<?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-yeast_uniprobe_GR09 /woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/YEAST/yeast_uniprobe_GR09.meme /woldlab/castor/home/georgi/genomes/sacCer3/sequence/sacCer3.fa</command-line>
<settings>
<setting name="output directory">FIMO-sacCer3-YEAST-yeast_uniprobe_GR09</setting>
<setting name="MEME file name">/woldlab/castor/home/georgi/programs/meme_4.11.2/motif_databases/YEAST/yeast_uniprobe_GR09.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="UP00344_1" alt="Aft1" width="21" best-possible-match="TTACATATTGCACCCGATTGG"/>
<motif name="UP00329_1" alt="Aro80" width="21" best-possible-match="GATAATTCTCGGCAAGTATGT"/>
<motif name="UP00350_1" alt="Asg1" width="16" best-possible-match="CCCGGCCGAGTTCCGG"/>
<motif name="UP00355_1" alt="Bas1" width="21" best-possible-match="GCACAGCCAGAGTCAAGTCAA"/>
<motif name="UP00309_1" alt="Cbf1" width="21" best-possible-match="GATCAGTCACGTGACTGATCG"/>
<motif name="UP00278_1" alt="Cep3" width="20" best-possible-match="GGCGACTTCGGAAATATGAG"/>
<motif name="UP00300_1" alt="Cha4" width="21" best-possible-match="GGGGGTATCTCCGCCGGTGTG"/>
<motif name="UP00308_1" alt="Cup9" width="20" best-possible-match="TTGCATATGTGTCACATTTT"/>
<motif name="UP00305_1" alt="Ecm22" width="18" best-possible-match="TTCCGGGTGGCCGGAAAT"/>
<motif name="UP00303_1" alt="Fhl1" width="20" best-possible-match="AAAATTGACGCAAATTCGTT"/>
<motif name="UP00353_1" alt="Fkh1" width="20" best-possible-match="TGAATTGTAAACAAAGAGGA"/>
<motif name="UP00312_1" alt="Fkh2" width="20" best-possible-match="TTAAAAGTAAACAAAGATGA"/>
<motif name="UP00322_1" alt="Gal4" width="19" best-possible-match="TCGGGAAAAAAAAAACCGA"/>
<motif name="UP00287_1" alt="Gat1" width="20" best-possible-match="CCATTTCCTTATCGGGTTTA"/>
<motif name="UP00319_1" alt="Gat3" width="20" best-possible-match="TAAATGAGATCTACAAGCTG"/>
<motif name="UP00336_1" alt="Gat4" width="20" best-possible-match="CCAGAATAGATCTATTCGCC"/>
<motif name="UP00285_1" alt="Gcn4" width="21" best-possible-match="CAAGGGATGAGTCATACTTCA"/>
<motif name="UP00318_1" alt="Gln3" width="21" best-possible-match="GTTTAGGCCTTATCAGCAATA"/>
<motif name="UP00301_1" alt="Gsm1" width="21" best-possible-match="ATTAAAAAACTCCGGAGTATA"/>
<motif name="UP00347_1" alt="Gzf3" width="20" best-possible-match="TTGCGGCTGATAAGGGATAA"/>
<motif name="UP00315_1" alt="Hal9" width="18" best-possible-match="TCCGAAAAAAAAAGCGGA"/>
<motif name="UP00277_1" alt="Leu3" width="21" best-possible-match="TCAAATACCGGCGAAATCTAA"/>
<motif name="UP00282_1" alt="Lys14" width="20" best-possible-match="CTCCCAAAATTCCGGGCGCT"/>
<motif name="UP00307_1" alt="Matalpha2" width="20" best-possible-match="TTGTAGAACAATAGACCTCC"/>
<motif name="UP00271_1" alt="Mbp1" width="20" best-possible-match="TGGGCGACGCGTCAGATGCA"/>
<motif name="UP00326_1" alt="Mcm1" width="20" best-possible-match="TGTTTCCCAATTCGGAAATG"/>
<motif name="UP00345_1" alt="Met32" width="21" best-possible-match="TCTCAAAGTGTGGCGCCCGTA"/>
<motif name="UP00339_1" alt="Mga1" width="21" best-possible-match="AGGACTATAGAACACTCTAAA"/>
<motif name="UP00291_1" alt="Mig1" width="21" best-possible-match="GTAAATAATGCGGGGGACTTG"/>
<motif name="UP00349_1" alt="Mig2" width="21" best-possible-match="ACGTGTTACCCCGCAATTAAT"/>
<motif name="UP00317_1" alt="Mig3" width="21" best-possible-match="ACGTGTTACCCCGCATTTAAT"/>
<motif name="UP00346_1" alt="Ndt80" width="21" best-possible-match="TTTCCGGCCACAAAAACGCAA"/>
<motif name="UP00352_1" alt="Nhp6a" width="21" best-possible-match="ATGACCTATATATAAAAATGA"/>
<motif name="UP00325_1" alt="Nhp6b" width="20" best-possible-match="TTTATTTATATATAATATGA"/>
<motif name="UP00270_1" alt="Nrg1" width="20" best-possible-match="CTAGATCAGGGTCCATCGCA"/>
<motif name="UP00298_1" alt="Oaf1" width="21" best-possible-match="TTTGCTTAAATCCGAAATGTA"/>
<motif name="UP00328_1" alt="Pbf1" width="21" best-possible-match="AGGCACAGCTCATCGCGTTTT"/>
<motif name="UP00280_1" alt="Pbf2" width="21" best-possible-match="TTCTGCACCTCATCGCATCCT"/>
<motif name="UP00290_1" alt="Pdr1" width="20" best-possible-match="GTGACTTTCCGGAATACTAA"/>
<motif name="UP00351_1" alt="Phd1" width="21" best-possible-match="GGGGAGCATGCATCAAGGTGG"/>
<motif name="UP00268_1" alt="Pho2" width="20" best-possible-match="CGCTGATTAATTAATGGGGC"/>
<motif name="UP00332_1" alt="Pho4" width="20" best-possible-match="GACCAAGCACGTGCTCGTAT"/>
<motif name="UP00335_1" alt="Put3" width="20" best-possible-match="ATCACTATCCCGGGAAGTTT"/>
<motif name="UP00321_1" alt="Rap1" width="20" best-possible-match="GGGTTAGGGTGTACGGGTAT"/>
<motif name="UP00269_1" alt="Rdr1" width="21" best-possible-match="TCAGACGTGCGGATATGGATC"/>
<motif name="UP00296_1" alt="Rds1" width="20" best-possible-match="CGTCCTTCGGCCGAAGGGGA"/>
<motif name="UP00302_1" alt="Rds2" width="21" best-possible-match="ATTTCGAAAACCCGAGGGAGT"/>
<motif name="UP00288_1" alt="Rgt1" width="20" best-possible-match="TTCTTCCGGAAAAATTTGCA"/>
<motif name="UP00348_1" alt="Rph1" width="21" best-possible-match="AAGAAAAATTAGGGGTGGAAT"/>
<motif name="UP00272_1" alt="Rpn4" width="20" best-possible-match="ACGTAACGCCACCCTAATCG"/>
<motif name="UP00286_1" alt="Rsc3" width="21" best-possible-match="TATAAGAGCGCGCGCTCTGTG"/>
<motif name="UP00279_1" alt="Rsc30" width="21" best-possible-match="CCCCCCGCGCGCGCGGTCGAC"/>
<motif name="UP00356_1" alt="Rtg3" width="20" best-possible-match="ATATTAGCACGTGCTTAGTC"/>
<motif name="UP00320_1" alt="Sfl1" width="21" best-possible-match="TAGAGAATAGAAGAAATAAAA"/>
<motif name="UP00342_1" alt="Sfp1" width="21" best-possible-match="ATTGAAAAAAATTTTCTACGG"/>
<motif name="UP00273_1" alt="Sip4" width="20" best-possible-match="CCCTATTTCCGGAAAGTTCC"/>
<motif name="UP00313_1" alt="Skn7" width="21" best-possible-match="CCAGTTATGGCCATATCTCCT"/>
<motif name="UP00294_1" alt="Smp1" width="21" best-possible-match="TTACCTATAATTAAATTAGCA"/>
<motif name="UP00337_1" alt="Spt15" width="21" best-possible-match="GACTAGATATATATATTCGAT"/>
<motif name="UP00304_1" alt="Srd1" width="20" best-possible-match="CAAATGAGATCTACAAACTG"/>
<motif name="UP00275_1" alt="Stb3" width="21" best-possible-match="GTCCAAAATTTTTCACTCTGG"/>
<motif name="UP00338_1" alt="Stp2" width="20" best-possible-match="TGATCGGCGCCGCACGACGA"/>
<motif name="UP00354_1" alt="Stp4" width="21" best-possible-match="CACTCGTGCGGCTGAAGCCGA"/>
<motif name="UP00341_1" alt="Sum1" width="20" best-possible-match="GCAAAAAATTAATTTTTAAC"/>
<motif name="UP00297_1" alt="Sut2" width="20" best-possible-match="ATGATAAACTCCGAAAATTT"/>
<motif name="UP00299_1" alt="Tbf1" width="20" best-possible-match="TTCCGTAACCCTAATACGCC"/>
<motif name="UP00306_1" alt="Tbs1" width="20" best-possible-match="TTTATGCGGATCCGCGGCTC"/>
<motif name="UP00333_1" alt="Tea1" width="20" best-possible-match="ATCTGCGGAAATTAAATACC"/>
<motif name="UP00340_1" alt="Tec1" width="20" best-possible-match="CAACCAACATTCTTGATATA"/>
<motif name="UP00324_1" alt="Tye7" width="20" best-possible-match="GATGCATCACGTGATGCACT"/>
<motif name="UP00334_1" alt="Ume6" width="20" best-possible-match="CTTTTCGGCGGCTATTTCGA"/>
<motif name="UP00343_1" alt="Usv1" width="20" best-possible-match="AAATTCCCCCTGAATTTGTG"/>
<motif name="UP00330_1" alt="Xbp1" width="20" best-possible-match="CTCGCATCTCGAGAGATGCG"/>
<motif name="UP00327_1" alt="Yap1" width="20" best-possible-match="ATTTGCTTACGTAAGCTCGT"/>
<motif name="UP00316_1" alt="Yap6" width="20" best-possible-match="GGTCTGATTACGTAAGCGAC"/>
<motif name="UP00331_1" alt="Ybr239c" width="20" best-possible-match="AGAATTTTCCGGAACAAACG"/>
<motif name="UP00323_1" alt="Ydr520c" width="20" best-possible-match="TAACATCGGAGATAATTTTA"/>
<motif name="UP00284_1" alt="Yer130c" width="20" best-possible-match="CTATGAAATAGGGGTAGGTA"/>
<motif name="UP00293_1" alt="Ygr067c" width="20" best-possible-match="TGGAGTGCGGGGTACTGTAA"/>
<motif name="UP00281_1" alt="Ykl222c" width="21" best-possible-match="CCGAGAACGGAAATAAGGCGG"/>
<motif name="UP00283_1" alt="Yll054c" width="18" best-possible-match="TCCGTAAAAAAAAACGGA"/>
<motif name="UP00289_1" alt="Yml081w" width="21" best-possible-match="ATGTACTACCCCGCACTTGTG"/>
<motif name="UP00292_1" alt="Ynr063w" width="20" best-possible-match="CCTTAAATCTCCGAGGCCGC"/>
<motif name="UP00274_1" alt="Yox1" width="20" best-possible-match="TTCCAATTAATTAATTTCTC"/>
<motif name="UP00311_1" alt="Ypr013c" width="20" best-possible-match="TTGAACGTAAATCACTTTAG"/>
<motif name="UP00276_1" alt="Ypr015c" width="20" best-possible-match="TGAAGACGTAAATCCTTACA"/>
<motif name="UP00314_1" alt="Ypr196w" width="21" best-possible-match="ATCTCAATTTCTCCGATGATT"/>
<motif name="UP00295_1" alt="Yrm1" width="21" best-possible-match="CACTCGCGGAAATAAGACGGT"/>
<motif name="UP00310_1" alt="Yrr1" width="21" best-possible-match="CGAGCGCGGAAATAACGGTCC"/>
<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>
