# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MCM1/seqs-shuffled # positives: 737 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MCM1/seqs-centered (Sun Jan 19 07:11:15 PST 2020) # negatives: 737 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--MCM1/seqs-shuffled (Sun Jan 19 07:11:15 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 07:27:37 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 0.198 G 0.199 T 0.300 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 92 10 4.1e-019 1.4e-014 # GGTTCGA TCGAACC 71 9 5.6e-014 1.9e-009 # GGATCGA TCGATCC 26 1 1.7e-007 5.8e-003 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 1.4e-014 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.260870 0.000000 0.000000 0.739130 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 AAAAAKAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAKAA TTMTTTTT 97 29 8.4e-011 2.9e-006 # AAAAAGAA TTCTTTTT 48 13 2.5e-006 8.5e-002 # AAAAATAA TTATTTTT 53 17 6.1e-006 2.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 105 E= 2.9e-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 0.000000 0.000000 0.466667 0.533333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAASA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCAASA TSTTGG 139 60 9.1e-010 3.1e-005 # CCAACA TGTTGG 72 28 3.1e-006 1.1e-001 # CCAAGA TCTTGG 73 34 5.9e-005 2.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 158 E= 3.1e-005 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 0.481013 0.518987 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACGRTG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACGRTG CAYCGT 78 26 6.1e-008 2.1e-003 # ACGGTG CACCGT 39 7 6.4e-007 2.2e-002 # ACGATG CATCGT 43 19 1.3e-003 4.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 83 E= 2.1e-003 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.518072 0.000000 0.481928 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTYGGCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 23 0 1.0e-007 3.4e-003 # CTCGGCCA TGGCCGAG 12 0 2.3e-004 7.8e+000 # CTTGGCCA TGGCCAAG 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.4e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.521739 0.000000 0.478261 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 CTTAAYCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTTAAYCA TGRTTAAG 29 2 1.8e-007 6.1e-003 # CTTAACCA TGGTTAAG 20 2 5.4e-005 1.8e+000 # CTTAATCA TGATTAAG 9 0 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.1e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.689655 0.000000 0.310345 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CKCTACC GGTAGMG 33 4 4.1e-007 1.4e-002 # CTCTACC GGTAGAG 17 2 3.4e-004 1.1e+001 # CGCTACC GGTAGCG 16 2 6.2e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.470588 0.529412 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 CCTTASCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCTTASCA TGSTAAGG 21 0 4.1e-007 1.4e-002 # CCTTACCA TGGTAAGG 12 0 2.3e-004 7.8e+000 # CCTTAGCA TGCTAAGG 9 0 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATAKTGTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATAKTGTA TACAMTAT 24 1 6.5e-007 2.2e-002 # ATATTGTA TACAATAT 11 0 4.7e-004 1.6e+001 # ATAGTGTA TACACTAT 13 1 8.7e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 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 0.000000 0.541667 0.458333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 46.83 seconds