# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MCM1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MCM1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MCM1/seqs-shuffled # positives: 877 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MCM1/seqs-centered (Sun Jan 19 06:29:48 PST 2020) # negatives: 877 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MCM1/seqs-shuffled (Sun Jan 19 06:29:48 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 06:44:38 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 0.298 C 0.200 G 0.205 T 0.297 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 119 16 2.4e-022 8.2e-018 # GGTTCGA TCGAACC 85 7 3.1e-019 1.1e-014 # GGTTCAA TTGAACC 35 9 4.4e-005 1.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 120 E= 8.2e-018 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 0.291667 0.000000 0.708333 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 65 4 5.2e-016 1.8e-011 # CGCCTTA TAAGGCG 51 3 7.5e-013 2.6e-008 # CGCGTTA TAACGCG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 1.8e-011 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 0.784615 0.215385 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 TAGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 49 2 3.1e-013 1.1e-008 # TAGTGGTA TACCACTA 27 1 8.9e-008 3.1e-003 # TAGTGGTT AACCACTA 22 1 2.5e-006 8.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 1.1e-008 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.551020 0.000000 0.000000 0.448980 MOTIF CCAACTK DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCAACTK MAGTTGG 84 17 1.0e-012 3.5e-008 # CCAACTG CAGTTGG 37 6 6.2e-007 2.2e-002 # CCAACTT AAGTTGG 47 11 7.0e-007 2.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 85 E= 3.5e-008 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.435294 0.564706 MOTIF ACGVTG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACGVTG CABCGT 128 49 1.7e-010 5.9e-006 # ACGGTG CACCGT 48 14 6.2e-006 2.1e-001 # ACGCTG CAGCGT 36 12 3.0e-004 1.0e+001 # ACGATG CATCGT 49 24 1.9e-003 6.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 136 E= 5.9e-006 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.367647 0.272059 0.360294 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CMAGAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CMAGAW WTCTKG 283 167 1.4e-010 4.7e-006 # CAAGAA TTCTTG 123 70 3.3e-005 1.1e+000 # CCAGAT ATCTGG 60 27 1.9e-004 6.5e+000 # CAAGAT ATCTTG 74 44 2.8e-003 9.4e+001 # CCAGAA TTCTGG 71 42 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 346 E= 4.7e-006 0.000000 1.000000 0.000000 0.000000 0.601156 0.398844 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 0.586705 0.000000 0.000000 0.413295 MOTIF CTCGKCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTCGKCCA TGGMCGAG 34 1 7.7e-010 2.6e-005 # CTCGGCCA TGGCCGAG 27 1 8.9e-008 3.0e-003 # CTCGTCCA TGGACGAG 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.6e-005 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 1.000000 0.000000 0.000000 0.000000 0.794118 0.205882 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 ATAGTKTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 29 1 2.3e-008 7.8e-004 # ATAGTGTA TACACTAT 19 0 1.7e-006 5.8e-002 # ATAGTTTA TAAACTAT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.8e-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 0.655172 0.344828 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGGYG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYG CRCCCAT 45 8 8.0e-008 2.7e-003 # ATGGGCG CGCCCAT 21 2 3.0e-005 1.0e+000 # ATGGGTG CACCCAT 25 6 4.0e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 2.7e-003 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 0.446809 0.000000 0.553191 0.000000 0.000000 1.000000 0.000000 MOTIF AGCGYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGCGYG CRCGCT 68 21 1.5e-007 5.2e-003 # AGCGCG CGCGCT 39 12 8.0e-005 2.7e+000 # AGCGTG CACGCT 29 9 7.4e-004 2.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 69 E= 5.2e-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 0.579710 0.000000 0.420290 0.000000 0.000000 1.000000 0.000000 MOTIF AGCARATG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGCARATG CATYTGCT 28 2 3.6e-007 1.2e-002 # AGCAAATG CATTTGCT 16 1 1.3e-004 4.3e+000 # AGCAGATG CATCTGCT 12 1 1.7e-003 5.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.2e-002 1.000000 0.000000 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 0.571429 0.000000 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGAGRT DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGAGRT AYCTCT 117 56 6.2e-007 2.1e-002 # AGAGAT ATCTCT 64 27 4.4e-005 1.5e+000 # AGAGGT ACCTCT 59 31 1.6e-003 5.5e+001 letter-probability matrix: alength= 4 w= 6 nsites= 127 E= 2.1e-002 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 0.000000 0.535433 0.000000 0.464567 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ATTAASAG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 24 1 6.7e-007 2.2e-002 # ATTAACAG CTGTTAAT 13 0 1.2e-004 3.9e+000 # ATTAAGAG CTCTTAAT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.541667 0.458333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CACTTKCG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 26 2 1.3e-006 4.3e-002 # CACTTGCG CGCAAGTG 13 1 8.8e-004 2.9e+001 # CACTTTCG CGAAAGTG 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.3e-002 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 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GAAGAMA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GAAGAMA TKTCTTC 88 37 1.3e-006 4.3e-002 # GAAGAAA TTTCTTC 64 30 2.1e-004 6.8e+000 # GAAGACA TGTCTTC 26 7 6.0e-004 2.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 91 E= 4.3e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.703297 0.296703 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 86.05 seconds