# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-shuffled # positives: 751 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-centered (Fri Jan 17 23:00:39 PST 2020) # negatives: 751 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--SWI1/seqs-shuffled (Fri Jan 17 23:00:39 PST 2020) # host: kali.stanford.edu # when: Fri Jan 17 23:16:58 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 0.301 C 0.205 G 0.198 T 0.296 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 108 8 2.3e-025 8.0e-021 # GGTTCGA TCGAACC 91 6 5.2e-022 1.8e-017 # GGATCGA TCGATCC 27 2 6.6e-007 2.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 108 E= 8.0e-021 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.203704 0.000000 0.000000 0.796296 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 GCCWTAAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 39 0 1.1e-012 3.8e-008 # GCCTTAAC GTTAAGGC 29 0 1.4e-009 4.9e-005 # GCCATAAC GTTATGGC 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 3.8e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.256410 0.000000 0.000000 0.743590 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ARAAAAR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAR YTTTTYT 274 160 5.2e-011 1.8e-006 # AAAAAAA TTTTTTT 169 96 4.8e-007 1.7e-002 # AAAAAAG CTTTTTT 112 56 2.8e-006 9.8e-002 # AGAAAAA TTTTTCT 96 49 2.6e-005 8.9e-001 # AGAAAAG CTTTTCT 41 21 6.6e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 366 E= 1.8e-006 1.000000 0.000000 0.000000 0.000000 0.672131 0.000000 0.327869 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 0.677596 0.000000 0.322404 0.000000 MOTIF TAGTGGTW DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 38 2 4.8e-010 1.7e-005 # TAGTGGTA TACCACTA 26 2 1.3e-006 4.3e-002 # TAGTGGTT AACCACTA 12 0 2.3e-004 8.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.7e-005 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 0.684211 0.000000 0.000000 0.315789 MOTIF ACTYGGCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACTYGGCC GGCCRAGT 30 0 6.9e-010 2.4e-005 # ACTTGGCC GGCCAAGT 20 0 8.4e-007 2.9e-002 # ACTCGGCC GGCCGAGT 18 0 3.4e-006 1.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.4e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 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 MOTIF GAMTTGAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GAMTTGAA TTCAAKTC 27 1 8.7e-008 3.0e-003 # GAATTGAA TTCAATTC 20 1 9.3e-006 3.2e-001 # GACTTGAA TTCAAGTC 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.0e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.740741 0.259259 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 GCGCYAC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCGCYAC GTRGCGC 32 3 1.6e-007 5.4e-003 # GCGCTAC GTAGCGC 21 2 2.9e-005 1.0e+000 # GCGCCAC GTGGCGC 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 5.4e-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 0.343750 0.000000 0.656250 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 97 40 1.8e-007 6.3e-003 # CGCCCA TGGGCG 44 15 7.6e-005 2.6e+000 # CACCCA TGGGTG 55 25 3.8e-004 1.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 125 E= 6.3e-003 0.000000 1.000000 0.000000 0.000000 0.640000 0.000000 0.360000 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 CTCTMCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTCTMCCA TGGKAGAG 21 0 4.1e-007 1.4e-002 # CTCTCCCA TGGGAGAG 14 0 5.7e-005 1.9e+000 # CTCTACCA TGGTAGAG 7 0 7.7e-003 2.6e+002 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.333333 0.666667 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 # Stopping reason: E-value threshold exceeded # Running time: 47.81 seconds