# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-shuffled # positives: 745 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-centered (Fri Jan 17 23:17:52 PST 2020) # negatives: 745 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--PHD1/seqs-shuffled (Fri Jan 17 23:17:52 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:36:11 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 0.296 C 0.205 G 0.202 T 0.296 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 111 17 8.5e-020 3.0e-015 # GGTTCGA TCGAACC 77 9 1.3e-015 4.7e-011 # GGTTCAA TTGAACC 36 8 9.8e-006 3.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 113 E= 3.0e-015 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 0.318584 0.000000 0.681416 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAAAD DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAAD HTTTTTTT 146 60 5.2e-011 1.8e-006 # AAAAAAAT ATTTTTTT 88 34 1.9e-007 6.6e-003 # AAAAAAAA TTTTTTTT 75 35 4.8e-005 1.7e+000 # AAAAAAAG CTTTTTTT 51 21 1.9e-004 6.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 169 E= 1.8e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.289941 0.000000 0.242604 0.467456 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 55 14 1.9e-007 6.8e-003 # AGTGGTA TACCACT 29 5 1.6e-005 5.6e-001 # AGTGGTT AACCACT 30 9 4.6e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 6.8e-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 0.467742 0.000000 0.000000 0.532258 MOTIF RCTATCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST RCTATCA TGATAGY 37 6 5.9e-007 2.1e-002 # ACTATCA TGATAGT 22 4 2.4e-004 8.4e+000 # GCTATCA TGATAGC 15 2 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.1e-002 0.594595 0.000000 0.405405 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GRAGAAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GRAGAAA TTTCTYC 66 22 7.2e-007 2.5e-002 # GAAGAAA TTTCTTC 48 16 2.7e-005 9.5e-001 # GGAGAAA TTTCTCC 20 6 4.4e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 2.5e-002 0.000000 0.000000 1.000000 0.000000 0.708333 0.000000 0.291667 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAACWG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCAACWG CWGTTGG 42 9 1.2e-006 4.1e-002 # CCAACAG CTGTTGG 22 5 6.9e-004 2.4e+001 # CCAACTG CAGTTGG 20 4 7.1e-004 2.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 4.1e-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 0.523810 0.000000 0.000000 0.476190 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 33.52 seconds