# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CUP9/seqs-shuffled # positives: 682 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CUP9/seqs-centered (Sat Jan 18 15:34:31 PST 2020) # negatives: 682 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CUP9/seqs-shuffled (Sat Jan 18 15:34:31 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 15:53:06 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 0.201 G 0.201 T 0.298 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 121 13 1.8e-025 5.8e-021 # GGTTCGA TCGAACC 89 8 7.7e-020 2.5e-015 # GGTTCAA TTGAACC 34 5 8.9e-007 2.8e-002 letter-probability matrix: alength= 4 w= 7 nsites= 123 E= 5.8e-021 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 0.276423 0.000000 0.723577 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTYGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTYGGTW WACCRACT 67 2 8.2e-019 2.6e-014 # AGTTGGTT AACCAACT 28 2 3.4e-007 1.1e-002 # AGTTGGTA TACCAACT 21 0 4.1e-007 1.3e-002 # AGTCGGTT AACCGACT 10 0 9.4e-004 3.0e+001 # AGTCGGTA TACCGACT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 2.6e-014 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 0.268657 0.000000 0.731343 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.432836 0.000000 0.000000 0.567164 MOTIF CCAYWC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCAYWC GWRTGG 183 74 1.8e-014 5.8e-010 # CCATAC GTATGG 63 22 2.5e-006 8.1e-002 # CCACAC GTGTGG 55 20 2.0e-005 6.4e-001 # CCACTC GAGTGG 39 14 3.2e-004 1.0e+001 # CCATTC GAATGG 40 21 8.9e-003 2.8e+002 letter-probability matrix: alength= 4 w= 6 nsites= 209 E= 5.8e-010 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 0.464115 0.000000 0.535885 0.622010 0.000000 0.000000 0.377990 0.000000 1.000000 0.000000 0.000000 MOTIF ATAGTDTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ATAGTDTA TAHACTAT 56 3 2.1e-014 6.4e-010 # ATAGTGTA TACACTAT 29 0 1.4e-009 4.3e-005 # ATAGTTTA TAAACTAT 19 3 3.9e-004 1.2e+001 # ATAGTATA TATACTAT 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 6.4e-010 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 0.140351 0.000000 0.508772 0.350877 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCYGTACA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TCYGTACA TGTACRGA 37 0 4.4e-012 1.4e-007 # TCCGTACA TGTACGGA 29 0 1.4e-009 4.3e-005 # TCTGTACA TGTACAGA 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.4e-007 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.714286 0.000000 0.285714 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGAW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST SAAGAW WTCTTS 251 147 3.6e-010 1.1e-005 # GAAGAT ATCTTC 60 23 1.8e-005 5.4e-001 # CAAGAT ATCTTG 75 36 7.4e-005 2.3e+000 # CAAGAA TTCTTG 92 49 8.5e-005 2.6e+000 # GAAGAA TTCTTC 88 51 6.0e-004 1.9e+001 letter-probability matrix: alength= 4 w= 6 nsites= 331 E= 1.1e-005 0.000000 0.540785 0.459215 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 0.561934 0.000000 0.000000 0.438066 MOTIF AGTGRTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AGTGRTA TAYCACT 54 8 3.8e-010 1.2e-005 # AGTGGTA TACCACT 33 5 1.6e-006 4.8e-002 # AGTGATA TATCACT 22 4 2.4e-004 7.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 1.2e-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 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAVGCG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AAVGCG CGCBTT 134 56 5.5e-010 1.7e-005 # AAGGCG CGCCTT 59 24 4.8e-005 1.4e+000 # AACGCG CGCGTT 37 16 2.3e-003 7.0e+001 # AAAGCG CGCTTT 41 20 4.1e-003 1.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 137 E= 1.7e-005 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.299270 0.270073 0.430657 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 MOTIF ACGKTGCC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACGKTGCC GGCAMCGT 30 0 6.7e-010 2.0e-005 # ACGTTGCC GGCAACGT 18 0 3.4e-006 1.0e-001 # ACGGTGCC GGCACCGT 12 0 2.3e-004 7.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.0e-005 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.600000 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 1.000000 0.000000 0.000000 MOTIF CCRTGGAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CCRTGGAG CTCCAYGG 27 0 5.7e-009 1.7e-004 # CCGTGGAG CTCCACGG 16 0 1.4e-005 4.2e-001 # CCATGGAG CTCCATGG 11 0 4.7e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 1.7e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.407407 0.000000 0.592593 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 MOTIF AASCACT DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AASCACT AGTGSTT 50 11 1.3e-007 3.8e-003 # AACCACT AGTGGTT 35 7 5.6e-006 1.7e-001 # AAGCACT AGTGCTT 15 4 9.2e-003 2.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 52 E= 3.8e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.711538 0.288462 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 MOTIF ATTRCGCC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATTRCGCC GGCGYAAT 22 0 2.0e-007 6.0e-003 # ATTGCGCC GGCGCAAT 12 0 2.3e-004 6.9e+000 # ATTACGCC GGCGTAAT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.0e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.454545 0.000000 0.545455 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 0.000000 MOTIF TAAGCARA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST TAAGCARA TYTGCTTA 24 1 6.4e-007 1.9e-002 # TAAGCAGA TCTGCTTA 15 1 2.4e-004 7.2e+000 # TAAGCAAA TTTGCTTA 9 0 1.9e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.9e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.000000 0.625000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCGCK DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCGCK MGCGC 119 59 8.8e-007 2.6e-002 # GCGCT AGCGC 91 43 8.0e-006 2.4e-001 # GCGCG CGCGC 63 31 4.2e-004 1.2e+001 letter-probability matrix: alength= 4 w= 5 nsites= 131 E= 2.6e-002 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 0.000000 0.381679 0.618321 # Stopping reason: E-value threshold exceeded # Running time: 63.53 seconds