# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/seqs-shuffled # positives: 476 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/seqs-centered (Sat Jan 18 21:13:43 PST 2020) # negatives: 476 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/seqs-shuffled (Sat Jan 18 21:13:43 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 21:23:07 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 0.293 C 0.209 G 0.207 T 0.291 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 80 2 2.2e-023 6.0e-019 # ACCCATAC GTATGGGT 39 2 1.9e-010 5.0e-006 # ATCCGTAC GTACGGAT 30 0 5.8e-010 1.6e-005 # ACCCGTAC GTACGGGT 12 0 2.3e-004 6.1e+000 # ATCCATAC GTATGGAT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 97 E= 6.0e-019 1.000000 0.000000 0.000000 0.000000 0.000000 0.546392 0.000000 0.453608 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.536082 0.000000 0.463918 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 MOTIF CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 78 4 1.7e-020 4.5e-016 # CGCCTTA TAAGGCG 61 3 3.7e-016 9.8e-012 # CGCGTTA TAACGCG 17 1 6.4e-005 1.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 4.5e-016 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 0.782051 0.217949 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 GGTTCRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 105 15 3.3e-020 8.7e-016 # GGTTCGA TCGAACC 81 7 9.7e-019 2.6e-014 # GGTTCAA TTGAACC 26 8 1.2e-003 3.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 107 E= 8.7e-016 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 0.242991 0.000000 0.757009 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 72 5 1.1e-017 2.9e-013 # ACCACTA TAGTGGT 45 4 1.7e-010 4.3e-006 # ACCACTC GAGTGGT 29 1 1.9e-008 5.0e-004 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 2.9e-013 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 0.608108 0.391892 0.000000 0.000000 MOTIF AAGAAAHA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAHA TDTTTCTT 66 4 9.6e-017 2.5e-012 # AAGAAAAA TTTTTCTT 39 1 1.7e-011 4.5e-007 # AAGAAATA TATTTCTT 19 1 1.7e-005 4.4e-001 # AAGAAACA TGTTTCTT 13 2 3.5e-003 9.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 2.5e-012 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.549296 0.183099 0.000000 0.267606 1.000000 0.000000 0.000000 0.000000 MOTIF AACTKGG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AACTKGG CCMAGTT 61 4 3.2e-015 8.4e-011 # AACTTGG CCAAGTT 40 3 7.2e-010 1.9e-005 # AACTGGG CCCAGTT 21 1 4.5e-006 1.2e-001 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 8.4e-011 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 0.344262 0.655738 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 2 9.5e-011 2.5e-006 # ATGGCAAC GTTGCCAT 28 1 3.8e-008 9.9e-004 # ATGGCATC GATGCCAT 12 1 1.6e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.5e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.700000 0.000000 0.000000 0.300000 0.000000 1.000000 0.000000 0.000000 MOTIF GACCAY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GACCAY RTGGTC 65 14 5.9e-010 1.5e-005 # GACCAC GTGGTC 29 3 9.0e-007 2.3e-002 # GACCAT ATGGTC 38 11 4.8e-005 1.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 69 E= 1.5e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.420290 0.000000 0.579710 MOTIF GCKCTACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 2 7.4e-010 1.9e-005 # GCGCTACC GGTAGCGC 25 2 2.1e-006 5.5e-002 # GCTCTACC GGTAGAGC 12 0 2.3e-004 5.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.9e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.675676 0.324324 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 CCCATKC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCCATKC GMATGGG 41 4 2.2e-009 5.7e-005 # CCCATGC GCATGGG 24 3 2.0e-005 5.0e-001 # CCCATTC GAATGGG 18 1 3.3e-005 8.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 5.7e-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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 1 2.4e-009 6.1e-005 # CTATCACG CGTGATAG 18 0 3.2e-006 8.2e-002 # CTATCACA TGTGATAG 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.1e-005 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 0.437500 0.000000 0.562500 0.000000 MOTIF CCGTGSA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 36 3 1.0e-008 2.6e-004 # CCGTGGA TCCACGG 23 2 7.7e-006 2.0e-001 # CCGTGCA TGCACGG 13 1 8.5e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.6e-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 0.378378 0.621622 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGMGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACTGMGC GCKCAGT 39 5 3.8e-008 9.5e-004 # ACTGAGC GCTCAGT 24 2 4.1e-006 1.0e-001 # ACTGCGC GCGCAGT 15 3 3.5e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 9.5e-004 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 0.615385 0.384615 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGCGCMAG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGCGCMAG CTKGCGCT 24 0 4.4e-008 1.1e-003 # AGCGCAAG CTTGCGCT 13 0 1.1e-004 2.8e+000 # AGCGCCAG CTGGCGCT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-003 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.541667 0.458333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATTAGAAR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATTAGAAR YTTCTAAT 26 1 1.5e-007 3.8e-003 # ATTAGAAA TTTCTAAT 13 0 1.1e-004 2.8e+000 # ATTAGAAG CTTCTAAT 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.8e-003 1.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.481481 0.000000 0.518519 0.000000 MOTIF SCACGCGA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST SCACGCGA TCGCGTGS 22 0 1.9e-007 4.7e-003 # GCACGCGA TCGCGTGC 12 0 2.3e-004 5.7e+000 # CCACGCGA TCGCGTGG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.7e-003 0.000000 0.454545 0.545455 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 1.000000 0.000000 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 AAAGCGWG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 21 0 3.8e-007 9.5e-003 # AAAGCGTG CACGCTTT 13 0 1.1e-004 2.8e+000 # AAAGCGAG CTCGCTTT 8 0 3.8e-003 9.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 9.5e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.380952 0.000000 0.000000 0.619048 0.000000 0.000000 1.000000 0.000000 MOTIF AAAARAAA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAAARAAA TTTYTTTT 64 22 1.2e-006 3.0e-002 # AAAAAAAA TTTTTTTT 46 17 1.1e-004 2.6e+000 # AAAAGAAA TTTCTTTT 22 7 3.6e-003 9.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 76 E= 3.0e-002 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 0.710526 0.000000 0.289474 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 MOTIF AKATCGG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AKATCGG CCGATMT 33 5 1.4e-006 3.5e-002 # AGATCGG CCGATCT 19 2 9.5e-005 2.4e+000 # ATATCGG CCGATAT 14 3 6.0e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 3.5e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.575758 0.424242 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATCGTGA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATCGTGA TCACGAT 19 0 1.6e-006 3.9e-002 # ATCGTGA TCACGAT 19 0 1.6e-006 3.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 19 E= 3.9e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 64.07 seconds