# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--FKH1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--FKH1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--FKH1/seqs-shuffled # positives: 1259 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--FKH1/seqs-centered (Sat Jan 18 06:15:56 PST 2020) # negatives: 1259 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/RM11-1A--FKH1/seqs-shuffled (Sat Jan 18 06:15:56 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:32:43 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 0.311 C 0.188 G 0.189 T 0.312 MOTIF GTAAAYA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTAAAYA TRTTTAC 181 53 2.1e-019 8.0e-015 # GTAAACA TGTTTAC 104 26 4.3e-013 1.6e-008 # GTAAATA TATTTAC 81 27 5.2e-008 2.0e-003 letter-probability matrix: alength= 4 w= 7 nsites= 192 E= 8.0e-015 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.557292 0.000000 0.442708 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 685 480 1.5e-016 5.9e-012 # CAAGA TCTTG 425 272 5.6e-012 2.2e-007 # GAAGA TCTTC 406 274 1.9e-009 7.3e-005 letter-probability matrix: alength= 4 w= 5 nsites= 991 E= 5.9e-012 0.000000 0.497477 0.502523 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 GGTTCRA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 103 24 1.0e-013 3.8e-009 # GGTTCGA TCGAACC 60 9 6.6e-011 2.5e-006 # GGTTCAA TTGAACC 45 15 5.6e-005 2.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 106 E= 3.8e-009 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 0.433962 0.000000 0.566038 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TACCR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TACCR YGGTA 365 246 1.9e-008 7.1e-004 # TACCA TGGTA 254 173 1.0e-005 3.8e-001 # TACCG CGGTA 141 80 1.1e-005 4.0e-001 letter-probability matrix: alength= 4 w= 5 nsites= 445 E= 7.1e-004 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 0.660674 0.000000 0.339326 0.000000 MOTIF AAAAAATA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAAAAATA TATTTTTT 82 27 3.4e-008 1.2e-003 # AAAAAATA TATTTTTT 82 27 3.4e-008 1.2e-003 letter-probability matrix: alength= 4 w= 8 nsites= 86 E= 1.2e-003 1.000000 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 0.000000 1.000000 0.000000 0.000000 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 MOTIF ATAAAYAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATAAAYAA TTRTTTAT 74 27 1.0e-006 3.7e-002 # ATAAACAA TTGTTTAT 46 13 7.7e-006 2.8e-001 # ATAAATAA TTATTTAT 31 14 7.6e-003 2.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 78 E= 3.7e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.602564 0.000000 0.397436 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAVCACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAVCACC GGTGBTG 52 14 1.1e-006 3.8e-002 # CAACACC GGTGTTG 23 5 4.3e-004 1.6e+001 # CAGCACC GGTGCTG 13 2 3.6e-003 1.3e+002 # CACCACC GGTGGTG 20 7 9.3e-003 3.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 56 E= 3.8e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.375000 0.250000 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 # Stopping reason: E-value threshold exceeded # Running time: 58.89 seconds