# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--RPD3/seqs-shuffled # positives: 1053 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--RPD3/seqs-centered (Sat Jan 18 06:49:33 PST 2020) # negatives: 1053 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--RPD3/seqs-shuffled (Sat Jan 18 06:49:33 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 07:04:26 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 0.303 C 0.195 G 0.196 T 0.307 MOTIF GGTTYGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTYGA TCRAACC 89 16 2.5e-014 9.2e-010 # GGTTCGA TCGAACC 65 7 1.5e-013 5.7e-009 # GGTTTGA TCAAACC 24 9 6.4e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 89 E= 9.2e-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 0.730337 0.000000 0.269663 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGAAM DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAGAAM KTTCTT 385 239 1.9e-012 7.0e-008 # AAGAAA TTTCTT 283 181 5.0e-008 1.8e-003 # AAGAAC GTTCTT 131 71 5.6e-006 2.0e-001 letter-probability matrix: alength= 4 w= 6 nsites= 471 E= 7.0e-008 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.717622 0.282378 0.000000 0.000000 MOTIF GCKCTACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 29 0 1.5e-009 5.6e-005 # GCGCTACC GGTAGCGC 18 0 3.5e-006 1.3e-001 # GCTCTACC GGTAGAGC 11 0 4.8e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.6e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.620690 0.379310 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 33 1 1.6e-009 5.8e-005 # CCTTAACC GGTTAAGG 22 1 2.6e-006 9.4e-002 # CCATAACC GGTTATGG 11 0 4.8e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 5.8e-005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 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 CTYGGCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 34 2 7.6e-009 2.8e-004 # CTCGGCCA TGGCCGAG 20 1 9.7e-006 3.5e-001 # CTTGGCCA TGGCCAAG 14 1 4.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.8e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.588235 0.000000 0.411765 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 TACTAACA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TACTAACA TGTTAGTA 30 1 1.2e-008 4.4e-004 # TACTAACA TGTTAGTA 30 1 1.2e-008 4.4e-004 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 4.4e-004 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 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 1.000000 0.000000 0.000000 0.000000 MOTIF CTTACCR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTTACCR YGGTAAG 49 10 9.4e-008 3.4e-003 # CTTACCA TGGTAAG 31 7 5.1e-005 1.8e+000 # CTTACCG CGGTAAG 18 3 7.1e-004 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 3.4e-003 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.632653 0.000000 0.367347 0.000000 MOTIF ATAYATA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATAYATA TATRTAT 75 25 1.5e-007 5.5e-003 # ATATATA TATATAT 46 14 1.6e-005 6.0e-001 # ATACATA TATGTAT 31 13 4.4e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 83 E= 5.5e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.385542 0.000000 0.614458 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCASM DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACCASM KSTGGT 205 117 6.0e-008 2.1e-003 # ACCAGC GCTGGT 56 20 1.6e-005 5.7e-001 # ACCACC GGTGGT 62 33 1.5e-003 5.6e+001 # ACCAGA TCTGGT 67 40 4.8e-003 1.7e+002 # ACCACA TGTGGT 62 38 9.0e-003 3.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 262 E= 2.1e-003 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 0.484733 0.515267 0.000000 0.511450 0.488550 0.000000 0.000000 MOTIF RATGGCAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST RATGGCAA TTGCCATY 27 2 7.0e-007 2.5e-002 # GATGGCAA TTGCCATC 15 0 2.9e-005 1.0e+000 # AATGGCAA TTGCCATT 12 2 6.3e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.5e-002 0.444444 0.000000 0.555556 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 71.33 seconds