# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-shuffled # positives: 604 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-centered (Sat Jan 18 17:07:16 PST 2020) # negatives: 604 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SMP1/seqs-shuffled (Sat Jan 18 17:07:16 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:23:33 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 0.304 C 0.200 G 0.196 T 0.301 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 95 8 8.6e-022 2.7e-017 # GGTTCGA TCGAACC 77 6 4.6e-018 1.5e-013 # GGATCGA TCGATCC 23 3 3.7e-005 1.2e+000 # GGCTCGA TCGAGCC 14 0 5.7e-005 1.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 2.7e-017 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.063158 0.000000 0.736842 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 ACCRCT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCRCT AGYGGT 106 28 2.1e-013 6.6e-009 # ACCACT AGTGGT 82 22 2.5e-010 7.9e-006 # ACCGCT AGCGGT 27 6 1.3e-004 4.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 120 E= 6.6e-009 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.775000 0.000000 0.225000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ARAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAA TTTTTYT 154 69 1.6e-010 4.9e-006 # AAAAAAA TTTTTTT 116 49 1.1e-008 3.4e-004 # AGAAAAA TTTTTCT 67 26 5.9e-006 1.8e-001 letter-probability matrix: alength= 4 w= 7 nsites= 186 E= 4.9e-006 1.000000 0.000000 0.000000 0.000000 0.672043 0.000000 0.327957 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 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 32 1 2.7e-009 8.2e-005 # CAACTTGG CCAAGTTG 23 1 1.2e-006 3.8e-002 # CAACTGGG CCCAGTTG 9 0 1.9e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.2e-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 0.281250 0.718750 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCSTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 54 10 4.3e-009 1.3e-004 # CGCCTTA TAAGGCG 40 7 3.4e-007 1.0e-002 # CGCGTTA TAACGCG 14 3 6.1e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 1.3e-004 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 0.740741 0.259259 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CRCCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 87 32 5.9e-008 1.8e-003 # CACCCA TGGGTG 57 20 8.0e-006 2.5e-001 # CGCCCA TGGGCG 33 13 1.9e-003 5.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 109 E= 1.8e-003 0.000000 1.000000 0.000000 0.000000 0.706422 0.000000 0.293578 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 1.000000 0.000000 0.000000 0.000000 MOTIF CTYACGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTYACGA TCGTRAG 26 2 1.2e-006 3.6e-002 # CTCACGA TCGTGAG 16 1 1.3e-004 3.8e+000 # CTTACGA TCGTAAG 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 26 E= 3.6e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.615385 0.000000 0.384615 1.000000 0.000000 0.000000 0.000000 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 CGTGYTAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 23 1 1.2e-006 3.7e-002 # CGTGCTAA TTAGCACG 11 0 4.7e-004 1.4e+001 # CGTGTTAA TTAACACG 12 1 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.7e-002 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 1.000000 0.000000 0.000000 0.478261 0.000000 0.521739 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGARGTC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGARGTC GACYTCT 31 4 1.3e-006 3.9e-002 # AGAAGTC GACTTCT 19 3 3.9e-004 1.2e+001 # AGAGGTC GACCTCT 12 1 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 3.9e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.612903 0.000000 0.387097 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 39.26 seconds