# DREME 4.12.0 # command: dreme -p UPINTRON_293_U1AMO_sorted_ext.fa -oc U1AMO_upintronsites_vs_Random -mink 4 -maxk 12 -m 20 # positives: 988 from UPINTRON_293_U1AMO_sorted_ext.fa (Thu Jan 11 12:18:24 PST 2018) # negatives: 988 from shuffled positives # host: compute-1-13.local # when: Sun Jan 14 21:33:19 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 0.297 C 0.175 G 0.190 T 0.338 MOTIF AATAAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AATAAA TTTATT 750 350 1.7e-075 9.4e-070 # AATAAA TTTATT 750 350 1.7e-075 9.4e-070 letter-probability matrix: alength= 4 w= 6 nsites= 1170 E= 9.4e-070 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 64 1 6.4e-019 3.4e-013 # CAGGCTGGA TCCAGCCTG 46 0 8.3e-015 4.3e-009 # CAGGCTGGT ACCAGCCTG 18 1 3.6e-005 1.9e+001 letter-probability matrix: alength= 4 w= 9 nsites= 65 E= 3.4e-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 0.707692 0.000000 0.000000 0.292308 MOTIF AAAVAAAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAVAAAAAAA TTTTTTTBTTT 83 12 4.3e-015 2.2e-009 # AAAAAAAAAAA TTTTTTTTTTT 56 8 1.5e-010 8.0e-005 # AAACAAAAAAA TTTTTTTGTTT 19 2 1.0e-004 5.4e+001 # AAAGAAAAAAA TTTTTTTCTTT 14 2 2.0e-003 1.1e+003 letter-probability matrix: alength= 4 w= 11 nsites= 94 E= 2.2e-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 0.670213 0.202128 0.127660 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 GGGAGRC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGGAGRC GYCTCCC 90 19 4.1e-013 2.1e-007 # GGGAGGC GCCTCCC 64 9 5.4e-012 2.8e-006 # GGGAGAC GTCTCCC 29 10 1.5e-003 8.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 2.1e-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 0.278846 0.000000 0.721154 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGGCTSA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTGGCTSA TSAGCCAC 49 3 3.0e-012 1.6e-006 # GTGGCTCA TGAGCCAC 39 3 2.0e-009 1.0e-003 # GTGGCTGA TCAGCCAC 10 0 9.5e-004 4.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 1.6e-006 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.795918 0.204082 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ABACAG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ABACAG CTGTVT 405 260 3.1e-012 1.6e-006 # ACACAG CTGTGT 169 91 1.3e-007 6.5e-002 # AGACAG CTGTCT 160 99 3.0e-005 1.5e+001 # ATACAG CTGTAT 149 105 1.9e-003 9.7e+002 letter-probability matrix: alength= 4 w= 6 nsites= 527 E= 1.6e-006 1.000000 0.000000 0.000000 0.000000 0.000000 0.354839 0.337761 0.307400 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 CACTGYA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACTGYA TRCAGTG 118 37 3.9e-012 1.9e-006 # CACTGCA TGCAGTG 81 22 8.1e-010 4.0e-004 # CACTGTA TACAGTG 38 15 9.5e-004 4.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 132 E= 1.9e-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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.704545 0.000000 0.295455 1.000000 0.000000 0.000000 0.000000 MOTIF AATCCCAGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AATCCCAGC GCTGGGATT 34 0 4.4e-011 2.1e-005 # AATCCCAGC GCTGGGATT 34 0 4.4e-011 2.1e-005 letter-probability matrix: alength= 4 w= 9 nsites= 35 E= 2.1e-005 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 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 MOTIF AMATRTAT DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AMATRTAT ATAYATKT 128 45 1.5e-011 7.4e-006 # AAATGTAT ATACATTT 40 12 5.2e-005 2.6e+001 # ACATGTAT ATACATGT 24 4 8.2e-005 4.0e+001 # ACATATAT ATATATGT 30 9 4.8e-004 2.3e+002 # AAATATAT ATATATTT 46 21 1.3e-003 6.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 146 E= 7.4e-006 1.000000 0.000000 0.000000 0.000000 0.616438 0.383562 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.554795 0.000000 0.445205 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CMRTCTC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CMRTCTC GAGAYKG 121 43 8.2e-011 4.0e-005 # CCGTCTC GAGACGG 27 2 7.0e-007 3.4e-001 # CCATCTC GAGATGG 46 17 1.4e-004 6.6e+001 # CAATCTC GAGATTG 29 13 9.1e-003 4.4e+003 # CAGTCTC GAGACTG 26 11 9.5e-003 4.6e+003 letter-probability matrix: alength= 4 w= 7 nsites= 131 E= 4.0e-005 0.000000 1.000000 0.000000 0.000000 0.427481 0.572519 0.000000 0.000000 0.587786 0.000000 0.412214 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 MOTIF CAGAGYGAGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAGAGYGAGA TCTCRCTCTG 31 0 3.7e-010 1.8e-004 # CAGAGTGAGA TCTCACTCTG 16 0 1.4e-005 6.9e+000 # CAGAGCGAGA TCTCGCTCTG 15 0 2.9e-005 1.4e+001 letter-probability matrix: alength= 4 w= 10 nsites= 31 E= 1.8e-004 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.483871 0.000000 0.516129 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 AAAATR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAAATR YATTTT 577 450 6.7e-009 3.2e-003 # AAAATA TATTTT 384 279 3.5e-007 1.7e-001 # AAAATG CATTTT 333 261 2.4e-004 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 905 E= 3.2e-003 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 0.000000 0.000000 0.000000 1.000000 0.542541 0.000000 0.457459 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 1295.47 seconds