# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--RIM101/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--RIM101/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--RIM101/seqs-shuffled # positives: 453 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--RIM101/seqs-centered (Sat Jan 18 03:13:11 PST 2020) # negatives: 453 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--RIM101/seqs-shuffled (Sat Jan 18 03:13:11 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:22:13 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 0.301 C 0.196 G 0.200 T 0.303 MOTIF GGHTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 72 7 4.2e-016 1.2e-011 # GGTTCGA TCGAACC 56 4 9.4e-014 2.7e-009 # GGATCGA TCGATCC 20 3 2.1e-004 6.0e+000 # GGCTCGA TCGAGCC 12 0 2.3e-004 6.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 1.2e-011 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.243243 0.094595 0.000000 0.662162 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 AARAAAWA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 86 22 1.6e-011 4.4e-007 # AAAAAATA TATTTTTT 33 7 1.4e-005 4.1e-001 # AAAAAAAA TTTTTTTT 35 9 3.6e-005 1.0e+000 # AAGAAAAA TTTTTCTT 24 4 7.2e-005 2.0e+000 # AAGAAATA TATTTCTT 14 3 6.0e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 98 E= 4.4e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.622449 0.000000 0.377551 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 0.571429 0.000000 0.000000 0.428571 1.000000 0.000000 0.000000 0.000000 MOTIF GCCWTAAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 25 0 2.1e-008 6.0e-004 # GCCTTAAC GTTAAGGC 18 0 3.2e-006 9.0e-002 # GCCATAAC GTTATGGC 7 0 7.6e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 6.0e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.280000 0.000000 0.000000 0.720000 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 TGGCCSA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TGGCCSA TSGGCCA 30 3 4.7e-007 1.3e-002 # TGGCCGA TCGGCCA 19 2 9.5e-005 2.7e+000 # TGGCCCA TGGGCCA 11 1 3.0e-003 8.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.3e-002 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 1.000000 0.000000 0.000000 0.000000 0.366667 0.633333 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CCRTACA TGTAYGG 31 4 1.2e-006 3.2e-002 # CCATACA TGTATGG 19 2 9.5e-005 2.7e+000 # CCGTACA TGTACGG 13 2 3.5e-003 9.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 3.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.611111 0.000000 0.388889 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 1.000000 0.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 19 0 1.6e-006 4.4e-002 # GTGATAGT ACTATCAC 10 0 9.3e-004 2.6e+001 # GTGATAGC GCTATCAC 9 0 1.9e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.4e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 0.473684 0.000000 0.526316 # Stopping reason: E-value threshold exceeded # Running time: 21.30 seconds