# dreme.py -p CHEN/Zfx.pos.fasta -n CHEN/Zfx.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/Zfx.pos.fasta -n CHEN/Zfx.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 GGCCTNB VNAGGCC 5969 10338 3072 10338 6.0e-366 7.5e-362 7.5e-362 GGCCTCC GGAGGCC 968 10338 551 10338 3.4e-029 4.2e-025 GGCCTGT ACAGGCC 634 10338 271 10338 5.4e-036 6.6e-032 GGCCTCT AGAGGCC 714 10338 398 10338 7.3e-023 9.1e-019 GGCCTGC GCAGGCC 1170 10338 615 10338 9.4e-044 1.2e-039 GGCCTAC GTAGGCC 463 10338 113 10338 7.4e-053 9.2e-049 GGCCTAG CTAGGCC 849 10338 224 10338 1.0e-090 1.3e-086 GGCCTTT AAAGGCC 362 10338 179 10338 6.0e-016 7.5e-012 GGCCTAT ATAGGCC 134 10338 76 10338 3.5e-005 4.3e-001 GGCCTTC GAAGGCC 620 10338 307 10338 1.8e-026 2.2e-022 GGCCTGG CCAGGCC 1544 10338 624 10338 1.1e-099 1.4e-095 GGCCTTG CAAGGCC 793 10338 319 10338 6.9e-050 8.6e-046 GGCCTCG CGAGGCC 667 10338 336 10338 2.2e-027 2.7e-023 MOTIF GGCCTNB 7.5e-362 letter-probability matrix: alength= 4 w= 7 nsites= 8009 E= 7.5e-362 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.157448 0.259458 0.389562 0.193532 0.000000 0.367087 0.431764 0.201149 BEST GGAAR YTTCC 4387 10338 3343 10338 3.2e-051 3.7e-047 5.6e-061 GGAAA TTTCC 1877 10338 1266 10338 1.1e-032 1.3e-028 GGAAG CTTCC 3162 10338 2414 10338 5.1e-032 5.9e-028 MOTIF GGAAR 3.7e-047 letter-probability matrix: alength= 4 w= 5 nsites= 5942 E= 3.7e-047 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 0.353416 0.000000 0.646584 0.000000 BEST AGGCCYD HRGGCCT 503 10338 211 10338 1.3e-029 1.5e-025 3.9e-269 AGGCCTT AAGGCCT 19 10338 6 10338 7.3e-003 8.2e+001 AGGCCTG CAGGCCT 52 10338 13 10338 5.6e-007 6.4e-003 AGGCCTA TAGGCCT 32 10338 8 10338 9.0e-005 1.0e+000 AGGCCCA TGGGCCT 192 10338 72 10338 3.1e-014 3.5e-010 AGGCCCG CGGGCCT 105 10338 49 10338 3.5e-006 3.9e-002 AGGCCCT AGGGCCT 132 10338 72 10338 1.5e-005 1.6e-001 MOTIF AGGCCYD 1.5e-025 letter-probability matrix: alength= 4 w= 7 nsites= 517 E= 1.5e-025 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 1.000000 0.000000 0.000000 0.000000 0.837524 0.000000 0.162476 0.423598 0.000000 0.284333 0.292070 BEST ATGGCG CGCCAT 549 10338 246 10338 1.0e-028 1.2e-024 3.0e-026 ATGGCG CGCCAT 549 10338 246 10338 1.0e-028 1.2e-024 MOTIF ATGGCG 1.2e-024 letter-probability matrix: alength= 4 w= 6 nsites= 568 E= 1.2e-024 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 CACGTG CACGTG 323 10338 106 10338 2.2e-027 2.5e-023 3.7e-024 CACGTG CACGTG 323 10338 106 10338 2.2e-027 2.5e-023 MOTIF CACGTG 2.5e-023 letter-probability matrix: alength= 4 w= 6 nsites= 331 E= 2.5e-023 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 AMACAVA TBTGTKT 583 10338 323 10338 4.1e-019 4.6e-015 1.8e-020 ACACACA TGTGTGT 147 10338 69 10338 5.1e-008 5.7e-004 AAACAGA TCTGTTT 101 10338 56 10338 2.0e-004 2.2e+000 AAACACA TGTGTTT 84 10338 47 10338 7.5e-004 8.4e+000 ACACAAA TTTGTGT 91 10338 46 10338 7.2e-005 8.0e-001 AAACAAA TTTGTTT 104 10338 51 10338 1.2e-005 1.3e-001 ACACAGA TCTGTGT 128 10338 78 10338 2.8e-004 3.2e+000 MOTIF AMACAVA 4.6e-015 letter-probability matrix: alength= 4 w= 7 nsites= 615 E= 4.6e-015 1.000000 0.000000 0.000000 0.000000 0.456911 0.543089 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 0.310569 0.334959 0.354472 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CSGGGAM KTCCCSG 714 10338 431 10338 3.5e-018 3.8e-014 1.3e-018 CGGGGAC GTCCCCG 309 10338 171 10338 9.5e-011 1.1e-006 CGGGGAA TTCCCCG 66 10338 38 10338 3.8e-003 4.2e+001 CCGGGAC GTCCCGG 279 10338 183 10338 3.6e-006 4.0e-002 CCGGGAA TTCCCGG 86 10338 49 10338 8.9e-004 9.9e+000 MOTIF CSGGGAM 3.8e-014 letter-probability matrix: alength= 4 w= 7 nsites= 757 E= 3.8e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.491413 0.508587 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 1.000000 0.000000 0.000000 0.000000 0.198151 0.801849 0.000000 0.000000 BEST CHGGGCC GGCCCDG 1521 10338 1140 10338 1.4e-015 1.5e-011 3.2e-078 CTGGGCC GGCCCAG 576 10338 391 10338 6.1e-010 6.7e-006 CCGGGCC GGCCCGG 559 10338 394 10338 2.5e-008 2.8e-004 CAGGGCC GGCCCTG 548 10338 436 10338 1.4e-004 1.6e+000 MOTIF CHGGGCC 1.5e-011 letter-probability matrix: alength= 4 w= 7 nsites= 1650 E= 1.5e-011 0.000000 1.000000 0.000000 0.000000 0.321818 0.336970 0.000000 0.341212 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 1.000000 0.000000 0.000000 BEST AKRAA TTYMT 2719 10338 2243 10338 5.0e-015 5.5e-011 9.2e-044 AGGAA TTCCT 763 10338 627 10338 8.8e-005 9.7e-001 ATAAA TTTAT 399 10338 285 10338 5.3e-006 5.9e-002 ATGAA TTCAT 670 10338 579 10338 4.3e-003 4.7e+001 AGAAA TTTCT 1324 10338 1061 10338 5.7e-009 6.3e-005 MOTIF AKRAA 5.5e-011 letter-probability matrix: alength= 4 w= 5 nsites= 3370 E= 5.5e-011 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.672404 0.327596 0.558160 0.000000 0.441840 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CGGARCC GGYTCCG 603 10338 385 10338 6.2e-013 6.6e-009 6.0e-013 CGGAACC GGTTCCG 137 10338 85 10338 2.7e-004 2.9e+000 CGGAGCC GGCTCCG 472 10338 302 10338 2.6e-010 2.8e-006 MOTIF CGGARCC 6.6e-009 letter-probability matrix: alength= 4 w= 7 nsites= 627 E= 6.6e-009 0.000000 1.000000 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 0.216906 0.000000 0.783094 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CDCCKCC GGMGGHG 2199 10338 1808 10338 3.3e-012 3.5e-008 4.6e-016 CTCCGCC GGCGGAG 382 10338 300 10338 8.0e-004 8.5e+000 CTCCTCC GGAGGAG 546 10338 419 10338 1.6e-005 1.7e-001 CGCCTCC GGAGGCG 437 10338 354 10338 1.5e-003 1.6e+001 CACCTCC GGAGGTG 327 10338 266 10338 6.2e-003 6.6e+001 CACCGCC GGCGGTG 295 10338 229 10338 2.0e-003 2.1e+001 CGCCGCC GGCGGCG 690 10338 509 10338 4.0e-008 4.3e-004 MOTIF CDCCKCC 3.5e-008 letter-probability matrix: alength= 4 w= 7 nsites= 2594 E= 3.5e-008 0.000000 1.000000 0.000000 0.000000 0.230918 0.000000 0.422128 0.346955 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.512336 0.487664 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST AKGTRA TYACMT 974 10338 710 10338 1.0e-011 1.1e-007 5.4e-012 AGGTAA TTACCT 226 10338 173 10338 4.2e-003 4.5e+001 ATGTGA TCACAT 206 10338 150 10338 1.6e-003 1.7e+001 ATGTAA TTACAT 92 10338 59 10338 4.4e-003 4.7e+001 AGGTGA TCACCT 487 10338 345 10338 2.9e-007 3.0e-003 MOTIF AKGTRA 1.1e-007 letter-probability matrix: alength= 4 w= 6 nsites= 1038 E= 1.1e-007 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.708092 0.291908 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.313102 0.000000 0.686898 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AGGAYG CRTCCT 873 10338 650 10338 1.6e-009 1.7e-005 1.6e-007 AGGATG CATCCT 454 10338 345 10338 4.8e-005 5.1e-001 AGGACG CGTCCT 432 10338 320 10338 1.8e-005 1.9e-001 MOTIF AGGAYG 1.7e-005 letter-probability matrix: alength= 4 w= 6 nsites= 905 E= 1.7e-005 1.000000 0.000000 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 0.000000 0.488398 0.000000 0.511602 0.000000 0.000000 1.000000 0.000000 BEST TTCCCR YGGGAA 386 10338 256 10338 1.1e-007 1.1e-003 3.5e-022 TTCCCA TGGGAA 247 10338 163 10338 1.6e-005 1.7e-001 TTCCCG CGGGAA 141 10338 94 10338 1.2e-003 1.3e+001 MOTIF TTCCCR 1.1e-003 letter-probability matrix: alength= 4 w= 6 nsites= 391 E= 1.1e-003 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 1.000000 0.000000 0.000000 0.636829 0.000000 0.363171 0.000000 BEST ACKGTG CACMGT 723 10338 550 10338 3.1e-007 3.3e-003 6.5e-005 ACGGTG CACCGT 280 10338 215 10338 1.8e-003 1.9e+001 ACTGTG CACAGT 454 10338 343 10338 3.5e-005 3.6e-001 MOTIF ACKGTG 3.3e-003 letter-probability matrix: alength= 4 w= 6 nsites= 756 E= 3.3e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.382275 0.617725 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 CHGCAGC GCTGCDG 1328 10338 1098 10338 3.7e-007 3.9e-003 1.0e-008 CTGCAGC GCTGCAG 451 10338 347 10338 9.8e-005 1.0e+000 CAGCAGC GCTGCTG 554 10338 444 10338 2.0e-004 2.1e+000 CCGCAGC GCTGCGG 454 10338 376 10338 3.2e-003 3.3e+001 MOTIF CHGCAGC 3.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 1447 E= 3.9e-003 0.000000 1.000000 0.000000 0.000000 0.373186 0.317208 0.000000 0.309606 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 AAGGTCA TGACCTT 135 10338 65 10338 3.7e-007 3.9e-003 4.8e-005 AAGGTCA TGACCTT 135 10338 65 10338 3.7e-007 3.9e-003 MOTIF AAGGTCA 3.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 137 E= 3.9e-003 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CACASCC GGSTGTG 577 10338 428 10338 8.2e-007 8.6e-003 6.4e-005 CACACCC GGGTGTG 221 10338 163 10338 1.6e-003 1.7e+001 CACAGCC GGCTGTG 366 10338 270 10338 6.3e-005 6.7e-001 MOTIF CACASCC 8.6e-003 letter-probability matrix: alength= 4 w= 7 nsites= 598 E= 8.6e-003 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 0.374582 0.625418 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST GGCCTR YAGGCC 315 10338 208 10338 1.2e-006 1.3e-002 1.4e-308 GGCCTG CAGGCC 218 10338 162 10338 2.2e-003 2.3e+001 GGCCTA TAGGCC 100 10338 46 10338 4.3e-006 4.5e-002 MOTIF GGCCTR 1.3e-002 letter-probability matrix: alength= 4 w= 6 nsites= 321 E= 1.3e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.311526 0.000000 0.688474 0.000000 # 19 motifs with E-value < 0.05 found. #elapsed time: 717.08 seconds