# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/seqs-shuffled # positives: 529 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/seqs-centered (Sat Jan 18 14:06:57 PST 2020) # negatives: 529 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/seqs-shuffled (Sat Jan 18 14:06:57 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 14:18:13 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 0.289 C 0.217 G 0.209 T 0.285 MOTIF SGGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCRA TYGAACCS 112 3 1.2e-032 3.2e-028 # GGGTTCGA TCGAACCC 47 0 2.4e-015 6.6e-011 # CGGTTCGA TCGAACCG 38 2 4.0e-010 1.1e-005 # GGGTTCAA TTGAACCC 17 1 6.5e-005 1.7e+000 # CGGTTCAA TTGAACCG 10 0 9.4e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 112 E= 3.2e-028 0.000000 0.428571 0.571429 0.000000 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.241071 0.000000 0.758929 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTWRACC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTWRACC GGTYWAG 110 15 2.0e-021 5.4e-017 # CTAGACC GGTCTAG 27 1 7.9e-008 2.1e-003 # CTTAACC GGTTAAG 43 8 1.9e-007 5.1e-003 # CTTGACC GGTCAAG 21 2 2.8e-005 7.5e-001 # CTAAACC GGTTTAG 20 4 6.9e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 111 E= 5.4e-017 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.423423 0.000000 0.000000 0.576577 0.567568 0.000000 0.432432 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 CCVTACA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCVTACA TGTABGG 102 14 9.5e-020 2.5e-015 # CCATACA TGTATGG 48 5 1.4e-010 3.8e-006 # CCGTACA TGTACGG 47 6 1.3e-009 3.4e-005 # CCCTACA TGTAGGG 16 3 2.0e-003 5.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 121 E= 2.5e-015 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.132231 0.413223 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 MOTIF GCKCTMCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTMCC GGKAGMGC 60 1 4.8e-018 1.3e-013 # GCGCTACC GGTAGCGC 34 0 3.4e-011 8.9e-007 # GCTCTACC GGTAGAGC 16 0 1.4e-005 3.6e-001 # GCGCTCCC GGGAGCGC 11 0 4.6e-004 1.2e+001 # GCTCTCCC GGGAGAGC 10 1 5.7e-003 1.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 60 E= 1.3e-013 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.566667 0.433333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.733333 0.266667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 71 5 2.9e-017 7.7e-013 # CTCGGCCA TGGCCGAG 37 2 7.9e-010 2.1e-005 # CTTGGCCA TGGCCAAG 22 1 2.3e-006 6.1e-002 # CTGGGCCA TGGCCCAG 12 2 6.2e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 7.7e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.521127 0.169014 0.309859 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 ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 47 1 6.2e-014 1.6e-009 # ATGGCAAC GTTGCCAT 31 0 3.0e-010 7.8e-006 # ATGGCATC GATGCCAT 16 1 1.2e-004 3.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 1.6e-009 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 0.659574 0.000000 0.000000 0.340426 0.000000 1.000000 0.000000 0.000000 MOTIF TAGTGTAR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAGTGTAR YTACACTA 31 0 3.0e-010 7.7e-006 # TAGTGTAG CTACACTA 16 0 1.4e-005 3.5e-001 # TAGTGTAA TTACACTA 15 0 2.8e-005 7.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 7.7e-006 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 0.483871 0.000000 0.516129 0.000000 MOTIF CYTGCGC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CYTGCGC GCGCARG 44 4 3.5e-010 9.1e-006 # CTTGCGC GCGCAAG 27 1 7.9e-008 2.1e-003 # CCTGCGC GCGCAGG 17 3 1.2e-003 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 9.1e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.361702 0.000000 0.638298 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGAAAW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAW WTTTCTT 94 31 8.7e-010 2.3e-005 # AAGAAAA TTTTCTT 63 19 2.1e-007 5.6e-003 # AAGAAAT ATTTCTT 35 12 4.2e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 2.3e-005 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.663462 0.000000 0.000000 0.336538 MOTIF CCGTGSA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 45 5 9.7e-010 2.5e-005 # CCGTGCA TGCACGG 20 1 8.9e-006 2.3e-001 # CCGTGGA TCCACGG 25 4 4.2e-005 1.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 2.5e-005 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 0.444444 0.555556 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACACSC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACACSC GSGTGT 113 45 2.4e-009 6.1e-005 # ACACGC GCGTGT 42 7 1.0e-007 2.6e-003 # ACACCC GGGTGT 72 38 4.1e-004 1.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 192 E= 6.1e-005 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 0.781250 0.218750 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCGTRAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATCGTRAG CTYACGAT 26 0 1.1e-008 2.8e-004 # ATCGTGAG CTCACGAT 17 0 6.7e-006 1.7e-001 # ATCGTAAG CTTACGAT 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.8e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.346154 0.000000 0.653846 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GTGATAGY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 33 2 1.2e-008 2.9e-004 # GTGATAGC GCTATCAC 17 1 6.5e-005 1.6e+000 # GTGATAGT ACTATCAC 16 1 1.2e-004 3.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.9e-004 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 0.515152 0.000000 0.484848 MOTIF ACTRCGCC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACTRCGCC GGCGYAGT 25 0 2.2e-008 5.6e-004 # ACTGCGCC GGCGCAGT 14 0 5.6e-005 1.4e+000 # ACTACGCC GGCGTAGT 11 0 4.6e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 5.6e-004 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.440000 0.000000 0.560000 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 MOTIF CSCATGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CSCATGC GCATGSG 37 4 3.0e-008 7.7e-004 # CCCATGC GCATGGG 27 3 3.2e-006 8.1e-002 # CGCATGC GCATGCG 10 1 5.7e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 7.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.729730 0.270270 0.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCCTTAS DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTAS STAAGGCG 28 1 4.0e-008 1.0e-003 # CGCCTTAG CTAAGGCG 16 1 1.2e-004 3.1e+000 # CGCCTTAC GTAAGGCG 12 0 2.3e-004 5.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.0e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.571429 0.000000 MOTIF GCGCCMA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GCGCCMA TKGGCGC 28 1 4.0e-008 9.9e-004 # GCGCCCA TGGGCGC 13 0 1.1e-004 2.8e+000 # GCGCCAA TTGGCGC 15 1 2.4e-004 5.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 9.9e-004 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 0.000000 1.000000 0.000000 0.000000 0.535714 0.464286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAKCTCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 41 6 4.9e-008 1.2e-003 # TAGCTCA TGAGCTA 23 3 3.7e-005 9.1e-001 # TATCTCA TGAGATA 18 3 6.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 1.2e-003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.511111 0.488889 0.000000 1.000000 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 MOTIF AATCAKAA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AATCAKAA TTMTGATT 27 1 7.9e-008 2.0e-003 # AATCATAA TTATGATT 14 0 5.6e-005 1.4e+000 # AATCAGAA TTCTGATT 14 1 4.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 2.0e-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 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 MOTIF ATCTGYTG DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATCTGYTG CARCAGAT 22 0 1.9e-007 4.7e-003 # ATCTGTTG CAACAGAT 15 0 2.8e-005 6.9e-001 # ATCTGCTG CAGCAGAT 7 0 7.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 4.7e-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 1.000000 0.000000 0.000000 0.318182 0.000000 0.681818 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGTTCGAW DREME-21 # Word RC Word Pos Neg P-value E-value # BEST AGTTCGAW WTCGAACT 25 1 3.1e-007 7.6e-003 # AGTTCGAT ATCGAACT 15 1 2.4e-004 5.9e+000 # AGTTCGAA TTCGAACT 10 0 9.4e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.6e-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 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 0.400000 0.000000 0.000000 0.600000 MOTIF RCGGGGA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST RCGGGGA TCCCCGY 33 4 3.6e-007 9.0e-003 # GCGGGGA TCCCCGC 16 1 1.2e-004 3.1e+000 # ACGGGGA TCCCCGT 17 3 1.2e-003 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 9.0e-003 0.515152 0.000000 0.484848 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGATTTC DREME-23 # Word RC Word Pos Neg P-value E-value # BEST AAGATTTC GAAATCTT 20 0 7.9e-007 2.0e-002 # AAGATTTC GAAATCTT 20 0 7.9e-007 2.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.0e-002 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATSTGGAG DREME-24 # Word RC Word Pos Neg P-value E-value # BEST ATSTGGAG CTCCASAT 20 0 7.9e-007 2.0e-002 # ATGTGGAG CTCCACAT 11 0 4.6e-004 1.1e+001 # ATCTGGAG CTCCAGAT 9 0 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.0e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.450000 0.550000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CKAGAATC DREME-25 # Word RC Word Pos Neg P-value E-value # BEST CKAGAATC GATTCTMG 23 1 1.2e-006 2.9e-002 # CGAGAATC GATTCTCG 13 0 1.1e-004 2.8e+000 # CTAGAATC GATTCTAG 10 1 5.7e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.9e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.565217 0.434783 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 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTCGCMC DREME-26 # Word RC Word Pos Neg P-value E-value # BEST AGTCGCMC GKGCGACT 19 0 1.6e-006 4.0e-002 # AGTCGCAC GTGCGACT 10 0 9.4e-004 2.3e+001 # AGTCGCCC GGGCGACT 9 0 1.9e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.0e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.526316 0.473684 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 85.71 seconds