# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-shuffled # positives: 824 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-centered (Sun Jan 19 01:26:37 PST 2020) # negatives: 824 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ARR1/seqs-shuffled (Sun Jan 19 01:26:37 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 01:42:08 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 0.320 C 0.181 G 0.173 T 0.326 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 104 7 6.7e-025 2.1e-020 # GGTTCGA TCGAACC 80 5 1.5e-019 4.8e-015 # GGTTCAA TTGAACC 25 2 2.4e-006 7.6e-002 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 2.1e-020 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 0.238095 0.000000 0.761905 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACTM DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ACCACTM KAGTGGT 90 13 1.8e-016 5.8e-012 # ACCACTA TAGTGGT 59 7 5.1e-012 1.6e-007 # ACCACTC GAGTGGT 33 6 5.7e-006 1.8e-001 letter-probability matrix: alength= 4 w= 7 nsites= 92 E= 5.8e-012 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 0.641304 0.358696 0.000000 0.000000 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 58 2 6.0e-016 1.9e-011 # CGCCTTA TAAGGCG 45 1 3.7e-013 1.2e-008 # CGCGTTA TAACGCG 13 1 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 1.9e-011 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 0.775862 0.224138 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 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 39 0 1.1e-012 3.6e-008 # AACTTGGC GCCAAGTT 27 0 6.0e-009 1.9e-004 # AACTGGGC GCCCAGTT 12 0 2.3e-004 7.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 3.6e-008 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 0.000000 1.000000 0.000000 0.000000 0.307692 0.692308 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAGAVAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAGAVAA TTBTCTT 170 76 4.1e-011 1.3e-006 # AAGAAAA TTTTCTT 117 52 7.5e-008 2.3e-003 # AAGACAA TTGTCTT 29 11 2.9e-003 9.1e+001 # AAGAGAA TTCTCTT 32 15 8.5e-003 2.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 192 E= 1.3e-006 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 0.682292 0.156250 0.161458 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCGCTWCC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCGCTWCC GGWAGCGC 29 1 2.3e-008 7.1e-004 # GCGCTACC GGTAGCGC 24 0 5.0e-008 1.6e-003 # GCGCTTCC GGAAGCGC 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.1e-004 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.724138 0.000000 0.000000 0.275862 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCCATDC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 49 10 8.4e-008 2.6e-003 # CCCATGC GCATGGG 11 0 4.7e-004 1.5e+001 # CCCATAC GTATGGG 26 7 5.9e-004 1.8e+001 # CCCATTC GAATGGG 15 4 9.3e-003 2.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 2.6e-003 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 0.000000 0.000000 0.000000 1.000000 0.527273 0.000000 0.200000 0.272727 0.000000 1.000000 0.000000 0.000000 MOTIF CACCGTGS DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 23 0 1.0e-007 3.2e-003 # CACCGTGC GCACGGTG 13 0 1.2e-004 3.6e+000 # CACCGTGG CCACGGTG 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.2e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.565217 0.434783 0.000000 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 32 3 1.6e-007 5.0e-003 # ATGGCAAC GTTGCCAT 20 3 2.2e-004 6.9e+000 # ATGGCATC GATGCCAT 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.0e-003 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 0.625000 0.000000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 25 1 3.4e-007 1.0e-002 # AGTCATAC GTATGACT 15 0 2.9e-005 8.8e-001 # AGTCAGAC GTCTGACT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-002 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 0.400000 0.600000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 57.53 seconds