# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MAC1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MAC1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MAC1/seqs-shuffled # positives: 637 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MAC1/seqs-centered (Sun Jan 19 05:32:40 PST 2020) # negatives: 637 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--MAC1/seqs-shuffled (Sun Jan 19 05:32:40 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:49:07 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 0.306 C 0.199 G 0.198 T 0.296 MOTIF RGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCRA TYGAACY 154 28 1.0e-025 3.2e-021 # GGTTCGA TCGAACC 80 5 8.7e-020 2.8e-015 # GGTTCAA TTGAACC 38 10 2.3e-005 7.2e-001 # AGTTCAA TTGAACT 23 7 2.4e-003 7.5e+001 # AGTTCGA TCGAACT 21 7 5.8e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 158 E= 3.2e-021 0.265823 0.000000 0.734177 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 0.386076 0.000000 0.613924 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 47 0 2.9e-015 9.3e-011 # CTCGGCCA TGGCCGAG 20 0 8.2e-007 2.6e-002 # CTTGGCCA TGGCCAAG 18 0 3.4e-006 1.1e-001 # CTGGGCCA TGGCCCAG 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 9.3e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.425532 0.191489 0.382979 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 AARAAAWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 147 50 1.8e-014 5.7e-010 # AAGAAAAA TTTTTCTT 45 8 6.8e-008 2.2e-003 # AAAAAAAA TTTTTTTT 63 23 4.8e-006 1.5e-001 # AAAAAATA TATTTTTT 49 19 1.2e-004 3.9e+000 # AAGAAATA TATTTCTT 19 5 3.1e-003 9.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 169 E= 5.7e-010 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.639053 0.000000 0.360947 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 0.609467 0.000000 0.000000 0.390533 1.000000 0.000000 0.000000 0.000000 MOTIF CCWTAACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CCWTAACC GGTTAWGG 42 1 2.6e-012 8.1e-008 # CCTTAACC GGTTAAGG 27 0 5.6e-009 1.8e-004 # CCATAACC GGTTATGG 15 1 2.4e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 8.1e-008 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.357143 0.000000 0.000000 0.642857 0.000000 0.000000 0.000000 1.000000 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 0.000000 MOTIF AGTGGWA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AGTGGWA TWCCACT 56 9 4.2e-010 1.3e-005 # AGTGGTA TACCACT 41 5 1.3e-008 4.1e-004 # AGTGGAA TTCCACT 15 4 9.2e-003 2.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 1.3e-005 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 1.000000 0.000000 0.254237 0.000000 0.000000 0.745763 1.000000 0.000000 0.000000 0.000000 MOTIF CSCGCTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CSCGCTA TAGCGSG 32 2 2.4e-008 7.6e-004 # CGCGCTA TAGCGCG 21 1 4.7e-006 1.5e-001 # CCCGCTA TAGCGGG 11 1 3.1e-003 9.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 7.6e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.343750 0.656250 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAGKCGC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AAGKCGC GCGMCTT 39 5 4.4e-008 1.4e-003 # AAGGCGC GCGCCTT 26 3 6.2e-006 1.9e-001 # AAGTCGC GCGACTT 13 2 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 1.4e-003 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 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGGAGAY DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTGGAGAY RTCTCCAC 23 1 1.2e-006 3.8e-002 # GTGGAGAT ATCTCCAC 13 0 1.1e-004 3.6e+000 # GTGGAGAC GTCTCCAC 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.8e-002 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 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 0.434783 0.000000 0.565217 # Stopping reason: E-value threshold exceeded # Running time: 36.97 seconds