# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--GAL11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--GAL11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--GAL11/seqs-shuffled # positives: 793 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--GAL11/seqs-centered (Sun Jan 19 08:34:02 PST 2020) # negatives: 793 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--GAL11/seqs-shuffled (Sun Jan 19 08:34:02 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 08:49:49 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 0.299 C 0.201 G 0.200 T 0.300 MOTIF CCRTACAY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 74 3 9.7e-020 3.3e-015 # CCGTACAT ATGTACGG 30 1 1.1e-008 3.9e-004 # CCATACAT ATGTATGG 31 2 5.0e-008 1.7e-003 # CCGTACAC GTGTACGG 13 0 1.2e-004 3.9e+000 # CCATACAC GTGTATGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 87 E= 3.3e-015 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.494253 0.000000 0.505747 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 0.252874 0.000000 0.747126 MOTIF BGGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST BGGTTCGA TCGAACCV 72 3 3.9e-019 1.3e-014 # GGGTTCGA TCGAACCC 39 0 1.1e-012 3.8e-008 # CGGTTCGA TCGAACCG 26 3 6.5e-006 2.2e-001 # TGGTTCGA TCGAACCA 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 72 E= 1.3e-014 0.000000 0.361111 0.541667 0.097222 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 64 2 8.6e-018 2.9e-013 # CTCGGCCA TGGCCGAG 32 1 2.9e-009 9.9e-005 # CTTGGCCA TGGCCAAG 19 1 1.8e-005 6.1e-001 # CTGGGCCA TGGCCCAG 13 0 1.2e-004 3.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 2.9e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.203125 0.296875 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 TAAGGCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 76 7 9.9e-017 3.3e-012 # TAAGGCG CGCCTTA 57 3 1.2e-014 4.1e-010 # TAAGGCA TGCCTTA 22 4 2.4e-004 8.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 79 E= 3.3e-012 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 0.278481 0.000000 0.721519 0.000000 MOTIF ARAAARAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ARAAARAA TTYTTTYT 175 78 1.4e-011 4.8e-007 # AAAAAAAA TTTTTTTT 102 46 8.0e-007 2.7e-002 # AGAAAAAA TTTTTTCT 59 23 2.8e-005 9.5e-001 # AAAAAGAA TTCTTTTT 48 19 2.0e-004 6.6e+000 # AGAAAGAA TTCTTTCT 19 3 4.0e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 215 E= 4.8e-007 1.000000 0.000000 0.000000 0.000000 0.716279 0.000000 0.283721 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 0.720930 0.000000 0.279070 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF RCACCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST RCACCCA TGGGTGY 53 6 4.3e-011 1.4e-006 # ACACCCA TGGGTGT 39 2 2.5e-010 8.5e-006 # GCACCCA TGGGTGC 16 4 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 1.4e-006 0.666667 0.000000 0.333333 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 41 2 6.7e-011 2.2e-006 # GCGCTACC GGTAGCGC 24 0 5.0e-008 1.7e-003 # GCTCTACC GGTAGAGC 17 2 3.4e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.2e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.585366 0.414634 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 TGGCGYAR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYAR YTRCGCCA 41 0 2.7e-013 8.9e-009 # TGGCGCAG CTGCGCCA 12 0 2.3e-004 7.8e+000 # TGGCGTAA TTACGCCA 12 0 2.3e-004 7.8e+000 # TGGCGCAA TTGCGCCA 10 0 9.5e-004 3.2e+001 # TGGCGTAG CTACGCCA 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 8.9e-009 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 0.536585 0.000000 0.463415 0.000000 MOTIF AACCACTD DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AACCACTD HAGTGGTT 44 3 7.2e-011 2.4e-006 # AACCACTA TAGTGGTT 20 1 9.4e-006 3.1e-001 # AACCACTT AAGTGGTT 19 2 1.0e-004 3.4e+000 # AACCACTG CAGTGGTT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 2.4e-006 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 0.434783 0.000000 0.152174 0.413043 MOTIF AAAGCRTG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAAGCRTG CAYGCTTT 28 0 2.9e-009 9.7e-005 # AAAGCGTG CACGCTTT 20 0 8.4e-007 2.8e-002 # AAAGCATG CATGCTTT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.7e-005 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 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACGCGWC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACGCGWC GWCGCGT 28 1 4.5e-008 1.5e-003 # ACGCGTC GACGCGT 17 1 6.7e-005 2.2e+000 # ACGCGAC GTCGCGT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 1.5e-003 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 0.392857 0.000000 0.000000 0.607143 0.000000 1.000000 0.000000 0.000000 MOTIF SAAGA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 374 272 1.2e-007 3.9e-003 # CAAGA TCTTG 219 141 1.8e-006 6.1e-002 # GAAGA TCTTC 208 160 2.6e-003 8.5e+001 letter-probability matrix: alength= 4 w= 5 nsites= 516 E= 3.9e-003 0.000000 0.513566 0.486434 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 GATGSCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GATGSCA TGSCATC 35 4 1.2e-007 4.0e-003 # GATGGCA TGCCATC 21 2 3.0e-005 9.5e-001 # GATGCCA TGGCATC 14 2 2.0e-003 6.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 4.0e-003 0.000000 0.000000 1.000000 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 0.378378 0.621622 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCACR DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 32 3 1.6e-007 5.1e-003 # CTATCACA TGTGATAG 17 0 7.0e-006 2.2e-001 # CTATCACG CGTGATAG 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.1e-003 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 0.531250 0.000000 0.468750 0.000000 MOTIF TCTCCACR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TCTCCACR YGTGGAGA 25 1 3.4e-007 1.1e-002 # TCTCCACG CGTGGAGA 14 1 4.6e-004 1.5e+001 # TCTCCACA TGTGGAGA 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.440000 0.000000 0.560000 0.000000 MOTIF CTAGACCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CTAGACCA TGGTCTAG 21 0 4.2e-007 1.3e-002 # CTAGACCA TGGTCTAG 21 0 4.2e-007 1.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 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 MOTIF CTGAGCTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 21 0 4.2e-007 1.3e-002 # CTGAGCTA TAGCTCAG 21 0 4.2e-007 1.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 86.89 seconds