# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-shuffled # positives: 505 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-centered (Sun Jan 19 06:46:45 PST 2020) # negatives: 505 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/YJM789--CUP9/seqs-shuffled (Sun Jan 19 06:46:45 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 06:58:15 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 0.300 C 0.198 G 0.200 T 0.302 MOTIF GTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GTTCGA TCGAAC 92 10 1.2e-019 3.6e-015 # GTTCGA TCGAAC 92 10 1.2e-019 3.6e-015 letter-probability matrix: alength= 4 w= 6 nsites= 92 E= 3.6e-015 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAGAAR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AAGAAR YTTCTT 170 88 2.0e-009 6.0e-005 # AAGAAA TTTCTT 128 63 1.1e-007 3.3e-003 # AAGAAG CTTCTT 60 33 2.2e-003 6.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 207 E= 6.0e-005 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 0.690821 0.000000 0.309179 0.000000 MOTIF ATAGTKTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 29 1 2.0e-008 5.7e-004 # ATAGTGTA TACACTAT 18 0 3.3e-006 9.6e-002 # ATAGTTTA TAAACTAT 11 1 3.0e-003 8.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.7e-004 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 0.620690 0.379310 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCABAC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCABAC GTVTGG 86 31 3.4e-008 9.9e-004 # CCATAC GTATGG 39 12 6.8e-005 2.0e+000 # CCAGAC GTCTGG 21 6 2.7e-003 7.7e+001 # CCACAC GTGTGG 34 16 6.5e-003 1.9e+002 letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 9.9e-004 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 0.462185 0.176471 0.361345 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGAYCGGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGGG CCCGRTCT 22 0 1.9e-007 5.4e-003 # AGATCGGG CCCGATCT 13 0 1.1e-004 3.3e+000 # AGACCGGG CCCGGTCT 9 0 1.9e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 5.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.409091 0.000000 0.590909 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 MOTIF ACCAACTK DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCAACTK MAGTTGGT 25 1 3.0e-007 8.7e-003 # ACCAACTG CAGTTGGT 12 0 2.3e-004 6.6e+000 # ACCAACTT AAGTTGGT 13 1 8.6e-004 2.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.7e-003 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 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 0.480000 0.520000 MOTIF AAWAAT DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAWAAT ATTWTT 230 154 5.5e-007 1.6e-002 # AATAAT ATTATT 96 46 3.9e-006 1.1e-001 # AAAAAT ATTTTT 168 127 2.8e-003 8.0e+001 letter-probability matrix: alength= 4 w= 6 nsites= 302 E= 1.6e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.652318 0.000000 0.000000 0.347682 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 # Stopping reason: E-value threshold exceeded # Running time: 26.84 seconds