# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-shuffled # positives: 769 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-centered (Sun Jan 19 05:15:21 PST 2020) # negatives: 769 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP3/seqs-shuffled (Sun Jan 19 05:15:21 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:31:54 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 0.310 C 0.188 G 0.186 T 0.316 MOTIF GGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 58 9 1.5e-010 5.2e-006 # GGTTCGA TCGAACC 58 9 1.5e-010 5.2e-006 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 5.2e-006 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RGAAGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST RGAAGA TCTTCY 161 77 1.8e-009 6.0e-005 # AGAAGA TCTTCT 106 48 5.0e-007 1.7e-002 # GGAAGA TCTTCC 63 32 6.9e-004 2.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 180 E= 6.0e-005 0.633333 0.000000 0.366667 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACCGW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCGW WCGGT 207 124 1.6e-007 5.4e-003 # ACCGA TCGGT 122 68 1.8e-005 6.1e-001 # ACCGT ACGGT 93 64 9.1e-003 3.0e+002 letter-probability matrix: alength= 4 w= 5 nsites= 224 E= 5.4e-003 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 0.566964 0.000000 0.000000 0.433036 MOTIF ATGGCAWC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 22 0 2.0e-007 6.7e-003 # ATGGCAAC GTTGCCAT 12 0 2.3e-004 7.6e+000 # ATGGCATC GATGCCAT 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.7e-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 0.545455 0.000000 0.000000 0.454545 0.000000 1.000000 0.000000 0.000000 MOTIF CTKACCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTKACCA TGGTMAG 41 7 2.1e-007 6.9e-003 # CTTACCA TGGTAAG 30 5 9.1e-006 3.0e-001 # CTGACCA TGGTCAG 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 6.9e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 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 MOTIF AGTGGTTW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTW WAACCACT 37 6 6.0e-007 1.9e-002 # AGTGGTTA TAACCACT 22 2 1.6e-005 5.1e-001 # AGTGGTTT AAACCACT 15 4 9.2e-003 3.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.9e-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 0.000000 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 0.594595 0.000000 0.000000 0.405405 MOTIF AAAAADAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 147 81 1.4e-006 4.4e-002 # AAAAATAA TTATTTTT 51 16 7.2e-006 2.3e-001 # AAAAAAAA TTTTTTTT 71 43 4.2e-003 1.4e+002 # AAAAAGAA TTCTTTTT 52 30 8.3e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 180 E= 4.4e-002 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 0.450000 0.000000 0.261111 0.288889 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 38.68 seconds