# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SRB8/seqs-shuffled # positives: 582 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SRB8/seqs-centered (Sun Jan 19 06:30:21 PST 2020) # negatives: 582 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SRB8/seqs-shuffled (Sun Jan 19 06:30:21 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 06:45:56 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 0.308 C 0.199 G 0.194 T 0.300 MOTIF GRHTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRHTCGAA TTCGADYC 82 5 1.7e-020 5.2e-016 # GGATCGAA TTCGATCC 27 1 8.1e-008 2.5e-003 # GGCTCGAA TTCGAGCC 15 0 2.8e-005 8.6e-001 # GAATCGAA TTCGATTC 16 1 1.3e-004 3.9e+000 # GGTTCGAA TTCGAACC 12 1 1.6e-003 5.0e+001 # GACTCGAA TTCGAGTC 10 1 5.7e-003 1.8e+002 # GATTCGAA TTCGAATC 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 5.2e-016 0.000000 0.000000 1.000000 0.000000 0.414634 0.000000 0.585366 0.000000 0.524390 0.304878 0.000000 0.170732 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 70 12 4.4e-012 1.4e-007 # AGTGGTT AACCACT 41 7 1.9e-007 5.8e-003 # AGTGGTA TACCACT 36 5 2.6e-007 7.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 1.4e-007 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 0.463415 0.000000 0.000000 0.536585 MOTIF AARAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AARAAA TTTYTT 299 189 4.1e-011 1.3e-006 # AAAAAA TTTTTT 213 128 2.8e-008 8.6e-004 # AAGAAA TTTCTT 150 90 8.9e-006 2.7e-001 letter-probability matrix: alength= 4 w= 6 nsites= 415 E= 1.3e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.626506 0.000000 0.373494 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 ACCCABAC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 36 2 1.6e-009 4.9e-005 # ACCCACAC GTGTGGGT 14 0 5.6e-005 1.7e+000 # ACCCATAC GTATGGGT 17 2 3.3e-004 1.0e+001 # ACCCAGAC GTCTGGGT 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 4.9e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.466667 0.155556 0.377778 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCHTAACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 37 3 5.9e-009 1.8e-004 # CCATAACC GGTTATGG 14 1 4.6e-004 1.4e+001 # CCTTAACC GGTTAAGG 14 1 4.6e-004 1.4e+001 # CCCTAACC GGTTAGGG 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.368421 0.263158 0.000000 0.368421 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCGCCW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCGCCW WGGCGC 55 12 2.2e-008 6.7e-004 # GCGCCT AGGCGC 26 3 6.1e-006 1.8e-001 # GCGCCA TGGCGC 35 9 3.9e-005 1.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 55 E= 6.7e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.563636 0.000000 0.000000 0.436364 MOTIF TAGKGTAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAGKGTAA TTACMCTA 20 0 8.1e-007 2.4e-002 # TAGTGTAA TTACACTA 11 0 4.7e-004 1.4e+001 # TAGGGTAA TTACCCTA 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-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 0.450000 0.550000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGYCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGYCCA TGGRCG 57 17 8.2e-007 2.4e-002 # CGCCCA TGGGCG 37 12 1.8e-004 5.3e+000 # CGTCCA TGGACG 21 5 1.1e-003 3.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 58 E= 2.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.637931 0.000000 0.362069 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 AGTCGMAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGTCGMAC GTKCGACT 19 0 1.6e-006 4.8e-002 # AGTCGAAC GTTCGACT 12 0 2.3e-004 6.8e+000 # AGTCGCAC GTGCGACT 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.8e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.631579 0.368421 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGCTWC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGCGCTWC GWAGCGCG 19 0 1.6e-006 4.8e-002 # CGCGCTAC GTAGCGCG 15 0 2.8e-005 8.2e-001 # CGCGCTTC GAAGCGCG 9 0 1.9e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.8e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.631579 0.000000 0.000000 0.368421 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 40.44 seconds