# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/seqs-shuffled # positives: 560 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/seqs-centered (Sat Jan 18 05:49:43 PST 2020) # negatives: 560 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/seqs-shuffled (Sat Jan 18 05:49:43 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 06:03:02 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 0.206 G 0.208 T 0.291 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 73 2 7.0e-021 2.1e-016 # ACCCATAC GTATGGGT 36 0 8.1e-012 2.4e-007 # ATCCGTAC GTACGGAT 27 0 5.4e-009 1.6e-004 # ACCCGTAC GTACGGGT 9 0 1.9e-003 5.7e+001 # ATCCATAC GTATGGAT 12 2 6.2e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 2.1e-016 1.000000 0.000000 0.000000 0.000000 0.000000 0.522727 0.000000 0.477273 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.556818 0.000000 0.443182 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 MOTIF RGTTCGA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 81 7 1.6e-018 4.8e-014 # GGTTCGA TCGAACC 68 3 3.5e-018 1.0e-013 # AGTTCGA TCGAACT 17 4 3.3e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 81 E= 4.8e-014 0.172840 0.000000 0.827160 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 81 8 9.8e-018 2.9e-013 # AGTGGTT AACCACT 60 4 8.5e-015 2.5e-010 # AGTGGTA TACCACT 35 4 1.1e-007 3.2e-003 letter-probability matrix: alength= 4 w= 7 nsites= 97 E= 2.9e-013 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 0.360825 0.000000 0.000000 0.639175 MOTIF ACCAACTK DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCAACTK MAGTTGGT 53 3 1.3e-013 3.8e-009 # ACCAACTT AAGTTGGT 34 3 4.0e-008 1.2e-003 # ACCAACTG CAGTTGGT 19 0 1.6e-006 4.8e-002 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 3.8e-009 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 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 0.358491 0.641509 MOTIF ATGGCAWC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 42 2 2.7e-011 8.0e-007 # ATGGCAAC GTTGCCAT 30 0 6.2e-010 1.8e-005 # ATGGCATC GATGCCAT 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 8.0e-007 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 0.697674 0.000000 0.000000 0.302326 0.000000 1.000000 0.000000 0.000000 MOTIF GCGCYAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCGCYAC GTRGCGC 36 2 1.6e-009 4.7e-005 # GCGCTAC GTAGCGC 20 0 8.0e-007 2.4e-002 # GCGCCAC GTGGCGC 16 2 6.0e-004 1.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 4.7e-005 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 1.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.555556 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCGTGGAR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCGTGGAR YTCCACGG 27 0 5.4e-009 1.6e-004 # CCGTGGAA TTCCACGG 14 0 5.6e-005 1.7e+000 # CCGTGGAG CTCCACGG 14 0 5.6e-005 1.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 1.6e-004 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.517241 0.000000 0.482759 0.000000 MOTIF CCAAVAGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CCAAVAGA TCTBTTGG 37 3 5.8e-009 1.7e-004 # CCAAGAGA TCTCTTGG 14 0 5.6e-005 1.6e+000 # CCAACAGA TCTGTTGG 11 1 3.0e-003 8.9e+001 # CCAAAAGA TCTTTTGG 12 2 6.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.7e-004 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 0.324324 0.297297 0.378378 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 CTATCACR DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 30 1 1.0e-008 3.0e-004 # CTATCACA TGTGATAG 14 0 5.6e-005 1.6e+000 # CTATCACG CGTGATAG 16 1 1.2e-004 3.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.0e-004 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 0.466667 0.000000 0.533333 0.000000 MOTIF GYGGTCTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GYGGTCTA TAGACCRC 26 0 1.1e-008 3.2e-004 # GTGGTCTA TAGACCAC 19 0 1.6e-006 4.8e-002 # GCGGTCTA TAGACCGC 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.2e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.269231 0.000000 0.730769 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGAW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST SAAGAW WTCTTS 210 125 1.9e-008 5.4e-004 # GAAGAT ATCTTC 50 18 4.0e-005 1.2e+000 # CAAGAT ATCTTG 65 31 1.9e-004 5.6e+000 # GAAGAA TTCTTC 77 43 6.8e-004 2.0e+001 # CAAGAA TTCTTG 75 48 6.4e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 277 E= 5.4e-004 0.000000 0.545126 0.454874 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 0.566787 0.000000 0.000000 0.433213 MOTIF CGSCCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 75 26 1.7e-007 4.9e-003 # CGCCCA TGGGCG 37 12 1.8e-004 5.0e+000 # CGGCCA TGGCCG 38 14 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 79 E= 4.9e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.518987 0.481013 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 ACAARGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ACAARGC GCYTTGT 39 7 5.7e-007 1.6e-002 # ACAAGGC GCCTTGT 18 2 1.8e-004 5.1e+000 # ACAAAGC GCTTTGT 22 5 6.7e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 1.6e-002 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 0.538462 0.000000 0.461538 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGCSCAA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GGCSCAA TTGSGCC 34 5 8.3e-007 2.3e-002 # GGCGCAA TTGCGCC 19 3 3.8e-004 1.1e+001 # GGCCCAA TTGGGCC 15 2 1.1e-003 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.3e-002 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 0.441176 0.558824 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 MOTIF GCACGS DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCACGS SCGTGC 56 17 1.3e-006 3.6e-002 # GCACGG CCGTGC 35 12 4.3e-004 1.2e+001 # GCACGC GCGTGC 21 5 1.1e-003 3.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 58 E= 3.6e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.362069 0.637931 0.000000 MOTIF GGRGATCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GGRGATCA TGATCYCC 19 0 1.6e-006 4.6e-002 # GGGGATCA TGATCCCC 10 0 9.4e-004 2.6e+001 # GGAGATCA TGATCTCC 9 0 1.9e-003 5.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.6e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.473684 0.000000 0.526316 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 60.61 seconds