# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP1/seqs-shuffled # positives: 715 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP1/seqs-centered (Sat Jan 18 23:32:55 PST 2020) # negatives: 715 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YAP1/seqs-shuffled (Sat Jan 18 23:32:55 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:49:35 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 0.311 C 0.191 G 0.185 T 0.313 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 89 16 1.3e-014 4.2e-010 # GGTTCGA TCGAACC 63 6 6.9e-014 2.3e-009 # GGTTCAA TTGAACC 27 10 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 4.2e-010 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 0.300000 0.000000 0.700000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AWAAAAAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AWAAAAAW WTTTTTWT 176 81 3.2e-011 1.1e-006 # AAAAAAAA TTTTTTTT 94 36 5.1e-008 1.7e-003 # AAAAAAAT ATTTTTTT 87 46 1.2e-004 4.1e+000 # ATAAAAAT ATTTTTAT 33 12 1.0e-003 3.5e+001 # ATAAAAAA TTTTTTAT 39 18 3.2e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 204 E= 1.1e-006 1.000000 0.000000 0.000000 0.000000 0.691176 0.000000 0.000000 0.308824 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 0.514706 0.000000 0.000000 0.485294 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 58 12 5.2e-009 1.7e-004 # AGTGGTT AACCACT 41 9 1.9e-006 6.4e-002 # AGTGGTA TACCACT 26 4 2.5e-005 8.3e-001 letter-probability matrix: alength= 4 w= 7 nsites= 69 E= 1.7e-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 0.376812 0.000000 0.000000 0.623188 MOTIF CGHTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGHTACC GGTADCG 36 4 6.5e-008 2.1e-003 # CGTTACC GGTAACG 14 1 4.6e-004 1.5e+001 # CGATACC GGTATCG 10 1 5.7e-003 1.9e+002 # CGCTACC GGTAGCG 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 2.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.277778 0.333333 0.000000 0.388889 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 CCWTAACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 21 0 4.1e-007 1.3e-002 # CCTTAACC GGTTAAGG 13 0 1.2e-004 3.8e+000 # CCATAACC GGTTATGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.380952 0.000000 0.000000 0.619048 0.000000 0.000000 0.000000 1.000000 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 0.000000 MOTIF ATGGCMA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCMA TKGCCAT 36 6 1.0e-006 3.4e-002 # ATGGCCA TGGCCAT 15 1 2.4e-004 8.0e+000 # ATGGCAA TTGCCAT 21 5 1.1e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.4e-002 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 0.583333 0.416667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 33.21 seconds