Mercurial > repos > iuc > homer_scanmotifgenomewide
changeset 0:db456c398880 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/homer_scanMotifGenomeWide.xml Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,94 @@ +<tool id="homer_scanMotifGenomeWide" name="scanMotifGenomeWide" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT"> + <description/> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +scanMotifGenomeWide.pl +'$motif' +#if str( $genome.source ) == "installed": + '$genome.all_fasta_source.fields.path' +#elif str( $genome.source ) == "history": + '$genome.fasta' +#end if +$bed +$keepAll +$mask +$Fivep +$homer1 +> +#if $bed: + '${output_bed}' +#else + '${output_text}' +#end if + ]]></command> + <inputs> + <param name="motif" type="data" format="txt" label="Motif file"/> + <conditional name="genome"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?"> + <option value="installed">Installed</option> + <option value="history">From History</option> + </param> + <when value="installed"> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No references are available"/> + </options> + </param> + </when> + <when value="history"> + <param name="fasta" type="data" format="fasta" label="Select reference genome"/> + </when> + </conditional> + <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" label="Output bed format"/> + <param argument="-keepAll" type="boolean" truevalue="-keepAll" falsevalue="" checked="false" label="Report all motifs even if overlap" + help="By default, HOMER will remove a motif that overlaps itself, useful for palindromes. To report all, specify this option."/> + <param argument="-mask" type="boolean" truevalue="-mask" falsevalue="" checked="false" + label="Do not look for motifs in RepeatMasked sequence (lower case sequence in FASTA files)"/> + <param argument="-5p" name="Fivep" type="boolean" truevalue="-5p" falsevalue="" checked="false" + label="Report motif positions based on the 5' end of the motif sequence"/> + <param argument="-homer1" type="boolean" truevalue="-homer1" falsevalue="" checked="false" + label="Use homer1 instead of homer2"/> + </inputs> + <outputs> + <data format="tabular" name="output_text" label="${tool.name} on ${on_string}"> + <filter>bed is False</filter> + </data> + <data format="bed" name="output_bed" label="${tool.name} on ${on_string}"> + <filter>bed is True</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="motif" value="motif_test1/homerResults/motif1.motif"/> + <conditional name="genome"> + <param name="source" value="installed"/> + <param name="all_fasta_source" value="phiX174"/> + </conditional> + <output name="output_text" file="scanMotif_res1.txt" ftype="tabular"/> + </test> + <test expect_num_outputs="1"> + <param name="motif" value="motif_test1/homerResults/motif1.motif"/> + <conditional name="genome"> + <param name="source" value="history"/> + <param name="fasta" value="phiX174.fasta"/> + </conditional> + <param name="bed" value="-bed"/> + <output name="output_bed" file="scanMotif_res1.bed" ftype="bed"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + + This is a wrapper for scanMotifGenomeWide.pl from HOMER but not all options are included. + + The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome. + + ]]></help> + <expand macro="citation"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,49 @@ +<macros> + <token name="@TOOL_VERSION@">4.11</token> + <!-- HOMER index version compatible with this version of HOMER + This is the HOMER version that introduced the preparsed structure expected + by the current version. --> + <token name="@IDX_VERSION@">4.11</token> + <token name="@VERSION_SUFFIX@">2</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">homer</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.11">homer</requirement> + </requirements> + </xml> + <xml name="choose_center"> + <conditional name="choose_center"> + <param name="center" type="select" label="Do you want to center your sequence on the peak center?"> + <option value="centered" selected="True">Yes</option> + <option value="manual">No, I want asymetric (raise an error if given was chosen above)</option> + </param> + <when value="centered"/> + <when value="manual"> + <param name="sizes" type="integer" value="-100" label="sequence start relative to center"/> + </when> + </conditional> + </xml> + <xml name="mask_size"> + <param argument="-mask" type="boolean" truevalue="True" falsevalue="False" label="mask repeats/lower case sequence"/> + <conditional name="fixed_size"> + <param name="size_fixed" type="select" label="Do you want a fixed fragment size?"> + <option value="fixed" selected="True">Yes</option> + <option value="given">No, I want to keep the size of my peaks (-size given)</option> + </param> + <when value="given"/> + <when value="fixed"> + <param argument="-size" type="integer" min="0" value="200" label="fragment size in bp"/> + <expand macro="choose_center"/> + </when> + </conditional> + </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1016/j.molcel.2010.05.004</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks.bed Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,66 @@ +chr10 95489848 95489849 chr10:95489648-95490124 9.37574 + 95489848 95489848 236,28,36 +chr10 95550657 95550658 chr10:95550458-95550913 22.4312 + 95550657 95550657 236,28,36 +chr10 95551883 95551884 chr10:95551647-95552156 9.8358 + 95551883 95551883 236,28,36 +chr10 95557476 95557477 chr10:95557210-95557760 15.8474 + 95557476 95557476 236,28,36 +chr10 95858373 95858374 chr10:95858061-95858620 8.91987 - 95858373 95858373 46,49,145 +chr10 95894941 95894942 chr10:95894657-95895156 14.5144 - 95894941 95894941 46,49,145 +chr10 95898656 95898657 chr10:95898384-95898961 12.5406 + 95898656 95898656 236,28,36 +chr10 96033867 96033868 chr10:96033562-96034101 20.0255 - 96033867 96033867 46,49,145 +chr10 96080634 96080635 chr10:96080279-96080903 6.11901 - 96080634 96080634 46,49,145 +chr10 96105359 96105360 chr10:96104999-96105605 12.8558 - 96105359 96105359 46,49,145 +chr10 96132305 96132306 chr10:96131980-96132540 14.3011 + 96132305 96132305 236,28,36 +chr10 96182451 96182452 chr10:96182221-96182632 9.96549 + 96182451 96182451 236,28,36 +chr10 96214052 96214053 chr10:96213797-96214300 26.3993 + 96214052 96214052 236,28,36 +chr10 96616854 96616855 chr10:96616623-96617093 4.72295 - 96616854 96616854 46,49,145 +chr10 96618518 96618519 chr10:96618332-96618740 7.7811 + 96618518 96618518 236,28,36 +chr10 96934833 96934834 chr10:96934538-96935160 10.7794 - 96934833 96934833 46,49,145 +chr10 97160696 97160697 chr10:97160138-97160734 9.26797 - 97160696 97160696 46,49,145 +chr10 97313143 97313144 chr10:97312750-97313424 16.1617 - 97313143 97313143 46,49,145 +chr10 97340069 97340070 chr10:97339748-97340355 8.23779 - 97340069 97340069 46,49,145 +chr10 97345534 97345535 chr10:97345244-97345845 21.9543 + 97345534 97345534 236,28,36 +chr10 97375992 97375993 chr10:97375737-97376277 17.1427 + 97375992 97375992 236,28,36 +chr10 97670411 97670412 chr10:97670243-97670641 15.0213 - 97670411 97670411 46,49,145 +chr10 97689620 97689621 chr10:97689400-97689842 6.20282 - 97689620 97689620 46,49,145 +chr10 97704766 97704767 chr10:97704497-97705056 12.2858 - 97704766 97704766 46,49,145 +chr10 97712886 97712887 chr10:97712528-97713193 16.5834 + 97712886 97712886 236,28,36 +chr10 97768453 97768454 chr10:97768293-97768873 -1.29559 . 97768453 97768453 0,0,0 +chr2 73745858 73745859 chr2:73745562-73746116 15.583 - 73745858 73745858 46,49,145 +chr2 73792430 73792431 chr2:73792224-73792669 11.3969 + 73792430 73792430 236,28,36 +chr2 73868302 73868303 chr2:73868052-73868532 16.5297 - 73868302 73868302 46,49,145 +chr2 73925250 73925251 chr2:73924997-73925519 6.64944 + 73925250 73925250 236,28,36 +chr2 73947567 73947568 chr2:73947347-73947809 11.7 - 73947567 73947567 46,49,145 +chr2 73965796 73965797 chr2:73965501-73966069 18.8918 + 73965796 73965796 236,28,36 +chr2 73987358 73987359 chr2:73987054-73987519 5.75056 - 73987358 73987358 46,49,145 +chr2 73998748 73998749 chr2:73998449-73999023 4.45417 - 73998748 73998748 46,49,145 +chr2 74027927 74027928 chr2:74027638-74028176 17.1136 + 74027927 74027927 236,28,36 +chr2 74066830 74066831 chr2:74066544-74067106 4.26306 + 74066830 74066830 236,28,36 +chr2 74247701 74247702 chr2:74247519-74247926 19.6437 - 74247701 74247701 46,49,145 +chr2 74300454 74300455 chr2:74300183-74300724 21.3163 + 74300454 74300454 236,28,36 +chr2 74305972 74305973 chr2:74305723-74306142 15.4325 - 74305972 74305972 46,49,145 +chr2 74655531 74655532 chr2:74655214-74655823 11.0865 - 74655531 74655531 46,49,145 +chr2 74661783 74661784 chr2:74661581-74662231 6.32635 - 74661783 74661783 46,49,145 +chr2 74663751 74663752 chr2:74663455-74664030 5.5749 - 74663751 74663751 46,49,145 +chr2 74673182 74673183 chr2:74672881-74673432 11.6759 - 74673182 74673182 46,49,145 +chr2 74686486 74686487 chr2:74686220-74686785 8.18583 + 74686486 74686486 236,28,36 +chr2 74691769 74691770 chr2:74691505-74692018 10.8344 + 74691769 74691769 236,28,36 +chr2 74694233 74694234 chr2:74693923-74694529 6.49186 - 74694233 74694233 46,49,145 +chr2 74702401 74702402 chr2:74702109-74702707 16.3674 + 74702401 74702401 236,28,36 +chr2 74715927 74715928 chr2:74715602-74716472 18.4944 + 74715927 74715927 236,28,36 +chr2 74964543 74964544 chr2:74964211-74964829 19.6671 - 74964543 74964543 46,49,145 +chr2 74977548 74977549 chr2:74977360-74977813 6.64332 + 74977548 74977548 236,28,36 +chr2 75055369 75055370 chr2:75055077-75055687 25.0987 - 75055369 75055369 46,49,145 +chr2 75138095 75138096 chr2:75137844-75138351 14.9999 - 75138095 75138095 46,49,145 +chr2 75151177 75151178 chr2:75150910-75151415 21.6232 - 75151177 75151177 46,49,145 +chr2 75152696 75152697 chr2:75152384-75152964 19.3701 - 75152696 75152696 46,49,145 +chr2 75208425 75208426 chr2:75208163-75208613 20.9151 - 75208425 75208425 46,49,145 +chr2 75312439 75312440 chr2:75312148-75312690 12.976 - 75312439 75312439 46,49,145 +chr2 75318398 75318399 chr2:75318086-75318603 15.8984 - 75318398 75318398 46,49,145 +chr2 75515510 75515511 chr2:75515254-75515778 6.45021 - 75515510 75515510 46,49,145 +chr2 75563785 75563786 chr2:75563556-75564002 6.81984 - 75563785 75563785 46,49,145 +chr2 75588782 75588783 chr2:75588511-75588998 13.9441 - 75588782 75588782 46,49,145 +chr2 75590417 75590418 chr2:75590116-75590691 15.844 - 75590417 75590417 46,49,145 +chr2 75603329 75603330 chr2:75603091-75603554 11.5679 - 75603329 75603329 46,49,145 +chr2 75605891 75605892 chr2:75605600-75606199 11.5138 + 75605891 75605891 236,28,36 +chr2 75658764 75658765 chr2:75658517-75658909 0.26272 + 75658764 75658764 236,28,36 +chr2 75781339 75781340 chr2:75781071-75781581 10.7504 - 75781339 75781339 46,49,145 +chr2 75786285 75786286 chr2:75786025-75786608 17.3776 + 75786285 75786285 236,28,36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_first.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,67 @@ +PeakID (cmd=annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf -ann test-data/annotations_default_simplified.txt) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type +chr10:96213797-96214300 chr10 96214053 96214053 + 26.3993 NA NA NA NA NA +chr2:75055077-75055687 chr2 75055370 75055370 - 25.0987 NA Intergenic NA -339374 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:95550458-95550913 chr10 95550658 95550658 + 22.4312 NA NA NA NA NA +chr10:97345244-97345845 chr10 97345535 97345535 + 21.9543 NA NA NA NA NA +chr2:75150910-75151415 chr2 75151178 75151178 - 21.6232 NA Intergenic NA -435182 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74300183-74300724 chr2 74300455 74300455 + 21.3163 NA Intergenic NA -367855 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:75208163-75208613 chr2 75208426 75208426 - 20.9151 NA Intergenic NA -492430 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:96033562-96034101 chr10 96033868 96033868 - 20.0255 NA NA NA NA NA +chr2:74964211-74964829 chr2 74964544 74964544 - 19.6671 NA Intergenic NA -248548 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74247519-74247926 chr2 74247702 74247702 - 19.6437 NA Intergenic NA -420608 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:75152384-75152964 chr2 75152697 75152697 - 19.3701 NA Intergenic NA -436701 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73965501-73966069 chr2 73965797 73965797 + 18.8918 NA Intergenic NA -702513 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74715602-74716472 chr2 74715928 74715928 + 18.4944 NA promoter-TSS (ENSMUST00000145799) NA 68 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:75786025-75786608 chr2 75786286 75786286 + 17.3776 NA Intergenic NA -1070290 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:97375737-97376277 chr10 97375993 97375993 + 17.1427 NA NA NA NA NA +chr2:74027638-74028176 chr2 74027928 74027928 + 17.1136 NA Intergenic NA -640382 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:97712528-97713193 chr10 97712887 97712887 + 16.5834 NA NA NA NA NA +chr2:73868052-73868532 chr2 73868303 73868303 - 16.5297 NA Intergenic NA -800007 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74702109-74702707 chr2 74702402 74702402 + 16.3674 NA Intergenic NA -1260 ENSMUST00000198895 ENSMUSG00000104570 ENSMUST00000198895 Gm44463 miRNA +chr10:97312750-97313424 chr10 97313144 97313144 - 16.1617 NA NA NA NA NA +chr2:75318086-75318603 chr2 75318399 75318399 - 15.8984 NA Intergenic NA -602403 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:95557210-95557760 chr10 95557477 95557477 + 15.8474 NA NA NA NA NA +chr2:75590116-75590691 chr2 75590418 75590418 - 15.844 NA Intergenic NA -874422 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73745562-73746116 chr2 73745859 73745859 - 15.583 NA Intergenic NA -922451 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74305723-74306142 chr2 74305973 74305973 - 15.4325 NA Intergenic NA -362337 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:97670243-97670641 chr10 97670412 97670412 - 15.0213 NA NA NA NA NA +chr2:75137844-75138351 chr2 75138096 75138096 - 14.9999 NA Intergenic NA -422100 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:95894657-95895156 chr10 95894942 95894942 - 14.5144 NA NA NA NA NA +chr10:96131980-96132540 chr10 96132306 96132306 + 14.3011 NA NA NA NA NA +chr2:75588511-75588998 chr2 75588783 75588783 - 13.9441 NA Intergenic NA -872787 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:75312148-75312690 chr2 75312440 75312440 - 12.976 NA Intergenic NA -596444 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:96104999-96105605 chr10 96105360 96105360 - 12.8558 NA NA NA NA NA +chr10:95898384-95898961 chr10 95898657 95898657 + 12.5406 NA NA NA NA NA +chr10:97704497-97705056 chr10 97704767 97704767 - 12.2858 NA NA NA NA NA +chr2:73947347-73947809 chr2 73947568 73947568 - 11.7 NA Intergenic NA -720742 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74672881-74673432 chr2 74673183 74673183 - 11.6759 NA Intergenic NA -1830 ENSMUST00000001878 ENSMUSG00000001823 ENSMUST00000001878 Hoxd12 protein_coding +chr2:75603091-75603554 chr2 75603330 75603330 - 11.5679 NA Intergenic NA -887334 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:75605600-75606199 chr2 75605892 75605892 + 11.5138 NA Intergenic NA -889896 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73792224-73792669 chr2 73792431 73792431 + 11.3969 NA Intergenic NA -875879 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74655214-74655823 chr2 74655532 74655532 - 11.0865 NA Intergenic NA -12778 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74691505-74692018 chr2 74691770 74691770 + 10.8344 NA promoter-TSS (ENSMUST00000061745) NA -154 ENSMUST00000061745 ENSMUSG00000050368 ENSMUST00000061745 Hoxd10 protein_coding +chr10:96934538-96935160 chr10 96934834 96934834 - 10.7794 NA NA NA NA NA +chr2:75781071-75781581 chr2 75781340 75781340 - 10.7504 NA Intergenic NA -1065344 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:96182221-96182632 chr10 96182452 96182452 + 9.96549 NA NA NA NA NA +chr10:95551647-95552156 chr10 95551884 95551884 + 9.8358 NA NA NA NA NA +chr10:95489648-95490124 chr10 95489849 95489849 + 9.37574 NA NA NA NA NA +chr10:97160138-97160734 chr10 97160697 97160697 - 9.26797 NA NA NA NA NA +chr10:95858061-95858620 chr10 95858374 95858374 - 8.91987 NA NA NA NA NA +chr10:97339748-97340355 chr10 97340070 97340070 - 8.23779 NA NA NA NA NA +chr2:74686220-74686785 chr2 74686487 74686487 + 8.18583 NA exon (ENSMUST00000048086, exon 2 of 2) NA 3041 ENSMUST00000136302 ENSMUSG00000099521 ENSMUST00000136302 Gm28309 processed_transcript +chr10:96618332-96618740 chr10 96618519 96618519 + 7.7811 NA NA NA NA NA +chr2:75563556-75564002 chr2 75563786 75563786 - 6.81984 NA Intergenic NA -847790 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73924997-73925519 chr2 73925251 73925251 + 6.64944 NA Intergenic NA -743059 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74977360-74977813 chr2 74977549 74977549 + 6.64332 NA Intergenic NA -261553 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74693923-74694529 chr2 74694234 74694234 - 6.49186 NA TTS (ENSMUST00000136302) NA -1286 ENSMUST00000126966 ENSMUSG00000086077 ENSMUST00000126966 Gm14396 lincRNA +chr2:75515254-75515778 chr2 75515511 75515511 - 6.45021 NA Intergenic NA -799515 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74661581-74662231 chr2 74661784 74661784 - 6.32635 NA Intergenic NA -6526 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:97689400-97689842 chr10 97689621 97689621 - 6.20282 NA NA NA NA NA +chr10:96080279-96080903 chr10 96080635 96080635 - 6.11901 NA NA NA NA NA +chr2:73987054-73987519 chr2 73987359 73987359 - 5.75056 NA Intergenic NA -680951 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74663455-74664030 chr2 74663752 74663752 - 5.5749 NA Intergenic NA -4558 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:96616623-96617093 chr10 96616855 96616855 - 4.72295 NA NA NA NA NA +chr2:73998449-73999023 chr2 73998749 73998749 - 4.45417 NA Intergenic NA -669561 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74066544-74067106 chr2 74066831 74066831 + 4.26306 NA Intergenic NA -601479 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:75658517-75658909 chr2 75658765 75658765 + 0.26272 NA Intergenic NA -942769 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:97768293-97768873 chr10 97768454 97768454 + -1.29559 NA NA NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_second.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,67 @@ +PeakID (cmd=annotatePeaks.pl test-data/CTCF_peaks.bed none -ann test-data/annotations_default.txt) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type +chr10:96213797-96214300 chr10 96214053 96214053 + 26.3993 NA NA NA NA NA +chr2:75055077-75055687 chr2 75055370 75055370 - 25.0987 NA Intergenic NA NA NA +chr10:95550458-95550913 chr10 95550658 95550658 + 22.4312 NA NA NA NA NA +chr10:97345244-97345845 chr10 97345535 97345535 + 21.9543 NA NA NA NA NA +chr2:75150910-75151415 chr2 75151178 75151178 - 21.6232 NA Intergenic NA NA NA +chr2:74300183-74300724 chr2 74300455 74300455 + 21.3163 NA Intergenic NA NA NA +chr2:75208163-75208613 chr2 75208426 75208426 - 20.9151 NA Intergenic NA NA NA +chr10:96033562-96034101 chr10 96033868 96033868 - 20.0255 NA NA NA NA NA +chr2:74964211-74964829 chr2 74964544 74964544 - 19.6671 NA Intergenic NA NA NA +chr2:74247519-74247926 chr2 74247702 74247702 - 19.6437 NA Intergenic NA NA NA +chr2:75152384-75152964 chr2 75152697 75152697 - 19.3701 NA Intergenic NA NA NA +chr2:73965501-73966069 chr2 73965797 73965797 + 18.8918 NA Intergenic NA NA NA +chr2:74715602-74716472 chr2 74715928 74715928 + 18.4944 NA promoter-TSS (ENSMUST00000145799) NA NA NA +chr2:75786025-75786608 chr2 75786286 75786286 + 17.3776 NA Intergenic NA NA NA +chr10:97375737-97376277 chr10 97375993 97375993 + 17.1427 NA NA NA NA NA +chr2:74027638-74028176 chr2 74027928 74027928 + 17.1136 NA Intergenic NA NA NA +chr10:97712528-97713193 chr10 97712887 97712887 + 16.5834 NA NA NA NA NA +chr2:73868052-73868532 chr2 73868303 73868303 - 16.5297 NA Intergenic NA NA NA +chr2:74702109-74702707 chr2 74702402 74702402 + 16.3674 NA TTS (ENSMUST00000132326) NA NA NA +chr10:97312750-97313424 chr10 97313144 97313144 - 16.1617 NA NA NA NA NA +chr2:75318086-75318603 chr2 75318399 75318399 - 15.8984 NA Intergenic NA NA NA +chr10:95557210-95557760 chr10 95557477 95557477 + 15.8474 NA NA NA NA NA +chr2:75590116-75590691 chr2 75590418 75590418 - 15.844 NA Intergenic NA NA NA +chr2:73745562-73746116 chr2 73745859 73745859 - 15.583 NA Intergenic NA NA NA +chr2:74305723-74306142 chr2 74305973 74305973 - 15.4325 NA Intergenic NA NA NA +chr10:97670243-97670641 chr10 97670412 97670412 - 15.0213 NA NA NA NA NA +chr2:75137844-75138351 chr2 75138096 75138096 - 14.9999 NA Intergenic NA NA NA +chr10:95894657-95895156 chr10 95894942 95894942 - 14.5144 NA NA NA NA NA +chr10:96131980-96132540 chr10 96132306 96132306 + 14.3011 NA NA NA NA NA +chr2:75588511-75588998 chr2 75588783 75588783 - 13.9441 NA Intergenic NA NA NA +chr2:75312148-75312690 chr2 75312440 75312440 - 12.976 NA Intergenic NA NA NA +chr10:96104999-96105605 chr10 96105360 96105360 - 12.8558 NA NA NA NA NA +chr10:95898384-95898961 chr10 95898657 95898657 + 12.5406 NA NA NA NA NA +chr10:97704497-97705056 chr10 97704767 97704767 - 12.2858 NA NA NA NA NA +chr2:73947347-73947809 chr2 73947568 73947568 - 11.7 NA Intergenic NA NA NA +chr2:74672881-74673432 chr2 74673183 74673183 - 11.6759 NA Intergenic NA NA NA +chr2:75603091-75603554 chr2 75603330 75603330 - 11.5679 NA Intergenic NA NA NA +chr2:75605600-75606199 chr2 75605892 75605892 + 11.5138 NA Intergenic NA NA NA +chr2:73792224-73792669 chr2 73792431 73792431 + 11.3969 NA Intergenic NA NA NA +chr2:74655214-74655823 chr2 74655532 74655532 - 11.0865 NA Intergenic NA NA NA +chr2:74691505-74692018 chr2 74691770 74691770 + 10.8344 NA promoter-TSS (ENSMUST00000061745) NA NA NA +chr10:96934538-96935160 chr10 96934834 96934834 - 10.7794 NA NA NA NA NA +chr2:75781071-75781581 chr2 75781340 75781340 - 10.7504 NA Intergenic NA NA NA +chr10:96182221-96182632 chr10 96182452 96182452 + 9.96549 NA NA NA NA NA +chr10:95551647-95552156 chr10 95551884 95551884 + 9.8358 NA NA NA NA NA +chr10:95489648-95490124 chr10 95489849 95489849 + 9.37574 NA NA NA NA NA +chr10:97160138-97160734 chr10 97160697 97160697 - 9.26797 NA NA NA NA NA +chr10:95858061-95858620 chr10 95858374 95858374 - 8.91987 NA NA NA NA NA +chr10:97339748-97340355 chr10 97340070 97340070 - 8.23779 NA NA NA NA NA +chr2:74686220-74686785 chr2 74686487 74686487 + 8.18583 NA exon (ENSMUST00000048086, exon 2 of 2) NA NA NA +chr10:96618332-96618740 chr10 96618519 96618519 + 7.7811 NA NA NA NA NA +chr2:75563556-75564002 chr2 75563786 75563786 - 6.81984 NA Intergenic NA NA NA +chr2:73924997-73925519 chr2 73925251 73925251 + 6.64944 NA Intergenic NA NA NA +chr2:74977360-74977813 chr2 74977549 74977549 + 6.64332 NA Intergenic NA NA NA +chr2:74693923-74694529 chr2 74694234 74694234 - 6.49186 NA TTS (ENSMUST00000136302) NA NA NA +chr2:75515254-75515778 chr2 75515511 75515511 - 6.45021 NA Intergenic NA NA NA +chr2:74661581-74662231 chr2 74661784 74661784 - 6.32635 NA Intergenic NA NA NA +chr10:97689400-97689842 chr10 97689621 97689621 - 6.20282 NA NA NA NA NA +chr10:96080279-96080903 chr10 96080635 96080635 - 6.11901 NA NA NA NA NA +chr2:73987054-73987519 chr2 73987359 73987359 - 5.75056 NA Intergenic NA NA NA +chr2:74663455-74664030 chr2 74663752 74663752 - 5.5749 NA Intergenic NA NA NA +chr10:96616623-96617093 chr10 96616855 96616855 - 4.72295 NA NA NA NA NA +chr2:73998449-73999023 chr2 73998749 73998749 - 4.45417 NA Intergenic NA NA NA +chr2:74066544-74067106 chr2 74066831 74066831 + 4.26306 NA Intergenic NA NA NA +chr2:75658517-75658909 chr2 75658765 75658765 + 0.26272 NA Intergenic NA NA NA +chr10:97768293-97768873 chr10 97768454 97768454 + -1.29559 NA NA NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_shifted.bed Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,24 @@ +mm10_dna 5858 5859 chr2:73745562-73746116 15.583 - 73745858 73745858 46,49,145 +mm10_dna 52430 52431 chr2:73792224-73792669 11.3969 + 73792430 73792430 236,28,36 +mm10_dna 128302 128303 chr2:73868052-73868532 16.5297 - 73868302 73868302 46,49,145 +mm10_dna 185250 185251 chr2:73924997-73925519 6.64944 + 73925250 73925250 236,28,36 +mm10_dna 207567 207568 chr2:73947347-73947809 11.7 - 73947567 73947567 46,49,145 +mm10_dna 225796 225797 chr2:73965501-73966069 18.8918 + 73965796 73965796 236,28,36 +mm10_dna 247358 247359 chr2:73987054-73987519 5.75056 - 73987358 73987358 46,49,145 +mm10_dna 258748 258749 chr2:73998449-73999023 4.45417 - 73998748 73998748 46,49,145 +mm10_dna 287927 287928 chr2:74027638-74028176 17.1136 + 74027927 74027927 236,28,36 +mm10_dna 326830 326831 chr2:74066544-74067106 4.26306 + 74066830 74066830 236,28,36 +mm10_dna 507701 507702 chr2:74247519-74247926 19.6437 - 74247701 74247701 46,49,145 +mm10_dna 560454 560455 chr2:74300183-74300724 21.3163 + 74300454 74300454 236,28,36 +mm10_dna 565972 565973 chr2:74305723-74306142 15.4325 - 74305972 74305972 46,49,145 +mm10_dna 915531 915532 chr2:74655214-74655823 11.0865 - 74655531 74655531 46,49,145 +mm10_dna 921783 921784 chr2:74661581-74662231 6.32635 - 74661783 74661783 46,49,145 +mm10_dna 923751 923752 chr2:74663455-74664030 5.5749 - 74663751 74663751 46,49,145 +mm10_dna 933182 933183 chr2:74672881-74673432 11.6759 - 74673182 74673182 46,49,145 +mm10_dna 946486 946487 chr2:74686220-74686785 8.18583 + 74686486 74686486 236,28,36 +mm10_dna 951769 951770 chr2:74691505-74692018 10.8344 + 74691769 74691769 236,28,36 +mm10_dna 954233 954234 chr2:74693923-74694529 6.49186 - 74694233 74694233 46,49,145 +mm10_dna 962401 962402 chr2:74702109-74702707 16.3674 + 74702401 74702401 236,28,36 +mm10_dna 975927 975928 chr2:74715602-74716472 18.4944 + 74715927 74715927 236,28,36 +mm10_dna 1224543 1224544 chr2:74964211-74964829 19.6671 - 74964543 74964543 46,49,145 +mm10_dna 1237548 1237549 chr2:74977360-74977813 6.64332 + 74977548 74977548 236,28,36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_third.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,67 @@ +PeakID (cmd=annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type +chr10:96213797-96214300 chr10 96214053 96214053 + 26.3993 NA NA NA NA NA +chr2:75055077-75055687 chr2 75055370 75055370 - 25.0987 NA Intergenic Intergenic -339374 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:95550458-95550913 chr10 95550658 95550658 + 22.4312 NA NA NA NA NA +chr10:97345244-97345845 chr10 97345535 97345535 + 21.9543 NA NA NA NA NA +chr2:75150910-75151415 chr2 75151178 75151178 - 21.6232 NA Intergenic Intergenic -435182 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74300183-74300724 chr2 74300455 74300455 + 21.3163 NA Intergenic Intergenic -367855 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:75208163-75208613 chr2 75208426 75208426 - 20.9151 NA Intergenic Intergenic -492430 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:96033562-96034101 chr10 96033868 96033868 - 20.0255 NA NA NA NA NA +chr2:74964211-74964829 chr2 74964544 74964544 - 19.6671 NA Intergenic Intergenic -248548 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74247519-74247926 chr2 74247702 74247702 - 19.6437 NA Intergenic Intergenic -420608 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:75152384-75152964 chr2 75152697 75152697 - 19.3701 NA Intergenic Intergenic -436701 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73965501-73966069 chr2 73965797 73965797 + 18.8918 NA Intergenic Intergenic -702513 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74715602-74716472 chr2 74715928 74715928 + 18.4944 NA promoter-TSS (ENSMUST00000145799) antisense-promoter-TSS (ENSMUST00000145799) 68 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:75786025-75786608 chr2 75786286 75786286 + 17.3776 NA Intergenic Intergenic -1070290 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:97375737-97376277 chr10 97375993 97375993 + 17.1427 NA NA NA NA NA +chr2:74027638-74028176 chr2 74027928 74027928 + 17.1136 NA Intergenic Intergenic -640382 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:97712528-97713193 chr10 97712887 97712887 + 16.5834 NA NA NA NA NA +chr2:73868052-73868532 chr2 73868303 73868303 - 16.5297 NA Intergenic Intergenic -800007 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74702109-74702707 chr2 74702402 74702402 + 16.3674 NA Intergenic Intergenic -1260 ENSMUST00000198895 ENSMUSG00000104570 ENSMUST00000198895 Gm44463 miRNA +chr10:97312750-97313424 chr10 97313144 97313144 - 16.1617 NA NA NA NA NA +chr2:75318086-75318603 chr2 75318399 75318399 - 15.8984 NA Intergenic Intergenic -602403 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:95557210-95557760 chr10 95557477 95557477 + 15.8474 NA NA NA NA NA +chr2:75590116-75590691 chr2 75590418 75590418 - 15.844 NA Intergenic Intergenic -874422 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73745562-73746116 chr2 73745859 73745859 - 15.583 NA Intergenic Intergenic -922451 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74305723-74306142 chr2 74305973 74305973 - 15.4325 NA Intergenic Intergenic -362337 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:97670243-97670641 chr10 97670412 97670412 - 15.0213 NA NA NA NA NA +chr2:75137844-75138351 chr2 75138096 75138096 - 14.9999 NA Intergenic Intergenic -422100 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:95894657-95895156 chr10 95894942 95894942 - 14.5144 NA NA NA NA NA +chr10:96131980-96132540 chr10 96132306 96132306 + 14.3011 NA NA NA NA NA +chr2:75588511-75588998 chr2 75588783 75588783 - 13.9441 NA Intergenic Intergenic -872787 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:75312148-75312690 chr2 75312440 75312440 - 12.976 NA Intergenic Intergenic -596444 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:96104999-96105605 chr10 96105360 96105360 - 12.8558 NA NA NA NA NA +chr10:95898384-95898961 chr10 95898657 95898657 + 12.5406 NA NA NA NA NA +chr10:97704497-97705056 chr10 97704767 97704767 - 12.2858 NA NA NA NA NA +chr2:73947347-73947809 chr2 73947568 73947568 - 11.7 NA Intergenic Intergenic -720742 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74672881-74673432 chr2 74673183 74673183 - 11.6759 NA Intergenic Intergenic -1830 ENSMUST00000001878 ENSMUSG00000001823 ENSMUST00000001878 Hoxd12 protein_coding +chr2:75603091-75603554 chr2 75603330 75603330 - 11.5679 NA Intergenic Intergenic -887334 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:75605600-75606199 chr2 75605892 75605892 + 11.5138 NA Intergenic Intergenic -889896 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73792224-73792669 chr2 73792431 73792431 + 11.3969 NA Intergenic Intergenic -875879 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74655214-74655823 chr2 74655532 74655532 - 11.0865 NA Intergenic Intergenic -12778 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74691505-74692018 chr2 74691770 74691770 + 10.8344 NA promoter-TSS (ENSMUST00000061745) protein_coding-promoter-TSS (ENSMUST00000061745) -154 ENSMUST00000061745 ENSMUSG00000050368 ENSMUST00000061745 Hoxd10 protein_coding +chr10:96934538-96935160 chr10 96934834 96934834 - 10.7794 NA NA NA NA NA +chr2:75781071-75781581 chr2 75781340 75781340 - 10.7504 NA Intergenic Intergenic -1065344 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:96182221-96182632 chr10 96182452 96182452 + 9.96549 NA NA NA NA NA +chr10:95551647-95552156 chr10 95551884 95551884 + 9.8358 NA NA NA NA NA +chr10:95489648-95490124 chr10 95489849 95489849 + 9.37574 NA NA NA NA NA +chr10:97160138-97160734 chr10 97160697 97160697 - 9.26797 NA NA NA NA NA +chr10:95858061-95858620 chr10 95858374 95858374 - 8.91987 NA NA NA NA NA +chr10:97339748-97340355 chr10 97340070 97340070 - 8.23779 NA NA NA NA NA +chr2:74686220-74686785 chr2 74686487 74686487 + 8.18583 NA exon (ENSMUST00000048086, exon 2 of 2) protein_coding-exon (ENSMUST00000048086, exon 2 of 2) 3041 ENSMUST00000136302 ENSMUSG00000099521 ENSMUST00000136302 Gm28309 processed_transcript +chr10:96618332-96618740 chr10 96618519 96618519 + 7.7811 NA NA NA NA NA +chr2:75563556-75564002 chr2 75563786 75563786 - 6.81984 NA Intergenic Intergenic -847790 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:73924997-73925519 chr2 73925251 73925251 + 6.64944 NA Intergenic Intergenic -743059 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74977360-74977813 chr2 74977549 74977549 + 6.64332 NA Intergenic Intergenic -261553 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74693923-74694529 chr2 74694234 74694234 - 6.49186 NA TTS (ENSMUST00000136302) processed_transcript-TTS (ENSMUST00000136302) -1286 ENSMUST00000126966 ENSMUSG00000086077 ENSMUST00000126966 Gm14396 lincRNA +chr2:75515254-75515778 chr2 75515511 75515511 - 6.45021 NA Intergenic Intergenic -799515 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr2:74661581-74662231 chr2 74661784 74661784 - 6.32635 NA Intergenic Intergenic -6526 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:97689400-97689842 chr10 97689621 97689621 - 6.20282 NA NA NA NA NA +chr10:96080279-96080903 chr10 96080635 96080635 - 6.11901 NA NA NA NA NA +chr2:73987054-73987519 chr2 73987359 73987359 - 5.75056 NA Intergenic Intergenic -680951 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74663455-74664030 chr2 74663752 74663752 - 5.5749 NA Intergenic Intergenic -4558 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr10:96616623-96617093 chr10 96616855 96616855 - 4.72295 NA NA NA NA NA +chr2:73998449-73999023 chr2 73998749 73998749 - 4.45417 NA Intergenic Intergenic -669561 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:74066544-74067106 chr2 74066831 74066831 + 4.26306 NA Intergenic Intergenic -601479 ENSMUST00000001872 ENSMUSG00000001819 ENSMUST00000001872 Hoxd13 protein_coding +chr2:75658517-75658909 chr2 75658765 75658765 + 0.26272 NA Intergenic Intergenic -942769 ENSMUST00000145799 ENSMUSG00000052371 ENSMUST00000145799 Hoxd3os1 antisense +chr10:97768293-97768873 chr10 97768454 97768454 + -1.29559 NA NA NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,7 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - dbkey (Database key) +# - name (Galaxy shows this in the UI) +# - path (the reference file) +# +phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_default.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,115 @@ +Intergenic chr2 1 74667309 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74667310 74668410 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668411 74669078 + E 59 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 158 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74670136 + E 61 +3' UTR (ENSMUST00000001872, exon 2 of 2) chr2 74670137 74671498 + 3UTR 60 +TTS (ENSMUST00000001872) chr2 74671499 74672599 + TTS 30 +Intergenic--2 chr2 74672600 74674012 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674013 74675113 + P 2 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675114 74675654 + E 63 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 158 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74676052 + E 65 +3' UTR (ENSMUST00000001878, exon 2 of 2) chr2 74676053 74677604 + 3UTR 64 +TTS (ENSMUST00000001878) chr2 74677605 74678556 + TTS 31 +promoter-TSS (ENSMUST00000048086) chr2 74678557 74679657 + P 6 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679658 74679809 + E 83 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74681322 + I 158 +promoter-TSS (ENSMUST00000142312) chr2 74681323 74682423 + P 20 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682424 74682445 + E 131 +promoter-TSS (ENSMUST00000136302) chr2 74682446 74683546 + P 17 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683547 74683902 + I 158 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684067 + E 84 +TTS (ENSMUST00000142312) chr2 74684068 74685168 + TTS 49 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74684357 74685168 + I 158 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74685169 74686915 + E 84 +TTS (ENSMUST00000048086) chr2 74686916 74688016 + TTS 35 +intron (ENSMUST00000136302, intron 2 of 2)--2 chr2 74688017 74690923 + I 158 +promoter-TSS (ENSMUST00000061745) chr2 74690924 74692024 + P 9 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74692025 74692724 + E 96 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 158 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694093 + E 98 +TTS (ENSMUST00000136302) chr2 74694094 74694519 + TTS 46 +promoter-TSS (ENSMUST00000126966) chr2 74694520 74695620 + P 15 +promoter-TSS (ENSMUST00000152027) chr2 74695621 74695701 + P 25 +TTS (ENSMUST00000061745) chr2 74695702 74696105 + TTS 38 +TTS (ENSMUST00000190845) chr2 74696106 74696726 - TTS 57 +promoter-TSS (ENSMUST00000059272) chr2 74696727 74697827 + P 8 +promoter-TSS (ENSMUST00000190845) chr2 74697828 74698586 - P 28 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698587 74698833 + E 92 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 158 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74699421 + E 94 +3' UTR (ENSMUST00000059272, exon 2 of 2) chr2 74699422 74700005 + 3UTR 93 +TTS (ENSMUST00000198895) chr2 74700006 74700107 - TTS 58 +TTS (ENSMUST00000059272) chr2 74700108 74701041 + TTS 37 +promoter-TSS (ENSMUST00000198895) chr2 74701042 74702142 - P 29 +Intergenic--3 chr2 74702143 74702247 + N 1900000000 +TTS (ENSMUST00000132326) chr2 74702248 74703348 - TTS 45 +exon (ENSMUST00000132326, exon 2 of 2) chr2 74703349 74703614 - E 120 +promoter-TSS (ENSMUST00000151380) chr2 74703615 74703904 + P 24 +promoter-TSS (ENSMUST00000019749) chr2 74703905 74705005 + P 3 +promoter-TSS (ENSMUST00000074721) chr2 74705006 74705252 + P 10 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74705253 74705547 + 5UTR 66 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 67 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 158 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706711 + E 69 +TTS (ENSMUST00000151380) chr2 74706712 74707206 + TTS 53 +TTS (ENSMUST00000074721) chr2 74707207 74707832 + TTS 39 +TTS (ENSMUST00000019749) chr2 74707833 74708933 + TTS 32 +intron (ENSMUST00000132326, intron 1 of 1) chr2 74708934 74709042 - I 158 +TTS (ENSMUST00000156342) chr2 74709043 74709192 - TTS 55 +TTS (ENSMUST00000145799) chr2 74709193 74710293 - TTS 52 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710294 74710926 - I 158 +promoter-TSS (ENSMUST00000111983) chr2 74710927 74712027 + P 14 +promoter-TSS (ENSMUST00000132326) chr2 74712028 74713054 - P 16 +promoter-TSS (ENSMUST00000156342) chr2 74713055 74713526 - P 26 +exon (ENSMUST00000139005, exon 2 of 2) chr2 74713527 74714401 - E 125 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 158 +exon (ENSMUST00000139005, exon 1 of 2) chr2 74715706 74715895 - E 126 +promoter-TSS (ENSMUST00000145799) chr2 74715896 74716029 - P 23 +promoter-TSS (ENSMUST00000139005) chr2 74716030 74717130 - P 18 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74717131 74720977 + I 158 +promoter-TSS (ENSMUST00000047904) chr2 74720978 74722078 + P 5 +5' UTR (ENSMUST00000047904, exon 1 of 6) chr2 74722079 74722177 + 5UTR 75 +intron (ENSMUST00000047904, intron 1 of 5) chr2 74722178 74722552 + I 158 +5' UTR (ENSMUST00000047904, exon 2 of 6) chr2 74722553 74722631 + 5UTR 76 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 158 +5' UTR (ENSMUST00000047904, exon 3 of 6) chr2 74723332 74723367 + 5UTR 77 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725069 + I 158 +promoter-TSS (ENSMUST00000083566) chr2 74725070 74725727 + P 11 +promoter-TSS (ENSMUST00000053932) chr2 74725728 74726828 + P 7 +promoter-TSS (ENSMUST00000111980) chr2 74726829 74727174 + P 12 +5' UTR (ENSMUST00000047904, exon 5 of 6) chr2 74727175 74727278 + 5UTR 79 +exon (ENSMUST00000047904, exon 5 of 6) chr2 74727279 74727705 + E 80 +intron (ENSMUST00000053932, intron 1 of 3) chr2 74727706 74728261 + I 158 +exon (ENSMUST00000047904, exon 6 of 6) chr2 74728262 74728587 + E 82 +3' UTR (ENSMUST00000047904, exon 6 of 6) chr2 74728588 74728767 + 3UTR 81 +TTS (ENSMUST00000144040) chr2 74728768 74729022 + TTS 50 +TTS (ENSMUST00000111980) chr2 74729023 74729059 + TTS 41 +TTS (ENSMUST00000047904) chr2 74729060 74730160 + TTS 34 +intron (ENSMUST00000053932, intron 2 of 3) chr2 74730161 74731912 + I 158 +promoter-TSS (ENSMUST00000144544) chr2 74731913 74733013 + P 22 +5' UTR (ENSMUST00000144544, exon 1 of 2) chr2 74733014 74733040 + 5UTR 141 +intron (ENSMUST00000144544, intron 1 of 1) chr2 74733041 74735514 + I 158 +promoter-TSS (ENSMUST00000111982) chr2 74735515 74736615 + P 13 +5' UTR (ENSMUST00000111982, exon 1 of 3) chr2 74736616 74736705 + 5UTR 108 +intron (ENSMUST00000111982, intron 1 of 2) chr2 74736706 74738618 + I 158 +promoter-TSS (ENSMUST00000047830) chr2 74738619 74739719 + P 4 +intron (ENSMUST00000047830, intron 1 of 2) chr2 74739720 74743927 + I 158 +5' UTR (ENSMUST00000047830, exon 2 of 3) chr2 74743928 74744011 + 5UTR 71 +exon (ENSMUST00000047830, exon 2 of 3) chr2 74744012 74744113 + E 72 +TTS (ENSMUST00000144544) chr2 74744114 74744673 + TTS 51 +promoter-TSS (ENSMUST00000140666) chr2 74744674 74745774 + P 19 +promoter-TSS (ENSMUST00000190553) chr2 74745775 74745822 + P 27 +5' UTR (ENSMUST00000140666, exon 1 of 2) chr2 74745823 74746156 + 5UTR 127 +exon (ENSMUST00000140666, exon 1 of 2) chr2 74746157 74746220 + E 128 +exon (ENSMUST00000190553, exon 1 of 1) chr2 74746221 74746321 + E 155 +exon (ENSMUST00000047830, exon 3 of 3) chr2 74746322 74746495 + E 74 +TTS (ENSMUST00000140666) chr2 74746496 74747596 + TTS 48 +3' UTR (ENSMUST00000111983, exon 3 of 3) chr2 74747080 74747799 + 3UTR 116 +3' UTR (ENSMUST00000047830, exon 3 of 3) chr2 74747597 74747799 + 3UTR 73 +TTS (ENSMUST00000047830) chr2 74747800 74748900 + TTS 33 +TTS (ENSMUST00000053932) chr2 74748901 74748918 + TTS 36 +TTS (ENSMUST00000111983) chr2 74748919 74749271 + TTS 43 +TTS (ENSMUST00000190553) chr2 74749272 74749442 + TTS 56 +Intergenic--4 chr2 74749443 1500000000 + N 1900000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_default_simplified.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,87 @@ +Intergenic chr2 1 74667309 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74667310 74668410 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668411 74669078 + E 33 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 88 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74670136 + E 35 +3' UTR (ENSMUST00000001872, exon 2 of 2) chr2 74670137 74671498 + 3UTR 34 +TTS (ENSMUST00000001872) chr2 74671499 74672599 + TTS 17 +Intergenic--2 chr2 74672600 74674012 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674013 74675113 + P 2 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675114 74675654 + E 37 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 88 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74676052 + E 39 +3' UTR (ENSMUST00000001878, exon 2 of 2) chr2 74676053 74677604 + 3UTR 38 +TTS (ENSMUST00000001878) chr2 74677605 74678556 + TTS 18 +promoter-TSS (ENSMUST00000048086) chr2 74678557 74679657 + P 4 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679658 74679809 + E 44 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74681322 + I 88 +promoter-TSS (ENSMUST00000142312) chr2 74681323 74682423 + P 11 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682424 74682445 + E 69 +promoter-TSS (ENSMUST00000136302) chr2 74682446 74683546 + P 10 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683547 74683902 + I 88 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684067 + E 45 +TTS (ENSMUST00000142312) chr2 74684068 74685168 + TTS 27 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74684357 74685168 + I 88 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74685169 74686915 + E 45 +TTS (ENSMUST00000048086) chr2 74686916 74688016 + TTS 20 +intron (ENSMUST00000136302, intron 2 of 2)--2 chr2 74688017 74690923 + I 88 +promoter-TSS (ENSMUST00000061745) chr2 74690924 74692024 + P 6 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74692025 74692724 + E 51 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 88 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694093 + E 53 +TTS (ENSMUST00000136302) chr2 74694094 74694519 + TTS 26 +promoter-TSS (ENSMUST00000126966) chr2 74694520 74695620 + P 9 +TTS (ENSMUST00000061745) chr2 74695621 74696105 + TTS 22 +TTS (ENSMUST00000190845) chr2 74696106 74696726 - TTS 31 +promoter-TSS (ENSMUST00000059272) chr2 74696727 74697827 + P 5 +promoter-TSS (ENSMUST00000190845) chr2 74697828 74698586 - P 15 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698587 74698833 + E 47 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 88 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74699421 + E 49 +3' UTR (ENSMUST00000059272, exon 2 of 2) chr2 74699422 74700005 + 3UTR 48 +TTS (ENSMUST00000198895) chr2 74700006 74700107 - TTS 32 +TTS (ENSMUST00000059272) chr2 74700108 74701041 + TTS 21 +promoter-TSS (ENSMUST00000198895) chr2 74701042 74702142 - P 16 +Intergenic--3 chr2 74702143 74703614 + N 1900000000 +promoter-TSS (ENSMUST00000151380) chr2 74703615 74703904 + P 14 +promoter-TSS (ENSMUST00000019749) chr2 74703905 74705005 + P 3 +promoter-TSS (ENSMUST00000074721) chr2 74705006 74705252 + P 7 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74705253 74705547 + 5UTR 40 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 41 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 88 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706711 + E 43 +TTS (ENSMUST00000151380) chr2 74706712 74707206 + TTS 30 +TTS (ENSMUST00000074721) chr2 74707207 74707832 + TTS 23 +TTS (ENSMUST00000019749) chr2 74707833 74708933 + TTS 19 +Intergenic--4 chr2 74708934 74709192 + N 1900000000 +TTS (ENSMUST00000145799) chr2 74709193 74710293 - TTS 29 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710294 74710926 - I 88 +promoter-TSS (ENSMUST00000111983) chr2 74710927 74712027 + P 8 +promoter-TSS (ENSMUST00000144040) chr2 74712028 74712029 + P 12 +5' UTR (ENSMUST00000111983, exon 1 of 3) chr2 74712030 74712316 + 5UTR 58 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74712317 74714270 + I 88 +exon (ENSMUST00000145799, exon 2 of 3) chr2 74714271 74714401 - E 80 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 88 +exon (ENSMUST00000145799, exon 1 of 3) chr2 74715706 74715895 - E 81 +promoter-TSS (ENSMUST00000145799) chr2 74715896 74716996 - P 13 +intron (ENSMUST00000111983, intron 1 of 2)--2 chr2 74716997 74722552 + I 88 +exon (ENSMUST00000144040, exon 2 of 7) chr2 74722553 74722631 + E 73 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 88 +exon (ENSMUST00000144040, exon 3 of 7) chr2 74723332 74723367 + E 74 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725462 + I 88 +exon (ENSMUST00000144040, exon 4 of 7) chr2 74725463 74725597 + E 75 +intron (ENSMUST00000144040, intron 4 of 6) chr2 74725598 74725844 + I 88 +exon (ENSMUST00000144040, exon 5 of 7) chr2 74725845 74725978 + E 76 +intron (ENSMUST00000144040, intron 5 of 6) chr2 74725979 74726875 + I 88 +exon (ENSMUST00000144040, exon 6 of 7) chr2 74726876 74726932 + E 77 +intron (ENSMUST00000144040, intron 6 of 6) chr2 74726933 74728358 + I 88 +exon (ENSMUST00000144040, exon 7 of 7) chr2 74728359 74728767 + E 78 +TTS (ENSMUST00000144040) chr2 74728768 74729868 + TTS 28 +intron (ENSMUST00000111983, intron 1 of 2)--3 chr2 74729869 74743927 + I 88 +5' UTR (ENSMUST00000111983, exon 2 of 3) chr2 74743928 74744011 + 5UTR 59 +exon (ENSMUST00000111983, exon 2 of 3) chr2 74744012 74744555 + E 60 +intron (ENSMUST00000111983, intron 2 of 2) chr2 74744556 74746321 + I 88 +exon (ENSMUST00000111983, exon 3 of 3) chr2 74746322 74747079 + E 62 +3' UTR (ENSMUST00000111983, exon 3 of 3) chr2 74747080 74748170 + 3UTR 61 +TTS (ENSMUST00000111983) chr2 74748171 74749271 + TTS 24 +Intergenic--5 chr2 74749272 1500000000 + N 1900000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_default_stats.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,8 @@ +Annotation Number of peaks Total size (bp) Log2 Ratio (obs/exp) LogP enrichment (+values depleted) +3UTR 5.0 4601 8.659 -26.809 +TTS 47.0 16013 10.092 -290.509 +Exon 32.0 8271 10.491 -205.971 +Intron 24.0 28234 8.304 -118.153 +Intergenic 0.0 74668827 -17.479 1369.495 +Promoter 81.0 23880 10.301 -519.342 +5UTR 12.0 1148 11.925 -89.692
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_exon_start.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,110 @@ +Intergenic chr2 1 74667309 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74667310 74668410 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668411 74669078 + E 59 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 145 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74671498 + E 60 +TTS (ENSMUST00000001872) chr2 74671499 74672599 + TTS 30 +Intergenic--2 chr2 74672600 74674012 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674013 74675113 + P 2 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675114 74675654 + E 62 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 145 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74677604 + E 63 +TTS (ENSMUST00000001878) chr2 74677605 74678556 + TTS 31 +promoter-TSS (ENSMUST00000048086) chr2 74678557 74679657 + P 6 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679658 74679809 + E 78 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74681322 + I 145 +promoter-TSS (ENSMUST00000142312) chr2 74681323 74682423 + P 20 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682424 74682445 + E 119 +promoter-TSS (ENSMUST00000136302) chr2 74682446 74683546 + P 17 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683547 74683902 + I 145 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684067 + E 79 +TTS (ENSMUST00000142312) chr2 74684068 74685168 + TTS 49 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74684357 74685168 + I 145 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74685169 74686915 + E 79 +TTS (ENSMUST00000048086) chr2 74686916 74688016 + TTS 35 +intron (ENSMUST00000136302, intron 2 of 2)--2 chr2 74688017 74690923 + I 145 +promoter-TSS (ENSMUST00000061745) chr2 74690924 74692024 + P 9 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74692025 74692724 + E 89 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 145 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694093 + E 90 +TTS (ENSMUST00000136302) chr2 74694094 74694519 + TTS 46 +promoter-TSS (ENSMUST00000126966) chr2 74694520 74695620 + P 15 +promoter-TSS (ENSMUST00000152027) chr2 74695621 74695701 + P 25 +TTS (ENSMUST00000061745) chr2 74695702 74696105 + TTS 38 +TTS (ENSMUST00000190845) chr2 74696106 74696726 - TTS 57 +promoter-TSS (ENSMUST00000059272) chr2 74696727 74697827 + P 8 +promoter-TSS (ENSMUST00000190845) chr2 74697828 74698586 - P 28 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698587 74698833 + E 86 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 145 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74700005 + E 87 +TTS (ENSMUST00000198895) chr2 74700006 74700107 - TTS 58 +TTS (ENSMUST00000059272) chr2 74700108 74701041 + TTS 37 +promoter-TSS (ENSMUST00000198895) chr2 74701042 74702142 - P 29 +Intergenic--3 chr2 74702143 74702247 + N 1900000000 +TTS (ENSMUST00000132326) chr2 74702248 74703348 - TTS 45 +exon (ENSMUST00000132326, exon 2 of 2) chr2 74703349 74703614 - E 108 +promoter-TSS (ENSMUST00000151380) chr2 74703615 74703904 + P 24 +promoter-TSS (ENSMUST00000019749) chr2 74703905 74705005 + P 3 +promoter-TSS (ENSMUST00000074721) chr2 74705006 74705252 + P 10 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74705253 74705547 + 5UTR 64 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 65 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 145 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706711 + E 66 +TTS (ENSMUST00000151380) chr2 74706712 74707206 + TTS 53 +TTS (ENSMUST00000074721) chr2 74707207 74707832 + TTS 39 +TTS (ENSMUST00000019749) chr2 74707833 74708933 + TTS 32 +intron (ENSMUST00000132326, intron 1 of 1) chr2 74708934 74709042 - I 145 +TTS (ENSMUST00000156342) chr2 74709043 74709192 - TTS 55 +TTS (ENSMUST00000145799) chr2 74709193 74710293 - TTS 52 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710294 74710926 - I 145 +promoter-TSS (ENSMUST00000111983) chr2 74710927 74712027 + P 14 +promoter-TSS (ENSMUST00000132326) chr2 74712028 74713054 - P 16 +promoter-TSS (ENSMUST00000156342) chr2 74713055 74713526 - P 26 +exon (ENSMUST00000139005, exon 2 of 2) chr2 74713527 74714401 - E 113 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 145 +exon (ENSMUST00000139005, exon 1 of 2) chr2 74715706 74715895 - E 114 +promoter-TSS (ENSMUST00000145799) chr2 74715896 74716029 - P 23 +promoter-TSS (ENSMUST00000139005) chr2 74716030 74717130 - P 18 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74717131 74720977 + I 145 +promoter-TSS (ENSMUST00000047904) chr2 74720978 74722078 + P 5 +5' UTR (ENSMUST00000047904, exon 1 of 6) chr2 74722079 74722177 + 5UTR 71 +intron (ENSMUST00000047904, intron 1 of 5) chr2 74722178 74722552 + I 145 +5' UTR (ENSMUST00000047904, exon 2 of 6) chr2 74722553 74722631 + 5UTR 72 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 145 +5' UTR (ENSMUST00000047904, exon 3 of 6) chr2 74723332 74723367 + 5UTR 73 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725069 + I 145 +promoter-TSS (ENSMUST00000083566) chr2 74725070 74725727 + P 11 +promoter-TSS (ENSMUST00000053932) chr2 74725728 74726828 + P 7 +promoter-TSS (ENSMUST00000111980) chr2 74726829 74727174 + P 12 +5' UTR (ENSMUST00000047904, exon 5 of 6) chr2 74727175 74727278 + 5UTR 75 +exon (ENSMUST00000047904, exon 5 of 6) chr2 74727279 74727705 + E 76 +intron (ENSMUST00000053932, intron 1 of 3) chr2 74727706 74728261 + I 145 +exon (ENSMUST00000047904, exon 6 of 6) chr2 74728262 74728767 + E 77 +TTS (ENSMUST00000144040) chr2 74728768 74729022 + TTS 50 +TTS (ENSMUST00000111980) chr2 74729023 74729059 + TTS 41 +TTS (ENSMUST00000047904) chr2 74729060 74730160 + TTS 34 +intron (ENSMUST00000053932, intron 2 of 3) chr2 74730161 74731912 + I 145 +promoter-TSS (ENSMUST00000144544) chr2 74731913 74733013 + P 22 +5' UTR (ENSMUST00000144544, exon 1 of 2) chr2 74733014 74733040 + 5UTR 128 +intron (ENSMUST00000144544, intron 1 of 1) chr2 74733041 74735514 + I 145 +promoter-TSS (ENSMUST00000111982) chr2 74735515 74736615 + P 13 +5' UTR (ENSMUST00000111982, exon 1 of 3) chr2 74736616 74736705 + 5UTR 98 +intron (ENSMUST00000111982, intron 1 of 2) chr2 74736706 74738618 + I 145 +promoter-TSS (ENSMUST00000047830) chr2 74738619 74739719 + P 4 +intron (ENSMUST00000047830, intron 1 of 2) chr2 74739720 74743927 + I 145 +5' UTR (ENSMUST00000047830, exon 2 of 3) chr2 74743928 74744011 + 5UTR 68 +exon (ENSMUST00000047830, exon 2 of 3) chr2 74744012 74744113 + E 69 +TTS (ENSMUST00000144544) chr2 74744114 74744673 + TTS 51 +promoter-TSS (ENSMUST00000140666) chr2 74744674 74745774 + P 19 +promoter-TSS (ENSMUST00000190553) chr2 74745775 74745822 + P 27 +5' UTR (ENSMUST00000140666, exon 1 of 2) chr2 74745823 74746156 + 5UTR 115 +exon (ENSMUST00000140666, exon 1 of 2) chr2 74746157 74746220 + E 116 +exon (ENSMUST00000190553, exon 1 of 1) chr2 74746221 74746321 + E 142 +exon (ENSMUST00000047830, exon 3 of 3) chr2 74746322 74746495 + E 70 +TTS (ENSMUST00000140666) chr2 74746496 74747596 + TTS 48 +exon (ENSMUST00000047830, exon 3 of 3)--2 chr2 74747597 74747799 + E 70 +TTS (ENSMUST00000047830) chr2 74747800 74748900 + TTS 33 +TTS (ENSMUST00000053932) chr2 74748901 74748918 + TTS 36 +TTS (ENSMUST00000111983) chr2 74748919 74749271 + TTS 43 +TTS (ENSMUST00000190553) chr2 74749272 74749442 + TTS 56 +Intergenic--4 chr2 74749443 1500000000 + N 1900000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_exon_start_stats.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,7 @@ +Annotation Number of peaks Total size (bp) Log2 Ratio (obs/exp) LogP enrichment (+values depleted) +TTS 41.0 16013 9.992 -250.473 +Exon 30.0 12152 9.939 -181.768 +Intron 24.0 28234 8.401 -119.856 +Intergenic 0.0 74668827 -17.395 1282.574 +Promoter 81.0 23880 10.397 -526.320 +5UTR 12.0 1148 12.021 -90.517
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_small_TSSTTS.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,164 @@ +Intergenic chr2 1 74668259 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74668260 74668360 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668361 74669078 + E 59 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 158 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74670136 + E 61 +3' UTR (ENSMUST00000001872, exon 2 of 2) chr2 74670137 74671548 + 3UTR 60 +TTS (ENSMUST00000001872) chr2 74671549 74671649 + TTS 30 +Intergenic--2 chr2 74671650 74674962 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674963 74675063 + P 2 +5' UTR (ENSMUST00000001878, exon 1 of 2) chr2 74675064 74675086 + 5UTR 62 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675087 74675654 + E 63 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 158 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74676052 + E 65 +3' UTR (ENSMUST00000001878, exon 2 of 2) chr2 74676053 74677654 + 3UTR 64 +TTS (ENSMUST00000001878) chr2 74677655 74677755 + TTS 31 +Intergenic--3 chr2 74677756 74679506 + N 1900000000 +promoter-TSS (ENSMUST00000048086) chr2 74679507 74679607 + P 6 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679608 74679809 + E 83 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74682272 + I 158 +promoter-TSS (ENSMUST00000142312) chr2 74682273 74682373 + P 20 +5' UTR (ENSMUST00000142312, exon 1 of 2) chr2 74682374 74682392 + 5UTR 130 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682393 74683167 + E 131 +intron (ENSMUST00000142312, intron 1 of 1) chr2 74683168 74683395 + I 158 +promoter-TSS (ENSMUST00000136302) chr2 74683396 74683496 + P 17 +exon (ENSMUST00000136302, exon 1 of 3) chr2 74683497 74683509 + E 122 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683510 74683902 + I 158 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684117 + E 84 +TTS (ENSMUST00000142312) chr2 74684118 74684218 + TTS 49 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74684219 74686965 + E 84 +TTS (ENSMUST00000048086) chr2 74686966 74687066 + TTS 35 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74687067 74691873 + I 158 +promoter-TSS (ENSMUST00000061745) chr2 74691874 74691974 + P 9 +5' UTR (ENSMUST00000061745, exon 1 of 2) chr2 74691975 74691979 + 5UTR 95 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74691980 74692724 + E 96 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 158 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694143 + E 98 +TTS (ENSMUST00000136302) chr2 74694144 74694244 + TTS 46 +exon (ENSMUST00000061745, exon 2 of 2)--2 chr2 74694245 74694368 + E 98 +3' UTR (ENSMUST00000061745, exon 2 of 2) chr2 74694369 74695054 + 3UTR 97 +TTS (ENSMUST00000061745) chr2 74695055 74695155 + TTS 38 +Intergenic--4 chr2 74695156 74695469 + N 1900000000 +promoter-TSS (ENSMUST00000126966) chr2 74695470 74695570 + P 15 +promoter-TSS (ENSMUST00000152027) chr2 74695571 74695651 + P 25 +exon (ENSMUST00000126966, exon 1 of 2) chr2 74695652 74695732 + E 118 +intron (ENSMUST00000126966, intron 1 of 1) chr2 74695733 74696717 + I 158 +TTS (ENSMUST00000190845) chr2 74696718 74696818 - TTS 57 +exon (ENSMUST00000190845, exon 2 of 2) chr2 74696819 74696841 - E 156 +intron (ENSMUST00000190845, intron 1 of 1) chr2 74696842 74697030 - I 158 +exon (ENSMUST00000126966, exon 2 of 2) chr2 74697031 74697314 + E 119 +TTS (ENSMUST00000126966) chr2 74697315 74697415 + TTS 44 +exon (ENSMUST00000190845, exon 1 of 2) chr2 74697416 74697535 - E 157 +promoter-TSS (ENSMUST00000190845) chr2 74697536 74697636 - P 28 +Intergenic--5 chr2 74697637 74697676 + N 1900000000 +promoter-TSS (ENSMUST00000059272) chr2 74697677 74697777 + P 8 +5' UTR (ENSMUST00000059272, exon 1 of 2) chr2 74697778 74698055 + 5UTR 91 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698056 74698833 + E 92 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 158 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74699421 + E 94 +3' UTR (ENSMUST00000059272, exon 2 of 2) chr2 74699422 74700157 + 3UTR 93 +TTS (ENSMUST00000059272) chr2 74700158 74700258 + TTS 37 +Intergenic--6 chr2 74700259 74700955 + N 1900000000 +TTS (ENSMUST00000198895) chr2 74700956 74701056 - TTS 58 +exon (ENSMUST00000198895, exon 1 of 1) chr2 74701057 74701091 - E 158 +promoter-TSS (ENSMUST00000198895) chr2 74701092 74701192 - P 29 +Intergenic--7 chr2 74701193 74703197 + N 1900000000 +TTS (ENSMUST00000132326) chr2 74703198 74703298 - TTS 45 +exon (ENSMUST00000132326, exon 2 of 2) chr2 74703299 74703622 - E 120 +intron (ENSMUST00000132326, intron 1 of 1) chr2 74703623 74704564 - I 158 +promoter-TSS (ENSMUST00000151380) chr2 74704565 74704665 + P 24 +5' UTR (ENSMUST00000151380, exon 1 of 3) chr2 74704666 74704724 + 5UTR 147 +intron (ENSMUST00000151380, intron 1 of 2) chr2 74704725 74704854 + I 158 +promoter-TSS (ENSMUST00000019749) chr2 74704855 74704955 + P 3 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74704956 74705101 + 5UTR 66 +promoter-TSS (ENSMUST00000074721) chr2 74705102 74705202 + P 10 +5' UTR (ENSMUST00000074721, exon 1 of 2) chr2 74705152 74705202 + 5UTR 99 +5' UTR (ENSMUST00000019749, exon 1 of 2)--2 chr2 74705203 74705547 + 5UTR 66 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 67 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 158 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706761 + E 69 +TTS (ENSMUST00000151380) chr2 74706762 74706862 + TTS 53 +3' UTR (ENSMUST00000019749, exon 2 of 2) chr2 74706863 74707256 + 3UTR 68 +TTS (ENSMUST00000074721) chr2 74707257 74707357 + TTS 39 +3' UTR (ENSMUST00000019749, exon 2 of 2)--2 chr2 74707358 74707882 + 3UTR 68 +TTS (ENSMUST00000019749) chr2 74707883 74707983 + TTS 32 +intron (ENSMUST00000132326, intron 1 of 1)--2 chr2 74707984 74709992 - I 158 +TTS (ENSMUST00000156342) chr2 74709993 74710093 - TTS 55 +exon (ENSMUST00000156342, exon 2 of 2) chr2 74710094 74710142 - E 153 +TTS (ENSMUST00000145799) chr2 74710143 74710243 - TTS 52 +exon (ENSMUST00000145799, exon 3 of 3) chr2 74710244 74710281 - E 144 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710282 74711876 - I 158 +promoter-TSS (ENSMUST00000111983) chr2 74711877 74711977 + P 14 +promoter-TSS (ENSMUST00000144040) chr2 74711978 74711979 + P 21 +5' UTR (ENSMUST00000111983, exon 1 of 3) chr2 74711980 74712003 + 5UTR 113 +promoter-TSS (ENSMUST00000132326) chr2 74712004 74712104 - P 16 +5' UTR (ENSMUST00000111983, exon 1 of 3)--2 chr2 74712105 74712316 + 5UTR 113 +exon (ENSMUST00000156342, exon 1 of 2) chr2 74712317 74712475 - E 154 +promoter-TSS (ENSMUST00000156342) chr2 74712476 74712576 - P 26 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74712577 74713075 + I 158 +TTS (ENSMUST00000139005) chr2 74713076 74713176 - TTS 47 +exon (ENSMUST00000139005, exon 2 of 2) chr2 74713177 74714401 - E 125 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 158 +exon (ENSMUST00000139005, exon 1 of 2) chr2 74715706 74715945 - E 126 +promoter-TSS (ENSMUST00000145799) chr2 74715946 74716046 - P 23 +exon (ENSMUST00000139005, exon 1 of 2)--2 chr2 74716047 74716079 - E 126 +promoter-TSS (ENSMUST00000139005) chr2 74716080 74716180 - P 18 +intron (ENSMUST00000111983, intron 1 of 2)--2 chr2 74716181 74721927 + I 158 +promoter-TSS (ENSMUST00000047904) chr2 74721928 74722028 + P 5 +5' UTR (ENSMUST00000047904, exon 1 of 6) chr2 74722029 74722177 + 5UTR 75 +intron (ENSMUST00000047904, intron 1 of 5) chr2 74722178 74722552 + I 158 +5' UTR (ENSMUST00000047904, exon 2 of 6) chr2 74722553 74722631 + 5UTR 76 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 158 +5' UTR (ENSMUST00000047904, exon 3 of 6) chr2 74723332 74723367 + 5UTR 77 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725462 + I 158 +5' UTR (ENSMUST00000047904, exon 4 of 6) chr2 74725463 74725978 + 5UTR 78 +intron (ENSMUST00000144040, intron 5 of 6) chr2 74725979 74726019 + I 158 +promoter-TSS (ENSMUST00000083566) chr2 74726020 74726120 + P 11 +TTS (ENSMUST00000083566) chr2 74726121 74726187 + TTS 40 +intron (ENSMUST00000144040, intron 5 of 6)--2 chr2 74726188 74726677 + I 158 +promoter-TSS (ENSMUST00000053932) chr2 74726678 74726778 + P 7 +5' UTR (ENSMUST00000053932, exon 1 of 4) chr2 74726779 74726875 + 5UTR 85 +5' UTR (ENSMUST00000047904, exon 5 of 6) chr2 74726876 74727023 + 5UTR 79 +promoter-TSS (ENSMUST00000111980) chr2 74727024 74727124 + P 12 +5' UTR (ENSMUST00000111980, exon 1 of 2) chr2 74727074 74727124 + 5UTR 104 +5' UTR (ENSMUST00000047904, exon 5 of 6)--2 chr2 74727125 74727278 + 5UTR 79 +exon (ENSMUST00000047904, exon 5 of 6) chr2 74727279 74727705 + E 80 +intron (ENSMUST00000053932, intron 1 of 3) chr2 74727706 74728261 + I 158 +exon (ENSMUST00000047904, exon 6 of 6) chr2 74728262 74728587 + E 82 +3' UTR (ENSMUST00000047904, exon 6 of 6) chr2 74728588 74728817 + 3UTR 81 +TTS (ENSMUST00000144040) chr2 74728818 74728918 + TTS 50 +3' UTR (ENSMUST00000047904, exon 6 of 6)--2 chr2 74728919 74729072 + 3UTR 81 +TTS (ENSMUST00000111980) chr2 74729073 74729109 + TTS 41 +TTS (ENSMUST00000047904) chr2 74729110 74729210 + TTS 34 +intron (ENSMUST00000053932, intron 2 of 3) chr2 74729211 74732862 + I 158 +promoter-TSS (ENSMUST00000144544) chr2 74732863 74732963 + P 22 +5' UTR (ENSMUST00000144544, exon 1 of 2) chr2 74732964 74733040 + 5UTR 141 +intron (ENSMUST00000144544, intron 1 of 1) chr2 74733041 74736464 + I 158 +promoter-TSS (ENSMUST00000111982) chr2 74736465 74736565 + P 13 +5' UTR (ENSMUST00000111982, exon 1 of 3) chr2 74736566 74736705 + 5UTR 108 +intron (ENSMUST00000111982, intron 1 of 2) chr2 74736706 74739568 + I 158 +promoter-TSS (ENSMUST00000047830) chr2 74739569 74739669 + P 4 +5' UTR (ENSMUST00000047830, exon 1 of 3) chr2 74739670 74739703 + 5UTR 70 +intron (ENSMUST00000047830, intron 1 of 2) chr2 74739704 74743927 + I 158 +5' UTR (ENSMUST00000047830, exon 2 of 3) chr2 74743928 74744011 + 5UTR 71 +exon (ENSMUST00000047830, exon 2 of 3) chr2 74744012 74744163 + E 72 +TTS (ENSMUST00000144544) chr2 74744164 74744264 + TTS 51 +exon (ENSMUST00000047830, exon 2 of 3)--2 chr2 74744265 74744555 + E 72 +intron (ENSMUST00000111983, intron 2 of 2) chr2 74744556 74745623 + I 158 +promoter-TSS (ENSMUST00000140666) chr2 74745624 74745724 + P 19 +promoter-TSS (ENSMUST00000190553) chr2 74745725 74745772 + P 27 +5' UTR (ENSMUST00000140666, exon 1 of 2) chr2 74745773 74746156 + 5UTR 127 +exon (ENSMUST00000140666, exon 1 of 2) chr2 74746157 74746220 + E 128 +exon (ENSMUST00000190553, exon 1 of 1) chr2 74746221 74746321 + E 155 +exon (ENSMUST00000047830, exon 3 of 3) chr2 74746322 74746545 + E 74 +TTS (ENSMUST00000140666) chr2 74746546 74746646 + TTS 48 +exon (ENSMUST00000047830, exon 3 of 3)--2 chr2 74746647 74747079 + E 74 +3' UTR (ENSMUST00000047830, exon 3 of 3) chr2 74747080 74747849 + 3UTR 73 +3' UTR (ENSMUST00000111983, exon 3 of 3) chr2 74747080 74747849 + 3UTR 116 +TTS (ENSMUST00000047830) chr2 74747850 74747950 + TTS 33 +TTS (ENSMUST00000053932) chr2 74747951 74747968 + TTS 36 +3' UTR (ENSMUST00000111983, exon 3 of 3)--2 chr2 74747969 74748220 + 3UTR 116 +TTS (ENSMUST00000111983) chr2 74748221 74748321 + TTS 43 +exon (ENSMUST00000190553, exon 1 of 1)--2 chr2 74748322 74748391 + E 155 +TTS (ENSMUST00000190553) chr2 74748392 74748492 + TTS 56 +Intergenic--8 chr2 74748493 1500000000 + N 1900000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_small_TSSTTS_stats.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,8 @@ +Annotation Number of peaks Total size (bp) Log2 Ratio (obs/exp) LogP enrichment (+values depleted) +3UTR 13.0 7531 9.326 -73.660 +TTS 38.0 2546 12.438 -296.106 +Exon 48.0 13188 10.403 -307.101 +Intron 36.0 43852 8.254 -176.111 +Intergenic 0.0 74676379 -17.650 1393.260 +Promoter 38.0 2757 12.324 -293.081 +5UTR 28.0 3111 11.709 -203.812
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_phix_peaks.bed Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,1 @@ +phiX174 1400 1500
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_phix_peaks.subset.bed Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,2 @@ +phiX174 1200 1300 +phiX174 1550 1800
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate_tests.sh Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,60 @@ +#! /usr/bin/bash +## Generate input data: +if [ ! -e test-data/small_simplified.gtf ]; then + wget http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz -O /tmp/Mus_musculus.GRCm38.102.gtf.gz + zcat /tmp/Mus_musculus.GRCm38.102.gtf.gz | head -n 5 > test-data/small.gtf + zcat /tmp/Mus_musculus.GRCm38.102.gtf.gz | awk -v OFS="\t" -v start=74667792 -v end=74748393 '$1 == "2" && $5 > start && $4 < end{print "chr"$0}' >> test-data/small.gtf + # annotatePeaks.pl gives different results all time. I need to simplify the gtf. + cat test-data/small.gtf | grep -v -P "ENSMUST00000152027|ENSMUST00000156342|ENSMUST00000139005|ENSMUST00000144544|ENSMUST00000111982|ENSMUST00000140666|ENSMUST00000190553|ENSMUST00000132326|ENSMUST00000047830|ENSMUST00000047904|ENSMUST00000111980|ENSMUSG00000065500|ENSMUSG00000100642" > test-data/small_simplified.gtf +fi +if [ ! -e test-data/CTCF_peaks.bed ]; then + wget https://raw.githubusercontent.com/lldelisle/scriptsForWilleminEtAl2021/main/CTCF/E12_Limbs_Wt_CTCF_colored.bed -O test-data/CTCF_peaks.bed +fi +if [ ! -e test-data/CTCF_peaks_shifted.bed ]; then + cat test-data/CTCF_peaks.bed | grep "chr2" | awk -v OFS="\t" '$3<75000000 && $2>73740000{$1="mm10_dna"; $2-=73740000; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed +fi +# chr2_subset.fa was downloaded from UCSC +# https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1234982067_JnS4z30UVCNarTg26Ztd1Oh6nfu6&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75000000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA + +. <(planemo conda_env homer_gtf_to_annotation.xml) +echo "$(which homer)" +## homer_gtf_to_annotation +## First test +parseGTF.pl test-data/small.gtf ann -features exon start_codon stop_codon > /tmp/annotations.txt +assignGenomeAnnotation /tmp/annotations.txt /tmp/annotations.txt -prioritize test-data/annotations_default.txt > test-data/annotations_default_stats.txt +## Second test +parseGTF.pl test-data/small.gtf ann -features exon start_codon > /tmp/annotations2.txt +assignGenomeAnnotation /tmp/annotations2.txt /tmp/annotations2.txt -prioritize test-data/annotations_exon_start.txt > test-data/annotations_exon_start_stats.txt +## Third test +parseGTF.pl test-data/small.gtf ann -features exon start_codon stop_codon -annTSSstartOffset -50 -annTSSendOffset 50 -annTTSstartOffset -50 -annTTSendOffset 50 > /tmp/annotations3.txt +assignGenomeAnnotation /tmp/annotations3.txt /tmp/annotations3.txt -prioritize test-data/annotations_small_TSSTTS.txt > test-data/annotations_small_TSSTTS_stats.txt + +## For annotatePeaks.pl +parseGTF.pl test-data/small_simplified.gtf ann -features exon start_codon stop_codon > /tmp/annotations.txt +assignGenomeAnnotation /tmp/annotations.txt /tmp/annotations.txt -prioritize test-data/annotations_default_simplified.txt + +## homer_annotatePeaks +## First test +annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf -ann test-data/annotations_default_simplified.txt > test-data/CTCF_peaks_first.txt +## Second test +annotatePeaks.pl test-data/CTCF_peaks.bed none -ann test-data/annotations_default.txt > test-data/CTCF_peaks_second.txt +## Third test +annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf > test-data/CTCF_peaks_third.txt +## Fourth test +annotatePeaks.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta -CpG > test-data/phiXcpg.txt +## Fifth test +annotatePeaks.pl test-data/fake_phix_peaks.bed none > test-data/phiX_nothing.txt + +## findMotifsGenome +# ! Genome preparsing is giving different results... +findMotifsGenome.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif +mv fake_phix_peaks_bed_motif test-data/motif_test1 +# Thus I needed to use has_text for the other outputs +# gunzip -c test-data/chr2_subset.fa.gz > test-data/chr2_subset.fa +# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif +# mv CTCF_peaks_shifted_bed_motif test-data/motif_test2 +# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mask +# mv CTCF_peaks_shifted_bed_motif test-data/motif_test3 +# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mset plants -nomotif +# mv CTCF_peaks_shifted_bed_motif test-data/motif_test4 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.all.motifs Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,165 @@ +>CTAATGAGCT 1-CTAATGAGCT 10.296193 -2.906976 0 T:1.0(100.00%),B:219.7(5.48%),P:1e-1 Tpos:101.0,Tstd:0.0,Bpos:96.2,Bstd:70.8,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +>ATCAAGATGA 2-ATCAAGATGA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:113.0,Tstd:0.0,Bpos:94.6,Bstd:75.6,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>GTTGCTGCCA 3-GTTGCTGCCA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.9(5.49%),P:1e-1 Tpos:140.0,Tstd:0.0,Bpos:103.4,Bstd:83.3,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>CCTGAGACTG 4-CCTGAGACTG 10.296193 -2.902420 0 T:1.0(100.00%),B:220.0(5.49%),P:1e-1 Tpos:181.0,Tstd:0.0,Bpos:96.7,Bstd:84.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>CGAGGCTAAC 5-CGAGGCTAAC 10.296193 -2.897885 0 T:1.0(100.00%),B:221.5(5.53%),P:1e-1 Tpos:90.0,Tstd:0.0,Bpos:103.4,Bstd:66.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +>ATGAGCTTAATC 1-ATGAGCTTAATC 12.355432 -2.920769 0 T:1.0(100.00%),B:216.0(5.39%),P:1e-1 Tpos:105.0,Tstd:0.0,Bpos:97.7,Bstd:71.4,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +>TGCCATCTCAAA 2-TGCCATCTCAAA 12.355432 -2.920769 0 T:1.0(100.00%),B:216.2(5.39%),P:1e-1 Tpos:146.0,Tstd:0.0,Bpos:105.7,Bstd:83.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +>CGAGGCTAACCC 3-CGAGGCTAACCC 12.355432 -2.916150 0 T:1.0(100.00%),B:217.8(5.43%),P:1e-1 Tpos:91.0,Tstd:0.0,Bpos:101.8,Bstd:65.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +>CTCCTGAGACTG 4-CTCCTGAGACTG 12.355432 -2.911553 0 T:1.0(100.00%),B:218.1(5.44%),P:1e-1 Tpos:180.0,Tstd:0.0,Bpos:95.7,Bstd:83.7,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>GATGATGCTCGT 5-GATGATGCTCGT 12.355432 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:119.0,Tstd:0.0,Bpos:93.3,Bstd:77.5,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +>CCCTAATG 1-CCCTAATG 8.236954 -2.897885 0 T:1.0(100.00%),B:221.6(5.53%),P:1e-1 Tpos:98.0,Tstd:0.0,Bpos:97.0,Bstd:70.2,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>TGCTGCCA 2-TGCTGCCA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.8(5.53%),P:1e-1 Tpos:141.0,Tstd:0.0,Bpos:102.6,Bstd:84.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GAGACTGA 3-GAGACTGA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.9(5.54%),P:1e-1 Tpos:183.0,Tstd:0.0,Bpos:97.7,Bstd:84.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>CTTAATCA 4-CTTAATCA 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:108.0,Tstd:0.0,Bpos:94.6,Bstd:75.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GATGATGC 5-GATGATGC 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:117.0,Tstd:0.0,Bpos:93.3,Bstd:78.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.motifs10 Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,55 @@ +>CTAATGAGCT 1-CTAATGAGCT 10.296193 -2.906976 0 T:1.0(100.00%),B:219.7(5.48%),P:1e-1 Tpos:101.0,Tstd:0.0,Bpos:96.2,Bstd:70.8,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +>ATCAAGATGA 2-ATCAAGATGA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:113.0,Tstd:0.0,Bpos:94.6,Bstd:75.6,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>GTTGCTGCCA 3-GTTGCTGCCA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.9(5.49%),P:1e-1 Tpos:140.0,Tstd:0.0,Bpos:103.4,Bstd:83.3,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>CCTGAGACTG 4-CCTGAGACTG 10.296193 -2.902420 0 T:1.0(100.00%),B:220.0(5.49%),P:1e-1 Tpos:181.0,Tstd:0.0,Bpos:96.7,Bstd:84.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>CGAGGCTAAC 5-CGAGGCTAAC 10.296193 -2.897885 0 T:1.0(100.00%),B:221.5(5.53%),P:1e-1 Tpos:90.0,Tstd:0.0,Bpos:103.4,Bstd:66.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.motifs12 Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,65 @@ +>ATGAGCTTAATC 1-ATGAGCTTAATC 12.355432 -2.920769 0 T:1.0(100.00%),B:216.0(5.39%),P:1e-1 Tpos:105.0,Tstd:0.0,Bpos:97.7,Bstd:71.4,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +>TGCCATCTCAAA 2-TGCCATCTCAAA 12.355432 -2.920769 0 T:1.0(100.00%),B:216.2(5.39%),P:1e-1 Tpos:146.0,Tstd:0.0,Bpos:105.7,Bstd:83.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +>CGAGGCTAACCC 3-CGAGGCTAACCC 12.355432 -2.916150 0 T:1.0(100.00%),B:217.8(5.43%),P:1e-1 Tpos:91.0,Tstd:0.0,Bpos:101.8,Bstd:65.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +>CTCCTGAGACTG 4-CTCCTGAGACTG 12.355432 -2.911553 0 T:1.0(100.00%),B:218.1(5.44%),P:1e-1 Tpos:180.0,Tstd:0.0,Bpos:95.7,Bstd:83.7,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>GATGATGCTCGT 5-GATGATGCTCGT 12.355432 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:119.0,Tstd:0.0,Bpos:93.3,Bstd:77.5,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.motifs8 Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,45 @@ +>CCCTAATG 1-CCCTAATG 8.236954 -2.897885 0 T:1.0(100.00%),B:221.6(5.53%),P:1e-1 Tpos:98.0,Tstd:0.0,Bpos:97.0,Bstd:70.2,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>TGCTGCCA 2-TGCTGCCA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.8(5.53%),P:1e-1 Tpos:141.0,Tstd:0.0,Bpos:102.6,Bstd:84.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GAGACTGA 3-GAGACTGA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.9(5.54%),P:1e-1 Tpos:183.0,Tstd:0.0,Bpos:97.7,Bstd:84.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>CTTAATCA 4-CTTAATCA 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:108.0,Tstd:0.0,Bpos:94.6,Bstd:75.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GATGATGC 5-GATGATGC 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:117.0,Tstd:0.0,Bpos:93.3,Bstd:78.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults.html Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,489 @@ +<HTML><HEAD><TITLE>fake_phix_peaks_bed_motif/ - Homer de novo Motif Results</TITLE></HEAD> +<BODY> +<H1>Homer <i>de novo</i> Motif Results (fake_phix_peaks_bed_motif/)</H1> +<A HREF="knownResults.html">Known Motif Enrichment Results</A><BR/> +<A HREF="geneOntology.html">Gene Ontology Enrichment Results</A><BR/> +If Homer is having trouble matching a motif to a known motif, try copy/pasting the matrix file into +<A HREF="http://www.benoslab.pitt.edu/stamp/">STAMP</A><BR/> +More information on motif finding results: <A HREF="http://biowhat.ucsd.edu/homer/">HOMER</A> + | <A HREF="http://biowhat.ucsd.edu/homer/motif/index.html">Description of Results</A> + | <A HREF="http://biowhat.ucsd.edu/homer/motif/practicalTips.html">Tips</A> +<BR/> +Total target sequences = 1<BR/> +Total background sequences = 4009<BR/> +<FONT color="red">* - possible false positive</FONT><BR/> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Motif</TD><TD>P-value</TD><TD>log P-pvalue</TD><TD>% of Targets</TD><TD>% of Background</TD> +<TD>STD(Bg STD)</TD> +<TD>Best Match/Details</TD><TD>Motif File</TD></TR> +<TR><TD>1 +<FONT color="red">*</FONT></TD><TD><svg width="305" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,2,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text> + 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HREF="homerResults/motif1.motif">motif file (matrix)</A></TD></TR> +<TR><TD>2 +<FONT color="red">*</FONT></TD><TD><svg width="305" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,1,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,25,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> + <text fill="#F9A500" x="0" 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HREF="homerResults/motif8.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif8.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif8.motif">motif file (matrix)</A></TD></TR> +</TABLE> +<P></P> +</BODY></HTML>
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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.921e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>216.0</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.39%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>105.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>97.7 +/- 71.4bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif1.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif1RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif1.logo.svg">forward logo</A><BR/><A HREF="motif1RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>Oc/dmmpmm(Noyes_hd)/fly</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.65</TD</TR> +<TR><TD>Offset:</TD><TD>4</TD</TR> +<TR><TD>Orientation:</TD><TD>forward strand</TD></TR> +<TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC--</FONT><BR><FONT face="courier">----NNTTAATCCN</FONT></TD></TR></TABLE> +</TD><TD> +<svg width="355" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#00BB00" x="0" y="0" 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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.921e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>216.0</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.39%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>105.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>97.7 +/- 71.4bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif1.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif1RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif1.similar1.motif Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,11 @@ +>CTAATGAGCT 1-CTAATGAGCT 10.296193 -2.906976 0 T:1.0(100.00%),B:219.7(5.48%),P:1e-1 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif1.similar2.motif Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,13 @@ +>GATGATGCTCGT 5-GATGATGCTCGT 12.355432 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif1.similar3.motif Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,9 @@ +>CTTAATCA 4-CTTAATCA 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100
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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.921e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>216.2</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.39%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>146.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>105.7 +/- 83.1bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif2.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif2RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif2.logo.svg">forward logo</A><BR/><A HREF="motif2RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>RFX1/RFX1_YPD/[](Harbison)/Yeast</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.64</TD</TR> +<TR><TD>Offset:</TD><TD>-2</TD</TR> +<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> +<TR><TD>Alignment:</TD><TD><FONT face="courier">--TGCCATCTCAAA</FONT><BR><FONT face="courier">GTTGCCATGGCAA-</FONT></TD></TR></TABLE> +</TD><TD> +<svg width="355" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.25,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.25,0,36.5)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.25,0,24)">G</text> + <text fill="#DD0000" x="0" y="0" 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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.921e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>216.2</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.39%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>146.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>105.7 +/- 83.1bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif2.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif2RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +</TABLE> +<P></P> +</BODY></HTML>
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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.916e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>217.8</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.43%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>91.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>101.8 +/- 65.4bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif3.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif3RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif3.logo.svg">forward logo</A><BR/><A HREF="motif3RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>PH0015.1_Crx/Jaspar</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.63</TD</TR> +<TR><TD>Offset:</TD><TD>2</TD</TR> +<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> +<TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC------</FONT><BR><FONT face="courier">--AGGCTAATCCCCAANG</FONT></TD></TR></TABLE> +</TD><TD> +<svg width="455" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#0000EE" x="0" y="0" 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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.916e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>217.8</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.43%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>91.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>101.8 +/- 65.4bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif3.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif3RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +<TR><TD>1</TD><TD>0.913</TD><TD><svg width="255" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#F9A500" x="0" y="0" 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transform="matrix(0.65,0,0,0.100,176,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,177,34)">A</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,200,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,202,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,226,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,225,34)">C</text> + + </g> +</svg> + +</TD><TD>1e-1</TD><TD>-2.897885</TD><TD>100.00%</TD><TD>5.53%</TD><TD><A target="_blank" HREF="motif3.similar1.motif">motif file (matrix)</A></TD></TR> +</TABLE> +<P></P> +</BODY></HTML>
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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.912e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>218.1</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.44%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>180.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>95.7 +/- 83.7bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif4.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif4RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif4.logo.svg">forward logo</A><BR/><A HREF="motif4RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>RAV1(2)(AP2/EREBP)/Arabidopsis thaliana/AthaMap</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.66</TD</TR> +<TR><TD>Offset:</TD><TD>-2</TD</TR> +<TR><TD>Orientation:</TD><TD>forward strand</TD></TR> +<TR><TD>Alignment:</TD><TD><FONT face="courier">--CTCCTGAGACTG</FONT><BR><FONT face="courier">ATCACCTGAGGC--</FONT></TD></TR></TABLE> +</TD><TD> +<svg width="355" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.25,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.25,0,36.5)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.25,0,24)">G</text> + <text fill="#DD0000" x="0" y="0" 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+<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.912e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>218.1</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.44%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>180.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>95.7 +/- 83.7bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif4.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif4RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +<TR><TD>1</TD><TD>0.913</TD><TD><svg width="255" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#0000EE" x="0" y="0" 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+<TR><TD>2</TD><TD>0.714</TD><TD><svg width="205" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,27,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text> + <text fill="#DD0000" 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motif</TD><TD>5.48%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>113.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>94.6 +/- 75.6bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif5.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif5RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif5.logo.svg">forward logo</A><BR/><A HREF="motif5RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>SNRNP70K(RRM)/Drosophila_melanogaster-RNCMPT00143-PBM/HughesRNA</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.79</TD</TR> +<TR><TD>Offset:</TD><TD>-1</TD</TR> 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motif</TD><TD>5.48%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>113.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>94.6 +/- 75.6bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif5.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif5RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +</TABLE> +<P></P> +</BODY></HTML>
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motif</TD><TD>5.49%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>140.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>103.4 +/- 83.3bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif6.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif6RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +<TR><TD>1</TD><TD>0.894</TD><TD><svg width="205" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + 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transform="matrix(0.53,0,0,0.100,77,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,100,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,125,34)">C</text> + + 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6.similar1.motif Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,9 @@ +>TGCTGCCA 2-TGCTGCCA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.8(5.53%),P:1e-1 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100
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target="_blank" HREF="motif7RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif7.logo.svg">forward logo</A><BR/><A HREF="motif7RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>HNRNPA1L2(RRM)/Homo_sapiens-RNCMPT00023-PBM/HughesRNA</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.81</TD</TR> +<TR><TD>Offset:</TD><TD>-1</TD</TR> +<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> +<TR><TD>Alignment:</TD><TD><FONT face="courier">-CCCTAATG</FONT><BR><FONT face="courier">TCCCTAA--</FONT></TD></TR></TABLE> +</TD><TD> +<svg width="230" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.25,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.25,0,36.5)">C</text> + <text fill="#F9A500" 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transform="matrix(0.55,0,0,0.700,175,34)">G</text> + + </g> +</svg> +<BR/> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.898e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>221.6</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.53%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>98.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>97.0 +/- 70.2bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif7.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif7RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +</TABLE> +<P></P> +</BODY></HTML>
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transform="matrix(0.59,0,0,0.700,175,34)">C</text> + + </g> +</svg> +<BR> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.889e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>223.5</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.58%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>117.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>93.3 +/- 78.0bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif8.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif8RV.motif">reverse opposite</A></TD></TR> +<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif8.logo.svg">forward logo</A><BR/><A HREF="motif8RV.logo.svg">reverse opposite</A></TD></TR> +</TABLE> +<H3>Matches to Known Motifs</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD> +<H4>AGL42/MA1201.1/Jaspar</H4> +<TABLE><TR><TD> +<TABLE> +<TR><TD>Match Rank:</TD><TD>1</TD></TR> +<TR><TD>Score:</TD><TD>0.90</TD</TR> +<TR><TD>Offset:</TD><TD>0</TD</TR> +<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR> +<TR><TD>Alignment:</TD><TD><FONT face="courier">GATGATGC</FONT><BR><FONT face="courier">GATGATG-</FONT></TD></TR></TABLE> +</TD><TD> +<svg width="205" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#DD0000" x="0" y="0" 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transform="matrix(0.59,0,0,0.700,175,34)">C</text> + + </g> +</svg> +<BR/> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>p-value:</TD><TD>1e-1</TD></TR> +<TR><TD>log p-value:</TD><TD>-2.889e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>223.5</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.58%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>117.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>93.3 +/- 78.0bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif8.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif8RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +</TABLE> +<P></P> +</BODY></HTML>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif8RV.logo.svg Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,44 @@ +<svg width="205" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,52,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,100,34)">C</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,127,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,150,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,151,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,175,34)">C</text> + + </g> +</svg>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif8RV.motif Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,9 @@ +>GCATCATC 5-GATGATGC 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/knownResults.html Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,11 @@ +<HTML><HEAD><TITLE>fake_phix_peaks_bed_motif - Homer Known Motif Enrichment Results</TITLE></HEAD> +<BODY> +<H1>Homer Known Motif Enrichment Results (fake_phix_peaks_bed_motif)</H1> +<A HREF="homerResults.html">Homer <i>de novo</i> Motif Results</A><BR/> +<A HREF="geneOntology.html">Gene Ontology Enrichment Results</A><BR/> +<A HREF="knownResults.txt">Known Motif Enrichment Results (txt file)</A><BR/> +Total Target Sequences = 1, Total Background Sequences = 4006</BR> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Motif</TD><TD>Name</TD><TD>P-value</TD><TD>log P-pvalue</TD><TD>q-value (Benjamini)</TD><TD># Target Sequences with Motif</TD><TD>% of Targets Sequences with Motif</TD><TD># Background Sequences with Motif</TD><TD>% of Background Sequences with Motif</TD><TD>Motif File</TD> +<TD>SVG</TD></TR> +</TABLE></BODY></HTML>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/knownResults.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,977 @@ +Motif Name Consensus P-value Log P-value q-value (Benjamini) # of Target Sequences with Motif(of 1) % of Target Sequences with Motif # of Background Sequences with Motif(of 4006) % of Background Sequences with Motif +EBF2(EBF)/BrownAdipose-EBF2-ChIP-Seq(GSE97114)/Homer NABTCCCWDGGGAVH 1e-1 -2.921e+00 1.0000 1.0 100.00% 216.3 5.40% +Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer YTAATYNRATTA 1e-1 -2.916e+00 1.0000 1.0 100.00% 217.9 5.44% +TBP3(MYBrelated)/col-TBP3-DAP-Seq(GSE60143)/Homer VYTAGGGCAN 1e-1 -2.898e+00 1.0000 1.0 100.00% 221.6 5.53% +Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer NRYTTCCGGY 1e-1 -2.889e+00 1.0000 1.0 100.00% 223.6 5.58% +EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer AVCAGGAAGT 1e-1 -2.871e+00 1.0000 1.0 100.00% 227.4 5.67% +ELF3(ETS)/PDAC-ELF3-ChIP-Seq(GSE64557)/Homer ANCAGGAAGT 1e-1 -2.871e+00 1.0000 1.0 100.00% 227.4 5.67% +Elf4(ETS)/BMDM-Elf4-ChIP-Seq(GSE88699)/Homer ACTTCCKGKT 1e-1 -2.871e+00 1.0000 1.0 100.00% 227.4 5.67% +ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer ACVAGGAAGT 1e-1 -2.871e+00 1.0000 1.0 100.00% 227.4 5.67% +OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer ATTTGCATAACAATG 1e-1 -2.779e+00 1.0000 1.0 100.00% 249.4 6.22% +CHR(?)/Hela-CellCycle-Expression/Homer SRGTTTCAAA 1e-1 -2.771e+00 1.0000 1.0 100.00% 251.3 6.27% +bZIP52(bZIP)/colamp-bZIP52-DAP-Seq(GSE60143)/Homer NDNHCAGCTGTCANN 1e-1 -2.755e+00 1.0000 1.0 100.00% 255.0 6.36% +Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967) NNAYTTCCTGHN 1e-1 -2.732e+00 1.0000 1.0 100.00% 261.1 6.51% +ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer ACAGGAAGTG 1e-1 -2.651e+00 1.0000 1.0 100.00% 283.5 7.07% +ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer ACAGGAAGTG 1e-1 -2.644e+00 1.0000 1.0 100.00% 285.4 7.12% +Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer CYAAAAATAG 1e-1 -2.609e+00 1.0000 1.0 100.00% 296.0 7.38% +Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer NRYTTCCGGH 1e-1 -2.450e+00 1.0000 1.0 100.00% 346.9 8.65% +AT2G20110(CPP)/colamp-AT2G20110-DAP-Seq(GSE60143)/Homer ATTYAAATHY 1e-1 -2.356e+00 1.0000 1.0 100.00% 380.2 9.49% +Prop1(Homeobox)/GHFT1-PROP1.biotin-ChIP-Seq(GSE77302)/Homer NTAATBNAATTA 1e-1 -2.343e+00 1.0000 1.0 100.00% 385.2 9.61% +IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer ACTGAAACCA 1e-1 -2.320e+00 1.0000 1.0 100.00% 394.7 9.85% +SPL14(SBP)/col-SPL14-DAP-Seq(GSE60143)/Homer NNWHTGTACGGAHNH 1e0 -2.285e+00 1.0000 1.0 100.00% 408.0 10.18% +bHLH28(bHLH)/col-bHLH28-DAP-Seq(GSE60143)/Homer NHHTGTACGGAH 1e0 -2.277e+00 1.0000 1.0 100.00% 411.7 10.27% +SPL13(SBP)/col-SPL13-DAP-Seq(GSE60143)/Homer WAHTGTACGGAH 1e0 -2.277e+00 1.0000 1.0 100.00% 411.7 10.27% +AT1G69570(C2C2dof)/col-AT1G69570-DAP-Seq(GSE60143)/Homer WAAAAGTGHH 1e0 -2.265e+00 1.0000 1.0 100.00% 416.9 10.40% +HIC1(Zf)/Treg-ZBTB29-ChIP-Seq(GSE99889)/Homer TGCCAGCB 1e0 -2.253e+00 1.0000 1.0 100.00% 421.8 10.52% +Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer TAATTAGN 1e0 -2.246e+00 1.0000 1.0 100.00% 424.3 10.59% +DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer TAGCGCGC 1e0 -2.169e+00 1.0000 1.0 100.00% 458.1 11.43% +Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer ATATGCAAAT 1e0 -2.054e+00 1.0000 1.0 100.00% 514.3 12.83% +AT1G72740(MYBrelated)/colamp-AT1G72740-DAP-Seq(GSE60143)/Homer NNWWAMCCTAAHWNN 1e0 -2.029e+00 1.0000 1.0 100.00% 527.4 13.16% +Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer GYMATAAAAH 1e0 -2.019e+00 1.0000 1.0 100.00% 532.9 13.30% +SPL5(SBP)/colamp-SPL5-DAP-Seq(GSE60143)/Homer NNHGTACGGHNN 1e0 -2.003e+00 1.0000 1.0 100.00% 541.8 13.52% +AT3G25990(Trihelix)/colamp-AT3G25990-DAP-Seq(GSE60143)/Homer TTAACCATAG 1e0 -1.992e+00 1.0000 1.0 100.00% 547.8 13.67% +PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer HAATAAAGNN 1e0 -1.945e+00 1.0000 1.0 100.00% 573.6 14.31% +RKD2(RWPRK)/colamp-RKD2-DAP-Seq(GSE60143)/Homer GACKTTTCRDCTTCC 1e0 -1.935e+00 1.0000 1.0 100.00% 579.4 14.46% +TCX2(CPP)/colamp-TCX2-DAP-Seq(GSE60143)/Homer NNWWTTYRAAHN 1e0 -1.913e+00 1.0000 1.0 100.00% 593.0 14.79% +SOL1(CPP)/colamp-SOL1-DAP-Seq(GSE60143)/Homer ATTTAAATHN 1e0 -1.902e+00 1.0000 1.0 100.00% 598.5 14.93% +Isl1(Homeobox)/Neuron-Isl1-ChIP-Seq(GSE31456)/Homer CTAATKGV 1e0 -1.883e+00 1.0000 1.0 100.00% 610.2 15.23% +Lhx1(Homeobox)/EmbryoCarcinoma-Lhx1-ChIP-Seq(GSE70957)/Homer NNYTAATTAR 1e0 -1.755e+00 1.0000 1.0 100.00% 693.4 17.30% +AT5G05550(Trihelix)/col-AT5G05550-DAP-Seq(GSE60143)/Homer HDNHDTCKCCGGMGA 1e0 -1.748e+00 1.0000 1.0 100.00% 698.8 17.44% +CCA(Myb)/Arabidopsis-CCA.GFP-ChIP-Seq(GSE70533)/Homer AGATATYTTT 1e0 -1.738e+00 1.0000 1.0 100.00% 705.2 17.60% +At4g01280(MYBrelated)/colamp-At4g01280-DAP-Seq(GSE60143)/Homer AAATATCT 1e0 -1.734e+00 1.0000 1.0 100.00% 709.0 17.69% +Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer ADBTAATTAR 1e0 -1.710e+00 1.0000 1.0 100.00% 725.1 18.09% +SPL15(SBP)/colamp-SPL15-DAP-Seq(GSE60143)/Homer WDWMMGTACADW 1e0 -1.699e+00 1.0000 1.0 100.00% 733.8 18.31% +Unknown6/Drosophila-Promoters/Homer AATTTTAAAA 1e0 -1.698e+00 1.0000 1.0 100.00% 734.5 18.33% +SPL1(SBP)/colamp-SPL1-DAP-Seq(GSE60143)/Homer HYGTACDTWH 1e0 -1.684e+00 1.0000 1.0 100.00% 744.9 18.59% +Sox6(HMG)/Myotubes-Sox6-ChIP-Seq(GSE32627)/Homer CCATTGTTNY 1e0 -1.624e+00 1.0000 1.0 100.00% 790.8 19.73% +ATHB23(ZFHD)/col-ATHB23-DAP-Seq(GSE60143)/Homer HTAATTARNN 1e0 -1.573e+00 1.0000 1.0 100.00% 831.1 20.73% +ATHB34(ZFHD)/colamp-ATHB34-DAP-Seq(GSE60143)/Homer TRATTARS 1e0 -1.567e+00 1.0000 1.0 100.00% 836.7 20.87% +ATHB24(ZFHD)/colamp-ATHB24-DAP-Seq(GSE60143)/Homer TAATTAAS 1e0 -1.478e+00 1.0000 1.0 100.00% 914.8 22.82% +RVE1(MYBrelated)/col-RVE1-DAP-Seq(GSE60143)/Homer AAATATCT 1e0 -1.437e+00 1.0000 1.0 100.00% 952.3 23.76% +MYB105(MYB)/colamp-MYB105-DAP-Seq(GSE60143)/Homer RATWCCGTTA 1e0 -1.367e+00 1.0000 1.0 100.00% 1022.5 25.51% +AT1G20910(ARID)/col-AT1G20910-DAP-Seq(GSE60143)/Homer THAATTRAWN 1e0 -1.358e+00 1.0000 1.0 100.00% 1032.0 25.75% +ATHB33(ZFHD)/col-ATHB33-DAP-Seq(GSE60143)/Homer NGTRATTAAK 1e0 -1.326e+00 1.0000 1.0 100.00% 1064.2 26.55% +EGL-5(Homeobox)/cElegans-L3-EGL5-ChIP-Seq(modEncode)/Homer ATTTAATGGG 1e0 -1.277e+00 1.0000 1.0 100.00% 1118.2 27.90% +Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer TGTCANYT 1e0 -1.203e+00 1.0000 1.0 100.00% 1204.7 30.06% +Initiator/Drosophila-Promoters/Homer NTCAGTYG 1e0 -1.181e+00 1.0000 1.0 100.00% 1230.5 30.70% +LHY(Myb)/Seedling-LHY-ChIP-Seq(GSE52175)/Homer ADAAATATCT 1e0 -1.172e+00 1.0000 1.0 100.00% 1241.5 30.98% +Hoxa13(Homeobox)/ChickenMSG-Hoxa13.Flag-ChIP-Seq(GSE86088)/Homer CYHATAAAAN 1e0 -1.148e+00 1.0000 1.0 100.00% 1272.7 31.75% +MYB83(MYB)/colamp-MYB83-DAP-Seq(GSE60143)/Homer CACCAACCWH 1e0 -1.126e+00 1.0000 1.0 100.00% 1300.4 32.44% +SeqBias: TA-repeat TATATATATA 1e0 -1.022e+00 1.0000 1.0 100.00% 1442.0 35.98% +ASL18(LOBAS2)/colamp-ASL18-DAP-Seq(GSE60143)/Homer CCGGAAAWTCMGGAR 1e0 -9.888e-01 1.0000 1.0 100.00% 1491.4 37.21% +ATHB25(ZFHD)/colamp-ATHB25-DAP-Seq(GSE60143)/Homer TAATTAVB 1e0 -9.096e-01 1.0000 1.0 100.00% 1614.2 40.27% +MYB81(MYB)/col-MYB81-DAP-Seq(GSE60143)/Homer NWAACSGWTWNN 1e0 -9.052e-01 1.0000 1.0 100.00% 1621.2 40.45% +ATY13(MYB)/col-ATY13-DAP-Seq(GSE60143)/Homer YYYAACYRHH 1e0 -8.809e-01 1.0000 1.0 100.00% 1661.1 41.44% +SeqBias: CA-repeat CACACACACA 1e0 -8.779e-01 1.0000 1.0 100.00% 1666.7 41.58% +Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer GKTAATGR 1e0 -8.218e-01 1.0000 1.0 100.00% 1762.4 43.97% +MYB(HTH)/ERMYB-Myb-ChIPSeq(GSE22095)/Homer GGCVGTTR 1e0 -7.731e-01 1.0000 1.0 100.00% 1850.5 46.17% +HuR(?)/HEK293-HuR-CLIP-Seq(GSE87887)/Homer BTTTGGTTTG 1e0 -6.807e-01 1.0000 1.0 100.00% 2029.7 50.64% +SeqBias: CG bias SSSSSSSSSS 1e0 -6.559e-01 1.0000 1.0 100.00% 2080.4 51.90% +MYB101(MYB)/colamp-MYB101-DAP-Seq(GSE60143)/Homer TAACNRMY 1e0 -6.392e-01 1.0000 1.0 100.00% 2115.2 52.77% +SUT1?/SacCer-Promoters/Homer CCCCGCGC 1e0 -5.162e-01 1.0000 1.0 100.00% 2392.4 59.69% +At3g24120(G2like)/col-At3g24120-DAP-Seq(GSE60143)/Homer NWWAGMATMW 1e0 -5.157e-01 1.0000 1.0 100.00% 2393.1 59.71% +STZ(C2H2)/colamp-STZ-DAP-Seq(GSE60143)/Homer HNBTCACT 1e0 -4.816e-01 1.0000 1.0 100.00% 2476.2 61.78% +Pitx1(Homeobox)/Chicken-Pitx1-ChIP-Seq(GSE38910)/Homer TAATCCCN 1e0 -4.696e-01 1.0000 1.0 100.00% 2506.1 62.53% +Nanog(Homeobox)/mES-Nanog-ChIP-Seq(GSE11724)/Homer RGCCATTAAC 1e0 -3.038e-01 1.0000 1.0 100.00% 2958.9 73.82% +SeqBias: polyA-repeat AAAAAAAAAA 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% +SeqBias: C/A-bias MMMMMMMMMM 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% +SeqBias: polyC-repeat CCCCCCCCCC 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% +SeqBias: G/A bias RRRRRRRRRR 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% +SeqBias: GCW-triplet GCWGCWGCWGCW 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% +SeqBias: A/T bias WWWWWWWWWW 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% + Ik-1 NHTTGGGAATRCC 1e0 -2.500e-04 1.0000 1.0 100.00% 4008.1 100.00% +AP-1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer VTGACTCATC 1e0 0.000e+00 1.0000 0.0 0.00% 505.0 12.60% +AP-2gamma(AP2)/MCF7-TFAP2C-ChIP-Seq(GSE21234)/Homer SCCTSAGGSCAW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AP-2alpha(AP2)/Hela-AP2alpha-ChIP-Seq(GSE31477)/Homer ATGCCCTGAGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Ap4(bHLH)/AML-Tfap4-ChIP-Seq(GSE45738)/Homer NAHCAGCTGD 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +FOXA1:AR(Forkhead,NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer AGTAAACAAAAAAGAACAND 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ARE(NR)/LNCAP-AR-ChIP-Seq(GSE27824)/Homer RGRACASNSTGTYCYB 1e0 0.000e+00 1.0000 0.0 0.00% 85.6 2.14% +AR-halfsite(NR)/LNCaP-AR-ChIP-Seq(GSE27824)/Homer CCAGGAACAG 1e0 0.000e+00 1.0000 0.0 0.00% 276.1 6.89% +Arnt:Ahr(bHLH)/MCF7-Arnt-ChIP-Seq(Lo_et_al.)/Homer TBGCACGCAA 1e0 0.000e+00 1.0000 0.0 0.00% 255.8 6.38% +Ascl1(bHLH)/NeuralTubes-Ascl1-ChIP-Seq(GSE55840)/Homer NNVVCAGCTGBN 1e0 0.000e+00 1.0000 0.0 0.00% 333.9 8.33% +Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer GATGACGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 272.7 6.80% +Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer NRRTGACGTCAT 1e0 0.000e+00 1.0000 0.0 0.00% 267.1 6.66% +Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer DATGASTCATHN 1e0 0.000e+00 1.0000 0.0 0.00% 227.7 5.68% +Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer MTGATGCAAT 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer NGRTGACGTCAY 1e0 0.000e+00 1.0000 0.0 0.00% 269.0 6.71% +Atoh1(bHLH)/Cerebellum-Atoh1-ChIP-Seq(GSE22111)/Homer VNRVCAGCTGGY 1e0 0.000e+00 1.0000 0.0 0.00% 171.4 4.28% +Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer AWWNTGCTGAGTCAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer TGCTGAGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 197.7 4.93% +Bapx1(Homeobox)/VertebralCol-Bapx1-ChIP-Seq(GSE36672)/Homer TTRAGTGSYK 1e0 0.000e+00 1.0000 0.0 0.00% 191.7 4.78% +Barx1(Homeobox)/Stomach-Barx1.3xFlag-ChIP-Seq(GSE69483)/Homer AAACMATTAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IRF:BATF(IRF:bZIP)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer CTTTCANTATGACTV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer DATGASTCAT 1e0 0.000e+00 1.0000 0.0 0.00% 335.8 8.38% +Bcl11a(Zf)/HSPC-BCL11A-ChIP-Seq(GSE104676)/Homer TYTGACCASWRG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer NNNCTTTCCAGGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 843.2 21.04% +bHLHE40(bHLH)/HepG2-BHLHE40-ChIP-Seq(GSE31477)/Homer KCACGTGMCN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bHLHE41(bHLH)/proB-Bhlhe41-ChIP-Seq(GSE93764)/Homer KCACGTGMCN 1e0 0.000e+00 1.0000 0.0 0.00% 669.4 16.70% +BMAL1(bHLH)/Liver-Bmal1-ChIP-Seq(GSE39860)/Homer GNCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 307.6 7.67% +BMYB(HTH)/Hela-BMYB-ChIP-Seq(GSE27030)/Homer NHAACBGYYV 1e0 0.000e+00 1.0000 0.0 0.00% 1946.0 48.55% +BORIS(Zf)/K562-CTCFL-ChIP-Seq(GSE32465)/Homer CNNBRGCGCCCCCTGSTGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Brachyury(T-box)/Mesoendoderm-Brachyury-ChIP-exo(GSE54963)/Homer ANTTMRCASBNNNGTGYKAAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Brn1(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer TATGCWAATBAV 1e0 0.000e+00 1.0000 0.0 0.00% 261.1 6.51% +Brn2(POU,Homeobox)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer ATGAATATTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bZIP:IRF(bZIP,IRF)/Th17-BatF-ChIP-Seq(GSE39756)/Homer NAGTTTCABTHTGACTNW 1e0 0.000e+00 1.0000 0.0 0.00% 213.1 5.32% +CDX4(Homeobox)/ZebrafishEmbryos-Cdx4.Myc-ChIP-Seq(GSE48254)/Homer NGYCATAAAWCH 1e0 0.000e+00 1.0000 0.0 0.00% 372.8 9.30% +CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer DRTGTTGCAA 1e0 0.000e+00 1.0000 0.0 0.00% 27.9 0.70% +CEBP:CEBP(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer NTNATGCAAYMNNHTGMAAY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CEBP(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer ATTGCGCAAC 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer ATTGCATCAT 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +CLOCK(bHLH)/Liver-Clock-ChIP-Seq(GSE39860)/Homer GHCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +c-Myc(bHLH)/LNCAP-cMyc-ChIP-Seq(Unpublished)/Homer VCCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 145.1 3.62% +c-Myc(bHLH)/mES-cMyc-ChIP-Seq(GSE11431)/Homer VVCCACGTGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +COUP-TFII(NR)/K562-NR2F1-ChIP-Seq(Encode)/Homer GKBCARAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 417.3 10.41% +COUP-TFII(NR)/Artia-Nr2f2-ChIP-Seq(GSE46497)/Homer AGRGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 141.4 3.53% +CRE(bZIP)/Promoter/Homer CSGTGACGTCAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer GCTAATCC 1e0 0.000e+00 1.0000 0.0 0.00% 1426.3 35.59% +CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer AYAGTGCCMYCTRGTGGCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CTCF-SatelliteElement(Zf?)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer TGCAGTTCCMVNWRTGGCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CUX1(Homeobox)/K562-CUX1-ChIP-Seq(GSE92882)/Homer TATCGATNAN 1e0 0.000e+00 1.0000 0.0 0.00% 460.0 11.48% +Cux2(Homeobox)/Liver-Cux2-ChIP-Seq(GSE35985)/Homer HNRAATCAAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Dlx3(Homeobox)/Kerainocytes-Dlx3-ChIP-Seq(GSE89884)/Homer NDGTAATTAC 1e0 0.000e+00 1.0000 0.0 0.00% 197.1 4.92% +Mouse_Recombination_Hotspot(Zf)/Testis-DMC1-ChIP-Seq(GSE24438)/Homer ACTYKNATTCGTGNTACTTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DMRT1(DM)/Testis-DMRT1-ChIP-Seq(GSE64892)/Homer TWGHWACAWTGTWDC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DMRT6(DM)/Testis-DMRT6-ChIP-Seq(GSE60440)/Homer YDGHTACAWTGTADC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer AGGTCAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RAR:RXR(NR),DR5/ES-RAR-ChIP-Seq(GSE56893)/Homer RGGTCADNNAGAGGTCAV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DUX4(Homeobox)/Myoblasts-DUX4.V5-ChIP-Seq(GSE75791)/Homer NWTAAYCYAATCAWN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DUX(Homeobox)/C2C12-Dux-ChIP-Seq(GSE87279)/Homer BCWGATTCAATCAAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E2A(bHLH)/proBcell-E2A-ChIP-Seq(GSE21978)/Homer DNRCAGCTGY 1e0 0.000e+00 1.0000 0.0 0.00% 168.1 4.19% +E2F1(E2F)/Hela-E2F1-ChIP-Seq(GSE22478)/Homer CWGGCGGGAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E2F3(E2F)/MEF-E2F3-ChIP-Seq(GSE71376)/Homer BTKGGCGGGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 104.2 2.60% +E2F4(E2F)/K562-E2F4-ChIP-Seq(GSE31477)/Homer GGCGGGAAAH 1e0 0.000e+00 1.0000 0.0 0.00% 695.6 17.35% +E2F6(E2F)/Hela-E2F6-ChIP-Seq(GSE31477)/Homer GGCGGGAARN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E2F7(E2F)/Hela-E2F7-ChIP-Seq(GSE32673)/Homer VDTTTCCCGCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E2F(E2F)/Hela-CellCycle-Expression/Homer TTSGCGCGAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E2A(bHLH),near_PU.1/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer NVCACCTGBN 1e0 0.000e+00 1.0000 0.0 0.00% 168.1 4.19% +EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer DGTCCCYRGGGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer GTCCCCWGGGGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +EBNA1(EBV-virus)/Raji-EBNA1-ChIP-Seq(GSE30709)/Homer GGYAGCAYDTGCTDCCCNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E-box(bHLH)/Promoter/Homer SSGGTCACGTGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Egr1(Zf)/K562-Egr1-ChIP-Seq(GSE32465)/Homer TGCGTGGGYG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Egr2(Zf)/Thymocytes-Egr2-ChIP-Seq(GSE34254)/Homer NGCGTGGGCGGR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +EKLF(Zf)/Erythrocyte-Klf1-ChIP-Seq(GSE20478)/Homer NWGGGTGTGGCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ELF1(ETS)/Jurkat-ELF1-ChIP-Seq(SRA014231)/Homer AVCCGGAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Elk1(ETS)/Hela-Elk1-ChIP-Seq(GSE31477)/Homer HACTTCCGGY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Eomes(T-box)/H9-Eomes-ChIP-Seq(GSE26097)/Homer ATTAACACCT 1e0 0.000e+00 1.0000 0.0 0.00% 986.3 24.61% +ERE(NR),IR3/MCF7-ERa-ChIP-Seq(Unpublished)/Homer VAGGTCACNSTGACC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Erra(NR)/HepG2-Erra-ChIP-Seq(GSE31477)/Homer CAAAGGTCAG 1e0 0.000e+00 1.0000 0.0 0.00% 152.9 3.82% +Unknown-ESC-element(?)/mES-Nanog-ChIP-Seq(GSE11724)/Homer CACAGCAGGGGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Esrrb(NR)/mES-Esrrb-ChIP-Seq(GSE11431)/Homer KTGACCTTGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Ets1-distal(ETS)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer MACAGGAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ETS:E-box(ETS,bHLH)/HPC7-Scl-ChIP-Seq(GSE22178)/Homer AGGAARCAGCTG 1e0 0.000e+00 1.0000 0.0 0.00% 48.6 1.21% +ETS(ETS)/Promoter/Homer AACCGGAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ETS:RUNX(ETS,Runt)/Jurkat-RUNX1-ChIP-Seq(GSE17954)/Homer RCAGGATGTGGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ETV1(ETS)/GIST48-ETV1-ChIP-Seq(GSE22441)/Homer AACCGGAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 58.0 1.45% +ETV4(ETS)/HepG2-ETV4-ChIP-Seq(ENCODE)/Homer ACCGGAAGTG 1e0 0.000e+00 1.0000 0.0 0.00% 35.5 0.89% +EWS:ERG-fusion(ETS)/CADO_ES1-EWS:ERG-ChIP-Seq(SRA014231)/Homer ATTTCCTGTN 1e0 0.000e+00 1.0000 0.0 0.00% 37.4 0.93% +EWS:FLI1-fusion(ETS)/SK_N_MC-EWS:FLI1-ChIP-Seq(SRA014231)/Homer VACAGGAAAT 1e0 0.000e+00 1.0000 0.0 0.00% 37.4 0.93% +Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer NATGASTCABNN 1e0 0.000e+00 1.0000 0.0 0.00% 225.8 5.63% +FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer WAAGTAAACA 1e0 0.000e+00 1.0000 0.0 0.00% 704.5 17.58% +FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer WAAGTAAACA 1e0 0.000e+00 1.0000 0.0 0.00% 704.5 17.58% +Foxa2(Forkhead)/Liver-Foxa2-ChIP-Seq(GSE25694)/Homer CYTGTTTACWYW 1e0 0.000e+00 1.0000 0.0 0.00% 583.6 14.56% +Foxa3(Forkhead)/Liver-Foxa3-ChIP-Seq(GSE77670)/Homer BSNTGTTTACWYWGN 1e0 0.000e+00 1.0000 0.0 0.00% 290.9 7.26% +Fox:Ebox(Forkhead,bHLH)/Panc1-Foxa2-ChIP-Seq(GSE47459)/Homer NNNVCTGWGYAAACASN 1e0 0.000e+00 1.0000 0.0 0.00% 78.2 1.95% +Foxf1(Forkhead)/Lung-Foxf1-ChIP-Seq(GSE77951)/Homer WWATRTAAACAN 1e0 0.000e+00 1.0000 0.0 0.00% 596.2 14.87% +Foxh1(Forkhead)/hESC-FOXH1-ChIP-Seq(GSE29422)/Homer NNTGTGGATTSS 1e0 0.000e+00 1.0000 0.0 0.00% 318.8 7.95% +FOXK1(Forkhead)/HEK293-FOXK1-ChIP-Seq(GSE51673)/Homer NVWTGTTTAC 1e0 0.000e+00 1.0000 0.0 0.00% 812.7 20.28% +FOXK2(Forkhead)/U2OS-FOXK2-ChIP-Seq(E-MTAB-2204)/Homer SCHTGTTTACAT 1e0 0.000e+00 1.0000 0.0 0.00% 772.4 19.27% +FoxL2(Forkhead)/Ovary-FoxL2-ChIP-Seq(GSE60858)/Homer WWTRTAAACAVG 1e0 0.000e+00 1.0000 0.0 0.00% 758.7 18.93% +FOXM1(Forkhead)/MCF7-FOXM1-ChIP-Seq(GSE72977)/Homer TRTTTACTTW 1e0 0.000e+00 1.0000 0.0 0.00% 798.2 19.91% +Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq(Fan_et_al.)/Homer CTGTTTAC 1e0 0.000e+00 1.0000 0.0 0.00% 964.5 24.06% +Foxo3(Forkhead)/U2OS-Foxo3-ChIP-Seq(E-MTAB-2701)/Homer DGTAAACA 1e0 0.000e+00 1.0000 0.0 0.00% 831.4 20.74% +FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer NYYTGTTTACHN 1e0 0.000e+00 1.0000 0.0 0.00% 304.2 7.59% +Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer NNATGASTCATH 1e0 0.000e+00 1.0000 0.0 0.00% 227.7 5.68% +Fra2(bZIP)/Striatum-Fra2-ChIP-Seq(GSE43429)/Homer GGATGACTCATC 1e0 0.000e+00 1.0000 0.0 0.00% 227.7 5.68% +FXR(NR),IR1/Liver-FXR-ChIP-Seq(Chong_et_al.)/Homer AGGTCANTGACCTB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GABPA(ETS)/Jurkat-GABPa-ChIP-Seq(GSE17954)/Homer RACCGGAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Gata2(Zf)/K562-GATA2-ChIP-Seq(GSE18829)/Homer BBCTTATCTS 1e0 0.000e+00 1.0000 0.0 0.00% 505.9 12.62% +GATA3(Zf),DR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer AGATGKDGAGATAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA3(Zf),DR8/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer AGATSTNDNNDSAGATAASN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer NNNNNBAGATAWYATCTVHN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA(Zf),IR4/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer NAGATWNBNATCTNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA3(Zf)/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer AGATAASR 1e0 0.000e+00 1.0000 0.0 0.00% 1397.7 34.87% +Gata4(Zf)/Heart-Gata4-ChIP-Seq(GSE35151)/Homer NBWGATAAGR 1e0 0.000e+00 1.0000 0.0 0.00% 968.1 24.15% +Gata6(Zf)/HUG1N-GATA6-ChIP-Seq(GSE51936)/Homer YCTTATCTBN 1e0 0.000e+00 1.0000 0.0 0.00% 778.0 19.41% +Gata1(Zf)/K562-GATA1-ChIP-Seq(GSE18829)/Homer SAGATAAGRV 1e0 0.000e+00 1.0000 0.0 0.00% 505.9 12.62% +GATA:SCL(Zf,bHLH)/Ter119-SCL-ChIP-Seq(GSE18720)/Homer CRGCTGBNGNSNNSAGATAA 1e0 0.000e+00 1.0000 0.0 0.00% 192.5 4.80% +Gfi1b(Zf)/HPC7-Gfi1b-ChIP-Seq(GSE22178)/Homer MAATCACTGC 1e0 0.000e+00 1.0000 0.0 0.00% 302.7 7.55% +GFX(?)/Promoter/Homer ATTCTCGCGAGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GFY(?)/Promoter/Homer ACTACAATTCCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GFY-Staf(?,Zf)/Promoter/Homer RACTACAATTCCCAGAAKGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GLI3(Zf)/Limb-GLI3-ChIP-Chip(GSE11077)/Homer CGTGGGTGGTCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GLIS3(Zf)/Thyroid-Glis3.GFP-ChIP-Seq(GSE103297)/Homer CTCCCTGGGAGGCCN 1e0 0.000e+00 1.0000 0.0 0.00% 189.9 4.74% +GRE(NR),IR3/A549-GR-ChIP-Seq(GSE32465)/Homer NRGVACABNVTGTYCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GRE(NR),IR3/RAW264.7-GRE-ChIP-Seq(Unpublished)/Homer VAGRACAKWCTGTYC 1e0 0.000e+00 1.0000 0.0 0.00% 87.5 2.18% +GRHL2(CP2)/HBE-GRHL2-ChIP-Seq(GSE46194)/Homer AAACYKGTTWDACMRGTTTB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GSC(Homeobox)/FrogEmbryos-GSC-ChIP-Seq(DRA000576)/Homer RGGATTAR 1e0 0.000e+00 1.0000 0.0 0.00% 1081.2 26.98% +Hand2(bHLH)/Mesoderm-Hand2-ChIP-Seq(GSE61475)/Homer TGACANARRCCAGRC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HEB(bHLH)/mES-Heb-ChIP-Seq(GSE53233)/Homer VCAGCTGBNN 1e0 0.000e+00 1.0000 0.0 0.00% 477.4 11.91% +HIF-1a(bHLH)/MCF7-HIF1a-ChIP-Seq(GSE28352)/Homer TACGTGCV 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +HIF-1b(HLH)/T47D-HIF1b-ChIP-Seq(GSE59937)/Homer RTACGTGC 1e0 0.000e+00 1.0000 0.0 0.00% 708.4 17.67% +HIF2a(bHLH)/785_O-HIF2a-ChIP-Seq(GSE34871)/Homer GCACGTACCC 1e0 0.000e+00 1.0000 0.0 0.00% 637.8 15.91% +HINFP(Zf)/K562-HINFP.eGFP-ChIP-Seq(Encode)/Homer TWVGGTCCGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HLF(bZIP)/HSC-HLF.Flag-ChIP-Seq(GSE69817)/Homer RTTATGYAAB 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +HNF1b(Homeobox)/PDAC-HNF1B-ChIP-Seq(GSE64557)/Homer GTTAATNATTAA 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +Hnf1(Homeobox)/Liver-Foxa2-Chip-Seq(GSE25694)/Homer GGTTAAWCATTAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HNF4a(NR),DR1/HepG2-HNF4a-ChIP-Seq(GSE25021)/Homer CARRGKBCAAAGTYCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HNF6(Homeobox)/Liver-Hnf6-ChIP-Seq(ERP000394)/Homer NTATYGATCH 1e0 0.000e+00 1.0000 0.0 0.00% 204.6 5.10% +Hoxa10(Homeobox)/ChickenMSG-Hoxa10.Flag-ChIP-Seq(GSE86088)/Homer GGYAATGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 354.0 8.83% +Hoxa11(Homeobox)/ChickenMSG-Hoxa11.Flag-ChIP-Seq(GSE86088)/Homer TTTTATGGCM 1e0 0.000e+00 1.0000 0.0 0.00% 1612.3 40.23% +HOXA1(Homeobox)/mES-Hoxa1-ChIP-Seq(SRP084292)/Homer TGATKGATGR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HOXA2(Homeobox)/mES-Hoxa2-ChIP-Seq(Donaldson_et_al.)/Homer GYCATCMATCAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Hoxa9(Homeobox)/ChickenMSG-Hoxa9.Flag-ChIP-Seq(GSE86088)/Homer RGCAATNAAA 1e0 0.000e+00 1.0000 0.0 0.00% 1597.1 39.85% +HOXB13(Homeobox)/ProstateTumor-HOXB13-ChIP-Seq(GSE56288)/Homer TTTTATKRGG 1e0 0.000e+00 1.0000 0.0 0.00% 331.3 8.26% +Hoxb4(Homeobox)/ES-Hoxb4-ChIP-Seq(GSE34014)/Homer TGATTRATGGCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Hoxc9(Homeobox)/Ainv15-Hoxc9-ChIP-Seq(GSE21812)/Homer GGCCATAAATCA 1e0 0.000e+00 1.0000 0.0 0.00% 244.3 6.09% +Hoxd10(Homeobox)/ChickenMSG-Hoxd10.Flag-ChIP-Seq(GSE86088)/Homer GGCMATGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 873.9 21.80% +Hoxd11(Homeobox)/ChickenMSG-Hoxd11.Flag-ChIP-Seq(GSE86088)/Homer VGCCATAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 1321.7 32.98% +Hoxd12(Homeobox)/ChickenMSG-Hoxd12.Flag-ChIP-Seq(GSE86088)/Homer HDGYAATGAAAN 1e0 0.000e+00 1.0000 0.0 0.00% 1343.8 33.53% +Hoxd13(Homeobox)/ChickenMSG-Hoxd13.Flag-ChIP-Seq(GSE86088)/Homer NCYAATAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 802.6 20.02% +HRE(HSF)/HepG2-HSF1-ChIP-Seq(GSE31477)/Homer BSTTCTRGAABVTTCYAGAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HRE(HSF)/Striatum-HSF1-ChIP-Seq(GSE38000)/Homer TTCTAGAABNTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IRF1(IRF)/PBMC-IRF1-ChIP-Seq(GSE43036)/Homer GAAAGTGAAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IRF2(IRF)/Erythroblas-IRF2-ChIP-Seq(GSE36985)/Homer GAAASYGAAASY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IRF3(IRF)/BMDM-Irf3-ChIP-Seq(GSE67343)/Homer AGTTTCAKTTTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IRF8(IRF)/BMDM-IRF8-ChIP-Seq(GSE77884)/Homer GRAASTGAAAST 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ISRE(IRF)/ThioMac-LPS-Expression(GSE23622)/Homer AGTTTCASTTTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer GATGASTCATCN 1e0 0.000e+00 1.0000 0.0 0.00% 225.8 5.63% +JunB(bZIP)/DendriticCells-Junb-ChIP-Seq(GSE36099)/Homer RATGASTCAT 1e0 0.000e+00 1.0000 0.0 0.00% 335.8 8.38% +c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer ATGACGTCATCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +JunD(bZIP)/K562-JunD-ChIP-Seq/Homer ATGACGTCATCN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +KLF10(Zf)/HEK293-KLF10.GFP-ChIP-Seq(GSE58341)/Homer GGGGGTGTGTCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +KLF14(Zf)/HEK293-KLF14.GFP-ChIP-Seq(GSE58341)/Homer RGKGGGCGKGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +KLF3(Zf)/MEF-Klf3-ChIP-Seq(GSE44748)/Homer NRGCCCCRCCCHBNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Klf4(Zf)/mES-Klf4-ChIP-Seq(GSE11431)/Homer GCCACACCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +KLF5(Zf)/LoVo-KLF5-ChIP-Seq(GSE49402)/Homer DGGGYGKGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +KLF6(Zf)/PDAC-KLF6-ChIP-Seq(GSE64557)/Homer MKGGGYGTGGCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Klf9(Zf)/GBM-Klf9-ChIP-Seq(GSE62211)/Homer GCCACRCCCACY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +LEF1(HMG)/H1-LEF1-ChIP-Seq(GSE64758)/Homer CCTTTGATST 1e0 0.000e+00 1.0000 0.0 0.00% 197.6 4.93% +Unknown(Homeobox)/Limb-p300-ChIP-Seq/Homer SSCMATWAAA 1e0 0.000e+00 1.0000 0.0 0.00% 414.8 10.35% +LRF(Zf)/Erythroblasts-ZBTB7A-ChIP-Seq(GSE74977)/Homer AAGACCCYYN 1e0 0.000e+00 1.0000 0.0 0.00% 147.0 3.67% +Nr5a2(NR)/Pancreas-LRH1-ChIP-Seq(GSE34295)/Homer BTCAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +LXRE(NR),DR4/RAW-LXRb.biotin-ChIP-Seq(GSE21512)/Homer RGGTTACTANAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer TGCTGACTCA 1e0 0.000e+00 1.0000 0.0 0.00% 274.6 6.85% +MafB(bZIP)/BMM-Mafb-ChIP-Seq(GSE75722)/Homer WNTGCTGASTCAGCANWTTY 1e0 0.000e+00 1.0000 0.0 0.00% 449.5 11.21% +MafF(bZIP)/HepG2-MafF-ChIP-Seq(GSE31477)/Homer HWWGTCAGCAWWTTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MafK(bZIP)/C2C12-MafK-ChIP-Seq(GSE36030)/Homer GCTGASTCAGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Max(bHLH)/K562-Max-ChIP-Seq(GSE31477)/Homer RCCACGTGGYYN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Maz(Zf)/HepG2-Maz-ChIP-Seq(GSE31477)/Homer GGGGGGGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Mef2b(MADS)/HEK293-Mef2b.V5-ChIP-Seq(GSE67450)/Homer GCTATTTTTGGM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Mef2c(MADS)/GM12878-Mef2c-ChIP-Seq(GSE32465)/Homer DCYAAAAATAGM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Mef2d(MADS)/Retina-Mef2d-ChIP-Seq(GSE61391)/Homer GCTATTTTTAGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer VGCTGWCAVB 1e0 0.000e+00 1.0000 0.0 0.00% 663.8 16.56% +MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer RTCATGTGAC 1e0 0.000e+00 1.0000 0.0 0.00% 512.8 12.79% +MNT(bHLH)/HepG2-MNT-ChIP-Seq(Encode)/Homer DGCACACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AMYB(HTH)/Testes-AMYB-ChIP-Seq(GSE44588)/Homer TGGCAGTTGG 1e0 0.000e+00 1.0000 0.0 0.00% 1024.8 25.57% +Myf5(bHLH)/GM-Myf5-ChIP-Seq(GSE24852)/Homer BAACAGCTGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYNN(Zf)/HEK293-MYNN.eGFP-ChIP-Seq(Encode)/Homer TTCAAAWTAAAAGTC 1e0 0.000e+00 1.0000 0.0 0.00% 151.3 3.77% +MyoD(bHLH)/Myotube-MyoD-ChIP-Seq(GSE21614)/Homer RRCAGCTGYTSY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MyoG(bHLH)/C2C12-MyoG-ChIP-Seq(GSE36024)/Homer AACAGCTG 1e0 0.000e+00 1.0000 0.0 0.00% 168.1 4.19% +NeuroD1(bHLH)/Islet-NeuroD1-ChIP-Seq(GSE30298)/Homer GCCATCTGTT 1e0 0.000e+00 1.0000 0.0 0.00% 261.1 6.51% +NeuroG2(bHLH)/Fibroblast-NeuroG2-ChIP-Seq(GSE75910)/Homer ACCATCTGTT 1e0 0.000e+00 1.0000 0.0 0.00% 661.9 16.51% +NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer WNTGTTTRYTTTGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer YTGCCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 469.5 11.71% +NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer CYTGGCABNSTGCCAR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NFAT:AP1(RHD,bZIP)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer SARTGGAAAAWRTGAGTCAB 1e0 0.000e+00 1.0000 0.0 0.00% 220.1 5.49% +NFAT(RHD)/Jurkat-NFATC1-ChIP-Seq(Jolma_et_al.)/Homer ATTTTCCATT 1e0 0.000e+00 1.0000 0.0 0.00% 968.4 24.16% +NFE2L2(bZIP)/HepG2-NFE2L2-ChIP-Seq(Encode)/Homer AWWWTGCTGAGTCAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NF-E2(bZIP)/K562-NFE2-ChIP-Seq(GSE31477)/Homer GATGACTCAGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NFIL3(bZIP)/HepG2-NFIL3-ChIP-Seq(Encode)/Homer VTTACGTAAYNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +NFkB-p65-Rel(RHD)/ThioMac-LPS-Expression(GSE23622)/Homer GGAAATTCCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NFY(CCAAT)/Promoter/Homer RGCCAATSRG 1e0 0.000e+00 1.0000 0.0 0.00% 374.5 9.34% +Nkx2.1(Homeobox)/LungAC-Nkx2.1-ChIP-Seq(GSE43252)/Homer RSCACTYRAG 1e0 0.000e+00 1.0000 0.0 0.00% 1459.1 36.40% +Nkx2.2(Homeobox)/NPC-Nkx2.2-ChIP-Seq(GSE61673)/Homer BTBRAGTGSN 1e0 0.000e+00 1.0000 0.0 0.00% 853.1 21.28% +Nkx2.5(Homeobox)/HL1-Nkx2.5.biotin-ChIP-Seq(GSE21529)/Homer RRSCACTYAA 1e0 0.000e+00 1.0000 0.0 0.00% 1485.3 37.06% +Nkx3.1(Homeobox)/LNCaP-Nkx3.1-ChIP-Seq(GSE28264)/Homer AAGCACTTAA 1e0 0.000e+00 1.0000 0.0 0.00% 528.5 13.19% +n-Myc(bHLH)/mES-nMyc-ChIP-Seq(GSE11431)/Homer VRCCACGTGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NPAS2(bHLH)/Liver-NPAS2-ChIP-Seq(GSE39860)/Homer KCCACGTGAC 1e0 0.000e+00 1.0000 0.0 0.00% 78.1 1.95% +NPAS(bHLH)/Liver-NPAS-ChIP-Seq(GSE39860)/Homer NVCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 480.7 11.99% +EAR2(NR)/K562-NR2F6-ChIP-Seq(Encode)/Homer NRBCARRGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 141.4 3.53% +Nr5a2(NR)/mES-Nr5a2-ChIP-Seq(GSE19019)/Homer BTCAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 340.9 8.51% +NRF1(NRF)/MCF7-NRF1-ChIP-Seq(Unpublished)/Homer CTGCGCATGCGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer HTGCTGAGTCAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NRF(NRF)/Promoter/Homer STGCGCATGCGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer TGACCTTTNCNT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Oct4(POU,Homeobox)/mES-Oct4-ChIP-Seq(GSE11431)/Homer ATTTGCATAW 1e0 0.000e+00 1.0000 0.0 0.00% 264.9 6.61% +Oct4:Sox17(POU,Homeobox,HMG)/F9-Sox17-ChIP-Seq(GSE44553)/Homer CCATTGTATGCAAAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Oct6(POU,Homeobox)/NPC-Pou3f1-ChIP-Seq(GSE35496)/Homer WATGCAAATGAG 1e0 0.000e+00 1.0000 0.0 0.00% 261.1 6.51% +OCT:OCT(POU,Homeobox,IR1)/NPC-Brn2-ChIP-Seq(GSE35496)/Homer ATGAATWATTCATGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +OCT:OCT(POU,Homeobox)/NPC-Brn1-ChIP-Seq(GSE35496)/Homer ATGAATATTCATGAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +OCT:OCT(POU,Homeobox)/NPC-OCT6-ChIP-Seq(GSE43916)/Homer YATGCATATRCATRT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +OCT:OCT-short(POU,Homeobox)/NPC-OCT6-ChIP-Seq(GSE43916)/Homer ATGCATWATGCATRW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Olig2(bHLH)/Neuron-Olig2-ChIP-Seq(GSE30882)/Homer RCCATMTGTT 1e0 0.000e+00 1.0000 0.0 0.00% 2022.6 50.46% +Otx2(Homeobox)/EpiLC-Otx2-ChIP-Seq(GSE56098)/Homer NYTAATCCYB 1e0 0.000e+00 1.0000 0.0 0.00% 419.1 10.46% +NFkB-p50,p52(RHD)/Monocyte-p50-ChIP-Chip(Schreiber_et_al.)/Homer GGGGGAATCCCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +p53(p53)/Saos-p53-ChIP-Seq(GSE15780)/Homer RRCATGYCYRGRCATGYYYN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +p53(p53)/mES-cMyc-ChIP-Seq(GSE11431)/Homer ACATGCCCGGGCAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +p53(p53)/Saos-p53-ChIP-Seq/Homer RRCATGYCYRGRCATGYYYN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +p63(p53)/Keratinocyte-p63-ChIP-Seq(GSE17611)/Homer NNDRCATGYCYNRRCATGYH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +NFkB-p65(RHD)/GM12787-p65-ChIP-Seq(GSE19485)/Homer WGGGGATTTCCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +p73(p53)/Trachea-p73-ChIP-Seq(PRJNA310161)/Homer NRRRCAWGTCCDGRCATGYY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PAX3:FKHR-fusion(Paired,Homeobox)/Rh4-PAX3:FKHR-ChIP-Seq(GSE19063)/Homer ACCRTGACTAATTNN 1e0 0.000e+00 1.0000 0.0 0.00% 265.2 6.62% +PAX5(Paired,Homeobox)/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer GCAGCCAAGCRTGACH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PAX5(Paired,Homeobox),condensed/GM12878-PAX5-ChIP-Seq(GSE32465)/Homer GTCACGCTCSCTGM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PAX6(Paired,Homeobox)/Forebrain-Pax6-ChIP-Seq(GSE66961)/Homer NGTGTTCAVTSAAGCGKAAA 1e0 0.000e+00 1.0000 0.0 0.00% 259.6 6.48% +Pax7(Paired,Homeobox),longest/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer NTAATTDGCYAATTANNWWD 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Pax7(Paired,Homeobox),long/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer TAATCHGATTAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Pax7(Paired,Homeobox)/Myoblast-Pax7-ChIP-Seq(GSE25064)/Homer TAATCAATTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Pax8(Paired,Homeobox)/Thyroid-Pax8-ChIP-Seq(GSE26938)/Homer GTCATGCHTGRCTGS 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PBX1(Homeobox)/MCF7-PBX1-ChIP-Seq(GSE28007)/Homer GSCTGTCACTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PBX2(Homeobox)/K562-PBX2-ChIP-Seq(Encode)/Homer RTGATTKATRGN 1e0 0.000e+00 1.0000 0.0 0.00% 244.3 6.09% +Pbx3(Homeobox)/GM12878-PBX3-ChIP-Seq(GSE32465)/Homer SCTGTCAMTCAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Pdx1(Homeobox)/Islet-Pdx1-ChIP-Seq(SRA008281)/Homer YCATYAATCA 1e0 0.000e+00 1.0000 0.0 0.00% 281.2 7.01% +PGR(NR)/EndoStromal-PGR-ChIP-Seq(GSE69539)/Homer AAGAACATWHTGTTC 1e0 0.000e+00 1.0000 0.0 0.00% 87.5 2.18% +Phox2b(Homeobox)/CLBGA-PHOX2B-ChIP-Seq(GSE90683)/Homer TTAATTNAATTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Pit1+1bp(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer ATGCATAATTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Pit1(Homeobox)/GCrat-Pit1-ChIP-Seq(GSE58009)/Homer ATGMATATDC 1e0 0.000e+00 1.0000 0.0 0.00% 339.9 8.48% +Pitx1:Ebox(Homeobox,bHLH)/Hindlimb-Pitx1-ChIP-Seq(GSE41591)/Homer YTAATTRAWWCCAGATGT 1e0 0.000e+00 1.0000 0.0 0.00% 214.5 5.35% +Pknox1(Homeobox)/ES-Prep1-ChIP-Seq(GSE63282)/Homer SCTGTCAVTCAV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PPARa(NR),DR1/Liver-Ppara-ChIP-Seq(GSE47954)/Homer VNAGGKCAAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PPARE(NR),DR1/3T3L1-Pparg-ChIP-Seq(GSE13511)/Homer TGACCTTTGCCCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PRDM10(Zf)/HEK293-PRDM10.eGFP-ChIP-Seq(Encode)/Homer TGGTACATTCCA 1e0 0.000e+00 1.0000 0.0 0.00% 419.9 10.48% +PRDM14(Zf)/H1-PRDM14-ChIP-Seq(GSE22767)/Homer RGGTCTCTAACY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PRDM15(Zf)/ESC-Prdm15-ChIP-Seq(GSE73694)/Homer YCCDNTCCAGGTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PRDM1(Zf)/Hela-PRDM1-ChIP-Seq(GSE31477)/Homer ACTTTCACTTTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer ADGGYAGYAGCATCT 1e0 0.000e+00 1.0000 0.0 0.00% 255.6 6.38% +PR(NR)/T47D-PR-ChIP-Seq(GSE31130)/Homer VAGRACAKNCTGTBC 1e0 0.000e+00 1.0000 0.0 0.00% 758.6 18.93% +PSE(SNAPc)/K562-mStart-Seq/Homer WAVTCACCMTAASYDAAAAG 1e0 0.000e+00 1.0000 0.0 0.00% 861.4 21.49% +Ptf1a(bHLH)/Panc1-Ptf1a-ChIP-Seq(GSE47459)/Homer ACAGCTGTTN 1e0 0.000e+00 1.0000 0.0 0.00% 567.0 14.15% +PU.1:IRF8(ETS:IRF)/pDC-Irf8-ChIP-Seq(GSE66899)/Homer GGAAGTGAAAST 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PU.1-IRF(ETS:IRF)/Bcell-PU.1-ChIP-Seq(GSE21512)/Homer MGGAAGTGAAAC 1e0 0.000e+00 1.0000 0.0 0.00% 166.3 4.15% +PU.1(ETS)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer AGAGGAAGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RARa(NR)/K562-RARa-ChIP-Seq(Encode)/Homer TTGAMCTTTG 1e0 0.000e+00 1.0000 0.0 0.00% 275.7 6.88% +RARg(NR)/ES-RARg-ChIP-Seq(GSE30538)/Homer AGGTCAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RBPJ:Ebox(?,bHLH)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer GGGRAARRGRMCAGMTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Rbpj1(?)/Panc1-Rbpj1-ChIP-Seq(GSE47459)/Homer HTTTCCCASG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +REST-NRSF(Zf)/Jurkat-NRSF-ChIP-Seq/Homer GGMGCTGTCCATGGTGCTGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Reverb(NR),DR2/RAW-Reverba.biotin-ChIP-Seq(GSE45914)/Homer GTRGGTCASTGGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Rfx1(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer KGTTGCCATGGCAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Rfx2(HTH)/LoVo-RFX2-ChIP-Seq(GSE49402)/Homer GTTGCCATGGCAACM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RFX(HTH)/K562-RFX3-ChIP-Seq(SRA012198)/Homer CGGTTGCCATGGCAAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Rfx5(HTH)/GM12878-Rfx5-ChIP-Seq(GSE31477)/Homer SCCTAGCAACAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Rfx6(HTH)/Min6b1-Rfx6.HA-ChIP-Seq(GSE62844)/Homer TGTTKCCTAGCAACM 1e0 0.000e+00 1.0000 0.0 0.00% 820.5 20.47% +Ronin(THAP)/ES-Thap11-ChIP-Seq(GSE51522)/Homer RACTACAACTCCCAGVAKGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RORa(NR)/Liver-Rora-ChIP-Seq(GSE101115)/Homer AAWCTAGGTCARDNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer AAYTAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RORg(NR)/Liver-Rorc-ChIP-Seq(GSE101115)/Homer WAABTAGGTCAV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RORgt(NR)/EL4-RORgt.Flag-ChIP-Seq(GSE56019)/Homer AAYTAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer SAAACCACAG 1e0 0.000e+00 1.0000 0.0 0.00% 244.7 6.11% +RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer AAACCACARM 1e0 0.000e+00 1.0000 0.0 0.00% 934.7 23.32% +RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer NWAACCACADNN 1e0 0.000e+00 1.0000 0.0 0.00% 244.7 6.11% +RUNX-AML(Runt)/CD4+-PolII-ChIP-Seq(Barski_et_al.)/Homer GCTGTGGTTW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RXR(NR),DR1/3T3L1-RXR-ChIP-Seq(GSE13511)/Homer TAGGGCAAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SCL(bHLH)/HPC7-Scl-ChIP-Seq(GSE13511)/Homer AVCAGCTG 1e0 0.000e+00 1.0000 0.0 0.00% 2259.3 56.37% +SCRT1(Zf)/HEK293-SCRT1.eGFP-ChIP-Seq(Encode)/Homer GCAACAGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SF1(NR)/H295R-Nr5a1-ChIP-Seq(GSE44220)/Homer CAAGGHCANV 1e0 0.000e+00 1.0000 0.0 0.00% 53.9 1.34% +Six1(Homeobox)/Myoblast-Six1-ChIP-Chip(GSE20150)/Homer GKVTCADRTTWC 1e0 0.000e+00 1.0000 0.0 0.00% 373.2 9.31% +Six2(Homeobox)/NephronProgenitor-Six2-ChIP-Seq(GSE39837)/Homer GWAAYHTGAKMC 1e0 0.000e+00 1.0000 0.0 0.00% 373.2 9.31% +Six4(Homeobox)/MCF7-SIX4-ChIP-Seq(Encode)/Homer TGWAAYCTGABACCB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Smad2(MAD)/ES-SMAD2-ChIP-Seq(GSE29422)/Homer CTGTCTGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Smad3(MAD)/NPC-Smad3-ChIP-Seq(GSE36673)/Homer TWGTCTGV 1e0 0.000e+00 1.0000 0.0 0.00% 464.0 11.58% +Smad4(MAD)/ESC-SMAD4-ChIP-Seq(GSE29422)/Homer VBSYGTCTGG 1e0 0.000e+00 1.0000 0.0 0.00% 158.7 3.96% +Slug(Zf)/Mesoderm-Snai2-ChIP-Seq(GSE61475)/Homer SNGCACCTGCHS 1e0 0.000e+00 1.0000 0.0 0.00% 164.3 4.10% +Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer CCWTTGTYYB 1e0 0.000e+00 1.0000 0.0 0.00% 405.6 10.12% +Sox15(HMG)/CPA-Sox15-ChIP-Seq(GSE62909)/Homer RAACAATGGN 1e0 0.000e+00 1.0000 0.0 0.00% 303.8 7.58% +Sox17(HMG)/Endoderm-Sox17-ChIP-Seq(GSE61475)/Homer CCATTGTTYB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Sox2(HMG)/mES-Sox2-ChIP-Seq(GSE11431)/Homer BCCATTGTTC 1e0 0.000e+00 1.0000 0.0 0.00% 68.9 1.72% +Sox3(HMG)/NPC-Sox3-ChIP-Seq(GSE33059)/Homer CCWTTGTY 1e0 0.000e+00 1.0000 0.0 0.00% 72.6 1.81% +Sox4(HMG)/proB-Sox4-ChIP-Seq(GSE50066)/Homer YCTTTGTTCC 1e0 0.000e+00 1.0000 0.0 0.00% 68.9 1.72% +Sox9(HMG)/Limb-SOX9-ChIP-Seq(GSE73225)/Homer AGGVNCCTTTGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Sp1(Zf)/Promoter/Homer GGCCCCGCCCCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Sp2(Zf)/HEK293-Sp2.eGFP-ChIP-Seq(Encode)/Homer YGGCCCCGCCCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Sp5(Zf)/mES-Sp5.Flag-ChIP-Seq(GSE72989)/Homer RGKGGGCGGAGC 1e0 0.000e+00 1.0000 0.0 0.00% 106.0 2.65% +SPDEF(ETS)/VCaP-SPDEF-ChIP-Seq(SRA014231)/Homer ASWTCCTGBT 1e0 0.000e+00 1.0000 0.0 0.00% 207.4 5.17% +SpiB(ETS)/OCILY3-SPIB-ChIP-Seq(GSE56857)/Homer AAAGRGGAAGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Srebp1a(bHLH)/HepG2-Srebp1a-ChIP-Seq(GSE31477)/Homer RTCACSCCAY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Srebp2(bHLH)/HepG2-Srebp2-ChIP-Seq(GSE31477)/Homer CGGTCACSCCAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CArG(MADS)/PUER-Srf-ChIP-Seq(Sullivan_et_al.)/Homer CCATATATGGNM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF143|STAF(Zf)/CUTLL-ZNF143-ChIP-Seq(GSE29600)/Homer ATTTCCCAGVAKSCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +STAT1(Stat)/HelaS3-STAT1-ChIP-Seq(GSE12782)/Homer NATTTCCNGGAAAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Stat3+il21(Stat)/CD4-Stat3-ChIP-Seq(GSE19198)/Homer SVYTTCCNGGAARB 1e0 0.000e+00 1.0000 0.0 0.00% 263.4 6.57% +Stat3(Stat)/mES-Stat3-ChIP-Seq(GSE11431)/Homer CTTCCGGGAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +STAT4(Stat)/CD4-Stat4-ChIP-Seq(GSE22104)/Homer NYTTCCWGGAAR 1e0 0.000e+00 1.0000 0.0 0.00% 779.2 19.44% +STAT5(Stat)/mCD4+-Stat5-ChIP-Seq(GSE12346)/Homer RTTTCTNAGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 158.1 3.95% +STAT6(Stat)/Macrophage-Stat6-ChIP-Seq(GSE38377)/Homer TTCCKNAGAA 1e0 0.000e+00 1.0000 0.0 0.00% 175.4 4.37% +STAT6(Stat)/CD4-Stat6-ChIP-Seq(GSE22104)/Homer ABTTCYYRRGAA 1e0 0.000e+00 1.0000 0.0 0.00% 175.4 4.37% +T1ISRE(IRF)/ThioMac-Ifnb-Expression/Homer ACTTTCGTTTCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TATA-Box(TBP)/Promoter/Homer CCTTTTAWAGSC 1e0 0.000e+00 1.0000 0.0 0.00% 436.7 10.90% +Tbet(T-box)/CD8-Tbet-ChIP-Seq(GSE33802)/Homer AGGTGTGAAM 1e0 0.000e+00 1.0000 0.0 0.00% 373.2 9.31% +Tbox:Smad(T-box,MAD)/ESCd5-Smad2_3-ChIP-Seq(GSE29422)/Homer AGGTGHCAGACA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tbr1(T-box)/Cortex-Tbr1-ChIP-Seq(GSE71384)/Homer AAGGTGTKAA 1e0 0.000e+00 1.0000 0.0 0.00% 389.4 9.72% +Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer GGTGYTGACAGS 1e0 0.000e+00 1.0000 0.0 0.00% 229.4 5.72% +Tbx21(T-box)/GM12878-TBX21-ChIP-Seq(Encode)/Homer AGGTGTGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 703.2 17.54% +Tbx5(T-box)/HL1-Tbx5.biotin-ChIP-Seq(GSE21529)/Homer AGGTGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 1041.9 26.00% +Tbx6(T-box)/ESC-Tbx6-ChIP-Seq(GSE93524)/Homer DAGGTGTBAA 1e0 0.000e+00 1.0000 0.0 0.00% 716.0 17.86% +Tcf12(bHLH)/GM12878-Tcf12-ChIP-Seq(GSE32465)/Homer VCAGCTGYTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tcf21(bHLH)/ArterySmoothMuscle-Tcf21-ChIP-Seq(GSE61369)/Homer NAACAGCTGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tcf3(HMG)/mES-Tcf3-ChIP-Seq(GSE11724)/Homer ASWTCAAAGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TCF4(bHLH)/SHSY5Y-TCF4-ChIP-Seq(GSE96915)/Homer SMCATCTGKH 1e0 0.000e+00 1.0000 0.0 0.00% 661.9 16.51% +TCFL2(HMG)/K562-TCF7L2-ChIP-Seq(GSE29196)/Homer ACWTCAAAGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tcf7(HMG)/GM12878-TCF7-ChIP-Seq(Encode)/Homer CTTTGATGTGSB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tcfcp2l1(CP2)/mES-Tcfcp2l1-ChIP-Seq(GSE11431)/Homer NRAACCRGTTYRAACCRGYT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TEAD1(TEAD)/HepG2-TEAD1-ChIP-Seq(Encode)/Homer CYRCATTCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TEAD2(TEA)/Py2T-Tead2-ChIP-Seq(GSE55709)/Homer CCWGGAATGY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TEAD3(TEA)/HepG2-TEAD3-ChIP-Seq(Encode)/Homer TRCATTCCAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer CCWGGAATGY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer YCWGGAATGY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TFE3(bHLH)/MEF-TFE3-ChIP-Seq(GSE75757)/Homer GTCACGTGACYV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tgif1(Homeobox)/mES-Tgif1-ChIP-Seq(GSE55404)/Homer YTGWCADY 1e0 0.000e+00 1.0000 0.0 0.00% 1367.1 34.11% +THRb(NR)/HepG2-THRb.Flag-ChIP-Seq(Encode)/Homer GGTCACCTGAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Tlx?(NR)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer CTGGCAGSCTGCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TR4(NR),DR1/Hela-TR4-ChIP-Seq(GSE24685)/Homer GAGGTCAAAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +THRa(NR)/C17.2-THRa-ChIP-Seq(GSE38347)/Homer GGTCANYTGAGGWCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +THRb(NR)/Liver-NR1A2-ChIP-Seq(GSE52613)/Homer TRAGGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 707.9 17.66% +Twist(bHLH)/HMLE-TWIST1-ChIP-Seq(Chang_et_al)/Homer VCAKCTGGNNNCCAGMTGBN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +USF1(bHLH)/GM12878-Usf1-ChIP-Seq(GSE32465)/Homer SGTCACGTGR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Usf2(bHLH)/C2C12-Usf2-ChIP-Seq(GSE36030)/Homer GTCACGTGGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +VDR(NR),DR3/GM10855-VDR+vitD-ChIP-Seq(GSE22484)/Homer ARAGGTCANWGAGTTCANNN 1e0 0.000e+00 1.0000 0.0 0.00% 390.0 9.73% +WT1(Zf)/Kidney-WT1-ChIP-Seq(GSE90016)/Homer MCTCCCMCRCAB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +X-box(HTH)/NPC-H3K4me1-ChIP-Seq(GSE16256)/Homer GGTTGCCATGGCAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +YY1(Zf)/Promoter/Homer CAAGATGGCGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Zac1(Zf)/Neuro2A-Plagl1-ChIP-Seq(GSE75942)/Homer HAWGRGGCCM 1e0 0.000e+00 1.0000 0.0 0.00% 151.1 3.77% +ZBTB12(Zf)/HEK293-ZBTB12.GFP-ChIP-Seq(GSE58341)/Homer NGNTCTAGAACCNGV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZBTB18(Zf)/HEK293-ZBTB18.GFP-ChIP-Seq(GSE58341)/Homer AACATCTGGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZBTB33(Zf)/GM12878-ZBTB33-ChIP-Seq(GSE32465)/Homer GGVTCTCGCGAGAAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZEB1(Zf)/PDAC-ZEB1-ChIP-Seq(GSE64557)/Homer VCAGGTRDRY 1e0 0.000e+00 1.0000 0.0 0.00% 399.8 9.97% +ZEB2(Zf)/SNU398-ZEB2-ChIP-Seq(GSE103048)/Homer GNMCAGGTGTGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Zfp281(Zf)/ES-Zfp281-ChIP-Seq(GSE81042)/Homer CCCCTCCCCCAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZFP3(Zf)/HEK293-ZFP3.GFP-ChIP-Seq(GSE58341)/Homer GGGTTTTGAAGGATGARTAGGAGTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Zfp809(Zf)/ES-Zfp809-ChIP-Seq(GSE70799)/Homer GGGGCTYGKCTGGGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZFX(Zf)/mES-Zfx-ChIP-Seq(GSE11431)/Homer AGGCCTRG 1e0 0.000e+00 1.0000 0.0 0.00% 193.7 4.83% +Zic3(Zf)/mES-Zic3-ChIP-Seq(GSE37889)/Homer GGCCYCCTGCTGDGH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Zic(Zf)/Cerebellum-ZIC1.2-ChIP-Seq(GSE60731)/Homer CCTGCTGAGH 1e0 0.000e+00 1.0000 0.0 0.00% 255.6 6.38% +ZKSCAN1(Zf)/HepG2-ZKSCAN1-ChIP-Seq(Encode)/Homer GCACAYAGTAGGKCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF136(Zf)/HEK293-ZNF136.GFP-ChIP-Seq(GSE58341)/Homer YTKGATAHAGTATTCTWGGTNGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF165(Zf)/WHIM12-ZNF165-ChIP-Seq(GSE65937)/Homer AAGGKGRCGCAGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF16(Zf)/HEK293-ZNF16.GFP-ChIP-Seq(GSE58341)/Homer MACCTTCYATGGCTCCCTAKTGCCY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF189(Zf)/HEK293-ZNF189.GFP-ChIP-Seq(GSE58341)/Homer TGGAACAGMA 1e0 0.000e+00 1.0000 0.0 0.00% 158.3 3.95% +Znf263(Zf)/K562-Znf263-ChIP-Seq(GSE31477)/Homer CVGTSCTCCC 1e0 0.000e+00 1.0000 0.0 0.00% 250.8 6.26% +ZNF264(Zf)/HEK293-ZNF264.GFP-ChIP-Seq(GSE58341)/Homer RGGGCACTAACY 1e0 0.000e+00 1.0000 0.0 0.00% 411.9 10.28% +ZNF317(Zf)/HEK293-ZNF317.GFP-ChIP-Seq(GSE58341)/Homer GTCWGCTGTYYCTCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF322(Zf)/HEK293-ZNF322.GFP-ChIP-Seq(GSE58341)/Homer GAGCCTGGTACTGWGCCTGR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF382(Zf)/HEK293-ZNF382.GFP-ChIP-Seq(GSE58341)/Homer GNCTGTASTRNTGBCTCHTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF415(Zf)/HEK293-ZNF415.GFP-ChIP-Seq(GSE58341)/Homer GRTGMTRGAGCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF416(Zf)/HEK293-ZNF416.GFP-ChIP-Seq(GSE58341)/Homer WDNCTGGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 180.8 4.51% +ZNF41(Zf)/HEK293-ZNF41.GFP-ChIP-Seq(GSE58341)/Homer CCTCATGGTGYCYTWYTCCCTTGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF467(Zf)/HEK293-ZNF467.GFP-ChIP-Seq(GSE58341)/Homer TGGGGAAGGGCM 1e0 0.000e+00 1.0000 0.0 0.00% 126.3 3.15% +ZNF519(Zf)/HEK293-ZNF519.GFP-ChIP-Seq(GSE58341)/Homer GAGSCCGAGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF528(Zf)/HEK293-ZNF528.GFP-ChIP-Seq(GSE58341)/Homer AGAAATGACTTCCCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF652/HepG2-ZNF652.Flag-ChIP-Seq(Encode)/Homer TTAACCCTTTVNKKN 1e0 0.000e+00 1.0000 0.0 0.00% 132.7 3.31% +ZNF669(Zf)/HEK293-ZNF669.GFP-ChIP-Seq(GSE58341)/Homer GARTGGTCATCGCCC 1e0 0.000e+00 1.0000 0.0 0.00% 106.2 2.65% +ZNF675(Zf)/HEK293-ZNF675.GFP-ChIP-Seq(GSE58341)/Homer ARGAGGMCAAAATGW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF692(Zf)/HEK293-ZNF692.GFP-ChIP-Seq(GSE58341)/Homer GTGGGCCCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZNF711(Zf)/SHSY5Y-ZNF711-ChIP-Seq(GSE20673)/Homer AGGCCTAG 1e0 0.000e+00 1.0000 0.0 0.00% 193.7 4.83% +ZNF7(Zf)/HepG2-ZNF7.Flag-ChIP-Seq(Encode)/Homer CTGCCWVCTTTTRTA 1e0 0.000e+00 1.0000 0.0 0.00% 152.5 3.81% +ZSCAN22(Zf)/HEK293-ZSCAN22.GFP-ChIP-Seq(GSE58341)/Homer SMCAGTCWGAKGGAGGAGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AARE(HLH)/mES-cMyc-ChIP-Seq/Homer GATTGCATCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SeqBias: CG-repeat CGCGCGCGCG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SeqBias: GA-repeat GAGAGAGAGA 1e0 0.000e+00 1.0000 0.0 0.00% 1452.3 36.23% +Tal1 CATCTG 1e0 0.000e+00 1.0000 0.0 0.00% 673.1 16.79% +bcd(Homeobox)/Embryo-Bcd-ChIP-Seq(GSE86966)/Homer VNNGGATTADNN 1e0 0.000e+00 1.0000 0.0 0.00% 812.3 20.27% +caudal(Homeobox)/Drosophila-Embryos-ChIP-Chip(modEncode)/Homer GGYCATAAAW 1e0 0.000e+00 1.0000 0.0 0.00% 765.8 19.11% +dHNF4(NR)/Fly-HNF4-ChIP-Seq(GSE73675)/Homer GGTCCAAAGTCCAMT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Dorsal(RHD)/Embryo-dl-ChIP-Seq(GSE65441)/Homer GGGAAAAMCCCG 1e0 0.000e+00 1.0000 0.0 0.00% 265.2 6.62% +DREF/Drosophila-Promoters/Homer AVYTATCGATAD 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +E-box/Drosophila-Promoters/Homer AACAGCTGTTHN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Trl(Zf)/S2-GAGAfactor-ChIP-Seq(GSE40646)/Homer RGAGAGAG 1e0 0.000e+00 1.0000 0.0 0.00% 426.7 10.65% +Unknown1(NR/Ini-like)/Drosophila-Promoters/Homer MYGGTCACACTG 1e0 0.000e+00 1.0000 0.0 0.00% 266.4 6.65% +M1BP(Zf)/S2R+-M1BP-ChIP-Seq(GSE49842)/Homer CAGTGTGACCGT 1e0 0.000e+00 1.0000 0.0 0.00% 305.5 7.62% +TATA-box/Drosophila-Promoters/Homer CTATAAAAGCSV 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Unknown2/Drosophila-Promoters/Homer CATCMCTA 1e0 0.000e+00 1.0000 0.0 0.00% 304.6 7.60% +Unknown3/Drosophila-Promoters/Homer ACVAKCTGGCAGCGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Unknown4/Drosophila-Promoters/Homer AAAAATACCRMA 1e0 0.000e+00 1.0000 0.0 0.00% 287.7 7.18% +Unknown5/Drosophila-Promoters/Homer GCTGATAASV 1e0 0.000e+00 1.0000 0.0 0.00% 691.9 17.26% +Zelda(Zf)/Embryo-zld-ChIP-Seq(GSE65441)/Homer KBCTACCTGW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HOXA9(Homeobox)/HSC-Hoxa9-ChIP-Seq(GSE33509)/Homer GGCCATAAATCA 1e0 0.000e+00 1.0000 0.0 0.00% 445.7 11.12% +HOXD13(Homeobox)/Chicken-Hoxd13-ChIP-Seq(GSE38910)/Homer NCYAATAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 531.0 13.25% +Tcf4(HMG)/Hct116-Tcf4-ChIP-Seq(SRA012054)/Homer ASATCAAAGGVA 1e0 0.000e+00 1.0000 0.0 0.00% 197.6 4.93% +ABF1(bZIP)/Arabidopsis-ABF1-ChIP-Seq(GSE80564)/Homer CACGTGGC 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +ABF2(bZIP)/col-ABF2-DAP-Seq(GSE60143)/Homer KGMCACGTGDCMHHH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ABI5(bZIP)/col-ABI5-DAP-Seq(GSE60143)/Homer GCCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +ABR1(AP2EREBP)/colamp-ABR1-DAP-Seq(GSE60143)/Homer AAATGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 358.1 8.93% +Adof1(C2C2dof)/col-Adof1-DAP-Seq(GSE60143)/Homer NRWAAAGYDV 1e0 0.000e+00 1.0000 0.0 0.00% 1661.4 41.45% +AGL13(MADS)/col-AGL13-DAP-Seq(GSE60143)/Homer TWCCAWWTWTGGWAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AGL15(MADS)/col-AGL15-DAP-Seq(GSE60143)/Homer TTTCCHWATWDGGAA 1e0 0.000e+00 1.0000 0.0 0.00% 189.7 4.73% +AGL16(MADS)/col-AGL16-DAP-Seq(GSE60143)/Homer TWCCHWATWDGGAAA 1e0 0.000e+00 1.0000 0.0 0.00% 187.9 4.69% +AGL25(MADS)/colamp-AGL25-DAP-Seq(GSE60143)/Homer TTTCCATWTWTGGAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AGL63(MADS)/col-AGL63-DAP-Seq(GSE60143)/Homer TTCCAAWWWTGG 1e0 0.000e+00 1.0000 0.0 0.00% 625.7 15.61% +AGL6(MADS)/col-AGL6-DAP-Seq(GSE60143)/Homer TTWCCWWAWWDGGWA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AGL95(ND)/col-AGL95-DAP-Seq(GSE60143)/Homer TTCTAGAAGCTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AIL7(AP2EREBP)/colamp-AIL7-DAP-Seq(GSE60143)/Homer KCACRAWTYYCGAGG 1e0 0.000e+00 1.0000 0.0 0.00% 249.9 6.24% +ANAC004(NAC)/colamp-ANAC004-DAP-Seq(GSE60143)/Homer WNCTTVYNNNRBAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ANAC005(NAC)/col-ANAC005-DAP-Seq(GSE60143)/Homer WVCTTVTWNHABAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ANAC011(NAC)/col-ANAC011-DAP-Seq(GSE60143)/Homer TDCTTGYRNNDCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ANAC013(NAC)/col-ANAC013-DAP-Seq(GSE60143)/Homer CTTGNNNNNCAAGNA 1e0 0.000e+00 1.0000 0.0 0.00% 236.8 5.91% +ANAC016(NAC)/col-ANAC016-DAP-Seq(GSE60143)/Homer WNCTTGNNNNNCAMG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +ANAC017(NAC)/colamp-ANAC017-DAP-Seq(GSE60143)/Homer TMCTTGNNNNNCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ANAC020(NAC)/col-ANAC020-DAP-Seq(GSE60143)/Homer DVCKTGHNNNDCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +ANAC028(NAC)/col-ANAC028-DAP-Seq(GSE60143)/Homer WRCTTGNNNNNCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +ANAC038(NAC)/col-ANAC038-DAP-Seq(GSE60143)/Homer ACACGTWAYC 1e0 0.000e+00 1.0000 0.0 0.00% 1031.7 25.74% +ANAC042(NAC)/col-ANAC042-DAP-Seq(GSE60143)/Homer CGTNDHNDHNACGKY 1e0 0.000e+00 1.0000 0.0 0.00% 364.1 9.08% +ANAC045(NAC)/col-ANAC045-DAP-Seq(GSE60143)/Homer DNCKTVNNNNNNAMG 1e0 0.000e+00 1.0000 0.0 0.00% 761.9 19.01% +ANAC046(NAC)/colamp-ANAC046-DAP-Seq(GSE60143)/Homer ACACGYWAYC 1e0 0.000e+00 1.0000 0.0 0.00% 1067.0 26.62% +ANAC047(NAC)/colamp-ANAC047-DAP-Seq(GSE60143)/Homer WACACGTAACTT 1e0 0.000e+00 1.0000 0.0 0.00% 27.9 0.70% +ANAC050(NAC)/colamp-ANAC050-DAP-Seq(GSE60143)/Homer WNCTTGNNNNNCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +ANAC053(NAC)/colamp-ANAC053-DAP-Seq(GSE60143)/Homer TDCTTGNNNNNCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +ANAC057(NAC)/colamp-ANAC057-DAP-Seq(GSE60143)/Homer DVCKTGNNNNNCAMG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +ANAC058(NAC)/col-ANAC058-DAP-Seq(GSE60143)/Homer TWCTTGTDNNACAAG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +ANAC062(NAC)/colamp-ANAC062-DAP-Seq(GSE60143)/Homer TACTTANTNWNYAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ANAC070(NAC)/colamp-ANAC070-DAP-Seq(GSE60143)/Homer CTTRHDNHNBAAGHW 1e0 0.000e+00 1.0000 0.0 0.00% 637.7 15.91% +ANAC071(NAC)/col-ANAC071-DAP-Seq(GSE60143)/Homer DNCKTNDNNNHNAAG 1e0 0.000e+00 1.0000 0.0 0.00% 411.7 10.27% +ANAC075(NAC)/col-ANAC075-DAP-Seq(GSE60143)/Homer CTTSWWNWWSAAGYT 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +ANAC079(NAC)/colamp-ANAC079-DAP-Seq(GSE60143)/Homer TACACGCAACCT 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +ANAC083(NAC)/col-ANAC083-DAP-Seq(GSE60143)/Homer CKTRWNNNWYAMGTA 1e0 0.000e+00 1.0000 0.0 0.00% 249.8 6.23% +ANAC087(NAC)/col-ANAC087-DAP-Seq(GSE60143)/Homer WVCKTGHNNNWCAMG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +ANAC092(NAC)/colamp-ANAC092-DAP-Seq(GSE60143)/Homer WRCKTGWNNNWCAMG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +ANAC094(NAC)/col-ANAC094-DAP-Seq(GSE60143)/Homer DVCGTRNNNNNYACG 1e0 0.000e+00 1.0000 0.0 0.00% 364.1 9.08% +ANAC096(NAC)/colamp-ANAC096-DAP-Seq(GSE60143)/Homer TACTTGWNNNWCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 411.7 10.27% +ANAC103(NAC)/col-ANAC103-DAP-Seq(GSE60143)/Homer AACTTGNWNWNCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +ANL2(HB)/col-ANL2-DAP-Seq(GSE60143)/Homer CATTAATTGC 1e0 0.000e+00 1.0000 0.0 0.00% 262.6 6.55% +AREB3(bZIP)/col-AREB3-DAP-Seq(GSE60143)/Homer NKGMCACGTGDCMNN 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +ARF16(ARF)/col-ARF16-DAP-Seq(GSE60143)/Homer ATTTTACGAT 1e0 0.000e+00 1.0000 0.0 0.00% 235.3 5.87% +ARF2(ARF)/col-ARF2-DAP-Seq(GSE60143)/Homer TTGTCGGMWN 1e0 0.000e+00 1.0000 0.0 0.00% 646.8 16.14% +AS2(LOBAS2)/col-AS2-DAP-Seq(GSE60143)/Homer CCGDAAWWHMCGSCG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ASHR1(ND)/col-ASHR1-DAP-Seq(GSE60143)/Homer NTGGTGAN 1e0 0.000e+00 1.0000 0.0 0.00% 644.0 16.07% +AT1G01250(AP2EREBP)/col-AT1G01250-DAP-Seq(GSE60143)/Homer YCACCGACAHTW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G04880(ARID)/colamp-AT1G04880-DAP-Seq(GSE60143)/Homer AAACTATATADTATA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G10720(BSD)/col-AT1G10720-DAP-Seq(GSE60143)/Homer TTCTAGAAKCTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G12630(AP2EREBP)/colamp-AT1G12630-DAP-Seq(GSE60143)/Homer TGTCGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 113.3 2.83% +At1g13300(G2like)/col-At1g13300-DAP-Seq(GSE60143)/Homer GAATCTWAGATTCYN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g14580(C2H2)/colamp-At1g14580-DAP-Seq(GSE60143)/Homer CASAAAAMGACAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g19000(MYBrelated)/colamp-At1g19000-DAP-Seq(GSE60143)/Homer WWTGGATAADDT 1e0 0.000e+00 1.0000 0.0 0.00% 213.9 5.34% +AT1G19040(NAC)/col-AT1G19040-DAP-Seq(GSE60143)/Homer CTTGNDNHNCAAGYW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g19210(AP2EREBP)/colamp-At1g19210-DAP-Seq(GSE60143)/Homer HCACCGACCAHN 1e0 0.000e+00 1.0000 0.0 0.00% 1634.2 40.77% +At1g22810(AP2EREBP)/colamp-At1g22810-DAP-Seq(GSE60143)/Homer BCACCGACANNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G23810(Orphan)/col-AT1G23810-DAP-Seq(GSE60143)/Homer TTCTAGAAGSTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G24250(Orphan)/col-AT1G24250-DAP-Seq(GSE60143)/Homer KTDGTTGGTDGTTGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g25550(G2like)/colamp-At1g25550-DAP-Seq(GSE60143)/Homer NAGATTCY 1e0 0.000e+00 1.0000 0.0 0.00% 503.5 12.56% +AT1G28160(AP2EREBP)/colamp-AT1G28160-DAP-Seq(GSE60143)/Homer GGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 420.0 10.48% +At1g36060(AP2EREBP)/colamp-At1g36060-DAP-Seq(GSE60143)/Homer NNWWKGTCGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 779.0 19.43% +AT1G44830(AP2EREBP)/col-AT1G44830-DAP-Seq(GSE60143)/Homer NCCACCGACA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G47655(C2C2dof)/colamp-AT1G47655-DAP-Seq(GSE60143)/Homer YHACTTTTTS 1e0 0.000e+00 1.0000 0.0 0.00% 2037.7 50.84% +At1g49010(MYBrelated)/col-At1g49010-DAP-Seq(GSE60143)/Homer RGATAASNTT 1e0 0.000e+00 1.0000 0.0 0.00% 998.3 24.91% +AT1G49560(G2like)/colamp-AT1G49560-DAP-Seq(GSE60143)/Homer GAWTCTNWDA 1e0 0.000e+00 1.0000 0.0 0.00% 1349.1 33.66% +At1g64620(C2C2dof)/colamp-At1g64620-DAP-Seq(GSE60143)/Homer CACTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 912.5 22.77% +At1g68670(G2like)/colamp-At1g68670-DAP-Seq(GSE60143)/Homer WNWWHNRAAGATTCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g69690(TCP)/colamp-At1g69690-DAP-Seq(GSE60143)/Homer NHGTGGGGCCCACHW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT1G71450(AP2EREBP)/col-AT1G71450-DAP-Seq(GSE60143)/Homer DHDWTGTCGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 1315.5 32.82% +At1g72010(TCP)/colamp-At1g72010-DAP-Seq(GSE60143)/Homer GGDCCCAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g74840(MYBrelated)/col100-At1g74840-DAP-Seq(GSE60143)/Homer YHTTATCCAWWT 1e0 0.000e+00 1.0000 0.0 0.00% 359.7 8.97% +At1g75490(AP2EREBP)/colamp-At1g75490-DAP-Seq(GSE60143)/Homer CACCGMCT 1e0 0.000e+00 1.0000 0.0 0.00% 2138.1 53.34% +At1g76110(ARID)/colamp-At1g76110-DAP-Seq(GSE60143)/Homer ATTTAATG 1e0 0.000e+00 1.0000 0.0 0.00% 762.1 19.01% +AT1G76870(Trihelix)/col-AT1G76870-DAP-Seq(GSE60143)/Homer AAAACCRGWW 1e0 0.000e+00 1.0000 0.0 0.00% 593.6 14.81% +AT1G76880(Trihelix)/col-AT1G76880-DAP-Seq(GSE60143)/Homer ACGGTAAAAW 1e0 0.000e+00 1.0000 0.0 0.00% 354.1 8.84% +AT1G77200(AP2EREBP)/colamp-AT1G77200-DAP-Seq(GSE60143)/Homer ACCGACAHWD 1e0 0.000e+00 1.0000 0.0 0.00% 710.7 17.73% +At1g77640(AP2EREBP)/col-At1g77640-DAP-Seq(GSE60143)/Homer TGTCGGTGGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At1g78700(BZR)/col-At1g78700-DAP-Seq(GSE60143)/Homer NNNNCACGTGNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At2g01060(G2like)/colamp-At2g01060-DAP-Seq(GSE60143)/Homer AGATKCBNWW 1e0 0.000e+00 1.0000 0.0 0.00% 2100.8 52.41% +AT2G01818(PLATZ)/col-AT2G01818-DAP-Seq(GSE60143)/Homer TCTAGAABSTTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At2g03500(G2like)/col-At2g03500-DAP-Seq(GSE60143)/Homer WWAGAATATTCT 1e0 0.000e+00 1.0000 0.0 0.00% 191.5 4.78% +AT2G15740(C2H2)/col-AT2G15740-DAP-Seq(GSE60143)/Homer DHNDWATCGATD 1e0 0.000e+00 1.0000 0.0 0.00% 1256.4 31.35% +AT2G20400(G2like)/colamp-AT2G20400-DAP-Seq(GSE60143)/Homer DNVGAATATTCBNHN 1e0 0.000e+00 1.0000 0.0 0.00% 187.7 4.68% +AT2G28810(C2C2dof)/colamp-AT2G28810-DAP-Seq(GSE60143)/Homer VAAAAAGTWA 1e0 0.000e+00 1.0000 0.0 0.00% 1057.5 26.38% +AT2G28920(ND)/col-AT2G28920-DAP-Seq(GSE60143)/Homer WAGATATTTWTW 1e0 0.000e+00 1.0000 0.0 0.00% 231.6 5.78% +AT2G31460(REMB3)/col-AT2G31460-DAP-Seq(GSE60143)/Homer WNWARWDGAAATGAT 1e0 0.000e+00 1.0000 0.0 0.00% 295.2 7.37% +AT2G33550(Trihelix)/colamp-AT2G33550-DAP-Seq(GSE60143)/Homer TTTAAGGGCAYTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 646.5 16.13% +At2g33710(AP2EREBP)/colamp-At2g33710-DAP-Seq(GSE60143)/Homer WTKGCGGCKR 1e0 0.000e+00 1.0000 0.0 0.00% 946.5 23.61% +AT2G38300(G2like)/col-AT2G38300-DAP-Seq(GSE60143)/Homer ADRGAATGTT 1e0 0.000e+00 1.0000 0.0 0.00% 91.2 2.28% +AT2G40260(G2like)/colamp-AT2G40260-DAP-Seq(GSE60143)/Homer WAAAYATTCTTT 1e0 0.000e+00 1.0000 0.0 0.00% 317.0 7.91% +At2g41835(C2H2)/col-At2g41835-DAP-Seq(GSE60143)/Homer TTTGAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At2g44940(AP2EREBP)/colamp-At2g44940-DAP-Seq(GSE60143)/Homer NYACCGACAHNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At2g45680(TCP)/colamp-At2g45680-DAP-Seq(GSE60143)/Homer GTGGGNCCCACNDND 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At3g04030(G2like)/col-At3g04030-DAP-Seq(GSE60143)/Homer DRGAATCT 1e0 0.000e+00 1.0000 0.0 0.00% 229.6 5.73% +At3g09600(MYBrelated)/colamp-At3g09600-DAP-Seq(GSE60143)/Homer AAAATATCTT 1e0 0.000e+00 1.0000 0.0 0.00% 300.7 7.50% +AT3G09735(S1Falike)/col-AT3G09735-DAP-Seq(GSE60143)/Homer TTCTAGAANMTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT3G10030(Trihelix)/colamp-AT3G10030-DAP-Seq(GSE60143)/Homer GCCGTTAA 1e0 0.000e+00 1.0000 0.0 0.00% 1135.7 28.34% +AT3G10113(MYBrelated)/col-AT3G10113-DAP-Seq(GSE60143)/Homer WNAAATATCWWN 1e0 0.000e+00 1.0000 0.0 0.00% 684.3 17.07% +AT3G10580(MYBrelated)/colamp-AT3G10580-DAP-Seq(GSE60143)/Homer TACCTAACWNHW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At3g11280(MYBrelated)/col-At3g11280-DAP-Seq(GSE60143)/Homer GATAAGRT 1e0 0.000e+00 1.0000 0.0 0.00% 513.4 12.81% +AT3G12130(C3H)/colamp-AT3G12130-DAP-Seq(GSE60143)/Homer TMACTTTTTV 1e0 0.000e+00 1.0000 0.0 0.00% 1408.2 35.13% +At3g12730(G2like)/colamp-At3g12730-DAP-Seq(GSE60143)/Homer AAGATTCT 1e0 0.000e+00 1.0000 0.0 0.00% 739.9 18.46% +AT3G16280(AP2EREBP)/colamp-AT3G16280-DAP-Seq(GSE60143)/Homer HCACCGACAHHDHHN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT3G42860(zfGRF)/col-AT3G42860-DAP-Seq(GSE60143)/Homer CGTTGACTTN 1e0 0.000e+00 1.0000 0.0 0.00% 464.5 11.59% +At3g45610(C2C2dof)/col-At3g45610-DAP-Seq(GSE60143)/Homer TWACTTTTTS 1e0 0.000e+00 1.0000 0.0 0.00% 1287.4 32.12% +AT3G51470(DBP)/col-AT3G51470-DAP-Seq(GSE60143)/Homer TTWHGGTGCACC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT3G52440(C2C2dof)/colamp-AT3G52440-DAP-Seq(GSE60143)/Homer DTHACTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 311.3 7.77% +AT3G57600(AP2EREBP)/col-AT3G57600-DAP-Seq(GSE60143)/Homer GGCGGTGG 1e0 0.000e+00 1.0000 0.0 0.00% 213.5 5.33% +AT3G58630(Trihelix)/col-AT3G58630-DAP-Seq(GSE60143)/Homer TCTCCGGCGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT3G60490(AP2EREBP)/colamp-AT3G60490-DAP-Seq(GSE60143)/Homer NNRCCGACANNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At3g60580(C2H2)/col-At3g60580-DAP-Seq(GSE60143)/Homer WTTYTACT 1e0 0.000e+00 1.0000 0.0 0.00% 2714.9 67.74% +AT4G00250(GeBP)/col-AT4G00250-DAP-Seq(GSE60143)/Homer WDTGGATAAKRT 1e0 0.000e+00 1.0000 0.0 0.00% 104.2 2.60% +AT4G12670(MYBrelated)/col-AT4G12670-DAP-Seq(GSE60143)/Homer AGGGTTTAGGGTTTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At4g16750(AP2EREBP)/col-At4g16750-DAP-Seq(GSE60143)/Homer HACCGACAHA 1e0 0.000e+00 1.0000 0.0 0.00% 470.0 11.73% +AT4G18450(AP2EREBP)/col-AT4G18450-DAP-Seq(GSE60143)/Homer ATGGCGGCKG 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +At4g18890(BZR)/col-At4g18890-DAP-Seq(GSE60143)/Homer NDBRCACGTGYR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT4G26030(C2H2)/col-AT4G26030-DAP-Seq(GSE60143)/Homer BYYACCWACY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT4G27900(C2C2COlike)/col-AT4G27900-DAP-Seq(GSE60143)/Homer TCTCVACCGTTSATT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At4g28140(AP2EREBP)/colamp-At4g28140-DAP-Seq(GSE60143)/Homer DCCACCGACCAW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At4g31060(AP2EREBP)/colamp-At4g31060-DAP-Seq(GSE60143)/Homer CACCGACAAW 1e0 0.000e+00 1.0000 0.0 0.00% 173.6 4.33% +At4g32800(AP2EREBP)/colamp-At4g32800-DAP-Seq(GSE60143)/Homer DYCACCGACAHWWWH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At4g36780(BZR)/col-At4g36780-DAP-Seq(GSE60143)/Homer NNNNNNCACGTGNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT4G37180(G2like)/col-AT4G37180-DAP-Seq(GSE60143)/Homer AGAATCTTNN 1e0 0.000e+00 1.0000 0.0 0.00% 797.4 19.89% +At4g38000(C2C2dof)/col-At4g38000-DAP-Seq(GSE60143)/Homer WWWTWACTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 454.9 11.35% +AT5G02460(C2C2dof)/col-AT5G02460-DAP-Seq(GSE60143)/Homer CHCCTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 880.1 21.96% +At5g04390(C2H2)/col200-At5g04390-DAP-Seq(GSE60143)/Homer AGTGANDN 1e0 0.000e+00 1.0000 0.0 0.00% 1934.1 48.25% +At5g05790(MYBrelated)/col-At5g05790-DAP-Seq(GSE60143)/Homer AYCTTATC 1e0 0.000e+00 1.0000 0.0 0.00% 513.4 12.81% +At5g08330(TCP)/col-At5g08330-DAP-Seq(GSE60143)/Homer GGRCCCAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At5g08520(MYBrelated)/colamp-At5g08520-DAP-Seq(GSE60143)/Homer ADBSTTATCY 1e0 0.000e+00 1.0000 0.0 0.00% 555.8 13.87% +At5g08750(C3H)/col-At5g08750-DAP-Seq(GSE60143)/Homer NWDTTGCGGCTR 1e0 0.000e+00 1.0000 0.0 0.00% 653.7 16.31% +At5g18450(AP2EREBP)/col-At5g18450-DAP-Seq(GSE60143)/Homer CACCGCTT 1e0 0.000e+00 1.0000 0.0 0.00% 1216.5 30.35% +At5g22890(C2H2)/col-At5g22890-DAP-Seq(GSE60143)/Homer NSAGGTKWTATCTGD 1e0 0.000e+00 1.0000 0.0 0.00% 241.9 6.03% +AT5G22990(C2H2)/col-AT5G22990-DAP-Seq(GSE60143)/Homer WCGAHDTCGWHN 1e0 0.000e+00 1.0000 0.0 0.00% 156.8 3.91% +AT5G23930(mTERF)/col-AT5G23930-DAP-Seq(GSE60143)/Homer GGCGGCTG 1e0 0.000e+00 1.0000 0.0 0.00% 416.6 10.39% +AT5G25475(ABI3VP1)/col-AT5G25475-DAP-Seq(GSE60143)/Homer RNNRNCAAGCADNDB 1e0 0.000e+00 1.0000 0.0 0.00% 1068.0 26.65% +At5g29000(G2like)/col-At5g29000-DAP-Seq(GSE60143)/Homer RGAATATTCYHH 1e0 0.000e+00 1.0000 0.0 0.00% 191.5 4.78% +AT5G45580(G2like)/colamp-AT5G45580-DAP-Seq(GSE60143)/Homer ADRGAATCTH 1e0 0.000e+00 1.0000 0.0 0.00% 760.8 18.98% +At5g47390(MYBrelated)/col-At5g47390-DAP-Seq(GSE60143)/Homer CTTATCCA 1e0 0.000e+00 1.0000 0.0 0.00% 372.7 9.30% +AT5G47660(Trihelix)/colamp-AT5G47660-DAP-Seq(GSE60143)/Homer AWTTTTACCG 1e0 0.000e+00 1.0000 0.0 0.00% 891.6 22.24% +At5g52660(MYBrelated)/colamp-At5g52660-DAP-Seq(GSE60143)/Homer HAAAAATATCTW 1e0 0.000e+00 1.0000 0.0 0.00% 684.2 17.07% +AT5G56840(MYBrelated)/colamp-AT5G56840-DAP-Seq(GSE60143)/Homer TGGATAAGGT 1e0 0.000e+00 1.0000 0.0 0.00% 868.9 21.68% +At5g58900(MYBrelated)/colamp-At5g58900-DAP-Seq(GSE60143)/Homer WWWTYTTATCTWWWW 1e0 0.000e+00 1.0000 0.0 0.00% 960.8 23.97% +AT5G59990(C2C2COlike)/colamp-AT5G59990-DAP-Seq(GSE60143)/Homer TCTCAACCGTTCATT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT5G60130(ABI3VP1)/col-AT5G60130-DAP-Seq(GSE60143)/Homer WTTYTAAGVAAA 1e0 0.000e+00 1.0000 0.0 0.00% 903.5 22.54% +AT5G61620(MYBrelated)/colamp-AT5G61620-DAP-Seq(GSE60143)/Homer CTTATCCA 1e0 0.000e+00 1.0000 0.0 0.00% 671.5 16.75% +At5g62940(C2C2dof)/col-At5g62940-DAP-Seq(GSE60143)/Homer WHWHHACTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 2306.3 57.54% +AT5G63260(C3H)/col-AT5G63260-DAP-Seq(GSE60143)/Homer RAAAAAGTRA 1e0 0.000e+00 1.0000 0.0 0.00% 1000.9 24.97% +At5g65130(AP2EREBP)/colamp-At5g65130-DAP-Seq(GSE60143)/Homer CCRCCGACAWTN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +At5g66730(C2H2)/colamp-At5g66730-DAP-Seq(GSE60143)/Homer TTTGTCKTTTTK 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +AT5G66940(C2C2dof)/col-AT5G66940-DAP-Seq(GSE60143)/Homer NNHACTTTWT 1e0 0.000e+00 1.0000 0.0 0.00% 720.4 17.97% +ATAF1(NAC)/col-ATAF1-DAP-Seq(GSE60143)/Homer YACGTMAY 1e0 0.000e+00 1.0000 0.0 0.00% 764.9 19.08% +AtGRF6(GRF)/col-AtGRF6-DAP-Seq(GSE60143)/Homer NTGTCAGADNNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 760.6 18.98% +ATHB13(Homeobox)/col-ATHB13-DAP-Seq(GSE60143)/Homer CAATAATT 1e0 0.000e+00 1.0000 0.0 0.00% 154.3 3.85% +ATHB15(HB)/col-ATHB15-DAP-Seq(GSE60143)/Homer GYAATSATTA 1e0 0.000e+00 1.0000 0.0 0.00% 361.5 9.02% +ATHB18(Homeobox)/colamp-ATHB18-DAP-Seq(GSE60143)/Homer YCAATSATTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ATHB20(Homeobox)/colamp-ATHB20-DAP-Seq(GSE60143)/Homer CAATHATT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ATHB21(HB)/colamp-ATHB21-DAP-Seq(GSE60143)/Homer YCAATWAT 1e0 0.000e+00 1.0000 0.0 0.00% 150.5 3.76% +AtHB32(ZFHD)/col200-AtHB32-DAP-Seq(GSE60143)/Homer CGAATTAT 1e0 0.000e+00 1.0000 0.0 0.00% 1107.5 27.63% +ATHB40(HB)/col-ATHB40-DAP-Seq(GSE60143)/Homer HCAATWATTG 1e0 0.000e+00 1.0000 0.0 0.00% 555.9 13.87% +ATHB53(HB)/col-ATHB53-DAP-Seq(GSE60143)/Homer CAATAATT 1e0 0.000e+00 1.0000 0.0 0.00% 152.4 3.80% +ATHB5(HB)/colamp-ATHB5-DAP-Seq(GSE60143)/Homer AATGATTG 1e0 0.000e+00 1.0000 0.0 0.00% 445.0 11.10% +ATHB6(Homeobox)/col-ATHB6-DAP-Seq(GSE60143)/Homer AATGATTG 1e0 0.000e+00 1.0000 0.0 0.00% 598.0 14.92% +ATHB7(Homeobox)/col-ATHB7-DAP-Seq(GSE60143)/Homer AATGATTG 1e0 0.000e+00 1.0000 0.0 0.00% 445.0 11.10% +AtIDD11(C2H2)/colamp-AtIDD11-DAP-Seq(GSE60143)/Homer TTTGTCGTTT 1e0 0.000e+00 1.0000 0.0 0.00% 268.3 6.69% +ATY19(MYB)/col-ATY19-DAP-Seq(GSE60143)/Homer YYCACCWACCAT 1e0 0.000e+00 1.0000 0.0 0.00% 145.3 3.63% +AZF1(C2H2)/colamp-AZF1-DAP-Seq(GSE60143)/Homer DKSWCACT 1e0 0.000e+00 1.0000 0.0 0.00% 2047.9 51.09% +BAM8(BES1)/col-BAM8-DAP-Seq(GSE60143)/Homer NNWSACACGTGTSWN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BBX31(Orphan)/col-BBX31-DAP-Seq(GSE60143)/Homer NAAAAAGTDA 1e0 0.000e+00 1.0000 0.0 0.00% 892.1 22.26% +bHLH10(bHLH)/colamp-bHLH10-DAP-Seq(GSE60143)/Homer YACCGACA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bHLH122(bHLH)/col100-bHLH122-DAP-Seq(GSE60143)/Homer NDDCAASTTGHHNWW 1e0 0.000e+00 1.0000 0.0 0.00% 526.9 13.15% +bHLH130(bHLH)/col-bHLH130-DAP-Seq(GSE60143)/Homer GCAACTTG 1e0 0.000e+00 1.0000 0.0 0.00% 388.5 9.69% +bHLH157(bHLH)/col-bHLH157-DAP-Seq(GSE60143)/Homer KACACGTCTCTY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bHLH18(bHLH)/col-bHLH18-DAP-Seq(GSE60143)/Homer CACGTGTTYCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bHLH34(bHLH)/colamp-bHLH34-DAP-Seq(GSE60143)/Homer HGWGRHWGACACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bHLH74(bHLH)/col-bHLH74-DAP-Seq(GSE60143)/Homer DRATCACGTGAB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bHLH80(bHLH)/col-bHLH80-DAP-Seq(GSE60143)/Homer NNNNDCAASTTGHNN 1e0 0.000e+00 1.0000 0.0 0.00% 526.9 13.15% +BIM1(bHLH)/colamp-BIM1-DAP-Seq(GSE60143)/Homer NNNNNNVTCACGTGM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BIM2(bHLH)/col-BIM2-DAP-Seq(GSE60143)/Homer NNNNCACGTGNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BIM3(bHLH)/col-BIM3-DAP-Seq(GSE60143)/Homer TWVTCACGTGAB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BOS1(MYB)/col-BOS1-DAP-Seq(GSE60143)/Homer NNRCCTAACT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BPC1(BBRBPC)/colamp-BPC1-DAP-Seq(GSE60143)/Homer GARGAGAGAGAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BPC6(BBRBPC)/col-BPC6-DAP-Seq(GSE60143)/Homer YTYTCTCTCTCTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bZIP16(bZIP)/colamp-bZIP16-DAP-Seq(GSE60143)/Homer TGCCACGTGD 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +bZIP18(bZIP)/colamp-bZIP18-DAP-Seq(GSE60143)/Homer KGMCAGCTND 1e0 0.000e+00 1.0000 0.0 0.00% 1355.8 33.83% +bZIP28(bZIP)/col-bZIP28-DAP-Seq(GSE60143)/Homer TGCCACGTSABH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bZIP3(bZIP)/col-bZIP3-DAP-Seq(GSE60143)/Homer DWKNHSACGTGGCAD 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +bZIP42(bZIP)/colamp-bZIP42-DAP-Seq(GSE60143)/Homer GCCACGTCAGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bZIP44(bZIP)/colamp-bZIP44-DAP-Seq(GSE60143)/Homer NDTGCCACGTCAGCH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +bZIP48(bZIP)/colamp-bZIP48-DAP-Seq(GSE60143)/Homer DDWWKVTSACGTGGC 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +bZIP50(bZIP)/colamp-bZIP50-DAP-Seq(GSE60143)/Homer GATGACGTCA 1e0 0.000e+00 1.0000 0.0 0.00% 492.8 12.29% +bZIP53(bZIP)/colamp-bZIP53-DAP-Seq(GSE60143)/Homer NDNHSACGTGKMNNN 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +bZIP68(bZIP)/col-bZIP68-DAP-Seq(GSE60143)/Homer WGCCACGTGK 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +bZIP69(bZIP)/col-bZIP69-DAP-Seq(GSE60143)/Homer GACAGCTGKCAW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +BZR1(BZR)/col-BZR1-DAP-Seq(GSE60143)/Homer NNCRCACGTGCG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CAMTA1(CAMTA)/col-CAMTA1-DAP-Seq(GSE60143)/Homer WWAACGCGTT 1e0 0.000e+00 1.0000 0.0 0.00% 423.3 10.56% +CAMTA5(CAMTA)/col-CAMTA5-DAP-Seq(GSE60143)/Homer ACGCGTTTTANACRC 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +CBF1(AP2EREBP)/colamp-CBF1-DAP-Seq(GSE60143)/Homer YRCCGACATN 1e0 0.000e+00 1.0000 0.0 0.00% 658.4 16.43% +CBF2(AP2EREBP)/colamp-CBF2-DAP-Seq(GSE60143)/Homer YBRCCGACATNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 643.5 16.05% +CBF3(AP2EREBP)/colamp-CBF3-DAP-Seq(GSE60143)/Homer YNRCCGACATNN 1e0 0.000e+00 1.0000 0.0 0.00% 470.1 11.73% +CBF4(AP2EREBP)/colamp-CBF4-DAP-Seq(GSE60143)/Homer NRCCGACDWNNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 462.2 11.53% +CDF3(C2C2dof)/colamp-CDF3-DAP-Seq(GSE60143)/Homer AAAAGTRM 1e0 0.000e+00 1.0000 0.0 0.00% 279.5 6.97% +CDM1(C3H)/colamp-CDM1-DAP-Seq(GSE60143)/Homer CCGAWAWTWTCGGAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +CEJ1(AP2EREBP)/col-CEJ1-DAP-Seq(GSE60143)/Homer WWTGTCGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 842.2 21.01% +COG1(C2C2dof)/col-COG1-DAP-Seq(GSE60143)/Homer DAAAAAGTGA 1e0 0.000e+00 1.0000 0.0 0.00% 509.5 12.71% +CRC(C2C2YABBY)/col-CRC-DAP-Seq(GSE60143)/Homer TWATSATA 1e0 0.000e+00 1.0000 0.0 0.00% 723.4 18.05% +CRF10(AP2EREBP)/col100-CRF10-DAP-Seq(GSE60143)/Homer DCCGCCGYHA 1e0 0.000e+00 1.0000 0.0 0.00% 466.1 11.63% +CRF4(AP2EREBP)/colamp-CRF4-DAP-Seq(GSE60143)/Homer CGCCGCCA 1e0 0.000e+00 1.0000 0.0 0.00% 244.0 6.09% +CUC1(NAC)/col-CUC1-DAP-Seq(GSE60143)/Homer TACTTGTNNNACAAG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +CUC2(NAC)/colamp-CUC2-DAP-Seq(GSE60143)/Homer TRCKTGTNNNWCAMG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +CUC3(NAC)/col-CUC3-DAP-Seq(GSE60143)/Homer TRCKTGWNNNACAMG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +DAG2(C2C2dof)/col-DAG2-DAP-Seq(GSE60143)/Homer WWTTHACTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 661.9 16.51% +DDF1(AP2EREBP)/col-DDF1-DAP-Seq(GSE60143)/Homer GCCGACAT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DDF2(AP2EREBP)/col-DDF2-DAP-Seq(GSE60143)/Homer GATGTCGRCR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DEAR2(AP2EREBP)/colamp-DEAR2-DAP-Seq(GSE60143)/Homer HCACCGACAWHD 1e0 0.000e+00 1.0000 0.0 0.00% 1283.4 32.02% +DEAR3(AP2EREBP)/colamp-DEAR3-DAP-Seq(GSE60143)/Homer BCACCGACAWNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 164.2 4.10% +DEAR5(AP2EREBP)/col-DEAR5-DAP-Seq(GSE60143)/Homer NDWTGTCGGTGRWDN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DEL1(E2FDP)/colamp-DEL1-DAP-Seq(GSE60143)/Homer TTCCCGCCAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DEL2(E2FDP)/col-DEL2-DAP-Seq(GSE60143)/Homer WTTTCSCGCC 1e0 0.000e+00 1.0000 0.0 0.00% 861.0 21.48% +dof24(C2C2dof)/col-dof24-DAP-Seq(GSE60143)/Homer TWMCTTTTTG 1e0 0.000e+00 1.0000 0.0 0.00% 1534.3 38.28% +dof42(C2C2dof)/col-dof42-DAP-Seq(GSE60143)/Homer AAAAAGGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +dof43(C2C2dof)/colamp-dof43-DAP-Seq(GSE60143)/Homer NAAAAAGTDA 1e0 0.000e+00 1.0000 0.0 0.00% 888.3 22.16% +dof45(C2C2dof)/col-dof45-DAP-Seq(GSE60143)/Homer NVAWAAAGTN 1e0 0.000e+00 1.0000 0.0 0.00% 1645.0 41.04% +DREB19(AP2EREBP)/colamp-DREB19-DAP-Seq(GSE60143)/Homer AATGTCGGTK 1e0 0.000e+00 1.0000 0.0 0.00% 135.9 3.39% +DREB26(AP2EREBP)/col-DREB26-DAP-Seq(GSE60143)/Homer CCACCGACAH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +DREB2(AP2EREBP)/col-DREB2-DAP-Seq(GSE60143)/Homer TMACCGACATWA 1e0 0.000e+00 1.0000 0.0 0.00% 134.1 3.34% +E2FA(E2FDP)/colamp-E2FA-DAP-Seq(GSE60143)/Homer WWTGGCGCCAWWWNN 1e0 0.000e+00 1.0000 0.0 0.00% 523.0 13.05% +E-box/Arabidopsis-Promoters/Homer GCCACGTG 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +EIN3(EIL)/col-EIN3-DAP-Seq(GSE60143)/Homer ARATTCAATGWATYT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +EMB1789(C3H)/col-EMB1789-DAP-Seq(GSE60143)/Homer TWTTTACCGYND 1e0 0.000e+00 1.0000 0.0 0.00% 523.9 13.07% +EPR1(MYBrelated)/colamp-EPR1-DAP-Seq(GSE60143)/Homer AAATATCT 1e0 0.000e+00 1.0000 0.0 0.00% 454.0 11.33% +ERF104(AP2EREBP)/col-ERF104-DAP-Seq(GSE60143)/Homer GGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ERF105(AP2EREBP)/colamp-ERF105-DAP-Seq(GSE60143)/Homer TGGCGGCT 1e0 0.000e+00 1.0000 0.0 0.00% 580.3 14.48% +ERF10(AP2EREBP)/col-ERF10-DAP-Seq(GSE60143)/Homer RTGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 197.4 4.93% +ERF115(AP2EREBP)/colamp-ERF115-DAP-Seq(GSE60143)/Homer WTKRCGGCGB 1e0 0.000e+00 1.0000 0.0 0.00% 752.8 18.78% +ERF11(AP2EREBP)/col-ERF11-DAP-Seq(GSE60143)/Homer RTGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 361.8 9.03% +ERF13(AP2EREBP)/colamp-ERF13-DAP-Seq(GSE60143)/Homer TYAGCCGCCATT 1e0 0.000e+00 1.0000 0.0 0.00% 427.8 10.67% +ERF15(AP2EREBP)/colamp-ERF15-DAP-Seq(GSE60143)/Homer WDHAGCMGCCAT 1e0 0.000e+00 1.0000 0.0 0.00% 409.1 10.21% +ERF1(AP2EREBP)/colamp-ERF1-DAP-Seq(GSE60143)/Homer GGCGGCTR 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ERF2(AP2EREBP)/colamp-ERF2-DAP-Seq(GSE60143)/Homer GGCGGCTG 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ERF38(AP2EREBP)/col-ERF38-DAP-Seq(GSE60143)/Homer CACCGACA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ERF3(AP2EREBP)/colamp-ERF3-DAP-Seq(GSE60143)/Homer ATGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 132.5 3.30% +ERF4(AP2EREBP)/colamp-ERF4-DAP-Seq(GSE60143)/Homer WDWTGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 620.5 15.48% +ERF5(AP2EREBP)/colamp-ERF5-DAP-Seq(GSE60143)/Homer DCMGCCGCCA 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ERF73(AP2EREBP)/col-ERF73-DAP-Seq(GSE60143)/Homer CCGCCGCC 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ERF7(AP2EREBP)/col-ERF7-DAP-Seq(GSE60143)/Homer ATGRCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 1319.6 32.92% +ERF8(AP2EREBP)/colamp-ERF8-DAP-Seq(GSE60143)/Homer CGCCGYCATW 1e0 0.000e+00 1.0000 0.0 0.00% 360.0 8.98% +ERF9(AP2EREBP)/colamp-ERF9-DAP-Seq(GSE60143)/Homer AWATGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ESE1(AP2EREBP)/col-ESE1-DAP-Seq(GSE60143)/Homer GGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 3.7 0.09% +ESE3(AP2EREBP)/col-ESE3-DAP-Seq(GSE60143)/Homer GACGGTGG 1e0 0.000e+00 1.0000 0.0 0.00% 213.5 5.33% +FAR1(FAR1)/col-FAR1-DAP-Seq(GSE60143)/Homer TKNNNYYCACGCGCY 1e0 0.000e+00 1.0000 0.0 0.00% 207.2 5.17% +FEA4(bZIP)/Corn-FEA4-ChIP-Seq(GSE61954)/Homer TGACGTCACS 1e0 0.000e+00 1.0000 0.0 0.00% 269.0 6.71% +FHY3(FAR1)/Arabidopsis-FHY3-ChIP-Seq(GSE30711)/Homer HHCACGCGCBTN 1e0 0.000e+00 1.0000 0.0 0.00% 210.9 5.26% +FRS9(ND)/col-FRS9-DAP-Seq(GSE60143)/Homer RGAGAGAGAAAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +FUS3(ABI3VP1)/col-FUS3-DAP-Seq(GSE60143)/Homer DNNWTNTGCATGKNN 1e0 0.000e+00 1.0000 0.0 0.00% 285.3 7.12% +GAGA-repeat/Arabidopsis-Promoters/Homer CTCTCTCTCY 1e0 0.000e+00 1.0000 0.0 0.00% 13.0 0.32% +GATA11(C2C2gata)/col-GATA11-DAP-Seq(GSE60143)/Homer DDHYYAGATCTR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA12(C2C2gata)/col-GATA12-DAP-Seq(GSE60143)/Homer YAGATCTRAW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA14(C2C2gata)/col-GATA14-DAP-Seq(GSE60143)/Homer AYCAGATCTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA15(C2C2gata)/col-GATA15-DAP-Seq(GSE60143)/Homer KATGATCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA19(C2C2gata)/colamp-GATA19-DAP-Seq(GSE60143)/Homer ATCSGATCVG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA1(C2C2gata)/colamp-GATA1-DAP-Seq(GSE60143)/Homer DDWWYYAGATCTRRW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA20(C2C2gata)/colamp-GATA20-DAP-Seq(GSE60143)/Homer TNGATCNDNM 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA4(C2C2gata)/col-GATA4-DAP-Seq(GSE60143)/Homer DDWTYAGATCTR 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GATA6(C2C2gata)/col200-GATA6-DAP-Seq(GSE60143)/Homer TAGATCTARAHH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GBF3(bZIP)/Arabidopsis-GBF3-ChIP-Seq(GSE80564)/Homer TGCCACGTSAYC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GBF5(bZIP)/colamp-GBF5-DAP-Seq(GSE60143)/Homer WKNWSACGTGGCAWN 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +GBF6(bZIP)/colamp-GBF6-DAP-Seq(GSE60143)/Homer WWTGMCACGTCABCW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GRF9(GRF)/colamp-GRF9-DAP-Seq(GSE60143)/Homer NWCTGACANNNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GT1(Trihelix)/col-GT1-DAP-Seq(GSE60143)/Homer TTAACCATGGTTAAD 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GT2(Trihelix)/colamp-GT2-DAP-Seq(GSE60143)/Homer AMGGTAAAWWWN 1e0 0.000e+00 1.0000 0.0 0.00% 1131.1 28.22% +GT3a(Trihelix)/col-GT3a-DAP-Seq(GSE60143)/Homer WNACACGTGTYWWAW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GTL1(Trihelix)/colamp-GTL1-DAP-Seq(GSE60143)/Homer WWTTTACCKY 1e0 0.000e+00 1.0000 0.0 0.00% 1203.2 30.02% +HAP3(CCAATHAP3)/col-HAP3-DAP-Seq(GSE60143)/Homer TGATGGAW 1e0 0.000e+00 1.0000 0.0 0.00% 165.8 4.14% +HAT1(Homeobox)/col-HAT1-DAP-Seq(GSE60143)/Homer SCAATCATTGNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HAT2(Homeobox)/colamp-HAT2-DAP-Seq(GSE60143)/Homer CYAATSATTR 1e0 0.000e+00 1.0000 0.0 0.00% 658.2 16.42% +HAT5(Homeobox)/colamp-HAT5-DAP-Seq(GSE60143)/Homer DCAATWATTG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ATHB6(Homeobox)/Arabidopsis-HB6-ChIP-Seq(GSE80564)/Homer CAATNATTBN 1e0 0.000e+00 1.0000 0.0 0.00% 154.3 3.85% +HDG1(Homeobox)/col100-HDG1-DAP-Seq(GSE60143)/Homer DDYAATTAATGH 1e0 0.000e+00 1.0000 0.0 0.00% 260.8 6.51% +HDG7(HB)/col-HDG7-DAP-Seq(GSE60143)/Homer WGCATTTAATGC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSF21(HSF)/col-HSF21-DAP-Seq(GSE60143)/Homer CTTCTAGAAGMTTYW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSF3(HSF)/colamp-HSF3-DAP-Seq(GSE60143)/Homer NTTCTAGAAKCTTCT 1e0 0.000e+00 1.0000 0.0 0.00% 142.0 3.54% +HSF6(HSF)/col-HSF6-DAP-Seq(GSE60143)/Homer TTYTAGAAGCTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSF7(HSF)/colamp-HSF7-DAP-Seq(GSE60143)/Homer TTCTAGAAGCTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSFA1E(HSF)/col-HSFA1E-DAP-Seq(GSE60143)/Homer TTCTAGAAGCTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSFA6A(HSF)/col-HSFA6A-DAP-Seq(GSE60143)/Homer RGAAGNTTCTAGAAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSFA6B(HSF)/colamp-HSFA6B-DAP-Seq(GSE60143)/Homer NTTCTAGAANHTTCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSFB3(HSF)/colamp-HSFB3-DAP-Seq(GSE60143)/Homer TTCTAGAAGMTTHTW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSFB4(HSF)/col-HSFB4-DAP-Seq(GSE60143)/Homer TTCTAGAAGCTTCTA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HSFC1(HSF)/col-HSFC1-DAP-Seq(GSE60143)/Homer HTTCTAGAADCTTCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HY5(bZIP)/colamp-HY5-DAP-Seq(GSE60143)/Homer RRTSACGTSD 1e0 0.000e+00 1.0000 0.0 0.00% 26.0 0.65% +IBL1(bHLH)/Seedling-IBL1-ChIP-Seq(GSE51120)/Homer CACGTGCC 1e0 0.000e+00 1.0000 0.0 0.00% 622.6 15.53% +IDD2(C2H2)/colamp-IDD2-DAP-Seq(GSE60143)/Homer HAVAAAAMGACAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IDD4(C2H2)/col-IDD4-DAP-Seq(GSE60143)/Homer TTTGTCTTTWTB 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IDD5(C2H2)/colamp-IDD5-DAP-Seq(GSE60143)/Homer TTTTGTCTTTTTBTK 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +IDD7(C2H2)/col-IDD7-DAP-Seq(GSE60143)/Homer TTTGTCKTTTTN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +JGL(C2H2)/col-JGL-DAP-Seq(GSE60143)/Homer ACYTTCAGTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +JKD(C2H2)/col-JKD-DAP-Seq(GSE60143)/Homer TTTTGTCGTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +KANADI1(Myb)/Seedling-KAN1-ChIP-Seq(GSE48081)/Homer ARGAATAWWN 1e0 0.000e+00 1.0000 0.0 0.00% 610.9 15.24% +KAN2(G2like)/colamp-KAN2-DAP-Seq(GSE60143)/Homer ATATTCTY 1e0 0.000e+00 1.0000 0.0 0.00% 193.3 4.82% +Knotted(Homeobox)/Corn-KN1-ChIP-Seq(GSE39161)/Homer GAYGNGACRGGN 1e0 0.000e+00 1.0000 0.0 0.00% 270.2 6.74% +LBD13(LOBAS2)/colamp-LBD13-DAP-Seq(GSE60143)/Homer KCCGTNWTTTBCGGC 1e0 0.000e+00 1.0000 0.0 0.00% 532.7 13.29% +LBD18(LOBAS2)/colamp-LBD18-DAP-Seq(GSE60143)/Homer CKGAWWTTCHGS 1e0 0.000e+00 1.0000 0.0 0.00% 1637.7 40.86% +LBD19(LOBAS2)/colamp-LBD19-DAP-Seq(GSE60143)/Homer CCKGAAWTTCMGGAW 1e0 0.000e+00 1.0000 0.0 0.00% 1949.5 48.64% +LBD23(LOBAS2)/colamp-LBD23-DAP-Seq(GSE60143)/Homer GCGNAWWWTNCGCYW 1e0 0.000e+00 1.0000 0.0 0.00% 451.2 11.26% +LBD2(LOBAS2)/colamp-LBD2-DAP-Seq(GSE60143)/Homer TCCGAWTTTTTCGGN 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +LCL1(MYBrelated)/colamp-LCL1-DAP-Seq(GSE60143)/Homer NAAAATATCTWHWWN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +LEP(AP2EREBP)/col-LEP-DAP-Seq(GSE60143)/Homer CDCCGCCGTC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +LHY1(MYBrelated)/col-LHY1-DAP-Seq(GSE60143)/Homer AAATATCT 1e0 0.000e+00 1.0000 0.0 0.00% 454.0 11.33% +LMI1(HB)/colamp-LMI1-DAP-Seq(GSE60143)/Homer AATTATTG 1e0 0.000e+00 1.0000 0.0 0.00% 154.3 3.85% +LOB(LOBAS2)/col-LOB-DAP-Seq(GSE60143)/Homer CGCCGKAWWTTHCGS 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MGP(C2H2)/colamp-MGP-DAP-Seq(GSE60143)/Homer TTTTGTCGTTTW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MS188(MYB)/colamp-MS188-DAP-Seq(GSE60143)/Homer WARKTAGGTRRA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB107(MYB)/col-MYB107-DAP-Seq(GSE60143)/Homer RGTWGGTRRR 1e0 0.000e+00 1.0000 0.0 0.00% 840.9 20.98% +MYB10(MYB)/col-MYB10-DAP-Seq(GSE60143)/Homer YCCACCTACCHH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB113(MYB)/col-MYB113-DAP-Seq(GSE60143)/Homer HNDAWTCMGTTAYWN 1e0 0.000e+00 1.0000 0.0 0.00% 241.8 6.03% +MYB116(MYB)/colamp-MYB116-DAP-Seq(GSE60143)/Homer AGTTAGGCAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB118(MYB)/colamp-MYB118-DAP-Seq(GSE60143)/Homer TAWCCGTTAC 1e0 0.000e+00 1.0000 0.0 0.00% 372.3 9.29% +MYB119(MYB)/colamp-MYB119-DAP-Seq(GSE60143)/Homer YRACCGTTACDD 1e0 0.000e+00 1.0000 0.0 0.00% 366.8 9.15% +MYB121(MYB)/col-MYB121-DAP-Seq(GSE60143)/Homer YNTACCTAACWW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB13(MYB)/col-MYB13-DAP-Seq(GSE60143)/Homer HYCACCWACCHH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB17(MYB)/colamp-MYB17-DAP-Seq(GSE60143)/Homer GGTAGGTGRG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB27(MYB)/colamp-MYB27-DAP-Seq(GSE60143)/Homer TACCTAACWT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB30(MYB)/colamp-MYB30-DAP-Seq(GSE60143)/Homer AGGTAGTTGG 1e0 0.000e+00 1.0000 0.0 0.00% 356.1 8.89% +MYB33(MYB)/col-MYB33-DAP-Seq(GSE60143)/Homer DDTYNGTTAN 1e0 0.000e+00 1.0000 0.0 0.00% 1277.8 31.88% +MYB39(MYB)/col-MYB39-DAP-Seq(GSE60143)/Homer WWAARKTAGGTGRAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB3(MYB)/Arabidopsis-MYB3-ChIP-Seq(GSE80564)/Homer GKTAGGTRGG 1e0 0.000e+00 1.0000 0.0 0.00% 210.8 5.26% +MYB3R1(MYB)/col-MYB3R1-DAP-Seq(GSE60143)/Homer WWDTDACCGTTR 1e0 0.000e+00 1.0000 0.0 0.00% 428.8 10.70% +MYB3R4(MYB)/col-MYB3R4-DAP-Seq(GSE60143)/Homer AWWTAACCGTTR 1e0 0.000e+00 1.0000 0.0 0.00% 490.0 12.23% +MYB3R5(MYB)/col-MYB3R5-DAP-Seq(GSE60143)/Homer THYAACGGTHAWAWT 1e0 0.000e+00 1.0000 0.0 0.00% 266.4 6.65% +MYB40(MYB)/col-MYB40-DAP-Seq(GSE60143)/Homer TGGTAGGTRARA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB41(MYB)/col-MYB41-DAP-Seq(GSE60143)/Homer BYTYACCTAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB44(MYB)/colamp-MYB44-DAP-Seq(GSE60143)/Homer CVGTTWWKTCNGTTA 1e0 0.000e+00 1.0000 0.0 0.00% 177.3 4.42% +MYB49(MYB)/col-MYB49-DAP-Seq(GSE60143)/Homer ARKTAGGTRR 1e0 0.000e+00 1.0000 0.0 0.00% 100.5 2.51% +MYB4(MYB)/col200-MYB4-DAP-Seq(GSE60143)/Homer WAGKTAGGTARR 1e0 0.000e+00 1.0000 0.0 0.00% 98.6 2.46% +MYB51(MYB)/col-MYB51-DAP-Seq(GSE60143)/Homer GGTAGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 592.6 14.79% +MYB55(MYB)/colamp-MYB55-DAP-Seq(GSE60143)/Homer YACCWAMC 1e0 0.000e+00 1.0000 0.0 0.00% 374.9 9.35% +MYB56(MYB)/colamp-MYB56-DAP-Seq(GSE60143)/Homer HTAACGRMHY 1e0 0.000e+00 1.0000 0.0 0.00% 660.2 16.47% +MYB57(MYB)/col-MYB57-DAP-Seq(GSE60143)/Homer TTACCTAACT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB58(MYB)/colamp-MYB58-DAP-Seq(GSE60143)/Homer YYYACCWACC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB61(MYB)/colamp-MYB61-DAP-Seq(GSE60143)/Homer HCYACCTACC 1e0 0.000e+00 1.0000 0.0 0.00% 490.3 12.23% +MYB62(MYB)/colamp-MYB62-DAP-Seq(GSE60143)/Homer NTACCTAACT 1e0 0.000e+00 1.0000 0.0 0.00% 130.4 3.25% +MYB63(MYB)/col-MYB63-DAP-Seq(GSE60143)/Homer BHYACCWACCHH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB65(MYB)/colamp-MYB65-DAP-Seq(GSE60143)/Homer RACNGTTA 1e0 0.000e+00 1.0000 0.0 0.00% 1542.6 38.49% +MYB67(MYB)/col-MYB67-DAP-Seq(GSE60143)/Homer YYYACCTAAC 1e0 0.000e+00 1.0000 0.0 0.00% 371.1 9.26% +MYB70(MYB)/col-MYB70-DAP-Seq(GSE60143)/Homer WTAACNGTTA 1e0 0.000e+00 1.0000 0.0 0.00% 1789.7 44.65% +MYB73(MYB)/col-MYB73-DAP-Seq(GSE60143)/Homer NNNNHAACNGHHDHN 1e0 0.000e+00 1.0000 0.0 0.00% 1405.3 35.06% +MYB74(MYB)/colamp-MYB74-DAP-Seq(GSE60143)/Homer YYYACCTACCWH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB77(MYB)/col-MYB77-DAP-Seq(GSE60143)/Homer NYAACBGYMC 1e0 0.000e+00 1.0000 0.0 0.00% 1369.7 34.17% +MYB88(MYB)/col-MYB88-DAP-Seq(GSE60143)/Homer HNACGCTCCT 1e0 0.000e+00 1.0000 0.0 0.00% 507.6 12.66% +MYB92(MYB)/colamp-MYB92-DAP-Seq(GSE60143)/Homer GGTAGGTR 1e0 0.000e+00 1.0000 0.0 0.00% 102.3 2.55% +MYB93(MYB)/colamp-MYB93-DAP-Seq(GSE60143)/Homer GGTAGGTGRD 1e0 0.000e+00 1.0000 0.0 0.00% 272.5 6.80% +MYB94(MYB)/col-MYB94-DAP-Seq(GSE60143)/Homer WGGTRGTTGGKA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +MYB96(MYB)/colamp-MYB96-DAP-Seq(GSE60143)/Homer WGGTRGTTGG 1e0 0.000e+00 1.0000 0.0 0.00% 682.3 17.02% +MYB98(MYB)/col-MYB98-DAP-Seq(GSE60143)/Homer NWDCCGTTAC 1e0 0.000e+00 1.0000 0.0 0.00% 172.7 4.31% +MYB99(MYB)/colamp-MYB99-DAP-Seq(GSE60143)/Homer GGTAGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 600.7 14.99% +NAC2(NAC)/colamp-NAC2-DAP-Seq(GSE60143)/Homer TDCTTGNNNNNCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +NAM(NAC)/col-NAM-DAP-Seq(GSE60143)/Homer RGTTRCGTRW 1e0 0.000e+00 1.0000 0.0 0.00% 283.9 7.08% +NAP(NAC)/col-NAP-DAP-Seq(GSE60143)/Homer ARGTTACGTRTN 1e0 0.000e+00 1.0000 0.0 0.00% 1.9 0.05% +NGA4(ABI3VP1)/col-NGA4-DAP-Seq(GSE60143)/Homer TKNTCAGGTG 1e0 0.000e+00 1.0000 0.0 0.00% 1053.7 26.29% +NLP7(RWPRK)/col-NLP7-DAP-Seq(GSE60143)/Homer TGRCCYTTCR 1e0 0.000e+00 1.0000 0.0 0.00% 1175.5 29.33% +NST1(NAC)/colamp-NST1-DAP-Seq(GSE60143)/Homer WRCTTRWWNWWYAAG 1e0 0.000e+00 1.0000 0.0 0.00% 249.8 6.23% +NTM1(NAC)/col-NTM1-DAP-Seq(GSE60143)/Homer ACTTRTARAASAAGT 1e0 0.000e+00 1.0000 0.0 0.00% 234.9 5.86% +NTM2(NAC)/col-NTM2-DAP-Seq(GSE60143)/Homer CTTRTNNNAYAAGBH 1e0 0.000e+00 1.0000 0.0 0.00% 259.1 6.46% +NUC(C2H2)/col-NUC-DAP-Seq(GSE60143)/Homer HAVAAAACGACAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +O2(bZIP)/Corn-O2-ChIP-Seq(GSE63991)/Homer GCTGACGTGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +OBP1(C2C2dof)/col-OBP1-DAP-Seq(GSE60143)/Homer NHHACTTTWT 1e0 0.000e+00 1.0000 0.0 0.00% 1808.6 45.12% +OBP3(C2C2dof)/col-OBP3-DAP-Seq(GSE60143)/Homer NYWACTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 1605.5 40.06% +OBP4(C2C2dof)/col-OBP4-DAP-Seq(GSE60143)/Homer WTTHACTTTTTB 1e0 0.000e+00 1.0000 0.0 0.00% 216.4 5.40% +PCF/Arabidopsis-Promoters/Homer NNWWWTGGGCYTDDN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PHV(HB)/col-PHV-DAP-Seq(GSE60143)/Homer RTAATSATTA 1e0 0.000e+00 1.0000 0.0 0.00% 361.5 9.02% +PIF4(bHLH)/Seedling-PIF4-ChIP-Seq(GSE35315)/Homer NNBCACGTGN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PIF5ox(bHLH)/Arabidopsis-PIF5ox-ChIP-Seq(GSE35062)/Homer BCACGTGVDN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PIF7(bHLH)/col-PIF7-DAP-Seq(GSE60143)/Homer CCACGTGGNH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PLT1(AP2EREBP)/colamp-PLT1-DAP-Seq(GSE60143)/Homer GCACGAWTYCCGAGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PLT3(AP2EREBP)/col-PLT3-DAP-Seq(GSE60143)/Homer GCACGNWTHYCGAGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PTF1(TCP)/colamp-PTF1-DAP-Seq(GSE60143)/Homer RDDGGGACCACA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +PUCHI(AP2EREBP)/colamp-PUCHI-DAP-Seq(GSE60143)/Homer GCGCCGTY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Rap210(AP2EREBP)/col-Rap210-DAP-Seq(GSE60143)/Homer TGTCGGCA 1e0 0.000e+00 1.0000 0.0 0.00% 662.2 16.52% +RAP211(AP2EREBP)/colamp-RAP211-DAP-Seq(GSE60143)/Homer RGCCGGCYWW 1e0 0.000e+00 1.0000 0.0 0.00% 388.7 9.70% +RAP212(AP2EREBP)/col-RAP212-DAP-Seq(GSE60143)/Homer CGCCGCCATTTT 1e0 0.000e+00 1.0000 0.0 0.00% 128.7 3.21% +RAP21(AP2EREBP)/colamp-RAP21-DAP-Seq(GSE60143)/Homer BCACCGACAHNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RAP26(AP2EREBP)/colamp-RAP26-DAP-Seq(GSE60143)/Homer HDATGGCGGCGG 1e0 0.000e+00 1.0000 0.0 0.00% 492.2 12.28% +RAV1(RAV)/colamp-RAV1-DAP-Seq(GSE60143)/Homer TWWTTTCTGTTG 1e0 0.000e+00 1.0000 0.0 0.00% 400.4 9.99% +REM16(ABI3VP1)/col-REM16-DAP-Seq(GSE60143)/Homer DTTTTTSCCGSMAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +REM19(REM)/colamp-REM19-DAP-Seq(GSE60143)/Homer AAAAAAAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Replumless(BLH)/Arabidopsis-RPL.GFP-ChIP-Seq(GSE78727)/Homer HGTCWHATCA 1e0 0.000e+00 1.0000 0.0 0.00% 170.0 4.24% +RRTF1(AP2EREBP)/colamp-RRTF1-DAP-Seq(GSE60143)/Homer CCGCCGCHATTT 1e0 0.000e+00 1.0000 0.0 0.00% 229.4 5.72% +SEP3(MADS)/Arabidoposis-Flower-Sep3-ChIP-Seq/Homer CCAAAAAGGG 1e0 0.000e+00 1.0000 0.0 0.00% 521.7 13.02% +SGR5(C2H2)/colamp-SGR5-DAP-Seq(GSE60143)/Homer TTTGTCTTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 148.8 3.71% +SHN3(AP2EREBP)/col-SHN3-DAP-Seq(GSE60143)/Homer CCGCCGCC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SMB(NAC)/colamp-SMB-DAP-Seq(GSE60143)/Homer CTTVNNNNDBAAGHW 1e0 0.000e+00 1.0000 0.0 0.00% 413.5 10.32% +SND2(NAC)/colamp-SND2-DAP-Seq(GSE60143)/Homer CTTVWNNNWBAAGNW 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +SND3(NAC)/col-SND3-DAP-Seq(GSE60143)/Homer CTTNHNNNDNAAGNH 1e0 0.000e+00 1.0000 0.0 0.00% 411.7 10.27% +SOC1(MADS)/Seedling-SOC1-ChIP-Seq(GSE45846)/Homer TWCCAWWTWTGG 1e0 0.000e+00 1.0000 0.0 0.00% 291.5 7.27% +SPCH(bHLH)/Seedling-SPCH-ChIP-Seq(GSE57497)/Homer WNBCACGTGA 1e0 0.000e+00 1.0000 0.0 0.00% 145.1 3.62% +SPL11(SBP)/col100-SPL11-DAP-Seq(GSE60143)/Homer YTGTACTTBH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SPL3(SBP)/colamp-SPL3-DAP-Seq(GSE60143)/Homer WDTTGTACGGAH 1e0 0.000e+00 1.0000 0.0 0.00% 184.7 4.61% +SPL9(SBP)/colamp-SPL9-DAP-Seq(GSE60143)/Homer BTGTACTT 1e0 0.000e+00 1.0000 0.0 0.00% 726.4 18.12% +SRS7(SRS)/colamp-SRS7-DAP-Seq(GSE60143)/Homer HATAGGTTTH 1e0 0.000e+00 1.0000 0.0 0.00% 531.5 13.26% +STOP1(C2H2)/colamp-STOP1-DAP-Seq(GSE60143)/Homer DTATCTGGKGRAGGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +SVP(MADS)/col-SVP-DAP-Seq(GSE60143)/Homer ANTTWCCHAATTTGG 1e0 0.000e+00 1.0000 0.0 0.00% 272.2 6.79% +TCP16(TCP)/colamp-TCP16-DAP-Seq(GSE60143)/Homer GTGGDCCYNNNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TCP17(TCP)/col-TCP17-DAP-Seq(GSE60143)/Homer GTGGTCCCCA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TCP1(TCP)/col-TCP1-DAP-Seq(GSE60143)/Homer GGGGGCCCMMCN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TCP20(TCP)/col-TCP20-DAP-Seq(GSE60143)/Homer GGDCCCAC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TCP3(TCP)/colamp-TCP3-DAP-Seq(GSE60143)/Homer WGTGGTCCCAAHWWW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TCP7(TCP)/col-TCP7-DAP-Seq(GSE60143)/Homer GTGGGSCCCACHHNN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TF3A(C2H2)/col-TF3A-DAP-Seq(GSE60143)/Homer NNDDGAGGAGGWNNN 1e0 0.000e+00 1.0000 0.0 0.00% 393.2 9.81% +TGA10(bZIP)/colamp-TGA10-DAP-Seq(GSE60143)/Homer ATGACGTC 1e0 0.000e+00 1.0000 0.0 0.00% 126.3 3.15% +TGA1(bZIP)/colamp-TGA1-DAP-Seq(GSE60143)/Homer TGACGTCAKC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TGA2(bZIP)/colamp-TGA2-DAP-Seq(GSE60143)/Homer ACGTCAYCHH 1e0 0.000e+00 1.0000 0.0 0.00% 460.1 11.48% +TGA3(bZIP)/colamp-TGA3-DAP-Seq(GSE60143)/Homer WTGATGACGTCATCW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TGA4(bZIP)/colamp-TGA4-DAP-Seq(GSE60143)/Homer RTGACGTCAKCW 1e0 0.000e+00 1.0000 0.0 0.00% 267.1 6.66% +TGA5(bZIP)/col-TGA5-DAP-Seq(GSE60143)/Homer NNGATGACGTCATCN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TGA6(bZIP)/colamp-TGA6-DAP-Seq(GSE60143)/Homer TGACGTCABC 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TGA9(bZIP)/colamp-TGA9-DAP-Seq(GSE60143)/Homer VTGACGTC 1e0 0.000e+00 1.0000 0.0 0.00% 608.3 15.18% +TINY(AP2EREBP)/col-TINY-DAP-Seq(GSE60143)/Homer NNCACCGACA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TRP2(MYBrelated)/colamp-TRP2-DAP-Seq(GSE60143)/Homer TAAACCCT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TSO1(CPP)/col-TSO1-DAP-Seq(GSE60143)/Homer RAATTTRAAW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Unknown2/Arabidopsis-Promoters/Homer AAACGACGTCGTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +Unknown3/Arabidopsis-Promoters/Homer AYTAAACCGG 1e0 0.000e+00 1.0000 0.0 0.00% 111.9 2.79% +Unknown4/Arabidopsis-Promoters/Homer CKTCKTCTTY 1e0 0.000e+00 1.0000 0.0 0.00% 152.7 3.81% +Unknown1/Arabidopsis-Promoters/Homer RGGGTAWWWTHGTAA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +VIP1(bZIP)/col-VIP1-DAP-Seq(GSE60143)/Homer NTTGACAGCTGTCAN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +VND1(NAC)/col-VND1-DAP-Seq(GSE60143)/Homer CTTRWDNHWYAAGYW 1e0 0.000e+00 1.0000 0.0 0.00% 249.8 6.23% +VND2(NAC)/col-VND2-DAP-Seq(GSE60143)/Homer DNCKTNNNNNNNAAG 1e0 0.000e+00 1.0000 0.0 0.00% 411.7 10.27% +VND3(NAC)/colamp-VND3-DAP-Seq(GSE60143)/Homer TRCTTGWDNHWCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 249.8 6.23% +VND4(NAC)/colamp-VND4-DAP-Seq(GSE60143)/Homer WRCTTGWANWWCAAG 1e0 0.000e+00 1.0000 0.0 0.00% 24.2 0.60% +VND6(NAC)/col-VND6-DAP-Seq(GSE60143)/Homer DCTTNHTTTTYAMGY 1e0 0.000e+00 1.0000 0.0 0.00% 411.7 10.27% +VRN1(ABI3VP1)/col-VRN1-DAP-Seq(GSE60143)/Homer TTTTTTTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +WIP5(C2H2)/colamp-WIP5-DAP-Seq(GSE60143)/Homer TDTTCTCMAGGT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +WRKY11(WRKY)/col-WRKY11-DAP-Seq(GSE60143)/Homer SCGTTGACTTTN 1e0 0.000e+00 1.0000 0.0 0.00% 458.9 11.45% +WRKY14(WRKY)/colamp-WRKY14-DAP-Seq(GSE60143)/Homer NCGTTGACTTTN 1e0 0.000e+00 1.0000 0.0 0.00% 985.0 24.58% +WRKY15(WRKY)/col-WRKY15-DAP-Seq(GSE60143)/Homer VGTTGACTWW 1e0 0.000e+00 1.0000 0.0 0.00% 994.3 24.81% +WRKY17(WRKY)/colamp-WRKY17-DAP-Seq(GSE60143)/Homer GCGTTGACTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +WRKY18(WRKY)/col-WRKY18-DAP-Seq(GSE60143)/Homer NNNTTGACYWNNNNN 1e0 0.000e+00 1.0000 0.0 0.00% 1383.6 34.52% +WRKY20(WRKY)/col-WRKY20-DAP-Seq(GSE60143)/Homer CKTTGACYWD 1e0 0.000e+00 1.0000 0.0 0.00% 1200.8 29.96% +WRKY21(WRKY)/colamp-WRKY21-DAP-Seq(GSE60143)/Homer DCGTTGACTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 163.7 4.08% +WRKY22(WRKY)/colamp-WRKY22-DAP-Seq(GSE60143)/Homer WWAAAGTCAACK 1e0 0.000e+00 1.0000 0.0 0.00% 1212.5 30.25% +WRKY24(WRKY)/colamp-WRKY24-DAP-Seq(GSE60143)/Homer CGTTGACTWW 1e0 0.000e+00 1.0000 0.0 0.00% 1200.8 29.96% +WRKY25(WRKY)/colamp-WRKY25-DAP-Seq(GSE60143)/Homer NNNNHRGTCAAMNNN 1e0 0.000e+00 1.0000 0.0 0.00% 1184.0 29.54% +WRKY26(WRKY)/colamp-WRKY26-DAP-Seq(GSE60143)/Homer CGTTGACTWDKN 1e0 0.000e+00 1.0000 0.0 0.00% 986.9 24.62% +WRKY27(WRKY)/colamp-WRKY27-DAP-Seq(GSE60143)/Homer NHGTTGACYTWD 1e0 0.000e+00 1.0000 0.0 0.00% 1690.0 42.16% +WRKY28(WRKY)/col-WRKY28-DAP-Seq(GSE60143)/Homer BGTTGACTWH 1e0 0.000e+00 1.0000 0.0 0.00% 1421.0 35.45% +WRKY29(WRKY)/colamp-WRKY29-DAP-Seq(GSE60143)/Homer MGTTGACTTT 1e0 0.000e+00 1.0000 0.0 0.00% 1421.0 35.45% +WRKY30(WRKY)/colamp-WRKY30-DAP-Seq(GSE60143)/Homer CGTTGACTTN 1e0 0.000e+00 1.0000 0.0 0.00% 718.2 17.92% +WRKY31(WRKY)/colamp-WRKY31-DAP-Seq(GSE60143)/Homer NCGTTGACTWWK 1e0 0.000e+00 1.0000 0.0 0.00% 1113.8 27.79% +WRKY33(WRKY)/col-WRKY33-DAP-Seq(GSE60143)/Homer CGTTGACYAW 1e0 0.000e+00 1.0000 0.0 0.00% 1125.0 28.07% +WRKY3(WRKY)/col-WRKY3-DAP-Seq(GSE60143)/Homer NCKTTGACYDDN 1e0 0.000e+00 1.0000 0.0 0.00% 1214.4 30.30% +WRKY40(WRKY)/colamp-WRKY40-DAP-Seq(GSE60143)/Homer AHWAGTCAAC 1e0 0.000e+00 1.0000 0.0 0.00% 994.3 24.81% +WRKY42(WRKY)/colamp-WRKY42-DAP-Seq(GSE60143)/Homer NAAAGTCAACGN 1e0 0.000e+00 1.0000 0.0 0.00% 547.1 13.65% +WRKY43(WRKY)/colamp-WRKY43-DAP-Seq(GSE60143)/Homer NCGTTGACTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 733.1 18.29% +WRKY45(WRKY)/col-WRKY45-DAP-Seq(GSE60143)/Homer HNNNKTTGACTWWNH 1e0 0.000e+00 1.0000 0.0 0.00% 723.8 18.06% +WRKY46(WRKY)/colamp-WRKY46-DAP-Seq(GSE60143)/Homer AAAGTCAACGSN 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +WRKY47(WRKY)/colamp-WRKY47-DAP-Seq(GSE60143)/Homer WAAGTCAACGBT 1e0 0.000e+00 1.0000 0.0 0.00% 712.6 17.78% +WRKY50(WRKY)/col-WRKY50-DAP-Seq(GSE60143)/Homer NNTTGACTWNNGNNN 1e0 0.000e+00 1.0000 0.0 0.00% 1178.4 29.40% +WRKY55(WRKY)/col-WRKY55-DAP-Seq(GSE60143)/Homer NCGTTGACTT 1e0 0.000e+00 1.0000 0.0 0.00% 1057.5 26.38% +WRKY65(WRKY)/colamp-WRKY65-DAP-Seq(GSE60143)/Homer AWWWAGTCAACG 1e0 0.000e+00 1.0000 0.0 0.00% 927.3 23.14% +WRKY6(WRKY)/colamp-WRKY6-DAP-Seq(GSE60143)/Homer NCGTTGACTWWD 1e0 0.000e+00 1.0000 0.0 0.00% 1113.8 27.79% +WRKY71(WRKY)/col-WRKY71-DAP-Seq(GSE60143)/Homer CKTTGACYWW 1e0 0.000e+00 1.0000 0.0 0.00% 994.3 24.81% +WRKY75(WRKY)/col-WRKY75-DAP-Seq(GSE60143)/Homer CGTTGACTWW 1e0 0.000e+00 1.0000 0.0 0.00% 1331.5 33.22% +WRKY7(WRKY)/colamp-WRKY7-DAP-Seq(GSE60143)/Homer AAAAGTCAACGSHWD 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +WRKY8(WRKY)/colamp-WRKY8-DAP-Seq(GSE60143)/Homer CGTTGACTTT 1e0 0.000e+00 1.0000 0.0 0.00% 276.1 6.89% +WUS1(Homeobox)/colamp-WUS1-DAP-Seq(GSE60143)/Homer CAWTCATTCA 1e0 0.000e+00 1.0000 0.0 0.00% 372.7 9.30% +ZIM(C2C2gata)/col-ZIM-DAP-Seq(GSE60143)/Homer ATCSRACGGTYRAGA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZML1(C2C2gata)/colamp-ZML1-DAP-Seq(GSE60143)/Homer ATCWYRACCGTTSRW 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ZML2(C2C2gata)/col-ZML2-DAP-Seq(GSE60143)/Homer CATCATCATC 1e0 0.000e+00 1.0000 0.0 0.00% 167.7 4.18% +CELF2(RRM)/JSL1-CELF2-CLIP-Seq(GSE71264)/Homer RGTGTCAG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer TGCATGCA 1e0 0.000e+00 1.0000 0.0 0.00% 496.1 12.38% +CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer AAATTSAATTTN 1e0 0.000e+00 1.0000 0.0 0.00% 258.9 6.46% +EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer TGCAARYGCGCTCYA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer AWTGATAAGA 1e0 0.000e+00 1.0000 0.0 0.00% 476.4 11.89% +GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer CCGACAYYTYACGGG 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer RACAGCTGTTBH 1e0 0.000e+00 1.0000 0.0 0.00% 168.1 4.19% +LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer CARTGGAGCGCRYTTGCATT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer ATGATTRATG 1e0 0.000e+00 1.0000 0.0 0.00% 1057.3 26.38% +PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer KTGTTTGC 1e0 0.000e+00 1.0000 0.0 0.00% 613.0 15.29% +PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer ACTGATAAGA 1e0 0.000e+00 1.0000 0.0 0.00% 601.6 15.01% +ABF1/SacCer-Promoters/Homer CGTRNAAARTGA 1e0 0.000e+00 1.0000 0.0 0.00% 83.7 2.09% +Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer TCACGTGAYH 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +GAGA-repeat/SacCer-Promoters/Homer CTYTCTYTCTCTCTC 1e0 0.000e+00 1.0000 0.0 0.00% 974.9 24.32% +Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer CCCACGTGCT 1e0 0.000e+00 1.0000 0.0 0.00% 41.0 1.02% +Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer AAGCACGTGBGD 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +REB1/SacCer-Promoters/Homer KCCGGGTAAYRR 1e0 0.000e+00 1.0000 0.0 0.00% 223.9 5.59% +RLR1?/SacCer-Promoters/Homer WTTTTCYYTTTT 1e0 0.000e+00 1.0000 0.0 0.00% 347.0 8.66% +SFP1/SacCer-Promoters/Homer DDAAAAATTTTY 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TATA-box/SacCer-Promoters/Homer BBHWTATATA 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00% +TOD6?/SacCer-Promoters/Homer GCGATGAGMT 1e0 0.000e+00 1.0000 0.0 0.00% 0.0 0.00%
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/motifFindingParameters.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,1 @@ +cmd = test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/seq.autonorm.tsv Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,85 @@ +Oligo TargetCounts BackgroundCounts NormalizationFactor +A 50.00% 28.55% 1.752 +C 50.00% 21.45% 2.331 +G 50.00% 21.45% 2.331 +T 50.00% 28.55% 1.752 +AA 50.00% 9.36% 5.343 +CA 50.00% 6.88% 7.271 +GA 50.00% 6.29% 7.951 +TA 50.00% 6.02% 8.305 +AC 50.00% 5.29% 9.450 +CC 50.00% 4.09% 12.224 +GC 50.00% 5.78% 8.644 +TC 50.00% 6.29% 7.951 +AG 50.00% 6.21% 8.053 +CG 50.00% 4.27% 11.696 +GG 50.00% 4.09% 12.224 +TG 50.00% 6.88% 7.271 +AT 50.00% 7.69% 6.499 +CT 50.00% 6.21% 8.053 +GT 50.00% 5.29% 9.450 +TT 50.00% 9.36% 5.343 +AAA 50.00% 3.00% 16.681 +CAA 50.00% 2.20% 22.680 +GAA 50.00% 1.98% 25.245 +TAA 50.00% 2.18% 22.960 +ACA 50.00% 1.18% 42.245 +CCA 50.00% 1.70% 29.393 +GCA 50.00% 1.65% 30.319 +TCA 50.00% 2.34% 21.350 +AGA 50.00% 1.81% 27.551 +CGA 50.00% 1.08% 46.235 +GGA 50.00% 1.05% 47.776 +TGA 50.00% 2.34% 21.350 +ATA 50.00% 1.81% 27.573 +CTA 50.00% 0.98% 50.945 +GTA 50.00% 1.05% 47.770 +TTA 50.00% 2.18% 22.960 +AAC 50.00% 2.00% 25.034 +CAC 50.00% 0.94% 52.984 +GAC 50.00% 1.30% 38.363 +TAC 50.00% 1.05% 47.770 +ACC 50.00% 1.52% 32.917 +CCC 50.00% 0.47% 105.420 +GCC 50.00% 1.05% 47.646 +TCC 50.00% 1.05% 47.776 +AGC 50.00% 1.87% 26.722 +CGC 50.00% 1.21% 41.155 +GGC 50.00% 1.05% 47.646 +TGC 50.00% 1.65% 30.319 +ATC 50.00% 1.61% 30.994 +CTC 50.00% 1.39% 35.864 +GTC 50.00% 1.30% 38.363 +TTC 50.00% 1.98% 25.245 +AAG 50.00% 2.09% 23.947 +CAG 50.00% 1.74% 28.691 +GAG 50.00% 1.39% 35.864 +TAG 50.00% 0.98% 50.945 +ACG 50.00% 1.19% 42.093 +CCG 50.00% 0.79% 63.182 +GCG 50.00% 1.21% 41.155 +TCG 50.00% 1.08% 46.235 +AGG 50.00% 1.12% 44.508 +CGG 50.00% 0.79% 63.182 +GGG 50.00% 0.47% 105.420 +TGG 50.00% 1.70% 29.393 +ATG 50.00% 1.99% 25.159 +CTG 50.00% 1.74% 28.691 +GTG 50.00% 0.94% 52.984 +TTG 50.00% 2.20% 22.680 +AAT 50.00% 2.28% 21.947 +CAT 50.00% 1.99% 25.159 +GAT 50.00% 1.61% 30.994 +TAT 50.00% 1.81% 27.573 +ACT 50.00% 1.40% 35.701 +CCT 50.00% 1.12% 44.508 +GCT 50.00% 1.87% 26.722 +TCT 50.00% 1.81% 27.551 +AGT 50.00% 1.40% 35.701 +CGT 50.00% 1.19% 42.093 +GGT 50.00% 1.52% 32.917 +TGT 50.00% 1.18% 42.245 +ATT 50.00% 2.28% 21.947 +CTT 50.00% 2.09% 23.947 +GTT 50.00% 2.00% 25.034 +TTT 50.00% 3.00% 16.681
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX_nothing.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,2 @@ +PeakID (cmd=annotatePeaks.pl test-data/fake_phix_peaks.bed none) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type +1 phiX174 1401 1500 + 0 NA NA NA NA NA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiXcpg.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,2 @@ +PeakID (cmd=annotatePeaks.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta -CpG) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type CpG% GC% +1 phiX174 1401 1500 + 0 NA NA NA NA NA 0.060606 0.470000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scanMotif_res1.bed Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,1 @@ +phiX174 1449 1460 1-ATGAGCTTAATC,BestGuess:Oc 12.355433 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scanMotif_res1.txt Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,1 @@ +1-ATGAGCTTAATC,BestGuess:Oc/dmmpmm(Noyes_hd)/fly(0.654)-1 phiX174 1449 1460 + 12.355433 ATGAGCTTAATC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.gtf Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,221 @@ +#!genome-build GRCm38.p6 +#!genome-version GRCm38 +#!genome-date 2012-01 +#!genome-build-accession NCBI:GCA_000001635.8 +#!genebuild-last-updated 2020-02 +chr2 ensembl_havana gene 74668310 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; +chr2 ensembl_havana transcript 74668310 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74668310 74669078 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000336629"; exon_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74668310 74669078 . + 0 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74668310 74668312 . + 0 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74669886 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000601614"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74669886 74670133 . + 2 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74670134 74670136 . + 0 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74670137 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74675013 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; +chr2 ensembl_havana transcript 74675013 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74675013 74675654 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "1"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; exon_id "ENSMUSE00000166083"; exon_version "5"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74675087 74675654 . + 0 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "1"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; protein_id "ENSMUSP00000001878"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74675087 74675089 . + 0 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "1"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74675814 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "2"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; exon_id "ENSMUSE00000359408"; exon_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74675814 74676049 . + 2 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "2"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; protein_id "ENSMUSP00000001878"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74676050 74676052 . + 0 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "2"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74675013 74675086 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74676053 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74679557 74687016 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; +chr2 havana transcript 74679557 74687016 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000048086"; transcript_version "8"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040002"; havana_transcript_version "5"; transcript_support_level "1"; +chr2 havana exon 74679557 74679809 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000048086"; transcript_version "8"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040002"; havana_transcript_version "5"; exon_id "ENSMUSE00000843165"; exon_version "3"; transcript_support_level "1"; +chr2 havana exon 74683903 74687016 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000048086"; transcript_version "8"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040002"; havana_transcript_version "5"; exon_id "ENSMUSE00000330347"; exon_version "4"; transcript_support_level "1"; +chr2 ensembl_havana transcript 74682323 74684168 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74682323 74683167 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; exon_id "ENSMUSE00000404559"; exon_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74682393 74683167 . + 0 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; protein_id "ENSMUSP00000122582"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74682393 74682395 . + 0 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74683903 74684168 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; exon_id "ENSMUSE00000746167"; exon_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74683903 74684135 . + 2 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; protein_id "ENSMUSP00000122582"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74684136 74684138 . + 0 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74682323 74682392 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74684139 74684168 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana gene 74683446 74694194 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; +chr2 havana transcript 74683446 74694194 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74683446 74683509 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; exon_number "1"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; exon_id "ENSMUSE00000731883"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74683903 74684357 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; exon_number "2"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; exon_id "ENSMUSE00000774488"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74694091 74694194 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; exon_number "3"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; exon_id "ENSMUSE00000858519"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl_havana gene 74691924 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; +chr2 ensembl_havana transcript 74691924 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74691924 74692724 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "1"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; exon_id "ENSMUSE00000341264"; exon_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74691980 74692724 . + 0 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "1"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; protein_id "ENSMUSP00000062412"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74691980 74691982 . + 0 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "1"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74694091 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "2"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; exon_id "ENSMUSE00000343683"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74694091 74694365 . + 2 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "2"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; protein_id "ENSMUSP00000062412"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74694366 74694368 . + 0 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "2"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74691924 74691979 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74694369 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana gene 74695520 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; +chr2 havana transcript 74695520 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000126966"; transcript_version "7"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-201"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040005"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74695520 74695732 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000126966"; transcript_version "7"; exon_number "1"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-201"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040005"; havana_transcript_version "3"; exon_id "ENSMUSE00000756210"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74697031 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000126966"; transcript_version "7"; exon_number "2"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-201"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040005"; havana_transcript_version "3"; exon_id "ENSMUSE00000777033"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana transcript 74695601 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000152027"; transcript_version "2"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-202"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040006"; havana_transcript_version "3"; transcript_support_level "2"; +chr2 havana exon 74695601 74695727 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000152027"; transcript_version "2"; exon_number "1"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-202"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040006"; havana_transcript_version "3"; exon_id "ENSMUSE00000772112"; exon_version "1"; transcript_support_level "2"; +chr2 havana exon 74697031 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000152027"; transcript_version "2"; exon_number "2"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-202"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040006"; havana_transcript_version "3"; exon_id "ENSMUSE00000777033"; exon_version "1"; transcript_support_level "2"; +chr2 havana gene 74696768 74697586 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; +chr2 havana transcript 74696768 74697586 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; transcript_id "ENSMUST00000190845"; transcript_version "1"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; transcript_name "Gm28793-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000119840"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74697248 74697586 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; transcript_id "ENSMUST00000190845"; transcript_version "1"; exon_number "1"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; transcript_name "Gm28793-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000119840"; havana_transcript_version "1"; exon_id "ENSMUSE00001327914"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74696768 74696841 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; transcript_id "ENSMUST00000190845"; transcript_version "1"; exon_number "2"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; transcript_name "Gm28793-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000119840"; havana_transcript_version "1"; exon_id "ENSMUSE00001329539"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl_havana gene 74697727 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; +chr2 ensembl_havana transcript 74697727 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74697727 74698833 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "1"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; exon_id "ENSMUSE00000385196"; exon_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74698056 74698833 . + 0 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "1"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; protein_id "ENSMUSP00000058490"; protein_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74698056 74698058 . + 0 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "1"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74699180 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "2"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; exon_id "ENSMUSE00000351804"; exon_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74699180 74699418 . + 2 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "2"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; protein_id "ENSMUSP00000058490"; protein_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74699419 74699421 . + 0 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "2"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74697727 74698055 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74699422 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl gene 74701006 74701142 . - . gene_id "ENSMUSG00000104570"; gene_version "1"; gene_name "Gm44463"; gene_source "ensembl"; gene_biotype "miRNA"; +chr2 ensembl transcript 74701006 74701142 . - . gene_id "ENSMUSG00000104570"; gene_version "1"; transcript_id "ENSMUST00000198895"; transcript_version "1"; gene_name "Gm44463"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "Gm44463-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA"; +chr2 ensembl exon 74701006 74701142 . - . gene_id "ENSMUSG00000104570"; gene_version "1"; transcript_id "ENSMUST00000198895"; transcript_version "1"; exon_number "1"; gene_name "Gm44463"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "Gm44463-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; exon_id "ENSMUSE00001352249"; exon_version "1"; tag "basic"; transcript_support_level "NA"; +chr2 ensembl_havana gene 74703248 74716130 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; +chr2 havana transcript 74703248 74712054 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000132326"; transcript_version "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040117"; havana_transcript_version "1"; transcript_support_level "3"; +chr2 havana exon 74711970 74712054 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000132326"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040117"; havana_transcript_version "1"; exon_id "ENSMUSE00000793320"; exon_version "1"; transcript_support_level "3"; +chr2 havana exon 74703248 74703622 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000132326"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040117"; havana_transcript_version "1"; exon_id "ENSMUSE00000821641"; exon_version "1"; transcript_support_level "3"; +chr2 ensembl_havana transcript 74710043 74712526 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000156342"; transcript_version "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-204"; transcript_source "ensembl_havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040116"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74711970 74712526 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000156342"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-204"; transcript_source "ensembl_havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040116"; havana_transcript_version "1"; exon_id "ENSMUSE00000842711"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74710043 74710281 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000156342"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-204"; transcript_source "ensembl_havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040116"; havana_transcript_version "1"; exon_id "ENSMUSE00000734798"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana transcript 74710193 74715996 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74715706 74715996 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; exon_id "ENSMUSE00000743618"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74714271 74714401 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; exon_id "ENSMUSE00000733703"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74710193 74710281 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; exon_number "3"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; exon_id "ENSMUSE00000841303"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana transcript 74713126 74716130 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000139005"; transcript_version "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-202"; transcript_source "ensembl_havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040115"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74715706 74716130 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000139005"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-202"; transcript_source "ensembl_havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040115"; havana_transcript_version "1"; exon_id "ENSMUSE00000734469"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74713126 74714401 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000139005"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-202"; transcript_source "ensembl_havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040115"; havana_transcript_version "1"; exon_id "ENSMUSE00000862774"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74704615 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; +chr2 havana transcript 74704615 74706812 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana exon 74704615 74704724 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; exon_id "ENSMUSE00000819713"; exon_version "1"; tag "basic"; transcript_support_level "2"; +chr2 havana exon 74705971 74706118 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; exon_id "ENSMUSE00000690072"; exon_version "1"; tag "basic"; transcript_support_level "2"; +chr2 havana CDS 74706094 74706118 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; protein_id "ENSMUSP00000118904"; protein_version "2"; tag "basic"; transcript_support_level "2"; +chr2 havana start_codon 74706094 74706096 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana exon 74706514 74706812 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; exon_id "ENSMUSE00000729425"; exon_version "1"; tag "basic"; transcript_support_level "2"; +chr2 havana CDS 74706514 74706809 . + 2 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; protein_id "ENSMUSP00000118904"; protein_version "2"; tag "basic"; transcript_support_level "2"; +chr2 havana stop_codon 74706810 74706812 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana five_prime_utr 74704615 74704724 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana five_prime_utr 74705971 74706093 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 ensembl_havana transcript 74704905 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74704905 74706118 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; exon_id "ENSMUSE00000387604"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74705548 74706118 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; protein_id "ENSMUSP00000019749"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74705548 74705550 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74706514 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; exon_id "ENSMUSE00000749776"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74706514 74706809 . + 2 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; protein_id "ENSMUSP00000019749"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74706810 74706812 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74704905 74705547 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74706813 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana transcript 74705152 74707307 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74705152 74706118 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; exon_id "ENSMUSE00000690069"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74705548 74706118 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; protein_id "ENSMUSP00000088094"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 havana start_codon 74705548 74705550 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74706517 74707307 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; exon_id "ENSMUSE00000690067"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74706517 74706809 . + 2 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; protein_id "ENSMUSP00000088094"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 havana stop_codon 74706810 74706812 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana five_prime_utr 74705152 74705547 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74706813 74707307 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74711927 74748442 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; +chr2 ensembl_havana transcript 74711927 74748271 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74711927 74712316 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; exon_id "ENSMUSE00001334697"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74743928 74744555 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; exon_id "ENSMUSE00001328611"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74744012 74744555 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; protein_id "ENSMUSP00000107614"; protein_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74744012 74744014 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74746322 74748271 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; exon_id "ENSMUSE00000690056"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74746322 74747076 . + 2 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; protein_id "ENSMUSP00000107614"; protein_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74747077 74747079 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74711927 74712316 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74743928 74744011 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74747080 74748271 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 havana transcript 74732913 74744214 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana exon 74732913 74733040 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; exon_id "ENSMUSE00000729707"; exon_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana exon 74743928 74744214 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; exon_id "ENSMUSE00000710772"; exon_version "2"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana CDS 74744012 74744214 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; protein_id "ENSMUSP00000134633"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana start_codon 74744012 74744014 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana five_prime_utr 74732913 74733040 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana five_prime_utr 74743928 74744011 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000144544"; transcript_version "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-205"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040125"; havana_transcript_version "5"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana transcript 74736515 74747915 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74736515 74736705 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; exon_id "ENSMUSE00000690055"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74743928 74744555 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; exon_id "ENSMUSE00001328611"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74744012 74744555 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; protein_id "ENSMUSP00000107613"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana start_codon 74744012 74744014 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74746322 74747915 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; exon_id "ENSMUSE00000690054"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74746322 74747076 . + 2 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; protein_id "ENSMUSP00000107613"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana stop_codon 74747077 74747079 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana five_prime_utr 74736515 74736705 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana five_prime_utr 74743928 74744011 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74747080 74747915 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111982"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040123"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana transcript 74739619 74747900 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74739619 74739703 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; exon_id "ENSMUSE00000690052"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74743928 74744555 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; exon_id "ENSMUSE00001328611"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana CDS 74744012 74744555 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; protein_id "ENSMUSP00000044809"; protein_version "6"; tag "basic"; transcript_support_level "5"; +chr2 havana start_codon 74744012 74744014 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74746322 74747900 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; exon_id "ENSMUSE00000566207"; exon_version "2"; tag "basic"; transcript_support_level "5"; +chr2 havana CDS 74746322 74747076 . + 2 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; protein_id "ENSMUSP00000044809"; protein_version "6"; tag "basic"; transcript_support_level "5"; +chr2 havana stop_codon 74747077 74747079 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana five_prime_utr 74739619 74739703 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana five_prime_utr 74743928 74744011 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana three_prime_utr 74747080 74747900 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000047830"; transcript_version "7"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-201"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040124"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana transcript 74745674 74746596 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana exon 74745674 74746220 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; exon_id "ENSMUSE00000738733"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana CDS 74746157 74746220 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; protein_id "ENSMUSP00000134616"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana start_codon 74746157 74746159 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana exon 74746322 74746596 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; exon_id "ENSMUSE00000837851"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana CDS 74746322 74746596 . + 2 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; protein_id "ENSMUSP00000134616"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana five_prime_utr 74745674 74746156 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000140666"; transcript_version "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-204"; transcript_source "havana"; transcript_biotype "protein_coding"; havana_transcript "OTTMUST00000040126"; havana_transcript_version "3"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "3"; +chr2 havana transcript 74745722 74748442 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000190553"; transcript_version "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-206"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTMUST00000120192"; havana_transcript_version "1"; tag "mRNA_end_NF"; transcript_support_level "NA"; +chr2 havana exon 74745722 74748442 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000190553"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-206"; transcript_source "havana"; transcript_biotype "retained_intron"; havana_transcript "OTTMUST00000120192"; havana_transcript_version "1"; exon_id "ENSMUSE00001319756"; exon_version "1"; tag "mRNA_end_NF"; transcript_support_level "NA"; +chr2 ensembl_havana gene 74711929 74729160 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; +chr2 havana transcript 74711929 74728868 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; transcript_support_level "1"; +chr2 havana exon 74711929 74712316 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000690059"; exon_version "2"; transcript_support_level "1"; +chr2 havana exon 74722553 74722631 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00001456804"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74723332 74723367 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00001459290"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74725463 74725597 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "4"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000766717"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74725845 74725978 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "5"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000795268"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74726876 74726932 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "6"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000795377"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74728359 74728868 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "7"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000723430"; exon_version "2"; transcript_support_level "1"; +chr2 ensembl transcript 74721978 74729160 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl exon 74721978 74722177 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; exon_id "ENSMUSE00000330193"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl exon 74722553 74722631 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; exon_id "ENSMUSE00001456804"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl exon 74723332 74723367 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; exon_id "ENSMUSE00001459290"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl exon 74725463 74725978 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "4"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; exon_id "ENSMUSE00000330175"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl exon 74726876 74727705 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "5"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; exon_id "ENSMUSE00000476301"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl CDS 74727279 74727705 . + 0 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "5"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; protein_id "ENSMUSP00000047949"; protein_version "3"; tag "basic"; transcript_support_level "5"; +chr2 ensembl start_codon 74727279 74727281 . + 0 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "5"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl exon 74728262 74729160 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "6"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; exon_id "ENSMUSE00000479221"; exon_version "2"; tag "basic"; transcript_support_level "5"; +chr2 ensembl CDS 74728262 74728584 . + 2 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "6"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; protein_id "ENSMUSP00000047949"; protein_version "3"; tag "basic"; transcript_support_level "5"; +chr2 ensembl stop_codon 74728585 74728587 . + 0 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; exon_number "6"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl five_prime_utr 74721978 74722177 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl five_prime_utr 74722553 74722631 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl five_prime_utr 74723332 74723367 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl five_prime_utr 74725463 74725978 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl five_prime_utr 74726876 74727278 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 ensembl three_prime_utr 74728588 74729160 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000047904"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-201"; transcript_source "ensembl"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; tag "basic"; transcript_support_level "5"; +chr2 havana transcript 74727074 74729123 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74727074 74727705 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; exon_id "ENSMUSE00000690044"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74727279 74727705 . + 0 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; protein_id "ENSMUSP00000107611"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana start_codon 74727279 74727281 . + 0 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74728262 74729123 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; exon_id "ENSMUSE00000690043"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74728262 74728584 . + 2 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; protein_id "ENSMUSP00000107611"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana stop_codon 74728585 74728587 . + 0 gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana five_prime_utr 74727074 74727278 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74728588 74729123 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000111980"; transcript_version "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16145"; havana_transcript "OTTMUST00000040129"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 mirbase gene 74726070 74726137 . + . gene_id "ENSMUSG00000065500"; gene_version "3"; gene_name "Mir10b"; gene_source "mirbase"; gene_biotype "miRNA"; +chr2 mirbase transcript 74726070 74726137 . + . gene_id "ENSMUSG00000065500"; gene_version "3"; transcript_id "ENSMUST00000083566"; transcript_version "3"; gene_name "Mir10b"; gene_source "mirbase"; gene_biotype "miRNA"; transcript_name "Mir10b-201"; transcript_source "mirbase"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA"; +chr2 mirbase exon 74726070 74726137 . + . gene_id "ENSMUSG00000065500"; gene_version "3"; transcript_id "ENSMUST00000083566"; transcript_version "3"; exon_number "1"; gene_name "Mir10b"; gene_source "mirbase"; gene_biotype "miRNA"; transcript_name "Mir10b-201"; transcript_source "mirbase"; transcript_biotype "miRNA"; exon_id "ENSMUSE00000522725"; exon_version "3"; tag "basic"; transcript_support_level "NA"; +chr2 havana gene 74726728 74747918 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; +chr2 havana transcript 74726728 74747918 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74726728 74727705 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "1"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; exon_id "ENSMUSE00000644413"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74727279 74727705 . + 0 gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "1"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; protein_id "ENSMUSP00000051355"; protein_version "6"; tag "basic"; transcript_support_level "1"; +chr2 havana start_codon 74727279 74727281 . + 0 gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "1"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74728359 74728682 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "2"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; exon_id "ENSMUSE00000644412"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74728359 74728363 . + 2 gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "2"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; protein_id "ENSMUSP00000051355"; protein_version "6"; tag "basic"; transcript_support_level "1"; +chr2 havana stop_codon 74728364 74728366 . + 0 gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "2"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74743928 74744555 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "3"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; exon_id "ENSMUSE00001323912"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74746322 74747918 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "4"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; exon_id "ENSMUSE00000601603"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana five_prime_utr 74726728 74727278 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74728367 74728682 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74743928 74744555 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74746322 74747918 . + . gene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_simplified.gtf Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,128 @@ +#!genome-build GRCm38.p6 +#!genome-version GRCm38 +#!genome-date 2012-01 +#!genome-build-accession NCBI:GCA_000001635.8 +#!genebuild-last-updated 2020-02 +chr2 ensembl_havana gene 74668310 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; +chr2 ensembl_havana transcript 74668310 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74668310 74669078 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000336629"; exon_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74668310 74669078 . + 0 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74668310 74668312 . + 0 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74669886 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000601614"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74669886 74670133 . + 2 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74670134 74670136 . + 0 gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74670137 74671599 . + . gene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74675013 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; +chr2 ensembl_havana transcript 74675013 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74675013 74675654 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "1"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; exon_id "ENSMUSE00000166083"; exon_version "5"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74675087 74675654 . + 0 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "1"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; protein_id "ENSMUSP00000001878"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74675087 74675089 . + 0 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "1"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74675814 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "2"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; exon_id "ENSMUSE00000359408"; exon_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74675814 74676049 . + 2 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "2"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; protein_id "ENSMUSP00000001878"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74676050 74676052 . + 0 gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; exon_number "2"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74675013 74675086 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74676053 74677705 . + . gene_id "ENSMUSG00000001823"; gene_version "5"; transcript_id "ENSMUST00000001878"; transcript_version "5"; gene_name "Hoxd12"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016555"; havana_gene_version "3"; transcript_name "Hoxd12-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38147"; havana_transcript "OTTMUST00000040008"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74679557 74687016 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; +chr2 havana transcript 74679557 74687016 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000048086"; transcript_version "8"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040002"; havana_transcript_version "5"; transcript_support_level "1"; +chr2 havana exon 74679557 74679809 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000048086"; transcript_version "8"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040002"; havana_transcript_version "5"; exon_id "ENSMUSE00000843165"; exon_version "3"; transcript_support_level "1"; +chr2 havana exon 74683903 74687016 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000048086"; transcript_version "8"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040002"; havana_transcript_version "5"; exon_id "ENSMUSE00000330347"; exon_version "4"; transcript_support_level "1"; +chr2 ensembl_havana transcript 74682323 74684168 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74682323 74683167 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; exon_id "ENSMUSE00000404559"; exon_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74682393 74683167 . + 0 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; protein_id "ENSMUSP00000122582"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74682393 74682395 . + 0 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "1"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74683903 74684168 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; exon_id "ENSMUSE00000746167"; exon_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74683903 74684135 . + 2 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; protein_id "ENSMUSP00000122582"; protein_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74684136 74684138 . + 0 gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; exon_number "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74682323 74682392 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74684139 74684168 . + . gene_id "ENSMUSG00000042499"; gene_version "13"; transcript_id "ENSMUST00000142312"; transcript_version "2"; gene_name "Hoxd11"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016551"; havana_gene_version "6"; transcript_name "Hoxd11-202"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16140"; havana_transcript "OTTMUST00000040001"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana gene 74683446 74694194 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; +chr2 havana transcript 74683446 74694194 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74683446 74683509 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; exon_number "1"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; exon_id "ENSMUSE00000731883"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74683903 74684357 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; exon_number "2"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; exon_id "ENSMUSE00000774488"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74694091 74694194 . + . gene_id "ENSMUSG00000099521"; gene_version "1"; transcript_id "ENSMUST00000136302"; transcript_version "2"; exon_number "3"; gene_name "Gm28309"; gene_source "havana"; gene_biotype "processed_transcript"; havana_gene "OTTMUSG00000049460"; havana_gene_version "1"; transcript_name "Gm28309-201"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000126087"; havana_transcript_version "1"; exon_id "ENSMUSE00000858519"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl_havana gene 74691924 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; +chr2 ensembl_havana transcript 74691924 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74691924 74692724 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "1"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; exon_id "ENSMUSE00000341264"; exon_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74691980 74692724 . + 0 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "1"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; protein_id "ENSMUSP00000062412"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74691980 74691982 . + 0 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "1"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74694091 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "2"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; exon_id "ENSMUSE00000343683"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74694091 74694365 . + 2 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "2"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; protein_id "ENSMUSP00000062412"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74694366 74694368 . + 0 gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; exon_number "2"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74691924 74691979 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74694369 74695105 . + . gene_id "ENSMUSG00000050368"; gene_version "4"; transcript_id "ENSMUST00000061745"; transcript_version "4"; gene_name "Hoxd10"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016554"; havana_gene_version "3"; transcript_name "Hoxd10-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16141"; havana_transcript "OTTMUST00000040007"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana gene 74695520 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; +chr2 havana transcript 74695520 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000126966"; transcript_version "7"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-201"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040005"; havana_transcript_version "3"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74695520 74695732 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000126966"; transcript_version "7"; exon_number "1"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-201"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040005"; havana_transcript_version "3"; exon_id "ENSMUSE00000756210"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74697031 74697365 . + . gene_id "ENSMUSG00000086077"; gene_version "7"; transcript_id "ENSMUST00000126966"; transcript_version "7"; exon_number "2"; gene_name "Gm14396"; gene_source "havana"; gene_biotype "lincRNA"; havana_gene "OTTMUSG00000037522"; havana_gene_version "2"; transcript_name "Gm14396-201"; transcript_source "havana"; transcript_biotype "lincRNA"; havana_transcript "OTTMUST00000040005"; havana_transcript_version "3"; exon_id "ENSMUSE00000777033"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana gene 74696768 74697586 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; +chr2 havana transcript 74696768 74697586 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; transcript_id "ENSMUST00000190845"; transcript_version "1"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; transcript_name "Gm28793-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000119840"; havana_transcript_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74697248 74697586 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; transcript_id "ENSMUST00000190845"; transcript_version "1"; exon_number "1"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; transcript_name "Gm28793-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000119840"; havana_transcript_version "1"; exon_id "ENSMUSE00001327914"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 havana exon 74696768 74696841 . - . gene_id "ENSMUSG00000100209"; gene_version "1"; transcript_id "ENSMUST00000190845"; transcript_version "1"; exon_number "2"; gene_name "Gm28793"; gene_source "havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000045856"; havana_gene_version "1"; transcript_name "Gm28793-201"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000119840"; havana_transcript_version "1"; exon_id "ENSMUSE00001329539"; exon_version "1"; tag "basic"; transcript_support_level "5"; +chr2 ensembl_havana gene 74697727 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; +chr2 ensembl_havana transcript 74697727 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74697727 74698833 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "1"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; exon_id "ENSMUSE00000385196"; exon_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74698056 74698833 . + 0 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "1"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; protein_id "ENSMUSP00000058490"; protein_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74698056 74698058 . + 0 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "1"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74699180 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "2"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; exon_id "ENSMUSE00000351804"; exon_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74699180 74699418 . + 2 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "2"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; protein_id "ENSMUSP00000058490"; protein_version "8"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74699419 74699421 . + 0 gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; exon_number "2"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74697727 74698055 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74699422 74700208 . + . gene_id "ENSMUSG00000043342"; gene_version "9"; transcript_id "ENSMUST00000059272"; transcript_version "9"; gene_name "Hoxd9"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016552"; havana_gene_version "4"; transcript_name "Hoxd9-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16142"; havana_transcript "OTTMUST00000040004"; havana_transcript_version "4"; tag "basic"; transcript_support_level "1"; +chr2 ensembl gene 74701006 74701142 . - . gene_id "ENSMUSG00000104570"; gene_version "1"; gene_name "Gm44463"; gene_source "ensembl"; gene_biotype "miRNA"; +chr2 ensembl transcript 74701006 74701142 . - . gene_id "ENSMUSG00000104570"; gene_version "1"; transcript_id "ENSMUST00000198895"; transcript_version "1"; gene_name "Gm44463"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "Gm44463-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA"; +chr2 ensembl exon 74701006 74701142 . - . gene_id "ENSMUSG00000104570"; gene_version "1"; transcript_id "ENSMUST00000198895"; transcript_version "1"; exon_number "1"; gene_name "Gm44463"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "Gm44463-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; exon_id "ENSMUSE00001352249"; exon_version "1"; tag "basic"; transcript_support_level "NA"; +chr2 ensembl_havana gene 74703248 74716130 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; +chr2 havana transcript 74710193 74715996 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74715706 74715996 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; exon_number "1"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; exon_id "ENSMUSE00000743618"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74714271 74714401 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; exon_number "2"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; exon_id "ENSMUSE00000733703"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74710193 74710281 . - . gene_id "ENSMUSG00000052371"; gene_version "5"; transcript_id "ENSMUST00000145799"; transcript_version "1"; exon_number "3"; gene_name "Hoxd3os1"; gene_source "ensembl_havana"; gene_biotype "antisense"; havana_gene "OTTMUSG00000016596"; havana_gene_version "1"; transcript_name "Hoxd3os1-203"; transcript_source "havana"; transcript_biotype "antisense"; havana_transcript "OTTMUST00000040114"; havana_transcript_version "1"; exon_id "ENSMUSE00000841303"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74704615 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; +chr2 havana transcript 74704615 74706812 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana exon 74704615 74704724 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; exon_id "ENSMUSE00000819713"; exon_version "1"; tag "basic"; transcript_support_level "2"; +chr2 havana exon 74705971 74706118 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; exon_id "ENSMUSE00000690072"; exon_version "1"; tag "basic"; transcript_support_level "2"; +chr2 havana CDS 74706094 74706118 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; protein_id "ENSMUSP00000118904"; protein_version "2"; tag "basic"; transcript_support_level "2"; +chr2 havana start_codon 74706094 74706096 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana exon 74706514 74706812 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; exon_id "ENSMUSE00000729425"; exon_version "1"; tag "basic"; transcript_support_level "2"; +chr2 havana CDS 74706514 74706809 . + 2 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; protein_id "ENSMUSP00000118904"; protein_version "2"; tag "basic"; transcript_support_level "2"; +chr2 havana stop_codon 74706810 74706812 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; exon_number "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana five_prime_utr 74704615 74704724 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 havana five_prime_utr 74705971 74706093 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000151380"; transcript_version "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS79809"; havana_transcript "OTTMUST00000040119"; havana_transcript_version "3"; tag "basic"; transcript_support_level "2"; +chr2 ensembl_havana transcript 74704905 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74704905 74706118 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; exon_id "ENSMUSE00000387604"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74705548 74706118 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; protein_id "ENSMUSP00000019749"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74705548 74705550 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74706514 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; exon_id "ENSMUSE00000749776"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74706514 74706809 . + 2 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; protein_id "ENSMUSP00000019749"; protein_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74706810 74706812 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74704905 74705547 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74706813 74707933 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000019749"; transcript_version "3"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16143"; havana_transcript "OTTMUST00000040000"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1"; +chr2 havana transcript 74705152 74707307 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74705152 74706118 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; exon_id "ENSMUSE00000690069"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74705548 74706118 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; protein_id "ENSMUSP00000088094"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 havana start_codon 74705548 74705550 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "1"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana exon 74706517 74707307 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; exon_id "ENSMUSE00000690067"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana CDS 74706517 74706809 . + 2 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; protein_id "ENSMUSP00000088094"; protein_version "4"; tag "basic"; transcript_support_level "1"; +chr2 havana stop_codon 74706810 74706812 . + 0 gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; exon_number "2"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana five_prime_utr 74705152 74705547 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 havana three_prime_utr 74706813 74707307 . + . gene_id "ENSMUSG00000027102"; gene_version "4"; transcript_id "ENSMUST00000074721"; transcript_version "5"; gene_name "Hoxd8"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000016550"; havana_gene_version "4"; transcript_name "Hoxd8-202"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS71077"; havana_transcript "OTTMUST00000040118"; havana_transcript_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74711927 74748442 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; +chr2 ensembl_havana transcript 74711927 74748271 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74711927 74712316 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "1"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; exon_id "ENSMUSE00001334697"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74743928 74744555 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; exon_id "ENSMUSE00001328611"; exon_version "1"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74744012 74744555 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; protein_id "ENSMUSP00000107614"; protein_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana start_codon 74744012 74744014 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "2"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana exon 74746322 74748271 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; exon_id "ENSMUSE00000690056"; exon_version "3"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana CDS 74746322 74747076 . + 2 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; protein_id "ENSMUSP00000107614"; protein_version "2"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana stop_codon 74747077 74747079 . + 0 gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; exon_number "3"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74711927 74712316 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana five_prime_utr 74743928 74744011 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana three_prime_utr 74747080 74748271 . + . gene_id "ENSMUSG00000079277"; gene_version "9"; transcript_id "ENSMUST00000111983"; transcript_version "8"; gene_name "Hoxd3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045589"; havana_gene_version "14"; transcript_name "Hoxd3-203"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS38149"; havana_transcript "OTTMUST00000040120"; havana_transcript_version "15"; tag "basic"; transcript_support_level "1"; +chr2 ensembl_havana gene 74711929 74729160 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; +chr2 havana transcript 74711929 74728868 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; transcript_support_level "1"; +chr2 havana exon 74711929 74712316 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000690059"; exon_version "2"; transcript_support_level "1"; +chr2 havana exon 74722553 74722631 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00001456804"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74723332 74723367 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00001459290"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74725463 74725597 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "4"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000766717"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74725845 74725978 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "5"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000795268"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74726876 74726932 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "6"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000795377"; exon_version "1"; transcript_support_level "1"; +chr2 havana exon 74728359 74728868 . + . gene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "7"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000723430"; exon_version "2"; transcript_support_level "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Mon Dec 13 15:13:33 2021 +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/homer_preparse.loc.sample Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,25 @@ +# homer_preparse.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Homer preparsed genomes. +# The file should include an one line entry for each index set. +# The path points to the "directory" for the set, not a specific file. +# It has six text columns seperated by TABS. +# +# <unique_preparse_id> <dbkey> <mask> <size> <display_name> <directory_path> <path_fasta> <version> +# +# So, for example, if you had phiX174 preparsed with 200bp stored in: +# +# /tmp/phix_200 +# +# containing phiX174.fasta.200.* files, such as: +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.cgbins +# -rw-r--r-- 1 ldelisle ldelisle 249K Jul 9 10:14 phiX174.fasta.200.cgfreq +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.gcbins +# -rw-r--r-- 1 ldelisle ldelisle 169K Jul 9 10:14 phiX174.fasta.200.pos +# -rw-r--r-- 1 ldelisle ldelisle 955K Jul 9 10:14 phiX174.fasta.200.seq +# +# then the homer_preparse.loc entry could look like this: +# +# phiX174_200 phiX174 False 200 phiX174 (200bp) /tmp/phix_200 /tmp/phiX174.fasta 4.11 +# +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of preparsed genomes --> + <table name="homer_preparse" comment_char="#"> + <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> + <file path="tool-data/homer_preparse.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Dec 13 15:13:33 2021 +0000 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of preparsed genomes --> + <table name="homer_preparse" comment_char="#"> + <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> + <file path="${__HERE__}/test-data/homer_preparse.loc" /> + </table> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables>