# dreme.py -p CHEN/E2f1.pos.fasta -n CHEN/E2f1.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/E2f1.pos.fasta -n CHEN/E2f1.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 VGGAAR YTTCCB 8349 20699 5626 20699 3.3e-177 4.1e-173 4.1e-173 AGGAAA TTTCCT 1685 20699 1043 20699 1.5e-037 1.9e-033 AGGAAG CTTCCT 2571 20699 1479 20699 6.4e-074 8.1e-070 GGGAAG CTTCCC 2402 20699 1630 20699 6.7e-038 8.4e-034 GGGAAA TTTCCC 1512 20699 1031 20699 3.3e-023 4.2e-019 CGGAAG CTTCCG 1694 20699 854 20699 2.0e-067 2.5e-063 CGGAAA TTTCCG 740 20699 471 20699 2.1e-015 2.7e-011 MOTIF VGGAAR 4.1e-173 letter-probability matrix: alength= 4 w= 6 nsites= 11266 E= 4.1e-173 0.399166 0.235576 0.365258 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 0.361442 0.000000 0.638558 0.000000 BEST ATGGCG CGCCAT 1274 20699 425 20699 1.5e-102 1.8e-098 8.1e-101 ATGGCG CGCCAT 1274 20699 425 20699 1.5e-102 1.8e-098 MOTIF ATGGCG 1.8e-098 letter-probability matrix: alength= 4 w= 6 nsites= 1308 E= 1.8e-098 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 BEST CDCCKCC GGMGGHG 3836 20699 2674 20699 6.5e-056 7.8e-052 9.1e-071 CTCCTCC GGAGGAG 1139 20699 719 20699 8.7e-024 1.1e-019 CGCCTCC GGAGGCG 730 20699 487 20699 8.1e-013 9.8e-009 CTCCGCC GGCGGAG 830 20699 479 20699 2.3e-023 2.8e-019 CACCTCC GGAGGTG 624 20699 501 20699 1.1e-004 1.3e+000 CACCGCC GGCGGTG 469 20699 325 20699 1.4e-007 1.7e-003 CGCCGCC GGCGGCG 831 20699 521 20699 4.7e-018 5.7e-014 MOTIF CDCCKCC 7.8e-052 letter-probability matrix: alength= 4 w= 7 nsites= 4460 E= 7.8e-052 0.000000 1.000000 0.000000 0.000000 0.237668 0.000000 0.332960 0.429372 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.459641 0.540359 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CNGGRA TYCCNG 6920 20699 5566 20699 6.1e-048 7.3e-044 1.1e-124 CTGGGA TCCCAG 1745 20699 1366 20699 8.6e-013 1.0e-008 CTGGAA TTCCAG 1512 20699 1146 20699 1.2e-013 1.4e-009 CCGGGA TCCCGG 1146 20699 766 20699 2.7e-019 3.2e-015 CCGGAA TTCCGG 372 20699 228 20699 1.7e-009 2.1e-005 CAGGGA TCCCTG 1584 20699 1446 20699 4.9e-003 5.8e+001 CAGGAA TTCCTG 712 20699 515 20699 6.3e-009 7.5e-005 CGGGAA TTCCCG 354 20699 242 20699 2.2e-006 2.6e-002 CGGGGA TCCCCG 1037 20699 835 20699 9.7e-007 1.2e-002 MOTIF CNGGRA 7.3e-044 letter-probability matrix: alength= 4 w= 6 nsites= 8612 E= 7.3e-044 0.000000 1.000000 0.000000 0.000000 0.275081 0.170924 0.160938 0.393056 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.342778 0.000000 0.657222 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CACGTGD HCACGTG 595 20699 218 20699 3.0e-042 3.5e-038 1.1e-037 CACGTGT ACACGTG 209 20699 77 20699 1.2e-015 1.4e-011 CACGTGA TCACGTG 271 20699 91 20699 2.3e-022 2.7e-018 CACGTGG CCACGTG 346 20699 129 20699 1.7e-024 1.9e-020 MOTIF CACGTGD 3.5e-038 letter-probability matrix: alength= 4 w= 7 nsites= 626 E= 3.5e-038 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 0.335463 0.000000 0.413738 0.250799 BEST TSTGTR YACASA 3814 20699 2814 20699 2.6e-041 3.0e-037 7.2e-038 TCTGTA TACAGA 676 20699 440 20699 4.1e-013 4.8e-009 TGTGTG CACACA 1482 20699 1036 20699 2.3e-020 2.7e-016 TGTGTA TACACA 631 20699 446 20699 6.2e-009 7.2e-005 TCTGTG CACAGA 1649 20699 1239 20699 1.4e-015 1.6e-011 MOTIF TSTGTR 3.0e-037 letter-probability matrix: alength= 4 w= 6 nsites= 4416 E= 3.0e-037 0.000000 0.000000 0.000000 1.000000 0.000000 0.526042 0.473958 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 0.289855 0.000000 0.710145 0.000000 BEST CMCRCCC GGGYGKG 2299 20699 1574 20699 8.2e-035 9.3e-031 3.4e-045 CCCGCCC GGGCGGG 837 20699 514 20699 1.8e-019 2.0e-015 CACACCC GGGTGTG 435 20699 335 20699 1.6e-004 1.8e+000 CCCACCC GGGTGGG 776 20699 503 20699 4.4e-015 5.0e-011 CACGCCC GGGCGTG 437 20699 300 20699 2.0e-007 2.3e-003 MOTIF CMCRCCC 9.3e-031 letter-probability matrix: alength= 4 w= 7 nsites= 2506 E= 9.3e-031 0.000000 1.000000 0.000000 0.000000 0.349561 0.650439 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.482442 0.000000 0.517558 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 RKAAA TTTMY 5854 20699 4841 20699 3.0e-030 3.4e-026 5.4e-080 GGAAA TTTCC 721 20699 590 20699 1.3e-004 1.5e+000 ATAAA TTTAT 1281 20699 923 20699 2.4e-015 2.7e-011 AGAAA TTTCT 3422 20699 2822 20699 9.2e-017 1.0e-012 GTAAA TTTAC 1393 20699 1219 20699 2.3e-004 2.6e+000 MOTIF RKAAA 3.4e-026 letter-probability matrix: alength= 4 w= 5 nsites= 7475 E= 3.4e-026 0.704749 0.000000 0.295251 0.000000 0.000000 0.000000 0.622475 0.377525 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 CHGSAGC GCTSCDG 3834 20699 3055 20699 4.5e-025 5.0e-021 5.2e-026 CAGGAGC GCTCCTG 713 20699 625 20699 7.8e-003 8.5e+001 CTGCAGC GCTGCAG 782 20699 604 20699 6.4e-007 7.0e-003 CAGCAGC GCTGCTG 1037 20699 703 20699 1.4e-016 1.5e-012 CTGGAGC GCTCCAG 673 20699 582 20699 4.9e-003 5.4e+001 CCGCAGC GCTGCGG 699 20699 487 20699 2.3e-010 2.5e-006 CCGGAGC GCTCCGG 514 20699 370 20699 5.5e-007 6.0e-003 MOTIF CHGSAGC 5.0e-021 letter-probability matrix: alength= 4 w= 7 nsites= 4384 E= 5.0e-021 0.000000 1.000000 0.000000 0.000000 0.394161 0.279197 0.000000 0.326642 0.000000 0.000000 1.000000 0.000000 0.000000 0.567062 0.432938 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 MTGCGCA TGCGCAK 564 20699 295 20699 6.1e-021 6.5e-017 3.0e-019 ATGCGCA TGCGCAT 252 20699 88 20699 6.6e-020 7.1e-016 CTGCGCA TGCGCAG 431 20699 246 20699 3.6e-013 3.9e-009 MOTIF MTGCGCA 6.5e-017 letter-probability matrix: alength= 4 w= 7 nsites= 595 E= 6.5e-017 0.331092 0.668908 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 HTTTAAA TTTAAAD 323 20699 158 20699 1.5e-014 1.6e-010 1.7e-010 TTTTAAA TTTAAAA 192 20699 88 20699 2.1e-010 2.2e-006 ATTTAAA TTTAAAT 120 20699 54 20699 2.9e-007 3.2e-003 CTTTAAA TTTAAAG 155 20699 82 20699 1.1e-006 1.2e-002 MOTIF HTTTAAA 1.6e-010 letter-probability matrix: alength= 4 w= 7 nsites= 332 E= 1.6e-010 0.265060 0.292169 0.000000 0.442771 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ATGGCYG CRGCCAT 538 20699 323 20699 6.4e-014 6.9e-010 1.0e-014 ATGGCCG CGGCCAT 191 20699 103 20699 1.5e-007 1.6e-003 ATGGCTG CAGCCAT 350 20699 222 20699 4.0e-008 4.3e-004 MOTIF ATGGCYG 6.9e-010 letter-probability matrix: alength= 4 w= 7 nsites= 545 E= 6.9e-010 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 0.352294 0.000000 0.647706 0.000000 0.000000 1.000000 0.000000 BEST AYGGTGA TCACCRT 345 20699 197 20699 8.1e-011 8.6e-007 5.1e-008 ACGGTGA TCACCGT 134 20699 70 20699 4.2e-006 4.5e-002 ATGGTGA TCACCAT 213 20699 128 20699 2.2e-006 2.4e-002 MOTIF AYGGTGA 8.6e-007 letter-probability matrix: alength= 4 w= 7 nsites= 349 E= 8.6e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.386819 0.000000 0.613181 0.000000 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 1.000000 0.000000 0.000000 0.000000 BEST GGAA TTCC 4410 20699 3905 20699 3.1e-010 3.3e-006 4.4e-130 GGAA TTCC 4410 20699 3905 20699 3.1e-010 3.3e-006 MOTIF GGAA 3.3e-006 letter-probability matrix: alength= 4 w= 4 nsites= 5094 E= 3.3e-006 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 CRSAGC GCTSYG 4774 20699 4262 20699 6.0e-010 6.2e-006 1.1e-029 CACAGC GCTGTG 1625 20699 1395 20699 7.5e-006 7.8e-002 CGCAGC GCTGCG 974 20699 861 20699 3.7e-003 3.9e+001 CAGAGC GCTCTG 1891 20699 1716 20699 1.2e-003 1.3e+001 CGGAGC GCTCCG 933 20699 775 20699 5.2e-005 5.4e-001 MOTIF CRSAGC 6.2e-006 letter-probability matrix: alength= 4 w= 6 nsites= 5622 E= 6.2e-006 0.000000 1.000000 0.000000 0.000000 0.652793 0.000000 0.347207 0.000000 0.000000 0.477054 0.522946 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 CCGCKGC GCMGCGG 797 20699 580 20699 1.5e-009 1.6e-005 3.6e-010 CCGCTGC GCAGCGG 356 20699 246 20699 3.6e-006 3.8e-002 CCGCGGC GCCGCGG 464 20699 344 20699 1.1e-005 1.2e-001 MOTIF CCGCKGC 1.6e-005 letter-probability matrix: alength= 4 w= 7 nsites= 841 E= 1.6e-005 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 0.000000 0.569560 0.430440 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST GTCYCCA TGGRGAC 790 20699 580 20699 4.4e-009 4.6e-005 1.8e-006 GTCTCCA TGGAGAC 390 20699 295 20699 1.4e-004 1.5e+000 GTCCCCA TGGGGAC 405 20699 289 20699 5.1e-006 5.3e-002 MOTIF GTCYCCA 4.6e-005 letter-probability matrix: alength= 4 w= 7 nsites= 805 E= 4.6e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.509317 0.000000 0.490683 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST TAWWTA TAWWTA 268 20699 158 20699 4.7e-008 4.9e-004 2.4e-014 TAATTA TAATTA 108 20699 64 20699 4.8e-004 5.0e+000 TAAATA TATTTA 102 20699 66 20699 3.3e-003 3.4e+001 TATATA TATATA 60 20699 31 20699 1.5e-003 1.6e+001 MOTIF TAWWTA 4.9e-004 letter-probability matrix: alength= 4 w= 6 nsites= 269 E= 4.9e-004 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.602230 0.000000 0.000000 0.397770 0.423792 0.000000 0.000000 0.576208 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 BEST AAACAMA TKTGTTT 349 20699 223 20699 6.3e-008 6.6e-004 1.3e-012 AAACAAA TTTGTTT 225 20699 133 20699 6.0e-007 6.2e-003 AAACACA TGTGTTT 132 20699 92 20699 4.4e-003 4.6e+001 MOTIF AAACAMA 6.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 366 E= 6.6e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.636612 0.363388 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AGGTAAS STTACCT 334 20699 211 20699 6.4e-008 6.6e-004 7.6e-005 AGGTAAG CTTACCT 215 20699 128 20699 1.4e-006 1.4e-002 AGGTAAC GTTACCT 119 20699 83 20699 6.7e-003 6.9e+001 MOTIF AGGTAAS 6.6e-004 letter-probability matrix: alength= 4 w= 7 nsites= 336 E= 6.6e-004 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.354167 0.645833 0.000000 BEST CTCCAKC GMTGGAG 713 20699 540 20699 3.9e-007 4.0e-003 6.9e-008 CTCCAGC GCTGGAG 444 20699 340 20699 1.0e-004 1.0e+000 CTCCATC GATGGAG 272 20699 206 20699 1.4e-003 1.4e+001 MOTIF CTCCAKC 4.0e-003 letter-probability matrix: alength= 4 w= 7 nsites= 726 E= 4.0e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.617080 0.382920 0.000000 1.000000 0.000000 0.000000 BEST KACGTCA TGACGTM 194 20699 109 20699 5.5e-007 5.7e-003 1.8e-007 GACGTCA TGACGTC 134 20699 73 20699 1.3e-005 1.3e-001 TACGTCA TGACGTA 60 20699 36 20699 9.1e-003 9.5e+001 MOTIF KACGTCA 5.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 195 E= 5.7e-003 0.000000 0.000000 0.692308 0.307692 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 BEST GGATGTR YACATCC 302 20699 201 20699 3.4e-006 3.5e-002 3.4e-005 GGATGTG CACATCC 212 20699 144 20699 1.7e-004 1.8e+000 GGATGTA TACATCC 92 20699 57 20699 2.5e-003 2.6e+001 MOTIF GGATGTR 3.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 305 E= 3.5e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.304918 0.000000 0.695082 0.000000 BEST AGGCAG CTGCCT 1959 20699 1697 20699 3.1e-006 3.2e-002 7.0e-009 AGGCAG CTGCCT 1959 20699 1697 20699 3.1e-006 3.2e-002 MOTIF AGGCAG 3.2e-002 letter-probability matrix: alength= 4 w= 6 nsites= 2081 E= 3.2e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # 24 motifs with E-value < 0.05 found. #elapsed time: 2501.24 seconds