# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SRB8/seqs-shuffled # positives: 804 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SRB8/seqs-centered (Sat Jan 18 04:47:40 PST 2020) # negatives: 804 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SRB8/seqs-shuffled (Sat Jan 18 04:47:40 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:03:11 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 0.280 C 0.220 G 0.221 T 0.279 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 123 14 5.5e-025 2.0e-020 # GGTTCGA TCGAACC 89 4 2.9e-023 1.1e-018 # GGTTCAA TTGAACC 35 10 1.0e-004 3.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 124 E= 2.0e-020 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 0.282258 0.000000 0.717742 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 41 0 2.7e-013 9.7e-009 # TAGTGGTA TACCACTA 24 0 5.0e-008 1.8e-003 # TAGTGGTT AACCACTA 17 0 7.0e-006 2.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 9.7e-009 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 0.585366 0.000000 0.000000 0.414634 MOTIF SAAGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 408 276 1.8e-011 6.3e-007 # CAAGA TCTTG 249 167 1.9e-006 6.8e-002 # GAAGA TCTTC 222 144 2.2e-006 7.9e-002 letter-probability matrix: alength= 4 w= 5 nsites= 587 E= 6.3e-007 0.000000 0.540034 0.459966 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 ATGTAYG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYG CRTACAT 50 6 2.8e-010 9.6e-006 # ATGTATG CATACAT 31 4 1.4e-006 4.8e-002 # ATGTACG CGTACAT 23 2 8.5e-006 3.0e-001 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 9.6e-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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.413793 0.000000 0.586207 0.000000 0.000000 1.000000 0.000000 MOTIF GGTASC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GGTASC GSTACC 78 20 4.8e-010 1.7e-005 # GGTAGC GCTACC 60 15 4.1e-008 1.4e-003 # GGTACC GGTACC 19 5 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 80 E= 1.7e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.237500 0.762500 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTYGGCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACTYGGCC GGCCRAGT 34 1 7.5e-010 2.6e-005 # ACTCGGCC GGCCGAGT 19 0 1.7e-006 5.9e-002 # ACTTGGCC GGCCAAGT 22 1 2.5e-006 8.7e-002 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.6e-005 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 0.470588 0.000000 0.529412 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 MOTIF GTGATAR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTGATAR YTATCAC 55 9 9.0e-010 3.1e-005 # GTGATAG CTATCAC 38 5 8.9e-008 3.1e-003 # GTGATAA TTATCAC 17 4 3.4e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 56 E= 3.1e-005 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 0.303571 0.000000 0.696429 0.000000 MOTIF CCTTAACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCTTAACC GGTTAAGG 29 0 1.4e-009 5.0e-005 # CCTTAACC GGTTAAGG 29 0 1.4e-009 5.0e-005 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.0e-005 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 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 CAASGATG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CAASGATG CATCSTTG 33 2 1.4e-008 4.7e-004 # CAACGATG CATCGTTG 21 1 4.9e-006 1.7e-001 # CAAGGATG CATCCTTG 12 1 1.7e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.7e-004 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 0.636364 0.363636 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 1.000000 0.000000 MOTIF CABACGC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CABACGC GCGTVTG 54 12 4.8e-008 1.7e-003 # CATACGC GCGTATG 14 1 4.6e-004 1.6e+001 # CAGACGC GCGTCTG 20 5 1.9e-003 6.6e+001 # CACACGC GCGTGTG 20 7 9.1e-003 3.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 1.7e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.370370 0.370370 0.259259 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 CACTATAK DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACTATAK MTATAGTG 23 0 1.0e-007 3.5e-003 # CACTATAT ATATAGTG 16 0 1.4e-005 4.9e-001 # CACTATAG CTATAGTG 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.5e-003 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 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 0.304348 0.695652 MOTIF CAAAGCAY DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CAAAGCAY RTGCTTTG 25 1 3.4e-007 1.2e-002 # CAAAGCAC GTGCTTTG 14 0 5.8e-005 2.0e+000 # CAAAGCAT ATGCTTTG 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.2e-002 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 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 0.560000 0.000000 0.440000 MOTIF GATTMGAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GATTMGAA TTCKAATC 31 4 1.4e-006 4.7e-002 # GATTAGAA TTCTAATC 21 3 1.3e-004 4.3e+000 # GATTCGAA TTCGAATC 10 1 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 4.7e-002 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 0.677419 0.322581 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 # Stopping reason: E-value threshold exceeded # Running time: 69.01 seconds