# dreme.py -p CHEN/Sox2.pos.fasta -n CHEN/Sox2.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/Sox2.pos.fasta -n CHEN/Sox2.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 ACAAWRG CYWTTGT 1713 4526 251 4526 2.2e-333 2.6e-329 2.6e-329 ACAAAGG CCTTTGT 674 4526 87 4526 1.2e-122 1.5e-118 ACAATGG CCATTGT 551 4526 48 4526 4.1e-116 4.8e-112 ACAATAG CTATTGT 322 4526 30 4526 2.4e-065 2.8e-061 ACAAAAG CTTTTGT 444 4526 93 4526 2.9e-059 3.4e-055 MOTIF ACAAWRG 2.6e-329 letter-probability matrix: alength= 4 w= 7 nsites= 2150 E= 2.6e-329 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 0.563256 0.000000 0.000000 0.436744 0.384186 0.000000 0.615814 0.000000 0.000000 0.000000 1.000000 0.000000 BEST ACAAWGM KCWTTGT 1027 4526 269 4526 6.0e-121 6.9e-117 1.3e-117 ACAAAGC GCTTTGT 285 4526 71 4526 6.1e-033 6.9e-029 ACAATGA TCATTGT 251 4526 62 4526 2.7e-029 3.0e-025 ACAATGC GCATTGT 226 4526 52 4526 4.5e-028 5.1e-024 ACAAAGA TCTTTGT 366 4526 93 4526 1.6e-041 1.8e-037 MOTIF ACAAWGM 6.9e-117 letter-probability matrix: alength= 4 w= 7 nsites= 1168 E= 6.9e-117 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 0.574486 0.000000 0.000000 0.425514 0.000000 0.000000 1.000000 0.000000 0.557363 0.442637 0.000000 0.000000 BEST ATGYWAA TTWRCAT 684 4526 158 4526 2.7e-086 3.0e-082 3.2e-085 ATGTAAA TTTACAT 110 4526 37 4526 4.9e-010 5.5e-006 ATGCTAA TTAGCAT 170 4526 23 4526 1.0e-029 1.1e-025 ATGCAAA TTTGCAT 366 4526 70 4526 6.0e-052 6.8e-048 ATGTTAA TTAACAT 83 4526 32 4526 9.3e-007 1.0e-002 MOTIF ATGYWAA 3.0e-082 letter-probability matrix: alength= 4 w= 7 nsites= 740 E= 3.0e-082 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 0.748649 0.000000 0.251351 0.658108 0.000000 0.000000 0.341892 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST CMCRCCC GGGYGKG 368 4526 164 4526 2.2e-020 2.4e-016 3.4e-017 CCCGCCC GGGCGGG 69 4526 29 4526 3.0e-005 3.3e-001 CCCACCC GGGTGGG 156 4526 81 4526 4.6e-007 5.1e-003 CACACCC GGGTGTG 123 4526 43 4526 1.4e-010 1.5e-006 CACGCCC GGGCGTG 41 4526 14 4526 1.7e-004 1.9e+000 MOTIF CMCRCCC 2.4e-016 letter-probability matrix: alength= 4 w= 7 nsites= 387 E= 2.4e-016 0.000000 1.000000 0.000000 0.000000 0.426357 0.573643 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.710594 0.000000 0.289406 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 CYATTCA TGAATRG 262 4526 97 4526 1.2e-019 1.4e-015 1.6e-015 CCATTCA TGAATGG 164 4526 65 4526 1.4e-011 1.5e-007 CTATTCA TGAATAG 101 4526 32 4526 6.1e-010 6.8e-006 MOTIF CYATTCA 1.4e-015 letter-probability matrix: alength= 4 w= 7 nsites= 278 E= 1.4e-015 0.000000 1.000000 0.000000 0.000000 0.000000 0.633094 0.000000 0.366906 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST RACAATR YATTGTY 193 4526 62 4526 1.5e-017 1.6e-013 3.1e-194 GACAATA TATTGTC 45 4526 15 4526 6.4e-005 7.1e-001 AACAATA TATTGTT 88 4526 24 4526 3.6e-010 4.0e-006 AACAATG CATTGTT 43 4526 19 4526 1.5e-003 1.7e+001 GACAATG CATTGTC 23 4526 4 4526 1.5e-004 1.7e+000 MOTIF RACAATR 1.6e-013 letter-probability matrix: alength= 4 w= 7 nsites= 202 E= 1.6e-013 0.663366 0.000000 0.336634 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 0.000000 0.000000 1.000000 0.663366 0.000000 0.336634 0.000000 BEST CTYCCBG CVGGRAG 422 4526 216 4526 1.1e-017 1.2e-013 1.8e-013 CTTCCGG CCGGAAG 33 4526 9 4526 1.3e-004 1.5e+000 CTCCCCG CGGGGAG 35 4526 15 4526 3.2e-003 3.6e+001 CTTCCTG CAGGAAG 173 4526 84 4526 9.4e-009 1.0e-004 CTCCCGG CCGGGAG 37 4526 13 4526 4.5e-004 5.0e+000 CTTCCCG CGGGAAG 39 4526 18 4526 3.7e-003 4.0e+001 CTCCCTG CAGGGAG 127 4526 83 4526 1.3e-003 1.4e+001 MOTIF CTYCCBG 1.2e-013 letter-probability matrix: alength= 4 w= 7 nsites= 446 E= 1.2e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.446188 0.000000 0.553812 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.165919 0.156951 0.677130 0.000000 0.000000 1.000000 0.000000 BEST ATAAWRG CYWTTAT 243 4526 112 4526 5.5e-013 6.0e-009 7.7e-010 ATAATAG CTATTAT 50 4526 18 4526 6.2e-005 6.8e-001 ATAAAAG CTTTTAT 71 4526 38 4526 9.6e-004 1.0e+001 ATAAAGG CCTTTAT 64 4526 25 4526 2.0e-005 2.2e-001 ATAATGG CCATTAT 59 4526 32 4526 2.9e-003 3.2e+001 MOTIF ATAAWRG 6.0e-009 letter-probability matrix: alength= 4 w= 7 nsites= 247 E= 6.0e-009 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 0.550607 0.000000 0.000000 0.449393 0.497976 0.000000 0.502024 0.000000 0.000000 0.000000 1.000000 0.000000 BEST ATGCAKA TMTGCAT 223 4526 101 4526 2.2e-012 2.4e-008 6.7e-009 ATGCATA TATGCAT 77 4526 24 4526 5.0e-008 5.5e-004 ATGCAGA TCTGCAT 152 4526 78 4526 4.4e-007 4.8e-003 MOTIF ATGCAKA 2.4e-008 letter-probability matrix: alength= 4 w= 7 nsites= 230 E= 2.4e-008 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 0.660870 0.339130 1.000000 0.000000 0.000000 0.000000 BEST CAGCAGG CCTGCTG 210 4526 100 4526 9.9e-011 1.1e-006 6.9e-008 CAGCAGG CCTGCTG 210 4526 100 4526 9.9e-011 1.1e-006 MOTIF CAGCAGG 1.1e-006 letter-probability matrix: alength= 4 w= 7 nsites= 218 E= 1.1e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 BEST ATTASCA TGSTAAT 120 4526 42 4526 2.4e-010 2.6e-006 1.1e-024 ATTAGCA TGCTAAT 57 4526 21 4526 2.6e-005 2.8e-001 ATTACCA TGGTAAT 65 4526 21 4526 9.7e-007 1.1e-002 MOTIF ATTASCA 2.6e-006 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 2.6e-006 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.532787 0.467213 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST RAGGTCA TGACCTY 209 4526 103 4526 5.1e-010 5.6e-006 8.0e-008 GAGGTCA TGACCTC 82 4526 41 4526 1.3e-004 1.4e+000 AAGGTCA TGACCTT 132 4526 62 4526 2.1e-007 2.3e-003 MOTIF RAGGTCA 5.6e-006 letter-probability matrix: alength= 4 w= 7 nsites= 223 E= 5.6e-006 0.618834 0.000000 0.381166 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 CYTCCTM KAGGARG 334 4526 197 4526 4.9e-010 5.3e-006 1.9e-007 CCTCCTC GAGGAGG 112 4526 60 4526 3.9e-005 4.2e-001 CCTCCTA TAGGAGG 54 4526 29 4526 3.9e-003 4.2e+001 CTTCCTC GAGGAAG 118 4526 77 4526 1.8e-003 2.0e+001 CTTCCTA TAGGAAG 68 4526 38 4526 2.2e-003 2.4e+001 MOTIF CYTCCTM 5.3e-006 letter-probability matrix: alength= 4 w= 7 nsites= 350 E= 5.3e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.468571 0.000000 0.531429 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 0.342857 0.657143 0.000000 0.000000 BEST CATTTCC GGAAATG 118 4526 46 4526 6.6e-009 7.1e-005 7.9e-009 CATTTCC GGAAATG 118 4526 46 4526 6.6e-009 7.1e-005 MOTIF CATTTCC 7.1e-005 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 7.1e-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 CCGCCTC GAGGCGG 37 4526 7 4526 2.5e-006 2.7e-002 1.1e-003 CCGCCTC GAGGCGG 37 4526 7 4526 2.5e-006 2.7e-002 MOTIF CCGCCTC 2.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.7e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 BEST TMTTTAA TTAAAKA 124 4526 62 4526 2.6e-006 2.8e-002 2.8e-003 TATTTAA TTAAATA 56 4526 24 4526 2.1e-004 2.3e+000 TCTTTAA TTAAAGA 71 4526 39 4526 1.4e-003 1.5e+001 MOTIF TMTTTAA 2.8e-002 letter-probability matrix: alength= 4 w= 7 nsites= 130 E= 2.8e-002 0.000000 0.000000 0.000000 1.000000 0.438462 0.561538 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 BEST TTCCTR YAGGAA 386 4526 273 4526 2.8e-006 3.0e-002 2.9e-016 TTCCTA TAGGAA 140 4526 85 4526 1.3e-004 1.4e+000 TTCCTG CAGGAA 257 4526 191 4526 8.0e-004 8.7e+000 MOTIF TTCCTR 3.0e-002 letter-probability matrix: alength= 4 w= 6 nsites= 405 E= 3.0e-002 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 0.000000 1.000000 0.348148 0.000000 0.651852 0.000000 BEST CGTGACM KGTCACG 32 4526 5 4526 3.6e-006 3.9e-002 6.9e-004 CGTGACA TGTCACG 18 4526 3 4526 7.4e-004 8.0e+000 CGTGACC GGTCACG 15 4526 2 4526 1.2e-003 1.3e+001 MOTIF CGTGACM 3.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 3.9e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.529412 0.470588 0.000000 0.000000 # 18 motifs with E-value < 0.05 found. #elapsed time: 262.99 seconds