# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR8/seqs-shuffled # positives: 555 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR8/seqs-centered (Sun Jan 19 05:49:52 PST 2020) # negatives: 555 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR8/seqs-shuffled (Sun Jan 19 05:49:52 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 06:03:52 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 0.306 C 0.202 G 0.190 T 0.303 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 82 7 8.0e-019 2.4e-014 # GGTTCGA TCGAACC 60 4 8.4e-015 2.6e-010 # GGATCGA TCGATCC 26 2 1.2e-006 3.6e-002 # GGCTCGA TCGAGCC 14 1 4.5e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 2.4e-014 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.268293 0.085366 0.000000 0.646341 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 CCWTAACC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 40 0 4.4e-013 1.3e-008 # CCTTAACC GGTTAAGG 26 0 1.1e-008 3.3e-004 # CCATAACC GGTTATGG 14 0 5.6e-005 1.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.3e-008 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.350000 0.000000 0.000000 0.650000 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 AAAAADA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAADA THTTTTT 196 95 3.0e-012 9.2e-008 # AAAAAAA TTTTTTT 117 53 5.7e-008 1.7e-003 # AAAAATA TATTTTT 80 36 1.0e-005 3.1e-001 # AAAAAGA TCTTTTT 66 29 4.7e-005 1.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 261 E= 9.2e-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 0.444444 0.000000 0.249042 0.306513 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 97 36 8.9e-009 2.7e-004 # ACCACT AGTGGT 67 23 7.4e-007 2.2e-002 # ACCTCT AGAGGT 32 13 2.8e-003 8.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 111 E= 2.7e-004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.702703 0.000000 0.000000 0.297297 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CRCCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 86 32 7.9e-008 2.4e-003 # CACCCA TGGGTG 60 19 9.3e-007 2.8e-002 # CGCCCA TGGGCG 30 13 6.0e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 115 E= 2.4e-003 0.000000 1.000000 0.000000 0.000000 0.747826 0.000000 0.252174 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 ACTBGGCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 23 1 1.2e-006 3.5e-002 # ACTTGGCC GGCCAAGT 13 1 8.6e-004 2.5e+001 # ACTCGGCC GGCCGAGT 8 0 3.8e-003 1.1e+002 # ACTGGGCC GGCCCAGT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.5e-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 0.304348 0.347826 0.347826 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 CGTGYTAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 23 1 1.2e-006 3.5e-002 # CGTGTTAA TTAACACG 13 1 8.6e-004 2.5e+001 # CGTGCTAA TTAGCACG 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.5e-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 1.000000 0.000000 0.000000 0.434783 0.000000 0.565217 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 30.01 seconds