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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Charles Plessy pushed to branch master at <a href="https://salsa.debian.org/med-team/last-align">Debian Med / last-align</a>
</h3>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Commits:
</h4>
<ul>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/3373b2271606113d5a2003a822837cf88d8a14ad">3373b227</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2024-02-21T08:04:42+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>New upstream version 1542</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/4a68474d8239f8a361c954457e3137e363d2fa54">4a68474d</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2024-02-21T08:04:42+09:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: New upstream version
</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/9b5762b705e72cc731faf54d3c633e2c630eb0eb">9b5762b7</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2024-02-21T08:04:49+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Update upstream source from tag 'upstream/1542'
Update to upstream version '1542'
with Debian dir 693a10483a78a1405bfacbf3fc63e6b23037fc82</pre>
</li>
<li>
<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/last-align/-/commit/4a58fc4334ab31dd6ff1af182535db0c43e0a5fa">4a58fc43</a></strong>
<div>
<span> by Charles Plessy </span> <i> at 2024-02-21T08:12:46+09:00 </i>
</div>
<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
11 changed files:
</h4>
<ul>
<li class="file-stats">
<a href="#b81b5de5f7bfd818c69285e09a1e8f1bef73444e">
bin/maf-convert
</a>
</li>
<li class="file-stats">
<a href="#f3dc1fa2ee7e2641f55cd910fd94c6ac54bac238">
data/MAM4.seed
</a>
</li>
<li class="file-stats">
<a href="#d8808ac5714f9c3554a3d03e80124554c92be191">
data/MAM8.seed
</a>
</li>
<li class="file-stats">
<a href="#056989fd476c60ee978d358e1eb6faa4ca231309">
data/YASS.seed
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#977fadb853a729d73f897f1532ab693a2edb5af2">
doc/last-seeds.rst
</a>
</li>
<li class="file-stats">
<a href="#92d9b0529e219d061bbcde273352ff9d2523754c">
doc/lastdb.rst
</a>
</li>
<li class="file-stats">
<a href="#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
src/makefile
</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="#e819333ce9c994404f6c3bb6ed8f32b3748b766c">
<span class="new-file">
+
test/toprev.maf
</span>
</a>
</li>
</ul>
<h4 style="margin-top: 10px; margin-bottom: 10px;">
Changes:
</h4>
<li id="b81b5de5f7bfd818c69285e09a1e8f1bef73444e">
<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#b81b5de5f7bfd818c69285e09a1e8f1bef73444e"><strong style="font-weight: bold;">bin/maf-convert</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -65,6 +65,14 @@ def myOpen(fileName):</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC65" class="line" lang="html">def maxlen(s):</span>
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66
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66
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC66" class="line" lang="html"> return max(map(len, s))</span>
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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="new_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
67
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC67" class="line" lang="html"></span>
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<td class="old_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
68
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC68" class="line" lang="html">complementLookup = bytearray(range(128))</span>
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<td class="old_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
69
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC69" class="line" lang="html">for x, y in zip("ACGTRYKMBDHVU",</span>
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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
70
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC70" class="line" lang="html"> "TGCAYRMKVHDBA"):</span>
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<td class="old_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
71
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC71" class="line" lang="html"> complementLookup[ord(x.upper())] = ord(y.upper())</span>
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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
72
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC72" class="line" lang="html"> complementLookup[ord(x.lower())] = ord(y.lower())</span>
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<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
73
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC73" class="line" lang="html">def revcomp(seq):</span>
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<td class="new_line diff-line-num new" data-linenumber="74" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
74
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC74" class="line" lang="html"> return "".join(chr(complementLookup[ord(i)]) for i in reversed(seq))</span>
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75
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC75" class="line" lang="html"></span>
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<td class="new_line diff-line-num" data-linenumber="76" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC76" class="line" lang="html">def pairOrDie(sLines, formatName):</span>
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69
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77
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC77" class="line" lang="html"> if len(sLines) != 2:</span>
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70
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78
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC78" class="line" lang="html"> e = "for %s, each alignment must have 2 sequences" % formatName</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="688" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="696" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -688,7 +696,8 @@ def cigarParts(alignmentColumns):</td>
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688
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696
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC696" class="line" lang="html"> yield str(size) + "X"</span>
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689
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<td class="new_line diff-line-num" data-linenumber="697" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
697
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC697" class="line" lang="html"></span>
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<td class="old_line diff-line-num" data-linenumber="690" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
690
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<td class="new_line diff-line-num" data-linenumber="698" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
698
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC698" class="line" lang="html">def writeSam(readGroup, mafs):</span>
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<td class="old_line diff-line-num old" data-linenumber="691" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
691
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<td class="new_line diff-line-num old" data-linenumber="699" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC691" class="line" lang="html"> seq = qual = cigar = score = evalue = ""</span>
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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
699
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC699" class="line" lang="html"> seq = qual = score = evalue = ""</span>
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<td class="old_line diff-line-num new" data-linenumber="692" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
700
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC700" class="line" lang="html"> cigar = []</span>
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692
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<td class="new_line diff-line-num" data-linenumber="701" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
701
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC701" class="line" lang="html"> mismapProb = 2.0</span>
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693
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702
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC702" class="line" lang="html"> editDistance = 0</span>
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<td class="old_line diff-line-num" data-linenumber="694" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
694
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<td class="new_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
703
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC703" class="line" lang="html"> for maf in mafs:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="697" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -697,11 +706,8 @@ def writeSam(readGroup, mafs):</td>
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<td class="old_line diff-line-num" data-linenumber="697" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
697
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<td class="new_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
706
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC706" class="line" lang="html"> seqNameA, seqLenA, strandA, letterSizeA, begA, endA, rowA = fieldsA</span>
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<td class="old_line diff-line-num" data-linenumber="698" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
698
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<td class="new_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
707
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC707" class="line" lang="html"> seqNameB, seqLenB, strandB, letterSizeB, begB, endB, rowB = fieldsB</span>
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699
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<td class="new_line diff-line-num" data-linenumber="708" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
708
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC708" class="line" lang="html"></span>
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<td class="old_line diff-line-num old" data-linenumber="700" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
700
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<td class="new_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC700" class="line" lang="html"> if letterSizeA > 1 or letterSizeB > 1:</span>
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<td class="old_line diff-line-num old" data-linenumber="701" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
701
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<td class="new_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC701" class="line" lang="html"> raise Exception("this looks like translated DNA - can't convert to SAM format")</span>
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702
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<td class="new_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC702" class="line" lang="html"></span>
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703
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<td class="new_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC703" class="line" lang="html"> if strandA != "+":</span>
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704
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<td class="new_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC704" class="line" lang="html"> raise Exception("for SAM, the 1st strand in each alignment must be +")</span>
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<td class="new_line diff-line-num new" data-linenumber="709" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
709
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC709" class="line" lang="html"> if letterSizeA * letterSizeB != 1:</span>
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<td class="old_line diff-line-num new" data-linenumber="705" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="710" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
710
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC710" class="line" lang="html"> raise RuntimeError("looks like DNA-to-protein alignment - can't convert to SAM format")</span>
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705
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711
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC711" class="line" lang="html"></span>
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<td class="old_line diff-line-num" data-linenumber="706" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
706
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712
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC712" class="line" lang="html"> isSplice = False</span>
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<td class="old_line diff-line-num" data-linenumber="707" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
707
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<td class="new_line diff-line-num" data-linenumber="713" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
713
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC713" class="line" lang="html"> for i in aLine.split():</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="716" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="722" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -716,15 +722,15 @@ def writeSam(readGroup, mafs):</td>
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716
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<td class="new_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
722
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC722" class="line" lang="html"></span>
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<td class="old_line diff-line-num" data-linenumber="717" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
717
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<td class="new_line diff-line-num" data-linenumber="723" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
723
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC723" class="line" lang="html"> if seq:</span>
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<td class="old_line diff-line-num" data-linenumber="718" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
718
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<td class="new_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
724
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC724" class="line" lang="html"> d = begA - oldEndA</span>
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<td class="old_line diff-line-num old" data-linenumber="719" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
719
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<td class="new_line diff-line-num old" data-linenumber="725" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC719" class="line" lang="html"> cigar<span class="idiff left right deletion" style="background-color: #fac5cd;"> += </span>str(d) + "DN"[isSplice]</span>
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<td class="old_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
725
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC725" class="line" lang="html"> cigar<span class="idiff left addition" style="background-color: #c7f0d2;">.append(</span>str(d) + "DN"[isSplice]<span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
720
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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
726
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC726" class="line" lang="html"> if not isSplice: editDistance += d</span>
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<td class="old_line diff-line-num" data-linenumber="721" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
721
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<td class="new_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
727
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC727" class="line" lang="html"> else:</span>
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<td class="old_line diff-line-num old" data-linenumber="722" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
722
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<td class="new_line diff-line-num old" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC722" class="line" lang="html"> pos = <span class="idiff left right deletion" style="background-color: #fac5cd;">str(begA + 1) # convert to 1-based coordinate</span></span>
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<td class="old_line diff-line-num old" data-linenumber="723" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
723
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<td class="new_line diff-line-num old" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC723" class="line" lang="html"> if begB: cigar<span class="idiff left right deletion" style="background-color: #fac5cd;"> += </span>str(begB) + "H"</span>
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<td class="old_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="728" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
728
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC728" class="line" lang="html"> pos = <span class="idiff left right addition" style="background-color: #c7f0d2;">begA</span></span>
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<td class="old_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
729
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC729" class="line" lang="html"> if begB: cigar<span class="idiff left addition" style="background-color: #c7f0d2;">.append(</span>str(begB) + "H"<span class="idiff right addition" style="background-color: #c7f0d2;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
724
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<td class="new_line diff-line-num" data-linenumber="730" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
730
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC730" class="line" lang="html"> oldEndA = endA</span>
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725
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<td class="new_line diff-line-num" data-linenumber="731" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
731
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC731" class="line" lang="html"></span>
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726
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<td class="new_line diff-line-num" data-linenumber="732" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
732
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC732" class="line" lang="html"> alignmentColumns = list(zip(rowA.upper(), rowB.upper()))</span>
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727
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<td class="new_line diff-line-num old" data-linenumber="733" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC727" class="line" lang="html"> cigar<span class="idiff left right deletion" style="background-color: #fac5cd;"> += "".join</span>(cigarParts(iter(alignmentColumns)))</span>
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<td class="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
733
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC733" class="line" lang="html"> cigar<span class="idiff left right addition" style="background-color: #c7f0d2;">.extend</span>(cigarParts(iter(alignmentColumns)))</span>
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728
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<td class="new_line diff-line-num" data-linenumber="734" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
734
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC734" class="line" lang="html"> editDistance += sum(x != y for x, y in alignmentColumns)</span>
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<td class="old_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
729
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<td class="new_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
735
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC735" class="line" lang="html"> # no special treatment of ambiguous bases: might be a minor bug</span>
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730
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736
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC736" class="line" lang="html"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="737" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="743" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -737,7 +743,13 @@ def writeSam(readGroup, mafs):</td>
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737
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<td class="new_line diff-line-num" data-linenumber="743" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
743
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC743" class="line" lang="html"> qual += ''.join(j for i, j in z if i != "-")</span>
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738
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<td class="new_line diff-line-num" data-linenumber="744" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
744
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC744" class="line" lang="html"></span>
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<td class="old_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
739
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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
745
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC745" class="line" lang="html"> revBegB = seqLenB - endB</span>
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<td class="old_line diff-line-num old" data-linenumber="740" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
740
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<td class="new_line diff-line-num old" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC740" class="line" lang="html"> if revBegB: cigar += str(revBegB) + "H"</span>
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<td class="old_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="746" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
746
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC746" class="line" lang="html"> if revBegB: cigar.append(str(revBegB) + "H")</span>
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<td class="new_line diff-line-num new" data-linenumber="747" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
747
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC747" class="line" lang="html"></span>
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<td class="new_line diff-line-num new" data-linenumber="748" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
748
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC748" class="line" lang="html"> if strandA == "-":</span>
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<td class="old_line diff-line-num new" data-linenumber="741" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="749" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
749
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC749" class="line" lang="html"> seq = revcomp(seq)</span>
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<td class="new_line diff-line-num new" data-linenumber="750" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
750
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC750" class="line" lang="html"> qual = qual[::-1]</span>
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<td class="new_line diff-line-num new" data-linenumber="751" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
751
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC751" class="line" lang="html"> cigar = reversed(cigar)</span>
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<td class="new_line diff-line-num new" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
752
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC752" class="line" lang="html"> pos = seqLenA - endA</span>
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741
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<td class="new_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC753" class="line" lang="html"></span>
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742
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<td class="new_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC754" class="line" lang="html"> if mismapProb > 1:</span>
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743
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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
755
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC755" class="line" lang="html"> mapq = mapqMissing</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -752,24 +764,26 @@ def writeSam(readGroup, mafs):</td>
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<td class="old_line diff-line-num" data-linenumber="752" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
752
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<td class="new_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
764
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC764" class="line" lang="html"> <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">I</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">'</span><span class="na" style="color: #008080;">m</span> <span class="na" style="color: #008080;">not</span> <span class="na" style="color: #008080;">sure</span> <span class="na" style="color: #008080;">whether</span> <span class="na" style="color: #008080;">to</span> <span class="na" style="color: #008080;">add</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="na" style="color: #008080;">and</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">/</span><span class="na" style="color: #008080;">or</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">8</span> <span class="na" style="color: #008080;">to</span> <span class="na" style="color: #008080;">flag.</span></span>
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<td class="old_line diff-line-num" data-linenumber="753" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
753
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<td class="new_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
765
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC765" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">seqNameB.endswith</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("/1")</span><span class="na" style="color: #008080;">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="754" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
754
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<td class="new_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
766
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC766" class="line" lang="html"> <span class="na" style="color: #008080;">seqNameB = </span><span class="s" style="color: #d14;">seqNameB[:-2]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
755
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<td class="new_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC755" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">strandB =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right deletion" style="background-color: #fac5cd;">"+"</span></span><span class="na" style="color: #008080;">:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"99"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">32</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">64</span></span>
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<td class="old_line diff-line-num old" data-linenumber="756" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
756
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<td class="new_line diff-line-num old" data-linenumber="767" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC756" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"83"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">16</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">64</span></span>
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<td class="old_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="767" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
767
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC767" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">strandB =</span><span class="s" style="color: #d14;">=</span> <span class="na" style="color: #008080;"><span class="idiff left right addition" style="background-color: #c7f0d2;">strandA</span>:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"99"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">32</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">64</span></span>
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<td class="old_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="768" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
768
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC768" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"83"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">16</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">64</span></span>
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<td class="old_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
757
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<td class="new_line diff-line-num" data-linenumber="769" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
769
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC769" class="line" lang="html"> <span class="na" style="color: #008080;">elif</span> <span class="na" style="color: #008080;">seqNameB.endswith</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("/2")</span><span class="na" style="color: #008080;">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="758" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
758
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<td class="new_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
770
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC770" class="line" lang="html"> <span class="na" style="color: #008080;">seqNameB = </span><span class="s" style="color: #d14;">seqNameB[:-2]</span></span>
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<td class="old_line diff-line-num old" data-linenumber="759" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
759
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<td class="new_line diff-line-num old" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC759" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">strandB =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right deletion" style="background-color: #fac5cd;">"+"</span></span><span class="na" style="color: #008080;">:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"163"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">32</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">128</span></span>
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<td class="old_line diff-line-num old" data-linenumber="760" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
760
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<td class="new_line diff-line-num old" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC760" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"147"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">16</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">128</span></span>
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<td class="old_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
771
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC771" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">strandB =</span><span class="s" style="color: #d14;">=</span> <span class="na" style="color: #008080;"><span class="idiff left right addition" style="background-color: #c7f0d2;">strandA</span>:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"163"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">32</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">128</span></span>
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<td class="old_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="772" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
772
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC772" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"147"</span> <span class="na" style="color: #008080;">#</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">16</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">+</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">128</span></span>
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<td class="old_line diff-line-num" data-linenumber="761" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
761
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<td class="new_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
773
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC773" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="762" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
762
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<td class="new_line diff-line-num old" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC762" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">strandB =</span><span class="s" style="color: #d14;">=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right deletion" style="background-color: #fac5cd;">"+"</span></span><span class="na" style="color: #008080;">:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"0"</span></span>
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<td class="old_line diff-line-num old" data-linenumber="763" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
763
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<td class="new_line diff-line-num old" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC763" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"16"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
774
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC774" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">strandB =</span><span class="s" style="color: #d14;">=</span> <span class="na" style="color: #008080;"><span class="idiff left right addition" style="background-color: #c7f0d2;">strandA</span>:</span> <span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"0"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="775" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
775
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC775" class="line" lang="html"> <span class="na" style="color: #008080;">else:</span> <span class="idiff left right addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;">flag = </span><span class="s" style="color: #d14;">"16"</span></span>
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<td class="old_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
764
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<td class="new_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
776
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC776" class="line" lang="html"></span>
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<td class="old_line diff-line-num" data-linenumber="765" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
765
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<td class="new_line diff-line-num" data-linenumber="777" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
777
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC777" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">len</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">qual</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;">len</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">seq</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span><span class="na" style="color: #008080;">:</span> <span class="na" style="color: #008080;">qual = </span><span class="s" style="color: #d14;">"*"</span></span>
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<td class="old_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="778" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
778
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC778" class="line" lang="html"> <span class="na" style="color: #008080;">pos</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 class="na" style="color: #008080;">convert</span> <span class="na" style="color: #008080;">to</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">1</span><span class="na" style="color: #008080;">-based</span> <span class="na" style="color: #008080;">coordinate</span></span>
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<td class="old_line diff-line-num new" data-linenumber="766" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="779" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
779
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC779" class="line" lang="html"> <span class="na" style="color: #008080;">cigar = </span><span class="s" style="color: #d14;">""</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">join</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">cigar</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="766" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
766
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<td class="new_line diff-line-num" data-linenumber="780" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
780
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC780" 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;">flag</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</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;">pos</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">mapq</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">cigar</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;">*</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="na" style="color: #008080;">t0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="na" style="color: #008080;">t0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">",</span> <span class="na" style="color: #008080;">seq</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span> <span class="na" style="color: #008080;">qual</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">]</span></span>
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<td class="old_line diff-line-num" data-linenumber="767" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
767
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<td class="new_line diff-line-num" data-linenumber="781" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
781
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC781" class="line" lang="html"> <span class="na" style="color: #008080;">out.append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">NM:i:</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;">str</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">editDistance</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>
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<td class="old_line diff-line-num" data-linenumber="768" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
768
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<td class="new_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
782
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC782" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">len</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="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">2</span><span class="na" style="color: #008080;">:</span></span>
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<td class="old_line diff-line-num" data-linenumber="769" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
769
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<td class="new_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
783
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC783" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">score.isdigit</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">()</span><span class="na" style="color: #008080;">:</span> <span class="na" style="color: #008080;">out.append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">AS:i:</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;">score</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span> <span class="na" style="color: #008080;">#</span> <span class="na" style="color: #008080;">must</span> <span class="na" style="color: #008080;">be</span> <span class="na" style="color: #008080;">an</span> <span class="na" style="color: #008080;">integer</span></span>
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<td class="old_line diff-line-num" data-linenumber="770" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
770
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<td class="new_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
784
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC784" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">evalue:</span> <span class="na" style="color: #008080;">out.append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">("</span><span class="na" style="color: #008080;">EV:Z:</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;">evalue</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="771" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
771
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<td class="new_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
785
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC785" class="line" lang="html"> <span class="na" style="color: #008080;">if</span> <span class="na" style="color: #008080;">readGroup:</span> <span class="na" style="color: #008080;">out.append</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(</span><span class="na" style="color: #008080;">readGroup</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>
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<td class="old_line diff-line-num old" data-linenumber="772" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
772
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<td class="new_line diff-line-num old" data-linenumber="786" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC772" class="line" lang="html"> <span class="na" style="color: #008080;">print</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">(<span class="idiff left deletion" style="background-color: #fac5cd;">"\</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">t</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff deletion" style="background-color: #fac5cd;">".</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">join</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff deletion" style="background-color: #fac5cd;">(</span></span><span class="na" style="color: #008080;"><span class="idiff deletion" style="background-color: #fac5cd;">out</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right deletion" style="background-color: #fac5cd;">)</span>)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="786" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
786
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC786" 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;"><span class="idiff left addition" style="background-color: #c7f0d2;">*out</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff addition" style="background-color: #c7f0d2;">,</span></span><span class="idiff addition" style="background-color: #c7f0d2;"> </span><span class="na" style="color: #008080;"><span class="idiff addition" style="background-color: #c7f0d2;">sep=</span></span><span class="s" style="color: #d14;"><span class="idiff right addition" style="background-color: #c7f0d2;">"\t"</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;">)</span></span>
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773
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<td class="new_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
787
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC787" class="line" lang="html"></span>
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<td class="old_line diff-line-num" data-linenumber="774" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
774
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<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
788
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC788" class="line" lang="html"><span class="na" style="color: #008080;">def</span> <span class="na" style="color: #008080;">mafConvertToSam</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>
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<td class="old_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
775
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<td class="new_line diff-line-num" data-linenumber="789" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
789
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC789" class="line" lang="html"> <span class="na" style="color: #008080;">readGroup = </span><span class="s" style="color: #d14;">""</span></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#f3dc1fa2ee7e2641f55cd910fd94c6ac54bac238"><strong style="font-weight: bold;">data/MAM4.seed</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,6 +2,8 @@</td>
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<td class="old_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
2
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext"># uses about half as much memory. [From Frith & Noé 2014 NAR 42:e59</span>
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<td class="old_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3
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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
3
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="plaintext"># Table S11, row 12.]</span>
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4
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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
4
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext">#lastdb -U100</span>
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6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"></span>
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5
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
7
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="plaintext">1 A C G T</span>
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6
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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
8
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">0 ACGT</span>
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7
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext">T AG CT</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#d8808ac5714f9c3554a3d03e80124554c92be191"><strong style="font-weight: bold;">data/MAM8.seed</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -3,6 +3,8 @@</td>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="plaintext"># mammal genomes). [From Frith & Noé 2014 NAR 42:e59 Table S12, row</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC8" class="line" lang="plaintext">1 A C G T</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext">0 ACGT</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#056989fd476c60ee978d358e1eb6faa4ca231309"><strong style="font-weight: bold;">data/YASS.seed</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -2,6 +2,8 @@</td>
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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="plaintext"># similarities. It is a good compromise for both protein-coding and</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC3" class="line" lang="plaintext"># non protein-coding DNA (L Noé & G Kucherov, NAR 2005 33:W540-W543).</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong style="font-weight: bold;">debian/changelog</strong></a>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext">last-align (1542-1) unstable; urgency=medium</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"></span>
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5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"> -- Charles Plessy <plessy@debian.org> Wed, 21 Feb 2024 08:06:34 +0900</span>
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6
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1
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC7" class="line" lang="plaintext">last-align (1540-1) unstable; urgency=medium</span>
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2
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3
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9
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC9" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#977fadb853a729d73f897f1532ab693a2edb5af2"><strong style="font-weight: bold;">doc/last-seeds.rst</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -99,6 +99,9 @@ And these patterns::</td>
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99
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC99" class="line" lang="plaintext"> 11TT010T01TT0001T</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC100" class="line" lang="plaintext"> 11TT10T1T101TT</span>
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101
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101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC101" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="102" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
102
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC102" class="line" lang="plaintext">It sets this lastdb default:</span>
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103
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC103" class="line" lang="plaintext">-U100</span>
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104
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC104" class="line" lang="plaintext"></span>
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102
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105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC105" class="line" lang="plaintext">MAM8</span>
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103
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106
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC106" class="line" lang="plaintext">----</span>
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104
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107
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="126" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -123,6 +126,9 @@ And these patterns::</td>
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123
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126
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC126" class="line" lang="plaintext"> 111100T011TTT00T0TT01T</span>
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127
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC127" class="line" lang="plaintext"> 1T1T10T1101101</span>
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125
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128
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129
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC129" class="line" lang="plaintext">It sets this lastdb default:</span>
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130
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131
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126
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132
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133
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134
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="196" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -190,6 +196,9 @@ And this pattern::</td>
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197
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192
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199
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC199" class="line" lang="plaintext">It sets this lastdb default:</span>
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200
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC200" class="line" lang="plaintext">-U100</span>
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201
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193
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<td class="new_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
202
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC202" class="line" lang="plaintext">RY4-9 (abbreviation: RY4)</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#92d9b0529e219d061bbcde273352ff9d2523754c"><strong style="font-weight: bold;">doc/lastdb.rst</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -105,9 +105,14 @@ Advanced Options</td>
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105
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC105" class="line" lang="plaintext"> repeat-finding slower. The default is 100 for DNA and 50 for</span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC106" class="line" lang="plaintext"> protein, which prevents non-homologous alignments.</span>
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107
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC107" class="line" lang="plaintext"></span>
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108
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<td class="new_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC108" class="line" lang="plaintext"> For DNA, however, if you specify -c (and don't specify AT-rich</span>
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109
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<td class="new_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC109" class="line" lang="plaintext"> tantan), the default is 400. This avoids hugely redundant</span>
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110
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<td class="new_line diff-line-num old" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC110" class="line" lang="plaintext"> alignments of human centromeric repeats.</span>
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<td class="old_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
108
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC108" class="line" lang="plaintext"> For DNA, however, the default is 400 if you:</span>
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109
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC109" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
110
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC110" class="line" lang="plaintext"> * specify ``-c`` AND</span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC111" class="line" lang="plaintext"> * don't specify AT-rich tantan AND</span>
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<td class="new_line diff-line-num new" data-linenumber="112" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
112
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC112" class="line" lang="plaintext"> * choose a seeding scheme other than MAM4, MAM8, or the default (YASS).</span>
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113
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC113" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC114" class="line" lang="plaintext"> This avoids hugely redundant alignments of human centromeric</span>
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115
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC115" class="line" lang="plaintext"> repeats.</span>
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116
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC116" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
117
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC117" class="line" lang="plaintext">-w STEP</span>
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118
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC118" class="line" lang="plaintext"> Allow initial matches to start only at every STEP-th position in</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong style="font-weight: bold;">src/makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -95,7 +95,7 @@ ScoreMatrixData.hh: ../data/*.mat</td>
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<td class="new_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC95" 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>
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96
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96
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC96" class="line" lang="make"></span>
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<td class="old_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
97
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC97" 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>
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98
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<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC98" 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: 154<span class="idiff left right deletion" style="background-color: #fac5cd;">0</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>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC98" 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: 154<span class="idiff left right addition" style="background-color: #c7f0d2;">2</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>
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99
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99
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC99" class="line" lang="make"></span>
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<td class="old_line diff-line-num" data-linenumber="100" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
100
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100
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC100" 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="p">$(</span>VERSION1<span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">$(</span>VERSION2<span class="p">)</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span></span>
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101
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101
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC101" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#fa1f2beb637146f5175aacd2f5469caf7be2e7eb"><strong style="font-weight: bold;">test/maf-convert-test.out</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23417" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23417" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -23417,6 +23417,15 @@ SRR359290.10000 16 chr12 110785492 255 27=1X47= * 0 0 AATGTTTGCGCATGTTCGAGATGAGT</td>
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23417
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<td class="new_line diff-line-num" data-linenumber="23417" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23417
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23417" class="line" lang="">102 16 chr6 65786102 255 453H13=1X5=1X3=223H * 0 0 AAGATGGCCCCAGCGCTCGCAAG * NM:i:2 AS:i:110 EV:Z:58</span>
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<td class="old_line diff-line-num" data-linenumber="23418" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23418
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<td class="new_line diff-line-num" data-linenumber="23418" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23418
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23418" class="line" lang="">102 16 chr6 170257702 255 191H17=1D1=1D6=484H * 0 0 AGCACCCAGCCTGCCCTGCCAGCC * NM:i:2 AS:i:110 EV:Z:58</span>
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<td class="old_line diff-line-num" data-linenumber="23419" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23419
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<td class="new_line diff-line-num" data-linenumber="23419" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23419
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23419" class="line" lang="">102 16 chr15 78230486 255 166H7=1X12=1D4=509H * 0 0 CAGGAGCGGCCACCATGGCCCAAG * NM:i:2 AS:i:110 EV:Z:58</span>
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<td class="new_line diff-line-num new" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23420
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23420" class="line" lang="">@HD VN:1.3 SO:unsorted</span>
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<td class="new_line diff-line-num new" data-linenumber="23421" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23421
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23421" class="line" lang="">@PG ID:lastal PN:lastal VN:1541</span>
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<td class="new_line diff-line-num new" data-linenumber="23422" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23422
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23422" class="line" lang="">chr15 0 L1P1_5end#LINE/L1 1 100 17013608H1=1X2=2X1=1X2=1X10=1X7=1X2=1X3=1X1=1X14=1X5=1X3=1X7=1X3=2X6=1X8=1X5=1X4=1X13=1X2=1X1=1X4=1X16=1X11=1X5=1X2=1X1=1X1=1X2=1X7=1X1=1X3=1X3=2X6=2X6=1X5=1X17=1X4=1X5=1X7=2X5=1X9=1X5=2X12=1X9=1X5=1X1=1X1=1X8=1X3=1X3=1X19=1X5=1X3=1X13=1X3=1X2=1X1=1X3=1X2=1X20=1X9=1X5=1X5=1X11=1X5=2X2=1D16=2X14=1X2=1X2=1X9=1X1=1X4=1X15=1X1=1X11=1X15=1X31=1X53=1X9=1X2=1X4=1X18=1X25=1X7=7I21=1X6=1X32=2X2=1X15=1X8=1X2=1X6=1X12=1X4=1X2=1X2=1X3=1X12=1X28=1X9=1X5=1X35=1X19=1X37=2X21=1X45=1X13=1X5=1X4=1X16=1X4=1X13=1X63=1X11=2X8=1X3=1X6=1X28=1X1D11=1X17=2X9=1X9=1X23=1X1=1X8=1X3=1X17=1X6=1X1=1X18=1X31=1X3=1X37=1X8=1X14=1X18=1X5=1X25=1X1=1X65=1D7=1X10=1X6=1X12=1X31=1X49=1X34=1X20=1X6=1X7=1X8=1X21=1X18=1X35=1X50=1X1=1X35=1X44=1X1=1X18=1X17=1X3=2X1=1X6=1X15=1X7=1X23=84975467H * 0 0 GAGGTGGCAGTCAAGATGGCCAAATAGGAGCACCTCTGTTCTACAGCTCCCAGTGTGAGTGACACAGAAGATGGGCAATTTCTTCATTTCCATCTGAGATACCTGGTTCATCTCACTAGGAATTGCCAGACAGTGGGCGCAGGatagtgggtgcaGTGCACCATGAGTGGGCAGAAGCAGAGTGAGTCATTTCCTCACTTGGGAAGTGCAAGTGGTCAGGGAGTTCCCTTACCTAATCAAATAAAGGGGCAACAGATGGCACCTGGGAAATCCAGTCACTCCCACCATAATACTGCTCTTTTTCAATGGGCTTAAAAAATGGCACACCAGGAGATTATATCCCACACCTTGCTTGGAGGGTCCTACGTCCATGGTGTCTCACTGATTGCTAGCACAGCAGTCTGTGATCAAACTACAAGGTGGCAGTGAGGCTGGGGGTGGGGCAACCCCATTGCCCAGGCTTGCTTAGGTAAACAAAGCTGCTGGAAAGCTCGAAGTAGGTGTAGCCCACCACAGCTCTACGAGGCCTGCCTTCCTCTGTAGGCTCCATCTCTGGGGGCAGGGCACAGACAAACAAAAAGGCAGCAGTAACCTCTGCAGACTTAAATGTCCCTGTCTGACAGCTTTGAAGAGAGAAGTGGTTCTACCGGCACACAGCTGGAGATCTGAGAATGGGCAGACTGCCTCCTCAAGTGGGTACCTGACCTCTGAACCCCGAGCAGCCTAACTGGGAGACACCCCTCAGTAGGGGCagactgacaccTCACACGGCCGTATAGTCCTCTGAGACAAAATTTCCAGAGCAAAGATCAGACAGCAGCATTCGTGGTTTACGAAAATCTGCTGTTCTGCAGTCACCGCTGCTGATACCCAGGCAAACAGGATCTGGAGTGTACCTCTAGCAAACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTTAGAAGGAAAACTAAGAAACAGAAAGGACATCCACACCAAAAACCCATCTGTATATCACCATCATCAAAGACCAAAAGTAGATAAAACCACAAAGATGGGGAAAAAACAGAGCAGAAAAACTAGAAACTCTAAAAAGCAGAGTGCCTTTCCTCCTCCAAAGGAATGCAGTTCCTCACCAGCAATGGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAATTACTCCGAGCTGCAGGAGGAAATTCAAACCAAAGGCAAAGAAGTTAAAAACTTtgaaaaaattTAGACGAATGTATAACTAGAATAACCAACACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAGCCAAGGCTCCAGAACTACTTGAAGAATGCAGAAGCCTCAGGAGCCGAGGTGATCAACTGGAAGAAAGGATATCAGTGATGGAAGATGAAATGAATGAAATAAAGTGAGAAGGGAAGTTTAGAGAAAAAAgaataaaaagaaATGAACAAAGACTCCAAGAAATATGAGACTATGTGAAAAGACCATATCTATGTCTGATTGGTGTACCTGAAAGTGATGCGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAGAAGGCAGACCAACATTCATATTCAGAAAATACAGAGAATGCCACAAAGATACTCCTCGAGAAGAGCAACTTCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATATTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGGAAGCCCATCAGACGAACAGCCGATCTCTTGGCAGAAAGTCTACAAGCCAGAAGAGAGTGTGGGCCAATATTCAACATTTTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATTCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTACAGACGATCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCTCTAAAAGAGCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAATCAGTACCAGCCACTGCAAAATCATGCCAAATTGTAAAGTCCACTGTGGCTAGTAAGAAACTGCATCAAGTAACGAGAAAAATAACCAGCTAACATCATAA * NM:i:188 AS:i:9472</span>
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23423
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23423" class="line" lang="">chr15 0 L1P1_orf2#LINE/L1 3 100 17015723H34=1X23=1X8=1D15=1X54=1X10=1X15=1X2=1X6=1X11=1X24=4D52=1X43=1X6=1X17=1X12=15D5=1X19=2X14=1X11=1X7=1X25=1X21=1X7=1X7=1X33=1X36=1X14=1X27=1X13=1X7=1X6=2X155=1X38=1X35=1X20=1X55=1X44=1X4=1X30=1X37=1X12=1X14=1X1=1X11=1X66=1X10=1D8=1X1=2X8=1X17=1X6=1X16=1X1=1X8=1X4=1X6=1X28=1X76=1X2=1X81=1X21=1X9=1X27=1X38=1X21=1X1=1X66=1X5=1X7=1X39=1X19=1X3=1X13=1X25=1X48=1X28=2X19=1X6=1X34=1X64=1X58=1X2=1X26=1X30=1X10=1X29=1X20=1X47=1X56=1X41=2X22=1X36=1X4=1X47=2X26=1X33=1X8=1X36=1X33=1X2=1X5=1X3=1X14=2X22=2X12=1X12=1X2=1X12=1X3=1X23=1X39=1X2=1X19=1X7=1X8=2X131=1X1=1X28=1X20=1X38=1X7=1X19=1X4=1X59=1X16=2X4=1X9=1X1=1X5=1X9=1X69=2X15=1X9=1X12=1X1=1D21=1D25=84972201H * 0 0 GACAGGATCAAATTCACACATAACAATATTAACTCTAAATGTAAATGGACTAAATGCTTCAATTAAAGACACAGACTGGCAATTTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACATGCAGAGACAAACATAGGCTCAAAATGAAAGGATGGTGGAAGATCTACAAAGCAAATGGAaaacaaaaaaaggggTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAACGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAGCAAGAAAAGCTAACTATCCTAAATGTATATGCACCCAGATTCTTAAAGCAAGTCCTGAGTGATGTACAAAGAGACTTACACTCCCACACAATAATAATTGGAGACTTTAACACCCCACTGTCAATATTAGACAGATCAACGAGACAAAAAGTTAGCAAGGATCCCCAGGAATTGAACTCAGCTCTGCACCAAGCGGGCCTAATAGACATCTACAGAACTCTCCACCCCAAATCGACAGAATATACATTTTTTTCAGCACCACAccacaCCTATTCCGAAATTGACCACATCGTTGGAAATAAAGCTATCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAAACTCACTCAAAACCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACAAAATGAAGGCAGAAATAAAGATGTTCTTTGAAACCAACAAGAACAAAGACACAACATACCAGAATCTCTGGGACACATTCAAAGCAGTGTGTAGAAGGAAATTTATAGCACTAAATGCCCACAAGAGAAAGCAGGAAAGATCCAAAATTGATACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACGCATTAAAAAGCTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATAGAGACACaaaaaaaCCTTCAAAAAATTAATGAATCCAGGAGATTGTTTTTTGAAAAGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGATGCAATAAAAATGATAAAGTGAGTATCACCATCGATCCCACAGAAATACGAACTACTATCAGAGAATACTACATAAACCTCTACACAAACAAACTACAAAATCTAGAAGAAATGGATAAATTCCTTGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGTGGTAATAATCAATAGCTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACAAGGAGGAACTGGTACCATTCCTTCTGAAATTATTCCAATGAATAGAAAAAGAGGGAATCCTCCCTAATTCATTTTATGAGGCCAGCATCATCCTGATACCAAAGCCGGGCAGAGACACAACCAAAAaaCAAAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGATTCCAGAAGCACATTAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTAGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAGAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGATAAAATTCAACAACCCTTCATGCTAAAAATACTCAATAAATTAGGTATTGTTGGGACATATCTCAAAATAATAAGAGCTATCTATGACAAACACACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACTGGCACAAGATAGGGATGCCCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCCATTAGGCAGGAGAAGGAAATAAAGGGTATGCAATTAGGAAAAGAGGAAGTCAAATTGTCCTTGTTTGCAGATGACATGATTGTATATCTAGAAAACCCCATTGTCTCAGCCCAAAATCTCCTGAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACAGAGAGCCAAATCATAAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATATGTAGGAATCCAACTTACAAGGGACGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGTTCAATGAAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCGTGAAAATGACCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCAACAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAGACTACTTTAAAGTTCATATGGAACCAAAAAAGATCCTGCATCACCATGTCAATCCTAAGCCGCAAGAACAAAGCTGGAGGCATCAGTCTACCTGACTTCGAACTATACTACAGGGATACAGTAACCAAGACATCATGGTACTGGTACCAAAACAGAAATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAATGCTGCATATCTACAACTATCTGTTCTTTGATAAACCTGAACAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAAAGTTaaacgttagacctaaaaccatAAAAATCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTTTAAAACAACAAAAGCAATGGCAACAAATGCCATAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAACAGGCAATGTACAAAATGGGAGATAGTTTTCACAACCTACTTATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAaaaaacaaacaaaGCCATCAAAAAGTGGGTGAAGGACATCAACAGACACTTCCCAAAGAAGACATTTATGCAGCCAAAAACACATGAAAAAATGCTCATC * NM:i:165 AS:i:15792</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="23424" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23424
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23424" class="line" lang="">chr15 0 L1PA3_3end#LINE/L1 150 52 17018992H24=1X20=1X14=1X35=1X22=1X4=1X9=1X3=1X4=1X10=1X4=1X35=2X4=1X10=1X27=1X1=2X7=1D51=1X14=1X3=2D9=1X15=1X4=1X1=1X3=1X13=1X11=2X2=1X13=1X7=1I42=1X27=1X5=1X8=1I8=1X4=1X24=1X1=1X48=1X4=1X12=1X15=1X19=1X11=1X10=1X5=1X13=1X18=1X3=1X43=84971448H * 0 0 ACTGGCCATCAGAGAAATGCAAATGAAAACCACAATGAGATACCACCTCACACCAGTTAGGATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGTTGGAGAGGATGTGGAGAAATAGAAACATTTTTACACTTTTGATGGGGCTGTAAACTAATTCAGCCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGAAGTAGAGCTAGAAATACAATTTGACCCAGCCATCCCATTACTGGGCACGTACCCAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTATTCACAATTGCAGACTTGGAAACAACCCAAATGTCCAGCAATAACAGAGTGGATTAAGAAAACGTGGCACATATGTACAATGGAATACTATGGAGCCATACAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAACTGGAAATCATCATTCTCAGTAAACTATTGCAAGGACAAAAAAACCAAACACTGCATGTTCTCACTCATAGGTGGGAATTGAGCGATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGATGTGAGGTGgggggaggagggaggGATAGCATTAGGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAACATGGCACATGTACACATATGTAACTAACCTGTACAATGTGCACATGTACCCTAAAACTTAAAGTATAataataataaaa * NM:i:53 AS:i:3398</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="23425" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23425
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23425" class="line" lang="">chr15 16 L1PA3_3end#LINE/L1 467 84 84955187H52=1X10=1X83=1X13=1X3=1X23=1X54=1X47=1X3=1X16=1X16=1X15=1X10=1X41=1X17=1X13=1X4=17035566H * 0 0 TAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAAAAAATGTGGCGCATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAATCAACATTCTCAGTAAAATATTGCAAGAACAAAAAACCAAACACCTCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATGGACACAGGAAAGGGAACATCACACTCTGGGGACTGTtgtggggtggggggagggGGGACGGAGAGCATTGGGAGATATATCTAATGCTAGATGACGGGTTAGTGGGTGCAGCACACCAGCATGTCACATGTATACATATGTAACTAACCTGCACATTGTGCACATTTACCCTAAAACTTAaagaataataataataagaaaa * NM:i:16 AS:i:2158</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="23426" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23426
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23426" class="line" lang="">chr15 0 L1PA3_3end#LINE/L1 40 81 17042713H2=1X3=1X7=1X6=1X12=1X14=1X16=1X1=2X78=1X8=1X7=1X11=1X64=2X2=1X5=1X13=1X10=1X35=1X39=1X59=1X6=1X15=1X35=1X12=1X64=1X41=1X7=1X4=1X27=1X43=2X3=1X23=1X2=1X2=1D2=1X1=1X12=2X18=1X11=1X10=1X7=1X3=1X12=1X58=84947620H * 0 0 aaaaaacaaacaaataaCCCCTTCAAAAAGTGGGTGAAGGACATGAACATACACTTCTCAAAAGAATATGTTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAAATACCATCACACACCAATTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACAAAGTGGGTGGCACTGTAAACTAGTACAACCATTGTAGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACCAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATGTACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTAGTCACAATAGCAAAGAGTTGGAACCAACCCAAATGTCCAACAATGATAGACTTGATTAAGAAAATATGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGTGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATTGCAAGAATAAAAGACCAAACACCGCATATTCTCACTCATAAGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAATGTCATACTCTGGGGACTGTTGTGGGGTGTGGTGAGGCGCAGGGATAGCATTATGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAGCGTGGTACATGTATACATGTGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataata * NM:i:47 AS:i:4053</span>
</pre></td>
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<td class="old_line diff-line-num new" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
</td>
<td class="new_line diff-line-num new" data-linenumber="23427" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23427
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23427" class="line" lang="">chr15 16 L1PA2_3end#LINE/L1 41 73 84941003H33=1X112=1X4=1X45=1X115=1X85=1X11=1X50=2X24=1X40=1X19=1X13=1X6=1X12=1X8=1X7=1D21=1X86=1X3=1X15=1X3=1X11=1X19=1X17=1X23=1X45=17049334H * 0 0 AGAaaaaaacaAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGTGATATCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACTACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACATATGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAACCATAGACTGGATTAAGAAAATGTGGTACATATACACCATGGAATACTATGCAGCCATAAAAAATGAAGAGTTCATGTCCTTTGTAGAGACATGGATGAAACTGGAAACCATCATTCTCAGCAAACTATCACAAGAACAAAAACCAAACACCGCATATTTTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTGGGGGCAGGAGGGAGGGATAGCATTAGGAAATATACCTAATACTAGATGACGAGTTAGTGGCTGCAGCGCACCAGCATGTCACATGTATACATATGTAACTAATCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAA * NM:i:26 AS:i:4305</span>
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<td class="old_line diff-line-num new" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="23428" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23428
</td>
<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23428" class="line" lang="">chr15 16 L1P1_orf2#LINE/L1 2609 100 84940427H4=1X17=1X92=1X22=1X25=1X103=1X20=1X45=1X3=1X39=1X28=1X14=1X70=1X16=1X63=17050187H * 0 0 TCACACTACCTGACTTCAAACTGTACTACAAGGCtacagtaaccaaaacagCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAACACCGCATATCTACAACTATCTGACCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAAGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATAGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC * NM:i:14 AS:i:2956</span>
</pre></td>
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<td class="old_line diff-line-num" data-linenumber="23420" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23420
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<td class="new_line diff-line-num" data-linenumber="23429" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23429
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23429" class="line" lang="">221 chr1 160106735 75 + 249250621 SRR359290.9001 0 75 - 75 75</span>
</pre></td>
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<td class="old_line diff-line-num" data-linenumber="23421" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23421
</td>
<td class="new_line diff-line-num" data-linenumber="23430" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23430
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23430" class="line" lang="">450 chr1 231468663 75 + 249250621 SRR359290.9002 0 75 + 75 75</span>
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<td class="old_line diff-line-num" data-linenumber="23422" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23422
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<td class="new_line diff-line-num" data-linenumber="23431" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
23431
</td>
<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC23431" class="line" lang="">120 chr15 50775672 24 + 102531392 SRR359290.9002 22 24 + 75 24</span>
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<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#91ede9ced121fa989c86d8e8721da9214813a826"><strong style="font-weight: bold;">test/maf-convert-test.sh</strong></a>
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<td class="line_content match" style="color: rgba(31,30,36,0.24); padding: inherit;" bgcolor="#fbfafd">@@ -46,6 +46,7 @@ maf2=bs100.maf</td>
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<td class="old_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC46" 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;">$r</span> <span class="nt" style="color: #000080;">-r</span> <span class="s1" style="color: #d14;">'ID:1 PL:ILLUMINA SM:x'</span> sam</span>
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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
47
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC47" class="line" lang="shell"> <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-d</span> sam <span class="nv" style="color: #008080;">$maf1</span></span>
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<td class="old_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
48
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC48" class="line" lang="shell"> <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-j1e9</span> sam 90089.maf 102.maf</span>
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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="shell"> <span class="nv" style="color: #008080;">$r</span> sam toprev.maf</span>
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<td class="old_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
49
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<td class="new_line diff-line-num" data-linenumber="50" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
50
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC50" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-n</span> tab</span>
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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
51
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC51" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n999</span> <span class="nv" style="color: #008080;">$maf1</span> | <span class="nv" style="color: #008080;">$r</span> tab</span>
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<td class="old_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
51
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<td class="new_line diff-line-num" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
52
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC52" class="line" lang="shell"> <span class="nv" style="color: #008080;">$r</span> <span class="nt" style="color: #000080;">-n</span> tab frameshift-new.maf</span>
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<li id="e819333ce9c994404f6c3bb6ed8f32b3748b766c">
<a href="https://salsa.debian.org/med-team/last-align/-/compare/52b5297cba13e88371f6fe2844d22f53da75892e...4a58fc4334ab31dd6ff1af182535db0c43e0a5fa#e819333ce9c994404f6c3bb6ed8f32b3748b766c"><strong style="font-weight: bold;">test/toprev.maf</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC1" class="line" lang="plaintext"># LAST version 1541</span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC2" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="plaintext"># a=26 b=1 A=29 B=1 e=138 d=77 x=137 y=46 z=137 D=1e+07 E=23646.3</span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC4" class="line" lang="plaintext"># R=01 u=0 s=1 S=1 M=0 T=0 m=100 l=1 n=100 k=1 w=1000 t=4.62434 j=3 Q=0</span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC5" class="line" lang="plaintext"># Reference sequences=2716 normal letters=3491686</span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC6" class="line" lang="plaintext"># lambda=0.21926 K=0.327014</span>
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7
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC7" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC8" class="line" lang="plaintext"># A C G T M S K W R Y B D H V</span>
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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
9
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC9" class="line" lang="plaintext"># A 5 -10 -5 -11 3 -7 -8 2 3 -11 -8 1 1 1</span>
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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
10
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC10" class="line" lang="plaintext"># C -10 6 -10 -3 2 3 -5 -5 -10 3 1 -6 1 1</span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC11" class="line" lang="plaintext"># G -3 -10 6 -10 -5 3 2 -5 3 -10 1 1 -6 1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC12" class="line" lang="plaintext"># T -11 -5 -10 5 -8 -7 3 2 -11 3 1 1 1 -8</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC13" class="line" lang="plaintext"># M 2 2 -7 -6 2 0 -6 0 0 -1 -2 -1 1 1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC14" class="line" lang="plaintext"># S -5 3 3 -5 0 3 0 -5 0 0 1 -1 -1 1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC15" class="line" lang="plaintext"># K -6 -7 2 2 -6 0 2 0 -1 0 1 1 -1 -2</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC16" class="line" lang="plaintext"># W 2 -7 -7 2 0 -7 0 2 0 0 -1 1 1 -1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC17" class="line" lang="plaintext"># R 3 -10 3 -11 1 0 -1 0 3 -10 -2 1 -1 1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC18" class="line" lang="plaintext"># Y -11 3 -10 3 -1 0 1 0 -10 3 1 -1 1 -2</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC19" class="line" lang="plaintext"># B -7 1 1 1 -2 1 1 -1 -2 1 1 -1 0 -1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC20" class="line" lang="plaintext"># D 1 -8 1 0 -1 -2 1 1 1 -1 -1 1 0 0</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC21" class="line" lang="plaintext"># H 0 1 -8 1 1 -2 -1 1 -1 1 0 0 1 -1</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC22" class="line" lang="plaintext"># V 1 1 1 -7 1 1 -2 -1 1 -2 -1 0 -1 1</span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC23" class="line" lang="plaintext"># N 0 0 0 0 0 0 0 0 0 0 0 0 0 0</span>
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<td class="new_line diff-line-num new" data-linenumber="24" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC24" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC25" class="line" lang="plaintext"># Coordinates are 0-based. For - strand matches, coordinates</span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC26" class="line" lang="plaintext"># in the reverse complement of the 2nd sequence are used.</span>
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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
27
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC27" class="line" lang="plaintext">#</span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC28" class="line" lang="plaintext"># name start alnSize strand seqSize alignment</span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC29" class="line" lang="plaintext">#</span>
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30
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC30" class="line" lang="plaintext"># m=1 s=138</span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC31" class="line" lang="plaintext">#</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC32" class="line" lang="plaintext">a score=9472 mismap=1e-10</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
33
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC33" class="line" lang="plaintext">s L1P1_5end#LINE/L1 0 2110 + 2259 GGGGGNGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAGCGACGCAGAAGACGGGTGATTTCTGCATTTCCANCTGAGGTACCGGGTTCATCTCACTGGGGAGTGCCGGACAGTGGgcgcaggacagtgggtgcagcgcaCCGTGCGCGAGCCGAAGCAGGGCGAGGCATCGCCTCACCCGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCTAGTCAAAGAAAGGGGTGACAGACGGCACCTGGAAAATCGGGTCACTCCCACCCTAATACTGCGCTTTTCCGACGGGCTTAANAAACGGCGCACCAGGAGATTATATCCCGCACCTGGCTCGGAGGGTCCTACGCCCACGGAGCCTCGCTCATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAGGCGGCAGCGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGANTAGGTAAACAAAGCGGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGTAGGCTCCACCTCTGGGGGCAGGGCACAGACAAACAAAAAGACAGCAGTAACCTCTGCAGACTTAAATGTCCCTGTCTGACAGCTTTGAAGAGAGCAGTGGTTCTCCCAGCACGCAGCTGGAGATCTGAGAACGGGCAGACTGCCTCCTCAAGTGGGTCCCTGACC-------CCCGAGCAGCCTAACTGGGAGGCACCCCCCAGTAGGGGCAGACTGACACCTCACACGGCCGGGTACTCCTCTGAGACAAAACTTCCAGAGGAACGATCAGGCAGCAGCATTCGCGGTTCACCAANATCCGCTGTTCTGCAGCCACCGCTGCTGATACCCAGGCAAACAGGGTCTGGAGTGGACCTCCAGCAAACTCCAACAGACCTGCAGCTGAGGGTCCTGNCTGTTAGAAGGAAAACTAACAAACAGAAAGGACATCCACACCAAAAACCCATCTGTACGTCACCATCATCAAAGACCAAAGGTAGATAAAACCACAAAGATGGGGAAAAAACAGAGCAGAAAAACTGGAAACTCTAAAAANCAGAGCGCCTCTCCTCCTCCAAAGGAACGCAGCTCCTCACCAGCAACGGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAACTACTCCGAGCTANAGGAGGAAGTTCGAACCAATGGCAAAGAAGTTAaaaactttgaaaaaaaaTTAGACGAATGGATAACTAGAATAACCAATGCAGAGAAGTCCTTAAAGGACCTGATGGAGCTGAAAGCCAAGGCNCGAGAACTACGTGANGAATGCAGAAGCCTCAGNAGCCGATGCGATCAACTGGAAGAAAGGGTATCAGTGATGGAAGATGAAATGAatgaaatgaaGCGAGAAGGGAAGTTTAGAGAAAAAagaataaaaagaaaCGAACAAAGCCTCCAAGAAATATGGGACTATGTGAAAAGACCAAATCTACGTCTGATTGGTGTACCTGAAAGTGACGGGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAGCAAGGCAGGCCAACATTCAGATTCAGGAAATACAGAGAACGCCACAAAGATACTCCTCGAGAAGAGCAACTCCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCACAAAGGGAAGCCCATCAGACTAACAGCNGATCTCTCGGCAGAAACTCTACAAGCCAGAAGAGAGTGGGGGCCAATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTACAGACAAGCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCCCTAAAAGAGCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAACCGGTACCAGCCACTGCAAAAACATGCCAAATTGTAAAGACCATCGAGGCTAGGAAGAAACTGCATCAACTAACGAGCAAAATAACCAGCTAACATCATAA</span>
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34
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC34" class="line" lang="plaintext">s chr15 17013608 2114 + 101991189 GAGGTGGCAGTCAAGATGGCCAAATAGGAGCACCTCTGTTCTACAGCTCCCAGTGTGAGTGACACAGAAGATGGGCAATTTCTTCATTTCCATCTGAGATACCTGGTTCATCTCACTAGGAATTGCCAGACAGTGGGCGCAGGatagtgggtgcaGTGCACCATGAGTGGGCAGAAGCAGAGTGAGTCATTTCCTCACTTGGGAAGTGCAAGTGGTCAGGGAGTTCCCTTACCTAATCAAATAAAGGGGCAACAGATGGCACCTGGGAAATCCAGTCACTCCCACCATAATACTGCTCTTTTTCAATGGGCTTAAAAAATGGCACACCAGGAGATTATATCCCACACCTTGCTTGGAGGGTCCTACGTCCATGGTGTCTCACTGATTGCTAGCACAGCAGTCTGTGATCAAACTACAAGGTGGCAGTGAGGCTGGGGGTGGGGCAACC-CCATTGCCCAGGCTTGCTTAGGTAAACAAAGCTGCTGGAAAGCTCGAAGTAGGTGTAGCCCACCACAGCTCTACGAGGCCTGCCTTCCTCTGTAGGCTCCATCTCTGGGGGCAGGGCACAGACAAACAAAAAGGCAGCAGTAACCTCTGCAGACTTAAATGTCCCTGTCTGACAGCTTTGAAGAGAGAAGTGGTTCTACCGGCACACAGCTGGAGATCTGAGAATGGGCAGACTGCCTCCTCAAGTGGGTACCTGACCTCTGAACCCCGAGCAGCCTAACTGGGAGACACCCCTCAGTAGGGGCagactgacaccTCACACGGCCGTATAGTCCTCTGAGACAAAATTTCCAGAGCAAAGATCAGACAGCAGCATTCGTGGTTTACGAAAATCTGCTGTTCTGCAGTCACCGCTGCTGATACCCAGGCAAACAGGATCTGGAGTGTACCTCTAGCAAACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTTAGAAGGAAAACTAAGAAACAGAAAGGACATCCACACCAAAAACCCATCTGTATATCACCATCATCAAAGACCAAAAGTAGATAAAACCACAAAGATGGGGAAAAAACAGAGCAGAAAAACTAGAAACTCTAAAAAGCAGAGTGCCTTTCCTCCTCCAAAGGAATGCAGTTCCTCACCAGCAATGGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAATTACTCCGAGCTGCAGGAGGAAATTCAAACCAAAGGCAAAGAAGTTAAAAACTTtgaaaaaat-tTAGACGAATGTATAACTAGAATAACCAACACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAGCCAAGGCTCCAGAACTACTTGAAGAATGCAGAAGCCTCAGGAGCCGAGGTGATCAACTGGAAGAAAGGATATCAGTGATGGAAGATGAAATGAATGAAATAAAGTGAGAAGGGAAGTTTAGAGAAAAAAgaataaaaagaaATGAACAAAGACTCCAAGAAATATGAGACTATGTGAAAAGACCATATCTATGTCTGATTGGTGTACCTGAAAGTGATGCGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAG-AAGGCAGACCAACATTCATATTCAGAAAATACAGAGAATGCCACAAAGATACTCCTCGAGAAGAGCAACTTCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATATTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGGAAGCCCATCAGACGAACAGCCGATCTCTTGGCAGAAAGTCTACAAGCCAGAAGAGAGTGTGGGCCAATATTCAACATTTTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATTCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTACAGACGATCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCTCTAAAAGAGCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAATCAGTACCAGCCACTGCAAAATCATGCCAAATTGTAAAGTCCACTGTGGCTAGTAAGAAACTGCATCAAGTAACGAGAAAAATAACCAGCTAACATCATAA</span>
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35
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC35" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC36" class="line" lang="plaintext">a score=15792 mismap=1e-10</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC37" class="line" lang="plaintext">s L1P1_orf2#LINE/L1 2 3288 + 3294 GACAGGATCAAATTCACACATAACAATATTaactttaaatgtaaatgGACTAAATGCTCCAATTAAAAGACACAGACTGGCAAATTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAGGGATGGAGGAAGATCTACCAAGCAAATGGAAAACAaaaaaAGGCAGGGGTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAAAGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAACAAGAAGAGCTAACTATCCTAAATATATATGCACCCAATACAGGAGCACCCAGATTCATAAAGCAAGTCCTGAGTGACCTACAAAGAGACTTAGACTCCCACACANTAATAATGGGAGACTTTAACACCCCACTGTCAACATTAGACAGATCAACGAGACAGAAAGTTAACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAGCGGACCTAATAGACATCTACAGAACTCTCCACCCCAAATCAACAGAATATACATTCTTTTCAGCACCACaccacaCCTATTCCAAAATTGACCACATAGTTGGAAGTAAAGCNCTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAAACTCACTCAAAACCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAAGGCAGAAATAAAGATGTTCTTTGAAACCAACGAGAACAAAGACACAACATACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAAATTTATAGCACTAAATGCCCACAAGAGAAAGCAGGAAAGATCCAAAATTGACACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAGCTAGCAGAAGGCAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAAATAGAGACACAaaaaaCCCTTCAAAAAATCAATGAATCCAGGAGCTGGTTTTTTGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGACGCAATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAATACAAACTACCATCAGAGAATACTACAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTCGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGNGGCAATAATCAATAGCTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACAAGGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAATCAATAGAAAAAGAGGGAATCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAGCCNGGCAGAGACACAACCAAAAAAGAGAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAATCCAGCATATAAACAGAACCAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGACAAAATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTATTGATGGGACGTATCTCAAAATAATAAGAGCTATCTATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACTGGCACAAGACAGGGATGCCCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGGAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAGACGACATGATTGTATATCTAGAAAACCCCATCGTCTCAGCCCAAAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACAGAGAGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAANGAAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGtactggtaccaaaacagAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAACGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC</span>
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38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="plaintext">s chr15 17015723 3265 + 101991189 GACAGGATCAAATTCACACATAACAATATTAACTCTAAATGTAAATGGACTAAATGCTTCAATTAAA-GACACAGACTGGCAATTTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACATGCAGAGACAAACATAGGCTCAAAATGAAAGGATGGTGGAAGATCTACAAAGCAAATGGAaaacaaaaaaagg----ggTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAACGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAGCAAGAAAAGCTAACTATCCTAAATGTATATGCACCCA---------------GATTCTTAAAGCAAGTCCTGAGTGATGTACAAAGAGACTTACACTCCCACACAATAATAATTGGAGACTTTAACACCCCACTGTCAATATTAGACAGATCAACGAGACAAAAAGTTAGCAAGGATCCCCAGGAATTGAACTCAGCTCTGCACCAAGCGGGCCTAATAGACATCTACAGAACTCTCCACCCCAAATCGACAGAATATACATTTTTTTCAGCACCACAccacaCCTATTCCGAAATTGACCACATCGTTGGAAATAAAGCTATCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAAACTCACTCAAAACCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACAAAATGAAGGCAGAAATAAAGATGTTCTTTGAAACCAACAAGAACAAAGACACAACATACCAGAATCTCTGGGACACATTCAAAGCAGTGTGTAGAAGGAAATTTATAGCACTAAATGCCCACAAGAGAAAGCAGGAAAGATCCAAAATTGATACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACGCATTAAAAAGCTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATAGAGACACaaaaaaaCCTTCAAAAAATTAATGAATCCAGGAGATTGTTTTTTGAAAAGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGATGCAATAAAAA-TGATAAAGTGAGTATCACCATCGATCCCACAGAAATACGAACTACTATCAGAGAATACTACATAAACCTCTACACAAACAAACTACAAAATCTAGAAGAAATGGATAAATTCCTTGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGTGGTAATAATCAATAGCTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACAAGGAGGAACTGGTACCATTCCTTCTGAAATTATTCCAATGAATAGAAAAAGAGGGAATCCTCCCTAATTCATTTTATGAGGCCAGCATCATCCTGATACCAAAGCCGGGCAGAGACACAACCAAAAaaCAAAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGATTCCAGAAGCACATTAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTAGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAGAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGATAAAATTCAACAACCCTTCATGCTAAAAATACTCAATAAATTAGGTATTGTTGGGACATATCTCAAAATAATAAGAGCTATCTATGACAAACACACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACTGGCACAAGATAGGGATGCCCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCCATTAGGCAGGAGAAGGAAATAAAGGGTATGCAATTAGGAAAAGAGGAAGTCAAATTGTCCTTGTTTGCAGATGACATGATTGTATATCTAGAAAACCCCATTGTCTCAGCCCAAAATCTCCTGAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACAGAGAGCCAAATCATAAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATATGTAGGAATCCAACTTACAAGGGACGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGTTCAATGAAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCGTGAAAATGACCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCAACAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAGACTACTTTAAAGTTCATATGGAACCAAAAAAGATCCTGCATCACCATGTCAATCCTAAGCCGCAAGAACAAAGCTGGAGGCATCAGTCTACCTGACTTCGAACTATACTACAGGGATACAGTAACCAAGACATCATGGTACTGGTACCAAAACAGAAATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAATGCTGCATATCTACAACTATCTGTTCTTTGATAAACCTGAACAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAAAGTTaaacgttagacctaaaaccatAAAAATCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTTTAAAACAACAAAAGCAATGGCAACAAATGCCATAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAACAGGCAATGTACAAAATGGGAGATAGTTTTCACAACCTACTTATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAaaaaacaaacaaaGCCATCAAAAAGTGGGTGAAGGACATCAACAGACACTTCCC-AAAGAAGACATTTATGCAGCC-AAAAACACATGAAAAAATGCTCATC</span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC39" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
40
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC40" class="line" lang="plaintext">a score=3398 mismap=6.76e-06</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
41
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC41" class="line" lang="plaintext">s L1PA3_3end#LINE/L1 149 750 + 902 ACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATA-AAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAA-CCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGgtggggggaggggggagggATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataataaaa</span>
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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
42
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC42" class="line" lang="plaintext">s chr15 17018992 749 + 101991189 ACTGGCCATCAGAGAAATGCAAATGAAAACCACAATGAGATACCACCTCACACCAGTTAGGATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGTTGGAGAGGATGTGGAGAAATAGAAACATTTTTACACTTTTGATGGGGCTGTAAACTAATTCAGCCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGAAGTAGAGCTAGAAATACAATTTGACCCAGCCATCCCATTACTGGGCACGTACCCAA-GGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTATTCACAATTGCA--GACTTGGAAACAACCCAAATGTCCAGCAATAACAGAGTGGATTAAGAAAACGTGGCACATATGTACAATGGAATACTATGGAGCCATACAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAACTGGAAATCATCATTCTCAGTAAACTATTGCAAGGACAAAAAAACCAAACACTGCATGTTCTCACTCATAGGTGGGAATTGAGCGATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGATGTGAGGTGgggggaggagggaggGATAGCATTAGGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAACATGGCACATGTACACATATGTAACTAACCTGTACAATGTGCACATGTACCCTAAAACTTAAAGTATAataataataaaa</span>
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<td class="new_line diff-line-num new" data-linenumber="43" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
43
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC43" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="44" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
44
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC44" class="line" lang="plaintext">a score=2158 mismap=3.89e-09</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="45" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
45
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC45" class="line" lang="plaintext">s L1PA3_3end#LINE/L1 0 436 - 902 TTTttttattattattatACTTTAAGTTTTAGGGTACATGTGCACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCccctccccccaccccacaACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTA</span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC46" class="line" lang="plaintext">s chr15 17035566 436 + 101991189 ttttcttattattattattcttTAAGTTTTAGGGTAAATGTGCACAATGTGCAGGTTAGTTACATATGTATACATGTGACATGCTGGTGTGCTGCACCCACTAACCCGTCATCTAGCATTAGATATATCTCCCAATGCTCTCCGTCCCccctccccccaccccacaACAGTCCCCAGAGTGTGATGTTCCCTTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGAGGTGTTTGGTTTTTTGTTCTTGCAATATTTTACTGAGAATGTTGATTTCCAATTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGCGCCACATTTTTTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTA</span>
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47
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC47" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="48" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
48
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC48" class="line" lang="plaintext">a score=4053 mismap=8.38e-09</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
49
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC49" class="line" lang="plaintext">s L1PA3_3end#LINE/L1 39 857 + 902 AAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGgtggggggaggggggagggATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataata</span>
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50
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC50" class="line" lang="plaintext">s chr15 17042713 856 + 101991189 aaaaaacaaacaaataaCCCCTTCAAAAAGTGGGTGAAGGACATGAACATACACTTCTCAAAAGAATATGTTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAAATACCATCACACACCAATTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACAAAGTGGGTGGCACTGTAAACTAGTACAACCATTGTAGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACCAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATGTACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTAGTCACAATAGCAAAGAGTTGGAACCAACCCAAATGTCCAACAATGATAGACTTGATTAAGAAAATATGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGTGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATTGCAAGAATAAAAGACCAAACACCGCATATTCTCACTCATAAGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAATGTCATACTCTGGGGACTGTTGTGGGGTGTGGTGA-GGCGCAGGGATAGCATTATGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAGCGTGGTACATGTATACATGTGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataata</span>
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<td class="new_line diff-line-num new" data-linenumber="51" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
51
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC51" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
52
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC52" class="line" lang="plaintext">a score=4305 mismap=5.26e-08</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
53
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC53" class="line" lang="plaintext">s L1PA2_3end#LINE/L1 9 853 - 902 ttttattatACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCcccctccccccaccccaccaCAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTttgtttttttcT</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="54" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
54
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC54" class="line" lang="plaintext">s chr15 17049334 852 + 101991189 TTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGATTAGTTACATATGTATACATGTGACATGCTGGTGCGCTGCAGCCACTAACTCGTCATCTAGTATTAGGTATATTTCCTAATGCTATCCCTCCCTCCTGCCCCCACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAAAATATGCGGTGTTTGGTTTTT-GTTCTTGTGATAGTTTGCTGAGAATGATGGTTTCCAGTTTCATCCATGTCTCTACAAAGGACATGAACTCTTCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTACCACATTTTCTTAATCCAGTCTATGGTTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATATGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTAGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGATATCACATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCACCCACTTTTTGATGGGGTTGTTtgttttttTCT</span>
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55
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC55" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
56
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC56" class="line" lang="plaintext">a score=2956 mismap=1e-10</span>
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<td class="new_line diff-line-num new" data-linenumber="57" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
57
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC57" class="line" lang="plaintext">s L1P1_orf2#LINE/L1 111 575 - 3294 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCGTTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGctgttttggttactgtaGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTGA</span>
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<td class="new_line diff-line-num new" data-linenumber="58" style="width: 35px; color: rgba(31,30,36,0.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
58
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #333238; position: relative; font-family: var(--default-mono-font, "GitLab Mono"),"JetBrains Mono","Menlo","DejaVu Sans Mono","Liberation Mono","Consolas","Ubuntu Mono","Courier New","andale mono","lucida console",monospace; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC58" class="line" lang="plaintext">s chr15 17050187 575 + 101991189 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCAAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCTATTTGTCAATTTTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTGGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCTTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAATCTTTAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTTCTTGTTTTTCTCAGGTTTGTCAAAGGTCAGATAGTTGTAGATATGCGGTGTTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGctgttttggttactgtaGCCTTGTAGTACAGTTTGAAGTCAGGTAGTGTGA</span>
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59
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