# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/seqs-shuffled # positives: 463 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/seqs-centered (Sun Jan 19 09:44:08 PST 2020) # negatives: 463 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/seqs-shuffled (Sun Jan 19 09:44:08 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 09:52:51 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 0.291 C 0.207 G 0.209 T 0.293 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 110 12 7.2e-024 1.9e-019 # GGTTCGA TCGAACC 81 4 1.7e-021 4.4e-017 # GGTTCAA TTGAACC 31 8 1.1e-004 2.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 112 E= 1.9e-019 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 0.276786 0.000000 0.723214 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 78 3 1.4e-021 3.5e-017 # CGCCTTA TAAGGCG 61 2 3.0e-017 7.8e-013 # CGCGTTA TAACGCG 17 1 6.3e-005 1.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 3.5e-017 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 0.782051 0.217949 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 CAYCCRTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAYCCRTA TAYGGRTG 69 2 8.1e-020 2.1e-015 # CACCCATA TATGGGTG 26 0 1.0e-008 2.7e-004 # CATCCGTA TACGGATG 24 0 4.4e-008 1.1e-003 # CACCCGTA TACGGGTG 11 0 4.6e-004 1.2e+001 # CATCCATA TATGGATG 12 2 6.1e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 77 E= 2.1e-015 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.506494 0.000000 0.493506 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.519481 0.000000 0.480519 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 66 3 9.5e-018 2.4e-013 # CTCGGCCA TGGCCGAG 34 1 5.8e-010 1.5e-005 # CTTGGCCA TGGCCAAG 20 2 5.1e-005 1.3e+000 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 5.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 66 E= 2.4e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.515152 0.181818 0.303030 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 GCKCTMCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTMCC GGKAGMGC 52 2 2.0e-014 5.1e-010 # GCGCTACC GGTAGCGC 25 2 2.1e-006 5.4e-002 # GCTCTACC GGTAGAGC 16 0 1.3e-005 3.4e-001 # GCTCTCCC GGGAGAGC 10 0 9.3e-004 2.4e+001 # GCGCTCCC GGGAGCGC 8 0 3.8e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 5.1e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.730769 0.269231 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCCATDC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 65 9 1.1e-012 2.8e-008 # CCCATAC GTATGGG 26 3 5.7e-006 1.5e-001 # CCCATGC GCATGGG 23 2 7.7e-006 1.9e-001 # CCCATTC GAATGGG 20 4 6.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 2.8e-008 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 0.000000 0.000000 0.000000 1.000000 0.402778 0.000000 0.319444 0.277778 0.000000 1.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 43 2 1.2e-011 2.9e-007 # TAGTGGTA TACCACTA 26 1 1.5e-007 3.7e-003 # TAGTGGTT AACCACTA 17 1 6.3e-005 1.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.9e-007 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 0.604651 0.000000 0.000000 0.395349 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 40 2 9.3e-011 2.3e-006 # ATGGCAAC GTTGCCAT 29 1 1.9e-008 4.7e-004 # ATGGCATC GATGCCAT 11 1 3.0e-003 7.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.3e-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 0.000000 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 GTSTGGS DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTSTGGS SCCASAC 51 4 2.9e-012 7.4e-008 # GTGTGGG CCCACAC 17 1 6.3e-005 1.6e+000 # GTCTGGC GCCAGAC 16 1 1.2e-004 3.1e+000 # GTCTGGG CCCAGAC 14 2 1.9e-003 4.9e+001 # GTGTGGC GCCACAC 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 7.4e-008 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.527273 0.472727 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 0.418182 0.581818 0.000000 MOTIF AARAAAW DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 180 93 2.2e-010 5.5e-006 # AAAAAAA TTTTTTT 93 40 4.2e-007 1.0e-002 # AAGAAAA TTTTCTT 58 25 9.9e-005 2.5e+000 # AAGAAAT ATTTCTT 34 11 3.1e-004 7.6e+000 # AAAAAAT ATTTTTT 80 46 7.4e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 238 E= 5.5e-006 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.634454 0.000000 0.365546 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 0.575630 0.000000 0.000000 0.424370 MOTIF CTTAABCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTTAABCA TGVTTAAG 31 0 2.8e-010 6.8e-006 # CTTAACCA TGGTTAAG 12 0 2.3e-004 5.5e+000 # CTTAATCA TGATTAAG 12 0 2.3e-004 5.5e+000 # CTTAAGCA TGCTTAAG 7 0 7.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 6.8e-006 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 0.387097 0.225806 0.387097 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGTCTCY DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GGTCTCY RGAGACC 33 1 1.2e-009 2.8e-005 # GGTCTCC GGAGACC 21 0 3.8e-007 9.2e-003 # GGTCTCT AGAGACC 12 1 1.6e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 2.8e-005 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 0.600000 0.000000 0.400000 MOTIF GYACGGA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GYACGGA TCCGTRC 29 0 1.2e-009 2.9e-005 # GTACGGA TCCGTAC 16 0 1.3e-005 3.3e-001 # GCACGGA TCCGTGC 13 0 1.1e-004 2.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.9e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.466667 0.000000 0.533333 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 1.000000 0.000000 0.000000 0.000000 MOTIF CACATYAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 27 0 5.0e-009 1.2e-004 # CACATCAC GTGATGTG 15 0 2.7e-005 6.6e-001 # CACATTAC GTAATGTG 12 0 2.3e-004 5.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.2e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.555556 0.000000 0.444444 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCKTGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 44 6 7.2e-009 1.7e-004 # ATCTTGA TCAAGAT 25 4 4.1e-005 9.9e-001 # ATCGTGA TCACGAT 19 2 9.5e-005 2.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 1.7e-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 0.431818 0.568182 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 0 1.0e-008 2.5e-004 # AGTCAGAC GTCTGACT 13 0 1.1e-004 2.7e+000 # AGTCATAC GTATGACT 13 0 1.1e-004 2.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.5e-004 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 ACTGAGCT DREME-17 # 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 CCGTGMTA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CCGTGMTA TAKCACGG 28 2 3.0e-007 7.2e-003 # CCGTGCTA TAGCACGG 12 0 2.3e-004 5.5e+000 # CCGTGATA TATCACGG 16 2 5.9e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 7.2e-003 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 0.571429 0.428571 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGTR DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TAGTGTR YACACTA 34 5 7.7e-007 1.8e-002 # TAGTGTA TACACTA 22 3 6.5e-005 1.5e+000 # TAGTGTG CACACTA 12 2 6.1e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.8e-002 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 0.647059 0.000000 0.352941 0.000000 MOTIF SCACGCGA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST SCACGCGA TCGCGTGS 20 0 7.7e-007 1.8e-002 # GCACGCGA TCGCGTGC 11 0 4.6e-004 1.1e+001 # CCACGCGA TCGCGTGG 9 0 1.9e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.8e-002 0.000000 0.450000 0.550000 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 1.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 62.63 seconds