# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/seqs-shuffled # positives: 560 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/seqs-centered (Sat Jan 18 10:20:01 PST 2020) # negatives: 560 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/seqs-shuffled (Sat Jan 18 10:20:01 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 10:32:53 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 0.208 G 0.196 T 0.296 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 90 3 3.5e-025 1.0e-020 # ATCCGTAC GTACGGAT 34 0 3.5e-011 1.0e-006 # ACCCATAC GTATGGGT 43 3 1.1e-010 3.2e-006 # ATCCATAC GTATGGAT 13 0 1.1e-004 3.3e+000 # ACCCGTAC GTACGGGT 12 0 2.3e-004 6.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 106 E= 1.0e-020 1.000000 0.000000 0.000000 0.000000 0.000000 0.528302 0.000000 0.471698 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.537736 0.000000 0.462264 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 MOTIF CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 73 3 9.6e-020 2.7e-015 # CTCGGCCA TGGCCGAG 39 0 9.2e-013 2.6e-008 # CTTGGCCA TGGCCAAG 22 2 1.5e-005 4.3e-001 # CTGGGCCA TGGCCCAG 12 1 1.6e-003 4.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 2.7e-015 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.534247 0.164384 0.301370 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 GCCWTAAC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 54 1 4.3e-016 1.2e-011 # GCCTTAAC GTTAAGGC 40 0 4.4e-013 1.3e-008 # GCCATAAC GTTATGGC 15 1 2.4e-004 6.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 1.2e-011 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.272727 0.000000 0.000000 0.727273 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 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 49 1 1.6e-014 4.5e-010 # GCGCTACC GGTAGCGC 33 0 7.2e-011 2.0e-006 # GCTCTACC GGTAGAGC 16 1 1.2e-004 3.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 4.5e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.673469 0.326531 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 CGARCCC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CGARCCC GGGYTCG 36 0 8.1e-012 2.3e-007 # CGAACCC GGGTTCG 26 0 1.1e-008 3.1e-004 # CGAGCCC GGGCTCG 17 0 6.7e-006 1.9e-001 letter-probability matrix: alength= 4 w= 7 nsites= 36 E= 2.3e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 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 CCASAC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CCASAC GTSTGG 124 44 9.0e-012 2.5e-007 # CCACAC GTGTGG 91 36 1.2e-007 3.5e-003 # CCAGAC GTCTGG 38 8 3.1e-006 8.7e-002 letter-probability matrix: alength= 4 w= 6 nsites= 236 E= 2.5e-007 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 0.838983 0.161017 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CACTAWA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CACTAWA TWTAGTG 59 9 6.1e-011 1.7e-006 # CACTATA TATAGTG 35 4 1.1e-007 3.0e-003 # CACTAAA TTTAGTG 25 5 1.4e-004 3.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 61 E= 1.7e-006 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 1.000000 0.000000 0.000000 0.000000 0.426230 0.000000 0.000000 0.573770 1.000000 0.000000 0.000000 0.000000 MOTIF ATCSTTG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATCSTTG CAASGAT 34 1 6.4e-010 1.8e-005 # ATCCTTG CAAGGAT 16 0 1.4e-005 3.8e-001 # ATCGTTG CAACGAT 19 1 1.7e-005 4.8e-001 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 1.8e-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 0.547619 0.452381 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 MOTIF CTTARACC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CTTARACC GGTYTAAG 29 0 1.3e-009 3.6e-005 # CTTAGACC GGTCTAAG 17 0 6.7e-006 1.9e-001 # CTTAAACC GGTTTAAG 12 0 2.3e-004 6.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.6e-005 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 0.413793 0.000000 0.586207 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 GGYTATCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 33 1 1.3e-009 3.6e-005 # GGCTATCA TGATAGCC 18 0 3.3e-006 9.2e-002 # GGTTATCA TGATAACC 15 1 2.4e-004 6.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 3.6e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.545455 0.000000 0.454545 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 GCGCAR DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GCGCAR YTGCGC 71 19 4.2e-009 1.2e-004 # GCGCAA TTGCGC 50 15 4.4e-006 1.2e-001 # GCGCAG CTGCGC 26 6 2.2e-004 6.2e+000 letter-probability matrix: alength= 4 w= 6 nsites= 75 E= 1.2e-004 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 1.000000 0.000000 0.000000 0.000000 0.653333 0.000000 0.346667 0.000000 MOTIF SAAGAAA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST SAAGAAA TTTCTTS 64 16 9.8e-009 2.7e-004 # CAAGAAA TTTCTTG 31 6 1.6e-005 4.3e-001 # GAAGAAA TTTCTTC 34 10 1.5e-004 4.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 2.7e-004 0.000000 0.477612 0.522388 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AATCSAAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AATCSAAC GTTSGATT 28 1 4.0e-008 1.1e-003 # AATCGAAC GTTCGATT 15 0 2.8e-005 7.6e-001 # AATCCAAC GTTGGATT 15 1 2.4e-004 6.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.1e-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 0.516129 0.483871 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 MOTIF CATYACGC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CATYACGC GCGTRATG 28 1 4.0e-008 1.1e-003 # CATTACGC GCGTAATG 14 0 5.6e-005 1.5e+000 # CATCACGC GCGTGATG 14 1 4.5e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.1e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 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 MOTIF ACCCRTGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ACCCRTGC GCAYGGGT 26 1 1.6e-007 4.3e-003 # ACCCATGC GCATGGGT 19 1 1.7e-005 4.7e-001 # ACCCGTGC GCACGGGT 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.3e-003 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 0.730769 0.000000 0.269231 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 MOTIF AMACCCAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AMACCCAA TTGGGTKT 25 1 3.1e-007 8.5e-003 # ACACCCAA TTGGGTGT 14 1 4.5e-004 1.2e+001 # AAACCCAA TTGGGTTT 11 0 4.6e-004 1.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 8.5e-003 1.000000 0.000000 0.000000 0.000000 0.440000 0.560000 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 1.000000 0.000000 0.000000 0.000000 MOTIF GTAKCTCA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GTAKCTCA TGAGMTAC 21 0 3.9e-007 1.1e-002 # GTATCTCA TGAGATAC 14 0 5.6e-005 1.5e+000 # GTAGCTCA TGAGCTAC 7 0 7.7e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 1.1e-002 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 0.000000 0.318182 0.681818 0.000000 1.000000 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 TCTCCACR DREME-18 # Word RC Word Pos Neg P-value E-value # BEST TCTCCACR YGTGGAGA 21 0 3.9e-007 1.1e-002 # TCTCCACG CGTGGAGA 12 0 2.3e-004 6.2e+000 # TCTCCACA TGTGGAGA 9 0 1.9e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.1e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.000000 0.571429 0.000000 MOTIF ACGGAKG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACGGAKG CMTCCGT 32 4 6.8e-007 1.8e-002 # ACGGATG CATCCGT 19 3 3.8e-004 1.0e+001 # ACGGAGG CCTCCGT 13 1 8.6e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 32 E= 1.8e-002 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.406250 0.593750 0.000000 0.000000 1.000000 0.000000 MOTIF AGTCAKAC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 2 1.2e-006 3.2e-002 # AGTCATAC GTATGACT 15 1 2.4e-004 6.4e+000 # AGTCAGAC GTCTGACT 11 1 3.0e-003 8.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.2e-002 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 0.423077 0.576923 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AAAAARAA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST AAAAARAA TTYTTTTT 69 25 1.2e-006 3.3e-002 # AAAAAAAA TTTTTTTT 47 16 3.7e-005 1.0e+000 # AAAAAGAA TTCTTTTT 30 13 6.0e-003 1.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 83 E= 3.3e-002 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 0.638554 0.000000 0.361446 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: 78.53 seconds