<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Begin document body -->
<fimo version="4.12.0" release="Tue Jun 27 16:22:50 2017 -0700">
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation=  xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
>
<command-line>/oak/stanford/groups/akundaje/marinovg/programs/meme_4.12.0/meme/bin/fimo --oc FIMO-Control_4_FGFR1_GSM2439179-MEMECHIP /oak/stanford/groups/akundaje/marinovg/various/2020-12-05-FGFR1-chrM/Control_4_FGFR1_GSM2439179-appMEMECHIP_5.3.01607328249702711587880/combined.meme /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM.fa</command-line>
<settings>
<setting name="output directory">FIMO-Control_4_FGFR1_GSM2439179-MEMECHIP</setting>
<setting name="MEME file name">/oak/stanford/groups/akundaje/marinovg/various/2020-12-05-FGFR1-chrM/Control_4_FGFR1_GSM2439179-appMEMECHIP_5.3.01607328249702711587880/combined.meme</setting>
<setting name="sequence file name">/oak/stanford/groups/akundaje/marinovg/genomes/hg20/bowtie-indexes/chrM.fa</setting>
<setting name="background file name">--nrdb--</setting>
<setting name="allow clobber">true</setting>
<setting name="compute q-values">true</setting>
<setting name="parse genomic coord.">false</setting>
<setting name="text only">false</setting>
<setting name="scan both strands">true</setting>
<setting name="output threshold">0.0001</setting>
<setting name="threshold type">p-value</setting>
<setting name="max stored scores">100000</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">2</setting>
</settings>
<sequence-data num-sequences="1" num-residues="16569" />
<alphabet name="DNA" like="dna">
<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/>
<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/>
<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/>
<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/>
<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/>
<letter id="V" symbol="V" equals="ACG" name="Not T"/>
<letter id="H" symbol="H" equals="ACT" name="Not G"/>
<letter id="D" symbol="D" equals="AGT" name="Not C"/>
<letter id="B" symbol="B" equals="CGT" name="Not A"/>
<letter id="M" symbol="M" equals="AC" name="Amino"/>
<letter id="R" symbol="R" equals="AG" name="Purine"/>
<letter id="W" symbol="W" equals="AT" name="Weak"/>
<letter id="S" symbol="S" equals="CG" name="Strong"/>
<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/>
<letter id="K" symbol="K" equals="GT" name="Keto"/>
</alphabet>
<motif name="1" alt="CCCCGCCCCCSCCCC-MEME-1" width="15" best-possible-match="CCCCGCCCCCCCCCC"/>
<motif name="2" alt="AAAAWAMAAAAAWWA-MEME-2" width="15" best-possible-match="AAAATAAAAAAATTA"/>
<motif name="3" alt="1-CCCCGCCCCCNCCC-STREME-1" width="14" best-possible-match="CCCCGCCCCCTCCC"/>
<motif name="4" alt="CTGTAATCCCAGCWM-MEME-3" width="15" best-possible-match="CTGTAATCCCAGCTA"/>
<motif name="5" alt="2-CGCCCYCTGSYGGC-STREME-2" width="14" best-possible-match="CGCCCCCTGGTGGC"/>
<motif name="6" alt="3-RCCGGAAGTGR-STREME-3" width="11" best-possible-match="ACCGGAAGTGA"/>
<motif name="7" alt="4-GCCTCRGCCTCCCAA-STREME-4" width="15" best-possible-match="GCCTCAGCCTCCCAA"/>
<motif name="8" alt="5-CTGTAATCCCAGCWM-STREME-5" width="15" best-possible-match="CTGTAATCCCAGCTA"/>
<motif name="9" alt="6-ACTACAAHTCC-STREME-6" width="11" best-possible-match="ACTACAAATCC"/>
<motif name="10" alt="7-GTTGCCATGGCAAC-STREME-7" width="14" best-possible-match="GTTGCCATGGCAAC"/>
<motif name="11" alt="8-YGCMGCCGCCRC-STREME-8" width="12" best-possible-match="CGCCGCCGCCGC"/>
<motif name="12" alt="9-RGCCAATSAGMR-STREME-9" width="12" best-possible-match="AGCCAATCAGAG"/>
<motif name="13" alt="10-CCCAGCCC-STREME-10" width="8" best-possible-match="CCCAGCCC"/>
<motif name="14" alt="11-AGGAGTTCRAGACCA-STREME-11" width="15" best-possible-match="AGGAGTTCGAGACCA"/>
<motif name="15" alt="12-CAASATGGYGR-STREME-12" width="11" best-possible-match="CAACATGGCGA"/>
<motif name="16" alt="13-YGCGCATGCGCR-STREME-13" width="12" best-possible-match="TGCGCATGCGCA"/>
<motif name="17" alt="14-AAATTAGCYRGGCRT-STREME-14" width="15" best-possible-match="AAATTAGCCGGGCGT"/>
<motif name="18" alt="15-GCRTGAGCCACYRY-STREME-15" width="14" best-possible-match="GCGTGAGCCACCGC"/>
<motif name="19" alt="16-GAGRATCRCTTGAR-STREME-16" width="14" best-possible-match="GAGGATCGCTTGAG"/>
<motif name="20" alt="17-GTCACGTGAC-STREME-17" width="10" best-possible-match="GTCACGTGAC"/>
<motif name="21" alt="18-AGGAAGCGG-STREME-18" width="9" best-possible-match="AGGAAGCGG"/>
<motif name="22" alt="19-NTCTCGCGAGAN-STREME-19" width="12" best-possible-match="GTCTCGCGAGAC"/>
<motif name="23" alt="20-CGGCTGCAG-STREME-20" width="9" best-possible-match="CGGCTGCAG"/>
<motif name="24" alt="21-CAGCACCRCGGACAG-STREME-21" width="15" best-possible-match="CAGCACCACGGACAG"/>
<motif name="25" alt="22-AGGGAGGGAGGGAG-STREME-22" width="14" best-possible-match="AGGGAGGGAGGGAG"/>
<motif name="26" alt="23-AACAAAG-STREME-23" width="7" best-possible-match="AACAAAG"/>
<motif name="27" alt="24-ACAAAG-STREME-24" width="6" best-possible-match="ACAAAG"/>
<motif name="28" alt="25-ACCCGGAAGY-STREME-25" width="10" best-possible-match="ACCCGGAAGC"/>
<motif name="29" alt="26-CGCCCCCTCCC-STREME-26" width="11" best-possible-match="CGCCCCCTCCC"/>
<motif name="30" alt="27-ACACACACACACA-STREME-27" width="13" best-possible-match="ACACACACACACA"/>
<motif name="31" alt="28-GTTGCTAKG-STREME-28" width="9" best-possible-match="GTTGCTATG"/>
<motif name="32" alt="29-AACCCYRTCTCT-STREME-29" width="12" best-possible-match="AACCCTGTCTCT"/>
<motif name="33" alt="30-CTCTGTYGCCCAG-STREME-30" width="13" best-possible-match="CTCTGTTGCCCAG"/>
<motif name="34" alt="31-AGAAAGAAAGAA-STREME-31" width="12" best-possible-match="AGAAAGAAAGAA"/>
<motif name="35" alt="32-GGCCCCGCCCC-STREME-32" width="11" best-possible-match="GGCCCCGCCCC"/>
<motif name="36" alt="33-CCCTTCCC-STREME-33" width="8" best-possible-match="CCCTTCCC"/>
<motif name="37" alt="34-GTGAGCYGAGATCRY-STREME-34" width="15" best-possible-match="GTGAGCCGAGATCGC"/>
<motif name="38" alt="35-AAATACAA-STREME-35" width="8" best-possible-match="AAATACAA"/>
<motif name="39" alt="36-TGAYRTCA-STREME-36" width="8" best-possible-match="TGACGTCA"/>
<motif name="40" alt="37-CAGCAGCTGC-STREME-37" width="10" best-possible-match="CAGCAGCTGC"/>
<motif name="41" alt="38-GCGCATGCGC-STREME-38" width="10" best-possible-match="GCGCATGCGC"/>
<motif name="42" alt="39-CTGAGTCAY-STREME-39" width="9" best-possible-match="CTGAGTCAC"/>
<motif name="43" alt="40-TCTCTACAAAAAAWA-STREME-40" width="15" best-possible-match="TCTCTACAAAAAAAA"/>
<motif name="44" alt="41-CCTCCTCCTCCTCCT-STREME-41" width="15" best-possible-match="CCTCCTCCTCCTCCT"/>
<motif name="45" alt="42-ATAAATAA-STREME-42" width="8" best-possible-match="ATAAATAA"/>
<motif name="46" alt="43-CCACTGCACTCCAGC-STREME-43" width="15" best-possible-match="CCACTGCACTCCAGC"/>
<motif name="47" alt="44-GACCTCGTGATCC-STREME-44" width="13" best-possible-match="GACCTCGTGATCC"/>
<motif name="48" alt="45-ATGCWAATSA-STREME-45" width="10" best-possible-match="ATGCAAATGA"/>
<motif name="49" alt="46-CCCGGCTC-STREME-46" width="8" best-possible-match="CCCGGCTC"/>
<motif name="50" alt="47-KGCCCCTTTAA-STREME-47" width="11" best-possible-match="GGCCCCTTTAA"/>
<motif name="51" alt="48-MTTCTGGGAADTG-STREME-48" width="13" best-possible-match="ATTCTGGGAAATG"/>
<motif name="52" alt="49-AGGCAGAGGCGAGG-STREME-49" width="14" best-possible-match="AGGCAGAGGCGAGG"/>
<motif name="53" alt="50-CAAGGTCA-STREME-50" width="8" best-possible-match="CAAGGTCA"/>
<motif name="54" alt="51-CGAGGCC-STREME-51" width="7" best-possible-match="CGAGGCC"/>
<background source="--nrdb--">
<value letter="A">0.275</value>
<value letter="C">0.225</value>
<value letter="G">0.225</value>
<value letter="T">0.275</value>
</background>
<cisml-file>cisml.xml</cisml-file>
</fimo>
