# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MSS11/seqs-shuffled # positives: 848 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MSS11/seqs-centered (Sat Jan 18 20:57:13 PST 2020) # negatives: 848 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MSS11/seqs-shuffled (Sat Jan 18 20:57:13 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 21:12:06 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 0.292 C 0.213 G 0.206 T 0.289 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 94 2 4.3e-027 1.5e-022 # ACCCATAC GTATGGGT 48 0 1.8e-015 6.2e-011 # ATCCGTAC GTACGGAT 31 0 3.5e-010 1.2e-005 # ATCCATAC GTATGGAT 16 1 1.3e-004 4.4e+000 # ACCCGTAC GTACGGGT 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 109 E= 1.5e-022 1.000000 0.000000 0.000000 0.000000 0.000000 0.541284 0.000000 0.458716 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.596330 0.000000 0.403670 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGWTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 132 15 9.2e-027 3.2e-022 # GGTTCGA TCGAACC 108 11 9.1e-023 3.1e-018 # GGATCGA TCGATCC 32 5 3.0e-006 1.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 132 E= 3.2e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.212121 0.000000 0.000000 0.787879 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 AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 110 13 6.7e-022 2.3e-017 # AGTGGTT AACCACT 75 10 2.5e-014 8.7e-010 # AGTGGTA TACCACT 49 3 2.8e-012 9.5e-008 letter-probability matrix: alength= 4 w= 7 nsites= 128 E= 2.3e-017 1.000000 0.000000 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 0.000000 1.000000 0.390625 0.000000 0.000000 0.609375 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 59 1 1.9e-017 6.5e-013 # CAACTTGG CCAAGTTG 47 1 9.3e-014 3.2e-009 # CAACTGGG CCCAGTTG 12 0 2.3e-004 8.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 6.5e-013 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.203390 0.796610 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF RAARAAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST RAARAAA TTTYTTY 274 153 7.5e-012 2.5e-007 # GAAAAAA TTTTTTC 116 62 1.2e-005 4.0e-001 # GAAGAAA TTTCTTC 61 25 4.4e-005 1.5e+000 # AAAAAAA TTTTTTT 142 87 5.9e-005 2.0e+000 # AAAGAAA TTTCTTT 85 43 7.3e-005 2.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 357 E= 2.5e-007 0.616246 0.000000 0.383754 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.633053 0.000000 0.366947 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 GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 2 6.9e-011 2.3e-006 # GCGCTACC GGTAGCGC 30 1 1.2e-008 3.9e-004 # GCTCTACC GGTAGAGC 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.3e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.731707 0.268293 0.000000 1.000000 0.000000 0.000000 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 MOTIF CACGGW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACGGW WCCGTG 105 35 2.7e-010 8.9e-006 # CACGGT ACCGTG 54 16 1.9e-006 6.3e-002 # CACGGA TCCGTG 52 20 7.6e-005 2.5e+000 letter-probability matrix: alength= 4 w= 6 nsites= 108 E= 8.9e-006 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 0.000000 1.000000 0.000000 0.490741 0.000000 0.000000 0.509259 MOTIF CGCSTTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 66 14 6.9e-010 2.3e-005 # CGCCTTA TAAGGCG 49 9 2.8e-008 9.2e-004 # CGCGTTA TAACGCG 17 5 8.1e-003 2.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 2.3e-005 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 0.731343 0.268657 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 MOTIF GATTWGAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 45 5 1.3e-009 4.3e-005 # GATTAGAA TTCTAATC 27 1 8.9e-008 3.0e-003 # GATTTGAA TTCAAATC 18 4 2.1e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 4.3e-005 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 0.600000 0.000000 0.000000 0.400000 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 ATCTK DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATCTK MAGAT 382 263 1.7e-009 5.5e-005 # ATCTT AAGAT 258 173 1.3e-006 4.4e-002 # ATCTG CAGAT 163 108 1.7e-004 5.5e+000 letter-probability matrix: alength= 4 w= 5 nsites= 477 E= 5.5e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.373166 0.626834 MOTIF CCACACSC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCACACSC GSGTGTGG 47 7 7.1e-009 2.3e-004 # CCACACGC GCGTGTGG 25 1 3.4e-007 1.1e-002 # CCACACCC GGGTGTGG 22 6 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 77 E= 2.3e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.675325 0.324675 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACATYAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 30 1 1.2e-008 3.7e-004 # CACATCAC GTGATGTG 15 0 2.9e-005 9.2e-001 # CACATTAC GTAATGTG 15 1 2.5e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.7e-004 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 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCCATGCW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCCATGCW WGCATGGG 26 1 1.7e-007 5.6e-003 # CCCATGCA TGCATGGG 16 1 1.3e-004 4.1e+000 # CCCATGCT AGCATGGG 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.6e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.615385 0.000000 0.000000 0.384615 MOTIF AGTYATAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGTYATAC GTATRACT 24 1 6.7e-007 2.1e-002 # AGTCATAC GTATGACT 15 1 2.5e-004 7.9e+000 # AGTTATAC GTATAACT 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.625000 0.000000 0.375000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCATCGTK DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CCATCGTK MACGATGG 26 2 1.3e-006 4.1e-002 # CCATCGTG CACGATGG 11 0 4.7e-004 1.5e+001 # CCATCGTT AACGATGG 15 2 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.1e-002 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 0.000000 0.000000 1.000000 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 0.423077 0.576923 MOTIF TAGTKTAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TAGTKTAA TTAMACTA 31 4 1.4e-006 4.5e-002 # TAGTGTAA TTACACTA 15 1 2.5e-004 7.9e+000 # TAGTTTAA TTAAACTA 16 3 2.1e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 4.5e-002 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.483871 0.516129 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 85.04 seconds