# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--STE12/seqs-shuffled # positives: 665 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--STE12/seqs-centered (Sun Jan 19 10:20:47 PST 2020) # negatives: 665 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--STE12/seqs-shuffled (Sun Jan 19 10:20:47 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 10:37:03 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 0.302 C 0.200 G 0.199 T 0.299 MOTIF CGCSTTA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 72 5 2.4e-017 7.7e-013 # CGCCTTA TAAGGCG 59 3 2.6e-015 8.2e-011 # CGCGTTA TAACGCG 13 2 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 7.7e-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 0.819444 0.180556 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 ACCCANAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 65 3 4.0e-017 1.3e-012 # ACCCATAC GTATGGGT 36 0 8.9e-012 2.9e-007 # ACCCACAC GTGTGGGT 13 1 8.7e-004 2.8e+001 # ACCCAAAC GTTTGGGT 11 1 3.1e-003 9.8e+001 # ACCCAGAC GTCTGGGT 11 1 3.1e-003 9.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 74 E= 1.3e-012 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.148649 0.202703 0.148649 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACCACTM DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 71 8 1.0e-014 3.2e-010 # ACCACTA TAGTGGT 42 5 7.3e-009 2.3e-004 # ACCACTC GAGTGGT 30 3 5.3e-007 1.7e-002 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 3.2e-010 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 0.583333 0.416667 0.000000 0.000000 MOTIF CAAGTTGS DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAAGTTGS SCAACTTG 40 0 5.0e-013 1.6e-008 # CAAGTTGG CCAACTTG 30 0 6.7e-010 2.1e-005 # CAAGTTGC GCAACTTG 10 0 9.4e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 1.6e-008 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 MOTIF GTTCGA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GTTCGA TCGAAC 67 12 3.1e-011 9.9e-007 # GTTCGA TCGAAC 67 12 3.1e-011 9.9e-007 letter-probability matrix: alength= 4 w= 6 nsites= 69 E= 9.9e-007 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 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 39 2 2.3e-010 7.4e-006 # GCGCTACC GGTAGCGC 27 1 8.4e-008 2.7e-003 # GCTCTACC GGTAGAGC 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 7.4e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.692308 0.307692 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 CCGTACAY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCGTACAY RTGTACGG 40 3 9.0e-010 2.8e-005 # CCGTACAT ATGTACGG 28 3 1.8e-006 5.8e-002 # CCGTACAC GTGTACGG 13 0 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.8e-005 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 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 0.302326 0.000000 0.697674 MOTIF TGGCGYA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 44 6 9.3e-009 2.9e-004 # TGGCGTA TACGCCA 20 2 5.4e-005 1.7e+000 # TGGCGCA TGCGCCA 24 4 7.8e-005 2.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 2.9e-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 0.545455 0.000000 0.454545 1.000000 0.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 28 1 4.3e-008 1.3e-003 # GTGATAGT ACTATCAC 13 0 1.2e-004 3.6e+000 # GTGATAGC GCTATCAC 16 1 1.3e-004 4.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 1.3e-003 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 0.551724 0.000000 0.448276 MOTIF AAGAAAWA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAWA TWTTTCTT 59 15 6.0e-008 1.9e-003 # AAGAAAAA TTTTTCTT 43 11 4.7e-006 1.5e-001 # AAGAAATA TATTTCTT 19 4 1.2e-003 3.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 1.9e-003 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 1.000000 0.000000 0.000000 0.000000 0.693548 0.000000 0.000000 0.306452 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 25 1 3.3e-007 1.0e-002 # AGTCATAC GTATGACT 15 0 2.8e-005 8.8e-001 # AGTCAGAC GTCTGACT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AACTGRGC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AACTGRGC GCYCAGTT 24 1 6.4e-007 2.0e-002 # AACTGAGC GCTCAGTT 15 1 2.4e-004 7.6e+000 # AACTGGGC GCCCAGTT 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-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 1.000000 0.000000 0.625000 0.000000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 56.11 seconds