# dreme.py -p CHEN/Klf4.pos.fasta -n CHEN/Klf4.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/Klf4.pos.fasta -n CHEN/Klf4.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 CMCRCCC GGGYGKG 5628 10875 1482 10875 1.1e-820 1.3e-816 1.3e-816 CCCGCCC GGGCGGG 1823 10875 519 10875 2.4e-188 2.9e-184 CACACCC GGGTGTG 1737 10875 311 10875 2.3e-262 2.8e-258 CCCACCC GGGTGGG 1615 10875 564 10875 2.6e-129 3.1e-125 CACGCCC GGGCGTG 1461 10875 203 10875 3.5e-252 4.1e-248 MOTIF CMCRCCC 1.3e-816 letter-probability matrix: alength= 4 w= 7 nsites= 7141 E= 1.3e-816 0.000000 1.000000 0.000000 0.000000 0.484946 0.515054 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.491528 0.000000 0.508472 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 BEST GGGCGKW WMCGCCC 1427 10875 531 10875 1.8e-103 2.1e-099 1.5e-113 GGGCGTA TACGCCC 117 10875 56 10875 1.9e-006 2.2e-002 GGGCGTT AACGCCC 283 10875 93 10875 4.4e-024 5.1e-020 GGGCGGT ACCGCCC 358 10875 173 10875 1.6e-016 1.9e-012 GGGCGGA TCCGCCC 737 10875 222 10875 3.4e-068 4.0e-064 MOTIF GGGCGKW 2.1e-099 letter-probability matrix: alength= 4 w= 7 nsites= 1554 E= 2.1e-099 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.741956 0.258044 0.579151 0.000000 0.000000 0.420849 BEST MGGAAR YTTCCK 2762 10875 1727 10875 5.2e-068 6.1e-064 1.7e-074 AGGAAG CTTCCT 1284 10875 802 10875 5.0e-029 5.8e-025 AGGAAA TTTCCT 815 10875 455 10875 7.5e-026 8.8e-022 CGGAAG CTTCCG 694 10875 382 10875 6.2e-023 7.3e-019 CGGAAA TTTCCG 300 10875 207 10875 1.7e-005 2.0e-001 MOTIF MGGAAR 6.1e-064 letter-probability matrix: alength= 4 w= 6 nsites= 3311 E= 6.1e-064 0.677741 0.322259 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 0.350045 0.000000 0.649955 0.000000 BEST CTCCDCC GGHGGAG 1379 10875 805 10875 6.5e-039 7.4e-035 5.9e-079 CTCCGCC GGCGGAG 254 10875 164 10875 5.1e-006 5.9e-002 CTCCTCC GGAGGAG 642 10875 361 10875 4.1e-020 4.7e-016 CTCCACC GGTGGAG 581 10875 316 10875 6.2e-020 7.1e-016 MOTIF CTCCDCC 7.4e-035 letter-probability matrix: alength= 4 w= 7 nsites= 1506 E= 7.4e-035 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 0.399070 0.000000 0.166667 0.434263 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST HRGGAA TTCCYD 2567 10875 1896 10875 9.6e-030 1.1e-025 2.4e-060 AAGGAA TTCCTT 227 10875 179 10875 9.2e-003 1.1e+002 TGGGAA TTCCCA 803 10875 574 10875 1.0e-010 1.1e-006 TAGGAA TTCCTA 151 10875 88 10875 2.5e-005 2.9e-001 CAGGAA TTCCTG 397 10875 270 10875 3.4e-007 3.8e-003 CGGGAA TTCCCG 552 10875 337 10875 9.0e-014 1.0e-009 AGGGAA TTCCCT 780 10875 628 10875 1.6e-005 1.8e-001 MOTIF HRGGAA 1.1e-025 letter-probability matrix: alength= 4 w= 6 nsites= 3017 E= 1.1e-025 0.347365 0.323169 0.000000 0.329466 0.260855 0.000000 0.739145 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 BEST ARABAAA TTTVTYT 774 10875 418 10875 8.5e-027 9.6e-023 2.3e-028 AAATAAA TTTATTT 61 10875 34 10875 3.6e-003 4.1e+001 AAACAAA TTTGTTT 183 10875 74 10875 3.0e-012 3.4e-008 AGACAAA TTTGTCT 170 10875 85 10875 4.7e-008 5.3e-004 AAAGAAA TTTCTTT 169 10875 88 10875 2.1e-007 2.4e-003 AGAGAAA TTTCTCT 198 10875 129 10875 7.2e-005 8.1e-001 AGATAAA TTTATCT 57 10875 23 10875 8.9e-005 1.0e+000 MOTIF ARABAAA 9.6e-023 letter-probability matrix: alength= 4 w= 7 nsites= 826 E= 9.6e-023 1.000000 0.000000 0.000000 0.000000 0.485472 0.000000 0.514528 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.426150 0.434625 0.139225 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 ASGTSAC GTSACST 563 10875 279 10875 5.1e-024 5.7e-020 3.2e-024 ACGTCAC GTGACGT 97 10875 41 10875 9.7e-007 1.1e-002 ACGTGAC GTCACGT 119 10875 34 10875 1.3e-012 1.4e-008 AGGTCAC GTGACCT 236 10875 123 10875 9.4e-010 1.0e-005 AGGTGAC GTCACCT 166 10875 109 10875 3.3e-004 3.6e+000 MOTIF ASGTSAC 5.7e-020 letter-probability matrix: alength= 4 w= 7 nsites= 582 E= 5.7e-020 1.000000 0.000000 0.000000 0.000000 0.000000 0.348797 0.651203 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.546392 0.453608 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST ACAAWGR YCWTTGT 536 10875 292 10875 2.1e-018 2.4e-014 3.0e-028 ACAAAGG CCTTTGT 175 10875 96 10875 7.9e-007 8.8e-003 ACAATGG CCATTGT 165 10875 83 10875 9.0e-008 1.0e-003 ACAAAGA TCTTTGT 128 10875 70 10875 2.1e-005 2.3e-001 ACAATGA TCATTGT 87 10875 45 10875 1.5e-004 1.7e+000 MOTIF ACAAWGR 2.4e-014 letter-probability matrix: alength= 4 w= 7 nsites= 565 E= 2.4e-014 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 0.546903 0.000000 0.000000 0.453097 0.000000 0.000000 1.000000 0.000000 0.389381 0.000000 0.610619 0.000000 BEST TAMAYA TRTKTA 636 10875 372 10875 7.4e-018 8.2e-014 1.2e-017 TACACA TGTGTA 244 10875 169 10875 1.1e-004 1.3e+000 TAAATA TATTTA 109 10875 41 10875 1.2e-008 1.3e-004 TACATA TATGTA 85 10875 55 10875 6.8e-003 7.6e+001 TAAACA TGTTTA 222 10875 113 10875 1.0e-009 1.1e-005 MOTIF TAMAYA 8.2e-014 letter-probability matrix: alength= 4 w= 6 nsites= 663 E= 8.2e-014 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.503771 0.496229 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.711916 0.000000 0.288084 1.000000 0.000000 0.000000 0.000000 BEST MTGCGCA TGCGCAK 300 10875 134 10875 2.8e-016 3.0e-012 6.6e-012 ATGCGCA TGCGCAT 109 10875 38 10875 1.7e-009 1.9e-005 CTGCGCA TGCGCAG 237 10875 111 10875 4.3e-012 4.7e-008 MOTIF MTGCGCA 3.0e-012 letter-probability matrix: alength= 4 w= 7 nsites= 310 E= 3.0e-012 0.277419 0.722581 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 1.000000 0.000000 0.000000 0.000000 BEST ATKCARA TYTGMAT 441 10875 236 10875 5.1e-016 5.6e-012 4.3e-016 ATTCAAA TTTGAAT 75 10875 46 10875 5.2e-003 5.7e+001 ATGCAAA TTTGCAT 146 10875 64 10875 6.5e-009 7.0e-005 ATGCAGA TCTGCAT 158 10875 81 10875 3.1e-007 3.4e-003 ATTCAGA TCTGAAT 76 10875 48 10875 7.4e-003 8.0e+001 MOTIF ATKCARA 5.6e-012 letter-probability matrix: alength= 4 w= 7 nsites= 468 E= 5.6e-012 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.675214 0.324786 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.485043 0.000000 0.514957 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AAGGWCA TGWCCTT 342 10875 177 10875 1.0e-013 1.1e-009 1.3e-024 AAGGACA TGTCCTT 155 10875 98 10875 1.9e-004 2.1e+000 AAGGTCA TGACCTT 193 10875 79 10875 1.3e-012 1.4e-008 MOTIF AAGGWCA 1.1e-009 letter-probability matrix: alength= 4 w= 7 nsites= 352 E= 1.1e-009 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 0.000000 1.000000 0.000000 0.443182 0.000000 0.000000 0.556818 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AGGCGKG CMCGCCT 538 10875 342 10875 8.1e-012 8.8e-008 4.4e-014 AGGCGTG CACGCCT 203 10875 124 10875 6.3e-006 6.9e-002 AGGCGGG CCCGCCT 343 10875 220 10875 8.5e-008 9.3e-004 MOTIF AGGCGKG 8.8e-008 letter-probability matrix: alength= 4 w= 7 nsites= 557 E= 8.8e-008 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 0.633752 0.366248 0.000000 0.000000 1.000000 0.000000 BEST CYGGRA TYCCRG 2196 10875 1816 10875 1.7e-011 1.8e-007 2.7e-038 CTGGGA TCCCAG 914 10875 762 10875 6.1e-005 6.7e-001 CTGGAA TTCCAG 755 10875 611 10875 3.2e-005 3.4e-001 CCGGGA TCCCGG 538 10875 452 10875 2.8e-003 3.1e+001 CCGGAA TTCCGG 193 10875 133 10875 4.8e-004 5.3e+000 MOTIF CYGGRA 1.8e-007 letter-probability matrix: alength= 4 w= 6 nsites= 2502 E= 1.8e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.298961 0.000000 0.701039 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.391687 0.000000 0.608313 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CCCTCCC GGGAGGG 745 10875 521 10875 4.8e-011 5.2e-007 3.4e-028 CCCTCCC GGGAGGG 745 10875 521 10875 4.8e-011 5.2e-007 MOTIF CCCTCCC 5.2e-007 letter-probability matrix: alength= 4 w= 7 nsites= 794 E= 5.2e-007 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 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 BEST KAKATAA TTATMTM 92 10875 27 10875 7.9e-010 8.5e-006 2.5e-008 GATATAA TTATATC 16 10875 4 10875 5.9e-003 6.4e+001 TATATAA TTATATA 17 10875 5 10875 8.4e-003 9.1e+001 GAGATAA TTATCTC 36 10875 13 10875 6.9e-004 7.5e+000 TAGATAA TTATCTA 23 10875 5 10875 4.5e-004 4.9e+000 MOTIF KAKATAA 8.5e-006 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 8.5e-006 0.000000 0.000000 0.565217 0.434783 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.641304 0.358696 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 BEST TTTAW WTAAA 921 10875 698 10875 4.6e-009 5.0e-005 1.2e-016 TTTAT ATAAA 376 10875 276 10875 4.0e-005 4.4e-001 TTTAA TTAAA 576 10875 456 10875 7.3e-005 7.9e-001 MOTIF TTTAW 5.0e-005 letter-probability matrix: alength= 4 w= 5 nsites= 987 E= 5.0e-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 0.608916 0.000000 0.000000 0.391084 BEST BCACGTG CACGTGV 187 10875 94 10875 1.3e-008 1.3e-004 3.5e-014 TCACGTG CACGTGA 61 10875 26 10875 1.1e-004 1.2e+000 GCACGTG CACGTGC 85 10875 54 10875 5.2e-003 5.6e+001 CCACGTG CACGTGG 107 10875 55 10875 2.5e-005 2.7e-001 MOTIF BCACGTG 1.3e-004 letter-probability matrix: alength= 4 w= 7 nsites= 193 E= 1.3e-004 0.000000 0.435233 0.352332 0.212435 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 BEST CGCSCAS STGSGCG 765 10875 571 10875 2.4e-008 2.6e-004 9.4e-087 CGCGCAC GTGCGCG 177 10875 130 10875 4.0e-003 4.3e+001 CGCGCAG CTGCGCG 267 10875 199 10875 8.4e-004 9.0e+000 CGCCCAG CTGGGCG 216 10875 169 10875 8.9e-003 9.6e+001 CGCCCAC GTGGGCG 156 10875 106 10875 1.1e-003 1.2e+001 MOTIF CGCSCAS 2.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 811 E= 2.6e-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 0.000000 0.462392 0.537608 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.408138 0.591862 0.000000 BEST ATTWGCA TGCWAAT 141 10875 65 10875 5.5e-008 5.9e-004 7.4e-009 ATTTGCA TGCAAAT 58 10875 31 10875 2.7e-003 2.9e+001 ATTAGCA TGCTAAT 85 10875 35 10875 2.7e-006 2.9e-002 MOTIF ATTWGCA 5.9e-004 letter-probability matrix: alength= 4 w= 7 nsites= 144 E= 5.9e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.604167 0.000000 0.000000 0.395833 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ATGGCGG CCGCCAT 129 10875 59 10875 1.6e-007 1.7e-003 1.4e-002 ATGGCGG CCGCCAT 129 10875 59 10875 1.6e-007 1.7e-003 MOTIF ATGGCGG 1.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 131 E= 1.7e-003 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 0.000000 0.000000 1.000000 0.000000 BEST CWGCAGC GCTGCWG 807 10875 622 10875 2.3e-007 2.5e-003 8.5e-005 CTGCAGC GCTGCAG 391 10875 309 10875 9.2e-004 9.8e+000 CAGCAGC GCTGCTG 451 10875 339 10875 2.8e-005 3.0e-001 MOTIF CWGCAGC 2.5e-003 letter-probability matrix: alength= 4 w= 7 nsites= 846 E= 2.5e-003 0.000000 1.000000 0.000000 0.000000 0.537825 0.000000 0.000000 0.462175 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST AGRATG CATYCT 815 10875 644 10875 2.0e-006 2.1e-002 1.4e-007 AGGATG CATCCT 476 10875 394 10875 2.5e-003 2.7e+001 AGAATG CATTCT 354 10875 265 10875 1.6e-004 1.7e+000 MOTIF AGRATG 2.1e-002 letter-probability matrix: alength= 4 w= 6 nsites= 851 E= 2.1e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.427732 0.000000 0.572268 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 BEST CAGAGM KCTCTG 1656 10875 1415 10875 1.5e-006 1.6e-002 2.0e-007 CAGAGC GCTCTG 1030 10875 864 10875 3.6e-005 3.8e-001 CAGAGA TCTCTG 699 10875 599 10875 2.3e-003 2.4e+001 MOTIF CAGAGM 1.6e-002 letter-probability matrix: alength= 4 w= 6 nsites= 1831 E= 1.6e-002 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 0.400328 0.599672 0.000000 0.000000 BEST GACTACA TGTAGTC 76 10875 30 10875 4.3e-006 4.6e-002 1.4e+000 GACTACA TGTAGTC 76 10875 30 10875 4.3e-006 4.6e-002 MOTIF GACTACA 4.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 4.6e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # 25 motifs with E-value < 0.05 found. #elapsed time: 915.03 seconds