# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PHD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PHD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PHD1/seqs-shuffled # positives: 814 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PHD1/seqs-centered (Sat Jan 18 23:04:34 PST 2020) # negatives: 814 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PHD1/seqs-shuffled (Sat Jan 18 23:04:34 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:20:07 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 0.287 C 0.216 G 0.215 T 0.282 MOTIF TCGAACCB DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TCGAACCB VGGTTCGA 73 3 2.0e-019 7.3e-015 # TCGAACCC GGGTTCGA 37 3 6.8e-009 2.5e-004 # TCGAACCG CGGTTCGA 25 0 2.5e-008 8.9e-004 # TCGAACCT AGGTTCGA 11 0 4.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 7.3e-015 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.506849 0.342466 0.150685 MOTIF ACCCANAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCCANAC GTNTGGGT 75 8 1.1e-015 3.9e-011 # ACCCATAC GTATGGGT 35 3 2.4e-008 8.8e-004 # ACCCACAC GTGTGGGT 17 1 6.7e-005 2.4e+000 # ACCCAAAC GTTTGGGT 15 2 1.1e-003 4.0e+001 # ACCCAGAC GTCTGGGT 15 2 1.1e-003 4.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 85 E= 3.9e-011 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 0.176471 0.211765 0.176471 0.435294 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 83 15 1.6e-013 5.6e-009 # AGTGGTT AACCACT 60 9 4.9e-011 1.8e-006 # AGTGGTA TACCACT 36 6 1.1e-006 3.8e-002 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 5.6e-009 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 0.370000 0.000000 0.000000 0.630000 MOTIF CGKTGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGKTGCC GGCAMCG 55 8 2.4e-010 8.7e-006 # CGTTGCC GGCAACG 32 3 1.6e-007 5.8e-003 # CGGTGCC GGCACCG 23 5 4.1e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 8.7e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.418182 0.581818 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 MOTIF ATGTACDG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGTACDG CHGTACAT 39 2 2.6e-010 9.1e-006 # ATGTACGG CCGTACAT 28 2 3.5e-007 1.3e-002 # ATGTACAG CTGTACAT 7 0 7.7e-003 2.7e+002 # ATGTACTG CAGTACAT 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 9.1e-006 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.162791 0.000000 0.674419 0.162791 0.000000 0.000000 1.000000 0.000000 MOTIF CGCSTTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 64 13 6.6e-010 2.3e-005 # CGCCTTA TAAGGCG 43 8 2.3e-007 8.3e-003 # CGCGTTA TAACGCG 21 5 1.2e-003 4.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 2.3e-005 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 0.671875 0.328125 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 CAACTKGG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 43 4 8.7e-010 3.1e-005 # CAACTTGG CCAAGTTG 31 4 1.4e-006 4.9e-002 # CAACTGGG CCCAGTTG 12 0 2.3e-004 8.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 3.1e-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 0.272727 0.727273 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GATTWGAA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 35 2 3.7e-009 1.3e-004 # GATTAGAA TTCTAATC 20 0 8.5e-007 3.0e-002 # GATTTGAA TTCAAATC 15 2 1.1e-003 4.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 1.3e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.555556 0.000000 0.000000 0.444444 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-9 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 351 248 7.5e-008 2.7e-003 # CAAGA TCTTG 205 136 1.6e-005 5.8e-001 # GAAGA TCTTC 186 137 1.4e-003 5.0e+001 letter-probability matrix: alength= 4 w= 5 nsites= 486 E= 2.7e-003 0.000000 0.532922 0.467078 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 GCKCTACC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 32 3 1.6e-007 5.5e-003 # GCGCTACC GGTAGCGC 21 3 1.3e-004 4.3e+000 # GCTCTACC GGTAGAGC 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.5e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.656250 0.343750 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 GCATGGGW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GCATGGGW WCCCATGC 22 0 2.1e-007 7.1e-003 # GCATGGGT ACCCATGC 13 0 1.2e-004 4.0e+000 # GCATGGGA TCCCATGC 9 0 1.9e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.1e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.409091 0.000000 0.000000 0.590909 MOTIF CATCTK DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CATCTK MAGATG 83 31 2.4e-007 8.3e-003 # CATCTT AAGATG 43 13 2.8e-005 9.5e-001 # CATCTG CAGATG 43 18 7.6e-004 2.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 87 E= 8.3e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.494253 0.505747 MOTIF GTGATAGY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 31 3 3.0e-007 1.0e-002 # GTGATAGT ACTATCAC 17 2 3.4e-004 1.2e+001 # GTGATAGC GCTATCAC 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.0e-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 0.451613 0.000000 0.548387 # Stopping reason: E-value threshold exceeded # Running time: 73.33 seconds