# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/seqs-shuffled # positives: 777 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/seqs-centered (Sun Jan 19 04:59:29 PST 2020) # negatives: 777 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/seqs-shuffled (Sun Jan 19 04:59:29 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:15:16 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 0.312 C 0.192 G 0.187 T 0.309 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 94 4 7.6e-025 2.4e-020 # ACCCATAC GTATGGGT 46 2 2.2e-012 7.1e-008 # ATCCGTAC GTACGGAT 35 1 3.7e-010 1.2e-005 # ACCCGTAC GTACGGGT 12 0 2.3e-004 7.4e+000 # ATCCATAC GTATGGAT 13 1 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 111 E= 2.4e-020 1.000000 0.000000 0.000000 0.000000 0.000000 0.540541 0.000000 0.459459 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.549550 0.000000 0.450450 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 AGTGGTWW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWW WWACCACT 82 7 1.8e-018 5.7e-014 # AGTGGTTA TAACCACT 45 3 3.7e-011 1.2e-006 # AGTGGTTT AAACCACT 23 1 1.3e-006 4.0e-002 # AGTGGTAA TTACCACT 17 1 6.7e-005 2.1e+000 # AGTGGTAT ATACCACT 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 98 E= 5.7e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.306122 0.000000 0.000000 0.693878 0.632653 0.000000 0.000000 0.367347 MOTIF GGHTCGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGHTCGA TCGADCC 80 10 1.0e-015 3.2e-011 # GGTTCGA TCGAACC 64 5 6.5e-015 2.0e-010 # GGCTCGA TCGAGCC 16 2 6.2e-004 1.9e+001 # GGATCGA TCGATCC 14 3 6.1e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 3.2e-011 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.158537 0.109756 0.000000 0.731707 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 MOTIF GCKCTACC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 52 3 3.5e-013 1.1e-008 # GCGCTACC GGTAGCGC 33 1 1.5e-009 4.6e-005 # GCTCTACC GGTAGAGC 19 2 1.0e-004 3.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 1.1e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.634615 0.365385 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 TTTCTTB DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 178 75 6.6e-013 2.1e-008 # TTTCTTC GAAGAAA 50 15 5.2e-006 1.6e-001 # TTTCTTG CAAGAAA 50 16 1.1e-005 3.5e-001 # TTTCTTT AAAGAAA 88 44 4.0e-005 1.3e+000 letter-probability matrix: alength= 4 w= 7 nsites= 196 E= 2.1e-008 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.255102 0.260204 0.484694 MOTIF CAACTKGG DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 53 4 1.3e-012 4.2e-008 # CAACTTGG CCAAGTTG 41 2 6.6e-011 2.0e-006 # CAACTGGG CCCAGTTG 12 2 6.3e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 4.2e-008 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.226415 0.773585 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCSTTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 63 8 1.9e-012 5.8e-008 # CGCCTTA TAAGGCG 50 7 1.2e-009 3.6e-005 # CGCGTTA TAACGCG 13 1 8.8e-004 2.7e+001 letter-probability matrix: alength= 4 w= 7 nsites= 63 E= 5.8e-008 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 0.793651 0.206349 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 MOTIF TGGCGYA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 50 5 5.5e-011 1.7e-006 # TGGCGCA TGCGCCA 27 3 3.5e-006 1.1e-001 # TGGCGTA TACGCCA 23 2 8.5e-006 2.6e-001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 1.7e-006 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 0.540000 0.000000 0.460000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCAVAC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 61 10 9.8e-011 3.0e-006 # ACCCACAC GTGTGGGT 35 5 5.2e-007 1.6e-002 # ACCCAGAC GTCTGGGT 14 1 4.6e-004 1.4e+001 # ACCCAAAC GTTTGGGT 16 4 5.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 113 E= 3.0e-006 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 0.141593 0.734513 0.123894 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTCAKAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GTCAKAC GTMTGAC 33 1 1.5e-009 4.5e-005 # GTCATAC GTATGAC 21 1 4.8e-006 1.5e-001 # GTCAGAC GTCTGAC 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 4.5e-005 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 0.352941 0.647059 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AATGGTCW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AATGGTCW WGACCATT 28 0 2.9e-009 8.9e-005 # AATGGTCA TGACCATT 21 0 4.2e-007 1.3e-002 # AATGGTCT AGACCATT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 8.9e-005 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 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 0.750000 0.000000 0.000000 0.250000 MOTIF GCCWTAAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 26 0 1.2e-008 3.7e-004 # GCCATAAC GTTATGGC 14 0 5.8e-005 1.8e+000 # GCCTTAAC GTTAAGGC 12 0 2.3e-004 7.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.7e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.538462 0.000000 0.000000 0.461538 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 GTGATAGY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 33 3 8.5e-008 2.6e-003 # GTGATAGC GCTATCAC 19 2 1.0e-004 3.1e+000 # GTGATAGT ACTATCAC 15 1 2.4e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.6e-003 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 0.558824 0.000000 0.441176 MOTIF CCCWTGCA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCCWTGCA TGCAWGGG 22 0 2.1e-007 6.3e-003 # CCCATGCA TGCATGGG 14 0 5.8e-005 1.8e+000 # CCCTTGCA TGCAAGGG 9 0 1.9e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 6.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.608696 0.000000 0.000000 0.391304 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGSTCTCC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CGSTCTCC GGAGASCG 22 0 2.1e-007 6.3e-003 # CGGTCTCC GGAGACCG 12 0 2.3e-004 7.1e+000 # CGCTCTCC GGAGAGCG 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.3e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.545455 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 1.000000 0.000000 0.000000 MOTIF CACGCCC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CACGCCC GGGCGTG 25 1 3.4e-007 1.0e-002 # CACGCCC GGGCGTG 25 1 3.4e-007 1.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 1.0e-002 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 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 MOTIF ACTGAGCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 21 0 4.2e-007 1.3e-002 # ACTGAGCT AGCTCAGT 21 0 4.2e-007 1.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-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 0.000000 1.000000 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 0.000000 1.000000 MOTIF AWAATA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AWAATA TATTWT 275 187 6.5e-007 2.0e-002 # AAAATA TATTTT 189 132 2.2e-004 6.7e+000 # ATAATA TATTAT 118 73 3.2e-004 9.8e+000 letter-probability matrix: alength= 4 w= 6 nsites= 345 E= 2.0e-002 1.000000 0.000000 0.000000 0.000000 0.634783 0.000000 0.000000 0.365217 1.000000 0.000000 0.000000 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 MOTIF ACACTATA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 27 1 8.7e-008 2.6e-003 # ACACTATA TATAGTGT 27 1 8.7e-008 2.6e-003 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.6e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF SAAGA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 304 215 1.1e-006 3.2e-002 # CAAGA TCTTG 174 108 8.8e-006 2.6e-001 # GAAGA TCTTC 164 127 9.6e-003 2.9e+002 letter-probability matrix: alength= 4 w= 5 nsites= 390 E= 3.2e-002 0.000000 0.525641 0.474359 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 MOTIF CGACWAG DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CGACWAG CTWGTCG 30 3 5.6e-007 1.6e-002 # CGACTAG CTAGTCG 15 1 2.4e-004 7.1e+000 # CGACAAG CTTGTCG 15 2 1.1e-003 3.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 30 E= 1.6e-002 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 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TCCGTRCA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST TCCGTRCA TGYACGGA 19 0 1.7e-006 5.0e-002 # TCCGTGCA TGCACGGA 12 0 2.3e-004 6.8e+000 # TCCGTACA TGTACGGA 7 0 7.7e-003 2.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 5.0e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.368421 0.000000 0.631579 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 106.62 seconds