<?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-sacCer3-YEAST-SwissRegulon_s_cer /woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/YEAST/SwissRegulon_s_cer.meme /woldlab/castor/home/georgi/genomes/sacCer3/sequence/sacCer3.fa</command-line>
<settings>
<setting name="output directory">FIMO-sacCer3-YEAST-SwissRegulon_s_cer</setting>
<setting name="MEME file name">/woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/YEAST/SwissRegulon_s_cer.meme</setting>
<setting name="sequence file name">/woldlab/castor/home/georgi/genomes/sacCer3/sequence/sacCer3.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="17" num-residues="12157105" />
<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="ABF1" alt="" width="13" best-possible-match="ATCACTATATACG"/>
<motif name="ABF2" alt="" width="6" best-possible-match="TCTAGA"/>
<motif name="ACE2" alt="" width="7" best-possible-match="GCTGGTT"/>
<motif name="ADR1" alt="" width="8" best-possible-match="ACCCCAAC"/>
<motif name="AFT1" alt="" width="10" best-possible-match="TATTGCACCC"/>
<motif name="AFT2" alt="" width="6" best-possible-match="ACACCC"/>
<motif name="ARO80" alt="" width="8" best-possible-match="CTCGGCAA"/>
<motif name="ASG1" alt="" width="15" best-possible-match="CCGGCCGAGTTCCGG"/>
<motif name="AZF1" alt="" width="9" best-possible-match="AAAAAGAAA"/>
<motif name="BAS1" alt="" width="10" best-possible-match="GCCAGAGTCA"/>
<motif name="CAD1" alt="" width="10" best-possible-match="ATTAGTAAGC"/>
<motif name="CAT8" alt="" width="5" best-possible-match="CCGGA"/>
<motif name="CBF1" alt="" width="7" best-possible-match="TCACGTG"/>
<motif name="CEP3" alt="" width="7" best-possible-match="CTCGGAA"/>
<motif name="CHA4" alt="" width="9" best-possible-match="ATCTCCGCC"/>
<motif name="CIN5" alt="" width="10" best-possible-match="TTACGTAATC"/>
<motif name="CRZ1" alt="" width="6" best-possible-match="AGCCAC"/>
<motif name="CST6" alt="" width="6" best-possible-match="TGACGT"/>
<motif name="CUP2" alt="" width="11" best-possible-match="CAGCAAAAATG"/>
<motif name="CUP9" alt="" width="9" best-possible-match="AATGTGTCA"/>
<motif name="DAL80" alt="" width="7" best-possible-match="CTTATCG"/>
<motif name="DAL82" alt="" width="14" best-possible-match="CAAGCGCAATTTTC"/>
<motif name="ECM22" alt="" width="13" best-possible-match="CCGGGTCTCCGGA"/>
<motif name="ECM23" alt="" width="6" best-possible-match="AGATCT"/>
<motif name="EDS1" alt="" width="9" best-possible-match="CGGAAAAAT"/>
<motif name="FHL1" alt="" width="8" best-possible-match="GACGCAAA"/>
<motif name="FKH1" alt="" width="13" best-possible-match="AAATGTAAACAAA"/>
<motif name="FKH2" alt="" width="13" best-possible-match="AAAAGTAAACAAA"/>
<motif name="FZF1" alt="" width="6" best-possible-match="CTATCA"/>
<motif name="GAL4" alt="" width="19" best-possible-match="TCGGGGAACAGTACTCCGA"/>
<motif name="GAL80" alt="" width="17" best-possible-match="CGGAGGATTGTCATCCG"/>
<motif name="GAT1" alt="" width="8" best-possible-match="CCTTATCG"/>
<motif name="GAT3" alt="" width="8" best-possible-match="AGATCTAC"/>
<motif name="GAT4" alt="" width="8" best-possible-match="TAGATCTA"/>
<motif name="GCN4" alt="" width="9" best-possible-match="ATGAGTCAT"/>
<motif name="GCR1" alt="" width="8" best-possible-match="TGGAAGCC"/>
<motif name="GIS1" alt="" width="7" best-possible-match="CCCCTAA"/>
<motif name="GLN3" alt="" width="11" best-possible-match="CTGATAAGGCC"/>
<motif name="GSM1" alt="" width="10" best-possible-match="AAACTCCGGA"/>
<motif name="GZF3" alt="" width="13" best-possible-match="ATCGCTTATCAGC"/>
<motif name="HAC1" alt="" width="7" best-possible-match="GACACGT"/>
<motif name="HAL9" alt="" width="18" best-possible-match="TCCGAAAAAAAAAGCGGA"/>
<motif name="HAP1" alt="" width="12" best-possible-match="CCGATATCTCCG"/>
<motif name="HAP2" alt="" width="5" best-possible-match="TTGGT"/>
<motif name="HAP3" alt="" width="15" best-possible-match="TCTGATTGGTTCAGA"/>
<motif name="HAP4" alt="" width="9" best-possible-match="TGATTGGTC"/>
<motif name="HAP5" alt="" width="14" best-possible-match="GGGATCTGATTGGT"/>
<motif name="HCM1" alt="" width="8" best-possible-match="ATAAACAA"/>
<motif name="HMRA2" alt="" width="8" best-possible-match="CATGTAAT"/>
<motif name="HSF1" alt="" width="14" best-possible-match="AGAACCTTATGGAA"/>
<motif name="INO2" alt="" width="11" best-possible-match="GCATGTGAAAA"/>
<motif name="INO4" alt="" width="11" best-possible-match="GCATGTGAAAA"/>
<motif name="LEU3" alt="" width="14" best-possible-match="CCGGTACCGGCGAA"/>
<motif name="LYS14" alt="" width="10" best-possible-match="AAATTCCGGG"/>
<motif name="MAC1" alt="" width="8" best-possible-match="TTTGCTCA"/>
<motif name="MATALPHA2" alt="" width="9" best-possible-match="AATTACATG"/>
<motif name="MBP1" alt="" width="9" best-possible-match="TGACGCGTC"/>
<motif name="MCM1" alt="" width="16" best-possible-match="TTTCCGAATTGGGAAA"/>
<motif name="MET31" alt="" width="10" best-possible-match="AACTGTGGCG"/>
<motif name="MET32" alt="" width="12" best-possible-match="AAACTGTGGCGC"/>
<motif name="MGA1" alt="" width="9" best-possible-match="ATAGAACAC"/>
<motif name="MIG1" alt="" width="14" best-possible-match="TCCCCCGCATTTTT"/>
<motif name="MIG2" alt="" width="13" best-possible-match="GTTACCCCGCAAT"/>
<motif name="MIG3" alt="" width="13" best-possible-match="GTTACCCCGCATT"/>
<motif name="MSN2" alt="" width="7" best-possible-match="TAAGGGG"/>
<motif name="MSN4" alt="" width="7" best-possible-match="TAAGGGG"/>
<motif name="NDT80" alt="" width="13" best-possible-match="GGCCACAAAAACG"/>
<motif name="NHP10" alt="" width="8" best-possible-match="GCCGGGGA"/>
<motif name="NHP6A" alt="" width="10" best-possible-match="CTATATATAA"/>
<motif name="NHP6B" alt="" width="11" best-possible-match="TATATATAATA"/>
<motif name="NRG1" alt="" width="9" best-possible-match="AGGACCCTG"/>
<motif name="OAF1" alt="" width="10" best-possible-match="TTATCTCCGA"/>
<motif name="ORC1" alt="" width="17" best-possible-match="TTTTTTTATGTTTAGTT"/>
<motif name="PBF1" alt="" width="10" best-possible-match="AGCTCATCGC"/>
<motif name="PBF2" alt="" width="11" best-possible-match="CACCTCATCGC"/>
<motif name="PDR1" alt="" width="10" best-possible-match="TTTCCGCGGA"/>
<motif name="PDR3" alt="" width="10" best-possible-match="TTTCCGCGGA"/>
<motif name="PDR8" alt="" width="7" best-possible-match="CGGAGAT"/>
<motif name="PHD1" alt="" width="9" best-possible-match="CATGCATCA"/>
<motif name="PHO2" alt="" width="10" best-possible-match="TTAATTAAAT"/>
<motif name="PHO4" alt="" width="8" best-possible-match="GCACGTGC"/>
<motif name="PUT3" alt="" width="10" best-possible-match="ATCCCGGGAA"/>
<motif name="RAP1" alt="" width="11" best-possible-match="CACCCATACAT"/>
<motif name="RDR1" alt="" width="9" best-possible-match="TGCGGAAAT"/>
<motif name="RDS1" alt="" width="8" best-possible-match="TCGGCCGA"/>
<motif name="RDS2" alt="" width="10" best-possible-match="GAAACCCCGA"/>
<motif name="REB1" alt="" width="11" best-possible-match="TCCGGGTAACA"/>
<motif name="REI1" alt="" width="7" best-possible-match="CCCCTGA"/>
<motif name="RFX1" alt="" width="13" best-possible-match="TTGCCATGGCAAC"/>
<motif name="RGM1" alt="" width="5" best-possible-match="AGGGG"/>
<motif name="RGT1" alt="" width="13" best-possible-match="TTTTCCGGAAAAA"/>
<motif name="RIM101" alt="" width="7" best-possible-match="CGCCAAG"/>
<motif name="RLM1" alt="" width="14" best-possible-match="AGCAAAATTTAAAA"/>
<motif name="ROX1" alt="" width="12" best-possible-match="TCCATTGTTCTC"/>
<motif name="RPH1" alt="" width="10" best-possible-match="AATTAGGGGT"/>
<motif name="RPN4" alt="" width="10" best-possible-match="GGTGGCAAAA"/>
<motif name="RSC3" alt="" width="10" best-possible-match="AGCGCGCGCT"/>
<motif name="RSC30" alt="" width="10" best-possible-match="CGCGCGCGCG"/>
<motif name="RTG3" alt="" width="9" best-possible-match="GTCACGTGC"/>
<motif name="SFL1" alt="" width="15" best-possible-match="ATAGAAGAAATAAAA"/>
<motif name="SFP1" alt="" width="12" best-possible-match="AAAAAATTTTCT"/>
<motif name="SIG1" alt="" width="5" best-possible-match="ATATA"/>
<motif name="SIP4" alt="" width="13" best-possible-match="CGGATGAATGGAG"/>
<motif name="SKN7" alt="" width="14" best-possible-match="CAGTTATGGCCATA"/>
<motif name="SKO1" alt="" width="8" best-possible-match="ACGTAATG"/>
<motif name="SMP1" alt="" width="13" best-possible-match="ACCTATAATTAAA"/>
<motif name="SNT2" alt="" width="10" best-possible-match="TGGTAGCGCC"/>
<motif name="SOK2" alt="" width="9" best-possible-match="ACCTGCAGG"/>
<motif name="SPT15" alt="" width="10" best-possible-match="GATATATATA"/>
<motif name="SRD1" alt="" width="9" best-possible-match="AGATCTACA"/>
<motif name="STB1" alt="" width="12" best-possible-match="AATTTTCGCGTT"/>
<motif name="STB3" alt="" width="11" best-possible-match="AATTTTTCACT"/>
<motif name="STB4" alt="" width="9" best-possible-match="TCGTTCCGA"/>
<motif name="STB5" alt="" width="10" best-possible-match="TATAACACCG"/>
<motif name="STE12" alt="" width="7" best-possible-match="TGTTTCA"/>
<motif name="STP2" alt="" width="9" best-possible-match="GGCGCCGCA"/>
<motif name="STP3" alt="" width="8" best-possible-match="GCTAGCGC"/>
<motif name="STP4" alt="" width="10" best-possible-match="GTGCGGCTGA"/>
<motif name="SUM1" alt="" width="11" best-possible-match="GTGTCACAAAA"/>
<motif name="SUT2" alt="" width="8" best-possible-match="AACTCCGA"/>
<motif name="SWI4" alt="" width="9" best-possible-match="ACGCGAAAA"/>
<motif name="SWI5" alt="" width="7" best-possible-match="TGCTGGT"/>
<motif name="SWI6" alt="" width="10" best-possible-match="AACGCGAAAA"/>
<motif name="TBF1" alt="" width="9" best-possible-match="TAACCCTAA"/>
<motif name="TBS1" alt="" width="10" best-possible-match="GCGGATCCGC"/>
<motif name="TEA1" alt="" width="19" best-possible-match="TCTGCGGAAATTAAATACC"/>
<motif name="TEC1" alt="" width="10" best-possible-match="AACATTCCCG"/>
<motif name="THI2" alt="" width="15" best-possible-match="GGAAACTCTAAGAAC"/>
<motif name="TOS8" alt="" width="8" best-possible-match="CTGTCAAA"/>
<motif name="TYE7" alt="" width="10" best-possible-match="ATCACGTGAT"/>
<motif name="UGA3" alt="" width="8" best-possible-match="CGGCGGGA"/>
<motif name="UME6" alt="" width="13" best-possible-match="ATTTAGCCGCCGA"/>
<motif name="UPC2" alt="" width="6" best-possible-match="ATACGA"/>
<motif name="USV1" alt="" width="11" best-possible-match="TTCCCCCTGAA"/>
<motif name="XBP1" alt="" width="7" best-possible-match="TCTCGAG"/>
<motif name="YAP1" alt="" width="12" best-possible-match="TGCTTACGAAAG"/>
<motif name="YAP3" alt="" width="8" best-possible-match="ATTACGTA"/>
<motif name="YAP6" alt="" width="15" best-possible-match="GTCTGATTACGTAAG"/>
<motif name="YAP7" alt="" width="11" best-possible-match="ATTAGTAAGCA"/>
<motif name="YBR239C" alt="" width="9" best-possible-match="TTCCGGAAC"/>
<motif name="YDR026c" alt="" width="9" best-possible-match="TTTACCCGG"/>
<motif name="YDR520C" alt="" width="9" best-possible-match="CGGAGATAA"/>
<motif name="YER130C" alt="" width="9" best-possible-match="AAATAGGGG"/>
<motif name="YER184C" alt="" width="6" best-possible-match="TCCGGA"/>
<motif name="YGR067C" alt="" width="13" best-possible-match="GCGGGGTACTGTA"/>
<motif name="YKL222C" alt="" width="11" best-possible-match="AACGGAAATAA"/>
<motif name="YLL054C" alt="" width="18" best-possible-match="TCCGTAAAAAAAAACGGA"/>
<motif name="YLR278C" alt="" width="8" best-possible-match="CCGGAGTT"/>
<motif name="YML081W" alt="" width="9" best-possible-match="TACCCCGCA"/>
<motif name="YNR063W" alt="" width="8" best-possible-match="ATCTCCGA"/>
<motif name="YOX1" alt="" width="19" best-possible-match="ATTAATTAATTTTCCTAAA"/>
<motif name="YPR013C" alt="" width="11" best-possible-match="AACGTAAATCA"/>
<motif name="YPR015C" alt="" width="12" best-possible-match="GACGTAAATCCT"/>
<motif name="YPR022C" alt="" width="6" best-possible-match="CCCCAC"/>
<motif name="YPR196W" alt="" width="10" best-possible-match="ATTTCTCCGA"/>
<motif name="YRM1" alt="" width="10" best-possible-match="ACGGAAATAA"/>
<motif name="YRR1" alt="" width="10" best-possible-match="GCGGAAATAA"/>
<motif name="ZMS1" alt="" width="9" best-possible-match="TTCCCCGCA"/>
<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>
