# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--TEC1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--TEC1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--TEC1/seqs-shuffled # positives: 741 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--TEC1/seqs-centered (Sun Jan 19 07:03:09 PST 2020) # negatives: 741 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--TEC1/seqs-shuffled (Sun Jan 19 07:03:09 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 07:18:43 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 0.299 C 0.200 G 0.197 T 0.304 MOTIF RGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST RGTTCGA TCGAACY 98 12 2.1e-019 7.0e-015 # GGTTCGA TCGAACC 85 8 1.4e-018 4.5e-014 # AGTTCGA TCGAACT 19 4 1.2e-003 4.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 98 E= 7.0e-015 0.173469 0.000000 0.826531 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 CTBGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 65 5 3.2e-015 1.0e-010 # CTCGGCCA TGGCCGAG 30 2 9.5e-008 3.1e-003 # CTTGGCCA TGGCCAAG 23 1 1.3e-006 4.2e-002 # CTGGGCCA TGGCCCAG 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 65 E= 1.0e-010 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.461538 0.184615 0.353846 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 ATGTAYGG DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ATGTAYGG CCRTACAT 62 4 3.2e-015 1.1e-010 # ATGTACGG CCGTACAT 32 0 1.7e-010 5.4e-006 # ATGTATGG CCATACAT 34 4 2.2e-007 7.3e-003 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 1.1e-010 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 0.000000 0.478873 0.000000 0.521127 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CTWAACCA DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CTWAACCA TGGTTWAG 50 2 1.4e-013 4.5e-009 # CTTAACCA TGGTTAAG 38 0 2.2e-012 7.3e-008 # CTAAACCA TGGTTTAG 12 2 6.3e-003 2.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 4.5e-009 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.240000 0.000000 0.000000 0.760000 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 MOTIF GCKCTAC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTAC GTAGMGC 44 2 8.4e-012 2.8e-007 # GCGCTAC GTAGCGC 26 0 1.2e-008 3.9e-004 # GCTCTAC GTAGAGC 18 2 1.9e-004 6.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 2.8e-007 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.590909 0.409091 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 GTWGCCA DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GTWGCCA TGGCWAC 49 4 1.8e-011 5.7e-007 # GTTGCCA TGGCAAC 34 3 4.5e-008 1.5e-003 # GTAGCCA TGGCTAC 15 1 2.4e-004 7.9e+000 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 5.7e-007 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.306122 0.000000 0.000000 0.693878 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 ACACSCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ACACSCA TGSGTGT 52 7 3.4e-010 1.1e-005 # ACACCCA TGGGTGT 39 5 4.7e-008 1.5e-003 # ACACGCA TGCGTGT 13 2 3.6e-003 1.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 1.1e-005 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 1.000000 0.000000 0.000000 0.000000 0.754717 0.245283 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CKCCACR DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CKCCACR YGTGGMG 58 10 5.3e-010 1.7e-005 # CGCCACG CGTGGCG 20 1 9.3e-006 3.0e-001 # CGCCACA TGTGGCG 19 2 1.0e-004 3.3e+000 # CTCCACG CGTGGAG 16 3 2.1e-003 6.8e+001 # CTCCACA TGTGGAG 15 4 9.2e-003 3.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 70 E= 1.7e-005 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.557143 0.442857 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 0.485714 0.000000 0.514286 0.000000 MOTIF AGAAAMA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AGAAAMA TKTTTCT 134 56 6.9e-010 2.2e-005 # AGAAAAA TTTTTCT 106 45 9.2e-008 3.0e-003 # AGAAACA TGTTTCT 30 11 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 140 E= 2.2e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.785714 0.214286 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCACR DREME-10 # 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 2.2e-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 ACTSACG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST ACTSACG CGTSAGT 38 4 1.9e-008 6.1e-004 # ACTCACG CGTGAGT 20 1 9.3e-006 3.0e-001 # ACTGACG CGTCAGT 18 3 6.9e-004 2.2e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 6.1e-004 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 0.526316 0.473684 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 MOTIF ACCAYTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACCAYTA TARTGGT 55 12 2.7e-008 8.6e-004 # ACCACTA TAGTGGT 31 5 5.1e-006 1.6e-001 # ACCATTA TAATGGT 24 8 3.2e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 55 E= 8.6e-004 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 0.563636 0.000000 0.436364 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTATWTC DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CTATWTC GAWATAG 46 9 1.4e-007 4.3e-003 # CTATTTC GAAATAG 28 5 2.8e-005 8.9e-001 # CTATATC GATATAG 19 4 1.2e-003 3.9e+001 letter-probability matrix: alength= 4 w= 7 nsites= 47 E= 4.3e-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 0.404255 0.000000 0.000000 0.595745 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CATTCTB DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CATTCTB VAGAATG 71 24 3.3e-007 1.1e-002 # CATTCTT AAGAATG 39 15 6.1e-004 2.0e+001 # CATTCTG CAGAATG 22 5 6.9e-004 2.2e+001 # CATTCTC GAGAATG 16 4 5.6e-003 1.8e+002 letter-probability matrix: alength= 4 w= 7 nsites= 82 E= 1.1e-002 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.195122 0.268293 0.536585 MOTIF AGARTCAT DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGARTCAT ATGAYTCT 25 1 3.3e-007 1.1e-002 # AGAGTCAT ATGACTCT 14 1 4.6e-004 1.5e+001 # AGAATCAT ATGATTCT 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.1e-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 0.440000 0.000000 0.560000 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 0.000000 1.000000 MOTIF ACTGAGCT DREME-16 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 21 0 4.1e-007 1.3e-002 # ACTGAGCT AGCTCAGT 21 0 4.1e-007 1.3e-002 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.3e-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 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 MOTIF GYACGGA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST GYACGGA TCCGTRC 30 3 5.5e-007 1.7e-002 # GTACGGA TCCGTAC 16 1 1.3e-004 4.1e+000 # GCACGGA TCCGTGC 14 2 2.0e-003 6.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 31 E= 1.7e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.483871 0.000000 0.516129 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 MOTIF GCARATGC DREME-18 # Word RC Word Pos Neg P-value E-value # BEST GCARATGC GCATYTGC 24 1 6.5e-007 2.1e-002 # GCAGATGC GCATCTGC 14 1 4.6e-004 1.5e+001 # GCAAATGC GCATTTGC 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.1e-002 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.416667 0.000000 0.583333 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 1.000000 0.000000 0.000000 MOTIF AGGAAGAS DREME-19 # Word RC Word Pos Neg P-value E-value # BEST AGGAAGAS STCTTCCT 20 0 8.4e-007 2.6e-002 # AGGAAGAC GTCTTCCT 11 0 4.7e-004 1.5e+001 # AGGAAGAG CTCTTCCT 9 0 1.9e-003 6.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 2.6e-002 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 0.000000 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 0.571429 0.428571 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 94.30 seconds