# DREME 4.11.4 # command: dreme -oc dreme_example_output_files -png -p Klf1.fna # positives: 904 from Klf1.fna (Thu Mar 09 19:29:18 PST 2017) # negatives: 904 from shuffled positives # host: glutamine.gs.washington.edu # when: Tue Apr 04 16:05:30 PDT 2017 MEME version 4.11.4 ALPHABET "DNA" DNA-LIKE A "Adenine" CC0000 ~ T "Thymine" 008000 C "Cytosine" 0000CC ~ G "Guanine" FFB300 N "Any base" = ACGT X = ACGT . = ACGT V "Not T" = ACG H "Not G" = ACT D "Not C" = AGT B "Not A" = CGT M "Amino" = AC R "Purine" = AG W "Weak" = AT S "Strong" = CG Y "Pyrimidine" = CT K "Keto" = GT U = T END ALPHABET strands: + - Background letter frequencies (from dataset): A 0.255 C 0.245 G 0.243 T 0.257 MOTIF CCMCRCCC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCMCRCCC GGGYGKGG 350 49 1.8e-071 7.6e-067 # CCACACCC GGGTGTGG 175 19 2.4e-036 1.0e-031 # CCCCACCC GGGTGGGG 128 25 1.5e-019 6.4e-015 # CCACGCCC GGGCGTGG 55 3 5.3e-014 2.3e-009 # CCCCGCCC GGGCGGGG 53 3 2.0e-013 8.6e-009 letter-probability matrix: alength= 4 w= 8 nsites= 454 E= 7.6e-067 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.550661 0.449339 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.733480 0.000000 0.266520 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 BTTATCW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BTTATCW WGATAAV 449 190 5.6e-038 2.4e-033 # CTTATCT AGATAAG 169 56 2.0e-016 8.6e-012 # CTTATCA TGATAAG 109 36 1.0e-010 4.3e-006 # TTTATCT AGATAAA 106 42 2.1e-008 9.0e-004 # GTTATCA TGATAAC 69 23 4.5e-007 1.9e-002 # GTTATCT AGATAAC 64 28 7.6e-005 3.2e+000 # TTTATCA TGATAAA 61 26 7.8e-005 3.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 613 E= 2.4e-033 0.000000 0.484502 0.216966 0.298532 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 0.415987 0.000000 0.000000 0.584013 MOTIF MCRCCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST MCRCCCA TGGGYGK 283 109 6.9e-024 2.9e-019 # CCACCCA TGGGTGG 129 48 6.2e-011 2.6e-006 # ACACCCA TGGGTGT 102 42 1.0e-007 4.4e-003 # ACGCCCA TGGGCGT 46 10 4.3e-007 1.8e-002 # CCGCCCA TGGGCGG 43 17 4.4e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 340 E= 2.9e-019 0.458824 0.541176 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.729412 0.000000 0.270588 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 1.000000 0.000000 0.000000 0.000000 MOTIF RARGAAA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RARGAAA TTTCYTY 398 215 4.8e-020 2.1e-015 # AAAGAAA TTTCTTT 149 68 2.5e-009 1.1e-004 # AAGGAAA TTTCCTT 130 57 9.3e-009 4.0e-004 # GAAGAAA TTTCTTC 122 54 3.8e-008 1.6e-003 # GAGGAAA TTTCCTC 110 67 4.2e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 539 E= 2.1e-015 0.543599 0.000000 0.456401 0.000000 1.000000 0.000000 0.000000 0.000000 0.534323 0.000000 0.465677 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 AKAAAM DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AKAAAM KTTTMT 585 415 5.3e-016 2.3e-011 # AGAAAA TTTTCT 302 208 5.6e-007 2.4e-002 # ATAAAA TTTTAT 192 117 1.7e-006 7.3e-002 # ATAAAC GTTTAT 128 75 5.0e-005 2.1e+000 # AGAAAC GTTTCT 211 145 5.8e-005 2.5e+000 letter-probability matrix: alength= 4 w= 6 nsites= 1018 E= 2.3e-011 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.629666 0.370334 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.617878 0.382122 0.000000 0.000000 MOTIF CTGTSTS DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTGTSTS SASACAG 384 235 9.1e-014 3.8e-009 # CTGTGTG CACACAG 139 72 5.6e-007 2.3e-002 # CTGTCTC GAGACAG 129 73 1.8e-005 7.6e-001 # CTGTCTG CAGACAG 127 77 1.3e-004 5.3e+000 # CTGTGTC GACACAG 87 55 3.3e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 516 E= 3.8e-009 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 0.000000 1.000000 0.000000 0.531008 0.468992 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.453488 0.546512 0.000000 MOTIF AGGGCGK DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGGGCGK MCGCCCT 96 28 8.3e-011 3.5e-006 # AGGGCGT ACGCCCT 50 10 5.1e-008 2.1e-003 # AGGGCGG CCGCCCT 48 18 1.1e-004 4.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 3.5e-006 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.514286 0.485714 MOTIF CCTKCCY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCTKCCY RGGMAGG 406 278 3.4e-010 1.4e-005 # CCTTCCT AGGAAGG 144 85 1.9e-005 7.9e-001 # CCTTCCC GGGAAGG 122 75 2.5e-004 1.0e+001 # CCTGCCC GGGCAGG 125 82 9.3e-004 3.9e+001 # CCTGCCT AGGCAGG 135 94 2.3e-003 9.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 576 E= 1.4e-005 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 0.491319 0.508681 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.467014 0.000000 0.532986 MOTIF TTAAAAW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TTAAAAW WTTTTAA 178 89 2.1e-009 8.5e-005 # TTAAAAA TTTTTAA 117 61 6.1e-006 2.5e-001 # TTAAAAT ATTTTAA 78 38 8.0e-005 3.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 203 E= 8.5e-005 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.605911 0.000000 0.000000 0.394089 MOTIF AAATAH DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAATAH DTATTT 350 242 3.9e-008 1.6e-003 # AAATAC GTATTT 123 71 4.9e-005 2.0e+000 # AAATAT ATATTT 149 100 5.1e-004 2.1e+001 # AAATAA TTATTT 147 105 2.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 494 E= 1.6e-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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.354251 0.277328 0.000000 0.368421 MOTIF CATYTCC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CATYTCC GGARATG 144 72 1.1e-007 4.3e-003 # CATTTCC GGAAATG 79 32 2.5e-006 1.0e-001 # CATCTCC GGAGATG 70 42 4.1e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 158 E= 4.3e-003 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 0.455696 0.000000 0.544304 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAGMCAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CAGMCAC GTGKCTG 162 88 2.8e-007 1.2e-002 # CAGACAC GTGTCTG 77 33 9.3e-006 3.8e-001 # CAGCCAC GTGGCTG 100 60 5.9e-004 2.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 191 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.434555 0.565445 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 MOTIF CACAGY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CACAGY RCTGTG 415 312 4.8e-007 2.0e-002 # CACAGC GCTGTG 263 184 1.0e-005 4.2e-001 # CACAGT ACTGTG 226 167 4.6e-004 1.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 574 E= 2.0e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.559233 0.000000 0.440767 MOTIF CTGGRGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTGGRGA TCYCCAG 205 125 6.9e-007 2.8e-002 # CTGGGGA TCCCCAG 117 69 1.3e-004 5.2e+000 # CTGGAGA TCTCCAG 102 66 2.2e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 233 E= 2.8e-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 0.463519 0.000000 0.536481 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SACGTGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST SACGTGA TCACGTS 43 9 7.4e-007 3.0e-002 # CACGTGA TCACGTG 25 6 4.0e-004 1.6e+001 # GACGTGA TCACGTC 18 3 7.0e-004 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 3.0e-002 0.000000 0.590909 0.409091 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 892.28 seconds