# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-shuffled # positives: 521 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-centered (Sun Jan 19 10:50:23 PST 2020) # negatives: 521 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAD1/seqs-shuffled (Sun Jan 19 10:50:23 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 11:02:41 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 0.303 C 0.196 G 0.198 T 0.302 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 68 4 2.9e-017 8.8e-013 # GGGTTCGA TCGAACCC 25 0 2.2e-008 6.8e-004 # CGGTTCGA TCGAACCG 22 2 1.5e-005 4.5e-001 # GAGTTCGA TCGAACTC 13 2 3.5e-003 1.1e+002 # CAGTTCGA TCGAACTG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 8.8e-013 0.000000 0.441176 0.558824 0.000000 0.308824 0.000000 0.691176 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 54 7 7.1e-011 2.2e-006 # AGTGGTT AACCACT 36 4 5.6e-008 1.7e-003 # AGTGGTA TACCACT 22 3 6.6e-005 2.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 2.2e-006 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 0.372881 0.000000 0.000000 0.627119 MOTIF AAAAAADA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAAADA THTTTTTT 109 45 1.3e-008 3.9e-004 # AAAAAAAA TTTTTTTT 54 21 5.0e-005 1.5e+000 # AAAAAAGA TCTTTTTT 34 12 6.4e-004 1.9e+001 # AAAAAATA TATTTTTT 42 18 9.9e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 118 E= 3.9e-004 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 1.000000 0.000000 0.000000 0.000000 0.440678 0.000000 0.254237 0.305085 1.000000 0.000000 0.000000 0.000000 MOTIF GGAMTTGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGAMTTGA TCAAKTCC 24 0 4.5e-008 1.4e-003 # GGAATTGA TCAATTCC 16 0 1.4e-005 4.1e-001 # GGACTTGA TCAAGTCC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCAACTKG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCAACTKG CMAGTTGG 21 0 3.9e-007 1.2e-002 # CCAACTTG CAAGTTGG 14 0 5.6e-005 1.7e+000 # CCAACTGG CCAGTTGG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 21.34 seconds