# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/seqs-shuffled # positives: 902 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/seqs-centered (Sat Jan 18 03:44:07 PST 2020) # negatives: 902 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/seqs-shuffled (Sat Jan 18 03:44:07 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:59:55 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 0.193 G 0.188 T 0.311 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 131 9 4.0e-031 1.3e-026 # GGTTCGA TCGAACC 109 6 3.2e-027 1.1e-022 # GGATCGA TCGATCC 33 3 8.9e-008 3.0e-003 letter-probability matrix: alength= 4 w= 7 nsites= 132 E= 1.3e-026 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.219697 0.000000 0.000000 0.780303 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 92 9 1.2e-019 4.1e-015 # TGTACGGA TCCGTACA 37 0 5.0e-012 1.7e-007 # TGTATGGG CCCATACA 40 5 2.8e-008 9.3e-004 # TGTACGGG CCCGTACA 12 1 1.7e-003 5.5e+001 # TGTATGGA TCCATACA 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 107 E= 4.1e-015 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 0.476636 0.000000 0.523364 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.514019 0.000000 0.485981 0.000000 MOTIF CTYGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 73 4 2.4e-018 8.0e-014 # CTCGGCC GGCCGAG 35 0 2.1e-011 6.9e-007 # CTTGGCC GGCCAAG 48 4 3.8e-011 1.3e-006 letter-probability matrix: alength= 4 w= 7 nsites= 73 E= 8.0e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.424658 0.000000 0.575342 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 1.000000 0.000000 0.000000 MOTIF ARAAAWA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ARAAAWA TWTTTYT 347 187 8.1e-017 2.7e-012 # AAAAAAA TTTTTTT 175 90 9.2e-009 3.0e-004 # AGAAAAA TTTTTCT 128 57 2.0e-008 6.6e-004 # AAAAATA TATTTTT 115 63 2.6e-005 8.4e-001 # AGAAATA TATTTCT 51 26 2.4e-003 8.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 445 E= 2.7e-012 1.000000 0.000000 0.000000 0.000000 0.635955 0.000000 0.364045 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 0.662921 0.000000 0.000000 0.337079 1.000000 0.000000 0.000000 0.000000 MOTIF CTWAACCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTWAACCA TGGTTWAG 57 1 8.5e-017 2.8e-012 # CTTAACCA TGGTTAAG 43 0 6.8e-014 2.2e-009 # CTAAACCA TGGTTTAG 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 2.8e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.245614 0.000000 0.000000 0.754386 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 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 50 2 1.6e-013 5.2e-009 # GCGCTACC GGTAGCGC 34 0 4.2e-011 1.4e-006 # GCTCTACC GGTAGAGC 16 2 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 5.2e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.680000 0.320000 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 GCGCM DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCGCM KGCGC 165 71 2.5e-011 8.2e-007 # GCGCA TGCGC 109 39 8.5e-010 2.8e-005 # GCGCC GGCGC 103 43 1.2e-007 4.1e-003 letter-probability matrix: alength= 4 w= 5 nsites= 181 E= 8.2e-007 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 0.530387 0.469613 0.000000 0.000000 MOTIF ACATYAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACATYAC GTRATGT 66 12 7.6e-011 2.4e-006 # ACATCAC GTGATGT 35 3 2.5e-008 8.1e-004 # ACATTAC GTAATGT 31 9 3.0e-004 9.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 2.4e-006 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 0.000000 1.000000 0.000000 0.530303 0.000000 0.469697 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 42 3 2.8e-010 9.1e-006 # ATGGCAAC GTTGCCAT 26 1 1.8e-007 5.6e-003 # ATGGCATC GATGCCAT 16 2 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 9.1e-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 0.619048 0.000000 0.000000 0.380952 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGGTTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTA TAACCACT 31 0 3.6e-010 1.1e-005 # AGTGGTTA TAACCACT 31 0 3.6e-010 1.1e-005 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.1e-005 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CDTTGGGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CDTTGGGC GCCCAAHG 32 1 3.0e-009 9.7e-005 # CTTTGGGC GCCCAAAG 14 0 5.8e-005 1.9e+000 # CGTTGGGC GCCCAACG 11 1 3.1e-003 9.9e+001 # CATTGGGC GCCCAATG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.7e-005 0.000000 1.000000 0.000000 0.000000 0.218750 0.000000 0.343750 0.437500 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTCYCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTCYCCA TGGRGAC 45 6 6.0e-009 1.9e-004 # GTCTCCA TGGAGAC 23 3 3.9e-005 1.3e+000 # GTCCCCA TGGGGAC 22 3 7.1e-005 2.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 1.9e-004 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 0.488889 0.000000 0.511111 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 GARTCATA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GARTCATA TATGAYTC 31 1 6.0e-009 1.9e-004 # GAATCATA TATGATTC 16 0 1.4e-005 4.5e-001 # GAGTCATA TATGACTC 15 1 2.5e-004 7.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.9e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.516129 0.000000 0.483871 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTGMTA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 26 0 1.2e-008 4.0e-004 # CCGTGATA TATCACGG 15 0 2.9e-005 9.2e-001 # CCGTGCTA TAGCACGG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.576923 0.423077 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTAGACC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTAGACC GGTCTAGT 29 1 2.3e-008 7.4e-004 # ACTAGACC GGTCTAGT 29 1 2.3e-008 7.4e-004 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.4e-004 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 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 ACCCAVAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 64 17 3.8e-008 1.2e-003 # ACCCACAC GTGTGGGT 34 11 3.6e-004 1.1e+001 # ACCCAGAC GTCTGGGT 16 2 6.2e-004 2.0e+001 # ACCCAAAC GTTTGGGT 18 4 2.1e-003 6.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 113 E= 1.2e-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 0.159292 0.699115 0.141593 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCAAMAGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCAAMAGA TCTKTTGG 28 1 4.6e-008 1.5e-003 # CCAACAGA TCTGTTGG 14 0 5.8e-005 1.8e+000 # CCAAAAGA TCTTTTGG 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.5e-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 0.500000 0.500000 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 TRTAYA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST TRTAYA TRTAYA 181 101 1.3e-007 4.1e-003 # TATACA TGTATA 89 48 1.7e-004 5.5e+000 # TATATA TATATA 88 49 3.4e-004 1.1e+001 # TGTACA TGTACA 37 16 2.4e-003 7.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 214 E= 4.1e-003 0.000000 0.000000 0.000000 1.000000 0.607477 0.000000 0.392523 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.359813 0.000000 0.640187 1.000000 0.000000 0.000000 0.000000 MOTIF ACAAAGCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACAAAGCA TGCTTTGT 23 0 1.0e-007 3.2e-003 # ACAAAGCA TGCTTTGT 23 0 1.0e-007 3.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-003 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 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 MOTIF CTCTCSC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSC GSGAGAG 29 2 1.9e-007 6.0e-003 # CTCTCCC GGGAGAG 15 1 2.5e-004 7.7e+000 # CTCTCGC GCGAGAG 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 6.0e-003 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 0.517241 0.482759 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-21 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 22 0 2.1e-007 6.6e-003 # ACTGAGCT AGCTCAGT 22 0 2.1e-007 6.6e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.6e-003 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 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 MOTIF ATRCTAAG DREME-22 # Word RC Word Pos Neg P-value E-value # BEST ATRCTAAG CTTAGYAT 22 0 2.1e-007 6.6e-003 # ATGCTAAG CTTAGCAT 13 0 1.2e-004 3.7e+000 # ATACTAAG CTTAGTAT 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.6e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.409091 0.000000 0.590909 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GGAWTTGA DREME-23 # Word RC Word Pos Neg P-value E-value # BEST GGAWTTGA TCAAWTCC 36 5 3.0e-007 9.4e-003 # GGAATTGA TCAATTCC 19 1 1.8e-005 5.8e-001 # GGATTTGA TCAAATCC 17 4 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 9.4e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.527778 0.000000 0.000000 0.472222 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCAKAAG DREME-24 # Word RC Word Pos Neg P-value E-value # BEST ATCAKAAG CTTMTGAT 30 3 5.7e-007 1.8e-002 # ATCATAAG CTTATGAT 16 1 1.3e-004 4.0e+000 # ATCAGAAG CTTCTGAT 14 2 2.0e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.8e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.466667 0.533333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACACGCCC DREME-25 # Word RC Word Pos Neg P-value E-value # BEST ACACGCCC GGGCGTGT 24 1 6.7e-007 2.1e-002 # ACACGCCC GGGCGTGT 24 1 6.7e-007 2.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF SATCGTGA DREME-26 # Word RC Word Pos Neg P-value E-value # BEST SATCGTGA TCACGATS 20 0 8.6e-007 2.7e-002 # CATCGTGA TCACGATG 13 0 1.2e-004 3.6e+000 # GATCGTGA TCACGATC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-002 0.000000 0.650000 0.350000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 142.09 seconds