# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-shuffled # positives: 472 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-centered (Sat Jan 18 18:28:43 PST 2020) # negatives: 472 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--HAA1/seqs-shuffled (Sat Jan 18 18:28:43 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:38:37 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 0.196 T 0.305 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 68 9 1.7e-013 4.9e-009 # GGTTCGA TCGAACC 47 4 4.4e-011 1.3e-006 # GGTTCAA TTGAACC 22 5 6.5e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 69 E= 4.9e-009 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 0.318841 0.000000 0.681159 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCCTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 31 0 2.8e-010 8.1e-006 # CGCCTTA TAAGGCG 31 0 2.8e-010 8.1e-006 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 8.1e-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 AARAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AARAAAA TTTTYTT 138 65 4.4e-009 1.3e-004 # AAAAAAA TTTTTTT 95 40 1.9e-007 5.5e-003 # AAGAAAA TTTTCTT 59 29 5.3e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 168 E= 1.3e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 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 MOTIF CTYGGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 25 0 2.2e-008 6.2e-004 # CTTGGCC GGCCAAG 16 0 1.3e-005 3.9e-001 # CTCGGCC GGCCGAG 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 6.2e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.440000 0.000000 0.560000 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 0.000000 MOTIF CACCCAD DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CACCCAD HTGGGTG 39 6 1.5e-007 4.3e-003 # CACCCAT ATGGGTG 22 4 2.3e-004 6.5e+000 # CACCCAA TTGGGTG 14 2 1.9e-003 5.6e+001 # CACCCAG CTGGGTG 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 4.3e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.311111 0.000000 0.200000 0.488889 MOTIF CTWGACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 26 1 1.5e-007 4.3e-003 # CTAGACC GGTCTAG 15 0 2.7e-005 7.8e-001 # CTTGACC GGTCAAG 11 1 3.0e-003 8.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 4.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.576923 0.000000 0.000000 0.423077 0.000000 0.000000 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 22.50 seconds