# dreme.py -p CHEN/cMyc.pos.fasta -n CHEN/cMyc.pos.shuf1.fasta -minw 3 -maxw 7 -mink 3 -maxk 7 -e 0.05 -g 100 -a 0.01 -r 1 # ( dreme.py -p CHEN/cMyc.pos.fasta -n CHEN/cMyc.pos.shuf1.fasta ) # Revision: 1663 MEME version 4.5 ALPHABET= ACGT strands: + - Background letter frequencies (from A 0.25 C 0.25 G 0.25 T 0.25 # VALUES AFTER ERASING BEST WORD # WORD RC_WORD p P n N p-value E-value BEST CACRTGS SCAYGTG 1035 3422 149 3422 3.6e-194 4.3e-190 4.3e-190 CACATGG CCATGTG 183 3422 41 3422 1.4e-023 1.7e-019 CACATGC GCATGTG 100 3422 39 3422 8.8e-008 1.0e-003 CACGTGG CCACGTG 578 3422 35 3422 2.2e-138 2.6e-134 CACGTGC GCACGTG 461 3422 55 3422 7.4e-087 8.7e-083 MOTIF CACRTGS 4.3e-190 letter-probability matrix: alength= 4 w= 7 nsites= 1118 E= 4.3e-190 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.259392 0.000000 0.740608 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.413238 0.586762 0.000000 BEST MGGAAR YTTCCK 945 3422 515 3422 1.9e-037 2.2e-033 1.6e-033 AGGAAG CTTCCT 356 3422 163 3422 3.9e-019 4.5e-015 AGGAAA TTTCCT 194 3422 112 3422 9.5e-007 1.1e-002 CGGAAG CTTCCG 367 3422 184 3422 1.7e-016 2.0e-012 CGGAAA TTTCCG 153 3422 86 3422 6.2e-006 7.1e-002 MOTIF MGGAAR 2.2e-033 letter-probability matrix: alength= 4 w= 6 nsites= 1138 E= 2.2e-033 0.505272 0.494728 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 0.315466 0.000000 0.684534 0.000000 BEST CGCCATB VATGGCG 320 3422 95 3422 1.4e-031 1.6e-027 5.9e-032 CGCCATC GATGGCG 137 3422 39 3422 1.4e-014 1.5e-010 CGCCATT AATGGCG 68 3422 16 3422 3.5e-009 3.9e-005 CGCCATG CATGGCG 125 3422 43 3422 5.4e-011 6.1e-007 MOTIF CGCCATB 1.6e-027 letter-probability matrix: alength= 4 w= 7 nsites= 332 E= 1.6e-027 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 0.000000 1.000000 0.000000 0.418675 0.379518 0.201807 BEST CACGHG CDCGTG 772 3422 438 3422 1.4e-026 1.5e-022 5.1e-145 CACGTG CACGTG 54 3422 12 3422 7.5e-008 8.3e-004 CACGCG CGCGTG 503 3422 266 3422 4.6e-020 5.2e-016 CACGAG CTCGTG 251 3422 183 3422 4.4e-004 4.9e+000 MOTIF CACGHG 1.5e-022 letter-probability matrix: alength= 4 w= 6 nsites= 877 E= 1.5e-022 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 0.291904 0.645382 0.000000 0.062714 0.000000 0.000000 1.000000 0.000000 BEST CBGGRA TYCCVG 1299 3422 974 3422 4.2e-017 4.6e-013 1.5e-023 CTGGGA TCCCAG 360 3422 283 3422 8.1e-004 9.0e+000 CTGGAA TTCCAG 240 3422 167 3422 1.1e-004 1.2e+000 CCGGGA TCCCGG 342 3422 235 3422 1.9e-006 2.1e-002 CCGGAA TTCCGG 93 3422 51 3422 2.6e-004 2.8e+000 CGGGAA TTCCCG 276 3422 180 3422 1.9e-006 2.1e-002 CGGGGA TCCCCG 334 3422 253 3422 2.7e-004 3.0e+000 MOTIF CBGGRA 4.6e-013 letter-probability matrix: alength= 4 w= 6 nsites= 1619 E= 4.6e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.243360 0.365658 0.390982 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.355158 0.000000 0.644842 0.000000 1.000000 0.000000 0.000000 0.000000 BEST GATGCAA TTGCATC 104 3422 23 3422 5.2e-014 5.7e-010 9.4e-010 GATGCAA TTGCATC 104 3422 23 3422 5.2e-014 5.7e-010 MOTIF GATGCAA 5.7e-010 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 5.7e-010 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 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 BEST CCTCCHC GDGGAGG 416 3422 245 3422 1.4e-012 1.5e-008 1.8e-013 CCTCCAC GTGGAGG 104 3422 64 3422 1.1e-003 1.2e+001 CCTCCCC GGGGAGG 166 3422 115 3422 1.1e-003 1.2e+001 CCTCCTC GAGGAGG 176 3422 88 3422 1.8e-008 2.0e-004 MOTIF CCTCCHC 1.5e-008 letter-probability matrix: alength= 4 w= 7 nsites= 451 E= 1.5e-008 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 1.000000 0.000000 0.000000 0.226164 0.381375 0.000000 0.392461 0.000000 1.000000 0.000000 0.000000 BEST ABAAA TTTVT 845 3422 610 3422 2.2e-012 2.4e-008 3.7e-009 ACAAA TTTGT 358 3422 285 3422 1.4e-003 1.5e+001 ATAAA TTTAT 130 3422 86 3422 1.4e-003 1.6e+001 AGAAA TTTCT 461 3422 306 3422 1.6e-009 1.8e-005 MOTIF ABAAA 2.4e-008 letter-probability matrix: alength= 4 w= 5 nsites= 1024 E= 2.4e-008 1.000000 0.000000 0.000000 0.000000 0.000000 0.375977 0.485352 0.138672 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AARATGG CCATYTT 85 3422 25 3422 3.0e-009 3.2e-005 1.6e-022 AAAATGG CCATTTT 23 3422 9 3422 9.9e-003 1.1e+002 AAGATGG CCATCTT 62 3422 16 3422 6.5e-008 6.9e-004 MOTIF AARATGG 3.2e-005 letter-probability matrix: alength= 4 w= 7 nsites= 89 E= 3.2e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.258427 0.000000 0.741573 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 0.000000 1.000000 0.000000 BEST CCGCCSC GSGGCGG 462 3422 336 3422 1.2e-006 1.3e-002 2.7e-008 CCGCCCC GGGGCGG 235 3422 169 3422 4.2e-004 4.5e+000 CCGCCGC GCGGCGG 256 3422 184 3422 2.3e-004 2.4e+000 MOTIF CCGCCSC 1.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 510 E= 1.3e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.470588 0.529412 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CMTGCGC GCGCAKG 259 3422 165 3422 1.4e-006 1.5e-002 1.1e-003 CATGCGC GCGCATG 79 3422 40 3422 2.0e-004 2.1e+000 CCTGCGC GCGCAGG 192 3422 127 3422 1.2e-004 1.2e+000 MOTIF CMTGCGC 1.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 279 E= 1.5e-002 0.000000 1.000000 0.000000 0.000000 0.297491 0.702509 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # 11 motifs with E-value < 0.05 found. #elapsed time: 156.04 seconds