# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-shuffled # positives: 577 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-centered (Sun Jan 19 06:14:41 PST 2020) # negatives: 577 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--AFT1/seqs-shuffled (Sun Jan 19 06:14:41 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 06:29:53 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 0.196 G 0.199 T 0.300 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 102 16 2.4e-018 7.5e-014 # GGTTCGA TCGAACC 69 4 1.8e-017 5.6e-013 # GGTTCAA TTGAACC 33 12 1.0e-003 3.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 102 E= 7.5e-014 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 0.323529 0.000000 0.676471 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAKAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAKAA TTMTTTTT 95 25 4.0e-012 1.3e-007 # AAAAAGAA TTCTTTTT 47 11 5.7e-007 1.8e-002 # AAAAATAA TTATTTTT 51 14 1.2e-006 3.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 99 E= 1.3e-007 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 0.474747 0.525253 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF DCGCCTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST DCGCCTTA TAAGGCGH 27 0 5.5e-009 1.7e-004 # TCGCCTTA TAAGGCGA 10 0 9.4e-004 2.9e+001 # GCGCCTTA TAAGGCGC 9 0 1.9e-003 5.9e+001 # ACGCCTTA TAAGGCGT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.7e-004 0.296296 0.000000 0.333333 0.370370 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RCGGGGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 31 3 2.7e-007 8.5e-003 # ACGGGGA TCCCCGT 18 2 1.8e-004 5.6e+000 # GCGGGGA TCCCCGC 13 1 8.6e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 8.5e-003 0.580645 0.000000 0.419355 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 MOTIF CGKTGCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGKTGCC GGCAMCG 23 1 1.2e-006 3.8e-002 # CGTTGCC GGCAACG 15 1 2.4e-004 7.4e+000 # CGGTGCC GGCACCG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.8e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.347826 0.652174 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 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 22.97 seconds