changeset 0:14f4c7a8a962 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/naltorfs/ commit cbedf7b5968b45a08df88d4ad799951d6f50a2bd"
author iuc
date Mon, 11 Apr 2022 20:37:19 +0000
parents
children
files find_nested_alt_orfs.xml macros.xml test-data/aa_freq_from_bicodon.tabular test-data/all_fasta.loc test-data/bed_out.bed test-data/bicodon_out.tabular test-data/cds_fasta_out.fasta test-data/codon_freq_from_bicodon.tabular test-data/codon_freq_from_bicodon_log.txt test-data/codon_out.tabular test-data/find_naltorfs_log.txt test-data/gencode_canonical.hg38.chr6_GL0002508.bed test-data/hg38.chr6_GL000250v2_alt.2bit.gz test-data/naltorfs_fasta_out.fasta test-data/peptide_fasta_out.fasta test-data/twobit.loc tool-data/all_fasta.loc.sample tool-data/twobit.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test
diffstat 20 files changed, 425 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_nested_alt_orfs.xml	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,115 @@
+<tool id="find_nested_alt_orfs" name="Find Nested Alternate ORFs (nAlt-ORFs)" version="@TOOL_VERSION@" profile="20.05">
+    <description>from BED and 2bit/FASTA</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements">
+        <requirement type="package" version="377">ucsc-fatotwobit</requirement>
+    </expand>
+    <version_command>find_nested_alt_orfs.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $ref.ref_source == 'history':
+            #if  $ref.ref_file.is_of_type('fasta'):
+                #set $twobit_filename = "out.2bit"
+                faToTwoBit '${ref.ref_file}' '$twobit_filename' -stripVersion &&
+            #else:
+                #set $twobit_filename = $ref.ref_file
+            #end if
+        #else:
+            #set $twobit_filename = $ref.ref_loc.fields.path
+        #end if
+        find_nested_alt_orfs.py
+            --twobit '$twobit_filename'
+
+            --min_length '$min_length'
+
+            --reference '${input.metadata.dbkey}'
+
+            --bed '$input'
+
+            #if $no_canonical_cds:
+                --no_canonical_cds '$no_canonical_cds'
+            #end if
+
+            --translation_table '$translation_table'
+
+            --bed_out '$bed_out'
+
+            --peptide_fasta_out '$peptide_fasta_out'
+
+            --naltorfs_fasta_out '$naltorfs_fasta_out'
+
+            --cds_fasta_out '$cds_fasta_out'
+
+            $unique_sequences
+
+            #if $write_log:
+                --log '$log'
+            #end if
+    ]]></command>
+    <inputs>
+        <param argument="--bed" name="input" type="data" format="bed" label="Gene BED" help="A BED file with 12 columns"/>
+        <conditional name="ref">
+            <param name="ref_source" type="select" label="Source for Genomic Sequence Data">
+                <option value="cached">Locally cached genome</option>
+                <option value="history">History dataset genome</option>
+            </param>
+            <when value="cached">
+                <param argument="--twobit" name="ref_loc" type="select" label="Select reference genome">
+                    <options from_data_table="twobit"/>
+                </param>
+            </when>
+            <when value="history">
+                <param argument="--twobit" name="ref_file" type="data" format="twobit,fasta" label="Reference genome"/>
+            </when>
+        </conditional>
+        <param argument="--min_length" type="integer" value="150" min="1" label="Minimum length of peptide translation to report"/>
+        <param argument="--unique_sequences" type="boolean" truevalue="--unique_sequences" falsevalue="" checked="True" label="Only report the first unique occurrence of an alternate sequence"/>
+        <param argument="--no_canonical_cds" type="data" format="bed" optional="True" label="Do not report any alternate sequences that match a provided canonical CDS" help="A BED file with 12 columns"/>
+        <expand macro="translation_table_select_parameter"/>
+        <param name="write_log" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Create log file"/>
+    </inputs>
+    <outputs>
+        <data name="bed_out" format="bed" label="Find Nested nAlt-ORFs on ${on_string}: nAlt-ORFs.proBed">
+            <actions>
+                <action name="column_names" type="metadata" default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,proteinAccession,peptideSequence,uniqueness,genomeReferenceVersion,psmScore,fdr,modifications,charge,expMassToCharge,calcMassToCharge,psmRank,datasetID,uri"/>
+            </actions>
+        </data>
+        <data name="peptide_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: peptide.fasta"/>
+        <data name="naltorfs_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: nAlt-ORFs.fasta"/>
+        <data name="cds_fasta_out" format="fasta" label="Find nAlt-ORFs on ${on_string}: canonical CDS.fasta"/>
+        <data name="log" format="txt" label="Find nAlt-ORFs on ${on_string}: log.txt">
+            <filter>write_log</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="gencode_canonical.hg38.chr6_GL0002508.bed" dbkey="hg38" ftype="bed12"/>
+            <conditional name="ref">
+                <param name="ref_source" value="history"/>
+                <param name="ref_file" value="hg38.chr6_GL000250v2_alt.2bit.gz" dbkey="hg38" ftype="twobit"/>
+            </conditional>
+            <param name="min_length" value="150"/>
+            <param name="unique_sequences" value="true"/>
+            <param name="no_canonical_cds" value="gencode_canonical.hg38.chr6_GL0002508.bed" dbkey="hg38" ftype="bed12"/>
+            <param name="translation_table" value="1"/>
+            <param name="write_log" value="true"/>
+            <output name="bed_out" value="bed_out.bed"/>
+            <output name="peptide_fasta_out" value="peptide_fasta_out.fasta"/>
+            <output name="naltorfs_fasta_out" value="naltorfs_fasta_out.fasta"/>
+            <output name="cds_fasta_out" value="cds_fasta_out.fasta"/>
+            <output name="log" value="find_naltorfs_log.txt"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Find Nested Alternate Open Reading Frames (nAlt-ORFs).
+
+Using a BED12 file containing the location of genes, and a matching reference genome,
+this tool searches in the alternate reading frames of the provided canonical coding sequence,
+and outputs nested alternate ORFs which match the provided thresholds.
+
+Translation table identifiers are based upon NCBI standards (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,63 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.2</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">naltorfs</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="translation_table_select_parameter">
+        <param argument="--translation_table" type="select" label="Translation table">
+            <option value="1" selected="true">Table 1 Standard, SGC0</option>
+            <option value="2">Table 2 Vertebrate Mitochondrial, SGC1</option>
+            <option value="3">Table 3 Yeast Mitochondrial, SGC2</option>
+            <option value="4">Table 4 Mold Mitochondrial, Protozoan Mitochondrial, Coelenterate Mitochondrial, Mycoplasma, Spiroplasma, SGC3</option>
+            <option value="5">Table 5 Invertebrate Mitochondrial, SGC4</option>
+            <option value="6">Table 6 Ciliate Nuclear, Dasycladacean Nuclear, Hexamita Nuclear, SGC5</option>
+            <option value="9">Table 9 Echinoderm Mitochondrial, Flatworm Mitochondrial, SGC8</option>
+            <option value="10">Table 10 Euplotid Nuclear, SGC9</option>
+            <option value="11">Table 11 Bacterial, Archaeal, Plant Plastid</option>
+            <option value="12">Table 12 Alternative Yeast Nuclear</option>
+            <option value="13">Table 13 Ascidian Mitochondrial</option>
+            <option value="14">Table 14 Alternative Flatworm Mitochondrial</option>
+            <option value="15">Table 15 Blepharisma Macronuclear</option>
+            <option value="16">Table 16 Chlorophycean Mitochondrial</option>
+            <option value="21">Table 21 Trematode Mitochondrial</option>
+            <option value="22">Table 22 Scenedesmus obliquus Mitochondrial</option>
+            <option value="23">Table 23 Thraustochytrium Mitochondrial</option>
+            <option value="24">Table 24 Pterobranchia Mitochondrial</option>
+            <option value="25">Table 25 Candidate Division SR1, Gracilibacteria</option>
+            <option value="26">Table 26 Pachysolen tannophilus Nuclear</option>
+            <option value="27">Table 27 Karyorelict Nuclear</option>
+            <option value="28">Table 28 Condylostoma Nuclear</option>
+            <option value="29">Table 29 Mesodinium Nuclear</option>
+            <option value="30">Table 30 Peritrich Nuclear</option>
+            <option value="31">Table 31 Blastocrithidia Nuclear</option>
+            <option value="32">Table 32 Balanophoraceae Plastid</option>
+            <option value="33">Table 33 Cephalodiscidae Mitochondrial</option>
+        </param>
+    </xml>
+    <xml name="edam_ontology">
+        <edam_topics>
+            <edam_topic>topic_0622</edam_topic>
+            <edam_topic>topic_0091</edam_topic>
+        </edam_topics>
+        <edam_operations>
+            <edam_operation>operation_0286</edam_operation>
+            <edam_operation>operation_0284</edam_operation>
+            <edam_operation>operation_0436</edam_operation>
+            <edam_operation>operation_0362</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @UNPUBLISHED{nAltORFs,
+                    author = "Kommireddy Vasu and Debjit Khan and Iyappan Ramachandiran and Daniel Blankenberg and Paul L. Fox",
+                    title = "Nested Alternate Open Reading Frames and their Encoded Proteins: The Hidden Orfeome",
+                    year = "2022"
+                }
+            </citation>
+        </citations>
+    </xml>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/aa_freq_from_bicodon.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,5 @@
+#frame	aa_count	*	A	C	D	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
+2-counts	855	20	74	27	11	20	27	52	15	42	18	95	31	20	81	20	72	86	59	44	26	15
+2-percent	855	2.3391812865497074724885351316	8.6549707602339189804752095370	3.1578947368421053099041273526	1.2865497076023393319132992474	2.3391812865497074724885351316	3.1578947368421053099041273526	6.0818713450292394284701913421	1.7543859649122806043664013487	4.9122807017543861363151336263	2.1052631578947367252396816184	11.1111111111111107163651467999	3.6257309941520468044018343790	2.3391812865497074724885351316	9.4736842105263168178908017580	2.3391812865497074724885351316	8.4210526315789469009587264736	10.0584795321637425757899109158	6.9005847953216372658857835631	5.1461988304093573276531969896	3.0409356725146197142350956710	1.7543859649122806043664013487
+3-counts	855	42	62	55	22	41	15	71	28	12	6	69	7	6	104	42	70	91	42	27	28	15
+3-percent	855	4.9122807017543861363151336263	7.2514619883040936088036687579	6.4327485380116957713880765368	2.5730994152046786638265984948	4.7953216374269000965568920947	1.7543859649122806043664013487	8.3040935672514617493789046421	3.2748538011695909055731590342	1.4035087719298244834931210789	0.7017543859649122417465605395	8.0701754385964914462192609790	0.8187134502923977263932897586	0.7017543859649122417465605395	12.1637426900584788569403826841	4.9122807017543861363151336263	8.1871345029239765977990828105	10.6432748538011701100458594738	4.9122807017543861363151336263	3.1578947368421053099041273526	3.2748538011695909055731590342	1.7543859649122806043664013487
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bed_out.bed	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,4 @@
+chr6_GL000250v2_alt	938210	938801	ENST00000432222.1	0	-	938210	938801	12,12,120	1	591	0	ENST00000432222.1_f2_40_3	MAQNQASVLKNQAPVTRTQAPITGTLCQDARSNSHPVKPSRLNVFCCPHCSLTFSKKSYLSRHQKAHLTEPPNYCFHCSKSFSSFSRLVRHQQTHWKQKSYLCPICDLSFGEKEGLMDHWRGYKGKDLCQSSHHKCRVILGQWLGFSHDVPTMAGEEWKHGGDQSPPRIHTPRRRGLREKACKGDKTKEAVSILKHK	unique	hg38	.	.	.	.	.	.	.	.	.
+chr6_GL000250v2_alt	2862985	2871389	ENST00000448800.5	0	-	2862985	2871389	12,12,120	8	14,148,145,110,132,119,184,78	0,342,616,859,2343,4930,6063,8326	ENST00000448800.5_f3_53_3	MCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR	unique	hg38	.	.	.	.	.	.	.	.	.
+chr6_GL000250v2_alt	3481820	3484425	ENST00000445122.5	0	-	3481820	3484425	12,12,120	4	176,186,216,19	0,314,1145,2586	ENST00000445122.5_f3_80_1	MSSEKSGDSLRGPTSPAAARCRRPAPAGASPDCPGPWLRGAHARGDCGHAAAGGLRSARIPPAAAALHCLRAGLPGGHAICRRDPGGNRSDLHSPPAAPGPRAGPTGAEAPATRLHAHRGADHHLLLLAYWHHCHLQGRAGAHGLGPRRHGVGRDRFTRGPELLLHLPGRGHRGHGALYHPHRSHHHRRAAPRELLGSL	unique	hg38	.	.	.	.	.	.	.	.	.
+chr6_GL000250v2_alt	3503057	3504078	ENST00000430777.2	0	-	3503057	3504078	12,12,120	3	145,134,180	0,481,841	ENST00000430777.2_f3_20_373	MDAAAAALPAAALPAAHPVVLQPQCQVLLQDGLLQWLDPLPGCARHPCVCRARTQRREHEDLASNAAPHQIPVRDPSGGARGSPLPSLAALCCCLQPPELSRSAWDDGGTARPLCAHCQARATVGWLCRAGLLAGRSHLHRPEAHGGCHQCHV	unique	hg38	.	.	.	.	.	.	.	.	.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bicodon_out.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,2 @@
+Division	Assembly	Taxid	Species	Organelle	Translation Table	# CDS	# Codon Pairs	aaaaaa	aaaaac	aaaaag	aaaaat	aaaaca	aaaacc	aaaacg	aaaact	aaaaga	aaaagc	aaaagg	aaaagt	aaaata	aaaatc	aaaatg	aaaatt	aaacaa	aaacac	aaacag	aaacat	aaacca	aaaccc	aaaccg	aaacct	aaacga	aaacgc	aaacgg	aaacgt	aaacta	aaactc	aaactg	aaactt	aaagaa	aaagac	aaagag	aaagat	aaagca	aaagcc	aaagcg	aaagct	aaagga	aaaggc	aaaggg	aaaggt	aaagta	aaagtc	aaagtg	aaagtt	aaataa	aaatac	aaatag	aaatat	aaatca	aaatcc	aaatcg	aaatct	aaatga	aaatgc	aaatgg	aaatgt	aaatta	aaattc	aaattg	aaattt	aacaaa	aacaac	aacaag	aacaat	aacaca	aacacc	aacacg	aacact	aacaga	aacagc	aacagg	aacagt	aacata	aacatc	aacatg	aacatt	aaccaa	aaccac	aaccag	aaccat	aaccca	aacccc	aacccg	aaccct	aaccga	aaccgc	aaccgg	aaccgt	aaccta	aacctc	aacctg	aacctt	aacgaa	aacgac	aacgag	aacgat	aacgca	aacgcc	aacgcg	aacgct	aacgga	aacggc	aacggg	aacggt	aacgta	aacgtc	aacgtg	aacgtt	aactaa	aactac	aactag	aactat	aactca	aactcc	aactcg	aactct	aactga	aactgc	aactgg	aactgt	aactta	aacttc	aacttg	aacttt	aagaaa	aagaac	aagaag	aagaat	aagaca	aagacc	aagacg	aagact	aagaga	aagagc	aagagg	aagagt	aagata	aagatc	aagatg	aagatt	aagcaa	aagcac	aagcag	aagcat	aagcca	aagccc	aagccg	aagcct	aagcga	aagcgc	aagcgg	aagcgt	aagcta	aagctc	aagctg	aagctt	aaggaa	aaggac	aaggag	aaggat	aaggca	aaggcc	aaggcg	aaggct	aaggga	aagggc	aagggg	aagggt	aaggta	aaggtc	aaggtg	aaggtt	aagtaa	aagtac	aagtag	aagtat	aagtca	aagtcc	aagtcg	aagtct	aagtga	aagtgc	aagtgg	aagtgt	aagtta	aagttc	aagttg	aagttt	aataaa	aataac	aataag	aataat	aataca	aatacc	aatacg	aatact	aataga	aatagc	aatagg	aatagt	aatata	aatatc	aatatg	aatatt	aatcaa	aatcac	aatcag	aatcat	aatcca	aatccc	aatccg	aatcct	aatcga	aatcgc	aatcgg	aatcgt	aatcta	aatctc	aatctg	aatctt	aatgaa	aatgac	aatgag	aatgat	aatgca	aatgcc	aatgcg	aatgct	aatgga	aatggc	aatggg	aatggt	aatgta	aatgtc	aatgtg	aatgtt	aattaa	aattac	aattag	aattat	aattca	aattcc	aattcg	aattct	aattga	aattgc	aattgg	aattgt	aattta	aatttc	aatttg	aatttt	acaaaa	acaaac	acaaag	acaaat	acaaca	acaacc	acaacg	acaact	acaaga	acaagc	acaagg	acaagt	acaata	acaatc	acaatg	acaatt	acacaa	acacac	acacag	acacat	acacca	acaccc	acaccg	acacct	acacga	acacgc	acacgg	acacgt	acacta	acactc	acactg	acactt	acagaa	acagac	acagag	acagat	acagca	acagcc	acagcg	acagct	acagga	acaggc	acaggg	acaggt	acagta	acagtc	acagtg	acagtt	acataa	acatac	acatag	acatat	acatca	acatcc	acatcg	acatct	acatga	acatgc	acatgg	acatgt	acatta	acattc	acattg	acattt	accaaa	accaac	accaag	accaat	accaca	accacc	accacg	accact	accaga	accagc	accagg	accagt	accata	accatc	accatg	accatt	acccaa	acccac	acccag	acccat	acccca	accccc	accccg	acccct	acccga	acccgc	acccgg	acccgt	acccta	accctc	accctg	accctt	accgaa	accgac	accgag	accgat	accgca	accgcc	accgcg	accgct	accgga	accggc	accggg	accggt	accgta	accgtc	accgtg	accgtt	acctaa	acctac	acctag	acctat	acctca	acctcc	acctcg	acctct	acctga	acctgc	acctgg	acctgt	acctta	accttc	accttg	accttt	acgaaa	acgaac	acgaag	acgaat	acgaca	acgacc	acgacg	acgact	acgaga	acgagc	acgagg	acgagt	acgata	acgatc	acgatg	acgatt	acgcaa	acgcac	acgcag	acgcat	acgcca	acgccc	acgccg	acgcct	acgcga	acgcgc	acgcgg	acgcgt	acgcta	acgctc	acgctg	acgctt	acggaa	acggac	acggag	acggat	acggca	acggcc	acggcg	acggct	acggga	acgggc	acgggg	acgggt	acggta	acggtc	acggtg	acggtt	acgtaa	acgtac	acgtag	acgtat	acgtca	acgtcc	acgtcg	acgtct	acgtga	acgtgc	acgtgg	acgtgt	acgtta	acgttc	acgttg	acgttt	actaaa	actaac	actaag	actaat	actaca	actacc	actacg	actact	actaga	actagc	actagg	actagt	actata	actatc	actatg	actatt	actcaa	actcac	actcag	actcat	actcca	actccc	actccg	actcct	actcga	actcgc	actcgg	actcgt	actcta	actctc	actctg	actctt	actgaa	actgac	actgag	actgat	actgca	actgcc	actgcg	actgct	actgga	actggc	actggg	actggt	actgta	actgtc	actgtg	actgtt	acttaa	acttac	acttag	acttat	acttca	acttcc	acttcg	acttct	acttga	acttgc	acttgg	acttgt	acttta	actttc	actttg	actttt	agaaaa	agaaac	agaaag	agaaat	agaaca	agaacc	agaacg	agaact	agaaga	agaagc	agaagg	agaagt	agaata	agaatc	agaatg	agaatt	agacaa	agacac	agacag	agacat	agacca	agaccc	agaccg	agacct	agacga	agacgc	agacgg	agacgt	agacta	agactc	agactg	agactt	agagaa	agagac	agagag	agagat	agagca	agagcc	agagcg	agagct	agagga	agaggc	agaggg	agaggt	agagta	agagtc	agagtg	agagtt	agataa	agatac	agatag	agatat	agatca	agatcc	agatcg	agatct	agatga	agatgc	agatgg	agatgt	agatta	agattc	agattg	agattt	agcaaa	agcaac	agcaag	agcaat	agcaca	agcacc	agcacg	agcact	agcaga	agcagc	agcagg	agcagt	agcata	agcatc	agcatg	agcatt	agccaa	agccac	agccag	agccat	agccca	agcccc	agcccg	agccct	agccga	agccgc	agccgg	agccgt	agccta	agcctc	agcctg	agcctt	agcgaa	agcgac	agcgag	agcgat	agcgca	agcgcc	agcgcg	agcgct	agcgga	agcggc	agcggg	agcggt	agcgta	agcgtc	agcgtg	agcgtt	agctaa	agctac	agctag	agctat	agctca	agctcc	agctcg	agctct	agctga	agctgc	agctgg	agctgt	agctta	agcttc	agcttg	agcttt	aggaaa	aggaac	aggaag	aggaat	aggaca	aggacc	aggacg	aggact	aggaga	aggagc	aggagg	aggagt	aggata	aggatc	aggatg	aggatt	aggcaa	aggcac	aggcag	aggcat	aggcca	aggccc	aggccg	aggcct	aggcga	aggcgc	aggcgg	aggcgt	aggcta	aggctc	aggctg	aggctt	agggaa	agggac	agggag	agggat	agggca	agggcc	agggcg	agggct	agggga	aggggc	aggggg	aggggt	agggta	agggtc	agggtg	agggtt	aggtaa	aggtac	aggtag	aggtat	aggtca	aggtcc	aggtcg	aggtct	aggtga	aggtgc	aggtgg	aggtgt	aggtta	aggttc	aggttg	aggttt	agtaaa	agtaac	agtaag	agtaat	agtaca	agtacc	agtacg	agtact	agtaga	agtagc	agtagg	agtagt	agtata	agtatc	agtatg	agtatt	agtcaa	agtcac	agtcag	agtcat	agtcca	agtccc	agtccg	agtcct	agtcga	agtcgc	agtcgg	agtcgt	agtcta	agtctc	agtctg	agtctt	agtgaa	agtgac	agtgag	agtgat	agtgca	agtgcc	agtgcg	agtgct	agtgga	agtggc	agtggg	agtggt	agtgta	agtgtc	agtgtg	agtgtt	agttaa	agttac	agttag	agttat	agttca	agttcc	agttcg	agttct	agttga	agttgc	agttgg	agttgt	agttta	agtttc	agtttg	agtttt	ataaaa	ataaac	ataaag	ataaat	ataaca	ataacc	ataacg	ataact	ataaga	ataagc	ataagg	ataagt	ataata	ataatc	ataatg	ataatt	atacaa	atacac	atacag	atacat	atacca	ataccc	ataccg	atacct	atacga	atacgc	atacgg	atacgt	atacta	atactc	atactg	atactt	atagaa	atagac	atagag	atagat	atagca	atagcc	atagcg	atagct	atagga	ataggc	ataggg	ataggt	atagta	atagtc	atagtg	atagtt	atataa	atatac	atatag	atatat	atatca	atatcc	atatcg	atatct	atatga	atatgc	atatgg	atatgt	atatta	atattc	atattg	atattt	atcaaa	atcaac	atcaag	atcaat	atcaca	atcacc	atcacg	atcact	atcaga	atcagc	atcagg	atcagt	atcata	atcatc	atcatg	atcatt	atccaa	atccac	atccag	atccat	atccca	atcccc	atcccg	atccct	atccga	atccgc	atccgg	atccgt	atccta	atcctc	atcctg	atcctt	atcgaa	atcgac	atcgag	atcgat	atcgca	atcgcc	atcgcg	atcgct	atcgga	atcggc	atcggg	atcggt	atcgta	atcgtc	atcgtg	atcgtt	atctaa	atctac	atctag	atctat	atctca	atctcc	atctcg	atctct	atctga	atctgc	atctgg	atctgt	atctta	atcttc	atcttg	atcttt	atgaaa	atgaac	atgaag	atgaat	atgaca	atgacc	atgacg	atgact	atgaga	atgagc	atgagg	atgagt	atgata	atgatc	atgatg	atgatt	atgcaa	atgcac	atgcag	atgcat	atgcca	atgccc	atgccg	atgcct	atgcga	atgcgc	atgcgg	atgcgt	atgcta	atgctc	atgctg	atgctt	atggaa	atggac	atggag	atggat	atggca	atggcc	atggcg	atggct	atggga	atgggc	atgggg	atgggt	atggta	atggtc	atggtg	atggtt	atgtaa	atgtac	atgtag	atgtat	atgtca	atgtcc	atgtcg	atgtct	atgtga	atgtgc	atgtgg	atgtgt	atgtta	atgttc	atgttg	atgttt	attaaa	attaac	attaag	attaat	attaca	attacc	attacg	attact	attaga	attagc	attagg	attagt	attata	attatc	attatg	attatt	attcaa	attcac	attcag	attcat	attcca	attccc	attccg	attcct	attcga	attcgc	attcgg	attcgt	attcta	attctc	attctg	attctt	attgaa	attgac	attgag	attgat	attgca	attgcc	attgcg	attgct	attgga	attggc	attggg	attggt	attgta	attgtc	attgtg	attgtt	atttaa	atttac	atttag	atttat	atttca	atttcc	atttcg	atttct	atttga	atttgc	atttgg	atttgt	atttta	attttc	attttg	attttt	caaaaa	caaaac	caaaag	caaaat	caaaca	caaacc	caaacg	caaact	caaaga	caaagc	caaagg	caaagt	caaata	caaatc	caaatg	caaatt	caacaa	caacac	caacag	caacat	caacca	caaccc	caaccg	caacct	caacga	caacgc	caacgg	caacgt	caacta	caactc	caactg	caactt	caagaa	caagac	caagag	caagat	caagca	caagcc	caagcg	caagct	caagga	caaggc	caaggg	caaggt	caagta	caagtc	caagtg	caagtt	caataa	caatac	caatag	caatat	caatca	caatcc	caatcg	caatct	caatga	caatgc	caatgg	caatgt	caatta	caattc	caattg	caattt	cacaaa	cacaac	cacaag	cacaat	cacaca	cacacc	cacacg	cacact	cacaga	cacagc	cacagg	cacagt	cacata	cacatc	cacatg	cacatt	caccaa	caccac	caccag	caccat	caccca	cacccc	cacccg	caccct	caccga	caccgc	caccgg	caccgt	caccta	cacctc	cacctg	cacctt	cacgaa	cacgac	cacgag	cacgat	cacgca	cacgcc	cacgcg	cacgct	cacgga	cacggc	cacggg	cacggt	cacgta	cacgtc	cacgtg	cacgtt	cactaa	cactac	cactag	cactat	cactca	cactcc	cactcg	cactct	cactga	cactgc	cactgg	cactgt	cactta	cacttc	cacttg	cacttt	cagaaa	cagaac	cagaag	cagaat	cagaca	cagacc	cagacg	cagact	cagaga	cagagc	cagagg	cagagt	cagata	cagatc	cagatg	cagatt	cagcaa	cagcac	cagcag	cagcat	cagcca	cagccc	cagccg	cagcct	cagcga	cagcgc	cagcgg	cagcgt	cagcta	cagctc	cagctg	cagctt	caggaa	caggac	caggag	caggat	caggca	caggcc	caggcg	caggct	caggga	cagggc	cagggg	cagggt	caggta	caggtc	caggtg	caggtt	cagtaa	cagtac	cagtag	cagtat	cagtca	cagtcc	cagtcg	cagtct	cagtga	cagtgc	cagtgg	cagtgt	cagtta	cagttc	cagttg	cagttt	cataaa	cataac	cataag	cataat	cataca	catacc	catacg	catact	cataga	catagc	catagg	catagt	catata	catatc	catatg	catatt	catcaa	catcac	catcag	catcat	catcca	catccc	catccg	catcct	catcga	catcgc	catcgg	catcgt	catcta	catctc	catctg	catctt	catgaa	catgac	catgag	catgat	catgca	catgcc	catgcg	catgct	catgga	catggc	catggg	catggt	catgta	catgtc	catgtg	catgtt	cattaa	cattac	cattag	cattat	cattca	cattcc	cattcg	cattct	cattga	cattgc	cattgg	cattgt	cattta	catttc	catttg	catttt	ccaaaa	ccaaac	ccaaag	ccaaat	ccaaca	ccaacc	ccaacg	ccaact	ccaaga	ccaagc	ccaagg	ccaagt	ccaata	ccaatc	ccaatg	ccaatt	ccacaa	ccacac	ccacag	ccacat	ccacca	ccaccc	ccaccg	ccacct	ccacga	ccacgc	ccacgg	ccacgt	ccacta	ccactc	ccactg	ccactt	ccagaa	ccagac	ccagag	ccagat	ccagca	ccagcc	ccagcg	ccagct	ccagga	ccaggc	ccaggg	ccaggt	ccagta	ccagtc	ccagtg	ccagtt	ccataa	ccatac	ccatag	ccatat	ccatca	ccatcc	ccatcg	ccatct	ccatga	ccatgc	ccatgg	ccatgt	ccatta	ccattc	ccattg	ccattt	cccaaa	cccaac	cccaag	cccaat	cccaca	cccacc	cccacg	cccact	cccaga	cccagc	cccagg	cccagt	cccata	cccatc	cccatg	cccatt	ccccaa	ccccac	ccccag	ccccat	ccccca	cccccc	cccccg	ccccct	ccccga	ccccgc	ccccgg	ccccgt	ccccta	cccctc	cccctg	cccctt	cccgaa	cccgac	cccgag	cccgat	cccgca	cccgcc	cccgcg	cccgct	cccgga	cccggc	cccggg	cccggt	cccgta	cccgtc	cccgtg	cccgtt	ccctaa	ccctac	ccctag	ccctat	ccctca	ccctcc	ccctcg	ccctct	ccctga	ccctgc	ccctgg	ccctgt	ccctta	cccttc	cccttg	cccttt	ccgaaa	ccgaac	ccgaag	ccgaat	ccgaca	ccgacc	ccgacg	ccgact	ccgaga	ccgagc	ccgagg	ccgagt	ccgata	ccgatc	ccgatg	ccgatt	ccgcaa	ccgcac	ccgcag	ccgcat	ccgcca	ccgccc	ccgccg	ccgcct	ccgcga	ccgcgc	ccgcgg	ccgcgt	ccgcta	ccgctc	ccgctg	ccgctt	ccggaa	ccggac	ccggag	ccggat	ccggca	ccggcc	ccggcg	ccggct	ccggga	ccgggc	ccgggg	ccgggt	ccggta	ccggtc	ccggtg	ccggtt	ccgtaa	ccgtac	ccgtag	ccgtat	ccgtca	ccgtcc	ccgtcg	ccgtct	ccgtga	ccgtgc	ccgtgg	ccgtgt	ccgtta	ccgttc	ccgttg	ccgttt	cctaaa	cctaac	cctaag	cctaat	cctaca	cctacc	cctacg	cctact	cctaga	cctagc	cctagg	cctagt	cctata	cctatc	cctatg	cctatt	cctcaa	cctcac	cctcag	cctcat	cctcca	cctccc	cctccg	cctcct	cctcga	cctcgc	cctcgg	cctcgt	cctcta	cctctc	cctctg	cctctt	cctgaa	cctgac	cctgag	cctgat	cctgca	cctgcc	cctgcg	cctgct	cctgga	cctggc	cctggg	cctggt	cctgta	cctgtc	cctgtg	cctgtt	ccttaa	ccttac	ccttag	ccttat	ccttca	ccttcc	ccttcg	ccttct	ccttga	ccttgc	ccttgg	ccttgt	ccttta	cctttc	cctttg	cctttt	cgaaaa	cgaaac	cgaaag	cgaaat	cgaaca	cgaacc	cgaacg	cgaact	cgaaga	cgaagc	cgaagg	cgaagt	cgaata	cgaatc	cgaatg	cgaatt	cgacaa	cgacac	cgacag	cgacat	cgacca	cgaccc	cgaccg	cgacct	cgacga	cgacgc	cgacgg	cgacgt	cgacta	cgactc	cgactg	cgactt	cgagaa	cgagac	cgagag	cgagat	cgagca	cgagcc	cgagcg	cgagct	cgagga	cgaggc	cgaggg	cgaggt	cgagta	cgagtc	cgagtg	cgagtt	cgataa	cgatac	cgatag	cgatat	cgatca	cgatcc	cgatcg	cgatct	cgatga	cgatgc	cgatgg	cgatgt	cgatta	cgattc	cgattg	cgattt	cgcaaa	cgcaac	cgcaag	cgcaat	cgcaca	cgcacc	cgcacg	cgcact	cgcaga	cgcagc	cgcagg	cgcagt	cgcata	cgcatc	cgcatg	cgcatt	cgccaa	cgccac	cgccag	cgccat	cgccca	cgcccc	cgcccg	cgccct	cgccga	cgccgc	cgccgg	cgccgt	cgccta	cgcctc	cgcctg	cgcctt	cgcgaa	cgcgac	cgcgag	cgcgat	cgcgca	cgcgcc	cgcgcg	cgcgct	cgcgga	cgcggc	cgcggg	cgcggt	cgcgta	cgcgtc	cgcgtg	cgcgtt	cgctaa	cgctac	cgctag	cgctat	cgctca	cgctcc	cgctcg	cgctct	cgctga	cgctgc	cgctgg	cgctgt	cgctta	cgcttc	cgcttg	cgcttt	cggaaa	cggaac	cggaag	cggaat	cggaca	cggacc	cggacg	cggact	cggaga	cggagc	cggagg	cggagt	cggata	cggatc	cggatg	cggatt	cggcaa	cggcac	cggcag	cggcat	cggcca	cggccc	cggccg	cggcct	cggcga	cggcgc	cggcgg	cggcgt	cggcta	cggctc	cggctg	cggctt	cgggaa	cgggac	cgggag	cgggat	cgggca	cgggcc	cgggcg	cgggct	cgggga	cggggc	cggggg	cggggt	cgggta	cgggtc	cgggtg	cgggtt	cggtaa	cggtac	cggtag	cggtat	cggtca	cggtcc	cggtcg	cggtct	cggtga	cggtgc	cggtgg	cggtgt	cggtta	cggttc	cggttg	cggttt	cgtaaa	cgtaac	cgtaag	cgtaat	cgtaca	cgtacc	cgtacg	cgtact	cgtaga	cgtagc	cgtagg	cgtagt	cgtata	cgtatc	cgtatg	cgtatt	cgtcaa	cgtcac	cgtcag	cgtcat	cgtcca	cgtccc	cgtccg	cgtcct	cgtcga	cgtcgc	cgtcgg	cgtcgt	cgtcta	cgtctc	cgtctg	cgtctt	cgtgaa	cgtgac	cgtgag	cgtgat	cgtgca	cgtgcc	cgtgcg	cgtgct	cgtgga	cgtggc	cgtggg	cgtggt	cgtgta	cgtgtc	cgtgtg	cgtgtt	cgttaa	cgttac	cgttag	cgttat	cgttca	cgttcc	cgttcg	cgttct	cgttga	cgttgc	cgttgg	cgttgt	cgttta	cgtttc	cgtttg	cgtttt	ctaaaa	ctaaac	ctaaag	ctaaat	ctaaca	ctaacc	ctaacg	ctaact	ctaaga	ctaagc	ctaagg	ctaagt	ctaata	ctaatc	ctaatg	ctaatt	ctacaa	ctacac	ctacag	ctacat	ctacca	ctaccc	ctaccg	ctacct	ctacga	ctacgc	ctacgg	ctacgt	ctacta	ctactc	ctactg	ctactt	ctagaa	ctagac	ctagag	ctagat	ctagca	ctagcc	ctagcg	ctagct	ctagga	ctaggc	ctaggg	ctaggt	ctagta	ctagtc	ctagtg	ctagtt	ctataa	ctatac	ctatag	ctatat	ctatca	ctatcc	ctatcg	ctatct	ctatga	ctatgc	ctatgg	ctatgt	ctatta	ctattc	ctattg	ctattt	ctcaaa	ctcaac	ctcaag	ctcaat	ctcaca	ctcacc	ctcacg	ctcact	ctcaga	ctcagc	ctcagg	ctcagt	ctcata	ctcatc	ctcatg	ctcatt	ctccaa	ctccac	ctccag	ctccat	ctccca	ctcccc	ctcccg	ctccct	ctccga	ctccgc	ctccgg	ctccgt	ctccta	ctcctc	ctcctg	ctcctt	ctcgaa	ctcgac	ctcgag	ctcgat	ctcgca	ctcgcc	ctcgcg	ctcgct	ctcgga	ctcggc	ctcggg	ctcggt	ctcgta	ctcgtc	ctcgtg	ctcgtt	ctctaa	ctctac	ctctag	ctctat	ctctca	ctctcc	ctctcg	ctctct	ctctga	ctctgc	ctctgg	ctctgt	ctctta	ctcttc	ctcttg	ctcttt	ctgaaa	ctgaac	ctgaag	ctgaat	ctgaca	ctgacc	ctgacg	ctgact	ctgaga	ctgagc	ctgagg	ctgagt	ctgata	ctgatc	ctgatg	ctgatt	ctgcaa	ctgcac	ctgcag	ctgcat	ctgcca	ctgccc	ctgccg	ctgcct	ctgcga	ctgcgc	ctgcgg	ctgcgt	ctgcta	ctgctc	ctgctg	ctgctt	ctggaa	ctggac	ctggag	ctggat	ctggca	ctggcc	ctggcg	ctggct	ctggga	ctgggc	ctgggg	ctgggt	ctggta	ctggtc	ctggtg	ctggtt	ctgtaa	ctgtac	ctgtag	ctgtat	ctgtca	ctgtcc	ctgtcg	ctgtct	ctgtga	ctgtgc	ctgtgg	ctgtgt	ctgtta	ctgttc	ctgttg	ctgttt	cttaaa	cttaac	cttaag	cttaat	cttaca	cttacc	cttacg	cttact	cttaga	cttagc	cttagg	cttagt	cttata	cttatc	cttatg	cttatt	cttcaa	cttcac	cttcag	cttcat	cttcca	cttccc	cttccg	cttcct	cttcga	cttcgc	cttcgg	cttcgt	cttcta	cttctc	cttctg	cttctt	cttgaa	cttgac	cttgag	cttgat	cttgca	cttgcc	cttgcg	cttgct	cttgga	cttggc	cttggg	cttggt	cttgta	cttgtc	cttgtg	cttgtt	ctttaa	ctttac	ctttag	ctttat	ctttca	ctttcc	ctttcg	ctttct	ctttga	ctttgc	ctttgg	ctttgt	ctttta	cttttc	cttttg	cttttt	gaaaaa	gaaaac	gaaaag	gaaaat	gaaaca	gaaacc	gaaacg	gaaact	gaaaga	gaaagc	gaaagg	gaaagt	gaaata	gaaatc	gaaatg	gaaatt	gaacaa	gaacac	gaacag	gaacat	gaacca	gaaccc	gaaccg	gaacct	gaacga	gaacgc	gaacgg	gaacgt	gaacta	gaactc	gaactg	gaactt	gaagaa	gaagac	gaagag	gaagat	gaagca	gaagcc	gaagcg	gaagct	gaagga	gaaggc	gaaggg	gaaggt	gaagta	gaagtc	gaagtg	gaagtt	gaataa	gaatac	gaatag	gaatat	gaatca	gaatcc	gaatcg	gaatct	gaatga	gaatgc	gaatgg	gaatgt	gaatta	gaattc	gaattg	gaattt	gacaaa	gacaac	gacaag	gacaat	gacaca	gacacc	gacacg	gacact	gacaga	gacagc	gacagg	gacagt	gacata	gacatc	gacatg	gacatt	gaccaa	gaccac	gaccag	gaccat	gaccca	gacccc	gacccg	gaccct	gaccga	gaccgc	gaccgg	gaccgt	gaccta	gacctc	gacctg	gacctt	gacgaa	gacgac	gacgag	gacgat	gacgca	gacgcc	gacgcg	gacgct	gacgga	gacggc	gacggg	gacggt	gacgta	gacgtc	gacgtg	gacgtt	gactaa	gactac	gactag	gactat	gactca	gactcc	gactcg	gactct	gactga	gactgc	gactgg	gactgt	gactta	gacttc	gacttg	gacttt	gagaaa	gagaac	gagaag	gagaat	gagaca	gagacc	gagacg	gagact	gagaga	gagagc	gagagg	gagagt	gagata	gagatc	gagatg	gagatt	gagcaa	gagcac	gagcag	gagcat	gagcca	gagccc	gagccg	gagcct	gagcga	gagcgc	gagcgg	gagcgt	gagcta	gagctc	gagctg	gagctt	gaggaa	gaggac	gaggag	gaggat	gaggca	gaggcc	gaggcg	gaggct	gaggga	gagggc	gagggg	gagggt	gaggta	gaggtc	gaggtg	gaggtt	gagtaa	gagtac	gagtag	gagtat	gagtca	gagtcc	gagtcg	gagtct	gagtga	gagtgc	gagtgg	gagtgt	gagtta	gagttc	gagttg	gagttt	gataaa	gataac	gataag	gataat	gataca	gatacc	gatacg	gatact	gataga	gatagc	gatagg	gatagt	gatata	gatatc	gatatg	gatatt	gatcaa	gatcac	gatcag	gatcat	gatcca	gatccc	gatccg	gatcct	gatcga	gatcgc	gatcgg	gatcgt	gatcta	gatctc	gatctg	gatctt	gatgaa	gatgac	gatgag	gatgat	gatgca	gatgcc	gatgcg	gatgct	gatgga	gatggc	gatggg	gatggt	gatgta	gatgtc	gatgtg	gatgtt	gattaa	gattac	gattag	gattat	gattca	gattcc	gattcg	gattct	gattga	gattgc	gattgg	gattgt	gattta	gatttc	gatttg	gatttt	gcaaaa	gcaaac	gcaaag	gcaaat	gcaaca	gcaacc	gcaacg	gcaact	gcaaga	gcaagc	gcaagg	gcaagt	gcaata	gcaatc	gcaatg	gcaatt	gcacaa	gcacac	gcacag	gcacat	gcacca	gcaccc	gcaccg	gcacct	gcacga	gcacgc	gcacgg	gcacgt	gcacta	gcactc	gcactg	gcactt	gcagaa	gcagac	gcagag	gcagat	gcagca	gcagcc	gcagcg	gcagct	gcagga	gcaggc	gcaggg	gcaggt	gcagta	gcagtc	gcagtg	gcagtt	gcataa	gcatac	gcatag	gcatat	gcatca	gcatcc	gcatcg	gcatct	gcatga	gcatgc	gcatgg	gcatgt	gcatta	gcattc	gcattg	gcattt	gccaaa	gccaac	gccaag	gccaat	gccaca	gccacc	gccacg	gccact	gccaga	gccagc	gccagg	gccagt	gccata	gccatc	gccatg	gccatt	gcccaa	gcccac	gcccag	gcccat	gcccca	gccccc	gccccg	gcccct	gcccga	gcccgc	gcccgg	gcccgt	gcccta	gccctc	gccctg	gccctt	gccgaa	gccgac	gccgag	gccgat	gccgca	gccgcc	gccgcg	gccgct	gccgga	gccggc	gccggg	gccggt	gccgta	gccgtc	gccgtg	gccgtt	gcctaa	gcctac	gcctag	gcctat	gcctca	gcctcc	gcctcg	gcctct	gcctga	gcctgc	gcctgg	gcctgt	gcctta	gccttc	gccttg	gccttt	gcgaaa	gcgaac	gcgaag	gcgaat	gcgaca	gcgacc	gcgacg	gcgact	gcgaga	gcgagc	gcgagg	gcgagt	gcgata	gcgatc	gcgatg	gcgatt	gcgcaa	gcgcac	gcgcag	gcgcat	gcgcca	gcgccc	gcgccg	gcgcct	gcgcga	gcgcgc	gcgcgg	gcgcgt	gcgcta	gcgctc	gcgctg	gcgctt	gcggaa	gcggac	gcggag	gcggat	gcggca	gcggcc	gcggcg	gcggct	gcggga	gcgggc	gcgggg	gcgggt	gcggta	gcggtc	gcggtg	gcggtt	gcgtaa	gcgtac	gcgtag	gcgtat	gcgtca	gcgtcc	gcgtcg	gcgtct	gcgtga	gcgtgc	gcgtgg	gcgtgt	gcgtta	gcgttc	gcgttg	gcgttt	gctaaa	gctaac	gctaag	gctaat	gctaca	gctacc	gctacg	gctact	gctaga	gctagc	gctagg	gctagt	gctata	gctatc	gctatg	gctatt	gctcaa	gctcac	gctcag	gctcat	gctcca	gctccc	gctccg	gctcct	gctcga	gctcgc	gctcgg	gctcgt	gctcta	gctctc	gctctg	gctctt	gctgaa	gctgac	gctgag	gctgat	gctgca	gctgcc	gctgcg	gctgct	gctgga	gctggc	gctggg	gctggt	gctgta	gctgtc	gctgtg	gctgtt	gcttaa	gcttac	gcttag	gcttat	gcttca	gcttcc	gcttcg	gcttct	gcttga	gcttgc	gcttgg	gcttgt	gcttta	gctttc	gctttg	gctttt	ggaaaa	ggaaac	ggaaag	ggaaat	ggaaca	ggaacc	ggaacg	ggaact	ggaaga	ggaagc	ggaagg	ggaagt	ggaata	ggaatc	ggaatg	ggaatt	ggacaa	ggacac	ggacag	ggacat	ggacca	ggaccc	ggaccg	ggacct	ggacga	ggacgc	ggacgg	ggacgt	ggacta	ggactc	ggactg	ggactt	ggagaa	ggagac	ggagag	ggagat	ggagca	ggagcc	ggagcg	ggagct	ggagga	ggaggc	ggaggg	ggaggt	ggagta	ggagtc	ggagtg	ggagtt	ggataa	ggatac	ggatag	ggatat	ggatca	ggatcc	ggatcg	ggatct	ggatga	ggatgc	ggatgg	ggatgt	ggatta	ggattc	ggattg	ggattt	ggcaaa	ggcaac	ggcaag	ggcaat	ggcaca	ggcacc	ggcacg	ggcact	ggcaga	ggcagc	ggcagg	ggcagt	ggcata	ggcatc	ggcatg	ggcatt	ggccaa	ggccac	ggccag	ggccat	ggccca	ggcccc	ggcccg	ggccct	ggccga	ggccgc	ggccgg	ggccgt	ggccta	ggcctc	ggcctg	ggcctt	ggcgaa	ggcgac	ggcgag	ggcgat	ggcgca	ggcgcc	ggcgcg	ggcgct	ggcgga	ggcggc	ggcggg	ggcggt	ggcgta	ggcgtc	ggcgtg	ggcgtt	ggctaa	ggctac	ggctag	ggctat	ggctca	ggctcc	ggctcg	ggctct	ggctga	ggctgc	ggctgg	ggctgt	ggctta	ggcttc	ggcttg	ggcttt	gggaaa	gggaac	gggaag	gggaat	gggaca	gggacc	gggacg	gggact	gggaga	gggagc	gggagg	gggagt	gggata	gggatc	gggatg	gggatt	gggcaa	gggcac	gggcag	gggcat	gggcca	gggccc	gggccg	gggcct	gggcga	gggcgc	gggcgg	gggcgt	gggcta	gggctc	gggctg	gggctt	ggggaa	ggggac	ggggag	ggggat	ggggca	ggggcc	ggggcg	ggggct	ggggga	gggggc	gggggg	gggggt	ggggta	ggggtc	ggggtg	ggggtt	gggtaa	gggtac	gggtag	gggtat	gggtca	gggtcc	gggtcg	gggtct	gggtga	gggtgc	gggtgg	gggtgt	gggtta	gggttc	gggttg	gggttt	ggtaaa	ggtaac	ggtaag	ggtaat	ggtaca	ggtacc	ggtacg	ggtact	ggtaga	ggtagc	ggtagg	ggtagt	ggtata	ggtatc	ggtatg	ggtatt	ggtcaa	ggtcac	ggtcag	ggtcat	ggtcca	ggtccc	ggtccg	ggtcct	ggtcga	ggtcgc	ggtcgg	ggtcgt	ggtcta	ggtctc	ggtctg	ggtctt	ggtgaa	ggtgac	ggtgag	ggtgat	ggtgca	ggtgcc	ggtgcg	ggtgct	ggtgga	ggtggc	ggtggg	ggtggt	ggtgta	ggtgtc	ggtgtg	ggtgtt	ggttaa	ggttac	ggttag	ggttat	ggttca	ggttcc	ggttcg	ggttct	ggttga	ggttgc	ggttgg	ggttgt	ggttta	ggtttc	ggtttg	ggtttt	gtaaaa	gtaaac	gtaaag	gtaaat	gtaaca	gtaacc	gtaacg	gtaact	gtaaga	gtaagc	gtaagg	gtaagt	gtaata	gtaatc	gtaatg	gtaatt	gtacaa	gtacac	gtacag	gtacat	gtacca	gtaccc	gtaccg	gtacct	gtacga	gtacgc	gtacgg	gtacgt	gtacta	gtactc	gtactg	gtactt	gtagaa	gtagac	gtagag	gtagat	gtagca	gtagcc	gtagcg	gtagct	gtagga	gtaggc	gtaggg	gtaggt	gtagta	gtagtc	gtagtg	gtagtt	gtataa	gtatac	gtatag	gtatat	gtatca	gtatcc	gtatcg	gtatct	gtatga	gtatgc	gtatgg	gtatgt	gtatta	gtattc	gtattg	gtattt	gtcaaa	gtcaac	gtcaag	gtcaat	gtcaca	gtcacc	gtcacg	gtcact	gtcaga	gtcagc	gtcagg	gtcagt	gtcata	gtcatc	gtcatg	gtcatt	gtccaa	gtccac	gtccag	gtccat	gtccca	gtcccc	gtcccg	gtccct	gtccga	gtccgc	gtccgg	gtccgt	gtccta	gtcctc	gtcctg	gtcctt	gtcgaa	gtcgac	gtcgag	gtcgat	gtcgca	gtcgcc	gtcgcg	gtcgct	gtcgga	gtcggc	gtcggg	gtcggt	gtcgta	gtcgtc	gtcgtg	gtcgtt	gtctaa	gtctac	gtctag	gtctat	gtctca	gtctcc	gtctcg	gtctct	gtctga	gtctgc	gtctgg	gtctgt	gtctta	gtcttc	gtcttg	gtcttt	gtgaaa	gtgaac	gtgaag	gtgaat	gtgaca	gtgacc	gtgacg	gtgact	gtgaga	gtgagc	gtgagg	gtgagt	gtgata	gtgatc	gtgatg	gtgatt	gtgcaa	gtgcac	gtgcag	gtgcat	gtgcca	gtgccc	gtgccg	gtgcct	gtgcga	gtgcgc	gtgcgg	gtgcgt	gtgcta	gtgctc	gtgctg	gtgctt	gtggaa	gtggac	gtggag	gtggat	gtggca	gtggcc	gtggcg	gtggct	gtggga	gtgggc	gtgggg	gtgggt	gtggta	gtggtc	gtggtg	gtggtt	gtgtaa	gtgtac	gtgtag	gtgtat	gtgtca	gtgtcc	gtgtcg	gtgtct	gtgtga	gtgtgc	gtgtgg	gtgtgt	gtgtta	gtgttc	gtgttg	gtgttt	gttaaa	gttaac	gttaag	gttaat	gttaca	gttacc	gttacg	gttact	gttaga	gttagc	gttagg	gttagt	gttata	gttatc	gttatg	gttatt	gttcaa	gttcac	gttcag	gttcat	gttcca	gttccc	gttccg	gttcct	gttcga	gttcgc	gttcgg	gttcgt	gttcta	gttctc	gttctg	gttctt	gttgaa	gttgac	gttgag	gttgat	gttgca	gttgcc	gttgcg	gttgct	gttgga	gttggc	gttggg	gttggt	gttgta	gttgtc	gttgtg	gttgtt	gtttaa	gtttac	gtttag	gtttat	gtttca	gtttcc	gtttcg	gtttct	gtttga	gtttgc	gtttgg	gtttgt	gtttta	gttttc	gttttg	gttttt	taaaaa	taaaac	taaaag	taaaat	taaaca	taaacc	taaacg	taaact	taaaga	taaagc	taaagg	taaagt	taaata	taaatc	taaatg	taaatt	taacaa	taacac	taacag	taacat	taacca	taaccc	taaccg	taacct	taacga	taacgc	taacgg	taacgt	taacta	taactc	taactg	taactt	taagaa	taagac	taagag	taagat	taagca	taagcc	taagcg	taagct	taagga	taaggc	taaggg	taaggt	taagta	taagtc	taagtg	taagtt	taataa	taatac	taatag	taatat	taatca	taatcc	taatcg	taatct	taatga	taatgc	taatgg	taatgt	taatta	taattc	taattg	taattt	tacaaa	tacaac	tacaag	tacaat	tacaca	tacacc	tacacg	tacact	tacaga	tacagc	tacagg	tacagt	tacata	tacatc	tacatg	tacatt	taccaa	taccac	taccag	taccat	taccca	tacccc	tacccg	taccct	taccga	taccgc	taccgg	taccgt	taccta	tacctc	tacctg	tacctt	tacgaa	tacgac	tacgag	tacgat	tacgca	tacgcc	tacgcg	tacgct	tacgga	tacggc	tacggg	tacggt	tacgta	tacgtc	tacgtg	tacgtt	tactaa	tactac	tactag	tactat	tactca	tactcc	tactcg	tactct	tactga	tactgc	tactgg	tactgt	tactta	tacttc	tacttg	tacttt	tagaaa	tagaac	tagaag	tagaat	tagaca	tagacc	tagacg	tagact	tagaga	tagagc	tagagg	tagagt	tagata	tagatc	tagatg	tagatt	tagcaa	tagcac	tagcag	tagcat	tagcca	tagccc	tagccg	tagcct	tagcga	tagcgc	tagcgg	tagcgt	tagcta	tagctc	tagctg	tagctt	taggaa	taggac	taggag	taggat	taggca	taggcc	taggcg	taggct	taggga	tagggc	tagggg	tagggt	taggta	taggtc	taggtg	taggtt	tagtaa	tagtac	tagtag	tagtat	tagtca	tagtcc	tagtcg	tagtct	tagtga	tagtgc	tagtgg	tagtgt	tagtta	tagttc	tagttg	tagttt	tataaa	tataac	tataag	tataat	tataca	tatacc	tatacg	tatact	tataga	tatagc	tatagg	tatagt	tatata	tatatc	tatatg	tatatt	tatcaa	tatcac	tatcag	tatcat	tatcca	tatccc	tatccg	tatcct	tatcga	tatcgc	tatcgg	tatcgt	tatcta	tatctc	tatctg	tatctt	tatgaa	tatgac	tatgag	tatgat	tatgca	tatgcc	tatgcg	tatgct	tatgga	tatggc	tatggg	tatggt	tatgta	tatgtc	tatgtg	tatgtt	tattaa	tattac	tattag	tattat	tattca	tattcc	tattcg	tattct	tattga	tattgc	tattgg	tattgt	tattta	tatttc	tatttg	tatttt	tcaaaa	tcaaac	tcaaag	tcaaat	tcaaca	tcaacc	tcaacg	tcaact	tcaaga	tcaagc	tcaagg	tcaagt	tcaata	tcaatc	tcaatg	tcaatt	tcacaa	tcacac	tcacag	tcacat	tcacca	tcaccc	tcaccg	tcacct	tcacga	tcacgc	tcacgg	tcacgt	tcacta	tcactc	tcactg	tcactt	tcagaa	tcagac	tcagag	tcagat	tcagca	tcagcc	tcagcg	tcagct	tcagga	tcaggc	tcaggg	tcaggt	tcagta	tcagtc	tcagtg	tcagtt	tcataa	tcatac	tcatag	tcatat	tcatca	tcatcc	tcatcg	tcatct	tcatga	tcatgc	tcatgg	tcatgt	tcatta	tcattc	tcattg	tcattt	tccaaa	tccaac	tccaag	tccaat	tccaca	tccacc	tccacg	tccact	tccaga	tccagc	tccagg	tccagt	tccata	tccatc	tccatg	tccatt	tcccaa	tcccac	tcccag	tcccat	tcccca	tccccc	tccccg	tcccct	tcccga	tcccgc	tcccgg	tcccgt	tcccta	tccctc	tccctg	tccctt	tccgaa	tccgac	tccgag	tccgat	tccgca	tccgcc	tccgcg	tccgct	tccgga	tccggc	tccggg	tccggt	tccgta	tccgtc	tccgtg	tccgtt	tcctaa	tcctac	tcctag	tcctat	tcctca	tcctcc	tcctcg	tcctct	tcctga	tcctgc	tcctgg	tcctgt	tcctta	tccttc	tccttg	tccttt	tcgaaa	tcgaac	tcgaag	tcgaat	tcgaca	tcgacc	tcgacg	tcgact	tcgaga	tcgagc	tcgagg	tcgagt	tcgata	tcgatc	tcgatg	tcgatt	tcgcaa	tcgcac	tcgcag	tcgcat	tcgcca	tcgccc	tcgccg	tcgcct	tcgcga	tcgcgc	tcgcgg	tcgcgt	tcgcta	tcgctc	tcgctg	tcgctt	tcggaa	tcggac	tcggag	tcggat	tcggca	tcggcc	tcggcg	tcggct	tcggga	tcgggc	tcgggg	tcgggt	tcggta	tcggtc	tcggtg	tcggtt	tcgtaa	tcgtac	tcgtag	tcgtat	tcgtca	tcgtcc	tcgtcg	tcgtct	tcgtga	tcgtgc	tcgtgg	tcgtgt	tcgtta	tcgttc	tcgttg	tcgttt	tctaaa	tctaac	tctaag	tctaat	tctaca	tctacc	tctacg	tctact	tctaga	tctagc	tctagg	tctagt	tctata	tctatc	tctatg	tctatt	tctcaa	tctcac	tctcag	tctcat	tctcca	tctccc	tctccg	tctcct	tctcga	tctcgc	tctcgg	tctcgt	tctcta	tctctc	tctctg	tctctt	tctgaa	tctgac	tctgag	tctgat	tctgca	tctgcc	tctgcg	tctgct	tctgga	tctggc	tctggg	tctggt	tctgta	tctgtc	tctgtg	tctgtt	tcttaa	tcttac	tcttag	tcttat	tcttca	tcttcc	tcttcg	tcttct	tcttga	tcttgc	tcttgg	tcttgt	tcttta	tctttc	tctttg	tctttt	tgaaaa	tgaaac	tgaaag	tgaaat	tgaaca	tgaacc	tgaacg	tgaact	tgaaga	tgaagc	tgaagg	tgaagt	tgaata	tgaatc	tgaatg	tgaatt	tgacaa	tgacac	tgacag	tgacat	tgacca	tgaccc	tgaccg	tgacct	tgacga	tgacgc	tgacgg	tgacgt	tgacta	tgactc	tgactg	tgactt	tgagaa	tgagac	tgagag	tgagat	tgagca	tgagcc	tgagcg	tgagct	tgagga	tgaggc	tgaggg	tgaggt	tgagta	tgagtc	tgagtg	tgagtt	tgataa	tgatac	tgatag	tgatat	tgatca	tgatcc	tgatcg	tgatct	tgatga	tgatgc	tgatgg	tgatgt	tgatta	tgattc	tgattg	tgattt	tgcaaa	tgcaac	tgcaag	tgcaat	tgcaca	tgcacc	tgcacg	tgcact	tgcaga	tgcagc	tgcagg	tgcagt	tgcata	tgcatc	tgcatg	tgcatt	tgccaa	tgccac	tgccag	tgccat	tgccca	tgcccc	tgcccg	tgccct	tgccga	tgccgc	tgccgg	tgccgt	tgccta	tgcctc	tgcctg	tgcctt	tgcgaa	tgcgac	tgcgag	tgcgat	tgcgca	tgcgcc	tgcgcg	tgcgct	tgcgga	tgcggc	tgcggg	tgcggt	tgcgta	tgcgtc	tgcgtg	tgcgtt	tgctaa	tgctac	tgctag	tgctat	tgctca	tgctcc	tgctcg	tgctct	tgctga	tgctgc	tgctgg	tgctgt	tgctta	tgcttc	tgcttg	tgcttt	tggaaa	tggaac	tggaag	tggaat	tggaca	tggacc	tggacg	tggact	tggaga	tggagc	tggagg	tggagt	tggata	tggatc	tggatg	tggatt	tggcaa	tggcac	tggcag	tggcat	tggcca	tggccc	tggccg	tggcct	tggcga	tggcgc	tggcgg	tggcgt	tggcta	tggctc	tggctg	tggctt	tgggaa	tgggac	tgggag	tgggat	tgggca	tgggcc	tgggcg	tgggct	tgggga	tggggc	tggggg	tggggt	tgggta	tgggtc	tgggtg	tgggtt	tggtaa	tggtac	tggtag	tggtat	tggtca	tggtcc	tggtcg	tggtct	tggtga	tggtgc	tggtgg	tggtgt	tggtta	tggttc	tggttg	tggttt	tgtaaa	tgtaac	tgtaag	tgtaat	tgtaca	tgtacc	tgtacg	tgtact	tgtaga	tgtagc	tgtagg	tgtagt	tgtata	tgtatc	tgtatg	tgtatt	tgtcaa	tgtcac	tgtcag	tgtcat	tgtcca	tgtccc	tgtccg	tgtcct	tgtcga	tgtcgc	tgtcgg	tgtcgt	tgtcta	tgtctc	tgtctg	tgtctt	tgtgaa	tgtgac	tgtgag	tgtgat	tgtgca	tgtgcc	tgtgcg	tgtgct	tgtgga	tgtggc	tgtggg	tgtggt	tgtgta	tgtgtc	tgtgtg	tgtgtt	tgttaa	tgttac	tgttag	tgttat	tgttca	tgttcc	tgttcg	tgttct	tgttga	tgttgc	tgttgg	tgttgt	tgttta	tgtttc	tgtttg	tgtttt	ttaaaa	ttaaac	ttaaag	ttaaat	ttaaca	ttaacc	ttaacg	ttaact	ttaaga	ttaagc	ttaagg	ttaagt	ttaata	ttaatc	ttaatg	ttaatt	ttacaa	ttacac	ttacag	ttacat	ttacca	ttaccc	ttaccg	ttacct	ttacga	ttacgc	ttacgg	ttacgt	ttacta	ttactc	ttactg	ttactt	ttagaa	ttagac	ttagag	ttagat	ttagca	ttagcc	ttagcg	ttagct	ttagga	ttaggc	ttaggg	ttaggt	ttagta	ttagtc	ttagtg	ttagtt	ttataa	ttatac	ttatag	ttatat	ttatca	ttatcc	ttatcg	ttatct	ttatga	ttatgc	ttatgg	ttatgt	ttatta	ttattc	ttattg	ttattt	ttcaaa	ttcaac	ttcaag	ttcaat	ttcaca	ttcacc	ttcacg	ttcact	ttcaga	ttcagc	ttcagg	ttcagt	ttcata	ttcatc	ttcatg	ttcatt	ttccaa	ttccac	ttccag	ttccat	ttccca	ttcccc	ttcccg	ttccct	ttccga	ttccgc	ttccgg	ttccgt	ttccta	ttcctc	ttcctg	ttcctt	ttcgaa	ttcgac	ttcgag	ttcgat	ttcgca	ttcgcc	ttcgcg	ttcgct	ttcgga	ttcggc	ttcggg	ttcggt	ttcgta	ttcgtc	ttcgtg	ttcgtt	ttctaa	ttctac	ttctag	ttctat	ttctca	ttctcc	ttctcg	ttctct	ttctga	ttctgc	ttctgg	ttctgt	ttctta	ttcttc	ttcttg	ttcttt	ttgaaa	ttgaac	ttgaag	ttgaat	ttgaca	ttgacc	ttgacg	ttgact	ttgaga	ttgagc	ttgagg	ttgagt	ttgata	ttgatc	ttgatg	ttgatt	ttgcaa	ttgcac	ttgcag	ttgcat	ttgcca	ttgccc	ttgccg	ttgcct	ttgcga	ttgcgc	ttgcgg	ttgcgt	ttgcta	ttgctc	ttgctg	ttgctt	ttggaa	ttggac	ttggag	ttggat	ttggca	ttggcc	ttggcg	ttggct	ttggga	ttgggc	ttgggg	ttgggt	ttggta	ttggtc	ttggtg	ttggtt	ttgtaa	ttgtac	ttgtag	ttgtat	ttgtca	ttgtcc	ttgtcg	ttgtct	ttgtga	ttgtgc	ttgtgg	ttgtgt	ttgtta	ttgttc	ttgttg	ttgttt	tttaaa	tttaac	tttaag	tttaat	tttaca	tttacc	tttacg	tttact	tttaga	tttagc	tttagg	tttagt	tttata	tttatc	tttatg	tttatt	tttcaa	tttcac	tttcag	tttcat	tttcca	tttccc	tttccg	tttcct	tttcga	tttcgc	tttcgg	tttcgt	tttcta	tttctc	tttctg	tttctt	tttgaa	tttgac	tttgag	tttgat	tttgca	tttgcc	tttgcg	tttgct	tttgga	tttggc	tttggg	tttggt	tttgta	tttgtc	tttgtg	tttgtt	ttttaa	ttttac	ttttag	ttttat	ttttca	ttttcc	ttttcg	ttttct	ttttga	ttttgc	ttttgg	ttttgt	ttttta	tttttc	tttttg	tttttt
+custom	hg38	9606	Homo sapiens	genomic	1	4	855	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	1	0	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	2	0	0	0	0	0	0	0	1	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	0	0	0	1	0	0	1	3	2	0	0	0	0	0	0	2	0	0	0	1	1	0	0	0	2	1	0	1	0	0	0	0	0	0	0	1	0	0	1	2	1	1	0	2	0	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	0	2	0	0	0	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	1	0	0	0	0	0	2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	2	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	2	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	3	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	0	2	0	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	1	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	1	1	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	1	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	2	0	1	0	0	0	1	0	0	0	1	0	1	1	2	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	2	1	0	1	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	2	2	0	0	0	1	0	0	0	2	0	1	0	0	0	0	1	0	1	1	0	1	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	2	0	0	0	0	1	0	2	2	0	1	1	0	0	0	1	0	0	0	1	0	0	0	0	3	0	0	1	0	0	0	0	1	0	1	1	0	0	1	0	1	2	2	0	0	0	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	0	0	1	1	1	0	0	0	1	2	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	1	3	1	1	0	1	1	3	1	0	0	1	1	2	1	0	0	1	0	1	0	0	1	0	1	2	0	1	0	0	0	0	0	0	0	0	0	0	0	3	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	0	0	0	1	0	0	0	0	0	0	1	0	1	1	0	0	1	0	0	0	2	1	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	2	0	0	3	0	0	1	0	0	0	1	2	1	0	2	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	1	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	0	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	1	1	0	0	2	0	2	0	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	1	0	0	0	1	0	0	0	2	0	0	1	0	0	0	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	2	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	0	1	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	2	0	0	0	1	0	0	0	0	0	0	3	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	0	0	1	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	1	0	2	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	0	1	0	1	0	0	0	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	2	0	1	0	2	1	1	0	0	0	1	0	0	0	1	0	0	0	0	0	1	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	2	0	0	2	0	1	0	3	1	0	0	1	1	1	2	1	1	0	1	0	0	0	1	0	0	2	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	2	1	0	0	0	0	0	0	0	0	1	0	0	1	0	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	2	2	0	0	1	0	0	0	1	0	0	0	0	0	0	0	2	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	0	0	1	0	3	1	0	0	1	0	0	0	1	0	1	2	0	0	0	0	1	0	0	0	1	0	0	1	1	0	0	1	1	0	1	0	1	1	1	0	1	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	1	0	1	1	0	2	0	0	0	0	0	1	2	0	3	2	0	2	0	1	1	1	0	0	0	3	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	2	0	1	0	1	0	1	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	2	1	1	0	1	1	0	1	0	3	2	2	1	1	0	0	0	1	1	0	1	0	1	0	0	0	1	0	0	3	0	1	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	1	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	1	2	0	1	0	0	1	2	0	7	0	3	2	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	2	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	1	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	1	1	0	1	2	1	2	0	1	3	1	0	1	3	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	1	1	0	1	1	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	2	0	1	0	2	0	0	0	0	0	0	1	0	0	0	0	1	2	0	0	0	0	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	1	2	2	0	0	1	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	0	0	0	0	0	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	1	1	2	0	0	1	0	0	0	1	0	0	0	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	1	0	1	0	1	1	0	0	0	1	1	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	1	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	2	0	2	0	0	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	1	0	0	0	0	1	2	0	1	2	1	1	1	1	0	2	2	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	2	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	1	2	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	1	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	1	0	1	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	1	0	1	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	0	0	0	1	0	0	0	0	1	0	0	0	0	0	1	1	0	1	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	1	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0	0	0	0	0	1	1	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	1	1	0	0	2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cds_fasta_out.fasta	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,8 @@
+>ENST00000432222.1
+GGCCAGGTCCCAGGAACCCATATTTAGAACTGAGGGTCCTATGGCCCAGAACCAGGCATCTGTACTTAAGAACCAAGCACCTGTGACCAGGACCCAGGCACCCATCACTGGAACCCTCTGTCAGGATGCCAGATCCAACTCTCATCCAGTGAAGCCCTCAAGACTCAATGTCTTCTGTTGCCCCCATTGTTCTTTGACTTTTAGCAAGAAATCCTATCTCTCCAGACACCAGAAGGCCCACCTCACAGAGCCGCCCAACTACTGCTTCCATTGCAGCAAGTCTTTCAGCTCATTTTCCAGGCTGGTCAGACACCAGCAGACCCACTGGAAGCAGAAGAGCTACCTTTGCCCTATCTGTGACCTCTCCTTTGGGGAGAAAGAGGGCCTTATGGATCACTGGAGGGGCTATAAAGGCAAGGACCTGTGCCAGAGCAGCCACCATAAATGCCGGGTGATCCTGGGCCAGTGGCTTGGCTTCTCTCATGATGTCCCCACTATGGCTGGGGAGGAATGGAAGCATGGAGGTGATCAATCTCCCCCCAGGATCCATACCCCCAGGAGAAGAGGCCTAAGAGAGAAGGCCTGCAAAGGAGACAAAACAAAGGAGGCAGTGAGCATCTTGAAACATAAATA
+>ENST00000448800.5
+TGGCCACACTGCAACAGCTGGAGCCAGTTACTGGGCAGGTGTCTGTACTGGTGATGTGTCACACTCGGGAGTTGGCTTTTCAGATCAGCAAGGAATATGAGCGCTTCTCTAAATACATGCCCAATGTCAAGGTTGCTGTTTTTTTTGGTGGTCTGTCTATCAAGAAGGATGAAGAGGTGCTGAAGAAGAACTGCCCGCATATCGTCGTGGGGACTCCAGGCCGTATCCTAGCCCTGGCTCGAAATAAGAGCCTCAACCTCAAACACATTAAACACTTTATTTTGGATGAATGTGATAAGATGCTTGAACAGCTCGACATGCGTCGGGATGTCCAGGAAATTTTTCGCATGACCCCCCACGAGAAGCAGGTCATGATGTTCAGTGCTACCTTGAGCAAAGAGATCCGTCCAGTCTGCCGCAAGTTCATGCAAGATCCAATGGAGATCTTCGTGGATGATGAGACGAAGTTGACGCTGCATGGGTTGCAGCAGTACTACGTGAAACTGAAGGACAACGAGAAGAACCGGAAGCTCTTTGACCTTCTGGATGTCCTTGAGTTCAACCAGGTGGTGATCTTTGTGAAGTCTGTGCAGCGGTGCATTGCCTTGGCCCAGCTACTAGTGGAGCAGAACTTCCCAGCCATTGCCATCCACCGTGGGATGCCCCAGGAGGAGAGGCTTTCTCGGTATCAGCAGTTTAAAGATTTTCAACGACGAATTCTTGTGGCTACCAACCTATTTGGCCGAGGCATGGACATCGAGCGGGTGAACATTGCTTTTAATTATGACATGCCTGAGGATTCTGACACCTACCTGCATCGGGTGGCCAGAGCAGGCCGGTTTGGCACCAAGGGCTTGGCTATCACATTTGTGTCCGATGAGAATGATGCCAAGATCCTCAATGATGTGCAGGATCGCTTTGAGGTCAATATTAGTGAGCTGCCTGATGAGATAGACATCTCCTCCTACATTGAACAGACACGGT
+>ENST00000445122.5
+ATGCCGGGCACCCAGACTCCAGCACCGGCCGAGGACCCCCACTCCGGCTGCAGGGACCCTGTCCCAGCGAGACCGCAGGCATGTCATCCGAAAAGTCAGGAGACTCGCTTCGAGGGCCCACTTcccccgccgccgcccgctgccgccgccccgcccccgccggcgccagccCAGACTGCCCAGGCCCCTGGCTTCGTGGTGCCCACGCACGCGGGGACTGTGGGCACGCTGCCGCTGGGGGGCTACGTAGCGCCCGGATACCCCCTGCAGCTGCAGCCTTGCACTGCTTACGTGCCGGTCTACCCGGTGGGCACGCCATATGCAGGCGGGACCCCGGGGGGAACAGGAGTGACCTCCACTCTCCCCCCGCCGCCCCAGGGCCCAGGGCTGGCCCTACTGGAGCCGAGGCGCCCGCCACACGACTACATGCCCATCGCGGTGCTGACCACCATCTGTTGCTTCTGGCCTACTGGCATCATTGCCATCTTCAAGGCCGTGCAGGTGCGCACGGCCTTGGCCCGCGGAGACATGGTGTCGGCCGAGATCGCTTCACGCGAGGCCCGGAACTTCTCCTTCATCTCCCTGGCCGTGGGCATCGCGGCCATGGTGCTCTGTACCATCCTCACCGTAGTCATCATCATCGCCGCGCAGCACCACGAGAACTACTGGGATCCCTAA
+>ENST00000430777.2
+ATGGATTTGTGGCCAGGGGCATGGAtgctgctgctgctgctcttcctgctgctgctcttcctgctgcCCACCCTGTGGTTCTGCAGCCCCAGTGCCAAGTACTTCTTCAAGATGGCCTTCTACAATGGCTGGATCCTCTTCCTGGCTGTGCTCGCCATCCCTGTGTGTGCCGTGCGAGGACGCAACGTCGAGAACATGAAGATCTTGCGTCTAATGCTGCTCCACATCAAATACCTGTACGGGATCCGAGTGGAGGTGCGAGGGGCTCACCACTTCCCTCCCTCGCAGCCCTATGTTGTTGTCTCCAACCACCAGAGCTCTCTCGATCTGCTTGGGATGATGGAGGTACTGCCAGGCCGCTGTGTGCCCATTGCCAAGCGCGAGCTACTGTGggctggctctgccgggctggcctgctggctggcaggAGTCATCTTCATCGACCGGAAGCGCACGGGGGATGCCATCAGTGTCATGTCTGAGGTCGCCCAGACCCTGCTCACCCAGGACGTGAGGGTCTGGGTGTTTCCTGAGGGAACGAGAAACCACAATGGCTCCATGCTGCCCTTCAAACGTGGCGCCTTCCATCTTGCAGTGCAGGCCCAGGTTCCCATTGTCCCCATAGTCATGTCCTCCTACCAAGACTTCTACTGCAAGAAGGAGCGTCGCTTCACCTCGGGACAATGTCAGGTGCGGGTGCTGCCCCCAGTGCCCACGGAAGGGCTGACACCAGATGACGTCCCAGCTCTGGCTGACAGAGTCCGGCACTCCATGCTCACTGTTTTCCGGGAAATCTCCACTGATGGCCGGGGTGGTGGTGACTATCTGAAGAAGCCTGGGGGCGGTGGGTGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/codon_freq_from_bicodon.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,5 @@
+#frame	codon_count	aaa	aac	aag	aat	aca	acc	acg	act	aga	agc	agg	agt	ata	atc	atg	att	caa	cac	cag	cat	cca	ccc	ccg	cct	cga	cgc	cgg	cgt	cta	ctc	ctg	ctt	gaa	gac	gag	gat	gca	gcc	gcg	gct	gga	ggc	ggg	ggt	gta	gtc	gtg	gtt	taa	tac	tag	tat	tca	tcc	tcg	tct	tga	tgc	tgg	tgt	tta	ttc	ttg	ttt
+2-counts	855	4	12	14	8	13	23	8	15	28	18	25	12	8	27	31	7	3	11	17	4	23	28	16	14	4	12	2	1	10	16	35	7	4	7	16	4	16	38	6	14	15	15	18	4	4	11	25	4	1	12	3	3	18	15	7	16	16	17	26	10	8	20	19	7
+2-percent	855	0.4678362573099415500088582576	1.4035087719298244834931210789	1.6374269005847954527865795171	0.9356725146198831000177165151	1.5204678362573098571175478355	2.6900584795321638154064203263	0.9356725146198831000177165151	1.7543859649122806043664013487	3.2748538011695909055731590342	2.1052631578947367252396816184	2.9239766081871341185660639894	1.4035087719298244834931210789	0.9356725146198831000177165151	3.1578947368421053099041273526	3.6257309941520468044018343790	0.8187134502923977263932897586	0.3508771929824561208732802697	1.2865497076023393319132992474	1.9883040935672515736598597869	0.4678362573099415500088582576	2.6900584795321638154064203263	3.2748538011695909055731590342	1.8713450292397662000354330303	1.6374269005847954527865795171	0.4678362573099415500088582576	1.4035087719298244834931210789	0.2339181286549707750044291288	0.1169590643274853875022145644	1.1695906432748537362442675658	1.8713450292397662000354330303	4.0935672514619882988995414053	0.8187134502923977263932897586	0.4678362573099415500088582576	0.8187134502923977263932897586	1.8713450292397662000354330303	0.4678362573099415500088582576	1.8713450292397662000354330303	4.4444444444444446418174266000	0.7017543859649122417465605395	1.6374269005847954527865795171	1.7543859649122806043664013487	1.7543859649122806043664013487	2.1052631578947367252396816184	0.4678362573099415500088582576	0.4678362573099415500088582576	1.2865497076023393319132992474	2.9239766081871341185660639894	0.4678362573099415500088582576	0.1169590643274853875022145644	1.4035087719298244834931210789	0.3508771929824561208732802697	0.3508771929824561208732802697	2.1052631578947367252396816184	1.7543859649122806043664013487	0.8187134502923977263932897586	1.8713450292397662000354330303	1.8713450292397662000354330303	1.9883040935672515736598597869	3.0409356725146197142350956710	1.1695906432748537362442675658	0.9356725146198831000177165151	2.3391812865497074724885351316	2.2222222222222223209087133000	0.8187134502923977263932897586
+3-counts	855	3	2	3	4	12	10	10	10	17	12	16	5	2	7	7	3	23	10	19	18	37	23	19	25	7	16	10	4	8	14	19	18	27	10	14	12	23	12	8	19	31	18	11	11	3	7	8	9	11	6	4	9	22	15	17	20	27	36	28	19	1	5	9	10
+3-percent	855	0.3508771929824561208732802697	0.2339181286549707750044291288	0.3508771929824561208732802697	0.4678362573099415500088582576	1.4035087719298244834931210789	1.1695906432748537362442675658	1.1695906432748537362442675658	1.1695906432748537362442675658	1.9883040935672515736598597869	1.4035087719298244834931210789	1.8713450292397662000354330303	0.5847953216374268681221337829	0.2339181286549707750044291288	0.8187134502923977263932897586	0.8187134502923977263932897586	0.3508771929824561208732802697	2.6900584795321638154064203263	1.1695906432748537362442675658	2.2222222222222223209087133000	2.1052631578947367252396816184	4.3274853801169594902376047685	2.6900584795321638154064203263	2.2222222222222223209087133000	2.9239766081871341185660639894	0.8187134502923977263932897586	1.8713450292397662000354330303	1.1695906432748537362442675658	0.4678362573099415500088582576	0.9356725146198831000177165151	1.6374269005847954527865795171	2.2222222222222223209087133000	2.1052631578947367252396816184	3.1578947368421053099041273526	1.1695906432748537362442675658	1.6374269005847954527865795171	1.4035087719298244834931210789	2.6900584795321638154064203263	1.4035087719298244834931210789	0.9356725146198831000177165151	2.2222222222222223209087133000	3.6257309941520468044018343790	2.1052631578947367252396816184	1.2865497076023393319132992474	1.2865497076023393319132992474	0.3508771929824561208732802697	0.8187134502923977263932897586	0.9356725146198831000177165151	1.0526315789473683626198408092	1.2865497076023393319132992474	0.7017543859649122417465605395	0.4678362573099415500088582576	1.0526315789473683626198408092	2.5730994152046786638265984948	1.7543859649122806043664013487	1.9883040935672515736598597869	2.3391812865497074724885351316	3.1578947368421053099041273526	4.2105263157894734504793632368	3.2748538011695909055731590342	2.2222222222222223209087133000	0.1169590643274853875022145644	0.5847953216374268681221337829	1.0526315789473683626198408092	1.1695906432748537362442675658
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/codon_freq_from_bicodon_log.txt	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,7 @@
+Using 4096 codon pairs
+Reporting 64 codons
+Found a total of 100.000000 percent for 2.
+Found a total of 100.000000 percent for 3.
+Reporting 21 amino acids
+Found a total of 100.000000 percent for 2-aa.
+Found a total of 100.000000 percent for 3-aa.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/codon_out.tabular	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,2 @@
+Division	Assembly	Taxid	Species	Organelle	Translation Table	# CDS	# Codons	aaa	aac	aag	aat	aca	acc	acg	act	aga	agc	agg	agt	ata	atc	atg	att	caa	cac	cag	cat	cca	ccc	ccg	cct	cga	cgc	cgg	cgt	cta	ctc	ctg	ctt	gaa	gac	gag	gat	gca	gcc	gcg	gct	gga	ggc	ggg	ggt	gta	gtc	gtg	gtt	taa	tac	tag	tat	tca	tcc	tcg	tct	tga	tgc	tgg	tgt	tta	ttc	ttg	ttt
+custom	hg38	9606	Homo sapiens	genomic	1	4	859	14	13	29	8	5	10	4	9	9	12	13	6	4	17	17	9	12	21	28	33	13	26	7	14	13	14	15	12	12	17	20	25	13	16	26	27	12	33	7	30	9	28	16	12	3	12	21	3	0	9	0	5	5	12	1	15	0	20	9	14	1	11	11	17
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/find_naltorfs_log.txt	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,7 @@
+{'chr6_GL000250v2_alt': 4672374}
+Excluding 77 unique canonical coding sequences from 77 BED lines.
+cds length is not divisible by 3!!!: 634. chr6_GL000250v2_alt	938190	938841	ENST00000432222.1	0	-	938207	938841	12,12,120	1	651	0
+cds length is not divisible by 3!!!: 271. chr6_GL000250v2_alt	2057211	2060006	ENST00000420604.1	0	-	2057618	2060006	12,12,120	3	437,165,76	0,2313,2719
+cds length is not divisible by 3!!!: 986. chr6_GL000250v2_alt	2862767	2871733	ENST00000448800.5	0	-	2862982	2871733	12,12,120	9	232,148,145,110,132,119,184,93,38	0,560,834,1077,2561,5148,6281,8544,8928
+cds length is not divisible by 3!!!: 580. chr6_GL000250v2_alt	3655068	3704125	ENST00000425722.1	0	-	3655068	3703952	12,12,120	19	21,21,24,21,21,21,21,21,21,39,90,21,21,21,30,33,33,87,186	0,637,1109,8114,9561,12963,13438,14141,16499,17121,26913,32289,32814,43342,43448,45110,45965,47083,48871
+transcripts: 77	unique LNO ORFs: 4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gencode_canonical.hg38.chr6_GL0002508.bed	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,77 @@
+chr6_GL000250v2_alt	168585	189574	ENST00000437160.6	0	-	169653	189217	12,12,120	8	1664,27,33,116,23,231,96,777,	0,4234,5806,5971,8695,17011,18891,20212,
+chr6_GL000250v2_alt	260408	270885	ENST00000426120.2	0	-	260624	269578	12,12,120	7	1802,105,127,92,82,269,253,	0,3949,4702,5171,8728,9161,10224,
+chr6_GL000250v2_alt	309837	310865	ENST00000421027.1	0	-	309837	310800	12,12,120	1	1028,	0,
+chr6_GL000250v2_alt	351929	352936	ENST00000420178.3	0	-	351929	352871	12,12,120	1	1007,	0,
+chr6_GL000250v2_alt	377510	378446	ENST00000428081.1	0	+	377510	378446	12,12,120	1	936,	0,
+chr6_GL000250v2_alt	438928	440200	ENST00000440124.4	0	+	439261	440200	12,12,120	1	1272,	0,
+chr6_GL000250v2_alt	572355	573321	ENST00000420495.4	0	+	572355	573321	12,12,120	1	966,	0,
+chr6_GL000250v2_alt	691168	722731	ENST00000435232.5	0	-	692358	693306	12,12,120	5	2229,48,125,124,85,	0,3408,4796,6359,31478,
+chr6_GL000250v2_alt	704969	706618	ENST00000455234.1	0	+	705679	706618	12,12,120	1	1649,	0,
+chr6_GL000250v2_alt	722840	729989	ENST00000453467.5	0	+	727430	728381	12,12,120	4	27,116,51,2830,	0,1273,3224,4319,
+chr6_GL000250v2_alt	752426	753563	ENST00000418003.3	0	-	752426	753563	12,12,120	1	1137,	0,
+chr6_GL000250v2_alt	821306	825621	ENST00000414436.2	0	-	821574	825397	12,12,120	2	739,251,	0,4064,
+chr6_GL000250v2_alt	821306	893756	ENST00000449163.5	0	-	869267	893509	12,12,120	19	739,176,144,129,128,94,108,117,133,151,78,64,243,192,66,102,171,135,553,	0,47959,48912,49278,49987,50809,51316,51521,53020,53648,55343,56970,57662,65507,66158,66510,67711,68296,71897,
+chr6_GL000250v2_alt	853147	854731	ENST00000453513.4	0	+	853637	854576	12,12,120	1	1584,	0,
+chr6_GL000250v2_alt	922689	938078	ENST00000548017.1	0	+	922918	936889	12,12,120	7	317,348,114,21,21,21,1203,	0,2336,9166,10657,10918,13715,14186,
+chr6_GL000250v2_alt	938190	938841	ENST00000432222.1	0	-	938207	938841	12,12,120	1	651,	0,
+chr6_GL000250v2_alt	1093432	1096751	ENST00000615098.4	0	+	1093456	1095994	12,12,120	7	97,270,276,276,117,33,372,	0,226,722,1597,1995,2557,2947,
+chr6_GL000250v2_alt	1147347	1267669	ENST00000640829.1	0	+	1147490	1266858	12,12,120	11	216,16,14,240,276,276,33,84,93,35,281,	0,340,39005,53186,53667,54522,68203,118979,119506,119955,120041,
+chr6_GL000250v2_alt	1319351	1323001	ENST00000443494.6	0	+	1319622	1322789	12,12,120	4	416,101,110,237,	0,663,970,3413,
+chr6_GL000250v2_alt	1324800	1328425	ENST00000441553.5	0	+	1326768	1327398	12,12,120	3	301,109,1230,	0,1881,2395,
+chr6_GL000250v2_alt	1328357	1333979	ENST00000450015.2	0	-	1329202	1333881	12,12,120	4	1426,92,23,665,	0,2891,3190,4957,
+chr6_GL000250v2_alt	1368538	1371196	ENST00000422484.1	0	-	1368538	1370895	12,12,120	4	231,96,500,43,	0,1199,1940,2615,
+chr6_GL000250v2_alt	1394223	1406831	ENST00000433713.5	0	+	1395132	1405908	12,12,120	6	62,649,96,225,23,1011,	0,605,9866,10857,11392,11597,
+chr6_GL000250v2_alt	1410040	1419029	ENST00000449208.6	0	-	1412064	1418953	12,12,120	7	2542,33,116,23,231,96,505,	0,3782,4994,5424,6453,7204,8484,
+chr6_GL000250v2_alt	1421285	1430769	ENST00000552062.2	0	+	1421971	1430429	12,12,120	8	860,96,231,9,14,116,33,858,	0,3970,5094,6035,6633,7295,7770,8626,
+chr6_GL000250v2_alt	1442505	1471482	ENST00000425523.5	0	-	1443926	1457164	12,12,120	9	2104,33,116,23,231,96,488,104,123,	0,4719,4970,5565,12071,13984,14221,16590,28854,
+chr6_GL000250v2_alt	1656333	1673225	ENST00000458607.5	0	+	1658808	1671755	12,12,120	8	152,153,460,96,231,23,116,2018,	0,2046,2468,3938,8907,13070,13667,14874,
+chr6_GL000250v2_alt	1658801	1676354	ENST00000550581.3	0	+	1658808	1676306	12,12,120	10	460,96,231,23,116,185,101,83,126,146,	0,1470,6439,10602,11199,12406,15992,16185,17126,17407,
+chr6_GL000250v2_alt	1870880	1883062	ENST00000383450.3	0	-	1875575	1883062	12,12,120	7	4937,141,163,179,195,96,208,	0,5319,5735,5975,11091,11708,11974,
+chr6_GL000250v2_alt	1988977	2002543	ENST00000450902.6	0	-	1988977	2002347	12,12,120	12	153,99,211,116,111,192,204,255,57,163,239,403,	0,264,560,3155,3439,5329,5599,6007,10938,11318,11564,13163,
+chr6_GL000250v2_alt	2005895	2017402	ENST00000438815.2	0	-	2006775	2015525	12,12,120	3	900,211,3488,	0,2790,8019,
+chr6_GL000250v2_alt	2017553	2020927	ENST00000427944.5	0	-	2018167	2020481	12,12,120	5	896,177,197,440,45,	0,1229,2000,2795,3329,
+chr6_GL000250v2_alt	2029311	2047393	ENST00000427406.6	0	-	2029969	2044679	12,12,120	15	826,111,126,183,120,2478,71,792,93,60,1481,70,381,139,645,	0,2746,2945,3297,3611,3814,7576,7758,11604,11859,12066,13840,13995,15232,17437,
+chr6_GL000250v2_alt	2049703	2054929	ENST00000421473.6	0	+	2050009	2053900	12,12,120	4	363,109,111,2087,	0,2336,2717,3139,
+chr6_GL000250v2_alt	2057211	2060006	ENST00000420604.1	0	-	2057618	2060006	12,12,120	3	437,165,76,	0,2313,2719,
+chr6_GL000250v2_alt	2217891	2218933	ENST00000434428.5	0	+	2218232	2218933	12,12,120	3	426,103,229,	0,519,813,
+chr6_GL000250v2_alt	2313217	2319398	ENST00000430305.2	0	+	2313458	2317689	12,12,120	3	302,1445,1904,	0,2514,4277,
+chr6_GL000250v2_alt	2827448	2843673	ENST00000619506.1	0	+	2838192	2842459	12,12,120	6	115,255,288,279,132,1342,	0,10718,11244,12123,12501,14883,
+chr6_GL000250v2_alt	2861265	2862781	ENST00000424816.2	0	+	2861563	2862484	12,12,120	2	469,486,	0,1030,
+chr6_GL000250v2_alt	2862767	2871733	ENST00000448800.5	0	-	2862982	2871733	12,12,120	9	232,148,145,110,132,119,184,93,38,	0,560,834,1077,2561,5148,6281,8544,8928,
+chr6_GL000250v2_alt	2909112	2910915	ENST00000445232.2	0	+	2909112	2910116	12,12,120	3	46,48,1221,	0,233,582,
+chr6_GL000250v2_alt	2913133	2915004	ENST00000457552.2	0	-	2913287	2914996	12,12,120	4	609,72,46,170,	0,1004,1259,1701,
+chr6_GL000250v2_alt	2918702	2921488	ENST00000433676.6	0	+	2919878	2921255	12,12,120	4	192,119,23,392,	0,1076,1820,2394,
+chr6_GL000250v2_alt	2921473	2925564	ENST00000432392.6	0	-	2921772	2925300	12,12,120	4	337,108,345,307,	0,631,887,3784,
+chr6_GL000250v2_alt	3089203	3095288	ENST00000430216.5	0	+	3090740	3095143	12,12,120	14	325,872,73,110,81,88,190,127,150,75,144,138,74,257,	0,830,1956,2174,2505,2833,3194,3498,4098,4596,4880,5226,5520,5828,
+chr6_GL000250v2_alt	3095410	3097463	ENST00000436320.5	0	+	3095666	3097143	12,12,120	4	370,141,96,413,	0,616,1265,1640,
+chr6_GL000250v2_alt	3098201	3109905	ENST00000452329.2	0	-	3098205	3109390	12,12,120	17	181,175,140,302,93,153,133,186,117,113,170,196,111,97,279,249,186,	0,293,655,873,1568,1772,2032,3427,4084,4410,7363,7651,8925,9742,10373,10955,11518,
+chr6_GL000250v2_alt	3130006	3139596	ENST00000432122.2	0	-	3130367	3139369	12,12,120	5	487,60,31,68,230,	0,594,1081,8680,9360,
+chr6_GL000250v2_alt	3142240	3147687	ENST00000426095.2	0	-	3142668	3144594	12,12,120	2	2367,177,	0,5270,
+chr6_GL000250v2_alt	3148164	3150568	ENST00000422919.1	0	+	3148378	3150304	12,12,120	2	289,1620,	0,784,
+chr6_GL000250v2_alt	3160359	3162874	ENST00000450744.1	0	+	3160575	3162501	12,12,120	1	2515,	0,
+chr6_GL000250v2_alt	3167532	3172376	ENST00000430690.5	0	+	3169944	3172278	12,12,120	5	283,41,219,200,219,	0,492,1382,2319,4625,
+chr6_GL000250v2_alt	3191667	3195522	ENST00000423382.2	0	-	3192334	3195392	12,12,120	6	894,223,183,263,193,289,	0,990,1387,2136,2947,3566,
+chr6_GL000250v2_alt	3195810	3211661	ENST00000550401.2	0	-	3196242	3211595	12,12,120	20	554,85,95,71,74,104,95,254,103,93,100,236,84,88,61,100,79,74,49,106,	0,1457,1621,1815,2120,2303,2495,2678,5960,6350,7406,7615,8117,8277,11264,11733,12656,12860,13838,15745,
+chr6_GL000250v2_alt	3212373	3230306	ENST00000421926.6	0	-	3212698	3230299	12,12,120	28	506,176,79,87,116,78,145,168,155,105,102,123,107,83,183,236,144,149,102,115,135,156,41,85,254,219,67,49,	0,914,1255,2940,3135,3603,4047,4633,4886,5153,6822,7016,7236,7818,8020,8282,8604,8840,9210,9469,9709,12652,12939,13071,16511,16854,17171,17884,
+chr6_GL000250v2_alt	3406267	3418718	ENST00000433037.1	0	-	3406267	3418718	12,12,120	6	306,333,306,291,297,369,	0,5366,7700,8368,10745,12082,
+chr6_GL000250v2_alt	3480956	3485682	ENST00000445122.5	0	-	3481819	3484701	12,12,120	6	1040,186,216,91,81,112,	0,1178,2009,3450,3737,4614,
+chr6_GL000250v2_alt	3497183	3500883	ENST00000414111.6	0	+	3498767	3500558	12,12,120	9	75,129,123,110,96,171,80,154,372,	0,1556,1916,2119,2328,2505,2768,2921,3328,
+chr6_GL000250v2_alt	3500813	3510698	ENST00000430777.2	0	-	3501877	3504098	12,12,120	7	1237,73,96,176,134,209,96,	0,1754,1953,2213,2725,3085,9789,
+chr6_GL000250v2_alt	3510955	3513395	ENST00000449794.2	0	+	3511113	3512928	12,12,120	6	298,19,113,55,118,565,	0,1187,1297,1523,1655,1875,
+chr6_GL000250v2_alt	3513569	3516924	ENST00000549839.5	0	-	3513744	3516824	12,12,120	5	272,83,123,107,152,	0,383,2660,2913,3203,
+chr6_GL000250v2_alt	3517334	3522785	ENST00000453487.2	0	-	3518980	3522514	12,12,120	9	1739,87,89,154,136,191,248,74,492,	0,1868,2077,2506,2911,3230,3521,3987,4959,
+chr6_GL000250v2_alt	3523364	3528122	ENST00000457070.1	0	-	3523964	3525112	12,12,120	8	738,200,103,59,84,81,93,98,	0,943,1382,1706,2275,3544,3971,4660,
+chr6_GL000250v2_alt	3527441	3536999	ENST00000425600.1	0	-	3528035	3536999	12,12,120	12	1308,98,148,296,139,82,220,176,384,524,113,253,	0,1481,2082,2456,3579,3807,4084,6000,6286,7245,8938,9305,
+chr6_GL000250v2_alt	3655068	3704125	ENST00000425722.1	0	-	3655068	3703952	12,12,120	19	21,21,24,21,21,21,21,21,21,39,90,21,21,21,30,33,33,87,186,	0,637,1109,8114,9561,12963,13438,14141,16499,17121,26913,32289,32814,43342,43448,45110,45965,47083,48871,
+chr6_GL000250v2_alt	3726193	3739359	ENST00000445928.5	0	-	3726199	3739352	12,12,120	7	95,282,348,21,282,348,86,	0,781,2076,7820,8970,10974,13080,
+chr6_GL000250v2_alt	3823888	3837634	ENST00000426847.2	0	-	3824827	3837535	12,12,120	6	953,24,111,282,270,199,	0,1752,2249,3043,5625,13547,
+chr6_GL000250v2_alt	4047519	4053351	ENST00000449560.5	0	+	4047581	4052533	12,12,120	4	144,249,282,973,	0,3778,4410,4859,
+chr6_GL000250v2_alt	4062236	4069674	ENST00000419685.6	0	-	4062591	4069610	12,12,120	6	369,24,111,282,267,161,	0,1184,1676,2753,5563,7277,
+chr6_GL000250v2_alt	4117786	4122072	ENST00000426644.6	0	-	4118239	4121975	12,12,120	6	489,32,111,282,270,188,	0,677,960,1557,2281,4098,
+chr6_GL000250v2_alt	4126846	4143590	ENST00000439425.6	0	-	4127302	4143099	12,12,120	12	486,137,160,174,189,129,198,206,131,115,497,75,	0,7419,7949,8286,8637,10352,10646,13173,13662,15556,15760,16669,
+chr6_GL000250v2_alt	4145581	4149568	ENST00000436627.2	0	-	4145823	4149278	12,12,120	6	331,205,130,112,148,425,	0,814,1417,1955,2225,3562,
+chr6_GL000250v2_alt	4150073	4158843	ENST00000418205.2	0	-	4150443	4158681	12,12,120	11	577,137,163,174,189,129,198,206,131,115,940,	0,1859,2304,2710,3443,3781,5109,5733,6900,7179,7830,
+chr6_GL000250v2_alt	4159070	4184429	ENST00000425855.2	0	+	4159094	4184317	12,12,120	6	84,68,130,142,93,156,	0,1932,3799,4158,22841,25203,
+chr6_GL000250v2_alt	4239473	4245915	ENST00000395312.7	0	-	4239815	4245652	12,12,120	6	359,36,117,285,282,318,	0,713,907,2543,4055,6124,
+chr6_GL000250v2_alt	4369248	4385378	ENST00000443117.5	0	-	4373329	4378232	12,12,120	6	779,167,282,246,199,31,	0,4069,4450,5072,8884,16099,
+chr6_GL000250v2_alt	4380587	4391853	ENST00000411749.6	0	+	4380703	4390890	12,12,120	6	216,264,282,111,24,663,	0,4752,9014,9843,10283,10603,
Binary file test-data/hg38.chr6_GL000250v2_alt.2bit.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/naltorfs_fasta_out.fasta	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,8 @@
+>ENST00000432222.1|chromosome:hg38:chr6_GL000250v2_alt:938210:938801:-
+ATGGCCCAGAACCAGGCATCTGTACTTAAGAACCAAGCACCTGTGACCAGGACCCAGGCACCCATCACTGGAACCCTCTGTCAGGATGCCAGATCCAACTCTCATCCAGTGAAGCCCTCAAGACTCAATGTCTTCTGTTGCCCCCATTGTTCTTTGACTTTTAGCAAGAAATCCTATCTCTCCAGACACCAGAAGGCCCACCTCACAGAGCCGCCCAACTACTGCTTCCATTGCAGCAAGTCTTTCAGCTCATTTTCCAGGCTGGTCAGACACCAGCAGACCCACTGGAAGCAGAAGAGCTACCTTTGCCCTATCTGTGACCTCTCCTTTGGGGAGAAAGAGGGCCTTATGGATCACTGGAGGGGCTATAAAGGCAAGGACCTGTGCCAGAGCAGCCACCATAAATGCCGGGTGATCCTGGGCCAGTGGCTTGGCTTCTCTCATGATGTCCCCACTATGGCTGGGGAGGAATGGAAGCATGGAGGTGATCAATCTCCCCCCAGGATCCATACCCCCAGGAGAAGAGGCCTAAGAGAGAAGGCCTGCAAAGGAGACAAAACAAAGGAGGCAGTGAGCATCTTGAAACATAAA
+>ENST00000448800.5|chromosome:hg38:chr6_GL000250v2_alt:2862985:2871389:-
+ATGTGTCACACTCGGGAGTTGGCTTTTCAGATCAGCAAGGAATATGAGCGCTTCTCTAAATACATGCCCAATGTCAAGGTTGCTGTTTTTTTTGGTGGTCTGTCTATCAAGAAGGATGAAGAGGTGCTGAAGAAGAACTGCCCGCATATCGTCGTGGGGACTCCAGGCCGTATCCTAGCCCTGGCTCGAAATAAGAGCCTCAACCTCAAACACATTAAACACTTTATTTTGGATGAATGTGATAAGATGCTTGAACAGCTCGACATGCGTCGGGATGTCCAGGAAATTTTTCGCATGACCCCCCACGAGAAGCAGGTCATGATGTTCAGTGCTACCTTGAGCAAAGAGATCCGTCCAGTCTGCCGCAAGTTCATGCAAGATCCAATGGAGATCTTCGTGGATGATGAGACGAAGTTGACGCTGCATGGGTTGCAGCAGTACTACGTGAAACTGAAGGACAACGAGAAGAACCGGAAGCTCTTTGACCTTCTGGATGTCCTTGAGTTCAACCAGGTGGTGATCTTTGTGAAGTCTGTGCAGCGGTGCATTGCCTTGGCCCAGCTACTAGTGGAGCAGAACTTCCCAGCCATTGCCATCCACCGTGGGATGCCCCAGGAGGAGAGGCTTTCTCGGTATCAGCAGTTTAAAGATTTTCAACGACGAATTCTTGTGGCTACCAACCTATTTGGCCGAGGCATGGACATCGAGCGGGTGAACATTGCTTTTAATTATGACATGCCTGAGGATTCTGACACCTACCTGCATCGGGTGGCCAGAGCAGGCCGGTTTGGCACCAAGGGCTTGGCTATCACATTTGTGTCCGATGAGAATGATGCCAAGATCCTCAATGATGTGCAGGATCGCTTTGAGGTCAATATTAGTGAGCTGCCTGATGAGATAGACATCTCCTCCTACATTGAACAGACACGG
+>ENST00000445122.5|chromosome:hg38:chr6_GL000250v2_alt:3481820:3484425:-
+ATGTCATCCGAAAAGTCAGGAGACTCGCTTCGAGGGCCCACTTcccccgccgccgcccgctgccgccgccccgcccccgccggcgccagccCAGACTGCCCAGGCCCCTGGCTTCGTGGTGCCCACGCACGCGGGGACTGTGGGCACGCTGCCGCTGGGGGGCTACGTAGCGCCCGGATACCCCCTGCAGCTGCAGCCTTGCACTGCTTACGTGCCGGTCTACCCGGTGGGCACGCCATATGCAGGCGGGACCCCGGGGGGAACAGGAGTGACCTCCACTCTCCCCCCGCCGCCCCAGGGCCCAGGGCTGGCCCTACTGGAGCCGAGGCGCCCGCCACACGACTACATGCCCATCGCGGTGCTGACCACCATCTGTTGCTTCTGGCCTACTGGCATCATTGCCATCTTCAAGGCCGTGCAGGTGCGCACGGCCTTGGCCCGCGGAGACATGGTGTCGGCCGAGATCGCTTCACGCGAGGCCCGGAACTTCTCCTTCATCTCCCTGGCCGTGGGCATCGCGGCCATGGTGCTCTGTACCATCCTCACCGTAGTCATCATCATCGCCGCGCAGCACCACGAGAACTACTGGGATCCCTA
+>ENST00000430777.2|chromosome:hg38:chr6_GL000250v2_alt:3503057:3504078:-
+ATGGAtgctgctgctgctgctcttcctgctgctgctcttcctgctgcCCACCCTGTGGTTCTGCAGCCCCAGTGCCAAGTACTTCTTCAAGATGGCCTTCTACAATGGCTGGATCCTCTTCCTGGCTGTGCTCGCCATCCCTGTGTGTGCCGTGCGAGGACGCAACGTCGAGAACATGAAGATCTTGCGTCTAATGCTGCTCCACATCAAATACCTGTACGGGATCCGAGTGGAGGTGCGAGGGGCTCACCACTTCCCTCCCTCGCAGCCCTATGTTGTTGTCTCCAACCACCAGAGCTCTCTCGATCTGCTTGGGATGATGGAGGTACTGCCAGGCCGCTGTGTGCCCATTGCCAAGCGCGAGCTACTGTGggctggctctgccgggctggcctgctggctggcaggAGTCATCTTCATCGACCGGAAGCGCACGGGGGATGCCATCAGTGTCATGTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptide_fasta_out.fasta	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,8 @@
+>ENST00000432222.1|chromosome:hg38:chr6_GL000250v2_alt:938210:938801:-
+MAQNQASVLKNQAPVTRTQAPITGTLCQDARSNSHPVKPSRLNVFCCPHCSLTFSKKSYLSRHQKAHLTEPPNYCFHCSKSFSSFSRLVRHQQTHWKQKSYLCPICDLSFGEKEGLMDHWRGYKGKDLCQSSHHKCRVILGQWLGFSHDVPTMAGEEWKHGGDQSPPRIHTPRRRGLREKACKGDKTKEAVSILKHK
+>ENST00000448800.5|chromosome:hg38:chr6_GL000250v2_alt:2862985:2871389:-
+MCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDETKLTLHGLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCIALAQLLVEQNFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLFGRGMDIERVNIAFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDENDAKILNDVQDRFEVNISELPDEIDISSYIEQTR
+>ENST00000445122.5|chromosome:hg38:chr6_GL000250v2_alt:3481820:3484425:-
+MSSEKSGDSLRGPTSPAAARCRRPAPAGASPDCPGPWLRGAHARGDCGHAAAGGLRSARIPPAAAALHCLRAGLPGGHAICRRDPGGNRSDLHSPPAAPGPRAGPTGAEAPATRLHAHRGADHHLLLLAYWHHCHLQGRAGAHGLGPRRHGVGRDRFTRGPELLLHLPGRGHRGHGALYHPHRSHHHRRAAPRELLGSL
+>ENST00000430777.2|chromosome:hg38:chr6_GL000250v2_alt:3503057:3504078:-
+MDAAAAALPAAALPAAHPVVLQPQCQVLLQDGLLQWLDPLPGCARHPCVCRARTQRREHEDLASNAAPHQIPVRDPSGGARGSPLPSLAALCCCLQPPELSRSAWDDGGTARPLCAHCQARATVGWLCRAGLLAGRSHLHRPEAHGGCHQCHV
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/twobit.loc	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>    <FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2    /depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1    /depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2    /depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/twobit.loc.sample	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that is used by some
+#tools.  The twobit.loc file has this format (white space characters 
+#are TAB characters):
+#
+#<Build>    <FullPathToFile>
+#
+#So, for example, if you had droPer1 twobit files stored in 
+#/depot/data2/galaxy/droPer1/, then the twobit.loc entry 
+#would look like this:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#
+#and your /depot/data2/galaxy/droPer1/ directory would 
+#contain all of your twobit files (e.g.):
+#
+#-rw-rw-r--   1 nate   galaxy 48972650 2007-05-04 11:27 droPer1.2bit
+#...etc...
+#
+#Your twobit.loc file should include an entry per line for each twobit 
+#file you have stored.  For example:
+#
+#droPer1    /depot/data2/galaxy/droPer1/droPer1.2bit
+#apiMel2    /depot/data2/galaxy/apiMel2/apiMel2.2bit
+#droAna1    /depot/data2/galaxy/droAna1/droAna1.2bit
+#droAna2    /depot/data2/galaxy/droAna2/droAna2.2bit
+#...etc...
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of reference fasta files -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the 2bit format -->
+    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, path</columns>
+        <file path="tool-data/twobit.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Mon Apr 11 20:37:19 2022 +0000
@@ -0,0 +1,13 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of reference fasta files -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+    <!-- Locations of indexes in the 2bit format -->
+    <table name="twobit" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, path</columns>
+        <file path="${__HERE__}/test-data/twobit.loc" />
+    </table>
+</tables>