# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CUP9/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CUP9/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CUP9/seqs-shuffled # positives: 825 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CUP9/seqs-centered (Sat Jan 18 11:54:43 PST 2020) # negatives: 825 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--CUP9/seqs-shuffled (Sat Jan 18 11:54:43 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 12:09:08 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 0.297 C 0.203 G 0.198 T 0.302 MOTIF GRNTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRNTCGAA TTCGANYC 134 17 5.2e-026 1.7e-021 # GGATCGAA TTCGATCC 31 3 3.0e-007 1.0e-002 # GAGTCGAA TTCGACTC 20 0 8.5e-007 2.8e-002 # GGCTCGAA TTCGAGCC 15 1 2.5e-004 8.1e+000 # GAATCGAA TTCGATTC 23 5 4.1e-004 1.4e+001 # GGGTCGAA TTCGACCC 13 1 8.8e-004 2.9e+001 # GACTCGAA TTCGAGTC 9 0 1.9e-003 6.3e+001 # GATTCGAA TTCGAATC 15 3 3.6e-003 1.2e+002 # GGTTCGAA TTCGAACC 16 4 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 134 E= 1.7e-021 0.000000 0.000000 1.000000 0.000000 0.485075 0.000000 0.514925 0.000000 0.402985 0.179104 0.246269 0.171642 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 1.000000 0.000000 0.000000 0.000000 MOTIF CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 71 1 3.3e-021 1.1e-016 # CCATACAT ATGTATGG 41 0 2.7e-013 8.9e-009 # CCGTACAT ATGTACGG 19 0 1.7e-006 5.6e-002 # CCATACAC GTGTATGG 8 0 3.8e-003 1.3e+002 # CCGTACAC GTGTACGG 10 1 5.7e-003 1.9e+002 letter-probability matrix: alength= 4 w= 8 nsites= 84 E= 1.1e-016 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.630952 0.000000 0.369048 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.226190 0.000000 0.773810 MOTIF CCWTAMC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCWTAMC GKTAWGG 123 27 1.8e-017 5.9e-013 # CCTTAAC GTTAAGG 38 8 3.5e-006 1.1e-001 # CCTTACC GGTAAGG 33 6 5.7e-006 1.9e-001 # CCATACC GGTATGG 28 7 2.2e-004 7.2e+000 # CCATAAC GTTATGG 26 7 5.9e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 126 E= 5.9e-013 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.436508 0.000000 0.000000 0.563492 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.507937 0.492063 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACTBGGCC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 52 1 2.7e-015 8.7e-011 # ACTTGGCC GGCCAAGT 27 1 8.8e-008 2.9e-003 # ACTCGGCC GGCCGAGT 21 0 4.2e-007 1.4e-002 # ACTGGGCC GGCCCAGT 12 0 2.3e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 8.7e-011 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 0.346154 0.230769 0.423077 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 AARAAAAW DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AARAAAAW WTTTTYTT 181 76 4.5e-013 1.4e-008 # AAGAAAAT ATTTTCTT 37 7 2.0e-006 6.5e-002 # AAAAAAAA TTTTTTTT 77 34 1.5e-005 4.9e-001 # AAAAAAAT ATTTTTTT 78 38 7.6e-005 2.5e+000 # AAGAAAAA TTTTTCTT 52 21 1.4e-004 4.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 206 E= 1.4e-008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.572816 0.000000 0.427184 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 0.524272 0.000000 0.000000 0.475728 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 39 1 2.4e-011 7.7e-007 # GCGCTACC GGTAGCGC 27 1 8.8e-008 2.8e-003 # GCTCTACC GGTAGAGC 12 0 2.3e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 7.7e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.692308 0.307692 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 TAGTGGTW DREME-7 # Word RC Word Pos Neg P-value E-value # BEST TAGTGGTW WACCACTA 41 3 5.2e-010 1.7e-005 # TAGTGGTA TACCACTA 23 2 8.5e-006 2.7e-001 # TAGTGGTT AACCACTA 18 1 3.5e-005 1.1e+000 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 1.7e-005 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 0.560976 0.000000 0.000000 0.439024 MOTIF AGAYCGGG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGGG CCCGRTCT 28 0 3.0e-009 9.5e-005 # AGATCGGG CCCGATCT 16 0 1.4e-005 4.5e-001 # AGACCGGG CCCGGTCT 12 0 2.3e-004 7.5e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.5e-005 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 0.428571 0.000000 0.571429 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 1.000000 0.000000 MOTIF CGRTGAAA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CGRTGAAA TTTCAYCG 28 0 3.0e-009 9.5e-005 # CGGTGAAA TTTCACCG 19 0 1.7e-006 5.5e-002 # CGATGAAA TTTCATCG 16 0 1.4e-005 4.5e-001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 9.5e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.321429 0.000000 0.678571 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AMAAAGCA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AMAAAGCA TGCTTTKT 47 7 7.0e-009 2.2e-004 # ACAAAGCA TGCTTTGT 31 3 3.0e-007 9.7e-003 # AAAAAGCA TGCTTTTT 16 4 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 2.2e-004 1.000000 0.000000 0.000000 0.000000 0.326531 0.673469 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CSGAAAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CSGAAAC GTTTCSG 44 6 1.0e-008 3.3e-004 # CGGAAAC GTTTCCG 22 1 2.5e-006 8.0e-002 # CCGAAAC GTTTCGG 22 5 6.9e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 3.3e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 0.000000 1.000000 0.000000 0.000000 MOTIF GTTGCYA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GTTGCYA TRGCAAC 59 15 6.9e-008 2.2e-003 # GTTGCCA TGGCAAC 35 7 5.9e-006 1.9e-001 # GTTGCTA TAGCAAC 24 8 3.2e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 59 E= 2.2e-003 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.593220 0.000000 0.406780 1.000000 0.000000 0.000000 0.000000 MOTIF CRCCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 139 68 7.8e-008 2.5e-003 # CACCCA TGGGTG 93 47 3.1e-005 9.8e-001 # CGCCCA TGGGCG 47 21 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 6 nsites= 206 E= 2.5e-003 0.000000 1.000000 0.000000 0.000000 0.766990 0.000000 0.233010 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 GCACGGW DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCACGGW WCCGTGC 35 4 1.3e-007 3.9e-003 # GCACGGA TCCGTGC 21 3 1.3e-004 4.0e+000 # GCACGGT ACCGTGC 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 37 E= 3.9e-003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.621622 0.000000 0.000000 0.378378 MOTIF AGAGGTKA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGAGGTKA TMACCTCT 22 0 2.1e-007 6.5e-003 # AGAGGTGA TCACCTCT 15 0 2.9e-005 9.0e-001 # AGAGGTTA TAACCTCT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.5e-003 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 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 0.681818 0.318182 1.000000 0.000000 0.000000 0.000000 MOTIF AGAYTATG DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGAYTATG CATARTCT 34 4 2.3e-007 7.2e-003 # AGATTATG CATAATCT 22 3 7.0e-005 2.2e+000 # AGACTATG CATAGTCT 12 1 1.7e-003 5.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 7.2e-003 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 0.352941 0.000000 0.647059 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 0.000000 1.000000 0.000000 MOTIF AGAWGC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AGAWGC GCWTCT 102 45 5.0e-007 1.6e-002 # AGAAGC GCTTCT 60 23 1.9e-005 6.0e-001 # AGATGC GCATCT 42 22 7.4e-003 2.3e+002 letter-probability matrix: alength= 4 w= 6 nsites= 103 E= 1.6e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.582524 0.000000 0.000000 0.417476 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCAKCGG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST ATCAKCGG CCGMTGAT 24 1 6.6e-007 2.1e-002 # ATCATCGG CCGATGAT 12 0 2.3e-004 7.3e+000 # ATCAGCGG CCGCTGAT 12 1 1.7e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 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 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGCCASAC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CGCCASAC GTSTGGCG 20 0 8.5e-007 2.6e-002 # CGCCACAC GTGTGGCG 13 0 1.2e-004 3.6e+000 # CGCCAGAC GTCTGGCG 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.650000 0.350000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTAGARG DREME-20 # Word RC Word Pos Neg P-value E-value # BEST ATTAGARG CYTCTAAT 26 2 1.3e-006 4.0e-002 # ATTAGAAG CTTCTAAT 14 1 4.7e-004 1.4e+001 # ATTAGAGG CCTCTAAT 12 1 1.7e-003 5.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-002 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.538462 0.000000 0.461538 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CACTTKCG DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CACTTKCG CGMAAGTG 26 2 1.3e-006 4.0e-002 # CACTTGCG CGCAAGTG 11 0 4.7e-004 1.5e+001 # CACTTTCG CGAAAGTG 15 2 1.1e-003 3.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.423077 0.576923 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CACTATA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST CACTATA TATAGTG 23 1 1.3e-006 4.0e-002 # CACTATA TATAGTG 23 1 1.3e-006 4.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 4.0e-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 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 # Stopping reason: E-value threshold exceeded # Running time: 111.87 seconds