# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP1/seqs-shuffled # positives: 877 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP1/seqs-centered (Sat Jan 18 22:30:30 PST 2020) # negatives: 877 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YAP1/seqs-shuffled (Sat Jan 18 22:30:30 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:46:40 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 0.329 C 0.167 G 0.166 T 0.338 MOTIF AACCACT DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AACCACT AGTGGTT 48 3 5.5e-012 1.8e-007 # AACCACT AGTGGTT 48 3 5.5e-012 1.8e-007 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 1.8e-007 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 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 TTTTCTB DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TTTTCTB VAGAAAA 203 103 1.8e-010 5.8e-006 # TTTTCTT AAGAAAA 137 67 1.1e-007 3.6e-003 # TTTTCTC GAGAAAA 50 22 5.1e-004 1.7e+001 # TTTTCTG CAGAAAA 33 16 9.8e-003 3.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 235 E= 5.8e-006 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 0.000000 0.000000 1.000000 0.000000 0.212766 0.140426 0.646809 MOTIF CGARCCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGARCCC GGGYTCG 34 1 7.7e-010 2.5e-005 # CGAACCC GGGTTCG 25 1 3.4e-007 1.1e-002 # CGAGCCC GGGCTCG 21 0 4.2e-007 1.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.5e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.617647 0.000000 0.382353 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 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 29 1 2.3e-008 7.6e-004 # GCTCTACC GGTAGAGC 13 0 1.2e-004 3.8e+000 # GCGCTACC GGTAGCGC 16 1 1.3e-004 4.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.6e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.551724 0.448276 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 AGTMATAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGTMATAC GTATKACT 32 3 1.6e-007 5.4e-003 # AGTAATAC GTATTACT 19 1 1.8e-005 6.0e-001 # AGTCATAC GTATGACT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.593750 0.406250 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 0.000000 1.000000 0.000000 0.000000 MOTIF AARAAATA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AARAAATA TATTTYTT 93 37 1.8e-007 6.0e-003 # AAAAAATA TATTTTTT 71 29 9.4e-006 3.1e-001 # AAGAAATA TATTTCTT 25 9 4.2e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 98 E= 6.0e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.734694 0.000000 0.265306 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATAKTGTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATAKTGTA TACAMTAT 38 6 3.5e-007 1.1e-002 # ATAGTGTA TACACTAT 18 1 3.5e-005 1.1e+000 # ATATTGTA TACAATAT 20 5 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.1e-002 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 0.473684 0.526316 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 # Stopping reason: E-value threshold exceeded # Running time: 45.50 seconds