# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MOT3/seqs-shuffled # positives: 707 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MOT3/seqs-centered (Sat Jan 18 03:39:26 PST 2020) # negatives: 707 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MOT3/seqs-shuffled (Sat Jan 18 03:39:26 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:55:27 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 0.297 C 0.206 G 0.202 T 0.295 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 127 7 2.4e-032 8.0e-028 # GGTTCGA TCGAACC 102 5 1.9e-026 6.5e-022 # AGTTCGA TCGAACT 33 2 1.3e-008 4.4e-004 letter-probability matrix: alength= 4 w= 7 nsites= 127 E= 8.0e-028 0.228346 0.000000 0.771654 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 90 16 6.9e-015 2.3e-010 # AGTGGTT AACCACT 56 9 4.6e-010 1.5e-005 # AGTGGTA TACCACT 44 7 3.7e-008 1.2e-003 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 2.3e-010 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 0.447619 0.000000 0.000000 0.552381 MOTIF ARAAAWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAWA TWTTTYT 247 130 1.1e-012 3.7e-008 # AAAAAAA TTTTTTT 129 59 2.4e-008 8.0e-004 # AAAAATA TATTTTT 89 45 4.2e-005 1.4e+000 # AGAAAAA TTTTTCT 85 47 3.4e-004 1.1e+001 # AGAAATA TATTTCT 33 13 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 313 E= 3.7e-008 1.000000 0.000000 0.000000 0.000000 0.654952 0.000000 0.345048 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 0.623003 0.000000 0.000000 0.376997 1.000000 0.000000 0.000000 0.000000 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 37 0 4.5e-012 1.5e-007 # CAACTTGG CCAAGTTG 30 0 6.8e-010 2.2e-005 # CAACTGGG CCCAGTTG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.5e-007 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 0.189189 0.810811 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AASGCG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AASGCG CGCSTT 97 32 8.2e-010 2.7e-005 # AAGGCG CGCCTT 64 16 1.2e-008 4.1e-004 # AACGCG CGCGTT 33 16 9.6e-003 3.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 97 E= 2.7e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.340206 0.659794 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 MOTIF ATCKTGAG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 29 1 2.2e-008 7.2e-004 # ATCGTGAG CTCACGAT 17 0 6.9e-006 2.3e-001 # ATCTTGAG CTCAAGAT 12 1 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.2e-004 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 0.586207 0.413793 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCGCW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCGCW WGCGCG 53 14 5.1e-007 1.7e-002 # CGCGCT AGCGCG 31 6 1.7e-005 5.4e-001 # CGCGCA TGCGCG 27 9 1.8e-003 5.7e+001 letter-probability matrix: alength= 4 w= 6 nsites= 54 E= 1.7e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.462963 0.000000 0.000000 0.537037 MOTIF CTCTCSCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSCA TGSGAGAG 24 1 6.5e-007 2.1e-002 # CTCTCCCA TGGGAGAG 16 1 1.3e-004 4.1e+000 # CTCTCGCA TGCGAGAG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCASCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACCASCA TGSTGGT 29 3 1.0e-006 3.3e-002 # ACCAGCA TGCTGGT 16 1 1.3e-004 4.1e+000 # ACCACCA TGGTGGT 13 2 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.3e-002 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 0.448276 0.551724 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: 44.21 seconds