# DREME 4.12.0 # command: dreme -v 1 -oc overlap_cut/dreme_out -png -dna -p overlap_cut/seqs-centered -n overlap_cut/seqs-shuffled # positives: 4485 from overlap_cut/seqs-centered (Mon Oct 21 03:56:37 PDT 2019) # negatives: 4485 from overlap_cut/seqs-shuffled (Mon Oct 21 03:56:37 PDT 2019) # host: surya.stanford.edu # when: Mon Oct 21 04:08:25 PDT 2019 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 0.275 C 0.224 G 0.226 T 0.276 MOTIF ATGYWAAT DREME-1 # Word RC Word Pos Neg P-value E-value # BEST ATGYWAAT ATTWRCAT 1252 88 4.2e-303 1.8e-298 # ATGCAAAT ATTTGCAT 588 30 7.8e-144 3.3e-139 # ATGCTAAT ATTAGCAT 322 19 7.7e-075 3.3e-070 # ATGTAAAT ATTTACAT 269 17 2.2e-061 9.5e-057 # ATGTTAAT ATTAACAT 216 22 1.9e-042 7.9e-038 letter-probability matrix: alength= 4 w= 8 nsites= 1493 E= 1.8e-298 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.659745 0.000000 0.340255 0.617549 0.000000 0.000000 0.382451 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GGTNCTGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTNCTGA TCAGNACC 568 42 2.7e-126 1.2e-121 # GGTGCTGA TCAGCACC 389 16 7.1e-098 3.0e-093 # GGTCCTGA TCAGGACC 108 10 1.9e-022 8.0e-018 # GGTACTGA TCAGTACC 35 3 3.2e-008 1.3e-003 # GGTTCTGA TCAGAACC 46 13 9.0e-006 3.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 601 E= 1.2e-121 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.058236 0.181364 0.683860 0.076539 0.000000 1.000000 0.000000 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 MOTIF GGACAGCD DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGACAGCD HGCTGTCC 416 40 7.2e-084 3.0e-079 # GGACAGCG CGCTGTCC 148 5 1.9e-038 7.9e-034 # GGACAGCT AGCTGTCC 157 15 8.2e-032 3.5e-027 # GGACAGCA TGCTGTCC 123 20 7.7e-020 3.2e-015 letter-probability matrix: alength= 4 w= 8 nsites= 436 E= 3.0e-079 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 1.000000 0.000000 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 0.284404 0.000000 0.346330 0.369266 MOTIF WTATGCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST WTATGCR YGCATAW 641 170 3.0e-071 1.3e-066 # TTATGCA TGCATAA 317 80 3.4e-036 1.4e-031 # ATATGCA TGCATAT 286 73 2.3e-032 9.8e-028 # ATATGCG CGCATAT 58 10 1.0e-009 4.4e-005 # TTATGCG CGCATAA 44 10 1.6e-006 6.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 713 E= 1.3e-066 0.493689 0.000000 0.000000 0.506311 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 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 0.862553 0.000000 0.137447 0.000000 MOTIF ACAAWRG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACAAWRG CYWTTGT 712 303 1.9e-043 8.0e-039 # ACAAAAG CTTTTGT 276 125 4.5e-015 1.9e-010 # ACAAAGG CCTTTGT 204 80 2.4e-014 1.0e-009 # ACAATAG CTATTGT 134 47 2.3e-011 9.6e-007 # ACAATGG CCATTGT 139 56 8.4e-010 3.5e-005 letter-probability matrix: alength= 4 w= 7 nsites= 768 E= 8.0e-039 1.000000 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 0.640625 0.000000 0.000000 0.359375 0.545573 0.000000 0.454427 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GGAATKY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GGAATKY RMATTCC 599 229 6.9e-043 2.9e-038 # GGAATGT ACATTCC 181 53 2.9e-018 1.2e-013 # GGAATTT AAATTCC 206 80 1.1e-014 4.7e-010 # GGAATGC GCATTCC 131 45 2.0e-011 8.4e-007 # GGAATTC GAATTCC 110 54 6.1e-006 2.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 655 E= 2.9e-038 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 0.496183 0.503817 0.000000 0.386260 0.000000 0.613740 MOTIF ATCTRCAT DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATCTRCAT ATGYAGAT 165 22 4.3e-029 1.8e-024 # ATCTACAT ATGTAGAT 83 8 2.8e-017 1.2e-012 # ATCTGCAT ATGCAGAT 83 14 1.6e-013 6.7e-009 letter-probability matrix: alength= 4 w= 8 nsites= 169 E= 1.8e-024 1.000000 0.000000 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 0.508876 0.000000 0.491124 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF TATGYWAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TATGYWAA TTWRCATA 186 37 6.2e-026 2.6e-021 # TATGCTAA TTAGCATA 57 8 1.4e-010 5.8e-006 # TATGTAAA TTTACATA 60 12 3.5e-009 1.5e-004 # TATGTTAA TTAACATA 43 12 1.6e-005 6.5e-001 # TATGCAAA TTTGCATA 26 5 9.4e-005 3.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 190 E= 2.6e-021 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.436842 0.000000 0.563158 0.468421 0.000000 0.000000 0.531579 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARAGRAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ARAGRAA TTYCTYT 785 455 2.3e-024 9.7e-020 # AAAGGAA TTCCTTT 233 103 1.9e-013 8.0e-009 # AGAGAAA TTTCTCT 207 112 3.4e-008 1.4e-003 # AAAGAAA TTTCTTT 283 185 1.9e-006 8.0e-002 # AGAGGAA TTCCTCT 143 87 1.1e-004 4.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 878 E= 9.7e-020 1.000000 0.000000 0.000000 0.000000 0.595672 0.000000 0.404328 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.571754 0.000000 0.428246 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGAATA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATGAATA TATTCAT 265 86 1.9e-023 7.7e-019 # ATGAATA TATTCAT 265 86 1.9e-023 7.7e-019 letter-probability matrix: alength= 4 w= 7 nsites= 269 E= 7.7e-019 1.000000 0.000000 0.000000 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 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 GGGHGGR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGGHGGR YCCDCCC 641 352 8.9e-023 3.7e-018 # GGGCGGG CCCGCCC 141 40 6.0e-015 2.5e-010 # GGGAGGG CCCTCCC 199 108 7.1e-008 2.9e-003 # GGGTGGG CCCACCC 134 71 5.1e-006 2.1e-001 # GGGAGGA TCCTCCC 126 69 2.2e-005 9.3e-001 # GGGTGGA TCCACCC 107 65 7.6e-004 3.2e+001 # GGGCGGA TCCGCCC 53 25 9.7e-004 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 756 E= 3.7e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.421958 0.280423 0.000000 0.297619 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.371693 0.000000 0.628307 0.000000 MOTIF CAGGWR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CAGGWR YWCCTG 1261 923 5.1e-017 2.1e-012 # CAGGTA TACCTG 276 169 1.1e-007 4.6e-003 # CAGGAA TTCCTG 373 266 6.5e-006 2.7e-001 # CAGGAG CTCCTG 414 308 2.2e-005 9.2e-001 # CAGGTG CACCTG 352 256 3.2e-005 1.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 1496 E= 2.1e-012 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.547460 0.000000 0.000000 0.452540 0.465241 0.000000 0.534759 0.000000 MOTIF AYGGACAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AYGGACAG CTGTCCRT 78 15 7.8e-012 3.2e-007 # ATGGACAG CTGTCCAT 56 11 9.6e-009 3.9e-004 # ACGGACAG CTGTCCGT 22 4 2.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 79 E= 3.2e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.278481 0.000000 0.721519 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CACGTG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CACGTG CACGTG 68 11 1.5e-011 6.1e-007 # CACGTG CACGTG 68 11 1.5e-011 6.1e-007 letter-probability matrix: alength= 4 w= 6 nsites= 68 E= 6.1e-007 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AASAATG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AASAATG CATTSTT 250 129 1.1e-010 4.4e-006 # AAGAATG CATTCTT 169 80 5.5e-009 2.3e-004 # AACAATG CATTGTT 83 49 1.8e-003 7.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 260 E= 4.4e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.326923 0.673077 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 0.000000 0.000000 1.000000 0.000000 MOTIF AGRGAGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGRGAGA TCTCYCT 283 157 3.9e-010 1.6e-005 # AGAGAGA TCTCTCT 182 92 1.8e-008 7.4e-004 # AGGGAGA TCTCCCT 123 72 1.4e-004 5.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 383 E= 1.6e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.671018 0.000000 0.328982 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGYGCTGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AGYGCTGA TCAGCRCT 71 17 2.2e-009 8.9e-005 # AGTGCTGA TCAGCACT 58 17 9.9e-007 4.0e-002 # AGCGCTGA TCAGCGCT 14 0 6.0e-005 2.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 72 E= 8.9e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.194444 0.000000 0.805556 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CATTTGHA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CATTTGHA TDCAAATG 141 61 6.2e-009 2.5e-004 # CATTTGTA TACAAATG 53 21 1.2e-004 4.9e+000 # CATTTGCA TGCAAATG 40 13 1.3e-004 5.3e+000 # CATTTGAA TTCAAATG 48 27 9.9e-003 4.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 143 E= 2.5e-004 0.000000 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 0.349650 0.279720 0.000000 0.370629 1.000000 0.000000 0.000000 0.000000 MOTIF AGGCGGG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AGGCGGG CCCGCCT 76 22 1.7e-008 6.7e-004 # AGGCGGG CCCGCCT 76 22 1.7e-008 6.7e-004 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 6.7e-004 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 1.000000 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 MOTIF ACAAAGM DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACAAAGM KCTTTGT 257 150 3.2e-008 1.3e-003 # ACAAAGA TCTTTGT 148 73 1.8e-007 7.4e-003 # ACAAAGC GCTTTGT 111 78 9.2e-003 3.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 263 E= 1.3e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.577947 0.422053 0.000000 0.000000 MOTIF ATGGARA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST ATGGARA TYTCCAT 241 145 3.4e-007 1.4e-002 # ATGGAGA TCTCCAT 109 62 1.8e-004 7.2e+000 # ATGGAAA TTTCCAT 135 84 3.0e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 250 E= 1.4e-002 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.544000 0.000000 0.456000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GACARAAC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GACARAAC GTTYTGTC 39 7 8.7e-007 3.5e-002 # GACAGAAC GTTCTGTC 17 2 3.6e-004 1.5e+001 # GACAAAAC GTTTTGTC 22 5 7.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.5e-002 0.000000 0.000000 1.000000 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 0.575000 0.000000 0.425000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 481.93 seconds