# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SOK2/seqs-shuffled # positives: 1129 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SOK2/seqs-centered (Sat Jan 18 22:13:42 PST 2020) # negatives: 1129 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SOK2/seqs-shuffled (Sat Jan 18 22:13:42 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:28:40 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 0.305 C 0.198 G 0.194 T 0.303 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 100 10 6.2e-021 2.3e-016 # GGTTCGA TCGAACC 84 6 1.3e-019 5.0e-015 # AGTTCGA TCGAACT 22 4 2.5e-004 9.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 2.3e-016 0.190000 0.000000 0.810000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 53 1 1.7e-015 6.2e-011 # ATGTATGG CCATACAT 35 0 2.2e-011 8.3e-007 # ATGTACGG CCGTACAT 23 1 1.3e-006 5.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 63 E= 6.2e-011 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.396825 0.000000 0.603175 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 49 3 3.3e-012 1.2e-007 # CTCGGCCA TGGCCGAG 23 0 1.1e-007 4.0e-003 # CTTGGCCA TGGCCAAG 17 3 1.2e-003 4.6e+001 # CTGGGCCA TGGCCCAG 9 0 1.9e-003 7.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 1.2e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.469388 0.183673 0.346939 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 AAAAARAA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAAAARAA TTYTTTTT 172 72 5.4e-012 2.0e-007 # AAAAAGAA TTCTTTTT 81 22 9.1e-010 3.4e-005 # AAAAAAAA TTTTTTTT 109 56 1.1e-005 4.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 192 E= 2.0e-007 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 0.588542 0.000000 0.411458 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCTTAMC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 48 3 6.3e-012 2.3e-007 # GCCTTAAC GTTAAGGC 29 1 2.4e-008 9.0e-004 # GCCTTACC GGTAAGGC 19 2 1.0e-004 3.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 2.3e-007 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.604167 0.395833 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF KACCACTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST KACCACTA TAGTGGTM 34 1 8.3e-010 3.1e-005 # TACCACTA TAGTGGTA 26 1 1.8e-007 6.8e-003 # GACCACTA TAGTGGTC 8 0 3.9e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 3.1e-005 0.000000 0.000000 0.235294 0.764706 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTGC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCGTGC GCACGG 67 17 9.9e-009 3.7e-004 # CCGTGC GCACGG 67 17 9.9e-009 3.7e-004 letter-probability matrix: alength= 4 w= 6 nsites= 68 E= 3.7e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF BGGAGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST BGGAGA TCTCCV 132 58 1.1e-008 4.0e-004 # GGGAGA TCTCCC 36 11 1.5e-004 5.5e+000 # TGGAGA TCTCCA 60 32 1.9e-003 7.1e+001 # CGGAGA TCTCCG 38 17 2.9e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 137 E= 4.0e-004 0.000000 0.284672 0.270073 0.445255 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 GATTWGAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 41 7 2.4e-007 8.8e-003 # GATTAGAA TTCTAATC 23 2 8.8e-006 3.2e-001 # GATTTGAA TTCAAATC 18 5 5.1e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 8.8e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.560976 0.000000 0.000000 0.439024 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TATATAWA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TATATAWA TWTATATA 40 7 4.2e-007 1.5e-002 # TATATAAA TTTATATA 25 3 1.2e-005 4.5e-001 # TATATATA TATATATA 19 4 1.2e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 1.5e-002 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.534884 0.000000 0.000000 0.465116 1.000000 0.000000 0.000000 0.000000 MOTIF RCGGGGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 35 5 5.7e-007 2.1e-002 # ACGGGGA TCCCCGT 17 2 3.5e-004 1.3e+001 # GCGGGGA TCCCCGC 19 3 4.0e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 2.1e-002 0.472222 0.000000 0.527778 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TACSCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TACSCCA TGGSGTA 39 7 7.3e-007 2.7e-002 # TACCCCA TGGGGTA 21 2 3.1e-005 1.1e+000 # TACGCCA TGGCGTA 18 5 5.1e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 2.7e-002 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 0.538462 0.461538 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 AACCRCT DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AACCRCT AGYGGTT 57 17 1.2e-006 4.3e-002 # AACCACT AGTGGTT 44 15 8.4e-005 3.1e+000 # AACCGCT AGCGGTT 13 2 3.6e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 4.3e-002 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 0.771930 0.000000 0.228070 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 100.56 seconds