# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/seqs-shuffled # positives: 1734 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/seqs-centered (Sat Jan 18 12:11:14 PST 2020) # negatives: 1734 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/seqs-shuffled (Sat Jan 18 12:11:14 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 12:21:01 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 0.296 C 0.201 G 0.205 T 0.298 MOTIF AAGWWG DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AAGWWG CWWCTT 753 436 3.5e-030 1.3e-025 # AAGAAG CTTCTT 347 160 8.6e-020 3.3e-015 # AAGATG CATCTT 216 117 6.5e-009 2.5e-004 # AAGTTG CAACTT 222 135 7.0e-007 2.6e-002 # AAGTAG CTACTT 122 71 9.9e-005 3.7e+000 letter-probability matrix: alength= 4 w= 6 nsites= 989 E= 1.3e-025 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.647118 0.000000 0.000000 0.352882 0.540950 0.000000 0.000000 0.459050 0.000000 0.000000 1.000000 0.000000 MOTIF AVCDTC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AVCDTC GAHGBT 797 514 2.0e-023 7.4e-019 # AGCTTC GAAGCT 126 53 1.1e-008 4.0e-004 # AGCGTC GACGCT 83 28 5.3e-008 2.0e-003 # ACCGTC GACGGT 86 34 7.6e-007 2.8e-002 # AACTTC GAAGTT 130 84 7.2e-004 2.7e+001 # AGCATC GATGCT 100 63 1.9e-003 7.0e+001 # ACCATC GATGGT 112 75 3.3e-003 1.2e+002 # ACCTTC GAAGGT 134 94 3.7e-003 1.4e+002 # AACGTC GACGTT 84 53 4.3e-003 1.6e+002 # AACATC GATGTT 150 110 5.9e-003 2.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 1064 E= 7.4e-019 1.000000 0.000000 0.000000 0.000000 0.375000 0.320489 0.304511 0.000000 0.000000 1.000000 0.000000 0.000000 0.354323 0.000000 0.239662 0.406015 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGTGVTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTGVTA TABCACC 141 33 3.6e-018 1.3e-013 # GGTGGTA TACCACC 64 17 5.2e-008 1.9e-003 # GGTGATA TATCACC 44 8 1.7e-007 6.0e-003 # GGTGCTA TAGCACC 33 8 5.1e-005 1.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 141 E= 1.3e-013 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 0.312057 0.234043 0.453901 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RDCCAA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RDCCAA TTGGHY 683 456 1.3e-016 4.6e-012 # GGCCAA TTGGCC 102 37 8.5e-009 3.1e-004 # AACCAA TTGGTT 229 135 1.1e-007 4.0e-003 # ATCCAA TTGGAT 176 107 1.1e-005 4.1e-001 # GACCAA TTGGTC 148 90 6.0e-005 2.2e+000 # GTCCAA TTGGAC 114 75 2.2e-003 7.8e+001 # AGCCAA TTGGCT 105 72 6.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 929 E= 4.6e-012 0.598493 0.000000 0.401507 0.000000 0.423036 0.000000 0.240043 0.336921 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 MOTIF CGSTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGSTA TASCG 352 181 3.7e-016 1.3e-011 # CGGTA TACCG 228 105 6.0e-013 2.1e-008 # CGCTA TAGCG 139 82 4.6e-005 1.6e+000 letter-probability matrix: alength= 4 w= 5 nsites= 394 E= 1.3e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.362944 0.637056 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGMAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGMAA TTKCCAT 147 47 3.8e-014 1.3e-009 # ATGGCAA TTGCCAT 85 16 3.8e-013 1.3e-008 # ATGGAAA TTTCCAT 76 32 1.0e-005 3.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 161 E= 1.3e-009 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 0.472050 0.527950 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCASC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCASC GSTGGT 202 94 2.5e-011 8.6e-007 # ACCAGC GCTGGT 103 43 2.1e-007 7.3e-003 # ACCACC GGTGGT 110 52 1.8e-006 6.2e-002 letter-probability matrix: alength= 4 w= 6 nsites= 231 E= 8.6e-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 0.519481 0.480519 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTTCTTS DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATTTCTTS SAAGAAAT 81 19 7.7e-011 2.6e-006 # ATTTCTTC GAAGAAAT 47 9 1.0e-007 3.5e-003 # ATTTCTTG CAAGAAAT 34 10 1.8e-004 6.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 81 E= 2.6e-006 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.580247 0.419753 0.000000 MOTIF AGAAAGG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGAAAGG CCTTTCT 79 20 5.4e-010 1.8e-005 # AGAAAGG CCTTTCT 79 20 5.4e-010 1.8e-005 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 1.8e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AATTRGGT DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AATTRGGT ACCYAATT 47 6 2.3e-009 7.7e-005 # AATTGGGT ACCCAATT 27 3 3.9e-006 1.3e-001 # AATTAGGT ACCTAATT 20 3 2.3e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 7.7e-005 1.000000 0.000000 0.000000 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 0.425532 0.000000 0.574468 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 MOTIF CTGCTRC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTGCTRC GYAGCAG 59 12 4.9e-009 1.7e-004 # CTGCTGC GCAGCAG 41 8 8.4e-007 2.8e-002 # CTGCTAC GTAGCAG 18 4 2.1e-003 7.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 1.7e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.305085 0.000000 0.694915 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GYTCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GYTCCA TGGARC 223 122 5.7e-009 1.9e-004 # GTTCCA TGGAAC 140 73 1.3e-006 4.3e-002 # GCTCCA TGGAGC 83 50 2.2e-003 7.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 232 E= 1.9e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.383621 0.000000 0.616379 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 MOTIF CCTTGDTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCTTGDTA TAHCAAGG 53 11 3.9e-008 1.3e-003 # CCTTGATA TATCAAGG 19 2 1.1e-004 3.6e+000 # CCTTGTTA TAACAAGG 20 4 7.4e-004 2.5e+001 # CCTTGGTA TACCAAGG 18 5 5.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 1.3e-003 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 0.000000 0.000000 1.000000 0.000000 0.351852 0.000000 0.277778 0.370370 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGAYGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGAYGA TCRTCG 148 71 4.2e-008 1.4e-003 # CGATGA TCATCG 96 41 9.4e-007 3.1e-002 # CGACGA TCGTCG 54 30 5.3e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 151 E= 1.4e-003 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 0.350993 0.000000 0.649007 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAGCTGGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CAGCTGGC GCCAGCTG 24 0 5.5e-008 1.8e-003 # CAGCTGGC GCCAGCTG 24 0 5.5e-008 1.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-003 0.000000 1.000000 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 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 MOTIF CWTACC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CWTACC GGTAWG 143 68 5.5e-008 1.8e-003 # CTTACC GGTAAG 82 36 1.0e-005 3.3e-001 # CATACC GGTATG 65 32 4.5e-004 1.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 148 E= 1.8e-003 0.000000 1.000000 0.000000 0.000000 0.445946 0.000000 0.000000 0.554054 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 CCAASAGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCAASAGA TCTSTTGG 33 3 1.0e-007 3.3e-003 # CCAAGAGA TCTCTTGG 19 1 1.9e-005 6.3e-001 # CCAACAGA TCTGTTGG 14 2 2.1e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 3.3e-003 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 0.424242 0.575758 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 CCAGAGGW DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CCAGAGGW WCCTCTGG 30 2 1.1e-007 3.6e-003 # CCAGAGGA TCCTCTGG 15 1 2.5e-004 8.3e+000 # CCAGAGGT ACCTCTGG 15 1 2.5e-004 8.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.6e-003 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 0.000000 1.000000 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 0.500000 0.000000 0.000000 0.500000 MOTIF AATKGCGT DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AATKGCGT ACGCMATT 29 2 2.1e-007 6.9e-003 # AATGGCGT ACGCCATT 20 2 5.8e-005 1.9e+000 # AATTGCGT ACGCAATT 9 0 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.9e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.689655 0.310345 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 MOTIF CAAKACC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CAAKACC GGTMTTG 69 22 3.0e-007 9.7e-003 # CAAGACC GGTCTTG 44 16 1.8e-004 5.8e+000 # CAATACC GGTATTG 25 6 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 9.7e-003 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 0.652778 0.347222 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 ACSGCTTC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST ACSGCTTC GAAGCSGT 24 1 7.2e-007 2.4e-002 # ACGGCTTC GAAGCCGT 16 1 1.3e-004 4.4e+000 # ACCGCTTC GAAGCGGT 8 0 3.9e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AYATACA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST AYATACA TGTATRT 92 38 7.8e-007 2.6e-002 # ACATACA TGTATGT 44 15 9.0e-005 3.0e+000 # ATATACA TGTATAT 49 26 4.9e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 2.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.484848 0.000000 0.515152 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAAGTCK DREME-23 # Word RC Word Pos Neg P-value E-value # BEST CCAAGTCK MGACTTGG 26 2 1.4e-006 4.6e-002 # CCAAGTCG CGACTTGG 14 0 5.9e-005 1.9e+000 # CCAAGTCT AGACTTGG 12 2 6.4e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.6e-002 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 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 0.538462 0.461538 # Stopping reason: E-value threshold exceeded # Running time: 219.60 seconds