# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/seqs-shuffled # positives: 923 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/seqs-centered (Sun Jan 19 08:06:57 PST 2020) # negatives: 923 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/seqs-shuffled (Sun Jan 19 08:06:57 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 08:22:20 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 0.311 C 0.192 G 0.188 T 0.308 MOTIF CGCSTTA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 99 8 2.1e-022 7.0e-018 # CGCCTTA TAAGGCG 78 4 8.2e-020 2.8e-015 # CGCGTTA TAACGCG 21 4 4.2e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 99 E= 7.0e-018 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 0.787879 0.212121 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 CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 78 2 5.3e-022 1.8e-017 # CTCGGCCA TGGCCGAG 41 1 6.3e-012 2.1e-007 # CTTGGCCA TGGCCAAG 24 1 6.7e-007 2.3e-002 # CTGGGCCA TGGCCCAG 13 0 1.2e-004 3.9e+000 letter-probability matrix: alength= 4 w= 8 nsites= 78 E= 1.8e-017 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.525641 0.166667 0.307692 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 GGTTCGA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST GGTTCGA TCGAACC 90 7 1.2e-020 4.2e-016 # GGTTCGA TCGAACC 90 7 1.2e-020 4.2e-016 letter-probability matrix: alength= 4 w= 7 nsites= 90 E= 4.2e-016 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACCACKA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACKA TMGTGGT 77 10 8.4e-015 2.8e-010 # ACCACTA TAGTGGT 63 7 4.8e-013 1.6e-008 # ACCACGA TCGTGGT 15 3 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 2.8e-010 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.192308 0.807692 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGGYG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ATGGGYG CRCCCAT 69 8 5.6e-014 1.9e-009 # ATGGGTG CACCCAT 46 7 1.3e-008 4.4e-004 # ATGGGCG CGCCCAT 23 1 1.3e-006 4.4e-002 letter-probability matrix: alength= 4 w= 7 nsites= 71 E= 1.9e-009 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 1.000000 0.000000 0.000000 0.323944 0.000000 0.676056 0.000000 0.000000 1.000000 0.000000 MOTIF TCCGBACA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST TCCGBACA TGTVCGGA 49 2 3.2e-013 1.1e-008 # TCCGTACA TGTACGGA 32 1 3.1e-009 1.0e-004 # TCCGGACA TGTCCGGA 10 1 5.7e-003 1.9e+002 # TCCGCACA TGTGCGGA 7 0 7.7e-003 2.6e+002 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 1.1e-008 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 0.137255 0.196078 0.666667 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 45 2 4.9e-012 1.6e-007 # GCGCTACC GGTAGCGC 32 1 3.1e-009 1.0e-004 # GCTCTACC GGTAGAGC 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 45 E= 1.6e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.711111 0.288889 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-8 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 217 110 3.8e-011 1.3e-006 # TTTCTTG CAAGAAA 59 23 3.0e-005 1.0e+000 # TTTCTTT AAAGAAA 122 70 4.7e-005 1.5e+000 # TTTCTTC GAAGAAA 59 24 5.5e-005 1.8e+000 letter-probability matrix: alength= 4 w= 7 nsites= 254 E= 1.3e-006 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 0.232283 0.236220 0.531496 MOTIF ATGGCAWC DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 43 4 9.2e-010 3.0e-005 # ATGGCAAC GTTGCCAT 29 2 1.9e-007 6.3e-003 # ATGGCATC GATGCCAT 14 2 2.0e-003 6.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 3.0e-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 0.674419 0.000000 0.000000 0.325581 0.000000 1.000000 0.000000 0.000000 MOTIF CACGGYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CACGGYG CRCCGTG 42 5 8.5e-009 2.8e-004 # CACGGTG CACCGTG 29 4 4.6e-006 1.5e-001 # CACGGCG CGCCGTG 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 43 E= 2.8e-004 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 0.000000 1.000000 0.000000 0.000000 0.325581 0.000000 0.674419 0.000000 0.000000 1.000000 0.000000 MOTIF CCCAYACA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCCAYACA TGTRTGGG 50 9 1.7e-008 5.5e-004 # CCCACACA TGTGTGGG 32 6 1.0e-005 3.3e-001 # CCCATACA TGTATGGG 18 3 7.0e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 74 E= 5.5e-004 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 0.000000 0.756757 0.000000 0.243243 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CTATCAC GTGATAG 35 3 2.5e-008 8.3e-004 # CTATCAC GTGATAG 35 3 2.5e-008 8.3e-004 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 8.3e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GATTWGAA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 39 5 5.1e-008 1.7e-003 # GATTAGAA TTCTAATC 25 3 1.2e-005 4.0e-001 # GATTTGAA TTCAAATC 14 2 2.0e-003 6.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 1.7e-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 0.641026 0.000000 0.000000 0.358974 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 CCACACSC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCACACSC GSGTGTGG 40 6 1.1e-007 3.7e-003 # CCACACGC GCGTGTGG 21 0 4.3e-007 1.4e-002 # CCACACCC GGGTGTGG 19 6 7.0e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 3.7e-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 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 0.580000 0.420000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 32 3 1.7e-007 5.5e-003 # ATCGTGAG CTCACGAT 19 1 1.8e-005 6.0e-001 # ATCTTGAG CTCAAGAT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.5e-003 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 0.593750 0.406250 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 AYTCTCG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AYTCTCG CGAGART 45 9 2.6e-007 8.4e-003 # ATTCTCG CGAGAAT 28 5 2.9e-005 9.4e-001 # ACTCTCG CGAGAGT 17 4 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 7 nsites= 45 E= 8.4e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.377778 0.000000 0.622222 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 0.000000 1.000000 0.000000 MOTIF CTGAGCTA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CTGAGCTA TAGCTCAG 25 1 3.5e-007 1.1e-002 # CTGAGCTA TAGCTCAG 25 1 3.5e-007 1.1e-002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 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 1.000000 0.000000 0.000000 0.000000 MOTIF CAWATATA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CAWATATA TATATWTG 40 7 4.0e-007 1.3e-002 # CATATATA TATATATG 23 3 4.0e-005 1.3e+000 # CAAATATA TATATTTG 17 4 3.4e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.3e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.404762 0.000000 0.000000 0.595238 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCKCCCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TCKCCCA TGGGMGA 38 7 1.2e-006 3.9e-002 # TCGCCCA TGGGCGA 19 2 1.0e-004 3.4e+000 # TCTCCCA TGGGAGA 19 5 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 3.9e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 ACCACTTK DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ACCACTTK MAAGTGGT 26 2 1.3e-006 4.2e-002 # ACCACTTG CAAGTGGT 17 2 3.4e-004 1.1e+001 # ACCACTTT AAAGTGGT 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 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 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 0.000000 1.000000 0.000000 0.000000 0.653846 0.346154 # Stopping reason: E-value threshold exceeded # Running time: 117.07 seconds