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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/6c273eac249079dddc97e6f2e1d4acdd749abe07">6c273eac</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-07-11T02:05:35+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1250</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/9e046023f3cb2515ca9e055a101bb363501bc98e">9e046023</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-07-11T02:05:35+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/last-align/-/commit/bf1432f5464effc0f937939646b03c87be267edf">bf1432f5</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-07-11T02:05:35+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry

</pre>

</li>

</ul>

<h4>18 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#b81b5de5f7bfd818c69285e09a1e8f1bef73444e">

bin/maf-convert

</a>

</li>

<li class="file-stats">

<a href="#63a0bbefe2fd66bf4c0908eacca1076fc04263b6">

bin/maf-swap

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">

debian/patches/2to3.patch

</a>

</li>

<li class="file-stats">

<a href="#1aed97b2ebfde2d21c24639963d42434bdcfddb8">

doc/lastal.rst

</a>

</li>

<li class="file-stats">

<a href="#4543c6ba972a23fa884543e091d830105a84288f">

doc/maf-convert.rst

</a>

</li>

<li class="file-stats">

<a href="#8758dc959aa5524be83960d0bfd56945bc432a26">

src/AlignmentWrite.cc

</a>

</li>

<li class="file-stats">

<a href="#4b7be8c3b80efc62977b307791d1a304c23e1fa4">

src/LastalArguments.cc

</a>

</li>

<li class="file-stats">

<a href="#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

src/lastal.cc

</a>

</li>

<li class="file-stats">

<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">

src/makefile

</a>

</li>

<li class="file-stats">

<a href="#1e8b7c6cdfd3ee5e24a1aadd55e212791c8bbf4b">

<span class="new-file">

+

test/frameshift-new.maf

</span>

</a>

</li>

<li class="file-stats">

<a href="#a81c2db8e6e690a6632a84731453a5a1b4e40d61">

<span class="new-file">

+

test/frameshift-old.maf

</span>

</a>

</li>

<li class="file-stats">

<a href="#6c90adec85ff9834658c43a287e5d780f52732ef">

test/last-test.out

</a>

</li>

<li class="file-stats">

<a href="#fcd3167fe23623673ee838f0da31855d3d479dff">

test/last-test.sh

</a>

</li>

<li class="file-stats">

<a href="#fa1f2beb637146f5175aacd2f5469caf7be2e7eb">

test/maf-convert-test.out

</a>

</li>

<li class="file-stats">

<a href="#91ede9ced121fa989c86d8e8721da9214813a826">

test/maf-convert-test.sh

</a>

</li>

<li class="file-stats">

<a href="#b6a13701586c2871af8117b9a92cc4d1efabc505">

test/maf-swap-test.out

</a>

</li>

<li class="file-stats">

<a href="#b6d5f875b0957cb0d3543c8c073a712d4ae0db6f">

test/maf-swap-test.sh

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="b81b5de5f7bfd818c69285e09a1e8f1bef73444e">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#b81b5de5f7bfd818c69285e09a1e8f1bef73444e"><strong>bin/maf-convert</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,6 +25,36 @@ try:</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="25" 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">

25

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<td class="new_line diff-line-num" data-linenumber="25" 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">

25

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC25" class="line" lang="html">except ImportError:</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="26" 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">

26

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<td class="new_line diff-line-num" data-linenumber="26" 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">

26

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="html">    pass</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="27" 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">

27

</td>

<td class="new_line diff-line-num" data-linenumber="27" 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">

27

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="html"></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="28" style="width: 35px; color: rgba(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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC28" class="line" lang="html">aminoAcidCodes = {"ALA": "A",</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="28" style="width: 35px; color: rgba(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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC29" class="line" lang="html">                  "CYS": "C",</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="28" style="width: 35px; color: rgba(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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC30" class="line" lang="html">                  "ASP": "D",</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="28" style="width: 35px; color: rgba(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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC31" class="line" lang="html">                  "GLU": "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="28" style="width: 35px; color: rgba(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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC32" class="line" lang="html">                  "PHE": "F",</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="28" style="width: 35px; color: rgba(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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC33" class="line" lang="html">                  "GLY": "G",</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="28" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="html">                  "HIS": "H",</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="28" style="width: 35px; color: rgba(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="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="html">                  "ILE": "I",</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="28" style="width: 35px; color: rgba(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="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="html">                  "LYS": "K",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="html">                  "LEU": "L",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="html">                  "MET": "M",</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="28" style="width: 35px; color: rgba(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="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">

39

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="html">                  "ASN": "N",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="html">                  "PRO": "P",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="html">                  "GLN": "Q",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="html">                  "ARG": "R",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC43" class="line" lang="html">                  "SER": "S",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="html">                  "THR": "T",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="html">                  "VAL": "V",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="html">                  "TRP": "W",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC47" class="line" lang="html">                  "TYR": "Y",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="html">                  "***": "*",</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC49" class="line" lang="html">                  "XAA": "X"}</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="28" style="width: 35px; color: rgba(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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="html"></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="28" style="width: 35px; color: rgba(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="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC51" class="line" lang="html">def standardGeneticCode():</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC52" class="line" lang="html">    aa = "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"</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="28" style="width: 35px; color: rgba(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="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

53

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC53" class="line" lang="html">    b1 = "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG"</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC54" class="line" lang="html">    b2 = "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG"</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="28" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC55" class="line" lang="html">    b3 = "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"</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="28" style="width: 35px; color: rgba(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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC56" class="line" lang="html">    return {x + y + z: a for a, x, y, z in zip(aa, b1, b2, b3)}</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="28" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC57" class="line" lang="html"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="28" 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">

28

</td>

<td class="new_line diff-line-num" data-linenumber="58" 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">

58

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC58" class="line" lang="html">def myOpen(fileName):</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="29" 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">

29

</td>

<td class="new_line diff-line-num" data-linenumber="59" 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">

59

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC59" class="line" lang="html">    if fileName == "-":</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="30" 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">

30

</td>

<td class="new_line diff-line-num" data-linenumber="60" 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">

60

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC60" class="line" lang="html">        return sys.stdin</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="97" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,24 +97,33 @@ def insertSize(row, letterSize):</td>

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<td class="old_line diff-line-num" data-linenumber="67" 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">

67

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<td class="new_line diff-line-num" data-linenumber="97" 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="LC97" class="line" lang="html">def matchAndInsertSizes(alignmentColumns, letterSizes):</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="68" 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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<td class="new_line diff-line-num" data-linenumber="98" 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="LC98" class="line" lang="html">    """Get sizes of gapless blocks, and of the inserts between them."""</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="69" 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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<td class="new_line diff-line-num" data-linenumber="99" 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="LC99" class="line" lang="html">    letterSizeA, letterSizeB = letterSizes</span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC100" class="line" lang="html">    delInc = max(letterSizeA, 1)</span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC101" class="line" lang="html">    delDiv = 1 if letterSizeA else 3</span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC102" class="line" lang="html">    insInc = max(letterSizeB, 1)</span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC103" class="line" lang="html">    insDiv = 1 if letterSizeB else 3</span>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC104" class="line" lang="html">    sizeDiv = max(delDiv, insDiv)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="70" 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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<td class="new_line diff-line-num" data-linenumber="105" 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="LC105" class="line" lang="html">    delSize = insSize = subSize = 0</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="71" 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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<td class="new_line diff-line-num" data-linenumber="106" 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="LC106" class="line" lang="html">    for x, y in alignmentColumns:</span>

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<td class="old_line diff-line-num" data-linenumber="72" 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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<td class="new_line diff-line-num" data-linenumber="107" 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="LC107" class="line" lang="html">        if x == "-":</span>

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<td class="old_line diff-line-num" data-linenumber="73" 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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<td class="new_line diff-line-num" data-linenumber="108" 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="LC108" class="line" lang="html">            if subSize:</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="74" 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="new_line diff-line-num old" data-linenumber="109" 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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<pre style="margin: 0;">-<span id="LC74" class="line" lang="html">                if delSize or insSize: yield str(delSize) + ":" + str(insSize)</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="109" 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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<pre style="margin: 0;">-<span id="LC75" class="line" lang="html">                yield str(subSize)</span>

</pre>

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<td class="old_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">

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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">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="html">                if delSize or insSize:</span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC110" class="line" lang="html">                    yield str(delSize // delDiv) + ":" + str(insSize // insDiv)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="html">                yield str(subSize // sizeDiv)</span>

</pre>

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76

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<td class="new_line diff-line-num" data-linenumber="112" 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="LC112" class="line" lang="html">                delSize = insSize = subSize = 0</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="77" 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="new_line diff-line-num old" data-linenumber="113" 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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<pre style="margin: 0;">-<span id="LC77" class="line" lang="html">            insSize += symbolSize(y, <span class="idiff left right">letterSizeB</span>)</span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="html">            insSize += symbolSize(y, <span class="idiff left right">insInc</span>)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="html">        elif y == "-":</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="79" 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">

79

</td>

<td class="new_line diff-line-num" data-linenumber="115" 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">

115

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="html">            if subSize:</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="80" 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">

80

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<td class="new_line diff-line-num old" data-linenumber="116" 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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<pre style="margin: 0;">-<span id="LC80" class="line" lang="html">                if delSize or insSize: yield str(delSize) + ":" + str(insSize)</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="81" 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">

81

</td>

<td class="new_line diff-line-num old" data-linenumber="116" 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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<pre style="margin: 0;">-<span id="LC81" class="line" lang="html">                yield str(subSize)</span>

</pre>

</td>

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<td class="old_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">

</td>

<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="html">                if delSize or insSize:</span>

</pre>

</td>

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<td class="old_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">

</td>

<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="html">                    yield str(delSize // delDiv) + ":" + str(insSize // insDiv)</span>

</pre>

</td>

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<td class="old_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">

</td>

<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="html">                yield str(subSize // sizeDiv)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="82" 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">

82

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<td class="new_line diff-line-num" data-linenumber="119" 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">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="html">                delSize = insSize = subSize = 0</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="83" 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">

83

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<td class="new_line diff-line-num old" data-linenumber="120" 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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<pre style="margin: 0;">-<span id="LC83" class="line" lang="html">            delSize += symbolSize(x, <span class="idiff left right">letterSizeA</span>)</span>

</pre>

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<td class="old_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">

</td>

<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="html">            delSize += symbolSize(x, <span class="idiff left right">delInc</span>)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="84" 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">

84

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<td class="new_line diff-line-num" data-linenumber="121" 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">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="html">        else:</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="85" 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">

85

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<td class="new_line diff-line-num" data-linenumber="122" 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">

122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="html">            subSize += 1</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="86" 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">

86

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<td class="new_line diff-line-num old" data-linenumber="123" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC86" class="line" lang="html">    if delSize or insSize: yield str(delSize) + ":" + str(insSize)</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="87" 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">

87

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<td class="new_line diff-line-num old" data-linenumber="123" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC87" class="line" lang="html">    if subSize: yield str(subSize)</span>

</pre>

</td>

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<td class="old_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">

</td>

<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="html">    if delSize or insSize:</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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="html">        yield str(delSize // delDiv) + ":" + str(insSize // insDiv)</span>

</pre>

</td>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC125" class="line" lang="html">    if subSize:</span>

</pre>

</td>

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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="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">

</td>

<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="html">        yield str(subSize // sizeDiv)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="88" 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">

88

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<td class="new_line diff-line-num" data-linenumber="127" 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">

127

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC127" class="line" lang="html"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="89" 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">

89

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<td class="new_line diff-line-num" data-linenumber="128" 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">

128

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="html">##### Routines for reading MAF format: #####</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="90" 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">

90

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<td class="new_line diff-line-num" data-linenumber="129" 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">

129

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="html"></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="159" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,8 +159,11 @@ def mafInput(opts, lines):</td>

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<td class="old_line diff-line-num" data-linenumber="120" 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="LC159" class="line" lang="html">            beg = int(beg)</span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="html">            span = int(span)</span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="html">            seqLen = int(seqLen)</span>

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<td class="old_line diff-line-num old" data-linenumber="123" 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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<pre style="margin: 0;">-<span id="LC123" class="line" lang="html">            if "\\" in row or "/" in row or len(row) - row.count("-") <span class="nt" style="color: #000080;"><</span> <span class="nt" style="color: #000080;">span:</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">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="html">            rowLetters = len(row) - row.count("-")</span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="html">            if "\\" in row or "/" in row or rowLetters <span class="nt" style="color: #000080;"><</span> <span class="nt" style="color: #000080;">span:</span></span>

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<td class="old_line diff-line-num" data-linenumber="124" 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="LC164" class="line" lang="html">                <span class="na" style="color: #008080;">letterSize = </span><span class="s" style="color: #d14;">3</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">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="html">            <span class="na" style="color: #008080;">elif</span> <span class="na" style="color: #008080;">rowLetters</span> <span class="nt" style="color: #000080;">></span> span:</span>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="html">                letterSize = 0  # xxx means 3-letter codes like AlaCysAsp</span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="html">            else:</span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="html">                letterSize = 1</span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="html">            fields = seqName, seqLen, strand, letterSize, beg, beg + span, row</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="306" 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">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -306,48 +348,83 @@ def mafConvertToChain(opts, lines):</td>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="html"><span class="na" style="color: #008080;">#####</span> <span class="na" style="color: #008080;">Routines</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">converting</span> <span class="na" style="color: #008080;">to</span> <span class="na" style="color: #008080;">PSL</span> <span class="na" style="color: #008080;">format:</span> <span class="na" style="color: #008080;">#####</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="html"></span>

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<pre style="margin: 0;">-<span id="LC309" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">pslBlocks</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">mafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">outCounts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC351" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">pslBlocks</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;"><span class="idiff left">geneticCode</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">mafs</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">outCounts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="html">    <span class="err" style="color: #a61717; background-color: #e3d2d2;">"""</span><span class="na" style="color: #008080;">Get</span> <span class="na" style="color: #008080;">sizes</span> <span class="na" style="color: #008080;">and</span> <span class="na" style="color: #008080;">start</span> <span class="na" style="color: #008080;">coordinates</span> <span class="na" style="color: #008080;">of</span> <span class="na" style="color: #008080;">gapless</span> <span class="na" style="color: #008080;">blocks</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">an</span> <span class="na" style="color: #008080;">alignment.</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="html">    <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">repMatches</span> <span class="na" style="color: #008080;">is</span> <span class="na" style="color: #008080;">always</span> <span class="na" style="color: #008080;">zero</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="312" 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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<td class="new_line diff-line-num" data-linenumber="354" 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="LC354" class="line" lang="html">    <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">proteins</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">nCount</span> <span class="na" style="color: #008080;">is</span> <span class="na" style="color: #008080;">always</span> <span class="na" style="color: #008080;">zero</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">because</span> <span class="na" style="color: #008080;">that</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">'</span><span class="na" style="color: #008080;">s</span> <span class="na" style="color: #008080;">what</span> <span class="na" style="color: #008080;">BLATv34</span> <span class="na" style="color: #008080;">does</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="313" 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="LC355" class="line" lang="html">    <span class="na" style="color: #008080;">normalBases = </span><span class="s" style="color: #d14;">"ACGTU"</span></span>

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<td class="old_line diff-line-num old" data-linenumber="314" 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="new_line diff-line-num old" data-linenumber="356" 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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<pre style="margin: 0;">-<span id="LC314" class="line" lang="html">    <span class="na" style="color: #008080;"><span class="idiff left right">matches = </span></span><span class="s" style="color: #d14;">mismatches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="na" style="color: #008080;">repMatches = </span><span class="s" style="color: #d14;">nCount</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span></span>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC356" class="line" lang="html">    <span class="na" style="color: #008080;">mismatches = </span><span class="s" style="color: #d14;">repMatches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="na" style="color: #008080;">nCount = </span><span class="s" style="color: #d14;">0</span></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="316" 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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<td class="new_line diff-line-num" data-linenumber="358" 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="LC358" class="line" lang="html">    <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">maf</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">mafs:</span></span>

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<td class="old_line diff-line-num" data-linenumber="317" 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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<td class="new_line diff-line-num" data-linenumber="359" 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="LC359" class="line" lang="html">        <span class="na" style="color: #008080;">sLines = </span><span class="s" style="color: #d14;">maf[1]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="318" 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="LC360" class="line" lang="html">        <span class="na" style="color: #008080;">fieldsA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">fieldsB = </span><span class="s" style="color: #d14;">pairOrDie(sLines,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">PSL</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="html">        <span class="na" style="color: #008080;">letterSizeA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowA = </span><span class="s" style="color: #d14;">fieldsA[3:7]</span></span>

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<td class="new_line diff-line-num" data-linenumber="362" 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="LC362" class="line" lang="html">        <span class="na" style="color: #008080;">letterSizeB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowB = </span><span class="s" style="color: #d14;">fieldsB[3:7]</span></span>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC322" class="line" lang="html">        <span class="na" style="color: #008080;">size = </span><span class="s" style="color: #d14;">0</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC323" class="line" lang="html">        <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">y</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">zip</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">rowA.upper</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(),</span> <span class="na" style="color: #008080;">rowB.upper</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">())</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="html">            <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">x =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="html">                <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">size:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC326" class="line" lang="html">                    <span class="na" style="color: #008080;">yield</span> <span class="na" style="color: #008080;">size</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="327" 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">

327

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="html">                    <span class="na" style="color: #008080;">begA</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="na" style="color: #008080;">size</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">letterSizeA</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="328" 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">

328

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<td class="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC328" class="line" lang="html">                    <span class="na" style="color: #008080;">begB</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="na" style="color: #008080;">size</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">letterSizeB</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="329" 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">

329

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<td class="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC329" class="line" lang="html">                    <span class="na" style="color: #008080;">size = </span><span class="s" style="color: #d14;">0</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="330" 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">

330

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<td class="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC330" class="line" lang="html">                <span class="na" style="color: #008080;">begB</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="na" style="color: #008080;">symbolSize</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">y</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="331" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC331" class="line" lang="html">            <span class="na" style="color: #008080;">elif</span> <span class="na" style="color: #008080;">y =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="332" 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">

332

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<td class="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC332" class="line" lang="html">                <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">size:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="333" 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">

333

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<td class="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC333" class="line" lang="html">                    <span class="na" style="color: #008080;">yield</span> <span class="na" style="color: #008080;">size</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="334" 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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<pre style="margin: 0;">-<span id="LC334" class="line" lang="html">                    <span class="na" style="color: #008080;">begA</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="na" style="color: #008080;">size</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">letterSizeA</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="335" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC335" class="line" lang="html">                    <span class="na" style="color: #008080;">begB</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="na" style="color: #008080;">size</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">letterSizeB</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="336" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC336" class="line" lang="html">                    <span class="na" style="color: #008080;">size = </span><span class="s" style="color: #d14;">0</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="337" 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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<pre style="margin: 0;">-<span id="LC337" class="line" lang="html">                <span class="na" style="color: #008080;">begA</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="na" style="color: #008080;">symbolSize</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="338" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC338" class="line" lang="html">            <span class="na" style="color: #008080;">else:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="339" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC339" class="line" lang="html">                <span class="na" style="color: #008080;">size</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="340" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC340" class="line" lang="html">                <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">x</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">normalBases</span> <span class="na" style="color: #008080;">and</span> <span class="na" style="color: #008080;">y</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">normalBases</span> <span class="na" style="color: #008080;">or</span> <span class="na" style="color: #008080;">opts.protein:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="341" 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="new_line diff-line-num old" data-linenumber="363" 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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<pre style="margin: 0;">-<span id="LC341" class="line" lang="html">                    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">x =</span><span class="s" style="color: #d14;">=</span> <span class="na" style="color: #008080;">y:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="342" 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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<pre style="margin: 0;">-<span id="LC342" class="line" lang="html">                        <span class="na" style="color: #008080;">matches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></span>

</pre>

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343

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="html">                    <span class="na" style="color: #008080;">else:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC363" class="line" lang="html">        <span class="na" style="color: #008080;">rowA = </span><span class="s" style="color: #d14;">rowA.upper()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC364" class="line" lang="html">        <span class="na" style="color: #008080;">rowB = </span><span class="s" style="color: #d14;">rowB.upper()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

365

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC366" class="line" lang="html">        <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">letterSizeA</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">letterSizeB</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC367" class="line" lang="html">            <span class="na" style="color: #008080;">letterSpanA = </span><span class="s" style="color: #d14;">3</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">letterSizeA</span> <span class="na" style="color: #008080;">*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC368" class="line" lang="html">            <span class="na" style="color: #008080;">letterSpanB = </span><span class="s" style="color: #d14;">3</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">letterSizeB</span> <span class="na" style="color: #008080;">*</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC369" class="line" lang="html">            <span class="na" style="color: #008080;">codeA = </span><span class="s" style="color: #d14;">geneticCode</span> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">letterSizeA</span> <span class="na" style="color: #008080;">else</span> <span class="na" style="color: #008080;">aminoAcidCodes</span></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC370" class="line" lang="html">            <span class="na" style="color: #008080;">codeB = </span><span class="s" style="color: #d14;">geneticCode</span> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">letterSizeB</span> <span class="na" style="color: #008080;">else</span> <span class="na" style="color: #008080;">aminoAcidCodes</span></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC371" class="line" lang="html">            <span class="na" style="color: #008080;">loopEnd = </span><span class="s" style="color: #d14;">len(rowA)</span></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC372" class="line" lang="html">            <span class="na" style="color: #008080;">i = </span><span class="s" style="color: #d14;">j</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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">

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="html">            <span class="na" style="color: #008080;">while</span> <span class="na" style="color: #008080;">j</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="na" style="color: #008080;">loopEnd:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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">

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<pre style="margin: 0;">+<span id="LC374" class="line" lang="html">                <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">rowA[j] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC375" class="line" lang="html">                    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">j</span> <span class="nt" style="color: #000080;">></span> i:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="html">                        size = j - i</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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">

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="html">                        yield size // 3, begA, begB</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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">

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="html">                        begA += size // letterSpanA</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-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

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="html">                        begB += size // letterSpanB</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(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="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="html">                    begB += 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="344" style="width: 35px; color: rgba(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="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="html">                    j += letterSpanB</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="344" style="width: 35px; color: rgba(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="html">                    i = j</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="344" style="width: 35px; color: rgba(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="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="html">                elif rowB[j] == "-":</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="344" style="width: 35px; color: rgba(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="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="html">                    if j > i:</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="344" style="width: 35px; color: rgba(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="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="html">                        size = j - i</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="344" style="width: 35px; color: rgba(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="html">                        yield size // 3, begA, begB</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="344" style="width: 35px; color: rgba(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="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="html">                        begA += size // letterSpanA</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="344" style="width: 35px; color: rgba(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="html">                        begB += size // letterSpanB</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="344" style="width: 35px; color: rgba(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="html">                    begA += 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="344" style="width: 35px; color: rgba(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="html">                    j += letterSpanA</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="344" style="width: 35px; color: rgba(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="html">                    i = j</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="344" style="width: 35px; color: rgba(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="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

</td>

<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="html">                else:</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="344" style="width: 35px; color: rgba(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="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

393

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC393" class="line" lang="html">                    k = j + 3</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="344" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC394" class="line" lang="html">                    if codeA.get(rowA[j:k], "X") != codeB.get(rowB[j:k], "X"):</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="344" 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">

344

</td>

<td class="new_line diff-line-num" data-linenumber="395" 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">

395

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC395" class="line" lang="html">                        mismatches += 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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                    j = k</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="345" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC397" class="line" lang="html">            if j > i:</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="345" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC398" class="line" lang="html">                yield (j - i) // 3, begA, begB</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">        else:</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="345" style="width: 35px; color: rgba(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="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

400

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC400" class="line" lang="html">            isProtein = opts.protein or letterSizeA * letterSizeB > 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="345" style="width: 35px; color: rgba(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="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="html">            size = 0</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="345" style="width: 35px; color: rgba(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="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="html">            for x, y in zip(rowA, rowB):</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                if x == "-":</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="345" style="width: 35px; color: rgba(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="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

404

</td>

<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="html">                    if size:</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="345" style="width: 35px; color: rgba(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="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

405

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC405" class="line" lang="html">                        yield size, begA, begB</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                        begA += size * letterSizeA</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="345" style="width: 35px; color: rgba(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="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

407

</td>

<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="html">                        begB += size * letterSizeB</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                        size = 0</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                    begB += symbolSize(y, letterSizeB)</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                elif y == "-":</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                    if size:</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                        yield size, begA, begB</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="345" style="width: 35px; color: rgba(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="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="html">                        begA += size * letterSizeA</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                        begB += size * letterSizeB</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="345" style="width: 35px; color: rgba(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="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="html">                        size = 0</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="345" style="width: 35px; color: rgba(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="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

</td>

<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="html">                    begA += symbolSize(x, letterSizeA)</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="345" 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">

345

</td>

<td class="new_line diff-line-num" data-linenumber="417" 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">

417

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC417" class="line" lang="html">                else:</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="346" 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">

346

</td>

<td class="new_line diff-line-num old" data-linenumber="418" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC346" class="line" lang="html">                    <span class="na" style="color: #008080;">nCount</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="347" 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">

347

</td>

<td class="new_line diff-line-num old" data-linenumber="418" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC347" class="line" lang="html">        <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">size:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="348" 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">

348

</td>

<td class="new_line diff-line-num old" data-linenumber="418" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC348" class="line" lang="html">            <span class="na" style="color: #008080;">yield</span> <span class="na" style="color: #008080;">size</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span></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="349" style="width: 35px; color: rgba(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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC418" class="line" lang="html">                    size += 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="349" style="width: 35px; color: rgba(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="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="html">                    if x in normalBases and y in normalBases or isProtein:</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="420" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC420" class="line" lang="html">                        if x != y:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="html">                            mismatches += 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="html">                    else:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="html">                        nCount += 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="html">            if size:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="html">                yield size, begA, begB</span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="html"></span>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="html">    <span class="na" style="color: #008080;">outCounts[0:<span class="idiff left">4</span>] = </span><span class="s" style="color: #d14;"><span class="idiff">matches,</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">mismatches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">repMatches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">nCount</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="html">    outCounts[0:<span class="idiff left right">3</span>] = mismatches, repMatches, nCount</span>

</pre>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="html"></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="html">def pslNumInserts(blocks, letterSizeA, letterSizeB):</span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="html">    numInsertA = numInsertB = 0</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="371" 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">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -371,31 +448,43 @@ def pslEnds(seqLen, strand, beg, end):</td>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="html">        return seqLen - end, seqLen - beg</span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="html">    return beg, end</span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="html"></span>

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="html">def writePsl(opts, mafs):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="html">    matchCounts = [0] * 4</span>

</pre>

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<pre style="margin: 0;">-<span id="LC376" class="line" lang="html">    blocks = list(pslBlocks(opts, mafs, matchCounts))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC377" class="line" lang="html">    matches, mismatches, repMatches, nCount = matchCounts</span>

</pre>

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="html">    numGaplessColumns = sum(matchCounts)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="html">def writePsl(opts, geneticCode, mafs):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="html">    matchCounts = [0] * 3</span>

</pre>

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="html">    blocks = list(pslBlocks(opts, geneticCode, mafs, matchCounts))</span>

</pre>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="html">    mismatches, repMatches, nCount = matchCounts</span>

</pre>

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="html">    numGaplessColumns = sum(i[0] for i in blocks)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="html">    matches = numGaplessColumns - sum(matchCounts)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="html">    if not blocks:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="html">        return</span>

</pre>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="html">    fieldsA, fieldsB = mafs[0][1]</span>

</pre>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC463" class="line" lang="html">    if fieldsA[3] <span class="nt" style="color: #000080;"><</span> <span class="nt" style="color: #000080;">fieldsB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[3]</span><span class="na" style="color: #008080;">:</span>  <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">protein-to-DNA</span> <span class="na" style="color: #008080;">alignment</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC464" class="line" lang="html">        <span class="na" style="color: #008080;">fieldsA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">fieldsB = </span><span class="s" style="color: #d14;">fieldsB,</span> <span class="na" style="color: #008080;">fieldsA</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC465" class="line" lang="html">        <span class="na" style="color: #008080;">blocks = </span><span class="s" style="color: #d14;">[(s,</span> <span class="na" style="color: #008080;">b</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">a</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">s</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">a</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">b</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">blocks</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC466" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC467" class="line" lang="html">    <span class="na" style="color: #008080;">seqNameA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">seqLenA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">strandA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeA = </span><span class="s" style="color: #d14;">fieldsA[0:4]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="html">    <span class="na" style="color: #008080;">seqNameB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">seqLenB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">strandB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeB = </span><span class="s" style="color: #d14;">fieldsB[0:4]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="html">    <span class="na" style="color: #008080;">sizeMulA = </span><span class="s" style="color: #d14;">3</span> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">letterSizeA</span> <span class="nt" style="color: #000080;">></span> letterSizeB else 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC471" class="line" lang="html">    sizeMulB = 3 if letterSizeB > letterSizeA else 1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC472" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="384" 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">

384

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="html">    headSize, headBegA, headBegB = blocks[0]</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="385" 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">

385

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="html">    tailSize, tailBegA, tailBegB = blocks[-1]</span>

</pre>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="html">    <span class="idiff left right">seqNameA, seqLenA, strandA, letterSizeA = fieldsA[0:4]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="html">    begA, endA = pslEnds(seqLenA, strandA, headBegA, tail<span class="idiff left right">BegA + tailSize</span>)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="html">    baseInsertA = endA - begA - numGaplessColumns * <span class="idiff left right">letterSize</span>A</span>

</pre>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="html">    <span class="idiff left right">tailEndA = tailBegA + tailSize * sizeMulA</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC477" class="line" lang="html">    begA, endA = pslEnds(seqLenA, strandA, headBegA, tail<span class="idiff left right">EndA</span>)</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC478" class="line" lang="html">    baseInsertA = endA - begA - numGaplessColumns * <span class="idiff left right">sizeMul</span>A</span>

</pre>

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390

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="html"></span>

</pre>

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391

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="html">    <span class="idiff left right">seqNameB, seqLenB, strandB, letterSizeB = fieldsB[0:4]</span></span>

</pre>

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392

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<td class="new_line diff-line-num old" data-linenumber="480" 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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<pre style="margin: 0;">-<span id="LC392" class="line" lang="html">    begB, endB = pslEnds(seqLenB, strandB, headBegB, tail<span class="idiff left right">BegB + tailSize</span>)</span>

</pre>

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393

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<td class="new_line diff-line-num old" data-linenumber="480" 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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<pre style="margin: 0;">-<span id="LC393" class="line" lang="html">    baseInsertB = endB - begB - numGaplessColumns * <span class="idiff left right">letterSize</span>B</span>

</pre>

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</td>

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<pre style="margin: 0;">+<span id="LC480" class="line" lang="html">    <span class="idiff left right">tailEndB = tailBegB + tailSize * sizeMulB</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC481" class="line" lang="html">    begB, endB = pslEnds(seqLenB, strandB, headBegB, tail<span class="idiff left right">EndB</span>)</span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC482" class="line" lang="html">    baseInsertB = endB - begB - numGaplessColumns * <span class="idiff left right">sizeMul</span>B</span>

</pre>

</td>

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC483" class="line" lang="html"></span>

</pre>

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395

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<td class="new_line diff-line-num old" data-linenumber="484" 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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<pre style="margin: 0;">-<span id="LC395" class="line" lang="html">    numInsertA, numInsertB = pslNumInserts(blocks, <span class="idiff left right">letterSizeA, letterSize</span>B)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="html">    numInsertA, numInsertB = pslNumInserts(blocks, <span class="idiff left right">sizeMulA, sizeMul</span>B)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="396" 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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<td class="new_line diff-line-num" data-linenumber="485" 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="LC485" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="397" 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="LC486" class="line" lang="html">    strand = strandB</span>

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<td class="new_line diff-line-num old" data-linenumber="487" 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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<pre style="margin: 0;">-<span id="LC398" class="line" lang="html">    if <span class="idiff left right">letterSizeA > 1 or letterSize</span>B > 1:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="html">    if <span class="idiff left right">sizeMulA > 1 or sizeMul</span>B > 1:</span>

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<td class="new_line diff-line-num" data-linenumber="488" 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="LC488" class="line" lang="html">        strand += strandA</span>

</pre>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="html">    elif strandA != "+":</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="401" 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="LC490" class="line" lang="html">        raise Exception("for non-translated PSL, the 1st strand in each alignment must be +")</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="409" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="498" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -409,15 +498,16 @@ def writePsl(opts, mafs):</td>

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<td class="old_line diff-line-num" data-linenumber="409" 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="LC498" class="line" lang="html">          blockCount, blockSizes, blockStartsB, blockStartsA, sep="\t")</span>

</pre>

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="html"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC500" class="line" lang="html">def mafConvertToPsl(opts, lines):</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">

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="html">    geneticCode = standardGeneticCode()</span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="html">    if opts.Join:</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="503" 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="LC503" class="line" lang="html">        for i in colinearMafInput(opts, lines):</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="504" 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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<pre style="margin: 0;">-<span id="LC414" class="line" lang="html">            writePsl(opts, i)</span>

</pre>

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<td class="old_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">

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="html">            writePsl(opts, <span class="idiff left right">geneticCode, </span>i)</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="505" 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="LC505" class="line" lang="html">    elif opts.join:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="416" 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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<td class="new_line diff-line-num" data-linenumber="506" 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="LC506" class="line" lang="html">        for i in mafGroupInput(opts, lines):</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="507" 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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<pre style="margin: 0;">-<span id="LC417" class="line" lang="html">            writePsl(opts, i)</span>

</pre>

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="html">            writePsl(opts, <span class="idiff left right">geneticCode, </span>i)</span>

</pre>

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418

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508

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="html">    else:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="419" 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">

419

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<td class="new_line diff-line-num" data-linenumber="509" 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">

509

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="html">        for i in mafInput(opts, lines):</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="420" 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">

420

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<td class="new_line diff-line-num old" data-linenumber="510" 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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<pre style="margin: 0;">-<span id="LC420" class="line" lang="html">            writePsl(opts, [i])</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="html">            writePsl(opts, <span class="idiff left right">geneticCode, </span>[i])</span>

</pre>

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421

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511

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC511" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="422" 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">

422

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<td class="new_line diff-line-num" data-linenumber="512" 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">

512

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="html">##### Routines for converting to SAM format: #####</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="423" 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">

423

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<td class="new_line diff-line-num" data-linenumber="513" 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">

513

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC513" class="line" lang="html"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="714" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="804" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -714,20 +804,61 @@ def blastDataFromMafFields(fields):</td>

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<td class="old_line diff-line-num" data-linenumber="714" 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">

714

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<td class="new_line diff-line-num" data-linenumber="804" 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">

804

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<pre style="margin: 0;"> <span id="LC804" class="line" lang="html">    else:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="715" 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">

715

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<td class="new_line diff-line-num" data-linenumber="805" 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">

805

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<pre style="margin: 0;"> <span id="LC805" class="line" lang="html">        beg = seqLen - beg</span>

</pre>

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716

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806

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC806" class="line" lang="html">        end = seqLen - end + 1</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="717" 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">

717

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<td class="new_line diff-line-num old" data-linenumber="807" 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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<pre style="margin: 0;">-<span id="LC717" class="line" lang="html">    return seqName, str(beg), str(end), row.upper()</span>

</pre>

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<td class="old_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">

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC807" class="line" lang="html">    return seqName, letterSize, str(beg), str(end), row.upper()</span>

</pre>

</td>

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<td class="old_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">

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC808" class="line" lang="html"></span>

</pre>

</td>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC809" class="line" lang="html">def codonMatchCounts(geneticCode, letterSizeA, letterSizeB, rowA, rowB):</span>

</pre>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC810" class="line" lang="html">    letterSpanA = 3 - letterSizeA * 2</span>

</pre>

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<td class="old_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">

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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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC811" class="line" lang="html">    letterSpanB = 3 - letterSizeB * 2</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC812" class="line" lang="html">    codeA = geneticCode if letterSizeA else aminoAcidCodes</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC813" class="line" lang="html">    codeB = geneticCode if letterSizeB else aminoAcidCodes</span>

</pre>

</td>

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</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC814" class="line" lang="html">    loopEnd = len(rowA)</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC815" class="line" lang="html">    matches = mismatches = gaps = dangles = 0</span>

</pre>

</td>

</tr>

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</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC816" class="line" lang="html">    i = 0</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC817" class="line" lang="html">    while i <span class="nt" style="color: #000080;"><</span> <span class="nt" style="color: #000080;">loopEnd:</span></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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC818" class="line" lang="html">        <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">rowA[i] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></span>

</pre>

</td>

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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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC819" class="line" lang="html">            <span class="na" style="color: #008080;">gaps</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></span>

</pre>

</td>

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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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC820" class="line" lang="html">            <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">rowA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">+1</span><span class="na" style="color: #008080;">] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span> <span class="na" style="color: #008080;">and</span> <span class="na" style="color: #008080;">rowA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">+2</span><span class="na" style="color: #008080;">] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></span>

</pre>

</td>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC821" class="line" lang="html">                <span class="na" style="color: #008080;">i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3</span></span>

</pre>

</td>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC822" class="line" lang="html">            <span class="na" style="color: #008080;">else:</span></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC823" class="line" lang="html">                <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">rowB[i-1] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></span>

</pre>

</td>

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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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC824" class="line" lang="html">                    <span class="na" style="color: #008080;">dangles</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC825" class="line" lang="html">                <span class="na" style="color: #008080;">i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC826" class="line" lang="html">        <span class="na" style="color: #008080;">elif</span> <span class="na" style="color: #008080;">rowB[i] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC827" class="line" lang="html">            <span class="na" style="color: #008080;">gaps</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC828" class="line" lang="html">            <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">rowB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">+1</span><span class="na" style="color: #008080;">] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span> <span class="na" style="color: #008080;">and</span> <span class="na" style="color: #008080;">rowB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">i</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">+2</span><span class="na" style="color: #008080;">] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC829" class="line" lang="html">                <span class="na" style="color: #008080;">i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3</span></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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC830" class="line" lang="html">            <span class="na" style="color: #008080;">else:</span></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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC831" class="line" lang="html">                <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">rowA[i-1] =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">:</span></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="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">

</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="html">                    <span class="na" style="color: #008080;">dangles</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></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="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">

</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="html">                <span class="na" style="color: #008080;">i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></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="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">

</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="html">        <span class="na" style="color: #008080;">else:</span></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC835" class="line" lang="html">            <span class="na" style="color: #008080;">j = </span><span class="s" style="color: #d14;">i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3</span></span>

</pre>

</td>

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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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC836" class="line" lang="html">            <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">codeA.get</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">rowA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">i:j</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">],</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">X</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">) =</span><span class="s" style="color: #d14;">=</span> <span class="na" style="color: #008080;">codeB.get</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">rowB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="na" style="color: #008080;">i:j</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">],</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">X</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<td class="old_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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC837" class="line" lang="html">                <span class="na" style="color: #008080;">matches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC838" class="line" lang="html">            <span class="na" style="color: #008080;">else:</span></span>

</pre>

</td>

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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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC839" class="line" lang="html">                <span class="na" style="color: #008080;">mismatches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span></span>

</pre>

</td>

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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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC840" class="line" lang="html">            <span class="na" style="color: #008080;">i = </span><span class="s" style="color: #d14;">j</span></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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC841" class="line" lang="html">    <span class="na" style="color: #008080;">return</span> <span class="na" style="color: #008080;">matches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">mismatches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">gaps</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">dangles</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="718" 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">

718

</td>

<td class="new_line diff-line-num" data-linenumber="842" 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">

842

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC842" class="line" lang="html"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="719" 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">

719

</td>

<td class="new_line diff-line-num old" data-linenumber="843" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC719" class="line" lang="html">def writeBlastTab(opts, maf):</span>

</pre>

</td>

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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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC843" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">writeBlastTab</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;"><span class="idiff left">geneticCode</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">maf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="720" 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">

720

</td>

<td class="new_line diff-line-num" data-linenumber="844" 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">

844

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC844" class="line" lang="html">    <span class="na" style="color: #008080;">aLine</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">sLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">qLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">pLines = </span><span class="s" style="color: #d14;">maf</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="721" 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">

721

</td>

<td class="new_line diff-line-num" data-linenumber="845" 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">

845

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC845" class="line" lang="html">    <span class="na" style="color: #008080;">fieldsA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">fieldsB = </span><span class="s" style="color: #d14;">pairOrDie(sLines,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">BlastTab</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="722" 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">

722

</td>

<td class="new_line diff-line-num old" data-linenumber="846" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC722" class="line" lang="html">    seqNameA, begA, endA, rowA = blastDataFromMafFields(fieldsA)</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="723" 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">

723

</td>

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<pre style="margin: 0;">-<span id="LC723" class="line" lang="html">    seqNameB, begB, endB, rowB = blastDataFromMafFields(fieldsB)</span>

</pre>

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846

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<pre style="margin: 0;">+<span id="LC846" class="line" lang="html">    <span class="na" style="color: #008080;">seqNameA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowA = </span><span class="s" style="color: #d14;">blastDataFromMafFields(fieldsA)</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC847" class="line" lang="html">    <span class="na" style="color: #008080;">seqNameB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowB = </span><span class="s" style="color: #d14;">blastDataFromMafFields(fieldsB)</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC848" class="line" lang="html">    <span class="na" style="color: #008080;">gapOpens = </span><span class="s" style="color: #d14;">gapRunCount(rowA)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="na" style="color: #008080;">gapRunCount</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">rowB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC849" class="line" lang="html"></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC850" class="line" lang="html">    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">letterSizeA</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">letterSizeB</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="html">        <span class="na" style="color: #008080;">c = </span><span class="s" style="color: #d14;">codonMatchCounts(geneticCode,</span> <span class="na" style="color: #008080;">letterSizeA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></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

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="html">        <span class="na" style="color: #008080;">matches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">mismatches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">gaps</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">dangles = </span><span class="s" style="color: #d14;">c</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="html">        <span class="na" style="color: #008080;">alnSize = </span><span class="s" style="color: #d14;">matches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="na" style="color: #008080;">mismatches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="na" style="color: #008080;">gaps</span></span>

</pre>

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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="html">        <span class="na" style="color: #008080;">gapOpens</span> <span class="na" style="color: #008080;">-= </span><span class="s" style="color: #d14;">dangles</span></span>

</pre>

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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="html">    <span class="na" style="color: #008080;">else:</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="html">        <span class="na" style="color: #008080;">alignmentColumns = </span><span class="s" style="color: #d14;">list(zip(rowA,</span> <span class="na" style="color: #008080;">rowB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="html">        <span class="na" style="color: #008080;">alnSize = </span><span class="s" style="color: #d14;">len(alignmentColumns)</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC858" class="line" lang="html">        <span class="na" style="color: #008080;">matches = </span><span class="s" style="color: #d14;">sum(x</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">==</span> <span class="na" style="color: #008080;">y</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">x</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">y</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">alignmentColumns</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC859" class="line" lang="html">        <span class="na" style="color: #008080;">mismatches = </span><span class="s" style="color: #d14;">alnSize</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">matches</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">rowA.count</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span> <span class="na" style="color: #008080;">-</span> <span class="na" style="color: #008080;">rowB.count</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">-</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

</pre>

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724

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<td class="new_line diff-line-num" data-linenumber="860" 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">

860

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="725" 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">

725

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<td class="new_line diff-line-num old" data-linenumber="861" 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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<pre style="margin: 0;">-<span id="LC725" class="line" lang="html">    alignmentColumns = list(zip(rowA, rowB))</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="726" 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">

726

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<td class="new_line diff-line-num old" data-linenumber="861" 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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<pre style="margin: 0;">-<span id="LC726" class="line" lang="html">    alnSize = len(alignmentColumns)</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="727" 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">

727

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<td class="new_line diff-line-num old" data-linenumber="861" 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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<pre style="margin: 0;">-<span id="LC727" class="line" lang="html">    matches = sum(x == y for x, y in alignmentColumns)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="728" 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">

728

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<td class="new_line diff-line-num" data-linenumber="861" 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">

861

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<pre style="margin: 0;"> <span id="LC861" class="line" lang="html">    <span class="na" style="color: #008080;">matchPercent = </span><span class="s" style="color: #d14;">"%.2f"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(100.0</span> <span class="na" style="color: #008080;">*</span> <span class="na" style="color: #008080;">matches</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">/</span> <span class="na" style="color: #008080;">alnSize</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="729" 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">

729

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<td class="new_line diff-line-num old" data-linenumber="862" 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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<pre style="margin: 0;">-<span id="LC729" class="line" lang="html">    mismatches = alnSize - matches - rowA.count("-") - rowB.count("-")</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="730" 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">

730

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<td class="new_line diff-line-num old" data-linenumber="862" 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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<pre style="margin: 0;">-<span id="LC730" class="line" lang="html">    gapOpens = gapRunCount(rowA) + gapRunCount(rowB)</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="731" 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">

731

</td>

<td class="new_line diff-line-num" data-linenumber="862" 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">

862

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<pre style="margin: 0;"> <span id="LC862" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="732" 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">

732

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<td class="new_line diff-line-num" data-linenumber="863" 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">

863

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<pre style="margin: 0;"> <span id="LC863" class="line" lang="html">    <span class="na" style="color: #008080;">out = </span><span class="s" style="color: #d14;">[seqNameB,</span> <span class="na" style="color: #008080;">seqNameA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">matchPercent</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">alnSize</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">mismatches</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="733" 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">

733

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<td class="new_line diff-line-num" data-linenumber="864" 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">

864

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<pre style="margin: 0;"> <span id="LC864" class="line" lang="html">           <span class="na" style="color: #008080;">gapOpens</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="742" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="873" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -742,8 +873,9 @@ def writeBlastTab(opts, maf):</td>

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<td class="old_line diff-line-num" data-linenumber="742" 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">

742

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<td class="new_line diff-line-num" data-linenumber="873" 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">

873

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<pre style="margin: 0;"> <span id="LC873" class="line" lang="html">    <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">*out</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">sep=</span><span class="s" style="color: #d14;">"\t"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="743" 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">

743

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<td class="new_line diff-line-num" data-linenumber="874" 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">

874

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<pre style="margin: 0;"> <span id="LC874" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="744" 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">

744

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<td class="new_line diff-line-num" data-linenumber="875" 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">

875

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<pre style="margin: 0;"> <span id="LC875" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">mafConvertToBlastTab</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="html">    <span class="na" style="color: #008080;">geneticCode = </span><span class="s" style="color: #d14;">standardGeneticCode()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="745" 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">

745

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<td class="new_line diff-line-num" data-linenumber="877" 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">

877

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="html">    <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">maf</span> <span class="na" style="color: #008080;">in</span> <span class="na" style="color: #008080;">mafInput</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">lines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="746" 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">

746

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<td class="new_line diff-line-num old" data-linenumber="878" 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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<pre style="margin: 0;">-<span id="LC746" class="line" lang="html">        writeBlastTab(opts, maf)</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="html">        <span class="na" style="color: #008080;">writeBlastTab</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">opts</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;"><span class="idiff left">geneticCode</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">maf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>

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879

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<pre style="margin: 0;"> <span id="LC879" class="line" lang="html"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="748" 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">

748

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<pre style="margin: 0;"> <span id="LC880" class="line" lang="html"><span class="na" style="color: #008080;">#####</span> <span class="na" style="color: #008080;">Routines</span> <span class="na" style="color: #008080;">for</span> <span class="na" style="color: #008080;">converting</span> <span class="na" style="color: #008080;">to</span> <span class="na" style="color: #008080;">GFF</span> <span class="na" style="color: #008080;">format:</span> <span class="na" style="color: #008080;">#####</span></span>

</pre>

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749

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<td class="new_line diff-line-num" data-linenumber="881" 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">

881

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<pre style="margin: 0;"> <span id="LC881" class="line" lang="html"></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -753,6 +885,10 @@ def writeGffHeader():</td>

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753

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">gffFromMaf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">maf</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="886" 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="LC886" class="line" lang="html">    <span class="na" style="color: #008080;">aLine</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">sLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">qLines</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">pLines = </span><span class="s" style="color: #d14;">maf</span></span>

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="html">    <span class="na" style="color: #008080;">fieldsA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">fieldsB = </span><span class="s" style="color: #d14;">pairOrDie(sLines,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">"</span><span class="na" style="color: #008080;">GFF</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">")</span></span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC888" class="line" lang="html"></span>

</pre>

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<td class="old_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">

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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">

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<pre style="margin: 0;">+<span id="LC889" class="line" lang="html">    <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">fieldsA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[3]</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="na" style="color: #008080;">fieldsB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">[3]</span><span class="na" style="color: #008080;">:</span>  <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">protein-to-DNA</span> <span class="na" style="color: #008080;">alignment</span></span>

</pre>

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<td class="old_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">

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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">

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<pre style="margin: 0;">+<span id="LC890" class="line" lang="html">        <span class="na" style="color: #008080;">fieldsA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">fieldsB = </span><span class="s" style="color: #d14;">fieldsB,</span> <span class="na" style="color: #008080;">fieldsA</span></span>

</pre>

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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">

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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="LC891" class="line" lang="html"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="892" 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="LC892" class="line" lang="html">    <span class="na" style="color: #008080;">seqNameA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">seqLenA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">strandA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endA</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowA = </span><span class="s" style="color: #d14;">fieldsA</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="893" 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="LC893" class="line" lang="html">    <span class="na" style="color: #008080;">seqNameB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">seqLenB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">strandB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">letterSizeB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">begB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">endB</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">rowB = </span><span class="s" style="color: #d14;">fieldsB</span></span>

</pre>

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758

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894

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<pre style="margin: 0;"> <span id="LC894" class="line" lang="html"></span>

</pre>

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</li>

<li id="63a0bbefe2fd66bf4c0908eacca1076fc04263b6">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#63a0bbefe2fd66bf4c0908eacca1076fc04263b6"><strong>bin/maf-swap</strong></a>

<hr>

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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="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>

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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">

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Author: Martin C. Frith</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># SPDX-License-Identifier: GPL-3.0-or-later</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="c1" style="color: #998; font-style: italic;"># Read MAF-format alignments, and write them, after moving the Nth</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;"># sequence to the top in each alignment.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" 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">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,8 +96,9 @@ def flippedMaf(mafLines):</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">    <span class="n" style="color: #333;">fieldWidths</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;">sLineFieldWidths</span><span class="p">(</span><span class="n" style="color: #333;">flippedLines</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">joinedMafLine</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">fieldWidths</span><span class="p">)</span> <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;">flippedLines</span><span class="p">)</span></span>

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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="LC97" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isCanonicalStrand</span><span class="p">(</span><span class="n" style="color: #333;">mafLine</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python">    <span class="n" style="color: #333;">words</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mafLine</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="LC99" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isCanonicalStrand</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python">    <span class="n" style="color: #333;">sLine1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC101" class="line" lang="python">    <span class="n" style="color: #333;">words</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sLine1</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="LC102" class="line" lang="python">    <span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">words</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="LC103" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strand</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;">return</span> <span class="bp" style="color: #999;">True</span></span>

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<td class="new_line diff-line-num" data-linenumber="104" 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="LC104" class="line" lang="python">    <span class="n" style="color: #333;">alnString</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">words</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,12 +106,18 @@ def isCanonicalStrand(mafLine):</td>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="n" style="color: #333;">alnSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">words</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="LC107" class="line" lang="python">    <span class="n" style="color: #333;">gapCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnString</span><span class="p">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num" data-linenumber="108" 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="LC108" 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;">alnString</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gapCount</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">alnSize</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span>  <span class="c1" style="color: #998; font-style: italic;"># translated DNA</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python">    <span class="n" style="color: #333;">sLine2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="n" style="color: #333;">indexOfNthSequence</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(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="110" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC110" class="line" lang="python">    <span class="n" style="color: #333;">words2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sLine2</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC111" class="line" lang="python">    <span class="n" style="color: #333;">alnSize2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">words2</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(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="112" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC112" class="line" lang="python">    <span class="n" style="color: #333;">alnString2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">words2</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;">+<span id="LC113" 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;">alnString2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alnString2</span><span class="p">.</span><span class="n" style="color: #333;">count</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="n" style="color: #333;">alnSize2</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="106" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span>  <span class="c1" style="color: #998; font-style: italic;"># 3-letter amino acids</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="106" 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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<td class="new_line diff-line-num" data-linenumber="115" 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="LC115" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="107" 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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<td class="new_line diff-line-num" data-linenumber="116" 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="LC116" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="108" 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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<td class="new_line diff-line-num" data-linenumber="117" 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">

117

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">swapOneMaf</span><span class="p">(</span><span class="n" style="color: #333;">opts</span><span class="p">,</span> <span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="109" 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">

109

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<td class="new_line diff-line-num" data-linenumber="118" 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="LC118" class="line" lang="python">    <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rangeOfNthSequence</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">,</span> <span class="n" style="color: #333;">opts</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="110" 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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<td class="new_line diff-line-num" data-linenumber="119" 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="LC119" class="line" lang="python">    <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">stop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">stop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">mafLines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="n" style="color: #333;">start</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="111" 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="new_line diff-line-num old" data-linenumber="120" 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="LC111" 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;">isCanonicalStrand</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p"><span class="idiff left">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(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="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">

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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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">isCanonicalStrand</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="112" 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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<td class="new_line diff-line-num" data-linenumber="121" 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="LC121" class="line" lang="python">        <span class="n" style="color: #333;">mafLines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">flippedMaf</span><span class="p">(</span><span class="n" style="color: #333;">mafLines</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="113" 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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<td class="new_line diff-line-num" data-linenumber="122" 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">

122

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<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;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mafLines</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="114" 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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123

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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<td class="old_line diff-line-num old" data-linenumber="1" 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">

1

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<td class="new_line diff-line-num old" data-linenumber="1" 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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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">last-align (12<span class="idiff left right">43</span>-1) UNRELEASED; urgency=medium</span>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">last-align (12<span class="idiff left right">50</span>-1) UNRELEASED; urgency=medium</span>

</pre>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="3" 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">

3

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<td class="new_line diff-line-num old" data-linenumber="3" 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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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">  * [skip ci] Update email</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" 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">

4

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<td class="new_line diff-line-num" data-linenumber="3" 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">  * d/watch: Fix fetch URL - last-align has moved to gitlab</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="5" 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">

5

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<td class="new_line diff-line-num old" data-linenumber="4" 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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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">  * New upstream version 12<span class="idiff left right">43</span></span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version 12<span class="idiff left right">50</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" 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">

6

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<td class="new_line diff-line-num" data-linenumber="5" 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">

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * d/p/2to3.patch: scripts has moved to bin, change</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="7" 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">

7

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<td class="new_line diff-line-num" data-linenumber="6" 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">

6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * d/p/helpMakefiles.patch: Refresh helpmakefile.patch</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" 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">

8

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<td class="new_line diff-line-num" data-linenumber="7" 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">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">  * d/p/simde: Attempt adapting simde to new upstream</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +10,7 @@ last-align (1243-1) UNRELEASED; urgency=medium</td>

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11

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<td class="new_line diff-line-num" data-linenumber="10" 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="LC10" class="line" lang="plaintext">  * d/debian/last-align.doc-base.last-align-manual:</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" 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">

12

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<td class="new_line diff-line-num" data-linenumber="11" 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="LC11" class="line" lang="plaintext">    The manual page has moved to last-cookbook.rst</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="13" 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">

13

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<td class="new_line diff-line-num" data-linenumber="12" 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">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" 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">

14

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<td class="new_line diff-line-num old" data-linenumber="13" 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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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org>  <span class="idiff left">Mo</span>n, 1<span class="idiff">9 Apr</span> 2021 <span class="idiff right">21:03:45</span> +0530</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC13" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org>  <span class="idiff left">Su</span>n, 1<span class="idiff">1 Jul</span> 2021 <span class="idiff right">02:05:04</span> +0530</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="14" 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">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="16" 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">

16

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<td class="new_line diff-line-num" data-linenumber="15" 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="LC15" class="line" lang="plaintext">last-align (1179-1) unstable; urgency=medium</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="17" 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">

17

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<td class="new_line diff-line-num" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>

</pre>

</td>

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<br>

</li>

<li id="555c85016bd79aa8bbb523506af81b69d9c69534">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -158,10 +158,10 @@ Last-Update: Fri, 22 Nov 2019 11:23:44 +0100</td>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#! /usr/bin/env python</span></span>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> # Author: Martin C. Frith</span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> # SPDX-License-Identifier: GPL-3.0-or-later</span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"> # Read MAF-format alignments, and write them, after moving the Nth</span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"> # sequence to the top in each alignment.</span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="diff"><span class="p">@@ -69,12 +69,12 @@</span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="p">@@ -71,12 +71,12 @@</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff"> </span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"> def sLineFieldWidths(mafLines):</span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="diff">     sLines = (i for i in mafLines if i[0] == "s")</span>

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<br>

</li>

<li id="1aed97b2ebfde2d21c24639963d42434bdcfddb8">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#1aed97b2ebfde2d21c24639963d42434bdcfddb8"><strong>doc/lastal.rst</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,10 +291,13 @@ Miscellaneous options</td>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext">    complemented matrix is used for query sequence reverse strands.</span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="plaintext">-K LIMIT</span>

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<td class="old_line diff-line-num old" data-linenumber="294" 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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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext">    Omit any alignment whose query range lies in LIMIT or more other</span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext">    alignments with higher score (and on the same strand).  This is</span>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="plaintext">    a useful way to get just the top few hits to each part of each</span>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext">    query (P Berman et al. 2000, J Comput Biol 7:293-302).</span>

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">    Omit any alignment whose query range is contained in LIMIT or more</span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">    other alignments with higher score (and on the same strand).  This</span>

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">    is a useful way to get just the top few hits to each part of each</span>

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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">    query (P Berman et al. 2000, J Comput Biol 7:293-302).  As a</span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">    special case, a LIMIT of 0 means: omit any alignment whose query</span>

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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">    range overlaps an alignment with higher score (and on the same</span>

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">    strand).</span>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="plaintext">-C LIMIT</span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="plaintext">    Before extending gapped alignments, discard any gapless</span>

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<br>

</li>

<li id="4543c6ba972a23fa884543e091d830105a84288f">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#4543c6ba972a23fa884543e091d830105a84288f"><strong>doc/maf-convert.rst</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +13,11 @@ It's often convenient to pipe in the input, like this::</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">This script takes the first (topmost) maf sequence as the "reference"</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">/ "subject" / "target", and the second sequence as the "query".</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">(Exception: when converting DNA-to-protein alignments to gff or psl,</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">the protein becomes the "query" and the DNA becomes the "reference".)</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">For html: if the input includes probability lines starting with 'p',</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">then the output will be colo<span class="idiff left right">u</span>red by column probability.  (To get lines</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">then the output will be colored by column probability.  (To get lines</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">starting with 'p', run lastal with option -j set to 4 or higher.)</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">.. _maf: http://genome.ucsc.edu/FAQ/FAQformat.html#format5</span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,7 +34,7 @@ Options</td>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">-p, --protein</span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">       Specify that the alignments are of proteins, rather than</span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">       nucleotides.  This affects psl format only (the first 4</span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">       columns).</span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">       columns)<span class="idiff left right">, and has no effect for DNA-to-protein alignments</span>.</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">-j N, --join=N</span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">       Join alignments that are co-linear (align different parts of</span>

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<br>

</li>

<li id="8758dc959aa5524be83960d0bfd56945bc432a26">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#8758dc959aa5524be83960d0bfd56945bc432a26"><strong>src/AlignmentWrite.cc</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -474,7 +474,7 @@ AlignmentText Alignment::writeBlastTab(const MultiSequence& seq1,</td>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">map2</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">translationType</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">codonToAmino</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">map1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matchCount</span><span class="p">(</span><span class="n" style="color: #333;">blocks</span><span class="p">,</span> <span class="n" style="color: #333;">seq1</span><span class="p">.</span><span class="n" style="color: #333;">seqReader</span><span class="p">(),</span> <span class="n" style="color: #333;">seqData2</span><span class="p">,</span> <span class="n" style="color: #333;">map1</span><span class="p">,</span> <span class="n" style="color: #333;">map2</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">mismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignedColumnCount</span><span class="p">(</span><span class="n" style="color: #333;">blocks</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">matches</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC477" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blocks</span><span class="p">.</span><span class="n" style="color: #333;">size</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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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC477" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">gapOpens</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">blocks</span><span class="p">.</span><span class="n" style="color: #333;">size</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="idiff left">  </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// xxx ???</span></span></span>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">matchPercent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">alnSize</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">blastAlnBeg1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alnBeg1</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// 1-based coordinate</span></span>

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<br>

</li>

<li id="4b7be8c3b80efc62977b307791d1a304c23e1fa4">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#4b7be8c3b80efc62977b307791d1a304c23e1fa4"><strong>src/LastalArguments.cc</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,7 +106,7 @@ LastalArguments::LastalArguments() :</td>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp">  <span class="n" style="color: #333;">maxGaplessAlignmentsPerQueryPosition</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on oneHitMultiplicity</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp">  <span class="n" style="color: #333;">maxAlignmentsPerQueryStrand</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="LC108" class="line" lang="cpp">  <span class="n" style="color: #333;">cullingLimitForGaplessAlignments</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="LC109" class="line" lang="cpp">  <span class="n" style="color: #333;">cullingLimitForFinalAlignments</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp">  <span class="n" style="color: #333;">cullingLimitForFinalAlignments</span><span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp">  <span class="n" style="color: #333;">queryStep</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="LC111" class="line" lang="cpp">  <span class="n" style="color: #333;">minimizerWindow</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on the reference's minimizer window</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp">  <span class="n" style="color: #333;">batchSize</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span>  <span class="c1" style="color: #998; font-style: italic;">// depends on the outputType, and voluming</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="649" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="649" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -649,7 +649,7 @@ void LastalArguments::writeCommented( std::ostream& stream ) const{</td>

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<pre style="margin: 0;"> <span id="LC649" class="line" lang="cpp">    <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" N="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">maxAlignmentsPerQueryStrand</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cullingLimitForGaplessAlignments</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp">    <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" C="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cullingLimitForGaplessAlignments</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cullingLimitForFinalAlignments</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">cullingLimitForFinalAlignments</span> <span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp">    <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" K="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">cullingLimitForFinalAlignments</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp">  <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" k="</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">queryStep</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">minimizerWindow</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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</li>

<li id="a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#a6e382f28bfc81d7455aa5cc9b1ac92939cbf40a"><strong>src/lastal.cc</strong></a>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">isCollatedAlignments</span><span class="p">()</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'b'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">outputFormat</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</span> <span class="o" style="font-weight: 600;">||</span></span>

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<pre style="margin: 0;">-<span id="LC546" class="line" lang="cpp">    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cullingLimitForFinalAlignments</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp">    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cullingLimitForFinalAlignments</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printAndDelete</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="846" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="846" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -846,12 +846,41 @@ static bool lessForCulling(const AlignmentText &x, const AlignmentText &y) {</td>

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<pre style="margin: 0;"> <span id="LC846" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">else</span>                            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">score</span>     <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC847" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC848" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC849" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Remove any alignment whose query range overlaps an alignment with</span></span>

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<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

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<pre style="margin: 0;">+<span id="LC850" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// higher score (and on the same strand):</span></span>

</pre>

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<td class="old_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">

</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

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<pre style="margin: 0;">+<span id="LC851" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">cullOverlappingAlignments</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignmentText</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span></span>

</pre>

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<td class="old_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">

</td>

<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

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<pre style="margin: 0;">+<span id="LC852" class="line" lang="cpp">                                <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</td>

<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

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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="old_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">

</td>

<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="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>

</pre>

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<td class="old_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">

</td>

<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="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</td>

<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

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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp">    <span class="n" style="color: #333;">AlignmentText</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textAlns</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>

</pre>

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<td class="old_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">

</td>

<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

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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="LC857" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</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;">k</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</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

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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="LC858" class="line" lang="cpp">      <span class="n" style="color: #333;">AlignmentText</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textAlns</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>

</pre>

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<td class="old_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">

</td>

<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

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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="LC859" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">strandNum</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;">strandNum</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">queryBeg</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;">queryEnd</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>

</pre>

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<td class="old_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">

</td>

<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="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">;</span></span>

</pre>

</td>

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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="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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC862" class="line" lang="cpp">  <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

</td>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC863" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC864" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">score</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;">score</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</td>

<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

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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="LC865" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">;</span></span>

</pre>

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</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC866" class="line" lang="cpp">  <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">text</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="old_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">

</td>

<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

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<pre style="margin: 0;">+<span id="LC867" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="old_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">

</td>

<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

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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="LC868" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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</td>

<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

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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="LC869" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</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

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<pre style="margin: 0;">+<span id="LC870" class="line" lang="cpp">      <span class="n" style="color: #333;">textAlns</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;">x</span><span class="p">;</span></span>

</pre>

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<td class="old_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">

</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

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<pre style="margin: 0;">+<span id="LC871" class="line" lang="cpp">      <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>

</pre>

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<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

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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_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">

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<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

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<pre style="margin: 0;">+<span id="LC873" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

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<td class="old_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">

</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

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp">  <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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</td>

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875

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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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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="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="849" 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">

849

</td>

<td class="new_line diff-line-num" data-linenumber="877" 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">

877

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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Remove any alignment whose query range lies in LIMIT or more other</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="850" 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">

850

</td>

<td class="new_line diff-line-num" data-linenumber="878" 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">

878

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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// alignments with higher score (and on the same strand):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="851" 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">

851

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<td class="new_line diff-line-num" data-linenumber="879" 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">

879

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<pre style="margin: 0;"> <span id="LC879" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">cullFinalAlignments</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">AlignmentText</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="852" 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">

852

</td>

<td class="new_line diff-line-num old" data-linenumber="880" 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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<pre style="margin: 0;">-<span id="LC852" class="line" lang="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="853" 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">

853

</td>

<td class="new_line diff-line-num old" data-linenumber="880" 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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<pre style="margin: 0;">-<span id="LC853" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">cullingLimitForFinalAlignments</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="old_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">

</td>

<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="cpp">                          <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">start</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">limit</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</td>

<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="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">limit</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="854" 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">

854

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<td class="new_line diff-line-num" data-linenumber="882" 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">

882

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<pre style="margin: 0;"> <span id="LC882" class="line" lang="cpp">  <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">lessForCulling</span><span class="p">);</span></span>

</pre>

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<td class="old_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">

</td>

<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="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">limit</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cullOverlappingAlignments</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="855" 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">

855

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<td class="new_line diff-line-num" data-linenumber="884" 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">

884

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<pre style="margin: 0;"> <span id="LC884" class="line" lang="cpp">  <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">stash</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// alignments that might dominate subsequent ones</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="856" 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">

856

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<td class="new_line diff-line-num" data-linenumber="885" 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">

885

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">// number of kept alignments so far</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="857" 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">

857

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<td class="new_line diff-line-num" data-linenumber="886" 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">

886

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<pre style="margin: 0;"> <span id="LC886" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="867" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="896" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -867,7 +896,7 @@ static void cullFinalAlignments(std::vector<AlignmentText> &textAlns,</td>

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<td class="old_line diff-line-num" data-linenumber="867" 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">

867

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<td class="new_line diff-line-num" data-linenumber="896" 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">

896

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<pre style="margin: 0;"> <span id="LC896" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">queryEnd</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;">queryEnd</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">score</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;">score</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">numOfDominators</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="868" 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">

868

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<td class="new_line diff-line-num" data-linenumber="897" 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">

897

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<pre style="margin: 0;"> <span id="LC897" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="869" 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">

869

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<td class="new_line diff-line-num" data-linenumber="898" 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">

898

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<pre style="margin: 0;"> <span id="LC898" class="line" lang="cpp">    <span class="n" style="color: #333;">stash</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="870" 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">

870

</td>

<td class="new_line diff-line-num old" data-linenumber="899" 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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<pre style="margin: 0;">-<span id="LC870" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numOfDominators</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;"><span class="idiff left">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">cullingLimitForFinalAlignments</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_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">

</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

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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">numOfDominators</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;"><span class="idiff left right">limit</span></span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="871" 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">

871

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<td class="new_line diff-line-num" data-linenumber="900" 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">

900

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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">text</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="872" 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">

872

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<td class="new_line diff-line-num" data-linenumber="901" 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">

901

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<pre style="margin: 0;"> <span id="LC901" class="line" lang="cpp">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="873" 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">

873

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<td class="new_line diff-line-num" data-linenumber="902" 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">

902

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<pre style="margin: 0;"> <span id="LC902" class="line" lang="cpp">      <span class="n" style="color: #333;">stash</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1037" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1066" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1037,7 +1066,7 @@ static void tantanMaskTranslatedQuery(size_t queryNum, uchar *querySeq) {</td>

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1037

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<td class="new_line diff-line-num" data-linenumber="1066" 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">

1066

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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1038" 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">

1038

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<td class="new_line diff-line-num" data-linenumber="1067" 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">

1067

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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Scan one query sequence strand against one database volume,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1039" 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">

1039

</td>

<td class="new_line diff-line-num" data-linenumber="1068" 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">

1068

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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// after optionally translating and/or masking the query</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="1040" 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">

1040

</td>

<td class="new_line diff-line-num old" data-linenumber="1069" 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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<pre style="margin: 0;">-<span id="LC1040" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1041" style="width: 35px; color: rgba(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="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1069

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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;"><span class="idiff left">&</span></span><span class="n" style="color: #333;">aligner</span><span class="p">,</span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">finalCullingLimit</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1041" 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">

1041

</td>

<td class="new_line diff-line-num" data-linenumber="1070" 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">

1070

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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="cpp">               <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SubstitutionMatrices</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">matrices</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1042" 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">

1042

</td>

<td class="new_line diff-line-num" data-linenumber="1071" 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">

1071

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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="cpp">  <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqWriter</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1043" 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">

1043

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<td class="new_line diff-line-num" data-linenumber="1072" 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">

1072

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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="cpp">  <span class="n" style="color: #333;">uchar</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">querySeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querySeqs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">padBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1069" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1098" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1069,7 +1098,7 @@ void translateAndScan(LastAligner& aligner,</td>

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<td class="old_line diff-line-num" data-linenumber="1069" 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">

1069

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<td class="new_line diff-line-num" data-linenumber="1098" 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">

1098

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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1070" 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">

1070

</td>

<td class="new_line diff-line-num" data-linenumber="1099" 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">

1099

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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">oldNumOfAlns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1071" 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">

1071

</td>

<td class="new_line diff-line-num" data-linenumber="1100" 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">

1100

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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="cpp">  <span class="n" style="color: #333;">scan</span><span class="p">(</span> <span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">matrices</span><span class="p">,</span> <span class="n" style="color: #333;">querySeq</span> <span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1072" 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">

1072

</td>

<td class="new_line diff-line-num old" data-linenumber="1101" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1072" class="line" lang="cpp">  <span class="n" style="color: #333;">cullFinalAlignments</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span> <span class="n" style="color: #333;">oldNumOfAlns</span><span class="idiff right"> </span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1073" style="width: 35px; color: rgba(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="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1101

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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="cpp">  <span class="n" style="color: #333;">cullFinalAlignments</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">.</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span> <span class="n" style="color: #333;">oldNumOfAlns</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">finalCullingLimit</span></span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1073" 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">

1073

</td>

<td class="new_line diff-line-num" data-linenumber="1102" 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">

1102

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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="cpp"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1074" 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">

1074

</td>

<td class="new_line diff-line-num" data-linenumber="1103" 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">

1103

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<pre style="margin: 0;"> <span id="LC1103" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">tantanSetting</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isKeepLowercase</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1075" 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">

1075

</td>

<td class="new_line diff-line-num" data-linenumber="1104" 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">

1104

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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqBeg</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">seqEnd</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1078" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1107" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1078,19 +1107,19 @@ void translateAndScan(LastAligner& aligner,</td>

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<td class="old_line diff-line-num" data-linenumber="1078" 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">

1078

</td>

<td class="new_line diff-line-num" data-linenumber="1107" 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">

1107

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1107" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1079" 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">

1079

</td>

<td class="new_line diff-line-num" data-linenumber="1108" 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">

1108

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1108" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1080" 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">

1080

</td>

<td class="new_line diff-line-num" data-linenumber="1109" 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">

1109

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1109" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1081" 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">

1081

</td>

<td class="new_line diff-line-num old" data-linenumber="1110" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1081" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span></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="1082" style="width: 35px; color: rgba(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="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1110

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">alignOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">LastAligner</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">finalCullingLimit</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1082" 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">

1082

</td>

<td class="new_line diff-line-num" data-linenumber="1111" 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">

1111

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1111" class="line" lang="cpp">                   <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isFirstVolume</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1083" 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">

1083

</td>

<td class="new_line diff-line-num" data-linenumber="1112" 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">

1112

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1112" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isFirstVolume</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1084" 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">

1084

</td>

<td class="new_line diff-line-num" data-linenumber="1113" 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">

1113

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1113" class="line" lang="cpp">    <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">reverseComplementOneSequence</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">queryAlph</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1085" 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">

1085

</td>

<td class="new_line diff-line-num" data-linenumber="1114" 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">

1114

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1114" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1086" 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">

1086

</td>

<td class="new_line diff-line-num" data-linenumber="1115" 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">

1115

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1115" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1087" 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">

1087

</td>

<td class="new_line diff-line-num old" data-linenumber="1116" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1087" class="line" lang="cpp">    <span class="n" style="color: #333;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">fwdMatrices</span><span class="p">);</span></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="1088" style="width: 35px; color: rgba(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="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1116

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1116" class="line" lang="cpp">    <span class="n" style="color: #333;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">finalCullingLimit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">fwdMatrices</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1088" 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">

1088

</td>

<td class="new_line diff-line-num" data-linenumber="1117" 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">

1117

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1117" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1089" 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">

1089

</td>

<td class="new_line diff-line-num" data-linenumber="1118" 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">

1118

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1118" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isFirstVolume</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1090" 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">

1090

</td>

<td class="new_line diff-line-num" data-linenumber="1119" 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">

1119

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1119" class="line" lang="cpp">    <span class="n" style="color: #333;">query</span><span class="p">.</span><span class="n" style="color: #333;">reverseComplementOneSequence</span><span class="p">(</span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span> <span class="n" style="color: #333;">queryAlph</span><span class="p">.</span><span class="n" style="color: #333;">complement</span><span class="p">);</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1091" 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">

1091

</td>

<td class="new_line diff-line-num" data-linenumber="1120" 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">

1120

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1092" 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">

1092

</td>

<td class="new_line diff-line-num" data-linenumber="1121" 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">

1121

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1093" 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">

1093

</td>

<td class="new_line diff-line-num old" data-linenumber="1122" 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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<pre style="margin: 0;">-<span id="LC1093" class="line" lang="cpp">    <span class="n" style="color: #333;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">queryNum</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1094" style="width: 35px; color: rgba(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="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1122

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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp">    <span class="n" style="color: #333;">translateAndScan</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">finalCullingLimit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">queryNum</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1094" 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">

1094

</td>

<td class="new_line diff-line-num" data-linenumber="1123" 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">

1123

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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="cpp">              <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">isQueryStrandMatrix</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">revMatrices</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fwdMatrices</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1095" 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">

1095

</td>

<td class="new_line diff-line-num" data-linenumber="1124" 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">

1124

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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1096" 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">

1096

</td>

<td class="new_line diff-line-num" data-linenumber="1125" 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">

1125

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1125" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1108" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1137" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1108,14 +1137,16 @@ static void alignSomeQueries(size_t chunkNum,</td>

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<td class="old_line diff-line-num" data-linenumber="1108" 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">

1108

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<td class="new_line diff-line-num" data-linenumber="1137" 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">

1137

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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSort</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isCollatedAlignments</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1109" 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">

1109

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<td class="new_line diff-line-num" data-linenumber="1138" 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">

1138

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<pre style="margin: 0;"> <span id="LC1138" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSortPerQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">isSort</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isMultiVolume</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1110" 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">

1110

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<td class="new_line diff-line-num" data-linenumber="1139" 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">

1139

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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isPrintPerQuery</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">isFirstThread</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">isSort</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isMultiVolume</span><span class="p">));</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1111" style="width: 35px; color: rgba(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="1140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1140

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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">finalCullingLimit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cullingLimitForFinalAlignments</span> <span class="o" style="font-weight: 600;">?</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1111" style="width: 35px; color: rgba(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="1141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1141

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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="LC1141" class="line" lang="cpp">    <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cullingLimitForFinalAlignments</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">isMultiVolume</span><span class="p">;</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1111" 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">

1111

</td>

<td class="new_line diff-line-num" data-linenumber="1142" 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">

1142

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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beg</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1112" 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">

1112

</td>

<td class="new_line diff-line-num" data-linenumber="1143" 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">

1143

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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">oldNumOfAlns</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="1113" 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">

1113

</td>

<td class="new_line diff-line-num old" data-linenumber="1144" 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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<pre style="margin: 0;">-<span id="LC1113" class="line" lang="cpp">    <span class="n" style="color: #333;">alignOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">isFirstVolume</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1114" style="width: 35px; color: rgba(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="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1144

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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp">    <span class="n" style="color: #333;">alignOneQuery</span><span class="p">(</span><span class="n" style="color: #333;">aligner</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">finalCullingLimit</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">isFirstVolume</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1114" 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">

1114

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<td class="new_line diff-line-num" data-linenumber="1145" 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">

1145

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<pre style="margin: 0;"> <span id="LC1145" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSortPerQuery</span><span class="p">)</span> <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">oldNumOfAlns</span><span class="p">,</span> <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1115" 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">

1115

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<td class="new_line diff-line-num" data-linenumber="1146" 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">

1146

</td>

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<pre style="margin: 0;"> <span id="LC1146" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isPrintPerQuery</span><span class="p">)</span> <span class="n" style="color: #333;">printAndClear</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">);</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1116" 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">

1116

</td>

<td class="new_line diff-line-num" data-linenumber="1147" 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">

1147

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1147" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1117" 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">

1117

</td>

<td class="new_line diff-line-num" data-linenumber="1148" 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">

1148

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<pre style="margin: 0;"> <span id="LC1148" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isFinalVolume</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isMultiVolume</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="1118" 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">

1118

</td>

<td class="new_line diff-line-num old" data-linenumber="1149" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1118" class="line" lang="cpp">    <span class="n" style="color: #333;">cullFinalAlignments</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></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="1119" style="width: 35px; color: rgba(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="1149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1149

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1149" class="line" lang="cpp">    <span class="n" style="color: #333;">cullFinalAlignments</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">cullingLimitForFinalAlignments</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1119" 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">

1119

</td>

<td class="new_line diff-line-num" data-linenumber="1150" 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">

1150

</td>

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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isSort</span><span class="p">)</span> <span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">textAlns</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">());</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="1120" 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">

1120

</td>

<td class="new_line diff-line-num" data-linenumber="1151" 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">

1151

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isFirstThread</span><span class="p">)</span> <span class="n" style="color: #333;">printAndClear</span><span class="p">(</span><span class="n" style="color: #333;">textAlns</span><span class="p">);</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1121" 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">

1121

</td>

<td class="new_line diff-line-num" data-linenumber="1152" 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">

1152

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cpp">  <span class="p">}</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat</td>

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<td class="old_line diff-line-num" data-linenumber="143" 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">

143

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<td class="new_line diff-line-num" data-linenumber="143" 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">

143

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="make"> ../build/mat-inc.sh ../data/<span class="k" style="font-weight: 600;">*</span>.mat <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$@</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="144" 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">

144

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<td class="new_line diff-line-num" data-linenumber="144" 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">

144

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC144" class="line" lang="make"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="145" 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">

145

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<td class="new_line diff-line-num" data-linenumber="145" 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">

145

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION1</span> <span class="o" style="font-weight: 600;">=</span> git describe <span class="nt" style="color: #000080;">--dirty</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="146" 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">

146

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<td class="new_line diff-line-num old" data-linenumber="146" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 12<span class="idiff left right">43, refs/keep-around/3243658001e5a2afe5329f23aab272c355465293</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>

</pre>

</td>

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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="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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC146" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">' (HEAD -> main, tag: 12<span class="idiff left right">50</span>) '</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/.*tag: *//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[,) ].*//'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="147" 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">

147

</td>

<td class="new_line diff-line-num" data-linenumber="147" 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">

147

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC147" class="line" lang="make"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="148" 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">

148

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<td class="new_line diff-line-num" data-linenumber="148" 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">

148

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC148" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">-e</span> ../.git <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: #008080;">$(VERSION1)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: #008080;">$(VERSION2)</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="149" 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">

149

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<td class="new_line diff-line-num" data-linenumber="149" 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">

149

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC149" class="line" lang="make"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="1e8b7c6cdfd3ee5e24a1aadd55e212791c8bbf4b">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#1e8b7c6cdfd3ee5e24a1aadd55e212791c8bbf4b"><strong>test/frameshift-new.maf</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># LAST version 1243</span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># a=21 b=1 A=27 B=1 F=-2,0,-3,0 e=165.797 d=70 x=165 y=42 z=165 D=1e+09 E=18.1715</span>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># R=01 u=2 s=2 S=0 M=0 T=0 m=500 l=1 n=500 K=1 k=1 w=1000 t=4.24284 j=3 Q=0</span>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># ../aant/hg38/last/rmsk-hg38</span>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># Reference sequences=38335 normal letters=27515653</span>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># lambda=0.235691 K=1.69939</span>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">#</span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">#   AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT</span>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># A  -7  -5  -7  -6   3   3   1   3  -6  -3  -6  -2  -2  -3  -2  -4  -7  -6  -5  -6  -1  -1  -3  -1  -5  -4  -7  -5  -5  -6  -4  -5  -2  -2  -3  -3   9   9   7  10  -1   0  -2   1   4   4   4   4  -5  -9  -6  -8   2   1   0   1  -8  -7 -11  -6  -4  -6  -2  -5</span>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># C -11  -4 -11  -5  -7  -4 -11  -5  -8   2  -7   2  -9  -6 -11  -8  -7   1  -6   2 -12  -7  -9  -7  -1   8  -2   8 -10  -6  -6  -4 -12  -6 -10  -6  -6  -6 -29  -5  -8   3  -6   1 -10  -6  -7  -6  -2   5   0   6  -6  -1  -4   0   3  13   1  13  -7   0  -6   1</span>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># D  -4   4  -3   4  -9  -3  -7  -4  -7   0  -7   1 -12  -7  -9  -8  -4   1  -5   0 -10  -7 -10  -6 -27  -1  -6  -3 -15  -9 -14 -10   2  11   3  10  -7  -1  -3  -1  -2   5  -2   5  -6   0  -6  -1  -2   1  -3   0  -9  -5 -16  -6  -8  -3 -12  -4 -13  -8 -10 -10</span>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># E   2  -2   1  -1  -5  -8  -8  -6  -3  -4  -4  -5  -7 -12  -7 -12   0  -5   0  -5  -8  -9 -11 -11  -2 -11  -5  -9 -10 -13 -10 -11   9   3   8   4  -1  -6  -1  -6   2  -2   2  -1  -2  -6  -3  -7   3  -6   0  -5  -9  -9  -9  -8  -4  -9 -10  -8  -9 -14  -8 -12</span>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># F -17  -9 -16  -8 -11  -6  -7  -6 -16  -8 -13  -8  -8  -2  -6  -2 -10  -3 -10  -1 -12  -5  -8  -6 -11  -5  -4  -1  -4   3  -2   2 -18 -11 -18 -11  -9 -10 -11  -7 -13 -10 -12  -9  -6   1  -7  -1  -6   2  -4   3  -6   1  -2   1  -7   1  -8   2   2  11   2  11</span>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># G  -4  -3  -3  -3  -6  -6  -5  -6   4   3   3   3  -8 -10  -8  -9  -4  -5  -4  -3 -10  -7  -3  -7   0   2   2   0 -13 -13 -14 -13   3   1   3   2  -1   0   1  -1  11  10  10  10  -1  -1  -2  -2  -2  -7  -4  -6 -10  -7  -8  -6   1  -2  -3  -1 -10 -13 -11 -10</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># H  -6   0  -5   0  -8  -4 -25  -4  -9  -3  -6  -1 -13  -9 -11  -9   3  11   3  11  -5   1  -1   0  -1   7   2   9  -6  -1  -8  -1  -7  -2  -4  -1 -10  -6  -4  -6  -7  -3  -6  -2 -11  -5 -10  -5  -1   6   0   6  -7  -1  -3  -2  -3   2  -6   4  -8  -3  -9  -3</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># I  -5  -5  -8  -4   1   1   1   2  -4  -2  -6  -2   7   7   3   7  -9 -10 -10  -9  -7  -8  -8  -9  -6  -6 -21  -7   1  -1  -2  -1 -11 -11 -10  -9  -4  -5  -2  -4  -8  -8  -9  -7   4   3   1   3  -6  -8  -8  -9  -6  -8  -7  -7  -7  -7 -15  -9   0  -3  -2  -2</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># K   7   1   7   1  -1  -5   0  -5   3  -2   2  -1  -3 -10  -3  -8   0  -5  -1  -5  -7 -10  -4 -10  -2  -8  -5  -5  -8 -13 -10 -13  -1  -7   0  -6  -6  -9  -5  -8  -3  -8  -4  -6  -6 -10  -7  -9   2  -9  -1  -8  -7 -10 -12 -10  -3  -9  -8 -10  -6 -14  -9 -10</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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># L -10 -10 -10 -11  -5  -7  -2  -4  -9  -8  -8  -8   0   0   1   0  -4  -2  -2  -2  -1  -1   3  -1   0   0  -3  -1   7   7   7   7 -12 -12 -10 -13  -8  -6  -1  -6 -11 -11  -8 -10   0  -1   0  -1  -3  -4  -4  -5  -2  -4   1  -4  -2  -4  -5  -3   7   3   6   3</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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># M  -6  -7  -2  -6   1  -3   7  -3  -4  -6   1  -6   4   1  11   2  -7  -8  -5  -9  -6  -8  -1  -9  -4 -10  -8  -3   0  -2   4  -2  -8 -12  -4 -10  -3  -5   2  -5 -10  -8  -4 -10   1  -3   6  -2  -5  -9  -3 -10  -4  -8   2  -8  -6 -12  -6  -8   1  -5   5  -3</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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># N   0   9   1   9  -5   1  -3   0  -3   5  -2   5  -7  -3  -7  -3  -3   1  -5   1  -9  -6 -11  -6  -6  -2  -5  -3 -14  -9 -13  -9  -4   2  -3   2  -8  -4  -9  -6  -6  -1  -6  -1  -9  -5  -9  -7  -2  -1  -5   0  -9  -5 -29  -6  -6  -4 -11  -4 -10  -9 -13  -7</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># P  -9  -9 -11  -9  -2  -2  -3  -1 -10  -9  -7  -7  -7  -8  -8  -8  -1  -1  -4  -2  10  10   9  10   1   2   0   2   4   2   2   2 -11  -8 -12  -9  -1   0   1  -1 -10  -7  -8  -8  -5  -6  -5  -6  -3  -5  -8  -5   5   5   4   5  -1  -3  -8  -4  -2  -3  -3  -3</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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># Q  -1  -4   0  -4  -6  -5  -6  -7  -4  -5  -3  -6 -10 -12  -7 -11  10   2  10   3   0  -4   2  -5   6   0   4   1  -2  -8  -2  -7   0  -3   1  -5  -7  -9  -7  -6  -4  -6  -3  -8  -7  -8  -6  -9   6  -2   5  -2  -3  -4  -1  -5   2  -4  -2  -5  -3  -9  -4  -8</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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># R   2  -4   3  -3  -1  -6  -1  -6   9   1   8   2  -3  -9  -3  -8   2   1   2   0  -7  -5  -6  -5   6   4   5   3  -8  -7  -8  -8  -4  -8  -4  -8  -7  -8  -3  -7   1  -4   2  -3  -7 -10  -6  -8   0  -5  -1  -4  -6  -7  -6  -6   5   1  -1   0  -6  -9  -7  -8</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># S  -6   0  -5  -1   0   2  -1   2  -3   6  -3   5  -5  -3  -5  -4  -5  -3  -4  -3   0   2  -1   1  -5   0  -4  -1  -5  -5  -4  -4  -6  -5  -6  -4   0   1  -1   1  -5   0  -4  -1  -5  -4  -4  -4  -1  -2  -4  -3   8   8   7   8  -1   0  -7  -1   1   0   1   0</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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># T  -3  -2  -3  -2   7   7   6   7  -2   1  -3   0   2   1   1   1  -5  -5  -5  -6  -2  -2  -2  -1  -5  -7  -4  -4  -4  -6  -3  -6  -6  -6  -6  -6   3   1   2   2  -5  -5  -6  -6   0  -1   0  -1  -4  -8  -6  -6   2   0   1   1  -5  -5 -12  -7  -3  -6  -3  -5</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"># V  -7  -6  -8  -7  -1   0  -1   1  -5  -5  -5  -4   3   4   2   4  -9  -6  -6  -7  -7  -5  -5  -5  -4  -7  -6  -5  -1  -2  -1  -1  -4  -5  -3  -4   1   2   4   2  -3  -3   0  -2   8   9   9   9  -5 -11  -6  -8  -5  -7  -3  -6  -7  -7 -11  -7   0  -3  -1  -1</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"># W -14 -18  -7 -13 -16 -15  -7 -14  -6  -9   1  -9 -13 -23 -10 -13  -5  -7   3  -5 -11 -14  -2 -26   4  -4  10  -1  -9 -10  -4 -11 -12 -14  -4 -19 -14 -12  -5 -19  -5  -9   4  -8 -12 -18  -7 -14   2  -3  11  -2  -3 -11   5  -8  10   4  14   4  -3  -9   4  -5</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC29" class="line" lang="plaintext"># Y -11  -2 -11  -2 -14  -7  -9  -8 -15  -5 -11  -4 -13  -9 -10  -8  -5   5  -3   6 -10  -6  -7  -5 -11   2  -4   3  -9  -4  -9  -5 -12  -4 -11  -2 -11  -9 -28  -8 -15  -7 -10  -5 -13  -5 -10  -8   3  11   4  11  -8   0  -6   0  -3   5  -5   6  -6   3  -5   2</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC30" class="line" lang="plaintext"># * -27 -29 -25 -27 -29 -28 -30 -28 -20 -19 -17   1 -28 -29 -28 -29   0 -20   5 -29 -29 -29 -29 -27   9 -29   4 -29 -25 -29 -26 -29 -24 -29 -28 -29 -29 -28 -29 -29   4 -29 -25 -25 -28 -30 -28 -30  14  -5  10 -12 -26 -29   6 -29  14 -27  -3  -8 -10 -29 -29 -29</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"># X   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">#</span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"># Coordinates are 0-based.  For - strand matches, coordinates</span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"># in the reverse complement of the 2nd sequence are used.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">#</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"># name start alnSize strand seqSize alignment</span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">#</span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"># batch 0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">a score=3177.2 EG2=0 E=0</span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">s UN-L1MA6_pol#LINE/L1   657  616 +  1275 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeu-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThrMetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeuProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrpAsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrpMetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">s chrUn_KI270748v1     13904 1811 + 93321 CAAGGGTGCCCACTCTCAGAACTTCTATTCAACATAGTACTGGATGTCCTAGCCAGAGCAATTAGGCAAAAGAAAGaaaTAAAAGGCATGAAAATTGGAAAGGAAGAAGTTAAATTGTTTCTGTTTGCAGTTGACATGATCTTATATATAGAAAACACCAATAACTCTGCCAAAAAA---TTTAGAATTCATAAATGAATTTAGTAAAGTTGCAGGATACAATGTGAACATACAAAATTCAGTAGCATTTCTACACATCAACAACAAACTATACAAAAAAagaaatcaagaaaacaATCCTATTTATAATAGCAACAAAA---------AATACTTAGATGTAAATTTAAACAAAGAGGTGAATGATCTTTACACTGAAAACTACAAAACATTGATGAAAACAATTGAAGAAGCCACAAATAAATGGAAAGATATCTCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAATGTCCATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAATTCCTATGACATTTTCCCACAGAAATAGAAAAACAACTCTCAAATCTGTATGGAATCACAAAAAACTCTGAAAAGCCAAAATAATCTTGATCGAAAAAAGCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCTATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATAGACCAATTACACAGAATAAAGAGCCCATAAATAAATCTACAT---ATTATAGTCAATTGACTTTCAACAAAGGTGCCAGGAACACA---CATGGGGAAAGAACAGTCTCTTCAAAAAATGGTGTTGAGAAAACTGAATGTCCACA------AGATTGATCTTAGGCCCTTATTTCATACCATATAAAAATATAAATTCAAAATAAGTT---AGACTTAAATGTAAGACCTAGCACTATAGAACTCCTAGAAGAAAAC---AGGGGAATAACTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGACTCTAAAGCACAGGCAAGAAAAGCAACAAAACACAAATGGAATAGCATCAACCTAAAAAGCTTCTGCGCAGCAAAAGAA---AGTCAACAGAGTGAAGTGATAACCTACAAAATGGGAGGAATTATCTGCAAACTATACATTTGATAAGAGGCTAATGTCCAAAATATCTTAGGAACTCAAACAACACAataataagaaAACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAACAGATATATA---AAAATGCTAATTATCACTGATCATCAGAGAAATGCATATTAAAACTACAATAAAATGCCATTTCACATCCGTTAGAATGGCTGTTACAGAAAAGGCAGAAGATACCAAGTGTTGGAGAGGATGTGGAGAAAAGGAAAACCTTGTA------ATTGTTGAGAATGTAAACTATTTCAGCCATTGTAAAAGACAGTATAAGTGATTCTG---------TAAAAATAGAATTACCATATGATTCAGTAATGCTATTTCTGGGCATATATTAAAAAGATATCAAATCAGTGTGTCAATGAGTTATCTGTACTCCCATATTTATTGTAGCATTATTCACAACAGCCAAGATGTGGAATTAACTTAAGTATCCATCGACACATGAGTGGATGAAGAAAATGTGGTACACATACACAATAGAATAGTATACAACCTTAaaaaataaaaaa---aGTATCATTTGTGACAACATGAATGAACCGGGAGGACATTATACTGAGTAAAATAATCCAGGCACAGAAAGCCAGATACTGCATAATCTCACTTGTATGTGGA</span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">a score=1775.7 EG2=2.9e-164 E=1.5e-169</span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">s UN-L1PA2_pol#LINE/L1 1048 227 +  1276 LeuIleSerArgIleTyrAsnGluLeuLysGlnIleTyrLysLysLysThrAsnAsnProIleLysLysTrpAlaLysAspMetAsnArgHisPheSerLysGluAspIleTyrAlaAlaLysLysHisMetLysLysCysSerSerSerLeuAlaIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysSerGlyAsnAsnArgCysTrpArgGlyCysGlyGluIleGlyThrLeuLeuHiscystrptrpaspcyslysLeuValGlnProLeuTrpLysSerValTrpArgPheLeuArgAspLeuGluLeuGluIleProPheAspProAlaIleProLeuLeuGlyIleTyrProLysAspTyrLysSerCysCysTyrLysAspThrCysThrArgMetPheIleAlaAlaLeuPheThrIleAlaLysThrTrpAsnGlnProLysCysProThrMetIleAspTrpIleLysLysMetTrpHisIleTyrThrMetGluTyrTyrAlaAlaIleLysAsnAspGluPheMetSerPheValGlyThrTrpMetLysLeuGluIleIleIleLeuSerLysLeuSerGlnGluGlnLysThrLysHisArgIlePheSerLeuIleGlyGlyAsn</span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">s chrUn_KI270748v1     3859 681 + 93321 CTAATATCCGGAATCTACAATGAACCCAAACAAATTTACAAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACTATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTTACACCAGTTAGAATGGCCATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACATTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGGTGATTCCGCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTACTGTGGCACTATTCACAATAGCAAAGACTTGGAACCAATCCAAATGTCCAACAATGATAGACTGGATTAAGAAAACGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAGCTGGAAACCATCATTCTCAGCAAACAATCACAAGGACAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAAT</span>

</pre>

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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">

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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="LC46" class="line" lang="plaintext"></span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">a score=1607.4 EG2=5e-147 E=2.5e-152</span>

</pre>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">s UN-L1MA6_pol#LINE/L1   517  362 +  1275 LysProAspLysAspThrThrLysLysGluAsn--TyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLys--IleLeuAlaAsnArgIleGlnGlnHisIleLysLysIle--IleHisHisAspGlnVal--GlyPheIleProGlyMetGln-GlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIleAsnArgMetLysAspLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAspLysIleGlnHisProPheMetIleLysThrLeuAsnLysLeuGlyIleGluGlyThrTyrLeuAsnThrIleLysAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGluLysLeuLysAlaPheProLeuArgSerGlyThrArgGlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGly-IleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeuLeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAla-PheLeuTyrAlaAsnSerGluLeuSerGluLysGlu-IleLyslysthrilepropheThrIleAlaThrLysLysIle------------------------------LysTyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGlu-IleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeu-ProAspPheLysIleTyrTyrLys</span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">s chrUn_KI270748v1     89660 1085 - 93321 aaggcaaacaAGGACACTATAAGAAAAGTA---TGGGCCAACCAATATCCCTGATGAACACAGATACAAAAGTCCTCAAAAAAAAGTACTAGCAAACAGAATTTAACAACATATTAGGAGA---ACATTTACCATGATAAA---GTGGATTTATCCTC---------CAGATGTTTCAGCAAACACAAATCA---AATGTGATAAACCACATTAACAGAATGAAGGATAAAAAA---ATAGCTATCTCTATATATGCAGAAAAAGCATTTGACTAAATTCAAAATCCTCTCATGACTAAACCTCTCAACAAATTGGGCATAGAAGGCATGTACCTTAACACAAAACAGGACATATATAACAAGCTCACAGCTCACATCATACCCAACAATGAAAAAGTGAAATCTTTTCTGCTAAGATCAAAAACAAGACAAGGATATTTATTCTCACTACTTCTATTCAACTTATTTCTGGAAGTCCTAGCCAGAGCAATTAAGCCAAATAAAGAAATAAAA---TATTCAAATTGAAAAGGaagaagtaaaaTTGTCTCTGTTTGATGAC------ATATTATATATAGGAAACCCTAAAAACTCCACCAAAAAGCTATTAGAAATGATAAATGAATTCAATAAAATTTCAGAATTCAAAATCAATGTACAAAACTCAGTA---GTTTCTTTACACTCACAACAAACTATATGACAAA---AATAAAGAAATCAATCTCATTCACAGTAGCATCAAaaaaaacgtattttttttGTTTAGGAGCACATTTAGGATAGTACttaggagtacatttaACCAAGGAGGTGAAAGATCTGTATTCTGAACACTATAAAACATTGATGAAA---AATTGTAGATGACACAAATACATGGAAAGATATTTTATGTTCATGGGTAGGAAGAATTAATATTCTTAAAATGTCCTTACTGCCCAAAGCGATTTATAGGTTTAATGCAATATTTATCAAAATTTCAATGTCATTCTTCACAGAAATAGAAAAAACAATTTGAAAATTTATATGGAACCACAAAGGATCCTGAATAACTAAAGGACTCTTGAGCAATAAGAACAAAGCTGAAGGCCTCACA---ATCTGACTTCAAAACATATTACAGG</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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC50" class="line" lang="plaintext"></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="51" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC51" class="line" lang="plaintext">a score=1559.7 EG2=3.8e-142 E=2e-147</span>

</pre>

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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">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">s UN-L1MA6_pol#LINE/L1  883 281 +  1275 LysThrAlaTrpTyrTrpHisLys--AsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIleTyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGlnTrp-GlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLysAspLeu-AsnValArgProGluThrMetLysLeuLeuGluGluAsnIleGlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThrIleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLys--GluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLysLysCysSerThrSerLeuIleIleArgGluMetGlnIle-LysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCysTrp--TrpGluCysLysLeuValGlnProLeuTrpLysThrVal--TrpArgPheLeuLysLysLeuLys</span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">s chrUn_KI270748v1     3232 818 - 93321 TaatcagcctggtaatcaCGT---AAAACAGACACATAGACCAGTGGAACAGAATAGAGAACCCAGATATAAATCCACACATTTACAGCCAGCTCATCTTCAGCAAAGGCACCAACAACATACGA---GCGAAAGGACGGTCTCTTCCATAAGTGGTGCAGGGGAAACTAGATAAAGATATGCAGAAGAATGAAACTAGACCCGTCTCTCTTACCATACACAGAAATCAAATCAGAATGGATTAAAGGT---AAAACTGAGACCTGAAAGTATAAAACTACTGGAAGAAAACATTAGGGAAGTGCTCCAGGACATTGTTCTCAGCAAAGACTTTTTCAGTAGGGCCCCAAAAGCACAGGCAACCAAAGCAAAAACAGACAAGTGAAATCACACCAAGCTAAGAACCCTCTGCAGACCAAAGGAAAAAGTCAACAAACTGAAGAGACAACCCACAGAATGGGAGAAAATACTTGCAAGCTACCCACCTGACAAGGGATTCATAACC------------AGGAGCTCAAACAA---------TAGCAAACAATTAATCGAATTTTAAAATGGGCAAGAGACCTGAGTAGACATTTCTCAAAAGAAGATGTACAAATGGCCAGCAGGTACATGAAAAAATGCTCAACATCACTAATCATCAGAGAAACGCAAATAAAAAACTGCAATGAGGTCTTCTCTCACCTCAGTTAAAATGGCTTTCGTCAAAAACGCAGGGAATAAGGGATGCTGGCGAGGATGTGGAGAAAGGGGGACCCTCACACACTGT---TGTGGGAACGTTGATTAGTACAACCACTATGGAAAACA---GATGGAGGCTCCTCAaaaaaccaaaa</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="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">

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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="LC54" class="line" lang="plaintext"></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="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">

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">a score=1508.0 EG2=7.4e-137 E=3.8e-142</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC56" class="line" lang="plaintext">s UN-L1PA16_pol#LINE/L1   526  338 +  1276 LysGluAsnTyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLysIleLeuAlaAsnArgIleGlnGlnHisIleLysLysLeuIleHisHisAspGlnValGlyPheIleProGlyMetGlnGlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIleAsnArgIleLysAsnLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAspLysIleGlnHisProPheMetIleLysThrLeuXaaLysLeuGlyIleGluGlyThrTyrLeuLysIleIleArgAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGlnLysLeuGluAlaPheProLeuArgThrGlyThrArgGlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrLeuGluAsnProLysAspSerAlaLysArgLeuLeuGluLeuIleAsnAspPheSerLysValSerGlyTyrLysIleAsnVal--GlnLysSerValAlaPheLeuTyrThrAsnAsnValGlnAla-----------------------------GluSerGlnIleLysAsnAlaIleProPheThrIleAlaThrLysLysIle--LysTyrLeuGlyIleHisLeu-ThrLysGluValLysAspLeuTyrLysGluAsnTyrLysThrLeuLeuLysGluIleIleAspAspThrAsnLysTrpLysAsnIleProCysSerTrpIleGlyArgIleAsnIle-ValLysMetAlaIleLeuProLys--AlaIleTyrArgPheAsnAlaIleProIleLysLeuProMetSerPhePheThrGluLeuGluLysThr-IleLeuLysPheIleTrpAsnGln-LysArgAlaGlnIleAlaLysAlaIleLeuSerLysLys</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">s chrUn_KI270748v1      17571 1017 + 93321 AAAGAAAACTACAAATCCTTATCCCTGATCAACACAGATGTAAAAATACTCAACAAAATTCTAGCAAACTGAAGCTAACAACACATCAAAAAGATAATTCATCATGATCAAGTGGGCTTTATTCCAGGGGTGCTTGAATGGTTCAAAATAGACAAATCAATAAACATGATTCACCACATAAATGGAACTGAGAACAAAAACCCTATGATCATCTCATTAGATGCAGAATaagcatttgataaaatccaacatctgtttatgataaaaaccctcaACAATATAGGTATAGATGGAGTATACCTCAAA---AAATGAGTCATCTATGACAAAGCCACAGCCAACATCATCCTGGATGGGCAAAAGTTAGAAGTGTTGCTTCTAGAAACTGGAAAAAAGCAAGGATGTTCACCTTCATCATTCCTATTCAATACAGTACTGGAAGTGCTAGCCAGAACTATCAGAAAGGAGAAAGAAATAAAAGGTATACAAATTAGAAAA---GAAGTCAAATGATCTCTGCTCACTGATGACATGACTGTAGGCCTAGAAAACCCTAAAGTCTTC---AGAAGACTCCTAGACTTGATACACGACTTCAGTAAAGTCTTGGGATAAACAAGC------CACAAAAATCAGTTGTATTTCTATACACCAAATACATTCAAGCTGTTTGAATGTTTGTTGAGATTAATTtgttgAGAACCAAATTAAGAACTCAACTGAATTTACAATAGCCATG---------AAAAATACCTAGGAATGCAT---AACTATATAAATGAAAGATCTCTACAAGGAGAACTACAAAATACTAATGAAAGAAATTATAGATGACATAAACAAATGGAAAAACATCCCATGCTCATGGATTAGAAAAATCAAT---AGCTAAAGTGACCATATCACCC---ATACAATCTATAGAGTTAATGCAATTCCCATCAAATTACCAACGTTATTTCTCACAaaattaaaaaaa---aaTCCTAAAGTTCACATGGAGCCAAAAAAAGATCCCTAATAGCCAAAGCACTTCTAAGCAAAAAa</span>

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58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span></pre>

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<br>

</li>

<li id="a81c2db8e6e690a6632a84731453a5a1b4e40d61">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#a81c2db8e6e690a6632a84731453a5a1b4e40d61"><strong>test/frameshift-old.maf</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># LAST version 1243</span>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#</span>

</pre>

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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="plaintext"># a=11 b=2 A=11 B=2 F=12 e=40 d=29 x=39 y=31 z=39 D=1e+06 E=8.45245e+08</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=3.08611 j=3 Q=0</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># /home/mcfrith/tmp/x</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># Reference sequences=1 normal letters=491</span>

</pre>

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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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># lambda=0.327048 K=0.105437</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">#</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">#    A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  J  Z  X  *</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1 -1 -1 -4</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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2  0 -1 -4</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  4 -3  0 -1 -4</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4 -3  1 -1 -4</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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4</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="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0 -2  4 -1 -4</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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1 -3  4 -1 -4</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -4 -2 -1 -4</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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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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="LC18" class="line" lang="plaintext"># H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0 -3  0 -1 -4</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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3  3 -3 -1 -4</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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4  3 -3 -1 -4</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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0 -3  1 -1 -4</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3  2 -1 -1 -4</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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3  0 -3 -1 -4</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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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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="LC24" class="line" lang="plaintext"># P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -3 -1 -1 -4</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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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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="LC25" class="line" lang="plaintext"># S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0 -2  0 -1 -4</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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

26

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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="LC26" class="line" lang="plaintext"># T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1 -1 -1 -4</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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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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="LC27" class="line" lang="plaintext"># W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -2 -2 -1 -4</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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"># Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -1 -2 -1 -4</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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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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="LC29" class="line" lang="plaintext"># V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3  2 -2 -1 -4</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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

30

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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="LC30" class="line" lang="plaintext"># B -2 -1  4  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4 -3  0 -1 -4</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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

31

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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="LC31" class="line" lang="plaintext"># J -1 -2 -3 -3 -1 -2 -3 -4 -3  3  3 -3  2  0 -3 -2 -1 -2 -1  2 -3  3 -3 -1 -4</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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"># Z -1  0  0  1 -3  4  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -2 -2 -2  0 -3  4 -1 -4</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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

33

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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="LC33" class="line" lang="plaintext"># X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4</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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"># * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC35" class="line" lang="plaintext">#</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"># Coordinates are 0-based.  For - strand matches, coordinates</span>

</pre>

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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="plaintext"># in the reverse complement of the 2nd sequence are used.</span>

</pre>

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">#</span>

</pre>

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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">

39

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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="LC39" class="line" lang="plaintext"># name start alnSize strand seqSize alignment</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="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="plaintext">#</span>

</pre>

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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="plaintext"># batch 0</span>

</pre>

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</td>

<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="plaintext">a score=118 EG2=1.8 E=2.4e-11</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="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="plaintext">s Q2LCP8  110 232 +   491 LILIYSSIIGMLISMEAHNLITLFLSLEISSICFYILALNKNSRKGIEGGLKYYIIGGIATTILLLGIVSIYKSTGSLMYTDLLVIVMENTDDYRIQMGIALIVLGLILKLGIAPFHGWLIDVYEGAGMLMTFYLTITQKlvtlmvlinlyqnliiytnaimftngliILILVTLVVGTIGSLRQQKLIRFIAYSAIVNSALLILMLAGSMSEELMVNSVYYLINYIIGLTV</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="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="plaintext">s chrM   5258 639 + 16775 LICTVSLIMGTSITISSNH*ILA*TGLEINTLAIIPLISKSHHPRAIEATIKYFLTQSTASALILFSSITNA*STGQ*DITQL------NHPTSCLILTIAIAI-----KLGLVPFHF*FPEVLQGSSLITALLLSTLIKLPPITLLLLTSQSL----Nttllt---llaISSTLIGG*MG-LNQTQTRKILAFSSISHLG*IIIIISYNPQLTILTFILYTIMTSTVFLSL</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">a score=72 EG2=6.3e+06 E=9e-05</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="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="plaintext">s Q2LCP8  379  52 +   491 ILVLMYLAGLPPMTNFISKILILLPYMVLGRVYLTMLAFFLSVGVMIYYMNL</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">s chrM   5972 156 + 16775 ILTLLSLAGLPPLTGFMPK*LIIQELTKQEITPiatiitilsllslfFYLRL</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

50

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">a score=55 EG2=1.6e+09 E=0.024</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="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">s Q2LCP8   101  87 +   491 KKTKITDEGLILIYSSIIGMLISMEAHNLITLFLSLEISSICFYILALN-KNSRKGIEGGLKYYIIGGIATTILLLGIVSIYKSTGSL</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">s chrM   11752 255 + 16775 KRKRIFISTLIIIQPFII---LAFSATELILFYISFEATLIPTLILITR*GNQPERLSAGIYLLFYTLISSLPLLVSILYLHTNTGTL</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="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

53

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">a score=51 EG2=6e+09 E=0.09</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">s Q2LCP8   170  49 +   491 TTILLLGIVS-IYKSTGSLMYTDLLVIVMENTDDYRIQMGIALIVLGLIL</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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

56

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">s chrM   13892 141 + 16775 TTCLCLGALSTLFAATCALTQNDIKKIIAFSTSS---QLGLIIVTIGLDL</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="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

58

</td>

<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">a score=48 EG2=1.6e+10 E=0.24</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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">s Q2LCP8   394 27 +   491 FISKILILLPYMVLGRVYLTMLAFFLS</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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">s chrM   11767 81 + 16775 FISTLIIIQPFIILAFSATELILFYIS</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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

61

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></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="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

62

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">a score=46 EG2=3.1e+10 E=0.47</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">s Q2LCP8    16  38 +   491 YILPLII-LIVLSISIKKDVQRVHIIIQSLKLtlivimi</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">s chrM   14080 115 + 16775 yiipmlr\LIIHSLNGEQDIRKIGCLQKTLPITTSCLTI</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="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">a score=44 EG2=5.9e+10 E=0.91</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">s Q2LCP8    27  57 +   491 SISIK-KDVQRVHIIIQSLKLtlivimiviGIEESIYVKLNGHLIKTELIKLFEYLLL</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="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">s chrM   13941 170 + 16775 ALSLK/NDIKKIIAFSTSSQLGLIIVTIGLDLPQLAFLHISTHAFFKAILFLCSGLII</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="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">a score=42 EG2=1.1e+11 E=1.8</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="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">s Q2LCP8 166 24 +   491 GGIATTILLLGIVSIYKSTGSLMY</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="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">s chrM    54 72 + 16775 GGILCIIVHTFIYHIYYGTGNIYY</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">a score=42 EG2=1.1e+11 E=1.8</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="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">s Q2LCP8   292 22 +   491 LRQQKLIRFIAYSAIVNSALLI</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">s chrM   12313 66 + 16775 LRQTDLKSLIAYSSVSHMGLVI</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">a score=42 EG2=1.1e+11 E=1.8</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">s Q2LCP8   388 15 +   491 LPPMTNFISKILILL</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="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

80

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">s chrM   12589 45 + 16775 LPPTTNLIAELTIIV</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">a score=41 EG2=1.6e+11 E=2.4</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">s Q2LCP8    10  66 +   491 MIKYSIYILPLIILIVLSISIKKDVQRVHIIIQSLKLtlivimiviGIEESI--YVKLNGHLIKTELI</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">s chrM   11677 204 + 16775 LLVLSCWFLPLIIIASQGHLQHEPHKRKRIFISTLIIIQPFIILAFSATELILFYISFEATLIPTLIL</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">a score=41 EG2=1.6e+11 E=2.4</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">s Q2LCP8   15  44 +   491 IYILPLIILIVLSISIKKDVQRVHIIIQSLKLtlivimiviGIE</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">s chrM   8444 129 + 16775 LYLLTLILIEKLS-SNTVDAQEVELI*TILPAIVlvllalpslq</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="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"></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="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">a score=41 EG2=1.6e+11 E=2.4</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="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

91

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">s Q2LCP8   117 200 +   491 IIGMLISMEAHNLITLFLSLE-ISSICFYILALNKNSRKGIEGGLKYYIIGGIATTILLLGIVSIYKSTGSLMYTDLLVIVMENTDDYRIQMGIALIVLGLILKLGIAPFHGWLIDVYEGAGMLMTFYLTITQKlvtlmvlinlyqnliiytnaimftngliILILVTLVVGTIGSLRQQKLIRFIAYSAIVNSALLILML</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="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

92

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">s chrM   13445 576 + 16775 liailTLTIANNIFLLFVG*EGVGIMSFLLIG**QGRAEANTAALQAIIYNRIGDIGLILSIA*L---ASSLNT*EIQQITHPNQTPTLPLLGLILAATGKSAQFGL---HP*LPAAIEGPTPVSALLHSSTIVVAGIFLLIRTHP--FLSSNKTALTTCLCLGALSTLFAATC-ALTQNDIKKIIAFSTSSQLGLIIVTI</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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

93

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">a score=41 EG2=1.6e+11 E=2.4</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="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

95

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">s Q2LCP8  375  42 +   491 AIVYILVLMYLAGLPPMTNFISKILILLPYMVLGRVYLTMLA</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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

96

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">s chrM   5606 108 + 16775 SLITALLLSTLIKLPPIT------LLLLTSQSLNttlltlla</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="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

97

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></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="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

98

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">a score=40 EG2=2.2e+11 E=3.4</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="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

99

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">s Q2LCP8  374 30 +   491 GAIVYILVLMYLAGLPPM---TNFISKILILLP</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="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

100

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">s chrM   7064 99 + 16775 gasvdlaifhylagVSSILGAINFITTIINIKP</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="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

101

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></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="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

102

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">a score=43 EG2=8.2e+10 E=1.3</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="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

103

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">s Q2LCP8  202 20 +   491 DYRIQMGIALIVLGLILKLG</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="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

104

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">s chrM   9413 57 - 16775 DRRIrigvg-iglglllqlG</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="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

105

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"></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="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

106

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">a score=41 EG2=1.6e+11 E=2.4</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="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">s Q2LCP8   0  34 +   491 MVCLFENLMNMIKYSIYILPLIILIVLSISIKKD</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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">s chrM   196 102 - 16775 LVSLGVSFVSLALFLVYLGGMLVVFVYSVSLAAD</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"></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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">a score=40 EG2=2.2e+11 E=3.4</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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">s Q2LCP8  406 20 +   491 VLGRVYLTMLAFFLSVGVMI</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="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

112

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">s chrM   2209 60 - 16775 IIPrvvtmmaavfvmvgivi</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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"></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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"># batch 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="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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"># Query sequences=2</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="6c90adec85ff9834658c43a287e5d780f52732ef">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#6c90adec85ff9834658c43a287e5d780f52732ef"><strong>test/last-test.out</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3939" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3939" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3939,6 +3939,92 @@ TEST lastal -D1000 -fTAB -K2 /tmp/last-test galGal3-M-32.fa</td>

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<td class="old_line diff-line-num" data-linenumber="3939" 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">

3939

</td>

<td class="new_line diff-line-num" data-linenumber="3939" 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">

3939

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3939" class="line" lang="plaintext">15 chrM    6590    19      +       16571   chr32   2       19      +       1028    19      EG2=2.4e+10     E=0.8</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3940" 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">

3940

</td>

<td class="new_line diff-line-num" data-linenumber="3940" 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">

3940

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3940" class="line" lang="plaintext"># Query sequences=2</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3941" 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">

3941

</td>

<td class="new_line diff-line-num" data-linenumber="3941" 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">

3941

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3941" class="line" lang="plaintext"></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="3942" style="width: 35px; color: rgba(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="3942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3942

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3942" class="line" lang="plaintext">TEST lastal -D1000 -fTAB -K0 /tmp/last-test galGal3-M-32.fa</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="3942" style="width: 35px; color: rgba(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="3943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3943

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3943" class="line" lang="plaintext">#</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="3942" style="width: 35px; color: rgba(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="3944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3944

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3944" class="line" lang="plaintext"># a=7 b=1 A=7 B=1 e=15 d=13 x=14 y=9 z=14 D=1000 E=2.43016e+10</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="3942" style="width: 35px; color: rgba(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="3945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3945

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3945" class="line" lang="plaintext"># R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 K=0 k=1 w=1000 t=0.910239 j=3 Q=0</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="3942" style="width: 35px; color: rgba(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="3946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3946

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3946" class="line" lang="plaintext"># /tmp/last-test</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="3942" style="width: 35px; color: rgba(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="3947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3947

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3947" class="line" lang="plaintext"># Reference sequences=1 normal letters=16571</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="3942" style="width: 35px; color: rgba(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="3948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3948

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3948" class="line" lang="plaintext"># lambda=1.09602 K=0.335388</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="3942" style="width: 35px; color: rgba(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="3949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3949

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3949" class="line" lang="plaintext">#</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="3942" style="width: 35px; color: rgba(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="3950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3950

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3950" class="line" lang="plaintext">#     A   C   G   T   M   S   K   W   R   Y   B   D   H   V</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="3942" style="width: 35px; color: rgba(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="3951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3951

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3951" class="line" lang="plaintext"># A   1  -1  -1  -1   0  -1  -1   0   0  -1  -1   0   0   0</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="3942" style="width: 35px; color: rgba(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="3952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3952

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3952" class="line" lang="plaintext"># C  -1   1  -1  -1   0   0  -1  -1  -1   0   0  -1   0   0</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="3942" style="width: 35px; color: rgba(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="3953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3953

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3953" class="line" lang="plaintext"># G  -1  -1   1  -1  -1   0   0  -1   0  -1   0   0  -1   0</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="3942" style="width: 35px; color: rgba(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="3954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3954

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3954" class="line" lang="plaintext"># T  -1  -1  -1   1  -1  -1   0   0  -1   0   0   0   0  -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="3942" style="width: 35px; color: rgba(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="3955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3955

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3955" class="line" lang="plaintext"># M   0   0  -1  -1   0   0  -1   0   0   0   0   0   0   0</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="3942" style="width: 35px; color: rgba(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="3956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3956

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3956" class="line" lang="plaintext"># S  -1   0   0  -1   0   0   0  -1   0   0   0   0   0   0</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="3942" style="width: 35px; color: rgba(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="3957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3957

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3957" class="line" lang="plaintext"># K  -1  -1   0   0  -1   0   0   0   0   0   0   0   0   0</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="3942" style="width: 35px; color: rgba(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="3958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3958

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3958" class="line" lang="plaintext"># W   0  -1  -1   0   0  -1   0   0   0   0   0   0   0   0</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="3942" style="width: 35px; color: rgba(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="3959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3959

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3959" class="line" lang="plaintext"># R   0  -1   0  -1   0   0   0   0   0  -1   0   0   0   0</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3960

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<pre style="margin: 0;">+<span id="LC3960" class="line" lang="plaintext"># Y  -1   0  -1   0   0   0   0   0  -1   0   0   0   0   0</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3961

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<pre style="margin: 0;">+<span id="LC3961" class="line" lang="plaintext"># B  -1   0   0   0   0   0   0   0   0   0   0   0   0   0</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3962

</td>

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<pre style="margin: 0;">+<span id="LC3962" class="line" lang="plaintext"># D   0  -1   0   0   0   0   0   0   0   0   0   0   0   0</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3963

</td>

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<pre style="margin: 0;">+<span id="LC3963" class="line" lang="plaintext"># H   0   0  -1   0   0   0   0   0   0   0   0   0   0   0</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3964

</td>

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<pre style="margin: 0;">+<span id="LC3964" class="line" lang="plaintext"># V   0   0   0  -1   0   0   0   0   0   0   0   0   0   0</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3965

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<pre style="margin: 0;">+<span id="LC3965" class="line" lang="plaintext">#</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3966

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<pre style="margin: 0;">+<span id="LC3966" class="line" lang="plaintext"># Coordinates are 0-based.  For - strand matches, coordinates</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3967

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<pre style="margin: 0;">+<span id="LC3967" class="line" lang="plaintext"># in the reverse complement of the 2nd sequence are used.</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3968

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<pre style="margin: 0;">+<span id="LC3968" class="line" lang="plaintext">#</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3969

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<pre style="margin: 0;">+<span id="LC3969" class="line" lang="plaintext"># score    name1   start1  alnSize1        strand1 seqSize1        name2   start2  alnSize2        strand2 seqSize2        blocks</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3970

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<pre style="margin: 0;">+<span id="LC3970" class="line" lang="plaintext"># batch 0</span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="3971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3971

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<pre style="margin: 0;">+<span id="LC3971" class="line" lang="plaintext">847        chrM    5902    1595    +       16571   chrM    6645    1589    +       16775   450,3:0,1085,3:0,54     EG2=0   E=0</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3972

</td>

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<pre style="margin: 0;">+<span id="LC3972" class="line" lang="plaintext">524        chrM    14756   1124    +       16571   chrM    14904   1124    +       16775   1124    EG2=1.3e-232    E=6.2e-242</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3973

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<pre style="margin: 0;">+<span id="LC3973" class="line" lang="plaintext">426        chrM    10944   1266    +       16571   chrM    11669   1266    +       16775   1266    EG2=5.6e-186    E=2.8e-195</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3974

</td>

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<pre style="margin: 0;">+<span id="LC3974" class="line" lang="plaintext">404        chrM    9109    918     +       16571   chrM    9824    918     +       16775   918     EG2=1.7e-175    E=8.4e-185</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3975

</td>

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<pre style="margin: 0;">+<span id="LC3975" class="line" lang="plaintext">366        chrM    3334    920     +       16571   chrM    4097    920     +       16775   920     EG2=2e-157      E=1e-166</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3976

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<pre style="margin: 0;">+<span id="LC3976" class="line" lang="plaintext">259        chrM    7524    722     +       16571   chrM    8266    721     +       16775   45,0:1,17,0:1,154,3:0,503       EG2=1.8e-106    E=9.1e-116</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3977

</td>

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<pre style="margin: 0;">+<span id="LC3977" class="line" lang="plaintext">249        chrM    13168   681     +       16571   chrM    13901   681     +       16775   681     EG2=1e-101      E=5.3e-111</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3978

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<pre style="margin: 0;">+<span id="LC3978" class="line" lang="plaintext">242        chrM    12461   671     +       16571   chrM    13197   668     +       16775   505,3:0,163     EG2=2.2e-98     E=1.1e-107</span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="3979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3979

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<pre style="margin: 0;">+<span id="LC3979" class="line" lang="plaintext">193        chrM    4321    800     +       16571   chrM    5093    798     +       16775   66,3:0,69,0:1,662       EG2=4.6e-75     E=2.4e-84</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3980

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<pre style="margin: 0;">+<span id="LC3980" class="line" lang="plaintext">160        chrM    2908    255     +       16571   chrM    3629    255     +       16775   146,0:1,53,1:0,55       EG2=2.3e-59     E=1.2e-68</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3981

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<pre style="margin: 0;">+<span id="LC3981" class="line" lang="plaintext">149        chrM    1042    401     +       16571   chrM    1702    407     +       16775   114,0:2,92,0:4,33,0:1,27,0:1,45,1:0,32,1:0,56   EG2=4e-54       E=2.1e-63</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3982

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<pre style="margin: 0;">+<span id="LC3982" class="line" lang="plaintext">122        chrM    2409    334     +       16571   chrM    3112    338     +       16775   41,2:0,38,0:1,32,0:2,37,0:3,184 EG2=2.8e-41     E=1.5e-50</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3983

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<pre style="margin: 0;">+<span id="LC3983" class="line" lang="plaintext">114        chrM    5208    523     +       16571   chrM    5978    529     +       16775   233,3:0,84,0:5,39,0:3,14,1:0,69,0:2,80  EG2=1.8e-37     E=9.9e-47</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3984

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<pre style="margin: 0;">+<span id="LC3984" class="line" lang="plaintext">108        chrM    595     352     +       16571   chrM    1243    356     +       16775   56,1:0,82,0:3,63,0:1,19,0:1,55,1:0,57,0:1,18    EG2=1.3e-34     E=7.1e-44</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3985

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<pre style="margin: 0;">+<span id="LC3985" class="line" lang="plaintext">95 chrM    1742    281     +       16571   chrM    2432    295     +       16775   26,0:1,12,0:4,25,0:4,11,0:2,57,1:0,42,0:1,24,0:3,83     EG2=2e-28       E=1.1e-37</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3986

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<pre style="margin: 0;">+<span id="LC3986" class="line" lang="plaintext">92 chrM    10106   346     +       16571   chrM    10825   349     +       16775   299,0:3,47      EG2=5.4e-27     E=2.9e-36</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3987

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<pre style="margin: 0;">+<span id="LC3987" class="line" lang="plaintext">90 chrM    10518   272     +       16571   chrM    11243   272     +       16775   272     EG2=4.9e-26     E=2.6e-35</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3988

</td>

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<pre style="margin: 0;">+<span id="LC3988" class="line" lang="plaintext">72 chrM    8638    216     +       16571   chrM    9353    216     +       16775   216     EG2=1.8e-17     E=9.8e-27</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3989

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<pre style="margin: 0;">+<span id="LC3989" class="line" lang="plaintext">67 chrM    8897    151     +       16571   chrM    9612    151     +       16775   151     EG2=4.3e-15     E=2.4e-24</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3990

</td>

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<pre style="margin: 0;">+<span id="LC3990" class="line" lang="plaintext">60 chrM    12211   128     +       16571   chrM    12944   128     +       16775   128     EG2=9.2e-12     E=5.1e-21</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3991

</td>

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<pre style="margin: 0;">+<span id="LC3991" class="line" lang="plaintext">48 chrM    14425   318     +       16571   chrM    16456   319     +       16775   247,0:2,54,1:0,16       EG2=4.8e-06     E=2.6e-15</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="3992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3992

</td>

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<pre style="margin: 0;">+<span id="LC3992" class="line" lang="plaintext">40 chrM    1546    60      +       16571   chrM    2216    60      +       16775   60      EG2=0.031       E=1.7e-11</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="3942" style="width: 35px; color: rgba(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="3993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3993

</td>

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<pre style="margin: 0;">+<span id="LC3993" class="line" lang="plaintext">36 chrM    5764    129     +       16571   chrM    6510    134     +       16775   78,0:2,33,0:3,18        EG2=2.5 E=1.4e-09</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="3942" style="width: 35px; color: rgba(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="3994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3994

</td>

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<pre style="margin: 0;">+<span id="LC3994" class="line" lang="plaintext">33 chrM    1450    53      +       16571   chrM    2122    53      +       16775   53      EG2=66  E=3.6e-08</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="3942" style="width: 35px; color: rgba(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="3995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3995

</td>

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<pre style="margin: 0;">+<span id="LC3995" class="line" lang="plaintext">26 chrM    198     48      +       16571   chrM    856     48      +       16775   48      EG2=1.4e+05     E=7.8e-05</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="3942" style="width: 35px; color: rgba(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="3996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3996

</td>

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<pre style="margin: 0;">+<span id="LC3996" class="line" lang="plaintext">25 chrM    3237    70      +       16571   chrM    3973    69      +       16775   38,1:0,31       EG2=4.2e+05     E=0.00023</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="3942" style="width: 35px; color: rgba(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="3997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3997

</td>

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<pre style="margin: 0;">+<span id="LC3997" class="line" lang="plaintext">24 chrM    2807    38      +       16571   chrM    3520    38      +       16775   38      EG2=1.3e+06     E=0.0007</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="3942" style="width: 35px; color: rgba(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="3998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3998

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3998" class="line" lang="plaintext">24 chrM    3279    28      +       16571   chrM    10177   28      -       16775   28      EG2=1.3e+06     E=0.0007</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="3942" style="width: 35px; color: rgba(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="3999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3999

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3999" class="line" lang="plaintext">23 chrM    15975   49      +       16571   chrM    16128   49      +       16775   49      EG2=3.8e+06     E=0.0021</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="3942" style="width: 35px; color: rgba(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="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4000

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4000" class="line" lang="plaintext">22 chrM    14065   78      +       16571   chrM    14801   78      +       16775   78      EG2=1.1e+07     E=0.0063</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="3942" style="width: 35px; color: rgba(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="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4001

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4001" class="line" lang="plaintext">19 chrM    14757   47      +       16571   chrM    14646   47      +       16775   47      EG2=3e+08       E=0.17</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="3942" style="width: 35px; color: rgba(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="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4002

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4002" class="line" lang="plaintext">18 chrM    10947   40      +       16571   chrM    13143   40      +       16775   40      EG2=9.1e+08     E=0.5</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="3942" style="width: 35px; color: rgba(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="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4003

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4003" class="line" lang="plaintext">17 chrM    2171    23      +       16571   chrM    2890    23      +       16775   23      EG2=2.7e+09     E=1.5</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="3942" style="width: 35px; color: rgba(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="4004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4004

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4004" class="line" lang="plaintext">17 chrM    2287    35      +       16571   chrM    2996    35      +       16775   35      EG2=2.7e+09     E=1.5</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="3942" style="width: 35px; color: rgba(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="4005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4005

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4005" class="line" lang="plaintext">17 chrM    4152    43      +       16571   chrM    2363    43      +       16775   43      EG2=2.7e+09     E=1.5</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="3942" style="width: 35px; color: rgba(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="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4006

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4006" class="line" lang="plaintext">17 chrM    5842    33      +       16571   chrM    3861    33      -       16775   33      EG2=2.7e+09     E=1.5</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="3942" style="width: 35px; color: rgba(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="4007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4007

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4007" class="line" lang="plaintext">17 chrM    8549    35      +       16571   chrM    473     35      +       16775   35      EG2=2.7e+09     E=1.5</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="3942" style="width: 35px; color: rgba(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="4008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4008

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4008" class="line" lang="plaintext">16 chrM    13128   26      +       16571   chrM    1473    26      -       16775   26      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4009

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4009" class="line" lang="plaintext">16 chrM    13647   60      +       16571   chrM    9068    60      +       16775   60      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4010

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4010" class="line" lang="plaintext">16 chrM    14155   42      +       16571   chrM    16201   42      +       16775   42      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4011

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4011" class="line" lang="plaintext">16 chrM    15450   32      +       16571   chrM    13086   32      +       16775   32      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4012

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4012" class="line" lang="plaintext">16 chrM    1668    36      +       16571   chrM    1653    36      +       16775   36      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4013

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4013" class="line" lang="plaintext">16 chrM    5427    26      +       16571   chrM    16421   26      +       16775   26      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4014

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4014" class="line" lang="plaintext">16 chrM    8312    24      +       16571   chrM    9034    24      +       16775   24      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4015

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4015" class="line" lang="plaintext">16 chrM    8362    42      +       16571   chrM    9080    42      +       16775   42      EG2=8.1e+09     E=4.5</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="3942" style="width: 35px; color: rgba(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="4016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4016

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4016" class="line" lang="plaintext">16 chrM    9094    38      +       16571   chrM    13088   38      +       16775   38      EG2=8.1e+09     E=4.5</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="3942" style="width: 35px; color: rgba(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="4017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4017

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4017" class="line" lang="plaintext">15 chrM    473     27      +       16571   chrM    5926    27      +       16775   27      EG2=2.4e+10     E=13</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="3942" style="width: 35px; color: rgba(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="4018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4018

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4018" class="line" lang="plaintext">15 chrM    4761    23      +       16571   chrM    9904    23      -       16775   23      EG2=2.4e+10     E=13</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="3942" style="width: 35px; color: rgba(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="4019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4019

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4019" class="line" lang="plaintext">15 chrM    6447    43      +       16571   chrM    9290    43      +       16775   43      EG2=2.4e+10     E=13</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="3942" style="width: 35px; color: rgba(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="4020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4020

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4020" class="line" lang="plaintext">15 chrM    6518    37      +       16571   chrM    3056    37      +       16775   37      EG2=2.4e+10     E=13</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="3942" style="width: 35px; color: rgba(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="4021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4021

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4021" class="line" lang="plaintext"># batch 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="3942" style="width: 35px; color: rgba(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="4022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4022

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4022" class="line" lang="plaintext">18 chrM    15816   34      +       16571   chr32   172     34      +       1028    34      EG2=9.1e+08     E=0.03</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="3942" style="width: 35px; color: rgba(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="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4023

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4023" class="line" lang="plaintext">15 chrM    13147   33      +       16571   chr32   78      33      +       1028    33      EG2=2.4e+10     E=0.8</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="3942" style="width: 35px; color: rgba(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="4024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4024

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4024" class="line" lang="plaintext">15 chrM    1676    23      +       16571   chr32   71      23      +       1028    23      EG2=2.4e+10     E=0.8</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="3942" style="width: 35px; color: rgba(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="4025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4025

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4025" class="line" lang="plaintext">15 chrM    6590    19      +       16571   chr32   2       19      +       1028    19      EG2=2.4e+10     E=0.8</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="3942" style="width: 35px; color: rgba(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="4026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4026

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4026" class="line" lang="plaintext"># Query sequences=2</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="3942" style="width: 35px; color: rgba(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="4027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4027

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4027" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3942" 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">

3942

</td>

<td class="new_line diff-line-num" data-linenumber="4028" 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">

4028

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4028" class="line" lang="plaintext">TEST lastal -W19 -fTAB /tmp/last-test hg19-M.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3943" 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">

3943

</td>

<td class="new_line diff-line-num" data-linenumber="4029" 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">

4029

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4029" class="line" lang="plaintext">#</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="3944" 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">

3944

</td>

<td class="new_line diff-line-num" data-linenumber="4030" 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">

4030

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4030" class="line" lang="plaintext"># a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 E=1.13155e+07</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="fcd3167fe23623673ee838f0da31855d3d479dff">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#fcd3167fe23623673ee838f0da31855d3d479dff"><strong>test/last-test.sh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="189" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,6 +189,7 @@ trap 'rm -f $db*' EXIT</td>

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<td class="old_line diff-line-num" data-linenumber="189" 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">

189

</td>

<td class="new_line diff-line-num" data-linenumber="189" 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">

189

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC189" class="line" lang="shell"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="190" 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">

190

</td>

<td class="new_line diff-line-num" data-linenumber="190" 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">

190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="shell">    <span class="c" style="color: #998; font-style: italic;"># culling</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="191" 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">

191

</td>

<td class="new_line diff-line-num" data-linenumber="191" 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">

191

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="shell">    try lastal <span class="nt" style="color: #000080;">-D1000</span> <span class="nt" style="color: #000080;">-fTAB</span> <span class="nt" style="color: #000080;">-K2</span> <span class="nv" style="color: #008080;">$db</span> galGal3-M-32.fa</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="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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC192" class="line" lang="shell">    try lastal <span class="nt" style="color: #000080;">-D1000</span> <span class="nt" style="color: #000080;">-fTAB</span> <span class="nt" style="color: #000080;">-K0</span> <span class="nv" style="color: #008080;">$db</span> galGal3-M-32.fa</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="192" 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">

192

</td>

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193

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC193" class="line" lang="shell"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="193" 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">

193

</td>

<td class="new_line diff-line-num" data-linenumber="194" 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">

194

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC194" class="line" lang="shell">    <span class="c" style="color: #998; font-style: italic;"># minimizers</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="194" 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">

194

</td>

<td class="new_line diff-line-num" data-linenumber="195" 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">

195

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC195" class="line" lang="shell">    lastdb <span class="nt" style="color: #000080;">-W3</span> <span class="nt" style="color: #000080;">-R10</span> <span class="nv" style="color: #008080;">$db</span> galGal3-M-32.fa</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="fa1f2beb637146f5175aacd2f5469caf7be2e7eb">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#fa1f2beb637146f5175aacd2f5469caf7be2e7eb"><strong>test/maf-convert-test.out</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8304" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8304" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8304,6 +8304,11 @@ Sbjct: 9000 TACGCCTAACCGCTAACATTACTGCAG 9026</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="8304" 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">

8304

</td>

<td class="new_line diff-line-num" data-linenumber="8304" 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">

8304

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8304" class="line" lang="">97  chrM    59.30   86      35      0       1       86      570     655</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8305" 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">

8305

</td>

<td class="new_line diff-line-num" data-linenumber="8305" 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">

8305

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8305" class="line" lang="">98  chrM    67.86   84      27      0       84      1       6926    7009</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8306" 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">

8306

</td>

<td class="new_line diff-line-num" data-linenumber="8306" 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">

8306

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8306" class="line" lang="">99  chrM    79.31   87      18      0       87      1       8940    9026</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="8307" style="width: 35px; color: rgba(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="8307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8307

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8307" class="line" lang="">chrUn_KI270748v1    UN-L1MA6_pol#LINE/L1    63.82   633     194     13      13905   15715   658     1273    0       1.08e+03</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="8307" style="width: 35px; color: rgba(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="8308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8308

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8308" class="line" lang="">chrUn_KI270748v1    UN-L1PA2_pol#LINE/L1    93.39   227     15      0       3860    4540    1049    1275    1.5e-169        603</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="8307" style="width: 35px; color: rgba(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="8309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8309

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8309" class="line" lang="">chrUn_KI270748v1    UN-L1MA6_pol#LINE/L1    62.18   386     107     14      3661    2577    518     879     2.5e-152        546</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="8307" style="width: 35px; color: rgba(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="8310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8310

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8310" class="line" lang="">chrUn_KI270748v1    UN-L1MA6_pol#LINE/L1    61.64   292     89      8       90089   89272   884     1164    2e-147  530</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="8307" style="width: 35px; color: rgba(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="8311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8311

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8311" class="line" lang="">chrUn_KI270748v1    UN-L1PA16_pol#LINE/L1   64.07   359     96      11      17572   18588   527     864     3.8e-142        512</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8307" 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">

8307

</td>

<td class="new_line diff-line-num" data-linenumber="8312" 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">

8312

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8312" class="line" lang="">chain 450 chr1 249250621 + 231468663 231468738 SRR359290.9002 75 + 0 75 1</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8308" 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">

8308

</td>

<td class="new_line diff-line-num" data-linenumber="8313" 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">

8313

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8313" class="line" lang="">75</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8309" 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">

8309

</td>

<td class="new_line diff-line-num" data-linenumber="8314" 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">

8314

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8314" class="line" lang="">chain 450 chr11 135006516 + 35273430 35273505 SRR359290.9010 75 + 0 75 2</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8933" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8938" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8933,6 +8938,12 @@ chr19   maf-convert     match   1395388 1395484 .       -       .       ID=102.72;Name=102:4-102</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8933" 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">

8933

</td>

<td class="new_line diff-line-num" data-linenumber="8938" 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">

8938

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8938" class="line" lang="">chr19       maf-convert     match_part      1395388 1395484 291     -       .       Target=102 4 102;Name=102:4-102;Parent=102.72</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8934" 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">

8934

</td>

<td class="new_line diff-line-num" data-linenumber="8939" 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">

8939

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8939" class="line" lang="">chr22       maf-convert     match   20726589        20726617        .       -       .       ID=102.73;Name=102:69-95</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8935" 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">

8935

</td>

<td class="new_line diff-line-num" data-linenumber="8940" 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">

8940

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8940" class="line" lang="">chr22       maf-convert     match_part      20726589        20726617        115     -       .       Target=102 69 95;Name=102:69-95;Parent=102.73</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="8936" style="width: 35px; color: rgba(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="8941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8941

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8941" class="line" lang="">##gff-version 3</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="8936" style="width: 35px; color: rgba(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="8942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8942

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8942" class="line" lang="">chrUn_KI270748v1    maf-convert     match   13905   15715   3177.2  +       .       Target=UN-L1MA6_pol#LINE/L1 658 1273;Name=UN-L1MA6_pol#LINE/L1:658-1273</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="8936" style="width: 35px; color: rgba(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="8943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8943

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8943" class="line" lang="">chrUn_KI270748v1    maf-convert     match   3860    4540    1775.7  +       .       Target=UN-L1PA2_pol#LINE/L1 1049 1275;Name=UN-L1PA2_pol#LINE/L1:1049-1275</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="8936" style="width: 35px; color: rgba(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="8944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8944

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8944" class="line" lang="">chrUn_KI270748v1    maf-convert     match   2577    3661    1607.4  -       .       Target=UN-L1MA6_pol#LINE/L1 518 879;Name=UN-L1MA6_pol#LINE/L1:518-879</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="8936" style="width: 35px; color: rgba(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="8945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8945

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8945" class="line" lang="">chrUn_KI270748v1    maf-convert     match   89272   90089   1559.7  -       .       Target=UN-L1MA6_pol#LINE/L1 884 1164;Name=UN-L1MA6_pol#LINE/L1:884-1164</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="8936" style="width: 35px; color: rgba(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="8946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8946

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8946" class="line" lang="">chrUn_KI270748v1    maf-convert     match   17572   18588   1508.0  +       .       Target=UN-L1PA16_pol#LINE/L1 527 864;Name=UN-L1PA16_pol#LINE/L1:527-864</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8936" 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">

8936

</td>

<td class="new_line diff-line-num" data-linenumber="8947" 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">

8947

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8947" class="line" lang=""></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8937" 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">

8937

</td>

<td class="new_line diff-line-num" data-linenumber="8948" 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">

8948

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8948" class="line" lang=""><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN"</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="8938" 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">

8938

</td>

<td class="new_line diff-line-num" data-linenumber="8949" 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">

8949

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8949" class="line" lang=""> "http://www.w3.org/TR/html4/strict.dtd"></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12112" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12123" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12112,6 +12123,29 @@ SRR359290.9033        1 CAAAGTGCTGGGATTGCAGGCATAAGCCACTGTGCGTGGCCA       42</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12112" 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">

12112

</td>

<td class="new_line diff-line-num" data-linenumber="12123" 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">

12123

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12123" class="line" lang="">606        8       0       0       4       8       17      34      +       90089   2478    48      670     chrX    156040895       23075589        23076237        22      9,31,26,2,35,9,4,43,7,56,10,9,13,90,10,40,50,5,68,65,2,30,      48,58,89,115,122,158,167,171,214,221,277,287,296,309,399,410,450,500,505,573,638,640,   23075589,23075598,23075630,23075663,23075665,23075700,23075710,23075716,23075760,23075770,23075827,23075838,23075848,23075864,23075956,23075966,23076007,23076058,23076064,23076135,23076203,23076207,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12113" 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">

12113

</td>

<td class="new_line diff-line-num" data-linenumber="12124" 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">

12124

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12124" class="line" lang="">100        1       0       0       0       0       5       6       -       90089   2478    675     776     chr7    159345973       121351142       121351249       6       9,10,41,2,20,19,        1702,1711,1721,1762,1764,1784,  121351142,121351152,121351164,121351206,121351209,121351230,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12114" 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">

12114

</td>

<td class="new_line diff-line-num" data-linenumber="12125" 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">

12125

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12125" class="line" lang="">1645       8       0       0       2       2       31      44      -       90089   2478    776     2431    chr7    159345973       121348853       121350550       34      45,14,4,43,11,65,37,114,184,15,47,75,120,53,3,25,117,94,52,69,19,94,51,8,84,40,4,46,1,8,13,26,22,50,    47,92,106,110,153,164,230,267,381,565,580,627,702,822,875,878,903,1020,1114,1166,1235,1254,1348,1399,1407,1491,1531,1535,1581,1582,1590,1604,1630,1652, 121348853,121348899,121348915,121348920,121348964,121348976,121349041,121349079,121349195,121349381,121349397,121349445,121349523,121349646,121349701,121349705,121349732,121349850,121349945,121349999,121350069,121350089,121350184,121350236,121350246,121350331,121350372,121350377,121350424,121350426,121350435,121350448,121350475,121350500,</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="12115" style="width: 35px; color: rgba(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="12126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12126

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12126" class="line" lang="">54 159     0       0       5       19      0       0       ++      Q2LCP8  491     110     342     chrM    16775   5258    5897    6       83,15,45,6,14,50,       110,199,219,268,277,292,        5258,5507,5552,5687,5705,5747,</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="12115" style="width: 35px; color: rgba(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="12127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12127

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12127" class="line" lang="">18 34      0       0       0       0       0       0       ++      Q2LCP8  491     379     431     chrM    16775   5972    6128    1       52,     379,    5972,</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="12115" style="width: 35px; color: rgba(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="12128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12128

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12128" class="line" lang="">24 60      0       0       1       3       1       3       ++      Q2LCP8  491     101     188     chrM    16775   11752   12007   3       18,28,38,       101,122,150,    11752,11806,11893,</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="12115" style="width: 35px; color: rgba(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="12129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12129

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12129" class="line" lang="">16 30      0       0       1       3       1       3       ++      Q2LCP8  491     170     219     chrM    16775   13892   14033   3       10,23,13,       170,180,206,    13892,13925,13994,</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="12115" style="width: 35px; color: rgba(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="12130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12130

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12130" class="line" lang="">8  19      0       0       0       0       0       0       ++      Q2LCP8  491     394     421     chrM    16775   11767   11848   1       27,     394,    11767,</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="12115" style="width: 35px; color: rgba(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="12131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12131

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12131" class="line" lang="">10 28      0       0       0       0       1       1       ++      Q2LCP8  491     16      54      chrM    16775   14080   14195   2       7,31,   16,23,  14080,14102,</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12132

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12132" class="line" lang="">11 46      0       0       0       0       0       -1      ++      Q2LCP8  491     27      84      chrM    16775   13941   14111   2       5,52,   27,32,  13941,13955,</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12133

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12133" class="line" lang="">10 14      0       0       0       0       0       0       ++      Q2LCP8  491     166     190     chrM    16775   54      126     1       24,     166,    54,</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12134

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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="LC12134" class="line" lang="">10 12      0       0       0       0       0       0       ++      Q2LCP8  491     292     314     chrM    16775   12313   12379   1       22,     292,    12313,</span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12135

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<pre style="margin: 0;">+<span id="LC12135" class="line" lang="">7  8       0       0       0       0       0       0       ++      Q2LCP8  491     388     403     chrM    16775   12589   12634   1       15,     388,    12589,</span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12136

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12136" class="line" lang="">17 49      0       0       0       0       1       6       ++      Q2LCP8  491     10      76      chrM    16775   11677   11881   2       52,14,  10,62,  11677,11839,</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12137

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12137" class="line" lang="">13 30      0       0       1       1       0       0       ++      Q2LCP8  491     15      59      chrM    16775   8444    8573    2       13,30,  15,29,  8444,8483,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12138

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12138" class="line" lang="">43 148     0       0       4       9       1       3       ++      Q2LCP8  491     117     317     chrM    16775   13445   14021   6       21,43,39,36,26,26,      117,138,184,226,264,291,        13445,13511,13640,13757,13865,13943,</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12139

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12139" class="line" lang="">15 21      0       0       1       6       0       0       ++      Q2LCP8  491     375     417     chrM    16775   5606    5714    2       18,18,  375,399,        5606,5660,</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12140

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12140" class="line" lang="">12 18      0       0       0       0       1       9       ++      Q2LCP8  491     374     404     chrM    16775   7064    7163    2       18,12,  374,392,        7064,7127,</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12141

</td>

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<pre style="margin: 0;">+<span id="LC12141" class="line" lang="">11 8       0       0       1       1       0       0       +-      Q2LCP8  491     202     222     chrM    16775   7305    7362    2       9,10,   202,212,        9413,9440,</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12142

</td>

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<pre style="margin: 0;">+<span id="LC12142" class="line" lang="">7  27      0       0       0       0       0       0       +-      Q2LCP8  491     0       34      chrM    16775   16477   16579   1       34,     0,      196,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12143

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<pre style="margin: 0;">+<span id="LC12143" class="line" lang="">8  12      0       0       0       0       0       0       +-      Q2LCP8  491     406     426     chrM    16775   14506   14566   1       20,     406,    2209,</span>

</pre>

</td>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12144

</td>

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<pre style="margin: 0;">+<span id="LC12144" class="line" lang="">404        194     0       0       12      18      12      17      ++      UN-L1MA6_pol#LINE/L1    1275    657     1273    chrUn_KI270748v1        93321   13904   15715   14      59,30,16,143,13,18,19,15,43,67,48,18,75,34,     657,717,747,766,910,924,944,964,980,1024,1092,1142,1163,1239,   13904,14082,14173,14223,14654,14695,14749,14807,14853,14983,15185,15331,15387,15613,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="12115" style="width: 35px; color: rgba(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="12145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12145

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12145" class="line" lang="">212        15      0       0       0       0       0       0       ++      UN-L1PA2_pol#LINE/L1    1276    1048    1275    chrUn_KI270748v1        93321   3859    4540    1       227,    1048,   3859,</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12146

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12146" class="line" lang="">240        107     0       0       12      15      11      44      +-      UN-L1MA6_pol#LINE/L1    1275    517     879     chrUn_KI270748v1        93321   2576    3661    15      10,16,12,5,4,8,13,92,15,35,11,14,24,80,8,       517,528,544,557,563,570,579,593,686,703,739,751,765,790,871,    89660,89692,89742,89780,89797,89810,89834,89873,90150,90195,90301,90335,90407,90480,90721,</span>

</pre>

</td>

</tr>

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</td>

<td class="new_line diff-line-num new" data-linenumber="12147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12147

</td>

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<pre style="margin: 0;">+<span id="LC12147" class="line" lang="">180        89      0       0       7       12      7       11      +-      UN-L1MA6_pol#LINE/L1    1275    883     1164    chrUn_KI270748v1        93321   89271   90089   9       7,33,40,84,4,44,37,12,8,        883,891,925,966,1054,1061,1105,1143,1156,       3232,3255,3355,3476,3730,3742,3875,3988,4026,</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12148

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12148" class="line" lang="">230        96      0       0       9       12      8       39      ++      UN-L1PA16_pol#LINE/L1   1276    526     864     chrUn_KI270748v1        93321   17571   18588   12      102,63,21,18,14,14,6,38,7,22,8,13,      526,629,693,715,735,749,766,773,812,820,843,851,        17571,17877,18066,18129,18185,18256,18300,18319,18434,18457,18524,18549,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12115" 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">

12115

</td>

<td class="new_line diff-line-num" data-linenumber="12149" 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">

12149

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12149" class="line" lang="">0  16      chrM    13914   71      3=1X11=1X28=2X21=1X15=1X3=      *       0       0       TCGAATTCTACCCTAACATCACACACCGCACAATCCCCTATCTAAACCTTCTTACGAGCCAAAACCTACCCCTACTCCTCCTAAACC C@A=<3CC@@CBCCC8CBAC?BBBC?BB@BCCBBBCCCCBBBCBCABCBBBCCCCBCBBAC@CCBBCCACCACCCCCCBCCACCA?B      NM:i:6  AS:i:429</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12116" 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">

12116

</td>

<td class="new_line diff-line-num" data-linenumber="12150" 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">

12150

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12150" class="line" lang="">1  0       chrM    1544    71      14=1X9=1X12=1X9=1X1=1X5=1X4=1X9=1X4=1X1=1X6=3X  *       0       0       TTATATAGAGGAGATAAGTCGTAATATGGTAAGTGTATTGGAAAGTGTATTTGGATGAACTAGAGTGTAGTTTAATATAAAGCATTT BB@1;?@B@BBBC@BBBCACBBA>B??=?A@B?B?B=7@4BB;B>@@@A?>=B@A@>@7>BA>BA6BA?@@B@@?B?AABBAB=<>B NM:i:13 AS:i:420</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="12117" 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">

12117

</td>

<td class="new_line diff-line-num" data-linenumber="12151" 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">

12151

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12151" class="line" lang="">10 0       chrM    3291    69      2=2X1=1X2=1X4=2X1=1X3=3X4=2X2=2X1=2X2=1X1=2X1=1X6=3X7=27H       *       0       0       TTTTTTTTTTTAATCATATATTTATGGTTAATTTTTTATTTTTTATTGTATTTATTCTAA    @6)>B+A9<)?>>A(?A=-(48/<5?=1>4>:B@@<-:@@5;/9==ABA47*5':B<### NM:i:23 AS:i:207</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23615" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23649" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23615,3 +23649,8 @@ SRR359290.9984 16      chrX    86355890        255     2H14=1X9=49H    *       0       0       GAAAGGGGAAGGAAAAGAAGGAAG</td>

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<td class="old_line diff-line-num" data-linenumber="23615" 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">

23615

</td>

<td class="new_line diff-line-num" data-linenumber="23649" 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">

23649

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23649" class="line" lang="">156        chr16   29595844        46      +       90354753        SRR359290.9033  0       46      +       75      46</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="23616" 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">

23616

</td>

<td class="new_line diff-line-num" data-linenumber="23650" 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">

23650

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23650" class="line" lang="">156        chr16   30335586        46      +       90354753        SRR359290.9033  0       46      +       75      46</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="23617" 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">

23617

</td>

<td class="new_line diff-line-num" data-linenumber="23651" 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">

23651

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23651" class="line" lang="">156        chr3    37456613        42      +       198022430       SRR359290.9033  0       42      +       75      42</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="23618" style="width: 35px; color: rgba(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="23652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23652

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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="LC23652" class="line" lang="">3177.2     UN-L1MA6_pol#LINE/L1    657     616     +       1275    chrUn_KI270748v1        13904   1811    +       93321   59,1:1,30,0:1,16,3:2,143,1:2,13,1:2,18,2:0,19,1:1,15,1:1,43,1:1,67,1:1,48,2:2,18,3:2,75,1:1,34  EG2=0   E=0</span>

</pre>

</td>

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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="23618" style="width: 35px; color: rgba(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="23653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23653

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<pre style="margin: 0;">+<span id="LC23653" class="line" lang="">1775.7     UN-L1PA2_pol#LINE/L1    1048    227     +       1276    chrUn_KI270748v1        3859    681     +       93321   227     EG2=2.9e-164    E=1.5e-169</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="23618" style="width: 35px; color: rgba(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="23654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23654

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<pre style="margin: 0;">+<span id="LC23654" class="line" lang="">1607.4     UN-L1MA6_pol#LINE/L1    517     362     +       1275    chrUn_KI270748v1        89660   1085    -       93321   10,1:2,16,0:2,12,1:2,5,1:2,4,3:1,8,1:0,13,1:0,92,1:1,15,2:0,35,1:1,11,1:1,14,0:30,24,1:1,80,1:1,8       EG2=5e-147      E=2.5e-152</span>

</pre>

</td>

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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="23618" style="width: 35px; color: rgba(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="23655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23655

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<pre style="margin: 0;">+<span id="LC23655" class="line" lang="">1559.7     UN-L1MA6_pol#LINE/L1    883     281     +       1275    chrUn_KI270748v1        3232    818     -       93321   7,1:2,33,1:1,40,1:1,84,4:2,4,3:0,44,0:1,37,1:2,12,1:2,8 EG2=3.8e-142    E=2e-147</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="23618" style="width: 35px; color: rgba(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="23656" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC23656" class="line" lang="">1508.0     UN-L1PA16_pol#LINE/L1   526     338     +       1276    chrUn_KI270748v1        17571   1017    +       93321   102,1:0,63,1:0,21,1:0,18,2:2,14,0:29,14,3:2,6,1:1,38,1:1,7,1:2,22,1:1,8,0:1,13  EG2=7.4e-137    E=3.8e-142</span></pre>

</td>

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</table>

<br>

</li>

<li id="91ede9ced121fa989c86d8e8721da9214813a826">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#91ede9ced121fa989c86d8e8721da9214813a826"><strong>test/maf-convert-test.sh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,9 +18,11 @@ maf2=bs100.maf</td>

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18

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<td class="new_line diff-line-num" data-linenumber="18" 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">

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-l100</span> blast</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="19" 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">

19

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<td class="new_line diff-line-num" data-linenumber="19" 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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> blast <span class="nv" style="color: #008080;">$maf2</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" 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">

20

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<td class="new_line diff-line-num" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> blasttab <span class="nv" style="color: #008080;">$maf2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC21" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> blasttab frameshift-new.maf</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="21" 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">

21

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<td class="new_line diff-line-num" data-linenumber="22" 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">

22

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> chain</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="22" 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">

22

</td>

<td class="new_line diff-line-num" data-linenumber="23" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> gff 102.maf</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="23" 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">

23

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<td class="new_line diff-line-num" data-linenumber="24" 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">

24

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-J1e9</span> gff 102.maf</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

25

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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="LC25" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> gff frameshift-new.maf</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="24" 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">

24

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<td class="new_line diff-line-num" data-linenumber="26" 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">

26

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> html <span class="nt" style="color: #000080;">-l100</span> <span class="nv" style="color: #008080;">$maf2</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="25" 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">

25

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<td class="new_line diff-line-num" data-linenumber="27" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-n</span> html</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" 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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<td class="new_line diff-line-num" data-linenumber="28" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> psl</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,9 +31,12 @@ maf2=bs100.maf</td>

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<td class="old_line diff-line-num" data-linenumber="29" 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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<td class="new_line diff-line-num" data-linenumber="31" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-j1e9</span> psl 102.maf</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="30" 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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<td class="new_line diff-line-num" data-linenumber="32" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-J1e9</span> psl 102.maf</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="31" 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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<td class="new_line diff-line-num" data-linenumber="33" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> psl 90089.maf</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="32" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC34" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> psl frameshift-old.maf</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="32" style="width: 35px; color: rgba(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="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC35" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> psl frameshift-new.maf</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="32" 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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<td class="new_line diff-line-num" data-linenumber="36" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-n</span> sam <span class="nv" style="color: #008080;">$maf2</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="33" 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">

33

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<td class="new_line diff-line-num" data-linenumber="37" 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">

37

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-r</span> <span class="s1" style="color: #d14;">'ID:1 PL:ILLUMINA SM:x'</span> sam</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="34" 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">

34

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<td class="new_line diff-line-num" data-linenumber="38" 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">

38

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC38" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-d</span> sam <span class="nv" style="color: #008080;">$maf1</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="35" 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">

35

</td>

<td class="new_line diff-line-num" data-linenumber="39" 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">

39

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-n</span> tab</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="36" 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">

36

</td>

<td class="new_line diff-line-num" data-linenumber="40" 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">

40

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell">    <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> tab</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">    <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-n</span> tab frameshift-new.maf</span>

</pre>

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37

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42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> | diff <span class="nt" style="color: #000080;">-u</span> maf-convert-test.out -</span></pre>

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<br>

</li>

<li id="b6a13701586c2871af8117b9a92cc4d1efabc505">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#b6a13701586c2871af8117b9a92cc4d1efabc505"><strong>test/maf-swap-test.out</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="769" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="769" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -769,3 +769,63 @@ p                                T\`hkkecba]\\`bbbceieae`]\[Z[ZZ[Z\^_^b^YY\[__cd</td>

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769

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769

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<pre style="margin: 0;"> <span id="LC769" class="line" lang="plaintext">p                                z~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}|yyyy}~~~~~}|yyyz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{zz{~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~||{{zz{~~~~~~~~~~~~~~~~~~~~~~|yywutsponnmmlllllmrw{~~~~~~~~~~~~~~~}}}}}~~~~~~~~~~|yxxxxx{|}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~zywwvssrqqqruwx}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{vrmlllkkkkkkllmnnooooppqrrrtuz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|{{{yyyyy{{~~~~~~~~~~~~~~~~~~~~~~~~~~~}|{{|~~~~~~}xxwwurrpnjea````````______________``bccdddefglqvz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~}~}||}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yuttssstvxxz{|{|{||{{zyxxyz{{{||}}||~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{wsnmmmmmmmllllllmnpqrrrrrrsvwx{}~~~~~~~~~~~~~~~~~~~|wsrpmid`[ZXXWWWWWWWWVTPLKJIHFEDA>98888888888888888888888763/+&%$</span>

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<td class="old_line diff-line-num" data-linenumber="770" 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">

770

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770

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="plaintext"></span>

</pre>

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771

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<td class="new_line diff-line-num" data-linenumber="771" 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">

771

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="plaintext"></span>

</pre>

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<td class="old_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">

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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">TEST maf-swap frameshift-new.maf</span>

</pre>

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<td class="old_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">

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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"># LAST version 1243</span>

</pre>

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<td class="old_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">

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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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC774" class="line" lang="plaintext">#</span>

</pre>

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<td class="old_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">

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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"># a=21 b=1 A=27 B=1 F=-2,0,-3,0 e=165.797 d=70 x=165 y=42 z=165 D=1e+09 E=18.1715</span>

</pre>

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<td class="old_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">

</td>

<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"># R=01 u=2 s=2 S=0 M=0 T=0 m=500 l=1 n=500 K=1 k=1 w=1000 t=4.24284 j=3 Q=0</span>

</pre>

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<td class="old_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">

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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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext"># ../aant/hg38/last/rmsk-hg38</span>

</pre>

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<td class="old_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">

</td>

<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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC778" class="line" lang="plaintext"># Reference sequences=38335 normal letters=27515653</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC779" class="line" lang="plaintext"># lambda=0.235691 K=1.69939</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC780" class="line" lang="plaintext">#</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC781" class="line" lang="plaintext">#   AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext"># A  -7  -5  -7  -6   3   3   1   3  -6  -3  -6  -2  -2  -3  -2  -4  -7  -6  -5  -6  -1  -1  -3  -1  -5  -4  -7  -5  -5  -6  -4  -5  -2  -2  -3  -3   9   9   7  10  -1   0  -2   1   4   4   4   4  -5  -9  -6  -8   2   1   0   1  -8  -7 -11  -6  -4  -6  -2  -5</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC783" class="line" lang="plaintext"># C -11  -4 -11  -5  -7  -4 -11  -5  -8   2  -7   2  -9  -6 -11  -8  -7   1  -6   2 -12  -7  -9  -7  -1   8  -2   8 -10  -6  -6  -4 -12  -6 -10  -6  -6  -6 -29  -5  -8   3  -6   1 -10  -6  -7  -6  -2   5   0   6  -6  -1  -4   0   3  13   1  13  -7   0  -6   1</span>

</pre>

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</td>

<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>

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<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext"># D  -4   4  -3   4  -9  -3  -7  -4  -7   0  -7   1 -12  -7  -9  -8  -4   1  -5   0 -10  -7 -10  -6 -27  -1  -6  -3 -15  -9 -14 -10   2  11   3  10  -7  -1  -3  -1  -2   5  -2   5  -6   0  -6  -1  -2   1  -3   0  -9  -5 -16  -6  -8  -3 -12  -4 -13  -8 -10 -10</span>

</pre>

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</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext"># E   2  -2   1  -1  -5  -8  -8  -6  -3  -4  -4  -5  -7 -12  -7 -12   0  -5   0  -5  -8  -9 -11 -11  -2 -11  -5  -9 -10 -13 -10 -11   9   3   8   4  -1  -6  -1  -6   2  -2   2  -1  -2  -6  -3  -7   3  -6   0  -5  -9  -9  -9  -8  -4  -9 -10  -8  -9 -14  -8 -12</span>

</pre>

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<td class="old_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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext"># F -17  -9 -16  -8 -11  -6  -7  -6 -16  -8 -13  -8  -8  -2  -6  -2 -10  -3 -10  -1 -12  -5  -8  -6 -11  -5  -4  -1  -4   3  -2   2 -18 -11 -18 -11  -9 -10 -11  -7 -13 -10 -12  -9  -6   1  -7  -1  -6   2  -4   3  -6   1  -2   1  -7   1  -8   2   2  11   2  11</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext"># G  -4  -3  -3  -3  -6  -6  -5  -6   4   3   3   3  -8 -10  -8  -9  -4  -5  -4  -3 -10  -7  -3  -7   0   2   2   0 -13 -13 -14 -13   3   1   3   2  -1   0   1  -1  11  10  10  10  -1  -1  -2  -2  -2  -7  -4  -6 -10  -7  -8  -6   1  -2  -3  -1 -10 -13 -11 -10</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext"># H  -6   0  -5   0  -8  -4 -25  -4  -9  -3  -6  -1 -13  -9 -11  -9   3  11   3  11  -5   1  -1   0  -1   7   2   9  -6  -1  -8  -1  -7  -2  -4  -1 -10  -6  -4  -6  -7  -3  -6  -2 -11  -5 -10  -5  -1   6   0   6  -7  -1  -3  -2  -3   2  -6   4  -8  -3  -9  -3</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext"># I  -5  -5  -8  -4   1   1   1   2  -4  -2  -6  -2   7   7   3   7  -9 -10 -10  -9  -7  -8  -8  -9  -6  -6 -21  -7   1  -1  -2  -1 -11 -11 -10  -9  -4  -5  -2  -4  -8  -8  -9  -7   4   3   1   3  -6  -8  -8  -9  -6  -8  -7  -7  -7  -7 -15  -9   0  -3  -2  -2</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext"># K   7   1   7   1  -1  -5   0  -5   3  -2   2  -1  -3 -10  -3  -8   0  -5  -1  -5  -7 -10  -4 -10  -2  -8  -5  -5  -8 -13 -10 -13  -1  -7   0  -6  -6  -9  -5  -8  -3  -8  -4  -6  -6 -10  -7  -9   2  -9  -1  -8  -7 -10 -12 -10  -3  -9  -8 -10  -6 -14  -9 -10</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext"># L -10 -10 -10 -11  -5  -7  -2  -4  -9  -8  -8  -8   0   0   1   0  -4  -2  -2  -2  -1  -1   3  -1   0   0  -3  -1   7   7   7   7 -12 -12 -10 -13  -8  -6  -1  -6 -11 -11  -8 -10   0  -1   0  -1  -3  -4  -4  -5  -2  -4   1  -4  -2  -4  -5  -3   7   3   6   3</span>

</pre>

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<td class="old_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">

</td>

<td class="new_line diff-line-num new" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

792

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext"># M  -6  -7  -2  -6   1  -3   7  -3  -4  -6   1  -6   4   1  11   2  -7  -8  -5  -9  -6  -8  -1  -9  -4 -10  -8  -3   0  -2   4  -2  -8 -12  -4 -10  -3  -5   2  -5 -10  -8  -4 -10   1  -3   6  -2  -5  -9  -3 -10  -4  -8   2  -8  -6 -12  -6  -8   1  -5   5  -3</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC793" class="line" lang="plaintext"># N   0   9   1   9  -5   1  -3   0  -3   5  -2   5  -7  -3  -7  -3  -3   1  -5   1  -9  -6 -11  -6  -6  -2  -5  -3 -14  -9 -13  -9  -4   2  -3   2  -8  -4  -9  -6  -6  -1  -6  -1  -9  -5  -9  -7  -2  -1  -5   0  -9  -5 -29  -6  -6  -4 -11  -4 -10  -9 -13  -7</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC794" class="line" lang="plaintext"># P  -9  -9 -11  -9  -2  -2  -3  -1 -10  -9  -7  -7  -7  -8  -8  -8  -1  -1  -4  -2  10  10   9  10   1   2   0   2   4   2   2   2 -11  -8 -12  -9  -1   0   1  -1 -10  -7  -8  -8  -5  -6  -5  -6  -3  -5  -8  -5   5   5   4   5  -1  -3  -8  -4  -2  -3  -3  -3</span>

</pre>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext"># Q  -1  -4   0  -4  -6  -5  -6  -7  -4  -5  -3  -6 -10 -12  -7 -11  10   2  10   3   0  -4   2  -5   6   0   4   1  -2  -8  -2  -7   0  -3   1  -5  -7  -9  -7  -6  -4  -6  -3  -8  -7  -8  -6  -9   6  -2   5  -2  -3  -4  -1  -5   2  -4  -2  -5  -3  -9  -4  -8</span>

</pre>

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</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext"># R   2  -4   3  -3  -1  -6  -1  -6   9   1   8   2  -3  -9  -3  -8   2   1   2   0  -7  -5  -6  -5   6   4   5   3  -8  -7  -8  -8  -4  -8  -4  -8  -7  -8  -3  -7   1  -4   2  -3  -7 -10  -6  -8   0  -5  -1  -4  -6  -7  -6  -6   5   1  -1   0  -6  -9  -7  -8</span>

</pre>

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</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC797" class="line" lang="plaintext"># S  -6   0  -5  -1   0   2  -1   2  -3   6  -3   5  -5  -3  -5  -4  -5  -3  -4  -3   0   2  -1   1  -5   0  -4  -1  -5  -5  -4  -4  -6  -5  -6  -4   0   1  -1   1  -5   0  -4  -1  -5  -4  -4  -4  -1  -2  -4  -3   8   8   7   8  -1   0  -7  -1   1   0   1   0</span>

</pre>

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</td>

<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

</td>

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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext"># T  -3  -2  -3  -2   7   7   6   7  -2   1  -3   0   2   1   1   1  -5  -5  -5  -6  -2  -2  -2  -1  -5  -7  -4  -4  -4  -6  -3  -6  -6  -6  -6  -6   3   1   2   2  -5  -5  -6  -6   0  -1   0  -1  -4  -8  -6  -6   2   0   1   1  -5  -5 -12  -7  -3  -6  -3  -5</span>

</pre>

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</td>

<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"># V  -7  -6  -8  -7  -1   0  -1   1  -5  -5  -5  -4   3   4   2   4  -9  -6  -6  -7  -7  -5  -5  -5  -4  -7  -6  -5  -1  -2  -1  -1  -4  -5  -3  -4   1   2   4   2  -3  -3   0  -2   8   9   9   9  -5 -11  -6  -8  -5  -7  -3  -6  -7  -7 -11  -7   0  -3  -1  -1</span>

</pre>

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</td>

<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

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<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext"># W -14 -18  -7 -13 -16 -15  -7 -14  -6  -9   1  -9 -13 -23 -10 -13  -5  -7   3  -5 -11 -14  -2 -26   4  -4  10  -1  -9 -10  -4 -11 -12 -14  -4 -19 -14 -12  -5 -19  -5  -9   4  -8 -12 -18  -7 -14   2  -3  11  -2  -3 -11   5  -8  10   4  14   4  -3  -9   4  -5</span>

</pre>

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</td>

<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"># Y -11  -2 -11  -2 -14  -7  -9  -8 -15  -5 -11  -4 -13  -9 -10  -8  -5   5  -3   6 -10  -6  -7  -5 -11   2  -4   3  -9  -4  -9  -5 -12  -4 -11  -2 -11  -9 -28  -8 -15  -7 -10  -5 -13  -5 -10  -8   3  11   4  11  -8   0  -6   0  -3   5  -5   6  -6   3  -5   2</span>

</pre>

</td>

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</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC802" class="line" lang="plaintext"># * -27 -29 -25 -27 -29 -28 -30 -28 -20 -19 -17   1 -28 -29 -28 -29   0 -20   5 -29 -29 -29 -29 -27   9 -29   4 -29 -25 -29 -26 -29 -24 -29 -28 -29 -29 -28 -29 -29   4 -29 -25 -25 -28 -30 -28 -30  14  -5  10 -12 -26 -29   6 -29  14 -27  -3  -8 -10 -29 -29 -29</span>

</pre>

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<td class="old_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">

</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

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="plaintext"># X   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0</span>

</pre>

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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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext">#</span>

</pre>

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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"># Coordinates are 0-based.  For - strand matches, coordinates</span>

</pre>

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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"># in the reverse complement of the 2nd sequence are used.</span>

</pre>

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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

</td>

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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext">#</span>

</pre>

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<td class="old_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">

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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"># name start alnSize strand seqSize alignment</span>

</pre>

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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">#</span>

</pre>

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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

</td>

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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext"># batch 0</span>

</pre>

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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">a score=3177.2 EG2=0 E=0</span>

</pre>

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</td>

<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">s chrUn_KI270748v1     13904 1811 + 93321 CAAGGGTGCCCACTCTCAGAACTTCTATTCAACATAGTACTGGATGTCCTAGCCAGAGCAATTAGGCAAAAGAAAGaaaTAAAAGGCATGAAAATTGGAAAGGAAGAAGTTAAATTGTTTCTGTTTGCAGTTGACATGATCTTATATATAGAAAACACCAATAACTCTGCCAAAAAA---TTTAGAATTCATAAATGAATTTAGTAAAGTTGCAGGATACAATGTGAACATACAAAATTCAGTAGCATTTCTACACATCAACAACAAACTATACAAAAAAagaaatcaagaaaacaATCCTATTTATAATAGCAACAAAA---------AATACTTAGATGTAAATTTAAACAAAGAGGTGAATGATCTTTACACTGAAAACTACAAAACATTGATGAAAACAATTGAAGAAGCCACAAATAAATGGAAAGATATCTCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAATGTCCATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAATTCCTATGACATTTTCCCACAGAAATAGAAAAACAACTCTCAAATCTGTATGGAATCACAAAAAACTCTGAAAAGCCAAAATAATCTTGATCGAAAAAAGCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCTATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATAGACCAATTACACAGAATAAAGAGCCCATAAATAAATCTACAT---ATTATAGTCAATTGACTTTCAACAAAGGTGCCAGGAACACA---CATGGGGAAAGAACAGTCTCTTCAAAAAATGGTGTTGAGAAAACTGAATGTCCACA------AGATTGATCTTAGGCCCTTATTTCATACCATATAAAAATATAAATTCAAAATAAGTT---AGACTTAAATGTAAGACCTAGCACTATAGAACTCCTAGAAGAAAAC---AGGGGAATAACTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGACTCTAAAGCACAGGCAAGAAAAGCAACAAAACACAAATGGAATAGCATCAACCTAAAAAGCTTCTGCGCAGCAAAAGAA---AGTCAACAGAGTGAAGTGATAACCTACAAAATGGGAGGAATTATCTGCAAACTATACATTTGATAAGAGGCTAATGTCCAAAATATCTTAGGAACTCAAACAACACAataataagaaAACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAACAGATATATA---AAAATGCTAATTATCACTGATCATCAGAGAAATGCATATTAAAACTACAATAAAATGCCATTTCACATCCGTTAGAATGGCTGTTACAGAAAAGGCAGAAGATACCAAGTGTTGGAGAGGATGTGGAGAAAAGGAAAACCTTGTA------ATTGTTGAGAATGTAAACTATTTCAGCCATTGTAAAAGACAGTATAAGTGATTCTG---------TAAAAATAGAATTACCATATGATTCAGTAATGCTATTTCTGGGCATATATTAAAAAGATATCAAATCAGTGTGTCAATGAGTTATCTGTACTCCCATATTTATTGTAGCATTATTCACAACAGCCAAGATGTGGAATTAACTTAAGTATCCATCGACACATGAGTGGATGAAGAAAATGTGGTACACATACACAATAGAATAGTATACAACCTTAaaaaataaaaaa---aGTATCATTTGTGACAACATGAATGAACCGGGAGGACATTATACTGAGTAAAATAATCCAGGCACAGAAAGCCAGATACTGCATAATCTCACTTGTATGTGGA</span>

</pre>

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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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC813" class="line" lang="plaintext">s UN-L1MA6_pol#LINE/L1   657  616 +  1275 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeu-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThrMetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeuProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrpAsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrpMetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly</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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC814" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext">a score=1775.7 EG2=2.9e-164 E=1.5e-169</span>

</pre>

</td>

</tr>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC816" class="line" lang="plaintext">s chrUn_KI270748v1     3859 681 + 93321 CTAATATCCGGAATCTACAATGAACCCAAACAAATTTACAAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACTATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTTACACCAGTTAGAATGGCCATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACATTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGGTGATTCCGCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTACTGTGGCACTATTCACAATAGCAAAGACTTGGAACCAATCCAAATGTCCAACAATGATAGACTGGATTAAGAAAACGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAGCTGGAAACCATCATTCTCAGCAAACAATCACAAGGACAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAAT</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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC817" class="line" lang="plaintext">s UN-L1PA2_pol#LINE/L1 1048 227 +  1276 LeuIleSerArgIleTyrAsnGluLeuLysGlnIleTyrLysLysLysThrAsnAsnProIleLysLysTrpAlaLysAspMetAsnArgHisPheSerLysGluAspIleTyrAlaAlaLysLysHisMetLysLysCysSerSerSerLeuAlaIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysSerGlyAsnAsnArgCysTrpArgGlyCysGlyGluIleGlyThrLeuLeuHiscystrptrpaspcyslysLeuValGlnProLeuTrpLysSerValTrpArgPheLeuArgAspLeuGluLeuGluIleProPheAspProAlaIleProLeuLeuGlyIleTyrProLysAspTyrLysSerCysCysTyrLysAspThrCysThrArgMetPheIleAlaAlaLeuPheThrIleAlaLysThrTrpAsnGlnProLysCysProThrMetIleAspTrpIleLysLysMetTrpHisIleTyrThrMetGluTyrTyrAlaAlaIleLysAsnAspGluPheMetSerPheValGlyThrTrpMetLysLeuGluIleIleIleLeuSerLysLeuSerGlnGluGlnLysThrLysHisArgIlePheSerLeuIleGlyGlyAsn</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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC818" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC819" class="line" lang="plaintext">a score=1607.4 EG2=5e-147 E=2.5e-152</span>

</pre>

</td>

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<td class="old_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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext">s chrUn_KI270748v1     89660 1085 - 93321 aaggcaaacaAGGACACTATAAGAAAAGTA---TGGGCCAACCAATATCCCTGATGAACACAGATACAAAAGTCCTCAAAAAAAAGTACTAGCAAACAGAATTTAACAACATATTAGGAGA---ACATTTACCATGATAAA---GTGGATTTATCCTC---------CAGATGTTTCAGCAAACACAAATCA---AATGTGATAAACCACATTAACAGAATGAAGGATAAAAAA---ATAGCTATCTCTATATATGCAGAAAAAGCATTTGACTAAATTCAAAATCCTCTCATGACTAAACCTCTCAACAAATTGGGCATAGAAGGCATGTACCTTAACACAAAACAGGACATATATAACAAGCTCACAGCTCACATCATACCCAACAATGAAAAAGTGAAATCTTTTCTGCTAAGATCAAAAACAAGACAAGGATATTTATTCTCACTACTTCTATTCAACTTATTTCTGGAAGTCCTAGCCAGAGCAATTAAGCCAAATAAAGAAATAAAA---TATTCAAATTGAAAAGGaagaagtaaaaTTGTCTCTGTTTGATGAC------ATATTATATATAGGAAACCCTAAAAACTCCACCAAAAAGCTATTAGAAATGATAAATGAATTCAATAAAATTTCAGAATTCAAAATCAATGTACAAAACTCAGTA---GTTTCTTTACACTCACAACAAACTATATGACAAA---AATAAAGAAATCAATCTCATTCACAGTAGCATCAAaaaaaacgtattttttttGTTTAGGAGCACATTTAGGATAGTACttaggagtacatttaACCAAGGAGGTGAAAGATCTGTATTCTGAACACTATAAAACATTGATGAAA---AATTGTAGATGACACAAATACATGGAAAGATATTTTATGTTCATGGGTAGGAAGAATTAATATTCTTAAAATGTCCTTACTGCCCAAAGCGATTTATAGGTTTAATGCAATATTTATCAAAATTTCAATGTCATTCTTCACAGAAATAGAAAAAACAATTTGAAAATTTATATGGAACCACAAAGGATCCTGAATAACTAAAGGACTCTTGAGCAATAAGAACAAAGCTGAAGGCCTCACA---ATCTGACTTCAAAACATATTACAGG</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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext">s UN-L1MA6_pol#LINE/L1   517  362 +  1275 LysProAspLysAspThrThrLysLysGluAsn--TyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLys--IleLeuAlaAsnArgIleGlnGlnHisIleLysLysIle--IleHisHisAspGlnVal--GlyPheIleProGlyMetGln-GlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIleAsnArgMetLysAspLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAspLysIleGlnHisProPheMetIleLysThrLeuAsnLysLeuGlyIleGluGlyThrTyrLeuAsnThrIleLysAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGluLysLeuLysAlaPheProLeuArgSerGlyThrArgGlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGly-IleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeuLeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAla-PheLeuTyrAlaAsnSerGluLeuSerGluLysGlu-IleLyslysthrilepropheThrIleAlaThrLysLysIle------------------------------LysTyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGlu-IleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeu-ProAspPheLysIleTyrTyrLys</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="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">

</td>

<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

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC822" class="line" lang="plaintext"></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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC823" class="line" lang="plaintext">a score=1559.7 EG2=3.8e-142 E=2e-147</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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC824" class="line" lang="plaintext">s chrUn_KI270748v1     3232 818 - 93321 TaatcagcctggtaatcaCGT---AAAACAGACACATAGACCAGTGGAACAGAATAGAGAACCCAGATATAAATCCACACATTTACAGCCAGCTCATCTTCAGCAAAGGCACCAACAACATACGA---GCGAAAGGACGGTCTCTTCCATAAGTGGTGCAGGGGAAACTAGATAAAGATATGCAGAAGAATGAAACTAGACCCGTCTCTCTTACCATACACAGAAATCAAATCAGAATGGATTAAAGGT---AAAACTGAGACCTGAAAGTATAAAACTACTGGAAGAAAACATTAGGGAAGTGCTCCAGGACATTGTTCTCAGCAAAGACTTTTTCAGTAGGGCCCCAAAAGCACAGGCAACCAAAGCAAAAACAGACAAGTGAAATCACACCAAGCTAAGAACCCTCTGCAGACCAAAGGAAAAAGTCAACAAACTGAAGAGACAACCCACAGAATGGGAGAAAATACTTGCAAGCTACCCACCTGACAAGGGATTCATAACC------------AGGAGCTCAAACAA---------TAGCAAACAATTAATCGAATTTTAAAATGGGCAAGAGACCTGAGTAGACATTTCTCAAAAGAAGATGTACAAATGGCCAGCAGGTACATGAAAAAATGCTCAACATCACTAATCATCAGAGAAACGCAAATAAAAAACTGCAATGAGGTCTTCTCTCACCTCAGTTAAAATGGCTTTCGTCAAAAACGCAGGGAATAAGGGATGCTGGCGAGGATGTGGAGAAAGGGGGACCCTCACACACTGT---TGTGGGAACGTTGATTAGTACAACCACTATGGAAAACA---GATGGAGGCTCCTCAaaaaaccaaaa</span>

</pre>

</td>

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<td class="old_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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC825" class="line" lang="plaintext">s UN-L1MA6_pol#LINE/L1  883 281 +  1275 LysThrAlaTrpTyrTrpHisLys--AsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIleTyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGlnTrp-GlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLysAspLeu-AsnValArgProGluThrMetLysLeuLeuGluGluAsnIleGlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThrIleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLys--GluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLysLysCysSerThrSerLeuIleIleArgGluMetGlnIle-LysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCysTrp--TrpGluCysLysLeuValGlnProLeuTrpLysThrVal--TrpArgPheLeuLysLysLeuLys</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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC826" class="line" lang="plaintext"></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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC827" class="line" lang="plaintext">a score=1508.0 EG2=7.4e-137 E=3.8e-142</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="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">

</td>

<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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC828" class="line" lang="plaintext">s chrUn_KI270748v1      17571 1017 + 93321 AAAGAAAACTACAAATCCTTATCCCTGATCAACACAGATGTAAAAATACTCAACAAAATTCTAGCAAACTGAAGCTAACAACACATCAAAAAGATAATTCATCATGATCAAGTGGGCTTTATTCCAGGGGTGCTTGAATGGTTCAAAATAGACAAATCAATAAACATGATTCACCACATAAATGGAACTGAGAACAAAAACCCTATGATCATCTCATTAGATGCAGAATaagcatttgataaaatccaacatctgtttatgataaaaaccctcaACAATATAGGTATAGATGGAGTATACCTCAAA---AAATGAGTCATCTATGACAAAGCCACAGCCAACATCATCCTGGATGGGCAAAAGTTAGAAGTGTTGCTTCTAGAAACTGGAAAAAAGCAAGGATGTTCACCTTCATCATTCCTATTCAATACAGTACTGGAAGTGCTAGCCAGAACTATCAGAAAGGAGAAAGAAATAAAAGGTATACAAATTAGAAAA---GAAGTCAAATGATCTCTGCTCACTGATGACATGACTGTAGGCCTAGAAAACCCTAAAGTCTTC---AGAAGACTCCTAGACTTGATACACGACTTCAGTAAAGTCTTGGGATAAACAAGC------CACAAAAATCAGTTGTATTTCTATACACCAAATACATTCAAGCTGTTTGAATGTTTGTTGAGATTAATTtgttgAGAACCAAATTAAGAACTCAACTGAATTTACAATAGCCATG---------AAAAATACCTAGGAATGCAT---AACTATATAAATGAAAGATCTCTACAAGGAGAACTACAAAATACTAATGAAAGAAATTATAGATGACATAAACAAATGGAAAAACATCCCATGCTCATGGATTAGAAAAATCAAT---AGCTAAAGTGACCATATCACCC---ATACAATCTATAGAGTTAATGCAATTCCCATCAAATTACCAACGTTATTTCTCACAaaattaaaaaaa---aaTCCTAAAGTTCACATGGAGCCAAAAAAAGATCCCTAATAGCCAAAGCACTTCTAAGCAAAAAa</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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC829" class="line" lang="plaintext">s UN-L1PA16_pol#LINE/L1   526  338 +  1276 LysGluAsnTyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLysIleLeuAlaAsnArgIleGlnGlnHisIleLysLysLeuIleHisHisAspGlnValGlyPheIleProGlyMetGlnGlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIleAsnArgIleLysAsnLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAspLysIleGlnHisProPheMetIleLysThrLeuXaaLysLeuGlyIleGluGlyThrTyrLeuLysIleIleArgAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGlnLysLeuGluAlaPheProLeuArgThrGlyThrArgGlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrLeuGluAsnProLysAspSerAlaLysArgLeuLeuGluLeuIleAsnAspPheSerLysValSerGlyTyrLysIleAsnVal--GlnLysSerValAlaPheLeuTyrThrAsnAsnValGlnAla-----------------------------GluSerGlnIleLysAsnAlaIleProPheThrIleAlaThrLysLysIle--LysTyrLeuGlyIleHisLeu-ThrLysGluValLysAspLeuTyrLysGluAsnTyrLysThrLeuLeuLysGluIleIleAspAspThrAsnLysTrpLysAsnIleProCysSerTrpIleGlyArgIleAsnIle-ValLysMetAlaIleLeuProLys--AlaIleTyrArgPheAsnAlaIleProIleLysLeuProMetSerPhePheThrGluLeuGluLysThr-IleLeuLysPheIleTrpAsnGln-LysArgAlaGlnIleAlaLysAlaIleLeuSerLysLys</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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext"></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="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">

</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>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC831" class="line" lang="plaintext"></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="b6d5f875b0957cb0d3543c8c073a712d4ae0db6f">

<a href="https://salsa.debian.org/med-team/last-align/-/compare/52919d393333dac9cca9b189947ac2b14d26b13a...bf1432f5464effc0f937939646b03c87be267edf#b6d5f875b0957cb0d3543c8c073a712d4ae0db6f"><strong>test/maf-swap-test.sh</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,4 +15,5 @@ PATH=../bin:$PATH</td>

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<td class="old_line diff-line-num" data-linenumber="15" 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">

15

</td>

<td class="new_line diff-line-num" data-linenumber="15" 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">

15

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">    try maf-swap bs100.maf</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="16" 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">

16

</td>

<td class="new_line diff-line-num" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell">    try maf-swap <span class="nt" style="color: #000080;">-n1</span> 90089.maf</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="17" 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">

17

</td>

<td class="new_line diff-line-num" data-linenumber="17" 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">

17

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell">    try maf-swap <span class="nt" style="color: #000080;">-n3</span> ../examples/multiMito.maf</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="18" style="width: 35px; color: rgba(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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">    try maf-swap frameshift-new.maf</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="18" 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">

18

</td>

<td class="new_line diff-line-num" data-linenumber="19" 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">

19

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span> 2>&1 | diff <span class="nt" style="color: #000080;">-u</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span> .sh<span class="si" style="color: #d14;">)</span>.out -</span></pre>

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