# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MCM1/seqs-shuffled # positives: 877 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MCM1/seqs-centered (Fri Jan 17 22:20:31 PST 2020) # negatives: 877 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MCM1/seqs-shuffled (Fri Jan 17 22:20:31 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:35:20 PST 2020 MEME version 4.12.0 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 0.285 C 0.219 G 0.217 T 0.280 MOTIF AACCACTH DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AACCACTH DAGTGGTT 64 4 1.0e-015 3.7e-011 # AACCACTT AAGTGGTT 23 1 1.3e-006 4.7e-002 # AACCACTA TAGTGGTT 20 1 9.5e-006 3.4e-001 # AACCACTC GAGTGGTT 22 2 1.6e-005 5.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 65 E= 3.7e-011 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 0.000000 1.000000 0.307692 0.338462 0.000000 0.353846 MOTIF GGYTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGYTCGA TCGARCC 65 6 2.4e-014 8.7e-010 # GGTTCGA TCGAACC 57 5 7.0e-013 2.5e-008 # GGCTCGA TCGAGCC 22 1 2.5e-006 9.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 8.7e-010 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.208955 0.000000 0.791045 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AMCAWC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AMCAWC GWTGKT 276 154 7.3e-012 2.6e-007 # AACATC GATGTT 73 30 7.7e-006 2.8e-001 # ACCATC GATGGT 70 32 6.9e-005 2.5e+000 # AACAAC GTTGTT 88 52 9.8e-004 3.5e+001 # ACCAAC GTTGGT 89 54 1.4e-003 5.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 326 E= 2.6e-007 1.000000 0.000000 0.000000 0.000000 0.496933 0.503067 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.555215 0.000000 0.000000 0.444785 0.000000 1.000000 0.000000 0.000000 MOTIF CCCAYACA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCCAYACA TGTRTGGG 54 7 1.1e-010 4.0e-006 # CCCATACA TGTATGGG 27 2 6.8e-007 2.4e-002 # CCCACACA TGTGTGGG 27 5 4.9e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 79 E= 4.0e-006 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 0.632911 0.000000 0.367089 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 43 3 1.5e-010 5.2e-006 # ATGGCAAC GTTGCCAT 32 2 2.7e-008 9.5e-004 # ATGGCATC GATGCCAT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 5.2e-006 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 1.000000 0.000000 0.000000 0.000000 0.744186 0.000000 0.000000 0.255814 0.000000 1.000000 0.000000 0.000000 MOTIF TACCGW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TACCGW WCGGTA 108 39 1.3e-009 4.4e-005 # TACCGA TCGGTA 63 15 9.5e-009 3.4e-004 # TACCGT ACGGTA 46 24 5.0e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 111 E= 4.4e-005 0.000000 0.000000 0.000000 1.000000 1.000000 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 0.567568 0.000000 0.000000 0.432432 MOTIF GAAGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GAAGA TCTTC 275 168 2.5e-009 8.8e-005 # GAAGA TCTTC 275 168 2.5e-009 8.8e-005 letter-probability matrix: alength= 4 w= 5 nsites= 351 E= 8.8e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCTTASC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCTTASC GSTAAGG 37 3 7.0e-009 2.4e-004 # CCTTAGC GCTAAGG 23 1 1.3e-006 4.5e-002 # CCTTACC GGTAAGG 14 2 2.0e-003 6.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.4e-004 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.378378 0.621622 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GYGGTCTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GYGGTCTA TAGACCRC 30 1 1.2e-008 4.1e-004 # GTGGTCTA TAGACCAC 22 1 2.5e-006 8.7e-002 # GCGGTCTA TAGACCGC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 4.1e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.266667 0.000000 0.733333 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GATTWGAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 34 3 4.7e-008 1.6e-003 # GATTAGAA TTCTAATC 23 2 8.6e-006 3.0e-001 # GATTTGAA TTCAAATC 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.6e-003 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 0.000000 1.000000 0.676471 0.000000 0.000000 0.323529 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 51 11 8.7e-008 3.0e-003 # TGGCGTA TACGCCA 25 5 1.5e-004 5.0e+000 # TGGCGCA TGCGCCA 26 6 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 3.0e-003 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 0.000000 1.000000 0.000000 0.000000 0.509804 0.000000 0.490196 1.000000 0.000000 0.000000 0.000000 MOTIF AAAARAAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAAARAAA TTTYTTTT 77 26 1.1e-007 3.9e-003 # AAAAGAAA TTTCTTTT 37 9 1.6e-005 5.6e-001 # AAAAAAAA TTTTTTTT 43 19 1.3e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 81 E= 3.9e-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 0.543210 0.000000 0.456790 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 CTCTMCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 22 0 2.1e-007 7.2e-003 # CTCTCCCA TGGGAGAG 13 0 1.2e-004 4.0e+000 # CTCTACCA TGGTAGAG 9 0 1.9e-003 6.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.2e-003 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 0.409091 0.590909 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 GGAAATW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GGAAATW WATTTCC 80 30 4.7e-007 1.6e-002 # GGAAATA TATTTCC 41 11 1.4e-005 4.7e-001 # GGAAATT AATTTCC 42 19 1.9e-003 6.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 1.6e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 # Stopping reason: E-value threshold exceeded # Running time: 79.58 seconds