# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--AFT2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--AFT2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--AFT2/seqs-shuffled # positives: 589 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--AFT2/seqs-centered (Sun Jan 19 10:33:58 PST 2020) # negatives: 589 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--AFT2/seqs-shuffled (Sun Jan 19 10:33:58 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:49:31 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 0.305 C 0.199 G 0.200 T 0.297 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 108 8 7.7e-026 2.4e-021 # GGTTCGA TCGAACC 91 6 2.4e-022 7.5e-018 # GGATCGA TCGATCC 25 2 2.3e-006 7.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 2.4e-021 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.194444 0.000000 0.000000 0.805556 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 ACCACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACT AGTGGT 92 21 4.1e-013 1.3e-008 # ACCACT AGTGGT 92 21 4.1e-013 1.3e-008 letter-probability matrix: alength= 4 w= 6 nsites= 106 E= 1.3e-008 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 0.000000 0.000000 1.000000 MOTIF RRAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST RRAAAAA TTTTTYY 204 110 3.6e-010 1.1e-005 # AAAAAAA TTTTTTT 121 64 3.2e-006 9.7e-002 # AGAAAAA TTTTTCT 78 34 7.8e-006 2.4e-001 # GAAAAAA TTTTTTC 92 47 3.1e-005 9.6e-001 # GGAAAAA TTTTTCC 46 20 6.8e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 245 E= 1.1e-005 0.689796 0.000000 0.310204 0.000000 0.604082 0.000000 0.395918 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 1.000000 0.000000 0.000000 0.000000 MOTIF AACCRACT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACCRACT AGTYGGTT 32 1 2.6e-009 8.0e-005 # AACCAACT AGTTGGTT 23 1 1.2e-006 3.7e-002 # AACCGACT AGTCGGTT 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.0e-005 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 0.000000 0.718750 0.000000 0.281250 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 MOTIF GMTACCGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 28 0 2.7e-009 8.1e-005 # GCTACCGA TCGGTAGC 20 0 8.1e-007 2.4e-002 # GATACCGA TCGGTATC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 8.1e-005 0.000000 0.000000 1.000000 0.000000 0.285714 0.714286 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 30 1 1.0e-008 3.1e-004 # ATGGCAAC GTTGCCAT 19 1 1.8e-005 5.3e-001 # ATGGCATC GATGCCAT 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.1e-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 0.633333 0.000000 0.000000 0.366667 0.000000 1.000000 0.000000 0.000000 MOTIF CCGTGSA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 31 2 4.6e-008 1.4e-003 # CCGTGCA TGCACGG 17 1 6.5e-005 2.0e+000 # CCGTGGA TCCACGG 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 1.4e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.548387 0.451613 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CRCCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 89 34 8.9e-008 2.7e-003 # CGCCCA TGGGCG 39 11 3.2e-005 9.6e-001 # CACCCA TGGGTG 52 23 3.7e-004 1.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 108 E= 2.7e-003 0.000000 1.000000 0.000000 0.000000 0.629630 0.000000 0.370370 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 MOTIF ACTSTTAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACTSTTAA TTAASAGT 22 0 2.0e-007 5.8e-003 # ACTCTTAA TTAAGAGT 12 0 2.3e-004 6.8e+000 # ACTGTTAA TTAACAGT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.8e-003 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 0.545455 0.454545 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 1.000000 0.000000 0.000000 0.000000 MOTIF GATTWGAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 31 4 1.3e-006 3.8e-002 # GATTTGAA TTCAAATC 16 2 6.1e-004 1.8e+001 # GATTAGAA TTCTAATC 15 2 1.1e-003 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 3.8e-002 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 0.483871 0.000000 0.000000 0.516129 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCACR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 19 0 1.6e-006 4.9e-002 # CTATCACG CGTGATAG 12 0 2.3e-004 6.8e+000 # CTATCACA TGTGATAG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.9e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.368421 0.000000 0.631579 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 44.94 seconds