# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MIG2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MIG2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MIG2/seqs-shuffled # positives: 875 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MIG2/seqs-centered (Sat Jan 18 08:27:06 PST 2020) # negatives: 875 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MIG2/seqs-shuffled (Sat Jan 18 08:27:06 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 08:43:32 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 0.208 G 0.203 T 0.294 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 119 14 1.1e-023 3.9e-019 # GGTTCGA TCGAACC 95 10 9.0e-020 3.3e-015 # GGATCGA TCGATCC 30 4 2.5e-006 9.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 119 E= 3.9e-019 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.235294 0.000000 0.000000 0.764706 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 ACCRACT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 66 9 1.5e-012 5.3e-008 # ACCAACT AGTTGGT 48 8 1.5e-008 5.3e-004 # ACCGACT AGTCGGT 18 1 3.5e-005 1.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 5.3e-008 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.727273 0.000000 0.272727 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 ARAAADA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAADA THTTTYT 359 227 1.4e-011 5.1e-007 # AAAAAAA TTTTTTT 158 89 1.3e-006 4.8e-002 # AGAAATA TATTTCT 47 14 9.9e-006 3.6e-001 # AGAAAAA TTTTTCT 103 59 1.8e-004 6.6e+000 # AAAAATA TATTTTT 117 71 2.4e-004 8.8e+000 # AAAAAGA TCTTTTT 87 54 2.4e-003 8.7e+001 # AGAAAGA TCTTTCT 36 16 3.5e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 485 E= 5.1e-007 1.000000 0.000000 0.000000 0.000000 0.655670 0.000000 0.344330 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 0.465979 0.000000 0.214433 0.319588 1.000000 0.000000 0.000000 0.000000 MOTIF TAGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 43 3 1.5e-010 5.2e-006 # TAGTGGTA TACCACTA 26 1 1.8e-007 6.3e-003 # TAGTGGTT AACCACTA 17 2 3.4e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 5.2e-006 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.604651 0.000000 0.000000 0.395349 MOTIF CGCSTTA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 57 10 1.1e-009 3.8e-005 # CGCCTTA TAAGGCG 41 6 6.2e-008 2.2e-003 # CGCGTTA TAACGCG 16 4 5.7e-003 2.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 3.8e-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 0.719298 0.280702 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 AASAAGG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AASAAGG CCTTSTT 54 11 1.8e-008 6.3e-004 # AAGAAGG CCTTCTT 31 5 5.3e-006 1.9e-001 # AACAAGG CCTTGTT 23 6 1.1e-003 3.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 6.3e-004 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.403509 0.596491 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 0.000000 1.000000 0.000000 MOTIF ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 29 1 2.3e-008 8.2e-004 # ATGGCATC GATGCCAT 13 0 1.2e-004 4.2e+000 # ATGGCAAC GTTGCCAT 16 1 1.3e-004 4.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 8.2e-004 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 0.551724 0.000000 0.000000 0.448276 0.000000 1.000000 0.000000 0.000000 MOTIF CTCGKCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTCGKCCA TGGMCGAG 27 1 8.9e-008 3.2e-003 # CTCGGCCA TGGCCGAG 20 1 9.5e-006 3.4e-001 # CTCGTCCA TGGACGAG 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.2e-003 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 0.740741 0.259259 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 AGTCAKAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 22 0 2.1e-007 7.4e-003 # AGTCATAC GTATGACT 14 0 5.8e-005 2.1e+000 # AGTCAGAC GTCTGACT 8 0 3.8e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.4e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.636364 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGATCKG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGATCKG CMGATCT 37 6 6.2e-007 2.2e-002 # AGATCGG CCGATCT 21 3 1.3e-004 4.5e+000 # AGATCTG CAGATCT 16 3 2.1e-003 7.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 2.2e-002 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.567568 0.432432 0.000000 0.000000 1.000000 0.000000 MOTIF CCRTGGAG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGAG CTCCAYGG 24 1 6.7e-007 2.4e-002 # CCATGGAG CTCCATGG 11 0 4.7e-004 1.7e+001 # CCGTGGAG CTCCACGG 13 1 8.8e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.4e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.458333 0.000000 0.541667 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 0.000000 0.000000 1.000000 0.000000 MOTIF ASACCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ASACCA TGGTST 107 50 1.1e-006 4.0e-002 # AGACCA TGGTCT 63 24 1.1e-005 3.9e-001 # ACACCA TGGTGT 48 27 8.9e-003 3.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 122 E= 4.0e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.467213 0.532787 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 MOTIF CGCCASAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGCCASAC GTSTGGCG 22 0 2.1e-007 7.3e-003 # CGCCACAC GTGTGGCG 12 0 2.4e-004 8.3e+000 # CGCCAGAC GTCTGGCG 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.3e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.545455 0.454545 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 73.23 seconds