# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/seqs-shuffled # positives: 851 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/seqs-centered (Sat Jan 18 01:01:07 PST 2020) # negatives: 851 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/seqs-shuffled (Sat Jan 18 01:01:07 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 01:16:43 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 0.202 G 0.204 T 0.293 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 121 16 5.9e-023 2.1e-018 # GGTTCGA TCGAACC 91 6 7.2e-022 2.5e-017 # GGTTCAA TTGAACC 31 11 1.3e-003 4.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 122 E= 2.1e-018 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.254098 0.000000 0.745902 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AYCCRTAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 78 2 4.6e-022 1.6e-017 # ACCCATAC GTATGGGT 37 1 9.7e-011 3.4e-006 # ATCCGTAC GTACGGAT 28 1 4.5e-008 1.6e-003 # ACCCGTAC GTACGGGT 11 0 4.7e-004 1.7e+001 # ATCCATAC GTATGGAT 11 0 4.7e-004 1.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 1.6e-017 1.000000 0.000000 0.000000 0.000000 0.000000 0.544444 0.000000 0.455556 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.544444 0.000000 0.455556 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 MOTIF AARAAAW DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AARAAAW WTTTYTT 357 208 1.0e-014 3.5e-010 # AAAAAAA TTTTTTT 198 110 1.8e-008 6.3e-004 # AAGAAAA TTTTCTT 119 57 4.8e-007 1.7e-002 # AAGAAAT ATTTCTT 61 32 1.3e-003 4.6e+001 # AAAAAAT ATTTTTT 145 104 3.0e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 471 E= 3.5e-010 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.615711 0.000000 0.384289 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 0.641189 0.000000 0.000000 0.358811 MOTIF CCRTGSA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCRTGSA TSCAYGG 89 16 1.8e-014 6.2e-010 # CCATGCA TGCATGG 27 3 3.6e-006 1.2e-001 # CCGTGGA TCCACGG 35 8 1.7e-005 5.8e-001 # CCATGGA TCCATGG 14 2 2.0e-003 6.9e+001 # CCGTGCA TGCACGG 15 4 9.3e-003 3.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 91 E= 6.2e-010 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.461538 0.000000 0.538462 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.461538 0.538462 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CAAMTTGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CAAMTTGG CCAAKTTG 37 0 4.9e-012 1.7e-007 # CAACTTGG CCAAGTTG 29 0 1.5e-009 5.0e-005 # CAAATTGG CCAATTTG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.7e-007 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.216216 0.783784 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 0.000000 0.000000 1.000000 0.000000 MOTIF TAAGGCR DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 71 13 1.4e-011 4.8e-007 # TAAGGCG CGCCTTA 47 8 2.6e-008 8.8e-004 # TAAGGCA TGCCTTA 25 6 4.0e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 72 E= 4.8e-007 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.347222 0.000000 0.652778 0.000000 MOTIF CRCCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 115 41 2.2e-010 7.5e-006 # CACCCA TGGGTG 64 24 7.2e-006 2.5e-001 # CGCCCA TGGGCG 53 19 2.7e-005 9.1e-001 letter-probability matrix: alength= 4 w= 6 nsites= 129 E= 7.5e-006 0.000000 1.000000 0.000000 0.000000 0.573643 0.000000 0.426357 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 GCKCTACC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 42 3 2.8e-010 9.4e-006 # GCGCTACC GGTAGCGC 26 1 1.7e-007 5.9e-003 # GCTCTACC GGTAGAGC 16 2 6.2e-004 2.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 9.4e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.619048 0.380952 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 MOTIF GTGATAGY DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 31 1 5.9e-009 2.0e-004 # GTGATAGC GCTATCAC 17 0 7.0e-006 2.4e-001 # GTGATAGT ACTATCAC 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.0e-004 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 0.548387 0.000000 0.451613 MOTIF TACCACYA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TACCACYA TRGTGGTA 27 0 6.0e-009 2.0e-004 # TACCACTA TAGTGGTA 20 0 8.5e-007 2.9e-002 # TACCACCA TGGTGGTA 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.0e-004 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 0.259259 0.000000 0.740741 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 30 1 1.2e-008 3.9e-004 # ATCGTGAG CTCACGAT 20 0 8.5e-007 2.9e-002 # ATCTTGAG CTCAAGAT 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.9e-004 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 0.666667 0.333333 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 1.000000 0.000000 MOTIF AKATGTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AKATGTA TACATMT 54 12 5.0e-008 1.7e-003 # AGATGTA TACATCT 29 5 1.6e-005 5.5e-001 # ATATGTA TACATAT 25 7 9.6e-004 3.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 56 E= 1.7e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.517857 0.482143 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTSGGCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTSGGCCA TGGCCSAG 31 2 5.1e-008 1.7e-003 # CTCGGCCA TGGCCGAG 20 1 9.5e-006 3.2e-001 # CTGGGCCA TGGCCCAG 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.7e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.645161 0.354839 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AWCACGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AWCACGC GCGTGWT 36 4 6.9e-008 2.3e-003 # AACACGC GCGTGTT 19 2 1.0e-004 3.4e+000 # ATCACGC GCGTGAT 17 2 3.4e-004 1.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 2.3e-003 1.000000 0.000000 0.000000 0.000000 0.527778 0.000000 0.000000 0.472222 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 0.000000 1.000000 0.000000 0.000000 MOTIF GCARATGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GCARATGC GCATYTGC 21 0 4.2e-007 1.4e-002 # GCAGATGC GCATCTGC 13 0 1.2e-004 3.9e+000 # GCAAATGC GCATTTGC 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.619048 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 1.000000 0.000000 0.000000 MOTIF GGATCRAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GGATCRAA TTYGATCC 30 3 5.7e-007 1.9e-002 # GGATCGAA TTCGATCC 21 3 1.3e-004 4.2e+000 # GGATCAAA TTTGATCC 9 0 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.9e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.300000 0.000000 0.700000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATAGTGTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATAGTGTA TACACTAT 27 2 6.8e-007 2.3e-002 # ATAGTGTA TACACTAT 27 2 6.8e-007 2.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.3e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGAAGAR DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GGAAGAR YTCTTCC 41 8 7.1e-007 2.4e-002 # GGAAGAA TTCTTCC 19 3 4.0e-004 1.3e+001 # GGAAGAG CTCTTCC 23 5 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 2.4e-002 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.452381 0.000000 0.547619 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 95.91 seconds