# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--AFT1/seqs-shuffled # positives: 769 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--AFT1/seqs-centered (Fri Jan 17 23:28:48 PST 2020) # negatives: 769 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--AFT1/seqs-shuffled (Fri Jan 17 23:28:48 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:44:51 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 0.281 C 0.221 G 0.220 T 0.277 MOTIF AGTGGTW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 111 16 2.3e-020 8.1e-016 # AGTGGTT AACCACT 76 9 2.6e-015 9.1e-011 # AGTGGTA TACCACT 49 7 2.1e-009 7.2e-005 letter-probability matrix: alength= 4 w= 7 nsites= 128 E= 8.1e-016 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 0.390625 0.000000 0.000000 0.609375 MOTIF GGTTCRA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 113 16 6.6e-021 2.3e-016 # GGTTCGA TCGAACC 78 7 2.5e-017 8.7e-013 # GGTTCAA TTGAACC 35 9 4.2e-005 1.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 113 E= 2.3e-016 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 0.309735 0.000000 0.690265 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACAY DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 82 8 1.1e-017 3.7e-013 # CCGTACAT ATGTACGG 31 2 5.0e-008 1.7e-003 # CCATACAT ATGTATGG 33 4 4.1e-007 1.4e-002 # CCGTACAC GTGTACGG 15 1 2.4e-004 8.4e+000 # CCATACAC GTGTATGG 12 1 1.6e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 96 E= 3.7e-013 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 0.291667 0.000000 0.708333 MOTIF ACCRACT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 92 13 4.6e-017 1.6e-012 # ACCAACT AGTTGGT 62 9 1.4e-011 4.9e-007 # ACCGACT AGTCGGT 30 4 2.5e-006 8.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 1.6e-012 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.673913 0.000000 0.326087 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 MOTIF ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 49 2 2.8e-013 9.7e-009 # ATGGCAAC GTTGCCAT 32 1 2.9e-009 9.9e-005 # ATGGCATC GATGCCAT 17 1 6.7e-005 2.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 9.7e-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 0.653061 0.000000 0.000000 0.346939 0.000000 1.000000 0.000000 0.000000 MOTIF RCACCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST RCACCCA TGGGTGY 88 20 2.3e-012 8.0e-008 # ACACCCA TGGGTGT 57 13 2.7e-008 9.2e-004 # GCACCCA TGGGTGC 34 7 1.0e-005 3.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 8.0e-008 0.688525 0.000000 0.311475 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 CACATYAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACATYAC GTRATGTG 34 0 4.0e-011 1.4e-006 # CACATCAC GTGATGTG 19 0 1.7e-006 5.8e-002 # CACATTAC GTAATGTG 15 0 2.8e-005 9.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.4e-006 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 0.558824 0.000000 0.441176 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 53 6 4.2e-011 1.4e-006 # CGCCTTA TAAGGCG 36 2 1.9e-009 6.3e-005 # CGCGTTA TAACGCG 17 4 3.4e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 1.4e-006 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 0.679245 0.320755 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 SAAGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 358 237 1.5e-010 5.1e-006 # CAAGA TCTTG 220 137 3.4e-007 1.1e-002 # GAAGA TCTTC 203 133 9.8e-006 3.3e-001 letter-probability matrix: alength= 4 w= 5 nsites= 509 E= 5.1e-006 0.000000 0.506876 0.493124 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 CTTGTTRG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTTGTTRG CYAACAAG 25 0 2.4e-008 8.0e-004 # CTTGTTGG CCAACAAG 17 0 7.0e-006 2.3e-001 # CTTGTTAG CTAACAAG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.0e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.320000 0.000000 0.680000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCGCTHCC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GCGCTHCC GGDAGCGC 34 3 4.5e-008 1.5e-003 # GCGCTCCC GGGAGCGC 12 0 2.3e-004 7.7e+000 # GCGCTTCC GGAAGCGC 8 0 3.8e-003 1.3e+002 # GCGCTACC GGTAGCGC 14 3 6.1e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.5e-003 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 0.000000 0.000000 1.000000 0.411765 0.352941 0.000000 0.235294 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCRTGGAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGAG CTCCAYGG 24 0 5.0e-008 1.6e-003 # CCGTGGAG CTCCACGG 15 0 2.8e-005 9.3e-001 # CCATGGAG CTCCATGG 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.000000 0.625000 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 CTCTMCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 27 1 8.7e-008 2.8e-003 # CTCTCCCA TGGGAGAG 20 1 9.4e-006 3.1e-001 # CTCTACCA TGGTAGAG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.8e-003 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 1.000000 0.259259 0.740741 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 ACACGCCC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ACACGCCC GGGCGTGT 24 1 6.6e-007 2.1e-002 # ACACGCCC GGGCGTGT 24 1 6.6e-007 2.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-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 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 1.000000 0.000000 0.000000 MOTIF AATCCMAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AATCCMAC GTKGGATT 26 2 1.3e-006 4.1e-002 # AATCCAAC GTTGGATT 19 2 1.0e-004 3.3e+000 # AATCCCAC GTGGGATT 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 4.1e-002 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 0.000000 1.000000 0.000000 0.000000 0.740741 0.259259 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTSTGGC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTSTGGC GCCASACT 23 1 1.3e-006 4.2e-002 # AGTGTGGC GCCACACT 11 0 4.7e-004 1.5e+001 # AGTCTGGC GCCAGACT 12 1 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.2e-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 0.521739 0.478261 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 # Stopping reason: E-value threshold exceeded # Running time: 78.64 seconds