# dreme.py -p CHEN/Oct4.pos.fasta -n CHEN/Oct4.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/Oct4.pos.fasta -n CHEN/Oct4.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 ATGBWAA TTWVCAT 885 3761 178 3761 2.4e-130 2.8e-126 2.8e-126 ATGGAAA TTTCCAT 95 3761 27 3761 1.7e-010 1.9e-006 ATGTAAA TTTACAT 125 3761 24 3761 2.8e-018 3.3e-014 ATGCTAA TTAGCAT 163 3761 21 3761 2.6e-029 3.0e-025 ATGCAAA TTTGCAT 462 3761 60 3761 3.3e-083 3.9e-079 ATGGTAA TTACCAT 52 3761 24 3761 8.4e-004 9.7e+000 ATGTTAA TTAACAT 74 3761 29 3761 4.7e-006 5.4e-002 MOTIF ATGBWAA 2.8e-126 letter-probability matrix: alength= 4 w= 7 nsites= 1012 E= 2.8e-126 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 0.659091 0.147233 0.193676 0.709486 0.000000 0.000000 0.290514 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ACAAWRG CYWTTGT 522 3761 151 3761 2.3e-053 2.6e-049 5.2e-050 ACAAAGG CCTTTGT 206 3761 36 3761 2.7e-031 3.1e-027 ACAATGG CCATTGT 119 3761 43 3761 6.5e-010 7.4e-006 ACAATAG CTATTGT 78 3761 20 3761 1.1e-009 1.3e-005 ACAAAAG CTTTTGT 150 3761 58 3761 3.9e-011 4.5e-007 MOTIF ACAAWRG 2.6e-049 letter-probability matrix: alength= 4 w= 7 nsites= 570 E= 2.6e-049 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 0.645614 0.000000 0.000000 0.354386 0.410526 0.000000 0.589474 0.000000 0.000000 0.000000 1.000000 0.000000 BEST WTATGCR YGCATAW 347 3761 68 3761 7.9e-049 9.0e-045 4.2e-097 TTATGCA TGCATAA 143 3761 24 3761 1.5e-022 1.7e-018 ATATGCG CGCATAT 41 3761 6 3761 8.2e-008 9.2e-004 ATATGCA TGCATAT 165 3761 36 3761 1.0e-021 1.1e-017 TTATGCG CGCATAA 27 3761 6 3761 1.6e-004 1.8e+000 MOTIF WTATGCR 9.0e-045 letter-probability matrix: alength= 4 w= 7 nsites= 365 E= 9.0e-045 0.553425 0.000000 0.000000 0.446575 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.835616 0.000000 0.164384 0.000000 BEST GGGHGGR YCCDCCC 707 3761 358 3761 2.0e-031 2.3e-027 5.9e-028 GGGCGGG CCCGCCC 161 3761 64 3761 2.1e-011 2.3e-007 GGGAGGG CCCTCCC 208 3761 99 3761 1.0e-010 1.2e-006 GGGCGGA TCCGCCC 93 3761 36 3761 2.2e-007 2.5e-003 GGGTGGG CCCACCC 181 3761 64 3761 7.9e-015 8.9e-011 GGGTGGA TCCACCC 84 3761 48 3761 1.0e-003 1.1e+001 GGGAGGA TCCTCCC 124 3761 76 3761 3.6e-004 4.0e+000 MOTIF GGGHGGR 2.3e-027 letter-probability matrix: alength= 4 w= 7 nsites= 844 E= 2.3e-027 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.386256 0.303318 0.000000 0.310427 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.354265 0.000000 0.645735 0.000000 BEST TTCCKGB VCMGGAA 461 3761 215 3761 9.3e-024 1.0e-019 4.1e-022 TTCCTGT ACAGGAA 96 3761 47 3761 2.2e-005 2.4e-001 TTCCTGC GCAGGAA 124 3761 61 3761 1.6e-006 1.8e-002 TTCCGGC GCCGGAA 50 3761 17 3761 3.1e-005 3.5e-001 TTCCGGT ACCGGAA 52 3761 11 3761 7.5e-008 8.4e-004 TTCCTGG CCAGGAA 119 3761 59 3761 3.2e-006 3.5e-002 TTCCGGG CCCGGAA 58 3761 24 3761 1.0e-004 1.1e+000 MOTIF TTCCKGB 1.0e-019 letter-probability matrix: alength= 4 w= 7 nsites= 509 E= 1.0e-019 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 0.000000 0.332024 0.667976 0.000000 0.000000 1.000000 0.000000 0.000000 0.349705 0.349705 0.300589 BEST ACAAWGM KCWTTGT 372 3761 169 3761 3.9e-020 4.3e-016 3.4e-020 ACAAAGC GCTTTGT 122 3761 46 3761 1.3e-009 1.5e-005 ACAATGC GCATTGT 60 3761 36 3761 8.8e-003 9.8e+001 ACAAAGA TCTTTGT 117 3761 59 3761 5.8e-006 6.4e-002 ACAATGA TCATTGT 91 3761 30 3761 9.7e-009 1.1e-004 MOTIF ACAAWGM 4.3e-016 letter-probability matrix: alength= 4 w= 7 nsites= 402 E= 4.3e-016 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 0.609453 0.000000 0.000000 0.390547 0.000000 0.000000 1.000000 0.000000 0.539801 0.460199 0.000000 0.000000 BEST ATGMATA TATKCAT 115 3761 28 3761 3.1e-014 3.4e-010 1.7e-036 ATGCATA TATGCAT 33 3761 11 3761 6.1e-004 6.7e+000 ATGAATA TATTCAT 83 3761 17 3761 4.9e-012 5.4e-008 MOTIF ATGMATA 3.4e-010 letter-probability matrix: alength= 4 w= 7 nsites= 117 E= 3.4e-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 0.717949 0.282051 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 BEST RGRAA TTYCY 1901 3761 1611 3761 1.2e-011 1.3e-007 1.6e-018 AGGAA TTCCT 730 3761 578 3761 2.1e-006 2.4e-002 GGAAA TTTCC 639 3761 554 3761 4.0e-003 4.4e+001 AGAAA TTTCT 796 3761 642 3761 3.6e-006 3.9e-002 GGGAA TTCCC 816 3761 682 3761 6.1e-005 6.7e-001 MOTIF RGRAA 1.3e-007 letter-probability matrix: alength= 4 w= 5 nsites= 2918 E= 1.3e-007 0.556888 0.000000 0.443112 0.000000 0.000000 0.000000 1.000000 0.000000 0.478067 0.000000 0.521933 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST GTCACS SGTGAC 250 3761 140 3761 5.9e-009 6.3e-005 3.0e-005 GTCACG CGTGAC 82 3761 45 3761 5.9e-004 6.4e+000 GTCACC GGTGAC 175 3761 97 3761 8.5e-007 9.2e-003 MOTIF GTCACS 6.3e-005 letter-probability matrix: alength= 4 w= 6 nsites= 262 E= 6.3e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.679389 0.320611 0.000000 BEST ATGCAGA TCTGCAT 113 3761 43 3761 6.9e-009 7.4e-005 4.8e-015 ATGCAGA TCTGCAT 113 3761 43 3761 6.9e-009 7.4e-005 MOTIF ATGCAGA 7.4e-005 letter-probability matrix: alength= 4 w= 7 nsites= 115 E= 7.4e-005 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST ATGCGCA TGCGCAT 65 3761 16 3761 1.6e-008 1.7e-004 4.8e-013 ATGCGCA TGCGCAT 65 3761 16 3761 1.6e-008 1.7e-004 MOTIF ATGCGCA 1.7e-004 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 1.7e-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 0.000000 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 TGAATR YATTCA 336 3761 212 3761 2.2e-008 2.3e-004 2.1e-017 TGAATA TATTCA 126 3761 75 3761 1.6e-004 1.8e+000 TGAATG CATTCA 216 3761 144 3761 6.0e-005 6.4e-001 MOTIF TGAATR 2.3e-004 letter-probability matrix: alength= 4 w= 6 nsites= 354 E= 2.3e-004 0.000000 0.000000 0.000000 1.000000 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 0.372881 0.000000 0.627119 0.000000 BEST CGGARCC GGYTCCG 97 3761 41 3761 8.4e-007 9.0e-003 7.4e-006 CGGAACC GGTTCCG 26 3761 8 3761 1.4e-003 1.5e+001 CGGAGCC GGCTCCG 74 3761 33 3761 4.1e-005 4.4e-001 MOTIF CGGARCC 9.0e-003 letter-probability matrix: alength= 4 w= 7 nsites= 103 E= 9.0e-003 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 0.252427 0.000000 0.747573 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 BEST CGGRAG CTYCCG 253 3761 159 3761 1.1e-006 1.2e-002 4.2e-009 CGGGAG CTCCCG 138 3761 100 3761 7.3e-003 7.8e+001 CGGAAG CTTCCG 119 3761 59 3761 3.2e-006 3.4e-002 MOTIF CGGRAG 1.2e-002 letter-probability matrix: alength= 4 w= 6 nsites= 269 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.453532 0.000000 0.546468 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST AAGGTCA TGACCTT 88 3761 38 3761 4.2e-006 4.4e-002 1.5e-003 AAGGTCA TGACCTT 88 3761 38 3761 4.2e-006 4.4e-002 MOTIF AAGGTCA 4.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 93 E= 4.4e-002 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 CACGCCC GGGCGTG 58 3761 19 3761 4.4e-006 4.7e-002 8.8e-003 CACGCCC GGGCGTG 58 3761 19 3761 4.4e-006 4.7e-002 MOTIF CACGCCC 4.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 4.7e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # 16 motifs with E-value < 0.05 found. #elapsed time: 209.33 seconds