# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SOK2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SOK2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SOK2/seqs-shuffled # positives: 771 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SOK2/seqs-centered (Sat Jan 18 23:15:07 PST 2020) # negatives: 771 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SOK2/seqs-shuffled (Sat Jan 18 23:15:07 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 23:31:25 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 0.294 C 0.211 G 0.208 T 0.287 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 140 14 4.3e-030 1.5e-025 # GGTTCGA TCGAACC 112 8 1.6e-026 5.4e-022 # GGATCGA TCGATCC 38 6 3.4e-007 1.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 140 E= 1.5e-025 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.242857 0.000000 0.000000 0.757143 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 AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 81 14 1.3e-013 4.6e-009 # AGTGGTT AACCACT 53 7 1.9e-010 6.6e-006 # AGTGGTA TACCACT 39 7 6.5e-007 2.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 95 E= 4.6e-009 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 0.421053 0.000000 0.000000 0.578947 MOTIF ARAAAAA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAA TTTTTYT 228 113 9.1e-013 3.1e-008 # AAAAAAA TTTTTTT 173 81 1.4e-010 5.0e-006 # AGAAAAA TTTTTCT 101 49 4.9e-006 1.7e-001 letter-probability matrix: alength= 4 w= 7 nsites= 271 E= 3.1e-008 1.000000 0.000000 0.000000 0.000000 0.667897 0.000000 0.332103 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 1.000000 0.000000 0.000000 0.000000 MOTIF ASACCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ASACCA TGGTST 102 36 1.8e-009 6.2e-005 # AGACCA TGGTCT 58 14 4.3e-008 1.5e-003 # ACACCA TGGTGT 46 23 3.2e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 114 E= 6.2e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.456140 0.543860 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 CGGGGAD DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGGGGAD HTCCCCG 50 8 4.4e-009 1.5e-004 # CGGGGAA TTCCCCG 23 3 3.9e-005 1.3e+000 # CGGGGAG CTCCCCG 14 2 2.0e-003 6.8e+001 # CGGGGAT ATCCCCG 14 3 6.1e-003 2.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 1.5e-004 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.450980 0.000000 0.274510 0.274510 MOTIF ACCRACT DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCRACT AGTYGGT 62 14 5.3e-009 1.8e-004 # ACCAACT AGTTGGT 46 11 1.1e-006 3.7e-002 # ACCGACT AGTCGGT 16 3 2.1e-003 7.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 1.8e-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 0.741935 0.000000 0.258065 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 CCTRCAG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCTRCAG CTGYAGG 35 3 2.4e-008 8.1e-004 # CCTGCAG CTGCAGG 18 1 3.5e-005 1.2e+000 # CCTACAG CTGTAGG 17 2 3.4e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 8.1e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.485714 0.000000 0.514286 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 ATAGTKTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 29 2 1.8e-007 6.2e-003 # ATAGTTTA TAAACTAT 16 1 1.3e-004 4.3e+000 # ATAGTGTA TACACTAT 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.2e-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 0.448276 0.551724 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCCATRGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GCCATRGA TCYATGGC 22 0 2.0e-007 6.9e-003 # GCCATGGA TCCATGGC 15 0 2.8e-005 9.6e-001 # GCCATAGA TCTATGGC 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.9e-003 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 0.000000 0.000000 1.000000 0.318182 0.000000 0.681818 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACGRTG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGRTG CAYCGTG 36 5 2.9e-007 9.7e-003 # CACGGTG CACCGTG 24 3 2.1e-005 7.2e-001 # CACGATG CATCGTG 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 9.7e-003 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 0.351351 0.000000 0.648649 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTCTCMCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CTCTCMCA TGKGAGAG 25 1 3.4e-007 1.1e-002 # CTCTCCCA TGGGAGAG 18 1 3.5e-005 1.2e+000 # CTCTCACA TGTGAGAG 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.280000 0.720000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGCAGATK DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGCAGATK MATCTGCT 21 0 4.2e-007 1.4e-002 # AGCAGATG CATCTGCT 14 0 5.8e-005 1.9e+000 # AGCAGATT AATCTGCT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-002 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 MOTIF CGCCASAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGCCASAC GTSTGGCG 21 0 4.2e-007 1.4e-002 # CGCCACAC GTGTGGCG 12 0 2.3e-004 7.9e+000 # CGCCAGAC GTCTGGCG 9 0 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCCGKAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATCCGKAC GTMCGGAT 20 0 8.4e-007 2.8e-002 # ATCCGTAC GTACGGAT 12 0 2.3e-004 7.9e+000 # ATCCGGAC GTCCGGAT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 2.8e-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 1.000000 0.000000 0.000000 0.000000 0.380952 0.619048 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGSCCA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGSCCA TGGSCG 90 38 9.4e-007 3.2e-002 # CGGCCA TGGCCG 44 15 7.7e-005 2.6e+000 # CGCCCA TGGGCG 47 24 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 91 E= 3.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.516484 0.483516 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 # Stopping reason: E-value threshold exceeded # Running time: 77.99 seconds