# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/seqs-shuffled # positives: 791 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/seqs-centered (Sat Jan 18 17:47:59 PST 2020) # negatives: 791 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/seqs-shuffled (Sat Jan 18 17:47:59 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:01:30 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 0.314 C 0.191 G 0.183 T 0.312 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 117 13 5.3e-024 1.7e-019 # GGTTCGA TCGAACC 82 5 3.6e-020 1.1e-015 # GGTTCAA TTGAACC 35 8 1.7e-005 5.2e-001 letter-probability matrix: alength= 4 w= 7 nsites= 117 E= 1.7e-019 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.299145 0.000000 0.700855 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 146 40 2.0e-017 6.3e-013 # ACCACT AGTGGT 95 27 4.7e-011 1.5e-006 # ACCTCT AGAGGT 57 14 7.3e-008 2.3e-003 letter-probability matrix: alength= 4 w= 6 nsites= 167 E= 6.3e-013 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.652695 0.000000 0.000000 0.347305 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ARAAAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAR YTTTTYT 299 167 1.9e-013 5.9e-009 # AAAAAAA TTTTTTT 163 90 3.4e-007 1.1e-002 # AGAAAAA TTTTTCT 111 51 3.9e-007 1.2e-002 # AAAAAAG CTTTTTT 103 63 6.6e-004 2.0e+001 # AGAAAAG CTTTTCT 45 25 9.8e-003 3.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 370 E= 5.9e-009 1.000000 0.000000 0.000000 0.000000 0.602703 0.000000 0.397297 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 0.643243 0.000000 0.356757 0.000000 MOTIF TAAGGCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 64 8 1.0e-012 3.2e-008 # TAAGGCG CGCCTTA 51 4 5.0e-012 1.5e-007 # TAAGGCA TGCCTTA 16 4 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 3.2e-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 0.238806 0.000000 0.761194 0.000000 MOTIF CCRTACA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 64 9 4.4e-012 1.4e-007 # CCATACA TGTATGG 40 6 1.1e-007 3.3e-003 # CCGTACA TGTACGG 30 3 5.6e-007 1.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 1.4e-007 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.589744 0.000000 0.410256 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAGATTTM DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGATTTM KAAATCTT 54 9 1.6e-009 4.8e-005 # AAGATTTC GAAATCTT 35 3 2.4e-008 7.3e-004 # AAGATTTA TAAATCTT 19 6 6.9e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 4.8e-005 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.363636 0.636364 0.000000 0.000000 MOTIF CTTRGC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTTRGC GCYAAG 98 35 5.5e-009 1.7e-004 # CTTGGC GCCAAG 64 20 4.2e-007 1.3e-002 # CTTAGC GCTAAG 35 15 2.9e-003 8.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 98 E= 1.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.346939 0.000000 0.653061 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACCTAAAS DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACCTAAAS STTTAGGT 26 0 1.2e-008 3.6e-004 # ACCTAAAC GTTTAGGT 15 0 2.9e-005 8.6e-001 # ACCTAAAG CTTTAGGT 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.6e-004 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 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 0.000000 0.576923 0.423077 0.000000 MOTIF GTCACTS DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTCACTS SAGTGAC 37 4 3.6e-008 1.1e-003 # GTCACTC GAGTGAC 15 0 2.9e-005 8.6e-001 # GTCACTG CAGTGAC 22 4 2.4e-004 7.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.1e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.405405 0.594595 0.000000 MOTIF AGCKCGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGCKCGC GCGMGCT 27 1 8.8e-008 2.6e-003 # AGCTCGC GCGAGCT 12 0 2.3e-004 7.0e+000 # AGCGCGC GCGCGCT 15 1 2.4e-004 7.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.6e-003 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 0.555556 0.444444 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATAATACA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATAATACA TGTATTAT 26 1 1.7e-007 5.2e-003 # ATAATACA TGTATTAT 26 1 1.7e-007 5.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.2e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 29 2 1.8e-007 5.5e-003 # ATGGCAAC GTTGCCAT 19 1 1.8e-005 5.4e-001 # ATGGCATC GATGCCAT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.5e-003 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 0.655172 0.000000 0.000000 0.344828 0.000000 1.000000 0.000000 0.000000 MOTIF CAMGGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CAMGGA TCCKTG 90 37 5.5e-007 1.6e-002 # CAAGGA TCCTTG 50 21 2.9e-004 8.7e+000 # CACGGA TCCGTG 41 16 5.1e-004 1.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 94 E= 1.6e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.563830 0.436170 0.000000 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 MOTIF AGAAGYCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGAAGYCA TGRCTTCT 24 1 6.6e-007 2.0e-002 # AGAAGTCA TGACTTCT 14 0 5.8e-005 1.7e+000 # AGAAGCCA TGGCTTCT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.416667 0.000000 0.583333 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCWGAAG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATCWGAAG CTTCWGAT 24 1 6.6e-007 2.0e-002 # ATCAGAAG CTTCTGAT 13 0 1.2e-004 3.4e+000 # ATCTGAAG CTTCAGAT 11 1 3.1e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.541667 0.000000 0.000000 0.458333 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 MOTIF RCGGGGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 34 5 9.3e-007 2.8e-002 # GCGGGGA TCCCCGC 15 1 2.4e-004 7.3e+000 # ACGGGGA TCCCCGT 19 4 1.2e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.8e-002 0.558824 0.000000 0.441176 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 82.51 seconds