# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SMP1/seqs-shuffled # positives: 504 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SMP1/seqs-centered (Sat Jan 18 22:15:00 PST 2020) # negatives: 504 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--SMP1/seqs-shuffled (Sat Jan 18 22:15:00 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:26:17 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 0.300 C 0.199 G 0.199 T 0.302 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 75 4 1.8e-019 5.4e-015 # GGTTCGA TCGAACC 55 3 2.8e-014 8.3e-010 # GGATCGA TCGATCC 25 2 2.2e-006 6.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 5.4e-015 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.320000 0.000000 0.000000 0.680000 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 CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 43 2 1.3e-011 3.7e-007 # CGCCTTA TAAGGCG 33 1 1.2e-009 3.6e-005 # CGCGTTA TAACGCG 10 1 5.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 3.7e-007 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 0.767442 0.232558 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 ACCRCT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCRCT AGYGGT 85 29 1.3e-008 3.8e-004 # ACCACT AGTGGT 66 23 1.0e-006 3.1e-002 # ACCGCT AGCGGT 21 6 2.6e-003 7.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 95 E= 3.8e-004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.778947 0.000000 0.221053 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ATGGCAW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAW WTGCCAT 46 8 3.3e-008 9.6e-004 # ATGGCAA TTGCCAT 26 3 5.9e-006 1.7e-001 # ATGGCAT ATGCCAT 20 5 1.8e-003 5.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 9.6e-004 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 0.553191 0.000000 0.000000 0.446809 MOTIF CCCATDC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 36 4 5.5e-008 1.6e-003 # CCCATGC GCATGGG 12 0 2.3e-004 6.7e+000 # CCCATAC GTATGGG 16 3 2.0e-003 5.9e+001 # CCCATTC GAATGGG 10 1 5.6e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.6e-003 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.421053 0.000000 0.315789 0.263158 0.000000 1.000000 0.000000 0.000000 MOTIF AAAAWAAT DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAAAWAAT ATTWTTTT 80 28 6.3e-008 1.8e-003 # AAAAAAAT ATTTTTTT 62 22 3.1e-006 9.0e-002 # AAAATAAT ATTATTTT 23 7 2.3e-003 6.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 1.8e-003 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 0.743902 0.000000 0.000000 0.256098 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CGCTWCC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCTWCC GGWAGCG 23 1 1.2e-006 3.4e-002 # CGCTACC GGTAGCG 15 1 2.4e-004 6.8e+000 # CGCTTCC GGAAGCG 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 3.4e-002 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 0.625000 0.000000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 28.68 seconds