# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ARR1/seqs-shuffled # positives: 797 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ARR1/seqs-centered (Sat Jan 18 04:02:29 PST 2020) # negatives: 797 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ARR1/seqs-shuffled (Sat Jan 18 04:02:29 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 04:17:34 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 0.298 C 0.206 G 0.201 T 0.295 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 123 12 1.8e-026 5.8e-022 # GGTTCGA TCGAACC 99 9 8.9e-022 2.9e-017 # GGATCGA TCGATCC 32 3 1.6e-007 5.3e-003 letter-probability matrix: alength= 4 w= 7 nsites= 124 E= 5.8e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.233871 0.000000 0.000000 0.766129 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 117 13 5.5e-024 1.8e-019 # AGTGGTT AACCACT 80 4 1.6e-020 5.2e-016 # AGTGGTA TACCACT 51 9 8.8e-009 2.9e-004 letter-probability matrix: alength= 4 w= 7 nsites= 137 E= 1.8e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.394161 0.000000 0.000000 0.605839 MOTIF AYCCRTAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 88 4 5.8e-023 1.9e-018 # ACCCATAC GTATGGGT 45 2 4.5e-012 1.5e-007 # ATCCGTAC GTACGGAT 30 0 7.1e-010 2.3e-005 # ACCCGTAC GTACGGGT 13 1 8.8e-004 2.9e+001 # ATCCATAC GTATGGAT 12 1 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 104 E= 1.9e-018 1.000000 0.000000 0.000000 0.000000 0.000000 0.567308 0.000000 0.432692 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.557692 0.000000 0.442308 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 MOTIF ACCRACT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 90 13 1.7e-016 5.6e-012 # ACCAACT AGTTGGT 62 10 5.6e-011 1.8e-006 # ACCGACT AGTCGGT 28 3 1.9e-006 6.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 5.6e-012 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.688889 0.000000 0.311111 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 MOTIF ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 42 3 2.7e-010 8.7e-006 # ATGGCAAC GTTGCCAT 27 2 6.7e-007 2.2e-002 # ATGGCATC GATGCCAT 15 1 2.4e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 8.7e-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 0.642857 0.000000 0.000000 0.357143 0.000000 1.000000 0.000000 0.000000 MOTIF ACCCAVAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 58 10 5.6e-010 1.8e-005 # ACCCAGAC GTCTGGGT 17 0 7.0e-006 2.3e-001 # ACCCACAC GTGTGGGT 31 8 1.2e-004 4.0e+000 # ACCCAAAC GTTTGGGT 14 2 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 92 E= 1.8e-005 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 0.152174 0.663043 0.184783 0.000000 1.000000 0.000000 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 274 167 1.3e-009 4.2e-005 # AAGAAAA TTTTCTT 92 47 4.2e-005 1.3e+000 # AAAAAAT ATTTTTT 119 70 9.4e-005 3.0e+000 # AAAAAAA TTTTTTT 132 81 1.1e-004 3.6e+000 # AAGAAAT ATTTCTT 53 26 1.2e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 355 E= 4.2e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.605634 0.000000 0.394366 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 0.577465 0.000000 0.000000 0.422535 MOTIF CGSCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 104 38 3.1e-009 1.0e-004 # CGGCCA TGGCCG 55 19 1.1e-005 3.5e-001 # CGCCCA TGGGCG 49 21 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 108 E= 1.0e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.490741 0.509259 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 CCGTGSA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 49 8 7.9e-009 2.5e-004 # CCGTGGA TCCACGG 26 4 2.6e-005 8.2e-001 # CCGTGCA TGCACGG 23 4 1.4e-004 4.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 2.5e-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 0.000000 0.469388 0.530612 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSACA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGCSACA TGTSGCG 38 4 2.0e-008 6.2e-004 # CGCGACA TGTCGCG 15 0 2.9e-005 9.1e-001 # CGCCACA TGTGGCG 23 4 1.4e-004 4.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 6.2e-004 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 0.605263 0.394737 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 MOTIF CSCATGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CSCATGC GCATGSG 45 7 2.2e-008 7.0e-004 # CCCATGC GCATGGG 35 6 1.9e-006 5.9e-002 # CGCATGC GCATGCG 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 7.0e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.222222 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 32 2 2.6e-008 8.3e-004 # GTGATAGT ACTATCAC 17 1 6.7e-005 2.1e+000 # GTGATAGC GCTATCAC 15 1 2.4e-004 7.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.3e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.468750 0.000000 0.531250 MOTIF CGCSTTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 58 14 4.4e-008 1.4e-003 # CGCCTTA TAAGGCG 40 10 9.0e-006 2.8e-001 # CGCGTTA TAACGCG 18 4 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 1.4e-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 0.689655 0.310345 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 ATATBTCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATATBTCA TGAVATAT 32 2 2.6e-008 8.2e-004 # ATATGTCA TGACATAT 11 0 4.7e-004 1.5e+001 # ATATCTCA TGAGATAT 13 1 8.8e-004 2.8e+001 # ATATTTCA TGAAATAT 11 1 3.1e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.2e-004 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 0.000000 1.000000 0.000000 0.406250 0.250000 0.343750 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 CGTMTGAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGTMTGAC GTCAKACG 28 1 4.5e-008 1.4e-003 # CGTATGAC GTCATACG 17 0 7.0e-006 2.2e-001 # CGTCTGAC GTCAGACG 11 1 3.1e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.4e-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 0.607143 0.392857 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 1.000000 0.000000 0.000000 MOTIF AGACTG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGACTG CAGTCT 47 10 2.4e-007 7.6e-003 # AGACTG CAGTCT 47 10 2.4e-007 7.6e-003 letter-probability matrix: alength= 4 w= 6 nsites= 47 E= 7.6e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGAAACAA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AGAAACAA TTGTTTCT 24 1 6.6e-007 2.1e-002 # AGAAACAA TTGTTTCT 24 1 6.6e-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 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATMTTS DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AATMTTS SAAKATT 107 39 1.7e-009 5.2e-005 # AATCTTC GAAGATT 32 11 8.3e-004 2.6e+001 # AATATTG CAATATT 27 8 8.4e-004 2.6e+001 # AATATTC GAATATT 26 8 1.3e-003 4.1e+001 # AATCTTG CAAGATT 31 13 4.3e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 114 E= 5.2e-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 0.447368 0.552632 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.508772 0.491228 0.000000 MOTIF GGAWTTGA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST GGAWTTGA TCAAWTCC 31 3 3.0e-007 9.3e-003 # GGAATTGA TCAATTCC 18 1 3.5e-005 1.1e+000 # GGATTTGA TCAAATCC 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 9.3e-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 0.580645 0.000000 0.000000 0.419355 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 # Stopping reason: E-value threshold exceeded # Running time: 96.12 seconds