# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--STE12/seqs-shuffled # positives: 806 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--STE12/seqs-centered (Fri Jan 17 23:56:50 PST 2020) # negatives: 806 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--STE12/seqs-shuffled (Fri Jan 17 23:56:50 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 00:16:27 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 0.304 C 0.198 G 0.193 T 0.305 MOTIF ACCWCT DREME-1 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 161 43 1.1e-019 3.6e-015 # ACCACT AGTGGT 119 26 5.4e-017 1.8e-012 # ACCTCT AGAGGT 49 18 7.1e-005 2.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 182 E= 3.6e-015 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.725275 0.000000 0.000000 0.274725 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF TCGAACCB DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 80 6 1.1e-018 3.6e-014 # TCGAACCG CGGTTCGA 27 0 6.0e-009 1.9e-004 # TCGAACCC GGGTTCGA 37 3 6.8e-009 2.2e-004 # TCGAACCT AGGTTCGA 16 3 2.1e-003 6.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 80 E= 3.6e-014 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 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 0.462500 0.337500 0.200000 MOTIF TGTAYGGR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 69 8 4.7e-014 1.5e-009 # TGTACGGA TCCGTACA 27 0 6.0e-009 1.9e-004 # TGTATGGG CCCATACA 30 6 2.9e-005 9.5e-001 # TGTATGGA TCCATACA 14 2 2.0e-003 6.5e+001 # TGTACGGG CCCGTACA 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 83 E= 1.5e-009 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.445783 0.000000 0.554217 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.530120 0.000000 0.469880 0.000000 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 47 1 9.0e-014 2.9e-009 # CAACTTGG CCAAGTTG 34 0 4.1e-011 1.3e-006 # CAACTGGG CCCAGTTG 13 1 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.9e-009 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 0.276596 0.723404 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TAAGGCR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 65 8 5.7e-013 1.8e-008 # TAAGGCG CGCCTTA 52 7 3.6e-010 1.2e-005 # TAAGGCA TGCCTTA 14 2 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 1.8e-008 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.212121 0.000000 0.787879 0.000000 MOTIF SAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 354 235 4.7e-010 1.5e-005 # CAAGA TCTTG 207 130 1.5e-006 4.8e-002 # GAAGA TCTTC 193 125 1.3e-005 4.2e-001 letter-probability matrix: alength= 4 w= 5 nsites= 485 E= 1.5e-005 0.000000 0.519588 0.480412 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 ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 36 2 1.9e-009 5.9e-005 # ATGGCAAC GTTGCCAT 20 0 8.5e-007 2.6e-002 # ATGGCATC GATGCCAT 16 2 6.2e-004 1.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 5.9e-005 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 0.555556 0.000000 0.000000 0.444444 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 35 2 3.7e-009 1.1e-004 # GCGCTACC GGTAGCGC 25 1 3.4e-007 1.0e-002 # GCTCTACC GGTAGAGC 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.1e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.285714 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 CACTATA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACTATA TATAGTG 30 2 9.7e-008 3.0e-003 # CACTATA TATAGTG 30 2 9.7e-008 3.0e-003 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 3.0e-003 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 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 AAAAADAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 119 54 9.8e-008 3.0e-003 # AAAAATAA TTATTTTT 41 16 5.2e-004 1.6e+001 # AAAAAGAA TTCTTTTT 42 18 1.1e-003 3.4e+001 # AAAAAAAA TTTTTTTT 49 28 9.5e-003 2.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 126 E= 3.0e-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 1.000000 0.000000 0.000000 0.000000 0.373016 0.000000 0.309524 0.317460 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGCGWGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 23 0 1.0e-007 3.1e-003 # AAGCGTGA TCACGCTT 13 0 1.2e-004 3.6e+000 # AAGCGAGA TCTCGCTT 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.1e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.434783 0.000000 0.000000 0.565217 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GATTRGAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GATTRGAA TTCYAATC 28 2 3.5e-007 1.1e-002 # GATTAGAA TTCTAATC 20 2 5.5e-005 1.7e+000 # GATTGGAA TTCCAATC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.1e-002 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 0.714286 0.000000 0.285714 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 MOTIF GTATGACW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTATGACW WGTCATAC 30 3 5.6e-007 1.7e-002 # GTATGACA TGTCATAC 17 1 6.7e-005 2.1e+000 # GTATGACT AGTCATAC 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.7e-002 0.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.566667 0.000000 0.000000 0.433333 MOTIF GAGATAY DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GAGATAY RTATCTC 41 8 7.0e-007 2.1e-002 # GAGATAC GTATCTC 20 1 9.4e-006 2.9e-001 # GAGATAT ATATCTC 30 7 8.1e-005 2.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 2.1e-002 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.423077 0.000000 0.576923 MOTIF GRTCTCCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GRTCTCCA TGGAGAYC 20 0 8.5e-007 2.6e-002 # GGTCTCCA TGGAGACC 13 0 1.2e-004 3.6e+000 # GATCTCCA TGGAGATC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-002 0.000000 0.000000 1.000000 0.000000 0.350000 0.000000 0.650000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 212.91 seconds