# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-shuffled # positives: 563 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-centered (Sat Jan 18 02:06:42 PST 2020) # negatives: 563 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR1/seqs-shuffled (Sat Jan 18 02:06:42 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 02:21:00 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 0.305 C 0.199 G 0.196 T 0.300 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 103 10 9.6e-023 3.0e-018 # GGTTCGA TCGAACC 73 3 9.7e-020 3.0e-015 # GGTTCAA TTGAACC 33 7 1.6e-005 4.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 106 E= 3.0e-018 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 0.311321 0.000000 0.688679 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 27 0 5.4e-009 1.7e-004 # CCTTAACC GGTTAAGG 17 0 6.7e-006 2.1e-001 # CCATAACC GGTTATGG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.370370 0.000000 0.000000 0.629630 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 AAAAADAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 133 61 7.7e-009 2.4e-004 # AAAAAGAA TTCTTTTT 54 19 1.4e-005 4.4e-001 # AAAAATAA TTATTTTT 44 17 2.6e-004 8.0e+000 # AAAAAAAA TTTTTTTT 59 30 9.2e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 157 E= 2.4e-004 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 0.414013 0.000000 0.312102 0.273885 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 95 38 8.0e-008 2.5e-003 # ACCTCT AGAGGT 43 15 1.1e-004 3.3e+000 # ACCACT AGTGGT 55 25 3.4e-004 1.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 107 E= 2.5e-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 0.579439 0.000000 0.000000 0.420561 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF SAAGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 285 199 1.5e-007 4.5e-003 # GAAGA TCTTC 173 119 1.5e-004 4.6e+000 # CAAGA TCTTG 150 112 4.5e-003 1.4e+002 letter-probability matrix: alength= 4 w= 5 nsites= 388 E= 4.5e-003 0.000000 0.458763 0.541237 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 ACTGGGS DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACTGGGS SCCCAGT 27 2 6.2e-007 1.8e-002 # ACTGGGG CCCCAGT 16 1 1.2e-004 3.7e+000 # ACTGGGC GCCCAGT 11 1 3.0e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 1.8e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.407407 0.592593 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 25.68 seconds