# DREME 4.12.0 # command: dreme -v 1 -oc cbf1_hg19/dreme_out -png -dna -p cbf1_hg19/seqs-centered -n cbf1_hg19/seqs-shuffled # positives: 6839 from cbf1_hg19/seqs-centered (Mon Sep 21 20:45:00 PDT 2020) # negatives: 6839 from cbf1_hg19/seqs-shuffled (Mon Sep 21 20:45:00 PDT 2020) # host: surya.stanford.edu # when: Mon Sep 21 20:56:53 PDT 2020 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 0.172 C 0.328 G 0.329 T 0.171 MOTIF TGACTMA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGACTMA TKAGTCA 606 68 5.8e-114 2.6e-109 # TGACTCA TGAGTCA 524 52 3.7e-103 1.6e-098 # TGACTAA TTAGTCA 93 16 8.9e-015 4.0e-010 letter-probability matrix: alength= 4 w= 7 nsites= 648 E= 2.6e-109 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.146605 0.853395 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGGYGGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGGYGGGR YCCCRCCC 1510 687 1.2e-083 5.5e-079 # GGGCGGGG CCCCGCCC 957 353 2.3e-071 1.0e-066 # GGGTGGGG CCCCACCC 322 147 6.7e-017 3.0e-012 # GGGCGGGA TCCCGCCC 293 158 5.1e-011 2.3e-006 # GGGTGGGA TCCCACCC 117 63 3.1e-005 1.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 1894 E= 5.5e-079 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 0.769271 0.000000 0.230729 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.218585 0.000000 0.781415 0.000000 MOTIF CHGGRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CHGGRA TYCCDG 3586 2540 8.8e-073 3.9e-068 # CTGGGA TCCCAG 1115 597 1.5e-041 6.7e-037 # CAGGAA TTCCTG 759 405 6.1e-028 2.7e-023 # CCGGAA TTCCGG 549 329 8.1e-015 3.6e-010 # CCGGGA TCCCGG 974 686 2.5e-014 1.1e-009 # CTGGAA TTCCAG 564 373 5.5e-011 2.4e-006 # CAGGGA TCCCTG 791 667 3.3e-004 1.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 5000 E= 3.9e-068 0.000000 1.000000 0.000000 0.000000 0.322000 0.325400 0.000000 0.352600 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.386400 0.000000 0.613600 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCKCCKCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCKCCKCC GGMGGMGG 1178 608 2.9e-048 1.3e-043 # CCGCCGCC GGCGGCGG 531 240 7.4e-028 3.2e-023 # CCTCCTCC GGAGGAGG 299 126 4.2e-018 1.8e-013 # CCGCCTCC GGAGGCGG 322 144 1.5e-017 6.7e-013 # CCTCCGCC GGCGGAGG 264 162 3.0e-007 1.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 1453 E= 1.3e-043 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.629732 0.370268 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.584308 0.415692 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RTGGGAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST RTGGGAA TTCCCAY 419 149 3.4e-032 1.5e-027 # GTGGGAA TTCCCAC 294 87 2.2e-028 9.6e-024 # ATGGGAA TTCCCAT 131 63 5.0e-007 2.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 434 E= 1.5e-027 0.301843 0.000000 0.698157 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGDAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGDAA TTHCT 2157 1619 4.2e-025 1.8e-020 # AGGAA TTCCT 1100 772 1.8e-016 7.7e-012 # AGAAA TTTCT 1025 785 7.8e-010 3.4e-005 # AGTAA TTACT 418 317 7.3e-005 3.2e+000 letter-probability matrix: alength= 4 w= 5 nsites= 2871 E= 1.8e-020 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.414838 0.000000 0.433647 0.151515 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACGTSAB DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACGTSAB VTSACGT 329 122 5.0e-024 2.1e-019 # ACGTGAC GTCACGT 94 20 4.8e-013 2.0e-008 # ACGTCAC GTGACGT 94 30 3.1e-009 1.3e-004 # ACGTCAG CTGACGT 89 32 9.5e-008 4.0e-003 # ACGTCAT ATGACGT 41 12 4.0e-005 1.7e+000 # ACGTGAT ATCACGT 27 9 1.9e-003 8.2e+001 # ACGTGAG CTCACGT 53 28 3.6e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 356 E= 2.1e-019 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 0.539326 0.460674 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.483146 0.348315 0.168539 MOTIF RRCCACA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST RRCCACA TGTGGYY 581 323 2.8e-019 1.2e-014 # AACCACA TGTGGTT 140 47 2.3e-012 9.5e-008 # GACCACA TGTGGTC 118 55 8.2e-007 3.4e-002 # AGCCACA TGTGGCT 156 96 8.3e-005 3.5e+000 # GGCCACA TGTGGCC 196 130 1.3e-004 5.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 616 E= 1.2e-014 0.483766 0.000000 0.516234 0.000000 0.425325 0.000000 0.574675 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCGCWGCY DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCGCWGCY RGCWGCGG 530 304 3.1e-016 1.3e-011 # CCGCAGCC GGCTGCGG 208 108 6.7e-009 2.8e-004 # CCGCTGCC GGCAGCGG 185 112 1.1e-005 4.6e-001 # CCGCAGCT AGCTGCGG 85 39 2.0e-005 8.5e-001 # CCGCTGCT AGCAGCGG 86 56 7.1e-003 3.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 572 E= 1.3e-011 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 1.000000 0.000000 0.000000 0.520979 0.000000 0.000000 0.479021 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.702797 0.000000 0.297203 MOTIF RTAAAYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RTAAAYA TRTTTAY 127 33 1.2e-014 5.0e-010 # ATAAATA TATTTAT 40 6 1.5e-007 6.2e-003 # GTAAACA TGTTTAC 44 11 4.2e-006 1.7e-001 # GTAAATA TATTTAC 19 4 1.3e-003 5.4e+001 # ATAAACA TGTTTAT 28 12 8.2e-003 3.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 131 E= 5.0e-010 0.519084 0.000000 0.480916 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.541985 0.000000 0.458015 1.000000 0.000000 0.000000 0.000000 MOTIF ATTGGCYG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATTGGCYG CRGCCAAT 118 31 1.4e-013 5.9e-009 # ATTGGCTG CAGCCAAT 76 20 3.3e-009 1.4e-004 # ATTGGCCG CGGCCAAT 43 11 6.8e-006 2.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 121 E= 5.9e-009 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.355372 0.000000 0.644628 0.000000 0.000000 1.000000 0.000000 MOTIF RTGATTCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST RTGATTCA TGAATCAY 79 15 5.0e-012 2.1e-007 # ATGATTCA TGAATCAT 35 5 6.7e-007 2.8e-002 # GTGATTCA TGAATCAC 44 10 1.6e-006 6.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 79 E= 2.1e-007 0.443038 0.000000 0.556962 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 0.000000 0.000000 1.000000 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 CTCCKCC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTCCKCC GGMGGAG 614 406 7.0e-012 2.9e-007 # CTCCTCC GGAGGAG 273 168 2.1e-007 8.9e-003 # CTCCGCC GGCGGAG 360 247 1.6e-006 6.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 659 E= 2.9e-007 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.572079 0.427921 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ADTTTCC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ADTTTCC GGAAAHT 118 39 7.9e-011 3.3e-006 # AGTTTCC GGAAACT 59 17 6.5e-007 2.7e-002 # ATTTTCC GGAAAAT 36 14 1.3e-003 5.3e+001 # AATTTCC GGAAATT 25 8 2.3e-003 9.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 3.3e-006 1.000000 0.000000 0.000000 0.000000 0.208333 0.000000 0.491667 0.300000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTBAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GTBAC GTVAC 1157 899 3.7e-010 1.6e-005 # GTCAC GTGAC 953 742 2.4e-008 1.0e-003 # GTTAC GTAAC 238 176 1.1e-003 4.8e+001 letter-probability matrix: alength= 4 w= 5 nsites= 1288 E= 1.6e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.395963 0.418478 0.185559 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCGRC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATGGCGRC GYCGCCAT 86 23 4.1e-010 1.7e-005 # ATGGCGGC GCCGCCAT 63 19 5.3e-007 2.2e-002 # ATGGCGAC GTCGCCAT 23 4 1.5e-004 6.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 86 E= 1.7e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.267442 0.000000 0.732558 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TTTAWW DREME-17 # Word RC Word Pos Neg P-value E-value # BEST TTTAWW WWTAAA 288 161 5.8e-010 2.4e-005 # TTTAAA TTTAAA 81 38 4.7e-005 1.9e+000 # TTTATA TATAAA 63 29 2.4e-004 1.0e+001 # TTTATT AATAAA 91 53 9.2e-004 3.8e+001 # TTTAAT ATTAAA 78 48 4.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 317 E= 2.4e-005 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.523659 0.000000 0.000000 0.476341 0.463722 0.000000 0.000000 0.536278 MOTIF GCGCABGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GCGCABGC GCVTGCGC 329 201 7.9e-009 3.2e-004 # GCGCATGC GCATGCGC 73 29 7.2e-006 2.9e-001 # GCGCAGGC GCCTGCGC 153 99 3.6e-004 1.5e+001 # GCGCACGC GCGTGCGC 117 77 2.3e-003 9.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 349 E= 3.2e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.340974 0.452722 0.206304 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTTCCS DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACTTCCS SGGAAGT 158 73 8.7e-009 3.5e-004 # ACTTCCG CGGAAGT 69 26 5.5e-006 2.2e-001 # ACTTCCC GGGAAGT 89 48 2.7e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 162 E= 3.5e-004 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.549383 0.450617 0.000000 MOTIF CCACGYCC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CCACGYCC GGRCGTGG 172 84 1.5e-008 6.1e-004 # CCACGCCC GGGCGTGG 144 76 2.2e-006 9.1e-002 # CCACGTCC GGACGTGG 29 8 3.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 184 E= 6.1e-004 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 1.000000 0.000000 0.000000 0.842391 0.000000 0.157609 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGAATGY DREME-21 # Word RC Word Pos Neg P-value E-value # BEST GGAATGY RCATTCC 120 50 3.3e-008 1.4e-003 # GGAATGT ACATTCC 57 18 3.4e-006 1.4e-001 # GGAATGC GCATTCC 64 32 6.9e-004 2.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 124 E= 1.4e-003 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 1.000000 0.000000 0.000000 0.540323 0.000000 0.459677 MOTIF GCGGCDGC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GCGGCDGC GCHGCCGC 422 290 2.1e-007 8.7e-003 # GCGGCAGC GCTGCCGC 134 81 1.6e-004 6.7e+000 # GCGGCTGC GCAGCCGC 143 93 6.2e-004 2.5e+001 # GCGGCGGC GCCGCCGC 181 129 1.7e-003 6.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 446 E= 8.7e-003 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 1.000000 0.000000 0.000000 0.289238 0.000000 0.396861 0.313901 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTGGYC DREME-23 # Word RC Word Pos Neg P-value E-value # BEST ATTGGYC GRCCAAT 129 62 6.0e-007 2.4e-002 # ATTGGTC GACCAAT 56 25 3.6e-004 1.5e+001 # ATTGGCC GGCCAAT 73 38 5.5e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 131 E= 2.4e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.564885 0.000000 0.435115 0.000000 1.000000 0.000000 0.000000 MOTIF ACTACAAY DREME-24 # Word RC Word Pos Neg P-value E-value # BEST ACTACAAY RTTGTAGT 30 3 6.8e-007 2.8e-002 # ACTACAAC GTTGTAGT 20 2 6.0e-005 2.4e+000 # ACTACAAT ATTGTAGT 11 1 3.2e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 2.8e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.656250 0.000000 0.343750 MOTIF ACAMACAC DREME-25 # Word RC Word Pos Neg P-value E-value # BEST ACAMACAC GTGTKTGT 58 17 1.0e-006 4.2e-002 # ACACACAC GTGTGTGT 44 13 2.3e-005 9.2e-001 # ACAAACAC GTGTTTGT 17 4 3.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 78 E= 4.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.217949 0.782051 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 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 713.54 seconds