# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP1/seqs-shuffled # positives: 726 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP1/seqs-centered (Fri Jan 17 22:03:52 PST 2020) # negatives: 726 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP1/seqs-shuffled (Fri Jan 17 22:03:52 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:19:34 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 0.301 C 0.196 G 0.197 T 0.307 MOTIF AGTGGTW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 86 13 1.6e-015 5.4e-011 # AGTGGTT AACCACT 66 8 2.7e-013 9.0e-009 # AGTGGTA TACCACT 32 5 2.9e-006 9.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 5.4e-011 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.320000 0.000000 0.000000 0.680000 MOTIF SGGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 54 4 6.6e-013 2.2e-008 # GGGTTCGA TCGAACCC 32 1 2.9e-009 9.5e-005 # CGGTTCGA TCGAACCG 22 3 6.9e-005 2.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 2.2e-008 0.000000 0.407407 0.592593 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 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 ACTBGGC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGC GCCVAGT 57 9 2.6e-010 8.6e-006 # ACTTGGC GCCAAGT 32 7 2.8e-005 9.4e-001 # ACTGGGC GCCCAGT 15 1 2.4e-004 8.1e+000 # ACTCGGC GCCGAGT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 8.6e-006 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 0.175439 0.263158 0.561404 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RCGCCTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RCGCCTTA TAAGGCGY 32 1 2.9e-009 9.4e-005 # GCGCCTTA TAAGGCGC 19 1 1.8e-005 5.9e-001 # ACGCCTTA TAAGGCGT 13 0 1.2e-004 3.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.4e-005 0.406250 0.000000 0.593750 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 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 ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 3 4.4e-008 1.5e-003 # ATGGCAAC GTTGCCAT 23 1 1.3e-006 4.2e-002 # ATGGCATC GATGCCAT 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.5e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.657143 0.000000 0.000000 0.342857 0.000000 1.000000 0.000000 0.000000 MOTIF AAGAAAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAW WTTTCTT 141 70 7.4e-008 2.5e-003 # AAGAAAA TTTTCTT 95 45 5.5e-006 1.8e-001 # AAGAAAT ATTTCTT 51 28 5.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 160 E= 2.5e-003 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.662500 0.000000 0.000000 0.337500 MOTIF AGTCAKAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 27 1 8.6e-008 2.8e-003 # AGTCATAC GTATGACT 16 0 1.4e-005 4.6e-001 # AGTCAGAC GTCTGACT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.8e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.407407 0.592593 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTMCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTMCC GGKAGMGC 43 5 4.1e-009 1.4e-004 # GCGCTACC GGTAGCGC 22 4 2.4e-004 7.9e+000 # GCTCTACC GGTAGAGC 13 1 8.7e-004 2.9e+001 # GCTCTCCC GGGAGAGC 8 0 3.8e-003 1.3e+002 # GCGCTCCC GGGAGCGC 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.4e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.511628 0.488372 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.744186 0.255814 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 37 5 1.6e-007 5.1e-003 # TGGCGTA TACGCCA 17 0 6.9e-006 2.3e-001 # TGGCGCA TGCGCCA 20 5 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 5.1e-003 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 0.540541 0.000000 0.459459 1.000000 0.000000 0.000000 0.000000 MOTIF CAAVAGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CAAVAGA TCTBTTG 82 29 8.6e-008 2.8e-003 # CAAGAGA TCTCTTG 26 7 5.8e-004 1.9e+001 # CAAAAGA TCTTTTG 37 15 1.3e-003 4.4e+001 # CAACAGA TCTGTTG 22 7 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 85 E= 2.8e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.435294 0.258824 0.305882 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 # Stopping reason: E-value threshold exceeded # Running time: 51.33 seconds