# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--GAL11/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--GAL11/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--GAL11/seqs-shuffled # positives: 738 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--GAL11/seqs-centered (Sat Jan 18 11:29:09 PST 2020) # negatives: 738 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--GAL11/seqs-shuffled (Sat Jan 18 11:29:09 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 11:51:08 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 0.298 C 0.201 G 0.205 T 0.296 MOTIF SGGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SGGTTCGA TCGAACCS 64 0 1.3e-020 4.3e-016 # GGGTTCGA TCGAACCC 42 0 1.2e-013 4.2e-009 # CGGTTCGA TCGAACCG 22 0 2.0e-007 6.8e-003 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 4.3e-016 0.000000 0.343750 0.656250 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 TGTAYGGR DREME-2 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 71 6 3.8e-016 1.3e-011 # TGTACGGA TCCGTACA 27 1 8.6e-008 2.9e-003 # TGTATGGG CCCATACA 30 3 5.5e-007 1.8e-002 # TGTACGGG CCCGTACA 10 0 9.5e-004 3.2e+001 # TGTATGGA TCCATACA 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 1.3e-011 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 0.475610 0.000000 0.524390 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.512195 0.000000 0.487805 0.000000 MOTIF CTYGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 53 1 1.2e-015 4.0e-011 # CTCGGCCA TGGCCGAG 31 1 5.7e-009 1.9e-004 # CTTGGCCA TGGCCAAG 22 0 2.0e-007 6.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 53 E= 4.0e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.584906 0.000000 0.415094 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 CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 75 12 3.3e-013 1.1e-008 # CGCCTTA TAAGGCG 59 8 2.0e-011 6.8e-007 # CGCGTTA TAACGCG 16 4 5.6e-003 1.9e+002 letter-probability matrix: alength= 4 w= 7 nsites= 75 E= 1.1e-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 0.786667 0.213333 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 AARAAA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AARAAA TTTYTT 372 241 2.8e-012 9.4e-008 # AAAAAA TTTTTT 250 155 1.9e-008 6.2e-004 # AAGAAA TTTCTT 200 131 1.0e-005 3.4e-001 letter-probability matrix: alength= 4 w= 6 nsites= 543 E= 9.4e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600368 0.000000 0.399632 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 ATGGCAWC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 36 0 9.4e-012 3.1e-007 # ATGGCAAC GTTGCCAT 26 0 1.2e-008 3.9e-004 # ATGGCATC GATGCCAT 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 3.1e-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 0.722222 0.000000 0.000000 0.277778 0.000000 1.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 1 1.1e-011 3.7e-007 # GCGCTACC GGTAGCGC 27 1 8.6e-008 2.8e-003 # GCTCTACC GGTAGAGC 13 0 1.2e-004 3.8e+000 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.7e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.675000 0.325000 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 CTATCACR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 33 1 1.4e-009 4.7e-005 # CTATCACA TGTGATAG 17 0 7.0e-006 2.3e-001 # CTATCACG CGTGATAG 16 1 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 4.7e-005 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 0.515152 0.000000 0.484848 0.000000 MOTIF CACGGTGM DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 26 0 1.2e-008 3.9e-004 # CACGGTGA TCACCGTG 15 0 2.8e-005 9.2e-001 # CACGGTGC GCACCGTG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 3.9e-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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.576923 0.423077 0.000000 0.000000 MOTIF TAGTGGTW DREME-10 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 37 4 3.5e-008 1.1e-003 # TAGTGGTA TACCACTA 21 0 4.1e-007 1.3e-002 # TAGTGGTT AACCACTA 16 4 5.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 37 E= 1.1e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.567568 0.000000 0.000000 0.432432 MOTIF CRCCCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 104 44 1.1e-007 3.7e-003 # CGCCCA TGGGCG 49 16 1.7e-005 5.6e-001 # CACCCA TGGGTG 56 30 2.6e-003 8.4e+001 letter-probability matrix: alength= 4 w= 6 nsites= 121 E= 3.7e-003 0.000000 1.000000 0.000000 0.000000 0.570248 0.000000 0.429752 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 MOTIF TGGCGYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 44 8 1.3e-007 4.1e-003 # TGGCGCA TGCGCCA 24 4 7.9e-005 2.5e+000 # TGGCGTA TACGCCA 20 4 7.1e-004 2.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 4.1e-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 0.545455 0.000000 0.454545 1.000000 0.000000 0.000000 0.000000 MOTIF AGTCAKAC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 26 1 1.7e-007 5.4e-003 # AGTCATAC GTATGACT 15 0 2.8e-005 9.1e-001 # AGTCAGAC GTCTGACT 11 1 3.1e-003 9.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 5.4e-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 0.423077 0.576923 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AKCGTGA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AKCGTGA TCACGMT 35 5 5.1e-007 1.6e-002 # AGCGTGA TCACGCT 17 1 6.7e-005 2.1e+000 # ATCGTGA TCACGAT 18 4 2.0e-003 6.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 1.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.485714 0.514286 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 1.000000 0.000000 0.000000 0.000000 MOTIF AACCRACT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AACCRACT AGTYGGTT 27 2 6.6e-007 2.1e-002 # AACCAACT AGTTGGTT 17 1 6.7e-005 2.1e+000 # AACCGACT AGTCGGTT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.1e-002 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 0.000000 0.629630 0.000000 0.370370 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 # Stopping reason: E-value threshold exceeded # Running time: 197.60 seconds