# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/seqs-shuffled # positives: 895 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/seqs-centered (Fri Jan 17 22:52:20 PST 2020) # negatives: 895 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/seqs-shuffled (Fri Jan 17 22:52:20 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:08:17 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 0.298 C 0.207 G 0.203 T 0.292 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 107 11 2.1e-022 7.4e-018 # GGTTCGA TCGAACC 90 7 1.2e-020 4.1e-016 # GGATCGA TCGATCC 26 4 2.6e-005 9.2e-001 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 7.4e-018 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.212963 0.000000 0.000000 0.787037 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 AYCCRTAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 93 8 1.0e-020 3.7e-016 # ACCCATAC GTATGGGT 46 4 1.4e-010 4.8e-006 # ATCCGTAC GTACGGAT 33 1 1.5e-009 5.4e-005 # ATCCATAC GTATGGAT 14 2 2.0e-003 7.1e+001 # ACCCGTAC GTACGGGT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 108 E= 3.7e-016 1.000000 0.000000 0.000000 0.000000 0.000000 0.537037 0.000000 0.462963 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.564815 0.000000 0.435185 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 AGTGGTW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 102 15 2.4e-018 8.3e-014 # AGTGGTT AACCACT 74 10 5.0e-014 1.8e-009 # AGTGGTA TACCACT 40 5 2.8e-008 9.8e-004 letter-probability matrix: alength= 4 w= 7 nsites= 118 E= 8.3e-014 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 0.338983 0.000000 0.000000 0.661017 MOTIF AGAAAH DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGAAAH DTTTCT 374 225 5.0e-014 1.7e-009 # AGAAAA TTTTCT 230 126 4.3e-010 1.5e-005 # AGAAAT ATTTCT 126 82 7.3e-004 2.6e+001 # AGAAAC GTTTCT 74 46 5.2e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 482 E= 1.7e-009 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 0.560166 0.157676 0.000000 0.282158 MOTIF CABACGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CABACGC GCGTVTG 67 9 8.2e-013 2.8e-008 # CACACGC GCGTGTG 28 3 2.0e-006 6.7e-002 # CAGACGC GCGTCTG 23 3 3.9e-005 1.4e+000 # CATACGC GCGTATG 16 3 2.1e-003 7.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 2.8e-008 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.417910 0.343284 0.238806 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 MOTIF CGCSTTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 73 13 4.8e-012 1.6e-007 # CGCCTTA TAAGGCG 54 7 1.2e-010 4.0e-006 # CGCGTTA TAACGCG 19 6 7.0e-003 2.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 73 E= 1.6e-007 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 0.739726 0.260274 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-7 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 51 4 5.5e-012 1.9e-007 # CTTGGCCA TGGCCAAG 20 1 9.5e-006 3.3e-001 # CTCGGCCA TGGCCGAG 18 1 3.5e-005 1.2e+000 # CTGGGCCA TGGCCCAG 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 1.9e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.352941 0.254902 0.392157 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 GCTACCGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCTACCGA TCGGTAGC 33 0 8.6e-011 2.9e-006 # GCTACCGA TCGGTAGC 33 0 8.6e-011 2.9e-006 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.9e-006 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 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 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 46 4 1.4e-010 4.6e-006 # ATGGCAAC GTTGCCAT 30 2 9.9e-008 3.4e-003 # ATGGCATC GATGCCAT 16 2 6.2e-004 2.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 4.6e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.652174 0.000000 0.000000 0.347826 0.000000 1.000000 0.000000 0.000000 MOTIF GCATGGGW DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCATGGGW WCCCATGC 28 0 3.0e-009 1.0e-004 # GCATGGGT ACCCATGC 16 0 1.4e-005 4.9e-001 # GCATGGGA TCCCATGC 12 0 2.4e-004 8.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.0e-004 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 0.428571 0.000000 0.000000 0.571429 MOTIF ACCCAMAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACCCAMAC GTKTGGGT 55 10 3.3e-009 1.1e-004 # ACCCACAC GTGTGGGT 38 9 9.8e-006 3.3e-001 # ACCCAAAC GTTTGGGT 17 1 6.8e-005 2.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 107 E= 1.1e-004 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 0.158879 0.841121 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGAGACCK DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GGAGACCK MGGTCTCC 24 0 5.1e-008 1.7e-003 # GGAGACCG CGGTCTCC 14 0 5.8e-005 2.0e+000 # GGAGACCT AGGTCTCC 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.7e-003 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 0.000000 1.000000 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 0.583333 0.416667 MOTIF CTATCACR DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 31 2 5.2e-008 1.8e-003 # CTATCACA TGTGATAG 17 1 6.8e-005 2.3e+000 # CTATCACG CGTGATAG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.8e-003 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 0.548387 0.000000 0.451613 0.000000 MOTIF AAAGCGWG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 27 1 9.0e-008 3.1e-003 # AAAGCGAG CTCGCTTT 12 0 2.4e-004 8.0e+000 # AAAGCGTG CACGCTTT 15 1 2.5e-004 8.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.1e-003 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.444444 0.000000 0.000000 0.555556 0.000000 0.000000 1.000000 0.000000 MOTIF ACTGAGCT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 22 0 2.1e-007 7.1e-003 # ACTGAGCT AGCTCAGT 22 0 2.1e-007 7.1e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.1e-003 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 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 MOTIF CAGAWCG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CAGAWCG CGWTCTG 42 8 4.2e-007 1.4e-002 # CAGAACG CGTTCTG 22 4 2.4e-004 8.3e+000 # CAGATCG CGATCTG 20 4 7.2e-004 2.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.4e-002 0.000000 1.000000 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 0.523810 0.000000 0.000000 0.476190 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF SATCGTGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST SATCGTGA TCACGATS 20 0 8.6e-007 2.9e-002 # CATCGTGA TCACGATG 12 0 2.4e-004 8.0e+000 # GATCGTGA TCACGATC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.9e-002 0.000000 0.600000 0.400000 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 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 MOTIF ATCTKCTG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATCTKCTG CAGMAGAT 29 3 1.1e-006 3.6e-002 # ATCTTCTG CAGAAGAT 21 3 1.3e-004 4.3e+000 # ATCTGCTG CAGCAGAT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.6e-002 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 0.275862 0.724138 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACACTATA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 26 2 1.3e-006 4.4e-002 # ACACTATA TATAGTGT 26 2 1.3e-006 4.4e-002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.4e-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 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 1.000000 0.000000 0.000000 0.000000 MOTIF ATCCKTGC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATCCKTGC GCAMGGAT 23 1 1.3e-006 4.4e-002 # ATCCGTGC GCACGGAT 14 1 4.7e-004 1.6e+001 # ATCCTTGC GCAAGGAT 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 4.4e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 110.66 seconds