# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-shuffled # positives: 569 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-centered (Sat Jan 18 10:00:12 PST 2020) # negatives: 569 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SRB8/seqs-shuffled (Sat Jan 18 10:00:12 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 10:14:50 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 0.201 G 0.201 T 0.298 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 90 11 3.6e-018 1.1e-013 # GGTTCGA TCGAACC 74 6 3.1e-017 9.8e-013 # AGTTCGA TCGAACT 26 5 7.9e-005 2.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 1.1e-013 0.244444 0.000000 0.755556 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 AAAAADAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 124 49 3.0e-010 9.2e-006 # AAAAAAAA TTTTTTTT 63 24 8.4e-006 2.6e-001 # AAAAATAA TTATTTTT 44 15 6.9e-005 2.1e+000 # AAAAAGAA TTCTTTTT 39 14 3.0e-004 9.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 143 E= 9.2e-006 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 0.419580 0.000000 0.265734 0.314685 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCCATDC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 44 6 8.5e-009 2.6e-004 # CCCATGC GCATGGG 14 1 4.6e-004 1.4e+001 # CCCATTC GAATGGG 15 2 1.1e-003 3.4e+001 # CCCATAC GTATGGG 16 4 5.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 2.6e-004 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 0.000000 0.000000 0.000000 1.000000 0.355556 0.000000 0.311111 0.333333 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 24 0 4.7e-008 1.4e-003 # GCGCTACC GGTAGCGC 14 0 5.6e-005 1.7e+000 # GCTCTACC GGTAGAGC 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.583333 0.416667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 GTGATAGY DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 22 0 1.9e-007 6.0e-003 # GTGATAGT ACTATCAC 14 0 5.6e-005 1.7e+000 # GTGATAGC GCTATCAC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.0e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 0.363636 0.000000 0.636364 MOTIF CTTAAYCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTTAAYCA TGRTTAAG 31 3 2.7e-007 8.3e-003 # CTTAATCA TGATTAAG 12 0 2.3e-004 7.1e+000 # CTTAACCA TGGTTAAG 19 3 3.8e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 8.3e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.612903 0.000000 0.387097 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGRTG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACGRTG CAYCGTG 28 2 3.2e-007 9.9e-003 # CACGGTG CACCGTG 21 2 2.8e-005 8.7e-001 # CACGATG CATCGTG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 9.9e-003 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 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GSGCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GSGCCA TGGCSC 46 10 3.5e-007 1.1e-002 # GCGCCA TGGCGC 29 5 1.5e-005 4.6e-001 # GGGCCA TGGCCC 17 5 7.9e-003 2.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 47 E= 1.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.617021 0.382979 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 # Stopping reason: E-value threshold exceeded # Running time: 32.98 seconds