<?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>/woldlab/castor/home/georgi/programs/meme_4.12.0/bin/fimo --max-stored-scores 10000000000 --oc FIMO-Schizosaccharomyces_pombe-YEAST-scpd_matrix /woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/YEAST/scpd_matrix.meme /woldlab/castor/home/georgi/genomes/Schizosaccharomyces_pombe/sequence/Schizosaccharomyces_pombe.ASM294v2.20.fa</command-line>
<settings>
<setting name="output directory">FIMO-Schizosaccharomyces_pombe-YEAST-scpd_matrix</setting>
<setting name="MEME file name">/woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/YEAST/scpd_matrix.meme</setting>
<setting name="sequence file name">/woldlab/castor/home/georgi/genomes/Schizosaccharomyces_pombe/sequence/Schizosaccharomyces_pombe.ASM294v2.20.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">-2147483648</setting>
<setting name="pseudocount">0.1</setting>
<setting name="verbosity">2</setting>
</settings>
<sequence-data num-sequences="6" num-residues="12631379" />
<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="RLM1" alt="" width="18" best-possible-match="AGTTCTATAAATAGATTC"/>
<motif name="SMP1" alt="" width="20" best-possible-match="ATGCTTCTATTTATAGCAAC"/>
<motif name="ABF1" alt="" width="12" best-possible-match="TCACTATACACG"/>
<motif name="CSRE" alt="" width="13" best-possible-match="TTCGGATGAATGG"/>
<motif name="SCB" alt="" width="7" best-possible-match="CACGAAA"/>
<motif name="GAL4" alt="" width="17" best-possible-match="CGGAGCACACTCCTCCG"/>
<motif name="GCN4" alt="" width="6" best-possible-match="TGACTC"/>
<motif name="GCR1" alt="" width="5" best-possible-match="CTTCC"/>
<motif name="MCB" alt="" width="6" best-possible-match="ACGCGT"/>
<motif name="MCM1" alt="" width="10" best-possible-match="CCCAATTAGG"/>
<motif name="MATalpha2" alt="" width="9" best-possible-match="CATGTAATT"/>
<motif name="MIG1" alt="" width="12" best-possible-match="CCCCAGATTTTT"/>
<motif name="PHO2" alt="" width="7" best-possible-match="TTAAATT"/>
<motif name="PDR1/PDR3" alt="" width="8" best-possible-match="TCCGCGGA"/>
<motif name="PHO4" alt="" width="10" best-possible-match="CGCACGTGGT"/>
<motif name="REB1" alt="" width="7" best-possible-match="TTACCCG"/>
<motif name="ROX1" alt="" width="12" best-possible-match="TCCATTGTTCTC"/>
<motif name="RAP1" alt="" width="12" best-possible-match="ACACCCATACAC"/>
<motif name="repressor_of_CAR1" alt="" width="9" best-possible-match="AGCCGCCAA"/>
<motif name="SWI5" alt="" width="12" best-possible-match="ATATCATGCTGG"/>
<motif name="STE12" alt="" width="8" best-possible-match="ATGAAACC"/>
<motif name="TBP" alt="" width="7" best-possible-match="TATAAAA"/>
<motif name="UASPHR" alt="" width="12" best-possible-match="TTTTCTTCCTCG"/>
<motif name="XBP1" alt="" width="12" best-possible-match="GCCTCGAGGCGA"/>
<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>
