# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-shuffled # positives: 701 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-centered (Sat Jan 18 16:05:41 PST 2020) # negatives: 701 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--STE12/seqs-shuffled (Sat Jan 18 16:05:41 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:22:03 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 0.207 G 0.204 T 0.293 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 104 10 1.2e-022 4.1e-018 # GGTTCGA TCGAACC 77 6 6.4e-018 2.2e-013 # GGCTCGA TCGAGCC 17 0 6.9e-006 2.3e-001 # GGATCGA TCGATCC 28 4 7.9e-006 2.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 4.1e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.247619 0.095238 0.000000 0.657143 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 ACCAYT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCAYT ARTGGT 158 57 2.5e-014 8.3e-010 # ACCACT AGTGGT 105 31 7.7e-012 2.6e-007 # ACCATT AATGGT 56 26 4.3e-004 1.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 175 E= 8.3e-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 0.674286 0.000000 0.325714 0.000000 0.000000 0.000000 1.000000 MOTIF CGCCTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 49 5 9.6e-011 3.2e-006 # CGCCTTA TAAGGCG 49 5 9.6e-011 3.2e-006 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 3.2e-006 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 AAAAWAT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAAAWAT ATWTTTT 158 76 2.4e-009 8.1e-005 # AAAAAAT ATTTTTT 123 62 9.2e-007 3.1e-002 # AAAATAT ATATTTT 60 19 1.1e-006 3.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 176 E= 8.1e-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 0.693182 0.000000 0.000000 0.306818 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CAACTTGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAACTTGG CCAAGTTG 29 1 2.2e-008 7.3e-004 # CAACTTGG CCAAGTTG 29 1 2.2e-008 7.3e-004 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.3e-004 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 0.000000 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 1.000000 0.000000 MOTIF GCGCTWCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCGCTWCC GGWAGCGC 29 1 2.2e-008 7.2e-004 # GCGCTACC GGTAGCGC 20 0 8.3e-007 2.7e-002 # GCGCTTCC GGAAGCGC 12 1 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.2e-004 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 0.000000 0.000000 1.000000 0.655172 0.000000 0.000000 0.344828 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACGATGGS DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACGATGGS SCCATCGT 20 0 8.3e-007 2.7e-002 # ACGATGGC GCCATCGT 10 0 9.5e-004 3.1e+001 # ACGATGGG CCCATCGT 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-002 1.000000 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 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 0.500000 0.500000 0.000000 MOTIF CCGYGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCGYGC GCRCGG 55 16 1.1e-006 3.5e-002 # CCGCGC GCGCGG 28 8 5.2e-004 1.7e+001 # CCGTGC GCACGG 28 8 5.2e-004 1.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 56 E= 3.5e-002 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 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACGCGAS DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACGCGAS STCGCGT 23 1 1.3e-006 4.1e-002 # ACGCGAC GTCGCGT 15 1 2.4e-004 8.0e+000 # ACGCGAG CTCGCGT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 4.1e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.652174 0.347826 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 44.42 seconds