# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-shuffled # positives: 792 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-centered (Fri Jan 17 22:43:10 PST 2020) # negatives: 792 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MOT3/seqs-shuffled (Fri Jan 17 22:43:10 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 22:59:35 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 0.202 G 0.200 T 0.298 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 120 6 7.3e-031 2.5e-026 # GGTTCGA TCGAACC 99 3 1.6e-027 5.6e-023 # GGATCGA TCGATCC 29 3 1.0e-006 3.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 2.5e-026 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.208333 0.000000 0.000000 0.791667 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 78 10 3.6e-015 1.3e-010 # AGTGGTT AACCACT 51 7 6.4e-010 2.2e-005 # AGTGGTA TACCACT 39 3 1.9e-009 6.5e-005 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 1.3e-010 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 0.436170 0.000000 0.000000 0.563830 MOTIF AAAAAWAW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWAW WTWTTTTT 199 90 6.4e-013 2.2e-008 # AAAAAAAT ATTTTTTT 97 43 1.1e-006 3.6e-002 # AAAAAAAA TTTTTTTT 85 41 2.8e-005 9.7e-001 # AAAAATAA TTATTTTT 57 23 6.2e-005 2.1e+000 # AAAAATAT ATATTTTT 41 16 5.1e-004 1.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 234 E= 2.2e-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 1.000000 0.000000 0.000000 0.000000 0.602564 0.000000 0.000000 0.397436 1.000000 0.000000 0.000000 0.000000 0.547009 0.000000 0.000000 0.452991 MOTIF ATGGCAWC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 31 2 5.0e-008 1.7e-003 # ATGGCAAC GTTGCCAT 22 2 1.6e-005 5.5e-001 # ATGGCATC GATGCCAT 9 0 1.9e-003 6.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.7e-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 0.709677 0.000000 0.000000 0.290323 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 23 0 1.0e-007 3.5e-003 # GCGCTACC GGTAGCGC 15 0 2.9e-005 9.8e-001 # GCTCTACC GGTAGAGC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.652174 0.347826 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 MOTIF CTTGRCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTTGRCC GGYCAAG 50 11 1.4e-007 4.8e-003 # CTTGACC GGTCAAG 22 3 7.0e-005 2.4e+000 # CTTGGCC GGCCAAG 28 8 5.3e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 4.8e-003 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 0.440000 0.000000 0.560000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 97 41 3.5e-007 1.2e-002 # CGCCCA TGGGCG 42 14 9.1e-005 3.1e+000 # CACCCA TGGGTG 56 27 7.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 116 E= 1.2e-002 0.000000 1.000000 0.000000 0.000000 0.620690 0.000000 0.379310 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAGGCG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AAGGCG CGCCTT 65 21 5.7e-007 1.9e-002 # AAGGCG CGCCTT 65 21 5.7e-007 1.9e-002 letter-probability matrix: alength= 4 w= 6 nsites= 65 E= 1.9e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTGGGGWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTGGGGWC GWCCCCAG 20 0 8.4e-007 2.9e-002 # CTGGGGAC GTCCCCAG 13 0 1.2e-004 3.9e+000 # CTGGGGTC GACCCCAG 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.9e-002 0.000000 1.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.650000 0.000000 0.000000 0.350000 0.000000 1.000000 0.000000 0.000000 MOTIF CACGGYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 31 4 1.4e-006 4.7e-002 # CACGGTG CACCGTG 21 3 1.3e-004 4.2e+000 # CACGGCG CGCCGTG 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 4.7e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.322581 0.000000 0.677419 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 54.26 seconds