# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/seqs-shuffled # positives: 755 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/seqs-centered (Sat Jan 18 16:48:32 PST 2020) # negatives: 755 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/seqs-shuffled (Sat Jan 18 16:48:32 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:03:56 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 0.198 G 0.189 T 0.304 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 116 13 8.6e-024 2.7e-019 # GGTTCGA TCGAACC 100 8 5.9e-023 1.9e-018 # GGATCGA TCGATCC 26 5 8.3e-005 2.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 2.7e-019 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.181034 0.000000 0.000000 0.818966 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 CCRTRCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTRCA TGYAYGG 132 20 1.0e-023 3.2e-019 # CCGTACA TGTACGG 58 6 1.8e-012 5.7e-008 # CCATACA TGTATGG 56 9 4.8e-010 1.5e-005 # CCGTGCA TGCACGG 18 2 1.9e-004 5.9e+000 # CCATGCA TGCATGG 18 3 6.9e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 159 E= 3.2e-019 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.515723 0.000000 0.484277 0.000000 0.000000 0.000000 0.000000 1.000000 0.779874 0.000000 0.220126 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTV DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCACTV BAGTGGT 111 15 5.1e-021 1.6e-016 # ACCACTA TAGTGGT 60 7 2.5e-012 8.0e-008 # ACCACTC GAGTGGT 39 6 1.9e-007 5.9e-003 # ACCACTG CAGTGGT 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 1.6e-016 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.535714 0.348214 0.116071 0.000000 MOTIF DCGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST DCGCCTTA TAAGGCGH 59 1 1.7e-017 5.3e-013 # GCGCCTTA TAAGGCGC 27 0 5.9e-009 1.8e-004 # TCGCCTTA TAAGGCGA 19 1 1.8e-005 5.6e-001 # ACGCCTTA TAAGGCGT 13 0 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 5.3e-013 0.220339 0.000000 0.457627 0.322034 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 ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 46 0 7.0e-015 2.2e-010 # ATGGCAAC GTTGCCAT 27 0 5.9e-009 1.8e-004 # ATGGCATC GATGCCAT 19 0 1.7e-006 5.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 2.2e-010 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 0.586957 0.000000 0.000000 0.413043 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 0 4.6e-012 1.4e-007 # GCGCTACC GGTAGCGC 26 0 1.2e-008 3.7e-004 # GCTCTACC GGTAGAGC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.4e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.702703 0.297297 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 CCAACTKG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCAACTKG CMAGTTGG 43 2 1.7e-011 5.2e-007 # CCAACTTG CAAGTTGG 30 1 1.1e-008 3.5e-004 # CCAACTGG CCAGTTGG 13 1 8.8e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 5.2e-007 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.302326 0.697674 0.000000 0.000000 1.000000 0.000000 MOTIF CCAAVAGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCAAVAGA TCTBTTGG 39 3 1.8e-009 5.7e-005 # CCAAAAGA TCTTTTGG 13 0 1.2e-004 3.6e+000 # CCAAGAGA TCTCTTGG 14 1 4.6e-004 1.4e+001 # CCAACAGA TCTGTTGG 12 2 6.3e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 5.7e-005 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 0.000000 0.333333 0.307692 0.358974 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 RAARAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST RAARAAA TTTYTTY 239 141 3.8e-009 1.2e-004 # AAAAAAA TTTTTTT 120 67 2.2e-005 6.8e-001 # AAAGAAA TTTCTTT 89 46 6.8e-005 2.1e+000 # GAAAAAA TTTTTTC 98 54 1.1e-004 3.4e+000 # GAAGAAA TTTCTTC 41 15 2.7e-004 8.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 307 E= 1.2e-004 0.667752 0.000000 0.332248 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.605863 0.000000 0.394137 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 TGGCGYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 40 4 5.5e-009 1.7e-004 # TGGCGCA TGCGCCA 22 2 1.6e-005 4.8e-001 # TGGCGTA TACGCCA 19 2 1.0e-004 3.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 1.7e-004 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 0.000000 1.000000 0.000000 0.000000 0.536585 0.000000 0.463415 1.000000 0.000000 0.000000 0.000000 MOTIF GATTWGAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 38 4 1.9e-008 5.9e-004 # GATTAGAA TTCTAATC 24 1 6.5e-007 2.0e-002 # GATTTGAA TTCAAATC 14 3 6.1e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 5.9e-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 0.615385 0.000000 0.000000 0.384615 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 ACCCABAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 50 10 4.7e-008 1.4e-003 # ACCCACAC GTGTGGGT 28 7 2.2e-004 6.7e+000 # ACCCAGAC GTCTGGGT 14 2 2.0e-003 6.1e+001 # ACCCATAC GTATGGGT 11 1 3.1e-003 9.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 91 E= 1.4e-003 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 0.714286 0.153846 0.131868 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACGGTGM DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 29 2 1.8e-007 5.6e-003 # CACGGTGC GCACCGTG 12 0 2.3e-004 7.1e+000 # CACGGTGA TCACCGTG 17 2 3.4e-004 1.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.6e-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 1.000000 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 0.586207 0.413793 0.000000 0.000000 MOTIF AAGCGWGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 25 1 3.3e-007 1.0e-002 # AAGCGAGA TCTCGCTT 12 0 2.3e-004 7.1e+000 # AAGCGTGA TCACGCTT 13 1 8.8e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-002 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 0.480000 0.000000 0.000000 0.520000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACTATAK DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CACTATAK MTATAGTG 21 0 4.1e-007 1.3e-002 # CACTATAT ATATAGTG 11 0 4.7e-004 1.4e+001 # CACTATAG CTATAGTG 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-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 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 0.476190 0.523810 MOTIF ACTCASG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTCASG CSTGAGT 30 3 5.5e-007 1.7e-002 # ACTCACG CGTGAGT 20 2 5.5e-005 1.7e+000 # ACTCAGG CCTGAGT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.7e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTWGACC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTWGACC GGTCWAGT 27 2 6.6e-007 2.0e-002 # ACTAGACC GGTCTAGT 17 1 6.7e-005 2.0e+000 # ACTTGACC GGTCAAGT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.0e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.629630 0.000000 0.000000 0.370370 0.000000 0.000000 1.000000 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 GCAYGCGA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GCAYGCGA TCGCRTGC 20 0 8.4e-007 2.5e-002 # GCACGCGA TCGCGTGC 10 0 9.5e-004 2.9e+001 # GCATGCGA TCGCATGC 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.5e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 87.51 seconds