# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/seqs-shuffled # positives: 812 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/seqs-centered (Sun Jan 19 07:49:09 PST 2020) # negatives: 812 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/seqs-shuffled (Sun Jan 19 07:49:09 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 08:05:14 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 0.315 C 0.189 G 0.183 T 0.312 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 85 8 1.7e-018 5.4e-014 # GGTTCGA TCGAACC 68 5 4.8e-016 1.6e-011 # AGTTCGA TCGAACT 21 3 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 85 E= 5.4e-014 0.223529 0.000000 0.776471 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 ATGYAYGG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATGYAYGG CCRTRCAT 75 5 4.4e-018 1.4e-013 # ATGTATGG CCATACAT 38 3 3.6e-009 1.2e-004 # ATGTACGG CCGTACAT 31 1 5.8e-009 1.9e-004 # ATGCATGG CCATGCAT 8 0 3.8e-003 1.2e+002 # ATGCACGG CCGTGCAT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 92 E= 1.4e-013 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 0.195652 0.000000 0.804348 1.000000 0.000000 0.000000 0.000000 0.000000 0.467391 0.000000 0.532609 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TAAGGCR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 83 8 6.2e-018 2.0e-013 # TAAGGCG CGCCTTA 65 4 4.8e-016 1.5e-011 # TAAGGCA TGCCTTA 21 4 4.2e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 2.0e-013 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.244186 0.000000 0.755814 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 67 6 6.0e-015 1.9e-010 # CTCGGCCA TGGCCGAG 34 0 4.1e-011 1.3e-006 # CTTGGCCA TGGCCAAG 22 5 6.9e-004 2.2e+001 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 9.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 1.9e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.507463 0.164179 0.328358 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 ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 45 1 3.7e-013 1.2e-008 # ATGGCAAC GTTGCCAT 29 0 1.4e-009 4.6e-005 # ATGGCATC GATGCCAT 16 1 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 1.2e-008 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 0.644444 0.000000 0.000000 0.355556 0.000000 1.000000 0.000000 0.000000 MOTIF TTTCTTB DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 193 91 1.4e-011 4.5e-007 # TTTCTTC GAAGAAA 59 19 1.9e-006 6.1e-002 # TTTCTTG CAAGAAA 53 19 2.6e-005 8.3e-001 # TTTCTTT AAAGAAA 97 57 4.5e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 220 E= 4.5e-007 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.272727 0.245455 0.481818 MOTIF GCGCTHCC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCGCTHCC GGDAGCGC 35 0 2.0e-011 6.3e-007 # GCGCTACC GGTAGCGC 30 0 7.1e-010 2.2e-005 # GCGCTTCC GGAAGCGC 9 0 1.9e-003 6.1e+001 # GCGCTCCC GGGAGCGC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 6.3e-007 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 0.685714 0.114286 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACCACTW DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AACCACTW WAGTGGTT 48 4 3.6e-011 1.1e-006 # AACCACTT AAGTGGTT 28 0 2.9e-009 9.3e-005 # AACCACTA TAGTGGTT 20 4 7.1e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 1.1e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.416667 0.000000 0.000000 0.583333 MOTIF TGGCGYA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 47 4 6.8e-011 2.1e-006 # TGGCGCA TGCGCCA 25 2 2.4e-006 7.6e-002 # TGGCGTA TACGCCA 22 2 1.6e-005 5.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 2.1e-006 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 0.000000 1.000000 0.000000 0.000000 0.531915 0.000000 0.468085 1.000000 0.000000 0.000000 0.000000 MOTIF CCCANACA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCCANACA TGTNTGGG 69 15 3.8e-010 1.2e-005 # CCCACACA TGTGTGGG 37 11 9.0e-005 2.8e+000 # CCCATACA TGTATGGG 13 1 8.8e-004 2.8e+001 # CCCAAACA TGTTTGGG 15 3 3.6e-003 1.1e+002 # CCCAGACA TGTCTGGG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 96 E= 1.2e-005 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 0.156250 0.635417 0.072917 0.135417 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTWGACC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 47 7 6.9e-009 2.2e-004 # CTAGACC GGTCTAG 29 4 4.5e-006 1.4e-001 # CTTGACC GGTCAAG 18 3 7.0e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 2.2e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.617021 0.000000 0.000000 0.382979 0.000000 0.000000 1.000000 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 ATAGTKTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 35 3 2.4e-008 7.6e-004 # ATAGTGTA TACACTAT 20 0 8.5e-007 2.7e-002 # ATAGTTTA TAAACTAT 15 3 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 7.6e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.555556 0.444444 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCTCCACR DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TCTCCACR YGTGGAGA 24 0 5.0e-008 1.6e-003 # TCTCCACA TGTGGAGA 13 0 1.2e-004 3.6e+000 # TCTCCACG CGTGGAGA 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.541667 0.000000 0.458333 0.000000 MOTIF RCGGGGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 27 1 8.8e-008 2.8e-003 # GCGGGGA TCCCCGC 16 1 1.3e-004 4.0e+000 # ACGGGGA TCCCCGT 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 2.8e-003 0.407407 0.000000 0.592593 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 CTCTMCCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 26 1 1.7e-007 5.4e-003 # CTCTCCCA TGGGAGAG 13 0 1.2e-004 3.6e+000 # CTCTACCA TGGTAGAG 13 1 8.8e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.4e-003 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 0.000000 0.000000 1.000000 0.500000 0.500000 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 TAKCTCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 48 11 4.0e-007 1.3e-002 # TAGCTCA TGAGCTA 21 3 1.3e-004 3.9e+000 # TATCTCA TGAGATA 27 8 8.4e-004 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 1.3e-002 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.396226 0.603774 0.000000 1.000000 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 CKTTGGGC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 21 0 4.2e-007 1.3e-002 # CGTTGGGC GCCCAACG 14 0 5.8e-005 1.8e+000 # CTTTGGGC GCCCAAAG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATATATR DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATATATR YATATAT 66 22 7.7e-007 2.4e-002 # ATATATA TATATAT 48 14 6.0e-006 1.9e-001 # ATATATG CATATAT 41 13 6.8e-005 2.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 2.4e-002 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 0.000000 0.000000 0.000000 1.000000 0.521127 0.000000 0.478873 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 95.02 seconds