# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-shuffled # positives: 536 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-centered (Sat Jan 18 04:28:29 PST 2020) # negatives: 536 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PDR3/seqs-shuffled (Sat Jan 18 04:28:29 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 04:41:25 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 0.305 C 0.196 G 0.203 T 0.296 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 89 5 8.2e-023 2.5e-018 # GGTTCGA TCGAACC 70 4 7.5e-018 2.3e-013 # GGATCGA TCGATCC 26 1 1.6e-007 4.8e-003 letter-probability matrix: alength= 4 w= 7 nsites= 89 E= 2.5e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.269663 0.000000 0.000000 0.730337 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 AAAARWAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAARWAA TTWYTTTT 120 51 4.8e-009 1.5e-004 # AAAAGAAA TTTCTTTT 34 10 1.5e-004 4.5e+000 # AAAAATAA TTATTTTT 48 19 1.7e-004 5.3e+000 # AAAAAAAA TTTTTTTT 48 21 5.4e-004 1.6e+001 # AAAAGTAA TTACTTTT 14 3 6.0e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 145 E= 1.5e-004 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 0.675862 0.000000 0.324138 0.000000 0.593103 0.000000 0.000000 0.406897 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTWCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTWCC GGWAG 191 117 3.8e-007 1.2e-002 # CTACC GGTAG 82 41 5.6e-005 1.7e+000 # CTTCC GGAAG 123 80 5.1e-004 1.6e+001 letter-probability matrix: alength= 4 w= 5 nsites= 234 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.380342 0.000000 0.000000 0.619658 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CAAGTKG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAAGTKG CMACTTG 31 4 1.2e-006 3.6e-002 # CAAGTTG CAACTTG 18 3 6.7e-004 2.0e+001 # CAAGTGG CCACTTG 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 3.6e-002 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.419355 0.580645 0.000000 0.000000 1.000000 0.000000 MOTIF CGYGGAGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGYGGAGA TCTCCRCG 19 0 1.6e-006 4.8e-002 # CGTGGAGA TCTCCACG 12 0 2.3e-004 6.8e+000 # CGCGGAGA TCTCCGCG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.8e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.368421 0.000000 0.631579 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 20.95 seconds