# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/seqs-shuffled # positives: 516 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/seqs-centered (Sat Jan 18 04:19:21 PST 2020) # negatives: 516 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/seqs-shuffled (Sat Jan 18 04:19:21 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 04:29:36 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 0.289 C 0.211 G 0.211 T 0.289 MOTIF GRNTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRNTCGAA TTCGANYC 151 9 1.1e-039 2.9e-035 # GAATCGAA TTCGATTC 32 1 2.5e-009 6.8e-005 # GGATCGAA TTCGATCC 31 1 5.0e-009 1.4e-004 # GAGTCGAA TTCGACTC 26 0 1.1e-008 3.0e-004 # GGGTCGAA TTCGACCC 15 0 2.8e-005 7.5e-001 # GGCTCGAA TTCGAGCC 11 0 4.6e-004 1.3e+001 # GGTTCGAA TTCGAACC 17 3 1.2e-003 3.2e+001 # GATTCGAA TTCGAATC 16 3 2.0e-003 5.6e+001 # GACTCGAA TTCGAGTC 12 2 6.2e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 152 E= 2.9e-035 0.000000 0.000000 1.000000 0.000000 0.539474 0.000000 0.460526 0.000000 0.421053 0.151316 0.269737 0.157895 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 75 2 1.3e-021 3.4e-017 # CCATACAT ATGTATGG 34 0 3.3e-011 9.0e-007 # CCGTACAT ATGTACGG 27 0 5.3e-009 1.4e-004 # CCGTACAC GTGTACGG 13 2 3.5e-003 9.5e+001 # CCATACAC GTGTATGG 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 88 E= 3.4e-017 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.534091 0.000000 0.465909 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 0.000000 0.250000 0.000000 0.750000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 57 0 1.4e-018 3.6e-014 # CTCGGCCA TGGCCGAG 28 0 2.6e-009 6.9e-005 # CTTGGCCA TGGCCAAG 17 0 6.7e-006 1.8e-001 # CTGGGCCA TGGCCCAG 12 0 2.3e-004 6.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 3.6e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.491228 0.210526 0.298246 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 CKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CKCTACC GGTAGMG 43 0 4.6e-014 1.2e-009 # CGCTACC GGTAGCG 27 0 5.3e-009 1.4e-004 # CTCTACC GGTAGAG 16 0 1.4e-005 3.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 1.2e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.627907 0.372093 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 GCCTTAMC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCCTTAMC GKTAAGGC 43 1 1.1e-012 2.8e-008 # GCCTTAAC GTTAAGGC 35 1 3.1e-010 8.2e-006 # GCCTTACC GGTAAGGC 8 0 3.8e-003 1.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 2.8e-008 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 0.813953 0.186047 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACCAYTA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACCAYTA TARTGGT 62 9 8.7e-012 2.3e-007 # ACCACTA TAGTGGT 39 3 1.5e-009 4.0e-005 # ACCATTA TAATGGT 24 6 6.1e-004 1.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 2.3e-007 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 0.000000 0.609375 0.000000 0.390625 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AMACCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AMACCCA TGGGTKT 56 8 8.6e-011 2.3e-006 # ACACCCA TGGGTGT 37 3 5.5e-009 1.5e-004 # AAACCCA TGGGTTT 21 5 1.1e-003 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 2.3e-006 1.000000 0.000000 0.000000 0.000000 0.360656 0.639344 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAAK DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAK MTTTTTT 164 77 8.8e-011 2.3e-006 # AAAAAAT ATTTTTT 104 46 1.8e-007 4.8e-003 # AAAAAAG CTTTTTT 77 36 2.9e-005 7.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 196 E= 2.3e-006 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.408163 0.591837 MOTIF CCGYGSA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CCGYGSA TSCRCGG 65 9 1.3e-012 3.5e-008 # CCGTGGA TCCACGG 27 3 3.2e-006 8.3e-002 # CCGTGCA TGCACGG 16 1 1.2e-004 3.2e+000 # CCGCGGA TCCGCGG 16 3 2.0e-003 5.3e+001 # CCGCGCA TGCGCGG 13 2 3.5e-003 9.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 3.5e-008 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 0.426667 0.000000 0.573333 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 36 2 1.5e-009 4.0e-005 # ATCGTGAG CTCACGAT 23 0 9.3e-008 2.4e-003 # ATCTTGAG CTCAAGAT 13 2 3.5e-003 9.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 4.0e-005 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 0.638889 0.361111 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 1.000000 0.000000 MOTIF GTGATAGY DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 32 1 2.5e-009 6.4e-005 # GTGATAGC GCTATCAC 18 1 3.3e-005 8.6e-001 # GTGATAGT ACTATCAC 14 0 5.6e-005 1.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 6.4e-005 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 0.562500 0.000000 0.437500 MOTIF ATGGCAWC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 34 2 5.9e-009 1.5e-004 # ATGGCAAC GTTGCCAT 24 2 4.2e-006 1.1e-001 # ATGGCATC GATGCCAT 10 0 9.3e-004 2.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.5e-004 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 0.705882 0.000000 0.000000 0.294118 0.000000 1.000000 0.000000 0.000000 MOTIF GATTRGAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GATTRGAA TTCYAATC 28 1 3.9e-008 1.0e-003 # GATTAGAA TTCTAATC 20 1 8.9e-006 2.3e-001 # GATTGGAA TTCCAATC 8 0 3.8e-003 9.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.0e-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 0.714286 0.000000 0.285714 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 TGGCGYA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 39 5 4.0e-008 1.0e-003 # TGGCGCA TGCGCCA 23 3 3.6e-005 9.3e-001 # TGGCGTA TACGCCA 16 2 6.0e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 39 E= 1.0e-003 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 0.589744 0.000000 0.410256 1.000000 0.000000 0.000000 0.000000 MOTIF RGCCCAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST RGCCCAA TTGGGCY 36 4 5.6e-008 1.4e-003 # GGCCCAA TTGGGCC 22 2 1.5e-005 3.8e-001 # AGCCCAA TTGGGCT 14 2 2.0e-003 5.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 1.4e-003 0.405405 0.000000 0.594595 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AACCCYG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AACCCYG CRGGGTT 33 3 7.3e-008 1.9e-003 # AACCCCG CGGGGTT 20 1 8.9e-006 2.3e-001 # AACCCTG CAGGGTT 13 2 3.5e-003 8.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 33 E= 1.9e-003 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.606061 0.000000 0.393939 0.000000 0.000000 1.000000 0.000000 MOTIF GWGCTAA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GWGCTAA TTAGCWC 33 3 7.3e-008 1.9e-003 # GAGCTAA TTAGCTC 19 0 1.6e-006 4.1e-002 # GTGCTAA TTAGCAC 15 3 3.5e-003 9.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.9e-003 0.000000 0.000000 1.000000 0.000000 0.558824 0.000000 0.000000 0.441176 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 1.000000 0.000000 0.000000 0.000000 MOTIF AAAGCGWG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAAGCGWG CWCGCTTT 23 0 9.3e-008 2.4e-003 # AAAGCGTG CACGCTTT 16 0 1.4e-005 3.4e-001 # AAAGCGAG CTCGCTTT 7 0 7.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.4e-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 0.304348 0.000000 0.000000 0.695652 0.000000 0.000000 1.000000 0.000000 MOTIF AGAAGWT DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AGAAGWT AWCTTCT 36 5 2.4e-007 6.2e-003 # AGAAGAT ATCTTCT 27 5 4.5e-005 1.1e+000 # AGAAGTT AACTTCT 9 0 1.9e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 6.2e-003 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 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 MOTIF CTTARCA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST CTTARCA TGYTAAG 30 3 4.9e-007 1.2e-002 # CTTAGCA TGCTAAG 14 1 4.5e-004 1.1e+001 # CTTAACA TGTTAAG 16 2 6.0e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.2e-002 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 0.533333 0.000000 0.466667 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTMTGAC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CGTMTGAC GTCAKACG 24 1 6.0e-007 1.5e-002 # CGTCTGAC GTCAGACG 12 0 2.3e-004 5.8e+000 # CGTATGAC GTCATACG 12 1 1.6e-003 4.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.500000 0.000000 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 1.000000 0.000000 0.000000 MOTIF CAGTCTKG DREME-22 # Word RC Word Pos Neg P-value E-value # BEST CAGTCTKG CMAGACTG 19 0 1.6e-006 4.1e-002 # CAGTCTGG CCAGACTG 10 0 9.3e-004 2.4e+001 # CAGTCTTG CAAGACTG 9 0 1.9e-003 4.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.1e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 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 0.526316 0.473684 0.000000 0.000000 1.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 73.00 seconds