# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/seqs-shuffled # positives: 520 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/seqs-centered (Sun Jan 19 07:20:26 PST 2020) # negatives: 520 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/seqs-shuffled (Sun Jan 19 07:20:26 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 07:31:46 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 0.296 C 0.204 G 0.206 T 0.294 MOTIF GGDTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGDTCGA TCGAHCC 86 2 3.2e-025 9.2e-021 # GGTTCGA TCGAACC 77 1 1.3e-023 3.8e-019 # GGGTCGA TCGACCC 12 0 2.3e-004 6.5e+000 # GGATCGA TCGATCC 15 1 2.4e-004 6.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 86 E= 9.2e-021 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.151163 0.000000 0.046512 0.802326 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 78 1 6.3e-024 1.8e-019 # TGTACGGA TCCGTACA 31 0 2.9e-010 8.3e-006 # TGTATGGG CCCATACA 34 1 6.2e-010 1.8e-005 # TGTATGGA TCCATACA 11 0 4.6e-004 1.3e+001 # TGTACGGG CCCGTACA 10 0 9.3e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 1.8e-019 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.477778 0.000000 0.522222 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 76 6 6.3e-018 1.8e-013 # CGCCTTA TAAGGCG 60 5 5.3e-014 1.5e-009 # CGCGTTA TAACGCG 16 1 1.2e-004 3.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 76 E= 1.8e-013 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 0.789474 0.210526 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 CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 65 3 2.5e-017 7.1e-013 # CTCGGCCA TGGCCGAG 32 0 1.4e-010 4.0e-006 # CTTGGCCA TGGCCAAG 21 2 2.8e-005 7.8e-001 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 4.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 65 E= 7.1e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.492308 0.184615 0.323077 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 1.000000 0.000000 0.000000 0.000000 MOTIF TGGGTGB DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TGGGTGB VCACCCA 56 6 4.2e-012 1.2e-007 # TGGGTGT ACACCCA 35 3 2.0e-008 5.7e-004 # TGGGTGC GCACCCA 17 1 6.4e-005 1.8e+000 # TGGGTGG CCACCCA 12 2 6.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 1.2e-007 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.171429 0.528571 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 1 9.1e-012 2.5e-007 # GCGCTACC GGTAGCGC 24 0 4.5e-008 1.3e-003 # GCTCTACC GGTAGAGC 16 1 1.2e-004 3.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 2.5e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 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 1.000000 0.000000 0.000000 MOTIF CTATCACR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 35 0 1.6e-011 4.4e-007 # CTATCACA TGTGATAG 18 0 3.3e-006 9.1e-002 # CTATCACG CGTGATAG 17 0 6.7e-006 1.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 4.4e-007 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.514286 0.000000 0.485714 0.000000 MOTIF GTWGCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTWGCCA TGGCWAC 48 5 1.4e-010 3.9e-006 # GTTGCCA TGGCAAC 36 3 1.1e-008 2.9e-004 # GTAGCCA TGGCTAC 12 2 6.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 3.9e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.000000 0.750000 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 MOTIF SAARAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST SAARAAA TTTYTTS 169 83 2.9e-010 7.8e-006 # GAAGAAA TTTCTTC 41 9 1.7e-006 4.6e-002 # GAAAAAA TTTTTTC 69 34 1.9e-004 5.1e+000 # CAAGAAA TTTCTTG 33 13 1.9e-003 5.1e+001 # CAAAAAA TTTTTTG 58 34 5.8e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 194 E= 7.8e-006 0.000000 0.463918 0.536082 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.675258 0.000000 0.324742 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 ACCACKA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACCACKA TMGTGGT 53 9 2.0e-009 5.4e-005 # ACCACTA TAGTGGT 42 8 3.3e-007 8.9e-003 # ACCACGA TCGTGGT 12 1 1.6e-003 4.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 5.4e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.222222 0.777778 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 44 6 7.9e-009 2.1e-004 # TGGCGTA TACGCCA 21 1 4.5e-006 1.2e-001 # TGGCGCA TGCGCCA 23 5 3.9e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 2.1e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.522727 0.000000 0.477273 1.000000 0.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 26 0 1.1e-008 2.9e-004 # CACCGTGC GCACGGTG 13 0 1.1e-004 3.0e+000 # CACCGTGG CCACGGTG 13 0 1.1e-004 3.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 2.9e-004 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 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 0.500000 0.500000 0.000000 MOTIF CACTTKCG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 23 0 9.3e-008 2.5e-003 # CACTTGCG CGCAAGTG 14 0 5.6e-005 1.5e+000 # CACTTTCG CGAAAGTG 9 0 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.5e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.608696 0.391304 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GGRAGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GGRAGA TCTYCC 70 23 1.7e-007 4.6e-003 # GGAAGA TCTTCC 41 15 2.4e-004 6.5e+000 # GGGAGA TCTCCC 29 9 6.8e-004 1.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 70 E= 4.6e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.585714 0.000000 0.414286 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 GACTSTTA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GACTSTTA TAASAGTC 22 0 1.9e-007 5.1e-003 # GACTCTTA TAAGAGTC 12 0 2.3e-004 6.1e+000 # GACTGTTA TAACAGTC 10 0 9.3e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.1e-003 0.000000 0.000000 1.000000 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 0.545455 0.454545 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 TCTAAYCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TCTAAYCA TGRTTAGA 20 0 7.9e-007 2.1e-002 # TCTAATCA TGATTAGA 13 0 1.1e-004 3.0e+000 # TCTAACCA TGGTTAGA 7 0 7.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.1e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 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 0.000000 0.350000 0.000000 0.650000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTGAGCTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 23 1 1.2e-006 3.1e-002 # CTGAGCTA TAGCTCAG 23 1 1.2e-006 3.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.1e-002 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 60.55 seconds