# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/seqs-shuffled # positives: 760 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/seqs-centered (Sat Jan 18 02:47:30 PST 2020) # negatives: 760 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/seqs-shuffled (Sat Jan 18 02:47:30 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 03:03:13 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 0.296 C 0.202 G 0.203 T 0.298 MOTIF CTBGGCCA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 67 4 1.1e-016 3.9e-012 # CTCGGCCA TGGCCGAG 33 0 8.2e-011 2.8e-006 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 8.0e+000 # CTTGGCCA TGGCCAAG 22 4 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 3.9e-012 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.492537 0.179104 0.328358 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 CGCCTTA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTA TAAGGCG 58 3 5.9e-015 2.0e-010 # CGCCTTA TAAGGCG 58 3 5.9e-015 2.0e-010 letter-probability matrix: alength= 4 w= 7 nsites= 58 E= 2.0e-010 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 MOTIF GGTTCGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 60 5 8.7e-014 3.0e-009 # GGTTCGA TCGAACC 60 5 8.7e-014 3.0e-009 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 3.0e-009 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 ATGGCAWC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 44 1 7.1e-013 2.4e-008 # ATGGCAAC GTTGCCAT 33 0 8.2e-011 2.8e-006 # ATGGCATC GATGCCAT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.4e-008 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 0.750000 0.000000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGTAYGG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 48 4 3.4e-011 1.2e-006 # ATGTACGG CCGTACAT 25 1 3.3e-007 1.1e-002 # ATGTATGG CCATACAT 26 3 6.4e-006 2.2e-001 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 1.2e-006 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.480769 0.000000 0.519231 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 38 1 4.6e-011 1.6e-006 # GCGCTACC GGTAGCGC 22 0 2.0e-007 6.9e-003 # GCTCTACC GGTAGAGC 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.6e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.578947 0.421053 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 SAAGAW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST SAAGAW WTCTTS 258 151 3.7e-010 1.3e-005 # GAAGAA TTCTTC 98 44 1.2e-006 4.0e-002 # GAAGAT ATCTTC 66 31 1.6e-004 5.4e+000 # CAAGAA TTCTTG 83 50 1.8e-003 6.0e+001 # CAAGAT ATCTTG 65 39 5.4e-003 1.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 329 E= 1.3e-005 0.000000 0.483283 0.516717 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 1.000000 0.000000 0.000000 0.000000 0.586626 0.000000 0.000000 0.413374 MOTIF ATAGTGTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATAGTGTA TACACTAT 26 0 1.2e-008 4.0e-004 # ATAGTGTA TACACTAT 26 0 1.2e-008 4.0e-004 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CACRCCC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACRCCC GGGYGTG 35 3 2.4e-008 8.0e-004 # CACGCCC GGGCGTG 21 1 4.8e-006 1.6e-001 # CACACCC GGGTGTG 15 2 1.1e-003 3.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 8.0e-004 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.461538 0.000000 0.538462 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 MOTIF AAAGCGWG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 24 0 5.0e-008 1.6e-003 # AAAGCGTG CACGCTTT 14 0 5.7e-005 1.9e+000 # AAAGCGAG CTCGCTTT 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.6e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.416667 0.000000 0.000000 0.583333 0.000000 0.000000 1.000000 0.000000 MOTIF GGAGASC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGAGASC GSTCTCC 29 2 1.8e-007 6.1e-003 # GGAGAGC GCTCTCC 12 0 2.3e-004 7.8e+000 # GGAGACC GGTCTCC 17 2 3.4e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 29 E= 6.1e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.586207 0.413793 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTAGACC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACTAGACC GGTCTAGT 22 0 2.0e-007 6.8e-003 # ACTAGACC GGTCTAGT 22 0 2.0e-007 6.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.8e-003 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 0.000000 0.000000 1.000000 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 GATTAGAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GATTAGAA TTCTAATC 22 0 2.0e-007 6.8e-003 # GATTAGAA TTCTAATC 22 0 2.0e-007 6.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.8e-003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AWGTGATA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AWGTGATA TATCACWT 28 2 3.5e-007 1.2e-002 # ATGTGATA TATCACAT 19 2 1.0e-004 3.3e+000 # AAGTGATA TATCACTT 9 0 1.9e-003 6.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.2e-002 1.000000 0.000000 0.000000 0.000000 0.321429 0.000000 0.000000 0.678571 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 MOTIF TGGCKCAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TGGCKCAA TTGMGCCA 20 0 8.4e-007 2.8e-002 # TGGCGCAA TTGCGCCA 12 0 2.3e-004 7.7e+000 # TGGCTCAA TTGAGCCA 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-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 0.600000 0.400000 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: 74.95 seconds