# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MAC1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MAC1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MAC1/seqs-shuffled # positives: 845 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MAC1/seqs-centered (Sun Jan 19 04:43:10 PST 2020) # negatives: 845 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MAC1/seqs-shuffled (Sun Jan 19 04:43:10 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 04:57:58 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 0.317 C 0.188 G 0.179 T 0.317 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 95 6 4.5e-023 1.5e-018 # GGTTCGA TCGAACC 79 3 3.2e-021 1.0e-016 # GGATCGA TCGATCC 26 3 6.5e-006 2.1e-001 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 1.5e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.231579 0.000000 0.000000 0.768421 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 ACCACTV DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACTV BAGTGGT 108 15 4.9e-020 1.6e-015 # ACCACTA TAGTGGT 58 4 5.4e-014 1.7e-009 # ACCACTC GAGTGGT 42 9 1.2e-006 3.9e-002 # ACCACTG CAGTGGT 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 1.6e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.517857 0.375000 0.107143 0.000000 MOTIF TGTAYGGR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 71 2 6.7e-020 2.1e-015 # TGTATGGG CCCATACA 31 0 3.5e-010 1.1e-005 # TGTACGGA TCCGTACA 29 2 1.9e-007 6.0e-003 # TGTATGGA TCCATACA 13 0 1.2e-004 3.7e+000 # TGTACGGG CCCGTACA 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 83 E= 2.1e-015 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 0.457831 0.000000 0.542169 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.542169 0.000000 0.457831 0.000000 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 73 5 1.8e-017 5.8e-013 # CGCCTTA TAAGGCG 58 2 6.2e-016 2.0e-011 # CGCGTTA TAACGCG 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 73 E= 5.8e-013 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 0.794521 0.205479 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 AAAAADAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 186 80 6.5e-013 2.1e-008 # AAAAAAAA TTTTTTTT 94 39 3.9e-007 1.2e-002 # AAAAAGAA TTCTTTTT 56 19 7.4e-006 2.3e-001 # AAAAATAA TTATTTTT 63 37 4.8e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 209 E= 2.1e-008 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 0.444976 0.000000 0.258373 0.296651 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGGYG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 35 1 3.8e-010 1.2e-005 # CACGGTG CACCGTG 24 0 5.1e-008 1.6e-003 # CACGGCG CGCCGTG 11 1 3.1e-003 9.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.2e-005 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 0.000000 0.314286 0.000000 0.685714 0.000000 0.000000 1.000000 0.000000 MOTIF CTTGGCC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTTGGCC GGCCAAG 41 3 5.3e-010 1.7e-005 # CTTGGCC GGCCAAG 41 3 5.3e-010 1.7e-005 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.7e-005 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGAARA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGAARA TYTTCT 266 169 4.2e-008 1.3e-003 # AGAAAA TTTTCT 209 133 2.6e-006 8.2e-002 # AGAAGA TCTTCT 83 45 3.1e-004 9.8e+000 letter-probability matrix: alength= 4 w= 6 nsites= 320 E= 1.3e-003 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 0.743750 0.000000 0.256250 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGRAGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGRAGA TCTYCC 98 40 1.4e-007 4.5e-003 # GGAAGA TCTTCC 67 28 2.4e-005 7.5e-001 # GGGAGA TCTCCC 32 12 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 101 E= 4.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.673267 0.000000 0.326733 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 ATCGTRAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATCGTRAG CTYACGAT 26 1 1.7e-007 5.4e-003 # ATCGTGAG CTCACGAT 15 0 2.9e-005 8.9e-001 # ATCGTAAG CTTACGAT 11 1 3.1e-003 9.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.4e-003 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 0.423077 0.000000 0.576923 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACCRACT DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 54 14 3.4e-007 1.1e-002 # ACCAACT AGTTGGT 34 10 1.6e-004 5.0e+000 # ACCGACT AGTCGGT 20 4 7.2e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 1.1e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.629630 0.000000 0.370370 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 MOTIF CWTGCGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CWTGCGC GCGCAWG 21 0 4.2e-007 1.3e-002 # CTTGCGC GCGCAAG 14 0 5.8e-005 1.8e+000 # CATGCGC GCGCATG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 1.3e-002 0.000000 1.000000 0.000000 0.000000 0.280000 0.000000 0.000000 0.720000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 35 5 5.3e-007 1.6e-002 # ATGGCAAC GTTGCCAT 18 0 3.5e-006 1.1e-001 # ATGGCATC GATGCCAT 17 5 8.1e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.6e-002 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 0.514286 0.000000 0.000000 0.485714 0.000000 1.000000 0.000000 0.000000 MOTIF RCACCCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST RCACCCA TGGGTGY 53 14 5.6e-007 1.7e-002 # ACACCCA TGGGTGT 39 12 7.9e-005 2.4e+000 # GCACCCA TGGGTGC 16 2 6.2e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 1.7e-002 0.787234 0.000000 0.212766 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGCSCAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GGCSCAA TTGSGCC 23 1 1.3e-006 4.0e-002 # GGCCCAA TTGGGCC 12 0 2.3e-004 7.2e+000 # GGCGCAA TTGCGCC 11 1 3.1e-003 9.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 4.0e-002 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 0.521739 0.478261 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 # Stopping reason: E-value threshold exceeded # Running time: 82.19 seconds