# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SOK2/seqs-shuffled # positives: 671 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SOK2/seqs-centered (Sat Jan 18 13:36:22 PST 2020) # negatives: 671 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SOK2/seqs-shuffled (Sat Jan 18 13:36:22 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 13:49:51 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 0.288 C 0.213 G 0.211 T 0.287 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 55 1 2.6e-016 8.8e-012 # TGTATGGG CCCATACA 25 0 2.4e-008 8.0e-004 # TGTACGGA TCCGTACA 20 1 9.2e-006 3.1e-001 # TGTACGGG CCCGTACA 8 0 3.8e-003 1.3e+002 # TGTATGGA TCCATACA 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 8.8e-012 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 0.468750 0.000000 0.531250 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.484375 0.000000 0.515625 0.000000 MOTIF GGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 48 5 1.8e-010 5.9e-006 # GGTTCGA TCGAACC 48 5 1.8e-010 5.9e-006 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 5.9e-006 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAACTKGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 31 0 3.3e-010 1.1e-005 # CAACTTGG CCAAGTTG 23 0 9.8e-008 3.3e-003 # CAACTGGG CCCAGTTG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.1e-005 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 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.258065 0.741935 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AARAAR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AARAAR YTTYTT 386 283 1.2e-008 4.1e-004 # AAGAAA TTTCTT 163 99 6.6e-006 2.2e-001 # AAAAAG CTTTTT 174 121 3.0e-004 1.0e+001 # AAGAAG CTTCTT 74 44 2.5e-003 8.4e+001 # AAAAAA TTTTTT 201 161 8.2e-003 2.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 594 E= 4.1e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.601010 0.000000 0.398990 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.612795 0.000000 0.387205 0.000000 MOTIF TACCGW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TACCGW WCGGTA 75 24 4.9e-008 1.6e-003 # TACCGA TCGGTA 34 9 6.7e-005 2.2e+000 # TACCGT ACGGTA 42 15 1.7e-004 5.7e+000 letter-probability matrix: alength= 4 w= 6 nsites= 78 E= 1.6e-003 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 0.000000 0.000000 1.000000 0.000000 0.448718 0.000000 0.000000 0.551282 MOTIF AGTGGTYA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTYA TRACCACT 28 2 3.4e-007 1.1e-002 # AGTGGTTA TAACCACT 20 2 5.4e-005 1.8e+000 # AGTGGTCA TGACCACT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.1e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.714286 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 30.60 seconds