# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/seqs-shuffled # positives: 871 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/seqs-centered (Sun Jan 19 09:08:27 PST 2020) # negatives: 871 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/seqs-shuffled (Sun Jan 19 09:08:27 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 09:24:02 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 0.205 G 0.198 T 0.297 MOTIF SGGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCRA TYGAACCS 120 5 9.9e-032 3.4e-027 # GGGTTCGA TCGAACCC 48 1 4.7e-014 1.6e-009 # CGGTTCGA TCGAACCG 40 0 5.8e-013 2.0e-008 # GGGTTCAA TTGAACCC 20 2 5.5e-005 1.9e+000 # CGGTTCAA TTGAACCG 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 120 E= 3.4e-027 0.000000 0.433333 0.566667 0.000000 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 0.266667 0.000000 0.733333 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 98 7 4.9e-023 1.7e-018 # TGTATGGG CCCATACA 43 2 1.8e-011 6.2e-007 # TGTACGGA TCCGTACA 39 3 1.9e-009 6.6e-005 # TGTACGGG CCCGTACA 13 1 8.8e-004 3.0e+001 # TGTATGGA TCCATACA 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 112 E= 1.7e-018 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 0.482143 0.000000 0.517857 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.491071 0.000000 0.508929 0.000000 MOTIF BTAAGGCG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 65 2 4.8e-018 1.6e-013 # TTAAGGCG CGCCTTAA 40 0 5.8e-013 1.9e-008 # CTAAGGCG CGCCTTAG 14 1 4.7e-004 1.6e+001 # GTAAGGCG CGCCTTAC 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 65 E= 1.6e-013 0.000000 0.215385 0.169231 0.615385 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTBGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 67 5 1.0e-015 3.5e-011 # CTCGGCCA TGGCCGAG 34 1 7.7e-010 2.6e-005 # CTTGGCCA TGGCCAAG 21 2 3.0e-005 1.0e+000 # CTGGGCCA TGGCCCAG 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 67 E= 3.5e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.507463 0.179104 0.313433 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 50 1 1.2e-014 3.9e-010 # GCGCTACC GGTAGCGC 34 0 4.2e-011 1.4e-006 # GCTCTACC GGTAGAGC 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 3.9e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.680000 0.320000 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 CCGTGSA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 57 3 1.3e-014 4.5e-010 # CCGTGGA TCCACGG 34 1 7.7e-010 2.6e-005 # CCGTGCA TGCACGG 23 2 8.6e-006 2.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 4.5e-010 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.383333 0.616667 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARARAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ARARAAA TTTYTYT 291 164 2.5e-012 8.3e-008 # AGAAAAA TTTTTCT 115 48 1.9e-008 6.4e-004 # AAAAAAA TTTTTTT 158 87 6.1e-007 2.0e-002 # AAAGAAA TTTCTTT 96 53 1.5e-004 5.0e+000 # AGAGAAA TTTCTCT 38 17 2.8e-003 9.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 374 E= 8.3e-008 1.000000 0.000000 0.000000 0.000000 0.663102 0.000000 0.336898 0.000000 1.000000 0.000000 0.000000 0.000000 0.697861 0.000000 0.302139 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 ATAGTDTA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATAGTDTA TAHACTAT 57 6 3.8e-012 1.3e-007 # ATAGTGTA TACACTAT 27 1 8.9e-008 3.0e-003 # ATAGTATA TATACTAT 10 0 9.5e-004 3.2e+001 # ATAGTTTA TAAACTAT 20 5 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 1.3e-007 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 0.172414 0.000000 0.465517 0.362069 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CRCCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 162 74 3.8e-010 1.3e-005 # CACCCA TGGGTG 109 47 1.1e-007 3.7e-003 # CGCCCA TGGGCG 57 30 2.0e-003 6.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 250 E= 1.3e-005 0.000000 1.000000 0.000000 0.000000 0.760000 0.000000 0.240000 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 CTARACCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 41 3 5.3e-010 1.8e-005 # CTAGACCA TGGTCTAG 27 0 6.1e-009 2.0e-004 # CTAAACCA TGGTTTAG 14 3 6.2e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.8e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.341463 0.000000 0.658537 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 ATGGCAWC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 42 4 1.7e-009 5.5e-005 # ATGGCAAC GTTGCCAT 27 3 3.6e-006 1.2e-001 # ATGGCATC GATGCCAT 15 1 2.5e-004 8.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 5.5e-005 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 0.642857 0.000000 0.000000 0.357143 0.000000 1.000000 0.000000 0.000000 MOTIF CTCTCSCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CTCTCSCA TGSGAGAG 31 1 6.0e-009 1.9e-004 # CTCTCCCA TGGGAGAG 21 1 4.9e-006 1.6e-001 # CTCTCGCA TGCGAGAG 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.9e-004 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 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.677419 0.322581 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCTTGAS DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATCTTGAS STCAAGAT 26 0 1.2e-008 4.0e-004 # ATCTTGAC GTCAAGAT 15 0 2.9e-005 9.4e-001 # ATCTTGAG CTCAAGAT 11 0 4.7e-004 1.5e+001 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 0.000000 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.576923 0.423077 0.000000 MOTIF AGTCAKAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 33 2 1.4e-008 4.6e-004 # AGTCATAC GTATGACT 17 1 6.8e-005 2.2e+000 # AGTCAGAC GTCTGACT 16 1 1.3e-004 4.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.6e-004 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.484848 0.515152 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AATCTTYT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AATCTTYT ARAAGATT 46 8 4.5e-008 1.5e-003 # AATCTTCT AGAAGATT 21 2 3.0e-005 9.7e-001 # AATCTTTT AAAAGATT 25 6 4.0e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 1.5e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.456522 0.000000 0.543478 0.000000 0.000000 0.000000 1.000000 MOTIF CCAGWTCG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CCAGWTCG CGAWCTGG 25 1 3.4e-007 1.1e-002 # CCAGATCG CGATCTGG 12 0 2.4e-004 7.7e+000 # CCAGTTCG CGAACTGG 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 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 0.000000 1.000000 0.000000 0.480000 0.000000 0.000000 0.520000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ACTSACGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTSACGA TCGTSAGT 27 2 6.8e-007 2.2e-002 # ACTCACGA TCGTGAGT 19 2 1.0e-004 3.3e+000 # ACTGACGA TCGTCAGT 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.703704 0.296296 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 32 4 7.8e-007 2.5e-002 # GGCTATCA TGATAGCC 16 1 1.3e-004 4.2e+000 # GGTTATCA TGATAACC 16 3 2.1e-003 6.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 2.5e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 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 MOTIF TGGCGYA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 48 12 1.1e-006 3.5e-002 # TGGCGCA TGCGCCA 28 7 2.2e-004 7.3e+000 # TGGCGTA TACGCCA 20 5 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 48 E= 3.5e-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 0.583333 0.000000 0.416667 1.000000 0.000000 0.000000 0.000000 MOTIF ACCGARAG DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACCGARAG CTYTCGGT 23 1 1.3e-006 4.2e-002 # ACCGAAAG CTTTCGGT 12 0 2.4e-004 7.6e+000 # ACCGAGAG CTCTCGGT 11 1 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.2e-002 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.521739 0.000000 0.478261 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 110.25 seconds