# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/seqs-shuffled # positives: 821 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/seqs-centered (Sat Jan 18 13:50:25 PST 2020) # negatives: 821 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/seqs-shuffled (Sat Jan 18 13:50:25 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 14:04:47 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 0.288 C 0.214 G 0.209 T 0.289 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 141 17 4.9e-028 1.7e-023 # GGTTCGA TCGAACC 105 8 2.5e-024 8.5e-020 # GGTTCAA TTGAACC 37 9 1.6e-005 5.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 142 E= 1.7e-023 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 0.260563 0.000000 0.739437 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 76 6 1.7e-017 5.6e-013 # ACCCATAC GTATGGGT 36 3 1.3e-008 4.4e-004 # ATCCGTAC GTACGGAT 29 1 2.3e-008 7.7e-004 # ACCCGTAC GTACGGGT 9 0 1.9e-003 6.4e+001 # ATCCATAC GTATGGAT 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 5.6e-013 1.000000 0.000000 0.000000 0.000000 0.000000 0.511111 0.000000 0.488889 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 CCTTAVC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCTTAVC GBTAAGG 105 20 1.9e-016 6.5e-012 # CCTTAAC GTTAAGG 47 7 7.0e-009 2.3e-004 # CCTTAGC GCTAAGG 30 4 2.5e-006 8.4e-002 # CCTTACC GGTAAGG 28 9 1.1e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 6.5e-012 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 0.447619 0.266667 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 70 7 5.0e-015 1.7e-010 # CTCGGCCA TGGCCGAG 35 3 2.4e-008 8.2e-004 # CTTGGCCA TGGCCAAG 23 4 1.4e-004 4.7e+000 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 7.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 70 E= 1.7e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.171429 0.328571 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 AAGAAAD DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAD HTTTCTT 170 68 3.6e-013 1.2e-008 # AAGAAAA TTTTCTT 105 42 2.8e-008 9.2e-004 # AAGAAAT ATTTCTT 58 20 6.2e-006 2.1e-001 # AAGAAAG CTTTCTT 23 8 5.0e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 196 E= 1.2e-008 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.591837 0.000000 0.112245 0.295918 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 47 2 1.2e-012 3.9e-008 # ATGGCAAC GTTGCCAT 31 1 5.9e-009 1.9e-004 # ATGGCATC GATGCCAT 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 3.9e-008 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.659574 0.000000 0.000000 0.340426 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 47 4 6.8e-011 2.3e-006 # GCGCTACC GGTAGCGC 31 1 5.9e-009 1.9e-004 # GCTCTACC GGTAGAGC 16 3 2.1e-003 7.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 2.3e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.659574 0.340426 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-8 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 29 0 1.4e-009 4.8e-005 # GTGATAGT ACTATCAC 16 0 1.4e-005 4.7e-001 # GTGATAGC GCTATCAC 13 0 1.2e-004 3.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 4.8e-005 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 0.448276 0.000000 0.551724 MOTIF KAATCATA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST KAATCATA TATGATTM 29 0 1.4e-009 4.8e-005 # TAATCATA TATGATTA 17 0 7.0e-006 2.3e-001 # GAATCATA TATGATTC 12 0 2.3e-004 7.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 4.8e-005 0.000000 0.000000 0.413793 0.586207 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 1.000000 0.000000 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 MOTIF ATAYAACA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATAYAACA TGTTRTAT 32 1 3.0e-009 9.8e-005 # ATACAACA TGTTGTAT 25 1 3.4e-007 1.1e-002 # ATATAACA TGTTATAT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 9.8e-005 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 0.757576 0.000000 0.242424 1.000000 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 MOTIF ATCTTYTG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 38 3 3.6e-009 1.2e-004 # ATCTTCTG CAGAAGAT 19 1 1.8e-005 6.0e-001 # ATCTTTTG CAAAAGAT 19 2 1.0e-004 3.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.2e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCGTGSA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 49 8 8.1e-009 2.7e-004 # CCGTGGA TCCACGG 29 4 4.5e-006 1.5e-001 # CCGTGCA TGCACGG 21 4 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 51 E= 2.7e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.431373 0.568627 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTGGTYTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTGGTYTA TARACCAC 36 3 1.3e-008 4.3e-004 # GTGGTCTA TAGACCAC 25 2 2.4e-006 7.9e-002 # GTGGTTTA TAAACCAC 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 4.3e-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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.694444 0.000000 0.305556 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 28 1 4.5e-008 1.5e-003 # AGTCATAC GTATGACT 16 1 1.3e-004 4.2e+000 # AGTCAGAC GTCTGACT 12 0 2.3e-004 7.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.5e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.571429 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TAGTGTAR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TAGTGTAR YTACACTA 28 1 4.5e-008 1.5e-003 # TAGTGTAG CTACACTA 15 0 2.9e-005 9.4e-001 # TAGTGTAA TTACACTA 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.5e-003 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 0.464286 0.000000 0.535714 0.000000 MOTIF CTGAGCTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 22 0 2.1e-007 6.8e-003 # CTGAGCTA TAGCTCAG 22 0 2.1e-007 6.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.8e-003 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF MACACCCA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST MACACCCA TGGGTGTK 43 8 2.4e-007 7.7e-003 # CACACCCA TGGGTGTG 26 5 8.4e-005 2.8e+000 # AACACCCA TGGGTGTT 17 3 1.2e-003 4.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 79 E= 7.7e-003 0.215190 0.784810 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 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 ACTSACG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ACTSACG CGTSAGT 36 5 2.9e-007 9.6e-003 # ACTCACG CGTGAGT 20 2 5.5e-005 1.8e+000 # ACTGACG CGTCAGT 16 3 2.1e-003 6.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 9.6e-003 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 0.555556 0.444444 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 MOTIF CAGWTAAC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CAGWTAAC GTTAWCTG 31 3 3.0e-007 9.9e-003 # CAGTTAAC GTTAACTG 17 1 6.7e-005 2.2e+000 # CAGATAAC GTTATCTG 14 2 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 9.9e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.451613 0.000000 0.000000 0.548387 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 ATGGTCAS DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATGGTCAS STGACCAT 24 1 6.6e-007 2.2e-002 # ATGGTCAG CTGACCAT 16 1 1.3e-004 4.2e+000 # ATGGTCAC GTGACCAT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 MOTIF CCAGWTCG DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CCAGWTCG CGAWCTGG 24 1 6.6e-007 2.2e-002 # CCAGTTCG CGAACTGG 12 0 2.3e-004 7.6e+000 # CCAGATCG CGATCTGG 12 1 1.7e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.2e-002 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 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CCTTARAC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST CCTTARAC GTYTAAGG 29 3 1.0e-006 3.4e-002 # CCTTAGAC GTCTAAGG 14 1 4.7e-004 1.5e+001 # CCTTAAAC GTTTAAGG 15 2 1.1e-003 3.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.4e-002 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 0.517241 0.000000 0.482759 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CKTTGGGC DREME-23 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 26 2 1.3e-006 4.1e-002 # CGTTGGGC GCCCAACG 16 1 1.3e-004 4.2e+000 # CTTTGGGC GCCCAAAG 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.1e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.615385 0.384615 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 117.70 seconds