# dreme.py -p CHEN/Nanog.pos.fasta -n CHEN/Nanog.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/Nanog.pos.fasta -n CHEN/Nanog.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 ACAAWRS SYWTTGT 2839 10343 994 10343 2.1e-247 2.6e-243 2.6e-243 ACAAAGC GCTTTGT 402 10343 143 10343 1.7e-030 2.0e-026 ACAAAGG CCTTTGT 718 10343 164 10343 5.6e-087 6.8e-083 ACAAAAC GTTTTGT 218 10343 165 10343 3.6e-003 4.4e+001 ACAATGG CCATTGT 519 10343 113 10343 3.7e-065 4.5e-061 ACAATAG CTATTGT 354 10343 83 10343 5.3e-042 6.4e-038 ACAATAC GTATTGT 165 10343 51 10343 1.2e-015 1.4e-011 ACAAAAG CTTTTGT 623 10343 235 10343 3.3e-043 4.0e-039 ACAATGC GCATTGT 304 10343 110 10343 8.0e-023 9.7e-019 MOTIF ACAAWRS 2.6e-243 letter-probability matrix: alength= 4 w= 7 nsites= 3413 E= 2.6e-243 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 0.589511 0.000000 0.000000 0.410489 0.407559 0.000000 0.592441 0.000000 0.000000 0.322883 0.677117 0.000000 BEST ATTWRCA TGYWAAT 1327 10343 463 10343 3.1e-105 3.7e-101 2.8e-102 ATTAACA TGTTAAT 275 10343 81 10343 1.6e-026 1.9e-022 ATTTACA TGTAAAT 328 10343 103 10343 2.9e-029 3.5e-025 ATTAGCA TGCTAAT 379 10343 107 10343 8.8e-038 1.1e-033 ATTTGCA TGCAAAT 447 10343 179 10343 1.8e-028 2.2e-024 MOTIF ATTWRCA 3.7e-101 letter-probability matrix: alength= 4 w= 7 nsites= 1451 E= 3.7e-101 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.455548 0.000000 0.000000 0.544452 0.423846 0.000000 0.576154 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CAGCRGG CCYGCTG 763 10343 234 10343 2.3e-069 2.7e-065 2.1e-065 CAGCAGG CCTGCTG 632 10343 196 10343 1.4e-056 1.6e-052 CAGCGGG CCCGCTG 139 10343 39 10343 9.0e-015 1.1e-010 MOTIF CAGCRGG 2.7e-065 letter-probability matrix: alength= 4 w= 7 nsites= 810 E= 2.7e-065 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 0.822222 0.000000 0.177778 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST CVATYA TRATBG 2832 10343 1788 10343 1.2e-068 1.4e-064 1.8e-077 CAATTA TAATTG 577 10343 380 10343 3.8e-011 4.5e-007 CCATCA TGATGG 925 10343 522 10343 1.4e-028 1.7e-024 CGATTA TAATCG 90 10343 60 10343 8.6e-003 1.0e+002 CCATTA TAATGG 615 10343 311 10343 4.5e-025 5.3e-021 CGATCA TGATCG 119 10343 82 10343 5.3e-003 6.2e+001 CAATCA TGATTG 930 10343 590 10343 6.0e-020 7.2e-016 MOTIF CVATYA 1.4e-064 letter-probability matrix: alength= 4 w= 6 nsites= 3439 E= 1.4e-064 0.000000 1.000000 0.000000 0.000000 0.463216 0.476010 0.060773 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.610933 0.000000 0.389067 1.000000 0.000000 0.000000 0.000000 BEST CMCRCCC GGGYGKG 758 10343 276 10343 2.2e-055 2.6e-051 1.1e-053 CCCGCCC GGGCGGG 115 10343 39 10343 2.9e-010 3.4e-006 CCCACCC GGGTGGG 324 10343 133 10343 3.7e-020 4.3e-016 CACACCC GGGTGTG 289 10343 89 10343 1.7e-026 1.9e-022 CACGCCC GGGCGTG 64 10343 25 10343 2.1e-005 2.4e-001 MOTIF CMCRCCC 2.6e-051 letter-probability matrix: alength= 4 w= 7 nsites= 805 E= 2.6e-051 0.000000 1.000000 0.000000 0.000000 0.449689 0.550311 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777640 0.000000 0.222360 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 AYAAWGA TCWTTRT 1120 10343 536 10343 1.0e-051 1.2e-047 2.3e-049 ACAAAGA TCTTTGT 487 10343 223 10343 1.5e-024 1.7e-020 ATAAAGA TCTTTAT 152 10343 111 10343 6.5e-003 7.5e+001 ATAATGA TCATTAT 142 10343 74 10343 1.9e-006 2.2e-002 ACAATGA TCATTGT 396 10343 138 10343 6.7e-031 7.8e-027 MOTIF AYAAWGA 1.2e-047 letter-probability matrix: alength= 4 w= 7 nsites= 1216 E= 1.2e-047 1.000000 0.000000 0.000000 0.000000 0.000000 0.754112 0.000000 0.245888 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.541118 0.000000 0.000000 0.458882 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST TRARTR YAYTYA 3290 10343 2427 10343 2.3e-041 2.6e-037 3.1e-047 TGAGTA TACTCA 427 10343 296 10343 4.0e-007 4.6e-003 TAAATG CATTTA 561 10343 345 10343 1.1e-013 1.3e-009 TGAATA TATTCA 559 10343 310 10343 2.5e-018 2.9e-014 TAAATA TATTTA 345 10343 255 10343 1.1e-004 1.3e+000 TAAGTG CACTTA 427 10343 346 10343 1.7e-003 1.9e+001 TAAGTA TACTTA 346 10343 222 10343 7.5e-008 8.6e-004 TGAATG CATTCA 857 10343 568 10343 1.1e-015 1.2e-011 TGAGTG CACTCA 661 10343 517 10343 8.7e-006 1.0e-001 MOTIF TRARTR 2.6e-037 letter-probability matrix: alength= 4 w= 6 nsites= 4243 E= 2.6e-037 0.000000 0.000000 0.000000 1.000000 0.392411 0.000000 0.607589 0.000000 1.000000 0.000000 0.000000 0.000000 0.556210 0.000000 0.443790 0.000000 0.000000 0.000000 0.000000 1.000000 0.389347 0.000000 0.610653 0.000000 BEST MGGAAR YTTCCK 2130 10343 1426 10343 6.9e-039 7.8e-035 1.1e-047 CGGAAG CTTCCG 231 10343 102 10343 4.0e-013 4.5e-009 AGGAAG CTTCCT 941 10343 625 10343 5.0e-017 5.6e-013 AGGAAA TTTCCT 972 10343 668 10343 2.7e-015 3.0e-011 CGGAAA TTTCCG 187 10343 115 10343 1.8e-005 2.0e-001 MOTIF MGGAAR 7.8e-035 letter-probability matrix: alength= 4 w= 6 nsites= 2490 E= 7.8e-035 0.826506 0.173494 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 0.497189 0.000000 0.502811 0.000000 BEST RAGGTCA TGACCTY 463 10343 213 10343 3.5e-023 3.8e-019 3.4e-025 GAGGTCA TGACCTC 163 10343 95 10343 1.2e-005 1.3e-001 AAGGTCA TGACCTT 308 10343 120 10343 8.1e-021 8.9e-017 MOTIF RAGGTCA 3.8e-019 letter-probability matrix: alength= 4 w= 7 nsites= 490 E= 3.8e-019 0.661224 0.000000 0.338776 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 TAATKA TMATTA 618 10343 333 10343 1.1e-021 1.2e-017 7.3e-043 TAATGA TCATTA 382 10343 220 10343 1.1e-011 1.2e-007 TAATTA TAATTA 249 10343 120 10343 5.6e-012 6.1e-008 MOTIF TAATKA 1.2e-017 letter-probability matrix: alength= 4 w= 6 nsites= 648 E= 1.2e-017 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.601852 0.398148 1.000000 0.000000 0.000000 0.000000 BEST TKTAAA TTTAMA 782 10343 514 10343 7.6e-015 8.3e-011 5.3e-044 TTTAAA TTTAAA 372 10343 242 10343 5.7e-008 6.2e-004 TGTAAA TTTACA 426 10343 280 10343 1.3e-008 1.4e-004 MOTIF TKTAAA 8.3e-011 letter-probability matrix: alength= 4 w= 6 nsites= 822 E= 8.3e-011 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.532847 0.467153 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 GAAARGA TCYTTTC 453 10343 260 10343 9.1e-014 1.0e-009 1.5e-017 GAAAGGA TCCTTTC 209 10343 102 10343 4.8e-010 5.3e-006 GAAAAGA TCTTTTC 253 10343 159 10343 1.7e-006 1.8e-002 MOTIF GAAARGA 1.0e-009 letter-probability matrix: alength= 4 w= 7 nsites= 466 E= 1.0e-009 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 0.545064 0.000000 0.454936 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ATGCADA THTGCAT 521 10343 313 10343 9.7e-014 1.1e-009 4.1e-041 ATGCATA TATGCAT 85 10343 54 10343 5.2e-003 5.7e+001 ATGCAAA TTTGCAT 219 10343 136 10343 5.2e-006 5.7e-002 ATGCAGA TCTGCAT 223 10343 127 10343 1.3e-007 1.4e-003 MOTIF ATGCADA 1.1e-009 letter-probability matrix: alength= 4 w= 7 nsites= 533 E= 1.1e-009 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 0.414634 0.000000 0.422139 0.163227 1.000000 0.000000 0.000000 0.000000 BEST CNCAGC GCTGNG 1692 10343 1325 10343 2.7e-013 2.9e-009 4.3e-038 CACAGC GCTGTG 650 10343 451 10343 3.9e-010 4.3e-006 CCCAGC GCTGGG 567 10343 450 10343 9.4e-005 1.0e+000 CGCAGC GCTGCG 130 10343 92 10343 6.2e-003 6.7e+001 CTCAGC GCTGAG 553 10343 431 10343 3.8e-005 4.1e-001 MOTIF CNCAGC 2.9e-009 letter-probability matrix: alength= 4 w= 6 nsites= 1962 E= 2.9e-009 0.000000 1.000000 0.000000 0.000000 0.344546 0.298675 0.067788 0.288991 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 CCTGBGG CCVCAGG 489 10343 303 10343 8.3e-012 9.0e-008 3.2e-010 CCTGTGG CCACAGG 209 10343 117 10343 1.6e-007 1.7e-003 CCTGCGG CCGCAGG 54 10343 30 10343 5.7e-003 6.2e+001 CCTGGGG CCCCAGG 233 10343 161 10343 1.5e-004 1.6e+000 MOTIF CCTGBGG 9.0e-008 letter-probability matrix: alength= 4 w= 7 nsites= 511 E= 9.0e-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 0.000000 1.000000 0.000000 0.000000 0.107632 0.473581 0.418787 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST GATGGCB VGCCATC 238 10343 120 10343 1.6e-010 1.7e-006 6.9e-032 GATGGCG CGCCATC 45 10343 17 10343 2.4e-004 2.6e+000 GATGGCT AGCCATC 117 10343 55 10343 1.2e-006 1.3e-002 GATGGCC GGCCATC 81 10343 49 10343 3.1e-003 3.3e+001 MOTIF GATGGCB 1.7e-006 letter-probability matrix: alength= 4 w= 7 nsites= 251 E= 1.7e-006 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.326693 0.203187 0.470120 BEST AAASAAA TTTSTTT 479 10343 308 10343 2.8e-010 3.0e-006 1.7e-043 AAACAAA TTTGTTT 225 10343 140 10343 4.2e-006 4.5e-002 AAAGAAA TTTCTTT 261 10343 170 10343 5.5e-006 5.9e-002 MOTIF AAASAAA 3.0e-006 letter-probability matrix: alength= 4 w= 7 nsites= 493 E= 3.0e-006 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 0.462475 0.537525 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 GGAATGY RCATTCC 284 10343 157 10343 5.1e-010 5.5e-006 1.4e-011 GGAATGC GCATTCC 119 10343 71 10343 2.9e-004 3.1e+000 GGAATGT ACATTCC 167 10343 89 10343 5.4e-007 5.7e-003 MOTIF GGAATGY 5.5e-006 letter-probability matrix: alength= 4 w= 7 nsites= 292 E= 5.5e-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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.410959 0.000000 0.589041 BEST CATTTCC GGAAATG 157 10343 69 10343 1.9e-009 2.0e-005 7.8e-039 CATTTCC GGAAATG 157 10343 69 10343 1.9e-009 2.0e-005 MOTIF CATTTCC 2.0e-005 letter-probability matrix: alength= 4 w= 7 nsites= 160 E= 2.0e-005 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 0.000000 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 BEST CCWCCC GGGWGG 972 10343 747 10343 8.1e-009 8.6e-005 3.3e-023 CCACCC GGGTGG 344 10343 278 10343 4.0e-003 4.3e+001 CCTCCC GGGAGG 662 10343 501 10343 6.6e-007 7.1e-003 MOTIF CCWCCC 8.6e-005 letter-probability matrix: alength= 4 w= 6 nsites= 1051 E= 8.6e-005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.325404 0.000000 0.000000 0.674596 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 ASAATAA TTATTST 273 10343 159 10343 1.6e-008 1.8e-004 7.8e-010 AGAATAA TTATTCT 128 10343 84 10343 1.5e-003 1.6e+001 ACAATAA TTATTGT 147 10343 75 10343 6.8e-007 7.3e-003 MOTIF ASAATAA 1.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 277 E= 1.8e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.530686 0.469314 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST GTCKTTA TAAMGAC 111 10343 44 10343 3.3e-008 3.5e-004 3.6e-006 GTCTTTA TAAAGAC 82 10343 38 10343 3.5e-005 3.7e-001 GTCGTTA TAACGAC 29 10343 6 10343 5.8e-005 6.2e-001 MOTIF GTCKTTA 3.5e-004 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 3.5e-004 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 0.000000 0.258929 0.741071 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 BEST CTGCRG CYGCAG 480 10343 342 10343 5.1e-007 5.5e-003 5.5e-007 CTGCAG CTGCAG 409 10343 296 10343 8.5e-006 9.1e-002 CTGCGG CCGCAG 77 10343 47 10343 4.4e-003 4.7e+001 MOTIF CTGCRG 5.5e-003 letter-probability matrix: alength= 4 w= 6 nsites= 500 E= 5.5e-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 1.000000 0.000000 0.000000 0.846000 0.000000 0.154000 0.000000 0.000000 0.000000 1.000000 0.000000 # 23 motifs with E-value < 0.05 found. #elapsed time: 723.09 seconds