# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR8/seqs-shuffled # positives: 469 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR8/seqs-centered (Sun Jan 19 05:05:07 PST 2020) # negatives: 469 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR8/seqs-shuffled (Sun Jan 19 05:05:07 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:14:50 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 0.293 C 0.200 G 0.203 T 0.304 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 82 9 1.6e-017 4.5e-013 # GGTTCGA TCGAACC 64 6 1.8e-014 5.2e-010 # GGATCGA TCGATCC 22 3 6.5e-005 1.9e+000 # GGCTCGA TCGAGCC 7 0 7.6e-003 2.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 4.5e-013 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.256098 0.060976 0.000000 0.682927 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 CGCCTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 35 0 1.5e-011 4.3e-007 # CGCCTTA TAAGGCG 35 0 1.5e-011 4.3e-007 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 4.3e-007 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 AAAAADAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 106 35 3.6e-011 1.0e-006 # AAAAAAAA TTTTTTTT 57 20 6.6e-006 1.9e-001 # AAAAAGAA TTCTTTTT 34 7 8.5e-006 2.4e-001 # AAAAATAA TTATTTTT 38 10 2.0e-005 5.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 118 E= 1.0e-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 0.457627 0.000000 0.245763 0.296610 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 107 39 4.4e-010 1.3e-005 # ACCACT AGTGGT 70 27 2.5e-006 7.0e-002 # ACCTCT AGAGGT 39 15 5.4e-004 1.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 1.3e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.655462 0.000000 0.000000 0.344538 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ATGTAYGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 30 2 8.1e-008 2.3e-003 # ATGTACGG CCGTACAT 17 0 6.6e-006 1.8e-001 # ATGTATGG CCATACAT 16 2 5.9e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 2.3e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.513514 0.000000 0.486486 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CRCCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 71 27 1.6e-006 4.5e-002 # CACCCA TGGGTG 43 17 3.6e-004 1.0e+001 # CGCCCA TGGGCG 29 10 1.4e-003 3.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 93 E= 4.5e-002 0.000000 1.000000 0.000000 0.000000 0.688172 0.000000 0.311828 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAW WTGCCAT 37 6 4.8e-007 1.3e-002 # ATGGCAT ATGCCAT 15 1 2.3e-004 6.5e+000 # ATGGCAA TTGCCAT 22 5 6.5e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.3e-002 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.578947 0.000000 0.000000 0.421053 # Stopping reason: E-value threshold exceeded # Running time: 25.34 seconds