<?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-CIS-BP-Schizosaccharomyces_pombe /woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/CIS-BP/Schizosaccharomyces_pombe.meme /woldlab/castor/home/georgi/genomes/Schizosaccharomyces_pombe/sequence/Schizosaccharomyces_pombe.ASM294v2.20.fa</command-line>
<settings>
<setting name="output directory">FIMO-Schizosaccharomyces_pombe-CIS-BP-Schizosaccharomyces_pombe</setting>
<setting name="MEME file name">/woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/CIS-BP/Schizosaccharomyces_pombe.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="M0121_1.02" alt="(cnp3)_(Brachypodium_distachyon)_(DBD_0.69)" width="9" best-possible-match="ACAAAATAA"/>
<motif name="M0232_1.02" alt="(sre1)_(Neurospora_crassa)_(DBD_0.63)" width="10" best-possible-match="ATCACGTGAT"/>
<motif name="M0341_1.02" alt="zip1" width="10" best-possible-match="ATTACGTAAT"/>
<motif name="M0744_1.02" alt="(sep1)_(Neurospora_crassa)_(DBD_0.61)" width="8" best-possible-match="ATAAACAA"/>
<motif name="M0792_1.02" alt="(gaf1)_(Neurospora_crassa)_(DBD_0.83)" width="8" best-possible-match="CAGATAAG"/>
<motif name="M1120_1.02" alt="SPAC32A11.03c" width="11" best-possible-match="TATTAATTACA"/>
<motif name="M1121_1.02" alt="SPBC21B10.13c" width="10" best-possible-match="ATTAATTAAT"/>
<motif name="M1742_1.02" alt="(SPBC15D4.02)_(Neurospora_crassa)_(DBD_0.75)" width="9" best-possible-match="TTAAGCGAG"/>
<motif name="M2118_1.02" alt="(hap2)_(Saccharomyces_cerevisiae)_(DBD_0.76)" width="5" best-possible-match="TTGGT"/>
<motif name="M2372_1.02" alt="(cdc5)_(Arabidopsis_thaliana)_(DBD_0.90)" width="11" best-possible-match="CGCGCTGAGCC"/>
<motif name="M4266_1.02" alt="(tbp1)_(Saccharomyces_cerevisiae)_(DBD_0.94)" width="21" best-possible-match="GACTAGATATATATATTCGAT"/>
<motif name="M4276_1.02" alt="(scr1)_(Saccharomyces_cerevisiae)_(DBD_0.75)" width="7" best-possible-match="GCGGGGG"/>
<motif name="M4343_1.02" alt="(sak1)_(Saccharomyces_cerevisiae)_(DBD_0.51)" width="16" best-possible-match="GGTTGCCATGGCAACG"/>
<motif name="M4376_1.02" alt="(fkh2)_(Saccharomyces_cerevisiae)_(DBD_0.52)" width="20" best-possible-match="TTAAAAGTAAACAAAGATGA"/>
<motif name="M6237_1.02" alt="(fhl1)_(Homo_sapiens)_(DBD_0.48)" width="9" best-possible-match="AAACAAACA"/>
<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>
