# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/seqs-shuffled # positives: 580 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/seqs-centered (Sat Jan 18 01:50:43 PST 2020) # negatives: 580 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/seqs-shuffled (Sat Jan 18 01:50:43 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 02:05:43 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 0.298 C 0.207 G 0.205 T 0.290 MOTIF GTTCGANY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGANY RNTCGAAC 130 5 4.2e-036 1.3e-031 # GTTCGATC GATCGAAC 26 0 1.1e-008 3.4e-004 # GTTCGATT AATCGAAC 29 1 2.1e-008 6.3e-004 # GTTCGAGC GCTCGAAC 16 0 1.4e-005 4.2e-001 # GTTCGACT AGTCGAAC 14 0 5.6e-005 1.7e+000 # GTTCGACC GGTCGAAC 10 0 9.4e-004 2.9e+001 # GTTCGAAC GTTCGAAC 9 0 1.9e-003 5.8e+001 # GTTCGAAT ATTCGAAC 16 3 2.1e-003 6.3e+001 # GTTCGAGT ACTCGAAC 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 130 E= 1.3e-031 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 0.192308 0.184615 0.200000 0.423077 0.000000 0.469231 0.000000 0.530769 MOTIF CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 74 3 5.1e-020 1.5e-015 # CGCCTTA TAAGGCG 58 1 2.4e-017 7.3e-013 # CGCGTTA TAACGCG 16 2 6.1e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 1.5e-015 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 0.783784 0.216216 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 MOTIF ACCWCT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 136 32 4.0e-019 1.2e-014 # ACCACT AGTGGT 102 16 2.4e-018 7.3e-014 # ACCTCT AGAGGT 38 16 1.5e-003 4.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 156 E= 1.2e-014 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.756410 0.000000 0.000000 0.243590 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 45 2 3.6e-012 1.1e-007 # AACTTGGC GCCAAGTT 35 1 3.3e-010 9.7e-006 # AACTGGGC GCCCAGTT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 1.1e-007 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 0.222222 0.777778 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 33 0 7.3e-011 2.2e-006 # GCGCTACC GGTAGCGC 25 0 2.3e-008 6.8e-004 # GCTCTACC GGTAGAGC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.2e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.757576 0.242424 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 AAAAADA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAAAADA THTTTTT 186 95 2.7e-010 7.9e-006 # AAAAAAA TTTTTTT 103 51 4.3e-006 1.3e-001 # AAAAATA TATTTTT 79 36 1.5e-005 4.6e-001 # AAAAAGA TCTTTTT 56 28 1.0e-003 3.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 222 E= 7.9e-006 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 0.436937 0.000000 0.234234 0.328829 1.000000 0.000000 0.000000 0.000000 MOTIF CCHTAACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 38 2 4.2e-010 1.2e-005 # CCCTAACC GGTTAGGG 14 0 5.6e-005 1.7e+000 # CCATAACC GGTTATGG 14 1 4.6e-004 1.3e+001 # CCTTAACC GGTTAAGG 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.2e-005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.368421 0.368421 0.000000 0.263158 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 ACTSTTAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACTSTTAA TTAASAGT 26 0 1.1e-008 3.3e-004 # ACTCTTAA TTAAGAGT 15 0 2.8e-005 8.2e-001 # ACTGTTAA TTAACAGT 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.3e-004 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 0.576923 0.423077 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 GCGTGTK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCGTGTK MACACGC 30 2 8.8e-008 2.6e-003 # GCGTGTG CACACGC 17 1 6.5e-005 1.9e+000 # GCGTGTT AACACGC 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.6e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.566667 0.433333 MOTIF CCGTGMTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 22 0 1.9e-007 5.7e-003 # CCGTGATA TATCACGG 12 0 2.3e-004 6.7e+000 # CCGTGCTA TAGCACGG 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.7e-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 0.545455 0.454545 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATGGTCW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AATGGTCW WGACCATT 25 1 3.2e-007 9.2e-003 # AATGGTCA TGACCATT 16 1 1.3e-004 3.7e+000 # AATGGTCT AGACCATT 9 0 1.9e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.2e-003 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.360000 MOTIF CRCCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 91 39 7.9e-007 2.3e-002 # CGCCCA TGGGCG 42 13 3.9e-005 1.1e+000 # CACCCA TGGGTG 52 27 2.4e-003 7.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 112 E= 2.3e-002 0.000000 1.000000 0.000000 0.000000 0.633929 0.000000 0.366071 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 CCAACRA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCAACRA TYGTTGG 42 8 3.5e-007 1.0e-002 # CCAACGA TCGTTGG 19 0 1.6e-006 4.7e-002 # CCAACAA TTGTTGG 27 8 8.0e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 1.0e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.586957 0.000000 0.413043 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 51.24 seconds