# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/seqs-shuffled # positives: 449 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/seqs-centered (Sun Jan 19 05:17:14 PST 2020) # negatives: 449 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/seqs-shuffled (Sun Jan 19 05:17:14 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 05:25:35 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 0.299 C 0.203 G 0.199 T 0.299 MOTIF TGTAYGGR DREME-1 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 80 2 1.8e-023 4.6e-019 # TGTACGGA TCCGTACA 33 0 6.3e-011 1.7e-006 # TGTATGGG CCCATACA 35 1 2.8e-010 7.3e-006 # TGTACGGG CCCGTACA 10 0 9.3e-004 2.4e+001 # TGTATGGA TCCATACA 12 1 1.6e-003 4.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 94 E= 4.6e-019 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 0.478723 0.000000 0.521277 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.510638 0.000000 0.489362 0.000000 MOTIF CTYGGCC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCC GGCCRAG 65 1 8.0e-020 2.1e-015 # CTTGGCC GGCCAAG 40 0 3.7e-013 9.5e-009 # CTCGGCC GGCCGAG 33 1 1.1e-009 3.0e-005 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 2.1e-015 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.446154 0.000000 0.553846 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 MOTIF CGCSTTA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 73 6 3.3e-017 8.6e-013 # CGCCTTA TAAGGCG 61 4 2.9e-015 7.4e-011 # CGCGTTA TAACGCG 12 2 6.1e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 73 E= 8.6e-013 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 0.835616 0.164384 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 ACCACKA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACCACKA TMGTGGT 56 2 1.1e-015 2.8e-011 # ACCACTA TAGTGGT 44 1 4.5e-013 1.2e-008 # ACCACGA TCGTGGT 13 1 8.5e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 57 E= 2.8e-011 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 0.228070 0.771930 1.000000 0.000000 0.000000 0.000000 MOTIF ACACSC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ACACSC GSGTGT 81 19 1.2e-011 3.2e-007 # ACACCC GGGTGT 52 13 2.4e-007 6.0e-003 # ACACGC GCGTGT 30 6 2.5e-005 6.4e-001 letter-probability matrix: alength= 4 w= 6 nsites= 88 E= 3.2e-007 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 0.659091 0.340909 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 39 1 1.6e-011 4.1e-007 # ATGGCAAC GTTGCCAT 28 0 2.4e-009 6.1e-005 # ATGGCATC GATGCCAT 11 1 3.0e-003 7.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 4.1e-007 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 0.717949 0.000000 0.000000 0.282051 0.000000 1.000000 0.000000 0.000000 MOTIF SGGTTCGA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 44 3 4.7e-011 1.2e-006 # GGGTTCGA TCGAACCC 29 1 1.9e-008 4.7e-004 # CGGTTCGA TCGAACCG 15 2 1.1e-003 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.2e-006 0.000000 0.340909 0.659091 0.000000 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 0.000000 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-8 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 37 1 6.8e-011 1.7e-006 # GCGCTACC GGTAGCGC 25 0 2.1e-008 5.3e-004 # GCTCTACC GGTAGAGC 12 1 1.6e-003 4.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.7e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.675676 0.324324 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 ATAGTKTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 34 1 5.7e-010 1.4e-005 # ATAGTGTA TACACTAT 19 1 1.7e-005 4.2e-001 # ATAGTTTA TAAACTAT 15 0 2.7e-005 6.8e-001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.4e-005 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.558824 0.441176 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGCTCAG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGCTCAG CTGAGCT 25 0 2.1e-008 5.3e-004 # AGCTCAG CTGAGCT 25 0 2.1e-008 5.3e-004 letter-probability matrix: alength= 4 w= 7 nsites= 25 E= 5.3e-004 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF AAGCGWGA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST AAGCGWGA TCWCGCTT 24 0 4.3e-008 1.1e-003 # AAGCGTGA TCACGCTT 14 0 5.5e-005 1.4e+000 # AAGCGAGA TCTCGCTT 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-003 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 0.416667 0.000000 0.000000 0.583333 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGCGCMAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGCGCMAG CTKGCGCT 24 0 4.3e-008 1.1e-003 # AGCGCAAG CTTGCGCT 14 0 5.5e-005 1.4e+000 # AGCGCCAG CTGGCGCT 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.1e-003 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 0.000000 1.000000 0.000000 0.000000 0.583333 0.416667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CACCGTGS DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CACCGTGS SCACGGTG 23 0 8.9e-008 2.2e-003 # CACCGTGG CCACGGTG 13 0 1.1e-004 2.8e+000 # CACCGTGC GCACGGTG 10 0 9.3e-004 2.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 2.2e-003 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 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 0.434783 0.565217 0.000000 MOTIF AGTCAKAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 1 1.5e-007 3.7e-003 # AGTCAGAC GTCTGACT 13 0 1.1e-004 2.8e+000 # AGTCATAC GTATGACT 13 1 8.5e-004 2.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.7e-003 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 ATGGGBG DREME-15 # Word RC Word Pos Neg P-value E-value # BEST ATGGGBG CVCCCAT 34 4 1.8e-007 4.5e-003 # ATGGGCG CGCCCAT 12 1 1.6e-003 4.0e+001 # ATGGGTG CACCCAT 13 2 3.5e-003 8.6e+001 # ATGGGGG CCCCCAT 10 1 5.6e-003 1.4e+002 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 4.5e-003 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 0.342857 0.285714 0.371429 0.000000 0.000000 1.000000 0.000000 MOTIF AAGAAAWA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AAGAAAWA TWTTTCTT 43 9 5.2e-007 1.3e-002 # AAGAAATA TATTTCTT 16 1 1.2e-004 3.0e+000 # AAGAAAAA TTTTTCTT 28 8 4.8e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 1.3e-002 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 0.636364 0.000000 0.000000 0.363636 1.000000 0.000000 0.000000 0.000000 MOTIF CGCGTGSC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CGCGTGSC GSCACGCG 19 0 1.6e-006 3.9e-002 # CGCGTGGC GCCACGCG 11 0 4.6e-004 1.1e+001 # CGCGTGCC GGCACGCG 8 0 3.8e-003 9.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 3.9e-002 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.421053 0.578947 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 53.39 seconds