# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAD1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAD1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAD1/seqs-shuffled # positives: 537 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAD1/seqs-centered (Sat Jan 18 05:14:27 PST 2020) # negatives: 537 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--CAD1/seqs-shuffled (Sat Jan 18 05:14:27 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:27:05 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 0.204 T 0.294 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 132 9 5.6e-033 1.6e-028 # GGTTCGA TCGAACC 97 3 1.5e-027 4.3e-023 # GGTTCAA TTGAACC 37 6 5.2e-007 1.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 134 E= 1.6e-028 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 0.276119 0.000000 0.723881 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 84 10 3.2e-017 9.4e-013 # AGTGGTT AACCACT 59 4 1.6e-014 4.6e-010 # AGTGGTA TACCACT 37 6 5.2e-007 1.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 9.4e-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 0.383838 0.000000 0.000000 0.616162 MOTIF CCCATDC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 67 7 1.8e-014 5.2e-010 # CCCATAC GTATGGG 25 1 3.1e-007 8.9e-003 # CCCATGC GCATGGG 23 1 1.2e-006 3.4e-002 # CCCATTC GAATGGG 21 5 1.1e-003 3.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 5.2e-010 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 0.000000 0.000000 0.000000 1.000000 0.371429 0.000000 0.328571 0.300000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTYGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 62 4 2.0e-015 5.8e-011 # AGTTGGTT AACCAACT 26 2 1.2e-006 3.3e-002 # AGTTGGTA TACCAACT 13 0 1.1e-004 3.2e+000 # AGTCGGTA TACCGACT 10 0 9.4e-004 2.7e+001 # AGTCGGTT AACCGACT 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 5.8e-011 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 0.370968 0.000000 0.629032 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.370968 0.000000 0.000000 0.629032 MOTIF CABACGC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CABACGC GCGTVTG 51 7 4.7e-010 1.3e-005 # CATACGC GCGTATG 18 2 1.8e-004 5.1e+000 # CACACGC GCGTGTG 18 3 6.7e-004 1.9e+001 # CAGACGC GCGTCTG 15 2 1.1e-003 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 1.3e-005 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.352941 0.294118 0.352941 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 ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 36 2 1.6e-009 4.4e-005 # ATGGCAAC GTTGCCAT 23 1 1.2e-006 3.4e-002 # ATGGCATC GATGCCAT 13 1 8.6e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 4.4e-005 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 0.638889 0.000000 0.000000 0.361111 0.000000 1.000000 0.000000 0.000000 MOTIF AARAAAR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AARAAAR YTTTYTT 180 99 1.1e-008 3.1e-004 # AAGAAAA TTTTCTT 66 23 1.1e-006 3.2e-002 # AAAAAAA TTTTTTT 103 52 6.1e-006 1.7e-001 # AAGAAAG CTTTCTT 24 6 6.2e-004 1.7e+001 # AAAAAAG CTTTTTT 70 40 1.7e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 224 E= 3.1e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.642857 0.000000 0.357143 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 0.669643 0.000000 0.330357 0.000000 MOTIF GTGATAGY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 24 0 4.6e-008 1.3e-003 # GTGATAGC GCTATCAC 13 0 1.1e-004 3.2e+000 # GTGATAGT ACTATCAC 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.3e-003 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 0.541667 0.000000 0.458333 MOTIF GGCGAAAK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GGCGAAAK MTTTCGCC 23 0 9.4e-008 2.6e-003 # GGCGAAAT ATTTCGCC 12 0 2.3e-004 6.4e+000 # GGCGAAAG CTTTCGCC 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.6e-003 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 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 0.478261 0.521739 MOTIF GCGCCW DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GCGCCW WGGCGC 62 18 1.5e-007 4.3e-003 # GCGCCA TGGCGC 41 11 1.2e-005 3.3e-001 # GCGCCT AGGCGC 28 8 4.9e-004 1.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 62 E= 4.3e-003 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 1.000000 0.000000 0.000000 0.596774 0.000000 0.000000 0.403226 MOTIF GAGACCR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GAGACCR YGGTCTC 26 1 1.6e-007 4.4e-003 # GAGACCG CGGTCTC 13 0 1.1e-004 3.2e+000 # GAGACCA TGGTCTC 13 1 8.6e-004 2.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 28 E= 4.4e-003 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 0.535714 0.000000 0.464286 0.000000 MOTIF AARGCGTG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AARGCGTG CACGCYTT 22 0 1.9e-007 5.3e-003 # AAAGCGTG CACGCTTT 12 0 2.3e-004 6.4e+000 # AAGGCGTG CACGCCTT 10 0 9.4e-004 2.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.3e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.545455 0.000000 0.454545 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 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CKTTGGGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 22 0 1.9e-007 5.3e-003 # CGTTGGGC GCCCAACG 15 0 2.8e-005 7.7e-001 # CTTTGGGC GCCCAAAG 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.681818 0.318182 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCTACCGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCTACCGA TCGGTAGC 20 0 8.0e-007 2.2e-002 # GCTACCGA TCGGTAGC 20 0 8.0e-007 2.2e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.2e-002 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 ACACTATA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 19 0 1.6e-006 4.5e-002 # ACACTATA TATAGTGT 19 0 1.6e-006 4.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.5e-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 # Stopping reason: E-value threshold exceeded # Running time: 54.12 seconds