# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-shuffled # positives: 637 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-centered (Sat Jan 18 21:57:57 PST 2020) # negatives: 637 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--MSS11/seqs-shuffled (Sat Jan 18 21:57:57 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 22:13:51 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 0.295 C 0.209 G 0.207 T 0.290 MOTIF GRNTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRNTCGAA TTCGANYC 136 12 5.0e-031 1.6e-026 # GGATCGAA TTCGATCC 29 2 1.7e-007 5.6e-003 # GAATCGAA TTCGATTC 27 2 6.4e-007 2.1e-002 # GACTCGAA TTCGAGTC 13 0 1.1e-004 3.7e+000 # GAGTCGAA TTCGACTC 15 1 2.4e-004 7.8e+000 # GATTCGAA TTCGAATC 17 2 3.3e-004 1.1e+001 # GGCTCGAA TTCGAGCC 17 2 3.3e-004 1.1e+001 # GGGTCGAA TTCGACCC 10 0 9.4e-004 3.0e+001 # GGTTCGAA TTCGAACC 17 3 1.2e-003 3.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 136 E= 1.6e-026 0.000000 0.000000 1.000000 0.000000 0.492647 0.000000 0.507353 0.000000 0.411765 0.220588 0.183824 0.183824 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 1.000000 0.000000 0.000000 0.000000 MOTIF ACCAYT DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCAYT ARTGGT 158 48 1.2e-017 3.8e-013 # ACCACT AGTGGT 106 20 5.0e-017 1.6e-012 # ACCATT AATGGT 55 29 2.3e-003 7.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 178 E= 3.8e-013 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 0.000000 0.679775 0.000000 0.320225 0.000000 0.000000 0.000000 1.000000 MOTIF DCGCCTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST DCGCCTTA TAAGGCGH 52 0 7.5e-017 2.4e-012 # GCGCCTTA TAAGGCGC 23 0 9.7e-008 3.1e-003 # TCGCCTTA TAAGGCGA 18 0 3.4e-006 1.1e-001 # ACGCCTTA TAAGGCGT 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 2.4e-012 0.211538 0.000000 0.442308 0.346154 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAWAT DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AAAAWAT ATWTTTT 163 71 1.4e-011 4.5e-007 # AAAATAT ATATTTT 59 16 1.4e-007 4.5e-003 # AAAAAAT ATTTTTT 125 63 6.0e-007 1.9e-002 letter-probability matrix: alength= 4 w= 7 nsites= 181 E= 4.5e-007 1.000000 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 0.000000 0.679558 0.000000 0.000000 0.320442 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF ACCRACT DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 61 9 2.1e-011 6.7e-007 # ACCAACT AGTTGGT 42 7 1.1e-007 3.5e-003 # ACCGACT AGTCGGT 19 2 9.9e-005 3.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 6.7e-007 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.688525 0.000000 0.311475 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 CRCCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 108 40 1.3e-009 4.2e-005 # CGCCCA TGGGCG 51 16 6.6e-006 2.1e-001 # CACCCA TGGGTG 60 25 5.6e-005 1.8e+000 letter-probability matrix: alength= 4 w= 6 nsites= 129 E= 4.2e-005 0.000000 1.000000 0.000000 0.000000 0.573643 0.000000 0.426357 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 MOTIF GAMTTGAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GAMTTGAA TTCAAKTC 36 2 1.7e-009 5.3e-005 # GAATTGAA TTCAATTC 28 2 3.3e-007 1.0e-002 # GACTTGAA TTCAAGTC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 5.3e-005 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.222222 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTCTGRC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTCTGRC GYCAGAC 31 1 5.4e-009 1.7e-004 # GTCTGGC GCCAGAC 18 0 3.4e-006 1.0e-001 # GTCTGAC GTCAGAC 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 1.7e-004 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 0.000000 0.000000 1.000000 0.000000 0.419355 0.000000 0.580645 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF MAAAAGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST MAAAAGA TCTTTTK 106 42 1.2e-008 3.6e-004 # AAAAAGA TCTTTTT 79 28 1.4e-007 4.3e-003 # CAAAAGA TCTTTTG 32 14 5.0e-003 1.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 116 E= 3.6e-004 0.724138 0.275862 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 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 DATGGCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST DATGGCA TGCCATH 65 17 1.7e-008 5.3e-004 # GATGGCA TGCCATC 25 5 1.4e-004 4.3e+000 # AATGGCA TGCCATT 21 6 2.7e-003 8.4e+001 # TATGGCA TGCCATA 19 6 6.9e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 5.3e-004 0.314286 0.000000 0.400000 0.285714 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 MOTIF CGCGGGSA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 25 0 2.3e-008 7.2e-004 # CGCGGGGA TCCCCGCG 13 0 1.1e-004 3.5e+000 # CGCGGGCA TGCCCGCG 12 0 2.3e-004 7.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.2e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.480000 0.520000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCWACAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCWACAG CTGTWGG 33 3 8.0e-008 2.4e-003 # CCAACAG CTGTTGG 18 2 1.8e-004 5.6e+000 # CCTACAG CTGTAGG 15 1 2.4e-004 7.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 2.4e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.000000 0.454545 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 0.000000 1.000000 0.000000 MOTIF AGARTCAT DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGARTCAT ATGAYTCT 26 1 1.6e-007 5.0e-003 # AGAGTCAT ATGACTCT 15 0 2.8e-005 8.6e-001 # AGAATCAT ATGATTCT 11 1 3.1e-003 9.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.0e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.423077 0.000000 0.576923 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 0.000000 1.000000 MOTIF CGCGCTMC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CGCGCTMC GKAGCGCG 20 0 8.2e-007 2.5e-002 # CGCGCTAC GTAGCGCG 14 0 5.7e-005 1.7e+000 # CGCGCTCC GGAGCGCG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.5e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.650000 0.350000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 60.18 seconds