# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YRR1/seqs-shuffled # positives: 562 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YRR1/seqs-centered (Sat Jan 18 12:51:01 PST 2020) # negatives: 562 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--YRR1/seqs-shuffled (Sat Jan 18 12:51:01 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 13:05:20 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 0.301 C 0.198 G 0.197 T 0.303 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 90 20 3.9e-013 1.2e-008 # GGTTCGA TCGAACC 63 13 7.8e-010 2.4e-005 # GGTTCAA TTGAACC 28 7 2.1e-004 6.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 91 E= 1.2e-008 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 0.307692 0.000000 0.692308 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 35 0 1.7e-011 5.2e-007 # ATGTATGG CCATACAT 19 0 1.6e-006 5.0e-002 # ATGTACGG CCGTACAT 17 0 6.7e-006 2.1e-001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 5.2e-007 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 0.475000 0.000000 0.525000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTTGKC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTTGKC GMCAAG 90 28 6.6e-010 2.0e-005 # CTTGGC GCCAAG 49 14 3.1e-006 9.6e-002 # CTTGTC GACAAG 41 16 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 94 E= 2.0e-005 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 0.531915 0.468085 0.000000 1.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 37 3 5.8e-009 1.7e-004 # CCTTAACC GGTTAAGG 23 0 9.5e-008 2.9e-003 # CCATAACC GGTTATGG 14 3 6.0e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.378378 0.000000 0.000000 0.621622 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 CTARACCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 31 2 4.5e-008 1.4e-003 # CTAGACCA TGGTCTAG 19 1 1.7e-005 5.3e-001 # CTAAACCA TGGTTTAG 12 1 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.4e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.387097 0.000000 0.612903 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 MOTIF AAHAAGAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAHAAGAA TTCTTDTT 65 19 8.6e-008 2.6e-003 # AAAAAGAA TTCTTTTT 41 16 4.7e-004 1.4e+001 # AACAAGAA TTCTTGTT 9 0 1.9e-003 5.7e+001 # AATAAGAA TTCTTATT 17 4 3.3e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 2.6e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.611940 0.134328 0.000000 0.253731 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 MOTIF GTGATAGY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 22 0 1.9e-007 5.8e-003 # GTGATAGT ACTATCAC 12 0 2.3e-004 6.9e+000 # GTGATAGC GCTATCAC 11 0 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 5.8e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.478261 0.000000 0.521739 MOTIF GCKCTACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 21 0 3.9e-007 1.2e-002 # GCGCTACC GGTAGCGC 14 0 5.6e-005 1.7e+000 # GCTCTACC GGTAGAGC 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.2e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 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 # Stopping reason: E-value threshold exceeded # Running time: 35.13 seconds