# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAT8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAT8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAT8/seqs-shuffled # positives: 558 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAT8/seqs-centered (Sat Jan 18 10:48:22 PST 2020) # negatives: 558 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAT8/seqs-shuffled (Sat Jan 18 10:48:22 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 11:02:32 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 0.300 C 0.203 G 0.199 T 0.297 MOTIF GTTCGABY DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGABY RVTCGAAC 82 2 8.6e-024 2.6e-019 # GTTCGATC GATCGAAC 18 0 3.3e-006 1.0e-001 # GTTCGATT AATCGAAC 21 1 4.6e-006 1.4e-001 # GTTCGAGC GCTCGAAC 14 0 5.6e-005 1.7e+000 # GTTCGACT AGTCGAAC 13 1 8.6e-004 2.6e+001 # GTTCGAGT ACTCGAAC 9 0 1.9e-003 5.8e+001 # GTTCGACC GGTCGAAC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 2.6e-019 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 0.000000 0.243902 0.280488 0.475610 0.000000 0.475610 0.000000 0.524390 MOTIF AAAAADAA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAAAADAA TTHTTTTT 123 35 1.0e-014 3.0e-010 # AAAAATAA TTATTTTT 42 7 1.0e-007 3.1e-003 # AAAAAGAA TTCTTTTT 37 8 5.2e-006 1.6e-001 # AAAAAAAA TTTTTTTT 58 23 3.5e-005 1.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 136 E= 3.0e-010 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 0.441176 0.000000 0.272059 0.286765 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCHTAACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 48 2 4.3e-013 1.3e-008 # CCTTAACC GGTTAAGG 24 1 6.1e-007 1.9e-002 # CCATAACC GGTTATGG 13 0 1.1e-004 3.4e+000 # CCCTAACC GGTTAGGG 12 1 1.6e-003 4.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 1.3e-008 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.265306 0.244898 0.000000 0.489796 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 AGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 65 15 2.1e-009 6.5e-005 # AGTGGTT AACCACT 41 9 1.8e-006 5.3e-002 # AGTGGTA TACCACT 34 6 2.9e-006 8.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 77 E= 6.5e-005 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 0.454545 0.000000 0.000000 0.545455 MOTIF CTACYGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTACYGA TCRGTAG 31 2 4.5e-008 1.4e-003 # CTACCGA TCGGTAG 21 2 2.8e-005 8.5e-001 # CTACTGA TCAGTAG 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.4e-003 0.000000 1.000000 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 0.617647 0.000000 0.382353 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTGSA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 33 4 3.7e-007 1.1e-002 # CCGTGGA TCCACGG 17 1 6.5e-005 2.0e+000 # CCGTGCA TGCACGG 16 3 2.1e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.1e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.484848 0.515152 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 33 4 3.7e-007 1.1e-002 # CGCCTTA TAAGGCG 22 3 6.7e-005 2.0e+000 # CGCGTTA TAACGCG 11 1 3.0e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.1e-002 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 0.666667 0.333333 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 GTGATAGY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 20 0 8.0e-007 2.4e-002 # GTGATAGC GCTATCAC 10 0 9.4e-004 2.8e+001 # GTGATAGT ACTATCAC 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 MOTIF GACAAS DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GACAAS STTGTC 60 19 9.4e-007 2.8e-002 # GACAAC GTTGTC 32 10 3.8e-004 1.1e+001 # GACAAG CTTGTC 29 9 6.9e-004 2.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 63 E= 2.8e-002 0.000000 0.000000 1.000000 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 0.539683 0.460317 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 36.18 seconds