# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HIR1/seqs-shuffled # positives: 565 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HIR1/seqs-centered (Sat Jan 18 03:56:18 PST 2020) # negatives: 565 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--HIR1/seqs-shuffled (Sat Jan 18 03:56:18 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 04:10:37 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 0.201 G 0.194 T 0.301 MOTIF TCGAACB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACB VGTTCGA 104 8 1.1e-024 3.4e-020 # TCGAACC GGTTCGA 76 3 1.1e-020 3.4e-016 # TCGAACT AGTTCGA 22 4 2.3e-004 7.1e+000 # TCGAACG CGTTCGA 11 1 3.0e-003 9.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 3.4e-020 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.711538 0.105769 0.182692 MOTIF ACCACTM DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 64 8 6.7e-013 2.0e-008 # ACCACTA TAGTGGT 42 5 6.6e-009 2.0e-004 # ACCACTC GAGTGGT 23 3 3.7e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 2.0e-008 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.646154 0.353846 0.000000 0.000000 MOTIF AAAADAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAADAAA TTTHTTTT 122 41 2.6e-012 7.9e-008 # AAAAGAAA TTTCTTTT 49 11 1.9e-007 5.9e-003 # AAAAAAAA TTTTTTTT 62 21 1.7e-006 5.1e-002 # AAAATAAA TTTATTTT 31 12 2.3e-003 7.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 139 E= 7.9e-008 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 0.467626 0.000000 0.316547 0.215827 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 CCAACTKG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCAACTKG CMAGTTGG 26 0 1.1e-008 3.4e-004 # CCAACTTG CAAGTTGG 19 0 1.6e-006 5.0e-002 # CCAACTGG CCAGTTGG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.4e-004 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.269231 0.730769 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 25 1 3.1e-007 9.5e-003 # ATGGCAAC GTTGCCAT 14 1 4.6e-004 1.4e+001 # ATGGCATC GATGCCAT 11 0 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.5e-003 1.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.560000 0.000000 0.000000 0.440000 0.000000 1.000000 0.000000 0.000000 MOTIF AMGGCTAT DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AMGGCTAT ATAGCCKT 21 0 3.9e-007 1.2e-002 # ACGGCTAT ATAGCCGT 11 0 4.6e-004 1.4e+001 # AAGGCTAT ATAGCCTT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 1.000000 0.000000 0.000000 0.000000 0.476190 0.523810 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GCGCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCGCTACC GGTAGCGC 21 0 3.9e-007 1.2e-002 # GCGCTACC GGTAGCGC 21 0 3.9e-007 1.2e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 0.000000 0.000000 1.000000 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 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 # Stopping reason: E-value threshold exceeded # Running time: 29.69 seconds