# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-shuffled # positives: 1005 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-centered (Sun Jan 19 00:37:29 PST 2020) # negatives: 1005 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--RPD3/seqs-shuffled (Sun Jan 19 00:37:29 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:54:16 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 0.304 C 0.197 G 0.197 T 0.302 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 103 22 8.9e-015 3.3e-010 # GGTTCGA TCGAACC 53 9 3.2e-009 1.2e-004 # GGTTCAA TTGAACC 50 13 1.1e-006 4.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 3.3e-010 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 0.490385 0.000000 0.509615 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SAAGAA TTCTTS 289 150 3.2e-014 1.2e-009 # CAAGAA TTCTTG 157 74 3.5e-009 1.3e-004 # GAAGAA TTCTTC 157 86 7.2e-007 2.7e-002 letter-probability matrix: alength= 4 w= 6 nsites= 342 E= 1.2e-009 0.000000 0.497076 0.502924 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 1.000000 0.000000 0.000000 0.000000 MOTIF YGGTAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST YGGTAR YTACCR 222 119 5.3e-010 2.0e-005 # TGGTAA TTACCA 94 49 6.0e-005 2.2e+000 # CGGTAG CTACCG 34 10 1.7e-004 6.2e+000 # TGGTAG CTACCA 65 34 9.3e-004 3.4e+001 # CGGTAA TTACCG 47 26 8.3e-003 3.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 246 E= 2.0e-005 0.000000 0.341463 0.000000 0.658537 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.597561 0.000000 0.402439 0.000000 MOTIF CTTGRC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTTGRC GYCAAG 109 49 3.8e-007 1.4e-002 # CTTGAC GTCAAG 56 23 9.9e-005 3.6e+000 # CTTGGC GCCAAG 55 27 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 115 E= 1.4e-002 0.000000 1.000000 0.000000 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 0.504348 0.000000 0.495652 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACCACT DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AACCACT AGTGGTT 42 9 1.3e-006 4.7e-002 # AACCACT AGTGGTT 42 9 1.3e-006 4.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 4.7e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GCCGCY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCCGCY RGCGGC 60 19 1.4e-006 4.9e-002 # GCCGCC GGCGGC 29 8 3.4e-004 1.2e+001 # GCCGCT AGCGGC 34 12 7.3e-004 2.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 67 E= 4.9e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.462687 0.000000 0.537313 # Stopping reason: E-value threshold exceeded # Running time: 44.65 seconds