# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-shuffled # positives: 864 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-centered (Fri Jan 17 23:36:50 PST 2020) # negatives: 864 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--AFT1/seqs-shuffled (Fri Jan 17 23:36:50 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:53:15 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 0.289 C 0.213 G 0.212 T 0.285 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 88 8 2.6e-019 9.7e-015 # GGGTTCGA TCGAACCC 34 2 7.2e-009 2.7e-004 # CGGTTCGA TCGAACCG 30 4 2.5e-006 9.3e-002 # GAGTTCGA TCGAACTC 14 1 4.7e-004 1.7e+001 # CAGTTCGA TCGAACTG 10 1 5.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 9.7e-015 0.000000 0.454545 0.545455 0.000000 0.272727 0.000000 0.727273 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 CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 55 2 5.0e-015 1.8e-010 # CTCGGCCA TGGCCGAG 24 0 5.1e-008 1.9e-003 # CTTGGCCA TGGCCAAG 22 2 1.6e-005 5.9e-001 # CTGGGCCA TGGCCCAG 9 0 1.9e-003 7.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 1.8e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.436364 0.163636 0.400000 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 AAAARWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAARWA TWYTTTT 251 132 3.0e-012 1.1e-007 # AAAAAAA TTTTTTT 128 64 5.8e-007 2.1e-002 # AAAAATA TATTTTT 84 39 1.6e-005 5.9e-001 # AAAAGAA TTCTTTT 75 37 1.3e-004 4.9e+000 # AAAAGTA TACTTTT 37 16 2.4e-003 8.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 315 E= 1.1e-007 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 0.647619 0.000000 0.352381 0.000000 0.628571 0.000000 0.000000 0.371429 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 83 18 5.1e-012 1.9e-007 # AGTGGTA TACCACT 45 9 2.5e-007 9.1e-003 # AGTGGTT AACCACT 45 9 2.5e-007 9.1e-003 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 1.9e-007 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 0.500000 0.000000 0.000000 0.500000 MOTIF CRCCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 145 56 1.0e-011 3.8e-007 # CACCCA TGGGTG 91 34 6.3e-008 2.3e-003 # CGCCCA TGGGCG 57 24 1.1e-004 4.1e+000 letter-probability matrix: alength= 4 w= 6 nsites= 165 E= 3.8e-007 0.000000 1.000000 0.000000 0.000000 0.654545 0.000000 0.345455 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 GCCWTAAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 42 2 3.5e-011 1.3e-006 # GCCTTAAC GTTAAGGC 31 1 5.9e-009 2.1e-004 # GCCATAAC GTTATGGC 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.3e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.261905 0.000000 0.000000 0.738095 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 MOTIF CGCTDCC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCTDCC GGHAGCG 37 3 7.0e-009 2.5e-004 # CGCTACC GGTAGCG 18 0 3.5e-006 1.3e-001 # CGCTTCC GGAAGCG 15 3 3.6e-003 1.3e+002 # CGCTGCC GGCAGCG 7 0 7.7e-003 2.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 2.5e-004 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 0.000000 1.000000 0.450000 0.000000 0.175000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF DTCTTC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST DTCTTC GAAGAH 207 123 1.7e-007 6.1e-003 # TTCTTC GAAGAA 111 60 2.5e-005 9.1e-001 # ATCTTC GAAGAT 76 43 1.1e-003 4.0e+001 # GTCTTC GAAGAC 48 27 8.8e-003 3.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 251 E= 6.1e-003 0.318725 0.000000 0.195219 0.486056 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 MOTIF CCATCGTK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCATCGTK MACGATGG 26 2 1.3e-006 4.6e-002 # CCATCGTG CACGATGG 11 0 4.7e-004 1.7e+001 # CCATCGTT AACGATGG 15 2 1.1e-003 4.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.6e-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 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 0.000000 0.000000 0.423077 0.576923 # Stopping reason: E-value threshold exceeded # Running time: 54.50 seconds