# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG2/seqs-shuffled # positives: 731 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG2/seqs-centered (Sat Jan 18 02:56:04 PST 2020) # negatives: 731 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--MIG2/seqs-shuffled (Sat Jan 18 02:56:04 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:12:37 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 0.298 C 0.197 G 0.202 T 0.303 MOTIF TCGAACCB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 59 4 2.4e-014 8.3e-010 # TCGAACCC GGGTTCGA 25 1 3.3e-007 1.2e-002 # TCGAACCG CGGTTCGA 21 1 4.8e-006 1.7e-001 # TCGAACCT AGGTTCGA 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 8.3e-010 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 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 0.423729 0.355932 0.220339 MOTIF AARAAARA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAARA TYTTTYTT 137 48 9.3e-013 3.2e-008 # AAAAAAAA TTTTTTTT 74 23 3.9e-008 1.4e-003 # AAGAAAAA TTTTTCTT 43 15 1.2e-004 4.0e+000 # AAAAAAGA TCTTTTTT 37 14 7.3e-004 2.5e+001 # AAGAAAGA TCTTTCTT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 153 E= 3.2e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.673203 0.000000 0.326797 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 0.732026 0.000000 0.267974 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TAYCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TAYCA TGRTA 302 206 8.5e-008 2.9e-003 # TATCA TGATA 186 121 1.9e-005 6.5e-001 # TACCA TGGTA 147 98 3.8e-004 1.3e+001 letter-probability matrix: alength= 4 w= 5 nsites= 370 E= 2.9e-003 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.435135 0.000000 0.564865 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGGWAG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGGWAG CTWCCG 72 23 9.9e-008 3.3e-003 # CGGTAG CTACCG 36 7 3.4e-006 1.1e-001 # CGGAAG CTTCCG 36 16 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 72 E= 3.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGTAYGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 21 0 4.1e-007 1.4e-002 # ATGTACGG CCGTACAT 12 0 2.3e-004 7.8e+000 # ATGTATGG CCATACAT 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 1.4e-002 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 0.538462 0.000000 0.461538 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 28.29 seconds