# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/seqs-shuffled # positives: 590 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/seqs-centered (Sat Jan 18 05:04:25 PST 2020) # negatives: 590 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/seqs-shuffled (Sat Jan 18 05:04:25 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:18:53 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 0.293 C 0.213 G 0.205 T 0.289 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 135 5 9.6e-038 2.8e-033 # GGTTCGA TCGAACC 110 1 1.7e-034 5.0e-030 # GGCTCGA TCGAGCC 24 1 6.2e-007 1.8e-002 # GGATCGA TCGATCC 27 3 3.3e-006 9.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 139 E= 2.8e-033 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.187050 0.107914 0.000000 0.705036 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 131 13 6.5e-029 1.9e-024 # CCGTACA TGTACGG 55 4 2.7e-013 7.7e-009 # CCATACA TGTATGG 58 6 1.4e-012 3.9e-008 # CCGTGCA TGCACGG 20 2 5.3e-005 1.5e+000 # CCATGCA TGCATGG 17 2 3.3e-004 9.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 158 E= 1.9e-024 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.512658 0.000000 0.487342 0.000000 0.000000 0.000000 0.000000 1.000000 0.772152 0.000000 0.227848 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTM DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 87 6 4.2e-021 1.2e-016 # ACCACTA TAGTGGT 53 3 1.4e-013 3.8e-009 # ACCACTC GAGTGGT 35 3 2.2e-008 6.1e-004 letter-probability matrix: alength= 4 w= 7 nsites= 89 E= 1.2e-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 0.595506 0.404494 0.000000 0.000000 MOTIF TAAGGCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 84 8 1.5e-018 4.2e-014 # TAAGGCG CGCCTTA 70 5 7.4e-017 2.1e-012 # TAAGGCA TGCCTTA 17 3 1.2e-003 3.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 87 E= 4.2e-014 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.195402 0.000000 0.804598 0.000000 MOTIF CAACTKGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 51 1 4.0e-015 1.1e-010 # CAACTTGG CCAAGTTG 39 1 2.0e-011 5.6e-007 # CAACTGGG CCCAGTTG 12 0 2.3e-004 6.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 1.1e-010 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 0.235294 0.764706 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 45 0 1.2e-014 3.3e-010 # GCGCTACC GGTAGCGC 34 0 3.6e-011 9.9e-007 # GCTCTACC GGTAGAGC 11 0 4.7e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 3.3e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.755556 0.244444 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 AARAAAW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 226 113 2.0e-013 5.5e-009 # AAAAAAA TTTTTTT 118 54 7.7e-008 2.1e-003 # AAGAAAA TTTTCTT 71 23 1.3e-007 3.5e-003 # AAGAAAT ATTTCTT 45 14 2.1e-005 5.9e-001 # AAAAAAT ATTTTTT 104 61 2.0e-004 5.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 292 E= 5.5e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.626712 0.000000 0.373288 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 0.537671 0.000000 0.000000 0.462329 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 2 1.1e-010 3.0e-006 # ATGGCAAC GTTGCCAT 24 1 6.2e-007 1.7e-002 # ATGGCATC GATGCCAT 16 1 1.3e-004 3.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.0e-006 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 0.600000 0.000000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 MOTIF GATTWGAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 38 2 4.3e-010 1.2e-005 # GATTAGAA TTCTAATC 23 0 9.6e-008 2.6e-003 # GATTTGAA TTCAAATC 15 2 1.1e-003 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.2e-005 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 0.605263 0.000000 0.000000 0.394737 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 ACSCAGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACSCAGA TCTGSGT 37 2 8.4e-010 2.3e-005 # ACGCAGA TCTGCGT 17 0 6.8e-006 1.9e-001 # ACCCAGA TCTGGGT 20 2 5.3e-005 1.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.3e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.540541 0.459459 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAKCTCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 49 7 1.7e-009 4.7e-005 # TAGCTCA TGAGCTA 25 2 2.3e-006 6.2e-002 # TATCTCA TGAGATA 24 5 2.3e-004 6.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 4.7e-005 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.471698 0.528302 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 MOTIF CASACGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CASACGC GCGTSTG 41 4 2.6e-009 7.0e-005 # CACACGC GCGTGTG 25 3 1.1e-005 3.0e-001 # CAGACGC GCGTCTG 16 1 1.3e-004 3.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 7.0e-005 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.609756 0.390244 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 MOTIF CCAAVAGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCAAVAGA TCTBTTGG 40 4 4.9e-009 1.3e-004 # CCAAGAGA TCTCTTGG 16 1 1.3e-004 3.4e+000 # CCAACAGA TCTGTTGG 14 2 2.0e-003 5.3e+001 # CCAAAAGA TCTTTTGG 10 1 5.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.3e-004 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 0.250000 0.350000 0.400000 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 AYTGCGCC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AYTGCGCC GGCGCART 27 0 5.5e-009 1.5e-004 # ACTGCGCC GGCGCAGT 14 0 5.6e-005 1.5e+000 # ATTGCGCC GGCGCAAT 13 0 1.1e-004 3.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.5e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.518519 0.000000 0.481481 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTCTCSCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSCA TGSGAGAG 27 0 5.5e-009 1.5e-004 # CTCTCCCA TGGGAGAG 20 0 8.1e-007 2.2e-002 # CTCTCGCA TGCGAGAG 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.5e-004 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.740741 0.259259 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCTCCACR DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TCTCCACR YGTGGAGA 27 0 5.5e-009 1.5e-004 # TCTCCACG CGTGGAGA 15 0 2.8e-005 7.5e-001 # TCTCCACA TGTGGAGA 12 0 2.3e-004 6.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.5e-004 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.444444 0.000000 0.555556 0.000000 MOTIF ATTAASAG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 32 3 1.5e-007 3.9e-003 # ATTAAGAG CTCTTAAT 21 2 2.8e-005 7.6e-001 # ATTAACAG CTGTTAAT 11 1 3.1e-003 8.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 3.9e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.343750 0.656250 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCGTGSC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CGCGTGSC GSCACGCG 22 0 2.0e-007 5.2e-003 # CGCGTGCC GGCACGCG 12 0 2.3e-004 6.2e+000 # CGCGTGGC GCCACGCG 10 0 9.4e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.2e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.454545 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGTTAYAC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CGTTAYAC GTRTAACG 22 0 2.0e-007 5.2e-003 # CGTTACAC GTGTAACG 14 0 5.6e-005 1.5e+000 # CGTTATAC GTATAACG 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.2e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.636364 0.000000 0.363636 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AWGTGATA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST AWGTGATA TATCACWT 28 2 3.3e-007 8.7e-003 # ATGTGATA TATCACAT 18 1 3.4e-005 9.1e-001 # AAGTGATA TATCACTT 10 1 5.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 8.7e-003 1.000000 0.000000 0.000000 0.000000 0.357143 0.000000 0.000000 0.642857 0.000000 0.000000 1.000000 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCCGCGY DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CCCGCGY RCGCGGG 27 2 6.2e-007 1.7e-002 # CCCGCGT ACGCGGG 11 0 4.7e-004 1.2e+001 # CCCGCGC GCGCGGG 16 2 6.1e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 1.7e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.592593 0.000000 0.407407 MOTIF ACCCAHAC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST ACCCAHAC GTDTGGGT 56 15 2.5e-007 6.6e-003 # ACCCACAC GTGTGGGT 31 11 1.2e-003 3.2e+001 # ACCCAAAC GTTTGGGT 15 3 3.6e-003 9.5e+001 # ACCCATAC GTATGGGT 10 1 5.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 93 E= 6.6e-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 0.161290 0.720430 0.000000 0.118280 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACYCCGAT DREME-23 # Word RC Word Pos Neg P-value E-value # BEST ACYCCGAT ATCGGRGT 20 0 8.1e-007 2.1e-002 # ACCCCGAT ATCGGGGT 10 0 9.4e-004 2.5e+001 # ACTCCGAT ATCGGAGT 10 0 9.4e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.1e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 0.000000 0.000000 0.000000 1.000000 MOTIF ATCKTGA DREME-24 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 51 14 1.2e-006 3.2e-002 # ATCTTGA TCAAGAT 30 8 1.9e-004 5.1e+000 # ATCGTGA TCACGAT 21 6 2.7e-003 7.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 3.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.403846 0.596154 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 88.22 seconds