# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ZAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ZAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ZAP1/seqs-shuffled # positives: 807 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ZAP1/seqs-centered (Sat Jan 18 13:53:34 PST 2020) # negatives: 807 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--ZAP1/seqs-shuffled (Sat Jan 18 13:53:34 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 14:09:43 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 0.302 C 0.201 G 0.199 T 0.298 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 118 11 9.4e-026 3.2e-021 # GGTTCGA TCGAACC 82 7 2.0e-018 6.8e-014 # GGTTCAA TTGAACC 38 4 2.0e-008 6.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 3.2e-021 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 0.316667 0.000000 0.683333 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 48 2 5.8e-013 2.0e-008 # CTCGGCCA TGGCCGAG 27 1 8.8e-008 3.0e-003 # CTTGGCCA TGGCCAAG 21 1 4.9e-006 1.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 2.0e-008 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.562500 0.000000 0.437500 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 1.000000 0.000000 0.000000 0.000000 MOTIF DCGCCTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST DCGCCTTA TAAGGCGH 50 3 1.4e-012 4.8e-008 # TCGCCTTA TAAGGCGA 18 0 3.5e-006 1.2e-001 # GCGCCTTA TAAGGCGC 21 2 3.0e-005 1.0e+000 # ACGCCTTA TAAGGCGT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 4.8e-008 0.220000 0.000000 0.420000 0.360000 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 ACCACBA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACBA TVGTGGT 85 20 1.3e-011 4.3e-007 # ACCACTA TAGTGGT 49 9 2.7e-008 9.3e-004 # ACCACGA TCGTGGT 18 3 7.0e-004 2.4e+001 # ACCACCA TGGTGGT 22 8 7.6e-003 2.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 4.3e-007 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 0.255556 0.200000 0.544444 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCADAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCCADAC GTHTGGGT 35 0 2.0e-011 6.9e-007 # ACCCATAC GTATGGGT 21 0 4.2e-007 1.4e-002 # ACCCAAAC GTTTGGGT 8 0 3.8e-003 1.3e+002 # ACCCAGAC GTCTGGGT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 6.9e-007 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 0.216216 0.000000 0.216216 0.567568 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAAAWAK DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAAAWAK MTWTTTT 277 166 3.6e-010 1.2e-005 # AAAAAAT ATTTTTT 133 80 6.2e-005 2.1e+000 # AAAAAAG CTTTTTT 102 60 3.2e-004 1.1e+001 # AAAATAT ATATTTT 68 38 1.7e-003 5.8e+001 # AAAATAG CTATTTT 33 14 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 331 E= 1.2e-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 0.712991 0.000000 0.000000 0.287009 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.413897 0.586103 MOTIF CRGTAGC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CRGTAGC GCTACYG 38 3 3.6e-009 1.2e-004 # CGGTAGC GCTACCG 26 2 1.3e-006 4.3e-002 # CAGTAGC GCTACTG 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.2e-004 0.000000 1.000000 0.000000 0.000000 0.315789 0.000000 0.684211 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCGTRAG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATCGTRAG CTYACGAT 24 0 5.0e-008 1.7e-003 # ATCGTGAG CTCACGAT 14 0 5.8e-005 2.0e+000 # ATCGTAAG CTTACGAT 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.416667 0.000000 0.583333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAGATTTC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AAGATTTC GAAATCTT 26 1 1.7e-007 5.9e-003 # AAGATTTC GAAATCTT 26 1 1.7e-007 5.9e-003 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.9e-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 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 MOTIF GYCAGA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GYCAGA TCTGRC 88 35 3.8e-007 1.3e-002 # GCCAGA TCTGGC 44 15 7.8e-005 2.6e+000 # GTCAGA TCTGAC 49 21 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 95 E= 1.3e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.463158 0.000000 0.536842 0.000000 1.000000 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 MOTIF GGCSCAA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGCSCAA TTGSGCC 30 3 5.6e-007 1.9e-002 # GGCCCAA TTGGGCC 18 1 3.5e-005 1.2e+000 # GGCGCAA TTGCGCC 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.9e-002 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 0.600000 0.400000 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 MOTIF CCAGTTSG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCAGTTSG CSAACTGG 20 0 8.5e-007 2.8e-002 # CCAGTTCG CGAACTGG 10 0 9.5e-004 3.2e+001 # CCAGTTGG CCAACTGG 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGTTGCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCCA TGGCAACG 20 0 8.5e-007 2.8e-002 # CGTTGCCA TGGCAACG 20 0 8.5e-007 2.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-002 0.000000 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 0.000000 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 69.49 seconds