# dreme.py -p CHEN/CTCF.pos.fasta -n CHEN/CTCF.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/CTCF.pos.fasta -n CHEN/CTCF.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 AGRKGGC GCCMYCT 15508 39609 2735 39609 9.3e-2732 1.2e-2727 1.2e-2727 AGAGGGC GCCCTCT 4705 39609 867 39609 3.9e-677 4.9e-673 AGGTGGC GCCACCT 4040 39609 652 39609 5.8e-627 7.2e-623 AGATGGC GCCATCT 2420 39609 452 39609 6.0e-335 7.5e-331 AGGGGGC GCCCCCT 5135 39609 846 39609 8.4e-799 1.1e-794 MOTIF AGRKGGC 1.2e-2727 letter-probability matrix: alength= 4 w= 7 nsites= 16582 E= 1.2e-2727 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.437523 0.000000 0.562477 0.000000 0.000000 0.000000 0.603606 0.396394 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CCACYAG CTRGTGG 3858 39609 1351 39609 4.5e-294 5.5e-290 7.9e-1031 CCACTAG CTAGTGG 2006 39609 467 39609 4.7e-233 5.8e-229 CCACCAG CTGGTGG 1907 39609 898 39609 9.6e-086 1.2e-081 MOTIF CCACYAG 5.5e-290 letter-probability matrix: alength= 4 w= 7 nsites= 3974 E= 5.5e-290 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 0.490438 0.000000 0.509562 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST RGAAA TTTCY 12985 39609 9298 39609 1.9e-187 2.3e-183 4.8e-183 GGAAA TTTCC 7082 39609 4793 39609 1.1e-115 1.3e-111 AGAAA TTTCT 7928 39609 5503 39609 2.1e-117 2.6e-113 MOTIF RGAAA 2.3e-183 letter-probability matrix: alength= 4 w= 5 nsites= 17449 E= 2.3e-183 0.535217 0.000000 0.464783 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 0.000000 BEST GTGGHCA TGDCCAC 2843 39609 1286 39609 4.7e-140 5.5e-136 1.1e-249 GTGGCCA TGGCCAC 1343 39609 522 39609 2.5e-085 2.9e-081 GTGGTCA TGACCAC 836 39609 381 39609 1.7e-040 2.0e-036 GTGGACA TGTCCAC 722 39609 400 39609 1.3e-022 1.5e-018 MOTIF GTGGHCA 5.5e-136 letter-probability matrix: alength= 4 w= 7 nsites= 2934 E= 5.5e-136 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 0.248807 0.462849 0.000000 0.288344 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CGCCNCC GGNGGCG 1897 39609 767 39609 2.4e-113 2.8e-109 4.6e-901 CGCCTCC GGAGGCG 618 39609 264 39609 4.2e-034 4.9e-030 CGCCGCC GGCGGCG 354 39609 184 39609 8.4e-014 9.8e-010 CGCCACC GGTGGCG 496 39609 133 39609 8.6e-051 1.0e-046 CGCCCCC GGGGGCG 529 39609 225 39609 1.2e-029 1.5e-025 MOTIF CGCCNCC 2.8e-109 letter-probability matrix: alength= 4 w= 7 nsites= 2013 E= 2.8e-109 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 0.245902 0.266269 0.178838 0.308992 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST AAYTRCA TGYARTT 2276 39609 1290 39609 5.4e-065 6.3e-061 1.4e-071 AACTACA TGTAGTT 408 39609 270 39609 5.7e-008 6.7e-004 AATTGCA TGCAATT 462 39609 323 39609 3.5e-007 4.1e-003 AATTACA TGTAATT 354 39609 178 39609 7.8e-015 9.1e-011 AACTGCA TGCAGTT 1117 39609 552 39609 2.2e-045 2.6e-041 MOTIF AAYTRCA 6.3e-061 letter-probability matrix: alength= 4 w= 7 nsites= 2339 E= 6.3e-061 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.657546 0.000000 0.342454 0.000000 0.000000 0.000000 1.000000 0.325780 0.000000 0.674220 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AGRKGGA TCCMYCT 3260 39609 2088 39609 1.7e-062 1.9e-058 7.3e-127 AGAGGGA TCCCTCT 1223 39609 684 39609 1.9e-036 2.2e-032 AGGTGGA TCCACCT 651 39609 483 39609 2.8e-007 3.3e-003 AGGGGGA TCCCCCT 1023 39609 655 39609 4.9e-020 5.7e-016 AGATGGA TCCATCT 508 39609 338 39609 2.3e-009 2.7e-005 MOTIF AGRKGGA 1.9e-058 letter-probability matrix: alength= 4 w= 7 nsites= 3459 E= 1.9e-058 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.508239 0.000000 0.491761 0.000000 0.000000 0.000000 0.663197 0.336803 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST TTTAWW WWTAAA 3360 39609 2241 39609 8.6e-055 1.0e-050 1.7e-057 TTTAAT ATTAAA 897 39609 681 39609 2.2e-008 2.5e-004 TTTATA TATAAA 710 39609 490 39609 8.4e-011 9.8e-007 TTTAAA TTTAAA 938 39609 504 39609 2.2e-031 2.5e-027 TTTATT AATAAA 1100 39609 729 39609 8.0e-019 9.3e-015 MOTIF TTTAWW 1.0e-050 letter-probability matrix: alength= 4 w= 6 nsites= 3688 E= 1.0e-050 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 0.501085 0.000000 0.000000 0.498915 0.452278 0.000000 0.000000 0.547722 BEST DCCACM KGTGGH 9095 39609 7444 39609 1.6e-047 1.8e-043 8.4e-388 ACCACC GGTGGT 1664 39609 1287 39609 8.1e-013 9.2e-009 ACCACA TGTGGT 2059 39609 1652 39609 4.2e-012 4.7e-008 TCCACC GGTGGA 1066 39609 908 39609 1.7e-004 1.9e+000 TCCACA TGTGGA 1803 39609 1645 39609 3.1e-003 3.5e+001 GCCACA TGTGGC 2489 39609 2021 39609 3.8e-013 4.4e-009 GCCACC GGTGGC 1612 39609 1070 39609 7.6e-027 8.6e-023 MOTIF DCCACM 1.8e-043 letter-probability matrix: alength= 4 w= 6 nsites= 10830 E= 1.8e-043 0.343952 0.000000 0.388643 0.267405 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 0.602308 0.397692 0.000000 0.000000 BEST RGGAA TTCCY 9487 39609 7973 39609 8.5e-039 9.6e-035 1.5e-091 AGGAA TTCCT 5742 39609 4631 39609 6.3e-032 7.1e-028 GGGAA TTCCC 4699 39609 4006 39609 1.8e-015 2.1e-011 MOTIF RGGAA 9.6e-035 letter-probability matrix: alength= 4 w= 5 nsites= 11474 E= 9.6e-035 0.556301 0.000000 0.443699 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 DAAATR YATTTH 3611 39609 2792 39609 6.6e-027 7.3e-023 2.4e-113 GAAATG CATTTC 495 39609 390 39609 2.2e-004 2.4e+000 TAAATG CATTTA 755 39609 644 39609 1.5e-003 1.6e+001 AAAATG CATTTT 1087 39609 848 39609 2.1e-008 2.3e-004 AAAATA TATTTT 737 39609 500 39609 5.9e-012 6.5e-008 GAAATA TATTTC 300 39609 200 39609 4.2e-006 4.6e-002 TAAATA TATTTA 484 39609 372 39609 6.7e-005 7.4e-001 MOTIF DAAATR 7.3e-023 letter-probability matrix: alength= 4 w= 6 nsites= 3934 E= 7.3e-023 0.475343 0.000000 0.203610 0.321047 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 0.391713 0.000000 0.608287 0.000000 BEST GTAYTRC GYARTAC 1094 39609 660 39609 4.0e-026 4.3e-022 1.4e-034 GTACTGC GCAGTAC 509 39609 289 39609 2.2e-015 2.4e-011 GTATTAC GTAATAC 140 39609 90 39609 5.8e-004 6.4e+000 GTATTGC GCAATAC 277 39609 165 39609 5.1e-008 5.6e-004 GTACTAC GTAGTAC 180 39609 129 39609 2.1e-003 2.3e+001 MOTIF GTAYTRC 4.3e-022 letter-probability matrix: alength= 4 w= 7 nsites= 1107 E= 4.3e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.623306 0.000000 0.376694 0.000000 0.000000 0.000000 1.000000 0.289973 0.000000 0.710027 0.000000 0.000000 1.000000 0.000000 0.000000 BEST AHACAMA TKTGTDT 2075 39609 1517 39609 7.9e-022 8.6e-018 6.4e-033 ACACACA TGTGTGT 614 39609 436 39609 1.8e-008 1.9e-004 ACACAAA TTTGTGT 427 39609 318 39609 3.4e-005 3.7e-001 ATACAAA TTTGTAT 191 39609 143 39609 4.9e-003 5.4e+001 ATACACA TGTGTAT 294 39609 185 39609 3.3e-007 3.6e-003 AAACAAA TTTGTTT 421 39609 299 39609 2.8e-006 3.1e-002 AAACACA TGTGTTT 399 39609 265 39609 1.0e-007 1.1e-003 MOTIF AHACAMA 8.6e-018 letter-probability matrix: alength= 4 w= 7 nsites= 2199 E= 8.6e-018 1.000000 0.000000 0.000000 0.000000 0.366075 0.429741 0.000000 0.204184 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.451569 0.548431 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST AGCGHCC GGDCGCT 804 39609 471 39609 2.1e-021 2.3e-017 1.8e-323 AGCGACC GGTCGCT 199 39609 117 39609 2.2e-006 2.4e-002 AGCGTCC GGACGCT 227 39609 135 39609 7.2e-007 7.8e-003 AGCGCCC GGGCGCT 389 39609 220 39609 3.0e-012 3.3e-008 MOTIF AGCGHCC 2.3e-017 letter-probability matrix: alength= 4 w= 7 nsites= 819 E= 2.3e-017 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 0.000000 1.000000 0.000000 0.245421 0.476190 0.000000 0.278388 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST AGCAGAG CTCTGCT 1398 39609 966 39609 9.1e-020 9.8e-016 1.3e-152 AGCAGAG CTCTGCT 1398 39609 966 39609 9.1e-020 9.8e-016 MOTIF AGCAGAG 9.8e-016 letter-probability matrix: alength= 4 w= 7 nsites= 1427 E= 9.8e-016 1.000000 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 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 BEST GTGTCRC GYGACAC 722 39609 419 39609 6.6e-020 7.1e-016 1.4e-020 GTGTCGC GCGACAC 201 39609 94 39609 2.0e-010 2.2e-006 GTGTCAC GTGACAC 523 39609 326 39609 5.5e-012 5.9e-008 MOTIF GTGTCRC 7.1e-016 letter-probability matrix: alength= 4 w= 7 nsites= 726 E= 7.1e-016 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.723140 0.000000 0.276860 0.000000 0.000000 1.000000 0.000000 0.000000 BEST RTTCTS SAGAAY 5345 39609 4644 39609 3.3e-014 3.6e-010 6.0e-024 GTTCTC GAGAAC 1451 39609 1231 39609 8.4e-006 9.0e-002 ATTCTC GAGAAT 1080 39609 948 39609 1.6e-003 1.7e+001 ATTCTG CAGAAT 1472 39609 1201 39609 5.3e-008 5.7e-004 GTTCTG CAGAAC 1732 39609 1555 39609 8.6e-004 9.2e+000 MOTIF RTTCTS 3.6e-010 letter-probability matrix: alength= 4 w= 6 nsites= 5887 E= 3.6e-010 0.441991 0.000000 0.558009 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 0.000000 1.000000 0.000000 0.439103 0.560897 0.000000 BEST GTGGTDA THACCAC 516 39609 316 39609 1.6e-012 1.7e-008 1.8e-047 GTGGTGA TCACCAC 249 39609 162 39609 9.9e-006 1.0e-001 GTGGTAA TTACCAC 147 39609 80 39609 5.0e-006 5.3e-002 GTGGTTA TAACCAC 125 39609 76 39609 3.3e-004 3.5e+000 MOTIF GTGGTDA 1.7e-008 letter-probability matrix: alength= 4 w= 7 nsites= 521 E= 1.7e-008 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 0.000000 1.000000 0.282150 0.000000 0.477927 0.239923 1.000000 0.000000 0.000000 0.000000 BEST GRACAC GTGTYC 2256 39609 1865 39609 2.1e-010 2.3e-006 2.8e-015 GAACAC GTGTTC 847 39609 683 39609 1.3e-005 1.3e-001 GGACAC GTGTCC 1438 39609 1214 39609 5.2e-006 5.6e-002 MOTIF GRACAC 2.3e-006 letter-probability matrix: alength= 4 w= 6 nsites= 2325 E= 2.3e-006 0.000000 0.000000 1.000000 0.000000 0.370753 0.000000 0.629247 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 1.000000 0.000000 0.000000 BEST CASCATC GATGSTG 957 39609 718 39609 2.0e-009 2.1e-005 6.1e-023 CAGCATC GATGCTG 604 39609 463 39609 7.8e-006 8.2e-002 CACCATC GATGGTG 360 39609 258 39609 2.2e-005 2.3e-001 MOTIF CASCATC 2.1e-005 letter-probability matrix: alength= 4 w= 7 nsites= 982 E= 2.1e-005 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.375764 0.624236 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 1.000000 0.000000 0.000000 BEST GATGTCA TGACATC 367 39609 232 39609 1.7e-008 1.8e-004 2.7e-014 GATGTCA TGACATC 367 39609 232 39609 1.7e-008 1.8e-004 MOTIF GATGTCA 1.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 368 E= 1.8e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ATGWACA TGTWCAT 462 39609 313 39609 4.2e-008 4.4e-004 1.3e-005 ATGTACA TGTACAT 214 39609 138 39609 2.9e-005 3.1e-001 ATGAACA TGTTCAT 248 39609 175 39609 2.2e-004 2.3e+000 MOTIF ATGWACA 4.4e-004 letter-probability matrix: alength= 4 w= 7 nsites= 467 E= 4.4e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.531049 0.000000 0.000000 0.468951 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CTGYCTC GAGRCAG 1712 39609 1427 39609 1.1e-007 1.2e-003 1.8e-010 CTGTCTC GAGACAG 681 39609 551 39609 1.0e-004 1.1e+000 CTGCCTC GAGGCAG 1051 39609 898 39609 2.4e-004 2.6e+000 MOTIF CTGYCTC 1.2e-003 letter-probability matrix: alength= 4 w= 7 nsites= 1771 E= 1.2e-003 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 0.608696 0.000000 0.391304 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 BEST GGAAGTS SACTTCC 367 39609 239 39609 1.0e-007 1.1e-003 1.8e-005 GGAAGTG CACTTCC 225 39609 138 39609 2.8e-006 2.9e-002 GGAAGTC GACTTCC 143 39609 101 39609 4.2e-003 4.4e+001 MOTIF GGAAGTS 1.1e-003 letter-probability matrix: alength= 4 w= 7 nsites= 373 E= 1.1e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.391421 0.608579 0.000000 BEST CTGYAG CTRCAG 3420 39609 3029 39609 2.0e-007 2.1e-003 1.5e-084 CTGTAG CTACAG 1509 39609 1372 39609 4.9e-003 5.2e+001 CTGCAG CTGCAG 2012 39609 1725 39609 8.1e-007 8.6e-003 MOTIF CTGYAG 2.1e-003 letter-probability matrix: alength= 4 w= 6 nsites= 3662 E= 2.1e-003 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 0.574823 0.000000 0.425177 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST CTGGYCA TGRCCAG 1279 39609 1055 39609 1.4e-006 1.4e-002 1.1e-027 CTGGCCA TGGCCAG 653 39609 524 39609 8.4e-005 8.8e-001 CTGGTCA TGACCAG 645 39609 542 39609 1.4e-003 1.5e+001 MOTIF CTGGYCA 1.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 1311 E= 1.4e-002 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 0.000000 0.502670 0.000000 0.497330 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST GTTTTM KAAAAC 1097 39609 898 39609 3.5e-006 3.7e-002 4.5e-030 GTTTTC GAAAAC 434 39609 358 39609 3.7e-003 3.9e+001 GTTTTA TAAAAC 670 39609 548 39609 2.4e-004 2.5e+000 MOTIF GTTTTM 3.7e-002 letter-probability matrix: alength= 4 w= 6 nsites= 1124 E= 3.7e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.608541 0.391459 0.000000 0.000000 BEST GAGGACA TGTCCTC 489 39609 359 39609 4.1e-006 4.3e-002 5.2e-005 GAGGACA TGTCCTC 489 39609 359 39609 4.1e-006 4.3e-002 MOTIF GAGGACA 4.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 495 E= 4.3e-002 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 0.000000 1.000000 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 # 28 motifs with E-value < 0.05 found. #elapsed time: 4237.85 seconds