# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/seqs-shuffled # positives: 863 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/seqs-centered (Sun Jan 19 03:46:11 PST 2020) # negatives: 863 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/seqs-shuffled (Sun Jan 19 03:46:11 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 04:01:54 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 0.312 C 0.194 G 0.186 T 0.308 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 141 19 1.4e-026 4.7e-022 # GGTTCGA TCGAACC 103 7 1.6e-024 5.1e-020 # GGTTCAA TTGAACC 39 12 8.0e-005 2.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 142 E= 4.7e-022 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 0.274648 0.000000 0.725352 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 8 1.9e-020 6.1e-016 # TGTACGGA TCCGTACA 38 3 3.7e-009 1.2e-004 # TGTATGGG CCCATACA 38 4 2.0e-008 6.6e-004 # TGTATGGA TCCATACA 13 0 1.2e-004 3.8e+000 # TGTACGGG CCCGTACA 12 1 1.7e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 105 E= 6.1e-016 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 0.495238 0.000000 0.504762 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.514286 0.000000 0.485714 0.000000 MOTIF ACTBGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 58 1 4.0e-017 1.3e-012 # ACTCGGCC GGCCGAGT 29 0 1.5e-009 4.8e-005 # ACTTGGCC GGCCAAGT 28 0 3.0e-009 9.7e-005 # ACTGGGCC GGCCCAGT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 1.3e-012 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 0.431034 0.189655 0.379310 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 84 10 9.8e-017 3.2e-012 # CGCCTTA TAAGGCG 68 6 3.4e-015 1.1e-010 # CGCGTTA TAACGCG 16 4 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 84 E= 3.2e-012 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 0.809524 0.190476 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 AGAAAMAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGAAAMAA TTKTTTCT 88 21 7.7e-012 2.5e-007 # AGAAAAAA TTTTTTCT 73 18 1.0e-009 3.2e-005 # AGAAACAA TTGTTTCT 16 3 2.1e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 93 E= 2.5e-007 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 0.827957 0.172043 0.000000 0.000000 1.000000 0.000000 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 47 3 1.1e-011 3.4e-007 # GCGCTACC GGTAGCGC 32 2 2.7e-008 8.7e-004 # GCTCTACC GGTAGAGC 15 1 2.5e-004 7.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 3.4e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.680851 0.319149 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 ACCCAVAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 62 11 2.1e-010 6.7e-006 # ACCCACAC GTGTGGGT 36 8 1.0e-005 3.3e-001 # ACCCAGAC GTCTGGGT 14 0 5.8e-005 1.9e+000 # ACCCAAAC GTTTGGGT 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 113 E= 6.7e-006 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 0.132743 0.743363 0.123894 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AASCACT DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AASCACT AGTGSTT 67 14 4.1e-010 1.3e-005 # AACCACT AGTGGTT 52 10 1.7e-008 5.4e-004 # AAGCACT AGTGCTT 15 4 9.3e-003 3.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 69 E= 1.3e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.782609 0.217391 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 MOTIF CTWGACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 49 7 2.2e-009 7.1e-005 # CTAGACC GGTCTAG 28 1 4.5e-008 1.5e-003 # CTTGACC GGTCAAG 21 6 2.8e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 7.1e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.571429 0.000000 0.000000 0.428571 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 CAASGATG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 28 0 3.0e-009 9.5e-005 # CAACGATG CATCGTTG 21 0 4.2e-007 1.3e-002 # CAAGGATG CATCCTTG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.5e-005 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 0.750000 0.250000 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 0.000000 0.000000 1.000000 0.000000 MOTIF CACCGTGS DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 27 0 6.1e-009 1.9e-004 # CACCGTGG CCACGGTG 17 0 7.0e-006 2.3e-001 # CACCGTGC GCACGGTG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.9e-004 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 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 0.370370 0.629630 0.000000 MOTIF TGGCGYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 45 7 2.3e-008 7.3e-004 # TGGCGCA TGCGCCA 25 2 2.4e-006 7.8e-002 # TGGCGTA TACGCCA 20 5 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 7.3e-004 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 0.000000 1.000000 0.000000 0.000000 0.555556 0.000000 0.444444 1.000000 0.000000 0.000000 0.000000 MOTIF ARAAWA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ARAAWA TWTTYT 516 404 4.1e-008 1.3e-003 # AAAATA TATTTT 242 174 7.9e-005 2.5e+000 # AGAAAA TTTTCT 173 118 2.5e-004 8.0e+000 # AAAAAA TTTTTT 255 204 3.2e-003 1.0e+002 # AGAATA TATTCT 88 58 6.0e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 814 E= 1.3e-003 1.000000 0.000000 0.000000 0.000000 0.670762 0.000000 0.329238 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.573710 0.000000 0.000000 0.426290 1.000000 0.000000 0.000000 0.000000 MOTIF CAGAYGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CAGAYGC GCRTCTG 34 3 4.7e-008 1.5e-003 # CAGACGC GCGTCTG 17 1 6.8e-005 2.1e+000 # CAGATGC GCATCTG 17 2 3.4e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.5e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TAKCTCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 47 9 8.4e-008 2.6e-003 # TATCTCA TGAGATA 27 5 4.9e-005 1.5e+000 # TAGCTCA TGAGCTA 20 4 7.2e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 2.6e-003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 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 GARTCATA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GARTCATA TATGAYTC 27 1 8.9e-008 2.8e-003 # GAGTCATA TATGACTC 13 0 1.2e-004 3.6e+000 # GAATCATA TATGATTC 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.8e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.518519 0.000000 0.481481 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 CAGTCTKG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CAGTCTKG CMAGACTG 21 0 4.2e-007 1.3e-002 # CAGTCTGG CCAGACTG 11 0 4.7e-004 1.5e+001 # CAGTCTTG CAAGACTG 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.523810 0.476190 0.000000 0.000000 1.000000 0.000000 MOTIF CTCTYCC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CTCTYCC GGRAGAG 43 9 7.3e-007 2.3e-002 # CTCTCCC GGGAGAG 22 4 2.4e-004 7.6e+000 # CTCTTCC GGAAGAG 21 5 1.2e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 2.3e-002 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 0.511628 0.000000 0.488372 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 112 53 8.2e-007 2.6e-002 # CACCCA TGGGTG 71 35 2.0e-004 6.3e+000 # CGCCCA TGGGCG 44 18 5.3e-004 1.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 124 E= 2.6e-002 0.000000 1.000000 0.000000 0.000000 0.629032 0.000000 0.370968 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 # Stopping reason: E-value threshold exceeded # Running time: 102.92 seconds