# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--STE12/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--STE12/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--STE12/seqs-shuffled # positives: 894 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--STE12/seqs-centered (Sat Jan 18 10:34:20 PST 2020) # negatives: 894 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--STE12/seqs-shuffled (Sat Jan 18 10:34:20 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 10:49:21 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 0.288 C 0.209 G 0.213 T 0.290 MOTIF GRRTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRRTCGAA TTCGAYYC 67 5 1.1e-015 3.8e-011 # GGATCGAA TTCGATCC 18 0 3.5e-006 1.3e-001 # GAATCGAA TTCGATTC 21 2 3.0e-005 1.1e+000 # GGGTCGAA TTCGACCC 13 0 1.2e-004 4.2e+000 # GAGTCGAA TTCGACTC 15 3 3.6e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 3.8e-011 0.000000 0.000000 1.000000 0.000000 0.537313 0.000000 0.462687 0.000000 0.582090 0.000000 0.417910 0.000000 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 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 471 307 3.1e-015 1.1e-010 # GAAGA TCTTC 283 175 3.0e-009 1.1e-004 # CAAGA TCTTG 268 163 3.9e-009 1.4e-004 letter-probability matrix: alength= 4 w= 5 nsites= 686 E= 1.1e-010 0.000000 0.475219 0.524781 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCHTAACC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCHTAACC GGTTADGG 46 2 2.4e-012 8.5e-008 # CCTTAACC GGTTAAGG 28 2 3.6e-007 1.3e-002 # CCCTAACC GGTTAGGG 10 0 9.5e-004 3.3e+001 # CCATAACC GGTTATGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 8.5e-008 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.173913 0.217391 0.000000 0.608696 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 ACCACYA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACYA TRGTGGT 73 15 4.8e-011 1.7e-006 # ACCACTA TAGTGGT 46 8 4.6e-008 1.6e-003 # ACCACCA TGGTGGT 27 7 3.7e-004 1.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 1.7e-006 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 0.378378 0.000000 0.621622 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 31 1 6.0e-009 2.1e-004 # GCGCTACC GGTAGCGC 21 1 4.9e-006 1.7e-001 # GCTCTACC GGTAGAGC 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.1e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.677419 0.322581 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 TCGSCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TCGSCCA TGGSCGA 46 7 1.3e-008 4.5e-004 # TCGGCCA TGGCCGA 31 4 1.4e-006 4.9e-002 # TCGCCCA TGGGCGA 15 3 3.6e-003 1.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 4.5e-004 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.326087 0.673913 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 AGTCAKAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 24 0 5.1e-008 1.8e-003 # AGTCAGAC GTCTGACT 12 0 2.4e-004 8.2e+000 # AGTCATAC GTATGACT 12 0 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-003 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 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAAC GTTGCCAT 27 1 9.0e-008 3.1e-003 # ATGGCAAC GTTGCCAT 27 1 9.0e-008 3.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.1e-003 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 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 MOTIF ATCTKTTG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATCTKTTG CAAMAGAT 29 2 1.9e-007 6.6e-003 # ATCTGTTG CAACAGAT 15 1 2.5e-004 8.6e+000 # ATCTTTTG CAAAAGAT 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 6.6e-003 1.000000 0.000000 0.000000 0.000000 0.000000 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 0.533333 0.466667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GKGGCCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GKGGCCCA TGGGCCMC 25 1 3.4e-007 1.2e-002 # GGGGCCCA TGGGCCCC 18 1 3.5e-005 1.2e+000 # GTGGCCCA TGGGCCAC 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.2e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.720000 0.280000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGRCTCGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGRCTCGA TCGAGYCC 21 0 4.2e-007 1.5e-002 # GGGCTCGA TCGAGCCC 14 0 5.8e-005 2.0e+000 # GGACTCGA TCGAGTCC 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.5e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCYGTACA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TCYGTACA TGTACRGA 24 1 6.7e-007 2.3e-002 # TCCGTACA TGTACGGA 18 1 3.5e-005 1.2e+000 # TCTGTACA TGTACAGA 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 2.3e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.678571 0.000000 0.321429 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 MOTIF CCWTAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCWTAC GTAWGG 102 46 9.2e-007 3.2e-002 # CCATAC GTATGG 65 28 5.2e-005 1.8e+000 # CCTTAC GTAAGG 39 18 3.3e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 108 E= 3.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.638889 0.000000 0.000000 0.361111 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AKACAACA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AKACAACA TGTTGTMT 26 2 1.3e-006 4.5e-002 # ATACAACA TGTTGTAT 18 2 1.9e-004 6.5e+000 # AGACAACA TGTTGTCT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.5e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.307692 0.692308 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 80.07 seconds