# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-shuffled # positives: 896 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-centered (Sun Jan 19 01:53:58 PST 2020) # negatives: 896 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SOK2/seqs-shuffled (Sun Jan 19 01:53:58 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:10:47 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 0.299 C 0.200 G 0.202 T 0.299 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 119 19 1.7e-020 6.4e-016 # GGTTCGA TCGAACC 75 10 2.7e-014 1.0e-009 # GGTTCAA TTGAACC 47 10 2.5e-007 9.4e-003 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 6.4e-016 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 0.385246 0.000000 0.614754 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAADAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 200 75 7.8e-017 2.9e-012 # AAAAATAA TTATTTTT 72 18 1.7e-009 6.4e-005 # AAAAAGAA TTCTTTTT 70 22 1.4e-007 5.0e-003 # AAAAAAAA TTTTTTTT 86 42 3.5e-005 1.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 230 E= 2.9e-012 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 0.382609 0.000000 0.300000 0.317391 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 28 1 4.6e-008 1.7e-003 # TAGTGGTA TACCACTA 18 1 3.5e-005 1.3e+000 # TAGTGGTT AACCACTA 10 0 9.5e-004 3.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.7e-003 0.000000 0.000000 0.000000 1.000000 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 0.642857 0.000000 0.000000 0.357143 MOTIF CGSTTGTC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGSTTGTC GACAASCG 21 0 4.2e-007 1.6e-002 # CGCTTGTC GACAAGCG 13 0 1.2e-004 4.3e+000 # CGGTTGTC GACAACCG 9 0 1.9e-003 7.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 1.6e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.590909 0.409091 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 1.000000 0.000000 0.000000 MOTIF RCGGGGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 39 7 6.9e-007 2.5e-002 # GCGGGGA TCCCCGC 17 1 6.8e-005 2.5e+000 # ACGGGGA TCCCCGT 23 6 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 2.5e-002 0.575000 0.000000 0.425000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 34.15 seconds