# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CUP9/seqs-shuffled # positives: 720 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CUP9/seqs-centered (Sat Jan 18 14:28:31 PST 2020) # negatives: 720 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CUP9/seqs-shuffled (Sat Jan 18 14:28:31 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 14:47:32 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 0.292 C 0.209 G 0.207 T 0.292 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 127 11 1.1e-028 3.6e-024 # GGTTCGA TCGAACC 103 7 8.5e-025 2.9e-020 # GGATCGA TCGATCC 32 4 7.4e-007 2.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 127 E= 3.6e-024 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.212598 0.000000 0.000000 0.787402 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 ACCACTM DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 79 10 1.6e-015 5.5e-011 # ACCACTA TAGTGGT 47 3 9.4e-012 3.2e-007 # ACCACTC GAGTGGT 33 7 1.7e-005 5.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 80 E= 5.5e-011 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 0.587500 0.412500 0.000000 0.000000 MOTIF AAAAADA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAADA THTTTTT 253 124 5.3e-015 1.8e-010 # AAAAAAA TTTTTTT 150 76 5.0e-008 1.7e-003 # AAAAAGA TCTTTTT 98 40 1.2e-007 3.9e-003 # AAAAATA TATTTTT 96 39 1.4e-007 4.9e-003 letter-probability matrix: alength= 4 w= 7 nsites= 327 E= 1.8e-010 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.434251 0.000000 0.281346 0.284404 1.000000 0.000000 0.000000 0.000000 MOTIF AACTTGRC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTTGRC GYCAAGTT 37 0 4.5e-012 1.5e-007 # AACTTGGC GCCAAGTT 30 0 6.8e-010 2.3e-005 # AACTTGAC GTCAAGTT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.5e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.189189 0.000000 0.810811 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 65 13 3.4e-010 1.1e-005 # CGCCTTA TAAGGCG 50 9 1.4e-008 4.8e-004 # CGCGTTA TAACGCG 15 4 9.2e-003 3.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 1.1e-005 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 0.769231 0.230769 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 ACCCAYA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCCAYA TRTGGGT 47 6 1.6e-009 5.3e-005 # ACCCATA TATGGGT 32 2 2.5e-008 8.5e-004 # ACCCACA TGTGGGT 15 4 9.2e-003 3.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 5.3e-005 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 0.000000 0.346154 0.000000 0.653846 1.000000 0.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 25 0 2.4e-008 8.0e-004 # AGATCGGG CCCGATCT 17 0 6.9e-006 2.3e-001 # AGATCGTG CACGATCT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.0e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.680000 0.320000 0.000000 0.000000 1.000000 0.000000 MOTIF GATGKCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GATGKCA TGMCATC 37 4 3.5e-008 1.2e-003 # GATGGCA TGCCATC 22 3 6.9e-005 2.3e+000 # GATGTCA TGACATC 15 1 2.4e-004 8.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 1.2e-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 0.000000 0.578947 0.421053 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAGTTGGK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAGTTGGK MCCAACTG 26 1 1.7e-007 5.6e-003 # CAGTTGGT ACCAACTG 15 0 2.8e-005 9.4e-001 # CAGTTGGG CCCAACTG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.6e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 0.000000 0.423077 0.576923 MOTIF CCGTGSA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 31 3 2.9e-007 9.7e-003 # CCGTGGA TCCACGG 17 1 6.7e-005 2.2e+000 # CCGTGCA TGCACGG 14 2 2.0e-003 6.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 9.7e-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 0.000000 0.451613 0.548387 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTATCAC GTGATAG 25 1 3.3e-007 1.1e-002 # CTATCAC GTGATAG 25 1 3.3e-007 1.1e-002 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 1.1e-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 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 GAAGAAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GAAGAAA TTTCTTC 50 12 3.6e-007 1.2e-002 # GAAGAAA TTTCTTC 50 12 3.6e-007 1.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 1.2e-002 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 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 MOTIF CTTAGCAW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTTAGCAW WTGCTAAG 21 0 4.1e-007 1.4e-002 # CTTAGCAT ATGCTAAG 12 0 2.3e-004 7.7e+000 # CTTAGCAA TTGCTAAG 9 0 1.9e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.428571 0.000000 0.000000 0.571429 MOTIF ACAGGGY DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACAGGGY RCCCTGT 32 4 7.4e-007 2.4e-002 # ACAGGGT ACCCTGT 17 1 6.7e-005 2.2e+000 # ACAGGGC GCCCTGT 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 2.4e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.468750 0.000000 0.531250 MOTIF GCMCCC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCMCCC GGGKGC 65 22 1.1e-006 3.6e-002 # GCCCCC GGGGGC 41 14 1.4e-004 4.5e+000 # GCACCC GGGTGC 25 8 2.1e-003 6.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 68 E= 3.6e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.397059 0.602941 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 MOTIF AAGRTTAG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AAGRTTAG CTAAYCTT 26 2 1.2e-006 4.1e-002 # AAGGTTAG CTAACCTT 16 1 1.3e-004 4.2e+000 # AAGATTAG CTAATCTT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.1e-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 0.384615 0.000000 0.615385 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 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 74.39 seconds