# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--INO80/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--INO80/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--INO80/seqs-shuffled # positives: 520 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--INO80/seqs-centered (Sat Jan 18 14:48:59 PST 2020) # negatives: 520 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--INO80/seqs-shuffled (Sat Jan 18 14:48:59 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 15:00:51 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 0.293 C 0.210 G 0.207 T 0.290 MOTIF RGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCRA TYGAACY 175 21 7.9e-038 2.3e-033 # GGTTCGA TCGAACC 95 2 3.2e-028 9.2e-024 # GGTTCAA TTGAACC 38 7 9.7e-007 2.8e-002 # AGTTCGA TCGAACT 27 3 3.2e-006 9.2e-002 # AGTTCAA TTGAACT 24 9 6.1e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 178 E= 2.3e-033 0.269663 0.000000 0.730337 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 0.348315 0.000000 0.651685 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 142 28 4.3e-023 1.2e-018 # ACCACT AGTGGT 107 18 9.1e-019 2.6e-014 # ACCTCT AGAGGT 39 12 6.9e-005 2.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 163 E= 1.2e-018 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.754601 0.000000 0.000000 0.245399 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AARAAAWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 108 31 6.6e-013 1.9e-008 # AAAAAATA TATTTTTT 40 8 1.0e-006 2.8e-002 # AAAAAAAA TTTTTTTT 48 13 2.1e-006 5.8e-002 # AAGAAAAA TTTTTCTT 32 10 3.7e-004 1.0e+001 # AAGAAATA TATTTCTT 14 3 6.0e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 123 E= 1.9e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 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 0.585366 0.000000 0.000000 0.414634 1.000000 0.000000 0.000000 0.000000 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 45 2 3.2e-012 9.0e-008 # AACTTGGC GCCAAGTT 33 1 1.2e-009 3.5e-005 # AACTGGGC GCCCAGTT 12 1 1.6e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 9.0e-008 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 0.000000 1.000000 0.000000 0.000000 0.266667 0.733333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 34 0 3.3e-011 9.3e-007 # GCGCTACC GGTAGCGC 24 0 4.5e-008 1.3e-003 # GCTCTACC GGTAGAGC 10 0 9.3e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 9.3e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.705882 0.294118 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 CCCATDC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 57 9 1.8e-010 5.2e-006 # CCCATAC GTATGGG 20 3 2.1e-004 6.0e+000 # CCCATGC GCATGGG 20 3 2.1e-004 6.0e+000 # CCCATTC GAATGGG 19 3 3.8e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 5.2e-006 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 0.338983 0.000000 0.338983 0.322034 0.000000 1.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 34 1 6.2e-010 1.7e-005 # CCTTAACC GGTTAAGG 20 0 7.9e-007 2.2e-002 # CCATAACC GGTTATGG 14 1 4.5e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.7e-005 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.411765 0.000000 0.000000 0.588235 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTMTCAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTMTCAC GTGAKAG 34 2 5.9e-009 1.6e-004 # CTATCAC GTGATAG 25 2 2.2e-006 6.1e-002 # CTCTCAC GTGAGAG 9 0 1.9e-003 5.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.6e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.714286 0.285714 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 MOTIF GACTSTTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 22 0 1.9e-007 5.3e-003 # GACTCTTA TAAGAGTC 13 0 1.1e-004 3.1e+000 # GACTGTTA TAACAGTC 9 0 1.9e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.3e-003 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 0.000000 1.000000 0.000000 0.590909 0.409091 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 CGCCTTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 45 9 1.9e-007 5.3e-003 # CGCCTTA TAAGGCG 45 9 1.9e-007 5.3e-003 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 5.3e-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 MOTIF CASACGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CASACGC GCGTSTG 31 3 2.6e-007 7.2e-003 # CACACGC GCGTGTG 18 1 3.3e-005 9.2e-001 # CAGACGC GCGTCTG 13 2 3.5e-003 9.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 7.2e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.580645 0.419355 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 MOTIF AAWGGTC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AAWGGTC GACCWTT 42 8 3.3e-007 9.0e-003 # AATGGTC GACCATT 26 5 7.8e-005 2.1e+000 # AAAGGTC GACCTTT 16 3 2.0e-003 5.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 9.0e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.000000 0.619048 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 MOTIF AAGATTTC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AAGATTTC GAAATCTT 24 1 6.0e-007 1.7e-002 # AAGATTTC GAAATCTT 24 1 6.0e-007 1.7e-002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.7e-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 CGCSACG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGCSACG CGTSGCG 20 0 7.9e-007 2.2e-002 # CGCCACG CGTGGCG 11 0 4.6e-004 1.3e+001 # CGCGACG CGTCGCG 9 0 1.9e-003 5.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 2.2e-002 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 0.550000 0.450000 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 MOTIF GTTGCCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GTTGCCA TGGCAAC 26 2 1.2e-006 3.1e-002 # GTTGCCA TGGCAAC 26 2 1.2e-006 3.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.1e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGGGSA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 23 1 1.2e-006 3.2e-002 # CGCGGGGA TCCCCGCG 13 1 8.6e-004 2.3e+001 # CGCGGGCA TGCCCGCG 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-002 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.434783 0.565217 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGCRGAT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AAGCRGAT ATCYGCTT 19 0 1.6e-006 4.4e-002 # AAGCAGAT ATCTGCTT 12 0 2.3e-004 6.2e+000 # AAGCGGAT ATCCGCTT 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.4e-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 0.000000 1.000000 0.000000 0.000000 0.631579 0.000000 0.368421 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 # Stopping reason: E-value threshold exceeded # Running time: 58.78 seconds