# HG changeset patch
# User iuc
# Date 1667504137 0
# Node ID 642d73815dd13e62087d797a6ce47f47ac5e239c

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628

diff -r 000000000000 -r 642d73815dd1 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,21 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">20.09</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">seqkit</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">seqkit</requirement>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1371/journal.pone.0163962</citation>
+        </citations>
+    </xml>
+</macros>
+
diff -r 000000000000 -r 642d73815dd1 seqkit_locate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqkit_locate.xml	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,177 @@
+<tool id="seqkit_locate" name="SeqKit locate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>subsequences/motifs, mismatch allowed</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+
+#set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
+ln -s '${input}' '${input_identifier}' &&
+
+seqkit locate 
+--threads \${GALAXY_SLOTS:-4}
+#if $conditional_pattern.mode == 'expression'
+    --pattern '"$conditional_pattern.pattern"'
+    $conditional_pattern.use_regexp
+#else
+    --pattern-file '$conditional_pattern.pattern_file'
+#end if
+$output_mode
+--validate-seq-length $advanced_options.validate_seq_length
+$advanced_options.circular
+$advanced_options.degenerate
+$advanced_options.hide_matched
+$advanced_options.ignore_case
+#if not $advanced_options.degenerate
+    --max-mismatch $advanced_options.max_mismatch
+    $advanced_options.use_fmi
+#end if
+$advanced_options.non_greedy
+$advanced_options.only_positive_strand
+$advanced_options.id_ncbi
+'${input_identifier}'
+> '$output'
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>
+        <conditional name="conditional_pattern">
+            <param name="mode" type="select" label="Pattern mode" 
+                help="Specify a pattern/motif sequence or a FASTA file with the motif of interest. Motifs could be EITHER plain sequence containing 'ACTGN' OR regular
+                    expression like 'A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)' for ORFs">
+                <option value="expression">Pattern/motif sequence</option>
+                <option value="file">FASTA file with the pattern/motif of interest</option>
+            </param>
+            <when value="expression">
+                <param argument="--pattern" type="text" value="" label="Pattern/motif sequence" help="Perl regular expressions are allowed">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.letters,string.digits">
+                        <add value="^"/>
+                        <add value="$"/>
+                        <add value="("/>
+                        <add value=")"/>
+                        <add value="|"/>
+                        <add value="?"/>
+                        <add value="*"/>
+                        <add value="+"/>
+                        <add value="{"/>
+                        <add value="}"/>
+                        <add value="\"/>
+                        <add value="["/>
+                        <add value="]"/>
+                        <add value="."/>
+                        <add value=","/>
+                        </valid>
+                    </sanitizer>
+                    <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
+                </param>
+                <param argument="--use-regexp" type="boolean" truevalue="--use-regexp" falsevalue="" checked="false" label="Pattern/motifs are regular expressions"/>
+            </when>
+            <when value="file">
+                <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
+            </when>
+        </conditional>
+        <param name="output_mode" type="select" label="Output mode">
+            <option value="">Tabular (default format)</option>
+            <option value="--gtf">GTF</option>
+            <option value="--bed">BED6</option>
+        </param>
+        <section name="advanced_options" title="Advanced options">
+            <param argument="--validate-seq-length" type="integer" min="0" value="10000" label="Lenth of the sequence to validate" help="Default: 10000" />
+            <param argument="--circular" type="boolean" truevalue="--circular" falsevalue="" checked="false" label="Circular genome" 
+                help="When using flag --circular, end position of matched subsequence that crossing genome sequence end would be greater than sequence length" />
+            <param argument="--degenerate" type="boolean" truevalue="--degenerate" falsevalue="" checked="false" label="Pattern/motif contains degenerate bases"
+                help="Do not use degenerate bases/residues in regular expression, you need convert them to regular expression, e.g., change 'N' or 'X'  to '.'"/>
+            <param argument="--hide-matched" type="boolean" truevalue="--hide-matched" falsevalue="" checked="false" label="Do not show matched sequences"/>
+            <param argument="--ignore-case" type="boolean" truevalue="--ignore-case" falsevalue="" checked="false" label="Ignore case"/>
+            <param argument="--max-mismatch" type="integer" min="0" value="0" label="Maximum mismatch" help="For large genomes like human genome, using mapping/alignment tools would be faster" />
+            <param argument="--non-greedy" type="boolean" truevalue="--non-greedy" falsevalue="" checked="false" label="Non-greedy mode" help="Faster, but muy miss motifs overlapping with others" />
+            <param argument="--only-positive-strand" type="boolean" truevalue="--only-positive-strand" falsevalue="" checked="false" label="Only search on positive strand"/>
+            <param argument="--use-fmi" type="boolean" truevalue="--use-fmi" falsevalue="" checked="false" label="FM-index" 
+                help="Use FM-index for much faster search of lots of sequence patterns. This option is not compatible with the --degenerate option"/>
+            <param argument="--id-ncbi" type="boolean" truevalue="--id-ncbi" falsevalue="" checked="false" label="FASTA head is NCBI stype" help="Example: >gi|110645304|ref|NC_002516.2| Pseud..." />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="output_mode" value="--gtf" format="gtf"/>
+                <when input="output_mode" value="--bed" format="bed"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <conditional name="conditional_pattern">
+                <param name="mode" value="expression"/>
+                <param name="pattern" value="ATAGAT"/>
+            </conditional>
+            <section name="advanced_options">
+                <param name="max_mismatch" value="1"/>
+            </section>
+            <output name="output" file="locate_output1.tabular" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <conditional name="conditional_pattern">
+                <param name="mode" value="expression"/>
+                <param name="pattern" value="A[TU]G"/>
+                <param name="use_regexp" value="true"/>
+            </conditional>
+            <param name="output_mode" value="--bed"/>
+            <section name="advanced_options">
+                <param name="circular" value="true"/>
+                <param name="hide_matched" value="true"/>
+                <param name="ignore_case" value="true"/>
+                <param name="only_positive_strand" value="true"/>
+                <param name="id_ncbi" value="true"/>
+            </section>
+            <output name="output" file="locate_output2.bed" ftype="bed"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <conditional name="conditional_pattern">
+                <param name="mode" value="file"/>
+                <param name="pattern_file" value="motif_sequence.fasta"/>
+            </conditional>
+            <param name="output_mode" value="--gtf"/>
+            <section name="advanced_options">
+                <param name="use_fmi" value="true"/>
+            </section>
+            <output name="output" file="locate_output3.gtf" ftype="gtf"/>
+        </test>
+    </tests>
+    <help>
+.. class:: infomark
+
+**Purpose**
+
+Locate subsequences/motifs, mismatch allowed.
+
+------
+
+.. class:: infomark
+
+**Attention**
+
+  1. Motifs could be EITHER plain sequence containing "ACTGN" OR regular
+     expression like "A[TU]G(?:.{3})+?[TU](?:AG|AA|GA)" for ORFs.     
+  2. Degenerate bases/residues like "RYMM.." are also supported by flag -d.
+     But do not use degenerate bases/residues in regular expression, you need
+     convert them to regular expression, e.g., change "N" or "X"  to ".".
+  3. When providing search patterns (motifs) via flag '-p',
+     please use double quotation marks for patterns containing comma, 
+     e.g., -p '"A{2,}"' or -p "\"A{2,}\"". Because the command line argument
+     parser accepts comma-separated-values (CSV) for multiple values (motifs).
+     Patterns in file do not follow this rule.     
+  4. Mismatch is allowed using flag "-m/--max-mismatch",
+     you can increase the value of "-j/--threads" to accelerate processing.
+  5. When using flag --circular, end position of matched subsequence that 
+     crossing genome sequence end would be greater than sequence length.
+    </help>
+    <expand macro="citations"/>
+</tool>
+
diff -r 000000000000 -r 642d73815dd1 test-data/fx2tab_output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output1.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,5 @@
+1/2	TATACTACTGTCATGTTTGCTTTTTTCGTGCTCATTACCTTATCGTATGCTTCCATCCAAAGATCTAGTTGTTTATAATATTCTCCCGGCCTTACTTCAAC	?@<DDDADDFAAC@>GG<FDCBHIIGB:8??DEAHGAFEDF<B?F9DBFFCDHF>48BBCF)8877=@=@C7=E??EBD:AADA;>C3;BB6:A@>>@:3>
+2/2	AAAAAAACTTTCTTTACAGGCGTAAAGAAAGTGAAATTGACAGTATTTATACATGAAATAGCAATGTCTTTCCCACTTCCCTACGCTGGCATTAACCAGAT	<@@DA6DDF42ABGF9F?F@C<EDDDFBGI>04BGC>BFF><?*88BDFDEAFFDGCGEFEEFIFFFEF>EBDBB@@:ACCCAB8@?=;B<@BABBBBB?#
+3/2	GTGCCATCATTTTCTATCCATTATTATGGATTATTGGCTCATCGTTTAATCCGGGTGATAGTTTATCTGGATCAAGTATTATTCCACAAAATGCAACGTTA	=BBFFFFFHHHHHJJJJJJJJJJJJIJIJEIIGIJJJHGIGGIIGHIDIJGHIIJ?FFHGIIJJJJJJJJHGIHHHCEHFFFFFFFFEAECCDADDDDDDD
+4/2	TTCAAAACACATAAAGCTAATTGCCGCATATGACAATATTGCTAAAATAATTTTTTTACCAGATATCGGTGTTAATCGAAATAATGTACTTTCGGTCATTT	BBCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJIIJJJJJJJIJJHHHHHFFDDCDEEEDDDDDDDDEDDDFFFEDDDDDDDDE
+5/2	ACTTGCCAATGCGATGCACCAATCTTTTCAGCAATAATCGGCAAAATTGGGTCGACTACTCCTATACCTGAAAAGGCAAGGAAAGTAGCCAACACTGTAAT	BCCFFFFFHHHHHIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIHIIJIJHHHHFFFFFFEEEEEEDDDDDDDDDDDDDCDDDDDDDDDDDDDED
diff -r 000000000000 -r 642d73815dd1 test-data/fx2tab_output2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output2.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,6 @@
+#id	length	avg.qual
+1/2	101	24.98
+2/2	101	20.44
+3/2	101	37.13
+4/2	101	37.61
+5/2	101	37.28
diff -r 000000000000 -r 642d73815dd1 test-data/fx2tab_output3.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output3.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,3 @@
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	GAGAGGACGAGGTGCCGCTGCCTGGAGAATCCTCCGCTGCCGTCGGCTCCCGGAGCCCAGCCCTTTCCTAACCCAACCCAACCTAGCCCAGTCCCAGCCGCCAGCGCCTGTCCCTGTCACGGACCCCAGCGTTACCATGCATCCTGCCGTCTTCCTATCCTTACCCGACCTCAGATGCTCCCTTCTGCTCCTGGTAACTTGGGTTTTTACTCCTGTAACAACTGAAATAACAAGTCTTGATACAGAGAATATAGATGAAATTTTAAACAATGCTGATGTTGCTTTAGTAAATTTTTATGCTGACTGGTGTCGTTTCAGTCAGATGTTGCATCCAATTTTTGAGGAAGCTTCCGATGTCATTAAGGAAGAATTTCCAAATGAAAATCAAGTAGTGTTTGCCAGAGTTGATTGTGATCAGCACTCTGACATAGCCCAGAGATACAGGATAAGCAAATACCCAACCCTCAAATTGTTTCGTAATGGGATGATGATGAAGAGAGAATACAGGGGTCAGCGATCAGTGAAAGCATTGGCAGATTACATCAGGCAACAAAAAAGTGACCCCATTCAAGAAATTCGGGACTTAGCAGAAATCACCACTCTTGATCGCAGCAAAAGAAATATCATTGGATATTTTGAGCAAAAGGACTCGGACAACTATAGAGTTTTTGAACGAGTAGCGAATATTTTGCATGATGACTGTGCCTTTCTTTCTGCATTTGGGGATGTTTCAAAACCGGAAAGATATAGTGGCGACAACATAATCTACAAACCACCAGGGCATTCTGCTCCGGATATGGTGTACTTGGGAGCTATGACAAATTTTGATGTGACTTACAATTGGATTCAAGATAAATGTGTTCCTCTTGTCCGAGAAATAACATTTGAAAATGGAGAGGAATTGACAGAAGAAGGACTGCCTTTTCTCATACTCTTTCACATGAAAGAAGATACAGAAAGTTTAGAAATATTCCAGAATGAAGTAGCTCGGCAATTAATAAGTGAAAAAGGTACAATAAACTTTTTACATGCCGATTGTGACAAATTTAGACATCCTCTTCTGCACATACAGAAAACTCCAGCAGATTGTCCTGTAATCGCTATTGACAGCTTTAGGCATATGTATGTGTTTGGAGACTTCAAAGATGTATTAATTCCTGGAAAACTCAAGCAATTCGTATTTGACTTACATTCTGGAAAACTGCACAGAGAATTCCATCATGGACCTGACCCAACTGATACAGCCCCAGGAGAGCAAGCCCAAGATGTAGCAAGCAGTCCACCTGAGAGCTCCTTCCAGAAACTAGCACCCAGTGAATATAGGTATACTCTATTGAGGGATCGAGATGAGCTTTAAAAACTTGAAAAACAGTTTGTAAGCCTTTCAACAGCAGCATCAACCTACGTGGTGGAAATAGTAAACCTATATTTTCATAATTCTATGTGTATTTTTATTTTGAATAAACAGAAAGAAATTTTGGGTTTTTAATTTTTTTCTCCCCGACTCAAAATGCATTGTCATTTAATATAGTAGCCTCTTAAAAAAAAAAAAACCTGCTAGGATTTAAAAATAAAAATCAGAGGCCTATCTCCACTTTAAATCTGTCCTGTAAAAGTTTTATAAATCAAATGAAAGGTGACATTGCCAGAAACTTACCATTAACTTGCACTACTAGGGTAGGGAGGACTTAGGATGTTTCCTGTGTCGTATGTGCTTTTCTTTCTTTCATATGATCAATTCTGTTGGTATTTTCAGTATCTCATTTCTCAAAGCTAAAGAGATATACATTCTGGATACTTGGGAGGGGAATAAATTAAAGTTTTCACACTGTGTACTGTGTTTTACTGATTGGTTGGATATTGCTTATGAAAATTCCATAGTGGTATTTTTTTGGATTCTTAATGTGTAACTTAAACATACTTTGAAGTGGAGGAGAGTCATAAGACAGAACATTTGGCAGGAATTGTCCTTATGAAACAAGAAAAAGAAAATGAAAAGTATTATTAAGCTTCTGTGTTTGTCTAAAAATGTGGCATATGGATGGCATTTAAAACTTTGAATGAATTATACCTAAATCTGGGACAGGGAGGTGACAGTGGAACAGGCTACCAATCAGAACTAGATGACTTTTAAGGCTCCTCCTATTATGAGACTTCAATTTCCAAAGAGAAGAACTAGCAGAGAAATTGTATTTCAGTAATTTTAAGCTCCTTCTGTCTTGTAGAGTCTTGTTATAGTTGTATAAATCAAAAACACAGAATAAGGAACATATTTAACTTTTTTTCATTATAAAATGGTTAGAGGACCCTACCCCCTCTAGATTCCCTGATTTCCCCAGGCCTGCAGCATACAGTAAGATGGGTCCCTGTGCCAGGCCTCAATACTGCCAGGGAATAAAACCAGAGGGAGAGGACCCTCAGTGTCATATCAGGAAGCCCAGTGCCAGAGGACAGACAGGTTCAAAACTGGCTTTTCCTCTGGGCCTGGGTTGGTGCTATAGGCCAAGGGTCATTTTATACTTGGGTATAAATCAATCCCAGTTTGGGAAAAGATTATTTTTAAGCTTAAAAGGCTGACATGTGCCATTATATGTAGTATGTAATATATGTAACATCTTCCAATTCTTTTAAAATAAAATTAATATTTATAATGGATATTTAATGATTGTTATTTTTAAAAACCAGCTTATAATTCCTCGTTATGCATGATTTATCCAAAGTTTCCATAGTTTTATTCAAAATAATAAATGTTAATAAGGTGATAAGGGGTATATTTAATGTATTGTATCAAATTGTGAATAAGAAAGTAGGATGGAGCTTTCTAGAGGTTGGGCCTTAGTTCTGTTATCCTCATTGCTTTTAACCAATAAGTTAAATGAAGTTAGAGTTATGGTCTTCAGGTTAGATTATGGACCAGATCTGTGAGGGTCAGCATGGAAATTCACATTCAACAAGGTAGCACACAGGACCAAGAGCAGCACATGCAATCAACTGGAATAATATAGTAATCCTGTAACTGGGTTTGAAAAAATAATCAACAAAAGATACAATTCAAGGGTTAGGTTGCAGAGAGCTGGCTTGAGAGTAGTTATTATGAAAAAGGCCTCAAGGAGTACGTGTTCAGTATGCTCTAAGATGATAAAGTGGCTGTTAAAAAGGGAGTTGATTTGAGGAAGTATTACTTAGCATTCATGCATATTGGGCTTAGGCTCTAGCCCTGCCACTATCATTGTCTTCTCTGGACTGTGAAGTCACTGAGGACAAGGAAACTAAATTTAATGTCTGTATCACTAGTGCCTAGAATTTCTGGACACTTAGTAGTCACCATCAGGCGTTTATTTAATGAATGAGAAGCAAAGTGACCTTGGTTACTTTTTTACCCTGAGGGGCTCAGCACTCATTAGGACTTGGTGCCTAATTTTATAAAAAGTCACTAAGCTCAAGTGCTTGGATGAAAGGACAGCGTGGATAAAAAGGTTTTTAAAACATGGATGTTAAGGCTGTTTTGCTTGGAGAAGACTTGGGACTGGGACAGTCTTTAGATATTATTTGAAATGCTGGCACTGTCTATCTGGATCCCAGGGCTTGAACTAGGATTTGAGGAAGTCACAGGGAAGCAGATTTCAGTCTGACATTTATTCAGTGCAAGTTTTTTGGTGCTGTAGTATATGATGAAAGATGTAAAGCTGAATAAAGCATTATTTCTGCCCTAGAGTTGTTCACAGCCTAGTCAGGCATATGGATATGTAAACAATGACTGTAACGTGTTATAGATGTAAAGACAAAATAAAGGTTAAAGAGGGCATAAAGGAGCACTCAATTGCAGAGATTTGAGGACATTATTTTTATTTTGAGCTTTAAAAAGATGAATAGGTGTTCTCAGGAGGTAGGGATCTGGCTGAGAGGGAATAATCTGAGCAAAGGTATGAAACAGCCTAATGCATTAGAGAAAAAAGTTCTTTTAGTAAGGCATTTGGGGTTGGGGAAGCTAGAAAAAGAAATGGGAGCTGGTCACACAGGGCCTTGTGTGCCAGACTAAGGGGTTTGTAGTATATATTGTAGGCAGAAGAGATCCATCAACAGATTGCAAGCAAGGAAGTATGTTCACTTTAAAGTTTGAGAAAGAATAGTGTGGAAGCACGTCTCAAATTTAGACTTACTTGTTCCCCCTCTGAACCGTGAATCAGACCATTTCAGGTAGAAGTCTTCCCCGGTTTATCTGATCTACTCGGGGCCTCAGGCTTCTCAGCTGGGAAGAGAGGATGCAAGACCAGACTGAAGAACACGGTTGAGTCCCCAGAACCAAAAGGGGGCCTTTCTGCTTCTTAGCCAGCTACCTCTTCGAGTTTTTCAAATTGTGAGGGGGACCATAAAAGGATGGAAACTTTTAGATGACATTCTACAAATTATTTTTTTCTTTAAATTAAAAGAACCTAGCCAATAAGATAGAGAATGGGCATCTAAGGCATCTCAGAGCTCTCTGATGAAGCCAGGTTGTCAAAGATCATTTGCAAAAGAAGGGAAAACTGGCATGACAAAAGCTACAGAGAGGAGAGTGAAATATAGAAGTGTTTGAAATGTTCAAGCTCACAATAAGCTTAAATTTATAGAAAATGCTAAGGTTGTCAAGAAGGCTTTTTTTTTTTTCTTTTTTAAACCTGAGGGCAAAAAGGAATGGATAAAGTAGTGTAATGGATTGACAATCAGGAAGAACAGAATAACTCAGTTTTTTTTTCTCCTACAAGGAGATATGGCTGGACCAAAATAAAATGACATGAAATTGCAAAAATGAAAAT	
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	GGGGGGCTGCGCGGCCGGGTCGGTGCGCACACGAGAAGGACGCGCGGCCCCCAGCGCTCTTGGGGGCCGCCTCGGAGCATGACCCCCGCGGGCCAGCGCCGCGCGCCTGATCCGAGGAGACCCCGCGCTCCCGCAGCCATGGGCACCGGGGGCCGGCGGGGGGCGGCGGCCGCGCCGCTGCTGGTGGCGGTGGCCGCGCTGCTACTGGGCGCCGCGGGCCACCTGTACCCCGGAGAGGTGTGTCCCGGCATGGATATCCGGAACAACCTCACTAGGTTGCATGAGCTGGAGAATTGCTCTGTCATCGAAGGACACTTGCAGATACTCTTGATGTTCAAAACGAGGCCCGAAGATTTCCGAGACCTCAGTTTCCCCAAACTCATCATGATCACTGATTACTTGCTGCTCTTCCGGGTCTATGGGCTCGAGAGCCTGAAGGACCTGTTCCCCAACCTCACGGTCATCCGGGGATCACGACTGTTCTTTAACTACGCGCTGGTCATCTTCGAGATGGTTCACCTCAAGGAACTCGGCCTCTACAACCTGATGAACATCACCCGGGGTTCTGTCCGCATCGAGAAGAACAATGAGCTCTGTTACTTGGCCACTATCGACTGGTCCCGTATCCTGGATTCCGTGGAGGATAATCACATCGTGTTGAACAAAGATGACAACGAGGAGTGTGGAGACATCTGTCCGGGTACCGCGAAGGGCAAGACCAACTGCCCCGCCACCGTCATCAACGGGCAGTTTGTCGAACGATGTTGGACTCATAGTCACTGCCAGAAAGTTTGCCCGACCATCTGTAAGTCACACGGCTGCACCGCCGAAGGCCTCTGTTGCCACAGCGAGTGCCTGGGCAACTGTTCTCAGCCCGACGACCCCACCAAGTGCGTGGCCTGCCGCAACTTCTACCTGGACGGCAGGTGTGTGGAGACCTGCCCGCCCCCGTACTACCACTTCCAGGACTGGCGCTGTGTGAACTTCAGCTTCTGCCAGGACCTGCACCACAAATGCAAGAACTCGCGGAGGCAGGGCTGCCACCAATACGTCATTCACAACAACAAGTGCATCCCTGAGTGTCCCTCCGGGTACACGATGAATTCCAGCAACTTGCTGTGCACCCCATGCCTGGGTCCCTGTCCCAAGGTGTGCCACCTCCTAGAAGGCGAGAAGACCATCGACTCGGTGACGTCTGCCCAGGAGCTCCGAGGATGCACCGTCATCAACGGGAGTCTGATCATCAACATTCGAGGAGGCAACAATCTGGCAGCTGAGCTAGAAGCCAACCTCGGCCTCATTGAAGAAATTTCAGGGTATCTAAAAATCCGCCGATCCTACGCTCTGGTGTCACTTTCCTTCTTCCGGAAGTTACGTCTGATTCGAGGAGAGACCTTGGAAATTGGGAACTACTCCTTCTATGCCTTGGACAACCAGAACCTAAGGCAGCTCTGGGACTGGAGCAAACACAACCTCACCACCACTCAGGGGAAACTCTTCTTCCACTATAACCCCAAACTCTGCTTGTCAGAAATCCACAAGATGGAAGAAGTTTCAGGAACCAAGGGGCGCCAGGAGAGAAACGACATTGCCCTGAAGACCAATGGGGACAAGGCATCCTGTGAAAATGAGTTACTTAAATTTTCTTACATTCGGACATCTTTTGACAAGATCTTGCTGAGATGGGAGCCGTACTGGCCCCCCGACTTCCGAGACCTCTTGGGGTTCATGCTGTTCTACAAAGAGGCCCCTTATCAGAATGTGACGGAGTTCGATGGGCAGGATGCGTGTGGTTCCAACAGTTGGACGGTGGTAGACATTGACCCACCCCTGAGGTCCAACGACCCCAAATCACAGAACCACCCAGGGTGGCTGATGCGGGGTCTCAAGCCCTGGACCCAGTATGCCATCTTTGTGAAGACCCTGGTCACCTTTTCGGATGAACGCCGGACCTATGGGGCCAAGAGTGACATCATTTATGTCCAGACAGATGCCACCAACCCCTCTGTGCCCCTGGATCCAATCTCAGTGTCTAACTCATCATCCCAGATTATTCTGAAGTGGAAACCACCCTCCGACCCCAATGGCAACATCACCCACTACCTGGTTTTCTGGGAGAGGCAGGCGGAAGACAGTGAGCTGTTCGAGCTGGATTATTGCCTCAAAGGGCTGAAGCTGCCCTCGAGGACCTGGTCTCCACCATTCGAGTCTGAAGATTCTCAGAAGCACAACCAGAGTGAGTATGAGGATTCGGCCGGCGAATGCTGCTCCTGTCCAAAGACAGACTCTCAGATCCTGAAGGAGCTGGAGGAGTCCTCGTTTAGGAAGACGTTTGAGGATTACCTGCACAACGTGGTTTTCGTCCCCAGAAAAACCTCTTCAGGCACTGGTGCCGAGGACCCTAGGCCATCTCGGAAACGCAGGTCCCTTGGCGATGTTGGGAATGTGACGGTGGCCGTGCCCACGGTGGCAGCTTTCCCCAACACTTCCTCGACCAGCGTGCCCACGAGTCCGGAGGAGCACAGGCCTTTTGAGAAGGTGGTGAACAAGGAGTCGCTGGTCATCTCCGGCTTGCGACACTTCACGGGCTATCGCATCGAGCTGCAGGCTTGCAACCAGGACACCCCTGAGGAACGGTGCAGTGTGGCAGCCTACGTCAGTGCGAGGACCATGCCTGAAGCCAAGGCTGATGACATTGTTGGCCCTGTGACGCATGAAATCTTTGAGAACAACGTCGTCCACTTGATGTGGCAGGAGCCGAAGGAGCCCAATGGTCTGATCGTGCTGTATGAAGTGAGTTATCGGCGATATGGTGATGAGGAGCTGCATCTCTGCGTCTCCCGCAAGCACTTCGCTCTGGAACGGGGCTGCAGGCTGCGTGGGCTGTCACCGGGGAACTACAGCGTGCGAATCCGGGCCACCTCCCTTGCGGGCAACGGCTCTTGGACGGAACCCACCTATTTCTACGTGACAGACTATTTAGACGTCCCGTCAAATATTGCAAAAATTATCATCGGCCCCCTCATCTTTGTCTTTCTCTTCAGTGTTGTGATTGGAAGTATTTATCTATTCCTGAGAAAGAGGCAGCCAGATGGGCCGCTGGGACCGCTTTACGCTTCTTCAAACCCTGAGTATCTCAGTGCCAGTGATGTGTTTCCATGCTCTGTGTACGTGCCGGACGAGTGGGAGGTGTCTCGAGAGAAGATCACCCTCCTTCGAGAGCTGGGGCAGGGCTCCTTCGGCATGGTGTATGAGGGCAATGCCAGGGACATCATCAAGGGTGAGGCAGAGACCCGCGTGGCGGTGAAGACGGTCAACGAGTCAGCCAGTCTCCGAGAGCGGATTGAGTTCCTCAATGAGGCCTCGGTCATGAAGGGCTTCACCTGCCATCACGTGGTGCGCCTCCTGGGAGTGGTGTCCAAGGGCCAGCCCACGCTGGTGGTGATGGAGCTGATGGCTCACGGAGACCTGAAGAGCTACCTCCGTTCTCTGCGGCCAGAGGCTGAGAATAATCCTGGCCGCCCTCCCCCTACCCTTCAAGAGATGATTCAGATGGCGGCAGAGATTGCTGACGGGATGGCCTACCTGAACGCCAAGAAGTTTGTGCATCGGGACCTGGCAGCGAGAAACTGCATGGTCGCCCATGATTTTACTGTCAAAATTGGAGACTTTGGAATGACCAGAGACATCTATGAAACGGATTACTACCGGAAAGGGGGCAAGGGTCTGCTCCCTGTACGGTGGATGGCACCGGAGTCCCTGAAGGATGGGGTCTTCACCACTTCTTCTGACATGTGGTCCTTTGGCGTGGTCCTTTGGGAAATCACCAGCTTGGCAGAACAGCCTTACCAAGGCCTGTCTAATGAACAGGTGTTGAAATTTGTCATGGATGGAGGGTATCTGGATCAACCCGACAACTGTCCAGAGAGAGTCACTGACCTCATGCGCATGTGCTGGCAATTCAACCCCAAGATGAGGCCAACCTTCCTGGAGATTGTCAACCTGCTCAAGGACGACCTGCACCCCAGCTTTCCAGAGGTGTCGTTCTTCCACAGCGAGGAGAACAAGGCTCCCGAGAGTGAGGAGCTGGAGATGGAGTTTGAGGACATGGAGAATGTGCCCCTGGACCGTTCCTCGCACTGTCAGAGGGAGGAGGCGGGGGGCCGGGATGGAGGGTCCTCGCTGGGTTTCAAGCGGAGCTACGAGGAACACATCCCTTACACACACATGAACGGAGGCAAGAAAAACGGGCGGATTCTGACCTTGCCTCGGTCCAATCCTTCCTAACAGTGCCTACCGTGGCGGGGGCGGGCAGGGGTTCCCATTTTCGCTTTCCTCTGGTTTGAAAGCCTCTGGAAAACTCAGGATTCTCACGACTCTACCATGTCCAGTGGAGTTCAGAGATCGTTCCTATACATTTCTGTTCATCTTAAGGTGGACTCGTTTGGTTACCAATTTAACTAGTCCTGCAGAGGATTTAACTGTGAACCTGGAGGGCAAGGGGTTTCCACAGTTGCTGCTCCTTTGGGGCAACGACGGTTTCAAACCAGGATTTTGTGTTTTTTCGTTCCCCCCACCCGCCCCCAGCAGATGGAAAGAAAGCACCTGTTTTTACAAATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTGCTGGTGTCTGAGCTTCAGTATAAAAGACAAAACTTCCTGTTTGTGGAACAAAATTTCGAAAGAAAAAACCAAA	
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	CCAGCTGGAGCCCTGAGTGGCTGAGCTCAGGCCTTCGCAGCATTCTTGGGTGGGAGCAGCCACGGGTCAGCCACAAGGGCCACAGCCATGAATGGCACAGAAGGCCCTAACTTCTACGTGCCCTTCTCCAATGCGACGGGTGTGGTACGCAGCCCCTTCGAGTACCCACAGTACTACCTGGCTGAGCCATGGCAGTTCTCCATGCTGGCCGCCTACATGTTTCTGCTGATCGTGCTGGGCTTCCCCATCAACTTCCTCACGCTCTACGTCACCGTCCAGCACAAGAAGCTGCGCACGCCTCTCAACTACATCCTGCTCAACCTAGCCGTGGCTGACCTCTTCATGGTCCTAGGTGGCTTCACCAGCACCCTCTACACCTCTCTGCATGGATACTTCGTCTTCGGGCCCACAGGATGCAATTTGGAGGGCTTCTTTGCCACCCTGGGCGGTGAAATTGCCCTGTGGTCCTTGGTGGTCCTGGCCATCGAGCGGTACGTGGTGGTGTGTAAGCCCATGAGCAACTTCCGCTTCGGGGAGAACCATGCCATCATGGGCGTTGCCTTCACCTGGGTCATGGCGCTGGCCTGCGCCGCACCCCCACTCGCCGGCTGGTCCAGGTACATCCCCGAGGGCCTGCAGTGCTCGTGTGGAATCGACTACTACACGCTCAAGCCGGAGGTCAACAACGAGTCTTTTGTCATCTACATGTTCGTGGTCCACTTCACCATCCCCATGATTATCATCTTTTTCTGCTATGGGCAGCTCGTCTTCACCGTCAAGGAGGCCGCTGCCCAGCAGCAGGAGTCAGCCACCACACAGAAGGCAGAGAAGGAGGTCACCCGCATGGTCATCATCATGGTCATCGCTTTCCTGATCTGCTGGGTGCCCTACGCCAGCGTGGCATTCTACATCTTCACCCACCAGGGCTCCAACTTCGGTCCCATCTTCATGACCATCCCAGCGTTCTTTGCCAAGAGCGCCGCCATCTACAACCCTGTCATCTATATCATGATGAACAAGCAGTTCCGGAACTGCATGCTCACCACCATCTGCTGCGGCAAGAACCCACTGGGTGACGATGAGGCCTCTGCTACCGTGTCCAAGACGGAGACGAGCCAGGTGGCCCCGGCCTAAGACCTGCCTAGGACTCTGTGGCCGACTATAGGCGTCTCCCATCCCCTACACCTTCCCCCAGCCACAGCCATCCCACCAG	
diff -r 000000000000 -r 642d73815dd1 test-data/fx2tab_output4.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fx2tab_output4.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,4 @@
+#id	length	GC	GC-Skew	alphabet	avg.qual	seq.hash
+ENA|AB011145|AB011145.1	4796	38.47	11.65	ACGT	0.00	c19cf05cadbdbc26e22efc2201acfcec
+ENA|M10051|M10051.1	4723	55.24	0.50	ACGT	0.00	4f6bbf79e427ef90b6f31de5023ad241
+ENA|BC112106|BC112106.1	1213	58.78	-15.01	ACGT	0.00	3b099f7df389373bb7e3269efc819599
diff -r 000000000000 -r 642d73815dd1 test-data/input1.fasta.gz
Binary file test-data/input1.fasta.gz has changed
diff -r 000000000000 -r 642d73815dd1 test-data/input1.fastq.gz
Binary file test-data/input1.fastq.gz has changed
diff -r 000000000000 -r 642d73815dd1 test-data/locate_output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output1.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,95 @@
+seqID	patternName	pattern	strand	start	end	matched
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	251	256	ATAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	435	440	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	660	665	ATAGAG
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	741	746	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	852	857	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1142	1147	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1320	1325	ATAGGT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1621	1626	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1778	1783	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1784	1789	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	1810	1815	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2038	2043	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2120	2125	CTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2235	2240	ATAGTT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2243	2248	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2318	2323	CTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2527	2532	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2549	2554	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2603	2608	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2651	2656	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2726	2731	ATAGTT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2744	2749	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	2902	2907	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3041	3046	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3488	3493	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3539	3544	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3675	3680	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3739	3744	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3770	3775	ATAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3825	3830	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3862	3867	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	3870	3875	ATAGGT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4052	4057	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4068	4073	AGAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4080	4085	ACAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4388	4393	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4446	4451	ATAGAG
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4500	4505	AAAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4563	4568	ATAGAA
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4607	4612	ATAGAA
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4675	4680	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	+	4692	4697	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4603	4608	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4459	4464	TTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4223	4228	GTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4072	4077	ATGGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	4052	4057	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	3634	3639	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	3566	3571	ATAGAC
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2918	2923	ACAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2778	2783	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2709	2714	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2644	2649	ATAAAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2603	2608	ATATAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	2531	2536	ATTGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1734	1739	ATTGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1601	1606	ACAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1438	1443	ATAGAA
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1422	1427	ATAGGT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1329	1334	ATAGAG
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1146	1151	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	1121	1126	ATACAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	811	816	ATAGCT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	764	769	GTAGAT
+ENA|AB011145|AB011145.1	ATAGAT	ATAGAT	-	656	661	ATAGTT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	250	255	ATGGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	664	669	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	1987	1992	ACAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	3540	3545	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	3561	3566	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	3886	3891	ATGGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	4400	4405	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	+	4413	4418	ATACAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3688	3693	ATAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3065	3070	ATAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3061	3066	ATAAAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	3025	3030	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	2956	2961	ATAGGT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	2828	2833	AGAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	2719	2724	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1975	1980	ATAAAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1951	1956	ATAGGT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1909	1914	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1659	1664	AAAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1417	1422	ATAGAA
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	1319	1324	TTAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	802	807	ACAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	691	696	ACAGAT
+ENA|M10051|M10051.1	ATAGAT	ATAGAT	-	415	420	ATAGAC
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	+	386	391	ATGGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	1000	1005	ATAGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	985	990	GTAGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	742	747	AAAGAT
+ENA|BC112106|BC112106.1	ATAGAT	ATAGAT	-	700	705	GTAGAT
diff -r 000000000000 -r 642d73815dd1 test-data/locate_output2.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output2.bed	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,202 @@
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	136	139	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	174	177	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	254	257	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	269	272	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	275	278	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	296	299	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	322	325	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	353	356	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	377	380	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	479	482	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	484	487	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	487	490	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	490	493	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	692	695	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	695	698	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	725	728	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	796	799	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	814	817	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	827	830	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	855	858	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	890	893	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	940	943	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	977	980	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1028	1031	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1120	1123	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1124	1127	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1145	1148	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1220	1223	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1265	1268	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1346	1349	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1441	1444	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1510	1513	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1629	1632	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1693	1696	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1709	1712	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1730	1733	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1866	1869	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1902	1905	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1972	1975	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	1991	1994	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2028	2031	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2037	2040	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2041	2044	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2060	2063	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2123	2126	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2147	2150	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2294	2297	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2358	2361	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2578	2581	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2590	2593	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2597	2600	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2606	2609	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2650	2653	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2661	2664	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2701	2704	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2705	2708	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2747	2750	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2777	2780	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2811	2814	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2875	2878	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2889	2892	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2908	2911	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2933	2936	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	2981	2984	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3093	3096	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3125	3128	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3135	3138	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3191	3194	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3278	3281	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3342	3345	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3346	3349	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3451	3454	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3487	3490	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3491	3494	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3554	3557	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3668	3671	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3671	3674	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3678	3681	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3738	3741	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3744	3747	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3753	3756	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3773	3776	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3865	3868	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3925	3928	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	3938	3941	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4000	4003	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4100	4103	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4262	4265	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4377	4380	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4391	4394	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4452	4455	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4483	4486	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4531	4534	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4577	4580	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4613	4616	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4674	4677	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4691	4694	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4750	4753	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4769	4772	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4774	4777	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4788	4791	A[TU]G	0	+
+ENA|AB011145|AB011145.1 Homo sapiens mRNA for KIAA0573 protein, partial cds.	4794	4797	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	78	81	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	138	141	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	249	252	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	280	283	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	330	333	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	384	387	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	418	421	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	510	513	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	546	549	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	586	589	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	667	670	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	761	764	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1013	1016	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1098	1101	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1127	1130	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1214	1217	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1420	1423	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1542	1545	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1603	1606	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1627	1630	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1682	1685	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1728	1731	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1759	1762	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1774	1777	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1783	1786	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1875	1878	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1903	1906	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1939	1942	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1954	1957	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1978	1981	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	1990	1993	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2083	2086	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2242	2245	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2261	2264	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2434	2437	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2443	2446	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2670	2673	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2689	2692	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2713	2716	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2745	2748	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2770	2773	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2788	2791	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2809	2812	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	2815	2818	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3091	3094	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3148	3151	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3158	3161	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3243	3246	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3250	3253	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3259	3262	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3355	3358	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3369	3372	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3444	3447	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3453	3456	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3543	3546	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3552	3555	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3576	3579	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3633	3636	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3643	3646	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3675	3678	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3691	3694	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3744	3747	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3766	3769	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3792	3795	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3862	3865	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3885	3888	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3889	3892	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3942	3945	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3948	3951	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	3972	3975	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4092	4095	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4107	4110	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4114	4117	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4168	4171	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4227	4230	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4383	4386	A[TU]G	0	+
+ENA|M10051|M10051.1 Human insulin receptor mRNA, complete cds.	4590	4593	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	87	90	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	91	94	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	130	133	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	188	191	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	201	204	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	216	219	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	342	345	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	385	388	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	413	416	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	513	516	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	541	544	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	549	552	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	573	576	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	705	708	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	732	735	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	754	757	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	843	846	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	855	858	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	948	951	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1008	1011	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1011	1014	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1035	1038	A[TU]G	0	+
+ENA|BC112106|BC112106.1 Homo sapiens rhodopsin, mRNA (cDNA clone MGC:138311 IMAGE:8327574), complete cds.	1078	1081	A[TU]G	0	+
diff -r 000000000000 -r 642d73815dd1 test-data/locate_output3.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/locate_output3.gtf	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,4 @@
+ENA|AB011145|AB011145.1	SeqKit	location	2270	2276	0	+	.	gene_id "test_motif2"; 
+ENA|AB011145|AB011145.1	SeqKit	location	2642	2648	0	+	.	gene_id "test_motif2"; 
+ENA|AB011145|AB011145.1	SeqKit	location	2655	2661	0	+	.	gene_id "test_motif2"; 
+ENA|AB011145|AB011145.1	SeqKit	location	2771	2777	0	+	.	gene_id "test_motif2"; 
diff -r 000000000000 -r 642d73815dd1 test-data/motif_sequence.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_sequence.fasta	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,4 @@
+>test_motif
+ATATACTAT
+>test_motif2
+ATATTTA
diff -r 000000000000 -r 642d73815dd1 test-data/stats_output1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats_output1.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,2 @@
+file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	Q20(%)	Q30(%)	GC(%)
+input1_fastq_gz	FASTQ	DNA	5	505	101	101.0	101	50.5	101.0	50.5	0	101	98.02	89.31	35.45
diff -r 000000000000 -r 642d73815dd1 test-data/stats_output2.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats_output2.tabular	Thu Nov 03 19:35:37 2022 +0000
@@ -0,0 +1,2 @@
+file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	Q20(%)	Q30(%)	GC(%)
+input1_fasta_gz	FASTA	DNA	3	10732	1213	3577.3	4796	2968.0	4723.0	4759.5	0	4723	0.00	0.00	48.15