# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--THP2/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--THP2/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--THP2/seqs-shuffled # positives: 939 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--THP2/seqs-centered (Sun Jan 19 03:33:04 PST 2020) # negatives: 939 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--THP2/seqs-shuffled (Sun Jan 19 03:33:04 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 03:43:54 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 0.303 C 0.197 G 0.196 T 0.304 MOTIF CAKCWTC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST CAKCWTC GAWGMTG 114 24 1.6e-016 5.2e-012 # CAGCTTC GAAGCTG 38 4 2.1e-008 6.9e-004 # CATCTTC GAAGATG 40 8 1.3e-006 4.2e-002 # CATCATC GATGATG 32 10 4.1e-004 1.4e+001 # CAGCATC GATGCTG 16 2 6.2e-004 2.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 124 E= 5.2e-012 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.435484 0.564516 0.000000 1.000000 0.000000 0.000000 0.362903 0.000000 0.000000 0.637097 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CTTCHA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTTCHA TDGAAG 298 157 1.6e-014 5.4e-010 # CTTCAA TTGAAG 153 75 2.1e-008 6.8e-004 # CTTCCA TGGAAG 90 40 3.3e-006 1.1e-001 # CTTCTA TAGAAG 88 53 1.4e-003 4.6e+001 letter-probability matrix: alength= 4 w= 6 nsites= 352 E= 5.4e-010 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 1.000000 0.000000 0.000000 0.468750 0.275568 0.000000 0.255682 1.000000 0.000000 0.000000 0.000000 MOTIF WTACCR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST WTACCR YGGTAW 256 124 1.6e-014 5.4e-010 # TTACCG CGGTAA 63 19 3.4e-007 1.1e-002 # ATACCA TGGTAT 85 34 7.8e-007 2.6e-002 # TTACCA TGGTAA 98 57 3.8e-004 1.2e+001 # ATACCG CGGTAT 36 16 3.5e-003 1.1e+002 letter-probability matrix: alength= 4 w= 6 nsites= 288 E= 5.4e-010 0.437500 0.000000 0.000000 0.562500 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 0.656250 0.000000 0.343750 0.000000 MOTIF TGGCCRA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TGGCCRA TYGGCCA 54 10 5.9e-009 1.9e-004 # TGGCCGA TCGGCCA 25 0 2.5e-008 8.2e-004 # TGGCCAA TTGGCCA 29 10 1.5e-003 4.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 1.9e-004 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 1.000000 0.000000 0.000000 0.537037 0.000000 0.462963 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CSAACCAG DREME-5 # Word RC Word Pos Neg P-value E-value # BEST CSAACCAG CTGGTTSG 31 1 6.1e-009 2.0e-004 # CCAACCAG CTGGTTGG 15 0 2.9e-005 9.3e-001 # CGAACCAG CTGGTTCG 16 1 1.3e-004 4.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.0e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.483871 0.516129 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 30 1 1.2e-008 3.8e-004 # GCTCTACC GGTAGAGC 20 1 9.6e-006 3.1e-001 # GCGCTACC GGTAGCGC 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.8e-004 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.666667 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 CGCCTTAR DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCCTTAR YTAAGGCG 26 0 1.3e-008 4.0e-004 # CGCCTTAA TTAAGGCG 18 0 3.5e-006 1.1e-001 # CGCCTTAG CTAAGGCG 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.692308 0.000000 0.307692 0.000000 MOTIF GVTGCCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GVTGCCA TGGCABC 61 15 2.8e-008 8.8e-004 # GATGCCA TGGCATC 30 8 2.1e-004 6.6e+000 # GGTGCCA TGGCACC 14 2 2.0e-003 6.5e+001 # GCTGCCA TGGCAGC 17 5 8.1e-003 2.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 62 E= 8.8e-004 0.000000 0.000000 1.000000 0.000000 0.483871 0.274194 0.241935 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CSAAGA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CSAAGA TCTTSG 125 56 3.8e-008 1.2e-003 # CCAAGA TCTTGG 79 38 5.8e-005 1.9e+000 # CGAAGA TCTTCG 51 19 6.3e-005 2.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 138 E= 1.2e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.623188 0.376812 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 CSGCTAC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CSGCTAC GTAGCSG 24 0 5.1e-008 1.6e-003 # CCGCTAC GTAGCGG 15 0 2.9e-005 9.1e-001 # CGGCTAC GTAGCCG 9 0 1.9e-003 6.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 24 E= 1.6e-003 0.000000 1.000000 0.000000 0.000000 0.000000 0.625000 0.375000 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 0.000000 1.000000 0.000000 0.000000 MOTIF ACCCABAC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACCCABAC GTVTGGGT 45 8 8.2e-008 2.6e-003 # ACCCATAC GTATGGGT 16 1 1.3e-004 4.1e+000 # ACCCAGAC GTCTGGGT 21 6 2.8e-003 8.8e+001 # ACCCACAC GTGTGGGT 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 2.6e-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 0.000000 0.224490 0.428571 0.346939 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATTTAGCM DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATTTAGCM KGCTAAAT 29 2 1.9e-007 6.0e-003 # ATTTAGCC GGCTAAAT 15 1 2.5e-004 7.8e+000 # ATTTAGCA TGCTAAAT 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.0e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.482759 0.517241 0.000000 0.000000 MOTIF CCTTAGC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCTTAGC GCTAAGG 31 3 3.1e-007 9.8e-003 # CCTTAGC GCTAAGG 31 3 3.1e-007 9.8e-003 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 9.8e-003 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AATAYTAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AATAYTAC GTARTATT 25 1 3.5e-007 1.1e-002 # AATATTAC GTAATATT 18 1 3.5e-005 1.1e+000 # AATACTAC GTAGTATT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-002 1.000000 0.000000 0.000000 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 0.280000 0.000000 0.720000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AYCGATGA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AYCGATGA TCATCGRT 21 0 4.3e-007 1.3e-002 # ATCGATGA TCATCGAT 12 0 2.4e-004 7.4e+000 # ACCGATGA TCATCGGT 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-002 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 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 ACCAMTAC DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACCAMTAC GTAKTGGT 20 0 8.6e-007 2.7e-002 # ACCACTAC GTAGTGGT 13 0 1.2e-004 3.7e+000 # ACCAATAC GTATTGGT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-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 0.350000 0.650000 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 MOTIF ATGYACGG DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ATGYACGG CCGTRCAT 20 0 8.6e-007 2.7e-002 # ATGTACGG CCGTACAT 15 0 2.9e-005 9.0e-001 # ATGCACGG CCGTGCAT 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 2.7e-002 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 0.318182 0.000000 0.681818 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 MOTIF TTTTGGW DREME-18 # Word RC Word Pos Neg P-value E-value # BEST TTTTGGW WCCAAAA 103 47 1.1e-006 3.5e-002 # TTTTGGA TCCAAAA 52 23 4.3e-004 1.3e+001 # TTTTGGT ACCAAAA 51 24 1.0e-003 3.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 104 E= 3.5e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.509615 0.000000 0.000000 0.490385 MOTIF ATCRGAAA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ATCRGAAA TTTCYGAT 26 2 1.3e-006 4.1e-002 # ATCGGAAA TTTCCGAT 11 0 4.7e-004 1.5e+001 # ATCAGAAA TTTCTGAT 15 2 1.1e-003 3.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.1e-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 0.576923 0.000000 0.423077 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 MOTIF SATCGTGA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST SATCGTGA TCACGATS 23 1 1.3e-006 4.1e-002 # CATCGTGA TCACGATG 16 1 1.3e-004 4.0e+000 # GATCGTGA TCACGATC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.1e-002 0.000000 0.695652 0.304348 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 # Stopping reason: E-value threshold exceeded # Running time: 118.82 seconds