# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/seqs-shuffled # positives: 513 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/seqs-centered (Sun Jan 19 00:07:05 PST 2020) # negatives: 513 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/seqs-shuffled (Sun Jan 19 00:07:05 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 00:17:28 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 0.290 C 0.216 G 0.210 T 0.284 MOTIF AGTYGGTW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 80 2 2.9e-023 8.1e-019 # AGTTGGTT AACCAACT 33 1 1.2e-009 3.4e-005 # AGTTGGTA TACCAACT 22 0 1.9e-007 5.3e-003 # AGTCGGTT AACCGACT 14 1 4.5e-004 1.3e+001 # AGTCGGTA TACCGACT 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 80 E= 8.1e-019 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 0.312500 0.000000 0.687500 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.412500 0.000000 0.000000 0.587500 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 80 4 5.1e-021 1.4e-016 # CCGTACAT ATGTACGG 30 0 6.0e-010 1.7e-005 # CCATACAT ATGTATGG 35 3 2.0e-008 5.6e-004 # CCGTACAC GTGTACGG 14 1 4.5e-004 1.3e+001 # CCATACAC GTGTATGG 10 0 9.3e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 95 E= 1.4e-016 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.515789 0.000000 0.484211 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 0.000000 0.263158 0.000000 0.736842 MOTIF GGTTCRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 81 8 7.6e-018 2.1e-013 # GGTTCGA TCGAACC 61 4 3.7e-015 1.0e-010 # GGTTCAA TTGAACC 20 4 6.8e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 81 E= 2.1e-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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.246914 0.000000 0.753086 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTM DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 89 12 2.3e-017 6.2e-013 # ACCACTA TAGTGGT 58 4 2.9e-014 8.0e-010 # ACCACTC GAGTGGT 33 8 4.1e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 91 E= 6.2e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.637363 0.362637 0.000000 0.000000 MOTIF CGCSTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 59 6 5.9e-013 1.6e-008 # CGCCTTA TAAGGCG 45 3 2.7e-011 7.4e-007 # CGCGTTA TAACGCG 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 1.6e-008 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 0.762712 0.237288 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-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 47 2 7.9e-013 2.1e-008 # ATGGCAAC GTTGCCAT 32 0 1.4e-010 3.8e-006 # ATGGCATC GATGCCAT 15 2 1.1e-003 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.1e-008 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 0.680851 0.000000 0.000000 0.319149 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGGNG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGGNG CNCCCAT 70 12 3.5e-012 9.6e-008 # ATGGGTG CACCCAT 33 8 4.1e-005 1.1e+000 # ATGGGCG CGCCCAT 15 1 2.4e-004 6.4e+000 # ATGGGAG CTCCCAT 11 1 3.0e-003 8.2e+001 # ATGGGGG CCCCCAT 12 2 6.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 9.6e-008 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 0.000000 1.000000 0.000000 0.152778 0.208333 0.166667 0.472222 0.000000 0.000000 1.000000 0.000000 MOTIF GCGCTHCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCGCTHCC GGDAGCGC 36 0 7.7e-012 2.1e-007 # GCGCTACC GGTAGCGC 17 0 6.7e-006 1.8e-001 # GCGCTCCC GGGAGCGC 10 0 9.3e-004 2.5e+001 # GCGCTTCC GGAAGCGC 9 0 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 2.1e-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 0.000000 0.000000 0.000000 1.000000 0.472222 0.277778 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGAAAWA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAWA TWTTTCTT 52 8 9.7e-010 2.6e-005 # AAGAAAAA TTTTTCTT 38 6 2.8e-007 7.6e-003 # AAGAAATA TATTTCTT 16 2 6.0e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 2.6e-005 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.703704 0.000000 0.000000 0.296296 1.000000 0.000000 0.000000 0.000000 MOTIF ATMCAAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATMCAAC GTTGKAT 50 8 3.2e-009 8.6e-005 # ATACAAC GTTGTAT 29 4 4.0e-006 1.1e-001 # ATCCAAC GTTGGAT 21 4 4.0e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 8.6e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.566038 0.433962 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 MOTIF CCASAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCASAC GTSTGG 110 44 4.3e-009 1.1e-004 # CCACAC GTGTGG 77 31 1.8e-006 4.7e-002 # CCAGAC GTCTGG 36 16 3.2e-003 8.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 204 E= 1.1e-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 0.000000 0.823529 0.176471 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GRTCTCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GRTCTCCA TGGAGAYC 27 0 5.2e-009 1.4e-004 # GGTCTCCA TGGAGACC 17 0 6.7e-006 1.8e-001 # GATCTCCA TGGAGATC 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.4e-004 0.000000 0.000000 1.000000 0.000000 0.370370 0.000000 0.629630 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CYATGGCC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CYATGGCC GGCCATRG 25 0 2.2e-008 5.8e-004 # CTATGGCC GGCCATAG 15 0 2.8e-005 7.2e-001 # CCATGGCC GGCCATGG 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 5.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 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 0.000000 1.000000 0.000000 0.000000 MOTIF AATCTTYT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AATCTTYT ARAAGATT 34 3 3.8e-008 1.0e-003 # AATCTTCT AGAAGATT 17 0 6.7e-006 1.7e-001 # AATCTTTT AAAAGATT 17 3 1.2e-003 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.0e-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 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 0.500000 0.000000 0.000000 0.000000 1.000000 MOTIF GCGCAAK DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCGCAAK MTTGCGC 34 3 3.8e-008 1.0e-003 # GCGCAAG CTTGCGC 20 0 7.9e-007 2.1e-002 # GCGCAAT ATTGCGC 17 3 1.2e-003 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.0e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.567568 0.432432 MOTIF AGTCAKAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 27 1 7.8e-008 2.0e-003 # AGTCAGAC GTCTGACT 13 0 1.1e-004 2.9e+000 # AGTCATAC GTATGACT 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.0e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.481481 0.518519 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGRTTAG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AAGRTTAG CTAAYCTT 23 0 9.3e-008 2.4e-003 # AAGGTTAG CTAACCTT 12 0 2.3e-004 6.0e+000 # AAGATTAG CTAATCTT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.4e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.478261 0.000000 0.521739 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 0.000000 1.000000 0.000000 MOTIF AAGCGWGA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 26 1 1.5e-007 4.0e-003 # AAGCGAGA TCTCGCTT 12 0 2.3e-004 6.0e+000 # AAGCGTGA TCACGCTT 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-003 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 0.461538 0.000000 0.000000 0.538462 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAASAG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CCAASAG CTSTTGG 34 4 1.9e-007 5.0e-003 # CCAAGAG CTCTTGG 20 3 2.1e-004 5.5e+000 # CCAACAG CTGTTGG 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 5.0e-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 0.411765 0.588235 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCGTGMTA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 26 2 1.1e-006 3.0e-002 # CCGTGATA TATCACGG 14 1 4.5e-004 1.2e+001 # CCGTGCTA TAGCACGG 12 1 1.6e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.0e-002 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 0.538462 0.461538 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGCTAYC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST GGCTAYC GRTAGCC 26 2 1.1e-006 3.0e-002 # GGCTATC GATAGCC 18 2 1.8e-004 4.6e+000 # GGCTACC GGTAGCC 8 0 3.8e-003 9.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.0e-002 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.307692 0.000000 0.692308 0.000000 1.000000 0.000000 0.000000 MOTIF CGCGRGC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST CGCGRGC GCYCGCG 19 0 1.6e-006 4.2e-002 # CGCGAGC GCTCGCG 11 0 4.6e-004 1.2e+001 # CGCGGGC GCCCGCG 8 0 3.8e-003 9.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 19 E= 4.2e-002 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 0.578947 0.000000 0.421053 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCGTGCSA DREME-23 # Word RC Word Pos Neg P-value E-value # BEST GCGTGCSA TSGCACGC 19 0 1.6e-006 4.2e-002 # GCGTGCGA TCGCACGC 11 0 4.6e-004 1.2e+001 # GCGTGCCA TGGCACGC 8 0 3.8e-003 9.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.2e-002 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 1.000000 0.000000 0.000000 0.000000 0.421053 0.578947 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTSACG DREME-24 # Word RC Word Pos Neg P-value E-value # BEST ACTSACG CGTSAGT 28 3 1.7e-006 4.4e-002 # ACTGACG CGTCAGT 14 0 5.6e-005 1.4e+000 # ACTCACG CGTGAGT 14 3 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 4.4e-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 0.500000 0.500000 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 # Stopping reason: E-value threshold exceeded # Running time: 79.69 seconds