# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-shuffled # positives: 814 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-centered (Sat Jan 18 05:28:09 PST 2020) # negatives: 814 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--SFL1/seqs-shuffled (Sat Jan 18 05:28:09 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 05:44:47 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 0.311 C 0.192 G 0.191 T 0.306 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 88 10 6.9e-018 2.4e-013 # GGTTCGA TCGAACC 71 5 6.6e-017 2.3e-012 # GGATCGA TCGATCC 21 5 1.2e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 88 E= 2.4e-013 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.215909 0.000000 0.000000 0.784091 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 AARAAAAW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAAAW WTTTTYTT 196 80 7.2e-015 2.5e-010 # AAAAAAAT ATTTTTTT 97 37 3.3e-008 1.1e-003 # AAGAAAAA TTTTTCTT 59 16 1.7e-007 5.9e-003 # AAAAAAAA TTTTTTTT 85 39 1.1e-005 3.8e-001 # AAGAAAAT ATTTTCTT 28 10 2.3e-003 8.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 226 E= 2.5e-010 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.632743 0.000000 0.367257 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 0.544248 0.000000 0.000000 0.455752 MOTIF TACCACYA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TACCACYA TRGTGGTA 31 0 3.5e-010 1.2e-005 # TACCACTA TAGTGGTA 20 0 8.5e-007 2.9e-002 # TACCACCA TGGTGGTA 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.2e-005 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.354839 0.000000 0.645161 1.000000 0.000000 0.000000 0.000000 MOTIF GCCTTAMC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 30 0 7.1e-010 2.5e-005 # GCCTTAAC GTTAAGGC 20 0 8.5e-007 2.9e-002 # GCCTTACC GGTAAGGC 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.5e-005 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 0.666667 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 33 1 1.5e-009 5.2e-005 # CTCGGCCA TGGCCGAG 13 0 1.2e-004 4.0e+000 # CTTGGCCA TGGCCAAG 12 1 1.7e-003 5.7e+001 # CTGGGCCA TGGCCCAG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 5.2e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.393939 0.242424 0.363636 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 1.000000 0.000000 0.000000 0.000000 MOTIF RGAAGA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST RGAAGA TCTTCY 161 78 3.5e-009 1.2e-004 # GGAAGA TCTTCC 74 29 2.8e-006 9.5e-002 # AGAAGA TCTTCT 94 54 3.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 6 nsites= 178 E= 1.2e-004 0.567416 0.000000 0.432584 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GMTACCGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GMTACCGA TCGGTAKC 22 0 2.1e-007 7.1e-003 # GCTACCGA TCGGTAGC 14 0 5.8e-005 2.0e+000 # GATACCGA TCGGTATC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.1e-003 0.000000 0.000000 1.000000 0.000000 0.363636 0.636364 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGATCGKG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGATCGKG CMCGATCT 20 0 8.5e-007 2.9e-002 # AGATCGGG CCCGATCT 13 0 1.2e-004 4.0e+000 # AGATCGTG CACGATCT 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.9e-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 1.000000 0.000000 0.000000 0.000000 0.650000 0.350000 0.000000 0.000000 1.000000 0.000000 MOTIF CTGGGGW DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTGGGGW WCCCCAG 29 3 1.0e-006 3.6e-002 # CTGGGGT ACCCCAG 18 2 1.9e-004 6.4e+000 # CTGGGGA TCCCCAG 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 3.6e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.379310 0.000000 0.000000 0.620690 # Stopping reason: E-value threshold exceeded # Running time: 51.56 seconds