# DREME 4.12.0 # command: dreme -v 1 -oc /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanDNase/M1SnareSeq/BICCN_huMOp_SNARE-Seq2_PVALB_reproduciblePeaks_enhancerShort.MemeChip4ResultsNoNeg/dreme_out -png -dna -p /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanDNase/M1SnareSeq/BICCN_huMOp_SNARE-Seq2_PVALB_reproduciblePeaks_enhancerShort.MemeChip4ResultsNoNeg/seqs-centered -n /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanDNase/M1SnareSeq/BICCN_huMOp_SNARE-Seq2_PVALB_reproduciblePeaks_enhancerShort.MemeChip4ResultsNoNeg/seqs-shuffled # positives: 5703 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanDNase/M1SnareSeq/BICCN_huMOp_SNARE-Seq2_PVALB_reproduciblePeaks_enhancerShort.MemeChip4ResultsNoNeg/seqs-centered (Sun Feb 07 10:47:26 EST 2021) # negatives: 5703 from /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/HumanDNase/M1SnareSeq/BICCN_huMOp_SNARE-Seq2_PVALB_reproduciblePeaks_enhancerShort.MemeChip4ResultsNoNeg/seqs-shuffled (Sun Feb 07 10:47:26 EST 2021) # host: compute-1-37.local # when: Sun Feb 07 11:46:45 EST 2021 MEME version 4.12.0 ALPHABET "DNA" DNA-LIKE A "Adenine" CC0000 ~ T "Thymine" 008000 C "Cytosine" 0000CC ~ G "Guanine" FFB300 N "Any base" = ACGT X = ACGT . = ACGT V "Not T" = ACG H "Not G" = ACT D "Not C" = AGT B "Not A" = CGT M "Amino" = AC R "Purine" = AG W "Weak" = AT S "Strong" = CG Y "Pyrimidine" = CT K "Keto" = GT U = T END ALPHABET strands: + - Background letter frequencies (from dataset): A 0.235 C 0.266 G 0.262 T 0.237 MOTIF RGRAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGRAA TTYCY 3995 3111 6.7e-066 2.9e-061 # GGAAA TTTCC 1637 1012 3.7e-044 1.7e-039 # AGAAA TTTCT 1789 1263 4.7e-029 2.1e-024 # AGGAA TTCCT 1782 1269 1.0e-027 4.4e-023 # GGGAA TTCCC 1533 1134 5.9e-019 2.6e-014 letter-probability matrix: alength= 4 w= 5 nsites= 6838 E= 2.9e-061 0.576046 0.000000 0.423954 0.000000 0.000000 0.000000 1.000000 0.000000 0.515940 0.000000 0.484060 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGRTGGCR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGRTGGCR YGCCAYCT 419 89 1.1e-054 4.8e-050 # AGATGGCA TGCCATCT 163 30 5.7e-024 2.4e-019 # AGGTGGCA TGCCACCT 140 40 1.1e-014 4.5e-010 # AGGTGGCG CGCCACCT 69 13 9.8e-011 4.2e-006 # AGATGGCG CGCCATCT 49 6 8.4e-010 3.6e-005 letter-probability matrix: alength= 4 w= 8 nsites= 423 E= 4.8e-050 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.503546 0.000000 0.496454 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.721040 0.000000 0.278960 0.000000 MOTIF CACAGH DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CACAGH DCTGTG 1810 1222 5.3e-036 2.3e-031 # CACAGC GCTGTG 901 570 1.1e-020 4.6e-016 # CACAGA TCTGTG 662 430 8.2e-014 3.5e-009 # CACAGT ACTGTG 462 336 2.1e-006 9.1e-002 letter-probability matrix: alength= 4 w= 6 nsites= 2178 E= 2.3e-031 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.321396 0.455464 0.000000 0.223140 MOTIF AGAGGGCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGAGGGCR YGCCCTCT 243 66 7.1e-026 3.0e-021 # AGAGGGCA TGCCCTCT 160 43 1.3e-017 5.5e-013 # AGAGGGCG CGCCCTCT 84 23 1.0e-009 4.3e-005 letter-probability matrix: alength= 4 w= 8 nsites= 245 E= 3.0e-021 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.657143 0.000000 0.342857 0.000000 MOTIF ATTTWTAD DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATTTWTAD HTAWAAAT 199 48 9.0e-024 3.8e-019 # ATTTTTAG CTAAAAAT 46 6 4.8e-009 2.0e-004 # ATTTTTAA TTAAAAAT 53 11 4.7e-008 2.0e-003 # ATTTATAA TTATAAAT 27 3 4.1e-006 1.7e-001 # ATTTATAG CTATAAAT 24 6 7.1e-004 3.0e+001 # ATTTATAT ATATAAAT 22 6 1.8e-003 7.7e+001 # ATTTTTAT ATAAAAAT 34 16 7.6e-003 3.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 203 E= 3.8e-019 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.359606 0.000000 0.000000 0.640394 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.389163 0.000000 0.344828 0.266010 MOTIF CAKCTGS DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CAKCTGS SCAGMTG 938 585 1.1e-022 4.8e-018 # CAGCTGC GCAGCTG 464 269 4.7e-014 2.0e-009 # CATCTGC GCAGATG 196 111 5.1e-007 2.1e-002 # CAGCTGG CCAGCTG 340 235 4.1e-006 1.7e-001 # CATCTGG CCAGATG 144 106 8.9e-003 3.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 1030 E= 4.8e-018 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.658252 0.341748 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.602913 0.397087 0.000000 MOTIF AAATA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAATA TATTT 755 488 5.3e-016 2.2e-011 # AAATA TATTT 755 488 5.3e-016 2.2e-011 letter-probability matrix: alength= 4 w= 5 nsites= 860 E= 2.2e-011 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGGRGGCG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGGRGGCG CGCCYCCT 126 30 1.1e-015 4.7e-011 # AGGGGGCG CGCCCCCT 90 19 1.2e-012 5.2e-008 # AGGAGGCG CGCCTCCT 39 11 4.4e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 134 E= 4.7e-011 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.298507 0.000000 0.701493 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF RTGASTCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RTGASTCA TGASTCAY 137 36 1.4e-015 5.9e-011 # ATGAGTCA TGACTCAT 49 11 3.6e-007 1.5e-002 # ATGACTCA TGAGTCAT 45 10 9.8e-007 4.1e-002 # GTGACTCA TGAGTCAC 48 12 1.5e-006 6.2e-002 # GTGAGTCA TGACTCAC 49 13 2.3e-006 9.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 139 E= 5.9e-011 0.496403 0.000000 0.503597 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.517986 0.482014 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CMGCCKCC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CMGCCKCC GGMGGCKG 278 127 8.2e-015 3.4e-010 # CAGCCTCC GGAGGCTG 117 47 1.8e-008 7.5e-004 # CCGCCGCC GGCGGCGG 61 24 3.5e-005 1.4e+000 # CCGCCTCC GGAGGCGG 64 26 3.6e-005 1.5e+000 # CAGCCGCC GGCGGCTG 58 32 3.9e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 300 E= 3.4e-010 0.000000 1.000000 0.000000 0.000000 0.580000 0.420000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.403333 0.596667 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCACTAGR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCACTAGR YCTAGTGG 109 26 1.0e-013 4.2e-009 # CCACTAGA TCTAGTGG 60 15 7.3e-008 3.0e-003 # CCACTAGG CCTAGTGG 49 11 3.6e-007 1.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 110 E= 4.2e-009 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.545455 0.000000 0.454545 0.000000 MOTIF GGGAGRR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GGGAGRR YYCTCCC 737 515 1.6e-011 6.7e-007 # GGGAGGA TCCTCCC 175 110 5.8e-005 2.4e+000 # GGGAGGG CCCTCCC 245 173 2.0e-004 8.1e+000 # GGGAGAA TTCTCCC 120 71 2.2e-004 8.9e+000 # GGGAGAG CTCTCCC 267 196 4.4e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 827 E= 6.7e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.476421 0.000000 0.523579 0.000000 0.366385 0.000000 0.633615 0.000000 MOTIF ACAYACAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACAYACAC GTGTRTGT 96 25 2.1e-011 8.8e-007 # ACACACAC GTGTGTGT 79 20 7.7e-010 3.2e-005 # ACATACAC GTGTATGT 24 7 1.6e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 146 E= 8.8e-007 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.856164 0.000000 0.143836 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTGBAG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTGBAG CTVCAG 1410 1152 4.0e-009 1.6e-004 # CTGCAG CTGCAG 557 409 3.7e-007 1.5e-002 # CTGGAG CTCCAG 697 596 1.6e-003 6.5e+001 # CTGTAG CTACAG 280 227 9.0e-003 3.7e+002 letter-probability matrix: alength= 4 w= 6 nsites= 1637 E= 1.6e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.359805 0.464875 0.175321 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GAYGTCAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GAYGTCAC GTGACRTC 42 4 2.4e-009 9.8e-005 # GACGTCAC GTGACGTC 20 0 9.4e-007 3.9e-002 # GATGTCAC GTGACATC 22 4 2.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 9.8e-005 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.476190 0.000000 0.523810 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTGCCWCC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CTGCCWCC GGWGGCAG 176 88 2.3e-008 9.5e-004 # CTGCCTCC GGAGGCAG 106 55 3.2e-005 1.3e+000 # CTGCCACC GGTGGCAG 70 34 2.5e-004 1.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 179 E= 9.5e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.396648 0.000000 0.000000 0.603352 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCCMGCCC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCCMGCCC GGGCKGGG 177 89 2.6e-008 1.1e-003 # CCCCGCCC GGGCGGGG 88 38 4.4e-006 1.8e-001 # CCCAGCCC GGGCTGGG 94 53 4.2e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 196 E= 1.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.474490 0.525510 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACACRG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACACRG CYGTGT 274 167 1.2e-007 4.8e-003 # ACACGG CCGTGT 126 63 2.2e-006 9.2e-002 # ACACAG CTGTGT 151 104 1.7e-003 7.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 282 E= 4.8e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.539007 0.000000 0.460993 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACGT DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACGT ACGT 490 348 2.0e-007 8.1e-003 # ACGT ACGT 490 348 2.0e-007 8.1e-003 letter-probability matrix: alength= 4 w= 4 nsites= 519 E= 8.1e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GAGASAGA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GAGASAGA TCTSTCTC 135 65 3.3e-007 1.3e-002 # GAGAGAGA TCTCTCTC 79 33 7.4e-006 3.0e-001 # GAGACAGA TCTGTCTC 60 32 2.2e-003 8.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 156 E= 1.3e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.403846 0.596154 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 1254.82 seconds