# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/seqs-shuffled # positives: 908 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/seqs-centered (Sat Jan 18 08:36:31 PST 2020) # negatives: 908 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/seqs-shuffled (Sat Jan 18 08:36:31 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 08:51:49 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 0.292 C 0.210 G 0.206 T 0.291 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 143 23 1.5e-024 5.3e-020 # GGTTCGA TCGAACC 107 11 2.2e-022 7.7e-018 # GGTTCAA TTGAACC 38 12 1.3e-004 4.5e+000 letter-probability matrix: alength= 4 w= 7 nsites= 145 E= 5.3e-020 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 0.262069 0.000000 0.737931 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ATGTAHGG DREME-2 # Word RC Word Pos Neg P-value E-value # BEST ATGTAHGG CCDTACAT 75 2 4.4e-021 1.6e-016 # ATGTATGG CCATACAT 39 1 2.5e-011 8.9e-007 # ATGTACGG CCGTACAT 35 1 3.9e-010 1.4e-005 # ATGTAAGG CCTTACAT 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 86 E= 1.6e-016 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 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.081395 0.430233 0.000000 0.488372 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 73 5 2.0e-017 7.1e-013 # CTCGGCCA TGGCCGAG 37 2 1.0e-009 3.6e-005 # CTTGGCCA TGGCCAAG 23 2 8.6e-006 3.1e-001 # CTGGGCCA TGGCCCAG 13 1 8.8e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 73 E= 7.1e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.506849 0.178082 0.315068 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 TTTCTTB DREME-4 # Word RC Word Pos Neg P-value E-value # BEST TTTCTTB VAAGAAA 200 77 3.3e-016 1.2e-011 # TTTCTTG CAAGAAA 56 15 3.2e-007 1.1e-002 # TTTCTTC GAAGAAA 69 23 4.5e-007 1.6e-002 # TTTCTTT AAAGAAA 98 46 3.9e-006 1.4e-001 letter-probability matrix: alength= 4 w= 7 nsites= 231 E= 1.2e-011 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 0.303030 0.242424 0.454545 MOTIF TAAGGCR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TAAGGCR YGCCTTA 91 16 6.3e-015 2.2e-010 # TAAGGCG CGCCTTA 69 10 1.0e-012 3.6e-008 # TAAGGCA TGCCTTA 25 6 4.0e-004 1.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 2.2e-010 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.265957 0.000000 0.734043 0.000000 MOTIF AGTGGTWW DREME-6 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWW WWACCACT 68 8 1.0e-013 3.5e-009 # AGTGGTTA TAACCACT 29 1 2.3e-008 8.2e-004 # AGTGGTAT ATACCACT 20 1 9.5e-006 3.3e-001 # AGTGGTAA TTACCACT 18 3 7.0e-004 2.5e+001 # AGTGGTTT AAACCACT 16 3 2.1e-003 7.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 83 E= 3.5e-009 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 0.457831 0.000000 0.000000 0.542169 0.566265 0.000000 0.000000 0.433735 MOTIF GCKCTACC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 51 3 7.7e-013 2.7e-008 # GCGCTACC GGTAGCGC 36 2 2.0e-009 6.9e-005 # GCTCTACC GGTAGAGC 15 1 2.5e-004 8.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 2.7e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.705882 0.294118 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 ATGGCAWC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 47 2 1.2e-012 4.3e-008 # ATGGCAAC GTTGCCAT 27 1 9.0e-008 3.1e-003 # ATGGCATC GATGCCAT 20 1 9.5e-006 3.3e-001 letter-probability matrix: alength= 4 w= 8 nsites= 47 E= 4.3e-008 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 0.574468 0.000000 0.000000 0.425532 0.000000 1.000000 0.000000 0.000000 MOTIF CACCCAK DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACCCAK MTGGGTG 63 9 9.2e-012 3.2e-007 # CACCCAT ATGGGTG 47 4 7.2e-011 2.5e-006 # CACCCAG CTGGGTG 18 5 5.1e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 67 E= 3.2e-007 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.283582 0.716418 MOTIF CTATCACR DREME-10 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 34 1 7.8e-010 2.7e-005 # CTATCACA TGTGATAG 17 0 7.1e-006 2.5e-001 # CTATCACG CGTGATAG 17 1 6.8e-005 2.4e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.7e-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 0.500000 0.000000 0.500000 0.000000 MOTIF ATCKTGAG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 29 0 1.5e-009 5.1e-005 # ATCGTGAG CTCACGAT 20 0 8.6e-007 3.0e-002 # ATCTTGAG CTCAAGAT 9 0 1.9e-003 6.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 5.1e-005 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 0.689655 0.310345 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 ATTAASAG DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ATTAASAG CTSTTAAT 36 2 2.0e-009 6.8e-005 # ATTAAGAG CTCTTAAT 24 1 6.7e-007 2.3e-002 # ATTAACAG CTGTTAAT 12 1 1.7e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 36 E= 6.8e-005 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 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 0.000000 MOTIF CTATATCK DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTATATCK MGATATAG 28 1 4.6e-008 1.6e-003 # CTATATCT AGATATAG 16 1 1.3e-004 4.5e+000 # CTATATCG CGATATAG 12 0 2.4e-004 8.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.6e-003 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.571429 MOTIF CCGGWCTC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CCGGWCTC GAGWCCGG 24 0 5.1e-008 1.8e-003 # CCGGTCTC GAGACCGG 16 0 1.4e-005 4.9e-001 # CCGGACTC GAGTCCGG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.8e-003 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 0.333333 0.000000 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CASACGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CASACGC GCGTSTG 50 10 5.2e-008 1.8e-003 # CAGACGC GCGTCTG 23 4 1.4e-004 4.9e+000 # CACACGC GCGTGTG 27 6 1.4e-004 5.0e+000 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 1.8e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.540000 0.460000 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 MOTIF GKGGCCCA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST GKGGCCCA TGGGCCMC 23 0 1.0e-007 3.6e-003 # GGGGCCCA TGGGCCCC 16 0 1.4e-005 4.9e-001 # GTGGCCCA TGGGCCAC 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.6e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.695652 0.304348 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCAACWGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CCAACWGA TCWGTTGG 29 2 1.9e-007 6.5e-003 # CCAACAGA TCTGTTGG 15 1 2.5e-004 8.5e+000 # CCAACTGA TCAGTTGG 14 1 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.5e-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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.517241 0.000000 0.000000 0.482759 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TGGCGCAR DREME-18 # Word RC Word Pos Neg P-value E-value # BEST TGGCGCAR YTGCGCCA 29 2 1.9e-007 6.5e-003 # TGGCGCAA TTGCGCCA 13 0 1.2e-004 4.0e+000 # TGGCGCAG CTGCGCCA 16 2 6.2e-004 2.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 6.5e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.448276 0.000000 0.551724 0.000000 MOTIF CCAGWTCG DREME-19 # Word RC Word Pos Neg P-value E-value # BEST CCAGWTCG CGAWCTGG 22 0 2.1e-007 7.2e-003 # CCAGATCG CGATCTGG 12 0 2.4e-004 8.1e+000 # CCAGTTCG CGAACTGG 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.2e-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 0.000000 1.000000 0.000000 0.545455 0.000000 0.000000 0.454545 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 GGRGATCA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GGRGATCA TGATCYCC 22 0 2.1e-007 7.2e-003 # GGGGATCA TGATCCCC 12 0 2.4e-004 8.1e+000 # GGAGATCA TGATCTCC 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.2e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.454545 0.000000 0.545455 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARAAAAAA DREME-21 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAAA TTTTTTYT 89 35 2.8e-007 9.7e-003 # AAAAAAAA TTTTTTTT 71 32 4.9e-005 1.7e+000 # AGAAAAAA TTTTTTCT 24 7 1.5e-003 5.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 97 E= 9.7e-003 1.000000 0.000000 0.000000 0.000000 0.793814 0.000000 0.206186 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTRCAC DREME-22 # Word RC Word Pos Neg P-value E-value # BEST CCGTRCAC GTGYACGG 30 3 5.7e-007 2.0e-002 # CCGTACAC GTGTACGG 17 2 3.4e-004 1.2e+001 # CCGTGCAC GTGCACGG 13 1 8.8e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.0e-002 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 0.566667 0.000000 0.433333 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 MOTIF AGMATGGG DREME-23 # Word RC Word Pos Neg P-value E-value # BEST AGMATGGG CCCATKCT 26 2 1.3e-006 4.4e-002 # AGAATGGG CCCATTCT 15 1 2.5e-004 8.4e+000 # AGCATGGG CCCATGCT 12 1 1.7e-003 5.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 4.4e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.555556 0.444444 0.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CGTGYTAA DREME-24 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 26 2 1.3e-006 4.4e-002 # CGTGTTAA TTAACACG 15 1 2.5e-004 8.4e+000 # CGTGCTAA TTAGCACG 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.4e-002 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 0.423077 0.000000 0.576923 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTAGAC DREME-25 # Word RC Word Pos Neg P-value E-value # BEST ACTAGAC GTCTAGT 23 1 1.3e-006 4.5e-002 # ACTAGAC GTCTAGT 23 1 1.3e-006 4.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 23 E= 4.5e-002 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 139.51 seconds