# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/seqs-shuffled # positives: 458 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/seqs-centered (Sun Jan 19 01:43:12 PST 2020) # negatives: 458 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/seqs-shuffled (Sun Jan 19 01:43:12 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 01:51:52 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 0.210 G 0.206 T 0.292 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 100 3 5.8e-029 1.5e-024 # GGTTCGA TCGAACC 83 3 3.0e-023 7.8e-019 # AGTTCGA TCGAACT 21 0 3.8e-007 9.7e-003 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 1.5e-024 0.190000 0.000000 0.810000 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 CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 82 1 1.8e-025 4.5e-021 # CCATACAT ATGTATGG 37 0 3.4e-012 8.7e-008 # CCGTACAT ATGTACGG 29 0 1.2e-009 3.0e-005 # CCGTACAC GTGTACGG 14 0 5.5e-005 1.4e+000 # CCATACAC GTGTATGG 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 95 E= 4.5e-021 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.536842 0.000000 0.463158 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.263158 0.000000 0.736842 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 64 0 5.1e-021 1.3e-016 # CTCGGCCA TGGCCGAG 33 0 6.4e-011 1.6e-006 # CTTGGCCA TGGCCAAG 20 0 7.7e-007 2.0e-002 # CTGGGCCA TGGCCCAG 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 1.3e-016 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.515625 0.171875 0.312500 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 74 3 2.6e-020 6.5e-016 # CGCCTTA TAAGGCG 59 3 1.4e-015 3.6e-011 # CGCGTTA TAACGCG 15 0 2.7e-005 6.8e-001 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 6.5e-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 0.797297 0.202703 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-5 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 50 1 5.9e-015 1.5e-010 # TAGTGGTA TACCACTA 32 0 1.3e-010 3.3e-006 # TAGTGGTT AACCACTA 18 1 3.3e-005 8.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 1.5e-010 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 0.640000 0.000000 0.000000 0.360000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 39 0 7.8e-013 2.0e-008 # GCGCTACC GGTAGCGC 28 0 2.4e-009 6.1e-005 # GCTCTACC GGTAGAGC 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 2.0e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.717949 0.282051 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 ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 1 8.2e-012 2.0e-007 # ATGGCAAC GTTGCCAT 29 1 1.9e-008 4.7e-004 # ATGGCATC GATGCCAT 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.0e-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 0.725000 0.000000 0.000000 0.275000 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 95 32 7.9e-010 2.0e-005 # CACCCA TGGGTG 60 19 7.7e-007 1.9e-002 # CGCCCA TGGGCG 35 13 7.9e-004 2.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 115 E= 2.0e-005 0.000000 1.000000 0.000000 0.000000 0.669565 0.000000 0.330435 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 MOTIF GTGATAGY DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 28 0 2.4e-009 6.0e-005 # GTGATAGC GCTATCAC 16 0 1.3e-005 3.3e-001 # GTGATAGT ACTATCAC 13 0 1.1e-004 2.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.0e-005 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 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 0.551724 0.000000 0.448276 MOTIF TGGCGYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 47 7 4.6e-009 1.1e-004 # TGGCGCA TGCGCCA 26 0 1.0e-008 2.5e-004 # TGGCGTA TACGCCA 21 7 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 1.1e-004 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 0.553191 0.000000 0.446809 1.000000 0.000000 0.000000 0.000000 MOTIF AAGCGWGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 26 0 1.0e-008 2.5e-004 # AAGCGTGA TCACGCTT 15 0 2.7e-005 6.6e-001 # AAGCGAGA TCTCGCTT 11 0 4.6e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.5e-004 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 0.423077 0.000000 0.000000 0.576923 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACTTKCG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 26 0 1.0e-008 2.5e-004 # CACTTGCG CGCAAGTG 14 0 5.5e-005 1.3e+000 # CACTTTCG CGAAAGTG 12 0 2.3e-004 5.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.5e-004 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 0.538462 0.461538 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCGTGSA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 38 4 1.5e-008 3.6e-004 # CCGTGGA TCCACGG 23 2 7.7e-006 1.9e-001 # CCGTGCA TGCACGG 15 2 1.1e-003 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 3.6e-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 0.394737 0.605263 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTGAGCT DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 0 9.0e-008 2.2e-003 # ACTGAGCT AGCTCAGT 23 0 9.0e-008 2.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.2e-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 0.000000 0.000000 0.000000 1.000000 MOTIF GTCAKAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GTCAKAC GTMTGAC 32 3 1.3e-007 3.2e-003 # GTCATAC GTATGAC 17 1 6.3e-005 1.5e+000 # GTCAGAC GTCTGAC 15 2 1.1e-003 2.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 3.2e-003 0.000000 0.000000 1.000000 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 0.000000 0.468750 0.531250 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCAKAAG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ATCAKAAG CTTMTGAT 22 0 1.8e-007 4.4e-003 # ATCAGAAG CTTCTGAT 11 0 4.6e-004 1.1e+001 # ATCATAAG CTTATGAT 11 0 4.6e-004 1.1e+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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATCTKTTG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATCTKTTG CAAMAGAT 25 1 2.9e-007 7.1e-003 # ATCTGTTG CAACAGAT 13 0 1.1e-004 2.7e+000 # ATCTTTTG CAAAAGAT 12 1 1.6e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.1e-003 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 0.000000 1.000000 0.000000 0.000000 0.520000 0.480000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GYGCCAGA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GYGCCAGA TCTGGCRC 20 0 7.7e-007 1.8e-002 # GTGCCAGA TCTGGCAC 11 0 4.6e-004 1.1e+001 # GCGCCAGA TCTGGCGC 9 0 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.8e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.450000 0.000000 0.550000 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAAAAA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST SAAAAAA TTTTTTS 110 55 1.5e-006 3.5e-002 # GAAAAAA TTTTTTC 74 33 1.6e-005 3.9e-001 # CAAAAAA TTTTTTG 46 25 6.5e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 125 E= 3.5e-002 0.000000 0.376000 0.624000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 58.81 seconds