# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YAP1/seqs-shuffled # positives: 693 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YAP1/seqs-centered (Sun Jan 19 03:31:05 PST 2020) # negatives: 693 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--YAP1/seqs-shuffled (Sun Jan 19 03:31:05 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 03:47:41 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 0.306 C 0.193 G 0.189 T 0.312 MOTIF GGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 65 5 2.9e-015 9.6e-011 # GGTTCGA TCGAACC 65 5 2.9e-015 9.6e-011 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 9.6e-011 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAADAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 154 73 2.3e-009 7.8e-005 # AAAAAGAA TTCTTTTT 51 18 2.9e-005 9.7e-001 # AAAAATAA TTATTTTT 51 22 3.3e-004 1.1e+001 # AAAAAAAA TTTTTTTT 71 38 6.6e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 170 E= 7.8e-005 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 0.429412 0.000000 0.270588 0.300000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTM DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 55 10 2.8e-009 9.1e-005 # ACCACTA TAGTGGT 35 5 5.0e-007 1.7e-002 # ACCACTC GAGTGGT 20 5 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 56 E= 9.1e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.625000 0.375000 0.000000 0.000000 MOTIF GGTAK DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGTAK MTACC 218 133 9.6e-008 3.2e-003 # GGTAT ATACC 126 80 3.3e-004 1.1e+001 # GGTAG CTACC 105 66 9.2e-004 3.1e+001 letter-probability matrix: alength= 4 w= 5 nsites= 254 E= 3.2e-003 0.000000 0.000000 1.000000 0.000000 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 0.000000 0.448819 0.551181 MOTIF ATAGMAG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATAGMAG CTKCTAT 42 7 1.2e-007 3.7e-003 # ATAGAAG CTTCTAT 26 4 2.5e-005 8.0e-001 # ATAGCAG CTGCTAT 16 3 2.1e-003 6.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 3.7e-003 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 0.627907 0.372093 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TATRTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TATRTA TAYATA 95 41 6.5e-007 2.1e-002 # TATATA TATATA 47 16 4.1e-005 1.3e+000 # TATGTA TACATA 52 26 1.7e-003 5.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 101 E= 2.1e-002 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.475248 0.000000 0.524752 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAASTTGG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAASTTGG CCAASTTG 27 2 6.5e-007 2.1e-002 # CAAGTTGG CCAACTTG 20 0 8.3e-007 2.6e-002 # CAACTTGG CCAAGTTG 23 2 8.3e-006 2.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.1e-002 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 0.703704 0.296296 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 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 35.82 seconds