# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ZAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ZAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ZAP1/seqs-shuffled # positives: 570 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ZAP1/seqs-centered (Sat Jan 18 13:06:00 PST 2020) # negatives: 570 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--ZAP1/seqs-shuffled (Sat Jan 18 13:06:00 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 13:20:54 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 0.315 C 0.195 G 0.188 T 0.302 MOTIF AGTGGTW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 69 7 5.4e-015 1.7e-010 # AGTGGTT AACCACT 37 2 8.3e-010 2.6e-005 # AGTGGTA TACCACT 40 6 9.2e-008 2.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 81 E= 1.7e-010 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 0.518519 0.000000 0.000000 0.481481 MOTIF GGWTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 68 9 2.4e-013 7.5e-009 # GGTTCGA TCGAACC 56 5 8.6e-013 2.7e-008 # GGATCGA TCGATCC 16 4 5.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 68 E= 7.5e-009 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.220588 0.000000 0.000000 0.779412 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 ARAAAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAR YTTTTYT 195 103 3.4e-010 1.0e-005 # AAAAAAA TTTTTTT 114 59 3.6e-006 1.1e-001 # AGAAAAA TTTTTCT 62 27 7.4e-005 2.3e+000 # AAAAAAG CTTTTTT 77 40 2.0e-004 6.2e+000 # AGAAAAG CTTTTCT 29 13 8.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 248 E= 1.0e-005 1.000000 0.000000 0.000000 0.000000 0.661290 0.000000 0.338710 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 0.649194 0.000000 0.350806 0.000000 MOTIF CCWTAACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 31 2 4.5e-008 1.4e-003 # CCATAACC GGTTATGG 15 0 2.8e-005 8.5e-001 # CCTTAACC GGTTAAGG 16 2 6.0e-004 1.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.4e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.483871 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGCCAAGW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GGCCAAGW WCTTGGCC 24 1 6.2e-007 1.9e-002 # GGCCAAGT ACTTGGCC 15 1 2.4e-004 7.3e+000 # GGCCAAGA TCTTGGCC 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.9e-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 1.000000 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 0.000000 0.375000 0.000000 0.000000 0.625000 MOTIF ACCCATA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCCATA TATGGGT 26 2 1.2e-006 3.6e-002 # ACCCATA TATGGGT 26 2 1.2e-006 3.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 3.6e-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 0.000000 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 26.65 seconds