# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/seqs-shuffled # positives: 629 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/seqs-centered (Sat Jan 18 00:44:24 PST 2020) # negatives: 629 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/seqs-shuffled (Sat Jan 18 00:44:24 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 00:59:45 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 0.288 C 0.212 G 0.210 T 0.290 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 114 9 1.1e-026 3.4e-022 # GGTTCGA TCGAACC 95 7 1.4e-022 4.5e-018 # GGATCGA TCGATCC 27 2 6.4e-007 2.0e-002 letter-probability matrix: alength= 4 w= 7 nsites= 114 E= 3.4e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.210526 0.000000 0.000000 0.789474 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 CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 62 2 2.6e-017 8.0e-013 # CTCGGCCA TGGCCGAG 32 0 1.6e-010 4.9e-006 # CTTGGCCA TGGCCAAG 17 1 6.6e-005 2.1e+000 # CTGGGCCA TGGCCCAG 13 1 8.7e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 62 E= 8.0e-013 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.516129 0.209677 0.274194 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 CCCATDC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCCATDC GHATGGG 81 13 2.5e-014 7.9e-010 # CCCATAC GTATGGG 44 5 2.1e-009 6.4e-005 # CCCATGC GCATGGG 22 4 2.4e-004 7.4e+000 # CCCATTC GAATGGG 20 4 7.0e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 89 E= 7.9e-010 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 0.000000 1.000000 0.528090 0.000000 0.247191 0.224719 0.000000 1.000000 0.000000 0.000000 MOTIF CGCSTTA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 74 11 1.2e-013 3.8e-009 # CGCCTTA TAAGGCG 58 7 7.3e-012 2.3e-007 # CGCGTTA TAACGCG 16 4 5.6e-003 1.7e+002 letter-probability matrix: alength= 4 w= 7 nsites= 74 E= 3.8e-009 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 0.783784 0.216216 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 GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 40 1 1.0e-011 3.2e-007 # GCGCTACC GGTAGCGC 26 0 1.1e-008 3.6e-004 # GCTCTACC GGTAGAGC 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.2e-007 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 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-6 # Word RC Word Pos Neg P-value E-value # BEST ATAGTKTA TAMACTAT 46 3 1.7e-011 5.1e-007 # ATAGTGTA TACACTAT 25 2 2.3e-006 7.1e-002 # ATAGTTTA TAAACTAT 21 2 2.9e-005 8.9e-001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 5.1e-007 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 0.543478 0.456522 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AARARAAA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST AARARAAA TTTYTYTT 127 46 1.4e-011 4.3e-007 # AAGAAAAA TTTTTCTT 45 12 4.2e-006 1.3e-001 # AAAAAAAA TTTTTTTT 62 23 7.3e-006 2.2e-001 # AAAAGAAA TTTCTTTT 41 14 1.3e-004 4.1e+000 # AAGAGAAA TTTCTCTT 16 3 2.1e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 154 E= 4.3e-007 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.681818 0.000000 0.318182 0.000000 1.000000 0.000000 0.000000 0.000000 0.662338 0.000000 0.337662 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 GTAMGGA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST GTAMGGA TCCKTAC 52 6 6.6e-011 2.0e-006 # GTACGGA TCCGTAC 36 4 6.2e-008 1.9e-003 # GTAAGGA TCCTTAC 16 2 6.1e-004 1.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 54 E= 2.0e-006 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.296296 0.703704 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 MOTIF CACGGTGM DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CACGGTGM KCACCGTG 28 1 4.2e-008 1.3e-003 # CACGGTGA TCACCGTG 16 0 1.4e-005 4.2e-001 # CACGGTGC GCACCGTG 12 1 1.6e-003 5.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.3e-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 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 0.571429 0.428571 0.000000 0.000000 MOTIF GATTRGAA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST GATTRGAA TTCYAATC 28 1 4.2e-008 1.3e-003 # GATTAGAA TTCTAATC 21 1 4.7e-006 1.4e-001 # GATTGGAA TTCCAATC 7 0 7.7e-003 2.4e+002 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.3e-003 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 0.000000 1.000000 0.750000 0.000000 0.250000 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 GGYTATCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 31 2 4.7e-008 1.4e-003 # GGCTATCA TGATAGCC 17 1 6.6e-005 2.0e+000 # GGTTATCA TGATAACC 14 1 4.6e-004 1.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.4e-003 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.548387 0.000000 0.451613 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 MOTIF CCASAC DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCASAC GTSTGG 92 36 9.8e-008 3.0e-003 # CCACAC GTGTGG 60 21 4.4e-006 1.4e-001 # CCAGAC GTCTGG 36 16 3.3e-003 1.0e+002 letter-probability matrix: alength= 4 w= 6 nsites= 101 E= 3.0e-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 0.643564 0.356436 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATGGCAW DREME-13 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAW WTGCCAT 46 9 1.2e-007 3.8e-003 # ATGGCAA TTGCCAT 29 6 4.7e-005 1.4e+000 # ATGGCAT ATGCCAT 17 3 1.2e-003 3.6e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 3.8e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.630435 0.000000 0.000000 0.369565 MOTIF ATCKTGAG DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 26 1 1.6e-007 4.9e-003 # ATCGTGAG CTCACGAT 16 1 1.3e-004 3.8e+000 # ATCTTGAG CTCAAGAT 10 0 9.4e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.9e-003 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 0.615385 0.384615 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 CACGGAW DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CACGGAW WTCCGTG 43 8 2.1e-007 6.3e-003 # CACGGAT ATCCGTG 22 3 6.8e-005 2.1e+000 # CACGGAA TTCCGTG 21 5 1.1e-003 3.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 6.3e-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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.477273 0.000000 0.000000 0.522727 MOTIF TACCACTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST TACCACTA TAGTGGTA 25 1 3.2e-007 9.7e-003 # TACCACTA TAGTGGTA 25 1 3.2e-007 9.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 9.7e-003 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 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 MOTIF AYTGCGCC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AYTGCGCC GGCGCART 23 1 1.2e-006 3.7e-002 # ACTGCGCC GGCGCAGT 12 0 2.3e-004 7.0e+000 # ATTGCGCC GGCGCAAT 11 1 3.1e-003 9.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.7e-002 1.000000 0.000000 0.000000 0.000000 0.000000 0.521739 0.000000 0.478261 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CKTTGGGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 23 1 1.2e-006 3.7e-002 # CGTTGGGC GCCCAACG 16 1 1.3e-004 3.8e+000 # CTTTGGGC GCCCAAAG 7 0 7.7e-003 2.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 3.7e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.695652 0.304348 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 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 75.71 seconds