# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SFL1/seqs-shuffled # positives: 832 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SFL1/seqs-centered (Sat Jan 18 06:33:51 PST 2020) # negatives: 832 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--SFL1/seqs-shuffled (Sat Jan 18 06:33:51 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:50:31 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 0.197 G 0.197 T 0.303 MOTIF GGTTCDA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCDA THGAACC 110 23 3.6e-016 1.3e-011 # GGTTCGA TCGAACC 59 8 2.3e-011 8.2e-007 # GGTTCTA TAGAACC 21 4 4.2e-004 1.5e+001 # GGTTCAA TTGAACC 32 11 8.4e-004 3.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 113 E= 1.3e-011 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 1.000000 0.000000 0.000000 0.292035 0.000000 0.522124 0.185841 1.000000 0.000000 0.000000 0.000000 MOTIF AARAAAR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAAR YTTTYTT 294 171 1.1e-011 3.9e-007 # AAGAAAA TTTTCTT 102 49 3.8e-006 1.3e-001 # AAAAAAA TTTTTTT 150 90 1.8e-005 6.4e-001 # AAAAAAG CTTTTTT 110 68 5.5e-004 2.0e+001 # AAGAAAG CTTTCTT 43 18 7.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 363 E= 3.9e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.617080 0.000000 0.382920 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 0.669421 0.000000 0.330579 0.000000 MOTIF TACCR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TACCR YGGTA 274 160 1.2e-010 4.2e-006 # TACCG CGGTA 118 51 3.0e-008 1.1e-003 # TACCA TGGTA 187 113 1.5e-006 5.2e-002 letter-probability matrix: alength= 4 w= 5 nsites= 340 E= 4.2e-006 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 0.626471 0.000000 0.373529 0.000000 MOTIF GYGGAGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GYGGAGA TCTCCRC 32 4 7.7e-007 2.6e-002 # GTGGAGA TCTCCAC 19 3 4.0e-004 1.4e+001 # GCGGAGA TCTCCGC 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 2.6e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.406250 0.000000 0.593750 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 AYATATA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AYATATA TATATRT 58 17 6.5e-007 2.2e-002 # ATATATA TATATAT 36 10 6.4e-005 2.2e+000 # ACATATA TATATGT 28 8 5.3e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 63 E= 2.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.412698 0.000000 0.587302 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTTGGM DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTTGGM KCCAAG 118 58 1.1e-006 3.6e-002 # CTTGGA TCCAAG 63 30 2.9e-004 9.8e+000 # CTTGGC GCCAAG 57 28 8.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 131 E= 3.6e-002 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.519084 0.480916 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 36.14 seconds