# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/seqs-shuffled # positives: 456 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/seqs-centered (Sun Jan 19 04:16:56 PST 2020) # negatives: 456 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/seqs-shuffled (Sun Jan 19 04:16:56 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 04:25:30 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 0.292 C 0.209 G 0.208 T 0.291 MOTIF CGCSTTA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 79 2 4.0e-023 1.1e-018 # CGCCTTA TAAGGCG 63 2 6.7e-018 1.8e-013 # CGCGTTA TAACGCG 16 0 1.3e-005 3.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 1.1e-018 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 0.797468 0.202532 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 MOTIF TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 83 6 2.9e-020 7.5e-016 # TGTATGGG CCCATACA 37 1 6.9e-011 1.8e-006 # TGTACGGA TCCGTACA 32 2 2.1e-008 5.5e-004 # TGTACGGG CCCGTACA 12 1 1.6e-003 4.2e+001 # TGTATGGA TCCATACA 12 2 6.1e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 97 E= 7.5e-016 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 0.474227 0.000000 0.525773 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.484536 0.000000 0.515464 0.000000 MOTIF GGTTCRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 97 13 3.0e-019 7.8e-015 # GGTTCGA TCGAACC 75 8 3.1e-016 8.1e-012 # GGTTCAA TTGAACC 24 5 2.2e-004 5.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 7.8e-015 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.242424 0.000000 0.757576 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTM DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 76 5 5.7e-019 1.5e-014 # ACCACTA TAGTGGT 48 3 3.1e-012 8.0e-008 # ACCACTC GAGTGGT 30 2 8.0e-008 2.1e-003 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 1.5e-014 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 0.620253 0.379747 0.000000 0.000000 MOTIF AACTKGGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 46 0 4.3e-015 1.1e-010 # AACTTGGC GCCAAGTT 35 0 1.5e-011 3.8e-007 # AACTGGGC GCCCAGTT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 1.1e-010 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 0.239130 0.760870 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 ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 41 1 4.0e-012 1.0e-007 # ATGGCAAC GTTGCCAT 29 0 1.2e-009 3.0e-005 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.0e-007 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 0.707317 0.000000 0.000000 0.292683 0.000000 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 33 0 6.4e-011 1.6e-006 # CTATCACG CGTGATAG 18 0 3.2e-006 8.2e-002 # CTATCACA TGTGATAG 15 0 2.7e-005 6.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 1.6e-006 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.000000 0.545455 0.000000 MOTIF ATGGGBG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGGBG CVCCCAT 53 7 1.1e-010 2.9e-006 # ATGGGCG CGCCCAT 15 0 2.7e-005 6.9e-001 # ATGGGTG CACCCAT 25 5 1.3e-004 3.3e+000 # ATGGGGG CCCCCAT 14 2 1.9e-003 4.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 2.9e-006 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 0.000000 1.000000 0.000000 0.000000 0.272727 0.254545 0.472727 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 36 1 1.4e-010 3.5e-006 # GCGCTACC GGTAGCGC 25 0 2.1e-008 5.4e-004 # GCTCTACC GGTAGAGC 11 1 3.0e-003 7.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 3.5e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.694444 0.305556 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 TGGCGYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 45 4 1.6e-010 4.0e-006 # TGGCGTA TACGCCA 21 0 3.8e-007 9.5e-003 # TGGCGCA TGCGCCA 24 4 7.2e-005 1.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 4.0e-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 0.533333 0.000000 0.466667 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 218 133 4.8e-009 1.2e-004 # GAAGA TCTTC 121 63 1.1e-006 2.8e-002 # CAAGA TCTTG 124 77 1.1e-004 2.9e+000 letter-probability matrix: alength= 4 w= 5 nsites= 298 E= 1.2e-004 0.000000 0.530201 0.469799 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCCAVACA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCCAVACA TGTBTGGG 33 2 1.1e-008 2.6e-004 # CCCACACA TGTGTGGG 14 1 4.5e-004 1.1e+001 # CCCAAACA TGTTTGGG 13 1 8.5e-004 2.1e+001 # CCCAGACA TGTCTGGG 7 0 7.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 2.6e-004 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 0.371429 0.428571 0.200000 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 MOTIF CGTGYTAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 24 0 4.4e-008 1.0e-003 # CGTGCTAA TTAGCACG 12 0 2.3e-004 5.4e+000 # CGTGTTAA TTAACACG 12 0 2.3e-004 5.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.0e-003 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 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGARTCAT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGARTCAT ATGAYTCT 22 0 1.8e-007 4.4e-003 # AGAGTCAT ATGACTCT 12 0 2.3e-004 5.4e+000 # AGAATCAT ATGATTCT 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.454545 0.000000 0.545455 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 0.000000 0.000000 0.000000 1.000000 MOTIF GRTCTCCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GRTCTCCA TGGAGAYC 22 0 1.8e-007 4.4e-003 # GGTCTCCA TGGAGACC 12 0 2.3e-004 5.4e+000 # GATCTCCA TGGAGATC 10 0 9.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.4e-003 0.000000 0.000000 1.000000 0.000000 0.454545 0.000000 0.545455 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGC GCTCAGT 21 0 3.8e-007 9.0e-003 # ACTGAGC GCTCAGT 21 0 3.8e-007 9.0e-003 letter-probability matrix: alength= 4 w= 7 nsites= 21 E= 9.0e-003 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 1.000000 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 MOTIF ACTTSTAA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTTSTAA TTASAAGT 21 0 3.8e-007 9.0e-003 # ACTTCTAA TTAGAAGT 14 0 5.5e-005 1.3e+000 # ACTTGTAA TTACAAGT 7 0 7.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.0e-003 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 0.000000 1.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAGWCGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CAGWCGC GCGWCTG 27 2 5.8e-007 1.4e-002 # CAGACGC GCGTCTG 18 2 1.8e-004 4.2e+000 # CAGTCGC GCGACTG 9 0 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 1.4e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACCACTTR DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACCACTTR YAAGTGGT 24 1 5.8e-007 1.4e-002 # ACCACTTG CAAGTGGT 16 1 1.2e-004 2.9e+000 # ACCACTTA TAAGTGGT 8 0 3.8e-003 9.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.4e-002 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 0.000000 0.000000 0.000000 1.000000 0.333333 0.000000 0.666667 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 59.08 seconds