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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/trnascan-se">Debian Med / trnascan-se</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/ca11dedea08701701140b444d70b16900c7713f8">ca11dede</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T20:19:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.7+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/2f0da5082f774f8b553555e16e0a3fb91398af16">2f0da508</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T20:19:11+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/700d1501e878b5c6d63941f4ea40eea8e4a14046">700d1501</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T20:19:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.7+ds'
Update to upstream version '2.0.7+ds'
with Debian dir c04a6330ec3582817eb1fcd40c610d1462a5f2cd</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/e355ed73c9a36eb854035a321619405c298398ba">e355ed73</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T20:26:29+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix typo in tRNAscan-SE.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/6620ef58a9e844b352db6fe745bd8285acccdf00">6620ef58</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T20:38:52+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bring back debugging symbols
The configure script now has a custom option to activate those,
but it needed to be enabled from dh_auto_donfigure to allow the
production of the -dbg package.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/92374a979ef1fc164bc4be8843ae9d1dcccbc241">92374a97</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-11-04T20:41:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#0948f9f528dc26687b578f11edc3473969de65fc">
debian/tRNAscan-SE.1
</a>
</li>
<li class="file-stats">
<a href="#1696dbcfa788b63fff64a0b01733bc7efa8fbb5e">
<span class="new-file">
+
lib/gcode/gcode.marsumito
</span>
</a>
</li>
<li class="file-stats">
<a href="#455f4b97ad0ab614b4ecf65badef3a917d40ace9">
lib/tRNAscanSE/ArraytRNA.pm
</a>
</li>
<li class="file-stats">
<a href="#d0be906675e24d75061810e58097b00c3f3a1825">
lib/tRNAscanSE/CM.pm
</a>
</li>
<li class="file-stats">
<a href="#abe03a0985881fbec53bce7bb3bd14d64974e28d">
lib/tRNAscanSE/GeneticCode.pm
</a>
</li>
<li class="file-stats">
<a href="#77e458ae8803b0156163559014803ef4b2c68443">
lib/tRNAscanSE/ScanResult.pm
</a>
</li>
<li class="file-stats">
<a href="#135e46eb045d916bfcb651303759ee4a4a861929">
lib/tRNAscanSE/tRNA.pm
</a>
</li>
<li class="file-stats">
<a href="#25626e186d050c301ec3d731d261ed5fe0bf4d5e">
tRNAscan-SE.conf.src
</a>
</li>
<li class="file-stats">
<a href="#10fd7c4f6f1e185010a4a71d1ef6b5fec8f9af8d">
tRNAscan-SE.src
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,9 +7,25 @@ AC_PREREQ([2.69])</td>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">AC_INIT([tRNAscan-SE],[2.0.0],[pchan@soe.ucsc.edu])</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">AC_CONFIG_HEADERS([config.h])</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">AC_ARG_ENABLE(debugging,</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> AS_HELP_STRING([--enable-debugging],[enable debugging, default: no]),</span>
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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">[</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">case "${enableval}" in</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> yes) enable_debugging=yes ;;</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> no) enable_debugging=no ;;</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> *) AC_MSG_ERROR([bad value ${enableval} for --enable-debugging]) ;;</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">esac],</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">[enable_debugging=no])</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># Checks for programs.</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">AC_PROG_CC</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">if test "$enable_debugging" != "no"; then</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> CFLAGS="-g -Wall"</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">else</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> CFLAGS="-O3"</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">fi</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"># standard install program</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">AC_PROG_INSTALL</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trnascan-se (2.0.7+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fixed typo in tRNAscan-SE.1.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <etienne.mollier@mailoo.org> Wed, 04 Nov 2020 20:40:45 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">trnascan-se (2.0.6+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,9 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> dh $@ --no-parallel</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> dh_auto_configure -- --enable-debugging</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"># tRNAscan can't handle compressed fasta files</span>
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9
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">override_dh_compress:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh_compress -X .fa</span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#0948f9f528dc26687b578f11edc3473969de65fc"><strong>debian/tRNAscan-SE.1</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -171,7 +171,7 @@ predictions per tRNA identification)</td>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext">\fB\-e\fR \fB\-\-eufind\fR</span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext">: search using Eukaryotic tRNA finder (EufindtRNA) only</span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext">(defaults to Normal seach parameters when run alone,</span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">(defaults to Normal sea<span class="idiff left right">r</span>ch parameters when run alone,</span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext">or to Relaxed search params when run with Cove)</span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext">\fB\-\-emode\fR <mode></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#1696dbcfa788b63fff64a0b01733bc7efa8fbb5e"><strong>lib/gcode/gcode.marsumito</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Marsupial mitochondrial translation codes</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># Format: <Codon> <3-letter AA abreviation> <One letter AA abrev></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">TGA Trp W</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ATA Met M</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">GGC Asp D</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">AGR Stp *</span></pre>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#455f4b97ad0ab614b4ecf65badef3a917d40ace9"><strong>lib/tRNAscanSE/ArraytRNA.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -210,7 +210,14 @@ sub bsearch_id</td>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$key</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$l</span><span class="p">,</span> <span class="nv" style="color: #008080;">$u</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}}</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span> </span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span><span class="p">;</span> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span><span class="p">;</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="perl"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@x_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$key</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">gtrnadb_id_parts</span><span class="p">")</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="perl"> <span class="p">{</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="perl"> <span class="nv" style="color: #008080;">@x_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\-/</span><span class="p">,</span> <span class="nv" style="color: #008080;">$x</span><span class="p">);</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="perl"> <span class="p">}</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="perl"></span>
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214
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nv" style="color: #008080;">$u</span><span class="p">)</span></span>
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215
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="perl"> <span class="p">{</span></span>
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216
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="perl"> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$u</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -259,6 +266,66 @@ sub bsearch_id</td>
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$i</span><span class="p">;</span> </span>
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260
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="perl"> <span class="p">}</span></span>
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261
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$key</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">gtrnadb_id_parts</span><span class="p">")</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ar_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\-/</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">gtrnadb_id</span><span class="p">());</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">lt</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="perl"> <span class="p">{</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="perl"> <span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="perl"> <span class="p">}</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">gt</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="perl"> <span class="p">{</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="perl"> <span class="nv" style="color: #008080;">$u</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="perl"> <span class="p">}</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="perl"> <span class="p">{</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">lt</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="perl"> <span class="p">{</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="perl"> <span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl"> <span class="p">}</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">gt</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="perl"> <span class="p">{</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="perl"> <span class="nv" style="color: #008080;">$u</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="perl"> <span class="p">}</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"> <span class="p">{</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">lt</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="perl"> <span class="p">{</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="perl"> <span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="perl"> <span class="p">}</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">gt</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"> <span class="p">{</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="perl"> <span class="nv" style="color: #008080;">$u</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="perl"> <span class="p">}</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="perl"> <span class="p">{</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="perl"> <span class="p">{</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="perl"> <span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="perl"> <span class="p">}</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="perl"> <span class="p">{</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="perl"> <span class="nv" style="color: #008080;">$u</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="perl"> <span class="p">}</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="perl"> <span class="p">{</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="perl"> <span class="p">{</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="perl"> <span class="nv" style="color: #008080;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl"> <span class="p">}</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$x_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="perl"> <span class="p">{</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="perl"> <span class="nv" style="color: #008080;">$u</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"> <span class="p">}</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"> <span class="p">}</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"> <span class="p">}</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"> <span class="p">}</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"> <span class="p">}</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"> <span class="p">}</span></span>
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$key</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">extdb_id</span><span class="p">")</span></span>
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263
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="perl"> <span class="p">{</span></span>
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264
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">extdb_id</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">lt</span> <span class="nv" style="color: #008080;">$x</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -295,6 +362,10 @@ sub sort_array</td>
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="perl"> <span class="p">{</span></span>
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296
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="perl"> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nv" style="color: #008080;">sort_by_gtrnadb_id</span> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}};</span></span>
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297
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="perl"> <span class="p">}</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$key</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">gtrnadb_id_parts</span><span class="p">")</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="perl"> <span class="p">{</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nv" style="color: #008080;">sort_by_gtrnadb_id_parts</span> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}};</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl"> <span class="p">}</span></span>
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298
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$key</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">extdb_id</span><span class="p">")</span></span>
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299
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="perl"> <span class="p">{</span></span>
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300
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="perl"> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nv" style="color: #008080;">sort_by_extdb_id</span> <span class="nv" style="color: #008080;">@</span><span class="p">{</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">ar_tRNAs</span><span class="p">}};</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -344,6 +415,18 @@ sub sort_by_gtrnadb_id</td>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$a</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">gtrnadb_id</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">cmp</span> <span class="nv" style="color: #008080;">$b</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">gtrnadb_id</span><span class="p">());</span> </span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">sort_by_gtrnadb_id_parts</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@a_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\-/</span><span class="p">,</span> <span class="nv" style="color: #008080;">$a</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">gtrnadb_id</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@b_parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\-/</span><span class="p">,</span> <span class="nv" style="color: #008080;">$b</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">gtrnadb_id</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$a_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">cmp</span> <span class="nv" style="color: #008080;">$b_parts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="perl"> <span class="nv" style="color: #008080;">$a_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">cmp</span> <span class="nv" style="color: #008080;">$b_parts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="perl"> <span class="nv" style="color: #008080;">$a_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">cmp</span> <span class="nv" style="color: #008080;">$b_parts</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: #008080;">$a_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><=></span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: #008080;">$b_parts</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: #008080;">$a_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><=></span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: #008080;">$b_parts</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]));</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">sort_by_extdb_id</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$a</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">extdb_id</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">cmp</span> <span class="nv" style="color: #008080;">$b</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">extdb_id</span><span class="p">());</span> </span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#d0be906675e24d75061810e58097b00c3f3a1825"><strong>lib/tRNAscanSE/CM.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -710,7 +710,6 @@ sub find_anticodon</td>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ss</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$model</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">model</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$undef_anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">undef_anticodon</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -720,29 +719,101 @@ sub find_anticodon</td>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># looking for second stem-loop structure ">>>>...<<<<"</span></span>
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># that should be the anitocodon stem-loop </span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$<span class="idiff left">opts</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">mito_mode</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$model</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">eq</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">SerGCT</span></span><span class="p"><span class="idiff right">"</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$<span class="idiff left">ss</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=~</span></span><span class="idiff"> </span><span class="sr" style="color: #009926;"><span class="idiff right">/^([>.]+<[<.]+>[>.]*)>([.]{4,})<+.+[>.]+<[<.]+/o</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+)>([.]{4,})<+.+[>.]+<[<.]+/o</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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<pre style="margin: 0;">-<span id="LC728" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length </span></span>
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="perl"> <span class="p">}</span></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">mito_mode</span><span class="p">())</span> </span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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733
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="perl"> <span class="p">{</span></span>
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734
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+<[<.]+[>.]*)>([.]{4,})<+.+[>.]+<[<.]+/o</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># index of end of anticodon loop</span></span>
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove '-' gaps from loop</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[\-]//g</span><span class="p">;</span> </span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Don't guess if even number of bp in </span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove introns & non-canonical bases</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[a-z]//g</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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735
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="perl"> <span class="p">{</span></span>
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736
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<pre style="margin: 0;">-<span id="LC736" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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737
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<pre style="margin: 0;">-<span id="LC737" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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738
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<pre style="margin: 0;">-<span id="LC738" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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739
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="perl"> <span class="p">}</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># get anticodon </span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="perl"> <span class="nv" style="color: #008080;">$verify_ac</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># check to see if anticodon extracted from the entire</span></span>
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># trna sequence (coveseq) is same as that extracted from</span></span>
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># just the anticodon loop sequence (antiloop)</span></span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$verify_ac</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: #008080;">$anticodon</span><span class="p">)</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">undetermined_ac</span><span class="p">");</span></span>
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span> </span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="perl"> <span class="p">}</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_end</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="perl"> <span class="p">}</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="perl"> <span class="p">{</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">undetermined_ac</span><span class="p">");</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="perl"> <span class="p">}</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="perl"><span class="p">}</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="perl"></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># find anticodon loop & a-codon from coves or cmsearch output</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">find_mito_anticodon</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="perl"><span class="p">{</span> </span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$self</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="nv" style="color: #008080;">$trna</span><span class="p">,</span> <span class="nv" style="color: #008080;">$gc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_end</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$verify_ac</span><span class="p">);</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="perl"></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">();</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ss</span><span class="p">();</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$model</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">model</span><span class="p">();</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$undef_anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">undef_anticodon</span><span class="p">();</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="perl"> </span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="perl"></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Match pattern in secondary structure output, </span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># looking for second stem-loop structure ">>>>...<<<<"</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># that should be the anitocodon stem-loop </span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="perl"></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerGCT</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+)>([.]{4,})<+.+[>.]+<[<.]+/o</span><span class="p">)</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="perl"> <span class="p">{</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length</span></span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">No D-arm</span><span class="p">");</span></span>
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="perl"> <span class="p">}</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+<[<.]+[>.]*)>([.]{4,})<[<.]+[.]{4,}<[<.]+$/o</span><span class="p">)</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="perl"> <span class="p">{</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length </span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">No T-arm</span><span class="p">");</span></span>
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740
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="perl"> <span class="p">}</span></span>
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741
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<pre style="margin: 0;">-<span id="LC741" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+<span class="idiff left right"><[<.]+>[>.]*)>([.]{4,})<+.+[>.]+<[<.]+</span>/o</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+<span class="idiff left right">[.]{4,}[>.]+)>([.]{4,})<[<.]+\.+[>.]+<[<.]+$</span>/o</span><span class="p">)</span></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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745
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length</span></span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">No D-arm</span><span class="p">");</span></span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="perl"> <span class="p">}</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ss</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([>.]+<[<.]+[>.]*)>([.]{4,})<+.+[>.]+<[<.]+/o</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># set to index position of first base in anticodon loop</span></span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$2</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop length </span></span>
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746
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="perl"> <span class="p">}</span></span>
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="perl"> </span>
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$antiloop_index</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$antiloop_len</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -757,65 +828,65 @@ sub find_anticodon</td>
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Don't guess if even number of bp in </span></span>
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># anticodon loop</span></span>
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: #008080;">$opts</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">mito_mode</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">);</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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761
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="perl"> <span class="p">{</span></span>
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762
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># remove introns & non-canonical bases</span></span>
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<td class="diff-line-num old old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
763
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[a-z]//g</span><span class="p">;</span> </span>
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764
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="perl"></span>
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765
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="perl"> <span class="p">{</span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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768
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
769
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<td class="diff-line-num new_line old" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># get anticodon </span></span>
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<td class="diff-line-num old old_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
770
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
771
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
772
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="perl"> <span class="nv" style="color: #008080;">$verify_ac</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">undetermined_ac</span><span class="p">");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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773
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<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="perl"> <span class="p">}</span></span>
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774
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<td class="diff-line-num new_line old" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="perl"> <span class="k" style="font-weight: 600;">els<span class="idiff left right">e</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="perl"> <span class="k" style="font-weight: 600;">els<span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$antiloop</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
775
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<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="perl"> <span class="p">{</span></span>
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776
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<td class="diff-line-num new_line old" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="perl"> <span class="nv" style="color: #008080;">$antiloop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">);</span></span>
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777
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<td class="diff-line-num new_line old" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC777" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$found</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_tRNA_type</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span> <span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">main_cm_file_path</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$model</span><span class="p">},</span> <span class="nv" style="color: #008080;">$model</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">cove_mode</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerGCT</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Ser</span><span class="p">")</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerTGA</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Ser</span><span class="p">")</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="perl"> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">LeuTAG</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Leu</span><span class="p">")</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">LeuTAA</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Leu</span><span class="p">"))</span></span>
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778
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="perl"> <span class="p">{</span></span>
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779
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;"><span class="idiff left right">undetermined_ac</span></span><span class="p">");</span></span>
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780
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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC780" class="line" lang="perl"> <span class="k" style="font-weight: 600;"><span class="idiff left">return</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$undef_anticodon</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;"><span class="idiff left right">mito_ac_mislocation</span></span><span class="p">");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="perl"> <span class="nv" style="color: #008080;"><span class="idiff left">$found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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781
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848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="perl"> <span class="p">}</span></span>
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782
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<td class="diff-line-num new_line old" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="perl"> <span class="k" style="font-weight: 600;">els<span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$antiloop</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">)</span></span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="perl"> <span class="k" style="font-weight: 600;">els<span class="idiff left right">e</span></span></span>
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783
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="perl"> <span class="p">{</span></span>
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784
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<pre style="margin: 0;">-<span id="LC784" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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785
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<td class="diff-line-num new_line" data-linenumber="852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
786
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<td class="diff-line-num new_line old" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC786" class="line" lang="perl"> <span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$isotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_tRNA_type</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span> <span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">main_cm_file_path</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$model</span><span class="p">},</span> <span class="nv" style="color: #008080;">$model</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">cove_mode</span><span class="p">());</span></span>
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<td class="diff-line-num new old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="perl"> <span class="nv" style="color: #008080;">$isotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_tRNA_type</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span> <span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">main_cm_file_path</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$model</span><span class="p">},</span> <span class="nv" style="color: #008080;">$model</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">cove_mode</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
787
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<td class="diff-line-num new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerGCT</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Ser</span><span class="p">")</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerTGA</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Ser</span><span class="p">")</span></span>
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<td class="diff-line-num old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
788
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<td class="diff-line-num new_line" data-linenumber="855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="perl"> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">LeuTAG</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Leu</span><span class="p">")</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">LeuTAA</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Leu</span><span class="p">"))</span></span>
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789
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<td class="diff-line-num new_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
790
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<td class="diff-line-num new_line" data-linenumber="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_ac_mislocation</span><span class="p">");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
791
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<td class="diff-line-num new_line old" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC791" class="line" lang="perl"> <span class="nv" style="color: #008080;">$<span class="idiff left">trna</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">note</span></span><span class="p"><span class="idiff">("</span></span><span class="s2" style="color: #d14;"><span class="idiff">(</span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$anticodon</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">)</span></span><span class="p"><span class="idiff right">");</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="perl"> <span class="nv" style="color: #008080;">$<span class="idiff left">found</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff right"> </span></span>
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792
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="perl"> <span class="p">}</span></span>
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793
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<td class="diff-line-num new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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794
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="perl"> <span class="p">{</span></span>
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795
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<td class="diff-line-num new_line old" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">((</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">$antiloop</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">3</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">;</span></span>
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796
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<td class="diff-line-num new_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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797
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="perl"> <span class="nv" style="color: #008080;">$isotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gc</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_tRNA_type</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span> <span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">main_cm_file_path</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">$model</span><span class="p">},</span> <span class="nv" style="color: #008080;">$model</span><span class="p">,</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">cove_mode</span><span class="p">());</span></span>
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798
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerGCT</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Ser</span><span class="p">")</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">SerTGA</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Ser</span><span class="p">")</span></span>
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799
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="perl"> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">LeuTAG</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Leu</span><span class="p">")</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="nv" style="color: #008080;">$model</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">LeuTAA</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">Leu</span><span class="p">"))</span></span>
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800
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867
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<pre style="margin: 0;"> <span id="LC867" class="line" lang="perl"> <span class="p">{</span></span>
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801
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_ac_mislocation</span><span class="p">");</span></span>
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802
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$anticodon</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">)</span><span class="p">");</span> </span>
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<pre style="margin: 0;">-<span id="LC803" class="line" lang="perl"> <span class="p">}</span></span>
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804
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<pre style="margin: 0;">-<span id="LC804" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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805
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<pre style="margin: 0;">-<span id="LC805" class="line" lang="perl"> <span class="p">{</span></span>
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806
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_mismatch_ac</span><span class="p">");</span></span>
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807
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$anticodon</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">)</span><span class="p">");</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="perl"> <span class="nv" style="color: #008080;">$found</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> </span>
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808
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="perl"> <span class="p">}</span></span>
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809
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="perl"> <span class="p">}</span></span>
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810
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="perl"> <span class="p">}</span></span>
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812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="perl"></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$found</span><span class="p">)</span></span>
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813
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># get anticodon </span></span>
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="perl"> <span class="nv" style="color: #008080;">$verify_ac</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">undetermined_ac</span><span class="p">");</span></span>
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="nv" style="color: #008080;">$undef_anticodon</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># get anticodon </span></span>
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$antiloop</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="perl"> <span class="nv" style="color: #008080;">$verify_ac</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ac_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># check to see if anticodon extracted from the entire</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1044,7 +1115,7 @@ sub decode_nci_tRNA_properties</td>
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<pre style="margin: 0;"> <span id="LC1115" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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1045
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="perl"> <span class="p">{</span> </span>
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1046
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<td class="diff-line-num new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$intron</span><span class="p">,</span> <span class="nv" style="color: #008080;">$istart</span><span class="p">,</span> <span class="nv" style="color: #008080;">$iend</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">find_intron</span><span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">(),</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_end</span><span class="p">);</span></span>
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1047
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<pre style="margin: 0;">-<span id="LC1047" class="line" lang="perl"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="perl"></span>
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1048
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<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$intron</span><span class="p">)</span></span>
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1049
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1050
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<td class="diff-line-num new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="perl"> <span class="nv" style="color: #008080;">$mat_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">(),</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nv" style="color: #008080;">$istart</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">(),</span> <span class="nv" style="color: #008080;">$iend</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1372,7 +1443,7 @@ sub decode_mito_tRNA_properties</td>
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1372
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1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1373
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<td class="diff-line-num new_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="perl"> <span class="nv" style="color: #008080;">$anticodon</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"</span><span class="s2" style="color: #d14;">ERR</span><span class="p">";</span></span>
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<td class="diff-line-num old_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1374
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1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="perl"></span>
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<td class="diff-line-num old old_line" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1375
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<td class="diff-line-num new_line old" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_end</span><span class="p">,</span> <span class="nv" style="color: #008080;">$acodon_index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">find_anticodon</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="nv" style="color: #008080;">$trna</span><span class="p">,</span> <span class="nv" style="color: #008080;">$gc</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: #008080;">$anticodon</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$antiloop_end</span><span class="p">,</span> <span class="nv" style="color: #008080;">$acodon_index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">find_<span class="idiff left right">mito_</span>anticodon</span><span class="p">(</span><span class="nv" style="color: #008080;">$opts</span><span class="p">,</span> <span class="nv" style="color: #008080;">$trna</span><span class="p">,</span> <span class="nv" style="color: #008080;">$gc</span><span class="p">);</span></span>
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1376
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<td class="diff-line-num new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">anticodon</span><span class="p">(</span><span class="nv" style="color: #008080;">$anticodon</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1377
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<td class="diff-line-num new_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">add_ac_pos</span><span class="p">(</span><span class="nv" style="color: #008080;">$acodon_index</span><span class="p">,</span> <span class="nv" style="color: #008080;">$acodon_index</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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1378
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<td class="diff-line-num new_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1449
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="perl"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1424,8 +1495,15 @@ sub decode_mito_tRNA_properties</td>
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1424
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1495
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
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<td class="diff-line-num new_line" data-linenumber="1496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"")</span></span>
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<td class="diff-line-num old_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
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<td class="diff-line-num new_line" data-linenumber="1497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1497
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<pre style="margin: 0;"> <span id="LC1497" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1427
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<td class="diff-line-num new_line old" data-linenumber="1498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1427" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_iso_conflict</span><span class="p">");</span></span>
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1428
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<pre style="margin: 0;">-<span id="LC1428" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$isotype</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">)</span><span class="p">");</span></span>
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1498
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<pre style="margin: 0;">+<span id="LC1498" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_inconsistent_isotype</span><span class="p">");</span></span>
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1499
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<pre style="margin: 0;">+<span id="LC1499" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span></span>
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1500
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<pre style="margin: 0;">+<span id="LC1500" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1501
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<pre style="margin: 0;">+<span id="LC1501" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$isotype</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">); </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">());</span></span>
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1502
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<pre style="margin: 0;">+<span id="LC1502" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1503
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<pre style="margin: 0;">+<span id="LC1503" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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1504
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<pre style="margin: 0;">+<span id="LC1504" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1505
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<pre style="margin: 0;">+<span id="LC1505" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$isotype</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">)</span><span class="p">");</span></span>
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1506
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<pre style="margin: 0;">+<span id="LC1506" class="line" lang="perl"> <span class="p">}</span></span>
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1429
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1507
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<pre style="margin: 0;"> <span id="LC1507" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1430
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<td class="diff-line-num new_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="perl"> <span class="nv" style="color: #008080;">$log</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">broadcast</span><span class="p">(</span><span class="nv" style="color: #008080;">$prescan_tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tRNAscan_id</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.trna</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">id</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> - isotype/anticondon conflict</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;"> Model: </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">model</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> Detected: </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$isotype</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$anticodon</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1431
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<td class="diff-line-num new_line" data-linenumber="1509" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ss</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1434,15 +1512,22 @@ sub decode_mito_tRNA_properties</td>
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1434
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1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1435
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<td class="diff-line-num new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"")</span></span>
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<td class="diff-line-num old_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1436
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<td class="diff-line-num new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<pre style="margin: 0;"> <span id="LC1514" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1437
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<td class="diff-line-num new_line old" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1437" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_mismatch_ac</span><span class="p">");</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1438
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<pre style="margin: 0;">-<span id="LC1438" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$model_ac</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">)</span><span class="p">");</span></span>
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1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_inconsistent_ac</span><span class="p">");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1517
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<pre style="margin: 0;">+<span id="LC1517" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1518
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<pre style="margin: 0;">+<span id="LC1518" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$model_ac</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">); </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1519
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<pre style="margin: 0;">+<span id="LC1519" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1520
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<pre style="margin: 0;">+<span id="LC1520" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1521
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<pre style="margin: 0;">+<span id="LC1521" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">("</span><span class="s2" style="color: #d14;">(</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$model_ac</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">)</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1439
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<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1440
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<td class="diff-line-num new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1525" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1441
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<td class="diff-line-num new_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1526
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$vert_mito_isotype</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"")</span></span>
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<td class="diff-line-num old_line" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1442
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<td class="diff-line-num new_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1527
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<pre style="margin: 0;"> <span id="LC1527" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1443
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<td class="diff-line-num new_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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<pre style="margin: 0;"> <span id="LC1528" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"")</span></span>
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<td class="diff-line-num old_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1444
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<td class="diff-line-num new_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<pre style="margin: 0;"> <span id="LC1529" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1445
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<td class="diff-line-num new_line old" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1445" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_<span class="idiff left right">noncanonical</span>_ac</span><span class="p">");</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1530
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<pre style="margin: 0;">+<span id="LC1530" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">("</span><span class="s2" style="color: #d14;">mito_<span class="idiff left right">unexpected</span>_ac</span><span class="p">");</span></span>
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1446
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<td class="diff-line-num new_line" data-linenumber="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1447
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<td class="diff-line-num new_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1532
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1532" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1448
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<td class="diff-line-num new_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="perl"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1581,7 +1666,7 @@ sub scan_noncanonical_introns</td>
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1581
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<td class="diff-line-num new_line" data-linenumber="1666" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$nci_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1582
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<td class="diff-line-num new_line" data-linenumber="1667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1667
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1583
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1668
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<pre style="margin: 0;"> <span id="LC1668" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$ci_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1584
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<td class="diff-line-num new_line old" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1584" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ci_index</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1669
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<pre style="margin: 0;">+<span id="LC1669" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ci_index</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">$tRNA</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">model</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">ne</span></span><span class="idiff"> </span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">SeC</span></span><span class="p"><span class="idiff right">"</span>)</span></span>
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1585
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1670
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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="perl"> <span class="p">{</span></span>
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1586
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1671
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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$add_ci</span><span class="p">)</span></span>
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1587
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1672
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<pre style="margin: 0;"> <span id="LC1672" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1640,7 +1725,7 @@ sub add_canonical_intron</td>
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1640
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1725
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<pre style="margin: 0;"> <span id="LC1725" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1641
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1726
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<pre style="margin: 0;"> <span id="LC1726" class="line" lang="perl"> <span class="p">}</span></span>
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1642
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<td class="diff-line-num new_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1727
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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="perl"> <span class="nv" style="color: #008080;">$mat_seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$precursor_seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$introns</span><span class="p">[</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@introns</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">});</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1643
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<pre style="margin: 0;">-<span id="LC1643" class="line" lang="perl"><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1728
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<pre style="margin: 0;">+<span id="LC1728" class="line" lang="perl"></span>
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1644
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1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$mat_seq</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">mat_seq</span><span class="p">()))</span></span>
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<td class="diff-line-num old_line" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1645
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1730
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="perl"> <span class="p">{</span></span>
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1646
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1731
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<pre style="margin: 0;"> <span id="LC1731" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$trna_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">tRNAscanSE::</span><span class="nv" style="color: #008080;">Sequence</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1785,12 +1870,13 @@ sub check_intron_validity</td>
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1785
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1870
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<pre style="margin: 0;"> <span id="LC1870" class="line" lang="perl"> <span class="p">}</span></span>
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1786
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1871
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<pre style="margin: 0;"> <span id="LC1871" class="line" lang="perl"> </span>
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1787
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1872
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<pre style="margin: 0;"> <span id="LC1872" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$clip_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$padded_seq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nv" style="color: #008080;">$cm_intron</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">start</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">$previous_intron_len</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$pre_intron_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">.</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$padded_seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$cm_intron</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">end</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">$previous_intron_len</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$post_intron_seq</span><span class="p">));</span></span>
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1873
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<pre style="margin: 0;">+<span id="LC1873" class="line" lang="perl"></span>
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1788
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1874
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<pre style="margin: 0;"> <span id="LC1874" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$trna_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">tRNAscanSE::</span><span class="nv" style="color: #008080;">Sequence</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">;</span></span>
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1789
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1875
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<pre style="margin: 0;"> <span id="LC1875" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna_file</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">open_file</span><span class="p">(</span><span class="nv" style="color: #008080;">$global_constants</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get</span><span class="p">("</span><span class="s2" style="color: #d14;">tmp_trnaseq_file</span><span class="p">"),</span> <span class="p">"</span><span class="s2" style="color: #d14;">write</span><span class="p">");</span></span>
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1790
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1876
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<pre style="margin: 0;"> <span id="LC1876" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna_file</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">set_seq_info</span><span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seqname</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;">.trna</span><span class="p">"</span><span class="o" style="font-weight: 600;">.&</span><span class="nv" style="color: #008080;">pad_num</span><span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">id</span><span class="p">(),</span> <span class="mi" style="color: #099;">6</span><span class="p">),</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tRNAscan_id</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$clip_seq</span><span class="p">),</span> <span class="nv" style="color: #008080;">$clip_seq</span><span class="p">);</span></span>
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1791
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1877
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<pre style="margin: 0;"> <span id="LC1877" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna_file</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">write_fasta</span><span class="p">();</span></span>
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1792
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1878
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<pre style="margin: 0;"> <span id="LC1878" class="line" lang="perl"> <span class="nv" style="color: #008080;">$trna_file</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">close_file</span><span class="p">();</span></span>
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1793
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<pre style="margin: 0;">-<span id="LC1793" class="line" lang="perl"><span class="idiff left right"> </span></span>
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1879
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<pre style="margin: 0;">+<span id="LC1879" class="line" lang="perl"></span>
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1794
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1880
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<pre style="margin: 0;"> <span id="LC1880" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$scan_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1795
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1881
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<pre style="margin: 0;"> <span id="LC1881" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$cms_output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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1796
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1882
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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$file_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1852,7 +1938,31 @@ sub check_intron_validity</td>
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1852
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1938
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<pre style="margin: 0;"> <span id="LC1938" class="line" lang="perl"> <span class="p">{</span></span>
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1853
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1939
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<pre style="margin: 0;"> <span id="LC1939" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1854
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1940
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<pre style="margin: 0;"> <span id="LC1940" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$intron_seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$pos</span><span class="p">;</span></span>
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1855
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<pre style="margin: 0;">-<span id="LC1855" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ar_introns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ar_introns</span><span class="p">();</span></span>
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1941
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<pre style="margin: 0;">+<span id="LC1941" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ar_introns_src</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ar_introns</span><span class="p">();</span></span>
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1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ar_introns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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1943
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<pre style="margin: 0;">+<span id="LC1943" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$intron_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{};</span></span>
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1944
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<pre style="margin: 0;">+<span id="LC1944" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Adjust intron relative start and end when round1 seq is different from round2 seq</span></span>
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1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ar_introns_src</span><span class="p">);</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1946
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<pre style="margin: 0;">+<span id="LC1946" class="line" lang="perl"> <span class="p">{</span></span>
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1947
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{};</span></span>
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1948
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<pre style="margin: 0;">+<span id="LC1948" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">};</span></span>
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1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">start</span><span class="p">};</span></span>
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1950
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<pre style="margin: 0;">+<span id="LC1950" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">end</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">end</span><span class="p">};</span></span>
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1951
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<pre style="margin: 0;">+<span id="LC1951" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">type</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">type</span><span class="p">};</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1952
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<pre style="margin: 0;">+<span id="LC1952" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">}))</span></span>
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1953
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<pre style="margin: 0;">+<span id="LC1953" class="line" lang="perl"> <span class="p">{</span></span>
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1954
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<pre style="margin: 0;">+<span id="LC1954" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$pos_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">}));</span></span>
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1955
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<pre style="margin: 0;">+<span id="LC1955" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$pos_i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">})</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$pos_i</span><span class="p">;</span></span>
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1957
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<pre style="margin: 0;">+<span id="LC1957" class="line" lang="perl"> <span class="p">}</span></span>
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1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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1959
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<pre style="margin: 0;">+<span id="LC1959" class="line" lang="perl"> <span class="p">{</span></span>
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1960
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<pre style="margin: 0;">+<span id="LC1960" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">};</span></span>
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1961
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<pre style="margin: 0;">+<span id="LC1961" class="line" lang="perl"> <span class="nv" style="color: #008080;">$intron_rec</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$ar_introns_src</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">};</span></span>
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1962
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<pre style="margin: 0;">+<span id="LC1962" class="line" lang="perl"> <span class="p">}</span></span>
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1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$intron_rec</span><span class="p">;</span></span>
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1964
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<pre style="margin: 0;">+<span id="LC1964" class="line" lang="perl"> <span class="p">}</span></span>
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1965
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<pre style="margin: 0;">+<span id="LC1965" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Check intron duplication</span></span>
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1856
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1966
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<pre style="margin: 0;"> <span id="LC1966" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ar_introns</span><span class="p">);</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1857
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1967
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<pre style="margin: 0;"> <span id="LC1967" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1858
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<td class="diff-line-num new_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1968
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<pre style="margin: 0;"> <span id="LC1968" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">$intron_start</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">}</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">$intron_end</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1879,6 +1989,13 @@ sub check_intron_validity</td>
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1879
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<td class="diff-line-num new_line" data-linenumber="1989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1989
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<pre style="margin: 0;"> <span id="LC1989" class="line" lang="perl"> <span class="nv" style="color: #008080;">$log</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">("</span><span class="s2" style="color: #d14;">Overlap with intron </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tRNAscan_id</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$intron_seq</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1880
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<td class="diff-line-num new_line" data-linenumber="1990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1990
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<pre style="margin: 0;"> <span id="LC1990" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
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1881
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<td class="diff-line-num new_line" data-linenumber="1991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1991
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<pre style="margin: 0;"> <span id="LC1991" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1992
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<pre style="margin: 0;">+<span id="LC1992" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">type</span><span class="p">}</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="p">"</span><span class="s2" style="color: #d14;">NCI</span><span class="p">"</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1993
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<pre style="margin: 0;">+<span id="LC1993" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">seg_overlap</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">},</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">},</span> <span class="nv" style="color: #008080;">$intron_start</span><span class="p">,</span> <span class="nv" style="color: #008080;">$intron_end</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1994
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<pre style="margin: 0;">+<span id="LC1994" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1995
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<pre style="margin: 0;">+<span id="LC1995" class="line" lang="perl"> <span class="nv" style="color: #008080;">$ret_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1996
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<pre style="margin: 0;">+<span id="LC1996" class="line" lang="perl"> <span class="nv" style="color: #008080;">$log</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">("</span><span class="s2" style="color: #d14;">Overlap with noncanonical intron </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">tRNAscan_id</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$intron_seq</span><span class="p">);</span></span>
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1997
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<pre style="margin: 0;">+<span id="LC1997" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span><span class="p">;</span></span>
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1998
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<pre style="margin: 0;">+<span id="LC1998" class="line" lang="perl"> <span class="p">}</span></span>
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1882
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1999
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<pre style="margin: 0;"> <span id="LC1999" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1883
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2000
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<pre style="margin: 0;"> <span id="LC2000" class="line" lang="perl"> <span class="p">}</span></span>
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1884
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2001
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<pre style="margin: 0;"> <span id="LC2001" class="line" lang="perl"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1901,6 +2018,16 @@ sub check_intron_validity</td>
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1901
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2018
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<pre style="margin: 0;"> <span id="LC2018" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$hit_overlap</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: #008080;">seg_overlap</span><span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">start</span><span class="p">(),</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">end</span><span class="p">(),</span> <span class="nv" style="color: #008080;">$start</span><span class="p">,</span> <span class="nv" style="color: #008080;">$end</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">);</span></span>
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1902
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2019
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<pre style="margin: 0;"> <span id="LC2019" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$ret_value</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$hit_overlap</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$cm_tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">score</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">score</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$cm_tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">())</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">min_tRNA_no_intron</span><span class="p">})</span></span>
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1903
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2020
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<pre style="margin: 0;"> <span id="LC2020" class="line" lang="perl"> <span class="p">{</span></span>
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2021
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<pre style="margin: 0;">+<span id="LC2021" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Adjust intron relative start and end when round1 seq is different from round2 seq</span></span>
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2022
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@ar_introns</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">ar_introns</span><span class="p">();</span></span>
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2023
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<pre style="margin: 0;">+<span id="LC2023" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: #008080;">@ar_introns</span><span class="p">);</span> <span class="nv" style="color: #008080;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2024
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<pre style="margin: 0;">+<span id="LC2024" class="line" lang="perl"> <span class="p">{</span></span>
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2025
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<pre style="margin: 0;">+<span id="LC2025" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_end</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">rel_start</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">}))</span></span>
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2026
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<pre style="margin: 0;">+<span id="LC2026" class="line" lang="perl"> <span class="p">{</span></span>
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2027
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<pre style="margin: 0;">+<span id="LC2027" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$pos_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">}));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">set_intron</span><span class="p">(</span><span class="nv" style="color: #008080;">$i</span><span class="p">,</span> <span class="nv" style="color: #008080;">$pos_i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">})</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: #008080;">$pos_i</span><span class="p">,</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">type</span><span class="p">},</span> <span class="nv" style="color: #008080;">$ar_introns</span><span class="p">[</span><span class="nv" style="color: #008080;">$i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">seq</span><span class="p">});</span></span>
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2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="perl"> <span class="p">}</span></span>
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2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="perl"> <span class="p">}</span></span>
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1904
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2031
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<pre style="margin: 0;"> <span id="LC2031" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">upstream</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$clip_seq</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nv" style="color: #008080;">$upstream_len</span><span class="p">));</span></span>
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1905
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2032
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<pre style="margin: 0;"> <span id="LC2032" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">downstream</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$clip_seq</span><span class="p">,</span> <span class="nv" style="color: #008080;">$cm_tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">end</span><span class="p">()));</span></span>
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1906
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2033
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="perl"> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">(</span><span class="nv" style="color: #008080;">$seq</span><span class="p">);</span></span>
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<li id="abe03a0985881fbec53bce7bb3bd14d64974e28d">
<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#abe03a0985881fbec53bce7bb3bd14d64974e28d"><strong>lib/tRNAscanSE/GeneticCode.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,7 +117,7 @@ sub initialize</td>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">GAA</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Phe</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">GTT</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Asn</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">TTT</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Lys</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">GTC</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Asp</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">TTC</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Glu</span><span class="p">',</span></span>
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118
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">GTG</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">His</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">TTG</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Gln</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">GTA</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Tyr</span><span class="p">',</span></span>
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119
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">GAT</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Ile</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">TAT</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Met</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">CAT</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Met</span><span class="p">',</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">GCA</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Cys</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">TCA</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Trp</span><span class="p">'</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="perl"> <span class="p">'</span><span class="s1" style="color: #d14;">GCA</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Cys</span><span class="p">',</span> <span class="p">'</span><span class="s1" style="color: #d14;">TCA</span><span class="p">'</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">Trp</span><span class="p">'<span class="idiff left">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">GCC</span></span><span class="p"><span class="idiff">'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=></span></span><span class="p"><span class="idiff">'</span></span><span class="s1" style="color: #d14;"><span class="idiff">Asp</span></span><span class="p"><span class="idiff right">',</span></span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"> <span class="p">};</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">trans_map</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">+</span><span class="p">{};</span></span>
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<li id="77e458ae8803b0156163559014803ef4b2c68443">
<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#77e458ae8803b0156163559014803ef4b2c68443"><strong>lib/tRNAscanSE/ScanResult.pm</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -548,15 +548,26 @@ sub save_allStruct_output</td>
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/_/ /g</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/mito //g</span><span class="p">;</span></span>
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551
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/iso/type/g</span><span class="p">;</span></span>
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552
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/ac/anticodon/g</span><span class="p">;</span></span>
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553
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$note</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$note</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^\(/</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="perl"> <span class="p">}</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="perl"> <span class="p">{</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;">;</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="perl"> <span class="p">}</span></span>
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="perl"> <span class="p">}</span></span>
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="perl"> <span class="nv" style="color: #008080;">$line</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">Note: </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$note</span><span class="p">;</span></span>
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="perl"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="perl"> <span class="nv" style="color: #008080;">$line</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="s2" style="color: #d14;">Note: </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$note</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="perl"> <span class="p">}</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="perl"> <span class="p">}</span></span>
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="perl"></span>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$line</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -832,13 +843,23 @@ sub construct_tab_output</td>
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832
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$opts</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">detail</span><span class="p">())</span></span>
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833
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="perl"> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
834
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845
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<pre style="margin: 0;"> <span id="LC845" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">category</span><span class="p">();</span></span>
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835
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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/mito //g</span><span class="p">;</span></span>
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836
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<td class="diff-line-num new_line old" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/iso/type/g</span><span class="p">;</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/mito_//g</span><span class="p">;</span></span>
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837
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<td class="diff-line-num new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">"")</span></span>
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838
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<td class="diff-line-num new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
848
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<pre style="margin: 0;"> <span id="LC848" class="line" lang="perl"> <span class="p">{</span></span>
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839
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<td class="diff-line-num new_line old" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC839" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^\(/</span><span class="p">)</span></span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="perl"> <span class="p">{</span></span>
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851
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="perl"> <span class="p">}</span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="perl"> <span class="p">{</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;">;</span><span class="p">"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="perl"> <span class="p">}</span></span>
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840
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="perl"> <span class="p">}</span></span>
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841
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="perl"> <span class="p">}</span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="p">""</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$opts</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">detail</span><span class="p">())</span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="perl"> <span class="p">{</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="perl"> <span class="nv" style="color: #008080;">$note</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">note</span><span class="p">();</span></span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="perl"> <span class="p">}</span></span>
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842
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result_line</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="se" style="color: #d14;">\t</span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: #008080;">$note</span><span class="p">;</span></span>
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843
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="perl"> <span class="p">}</span></span>
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844
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="perl"> <span class="nv" style="color: #008080;">$result_line</span> <span class="o" style="font-weight: 600;">.=</span> <span class="p">"</span><span class="se" style="color: #d14;">\n</span><span class="p">";</span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#135e46eb045d916bfcb651303759ee4a4a861929"><strong>lib/tRNAscanSE/tRNA.pm</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1274,6 +1274,22 @@ sub get_base_at_rel_align_pos</td>
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1274
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1274
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<pre style="margin: 0;"> <span id="LC1274" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$base</span><span class="p">;</span></span>
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1275
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1275
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<pre style="margin: 0;"> <span id="LC1275" class="line" lang="perl"><span class="p">}</span></span>
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1276
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1276
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="perl"></span>
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1277
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">get_seq_at_rel_align_pos</span></span>
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1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="perl"><span class="p">{</span></span>
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1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$self</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$rel_pos_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$rel_pos_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="perl"></span>
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1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$rel_pos_end</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: #008080;">$rel_pos_start</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="perl"></span>
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1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">"";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$rel_pos_start</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: #008080;">$len</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="perl"> <span class="p">{</span></span>
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1288
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="perl"> <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: #008080;">data</span><span class="p">}</span><span class="o" style="font-weight: 600;">-></span><span class="p">[</span><span class="nv" style="color: #008080;">_sprinzl_align</span><span class="p">],</span> <span class="nv" style="color: #008080;">$rel_pos_start</span><span class="p">,</span> <span class="nv" style="color: #008080;">$len</span><span class="p">);</span></span>
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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="perl"> <span class="p">}</span></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">;</span></span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">get_rel_pos</span></span>
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="perl"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$self</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#25626e186d050c301ec3d731d261ed5fe0bf4d5e"><strong>tRNAscan-SE.conf.src</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -82,6 +82,7 @@ gc_invert_mito: {lib_dir}/gcode/gcode.invmito</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext">gc_ciliate_cyto: {lib_dir}/gcode/gcode.cilnuc</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext">gc_echinoderm_mito: {lib_dir}/gcode/gcode.echdmito</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">gc_other_mito: {lib_dir}/gcode/gcode.othmito</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">gc_marsu_mito: {lib_dir}/gcode/gcode.marsumito</span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"># Infernal 1.1 covariance models</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">cm_dir: {lib_dir}/models</span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/aec148d60d97f347982a95905b4c01ad0178e6f5...92374a979ef1fc164bc4be8843ae9d1dcccbc241#10fd7c4f6f1e185010a4a71d1ef6b5fec8f9af8d"><strong>tRNAscan-SE.src</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># tRNAscan-SE: a program for improved detection of transfer RNA</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># genes in genomic sequence</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># Version 2.0.<span class="idiff left right">6</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># Version 2.0.<span class="idiff left right">7</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">#</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"># Copyright (C) 2020 Patricia Chan and Todd Lowe </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">use tRNAscanSE::MultiResultFile;</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">use tRNAscanSE::SS;</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">our $version = "2.0.<span class="idiff left right">6</span>"; </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">our $release_date = "<span class="idiff left right">May</span> 2020";</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">our $version = "2.0.<span class="idiff left right">7</span>"; </span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">our $release_date = "<span class="idiff left right">Oct</span> 2020";</span>
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44
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">our $program_id = "tRNAscan-SE-".$version;</span>
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45
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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46
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"># modified by 'make'</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -621,7 +621,7 @@ sub error_handler</td>
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621
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621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="plaintext"></span>
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622
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="plaintext">sub display_credits</span>
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623
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="plaintext">{</span>
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624
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<pre style="margin: 0;">-<span id="LC624" class="line" lang="plaintext"> print STDERR "Copyright (C) 20<span class="idiff left right">19</span> Patricia Chan and Todd Lowe\n",</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext"> print STDERR "Copyright (C) 20<span class="idiff left right">20</span> Patricia Chan and Todd Lowe\n",</span>
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625
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="plaintext"> " University of California Santa Cruz\n",</span>
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<td class="diff-line-num old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
626
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626
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="plaintext"> "Freely distributed under the GNU General Public License (GPLv3)\n\n";</span>
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627
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="plaintext">}</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1063,7 +1063,7 @@ sub set_options</td>
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1063
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="plaintext"> $opts->no_isotype(0);</span>
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1064
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="plaintext"> if ($opt_isocm eq "off")</span>
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1065
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="plaintext"> {</span>
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1066
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<pre style="margin: 0;">-<span id="LC1066" class="line" lang="plaintext"> $opts->no_isotype(<span class="idiff left right">0</span>);</span>
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1066
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<pre style="margin: 0;">+<span id="LC1066" class="line" lang="plaintext"> $opts->no_isotype(<span class="idiff left right">1</span>);</span>
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1067
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1067
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<pre style="margin: 0;"> <span id="LC1067" class="line" lang="plaintext"> }</span>
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1068
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1068
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<pre style="margin: 0;"> <span id="LC1068" class="line" lang="plaintext"></span>
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1069
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="plaintext"> if ($opt_mt ne '')</span>
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