# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--CUP9/seqs-shuffled # positives: 709 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--CUP9/seqs-centered (Sat Jan 18 16:22:55 PST 2020) # negatives: 709 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--CUP9/seqs-shuffled (Sat Jan 18 16:22:55 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 16:42:36 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 0.198 G 0.199 T 0.301 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 92 18 2.4e-014 8.1e-010 # GGTTCGA TCGAACC 75 13 1.1e-012 3.8e-008 # GGATCGA TCGATCC 24 5 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 8.1e-010 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.228261 0.000000 0.000000 0.771739 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 AAAAADAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 139 61 1.4e-009 4.8e-005 # AAAAAAAA TTTTTTTT 72 30 9.9e-006 3.3e-001 # AAAAATAA TTATTTTT 45 15 4.8e-005 1.6e+000 # AAAAAGAA TTCTTTTT 49 18 6.8e-005 2.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 166 E= 4.8e-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 1.000000 0.000000 0.000000 0.000000 0.469880 0.000000 0.277108 0.253012 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTA TAACCACT 27 0 5.8e-009 1.9e-004 # AGTGGTTA TAACCACT 27 0 5.8e-009 1.9e-004 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.9e-004 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCTTCB DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TCTTCB VGAAGA 167 85 7.2e-009 2.4e-004 # TCTTCT AGAAGA 89 42 1.0e-005 3.5e-001 # TCTTCC GGAAGA 55 26 6.1e-004 2.1e+001 # TCTTCG CGAAGA 42 21 4.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 6 nsites= 197 E= 2.4e-004 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 0.309645 0.208122 0.482234 MOTIF CAACTTG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAACTTG CAAGTTG 33 2 1.3e-008 4.4e-004 # CAACTTG CAAGTTG 33 2 1.3e-008 4.4e-004 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 4.4e-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 MOTIF CGHTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGHTACC GGTADCG 32 3 1.6e-007 5.2e-003 # CGATACC GGTATCG 10 0 9.5e-004 3.1e+001 # CGTTACC GGTAACG 8 0 3.8e-003 1.3e+002 # CGCTACC GGTAGCG 14 3 6.1e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 5.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.312500 0.437500 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACRATGG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACRATGG CCATYGT 29 3 1.0e-006 3.3e-002 # ACGATGG CCATCGT 15 0 2.8e-005 9.4e-001 # ACAATGG CCATTGT 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 3.3e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 # Stopping reason: E-value threshold exceeded # Running time: 35.96 seconds