# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--NOT3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--NOT3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--NOT3/seqs-shuffled # positives: 752 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--NOT3/seqs-centered (Sat Jan 18 17:05:33 PST 2020) # negatives: 752 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--NOT3/seqs-shuffled (Sat Jan 18 17:05:33 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 17:21:37 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 0.324 C 0.178 G 0.175 T 0.324 MOTIF GGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 57 1 7.1e-017 2.2e-012 # GGTTCGA TCGAACC 57 1 7.1e-017 2.2e-012 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 2.2e-012 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 47 1 8.5e-014 2.7e-009 # CTTGGCC GGCCAAG 33 1 1.5e-009 4.5e-005 # CTCGGCC GGCCGAG 21 0 4.1e-007 1.3e-002 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 2.7e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.404255 0.000000 0.595745 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 MOTIF GCGCYAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCGCYAC GTRGCGC 34 0 4.0e-011 1.2e-006 # GCGCTAC GTAGCGC 22 0 2.0e-007 6.3e-003 # GCGCCAC GTGGCGC 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.2e-006 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 0.352941 0.000000 0.647059 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCACTAVA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCACTAVA TBTAGTGG 36 2 1.8e-009 5.7e-005 # CCACTACA TGTAGTGG 12 0 2.3e-004 7.2e+000 # CCACTAAA TTTAGTGG 16 2 6.2e-004 1.9e+001 # CCACTAGA TCTAGTGG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 5.7e-005 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 1.000000 0.000000 0.000000 0.000000 0.444444 0.333333 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGCCTTAR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTAR YTAAGGCG 32 1 2.9e-009 8.9e-005 # CGCCTTAA TTAAGGCG 24 1 6.5e-007 2.0e-002 # CGCCTTAG CTAAGGCG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 8.9e-005 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 MOTIF TCCRTACA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TCCRTACA TGTAYGGA 33 2 1.3e-008 4.1e-004 # TCCGTACA TGTACGGA 22 0 2.0e-007 6.3e-003 # TCCATACA TGTATGGA 12 2 6.3e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 4.1e-004 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.351351 0.000000 0.648649 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGAAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGAAAA TTTTCT 181 97 1.5e-008 4.5e-004 # AGAAAA TTTTCT 181 97 1.5e-008 4.5e-004 letter-probability matrix: alength= 4 w= 6 nsites= 200 E= 4.5e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTWGCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGTWGCCA TGGCWACG 25 0 2.4e-008 7.4e-004 # CGTTGCCA TGGCAACG 18 0 3.4e-006 1.1e-001 # CGTAGCCA TGGCTACG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.4e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.280000 0.000000 0.000000 0.720000 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 CTATCAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTATCAC GTGATAG 25 0 2.4e-008 7.4e-004 # CTATCAC GTGATAG 25 0 2.4e-008 7.4e-004 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 7.4e-004 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CRCCCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 92 34 3.5e-008 1.1e-003 # CACCCA TGGGTG 63 23 5.3e-006 1.6e-001 # CGCCCA TGGGCG 29 11 2.9e-003 8.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 161 E= 1.1e-003 0.000000 1.000000 0.000000 0.000000 0.801242 0.000000 0.198758 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 AGGAAGW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AGGAAGW WCTTCCT 42 9 1.2e-006 3.5e-002 # AGGAAGA TCTTCCT 27 5 4.8e-005 1.5e+000 # AGGAAGT ACTTCCT 19 4 1.2e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 3.5e-002 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.586957 0.000000 0.000000 0.413043 MOTIF TGGCGYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 33 5 1.6e-006 4.9e-002 # TGGCGCA TGCGCCA 16 2 6.2e-004 1.9e+001 # TGGCGTA TACGCCA 17 3 1.2e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 4.9e-002 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 0.000000 1.000000 0.000000 0.000000 0.484848 0.000000 0.515152 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 63.63 seconds