# DREME 4.8.0 # command: dreme -png -p sample-dna-Klf1.fa # host: tlb-takumi-lt.imb.uq.edu.au # when: Wed Jan 11 17:53:34 EST 2012 # positives: 904 # from: sample-dna-Klf1.fa (Wed Jan 11 16:31:12 EST 2012) # negatives: 904 # from: shuffled positives MEME version 4.8.0 ALPHABET= ACGT strands: + - Background letter frequencies (from dataset): A 0.255 C 0.244 G 0.243 T 0.258 MOTIF CCMCRCCC # Word RC Word Pos Neg P-value E-value # BEST CCMCRCCC GGGYGKGG 369 51 8.6e-077 3.7e-072 # CCACACCC GGGTGTGG 188 20 1.5e-039 6.5e-035 # CCCCACCC GGGTGGGG 139 24 6.3e-023 2.7e-018 # CCACGCCC GGGCGTGG 59 2 3.3e-016 1.4e-011 # CCCCGCCC GGGCGGGG 65 7 1.3e-013 5.7e-009 letter-probability matrix: alength= 4 w= 8 nsites= 510 E= 3.7e-072 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.549020 0.450980 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.725490 0.000000 0.274510 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 MOTIF TTATCW # Word RC Word Pos Neg P-value E-value # BEST TTATCW WGATAA 497 244 3.0e-034 1.3e-029 # TTATCT AGATAA 356 138 2.0e-031 8.5e-027 # TTATCA TGATAA 250 128 9.1e-013 3.9e-008 letter-probability matrix: alength= 4 w= 6 nsites= 722 E= 1.3e-029 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.414127 0.000000 0.000000 0.585873 MOTIF CACRCMC # Word RC Word Pos Neg P-value E-value # BEST CACRCMC GKGYGTG 270 95 1.8e-025 7.7e-021 # CACACCC GGGTGTG 129 32 1.5e-016 6.5e-012 # CACACAC GTGTGTG 123 54 2.6e-008 1.1e-003 # CACGCCC GGGCGTG 46 9 1.5e-007 6.3e-003 # CACGCAC GTGCGTG 25 9 4.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 350 E= 7.7e-021 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.785714 0.000000 0.214286 0.000000 0.000000 1.000000 0.000000 0.000000 0.457143 0.542857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RARGAAA # Word RC Word Pos Neg P-value E-value # BEST RARGAAA TTTCYTY 412 240 2.0e-017 8.5e-013 # AAAGAAA TTTCTTT 161 82 3.0e-008 1.3e-003 # GAGGAAA TTTCCTC 113 50 1.3e-007 5.6e-003 # GAAGAAA TTTCTTC 125 68 8.9e-006 3.8e-001 # AAGGAAA TTTCCTT 138 80 1.8e-005 7.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 568 E= 8.5e-013 0.556338 0.000000 0.443662 0.000000 1.000000 0.000000 0.000000 0.000000 0.538732 0.000000 0.461268 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 MOTIF TTTTAWW # Word RC Word Pos Neg P-value E-value # BEST TTTTAWW WWTAAAA 292 154 2.7e-014 1.1e-009 # TTTTAAA TTTAAAA 124 54 1.8e-008 7.6e-004 # TTTTATT AATAAAA 103 54 2.7e-005 1.1e+000 # TTTTAAT ATTAAAA 75 37 1.4e-004 5.8e+000 # TTTTATA TATAAAA 66 36 1.5e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 396 E= 1.1e-009 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 1.000000 0.000000 0.000000 0.000000 0.537879 0.000000 0.000000 0.462121 0.517677 0.000000 0.000000 0.482323 MOTIF CTCCDCCC # Word RC Word Pos Neg P-value E-value # BEST CTCCDCCC GGGHGGAG 164 61 7.7e-014 3.2e-009 # CTCCACCC GGGTGGAG 80 24 6.4e-009 2.7e-004 # CTCCTCCC GGGAGGAG 75 33 1.9e-005 8.2e-001 # CTCCGCCC GGGCGGAG 24 8 3.3e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 191 E= 3.2e-009 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 1.000000 0.000000 0.000000 0.455497 0.000000 0.125654 0.418848 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACACRK # Word RC Word Pos Neg P-value E-value # BEST ACACRK MYGTGT 476 335 1.6e-011 6.9e-007 # ACACAG CTGTGT 309 200 7.4e-009 3.1e-004 # ACACGG CCGTGT 69 31 6.0e-005 2.5e+000 # ACACAT ATGTGT 182 125 2.2e-004 9.2e+000 # ACACGT ACGTGT 56 32 5.8e-003 2.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 716 E= 6.9e-007 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 0.818436 0.000000 0.181564 0.000000 0.000000 0.000000 0.613128 0.386872 MOTIF MCGCCCW # Word RC Word Pos Neg P-value E-value # BEST MCGCCCW WGGGCGK 137 48 1.8e-012 7.4e-008 # ACGCCCT AGGGCGT 30 7 8.3e-005 3.4e+000 # ACGCCCA TGGGCGT 37 11 9.2e-005 3.8e+000 # CCGCCCA TGGGCGG 35 14 1.7e-003 7.0e+001 # CCGCCCT AGGGCGG 40 19 3.8e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 147 E= 7.4e-008 0.455782 0.544218 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 0.489796 0.000000 0.000000 0.510204 MOTIF TTCTCTB # Word RC Word Pos Neg P-value E-value # BEST TTCTCTB VAGAGAA 305 188 3.9e-010 1.6e-005 # TTCTCTT AAGAGAA 121 65 9.1e-006 3.8e-001 # TTCTCTG CAGAGAA 122 75 2.5e-004 1.0e+001 # TTCTCTC GAGAGAA 114 74 1.3e-003 5.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 383 E= 1.6e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.310705 0.344648 0.344648 MOTIF AAATRT # Word RC Word Pos Neg P-value E-value # BEST AAATRT AYATTT 319 202 7.6e-010 3.1e-005 # AAATGT ACATTT 207 129 1.5e-006 6.2e-002 # AAATAT ATATTT 163 98 8.5e-006 3.5e-001 letter-probability matrix: alength= 4 w= 6 nsites= 447 E= 3.1e-005 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 0.445190 0.000000 0.554810 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AKATA # Word RC Word Pos Neg P-value E-value # BEST AKATA TATMT 484 370 4.9e-008 2.0e-003 # AGATA TATCT 370 282 1.0e-005 4.1e-001 # ATATA TATAT 212 158 9.9e-004 4.1e+001 letter-probability matrix: alength= 4 w= 5 nsites= 734 E= 2.0e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.652589 0.347411 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAHAAA # Word RC Word Pos Neg P-value E-value # BEST AAAAHAAA TTTDTTTT 126 58 7.0e-008 2.9e-003 # AAAAAAAA TTTTTTTT 58 24 7.9e-005 3.2e+000 # AAAATAAA TTTATTTT 26 7 6.0e-004 2.4e+001 # AAAACAAA TTTGTTTT 52 29 6.0e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 148 E= 2.9e-003 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 0.000000 0.000000 0.000000 0.445946 0.371622 0.000000 0.182432 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTGGGRAC # Word RC Word Pos Neg P-value E-value # BEST CTGGGRAC GTYCCCAG 59 17 4.2e-007 1.7e-002 # CTGGGAAC GTTCCCAG 29 5 1.6e-005 6.7e-001 # CTGGGGAC GTCCCCAG 32 13 3.0e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 61 E= 1.7e-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 0.000000 1.000000 0.000000 0.475410 0.000000 0.524590 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF SACAGA # Word RC Word Pos Neg P-value E-value # BEST SACAGA TCTGTS 425 322 5.4e-007 2.2e-002 # GACAGA TCTGTC 263 188 2.8e-005 1.1e+000 # CACAGA TCTGTG 232 175 8.0e-004 3.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 590 E= 2.2e-002 0.000000 0.461017 0.538983 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000