# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--GAL11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--GAL11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--GAL11/seqs-shuffled # positives: 655 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--GAL11/seqs-centered (Sat Jan 18 12:16:33 PST 2020) # negatives: 655 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--GAL11/seqs-shuffled (Sat Jan 18 12:16:33 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 12:33:23 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 0.304 C 0.197 G 0.197 T 0.302 MOTIF RGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCRA TYGAACY 109 26 7.5e-015 2.5e-010 # GGTTCGA TCGAACC 48 8 1.3e-008 4.2e-004 # GGTTCAA TTGAACC 29 8 3.2e-004 1.1e+001 # AGTTCAA TTGAACT 21 7 5.8e-003 1.9e+002 # AGTTCGA TCGAACT 15 4 9.2e-003 3.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 111 E= 2.5e-010 0.324324 0.000000 0.675676 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 0.450450 0.000000 0.549550 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 32 0 1.6e-010 5.3e-006 # CTCGGCCA TGGCCGAG 15 0 2.8e-005 9.4e-001 # CTTGGCCA TGGCCAAG 10 0 9.4e-004 3.1e+001 # CTGGGCCA TGGCCCAG 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.3e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.468750 0.218750 0.312500 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 AGAAWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGAAWA TWTTCT 201 116 2.6e-008 8.7e-004 # AGAAAA TTTTCT 140 86 5.0e-005 1.7e+000 # AGAATA TATTCT 73 36 1.4e-004 4.7e+000 letter-probability matrix: alength= 4 w= 6 nsites= 239 E= 8.7e-004 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 0.682008 0.000000 0.000000 0.317992 1.000000 0.000000 0.000000 0.000000 MOTIF CCAACWGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCAACWGA TCWGTTGG 24 1 6.4e-007 2.1e-002 # CCAACTGA TCAGTTGG 13 0 1.1e-004 3.8e+000 # CCAACAGA TCTGTTGG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-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 0.458333 0.000000 0.000000 0.541667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 27 2 6.4e-007 2.1e-002 # CCTTAACC GGTTAAGG 19 2 9.9e-005 3.3e+000 # CCATAACC GGTTATGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.1e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.296296 0.000000 0.000000 0.703704 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GAAAKA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GAAAKA TMTTTC 156 89 1.3e-006 4.3e-002 # GAAATA TATTTC 93 56 8.3e-004 2.7e+001 # GAAAGA TCTTTC 66 36 1.3e-003 4.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 163 E= 4.3e-002 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 0.000000 0.000000 0.411043 0.588957 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 29.19 seconds