# HG changeset patch
# User iuc
# Date 1639408413 0
# Node ID db456c398880a54563078bf72ecba0131846b51a

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd"

diff -r 000000000000 -r db456c398880 homer_scanMotifGenomeWide.xml
--- /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>
diff -r 000000000000 -r db456c398880 macros.xml
--- /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>
diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks.bed
--- /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
diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_first.txt
--- /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								
diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_second.txt
--- /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								
diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_shifted.bed
--- /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
diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_third.txt
--- /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								
diff -r 000000000000 -r db456c398880 test-data/all_fasta.loc
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_default.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_default_simplified.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_default_stats.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_exon_start.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_exon_start_stats.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_small_TSSTTS.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/annotations_small_TSSTTS_stats.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/chr2_subset.fa.gz
Binary file test-data/chr2_subset.fa.gz has changed
diff -r 000000000000 -r db456c398880 test-data/fake_phix_peaks.bed
--- /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
diff -r 000000000000 -r db456c398880 test-data/fake_phix_peaks.subset.bed
--- /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
diff -r 000000000000 -r db456c398880 test-data/generate_tests.sh
--- /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
+
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.all.motifs
--- /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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.motifs10
--- /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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.motifs12
--- /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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.motifs8
--- /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
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+>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
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+0.100	0.700	0.100	0.100
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults.html
--- /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
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+</TD><TD>1e-1</TD><TD>-2.921e+00</TD><TD>100.00%</TD><TD>5.39%</TD><TD>0.0bp (71.4bp)</TD><TD>Oc/dmmpmm(Noyes_hd)/fly(0.654)<BR/><A target="_blank" HREF="homerResults/motif1.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif1.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif1.motif">motif file (matrix)</A></TD></TR>
+<TR><TD>2
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+<TR><TD>4
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+<TR><TD>5
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+<TR><TD>6
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+<TR><TD>7
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+  <text fill="#0000EE" x="0" y="0"  transform="matrix(0.59,0,0,0.100,175,44)">C</text>
+  <text fill="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.100,176,39)">T</text>
+  <text fill="#F9A500" x="0" y="0"  transform="matrix(0.55,0,0,0.700,175,34)">G</text>
+  
+ </g>
+</svg>
+</TD><TD>1e-1</TD><TD>-2.898e+00</TD><TD>100.00%</TD><TD>5.53%</TD><TD>0.0bp (70.2bp)</TD><TD>HNRNPA1L2(RRM)/Homo_sapiens-RNCMPT00023-PBM/HughesRNA(0.812)<BR/><A target="_blank" HREF="homerResults/motif7.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif7.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif7.motif">motif file (matrix)</A></TD></TR>
+<TR><TD>8
+<FONT color="red">*</FONT></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>
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+  <text fill="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.700,51,34)">T</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>
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+  
+  <text fill="#0000EE" x="0" y="0"  transform="matrix(0.59,0,0,0.100,100,49)">C</text>
+  <text fill="#F9A500" x="0" y="0"  transform="matrix(0.55,0,0,0.100,100,44)">G</text>
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+  <text fill="#00BB00" x="0" y="0"  transform="matrix(0.53,0,0,0.700,102,34)">A</text>
+  
+  <text fill="#00BB00" x="0" y="0"  transform="matrix(0.53,0,0,0.100,127,49)">A</text>
+  <text fill="#0000EE" x="0" y="0"  transform="matrix(0.59,0,0,0.100,125,44)">C</text>
+  <text fill="#F9A500" x="0" y="0"  transform="matrix(0.55,0,0,0.100,125,39)">G</text>
+  <text fill="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.700,126,34)">T</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="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.100,151,39)">T</text>
+  <text fill="#F9A500" x="0" y="0"  transform="matrix(0.55,0,0,0.700,150,34)">G</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>
+</TD><TD>1e-1</TD><TD>-2.889e+00</TD><TD>100.00%</TD><TD>5.58%</TD><TD>0.0bp (78.0bp)</TD><TD>AGL42/MA1201.1/Jaspar(0.903)<BR/><A target="_blank" 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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1.info.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif1.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1753 @@
+<HTML><HEAD><TITLE>Motif 1</TITLE></HEAD>
+<H2>Information for 1-ATGAGCTTAATC (Motif 1)</H2>
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+</svg>
+
+<BR>
+Reverse Opposite:<BR/><svg width="305" height="50">
+ <g font-family="Arial" font-weight="bold" font-size="66.5">
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+</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>-2.921e+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">
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+<TR><TD>
+<H4>PHO2(MacIsaac)/Yeast</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>2</TD></TR>
+<TR><TD>Score:</TD><TD>0.65</TD</TR>
+<TR><TD>Offset:</TD><TD>5</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">ATGAGCTTAATC</FONT><BR><FONT face="courier">-----CTTAAT-</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>oc/dmmpmm(Noyes)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>3</TD></TR>
+<TR><TD>Score:</TD><TD>0.65</TD</TR>
+<TR><TD>Offset:</TD><TD>6</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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+<H4>Gsc/dmmpmm(Noyes_hd)/fly</H4>
+<TABLE><TR><TD>
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+<TR><TD>Match Rank:</TD><TD>4</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</TD</TR>
+<TR><TD>Offset:</TD><TD>4</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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+<TR><TD>
+<H4>bcd/dmmpmm(Noyes_hd)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>5</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</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">----GGTTAATCCN</FONT></TD></TR></TABLE>
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+<H4>OTX2/MA0712.1/Jaspar</H4>
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+<TABLE>
+<TR><TD>Match Rank:</TD><TD>6</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</TD</TR>
+<TR><TD>Offset:</TD><TD>6</TD</TR>
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+<TR><TD>
+<H4>OTX1/MA0711.1/Jaspar</H4>
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+<TR><TD>Match Rank:</TD><TD>7</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>6</TD</TR>
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+<TR><TD>
+<H4>ESRRB/MA0141.3/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>8</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</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">-ATGAGCTTAATC</FONT><BR><FONT face="courier">NATGACCTTGA--</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>GSC2/MA0891.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>9</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>5</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">-----CCTAATCCGC</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>Pitx1/MA0682.1/Jaspar</H4>
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+<TR><TD>Match Rank:</TD><TD>10</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>6</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">------TTAATCCC</FONT></TD></TR></TABLE>
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif1.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,13 @@
+>ATGAGCTTAATC	1-ATGAGCTTAATC,BestGuess:Oc/dmmpmm(Noyes_hd)/fly(0.654)	12.355432	-2.920769	0	T:1.0(100.00%),B:216.0(5.39%),P:1e-1
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1.similar.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif1.similar.html	Mon Dec 13 15:13:33 2021 +0000
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+<TABLE border="1" cellpading="0" cellspacing="0">
+<TR><TD>p-value:</TD><TD>1e-1</TD></TR>
+<TR><TD>log p-value:</TD><TD>-2.921e+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 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>
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+</TABLE>
+<P></P>
+</BODY></HTML>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1.similar1.motif
--- /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 @@
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1.similar2.motif
--- /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
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--- /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
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif1RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,13 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif2.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1783 @@
+<HTML><HEAD><TITLE>Motif 2</TITLE></HEAD>
+<H2>Information for 2-TGCCATCTCAAA (Motif 2)</H2>
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+</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>-2.921e+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>
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+<H4>HIC1(Zf)/Treg-ZBTB29-ChIP-Seq(GSE99889)/Homer</H4>
+<TABLE><TR><TD>
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+<TR><TD>Match Rank:</TD><TD>2</TD></TR>
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+<H4>O2/MA1417.1/Jaspar</H4>
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+<TR><TD>Match Rank:</TD><TD>3</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>-1</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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+<TR><TD>
+<H4>Hic1/MA0739.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>4</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>-1</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">-TGCCATCTCAAA</FONT><BR><FONT face="courier">ATGCCAACC----</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>exd/dmmpmm(Noyes_hd)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>5</TD></TR>
+<TR><TD>Score:</TD><TD>0.62</TD</TR>
+<TR><TD>Offset:</TD><TD>3</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">---NTTGTCAAAN</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>PB0098.1_Zfp410_1/Jaspar</H4>
+<TABLE><TR><TD>
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+<TR><TD>Match Rank:</TD><TD>6</TD></TR>
+<TR><TD>Score:</TD><TD>0.61</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">NNNTCCATCCCATAANN</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>Tgif2(Homeobox)/mES-Tgif2-ChIP-Seq(GSE55404)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>7</TD></TR>
+<TR><TD>Score:</TD><TD>0.60</TD</TR>
+<TR><TD>Offset:</TD><TD>0</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">TGCCATCTCAAA</FONT><BR><FONT face="courier">TGTCANYT----</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>NF1:FOXA1(CTF,Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>8</TD></TR>
+<TR><TD>Score:</TD><TD>0.60</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">TGCCATCTCAAA----</FONT><BR><FONT face="courier">TGCCAAAATAAACANN</FONT></TD></TR></TABLE>
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+<H4>PB0029.1_Hic1_1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>9</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>-4</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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+<TR><TD>
+<H4>RFX1(MacIsaac)/Yeast</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>10</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</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">GTTGCCATGGCAAC</FONT></TD></TR></TABLE>
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif2.similar.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif2.similar.html	Mon Dec 13 15:13:33 2021 +0000
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+</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>-2.921e+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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif2RV.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif2RV.logo.svg	Mon Dec 13 15:13:33 2021 +0000
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif2RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif2RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,13 @@
+>TTTGAGATGGCA	2-TGCCATCTCAAA	12.355432	-2.920769	0	T:1.0(100.00%),B:216.2(5.39%),P:1e-1
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3.info.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif3.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1723 @@
+<HTML><HEAD><TITLE>Motif 3</TITLE></HEAD>
+<H2>Information for 3-CGAGGCTAACCC (Motif 3)</H2>
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+<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>-2.916e+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>
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+<TR><TD>
+<H4>CRX(Homeobox)/Retina-Crx-ChIP-Seq(GSE20012)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>2</TD></TR>
+<TR><TD>Score:</TD><TD>0.62</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">CGAGGCTAACCC</FONT><BR><FONT face="courier">----GCTAATCC</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>ttk/dmmpmm(Noyes)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>3</TD></TR>
+<TR><TD>Score:</TD><TD>0.61</TD</TR>
+<TR><TD>Offset:</TD><TD>0</TD</TR>
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+<TR><TD>
+<H4>bcd/dmmpmm(Bergman)/fly</H4>
+<TABLE><TR><TD>
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+<TR><TD>Match Rank:</TD><TD>4</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>2</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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+</TD></TR>
+<TR><TD>
+<H4>bcd/dmmpmm(Noyes_hd)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>5</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>3</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC-</FONT><BR><FONT face="courier">---GGTTAATCCN</FONT></TD></TR></TABLE>
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+<H4>HOW(KH)/Drosophila_melanogaster-RNCMPT00118-PBM/HughesRNA</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>6</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>4</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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+<H4>GT-1/MA1020.1/Jaspar</H4>
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+<TR><TD>Match Rank:</TD><TD>7</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
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+</TD></TR>
+<TR><TD>
+<H4>Kr/dmmpmm(Papatsenko)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>8</TD></TR>
+<TR><TD>Score:</TD><TD>0.58</TD</TR>
+<TR><TD>Offset:</TD><TD>6</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">CGAGGCTAACCC---</FONT><BR><FONT face="courier">------TAACCCTTT</FONT></TD></TR></TABLE>
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+<H4>HNRNPK(KH)/Homo_sapiens-RNCMPT00026-PBM/HughesRNA</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>9</TD></TR>
+<TR><TD>Score:</TD><TD>0.58</TD</TR>
+<TR><TD>Offset:</TD><TD>5</TD</TR>
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+<TR><TD>
+<H4>bcd/dmmpmm(Papatsenko)/fly</H4>
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+<TR><TD>Match Rank:</TD><TD>10</TD></TR>
+<TR><TD>Score:</TD><TD>0.58</TD</TR>
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+  
+ </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>-2.916e+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">
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+  <text fill="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.100,201,39)">T</text>
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+  
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+  <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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3.similar1.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif3.similar1.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,11 @@
+>CGAGGCTAAC	5-CGAGGCTAAC	10.296193	-2.897885	0	T:1.0(100.00%),B:221.5(5.53%),P:1e-1
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3RV.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif3RV.logo.svg	Mon Dec 13 15:13:33 2021 +0000
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif3RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,13 @@
+>GGGTTAGCCTCG	3-CGAGGCTAACCC	12.355432	-2.916150	0	T:1.0(100.00%),B:217.8(5.43%),P:1e-1
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4.info.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif4.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1733 @@
+<HTML><HEAD><TITLE>Motif 4</TITLE></HEAD>
+<H2>Information for 4-CTCCTGAGACTG (Motif 4)</H2>
+<svg width="305" height="50">
+ <g font-family="Arial" font-weight="bold" font-size="66.5">
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+<TABLE border="1" cellpading="0" cellspacing="0">
+<TR><TD>p-value:</TD><TD>1e-1</TD></TR>
+<TR><TD>log p-value:</TD><TD>-2.912e+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>
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+<TR><TD>
+<H4>RAV1(var.2)/MA0583.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>2</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>
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+<TR><TD>
+<H4>CELF2(RRM)/JSL1-CELF2-CLIP-Seq(GSE71264)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>3</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</TD</TR>
+<TR><TD>Offset:</TD><TD>3</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">---CTGACACY-</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>YML081W(MacIsaac)/Yeast</H4>
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+<TABLE>
+<TR><TD>Match Rank:</TD><TD>4</TD></TR>
+<TR><TD>Score:</TD><TD>0.61</TD</TR>
+<TR><TD>Offset:</TD><TD>3</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG-</FONT><BR><FONT face="courier">---TTCAGACTGG</FONT></TD></TR></TABLE>
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+<H4>SRSF2(RRM)/Homo_sapiens-RNCMPT00072-PBM/HughesRNA</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>5</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>-3</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
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+</TD></TR>
+<TR><TD>
+<H4>REI1/MA0364.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>6</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>0</TD</TR>
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+<TR><TD>Alignment:</TD><TD><FONT face="courier">CTCCTGAGACTG</FONT><BR><FONT face="courier">CCCCTGA-----</FONT></TD></TR></TABLE>
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+</TD></TR>
+<TR><TD>
+<H4>REI1/MA0364.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>7</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>0</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">CCCCTGA-----</FONT></TD></TR></TABLE>
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+</TD></TR>
+<TR><TD>
+<H4>AT5G05550(Trihelix)/col-AT5G05550-DAP-Seq(GSE60143)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>8</TD></TR>
+<TR><TD>Score:</TD><TD>0.59</TD</TR>
+<TR><TD>Offset:</TD><TD>-6</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">HDNHDTCKCCGGMGA---</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>GFX(?)/Promoter/Homer</H4>
+<TABLE><TR><TD>
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+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">-CTCCTGAGACTG</FONT><BR><FONT face="courier">TCTCGCGAGAAT-</FONT></TD></TR></TABLE>
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+<H4>ZmHOX2a(1)(HD-HOX)/Zea mays/AthaMap</H4>
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+  
+ </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>-2.912e+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">
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+</svg>
+
+</TD><TD>1e-1</TD><TD>-2.902420</TD><TD>100.00%</TD><TD>5.49%</TD><TD><A target="_blank" HREF="motif4.similar1.motif">motif file (matrix)</A></TD></TR>
+<TR><TD>2</TD><TD>0.714</TD><TD><svg width="205" height="50">
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+</svg>
+
+</TD><TD>1e-1</TD><TD>-2.897885</TD><TD>100.00%</TD><TD>5.54%</TD><TD><A target="_blank" HREF="motif4.similar2.motif">motif file (matrix)</A></TD></TR>
+</TABLE>
+<P></P>
+</BODY></HTML>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4.similar1.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif4.similar1.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,11 @@
+>CCTGAGACTG	4-CCTGAGACTG	10.296193	-2.902420	0	T:1.0(100.00%),B:220.0(5.49%),P:1e-1
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4.similar2.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif4.similar2.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,9 @@
+>GAGACTGA	3-GAGACTGA	8.236954	-2.897885	0	T:1.0(100.00%),B:221.9(5.54%),P:1e-1
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+0.700	0.100	0.100	0.100
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4RV.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif4RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,13 @@
+>CAGTCTCAGGAG	4-CTCCTGAGACTG	12.355432	-2.911553	0	T:1.0(100.00%),B:218.1(5.44%),P:1e-1
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+0.100	0.100	0.700	0.100
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5.info.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif5.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1593 @@
+<HTML><HEAD><TITLE>Motif 5</TITLE></HEAD>
+<H2>Information for 2-ATCAAGATGA (Motif 5)</H2>
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+<TABLE border="1" cellpading="0" cellspacing="0">
+<TR><TD>p-value:</TD><TD>1e-1</TD></TR>
+<TR><TD>log p-value:</TD><TD>-2.907e+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>219.8</TD></TR>
+<TR><TD>Percentage of Background Sequences with 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>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">-ATCAAGATGA</FONT><BR><FONT face="courier">GATCAAGA---</FONT></TD></TR></TABLE>
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+<H4>SNRNP70(RRM)/Homo_sapiens-RNCMPT00070-PBM/HughesRNA</H4>
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+</TD></TR>
+<TR><TD>
+<H4>At5g05790/MA1196.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>4</TD></TR>
+<TR><TD>Score:</TD><TD>0.68</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">-ATCAAGATGA----</FONT><BR><FONT face="courier">GATNAAGATAAGGTT</FONT></TD></TR></TABLE>
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+<H4>Rbm47(RRM)/Xenopus_tropicalis-RNCMPT00280-PBM/HughesRNA</H4>
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+<H4>RIN(RRM)/Drosophila_melanogaster-RNCMPT00138-PBM/HughesRNA</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>7</TD></TR>
+<TR><TD>Score:</TD><TD>0.65</TD</TR>
+<TR><TD>Offset:</TD><TD>4</TD</TR>
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+<H4>ZBTB18/MA0698.1/Jaspar</H4>
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+<TR><TD>Match Rank:</TD><TD>8</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</TD</TR>
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+</TD></TR>
+<TR><TD>
+<H4>At3g11280/MA1188.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>9</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</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">ATCAAGATGA----</FONT><BR><FONT face="courier">ATNAAGATAAGGAT</FONT></TD></TR></TABLE>
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+<H4>onecut/dmmpmm(Noyes_hd)/fly</H4>
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+<TR><TD>Match Rank:</TD><TD>10</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>-3</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">---ATCAAGATGA</FONT><BR><FONT face="courier">CAAATCAANN---</FONT></TD></TR></TABLE>
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5.logo.svg
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif5.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,11 @@
+>ATCAAGATGA	2-ATCAAGATGA,BestGuess:SNRNP70K(RRM)/Drosophila_melanogaster-RNCMPT00143-PBM/HughesRNA(0.785)	10.296193	-2.906976	0	T:1.0(100.00%),B:219.8(5.48%),P:1e-1
+0.700	0.100	0.100	0.100
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+0.700	0.100	0.100	0.100
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+0.100	0.100	0.700	0.100
+0.700	0.100	0.100	0.100
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5.similar.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif5.similar.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,132 @@
+<HTML><HEAD><TITLE>motif5</TITLE></HEAD>
+<H2>Information for motif5</H2>
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+</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>-2.907e+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>219.8</TD></TR>
+<TR><TD>Percentage of Background Sequences with 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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5RV.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif5RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,11 @@
+>TCATCTTGAT	2-ATCAAGATGA	10.296193	-2.906976	0	T:1.0(100.00%),B:219.8(5.48%),P:1e-1
+0.100	0.100	0.100	0.700
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.info.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif6.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1593 @@
+<HTML><HEAD><TITLE>Motif 6</TITLE></HEAD>
+<H2>Information for 3-GTTGCTGCCA (Motif 6)</H2>
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+<TABLE border="1" cellpading="0" cellspacing="0">
+<TR><TD>p-value:</TD><TD>1e-1</TD></TR>
+<TR><TD>log p-value:</TD><TD>-2.907e+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>219.9</TD></TR>
+<TR><TD>Percentage of Background Sequences with 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>
+<TR><TD>SVG Files for Logos:</TD><TD><A HREF="motif6.logo.svg">forward logo</A><BR/><A HREF="motif6RV.logo.svg">reverse opposite</A></TD></TR>
+</TABLE>
+<H3>Matches to Known Motifs</H3>
+<TABLE border="1" cellpading="0" cellspacing="0">
+<TR><TD>
+<H4>DEL1(E2FDP)/colamp-DEL1-DAP-Seq(GSE60143)/Homer</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>1</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">GTTGCTGCCA-</FONT><BR><FONT face="courier">-TTCCCGCCAA</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>2</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">GTTGCTGCCA--</FONT><BR><FONT face="courier">----TTGCCAAG</FONT></TD></TR></TABLE>
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+<TR><TD>
+<H4>HIC1(Zf)/Treg-ZBTB29-ChIP-Seq(GSE99889)/Homer</H4>
+<TABLE><TR><TD>
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+<TR><TD>Match Rank:</TD><TD>3</TD></TR>
+<TR><TD>Score:</TD><TD>0.65</TD</TR>
+<TR><TD>Offset:</TD><TD>2</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
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+<TR><TD>
+<H4>PRDM9(Zf)/Testis-DMC1-ChIP-Seq(GSE35498)/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>4</TD></TR>
+<TR><TD>Score:</TD><TD>0.65</TD</TR>
+<TR><TD>Offset:</TD><TD>-4</TD</TR>
+<TR><TD>Orientation:</TD><TD>reverse strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">----GTTGCTGCCA-</FONT><BR><FONT face="courier">AGATGCTRCTRCCHT</FONT></TD></TR></TABLE>
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+</TD></TR>
+<TR><TD>
+<H4>NFIX/MA0671.1/Jaspar</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>5</TD></TR>
+<TR><TD>Score:</TD><TD>0.64</TD</TR>
+<TR><TD>Offset:</TD><TD>3</TD</TR>
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+<TR><TD>
+<H4>Aef1/dmmpmm(Pollard)/fly</H4>
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+<TABLE>
+<TR><TD>Match Rank:</TD><TD>6</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</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">-GTTGCTGCCA</FONT><BR><FONT face="courier">TGTTGTTG---</FONT></TD></TR></TABLE>
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+<H4>SUM1(MacIsaac)/Yeast</H4>
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+<TABLE>
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+<TR><TD>
+<H4>Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer</H4>
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+<TR><TD>Match Rank:</TD><TD>8</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</TD</TR>
+<TR><TD>Offset:</TD><TD>0</TD</TR>
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+</TD></TR>
+<TR><TD>
+<H4>Unknown3/Drosophila-Promoters/Homer</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>9</TD></TR>
+<TR><TD>Score:</TD><TD>0.63</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">GTTGCTGCCA------</FONT><BR><FONT face="courier">-GCGCTGCCAGMTBGT</FONT></TD></TR></TABLE>
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+<H4>CRZ1(MacIsaac)/Yeast</H4>
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+<TR><TD>Offset:</TD><TD>0</TD</TR>
+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
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+  <text fill="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.100,226,39)">T</text>
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+  
+ </g>
+</svg>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif6.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,11 @@
+>GTTGCTGCCA	3-GTTGCTGCCA,BestGuess:DEL1(E2FDP)/colamp-DEL1-DAP-Seq(GSE60143)/Homer(0.657)	10.296193	-2.906976	0	T:1.0(100.00%),B:219.9(5.49%),P:1e-1
+0.100	0.100	0.700	0.100
+0.100	0.100	0.100	0.700
+0.100	0.100	0.100	0.700
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+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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.similar.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif6.similar.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,178 @@
+<HTML><HEAD><TITLE>motif6</TITLE></HEAD>
+<H2>Information for motif6</H2>
+<svg width="255" height="50">
+ <g font-family="Arial" font-weight="bold" font-size="66.5">
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+</svg>
+<BR/>
+Reverse Opposite:<BR/><svg width="255" height="50">
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+  
+ </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>-2.907e+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>219.9</TD></TR>
+<TR><TD>Percentage of Background Sequences with 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">
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+ </g>
+</svg>
+
+</TD><TD>1e-1</TD><TD>-2.897885</TD><TD>100.00%</TD><TD>5.53%</TD><TD><A target="_blank" HREF="motif6.similar1.motif">motif file (matrix)</A></TD></TR>
+</TABLE>
+<P></P>
+</BODY></HTML>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.similar1.motif
--- /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
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6RV.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif6RV.logo.svg	Mon Dec 13 15:13:33 2021 +0000
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif6RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,11 @@
+>TGGCAGCAAC	3-GTTGCTGCCA	10.296193	-2.906976	0	T:1.0(100.00%),B:219.9(5.49%),P:1e-1
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+0.700	0.100	0.100	0.100
+0.100	0.700	0.100	0.100
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.info.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif7.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1363 @@
+<HTML><HEAD><TITLE>Motif 7</TITLE></HEAD>
+<H2>Information for 1-CCCTAATG (Motif 7)</H2>
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+<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>
+<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>
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+<TR><TD>
+<H4>zen/dmmpmm(Noyes_hd)/fly</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>2</TD></TR>
+<TR><TD>Score:</TD><TD>0.80</TD</TR>
+<TR><TD>Offset:</TD><TD>0</TD</TR>
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+<H4>HNRNPA1(RRM)/Homo_sapiens-RNCMPT00022-PBM/HughesRNA</H4>
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+<TR><TD>
+<H4>HNRNPA2B1(RRM)/Homo_sapiens-RNCMPT00024-PBM/HughesRNA</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>6</TD></TR>
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+<TR><TD>Offset:</TD><TD>-1</TD</TR>
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+<H4>TBP3/MA1355.1/Jaspar</H4>
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+<H4>RPH1/MA0372.1/Jaspar</H4>
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+<TR><TD>
+<H4>RPH1/MA0372.1/Jaspar</H4>
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+<TABLE>
+<TR><TD>Match Rank:</TD><TD>10</TD></TR>
+<TR><TD>Score:</TD><TD>0.75</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">--CCCTAATG</FONT><BR><FONT face="courier">ACCCCTAA--</FONT></TD></TR></TABLE>
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+  <text fill="#DD0000" x="0" y="0"  transform="matrix(0.65,0,0,0.100,176,39)">T</text>
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+</svg>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif7.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,9 @@
+>CCCTAATG	1-CCCTAATG,BestGuess:HNRNPA1L2(RRM)/Homo_sapiens-RNCMPT00023-PBM/HughesRNA(0.812)	8.236954	-2.897885	0	T:1.0(100.00%),B:221.6(5.53%),P:1e-1
+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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.similar.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif7.similar.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,112 @@
+<HTML><HEAD><TITLE>motif7</TITLE></HEAD>
+<H2>Information for motif7</H2>
+<svg width="205" height="50">
+ <g font-family="Arial" font-weight="bold" font-size="66.5">
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+ </g>
+</svg>
+<BR/>
+Reverse Opposite:<BR/><svg width="205" height="50">
+ <g font-family="Arial" font-weight="bold" font-size="66.5">
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+  <text fill="#F9A500" x="0" y="0"  transform="matrix(0.55,0,0,0.700,150,34)">G</text>
+  
+  <text fill="#00BB00" x="0" y="0"  transform="matrix(0.53,0,0,0.100,177,49)">A</text>
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+  
+ </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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7RV.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif7RV.logo.svg	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,44 @@
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7RV.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif7RV.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,9 @@
+>CATTAGGG	1-CCCTAATG	8.236954	-2.897885	0	T:1.0(100.00%),B:221.6(5.53%),P:1e-1
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif8.info.html	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,1343 @@
+<HTML><HEAD><TITLE>Motif 8</TITLE></HEAD>
+<H2>Information for 5-GATGATGC (Motif 8)</H2>
+<svg width="205" height="50">
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+</svg>
+
+<BR>
+Reverse Opposite:<BR/><svg width="205" height="50">
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+</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>
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+<TR><TD>
+<H4>RBM47(RRM)/Gallus_gallus-RNCMPT00279-PBM/HughesRNA</H4>
+<TABLE><TR><TD>
+<TABLE>
+<TR><TD>Match Rank:</TD><TD>2</TD></TR>
+<TR><TD>Score:</TD><TD>0.83</TD</TR>
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+<TR><TD>Orientation:</TD><TD>forward strand</TD></TR>
+<TR><TD>Alignment:</TD><TD><FONT face="courier">GATGATGC</FONT><BR><FONT face="courier">GATGATN-</FONT></TD></TR></TABLE>
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+<H4>RIN(RRM)/Drosophila_melanogaster-RNCMPT00138-PBM/HughesRNA</H4>
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+<H4>ZML2(C2C2gata)/col-ZML2-DAP-Seq(GSE60143)/Homer</H4>
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+<H4>Rbm47(RRM)/Xenopus_tropicalis-RNCMPT00280-PBM/HughesRNA</H4>
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+<H4>ATF4/MA0833.1/Jaspar</H4>
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+<TR><TD>Offset:</TD><TD>-1</TD</TR>
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+<H4>Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer</H4>
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+<TR><TD>Score:</TD><TD>0.74</TD</TR>
+<TR><TD>Offset:</TD><TD>1</TD</TR>
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+<H4>Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer</H4>
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+<H4>AARE(HLH)/mES-cMyc-ChIP-Seq/Homer</H4>
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8.logo.svg
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif8.logo.svg	Mon Dec 13 15:13:33 2021 +0000
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8.motif
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif8.motif	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,9 @@
+>GATGATGC	5-GATGATGC,BestGuess:AGL42/MA1201.1/Jaspar(0.903)	8.236954	-2.888876	0	T:1.0(100.00%),B:223.5(5.58%),P:1e-1
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8.similar.html
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif_test1/homerResults/motif8.similar.html	Mon Dec 13 15:13:33 2021 +0000
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+<HTML><HEAD><TITLE>motif8</TITLE></HEAD>
+<H2>Information for motif8</H2>
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+<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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8RV.logo.svg
--- /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
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diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8RV.motif
--- /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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/knownResults.html
--- /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>
diff -r 000000000000 -r db456c398880 test-data/motif_test1/knownResults.txt
--- /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%
diff -r 000000000000 -r db456c398880 test-data/motif_test1/motifFindingParameters.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/motif_test1/seq.autonorm.tsv
--- /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
diff -r 000000000000 -r db456c398880 test-data/phiX174.fasta
--- /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
+
diff -r 000000000000 -r db456c398880 test-data/phiX_nothing.txt
--- /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								
diff -r 000000000000 -r db456c398880 test-data/phiXcpg.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/scanMotif_res1.bed
--- /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	+
diff -r 000000000000 -r db456c398880 test-data/scanMotif_res1.txt
--- /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
diff -r 000000000000 -r db456c398880 test-data/small.gtf
--- /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";
diff -r 000000000000 -r db456c398880 test-data/small_simplified.gtf
--- /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";
diff -r 000000000000 -r db456c398880 tool-data/all_fasta.loc.sample
--- /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.
+#
diff -r 000000000000 -r db456c398880 tool-data/homer_preparse.loc.sample
--- /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
+#
+#
diff -r 000000000000 -r db456c398880 tool_data_table_conf.xml.sample
--- /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>
diff -r 000000000000 -r db456c398880 tool_data_table_conf.xml.test
--- /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>