# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-shuffled # positives: 782 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-centered (Sun Jan 19 02:59:16 PST 2020) # negatives: 782 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--HIR1/seqs-shuffled (Sun Jan 19 02:59:16 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 03:15:09 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 0.319 C 0.183 G 0.181 T 0.318 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 82 7 1.8e-018 5.8e-014 # TGTACGGA TCCGTACA 34 1 7.4e-010 2.3e-005 # TGTATGGG CCCATACA 34 5 9.3e-007 2.9e-002 # TGTACGGG CCCGTACA 11 0 4.7e-004 1.5e+001 # TGTATGGA TCCATACA 14 3 6.1e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 96 E= 5.8e-014 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 0.489583 0.000000 0.510417 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.531250 0.000000 0.468750 0.000000 MOTIF BTAAGGCG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 57 0 2.4e-018 7.6e-014 # TTAAGGCG CGCCTTAA 33 0 8.2e-011 2.6e-006 # CTAAGGCG CGCCTTAG 13 0 1.2e-004 3.6e+000 # GTAAGGCG CGCCTTAC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 7.6e-014 0.000000 0.228070 0.192982 0.578947 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 0.000000 0.000000 1.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 65 2 4.2e-018 1.3e-013 # CTCGGCCA TGGCCGAG 33 1 1.5e-009 4.6e-005 # CTTGGCCA TGGCCAAG 21 0 4.2e-007 1.3e-002 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 65 E= 1.3e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.507692 0.169231 0.323077 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 GGHTCGA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 76 8 5.4e-016 1.7e-011 # GGTTCGA TCGAACC 61 5 4.7e-014 1.5e-009 # GGCTCGA TCGAGCC 18 1 3.5e-005 1.1e+000 # GGATCGA TCGATCC 14 2 2.0e-003 6.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 1.7e-011 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.131579 0.144737 0.000000 0.723684 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 GCKCTMCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTMCC GGKAGMGC 47 0 3.5e-015 1.1e-010 # GCGCTACC GGTAGCGC 25 0 2.5e-008 7.6e-004 # GCTCTACC GGTAGAGC 13 0 1.2e-004 3.6e+000 # GCTCTCCC GGGAGAGC 9 0 1.9e-003 5.9e+001 # GCGCTCCC GGGAGCGC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 1.1e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.531915 0.468085 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.744681 0.255319 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTARACCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 42 2 3.4e-011 1.0e-006 # CTAGACCA TGGTCTAG 28 2 3.5e-007 1.1e-002 # CTAAACCA TGGTTTAG 14 0 5.8e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.0e-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 0.333333 0.000000 0.666667 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 MOTIF ACCCANAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 60 12 1.9e-009 5.8e-005 # ACCCAGAC GTCTGGGT 14 0 5.8e-005 1.8e+000 # ACCCACAC GTGTGGGT 29 10 1.5e-003 4.7e+001 # ACCCAAAC GTTTGGGT 13 2 3.6e-003 1.1e+002 # ACCCATAC GTATGGGT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 115 E= 5.8e-005 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 1.000000 0.000000 0.000000 0.000000 0.113043 0.686957 0.121739 0.078261 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AARAAAWA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 172 87 4.3e-009 1.3e-004 # AAAAAAAA TTTTTTTT 89 38 1.4e-006 4.3e-002 # AAAAAATA TATTTTTT 46 19 4.3e-004 1.3e+001 # AAGAAAAA TTTTTCTT 51 27 3.6e-003 1.1e+002 # AAGAAATA TATTTCTT 27 11 6.4e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 195 E= 1.3e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.646154 0.000000 0.353846 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 0.661538 0.000000 0.000000 0.338462 1.000000 0.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 29 1 2.3e-008 6.9e-004 # CCTTAACC GGTTAAGG 16 0 1.4e-005 4.3e-001 # CCATAACC GGTTATGG 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 6.9e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.466667 0.000000 0.000000 0.533333 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CATYACGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CATYACGC GCGTRATG 24 0 5.0e-008 1.5e-003 # CATCACGC GCGTGATG 12 0 2.3e-004 7.2e+000 # CATTACGC GCGTAATG 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-003 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 0.500000 0.000000 0.500000 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 MOTIF TGGCGCAR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TGGCGCAR YTGCGCCA 25 1 3.4e-007 1.0e-002 # TGGCGCAA TTGCGCCA 14 1 4.6e-004 1.4e+001 # TGGCGCAG CTGCGCCA 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.560000 0.000000 0.440000 0.000000 MOTIF ACTGAGCT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 21 0 4.2e-007 1.3e-002 # ACTGAGCT AGCTCAGT 21 0 4.2e-007 1.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 0.000000 0.000000 0.000000 1.000000 MOTIF CYACACTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CYACACTA TAGTGTRG 30 3 5.6e-007 1.7e-002 # CTACACTA TAGTGTAG 17 2 3.4e-004 1.0e+001 # CCACACTA TAGTGTGG 13 1 8.8e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.7e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.433333 0.000000 0.566667 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 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 69.85 seconds