# DREME 4.12.0 # command: dreme -p UPINTRON_Union.fa -oc Both_upintronsite_vs_Random -mink 4 -maxk 12 -m 20 # positives: 1028 from UPINTRON_Union.fa (Thu Jan 11 12:43:36 PST 2018) # negatives: 1028 from shuffled positives # host: compute-1-13.local # when: Mon Jan 15 14:06:30 PST 2018 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 0.296 C 0.176 G 0.191 T 0.337 MOTIF AATAAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AATAAA TTTATT 778 371 4.1e-075 2.3e-069 # AATAAA TTTATT 778 371 4.1e-075 2.3e-069 letter-probability matrix: alength= 4 w= 6 nsites= 1210 E= 2.3e-069 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAGGCTGGW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CAGGCTGGW WCCAGCCTG 67 2 1.4e-018 7.7e-013 # CAGGCTGGA TCCAGCCTG 49 2 3.4e-013 1.8e-007 # CAGGCTGGT ACCAGCCTG 18 0 3.5e-006 1.9e+000 letter-probability matrix: alength= 4 w= 9 nsites= 68 E= 7.7e-013 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.720588 0.000000 0.000000 0.279412 MOTIF AAAVAAAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAVAAAAAAA TTTTTTTBTTT 89 14 1.9e-015 1.0e-009 # AAAAAAAAAAA TTTTTTTTTTT 60 11 7.2e-010 3.9e-004 # AAACAAAAAAA TTTTTTTGTTT 22 2 1.6e-005 8.8e+000 # AAAGAAAAAAA TTTTTTTCTTT 14 1 4.7e-004 2.5e+002 letter-probability matrix: alength= 4 w= 11 nsites= 101 E= 1.0e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.663366 0.217822 0.118812 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 1.000000 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 0.000000 MOTIF ASAGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ASAGA TCTST 759 592 5.0e-015 2.7e-009 # ACAGA TCTGT 546 379 8.2e-014 4.4e-008 # AGAGA TCTCT 475 366 6.2e-007 3.3e-001 letter-probability matrix: alength= 4 w= 5 nsites= 1370 E= 2.7e-009 1.000000 0.000000 0.000000 0.000000 0.000000 0.555474 0.444526 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 CCAYTGCAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCAYTGCAC GTGCARTGG 45 1 4.2e-013 2.0e-007 # CCACTGCAC GTGCAGTGG 36 1 2.1e-010 1.0e-004 # CCATTGCAC GTGCAATGG 9 0 1.9e-003 9.4e+002 letter-probability matrix: alength= 4 w= 9 nsites= 45 E= 2.0e-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 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 MOTIF GCCTCYC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCCTCYC GRGAGGC 79 14 6.2e-013 3.1e-007 # GCCTCCC GGGAGGC 66 11 2.5e-011 1.2e-005 # GCCTCTC GAGAGGC 15 3 3.6e-003 1.8e+003 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 3.1e-007 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 1.000000 0.000000 0.000000 0.000000 0.840426 0.000000 0.159574 0.000000 1.000000 0.000000 0.000000 MOTIF GCTGGGAY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCTGGGAY RTCCCAGC 44 1 8.3e-013 4.1e-007 # GCTGGGAT ATCCCAGC 38 1 5.2e-011 2.5e-005 # GCTGGGAC GTCCCAGC 9 0 1.9e-003 9.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 4.1e-007 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.187500 0.000000 0.812500 MOTIF CACWGTR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CACWGTR YACWGTG 135 48 6.0e-012 2.9e-006 # CACAGTG CACTGTG 48 11 4.4e-007 2.2e-001 # CACTGTA TACAGTG 52 21 1.5e-004 7.1e+001 # CACAGTA TACTGTG 44 16 1.6e-004 7.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 147 E= 2.9e-006 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.462585 0.000000 0.000000 0.537415 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.659864 0.000000 0.340136 0.000000 MOTIF GAGGYTGC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GAGGYTGC GCARCCTC 41 3 5.7e-010 2.7e-004 # GAGGTTGC GCAACCTC 24 0 5.2e-008 2.5e-002 # GAGGCTGC GCAGCCTC 17 3 1.2e-003 5.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.7e-004 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 0.414634 0.000000 0.585366 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AMATRTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AMATRTA TAYATKT 318 197 4.4e-010 2.1e-004 # AAATGTA TACATTT 108 61 1.0e-004 4.9e+001 # ACATGTA TACATGT 54 23 2.1e-004 1.0e+002 # AAATATA TATATTT 132 92 2.8e-003 1.4e+003 # ACATATA TATATGT 68 42 7.0e-003 3.3e+003 letter-probability matrix: alength= 4 w= 7 nsites= 397 E= 2.1e-004 1.000000 0.000000 0.000000 0.000000 0.667506 0.332494 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.569270 0.000000 0.430730 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTGAGCCR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GTGAGCCR YGGCTCAC 41 3 5.7e-010 2.7e-004 # GTGAGCCA TGGCTCAC 30 3 5.9e-007 2.8e-001 # GTGAGCCG CGGCTCAC 11 0 4.8e-004 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.7e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.744186 0.000000 0.255814 0.000000 MOTIF RCACACACA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST RCACACACA TGTGTGTGY 32 1 3.1e-009 1.5e-003 # ACACACACA TGTGTGTGT 24 1 6.8e-007 3.2e-001 # GCACACACA TGTGTGTGC 10 0 9.6e-004 4.5e+002 letter-probability matrix: alength= 4 w= 9 nsites= 35 E= 1.5e-003 0.685714 0.000000 0.314286 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 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 GBGAGAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GBGAGAC GTCTCVC 85 26 3.5e-009 1.6e-003 # GCGAGAC GTCTCGC 20 3 2.3e-004 1.1e+002 # GTGAGAC GTCTCAC 37 13 4.1e-004 1.9e+002 # GGGAGAC GTCTCCC 28 10 2.4e-003 1.1e+003 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 1.6e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.232558 0.325581 0.441860 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 1.000000 0.000000 0.000000 MOTIF TCCRTCTCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TCCRTCTCA TGAGAYGGA 24 0 5.2e-008 2.4e-002 # TCCATCTCA TGAGATGGA 13 0 1.2e-004 5.4e+001 # TCCGTCTCA TGAGACGGA 11 0 4.8e-004 2.2e+002 letter-probability matrix: alength= 4 w= 9 nsites= 24 E= 2.4e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.541667 0.000000 0.458333 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 1522.66 seconds