# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAT8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAT8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAT8/seqs-shuffled # positives: 586 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAT8/seqs-centered (Sat Jan 18 16:51:13 PST 2020) # negatives: 586 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--CAT8/seqs-shuffled (Sat Jan 18 16:51:13 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:06:35 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 0.300 C 0.200 G 0.201 T 0.298 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 98 7 1.3e-023 4.1e-019 # GGTTCGA TCGAACC 76 6 8.5e-018 2.7e-013 # GGATCGA TCGATCC 28 1 4.1e-008 1.3e-003 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 4.1e-019 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.275510 0.000000 0.000000 0.724490 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 AAAAADAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 113 39 5.2e-011 1.6e-006 # AAAAAAAA TTTTTTTT 55 15 4.0e-007 1.3e-002 # AAAAAGAA TTCTTTTT 38 8 3.1e-006 9.8e-002 # AAAAATAA TTATTTTT 41 20 4.0e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 133 E= 1.6e-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 0.436090 0.000000 0.263158 0.300752 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GAATTGAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GAATTGAA TTCAATTC 31 1 5.2e-009 1.6e-004 # GAATTGAA TTCAATTC 31 1 5.2e-009 1.6e-004 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.6e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 55 13 6.2e-008 1.9e-003 # AGTGGTT AACCACT 33 4 3.8e-007 1.2e-002 # AGTGGTA TACCACT 25 9 4.0e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 1.9e-003 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 0.442623 0.000000 0.000000 0.557377 MOTIF CCCMTACA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCCMTACA TGTAKGGG 22 0 2.0e-007 6.1e-003 # CCCATACA TGTATGGG 12 0 2.3e-004 7.2e+000 # CCCCTACA TGTAGGGG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.1e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.454545 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 1.000000 0.000000 0.000000 0.000000 MOTIF GCCASAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCCASAC GTSTGGC 27 2 6.2e-007 1.9e-002 # GCCAGAC GTCTGGC 15 0 2.8e-005 8.7e-001 # GCCACAC GTGTGGC 12 2 6.2e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 1.9e-002 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 0.000000 0.444444 0.555556 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGYGGAGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGYGGAGA TCTCCRCG 20 0 8.1e-007 2.5e-002 # CGTGGAGA TCTCCACG 11 0 4.7e-004 1.4e+001 # CGCGGAGA TCTCCGCG 9 0 1.9e-003 5.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.5e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.450000 0.000000 0.550000 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 MOTIF AMACTATA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AMACTATA TATAGTKT 23 1 1.2e-006 3.8e-002 # ACACTATA TATAGTGT 16 1 1.3e-004 3.9e+000 # AAACTATA TATAGTTT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.8e-002 1.000000 0.000000 0.000000 0.000000 0.304348 0.695652 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 1.000000 0.000000 0.000000 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: 34.76 seconds