<dreme version="5.0.4" release="Wed Jan 23 14:05:40 2019 -0800"> <model> <command_line>dreme -oc StrongEnhancerVsSilencer -p strongEnhancer.fasta -n silencer.fasta -dna -eps -mink 6 -maxk 12 -e 0.05</command_line> <positives name="strongEnhancer" count="1051" file="strongEnhancer.fasta" last_mod_date="Tue Jul 28 11:35:47 CDT 2020" /> <negatives name="silencer" count="837" from="file" file="silencer.fasta" last_mod_date="Tue Jul 28 11:35:47 CDT 2020" /> <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> <strands>both</strands> <background A="0.248" C="0.260" G="0.236" T="0.256" from="dataset"/> <stop evalue="0.05"/> <ngen>100</ngen> <add_pv_thresh>0.01</add_pv_thresh> <seed>1</seed> <host>n171</host> <when>Tue Jul 28 11:40:48 CDT 2020</when> </model> <motifs> <motif id="m01" alt="DREME-1" seq="RGGKCA" length="6" nsites="773" p="574" n="266" pvalue="1.4e-023" evalue="7.4e-018" unerased_evalue="7.4e-018"> <pos A="0.614489" C="0.000000" G="0.385511" T="0.000000"/> <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/> <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/> <pos A="0.000000" C="0.000000" G="0.455369" T="0.544631"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/> <match seq="AGGTCA" p="248" n="100" pvalue="3.3e-011" evalue="1.7e-005"/> <match seq="GGGTCA" p="141" n="46" pvalue="3.4e-009" evalue="1.8e-003"/> <match seq="GGGGCA" p="136" n="53" pvalue="9.5e-007" evalue="4.9e-001"/> <match seq="AGGGCA" p="185" n="103" pvalue="8.6e-004" evalue="4.5e+002"/> </motif> <motif id="m02" alt="DREME-2" seq="CAKMTGG" length="7" nsites="253" p="229" n="62" pvalue="6.0e-019" evalue="2.9e-013" unerased_evalue="1.1e-013"> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="1.000000" C="0.000000" G="0.000000" T="0.000000"/> <pos A="0.000000" C="0.000000" G="0.707510" T="0.292490"/> <pos A="0.509881" C="0.490119" G="0.000000" T="0.000000"/> <pos A="0.000000" C="0.000000" G="0.000000" T="1.000000"/> <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/> <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/> <match seq="CAGATGG" p="121" n="20" pvalue="2.1e-015" evalue="1.1e-009"/> <match seq="CATCTGG" p="62" n="10" pvalue="1.9e-008" evalue="9.6e-003"/> <match seq="CATATGG" p="26" n="5" pvalue="8.3e-004" evalue="4.1e+002"/> <match seq="CAGCTGG" p="75" n="32" pvalue="1.2e-003" evalue="5.9e+002"/> </motif> <motif id="m03" alt="DREME-3" seq="CCNCCCC" length="7" nsites="361" p="272" n="102" pvalue="3.3e-014" evalue="1.6e-008" unerased_evalue="2.4e-009"> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.229917" C="0.124654" G="0.238227" T="0.407202"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <match seq="CCTCCCC" p="129" n="41" pvalue="8.8e-009" evalue="4.3e-003"/> <match seq="CCACCCC" p="82" n="28" pvalue="2.0e-005" evalue="9.7e+000"/> <match seq="CCGCCCC" p="73" n="30" pvalue="8.3e-004" evalue="4.0e+002"/> <match seq="CCCCCCC" p="46" n="17" pvalue="3.0e-003" evalue="1.5e+003"/> </motif> <motif id="m04" alt="DREME-4" seq="CWGCWG" length="6" nsites="521" p="415" n="201" pvalue="4.9e-013" evalue="2.3e-007" unerased_evalue="5.9e-009"> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.476008" C="0.000000" G="0.000000" T="0.523992"/> <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/> <pos A="0.000000" C="1.000000" G="0.000000" T="0.000000"/> <pos A="0.508637" C="0.000000" G="0.000000" T="0.491363"/> <pos A="0.000000" C="0.000000" G="1.000000" T="0.000000"/> <match seq="CAGCAG" p="274" n="127" pvalue="4.2e-009" evalue="2.0e-003"/> <match seq="CAGCTG" p="101" n="40" pvalue="3.9e-005" evalue="1.8e+001"/> <match seq="CTGCAG" p="121" n="60" pvalue="8.5e-004" evalue="4.0e+002"/> </motif> <motif id="m05" alt="DREME-5" seq="CAGSCTGY" 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