# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-shuffled # positives: 486 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-centered (Sat Jan 18 00:29:30 PST 2020) # negatives: 486 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HIR1/seqs-shuffled (Sat Jan 18 00:29:30 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 00:39:51 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 0.298 C 0.198 G 0.199 T 0.304 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 68 4 2.4e-017 7.2e-013 # CGGTTCGA TCGAACCG 24 1 5.9e-007 1.7e-002 # GGGTTCGA TCGAACCC 23 2 7.8e-006 2.3e-001 # GAGTTCGA TCGAACTC 14 1 4.5e-004 1.3e+001 # CAGTTCGA TCGAACTG 7 0 7.6e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 7.2e-013 0.000000 0.455882 0.544118 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 ACCAST DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCAST ASTGGT 79 17 5.6e-012 1.6e-007 # ACCACT AGTGGT 62 12 3.6e-010 1.0e-005 # ACCAGT ACTGGT 22 7 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 95 E= 1.6e-007 1.000000 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 0.000000 0.000000 0.000000 0.768421 0.231579 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ARAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAA TTTTTYT 142 58 1.3e-011 3.8e-007 # AAAAAAA TTTTTTT 106 47 1.2e-007 3.5e-003 # AGAAAAA TTTTTCT 63 20 4.3e-007 1.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 172 E= 3.8e-007 1.000000 0.000000 0.000000 0.000000 0.674419 0.000000 0.325581 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 MOTIF CGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 29 1 1.9e-008 5.5e-004 # CGCCTTA TAAGGCG 29 1 1.9e-008 5.5e-004 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 5.5e-004 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 CGSCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 62 17 5.8e-008 1.7e-003 # CGCCCA TGGGCG 36 8 8.4e-006 2.4e-001 # CGGCCA TGGCCG 27 9 1.7e-003 4.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 64 E= 1.7e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.578125 0.421875 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 GAAGAAR DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GAAGAAR YTTCTTC 51 12 1.6e-007 4.6e-003 # GAAGAAA TTTCTTC 33 6 4.9e-006 1.4e-001 # GAAGAAG CTTCTTC 21 6 2.6e-003 7.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 4.6e-003 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.603774 0.000000 0.396226 0.000000 MOTIF CCGTSG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCGTSG CSACGG 31 3 2.6e-007 7.2e-003 # CCGTCG CGACGG 15 1 2.4e-004 6.6e+000 # CCGTGG CCACGG 17 2 3.3e-004 9.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 32 E= 7.2e-003 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 1.000000 0.000000 0.468750 0.531250 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTATCACR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 21 0 3.8e-007 1.1e-002 # CTATCACG CGTGATAG 11 0 4.6e-004 1.3e+001 # CTATCACA TGTGATAG 10 0 9.3e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.000000 0.523810 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 28.96 seconds