# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-shuffled # positives: 524 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-centered (Sat Jan 18 05:45:47 PST 2020) # negatives: 524 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--PDR3/seqs-shuffled (Sat Jan 18 05:45:47 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:58:11 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 0.301 C 0.198 G 0.201 T 0.301 MOTIF GRTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRTTCGA TCGAAYC 58 6 1.2e-012 3.6e-008 # GGTTCGA TCGAACC 52 4 1.8e-012 5.4e-008 # GATTCGA TCGAATC 14 2 2.0e-003 6.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 3.6e-008 0.000000 0.000000 1.000000 0.000000 0.203390 0.000000 0.796610 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 SAAGAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SAAGAA TTCTTS 143 62 1.5e-010 4.6e-006 # GAAGAA TTCTTC 89 37 4.7e-007 1.4e-002 # CAAGAA TTCTTG 66 30 7.7e-005 2.3e+000 letter-probability matrix: alength= 4 w= 6 nsites= 166 E= 4.6e-006 0.000000 0.421687 0.578313 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACCWCT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCWCT AGWGGT 94 30 3.9e-010 1.2e-005 # ACCACT AGTGGT 62 20 7.5e-007 2.2e-002 # ACCTCT AGAGGT 33 10 2.3e-004 7.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 102 E= 1.2e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.656863 0.000000 0.000000 0.343137 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF CCRTACA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 47 7 5.2e-009 1.5e-004 # CCGTACA TGTACGG 20 0 7.9e-007 2.4e-002 # CCATACA TGTATGG 29 7 1.2e-004 3.7e+000 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 1.5e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.592593 0.000000 0.407407 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 1.000000 0.000000 0.000000 0.000000 MOTIF GCCWTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCWTA TAWGGC 69 20 2.6e-008 7.6e-004 # GCCTTA TAAGGC 50 12 2.9e-007 8.7e-003 # GCCATA TATGGC 25 10 7.5e-003 2.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 77 E= 7.6e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.337662 0.000000 0.000000 0.662338 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF BTCCGCG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST BTCCGCG CGCGGAV 30 3 4.9e-007 1.4e-002 # CTCCGCG CGCGGAG 13 1 8.6e-004 2.5e+001 # TTCCGCG CGCGGAA 14 2 2.0e-003 5.7e+001 # GTCCGCG CGCGGAC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.4e-002 0.000000 0.393939 0.242424 0.363636 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAAAAWAT DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWAT ATWTTTTT 74 27 5.0e-007 1.4e-002 # AAAAAAAT ATTTTTTT 59 21 6.0e-006 1.8e-001 # AAAAATAT ATATTTTT 22 6 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 76 E= 1.4e-002 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 0.750000 0.000000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF AACTTGGY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AACTTGGY RCCAAGTT 23 1 1.2e-006 3.5e-002 # AACTTGGC GCCAAGTT 15 1 2.4e-004 6.9e+000 # AACTTGGT ACCAAGTT 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.5e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.652174 0.000000 0.347826 # Stopping reason: E-value threshold exceeded # Running time: 30.57 seconds