# DREME 4.12.0 # command: dreme -v 1 -oc /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/USF2-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/dreme_out -png -dna -p /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/USF2-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/seqs-centered -n /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/USF2-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/seqs-shuffled # positives: 3542 from /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/USF2-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/seqs-centered (Wed Nov 22 12:43:45 PST 2017) # negatives: 3542 from /srv/scratch/shared/surya/imk1/TFBindingPredictionProject/EncodeK562eGFPComparisons/USF2-Antibody.IDR0.05.filt.narrowPeak.summitPlusMinus250bp.MemeChipResultsDefaultMax/seqs-shuffled (Wed Nov 22 12:43:45 PST 2017) # host: indra # when: Wed Nov 22 12:57:46 PST 2017 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 0.216 C 0.284 G 0.283 T 0.217 MOTIF BCACRTG DREME-1 # Word RC Word Pos Neg P-value E-value # BEST BCACRTG CAYGTGV 2769 287 8.8e-866 3.8e-861 # TCACGTG CACGTGA 1540 28 6.0e-504 2.6e-499 # CCACGTG CACGTGG 1027 47 3.1e-276 1.4e-271 # TCACATG CATGTGA 813 71 4.3e-180 1.9e-175 # GCACGTG CACGTGC 454 29 1.6e-105 7.1e-101 # GCACATG CATGTGC 139 74 3.7e-006 1.6e-001 # CCACATG CATGTGG 127 79 4.2e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 3278 E= 3.8e-861 0.000000 0.244356 0.123551 0.632093 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.355095 0.000000 0.644905 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATTGGYY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATTGGYY RRCCAAT 861 159 4.1e-135 1.8e-130 # ATTGGCC GGCCAAT 391 48 4.5e-072 1.9e-067 # ATTGGCT AGCCAAT 313 41 1.1e-055 4.8e-051 # ATTGGTC GACCAAT 159 31 9.7e-023 4.1e-018 # ATTGGTT AACCAAT 161 41 9.2e-019 3.9e-014 letter-probability matrix: alength= 4 w= 7 nsites= 1090 E= 1.8e-130 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 0.689908 0.000000 0.310092 0.000000 0.532110 0.000000 0.467890 MOTIF VGGAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST VGGAAR YTTCCB 1583 953 1.7e-055 7.1e-051 # GGGAAA TTTCCC 487 172 2.0e-039 8.7e-035 # AGGAAG CTTCCT 412 258 2.2e-010 9.5e-006 # AGGAAA TTTCCT 295 168 5.6e-010 2.4e-005 # GGGAAG CTTCCC 431 284 3.8e-009 1.6e-004 # CGGAAG CTTCCG 237 134 2.2e-008 9.5e-004 # CGGAAA TTTCCG 112 69 7.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 2066 E= 7.1e-051 0.355760 0.181510 0.462730 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 0.441433 0.000000 0.558567 0.000000 MOTIF CYCCKCCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CYCCKCCC GGGMGGRG 425 159 1.3e-031 5.3e-027 # CCCCGCCC GGGCGGGG 203 52 2.8e-023 1.2e-018 # CTCCTCCC GGGAGGAG 82 28 1.0e-007 4.3e-003 # CTCCGCCC GGGCGGAG 73 26 1.1e-006 4.4e-002 # CCCCTCCC GGGAGGGG 115 57 4.5e-006 1.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 482 E= 5.3e-027 0.000000 1.000000 0.000000 0.000000 0.000000 0.690871 0.000000 0.309129 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.603734 0.396266 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 RACTACA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST RACTACA TGTAGTY 184 51 1.1e-019 4.4e-015 # GACTACA TGTAGTC 120 28 2.5e-015 1.0e-010 # AACTACA TGTAGTT 67 23 1.7e-006 6.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 187 E= 4.4e-015 0.352941 0.000000 0.647059 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCAARGGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCAARGGA TCCYTTGC 121 26 2.0e-016 8.2e-012 # GCAAGGGA TCCCTTGC 82 17 8.1e-012 3.4e-007 # GCAAAGGA TCCTTTGC 40 9 4.3e-006 1.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 122 E= 8.2e-012 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 0.000000 0.327869 0.000000 0.672131 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 MOTIF ATGGCBGC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCBGC GCVGCCAT 110 29 8.3e-013 3.4e-008 # ATGGCGGC GCCGCCAT 54 10 8.7e-009 3.6e-004 # ATGGCTGC GCAGCCAT 35 13 1.0e-003 4.2e+001 # ATGGCCGC GCGGCCAT 21 6 2.9e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 110 E= 3.4e-008 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 0.190909 0.490909 0.318182 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCAATCAS DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCAATCAS STGATTGG 87 19 5.0e-012 2.1e-007 # CCAATCAG CTGATTGG 63 9 1.7e-011 7.1e-007 # CCAATCAC GTGATTGG 26 10 5.6e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 2.1e-007 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 0.000000 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 0.300000 0.700000 0.000000 MOTIF CACMTGAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACMTGAC GTCAKGTG 85 22 2.4e-010 1.0e-005 # CACCTGAC GTCAGGTG 72 20 1.9e-008 7.9e-004 # CACATGAC GTCATGTG 13 2 3.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 87 E= 1.0e-005 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.149425 0.850575 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 0.000000 1.000000 0.000000 0.000000 MOTIF RKAAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RKAAA TTTMY 1264 1019 2.7e-010 1.1e-005 # AGAAA TTTCT 696 560 1.3e-005 5.5e-001 # ATAAA TTTAT 316 222 1.5e-005 6.1e-001 # GTAAA TTTAC 303 239 2.4e-003 1.0e+002 # GGAAA TTTCC 243 186 2.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 5 nsites= 1715 E= 1.1e-005 0.662974 0.000000 0.337026 0.000000 0.000000 0.000000 0.618076 0.381924 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GAGGCGGR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GAGGCGGR YCCGCCTC 103 35 2.1e-009 8.4e-005 # GAGGCGGG CCCGCCTC 77 31 4.8e-006 1.9e-001 # GAGGCGGA TCCGCCTC 28 4 9.3e-006 3.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 108 E= 8.4e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.277778 0.000000 0.722222 0.000000 MOTIF GGGMGGGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GGGMGGGA TCCCKCCC 101 35 4.8e-009 1.9e-004 # GGGCGGGA TCCCGCCC 54 15 1.2e-006 4.7e-002 # GGGAGGGA TCCCTCCC 47 20 6.2e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 101 E= 1.9e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.465347 0.534653 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 1.000000 0.000000 0.000000 0.000000 MOTIF TGACGTCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TGACGTCA TGACGTCA 31 1 7.2e-009 2.9e-004 # TGACGTCA TGACGTCA 31 1 7.2e-009 2.9e-004 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.9e-004 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 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 MOTIF CGCAKGCG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGCAKGCG CGCMTGCG 70 19 2.1e-008 8.3e-004 # CGCAGGCG CGCCTGCG 55 15 7.4e-007 3.0e-002 # CGCATGCG CGCATGCG 16 4 5.9e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 8.3e-004 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 0.000000 0.780822 0.219178 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 AGAWGGCG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGAWGGCG CGCCWTCT 38 5 1.2e-007 4.7e-003 # AGATGGCG CGCCATCT 18 2 2.0e-004 8.0e+000 # AGAAGGCG CGCCTTCT 20 3 2.4e-004 9.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 4.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.526316 0.000000 0.000000 0.473684 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 AAAGCAAG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AAAGCAAG CTTGCTTT 35 5 6.5e-007 2.6e-002 # AAAGCAAG CTTGCTTT 35 5 6.5e-007 2.6e-002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 2.6e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CKCGTGAC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CKCGTGAC GTCACGMG 62 19 7.8e-007 3.1e-002 # CGCGTGAC GTCACGCG 42 12 2.4e-005 9.8e-001 # CTCGTGAC GTCACGAG 20 7 9.5e-003 3.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 3.1e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.677419 0.322581 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTTCTGY DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACTTCTGY RCAGAAGT 49 12 8.9e-007 3.6e-002 # ACTTCTGC GCAGAAGT 34 8 3.3e-005 1.3e+000 # ACTTCTGT ACAGAAGT 15 4 9.5e-003 3.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 3.6e-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 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 1.000000 0.000000 0.000000 0.693878 0.000000 0.306122 # Stopping reason: E-value threshold exceeded # Running time: 321.35 seconds