# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/seqs-shuffled # positives: 529 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/seqs-centered (Sun Jan 19 00:55:11 PST 2020) # negatives: 529 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/seqs-shuffled (Sun Jan 19 00:55:11 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 01:07:30 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 0.297 C 0.206 G 0.206 T 0.291 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 107 11 2.5e-023 7.3e-019 # GGTTCGA TCGAACC 78 3 2.1e-021 6.3e-017 # GGTTCAA TTGAACC 29 8 3.0e-004 9.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 107 E= 7.3e-019 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 0.271028 0.000000 0.728972 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AACCACTH DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AACCACTH DAGTGGTT 56 1 9.1e-017 2.7e-012 # AACCACTA TAGTGGTT 19 0 1.6e-006 4.8e-002 # AACCACTT AAGTGGTT 19 0 1.6e-006 4.8e-002 # AACCACTC GAGTGGTT 18 1 3.3e-005 9.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 56 E= 2.7e-012 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 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 0.339286 0.321429 0.000000 0.339286 MOTIF CAASTTGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CAASTTGG CCAASTTG 35 0 1.6e-011 4.8e-007 # CAACTTGG CCAAGTTG 31 0 3.0e-010 8.7e-006 # CAAGTTGG CCAACTTG 25 0 2.2e-008 6.6e-004 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 4.8e-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 0.000000 0.685714 0.314286 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 GYGGTCTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GYGGTCTA TAGACCRC 40 2 1.0e-010 3.0e-006 # GTGGTCTA TAGACCAC 27 1 7.9e-008 2.3e-003 # GCGGTCTA TAGACCGC 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.0e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.325000 0.000000 0.675000 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 29 0 1.3e-009 3.7e-005 # GCGCTACC GGTAGCGC 19 0 1.6e-006 4.7e-002 # GCTCTACC GGTAGAGC 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.7e-005 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.655172 0.344828 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 AAAAARAA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AAAAARAA TTYTTTTT 82 25 2.7e-009 7.8e-005 # AAAAAAAA TTTTTTTT 54 18 6.7e-006 2.0e-001 # AAAAAGAA TTCTTTTT 30 8 1.9e-004 5.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 7.8e-005 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 0.659091 0.000000 0.340909 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGGYG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYG CRCCCAT 45 6 4.4e-009 1.3e-004 # ATGGGTG CACCCAT 26 3 5.9e-006 1.7e-001 # ATGGGCG CGCCCAT 19 3 3.8e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 1.3e-004 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 1.000000 0.000000 0.000000 0.422222 0.000000 0.577778 0.000000 0.000000 1.000000 0.000000 MOTIF ATCKTGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGA TCAMGAT 44 6 8.0e-009 2.3e-004 # ATCTTGA TCAAGAT 24 3 2.0e-005 5.8e-001 # ATCGTGA TCACGAT 20 3 2.1e-004 6.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 2.3e-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 0.454545 0.545455 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGARGTC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGARGTC GACYTCT 30 1 1.0e-008 2.9e-004 # AGAGGTC GACCTCT 15 0 2.8e-005 8.0e-001 # AGAAGTC GACTTCT 15 1 2.4e-004 6.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 2.9e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 MOTIF CCWTAACC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 26 0 1.1e-008 3.1e-004 # CCATAACC GGTTATGG 20 0 7.9e-007 2.3e-002 # CCTTAACC GGTTAAGG 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 3.1e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.740741 0.000000 0.000000 0.259259 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 0.000000 1.000000 0.000000 0.000000 MOTIF ATCCGTRC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCCGTRC GYACGGAT 26 1 1.6e-007 4.5e-003 # ATCCGTAC GTACGGAT 18 1 3.3e-005 9.6e-001 # ATCCGTGC GCACGGAT 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 4.5e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.666667 0.000000 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCRTGGAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGAG CTCCAYGG 21 0 3.9e-007 1.1e-002 # CCGTGGAG CTCCACGG 11 0 4.6e-004 1.3e+001 # CCATGGAG CTCCATGG 10 0 9.4e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-002 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.476190 0.000000 0.523810 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATGGTCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATGGTCA TGACCAT 23 1 1.2e-006 3.4e-002 # ATGGTCA TGACCAT 23 1 1.2e-006 3.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 3.4e-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 MOTIF AARGCGTG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AARGCGTG CACGCYTT 19 0 1.6e-006 4.6e-002 # AAGGCGTG CACGCCTT 10 0 9.4e-004 2.7e+001 # AAAGCGTG CACGCTTT 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.6e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.473684 0.000000 0.526316 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 1.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 52.06 seconds