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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-pangolearn">Debian Med / python-pangolearn</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pangolearn/-/commit/b4683525cac13f41a979b91cfca2cd7b216aa860">b4683525</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-08T08:21:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021-10-18</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pangolearn/-/commit/fca780e7500c2a9c01f3b7a2b96c58b9298104e1">fca780e7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-11-08T09:31:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021-10-18+dfsg</pre>
</li>
</ul>
<h4>20 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f7fd31b58e23b24a94dabd755beefdb3dc581946">
pangoLEARN/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#68251621b214b574e568fad115e86bfce9596ee0">
<span class="deleted-file">
−
pangoLEARN/data/decisionTreeHeaders_v1.joblib
</span>
</a>
</li>
<li class="file-stats">
<a href="#a534afca042d64405d1ba1e342dac1744360261e">
<span class="deleted-file">
−
pangoLEARN/data/decisionTree_v1.joblib
</span>
</a>
</li>
<li class="file-stats">
<a href="#e1cc4ccd0d52e1672534dd610e3ef13582bbd449">
<span class="deleted-file">
−
pangoLEARN/data/decision_tree_rules.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#1d231c3872591086b8ed3f7f1b2d540a4474c0f1">
<span class="new-file">
+
pangoLEARN/data/decision_tree_rules.zip
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<li class="file-stats">
<a href="#7258cdcff4b6897a9309b8a5bca162a07c95fae8">
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+
pangoLEARN/data/lineageTree.pb
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<li class="file-stats">
<a href="#3c5a0b1c53ce223f9b1a4547dfe649271aca7ed2">
pangoLEARN/data/lineages.downsample.csv
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<li class="file-stats">
<a href="#9426378f0cbae2a52b684961cbae2a7245342989">
pangoLEARN/data/lineages.metadata.csv
→
pangoLEARN/data/lineages.hash.csv
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<li class="file-stats">
<a href="#d4ae0f4b08b62a7970ca0bd91742a513cfe38a20">
<span class="new-file">
+
pangoLEARN/scripts/__init__.py
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<li class="file-stats">
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<span class="new-file">
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pangoLEARN/scripts/curate_alignment.smk
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<li class="file-stats">
<a href="#cdeb1cfde1d40372850708a583fa144fd3b3cc5a">
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pangoLEARN/scripts/training_runner.sh
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pangoLEARN/supporting_information/.DS_Store
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pangoLEARN/supporting_information/data_prep_description.md
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<span class="new-file">
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pangoLEARN/training/WH04.gb
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<li class="file-stats">
<a href="#615ab5a7dac3179a14b1392ca1c88953381cbc7e">
<span class="new-file">
+
pangoLEARN/training/__init__.py
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<li class="file-stats">
<a href="#efe721a7f83615610271fb571e2e0d610474eebf">
<span class="new-file">
+
pangoLEARN/training/downsample.py
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<li class="file-stats">
<a href="#927dbe358afc82a665cde7bc081ffcbdb5e6ad62">
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+
pangoLEARN/training/getDecisionTreeRules.py
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<li class="file-stats">
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pangoLEARN/training/outgroups.csv
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pangoLEARN/training/pangoLEARNDecisionTree_v1.py
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<li class="file-stats">
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<span class="new-file">
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pangoLEARN/training/processOutputFile.py
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</li>
</ul>
<h4>Changes:</h4>
<li id="f7fd31b58e23b24a94dabd755beefdb3dc581946">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#f7fd31b58e23b24a94dabd755beefdb3dc581946"><strong>pangoLEARN/__init__.py</strong></a>
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1
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<td class="new_line diff-line-num" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">_program</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"pangoLEARN"</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2
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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2021-04-01"</span></span></pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2021-10-18"</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">PANGO_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"v1.2.88"</span></span></pre>
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<br>
</li>
<li id="68251621b214b574e568fad115e86bfce9596ee0">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#68251621b214b574e568fad115e86bfce9596ee0"><strong>pangoLEARN/data/decisionTreeHeaders_v1.joblib</strong>
deleted
</a>
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No preview for this file type
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<li id="a534afca042d64405d1ba1e342dac1744360261e">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#a534afca042d64405d1ba1e342dac1744360261e"><strong>pangoLEARN/data/decisionTree_v1.joblib</strong>
deleted
</a>
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No preview for this file type
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</li>
<li id="e1cc4ccd0d52e1672534dd610e3ef13582bbd449">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#e1cc4ccd0d52e1672534dd610e3ef13582bbd449"><strong>pangoLEARN/data/decision_tree_rules.txt</strong>
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<li id="1d231c3872591086b8ed3f7f1b2d540a4474c0f1">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#1d231c3872591086b8ed3f7f1b2d540a4474c0f1"><strong>pangoLEARN/data/decision_tree_rules.zip</strong></a>
<hr>
No preview for this file type
<br>
</li>
<li id="7258cdcff4b6897a9309b8a5bca162a07c95fae8">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#7258cdcff4b6897a9309b8a5bca162a07c95fae8"><strong>pangoLEARN/data/lineageTree.pb</strong></a>
The diff for this file was not included because it is too large.
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<li id="3c5a0b1c53ce223f9b1a4547dfe649271aca7ed2">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#3c5a0b1c53ce223f9b1a4547dfe649271aca7ed2"><strong>pangoLEARN/data/lineages.downsample.csv</strong></a>
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<li id="9426378f0cbae2a52b684961cbae2a7245342989">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#9426378f0cbae2a52b684961cbae2a7245342989"><strong>pangoLEARN/data/lineages.metadata.csv</strong>
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<li id="d4ae0f4b08b62a7970ca0bd91742a513cfe38a20">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#d4ae0f4b08b62a7970ca0bd91742a513cfe38a20"><strong>pangoLEARN/scripts/__init__.py</strong></a>
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<li id="a2253f9fe6157858d6b1e963fb726c6d61acc28c">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#a2253f9fe6157858d6b1e963fb726c6d61acc28c"><strong>pangoLEARN/scripts/curate_alignment.smk</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">csv</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">os</span></span>
</pre>
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4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">collections</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">hashlib</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">collections</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">csv</span></span>
</pre>
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</tr>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">Bio</span> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">pangoLEARN</span><span class="p">.</span><span class="n" style="color: #333;">training</span> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">downsample</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="k" style="font-weight: 600;">from</span> <span class="n" style="color: #333;">datetime</span> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">date</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">today</span> <span class="p">=</span> <span class="n" style="color: #333;">date</span><span class="p">.</span><span class="n" style="color: #333;">today</span><span class="p">()</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"><span class="n" style="color: #333;">def</span> <span class="n" style="color: #333;">get_hash_string</span><span class="p">(</span><span class="k" style="font-weight: 600;">record</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">seq</span> <span class="p">=</span> <span class="n" style="color: #333;">str</span><span class="p">(</span><span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">upper</span><span class="p">().</span><span class="n" style="color: #333;">encode</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">hash_object</span> <span class="p">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">hash_string</span> <span class="p">=</span> <span class="n" style="color: #333;">hash_object</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"> <span class="n" style="color: #333;">return</span> <span class="n" style="color: #333;">hash_string</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"><span class="n" style="color: #333;">def</span> <span class="n" style="color: #333;">get_dict</span><span class="p">(</span><span class="n" style="color: #333;">in_csv</span><span class="p">,</span><span class="n" style="color: #333;">name_column</span><span class="p">,</span><span class="n" style="color: #333;">data_column</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"> <span class="n" style="color: #333;">this_dict</span> <span class="p">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">in_csv</span><span class="p">,</span><span class="s2" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">reader</span> <span class="p">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">row</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">this_dict</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">name_column</span><span class="p">]]</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="n" style="color: #333;">data_column</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"> <span class="n" style="color: #333;">return</span> <span class="n" style="color: #333;">this_dict</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="n" style="color: #333;">def</span> <span class="n" style="color: #333;">add_to_hash</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">hash_map</span> <span class="p">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">seq_hash</span> <span class="p">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="k" style="font-weight: 600;">record</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">seq_file</span><span class="p">,</span> <span class="s2" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">seq</span> <span class="p">=</span> <span class="n" style="color: #333;">str</span><span class="p">(</span><span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">).</span><span class="n" style="color: #333;">upper</span><span class="p">().</span><span class="n" style="color: #333;">encode</span><span class="p">()</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">hash_object</span> <span class="p">=</span> <span class="n" style="color: #333;">hashlib</span><span class="p">.</span><span class="n" style="color: #333;">md5</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">hash_map</span><span class="p">[</span><span class="n" style="color: #333;">hash_object</span><span class="p">.</span><span class="n" style="color: #333;">hexdigest</span><span class="p">()]</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"> <span class="n" style="color: #333;">seq_hash</span><span class="p">[</span><span class="n" style="color: #333;">str</span><span class="p">(</span><span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)]</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"> <span class="n" style="color: #333;">return</span> <span class="n" style="color: #333;">hash_map</span><span class="p">,</span><span class="n" style="color: #333;">seq_hash</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"><span class="n" style="color: #333;">pangoLEARN_path</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"pangoLEARN_path"</span><span class="p">].</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s2" style="color: #d14;">"/"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"><span class="n" style="color: #333;">pangolin_path</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"pangolin_path"</span><span class="p">].</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s2" style="color: #d14;">"/"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"><span class="n" style="color: #333;">pango_designation_path</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"pango_designation_path"</span><span class="p">].</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s2" style="color: #d14;">"/"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="n" style="color: #333;">quokka_path</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"quokka_path"</span><span class="p">].</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s2" style="color: #d14;">"/"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"><span class="n" style="color: #333;">data_date</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"data_date"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"trim_start"</span><span class="p">]</span> <span class="p">=</span> <span class="m" style="color: #099;">265</span></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"trim_end"</span><span class="p">]</span> <span class="p">=</span> <span class="m" style="color: #099;">29674</span></span>
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"lineages_csv"</span><span class="p">]=</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{pango_designation_path}/lineages.csv"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"reference"</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{pangolin_path}/pangolin/data/reference.fasta"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outgroups"</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{pangoLEARN_path}/pangoLEARN/training/outgroups.csv"</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"genbank_ref"</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{pangoLEARN_path}/pangoLEARN/training/WH04.gb"</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"datadir"</span><span class="p">]=</span> <span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"/localdisk/home/shared/raccoon-dog/{data_date}_gisaid/publish/gisaid"</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">all</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.filtered.fasta"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"decision_tree_rules.zip"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"pangolearn.init.py"</span><span class="p">),</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="mosel"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineage.hash.csv"</span><span class="p">)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="mosel"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">make_init</span><span class="p">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="mosel"> <span class="n" style="color: #333;">init</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"pangolearn.init.py"</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">:</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="mosel"> <span class="n" style="color: #333;">pangolearn_new_v</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"pangolearn_version"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="mosel"> <span class="n" style="color: #333;">pango_version</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"pango_version"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">,</span><span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s1" style="color: #d14;">'''_program = "pangoLEARN"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="mosel"><span class="s1" style="color: #d14;">__version__ = "{pangolearn_new_v}"</span></span>
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<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="mosel"><span class="s1" style="color: #d14;">PANGO_VERSION = "{pango_version}"</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;">'''</span><span class="p">)</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">filter_alignment</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"lineages_csv"</span><span class="p">],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"datadir"</span><span class="p">],</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"gisaid_{data_date}_all_alignment.fa"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel"> <span class="n" style="color: #333;">full_csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"datadir"</span><span class="p">],</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"gisaid_{data_date}_all_metadata.csv"</span><span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.filtered.fasta"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineages.metadata.filtered.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"> <span class="n" style="color: #333;">csv_all</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineages.designated.csv"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel"> <span class="n" style="color: #333;">csv_len</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel"> <span class="n" style="color: #333;">seqs_len</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="mosel"> <span class="n" style="color: #333;">lineages</span> <span class="p">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="mosel"> <span class="n" style="color: #333;">all_lineages</span> <span class="p">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="mosel"> <span class="n" style="color: #333;">all_len</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span><span class="s2" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">l</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"> <span class="n" style="color: #333;">l</span> <span class="p">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="mosel"> <span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">lineage</span> <span class="p">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s2" style="color: #d14;">","</span><span class="p">)</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="mosel"> </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"> <span class="n" style="color: #333;">lineages</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]=</span><span class="n" style="color: #333;">lineage</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="mosel"> <span class="n" style="color: #333;">csv_len</span> <span class="p">+=</span><span class="m" style="color: #099;">1</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="mosel"> <span class="n" style="color: #333;">all_lineages</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]=</span><span class="n" style="color: #333;">lineage</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="mosel"> <span class="n" style="color: #333;">all_len</span> <span class="p">+=</span><span class="m" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span><span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">csv_all</span><span class="p">,</span><span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw2</span><span class="p">:</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">full_csv</span><span class="p">,</span><span class="s2" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="mosel"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="mosel"> <span class="n" style="color: #333;">reader</span> <span class="p">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="mosel"> <span class="n" style="color: #333;">header</span> <span class="p">=</span> <span class="n" style="color: #333;">reader</span><span class="p">.</span><span class="n" style="color: #333;">fieldnames</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="mosel"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="mosel"> <span class="n" style="color: #333;">writer</span> <span class="p">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictWriter</span><span class="p">(</span><span class="n" style="color: #333;">fw</span><span class="p">,</span> <span class="n" style="color: #333;">fieldnames</span><span class="p">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">lineterminator</span><span class="p">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="mosel"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writeheader</span><span class="p">()</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="mosel"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="mosel"> <span class="n" style="color: #333;">writer2</span> <span class="p">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictWriter</span><span class="p">(</span><span class="n" style="color: #333;">fw2</span><span class="p">,</span> <span class="n" style="color: #333;">fieldnames</span><span class="p">=</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">lineterminator</span><span class="p">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="mosel"> <span class="n" style="color: #333;">writer2</span><span class="p">.</span><span class="n" style="color: #333;">writeheader</span><span class="p">()</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="mosel"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">row</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="mosel"> <span class="n" style="color: #333;">name</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s2" style="color: #d14;">"sequence_name"</span><span class="p">].</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s2" style="color: #d14;">"SouthAfrica"</span><span class="p">,</span><span class="s2" style="color: #d14;">"South_Africa"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineages</span><span class="p">:</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="mosel"> <span class="n" style="color: #333;">new_row</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="mosel"> <span class="n" style="color: #333;">new_row</span><span class="p">[</span><span class="s2" style="color: #d14;">"lineage"</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">lineages</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="mosel"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">new_row</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_lineages</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="mosel"> <span class="n" style="color: #333;">all_row</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span></span>
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<td class="new_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="mosel"> <span class="n" style="color: #333;">all_row</span><span class="p">[</span><span class="s2" style="color: #d14;">"lineage"</span><span class="p">]</span> <span class="p">=</span> <span class="n" style="color: #333;">all_lineages</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="mosel"> <span class="n" style="color: #333;">writer2</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">all_row</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="mosel"> <span class="n" style="color: #333;">written</span> <span class="p">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span><span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="k" style="font-weight: 600;">record</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="s2" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="p">=</span> <span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s2" style="color: #d14;">"SouthAfrica"</span><span class="p">,</span><span class="s2" style="color: #d14;">"South_Africa"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">if</span> <span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineages</span> <span class="k" style="font-weight: 600;">and</span> <span class="k" style="font-weight: 600;">not</span> <span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">written</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">">{record.id}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">{record.seq}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="mosel"> <span class="n" style="color: #333;">written</span><span class="p">[</span><span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">]=</span><span class="m" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="mosel"> <span class="n" style="color: #333;">seqs_len</span> <span class="p">+=</span><span class="m" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="mosel"> </span>
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<td class="new_line diff-line-num new" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="mosel"> <span class="n" style="color: #333;">print</span><span class="p">(</span><span class="s2" style="color: #d14;">"Number of sequences in gisaid designated"</span><span class="p">,</span> <span class="n" style="color: #333;">all_len</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="mosel"> <span class="n" style="color: #333;">print</span><span class="p">(</span><span class="s2" style="color: #d14;">"Number of sequences going into pangolearn training"</span><span class="p">,</span><span class="n" style="color: #333;">csv_len</span><span class="p">)</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="mosel"> <span class="n" style="color: #333;">print</span><span class="p">(</span><span class="s2" style="color: #d14;">"Number of sequences found on gisaid"</span><span class="p">,</span> <span class="n" style="color: #333;">seqs_len</span><span class="p">)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="mosel"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">align_with_minimap2</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.filtered.fasta"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="mosel"> <span class="n" style="color: #333;">reference</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"reference"</span><span class="p">]</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="mosel"> <span class="n" style="color: #333;">sam</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.sam"</span><span class="p">)</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="mosel"> <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"""</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="mosel"><span class="s2" style="color: #d14;"> minimap2 -a -x asm5 -t {workflow.cores} \</span></span>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.reference:q} \</span></span>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.fasta:q} > {output.sam:q}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="mosel"><span class="s2" style="color: #d14;"> """</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="mosel"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">get_variants</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="mosel"> <span class="n" style="color: #333;">sam</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.sam"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"variants.csv"</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="mosel"> <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>
</pre>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"""</span></span>
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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="mosel"><span class="s2" style="color: #d14;"> gofasta sam variants -t {workflow.cores} \</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="mosel"><span class="s2" style="color: #d14;"> --samfile {input.sam:q} \</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="mosel"><span class="s2" style="color: #d14;"> --reference {config[reference]} \</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="mosel"><span class="s2" style="color: #d14;"> --genbank {config[genbank_ref]} \</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="mosel"><span class="s2" style="color: #d14;"> --outfile {output.csv}</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="mosel"><span class="s2" style="color: #d14;"> """</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">add_lineage</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"variants.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="mosel"> <span class="n" style="color: #333;">lineages</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineages.designated.csv"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"variants.lineages.csv"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="mosel"> <span class="n" style="color: #333;">lineages_dict</span> <span class="p">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">lineages</span><span class="p">,</span><span class="s2" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="mosel"> <span class="n" style="color: #333;">reader</span><span class="p">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">row</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="mosel"> <span class="n" style="color: #333;">lineages_dict</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s2" style="color: #d14;">"sequence_name"</span><span class="p">]]</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s2" style="color: #d14;">"lineage"</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span> <span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"sequence_name,nucleotide_variants,lineage,why_excluded</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span><span class="s2" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">l</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="mosel"> <span class="n" style="color: #333;">l</span> <span class="p">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="mosel"> <span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">variants</span> <span class="p">=</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s2" style="color: #d14;">","</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="p">==</span><span class="s2" style="color: #d14;">"query"</span><span class="p">:</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="mosel"> <span class="n" style="color: #333;">pass</span></span>
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineages_dict</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{name},{variants},{lineages_dict[name]},</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="mosel"> </span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">downsample</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"variants.lineages.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.filtered.fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"metadata.copy.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.downsample.fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="mosel"> <span class="n" style="color: #333;">downsample</span><span class="p">.</span><span class="n" style="color: #333;">downsample</span><span class="p">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="mosel"> <span class="m" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outgroups"</span><span class="p">],</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="mosel"> <span class="nb" style="color: #0086b3;">False</span><span class="p">,</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="mosel"> <span class="nb" style="color: #0086b3;">False</span><span class="p">,</span> </span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="mosel"> <span class="m" style="color: #099;">10</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">filter_metadata</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"metadata.copy.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.downsample.fasta"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"metadata.downsample.csv"</span><span class="p">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">:</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="mosel"> <span class="n" style="color: #333;">in_downsample</span> <span class="p">=</span> <span class="p">{}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="k" style="font-weight: 600;">record</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span><span class="s2" style="color: #d14;">"fasta"</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="mosel"> <span class="n" style="color: #333;">in_downsample</span><span class="p">[</span><span class="k" style="font-weight: 600;">record</span><span class="p">.</span><span class="n" style="color: #333;">id</span><span class="p">]</span> <span class="p">=</span> <span class="m" style="color: #099;">1</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="mosel"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span> <span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"sequence_name,lineage</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span> <span class="s2" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="mosel"> <span class="n" style="color: #333;">reader</span> <span class="p">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">row</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s2" style="color: #d14;">"sequence_name"</span><span class="p">]</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">in_downsample</span><span class="p">:</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="mosel"> <span class="n" style="color: #333;">name</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s2" style="color: #d14;">"sequence_name"</span><span class="p">]</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="mosel"> <span class="n" style="color: #333;">lineage</span> <span class="p">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s2" style="color: #d14;">"lineage"</span><span class="p">]</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{name},{lineage}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="mosel"></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">get_relevant_postions</span><span class="p">:</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.downsample.fasta"</span><span class="p">),</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"metadata.downsample.csv"</span><span class="p">),</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="mosel"> <span class="n" style="color: #333;">reference</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"reference"</span><span class="p">]</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="mosel"> <span class="n" style="color: #333;">params</span><span class="p">:</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="mosel"> <span class="n" style="color: #333;">path_to_script</span> <span class="p">=</span> <span class="n" style="color: #333;">quokka_path</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="mosel"> <span class="n" style="color: #333;">relevant_pos_obj</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"relevantPositions.pickle"</span><span class="p">),</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="mosel"> <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"""</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="mosel"><span class="s2" style="color: #d14;"> python {params.path_to_script}/quokka/getRelevantLocationsObject.py \</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.reference:q} \</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.fasta} \</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.csv:q} \</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {config[outdir]}</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="mosel"><span class="s2" style="color: #d14;"> """</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="mosel"></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">run_training</span><span class="p">:</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.downsample.fasta"</span><span class="p">),</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"metadata.downsample.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="mosel"> <span class="n" style="color: #333;">reference</span> <span class="p">=</span> <span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"reference"</span><span class="p">],</span></span>
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<td class="new_line diff-line-num new" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="mosel"> <span class="n" style="color: #333;">relevant_pos_obj</span> <span class="p">=</span> <span class="n" style="color: #333;">rules</span><span class="p">.</span><span class="n" style="color: #333;">get_relevant_postions</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">relevant_pos_obj</span></span>
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<td class="new_line diff-line-num new" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="mosel"> <span class="n" style="color: #333;">params</span><span class="p">:</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="mosel"> <span class="n" style="color: #333;">path_to_script</span> <span class="p">=</span> <span class="n" style="color: #333;">pangoLEARN_path</span></span>
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<td class="new_line diff-line-num new" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="mosel"> <span class="n" style="color: #333;">headers</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"decisionTreeHeaders_v1.joblib"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"decisionTree_v1.joblib"</span><span class="p">),</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="mosel"> <span class="n" style="color: #333;">txt</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"training_summary.txt"</span><span class="p">)</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="mosel"> <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"""</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="mosel"><span class="s2" style="color: #d14;"> python {params.path_to_script}/pangoLEARN/training/pangoLEARNDecisionTree_v1.py \</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.csv:q} \</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.fasta} \</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.reference:q} \</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {config[outdir]} \</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.relevant_pos_obj} \</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="mosel"><span class="s2" style="color: #d14;"> > {output.txt:q}</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="mosel"><span class="s2" style="color: #d14;"> """</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="mosel"></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">get_recall</span><span class="p">:</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="mosel"> <span class="n" style="color: #333;">txt</span> <span class="p">=</span> <span class="n" style="color: #333;">rules</span><span class="p">.</span><span class="n" style="color: #333;">run_training</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">txt</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="mosel"> <span class="n" style="color: #333;">params</span><span class="p">:</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="mosel"> <span class="n" style="color: #333;">path_to_script</span> <span class="p">=</span> <span class="n" style="color: #333;">pangoLEARN_path</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="mosel"> <span class="n" style="color: #333;">txt</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineage_recall_report.txt"</span><span class="p">)</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="mosel"> <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"""</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="mosel"><span class="s2" style="color: #d14;"> python {params.path_to_script}/pangoLEARN/training/processOutputFile.py {input.txt} > {output.txt}</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="mosel"><span class="s2" style="color: #d14;"> """</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="mosel"></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">get_decisions</span><span class="p">:</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="mosel"> <span class="n" style="color: #333;">headers</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"decisionTreeHeaders_v1.joblib"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">model</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"decisionTree_v1.joblib"</span><span class="p">),</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="mosel"> <span class="n" style="color: #333;">txt</span> <span class="p">=</span> <span class="n" style="color: #333;">rules</span><span class="p">.</span><span class="n" style="color: #333;">run_training</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">txt</span></span>
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<td class="new_line diff-line-num new" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="mosel"> <span class="n" style="color: #333;">params</span><span class="p">:</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="mosel"> <span class="n" style="color: #333;">path_to_script</span> <span class="p">=</span> <span class="n" style="color: #333;">pangoLEARN_path</span></span>
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<td class="new_line diff-line-num new" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="mosel"> <span class="n" style="color: #333;">txt</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"tree_rules.txt"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="mosel"> <span class="n" style="color: #333;">zipped</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"decision_tree_rules.zip"</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="mosel"> <span class="n" style="color: #333;">shell</span><span class="p">:</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="mosel"> <span class="s2" style="color: #d14;">"""</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="mosel"><span class="s2" style="color: #d14;"> python {params.path_to_script}/pangoLEARN/training/getDecisionTreeRules.py \</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="mosel"><span class="s2" style="color: #d14;"> {input.model:q} {input.headers:q} {input.txt:q} \</span></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="mosel"><span class="s2" style="color: #d14;"> > {output.txt:q} && zip {output.zipped:q} {output.txt:q}</span></span>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="mosel"><span class="s2" style="color: #d14;"> """</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="mosel"><span class="n" style="color: #333;">rule</span> <span class="n" style="color: #333;">create_hash</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="mosel"> <span class="n" style="color: #333;">input</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"alignment.filtered.fasta"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="mosel"> <span class="n" style="color: #333;">lin_designation</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineages.designated.csv"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="mosel"> <span class="n" style="color: #333;">output</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="mosel"> <span class="n" style="color: #333;">csv</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineage.hash.csv"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="mosel"> <span class="n" style="color: #333;">fasta</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"lineage.hash.fasta"</span><span class="p">),</span></span>
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="mosel"> <span class="n" style="color: #333;">hashed_designations</span> <span class="p">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">[</span><span class="s2" style="color: #d14;">"outdir"</span><span class="p">],</span><span class="s2" style="color: #d14;">"designations.hash.csv"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="mosel"> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="mosel"> <span class="n" style="color: #333;">designated</span> <span class="p">=</span> <span class="n" style="color: #333;">get_dict</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">lin_designation</span><span class="p">,</span><span class="s2" style="color: #d14;">"sequence_name"</span><span class="p">,</span><span class="s2" style="color: #d14;">"lineage"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="mosel"></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="mosel"> <span class="n" style="color: #333;">hash_map</span><span class="p">,</span><span class="n" style="color: #333;">seq_hash_dict</span> <span class="p">=</span> <span class="n" style="color: #333;">add_to_hash</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">)</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="mosel"></span>
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">csv</span><span class="p">,</span><span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"seq_hash,lineage</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">seq_hash</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hash_map</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="mosel"> <span class="n" style="color: #333;">seq_name</span> <span class="p">=</span> <span class="n" style="color: #333;">hash_map</span><span class="p">[</span><span class="n" style="color: #333;">seq_hash</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="mosel"> <span class="n" style="color: #333;">set_name</span> <span class="p">=</span> <span class="n" style="color: #333;">designated</span><span class="p">[</span><span class="n" style="color: #333;">seq_name</span><span class="p">]</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{seq_hash},{set_name}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="mosel"> </span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="mosel"> <span class="n" style="color: #333;">num_seqs</span> <span class="p">=</span> <span class="m" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">hashed_designations</span><span class="p">,</span> <span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw2</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="mosel"> <span class="n" style="color: #333;">fw2</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"taxon,lineage</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="s2" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fw</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">seq</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_hash_dict</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="mosel"> <span class="n" style="color: #333;">num_seqs</span> <span class="p">+=</span><span class="m" style="color: #099;">1</span></span>
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<td class="new_line diff-line-num new" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="mosel"> <span class="n" style="color: #333;">fw</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">">{seq_hash_dict[seq]}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">{seq}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="mosel"> <span class="n" style="color: #333;">fw2</span><span class="p">.</span><span class="nb" style="color: #0086b3;">write</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{seq_hash_dict[seq]},{designated[seq_hash_dict[seq]]}</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="mosel"></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="mosel"> <span class="n" style="color: #333;">print</span><span class="p">(</span><span class="s2" style="color: #d14;">"Number of seqs going into training: "</span><span class="p">,</span><span class="n" style="color: #333;">f</span><span class="s2" style="color: #d14;">"{num_seqs}"</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#cdeb1cfde1d40372850708a583fa144fd3b3cc5a"><strong>pangoLEARN/scripts/training_runner.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#source /localdisk/home/s1680070/.bashrc</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#conda activate pangolin</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">TODAY</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span> +%F<span class="si" style="color: #d14;">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">OUT</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TODAY</span><span class="k" style="font-weight: 600;">}</span>_pangoLEARN</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">OUTDIR</span><span class="o" style="font-weight: 600;">=</span>/localdisk/home/shared/raccoon-dog/<span class="nv" style="color: #008080;">$OUT</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$OUTDIR</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$OUTDIR</span> <span class="o" style="font-weight: 600;">]</span> </span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Directory </span><span class="nv" style="color: #008080;">$OUTDIR</span><span class="s2" style="color: #d14;"> exists."</span> </span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$OUTDIR</span> </span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Directory </span><span class="nv" style="color: #008080;">$OUTDIR</span><span class="s2" style="color: #d14;"> does not exist, making it."</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Training model version: </span><span class="nv" style="color: #008080;">$TODAY</span><span class="s2" style="color: #d14;">"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">DATA_DATE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TODAY</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">DATA_DATE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># LATEST_DATA=$(ls -td /localdisk/home/shared/raccoon-dog/2021*_gisaid/publish/gisaid | head -n 1)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nv" style="color: #008080;">REPO_PATH</span><span class="o" style="font-weight: 600;">=</span>/localdisk/home/s1362711/repositories</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nv" style="color: #008080;">PANGO_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$REPO_PATH</span>/pango-designation</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="nv" style="color: #008080;">PLEARN_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$REPO_PATH</span>/pangoLEARN</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nv" style="color: #008080;">PANGOLIN_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$REPO_PATH</span>/pangolin</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nv" style="color: #008080;">QUOKKA_PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$REPO_PATH</span>/quokka</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pango designation path </span><span class="nv" style="color: #008080;">$PANGO_PATH</span><span class="s2" style="color: #d14;">"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pangoLEARN path </span><span class="nv" style="color: #008080;">$PLEARN_PATH</span><span class="s2" style="color: #d14;">"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pangolin path </span><span class="nv" style="color: #008080;">$PANGOLIN_PATH</span><span class="s2" style="color: #d14;">"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$PANGO_PATH</span> <span class="o" style="font-weight: 600;">&&</span> git pull <span class="c" style="color: #998; font-style: italic;">#gets any updates to the reports in the data directory</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nv" style="color: #008080;">PANGO_V</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>git tag <span class="nt" style="color: #000080;">--points-at</span> HEAD<span class="si" style="color: #d14;">)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pango version </span><span class="nv" style="color: #008080;">$PANGO_V</span><span class="s2" style="color: #d14;">"</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> /localdisk/home/shared/raccoon-dog/ <span class="c" style="color: #998; font-style: italic;">#gets any updates to the reports in the data directory</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"--config outdir=</span><span class="nv" style="color: #008080;">$OUTDIR</span><span class="s2" style="color: #d14;"> data_date=</span><span class="nv" style="color: #008080;">$DATA_DATE</span><span class="s2" style="color: #d14;"> pangolearn_version=</span><span class="nv" style="color: #008080;">$TODAY</span><span class="s2" style="color: #d14;"> pango_version=</span><span class="nv" style="color: #008080;">$PANGO_V</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"pangoLEARN training starting"</span> | mail <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"update lineageTree.pb with pango designation version </span><span class="nv" style="color: #008080;">$PANGO_V</span><span class="s2" style="color: #d14;">"</span> angie@soe.ucsc.edu</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">snakemake <span class="nt" style="color: #000080;">--snakefile</span> <span class="nv" style="color: #008080;">$PLEARN_PATH</span>/pangoLEARN/scripts/curate_alignment.smk <span class="nt" style="color: #000080;">--rerun-incomplete</span> <span class="nt" style="color: #000080;">--nolock</span> <span class="nt" style="color: #000080;">--cores</span> 1 <span class="nt" style="color: #000080;">--config</span> <span class="nv" style="color: #008080;">pango_designation_path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PANGO_PATH</span> <span class="nv" style="color: #008080;">pangolin_path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PANGOLIN_PATH</span> <span class="nv" style="color: #008080;">pangoLEARN_path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PLEARN_PATH</span> <span class="nv" style="color: #008080;">quokka_path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$QUOKKA_PATH</span> <span class="nv" style="color: #008080;">outdir</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OUTDIR</span> <span class="nv" style="color: #008080;">data_date</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DATA_DATE</span> <span class="nv" style="color: #008080;">pangolearn_version</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TODAY</span> <span class="nv" style="color: #008080;">pango_version</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$PANGO_V</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cp $OUTDIR/pangolearn.init.py /localdisk/home/s1680070/repositories/pangoLEARN/pangoLEARN/__init__.py</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cp $OUTDIR/decision* /localdisk/home/s1680070/repositories/pangoLEARN/pangoLEARN/data/</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cp $OUTDIR/metadata.downsample.csv /localdisk/home/s1680070/repositories/pangoLEARN/pangoLEARN/data/lineages.downsample.csv</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># cp $OUTDIR/lineage.hash.csv /localdisk/home/s1680070/repositories/pangoLEARN/pangoLEARN/data/lineages.hash.csv</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#33af78f63936739c6f95568aa35cf093e1933aaa"><strong>pangoLEARN/supporting_information/.DS_Store</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Data preparation</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Source</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">All GISAID data is downloaded and run through <span class="p">[</span><span class="nv" style="color: #008080;">`grapevine`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/cov-ert/grapevine</span><span class="p">)</span> which excludes records without proper dates, removes duplicate sequences (taking the earliest sample of the duplicates), omits some sequences with known issues, filters by length and coverage, and trims the sequences to CDS.</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">It also aligns the sequences using <span class="sb" style="color: #d14;">`mafft`</span> and builds an ML tree using <span class="sb" style="color: #d14;">`iqtree`</span>. A lineages is assigned to each sequence using <span class="sb" style="color: #d14;">`pangolin`</span> with the previous data release.</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Lineage Curation</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">The phylogeny is annotated with lineage and then in <span class="sb" style="color: #d14;">`FigTree`</span> the lineages are manually curated, drawing together a number of pieces of information including monophyly in the ML phylogeny (generally a bootstrap > 70 is required) and epidemiological data such as country and travel history. Any changes to lineage definitions and new lineages are documented during this process.</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="p">-</span> The lineage may have been defined earlier in the outbreak and with added sequence data, there is less support for that lineage. In these cases the associated epidemiological metadata is examined and the lineage may be refined or even dropped entirely. The lineage number will not be 'recycled', but the members will get reassigned the parent lineage designation.</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">-</span> The lineage may have very clear epidemiological support and ambiguities or homoplasies in the sequences/ tree could contribute to low bootstrap values. In these cases, if the support is strong, the lineages are called. Recall rates for these lingeages within <span class="sb" style="color: #d14;">`pangolin`</span> may be lower however.</span>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#cbe119ab0ae099c312d6d5d20d27eecc11b48c74"><strong>pangoLEARN/training/WH04.gb</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">LOCUS MT291829 29774 bp RNA linear VRL 14-MAY-2020</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">DEFINITION Severe acute respiratory syndrome coronavirus 2 isolate</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> SARS-CoV-2/human/CHN/Wuhan_IME-WH04/2019, complete genome.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ACCESSION MT291829 GWHACAV01000001</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">VERSION MT291829.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">KEYWORDS .</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">SOURCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> ORGANISM Severe acute respiratory syndrome coronavirus 2</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Nidovirales; Cornidovirineae; Coronaviridae; Orthocoronavirinae;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Betacoronavirus; Sarbecovirus.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">REFERENCE 1 (bases 1 to 29774)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> AUTHORS Fan,H., Qin,E., Wu,Y., Guo,Y., Zhang,X., Yong,Y., Hou,J., Xu,Z.,</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Mu,J., Teng,Y., Mi,Z., Yang,R., Song,Y., Li,B. and Cui,Y.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> TITLE Direct Submission</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> JOURNAL Submitted (06-APR-2020) Beijing Institute of Microbiology and</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Epidemiology, Fengtai District, Beijing 100071, China</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">COMMENT This record was submitted to GenBank on behalf of the original</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> #submitter through Genome Warehouse (GWH,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> https://bigd.big.ac.cn/gwh/) of the China National Center for</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> Bioinformation (CNCB)/National Genomics Data Center (NGDC,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> https://bigd.big.ac.cn).</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ##Assembly-Data-START##</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> Assembly Method :: CLC Genomic Workbench v. V9.0</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Assembly Name :: IME-WH04</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Coverage :: 46</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> Sequencing Technology :: Ion Torrent X5Plus</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ##Assembly-Data-END##</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">FEATURES Location/Qualifiers</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> source 1..29774</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> /organism="Severe acute respiratory syndrome coronavirus</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> 2"</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> /mol_type="genomic RNA"</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> /isolate="SARS-CoV-2/human/CHN/Wuhan_IME-WH04/2019"</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> /isolation_source="bronchoalveolar lavage fluid"</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> /host="Homo sapiens"</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> /db_xref="taxon:2697049"</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> /country="China: Wuhan"</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> /collection_date="2019-12-30"</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> /collected_by="Beijing Institute of Micribiology and</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> Epidemiology"</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> gene 178..21467</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> CDS join(178..13380,13380..21467)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> /ribosomal_slippage</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> /codon_start=1</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> /product="ORF1ab polyprotein"</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> /protein_id="QIU81799.1"</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> /translation="MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQ</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> HLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGE</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> TLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> WNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQ</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> LDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFP</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> LNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTG</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> DFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESG</span>
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58
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> LKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNL</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> LEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> FKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAA</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> ITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKL</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> KPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLV</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> NKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEII</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEK</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> YCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> CSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEF</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> KLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPE</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> EEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSG</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> YLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESD</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> DYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLA</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> PLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIA</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> EIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGN</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> LHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLIN</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> TLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSS</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> KTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVIT</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> FDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPH</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> NSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIK</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> WADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELG</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> DVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQ</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> IPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSK</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> ETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYY</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> KKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVT</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> FFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGD</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> IILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNS</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> VPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRI</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> KASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTA</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> ALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLET</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> IQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWL</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> MWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVE</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> CTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRP</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> INPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPI</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> NVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVN</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> TFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVEC</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> LKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALI</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> WNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWL</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> KQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFA</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> NKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLP</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> RVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVA</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> YESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSG</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> RWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTN</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> DVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFE</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> EAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHL</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> AKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNG</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> LWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVL</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> KLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSC</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> GSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVN</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> VLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAV</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> LDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHW</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> LLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFL</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> LPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTAR</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> TVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLAR</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> GIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYL</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> VSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVL</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> LSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKL</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> CEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAK</span>
</pre>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> SEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALN</span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> NIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTA</span>
</pre>
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</tr>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> CTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTP</span>
</pre>
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</tr>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAK</span>
</pre>
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</tr>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> AYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDH</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> PNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSA</span>
</pre>
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</tr>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> DAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKD</span>
</pre>
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</tr>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> EDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQR</span>
</pre>
</td>
</tr>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> LTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKKDWYDFVENPDILRVYA</span>
</pre>
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</tr>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> NLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVV</span>
</pre>
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</tr>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> DSYYSLLMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQ</span>
</pre>
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</tr>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> TYHPNCVNCLDDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRE</span>
</pre>
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</tr>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> LGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVAFQ</span>
</pre>
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</tr>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> TVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDI</span>
</pre>
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</tr>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> RQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQ</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> DALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGVSICSTMTNRQFHQKLLKSIAAT</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> RGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLAR</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> KHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQ</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> AVTANVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMM</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> ILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLTKGPHEFCS</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> QHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKH</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> PNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTV</span>
</pre>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> LQAVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCD</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> VTDVTQLYLGGMSYYCKSHKPPISFPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDW</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> TNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSDRELHLSWEVGKP</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> RPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSH</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> TVMPLSAPTLVPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGK</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> SHFAIGLALYYPSARIVYTACSHAAVDALCEKALKYLPIDKCSRIIPARARVECFDKF</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> KVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIGDPAQ</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> LPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLK</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> AHKDKSAQCFKMFYKGVITHDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNA</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> VASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNRFNVAITRAKVGILCIMSD</span>
</pre>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> RDLYDKLQFTSLEIPRRNVATLQAENVTGLFKDCSKVITGLHPTQAPTHLSVDTKFKT</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> EGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEG</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> CHATREAVGTNLPLQLGFSTGVNLVAVPTGYVDTPNNTDFSRVSAKPPPGDQFKHLIP</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> LMYKGLPWNVVRIKIVQMLSDTLKNLSDRVVFVLWAHGFELTSMKYFVKIGPERTCCL</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> CDRRATCFSTASDTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNA</span>
</pre>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> HVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHMVVKAALLADK</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> FPVLHDIGNPKAIKCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCL</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> FWNCNVDRYPANSIVCRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQ</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> LPFFYYSDSPCESHGKQVVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYN</span>
</pre>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> MMISAGFSLWVYKQFDTYNLWNTFTRLQSLENVAFNVVNKGHFDGQQGEVPVSIINNT</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> VYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDY</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> KRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEG</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> SVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFK</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> PRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESP</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> FELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKV</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> TIDYTEISFMLWCKDGHVETFYPKLQSSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGD</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> SATLPKGIMMNVAKYTQLCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLP</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> TGTLLVDSDLNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEG</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> FFTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASSSEAFL</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> IGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFPLKLRGTAVMSLKE</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> GQINDMILSLLSKGRLIIRENNRVVISSDVLVNN"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> mat_peptide 178..717</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> /product="leader protein"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> mat_peptide 718..2631</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> /product="nsp2"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> mat_peptide 2632..8466</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> /product="nsp3"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> mat_peptide 8467..9966</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> /product="nsp4"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> mat_peptide 9967..10884</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> /product="3C-like proteinase"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> mat_peptide 10885..11754</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> /product="nsp6"</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> mat_peptide 11755..12003</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> /product="nsp7"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> mat_peptide 12004..12597</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> /product="nsp8"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> mat_peptide 12598..12936</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> /product="nsp9"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> mat_peptide 12937..13353</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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203
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> /product="nsp10"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> mat_peptide join(13354..13380,13380..13382,13378..13380,13380..16148)</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> /product="RNA-dependent RNA polymerase"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> mat_peptide 16149..17951</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> /product="helicase"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> mat_peptide 17952..19532</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> /product="3'-to-5' exonuclease"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> mat_peptide 19533..20570</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
214
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
215
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> /product="endoRNAse"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> mat_peptide 20571..21464</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
</td>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> /product="2'-O-ribose methyltransferase"</span>
</pre>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> CDS 178..13395</span>
</pre>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> /codon_start=1</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> /product="ORF1a polyprotein"</span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> /protein_id="QIU81800.1"</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> /translation="MESLVPGFNEKTHVQLSLPVLQVRDVLVRGFGDSVEEVLSEARQ</span>
</pre>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> HLKDGTCGLVEVEKGVLPQLEQPYVFIKRSDARTAPHGHVMVELVAELEGIQYGRSGE</span>
</pre>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> TLGVLVPHVGEIPVAYRKVLLRKNGNKGAGGHSYGADLKSFDLGDELGTDPYEDFQEN</span>
</pre>
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</tr>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> WNTKHSSGVTRELMRELNGGAYTRYVDNNFCGPDGYPLECIKDLLARAGKASCTLSEQ</span>
</pre>
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</tr>
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228
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> LDFIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEIKLAKKFDTFNGECPNFVFP</span>
</pre>
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</tr>
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229
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> LNSIIKTIQPRVEKKKLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTG</span>
</pre>
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</tr>
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230
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> DFVKATCEFCGTENLTKEGATTCGYLPQNAVVKIYCPACHNSEVGPEHSLAEYHNESG</span>
</pre>
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</tr>
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231
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> LKTILRKGGRTIAFGGCVFSYVGCHNKCAYWVPRASANIGCNHTGVVGEGSEGLNDNL</span>
</pre>
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</tr>
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232
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> LEILQKEKVNINIVGDFKLNEEIAIILASFSASTSAFVETVKGLDYKAFKQIVESCGN</span>
</pre>
</td>
</tr>
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233
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> FKVTKGKAKKGAWNIGEQKSILSPLYAFASEAARVVRSIFSRTLETAQNSVRVLQKAA</span>
</pre>
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</tr>
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234
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> ITILDGISQYSLRLIDAMMFTSDLATNNLVVMAYITGGVVQLTSQWLTNIFGTVYEKL</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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235
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> KPVLDWLEEKFKEGVEFLRDGWEIVKFISTCACEIVGGQIVTCAKEIKESVQTFFKLV</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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236
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> NKFLALCADSIIIGGAKLKALNLGETFVTHSKGLYRKCVKSREETGLLMPLKAPKEII</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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237
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> FLEGETLPTEVLTEEVVLKTGDLQPLEQPTSEAVEAPLVGTPVCINGLMLLEIKDTEK</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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238
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> YCALAPNMMVTNNTFTLKGGAPTKVTFGDDTVIEVQGYKSVNITFELDERIDKVLNEK</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> CSAYTVELGTEVNEFACVVADAVIKTLQPVSELLTPLGIDLDEWSMATYYLFDESGEF</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
240
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> KLASHMYCSFYPPDEDEEEGDCEEEEFEPSTQYEYGTEDDYQGKPLEFGATSAALQPE</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
241
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> EEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQLEMELTPVVQTIEVNSFSG</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> YLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALNKATNNAMQVESD</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> DYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGEDIQLLKSAYENFNQHEVLLA</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> PLLSAGIFGADPIHSLRVCVDTVRTNVYLAVFDKNLYDKLVSSFLEMKSEKQVEQKIA</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> EIPKEEVKPFITESKPSVEQRKQDDKKIKACVEEVTTTLEETKFLTENLLLYIDINGN</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> LHPDSATLVSDIDITFLKKDAPYIVGDVVQEGVLTAVVIPTKKAGGTTEMLAKALRKV</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> PTDNYITTYPGQGLNGYTVEEAKTVLKKCKSAFYILPSIISNEKQEILGTVSWNLREM</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> LAHAEETRKLMPVCVETKAIVSTIQRKYKGIKIQEGVVDYGARFYFYTSKTTVASLIN</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> TLNDLNETLVTMPLGYVTHGLNLEEAARYMRSLKVPATVSVSSPDAVTAYNGYLTSSS</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> KTPEEHFIETISLAGSYKDWSYSGQSTQLGIEFLKRGDKSVYYTSNPTTFHLDGEVIT</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"> FDNLKTLLSLREVRTIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPH</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> NSHEGKTFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTSIK</span>
</pre>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> WADNNCYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILAYCNKTVGELG</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> DVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVEAVMYMGTLSYEQFKKGVQ</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> IPCTCGKQATKYLVQQESPFVMMSAPPAQYELKHGTFTCASEYTGNYQCGHYKHITSK</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> ETLYCIDGALLTKSSEYKGPITDVFYKENSYTTTIKPVTYKLDGVVCTEIDPKLDNYY</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> KKDNSYFTEQPIDLVPNQPYPNASFDNFKFVCDNIKFADDLNQLTGYKKPASRELKVT</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> FFPDLNGDVVAIDYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWST</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> KPVETSNSFDVLKSEDAQGMDNLACEDLKPVSEEVVENPTIQKDVLECNVKTTEVVGD</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> IILKPANNSLKITEEVGHTDLMAAYVDNSSLTIKKPNELSRVLGLKTLATHGLAAVNS</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> VPWDTIANYAKPFLNKVVSTTTNIVTRCLNRVCTNYMPYFFTLLLQLCTFTRSTNSRI</span>
</pre>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> KASMPTTIAKNTVKSVGKFCLEASFNYLKSPNFSKLINIIIWFLLLSVCLGSLIYSTA</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> ALGVLMSNLGMPSYCTGYREGYLNSTNVTIATYCTGSIPCSVCLSGLDSLDTYPSLET</span>
</pre>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> IQITISSFKWDLTAFGLVAEWFLAYILFTRFFYVLGLAAIMQLFFSYFAVHFISNSWL</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> MWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVE</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> CTTIVNGVRRSFYVYANGGKGFCKLHNWNCVNCDTFCAGSTFISDEVARDLSLQFKRP</span>
</pre>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> INPTDQSSYIVDSVTVKNGSIHLYFDKAGQKTYERHSLSHFVNLDNLRANNTKGSLPI</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> NVIVFDGKSKCEESSAKSASVYYSQLMCQPILLLDQALVSDVGDSAEVAVKMFDAYVN</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> TFSSTFNVPMEKLKTLVATAEAELAKNVSLDNVLSTFISAARQGFVDSDVETKDVVEC</span>
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</tr>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> LKLSHQSDIEVTGDSCNNYMLTYNKVENMTPRDLGACIDCSARHINAQVAKSHNIALI</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> WNVKDFMSLSEQLRKQIRSAAKKNNLPFKLTCATTRQVVNVVTTKIALKGGKIVNNWL</span>
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</tr>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> KQLIKVTLVFLFVAAIFYLITPVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFA</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> NKHADFDTWFSQRGGSYTNDKACPLIAAVITREVGFVVPGLPGTILRTTNGDFLHFLP</span>
</pre>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> RVFSAVGNICYTPSKLIEYTDFATSACVLAAECTIFKDASGKPVPYCYDTNVLEGSVA</span>
</pre>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> YESLRPDTRYVLMDGSIIQFPNTYLEGSVRVVTTFDSEYCRHGTCERSEAGVCVSTSG</span>
</pre>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> RWVLNNDYYRSLPGVFCGVDAVNLLTNMFTPLIQPIGALDISASIVAGGIVAIVVTCL</span>
</pre>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> AYYFMRFRRAFGEYSHVVAFNTLLFLMSFTVLCLTPVYSFLPGVYSVIYLYLTFYLTN</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext"> DVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRRVVFNGVSFSTFE</span>
</pre>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"> EAALCTFLLNKEMYLKLRSDVLLPLTQYNRYLALYNKYKYFSGAMDTTSYREAACCHL</span>
</pre>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> AKALNDFSNSGSDVLYQPPQTSITSAVLQSGFRKMAFPSGKVEGCMVQVTCGTTTLNG</span>
</pre>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext"> LWLDDVVYCPRHVICTSEDMLNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVL</span>
</pre>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext"> KLKVDTANPKTPKYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSC</span>
</pre>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext"> GSVGFNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVN</span>
</pre>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"> VLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQTGIAV</span>
</pre>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"> LDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSGVTFQSAVKRTIKGTHHW</span>
</pre>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> LLLTILTSLLVLVQSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKHKHAFLCLFL</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"> LPSLATVAYFNMVYMPASWVMRIMTWLDMVDTSLSGFKLKDCVMYASAVVLLILMTAR</span>
</pre>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"> TVYDDGARRVWTLMNVLTLVYKVYYGNALDQAISMWALIISVTSNYSGVVTTVMFLAR</span>
</pre>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> GIVFMCVEYCPIFFITGNTLQCIMLVYCFLGYFCTCYFGLFCLLNRYFRLTLGVYDYL</span>
</pre>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> VSTQEFRYMNSQGLLPPKNSIDAFKLNIKLLGVGGKPCIKVATVQSKMSDVKCTSVVL</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> LSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKL</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"> CEEMLDNRATLQAIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAK</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> SEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTMLFTMLRKLDNDALN</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> NIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVVDA</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> DSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQNNELSPVALRQMSCAAGTTQTA</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> CTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTP</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQAGNATEVPANSTVLSFCAFAVDAAK</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> AYKDYLASGGQPITNCVKMLCTHTGTGQAITVTPEANMDQESFGGASCCLYCRCHIDH</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> PNPKGFCDLKGKYVQIPTTCANDPVGFTLKNTVCTVCGMWKGYGCSCDQLREPMLQSA</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> DAQSFLNGFAV"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> mat_peptide 178..717</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> /product="leader protein"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> mat_peptide 718..2631</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> /product="nsp2"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> mat_peptide 2632..8466</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> /product="nsp3"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> mat_peptide 8467..9966</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> /product="nsp4"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> mat_peptide 9967..10884</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> /product="3C-like proteinase"</span>
</pre>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> mat_peptide 10885..11754</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> /product="nsp6"</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> mat_peptide 11755..12003</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"> /product="nsp7"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> mat_peptide 12004..12597</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> /product="nsp8"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> mat_peptide 12598..12936</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> /product="nsp9"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"> mat_peptide 12937..13353</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext"> /product="nsp10"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> mat_peptide 13354..13392</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> /product="nsp11"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"> stem_loop 13388..13415</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"> /gene="ORF1ab"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext"> /note="Coronavirus frameshifting stimulation element</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
337
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"> stem-loop 1"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
338
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> stem_loop 13400..13454</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
339
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> /gene="ORF1ab"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
340
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> /note="Coronavirus frameshifting stimulation element</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
341
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> stem-loop 2"</span>
</pre>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> gene 21475..25296</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> /gene="S"</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"> CDS 21475..25296</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"> /gene="S"</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"> /codon_start=1</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext"> /product="surface glycoprotein"</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"> /protein_id="QIU81801.1"</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"> /translation="MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFR</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext"> SSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIR</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> GWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQ</span>
</pre>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext"> GFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFL</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext"> LKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITN</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext"> LCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCF</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext"> TNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYN</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"> YLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPY</span>
</pre>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext"> RVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFG</span>
</pre>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext"> RDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAI</span>
</pre>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> HADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPR</span>
</pre>
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</tr>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext"> RARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTM</span>
</pre>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext"> YICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFG</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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363
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext"> GFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFN</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext"> GLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQN</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext"> VLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGA</span>
</pre>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext"> ISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMS</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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<td class="new_line diff-line-num new" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
367
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext"> ECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAH</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
368
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext"> FPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELD</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
369
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"> SFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELG</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
370
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext"> KYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSE</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
371
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext"> PVLKGVKLHYT"</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
372
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"> gene 25305..26132</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext"> /gene="ORF3a"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
374
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"> CDS 25305..26132</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext"> /gene="ORF3a"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
376
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext"> /product="ORF3a protein"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
378
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext"> /protein_id="QIU81802.1"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
379
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext"> /translation="MDLFMRIFTIGTVTLKQGEIKDATPSDFVRATATIPIQASLPFG</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
380
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext"> WLIVGVALLAVFQSASKIITLKKRWQLALSKGVHFVCNLLLLFVTVYSHLLLVAAGLE</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext"> APFLYLYALVYFLQSINFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPY</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
382
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext"> NSVTSSIVITSGDGTTSPISEHDYQIGGYTEKWESGVKDCVVLHSYFTSDYYQLYSTQ</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
383
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext"> LSTDTGVEHVTFFIYNKIVDEPEEHVQIHTIDGSSGVVNPVMEPIYDEPTTTTSVPL"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
384
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"> gene 26157..26384</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext"> /gene="E"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext"> CDS 26157..26384</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext"> /gene="E"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
389
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext"> /product="envelope protein"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext"> /protein_id="QIU81803.1"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
391
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext"> /translation="MYSFVSEETGTLIVNSVLLFLAFVVFLLVTLAILTALRLCAYCC</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"> NIVNVSLVKPSFYVYSRVKNLNSSRVPDLLV"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext"> gene 26435..27103</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext"> /gene="M"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext"> CDS 26435..27103</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
396
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext"> /gene="M"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext"> /product="membrane glycoprotein"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
399
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext"> /protein_id="QIU81804.1"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> /translation="MADSNGTITVEELKKLLEQWNLVIGFLFLTWICLLQFAYANRNR</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
401
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"> FLYIIKLIFLWLLWPVTLACFVLAAVYRINWITGGIAIAMACLVGLMWLSYFIASFRL</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
402
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> FARTRSMWSFNPETNILLNVPLHGTILTRPLLESELVIGAVILRGHLRIAGHHLGRCD</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
403
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> IKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDNIA</span>
</pre>
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</tr>
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404
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"> LLVQ"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext"> gene 27114..27299</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
406
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext"> /gene="ORF6"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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407
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext"> CDS 27114..27299</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
408
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext"> /gene="ORF6"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
409
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
410
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext"> /product="ORF6 protein"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
411
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext"> /protein_id="QIU81805.1"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
412
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"> /translation="MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSL</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
413
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"> TENKYSQLDEEQPMEID"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
414
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> gene 27306..27671</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
415
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext"> /gene="ORF7a"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
416
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> CDS 27306..27671</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> /gene="ORF7a"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> /codon_start=1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> /product="ORF7a protein"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext"> /protein_id="QIU81806.1"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext"> /translation="MKIILFLALITLATCELYHYQECVRGTTVLLKEPCSSGTYEGNS</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
422
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext"> PFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFL</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
423
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext"> IVAAIVFITLCFTLKRKTE"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext"> gene 27668..27799</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"> /gene="ORF7b"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext"> CDS 27668..27799</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext"> /gene="ORF7b"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext"> /product="ORF7b"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext"> /protein_id="QIU81807.1"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext"> /translation="MIELSLIDFYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA"</span>
</pre>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext"> gene 27806..28171</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext"> /gene="ORF8"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext"> CDS 27806..28171</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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435
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext"> /gene="ORF8"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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436
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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437
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext"> /product="ORF8 protein"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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438
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext"> /protein_id="QIU81808.1"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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439
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext"> /translation="MKFLVFLGIITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSK</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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440
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext"> WYIRVGARKSAPLIELCVDEAGSKSPIQYIDIGNYTVSCLPFTINCQEPKLGSLVVRC</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
441
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext"> SFYEDFLEYHDVRVVLDFI"</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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442
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext"> gene 28186..29445</span>
</pre>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext"> /gene="N"</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext"> CDS 28186..29445</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext"> /gene="N"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> /codon_start=1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext"> /product="nucleocapsid phosphoprotein"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext"> /protein_id="QIU81809.1"</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext"> /translation="MSDNGPQNQRNAPRITFGGPSDSTGSNQNGERSGARSKQRRPQG</span>
</pre>
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450
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext"> LPNNTASWFTALTQHGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMK</span>
</pre>
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</tr>
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451
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext"> DLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQ</span>
</pre>
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</tr>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext"> LPQGTTLPKGFYAEGSRGGSQASSRSSSRSRNSSRNSTPGSSRGTSPARMAGNGGDAA</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext"> LALLLLDRLNQLESKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATKAYNVTQAFGR</span>
</pre>
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</tr>
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454
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext"> RGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYT</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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455
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext"> GAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKDKKKKADETQALPQRQKKQQTV</span>
</pre>
</td>
</tr>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext"> TLLPAADLDDFSKQLQQSMSSADSTQA"</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"> gene 29470..29586</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext"> /gene="ORF10"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"> CDS 29470..29586</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext"> /gene="ORF10"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext"> /codon_start=1</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> /product="ORF10 protein"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext"> /protein_id="QIU81810.1"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext"> /translation="MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT"</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext"> stem_loop 29521..29556</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext"> /gene="ORF10"</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext"> /note="Coronavirus 3' UTR pseudoknot stem-loop 1"</span>
</pre>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"> stem_loop 29541..29569</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext"> /gene="ORF10"</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext"> /note="Coronavirus 3' UTR pseudoknot stem-loop 2"</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext"> stem_loop 29640..29680</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext"> /note="Coronavirus 3' stem-loop II-like motif (s2m)"</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">ORIGIN </span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"> 1 tggctgtcac tcggctgcat gcttagtgca ctcacgcagt ataattaata actaattact</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext"> 61 gtcgttgaca ggacacgagt aactcgtcta tcttctgcag gctgcttacg gtttcgtccg</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext"> 121 tgttgcagcc gatcatcagc acatctaggt ttcgtccggg tgtgaccgaa aggtaagatg</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext"> 181 gagagccttg tccctggttt caacgagaaa acacacgtcc aactcagttt gcctgtttta</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> 241 caggttcgcg acgtgctcgt acgtggcttt ggagactccg tggaggaggt cttatcagag</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"> 301 gcacgtcaac atcttaaaga tggcacttgt ggcttagtag aagttgaaaa aggcgttttg</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"> 361 cctcaacttg aacagcccta tgtgttcatc aaacgttcgg atgctcgaac tgcacctcat</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> 421 ggtcatgtta tggttgagct ggtagcagaa ctcgaaggca ttcagtacgg tcgtagtggt</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> 481 gagacacttg gtgtccttgt ccctcatgtg ggcgaaatac cagtggctta ccgcaaggtt</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"> 541 cttcttcgta agaacggtaa taaaggagct ggtggccata gttacggcgc cgatctaaag</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext"> 601 tcatttgact taggcgacga gcttggcact gatccttatg aagattttca agaaaactgg</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext"> 661 aacactaaac atagcagtgg tgttacccgt gaactcatgc gtgagcttaa cggaggggca</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"> 721 tacactcgct atgtcgataa caacttctgt ggccctgatg gctaccctct tgagtgcatt</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext"> 781 aaagaccttc tagcacgtgc tggtaaagct tcatgcactt tgtccgaaca actggacttt</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"> 841 attgacacta agaggggtgt atactgctgc cgtgaacatg agcatgaaat tgcttggtac</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext"> 901 acggaacgtt ctgaaaagag ctatgaattg cagacacctt ttgaaattaa attggcaaag</span>
</pre>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext"> 961 aaatttgaca ccttcaatgg ggaatgtcca aattttgtat ttcccttaaa ttccataatc</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext"> 1021 aagactattc aaccaagggt tgaaaagaaa aagcttgatg gctttatggg tagaattcga</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext"> 1081 tctgtctatc cagttgcgtc accaaatgaa tgcaaccaaa tgtgcctttc aactctcatg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext"> 1141 aagtgtgatc attgtggtga aacttcatgg cagacgggcg attttgttaa agccacttgc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"> 1201 gaattttgtg gcactgagaa tttgactaaa gaaggtgcca ctacttgtgg ttacttaccc</span>
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<td class="new_line diff-line-num new" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"> 1261 caaaatgctg ttgttaaaat ttattgtcca gcatgtcaca attcagaagt aggacctgag</span>
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<td class="new_line diff-line-num new" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> 1321 catagtcttg ccgaatacca taatgaatct ggcttgaaaa ccattcttcg taagggtggt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext"> 1381 cgcactattg cctttggagg ctgtgtgttc tcttatgttg gttgccataa caagtgtgcc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext"> 1441 tattgggttc cacgtgctag cgctaacata ggttgtaacc atacaggtgt tgttggagaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> 1501 ggttccgaag gtcttaatga caaccttctt gaaatactcc aaaaagagaa agtcaacatc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> 1561 aatattgttg gtgactttaa acttaatgaa gagatcgcca ttattttggc atctttttct</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext"> 1621 gcttccacaa gtgcttttgt ggaaactgtg aaaggtttgg attataaagc attcaaacaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> 1681 attgttgaat cctgtggtaa ttttaaagtt acaaaaggaa aagctaaaaa aggtgcctgg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> 1741 aatattggtg aacagaaatc aatactgagt cctctttatg catttgcatc agaggctgct</span>
</pre>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> 1801 cgtgttgtac gatcaatttt ctcccgcact cttgaaactg ctcaaaattc tgtgcgtgtt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext"> 1861 ttacagaagg ccgctataac aatactagat ggaatttcac agtattcact gagactcatt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext"> 1921 gatgctatga tgttcacatc tgatttggct actaacaatc tagttgtaat ggcctacatt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext"> 1981 acaggtggtg ttgttcagtt gacttcgcag tggctaacta acatctttgg cactgtttat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext"> 2041 gaaaaactca aacccgtcct tgattggctt gaagagaagt ttaaggaagg tgtagagttt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext"> 2101 cttagagacg gttgggaaat tgttaaattt atctcaacct gtgcttgtga aattgtcggt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> 2161 ggacaaattg tcacctgtgc aaaggaaatt aaggagagtg ttcagacatt ctttaagctt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext"> 2221 gtaaataaat ttttggcttt gtgtgctgac tctatcatta ttggtggagc taaacttaaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext"> 2281 gccttgaatt taggtgaaac atttgtcacg cactcaaagg gattgtacag aaagtgtgtt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext"> 2341 aaatccagag aagaaactgg cctactcatg cctctaaaag ccccaaaaga aattatcttc</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext"> 2401 ttagagggag aaacacttcc cacagaagtg ttaacagagg aagttgtctt gaaaactggt</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext"> 2461 gatttacaac cattagaaca acctactagt gaagctgttg aagctccatt ggttggtaca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"> 2521 ccagtttgta ttaacgggct tatgttgctc gaaatcaaag acacagaaaa gtactgtgcc</span>
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<td class="new_line diff-line-num new" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext"> 2581 cttgcaccta atatgatggt aacaaacaat accttcacac tcaaaggcgg tgcaccaaca</span>
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<td class="new_line diff-line-num new" data-linenumber="518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> 2641 aaggttactt ttggtgatga cactgtgata gaagtgcaag gttacaagag tgtgaatatc</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext"> 2701 acttttgaac ttgatgaaag gattgataaa gtacttaatg agaagtgctc tgcctataca</span>
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<td class="new_line diff-line-num new" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"> 2761 gttgaactcg gtacagaagt aaatgagttc gcctgtgttg tggcagatgc tgtcataaaa</span>
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<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext"> 2821 actttgcaac cagtatctga attacttaca ccactgggca ttgatttaga tgagtggagt</span>
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<td class="new_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> 2881 atggctacat actacttatt tgatgagtct ggtgagttta aattggcttc acatatgtat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext"> 2941 tgttctttct accctccaga tgaggatgaa gaagaaggtg attgtgaaga agaagagttt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> 3001 gagccatcaa ctcaatatga gtatggtact gaagatgatt accaaggtaa acctttggaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext"> 3061 tttggtgcca cttctgctgc tcttcaacct gaagaagagc aagaagaaga ttggttagat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> 3121 gatgatagtc aacaaactgt tggtcaacaa gacggcagtg aggacaatca gacaactact</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> 3181 attcaaacaa ttgttgaggt tcaacctcaa ttagagatgg aacttacacc agttgttcag</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> 3241 actattgaag tgaatagttt tagtggttat ttaaaactta ctgacaatgt atacattaaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext"> 3301 aatgcagaca ttgtggaaga agctaaaaag gtaaaaccaa cagtggttgt taatgcagcc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> 3361 aatgtttacc ttaaacatgg aggaggtgtt gcaggagcct taaataaggc tactaacaat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext"> 3421 gccatgcaag ttgaatctga tgattacata gctactaatg gaccacttaa agtgggtggt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"> 3481 agttgtgttt taagcggaca caatcttgct aaacactgtc ttcatgttgt cggcccaaat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext"> 3541 gttaacaaag gtgaagacat tcaacttctt aagagtgctt atgaaaattt taatcagcac</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"> 3601 gaagttctac ttgcaccatt attatcagct ggtatttttg gtgctgaccc tatacattct</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext"> 3661 ttaagagttt gtgtagatac tgttcgcaca aatgtctact tagctgtctt tgataaaaat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext"> 3721 ctctatgaca aacttgtttc aagctttttg gaaatgaaga gtgaaaagca agttgaacaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext"> 3781 aagatcgctg agattcctaa agaggaagtt aagccattta taactgaaag taaaccttca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext"> 3841 gttgaacaga gaaaacaaga tgataagaaa atcaaagctt gtgttgaaga agttacaaca</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext"> 3901 actctggaag aaactaagtt cctcacagaa aacttgttac tttatattga cattaatggc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"> 3961 aatcttcatc cagattctgc cactcttgtt agtgacattg acatcacttt cttaaagaaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext"> 4021 gatgctccat atatagtggg tgatgttgtt caagagggtg ttttaactgc tgtggttata</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext"> 4081 cctactaaaa aggctggtgg cactactgaa atgctagcga aagctttgag aaaagtgcca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext"> 4141 acagacaatt atataaccac ttacccgggt cagggtttaa atggttacac tgtagaggag</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="544" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext"> 4201 gcaaagacag tgcttaaaaa gtgtaaaagt gccttttaca ttctaccatc tattatctct</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext"> 4261 aatgagaagc aagaaattct tggaactgtt tcttggaatt tgcgagaaat gcttgcacat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="546" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext"> 4321 gcagaagaaa cacgcaaatt aatgcctgtc tgtgtggaaa ctaaagccat agtttcaact</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="547" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext"> 4381 atacagcgta aatataaggg tattaaaata caagagggtg tggttgatta tggtgctaga</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext"> 4441 ttttactttt acaccagtaa aacaactgta gcgtcactta tcaacacact taacgatcta</span>
</pre>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext"> 4501 aatgaaactc ttgttacaat gccacttggc tatgtaacac atggcttaaa tttggaagaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext"> 4561 gctgctcggt atatgagatc tctcaaagtg ccagctacag tttctgtttc ttcacctgat</span>
</pre>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext"> 4621 gctgttacag cgtataatgg ttatcttact tcttcttcta aaacacctga agaacatttt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext"> 4681 attgaaacca tctcacttgc tggttcctat aaagattggt cctattctgg acaatctaca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext"> 4741 caactaggta tagaatttct taagagaggt gataaaagtg tatattacac tagtaatcct</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext"> 4801 accacattcc acctagatgg tgaagttatc acctttgaca atcttaagac acttctttct</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext"> 4861 ttgagagaag tgaggactat taaggtgttt acaacagtag acaacattaa cctccacacg</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext"> 4921 caagttgtgg acatgtcaat gacatatgga caacagtttg gtccaactta tttggatgga</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext"> 4981 gctgatgtta ctaaaataaa acctcataat tcacatgaag gtaaaacatt ttatgtttta</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
558
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext"> 5041 cctaatgatg acactctacg tgttgaggct tttgagtact accacacaac tgatcctagt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
559
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext"> 5101 tttctgggta ggtacatgtc agcattaaat cacactaaaa agtggaaata cccacaagtt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
560
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext"> 5161 aatggtttaa cttctattaa atgggcagat aacaactgtt atcttgccac tgcattgtta</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
561
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext"> 5221 acactccaac aaatagagtt gaagtttaat ccacctgctc tacaagatgc ttattacaga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
562
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext"> 5281 gcaagggctg gtgaagctgc taacttttgt gcacttatct tagcctactg taataagaca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
563
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext"> 5341 gtaggtgagt taggtgatgt tagagaaaca atgagttact tgtttcaaca tgccaattta</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext"> 5401 gattcttgca aaagagtctt gaacgtggtg tgtaaaactt gtggacaaca gcagacaacc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
565
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext"> 5461 cttaagggtg tagaagctgt tatgtacatg ggcacacttt cttatgaaca atttaagaaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext"> 5521 ggtgttcaga taccttgtac gtgtggtaaa caagctacaa aatatctagt acaacaggag</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext"> 5581 tcaccttttg ttatgatgtc agcaccacct gctcagtatg aacttaagca tggtacattt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext"> 5641 acttgtgcta gtgagtacac tggtaattac cagtgtggtc actataaaca tataacttct</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext"> 5701 aaagaaactt tgtattgcat agacggtgct ttacttacaa agtcctcaga atacaaaggt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext"> 5761 cctattacgg atgttttcta caaagaaaac agttacacaa caaccataaa accagttact</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext"> 5821 tataaattgg atggtgttgt ttgtacagaa attgacccta agttggacaa ttattataag</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext"> 5881 aaagacaatt cttatttcac agagcaacca attgatcttg taccaaacca accatatcca</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext"> 5941 aacgcaagct tcgataattt taagtttgta tgtgataata tcaaatttgc tgatgattta</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"> 6001 aaccagttaa ctggttataa gaaacctgct tcaagagagc ttaaagttac atttttccct</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext"> 6061 gacttaaatg gtgatgtggt ggctattgat tataaacact acacaccctc ttttaagaaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext"> 6121 ggagctaaat tgttacataa acctattgtt tggcatgtta acaatgcaac taataaagcc</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext"> 6181 acgtataaac caaatacctg gtgtatacgt tgtctttgga gcacaaaacc agttgaaaca</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"> 6241 tcaaattcgt ttgatgtact gaagtcagag gacgcgcagg gaatggataa tcttgcctgc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext"> 6301 gaagatctaa aaccagtctc tgaagaagta gtggaaaatc ctaccataca gaaagacgtt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> 6361 cttgagtgta atgtgaaaac taccgaagtt gtaggagaca ttatacttaa accagcaaat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
581
</td>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext"> 6421 aatagtttaa aaattacaga agaggttggc cacacagatc taatggctgc ttatgtagac</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
582
</td>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> 6481 aattctagtc ttactattaa gaaacctaat gaattatcta gagtattagg tttgaaaacc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
583
</td>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext"> 6541 cttgctactc atggtttagc tgctgttaat agtgtccctt gggatactat agctaattat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
584
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> 6601 gctaagcctt ttcttaacaa agttgttagt acaactacta acatagttac acggtgttta</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
585
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext"> 6661 aaccgtgttt gtactaatta tatgccttat ttctttactt tattgctaca attgtgtact</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
586
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext"> 6721 tttactagaa gtacaaattc tagaattaaa gcatctatgc cgactactat agcaaagaat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
587
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext"> 6781 actgttaaga gtgtcggtaa attttgtcta gaggcttcat ttaattattt gaagtcacct</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext"> 6841 aatttttcta aactgataaa tattataatt tggtttttac tattaagtgt ttgcctaggt</span>
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<td class="new_line diff-line-num new" data-linenumber="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext"> 6901 tctttaatct actcaaccgc tgctttaggt gttttaatgt ctaatttagg catgccttct</span>
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<td class="new_line diff-line-num new" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext"> 6961 tactgtactg gttacagaga aggctatttg aactctacta atgtcactat tgcaacctac</span>
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<td class="new_line diff-line-num new" data-linenumber="591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext"> 7021 tgtactggtt ctataccttg tagtgtttgt cttagtggtt tagattcttt agacacctat</span>
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<td class="new_line diff-line-num new" data-linenumber="592" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"> 7081 ccttctttag aaactataca aattaccatt tcatctttta aatgggattt aactgctttt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="593" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext"> 7141 ggcttagttg cagagtggtt tttggcatat attcttttca ctaggttttt ctatgtactt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext"> 7201 ggattggctg caatcatgca attgtttttc agctattttg cagtacattt tattagtaat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext"> 7261 tcttggctta tgtggttaat aattaatctt gtacaaatgg ccccgatttc agctatggtt</span>
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<td class="new_line diff-line-num new" data-linenumber="596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext"> 7321 agaatgtaca tcttctttgc atcattttat tatgtatgga aaagttatgt gcatgttgta</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext"> 7381 gacggttgta attcatcaac ttgtatgatg tgttacaaac gtaatagagc aacaagagtc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="598" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext"> 7441 gaatgtacaa ctattgttaa tggtgttaga aggtcctttt atgtctatgc taatggaggt</span>
</pre>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext"> 7501 aaaggctttt gcaaactaca caattggaat tgtgttaatt gtgatacatt ctgtgctggt</span>
</pre>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext"> 7561 agtacattta ttagtgatga agttgcgaga gacttgtcac tacagtttaa aagaccaata</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext"> 7621 aatcctactg accagtcttc ttacatcgtt gatagtgtta cagtgaagaa tggttccatc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext"> 7681 catctttact ttgataaagc tggtcaaaag acttatgaaa gacattctct ctctcatttt</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext"> 7741 gttaacttag acaacctgag agctaataac actaaaggtt cattgcctat taatgttata</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext"> 7801 gtttttgatg gtaaatcaaa atgtgaagaa tcatctgcaa aatcagcgtc tgtttactac</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext"> 7861 agtcagctta tgtgtcaacc tatactgtta ctagatcagg cattagtgtc tgatgttggt</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext"> 7921 gatagtgcgg aagttgcagt taaaatgttt gatgcttacg ttaatacgtt ttcatcaact</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
607
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext"> 7981 tttaacgtac caatggaaaa actcaaaaca ctagttgcaa ctgcagaagc tgaacttgca</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
608
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext"> 8041 aagaatgtgt ccttagacaa tgtcttatct acttttattt cagcagctcg gcaagggttt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
609
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext"> 8101 gttgattcag atgtagaaac taaagatgtt gttgaatgtc ttaaattgtc acatcaatct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
610
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext"> 8161 gacatagaag ttactggcga tagttgtaat aactatatgc tcacctataa caaagttgaa</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
611
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext"> 8221 aacatgacac cccgtgacct tggtgcttgt attgactgta gtgcgcgtca tattaatgcg</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"> 8281 caggtagcaa aaagtcacaa cattgctttg atatggaacg ttaaagattt catgtcattg</span>
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<td class="new_line diff-line-num new" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext"> 8341 tctgaacaac tacgaaaaca aatacgtagt gctgctaaaa agaataactt accttttaag</span>
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<td class="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext"> 8401 ttgacatgtg caactactag acaagttgtt aatgttgtaa caacaaagat agcacttaag</span>
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<td class="new_line diff-line-num new" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext"> 8461 ggtggtaaaa ttgttaataa ttggttgaag cagttaatta aagttacact tgtgttcctt</span>
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<td class="new_line diff-line-num new" data-linenumber="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext"> 8521 tttgttgctg ctattttcta tttaataaca cctgttcatg tcatgtctaa acatactgac</span>
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<td class="new_line diff-line-num new" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext"> 8581 ttttcaagtg aaatcatagg atacaaggct attgatggtg gtgtcactcg tgacatagca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext"> 8641 tctacagata cttgttttgc taacaaacat gctgattttg acacatggtt tagccagcgt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext"> 8701 ggtggtagtt atactaatga caaagcttgc ccattgattg ctgcagtcat aacaagagaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext"> 8761 gtgggttttg tcgtgcctgg tttgcctggc acgatattac gcacaactaa tggtgacttt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext"> 8821 ttgcatttct tacctagagt ttttagtgca gttggtaaca tctgttacac accatcaaaa</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext"> 8881 cttatagagt acactgactt tgcaacatca gcttgtgttt tggctgctga atgtacaatt</span>
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<td class="new_line diff-line-num new" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext"> 8941 tttaaagatg cttctggtaa gccagtacca tattgttatg ataccaatgt actagaaggt</span>
</pre>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext"> 9001 tctgttgctt atgaaagttt acgccctgac acacgttatg tgctcatgga tggctctatt</span>
</pre>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext"> 9061 attcaatttc ctaacaccta ccttgaaggt tctgttagag tggtaacaac ttttgattct</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext"> 9121 gagtactgta ggcacggcac ttgtgaaaga tcagaagctg gtgtttgtgt atctactagt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext"> 9181 ggtagatggg tacttaacaa tgattattac agatctttac caggagtttt ctgtggtgta</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext"> 9241 gatgctgtaa atttacttac taatatgttt acaccactaa ttcaacctat tggtgctttg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext"> 9301 gacatatcag catctatagt agctggtggt attgtagcta tcgtagtaac atgccttgcc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext"> 9361 tactatttta tgaggtttag aagagctttt ggtgaataca gtcatgtagt tgcctttaat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext"> 9421 actttactat tccttatgtc attcactgta ctctgtttaa caccagttta ctcattctta</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext"> 9481 cctggtgttt attctgttat ttacttgtac ttgacatttt atcttactaa tgatgtttct</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext"> 9541 tttttagcac atattcagtg gatggttatg ttcacacctt tagtaccttt ctggataaca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext"> 9601 attgcttata tcatttgtat ttccacaaag catttctatt ggttctttag taattaccta</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext"> 9661 aagagacgtg tagtctttaa tggtgtttcc tttagtactt ttgaagaagc tgcgctgtgc</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext"> 9721 acctttttgt taaataaaga aatgtatcta aagttgcgta gtgatgtgct attacctctt</span>
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<td class="new_line diff-line-num new" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext"> 9781 acgcaatata atagatactt agctctttat aataagtaca agtattttag tggagcaatg</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext"> 9841 gatacaacta gctacagaga agctgcttgt tgtcatctcg caaaggctct caatgacttc</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext"> 9901 agtaactcag gttctgatgt tctttaccaa ccaccacaaa cctctatcac ctcagctgtt</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext"> 9961 ttgcagagtg gttttagaaa aatggcattc ccatctggta aagttgaggg ttgtatggta</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext"> 10021 caagtaactt gtggtacaac tacacttaac ggtctttggc ttgatgacgt agtttactgt</span>
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<td class="new_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext"> 10081 ccaagacatg tgatctgcac ctctgaagac atgcttaacc ctaattatga agatttactc</span>
</pre>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext"> 10141 attcgtaagt ctaatcataa tttcttggta caggctggta atgttcaact cagggttatt</span>
</pre>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext"> 10201 ggacattcta tgcaaaattg tgtacttaag cttaaggttg atacagccaa tcctaagaca</span>
</pre>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext"> 10261 cctaagtata agtttgttcg cattcaacca ggacagactt tttcagtgtt agcttgttac</span>
</pre>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext"> 10321 aatggttcac catctggtgt ttaccaatgt gctatgaggc ccaatttcac tattaagggt</span>
</pre>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext"> 10381 tcattcctta atggttcatg tggtagtgtt ggttttaaca tagattatga ctgtgtctct</span>
</pre>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext"> 10441 ttttgttaca tgcaccatat ggaattacca actggagttc atgctggcac agacttagaa</span>
</pre>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext"> 10501 ggtaactttt atggaccttt tgttgacagg caaacagcac aagcagctgg tacggacaca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext"> 10561 actattacag ttaatgtttt agcttggttg tacgctgctg ttataaatgg agacaggtgg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext"> 10621 tttctcaatc gatttaccac aactcttaat gactttaacc ttgtggctat gaagtacaat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext"> 10681 tatgaacctc taacacaaga ccatgttgac atactaggac ctctttctgc tcaaactgga</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext"> 10741 attgccgttt tagatatgtg tgcttcatta aaagaattac tgcaaaatgg tatgaatgga</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext"> 10801 cgtaccatat tgggtagtgc tttattagaa gatgaattta caccttttga tgttgttaga</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
655
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext"> 10861 caatgctcag gtgttacttt ccaaagtgca gtgaaaagaa caatcaaggg tacacaccac</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
656
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext"> 10921 tggttgttac tcacaatttt gacttcactt ttagttttag tccagagtac tcaatggtct</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext"> 10981 ttgttctttt ttttgtatga aaatgccttt ttaccttttg ctatgggtat tattgctatg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
658
</td>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext"> 11041 tctgcttttg caatgatgtt tgtcaaacat aagcatgcat ttctctgttt gtttttgtta</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext"> 11101 ccttctcttg ccactgtagc ttattttaat atggtctata tgcctgctag ttgggtgatg</span>
</pre>
</td>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext"> 11161 cgtattatga catggttgga tatggttgat actagtttgt ctggttttaa gctaaaagac</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext"> 11221 tgtgttatgt atgcatcagc tgtagtgtta ctaatcctta tgacagcaag aactgtgtat</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext"> 11281 gatgatggtg ctaggagagt gtggacactt atgaatgtct tgacactcgt ttataaagtt</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext"> 11341 tattatggta atgctttaga tcaagccatt tccatgtggg ctcttataat ctctgttact</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext"> 11401 tctaactact caggtgtagt tacaactgtc atgtttttgg ccagaggtat tgtttttatg</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext"> 11461 tgtgttgagt attgccctat tttcttcata actggtaata cacttcagtg tataatgcta</span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext"> 11521 gtttattgtt tcttaggcta tttttgtact tgttactttg gcctcttttg tttactcaac</span>
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<td class="new_line diff-line-num new" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext"> 11581 cgctacttta gactgactct tggtgtttat gattacttag tttctacaca ggagtttaga</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext"> 11641 tatatgaatt cacagggact actcccaccc aagaatagca tagatgcctt caaactcaac</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext"> 11701 attaaattgt tgggtgttgg tggcaaacct tgtatcaaag tagccactgt acagtctaaa</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext"> 11761 atgtcagatg taaagtgcac atcagtagtc ttactctcag ttttgcaaca actcagagta</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext"> 11821 gaatcatcat ctaaattgtg ggctcaatgt gtccagttac acaatgacat tctcttagct</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext"> 11881 aaagatacta ctgaagcctt tgaaaaaatg gtttcactac tttctgtttt gctttccatg</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext"> 11941 cagggtgctg tagacataaa caagctttgt gaagaaatgc tggacaacag ggcaacctta</span>
</pre>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext"> 12001 caagctatag cctcagagtt tagttccctt ccatcatatg cagcttttgc tactgctcaa</span>
</pre>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext"> 12061 gaagcttatg agcaggctgt tgctaatggt gattctgaag ttgttcttaa aaagttgaag</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext"> 12121 aagtctttga atgtggctaa atctgaattt gaccgtgatg cagccatgca acgtaagttg</span>
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<td class="new_line diff-line-num new" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext"> 12181 gaaaagatgg ctgatcaagc tatgacccaa atgtataaac aggctagatc tgaggacaag</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext"> 12241 agggcaaaag ttactagtgc tatgcagaca atgcttttca ctatgcttag aaagttggat</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext"> 12301 aatgatgcac tcaacaacat tatcaacaat gcaagagatg gttgtgttcc cttgaacata</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext"> 12361 atacctctta caacagcagc caaactaatg gttgtcatac cagactataa cacatataaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext"> 12421 aatacgtgtg atggtacaac atttacttat gcatcagcat tgtgggaaat ccaacaggtt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext"> 12481 gtagatgcag atagtaaaat tgttcaactt agtgaaatta gtatggacaa ttcacctaat</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext"> 12541 ttagcatggc ctcttattgt aacagcttta agggccaatt ctgctgtcaa attacagaat</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="684" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext"> 12601 aatgagctta gtcctgttgc actacgacag atgtcttgtg ctgccggtac tacacaaact</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext"> 12661 gcttgcactg atgacaatgc gttagcttac tacaacacaa caaagggagg taggtttgta</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="plaintext"> 12721 cttgcactgt tatccgattt acaggatttg aaatgggcta gattccctaa gagtgatgga</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="plaintext"> 12781 actggtacta tctatacaga actggaacca ccttgtaggt ttgttacaga cacacctaaa</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="plaintext"> 12841 ggtcctaaag tgaagtattt atactttatt aaaggattaa acaacctaaa tagaggtatg</span>
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<td class="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext"> 12901 gtacttggta gtttagctgc cacagtacgt ctacaagctg gtaatgcaac agaagtgcct</span>
</pre>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="plaintext"> 12961 gccaattcaa ctgtattatc tttctgtgct tttgctgtag atgctgctaa agcttacaaa</span>
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<td class="new_line diff-line-num new" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="plaintext"> 13021 gattatctag ctagtggggg acaaccaatc actaattgtg ttaagatgtt gtgtacacac</span>
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<td class="new_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="plaintext"> 13081 actggtactg gtcaggcaat aacagttaca ccggaagcca atatggatca agaatccttt</span>
</pre>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="plaintext"> 13141 ggtggtgcat cgtgttgtct gtactgccgt tgccacatag atcatccaaa tcctaaagga</span>
</pre>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="plaintext"> 13201 ttttgtgact taaaaggtaa gtatgtacaa atacctacaa cttgtgctaa tgaccctgtg</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="plaintext"> 13261 ggttttacac ttaaaaacac agtctgtacc gtctgcggta tgtggaaagg ttatggctgt</span>
</pre>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="plaintext"> 13321 agttgtgatc aactccgcga acccatgctt cagtcagctg atgcacaatc gtttttaaac</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="plaintext"> 13381 gggtttgcgg tgtaagtgca gcccgtctta caccgtgcgg cacaggcact agtactgatg</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="plaintext"> 13441 tcgtatacag ggcttttgac atctacaatg ataaagtagc tggttttgct aaattcctaa</span>
</pre>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="plaintext"> 13501 aaactaattg ttgtcgcttc caagaaaagg acgaagatga caatttaatt gattcttact</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext"> 13561 ttgtagttaa gagacacact ttctctaact accaacatga agaaacaatt tataatttac</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext"> 13621 ttaaggattg tccagctgtt gctaaacatg acttctttaa gtttagaata gacggtgaca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext"> 13681 tggtaccaca tatatcacgt caacgtctta ctaaatacac aatggcagac ctcgtctatg</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="plaintext"> 13741 ctttaaggca ttttgatgaa ggtaattgtg acacattaaa agaaatactt gtcacataca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
704
</td>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="plaintext"> 13801 attgttgtga tgatgattat ttcaataaaa aggactggta tgattttgta gaaaacccag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
705
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext"> 13861 atatattacg cgtatacgcc aacttaggtg aacgtgtacg ccaagctttg ttaaaaacag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
706
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC706" class="line" lang="plaintext"> 13921 tacaattctg tgatgccatg cgaaatgctg gtattgttgg tgtactgaca ttagataatc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
707
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC707" class="line" lang="plaintext"> 13981 aagatctcaa tggtaactgg tatgatttcg gtgatttcat acaaaccacg ccaggtagtg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext"> 14041 gagttcctgt tgtagattct tattattcat tgttaatgcc tatattaacc ttgaccaggg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext"> 14101 ctttaactgc agagtcacat gttgacactg acttaacaaa gccttacatt aagtgggatt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext"> 14161 tgttaaaata tgacttcacg gaagagaggt taaaactctt tgaccgttat tttaaatatt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext"> 14221 gggatcagac ataccaccca aattgtgtta actgtttgga tgacagatgc attctgcatt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext"> 14281 gtgcaaactt taatgtttta ttctctacag tgttcccacc tacaagtttt ggaccactag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext"> 14341 tgagaaaaat atttgttgat ggtgttccat ttgtagtttc aactggatac cacttcagag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext"> 14401 agctaggtgt tgtacataat caggatgtaa acttacatag ctctagactt agttttaagg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext"> 14461 aattacttgt gtatgctgct gaccctgcta tgcacgctgc ttctggtaat ctattactag</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext"> 14521 ataaacgcac tacgtgcttt tcagtagctg cacttactaa caatgttgct tttcaaactg</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="plaintext"> 14581 tcaaacccgg taattttaac aaagacttct atgactttgc tgtgtctaag ggtttcttta</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="plaintext"> 14641 aggaaggaag ttctgttgaa ttaaaacact tcttctttgc tcaggatggt aatgctgcta</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext"> 14701 tcagcgatta tgactactat cgttataatc taccaacaat gtgtgatatc agacaactac</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="plaintext"> 14761 tatttgtagt tgaagttgtt gataagtact ttgattgtta cgatggtggc tgtattaatg</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext"> 14821 ctaaccaagt catcgtcaac aacctagaca aatcagctgg ttttccattt aataaatggg</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="plaintext"> 14881 gtaaggctag actttattat gattcaatga gttatgagga tcaagatgca cttttcgcat</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="plaintext"> 14941 atacaaaacg taatgtcatc cctactataa ctcaaatgaa tcttaagtat gccattagtg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="plaintext"> 15001 caaagaatag agctcgcacc gtagctggtg tctctatctg tagtactatg accaatagac</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="plaintext"> 15061 agtttcatca aaaattattg aaatcaatag ccgccactag aggagctact gtagtaattg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="plaintext"> 15121 gaacaagcaa attctatggt ggttggcaca acatgttaaa aactgtttat agtgatgtag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="plaintext"> 15181 aaaaccctca ccttatgggt tgggattatc ctaaatgtga tagagccatg cctaacatgc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
728
</td>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="plaintext"> 15241 ttagaattat ggcctcactt gttcttgctc gcaaacatac aacgtgttgt agcttgtcac</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
729
</td>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="plaintext"> 15301 accgtttcta tagattagct aatgagtgtg ctcaagtatt gagtgaaatg gtcatgtgtg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="plaintext"> 15361 gcggttcact atatgttaaa ccaggtggaa cctcatcagg agatgccaca actgcttatg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
</td>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="plaintext"> 15421 ctaatagtgt ttttaacatt tgtcaagctg tcacggccaa tgttaatgca cttttatcta</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="plaintext"> 15481 ctgatggtaa caaaattgcc gataagtatg tccgcaattt acaacacaga ctttatgagt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="plaintext"> 15541 gtctctatag aaatagagat gttgacacag actttgtgaa tgagttttac gcatatttgc</span>
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<td class="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="plaintext"> 15601 gtaaacattt ctcaatgatg atactctctg acgatgctgt tgtgtgtttc aatagcactt</span>
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<td class="new_line diff-line-num new" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="plaintext"> 15661 atgcatctca aggtctagtg gctagcataa agaactttaa gtcagttctt tattatcaaa</span>
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<td class="new_line diff-line-num new" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="plaintext"> 15721 acaatgtttt tatgtctgaa gcaaaatgtt ggactgagac tgaccttact aaaggacctc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="plaintext"> 15781 atgaattttg ctctcaacat acaatgctag ttaaacaggg tgatgattat gtgtaccttc</span>
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<td class="new_line diff-line-num new" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="plaintext"> 15841 cttacccaga tccatcaaga atcctagggg ccggctgttt tgtagatgat atcgtaaaaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="plaintext"> 15901 cagatggtac acttatgatt gaacggttcg tgtctttagc tatagatgct tacccactta</span>
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<td class="new_line diff-line-num new" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="plaintext"> 15961 ctaaacatcc taatcaggag tatgctgatg tctttcattt gtacttacaa tacataagaa</span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="plaintext"> 16021 agctacatga tgagttaaca ggacacatgt tagacatgta ttctgttatg cttactaatg</span>
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<td class="new_line diff-line-num new" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="plaintext"> 16081 ataacacttc aaggtattgg gaacctgagt tttatgaggc tatgtacaca ccgcatacag</span>
</pre>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="plaintext"> 16141 tcttacaggc tgttggggct tgtgttcttt gcaattcaca gacttcatta agatgtggtg</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="plaintext"> 16201 cttgcatacg tagaccattc ttatgttgta aatgctgtta cgaccatgtc atatcaacat</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext"> 16261 cacataaatt agtcttgtct gttaatccgt atgtttgcaa tgctccaggt tgtgatgtca</span>
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<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="plaintext"> 16321 cagatgtgac tcaactttac ttaggaggta tgagctatta ttgtaaatca cataaaccac</span>
</pre>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="plaintext"> 16381 ccattagttt tccattgtgt gctaatggac aagtttttgg tttatataaa aatacatgtg</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="plaintext"> 16441 ttggtagcga taatgttact gactttaatg caattgcaac atgtgactgg acaaatgctg</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="plaintext"> 16501 gtgattacat tttagctaac acctgtactg aaagactcaa gctttttgca gcagaaacgc</span>
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<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="plaintext"> 16561 tcaaagctac tgaggagaca tttaaactgt cttatggtat tgctactgta cgtgaagtgc</span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="plaintext"> 16621 tgtctgacag agaattacat ctttcatggg aagttggtaa acctagacca ccacttaacc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="plaintext"> 16681 gaaattatgt ctttactggt tatcgtgtaa ctaaaaacag taaagtacaa ataggagagt</span>
</pre>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="plaintext"> 16741 acacctttga aaaaggtgac tatggtgatg ctgttgttta ccgaggtaca acaacttaca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="plaintext"> 16801 aattaaatgt tggtgattat tttgtgctga catcacatac agtaatgcca ttaagtgcac</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="plaintext"> 16861 ctacactagt gccacaagag cactatgtta gaattactgg cttataccca acactcaata</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="plaintext"> 16921 tctcagatga gttttctagc aatgttgcaa attatcaaaa ggttggtatg caaaagtatt</span>
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<td class="new_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="plaintext"> 16981 ctacactcca gggaccacct ggtactggta agagtcattt tgctattggc ctagctctct</span>
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<td class="new_line diff-line-num new" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="plaintext"> 17041 actacccttc tgctcgcata gtgtatacag cttgctctca tgccgctgtt gatgcactat</span>
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<td class="new_line diff-line-num new" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="plaintext"> 17101 gtgagaaggc attaaaatat ttgcctatag ataaatgtag tagaattata cctgcacgtg</span>
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<td class="new_line diff-line-num new" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="plaintext"> 17161 ctcgtgtaga gtgttttgat aaattcaaag tgaattcaac attagaacag tatgtctttt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="plaintext"> 17221 gtactgtaaa tgcattgcct gagacgacag cagatatagt tgtctttgat gaaatttcaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="plaintext"> 17281 tggccacaaa ttatgatttg agtgttgtca atgccagatt acgtgctaag cactatgtgt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="plaintext"> 17341 acattggcga ccctgctcaa ttacctgcac cacgcacatt gctaactaag ggcacactag</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="plaintext"> 17401 aaccagaata tttcaattca gtgtgtagac ttatgaaaac tataggtcca gacatgttcc</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="plaintext"> 17461 tcggaacttg tcggcgttgt cctgctgaaa ttgttgacac tgtgagtgct ttggtttatg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="plaintext"> 17521 ataataagct taaagcacat aaagacaaat cagctcaatg ctttaaaatg ttttataagg</span>
</pre>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="plaintext"> 17581 gtgttatcac gcatgatgtt tcatctgcaa ttaacaggcc acaaataggc gtggtaagag</span>
</pre>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="plaintext"> 17641 aattccttac acgtaaccct gcttggagaa aagctgtctt tatttcacct tataattcac</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="plaintext"> 17701 agaatgctgt agcctcaaag attttgggac taccaactca aactgttgat tcatcacagg</span>
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<td class="new_line diff-line-num new" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="plaintext"> 17761 gctcagaata tgactatgtc atattcactc aaaccactga aacagctcac tcttgtaatg</span>
</pre>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="plaintext"> 17821 taaacagatt taatgttgct attaccagag caaaagtagg catactttgc ataatgtctg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="plaintext"> 17881 atagagacct ttatgacaag ttgcaattta caagtcttga aattccacgt aggaatgtgg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="plaintext"> 17941 caactttaca agctgaaaat gtaacaggac tctttaaaga ttgtagtaag gtaatcactg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="plaintext"> 18001 ggttacatcc tacacaggca cctacacacc tcagtgttga cactaaattc aaaactgaag</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="plaintext"> 18061 gtttatgtgt tgacatacct ggcataccta aggacatgac ctatagaaga ctcatctcta</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="plaintext"> 18121 tgatgggttt taaaatgaat tatcaagtta atggttaccc taacatgttt atcacccgcg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext"> 18181 aagaagctat aagacatgta cgtgcatgga ttggcttcga tgtcgagggg tgtcatgcta</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="plaintext"> 18241 ctagagaagc tgttggtacc aatttacctt tacagctagg tttttctaca ggtgttaacc</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="plaintext"> 18301 tagttgctgt acctacaggt tatgttgata cacctaataa tacagatttt tccagagtta</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="plaintext"> 18361 gtgctaaacc accgcctgga gatcaattta aacacctcat accacttatg tacaaaggac</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="plaintext"> 18421 ttccttggaa tgtagtgcgt ataaagattg tacaaatgtt aagtgacaca cttaaaaatc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext"> 18481 tctctgacag agtcgtattt gtcttatggg cacatggctt tgagttgaca tctatgaagt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="plaintext"> 18541 attttgtgaa aataggacct gagcgcacct gttgtctatg tgatagacgt gccacatgct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
784
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext"> 18601 tttccactgc ttcagacact tatgcctgtt ggcatcattc tattggattt gattacgtct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext"> 18661 ataatccgtt tatgattgat gttcaacaat ggggttttac aggtaaccta caaagcaacc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
786
</td>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext"> 18721 atgatctgta ttgtcaagtc catggtaatg cacatgtagc tagttgtgat gcaatcatga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext"> 18781 ctaggtgtct agctgtccac gagtgctttg ttaagcgtgt tgactggact attgaatatc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext"> 18841 ctataattgg tgatgaactg aagattaatg cggcttgtag aaaggttcaa cacatggttg</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext"> 18901 ttaaagctgc attattagca gacaaattcc cagttcttca cgacattggt aaccctaaag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext"> 18961 ctattaagtg tgtacctcaa gctgatgtag aatggaagtt ctatgatgca cagccttgta</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext"> 19021 gtgacaaagc ttataaaata gaagaattat tctattctta tgccacacat tctgacaaat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext"> 19081 tcacagatgg tgtatgccta ttttggaatt gcaatgtcga tagatatcct gctaattcca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="plaintext"> 19141 ttgtttgtag atttgacact agagtgctat ctaaccttaa cttgcctggt tgtgatggtg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="plaintext"> 19201 gcagtttgta tgtaaataaa catgcattcc acacaccagc ttttgataaa agtgcttttg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext"> 19261 ttaatttaaa acaattacca tttttctatt actctgacag tccatgtgag tctcatggaa</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext"> 19321 aacaagtagt gtcagatata gattatgtac cactaaagtc tgctacgtgt ataacacgtt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="plaintext"> 19381 gcaatttagg tggtgctgtc tgtagacatc atgctaatga gtacagattg tatctcgatg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext"> 19441 cttataacat gatgatctca gctggcttta gcttgtgggt ttacaaacaa tttgatactt</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="plaintext"> 19501 ataacctctg gaacactttt acaagacttc agagtttaga aaatgtggct tttaatgttg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
800
</td>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext"> 19561 taaataaggg acactttgat ggacaacagg gtgaagtacc agtttctatc attaataaca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext"> 19621 ctgtttacac aaaagttgat ggtgttgatg tagaattgtt tgaaaataaa acaacattac</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
802
</td>
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="plaintext"> 19681 ctgttaatgt agcatttgag ctttgggcta agcgcaacat taaaccagta ccagaggtga</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
803
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC803" class="line" lang="plaintext"> 19741 aaatactcaa taatttgggt gtggacattg ctgctaatac tgtgatctgg gactacaaaa</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext"> 19801 gagatgctcc agcacatata tctactattg gtgtttgttc tatgactgac atagccaaga</span>
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<td class="new_line diff-line-num new" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="plaintext"> 19861 aaccaactga aacgatttgt gcaccactca ctgtcttttt tgatggtaga gttgatggtc</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="plaintext"> 19921 aagtagactt atttagaaat gcccgtaatg gtgttcttat tacagaaggt agtgttaaag</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext"> 19981 gtttacaacc atctgtaggt cccaaacaag ctagtcttaa tggagtcaca ttaattggag</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext"> 20041 aagccgtaaa aacacagttc aattattata agaaagttga tggtgttgtc caacaattac</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext"> 20101 ctgaaactta ctttactcag agtagaaatt tacaagaatt taaacccagg agtcaaatgg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext"> 20161 aaattgattt cttagaatta gctatggatg aattcattga acggtataaa ttagaaggct</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="plaintext"> 20221 atgccttcga acatatcgtt tatggagatt ttagtcatag tcagttaggt ggtttacatc</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="plaintext"> 20281 tactgattgg actagctaaa cgttttaagg aatcaccttt tgaattagaa gattttattc</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="plaintext"> 20341 ctatggacag tacagttaaa aactatttca taacagatgc gcaaacaggt tcatctaagt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="plaintext"> 20401 gtgtgtgttc tgttattgat ttattacttg atgattttgt tgaaataata aaatcccaag</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext"> 20461 atttatctgt agtttctaag gttgtcaaag tgactattga ctatacagaa atttcattta</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="plaintext"> 20521 tgctttggtg taaagatggc catgtagaaa cattttaccc aaaattacaa tctagtcaag</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="plaintext"> 20581 cgtggcaacc gggtgttgct atgcctaatc tttacaaaat gcaaagaatg ctattagaaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="plaintext"> 20641 agtgtgacct tcaaaattat ggtgatagtg caacattacc taaaggcata atgatgaatg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="plaintext"> 20701 tcgcaaaata tactcaactg tgtcaatatt taaacacatt aacattagct gtaccctata</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext"> 20761 atatgagagt tatacatttt ggtgctggtt ctgataaagg agttgcacca ggtacagctg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext"> 20821 ttttaagaca gtggttgcct acgggtacgc tgcttgtcga ttcagatctt aatgactttg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="plaintext"> 20881 tctctgatgc agattcaact ttgattggtg attgtgcaac tgtacataca gctaataaat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
823
</td>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="plaintext"> 20941 gggatctcat tattagtgat atgtacgacc ctaagactaa aaatgttaca aaagaaaatg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
824
</td>
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="plaintext"> 21001 actctaaaga gggttttttc acttacattt gtgggtttat acaacaaaag ctagctcttg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
825
</td>
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="plaintext"> 21061 gaggttccgt ggctataaag ataacagaac attcttggaa tgctgatctt tataagctca</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
826
</td>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="plaintext"> 21121 tgggacactt cgcatggtgg acagcctttg ttactaatgt gaatgcgtca tcatctgaag</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
827
</td>
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="plaintext"> 21181 catttttaat tggatgtaat tatcttggca aaccacgcga acaaatagat ggttatgtca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
828
</td>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="plaintext"> 21241 tgcatgcaaa ttacatattt tggaggaata caaatccaat tcagttgtct tcctattctt</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
829
</td>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="plaintext"> 21301 tatttgacat gagtaaattt ccccttaaat taaggggtac tgctgttatg tctttaaaag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
830
</td>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext"> 21361 aaggtcaaat caatgatatg attttatctc ttcttagtaa aggtagactt ataattagag</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
831
</td>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="plaintext"> 21421 aaaacaacag agttgttatt tctagtgatg ttcttgttaa caactaaacg aacaatgttt</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
832
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC832" class="line" lang="plaintext"> 21481 gtttttcttg ttttattgcc actagtctct agtcagtgtg ttaatcttac aaccagaact</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
833
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC833" class="line" lang="plaintext"> 21541 caattacccc ctgcatacac taattctttc acacgtggtg tttattaccc tgacaaagtt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC834" class="line" lang="plaintext"> 21601 ttcagatcct cagttttaca ttcaactcag gacttgttct tacctttctt ttccaatgtt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
835
</td>
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="plaintext"> 21661 acttggttcc atgctataca tgtctctggg accaatggta ctaagaggtt tgataaccct</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
836
</td>
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="plaintext"> 21721 gtcctaccat ttaatgatgg tgtttatttt gcttccactg agaagtctaa cataataaga</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
</td>
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="plaintext"> 21781 ggctggattt ttggtactac tttagattcg aagacccagt ccctacttat tgttaataac</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
838
</td>
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="plaintext"> 21841 gctactaatg ttgttattaa agtctgtgaa tttcaatttt gtaatgatcc atttttgggt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
839
</td>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="plaintext"> 21901 gtttattacc acaaaaacaa caaaagttgg atggaaagtg agttcagagt ttattctagt</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="plaintext"> 21961 gcgaataatt gcacttttga atatgtctct cagccttttc ttatggacct tgaaggaaaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="plaintext"> 22021 cagggtaatt tcaaaaatct tagggaattt gtgtttaaga atattgatgg ttattttaaa</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="plaintext"> 22081 atatattcta agcacacgcc tattaattta gtgcgtgatc tccctcaggg tttttcggct</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="plaintext"> 22141 ttagaaccat tggtagattt gccaataggt attaacatca ctaggtttca aactttactt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
844
</td>
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="plaintext"> 22201 gctttacata gaagttattt gactcctggt gattcttctt caggttggac agctggtgct</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
845
</td>
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="plaintext"> 22261 gcagcttatt atgtgggtta tcttcaacct aggacttttc tattaaaata taatgaaaat</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
846
</td>
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="plaintext"> 22321 ggaaccatta cagatgctgt agactgtgca cttgaccctc tctcagaaac aaagtgtacg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
847
</td>
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="plaintext"> 22381 ttgaaatcct tcactgtaga aaaaggaatc tatcaaactt ctaactttag agtccaacca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
848
</td>
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="plaintext"> 22441 acagaatcta ttgttagatt tcctaatatt acaaacttgt gcccttttgg tgaagttttt</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
849
</td>
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="plaintext"> 22501 aacgccacca gatttgcatc tgtttatgct tggaacagga agagaatcag caactgtgtt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
850
</td>
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="plaintext"> 22561 gctgattatt ctgtcctata taattccgca tcattttcca cttttaagtg ttatggagtg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
851
</td>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="plaintext"> 22621 tctcctacta aattaaatga tctctgcttt actaatgtct atgcagattc atttgtaatt</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
852
</td>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="plaintext"> 22681 agaggtgatg aagtcagaca aatcgctcca gggcaaactg gaaagattgc tgattataat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
853
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC853" class="line" lang="plaintext"> 22741 tataaattac cagatgattt tacaggctgc gttatagctt ggaattctaa caatcttgat</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="plaintext"> 22801 tctaaggttg gtggtaatta taattacctg tatagattgt ttaggaagtc taatctcaaa</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="plaintext"> 22861 ccttttgaga gagatatttc aactgaaatc tatcaggccg gtagcacacc ttgtaatggt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
856
</td>
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="plaintext"> 22921 gttgaaggtt ttaattgtta ctttccttta caatcatatg gtttccaacc cactaatggt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
857
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC857" class="line" lang="plaintext"> 22981 gttggttacc aaccatacag agtagtagta ctttcttttg aacttctaca tgcaccagca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
858
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC858" class="line" lang="plaintext"> 23041 actgtttgtg gacctaaaaa gtctactaat ttggttaaaa acaaatgtgt caatttcaac</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
859
</td>
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="plaintext"> 23101 ttcaatggtt taacaggcac aggtgttctt actgagtcta acaaaaagtt tctgcctttc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="plaintext"> 23161 caacaatttg gcagagacat tgctgacact actgatgctg tccgtgatcc acagacactt</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="plaintext"> 23221 gagattcttg acattacacc atgttctttt ggtggtgtca gtgttataac accaggaaca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="plaintext"> 23281 aatacttcta accaggttgc tgttctttat caggatgtta actgcacaga agtccctgtt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="plaintext"> 23341 gctattcatg cagatcaact tactcctact tggcgtgttt attctacagg ttctaatgtt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="plaintext"> 23401 tttcaaacac gtgcaggctg tttaataggg gctgaacatg tcaacaactc atatgagtgt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
865
</td>
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="plaintext"> 23461 gacataccca ttggtgcagg tatatgcgct agttatcaga ctcagactaa ttctcctcgg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="866" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
866
</td>
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="plaintext"> 23521 cgggcacgta gtgtagctag tcaatccatc attgcctaca ctatgtcact tggtgcagaa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
867
</td>
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="plaintext"> 23581 aattcagttg cttactctaa taactctatt gccataccca caaattttac tattagtgtt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
868
</td>
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="plaintext"> 23641 accacagaaa ttctaccagt gtctatgacc aagacatcag tagattgtac aatgtacatt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
869
</td>
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="plaintext"> 23701 tgtggtgatt caactgaatg cagcaatctt ttgttgcaat atggcagttt ttgtacacaa</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
870
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC870" class="line" lang="plaintext"> 23761 ttaaaccgtg ctttaactgg aatagctgtt gaacaagaca aaaacaccca agaagttttt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="871" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
871
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC871" class="line" lang="plaintext"> 23821 gcacaagtca aacaaattta caaaacacca ccaattaaag attttggtgg ttttaatttt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
872
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC872" class="line" lang="plaintext"> 23881 tcacaaatat taccagatcc atcaaaacca agcaagaggt catttattga agatctactt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
873
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC873" class="line" lang="plaintext"> 23941 ttcaacaaag tgacacttgc agatgctggc ttcatcaaac aatatggtga ttgccttggt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
874
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC874" class="line" lang="plaintext"> 24001 gatattgctg ctagagacct catttgtgca caaaagttta acggccttac tgttttgcca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="875" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
875
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC875" class="line" lang="plaintext"> 24061 cctttgctca cagatgaaat gattgctcaa tacacttctg cactgttagc gggtacaatc</span>
</pre>
</td>
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<td class="new_line diff-line-num new" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="plaintext"> 24121 acttctggtt ggacctttgg tgcaggtgct gcattacaaa taccatttgc tatgcaaatg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="plaintext"> 24181 gcttataggt ttaatggtat tggagttaca cagaatgttc tctatgagaa ccaaaaattg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="878" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="plaintext"> 24241 attgccaacc aatttaatag tgctattggc aaaattcaag actcactttc ttccacagca</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="plaintext"> 24301 agtgcacttg gaaaacttca agatgtggtc aaccaaaatg cacaagcttt aaacacgctt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="plaintext"> 24361 gttaaacaac ttagctccaa ttttggtgca atttcaagtg ttttaaatga tatcctttca</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="plaintext"> 24421 cgtcttgaca aagttgaggc tgaagtgcaa attgataggt tgatcacagg cagacttcaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="plaintext"> 24481 agtttgcaga catatgtgac tcaacaatta attagagctg cagaaatcag agcttctgct</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="plaintext"> 24541 aatcttgctg ctactaaaat gtcagagtgt gtacttggac aatcaaaaag agttgatttt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="plaintext"> 24601 tgtggaaagg gctatcatct tatgtccttc cctcagtcag cacctcatgg tgtagtcttc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="plaintext"> 24661 ttgcatgtga cttatgtccc tgcacaagaa aagaacttca caactgctcc tgccatttgt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="plaintext"> 24721 catgatggaa aagcacactt tcctcgtgaa ggtgtctttg tttcaaatgg cacacactgg</span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="plaintext"> 24781 tttgtaacac aaaggaattt ttatgaacca caaatcatta ctacagacaa cacatttgtg</span>
</pre>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="plaintext"> 24841 tctggtaact gtgatgttgt aataggaatt gtcaacaaca cagtttatga tcctttgcaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="plaintext"> 24901 cctgaattag actcattcaa ggaggagtta gataaatatt ttaagaatca tacatcacca</span>
</pre>
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</tr>
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<td class="new_line diff-line-num new" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="plaintext"> 24961 gatgttgatt taggtgacat ctctggcatt aatgcttcag ttgtaaacat tcaaaaagaa</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="plaintext"> 25021 attgaccgcc tcaatgaggt tgccaagaat ttaaatgaat ctctcatcga tctccaagaa</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="plaintext"> 25081 cttggaaagt atgagcagta tataaaatgg ccatggtaca tttggctagg ttttatagct</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="plaintext"> 25141 ggcttgattg ccatagtaat ggtgacaatt atgctttgct gtatgaccag ttgctgtagt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="plaintext"> 25201 tgtctcaagg gctgttgttc ttgtggatcc tgctgcaaat ttgatgaaga cgactctgag</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
895
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC895" class="line" lang="plaintext"> 25261 ccagtgctca aaggagtcaa attacattac acataaacga acttatggat ttgtttatga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
896
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC896" class="line" lang="plaintext"> 25321 gaatcttcac aattggaact gtaactttga agcaaggtga aatcaaggat gctactcctt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
897
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC897" class="line" lang="plaintext"> 25381 cagattttgt tcgcgctact gcaacgatac cgatacaagc ctcactccct ttcggatggc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
898
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC898" class="line" lang="plaintext"> 25441 ttattgttgg cgttgcactt cttgctgttt ttcagagcgc ttccaaaatc ataaccctca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
899
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC899" class="line" lang="plaintext"> 25501 aaaagagatg gcaactagca ctctccaagg gtgttcactt tgtttgcaac ttgctgttgt</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="plaintext"> 25561 tgtttgtaac agtttactca caccttttgc tcgttgctgc tggccttgaa gccccttttc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
901
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC901" class="line" lang="plaintext"> 25621 tctatcttta tgctttagtc tacttcttgc agagtataaa ctttgtaaga ataataatga</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="plaintext"> 25681 ggctttggct ttgctggaaa tgccgttcca aaaacccatt actttatgat gccaactatt</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="plaintext"> 25741 ttctttgctg gcatactaat tgttacgact attgtatacc ttacaatagt gtaacttctt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
904
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC904" class="line" lang="plaintext"> 25801 caattgtcat tacttcaggt gatggcacaa caagtcctat ttctgaacat gactaccaga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
905
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC905" class="line" lang="plaintext"> 25861 ttggtggtta tactgaaaaa tgggaatctg gagtaaaaga ctgtgttgta ttacacagtt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
906
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC906" class="line" lang="plaintext"> 25921 acttcacttc agactattac cagctgtact caactcaatt gagtacagac actggtgttg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
907
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC907" class="line" lang="plaintext"> 25981 aacatgttac cttcttcatc tacaataaaa ttgttgatga gcctgaagaa catgtccaaa</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="plaintext"> 26041 ttcacacaat cgacggttca tccggagttg ttaatccagt aatggaacca atttatgatg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="plaintext"> 26101 aaccgacgac gactactagc gtgcctttgt aagcacaagc tgatgagtac gaacttatgt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="plaintext"> 26161 actcattcgt ttcggaagag acaggtacgt taatagttaa tagcgtactt ctttttcttg</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="plaintext"> 26221 ctttcgtggt attcttgcta gttacactag ccatccttac tgcgcttcga ttgtgtgcgt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="plaintext"> 26281 actgctgcaa tattgttaac gtgagtcttg taaaaccttc tttttacgtt tactctcgtg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
913
</td>
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="plaintext"> 26341 ttaaaaatct gaattcttct agagttcctg atcttctggt ctaaacgaac taaatattat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
914
</td>
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="plaintext"> 26401 attagttttt ctgtttggaa ctttaatttt agccatggca gattccaacg gtactattac</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="plaintext"> 26461 cgttgaagag cttaaaaagc tccttgaaca atggaaccta gtaataggtt tcctattcct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
916
</td>
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="plaintext"> 26521 tacatggatt tgtcttctac aatttgccta tgccaacagg aataggtttt tgtatataat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
917
</td>
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="plaintext"> 26581 taagttaatt ttcctctggc tgttatggcc agtaacttta gcttgttttg tgcttgctgc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
918
</td>
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="plaintext"> 26641 tgtttacaga ataaattgga tcaccggtgg aattgctatc gcaatggctt gtcttgtagg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
919
</td>
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="plaintext"> 26701 cttgatgtgg ctcagctact tcattgcttc tttcagactg tttgcgcgta cgcgttccat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
920
</td>
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="plaintext"> 26761 gtggtcattc aatccagaaa ctaacattct tctcaacgtg ccactccatg gcactattct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
</td>
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="plaintext"> 26821 gaccagaccg cttctagaaa gtgaactcgt aatcggagct gtgatccttc gtggacatct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC922" class="line" lang="plaintext"> 26881 tcgtattgct ggacaccatc taggacgctg tgacatcaag gacctgccta aagaaatcac</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
923
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC923" class="line" lang="plaintext"> 26941 tgttgctaca tcacgaacgc tttcttatta caaattggga gcttcgcagc gtgtagcagg</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="plaintext"> 27001 tgactcaggt tttgctgcat acagtcgcta caggattggc aactataaat taaacacaga</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
925
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC925" class="line" lang="plaintext"> 27061 ccattccagt agcagtgaca atattgcttt gcttgtacag taagtgacaa cagatgtttc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
926
</td>
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="plaintext"> 27121 atctcgttga ctttcaggtt actatagcag agatattact aattattatg aggactttta</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
</td>
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="plaintext"> 27181 aagtttccat ttggaatctt gattacatca taaacctcat aattaaaaat ttatctaagt</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC928" class="line" lang="plaintext"> 27241 cactaactga gaataaatat tctcaattag atgaagagca accaatggag attgattaaa</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
929
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC929" class="line" lang="plaintext"> 27301 cgaacatgaa aattattctt ttcttggcac tgataacact cgctacttgt gagctttatc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
930
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC930" class="line" lang="plaintext"> 27361 actaccaaga gtgtgttaga ggtacaacag tacttttaaa agaaccttgc tcttctggaa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
931
</td>
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="plaintext"> 27421 catacgaggg caattcacca tttcatcctc tagctgataa caaatttgca ctgacttgct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC932" class="line" lang="plaintext"> 27481 ttagcactca atttgctttt gcttgtcctg acggcgtaaa acacgtctat cagttacgtg</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC933" class="line" lang="plaintext"> 27541 ccagatcagt ttcacctaaa ctgttcatca gacaagagga agttcaagaa ctttactctc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
</td>
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="plaintext"> 27601 caatttttct tattgttgcg gcaatagtgt ttataacact ttgcttcaca ctcaaaagaa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
</td>
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="plaintext"> 27661 agacagaatg attgaacttt cattaattga cttctatttg tgctttttag cctttctgct</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
</td>
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="plaintext"> 27721 attccttgtt ttaattatgc ttattatctt ttggttctca cttgaactgc aagatcataa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
</td>
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="plaintext"> 27781 tgaaacttgt cacgcctaaa cgaacatgaa atttcttgtt ttcttaggaa tcatcacaac</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
</td>
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="plaintext"> 27841 tgtagctgca tttcaccaag aatgtagttt acagtcatgt actcaacatc aaccatatgt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
</td>
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="plaintext"> 27901 agttgatgac ccgtgtccta ttcacttcta ttctaaatgg tatattagag taggagctag</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="plaintext"> 27961 aaaatcagca cctttaattg aattgtgcgt ggatgaggct ggttctaaat cacccattca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
941
</td>
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="plaintext"> 28021 gtacatcgat atcggtaatt atacagtttc ctgtttacct tttacaatta attgccagga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
942
</td>
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="plaintext"> 28081 acctaaattg ggtagtcttg tagtgcgttg ttcgttctat gaagactttt tagagtatca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
943
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC943" class="line" lang="plaintext"> 28141 tgacgttcgt gttgttttag atttcatcta aacgaacaaa ctaaaatgtc tgataatgga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
944
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC944" class="line" lang="plaintext"> 28201 ccccaaaatc agcgaaatgc accccgcatt acgtttggtg gaccctcaga ttcaactggc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
945
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC945" class="line" lang="plaintext"> 28261 agtaaccaga atggagaacg cagtggggcg cgatcaaaac aacgtcggcc ccaaggttta</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
946
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC946" class="line" lang="plaintext"> 28321 cccaataata ctgcgtcttg gttcaccgct ctcactcaac atggcaagga agaccttaaa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
947
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC947" class="line" lang="plaintext"> 28381 ttccctcgag gacaaggcgt tccaattaac accaatagca gtccagatga ccaaattggc</span>
</pre>
</td>
</tr>
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<td class="new_line diff-line-num new" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="plaintext"> 28441 tactaccgaa gagctaccag acgaattcgt ggtggtgacg gtaaaatgaa agatctcagt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
949
</td>
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="plaintext"> 28501 ccaagatggt atttctacta cctaggaact gggccagaag ctggacttcc ctatggtgct</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="plaintext"> 28561 aacaaagacg gcatcatatg ggttgcaact gagggagcct tgaatacacc aaaagatcac</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="plaintext"> 28621 attggcaccc gcaatcctgc taacaatgct gcaatcgtgc tacaacttcc tcaaggaaca</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="plaintext"> 28681 acattgccaa aaggcttcta cgcagaaggg agcagaggcg gcagtcaagc ctcttctcgt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="plaintext"> 28741 tcctcatcac gtagtcgcaa cagttcaaga aattcaactc caggcagcag taggggaact</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="plaintext"> 28801 tctcctgcta gaatggctgg caatggcggt gatgctgctc ttgctttgct gctgcttgac</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="plaintext"> 28861 agattgaacc agcttgagag caaaatgtct ggtaaaggcc aacaacaaca aggccaaact</span>
</pre>
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</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="plaintext"> 28921 gtcactaaga aatctgctgc tgaggcttct aagaagcctc ggcaaaaacg tactgccact</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="plaintext"> 28981 aaagcataca atgtaacaca agctttcggc agacgtggtc cagaacaaac ccaaggaaat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="plaintext"> 29041 tttggggacc aggaactaat cagacaagga actgattaca aacattggcc gcaaattgca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="plaintext"> 29101 caatttgccc ccagcgcttc agcgttcttc ggaatgtcgc gcattggcat ggaagtcaca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="plaintext"> 29161 ccttcgggaa cgtggttgac ctacacaggt gccatcaaat tggatgacaa agatccaaat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="plaintext"> 29221 ttcaaagatc aagtcatttt gctgaataag catattgacg catacaaaac attcccacca</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
962
</td>
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="plaintext"> 29281 acagagccta aaaaggacaa aaagaagaag gctgatgaaa ctcaagcctt accgcagaga</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="plaintext"> 29341 cagaagaaac agcaaactgt gactcttctt cctgctgcag atttggatga tttctccaaa</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
964
</td>
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="plaintext"> 29401 caattgcaac aatccatgag cagtgctgac tcaactcagg cctaaactca tgcagaccac</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="plaintext"> 29461 acaaggcaga tgggctatat aaacgttttc gcttttccgt ttacgatata tagtctactc</span>
</pre>
</td>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
966
</td>
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="plaintext"> 29521 ttgtgcagaa tgaattctcg taactacata gcacaagtag atgtagttaa ctttaatctc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
967
</td>
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="plaintext"> 29581 acatagcaat ctttaatcag tgtgtaacat tagggaggac ttgaaagagc caccacattt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
968
</td>
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="plaintext"> 29641 tcaccgaggc cacgcggagt acgatcgagt gtacagtgaa caatgctagg gagagctgcc</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
969
</td>
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="plaintext"> 29701 tatatggaag agccctaatg tgtaaaatta attttagtag tgctatcccc atgtgatttt</span>
</pre>
</td>
</tr>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="plaintext"> 29761 aatagcttct tagg</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
971
</td>
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="plaintext">//</span>
</pre>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#615ab5a7dac3179a14b1392ca1c88953381cbc7e"><strong>pangoLEARN/training/__init__.py</strong></a>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#efe721a7f83615610271fb571e2e0d610474eebf"><strong>pangoLEARN/training/downsample.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">csv</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">datetime</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">operator</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># import argparse</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># def parse_args():</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser = argparse.ArgumentParser(description="""Pick a representative sample for each unique sequence""",</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># formatter_class=argparse.RawTextHelpFormatter)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--in-metadata', dest = 'in_metadata', required=True, help='CSV of containing sequence_name and nucleotide_variants columns, the latter being | separated list of variants')</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--in-fasta', dest = 'in_fasta', required=True, help='FASTA of all input seqs')</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--diff', dest = 'diff', required=True, type=int, help='Samples within distance DIFF of included others may be excluded by the downsampler')</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--out-metadata', dest = 'out_metadata', required=True, help='CSV to write out')</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--out-fasta', dest = 'out_fasta', required=True, help='FASTA to write downsampled seqs')</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--outgroups', dest = 'outgroups', required=False, help='Lineage splits file containing representative outgroups to protect')</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--downsample_date_excluded', action='store_true', help='Downsample from those excluded as outside date window')</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--downsample_included', action='store_true', help='Downsample from all included sequences')</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># parser.add_argument('--downsample_lineage_size', type=int, default=None, help='Min size of lineages to downsample, if unspecified no lineage-aware downsampling')</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># args = parser.parse_args()</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># return args</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_outgroups</span><span class="p">(</span><span class="n" style="color: #333;">outgroup_file</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;"> input is CSV, last column being the representative outgroups:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">outgroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">outgroup_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">outgroups</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outgroup_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">outgroup_handle</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outgroup_handle</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">outgroup</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">outgroups</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">outgroup</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outgroup_handle</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">outgroups</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_count_dict</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">count_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">num_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">num_samples</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">var</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"nucleotide_variants"</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"|"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">var</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">count_dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">count_dict</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">count_dict</span><span class="p">[</span><span class="n" style="color: #333;">var</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Found"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">count_dict</span><span class="p">),</span> <span class="s" style="color: #d14;">"variants"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">sorted_tuples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">count_dict</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">operator</span><span class="p">.</span><span class="n" style="color: #333;">itemgetter</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">count_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="n" style="color: #333;">v</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_tuples</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count_dict</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_lineage_dict</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">min_size</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">lineage_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_size</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lineage_dict</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"lineage"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">lin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"lineage"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineage_dict</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">lineage_dict</span><span class="p">[</span><span class="n" style="color: #333;">lin</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"sequence_name"</span><span class="p">])</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">lineage_dict</span><span class="p">[</span><span class="n" style="color: #333;">lin</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"sequence_name"</span><span class="p">]]</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Found"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lineage_dict</span><span class="p">),</span> <span class="s" style="color: #d14;">"lineages"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">small_lineages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">lin</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineage_dict</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lineage_dict</span><span class="p">[</span><span class="n" style="color: #333;">lin</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_size</span><span class="p">]</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">small_lineages</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">lineage_dict</span><span class="p">[</span><span class="n" style="color: #333;">lin</span><span class="p">]</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Found"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lineage_dict</span><span class="p">),</span> <span class="s" style="color: #d14;">"lineages with at least"</span><span class="p">,</span> <span class="n" style="color: #333;">min_size</span><span class="p">,</span> <span class="s" style="color: #d14;">"representative sequences"</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lineage_dict</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_by_frequency</span><span class="p">(</span><span class="n" style="color: #333;">count_dict</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span><span class="mf" style="color: #099;">1.0</span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">num_samples</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">band</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">upper_bound</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">num_samples</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">band</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">most_frequent</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">k</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">k</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">count_dict</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lower_bound</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">count_dict</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">upper_bound</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">most_frequent</span><span class="p">),</span> <span class="s" style="color: #d14;">"lie in frequency band"</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">most_frequent</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">num_unique</span><span class="p">(</span><span class="n" style="color: #333;">muts1</span><span class="p">,</span> <span class="n" style="color: #333;">muts2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">u1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">m</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">u2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">m</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">u1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">u2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">should_downsample_row</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_date_excluded</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_included</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_lineage_size</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">lineage_dict</span><span class="o" style="font-weight: 600;">=</span><span class="p">{}):</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">downsample_included</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"why_excluded"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">downsample_date_excluded</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"why_excluded"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"date_filter"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"date_filter"</span><span class="p">].</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"sample_date older than"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">downsample_lineage_size</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"lineage"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineage_dict</span><span class="p">:</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">downsample</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">out_metadata</span><span class="p">,</span> <span class="n" style="color: #333;">in_fasta</span><span class="p">,</span> <span class="n" style="color: #333;">out_fasta</span><span class="p">,</span> <span class="n" style="color: #333;">max_diff</span><span class="p">,</span> <span class="n" style="color: #333;">outgroup_file</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_date_excluded</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_included</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_lineage_size</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">original_num_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">sample_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">var_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">count_dict</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_count_dict</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">most_frequent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_by_frequency</span><span class="p">(</span><span class="n" style="color: #333;">count_dict</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mf" style="color: #099;">0.05</span><span class="p">,</span><span class="mf" style="color: #099;">1.0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">very_most_frequent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_by_frequency</span><span class="p">(</span><span class="n" style="color: #333;">count_dict</span><span class="p">,</span> <span class="n" style="color: #333;">num_samples</span><span class="p">,</span> <span class="n" style="color: #333;">band</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span><span class="mf" style="color: #099;">1.0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">lineage_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_lineage_dict</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">,</span><span class="n" style="color: #333;">downsample_lineage_size</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">outgroups</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_outgroups</span><span class="p">(</span><span class="n" style="color: #333;">outgroup_file</span><span class="p">)</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">indexed_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">in_fasta</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">in_metadata</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">,</span> <span class="n" style="color: #333;">newline</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">csv_in</span><span class="p">,</span> \</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_fasta</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">newline</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fa_out</span><span class="p">,</span> \</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_metadata</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">newline</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">csv_out</span><span class="p">:</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">csv_in</span><span class="p">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">quotechar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">dialect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unix"</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictWriter</span><span class="p">(</span><span class="n" style="color: #333;">csv_out</span><span class="p">,</span> <span class="n" style="color: #333;">fieldnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reader</span><span class="p">.</span><span class="n" style="color: #333;">fieldnames</span><span class="p">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">quotechar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">quoting</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">QUOTE_MINIMAL</span><span class="p">,</span> <span class="n" style="color: #333;">dialect</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unix"</span><span class="p">)</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writeheader</span><span class="p">()</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">fasta_header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"sequence_name"</span><span class="p">]</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fasta_header</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indexed_fasta</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">original_num_seqs</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">1000</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%s Downsampled from %i seqs to %i seqs"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">),</span> <span class="n" style="color: #333;">original_num_seqs</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sample_dict</span><span class="p">)))</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">original_num_seqs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fasta_header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outgroups</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">should_downsample_row</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span><span class="n" style="color: #333;">downsample_date_excluded</span><span class="p">,</span> <span class="n" style="color: #333;">downsample_included</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">downsample_lineage_size</span><span class="p">,</span><span class="n" style="color: #333;">lineage_dict</span><span class="p">):</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fasta_header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outgroups</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"why_excluded"</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"why_excluded"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"None"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">fasta_header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indexed_fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">seq_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexed_fasta</span><span class="p">[</span><span class="n" style="color: #333;">fasta_header</span><span class="p">]</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">fa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">fa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seq_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"why_excluded"</span><span class="p">],</span> <span class="n" style="color: #333;">fasta_header</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">fasta_header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indexed_fasta</span><span class="p">))</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">muts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"nucleotide_variants"</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"|"</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">muts</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_diff</span><span class="p">:</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if not row["why_excluded"]:</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># row["why_excluded"] = "downsampled with diff threshold %i" %max_diff</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">found_close_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">low_frequency_muts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mut</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">most_frequent</span><span class="p">]</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">low_frequency_muts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">low_frequency_muts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">mut</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">very_most_frequent</span><span class="p">]</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">low_frequency_muts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">low_frequency_muts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">muts</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">low_frequency_muts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_diff</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">low_frequency_muts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">low_frequency_muts</span><span class="p">[:</span><span class="n" style="color: #333;">max_diff</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">low_frequency_muts</span><span class="p">:</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">var_dict</span><span class="p">:</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">samples</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">var_dict</span><span class="p">[</span><span class="n" style="color: #333;">mut</span><span class="p">])</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">downsample_lineage_size</span><span class="p">:</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">&</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">lineage_dict</span><span class="p">[</span><span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"lineage"</span><span class="p">]])</span> <span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num_unique</span><span class="p">(</span><span class="n" style="color: #333;">muts</span><span class="p">,</span> <span class="n" style="color: #333;">sample_dict</span><span class="p">[</span><span class="n" style="color: #333;">sample</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">max_diff</span><span class="p">:</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">found_close_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#if not row["why_excluded"]:</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># row["why_excluded"] = "downsampled with diff threshold %i" %max_diff</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">found_close_seq</span><span class="p">:</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">sample_dict</span><span class="p">[</span><span class="n" style="color: #333;">fasta_header</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">muts</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">muts</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">var_dict</span><span class="p">:</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">var_dict</span><span class="p">[</span><span class="n" style="color: #333;">mut</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">fasta_header</span><span class="p">]</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">var_dict</span><span class="p">[</span><span class="n" style="color: #333;">mut</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">fasta_header</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">row</span><span class="p">[</span><span class="s" style="color: #d14;">"why_excluded"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">writerow</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fasta_header</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indexed_fasta</span><span class="p">:</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">seq_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indexed_fasta</span><span class="p">[</span><span class="n" style="color: #333;">fasta_header</span><span class="p">]</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">fa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">seq_rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">fa_out</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">seq_rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">now</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%s Downsampled from %i seqs to %i seqs"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">now</span><span class="p">),</span> <span class="n" style="color: #333;">original_num_seqs</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sample_dict</span><span class="p">)))</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return sample_dict.keys()</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># def main():</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># args = parse_args()</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># subsample = downsample(args.in_metadata, args.out_metadata, args.in_fasta, args.out_fasta, args.diff, args.outgroups, args.downsample_date_excluded, args.downsample_included, args.downsample_lineage_size)</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># if __name__ == '__main__':</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># main()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#927dbe358afc82a665cde7bc081ffcbdb5e6ad62"><strong>pangoLEARN/training/getDecisionTreeRules.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.tree</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DecisionTreeClassifier</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.tree</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">export_text</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">joblib</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.tree</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_tree</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">setrecursionlimit</span><span class="p">(</span><span class="mi" style="color: #099;">4000</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">loaded_model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">joblib</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">joblib</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">finalHeaders</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"["</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1000</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">finalHeaders</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">finalHeaders</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">finalHeaders</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finalHeaders</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">finalHeaders</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finalHeaders</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"'"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">finalHeaders</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="n" style="color: #333;">categories</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">loaded_model</span><span class="p">.</span><span class="n" style="color: #333;">classes_</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getClass</span><span class="p">(</span><span class="n" style="color: #333;">weightArray</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">weightArray</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weightArray</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">maxIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">weightArray</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">weightArray</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">maxValue</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">maxValue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weightArray</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">maxIndex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">classes</span><span class="p">[</span><span class="n" style="color: #333;">maxIndex</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reformatRule</span><span class="p">(</span><span class="n" style="color: #333;">sign</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">letter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"_"</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"=="</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sign</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"<="</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"!="</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">position</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">symbol</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">letter</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="n" style="color: #333;">outcomesToRules</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tree_to_code</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">feature_names</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">tree_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">.</span><span class="n" style="color: #333;">tree_</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">feature_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">feature_names</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">_tree</span><span class="p">.</span><span class="n" style="color: #333;">TREE_UNDEFINED</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"undefined!"</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree_</span><span class="p">.</span><span class="n" style="color: #333;">feature</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">prevRules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">recurse</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">prevRules</span><span class="p">):</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">indent</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">depth</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tree_</span><span class="p">.</span><span class="n" style="color: #333;">feature</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">_tree</span><span class="p">.</span><span class="n" style="color: #333;">TREE_UNDEFINED</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature_name</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">]</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree_</span><span class="p">.</span><span class="n" style="color: #333;">threshold</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">]</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">prevRulesRight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prevRules</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">prevRulesLeft</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prevRules</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">prevRulesLeft</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">reformatRule</span><span class="p">(</span><span class="s" style="color: #d14;">"<="</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">))</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">prevRulesRight</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">reformatRule</span><span class="p">(</span><span class="s" style="color: #d14;">">"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">))</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">recurse</span><span class="p">(</span><span class="n" style="color: #333;">tree_</span><span class="p">.</span><span class="n" style="color: #333;">children_left</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">],</span> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">prevRulesLeft</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">recurse</span><span class="p">(</span><span class="n" style="color: #333;">tree_</span><span class="p">.</span><span class="n" style="color: #333;">children_right</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">],</span> <span class="n" style="color: #333;">depth</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">prevRulesRight</span><span class="p">)</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">rulesString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prevRules</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rule</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">prevRules</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">rule</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rule</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">rulesString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rulesString</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rule</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">outcome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getClass</span><span class="p">(</span><span class="n" style="color: #333;">tree_</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outcome</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outcomesToRules</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">outcomesToRules</span><span class="p">[</span><span class="n" style="color: #333;">outcome</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">outcome</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rulesString</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">recurse</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">prevRules</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="n" style="color: #333;">tree_to_code</span><span class="p">(</span><span class="n" style="color: #333;">loaded_model</span><span class="p">,</span> <span class="n" style="color: #333;">finalHeaders</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">formatCommonRules</span><span class="p">(</span><span class="n" style="color: #333;">ruleSets</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">splitRuleSets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">totalRules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">commonRules</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ruleSets</span><span class="p">:</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">splitRuleSets</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">):</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">totalRules</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">totalRules</span><span class="p">:</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">addRule</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">splitRuleSets</span><span class="p">:</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">addRule</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">addRule</span><span class="p">:</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="n" style="color: #333;">commonRules</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">splitRuleSets</span><span class="p">:</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">commonRules</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">commonRules</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">commonRules</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">c</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" AND "</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">splitRuleSets</span><span class="p">:</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"("</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]:</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">retString</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">") OR "</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">retString</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span></pre>
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<li id="5ef06f9b6b28b5d4448f18c67a9e053f21440b54">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#5ef06f9b6b28b5d4448f18c67a9e053f21440b54"><strong>pangoLEARN/training/outgroups.csv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">lineage,outgroup</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">A,Wuhan/WH04/2020</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">B,Wuhan/WHU01/2020</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">B.1,Italy/ABR-IZSGC-TE5166/2020</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">B.1.1,Germany/BY-MVP-V2010837/2020</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">B.1.177,Spain/VC-IBV-98006461/2020</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">B.1.1.7,England/MILK-9E05B3/2020</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">B.1.160,Belgium/rega-10021225/2020</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">B.1.2,USA/TX-HMH-MCoV-16306/2020</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">B.1.258,England/LEED-2A8A64/2020</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">B.1.243,USA/TX-HMH-MCoV-18678/2020</span></pre>
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<li id="2c879efa6cd87c47e13035644f01174136dffa47">
<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#2c879efa6cd87c47e13035644f01174136dffa47"><strong>pangoLEARN/training/pangoLEARNDecisionTree_v1.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.model_selection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">train_test_split</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">metrics</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.datasets</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">make_classification</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.model_selection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StratifiedShuffleSplit</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.tree</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DecisionTreeClassifier</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.metrics</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">accuracy_score</span><span class="p">,</span> <span class="n" style="color: #333;">f1_score</span><span class="p">,</span> <span class="n" style="color: #333;">precision_score</span><span class="p">,</span> <span class="n" style="color: #333;">recall_score</span><span class="p">,</span> <span class="n" style="color: #333;">classification_report</span><span class="p">,</span> <span class="n" style="color: #333;">confusion_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">make_scorer</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">datetime</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datetime</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">joblib</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.model_selection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cross_val_score</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pickle</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># file with lineage assignments</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">lineage_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># file with sequences</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="n" style="color: #333;">sequence_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># how much of the data will be used for testing, instead of training</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="n" style="color: #333;">testing_percentage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0000000001</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">relevant_positions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pickle</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">relevant_positions</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># the path to the reference file. </span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This reference sequence must be the same as is used in the pangolearn script!!</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">referenceFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># data storage</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="n" style="color: #333;">dataList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># dict for lookup efficiency</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">indiciesToKeep</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">referenceId</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Wuhan/WH04/2020"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="n" style="color: #333;">referenceSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="n" style="color: #333;">idToLineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"><span class="n" style="color: #333;">idToSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">mustKeepIds</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">mustKeepLineages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># function for handling weird sequence characters</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clean</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'T'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'A'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'G'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'C'</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'-'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'U'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'T'</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># otherwise return value from reference</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">referenceSeq</span><span class="p">[</span><span class="n" style="color: #333;">loc</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findReferenceSeq</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">referenceFile</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">currentSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">">"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">currentSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">currentSeq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">currentSeq</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">getDataLine</span><span class="p">(</span><span class="n" style="color: #333;">seqId</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">dataLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">dataLine</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqId</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">newSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for each character in the sequence</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">newSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newSeq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">clean</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">],</span> <span class="n" style="color: #333;">index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">dataLine</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">newSeq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> </span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dataLine</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">readInAndFormatData</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># add the data line for the reference seq</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">idToLineage</span><span class="p">[</span><span class="n" style="color: #333;">referenceId</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"A"</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">dataList</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">getDataLine</span><span class="p">(</span><span class="n" style="color: #333;">referenceId</span><span class="p">,</span> <span class="n" style="color: #333;">referenceSeq</span><span class="p">))</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># create a dictionary of sequence ids to their assigned lineages</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">lineage_file</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">idToLineage</span><span class="p">[</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># close the file</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">seq_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span> <span class="p">:</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">seq</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">sequence_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta"</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"files read in, now processing"</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idToLineage</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">dataList</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">getDataLine</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">seq_dict</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]))</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"unable to find the lineage classification for: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">key</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># find columns in the data list which always have the same value</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">findColumnsWithoutSNPs</span><span class="p">():</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for each index in the length of each sequence</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dataList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])):</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># loop through all lines</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dataList</span><span class="p">:</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if there is a difference somewhere, then we want to keep it</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">dataList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># otherwise, save it</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">relevant_positions</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">indiciesToKeep</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># remove columns from the data list which don't have any SNPs. We do this because</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># these columns won't be relevant for a logistic regression which is trying to use</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># differences between sequences to assign lineages</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">removeOtherIndices</span><span class="p">(</span><span class="n" style="color: #333;">indiciesToKeep</span><span class="p">):</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># instantiate the final list</span></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">finalList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">indicies</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">indiciesToKeep</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">indicies</span><span class="p">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># while the dataList isn't empty</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dataList</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pop the first line</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dataList</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">seqId</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># initialize the finalLine</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">finalLine</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">indicies</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if its the first index, then that's the lineage assignment, so keep it</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">finalLine</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">seqId</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># otherwise keep everything at the indices in indiciesToKeep</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">finalLine</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">])</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># save the finalLine to the finalList</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">finalList</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">finalLine</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">finalList</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">allEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">entries</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">:</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">entries</span><span class="p">:</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">entries</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">entries</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">removeAmbiguous</span><span class="p">():</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">idsToRemove</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">lineMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">idMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dataList</span><span class="p">:</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">keyString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">","</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:])</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keyString</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineMap</span><span class="p">:</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">lineMap</span><span class="p">[</span><span class="n" style="color: #333;">keyString</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">idMap</span><span class="p">[</span><span class="n" style="color: #333;">keyString</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> </span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idToLineage</span><span class="p">:</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">lineMap</span><span class="p">[</span><span class="n" style="color: #333;">keyString</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">idToLineage</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">idMap</span><span class="p">[</span><span class="n" style="color: #333;">keyString</span><span class="p">].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"diagnostics"</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">keyString</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineMap</span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">allEqual</span><span class="p">(</span><span class="n" style="color: #333;">lineMap</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]):</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">skipRest</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># see if any protected lineages are contained in the set, if so keep those ids</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lineage</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineMap</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]:</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineage</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mustKeepLineages</span><span class="p">:</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">skipRest</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idMap</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]:</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineage</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">idToLineage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mustKeepIds</span><span class="p">:</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">idsToRemove</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># none of the lineages are protected, fire at will</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">skipRest</span><span class="p">:</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">lineageToCounts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">aLineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># find most common lineage</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lineage</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineMap</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]:</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineage</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">:</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">[</span><span class="n" style="color: #333;">lineage</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">[</span><span class="n" style="color: #333;">lineage</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">[</span><span class="n" style="color: #333;">lineage</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">aLineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aLineage</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lineage</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">:</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">[</span><span class="n" style="color: #333;">lineage</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lineageToCounts</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">]:</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lineage</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idMap</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]:</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">idToLineage</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]:</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">idsToRemove</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">newList</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"keeping indicies:"</span><span class="p">)</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">dataList</span><span class="p">:</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">idsToRemove</span><span class="p">:</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idToLineage</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">newList</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">newList</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"reading in data "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y, %H:%M:%S"</span><span class="p">),</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"><span class="n" style="color: #333;">referenceSeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findReferenceSeq</span><span class="p">()</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"><span class="n" style="color: #333;">readInAndFormatData</span><span class="p">()</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"processing snps, formatting data "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y, %H:%M:%S"</span><span class="p">),</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"><span class="n" style="color: #333;">findColumnsWithoutSNPs</span><span class="p">()</span></span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"><span class="n" style="color: #333;">dataList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeOtherIndices</span><span class="p">(</span><span class="n" style="color: #333;">indiciesToKeep</span><span class="p">)</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# sequences before blacklisting"</span><span class="p">)</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dataList</span><span class="p">))</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"><span class="n" style="color: #333;">dataList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">removeAmbiguous</span><span class="p">()</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"# sequences after blacklisting"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dataList</span><span class="p">))</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># headers are the original genome locations</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"><span class="n" style="color: #333;">headers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">indiciesToKeep</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"><span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"lineage"</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"setting up training "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y, %H:%M:%S"</span><span class="p">),</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"><span class="n" style="color: #333;">pima</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">dataList</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">headers</span><span class="p">)</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># nucleotide symbols which can appear</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="n" style="color: #333;">categories</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-'</span><span class="p">]</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># one hot encoding of all headers other than the first which is the lineage</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="n" style="color: #333;">dummyHeaders</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">headers</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add extra rows to ensure all of the categories are represented, as otherwise </span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># not enough columns will be created when we call get_dummies</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">categories</span><span class="p">:</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">dataList</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">pima</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pima</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># get one-hot encoding</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"><span class="n" style="color: #333;">pima</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">get_dummies</span><span class="p">(</span><span class="n" style="color: #333;">pima</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dummyHeaders</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># get rid of the fake data we just added</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"><span class="n" style="color: #333;">pima</span><span class="p">.</span><span class="n" style="color: #333;">drop</span><span class="p">(</span><span class="n" style="color: #333;">pima</span><span class="p">.</span><span class="n" style="color: #333;">tail</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">categories</span><span class="p">)).</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"><span class="n" style="color: #333;">feature_cols</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">pima</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">feature_cols</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># remove the last column from the data frame. This is because we are trying to predict these values.</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"><span class="n" style="color: #333;">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">feature_cols</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"><span class="n" style="color: #333;">X</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pima</span><span class="p">[</span><span class="n" style="color: #333;">feature_cols</span><span class="p">]</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pima</span><span class="p">[</span><span class="n" style="color: #333;">h</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># separate the data frame into testing/training data sets. 25% of the data will be used for training, 75% for test.</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"><span class="n" style="color: #333;">X_train</span><span class="p">,</span><span class="n" style="color: #333;">X_test</span><span class="p">,</span><span class="n" style="color: #333;">y_train</span><span class="p">,</span><span class="n" style="color: #333;">y_test</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">train_test_split</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">,</span><span class="n" style="color: #333;">test_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">testing_percentage</span><span class="p">,</span><span class="n" style="color: #333;">random_state</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"training "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y, %H:%M:%S"</span><span class="p">),</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="python"><span class="n" style="color: #333;">header_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="s" style="color: #d14;">"decisionTreeHeaders_v1.joblib"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"><span class="n" style="color: #333;">joblib</span><span class="p">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">headers</span><span class="p">,</span> <span class="n" style="color: #333;">header_out</span><span class="p">,</span> <span class="n" style="color: #333;">compress</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">9</span><span class="p">)</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># instantiate the random forest with 1000 trees</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"><span class="n" style="color: #333;">dt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DecisionTreeClassifier</span><span class="p">()</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># fit the model</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"><span class="n" style="color: #333;">dt</span><span class="p">.</span><span class="n" style="color: #333;">fit</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="p">)</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"testing "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y, %H:%M:%S"</span><span class="p">),</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># classify the test data</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"><span class="n" style="color: #333;">y_pred</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">dt</span><span class="p">.</span><span class="n" style="color: #333;">predict</span><span class="p">(</span><span class="n" style="color: #333;">X_test</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">y_pred</span><span class="p">)</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># get the scores from these predictions</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"><span class="n" style="color: #333;">y_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dt</span><span class="p">.</span><span class="n" style="color: #333;">predict_proba</span><span class="p">(</span><span class="n" style="color: #333;">X_test</span><span class="p">)</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"generating statistics "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datetime</span><span class="p">.</span><span class="n" style="color: #333;">now</span><span class="p">().</span><span class="n" style="color: #333;">strftime</span><span class="p">(</span><span class="s" style="color: #d14;">"%m/%d/%Y, %H:%M:%S"</span><span class="p">),</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#print the confusion matrix</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"--------------------------------------------"</span><span class="p">)</span></span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Confusion Matrix"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"><span class="n" style="color: #333;">cnf_matrix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">metrics</span><span class="p">.</span><span class="n" style="color: #333;">confusion_matrix</span><span class="p">(</span><span class="n" style="color: #333;">y_test</span><span class="p">,</span> <span class="n" style="color: #333;">y_pred</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">cnf_matrix</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"--------------------------------------------"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Classification report"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">metrics</span><span class="p">.</span><span class="n" style="color: #333;">classification_report</span><span class="p">(</span><span class="n" style="color: #333;">y_test</span><span class="p">,</span> <span class="n" style="color: #333;">y_pred</span><span class="p">,</span> <span class="n" style="color: #333;">digits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># save the model files to compressed joblib files</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># using joblib instead of pickle because these large files need to be compressed</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"><span class="n" style="color: #333;">model_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="s" style="color: #d14;">"decisionTree_v1.joblib"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"><span class="n" style="color: #333;">joblib</span><span class="p">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">dt</span><span class="p">,</span> <span class="n" style="color: #333;">model_out</span><span class="p">,</span> <span class="n" style="color: #333;">compress</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">9</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"model files created"</span><span class="p">,</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># this method is used below when running 10-fold cross validation. It ensures</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># that the per-lineage statistics are generated for each cross-fold</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">classification_report_with_accuracy_score</span><span class="p">(</span><span class="n" style="color: #333;">y_true</span><span class="p">,</span> <span class="n" style="color: #333;">y_pred</span><span class="p">):</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"--------------------------------------------"</span><span class="p">)</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Crossfold Classification Report"</span><span class="p">)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">metrics</span><span class="p">.</span><span class="n" style="color: #333;">classification_report</span><span class="p">(</span><span class="n" style="color: #333;">y_true</span><span class="p">,</span> <span class="n" style="color: #333;">y_pred</span><span class="p">,</span> <span class="n" style="color: #333;">digits</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">accuracy_score</span><span class="p">(</span><span class="n" style="color: #333;">y_true</span><span class="p">,</span> <span class="n" style="color: #333;">y_pred</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># optionally, run 10-fold cross validation (comment this out if not needed as it takes a while to run)</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># cross_validation_scores = cross_val_score(dt, X=X, y=y, cv=10, scoring=make_scorer(classification_report_with_accuracy_score))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-pangolearn/-/compare/7b3b78fc1ec5653665c23ed8a3ae1ad8c87e3f0a...fca780e7500c2a9c01f3b7a2b96c58b9298104e1#bcb931320871a58344d28fa6ff020be9d89f9721"><strong>pangoLEARN/training/processOutputFile.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">outputfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">nameToLineage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Lineage</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">precisions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">recalls</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f1s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">supports</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">printStats</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">avgPrec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">precisions</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">precisions</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">avgRec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">recalls</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">recalls</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">avgF1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f1s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">f1s</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">totalSupport</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">supports</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">avgPrec</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">avgRec</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">avgF1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">","</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">totalSupport</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">outputfile</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">split</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"macro avg"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"weighted avg"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nameToLineage</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Lineage</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">precisions</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">recalls</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">f1s</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">supports</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">":"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">line</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nameToLineage</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Lineage</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">precisions</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">recalls</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">f1s</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">].</span><span class="n" style="color: #333;">supports</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">split</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"lineage,precision,recall,f1_score,support"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nameToLineage</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"macro"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"weighted"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">key</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">].</span><span class="n" style="color: #333;">printStats</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="s" style="color: #d14;">"macro avg"</span><span class="p">].</span><span class="n" style="color: #333;">printStats</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="n" style="color: #333;">nameToLineage</span><span class="p">[</span><span class="s" style="color: #d14;">"weighted avg"</span><span class="p">].</span><span class="n" style="color: #333;">printStats</span><span class="p">()</span></span></pre>
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