# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SRB8/seqs-shuffled # positives: 544 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SRB8/seqs-centered (Sat Jan 18 22:44:23 PST 2020) # negatives: 544 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SRB8/seqs-shuffled (Sat Jan 18 22:44:23 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:57:53 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 0.301 C 0.200 G 0.202 T 0.297 MOTIF GGDTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGDTCGA TCGAHCC 82 10 1.3e-016 3.9e-012 # GGTTCGA TCGAACC 63 6 4.6e-014 1.4e-009 # GGATCGA TCGATCC 25 4 4.2e-005 1.3e+000 # GGGTCGA TCGACCC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 3.9e-012 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.280488 0.000000 0.073171 0.646341 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 AAAAAWAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWAW WTWTTTTT 120 45 1.1e-010 3.3e-006 # AAAAAAAT ATTTTTTT 66 23 1.1e-006 3.5e-002 # AAAAAAAA TTTTTTTT 58 21 9.6e-006 3.0e-001 # AAAAATAA TTATTTTT 36 11 1.3e-004 4.0e+000 # AAAAATAT ATATTTTT 21 7 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 146 E= 3.3e-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 0.636986 0.000000 0.000000 0.363014 1.000000 0.000000 0.000000 0.000000 0.575342 0.000000 0.000000 0.424658 MOTIF CTYGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 28 1 4.0e-008 1.2e-003 # CTCGGCCA TGGCCGAG 15 0 2.8e-005 8.5e-001 # CTTGGCCA TGGCCAAG 13 1 8.6e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.535714 0.000000 0.464286 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCTTAMC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 27 1 7.9e-008 2.4e-003 # GCCTTAAC GTTAAGGC 19 1 1.7e-005 5.3e-001 # GCCTTACC GGTAAGGC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.4e-003 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 0.703704 0.296296 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTACCGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTACCGA TCGGTAG 21 0 3.9e-007 1.2e-002 # CTACCGA TCGGTAG 21 0 3.9e-007 1.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 21 E= 1.2e-002 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTKTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TAGTKTA TAMACTA 41 8 5.9e-007 1.8e-002 # TAGTGTA TACACTA 19 2 9.7e-005 3.0e+000 # TAGTTTA TAAACTA 22 6 1.7e-003 5.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.8e-002 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 0.476190 0.523810 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST SAAGAA TTCTTS 122 63 1.2e-006 3.7e-002 # GAAGAA TTCTTC 72 32 2.4e-005 7.4e-001 # CAAGAA TTCTTG 58 33 4.1e-003 1.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 138 E= 3.7e-002 0.000000 0.442029 0.557971 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 28.49 seconds