# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--IES2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--IES2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--IES2/seqs-shuffled # positives: 591 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--IES2/seqs-centered (Sat Jan 18 17:24:18 PST 2020) # negatives: 591 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--IES2/seqs-shuffled (Sat Jan 18 17:24:18 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:40:19 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 0.311 C 0.194 G 0.188 T 0.306 MOTIF SGGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCRA TYGAACCS 59 1 1.2e-017 3.8e-013 # CGGTTCGA TCGAACCG 21 0 4.0e-007 1.2e-002 # GGGTTCGA TCGAACCC 22 1 2.4e-006 7.5e-002 # GGGTTCAA TTGAACCC 9 0 1.9e-003 5.9e+001 # CGGTTCAA TTGAACCG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 3.8e-013 0.000000 0.474576 0.525424 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.271186 0.000000 0.728814 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 66 13 1.5e-010 4.8e-006 # AGTGGTA TACCACT 36 5 2.6e-007 8.1e-003 # AGTGGTT AACCACT 42 8 3.5e-007 1.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 80 E= 4.8e-006 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 0.462500 0.000000 0.000000 0.537500 MOTIF AAAAAAKA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAKA TMTTTTTT 87 31 2.8e-008 8.9e-004 # AAAAAATA TATTTTTT 53 14 4.5e-007 1.4e-002 # AAAAAAGA TCTTTTTT 36 18 8.6e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 95 E= 8.9e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.389474 0.610526 1.000000 0.000000 0.000000 0.000000 MOTIF GCCAAGW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCCAAGW WCTTGGC 35 4 1.1e-007 3.5e-003 # GCCAAGT ACTTGGC 24 2 4.3e-006 1.3e-001 # GCCAAGA TCTTGGC 12 2 6.2e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.5e-003 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 0.333333 0.000000 0.000000 0.666667 MOTIF ACTCWCG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACTCWCG CGWGAGT 25 1 3.2e-007 9.8e-003 # ACTCACG CGTGAGT 13 0 1.1e-004 3.5e+000 # ACTCTCG CGAGAGT 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 9.8e-003 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 1.000000 0.000000 0.000000 0.520000 0.000000 0.000000 0.480000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCGCCW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCGCCW WGGCGC 44 9 3.6e-007 1.1e-002 # GCGCCA TGGCGC 31 5 4.8e-006 1.5e-001 # GCGCCT AGGCGC 19 4 1.2e-003 3.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 44 E= 1.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.636364 0.000000 0.000000 0.363636 MOTIF CGTTGCY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCY RGCAACG 26 2 1.2e-006 3.7e-002 # CGTTGCC GGCAACG 19 2 9.8e-005 3.0e+000 # CGTTGCT AGCAACG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.7e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.730769 0.000000 0.269231 # Stopping reason: E-value threshold exceeded # Running time: 31.79 seconds