# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--INO80/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--INO80/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--INO80/seqs-shuffled # positives: 537 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--INO80/seqs-centered (Sun Jan 19 04:03:47 PST 2020) # negatives: 537 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--INO80/seqs-shuffled (Sun Jan 19 04:03:47 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 04:16:03 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 0.307 C 0.194 G 0.193 T 0.306 MOTIF AGTGGTW DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 83 5 6.4e-021 1.8e-016 # AGTGGTT AACCACT 61 5 2.8e-014 8.3e-010 # AGTGGTA TACCACT 35 0 1.6e-011 4.8e-007 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 1.8e-016 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 0.353535 0.000000 0.000000 0.646465 MOTIF AYCCRTAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 67 3 6.5e-018 1.9e-013 # ATCCGTAC GTACGGAT 25 0 2.2e-008 6.5e-004 # ACCCATAC GTATGGGT 32 2 2.3e-008 6.6e-004 # ACCCGTAC GTACGGGT 9 0 1.9e-003 5.5e+001 # ATCCATAC GTATGGAT 10 1 5.7e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 81 E= 1.9e-013 1.000000 0.000000 0.000000 0.000000 0.000000 0.530864 0.000000 0.469136 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.543210 0.000000 0.456790 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 ACCRACT DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 68 7 9.3e-015 2.7e-010 # ACCAACT AGTTGGT 52 6 5.7e-011 1.6e-006 # ACCGACT AGTCGGT 16 1 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 68 E= 2.7e-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 0.764706 0.000000 0.235294 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 MOTIF AAGGCG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAGGCG CGCCTT 69 10 4.9e-013 1.4e-008 # AAGGCG CGCCTT 69 10 4.9e-013 1.4e-008 letter-probability matrix: alength= 4 w= 6 nsites= 70 E= 1.4e-008 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CAASAAR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAASAAR YTTSTTG 103 37 1.1e-009 3.0e-005 # CAAGAAA TTTCTTG 37 13 3.5e-004 1.0e+001 # CAACAAG CTTGTTG 23 5 3.9e-004 1.1e+001 # CAACAAA TTTGTTG 29 13 8.6e-003 2.5e+002 # CAAGAAG CTTCTTG 20 7 8.9e-003 2.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 110 E= 3.0e-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 0.472727 0.527273 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.609091 0.000000 0.390909 0.000000 MOTIF CCACAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCACAC GTGTGG 50 8 3.3e-009 9.4e-005 # CCACAC GTGTGG 50 8 3.3e-009 9.4e-005 letter-probability matrix: alength= 4 w= 6 nsites= 53 E= 9.4e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCTACYGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCTACYGA TCRGTAGC 26 0 1.1e-008 3.1e-004 # GCTACCGA TCGGTAGC 19 0 1.6e-006 4.6e-002 # GCTACTGA TCAGTAGC 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.1e-004 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 0.730769 0.000000 0.269231 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 3 3.9e-008 1.1e-003 # ATGGCAAC GTTGCCAT 23 2 7.9e-006 2.2e-001 # ATGGCATC GATGCCAT 11 1 3.0e-003 8.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.1e-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 0.676471 0.000000 0.000000 0.323529 0.000000 1.000000 0.000000 0.000000 MOTIF GGTTCGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 38 5 7.5e-008 2.1e-003 # GGTTCGA TCGAACC 38 5 7.5e-008 2.1e-003 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 2.1e-003 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 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 ATAGTKTA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 30 2 8.6e-008 2.4e-003 # ATAGTGTA TACACTAT 17 1 6.5e-005 1.8e+000 # ATAGTTTA TAAACTAT 13 1 8.6e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.4e-003 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.566667 0.433333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGGCYA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGGCYA TRGCCG 65 20 1.9e-007 5.2e-003 # CGGCCA TGGCCG 43 12 1.0e-005 2.9e-001 # CGGCTA TAGCCG 23 9 9.1e-003 2.5e+002 letter-probability matrix: alength= 4 w= 6 nsites= 66 E= 5.2e-003 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 0.000000 0.651515 0.000000 0.348485 1.000000 0.000000 0.000000 0.000000 MOTIF GAGCGYC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GAGCGYC GRCGCTC 20 0 8.0e-007 2.2e-002 # GAGCGCC GGCGCTC 12 0 2.3e-004 6.3e+000 # GAGCGTC GACGCTC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 20 E= 2.2e-002 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 1.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 MOTIF AKATATG DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AKATATG CATATMT 34 5 8.2e-007 2.3e-002 # AGATATG CATATCT 14 1 4.5e-004 1.3e+001 # ATATATG CATATAT 20 4 6.9e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 2.3e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.411765 0.588235 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 47.84 seconds