# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YKL222C/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YKL222C/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YKL222C/seqs-shuffled # positives: 579 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YKL222C/seqs-centered (Sun Jan 19 03:15:05 PST 2020) # negatives: 579 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YKL222C/seqs-shuffled (Sun Jan 19 03:15:05 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 03:30:31 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 0.307 C 0.197 G 0.191 T 0.305 MOTIF GGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 60 1 5.6e-018 1.8e-013 # GGTTCGA TCGAACC 60 1 5.6e-018 1.8e-013 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 1.8e-013 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 CCWTAACC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 37 1 8.1e-011 2.5e-006 # CCTTAACC GGTTAAGG 27 1 8.1e-008 2.5e-003 # CCATAACC GGTTATGG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 2.5e-006 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.270270 0.000000 0.000000 0.729730 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 CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 37 2 8.3e-010 2.6e-005 # CTTGGCCA TGGCCAAG 12 0 2.3e-004 7.1e+000 # CTCGGCCA TGGCCGAG 17 2 3.3e-004 1.0e+001 # CTGGGCCA TGGCCCAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 2.6e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.459459 0.216216 0.324324 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 MOTIF ARAARAA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ARAARAA TTYTTYT 200 110 1.4e-009 4.5e-005 # AAAAAAA TTTTTTT 115 61 6.3e-006 2.0e-001 # AAAAGAA TTCTTTT 67 31 9.6e-005 3.0e+000 # AGAAGAA TTCTTCT 34 14 2.3e-003 7.1e+001 # AGAAAAA TTTTTCT 57 31 2.7e-003 8.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 254 E= 4.5e-005 1.000000 0.000000 0.000000 0.000000 0.696850 0.000000 0.303150 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.649606 0.000000 0.350394 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 55 13 6.2e-008 1.9e-003 # AGTGGTT AACCACT 32 7 2.7e-005 8.2e-001 # AGTGGTA TACCACT 28 6 7.9e-005 2.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 1.9e-003 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 0.468750 0.000000 0.000000 0.531250 MOTIF CCGTGCW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCGTGCW WGCACGG 26 2 1.2e-006 3.6e-002 # CCGTGCA TGCACGG 15 1 2.4e-004 7.3e+000 # CCGTGCT AGCACGG 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 3.6e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.535714 0.000000 0.000000 0.464286 # Stopping reason: E-value threshold exceeded # Running time: 27.62 seconds