# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SRB8/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SRB8/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SRB8/seqs-shuffled # positives: 628 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SRB8/seqs-centered (Sat Jan 18 21:40:21 PST 2020) # negatives: 628 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SRB8/seqs-shuffled (Sat Jan 18 21:40:21 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 21:55:53 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 0.290 C 0.212 G 0.211 T 0.287 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 102 2 3.6e-030 1.1e-025 # GGGTTCGA TCGAACCC 46 2 1.9e-012 6.0e-008 # CGGTTCGA TCGAACCG 36 0 8.7e-012 2.7e-007 # GAGTTCGA TCGAACTC 11 0 4.7e-004 1.5e+001 # CAGTTCGA TCGAACTG 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 102 E= 1.1e-025 0.000000 0.441176 0.558824 0.000000 0.196078 0.000000 0.803922 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 1.000000 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 82 4 2.2e-021 6.9e-017 # TGTATGGG CCCATACA 36 0 8.7e-012 2.7e-007 # TGTACGGA TCCGTACA 30 1 1.1e-008 3.3e-004 # TGTACGGG CCCGTACA 12 1 1.6e-003 5.1e+001 # TGTATGGA TCCATACA 14 2 2.0e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 96 E= 6.9e-017 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 0.458333 0.000000 0.541667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.489583 0.000000 0.510417 0.000000 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 78 6 2.6e-018 7.9e-014 # CGCCTTA TAAGGCG 62 2 2.6e-017 7.9e-013 # CGCGTTA TAACGCG 16 4 5.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 7.9e-014 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 0.794872 0.205128 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 CTYGGCCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 57 2 8.9e-016 2.7e-011 # CTCGGCCA TGGCCGAG 35 1 3.4e-010 1.1e-005 # CTTGGCCA TGGCCAAG 22 1 2.4e-006 7.5e-002 letter-probability matrix: alength= 4 w= 8 nsites= 57 E= 2.7e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.614035 0.000000 0.385965 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 41 0 2.3e-013 7.2e-009 # GCGCTACC GGTAGCGC 26 0 1.1e-008 3.5e-004 # GCTCTACC GGTAGAGC 15 0 2.8e-005 8.7e-001 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 7.2e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.634146 0.365854 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 CTWGACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST CTWGACC GGTCWAG 50 5 4.7e-011 1.4e-006 # CTTGACC GGTCAAG 25 2 2.3e-006 7.1e-002 # CTAGACC GGTCTAG 25 3 1.1e-005 3.5e-001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 1.4e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF SAAGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST SAAGA TCTTS 316 203 6.1e-011 1.9e-006 # CAAGA TCTTG 175 111 1.1e-005 3.3e-001 # GAAGA TCTTC 184 120 1.6e-005 4.9e-001 letter-probability matrix: alength= 4 w= 5 nsites= 426 E= 1.9e-006 0.000000 0.483568 0.516432 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 ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 46 4 1.1e-010 3.2e-006 # ATGGCAAC GTTGCCAT 33 2 1.3e-008 3.7e-004 # ATGGCATC GATGCCAT 14 2 2.0e-003 5.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 3.2e-006 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 0.702128 0.000000 0.000000 0.297872 0.000000 1.000000 0.000000 0.000000 MOTIF ACACSCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ACACSCA TGSGTGT 52 7 3.0e-010 8.8e-006 # ACACCCA TGGGTGT 40 6 9.7e-008 2.9e-003 # ACACGCA TGCGTGT 12 1 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 8.8e-006 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 0.777778 0.222222 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTGATAGY DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GTGATAGY RCTATCAC 35 1 3.4e-010 1.0e-005 # GTGATAGC GCTATCAC 18 0 3.4e-006 9.9e-002 # GTGATAGT ACTATCAC 18 1 3.4e-005 1.0e+000 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 1.0e-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 0.500000 0.000000 0.500000 MOTIF CACGRTG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CACGRTG CAYCGTG 42 4 1.4e-009 4.2e-005 # CACGGTG CACCGTG 29 2 1.7e-007 5.1e-003 # CACGATG CATCGTG 13 2 3.5e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 42 E= 4.2e-005 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 0.309524 0.000000 0.690476 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AGTCAKAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 28 0 2.7e-009 8.1e-005 # AGTCAGAC GTCTGACT 14 0 5.7e-005 1.7e+000 # AGTCATAC GTATGACT 14 0 5.7e-005 1.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 8.1e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AGTGGTTW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTW WAACCACT 36 3 1.2e-008 3.4e-004 # AGTGGTTT AAACCACT 18 1 3.4e-005 1.0e+000 # AGTGGTTA TAACCACT 19 2 9.9e-005 2.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 3.4e-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 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 0.513514 0.000000 0.000000 0.486486 MOTIF CCAACWGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCAACWGA TCWGTTGG 26 1 1.6e-007 4.8e-003 # CCAACAGA TCTGTTGG 14 0 5.7e-005 1.7e+000 # CCAACTGA TCAGTTGG 12 1 1.6e-003 4.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.8e-003 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 0.000000 1.000000 0.000000 0.000000 0.538462 0.000000 0.000000 0.461538 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGYA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 43 8 2.1e-007 6.1e-003 # TGGCGTA TACGCCA 21 3 1.2e-004 3.6e+000 # TGGCGCA TGCGCCA 22 5 6.8e-004 2.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 6.1e-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 0.511628 0.000000 0.488372 1.000000 0.000000 0.000000 0.000000 MOTIF ACCCAVAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 25 1 3.2e-007 9.4e-003 # ACCCACAC GTGTGGGT 10 0 9.4e-004 2.8e+001 # ACCCAGAC GTCTGGGT 8 0 3.8e-003 1.1e+002 # ACCCAAAC GTTTGGGT 10 1 5.7e-003 1.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.4e-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 1.000000 0.000000 0.000000 0.000000 0.357143 0.357143 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF RCCGATGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST RCCGATGA TCATCGGY 20 0 8.2e-007 2.4e-002 # ACCGATGA TCATCGGT 12 0 2.3e-004 6.8e+000 # GCCGATGA TCATCGGC 8 0 3.8e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.4e-002 0.600000 0.000000 0.400000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAAAAAR DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAAAAAAR YTTTTTTT 77 30 1.2e-006 3.5e-002 # AAAAAAAA TTTTTTTT 63 24 9.1e-006 2.6e-001 # AAAAAAAG CTTTTTTT 45 18 3.3e-004 9.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 95 E= 3.5e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.642105 0.000000 0.357895 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 74.48 seconds