# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/seqs-shuffled # positives: 581 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/seqs-centered (Sun Jan 19 09:48:49 PST 2020) # negatives: 581 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--PDR1/seqs-shuffled (Sun Jan 19 09:48:49 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:03:51 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 0.210 G 0.204 T 0.289 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 127 12 1.7e-028 5.2e-024 # GGTTCGA TCGAACC 90 5 5.4e-023 1.7e-018 # GGTTCAA TTGAACC 37 7 1.8e-006 5.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 127 E= 5.2e-024 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 0.291339 0.000000 0.708661 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARAAARA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ARAAARA TYTTTYT 203 83 1.2e-016 3.7e-012 # AGAAAAA TTTTTCT 73 18 6.2e-010 1.9e-005 # AAAAAAA TTTTTTT 116 48 5.5e-009 1.7e-004 # AAAAAGA TCTTTTT 69 23 3.1e-007 9.5e-003 # AGAAAGA TCTTTCT 23 9 9.2e-003 2.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 252 E= 3.7e-012 1.000000 0.000000 0.000000 0.000000 0.674603 0.000000 0.325397 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 0.694444 0.000000 0.305556 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAAGGCR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 69 5 1.4e-016 4.3e-012 # TAAGGCG CGCCTTA 58 4 3.5e-014 1.1e-009 # TAAGGCA TGCCTTA 13 1 8.6e-004 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 4.3e-012 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.183099 0.000000 0.816901 0.000000 MOTIF ACCACTH DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACTH DAGTGGT 91 18 2.6e-014 7.8e-010 # ACCACTA TAGTGGT 47 5 2.9e-010 8.9e-006 # ACCACTC GAGTGGT 32 7 2.7e-005 8.1e-001 # ACCACTT AAGTGGT 28 6 7.9e-005 2.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 7.8e-010 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 0.435185 0.296296 0.000000 0.268519 MOTIF ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 0 3.5e-011 1.1e-006 # ATGGCAAC GTTGCCAT 22 0 1.9e-007 5.8e-003 # ATGGCATC GATGCCAT 12 0 2.3e-004 6.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.1e-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 0.647059 0.000000 0.000000 0.352941 0.000000 1.000000 0.000000 0.000000 MOTIF ACCRACT DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 58 9 1.2e-010 3.5e-006 # ACCAACT AGTTGGT 37 7 1.8e-006 5.3e-002 # ACCGACT AGTCGGT 21 2 2.8e-005 8.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 3.5e-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 0.637931 0.000000 0.362069 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 ATCGTRAG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATCGTRAG CTYACGAT 26 0 1.1e-008 3.3e-004 # ATCGTGAG CTCACGAT 18 0 3.3e-006 1.0e-001 # ATCGTAAG CTTACGAT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.3e-004 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 0.307692 0.000000 0.692308 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGYCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGYCA TGRCCAT 40 6 9.3e-008 2.8e-003 # ATGGCCA TGGCCAT 19 2 9.8e-005 2.9e+000 # ATGGTCA TGACCAT 21 4 4.0e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 2.8e-003 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 0.475000 0.000000 0.525000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTGMTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 22 0 1.9e-007 5.8e-003 # CCGTGATA TATCACGG 11 0 4.7e-004 1.4e+001 # CCGTGCTA TAGCACGG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.8e-003 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 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCGGYCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TCGGYCA TGRCCGA 31 3 2.7e-007 8.1e-003 # TCGGTCA TGACCGA 17 0 6.8e-006 2.0e-001 # TCGGCCA TGGCCGA 14 3 6.1e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 8.1e-003 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 0.451613 0.000000 0.548387 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ASACCAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ASACCAC GTGGTST 33 4 3.8e-007 1.1e-002 # AGACCAC GTGGTCT 17 0 6.8e-006 2.0e-001 # ACACCAC GTGGTGT 18 4 2.0e-003 5.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 1.1e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.564103 0.435897 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 0.000000 1.000000 0.000000 0.000000 MOTIF GYCCGGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GYCCGGA TCCGGRC 27 2 6.2e-007 1.8e-002 # GCCCGGA TCCGGGC 12 0 2.3e-004 6.8e+000 # GTCCGGA TCCGGAC 15 2 1.1e-003 3.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 1.8e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.444444 0.000000 0.555556 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 0.000000 MOTIF CRCCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 90 38 6.6e-007 2.0e-002 # CGCCCA TGGGCG 44 14 3.4e-005 9.9e-001 # CACCCA TGGGTG 49 25 2.7e-003 8.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 104 E= 2.0e-002 0.000000 1.000000 0.000000 0.000000 0.576923 0.000000 0.423077 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 MOTIF RCGGGGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 35 5 4.7e-007 1.4e-002 # GCGGGGA TCCCCGC 19 1 1.8e-005 5.1e-001 # ACGGGGA TCCCCGT 16 4 5.6e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.4e-002 0.457143 0.000000 0.542857 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGATCGAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GGATCGAA TTCGATCC 20 0 8.1e-007 2.3e-002 # GGATCGAA TTCGATCC 20 0 8.1e-007 2.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.3e-002 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 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 59.30 seconds