# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/seqs-shuffled # positives: 685 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/seqs-centered (Sat Jan 18 22:47:30 PST 2020) # negatives: 685 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/seqs-shuffled (Sat Jan 18 22:47:30 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:03:07 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 0.287 C 0.214 G 0.214 T 0.286 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 106 13 4.3e-021 1.4e-016 # GGTTCGA TCGAACC 88 8 1.5e-019 5.1e-015 # GGCTCGA TCGAGCC 18 3 6.9e-004 2.3e+001 # GGATCGA TCGATCC 17 3 1.2e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 109 E= 1.4e-016 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.146789 0.137615 0.000000 0.715596 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 ACCCANAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 76 4 1.9e-019 6.2e-015 # ACCCATAC GTATGGGT 42 0 1.2e-013 3.9e-009 # ACCCAGAC GTCTGGGT 14 1 4.6e-004 1.5e+001 # ACCCACAC GTGTGGGT 15 2 1.1e-003 3.6e+001 # ACCCAAAC GTTTGGGT 12 1 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 87 E= 6.2e-015 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 0.137931 0.183908 0.160920 0.517241 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 68 2 4.0e-019 1.3e-014 # CTCGGCCA TGGCCGAG 33 1 1.4e-009 4.6e-005 # CTTGGCCA TGGCCAAG 23 1 1.3e-006 4.1e-002 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 68 E= 1.3e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.485294 0.176471 0.338235 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 76 7 7.6e-017 2.5e-012 # CGCCTTA TAAGGCG 61 5 4.0e-014 1.3e-009 # CGCGTTA TAACGCG 15 2 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 2.5e-012 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 0.802632 0.197368 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 0 2.5e-013 8.0e-009 # GCGCTACC GGTAGCGC 25 0 2.4e-008 7.8e-004 # GCTCTACC GGTAGAGC 16 0 1.4e-005 4.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 8.0e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.609756 0.390244 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 AACCACTW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AACCACTW WAGTGGTT 44 2 8.0e-012 2.6e-007 # AACCACTT AAGTGGTT 23 0 9.9e-008 3.2e-003 # AACCACTA TAGTGGTT 21 2 2.9e-005 9.4e-001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.6e-007 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.477273 0.000000 0.000000 0.522727 MOTIF SAAGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 344 223 2.0e-011 6.6e-007 # CAAGA TCTTG 215 123 5.0e-009 1.6e-004 # GAAGA TCTTC 193 134 1.2e-004 3.7e+000 letter-probability matrix: alength= 4 w= 5 nsites= 502 E= 6.6e-007 0.000000 0.549801 0.450199 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 ATGYACGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGYACGG CCGTRCAT 36 1 1.8e-010 5.5e-006 # ATGTACGG CCGTACAT 30 1 1.1e-008 3.4e-004 # ATGCACGG CCGTGCAT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 5.5e-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 0.205128 0.000000 0.794872 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 0.000000 1.000000 0.000000 MOTIF TGGCGYA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 41 4 2.8e-009 8.8e-005 # TGGCGCA TGCGCCA 22 2 1.6e-005 4.8e-001 # TGGCGTA TACGCCA 19 2 1.0e-004 3.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 41 E= 8.8e-005 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 0.536585 0.000000 0.463415 1.000000 0.000000 0.000000 0.000000 MOTIF ACGRTG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACGRTG CAYCGT 91 30 2.8e-009 8.8e-005 # ACGATG CATCGT 47 13 3.9e-006 1.2e-001 # ACGGTG CACCGT 45 17 1.8e-004 5.7e+000 letter-probability matrix: alength= 4 w= 6 nsites= 93 E= 8.8e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.505376 0.000000 0.494624 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGWGATA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATGWGATA TATCWCAT 29 1 2.2e-008 6.7e-004 # ATGTGATA TATCACAT 21 1 4.8e-006 1.5e-001 # ATGAGATA TATCTCAT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.7e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.275862 0.000000 0.000000 0.724138 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 MOTIF AGTCAKAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 28 1 4.3e-008 1.3e-003 # AGTCATAC GTATGACT 14 0 5.7e-005 1.8e+000 # AGTCAGAC GTCTGACT 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.3e-003 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 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 0.000000 1.000000 0.000000 0.000000 MOTIF CTWGACC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 34 3 4.3e-008 1.3e-003 # CTAGACC GGTCTAG 24 3 2.1e-005 6.5e-001 # CTTGACC GGTCAAG 10 0 9.4e-004 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.705882 0.000000 0.000000 0.294118 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 MOTIF AAAGCGWG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 29 2 1.8e-007 5.5e-003 # AAAGCGTG CACGCTTT 19 1 1.8e-005 5.5e-001 # AAAGCGAG CTCGCTTT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.5e-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 0.344828 0.000000 0.000000 0.655172 0.000000 0.000000 1.000000 0.000000 MOTIF AATGGTCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AATGGTCA TGACCATT 22 0 2.0e-007 6.2e-003 # AATGGTCA TGACCATT 22 0 2.0e-007 6.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.2e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTTAAYCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CTTAAYCA TGRTTAAG 25 1 3.3e-007 1.0e-002 # CTTAATCA TGATTAAG 14 1 4.6e-004 1.4e+001 # CTTAACCA TGGTTAAG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-002 0.000000 1.000000 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 0.440000 0.000000 0.560000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATAGTGTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATAGTGTA TACACTAT 21 0 4.1e-007 1.3e-002 # ATAGTGTA TACACTAT 21 0 4.1e-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 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGTCTCY DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GGTCTCY RGAGACC 39 7 6.3e-007 1.9e-002 # GGTCTCC GGAGACC 26 6 2.3e-004 7.1e+000 # GGTCTCT AGAGACC 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 40 E= 1.9e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.650000 0.000000 0.350000 # Stopping reason: E-value threshold exceeded # Running time: 79.67 seconds