# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RPD3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RPD3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RPD3/seqs-shuffled # positives: 944 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RPD3/seqs-centered (Sat Jan 18 07:20:42 PST 2020) # negatives: 944 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--RPD3/seqs-shuffled (Sat Jan 18 07:20:42 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 07:37:13 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 0.298 C 0.201 G 0.200 T 0.301 MOTIF GRVTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRVTCGAA TTCGABYC 105 11 8.9e-022 3.3e-017 # GGATCGAA TTCGATCC 24 1 6.8e-007 2.5e-002 # GAATCGAA TTCGATTC 31 6 1.7e-005 6.5e-001 # GAGTCGAA TTCGACTC 11 0 4.7e-004 1.8e+001 # GGCTCGAA TTCGAGCC 16 2 6.2e-004 2.3e+001 # GGGTCGAA TTCGACCC 10 0 9.5e-004 3.5e+001 # GACTCGAA TTCGAGTC 13 2 3.6e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 105 E= 3.3e-017 0.000000 0.000000 1.000000 0.000000 0.523810 0.000000 0.476190 0.000000 0.523810 0.276190 0.200000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF KCTACCR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST KCTACCR YGGTAGM 74 10 5.3e-014 2.0e-009 # TCTACCA TGGTAGA 28 4 8.3e-006 3.0e-001 # GCTACCG CGGTAGC 20 1 9.6e-006 3.5e-001 # GCTACCA TGGTAGC 15 3 3.6e-003 1.3e+002 # TCTACCG CGGTAGA 12 2 6.3e-003 2.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 2.0e-009 0.000000 0.000000 0.466667 0.533333 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 0.573333 0.000000 0.426667 0.000000 MOTIF AAAAAWR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AAAAAWR YWTTTTT 355 219 6.1e-012 2.2e-007 # AAAAATA TATTTTT 143 70 6.4e-008 2.3e-003 # AAAAAAA TTTTTTT 189 119 8.1e-006 3.0e-001 # AAAAATG CATTTTT 69 39 1.9e-003 7.1e+001 # AAAAAAG CTTTTTT 116 81 5.2e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 443 E= 2.2e-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 1.000000 0.000000 0.000000 0.000000 0.534989 0.000000 0.000000 0.465011 0.641084 0.000000 0.358916 0.000000 MOTIF ACCACTM DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 59 9 9.9e-011 3.6e-006 # ACCACTA TAGTGGT 36 5 3.0e-007 1.1e-002 # ACCACTC GAGTGGT 23 4 1.4e-004 5.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 3.6e-006 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.610169 0.389831 0.000000 0.000000 MOTIF TGCCAKA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TGCCAKA TMTGGCA 47 9 8.7e-008 3.2e-003 # TGCCAGA TCTGGCA 24 3 2.2e-005 8.0e-001 # TGCCATA TATGGCA 24 6 6.6e-004 2.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 3.2e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.489796 0.510204 1.000000 0.000000 0.000000 0.000000 MOTIF GCCAAGW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCCAAGW WCTTGGC 58 15 1.2e-007 4.5e-003 # GCCAAGT ACTTGGC 26 5 8.6e-005 3.1e+000 # GCCAAGA TCTTGGC 34 10 1.7e-004 6.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 4.5e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.566667 0.000000 0.000000 0.433333 MOTIF CGYCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGYCCA TGGRCG 77 27 2.4e-007 8.7e-003 # CGCCCA TGGGCG 46 12 3.0e-006 1.1e-001 # CGTCCA TGGACG 33 15 6.1e-003 2.2e+002 letter-probability matrix: alength= 4 w= 6 nsites= 80 E= 8.7e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.575000 0.000000 0.425000 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 AGCATGSG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGCATGSG CSCATGCT 20 0 8.6e-007 3.1e-002 # AGCATGCG CGCATGCT 11 0 4.7e-004 1.7e+001 # AGCATGGG CCCATGCT 9 0 1.9e-003 6.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 3.1e-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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.550000 0.450000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TATATANA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST TATATANA TNTATATA 48 12 1.1e-006 4.0e-002 # TATATATA TATATATA 19 3 4.0e-004 1.4e+001 # TATATAGA TCTATATA 12 1 1.7e-003 6.0e+001 # TATATACA TGTATATA 16 4 5.7e-003 2.0e+002 # TATATAAA TTTATATA 15 4 9.3e-003 3.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 4.0e-002 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.245283 0.245283 0.132075 0.377358 1.000000 0.000000 0.000000 0.000000 MOTIF GGGAATTK DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GGGAATTK MAATTCCC 23 1 1.3e-006 4.7e-002 # GGGAATTG CAATTCCC 15 1 2.5e-004 8.9e+000 # GGGAATTT AAATTCCC 8 0 3.8e-003 1.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.7e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.652174 0.347826 # Stopping reason: E-value threshold exceeded # Running time: 63.57 seconds