# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-shuffled # positives: 966 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-centered (Sat Jan 18 05:33:54 PST 2020) # negatives: 966 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SFL1/seqs-shuffled (Sat Jan 18 05:33:54 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:48:30 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 0.323 C 0.175 G 0.171 T 0.331 MOTIF CCHTAACC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 47 1 1.0e-013 3.4e-009 # CCTTAACC GGTTAAGG 27 0 6.2e-009 2.1e-004 # CCCTAACC GGTTAGGG 9 0 1.9e-003 6.4e+001 # CCATAACC GGTTATGG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 3.4e-009 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.234043 0.191489 0.000000 0.574468 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 RAGAAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST RAGAAA TTTCTY 363 223 2.5e-012 8.5e-008 # AAGAAA TTTCTT 287 172 4.7e-010 1.6e-005 # GAGAAA TTTCTC 123 69 2.5e-005 8.5e-001 letter-probability matrix: alength= 4 w= 6 nsites= 460 E= 8.5e-008 0.723913 0.000000 0.276087 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 1.000000 0.000000 0.000000 0.000000 MOTIF GGHTCGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 81 18 1.7e-011 5.7e-007 # GGTTCGA TCGAACC 56 10 2.0e-009 6.5e-005 # GGATCGA TCGATCC 18 5 5.1e-003 1.7e+002 # GGCTCGA TCGAGCC 16 4 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 81 E= 5.7e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.185185 0.185185 0.000000 0.629630 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 GCCAAGW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCCAAGW WCTTGGC 51 6 1.7e-010 5.5e-006 # GCCAAGT ACTTGGC 33 4 4.4e-007 1.4e-002 # GCCAAGA TCTTGGC 18 2 1.9e-004 6.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 5.5e-006 0.000000 0.000000 1.000000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.352941 0.000000 0.000000 0.647059 MOTIF AGCKAGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGCKAGA TCTMGCT 32 2 2.8e-008 9.1e-004 # AGCGAGA TCTCGCT 17 0 7.1e-006 2.3e-001 # AGCTAGA TCTAGCT 15 2 1.1e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 9.1e-004 1.000000 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 0.531250 0.468750 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 CGMTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGMTACC GGTAKCG 32 2 2.8e-008 9.1e-004 # CGCTACC GGTAGCG 17 1 6.8e-005 2.2e+000 # CGATACC GGTATCG 15 1 2.5e-004 8.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 9.1e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.468750 0.531250 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 MOTIF ATATAYA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATATAYA TRTATAT 125 57 6.7e-008 2.2e-003 # ATATATA TATATAT 85 36 2.5e-006 8.3e-002 # ATATACA TGTATAT 63 25 2.1e-005 6.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 140 E= 2.2e-003 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.407143 0.000000 0.592857 1.000000 0.000000 0.000000 0.000000 MOTIF AMGATGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AMGATGG CCATCKT 55 13 8.6e-008 2.8e-003 # ACGATGG CCATCGT 22 2 1.6e-005 5.3e-001 # AAGATGG CCATCTT 33 11 5.5e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 2.8e-003 1.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACCACTR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACCACTR YAGTGGT 47 9 8.8e-008 2.9e-003 # ACCACTA TAGTGGT 40 9 3.6e-006 1.2e-001 # ACCACTG CAGTGGT 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 2.9e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.851064 0.000000 0.148936 0.000000 MOTIF CACGGYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 35 4 1.3e-007 4.3e-003 # CACGGTG CACCGTG 25 4 4.6e-005 1.5e+000 # CACGGCG CGCCGTG 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 4.3e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 65.45 seconds