# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/seqs-shuffled # positives: 664 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/seqs-centered (Sat Jan 18 18:03:03 PST 2020) # negatives: 664 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/seqs-shuffled (Sat Jan 18 18:03:03 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:18:23 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 0.299 C 0.201 G 0.201 T 0.299 MOTIF AGTGGTH DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTH DACCACT 109 16 4.8e-020 1.5e-015 # AGTGGTT AACCACT 70 5 9.3e-017 2.9e-012 # AGTGGTA TACCACT 36 7 3.3e-006 1.0e-001 # AGTGGTC GACCACT 16 4 5.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 126 E= 1.5e-015 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 0.293651 0.126984 0.000000 0.579365 MOTIF GGHTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 84 7 3.3e-019 1.0e-014 # GGTTCGA TCGAACC 68 4 4.6e-017 1.4e-012 # GGCTCGA TCGAGCC 14 1 4.6e-004 1.4e+001 # GGATCGA TCGATCC 15 2 1.1e-003 3.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 84 E= 1.0e-014 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.154762 0.107143 0.000000 0.738095 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 ACCCABAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 60 1 7.0e-018 2.2e-013 # ACCCATAC GTATGGGT 38 0 2.1e-012 6.5e-008 # ACCCACAC GTGTGGGT 13 0 1.2e-004 3.6e+000 # ACCCAGAC GTCTGGGT 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 2.2e-013 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 0.208955 0.194030 0.597015 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AASGCG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AASGCG CGCSTT 106 27 1.1e-013 3.3e-009 # AAGGCG CGCCTT 74 13 1.8e-012 5.6e-008 # AACGCG CGCGTT 32 14 5.0e-003 1.5e+002 letter-probability matrix: alength= 4 w= 6 nsites= 107 E= 3.3e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.299065 0.700935 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 MOTIF AACTKGGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 46 2 2.0e-012 6.1e-008 # AACTTGGC GCCAAGTT 34 1 7.0e-010 2.1e-005 # AACTGGGC GCCCAGTT 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 6.1e-008 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 0.260870 0.739130 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF SAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 347 225 8.7e-012 2.7e-007 # CAAGA TCTTG 220 140 5.0e-007 1.5e-002 # GAAGA TCTTC 185 116 3.9e-006 1.2e-001 letter-probability matrix: alength= 4 w= 5 nsites= 515 E= 2.7e-007 0.000000 0.545631 0.454369 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 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 33 0 7.7e-011 2.3e-006 # GCGCTACC GGTAGCGC 22 0 2.0e-007 5.9e-003 # GCTCTACC GGTAGAGC 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.3e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 MOTIF TGTACGGR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TGTACGGR YCCGTACA 39 2 2.3e-010 6.8e-006 # TGTACGGA TCCGTACA 30 2 9.2e-008 2.7e-003 # TGTACGGG CCCGTACA 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 6.8e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.756098 0.000000 0.243902 0.000000 MOTIF CACGGYG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 38 4 1.8e-008 5.3e-004 # CACGGTG CACCGTG 27 4 1.4e-005 4.1e-001 # CACGGCG CGCCGTG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 5.3e-004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.289474 0.000000 0.710526 0.000000 0.000000 1.000000 0.000000 MOTIF GATTRGAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GATTRGAA TTCYAATC 29 1 2.2e-008 6.3e-004 # GATTAGAA TTCTAATC 19 0 1.7e-006 4.9e-002 # GATTGGAA TTCCAATC 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.3e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.655172 0.000000 0.344828 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 CTATCACR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 2 2.5e-008 7.2e-004 # CTATCACA TGTGATAG 17 0 6.9e-006 2.0e-001 # CTATCACG CGTGATAG 15 2 1.1e-003 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 7.2e-004 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 0.531250 0.000000 0.468750 0.000000 MOTIF AAACCCAW DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAACCCAW WTGGGTTT 22 0 2.0e-007 5.8e-003 # AAACCCAA TTGGGTTT 15 0 2.8e-005 8.2e-001 # AAACCCAT ATGGGTTT 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.8e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 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 0.681818 0.000000 0.000000 0.318182 MOTIF CACTATAK DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CACTATAK MTATAGTG 22 0 2.0e-007 5.8e-003 # CACTATAT ATATAGTG 14 0 5.7e-005 1.7e+000 # CACTATAG CTATAGTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.8e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.636364 MOTIF ATTRCGCC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATTRCGCC GGCGYAAT 25 1 3.3e-007 9.4e-003 # ATTGCGCC GGCGCAAT 13 0 1.2e-004 3.3e+000 # ATTACGCC GGCGTAAT 12 1 1.6e-003 4.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.480000 0.000000 0.520000 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 MOTIF AAAGCGWG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 28 2 3.4e-007 9.8e-003 # AAAGCGTG CACGCTTT 18 1 3.4e-005 9.9e-001 # AAAGCGAG CTCGCTTT 10 1 5.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.8e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.357143 0.000000 0.000000 0.642857 0.000000 0.000000 1.000000 0.000000 MOTIF RAAAAAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST RAAAAAA TTTTTTY 138 72 4.3e-007 1.2e-002 # AAAAAAA TTTTTTT 103 53 1.3e-005 3.8e-001 # GAAAAAA TTTTTTC 72 37 3.1e-004 8.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 161 E= 1.2e-002 0.621118 0.000000 0.378882 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 1.000000 0.000000 0.000000 0.000000 MOTIF GATKGCAA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GATKGCAA TTGCMATC 22 0 2.0e-007 5.7e-003 # GATGGCAA TTGCCATC 15 0 2.8e-005 8.1e-001 # GATTGCAA TTGCAATC 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.7e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.681818 0.318182 0.000000 0.000000 1.000000 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 MOTIF CACGCCC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CACGCCC GGGCGTG 20 0 8.2e-007 2.4e-002 # CACGCCC GGGCGTG 20 0 8.2e-007 2.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 2.4e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTGAGCTA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 20 0 8.2e-007 2.4e-002 # CTGAGCTA TAGCTCAG 20 0 8.2e-007 2.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCGARAG DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACCGARAG CTYTCGGT 19 0 1.7e-006 4.8e-002 # ACCGAAAG CTTTCGGT 11 0 4.7e-004 1.3e+001 # ACCGAGAG CTCTCGGT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.8e-002 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 0.578947 0.000000 0.421053 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 84.47 seconds