# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP3/seqs-shuffled # positives: 691 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP3/seqs-centered (Sat Jan 18 19:10:37 PST 2020) # negatives: 691 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YAP3/seqs-shuffled (Sat Jan 18 19:10:37 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 19:26:25 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 0.312 C 0.187 G 0.186 T 0.315 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 83 6 1.0e-019 3.3e-015 # GGTTCGA TCGAACC 60 1 7.4e-018 2.3e-013 # GGTTCAA TTGAACC 24 5 2.4e-004 7.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 84 E= 3.3e-015 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 0.285714 0.000000 0.714286 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 54 0 1.9e-017 6.0e-013 # CTCGGCCA TGGCCGAG 32 0 1.6e-010 5.1e-006 # CTTGGCCA TGGCCAAG 22 0 2.0e-007 6.3e-003 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 6.0e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.592593 0.000000 0.407407 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 CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 66 7 5.2e-014 1.6e-009 # CGCCTTA TAAGGCG 54 6 2.1e-011 6.5e-007 # CGCGTTA TAACGCG 12 1 1.6e-003 5.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 66 E= 1.6e-009 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 0.818182 0.181818 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 GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 35 0 1.9e-011 5.9e-007 # GCGCTACC GGTAGCGC 21 0 4.1e-007 1.3e-002 # GCTCTACC GGTAGAGC 14 0 5.7e-005 1.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 5.9e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 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 AGAAAAW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGAAAAW WTTTTCT 150 71 3.8e-009 1.2e-004 # AGAAAAA TTTTTCT 96 44 2.2e-006 6.9e-002 # AGAAAAT ATTTTCT 63 30 2.6e-004 8.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 171 E= 1.2e-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 0.619883 0.000000 0.000000 0.380117 MOTIF CTARACCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 34 2 6.7e-009 2.1e-004 # CTAGACCA TGGTCTAG 19 1 1.8e-005 5.6e-001 # CTAAACCA TGGTTTAG 15 1 2.4e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.1e-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 0.441176 0.000000 0.558824 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 MOTIF GTGATAGY DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 25 0 2.4e-008 7.4e-004 # GTGATAGC GCTATCAC 15 0 2.8e-005 8.8e-001 # GTGATAGT ACTATCAC 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 7.4e-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 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 0.576923 0.000000 0.423077 MOTIF ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 3 4.4e-008 1.4e-003 # ATGGCAAC GTTGCCAT 22 3 6.9e-005 2.1e+000 # ATGGCATC GATGCCAT 13 0 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 1.4e-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 0.628571 0.000000 0.000000 0.371429 0.000000 1.000000 0.000000 0.000000 MOTIF GTTGRA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GTTGRA TYCAAC 123 60 3.5e-007 1.1e-002 # GTTGAA TTCAAC 77 35 2.2e-005 6.9e-001 # GTTGGA TCCAAC 51 29 7.5e-003 2.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 135 E= 1.1e-002 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 0.600000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATATATA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AATATATA TATATATT 35 5 5.0e-007 1.5e-002 # AATATATA TATATATT 35 5 5.0e-007 1.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 1.5e-002 1.000000 0.000000 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 0.000000 0.000000 0.000000 1.000000 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 ATAGTGTA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATAGTGTA TACACTAT 24 1 6.4e-007 2.0e-002 # ATAGTGTA TACACTAT 24 1 6.4e-007 2.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGSGCCAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGSGCCAA TTGGCSCA 24 1 6.4e-007 2.0e-002 # TGCGCCAA TTGGCGCA 11 0 4.7e-004 1.4e+001 # TGGGCCAA TTGGCCCA 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.458333 0.541667 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 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 56.59 seconds