# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP3/seqs-shuffled # positives: 866 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP3/seqs-centered (Sun Jan 19 04:26:37 PST 2020) # negatives: 866 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP3/seqs-shuffled (Sun Jan 19 04:26:37 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 04:42:18 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 0.334 C 0.164 G 0.163 T 0.340 MOTIF CTYGGCC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 42 2 3.5e-011 1.1e-006 # CTTGGCC GGCCAAG 28 1 4.5e-008 1.4e-003 # CTCGGCC GGCCGAG 20 1 9.5e-006 3.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.1e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.404762 0.000000 0.595238 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 ATATAKAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATATAKAY RTMTATAT 86 23 1.4e-010 4.5e-006 # ATATATAT ATATATAT 36 11 1.4e-004 4.6e+000 # ATATATAC GTATATAT 32 9 1.8e-004 5.9e+000 # ATATAGAT ATCTATAT 18 3 7.0e-004 2.2e+001 # ATATAGAC GTCTATAT 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 91 E= 4.5e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.318681 0.681319 1.000000 0.000000 0.000000 0.000000 0.000000 0.417582 0.000000 0.582418 MOTIF GCKCTACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 31 0 3.5e-010 1.1e-005 # GCGCTACC GGTAGCGC 17 0 7.0e-006 2.2e-001 # GCTCTACC GGTAGAGC 14 0 5.8e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.1e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.548387 0.451613 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 GGGYTCGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGGYTCGA TCGARCCC 33 1 1.5e-009 4.8e-005 # GGGTTCGA TCGAACCC 24 1 6.7e-007 2.1e-002 # GGGCTCGA TCGAGCCC 19 0 1.7e-006 5.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.8e-005 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 0.363636 0.000000 0.636364 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 AAAAADAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 211 118 7.3e-009 2.3e-004 # AAAAAGAA TTCTTTTT 68 27 9.3e-006 2.9e-001 # AAAAAAAA TTTTTTTT 101 57 1.5e-004 4.9e+000 # AAAAATAA TTATTTTT 84 52 2.7e-003 8.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 250 E= 2.3e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.380000 0.000000 0.256000 0.364000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF KGCGCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST KGCGCCA TGGCGCM 22 0 2.1e-007 6.5e-003 # TGCGCCA TGGCGCA 15 0 2.9e-005 9.0e-001 # GGCGCCA TGGCGCC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 22 E= 6.5e-003 0.000000 0.000000 0.318182 0.681818 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCRCT DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCRCT AGYGGT 95 39 2.7e-007 8.4e-003 # ACCACT AGTGGT 75 31 6.3e-006 2.0e-001 # ACCGCT AGCGGT 22 8 7.6e-003 2.4e+002 letter-probability matrix: alength= 4 w= 6 nsites= 113 E= 8.4e-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 0.805310 0.000000 0.194690 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 46.05 seconds