# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ZAP1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ZAP1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ZAP1/seqs-shuffled # positives: 776 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ZAP1/seqs-centered (Sat Jan 18 13:19:54 PST 2020) # negatives: 776 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--ZAP1/seqs-shuffled (Sat Jan 18 13:19:54 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 13:34:48 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 0.301 C 0.205 G 0.200 T 0.294 MOTIF AYCCRTAC DREME-1 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 95 5 4.0e-024 1.3e-019 # ACCCATAC GTATGGGT 47 2 1.1e-012 3.7e-008 # ATCCGTAC GTACGGAT 33 1 1.5e-009 4.8e-005 # ACCCGTAC GTACGGGT 14 1 4.6e-004 1.5e+001 # ATCCATAC GTATGGAT 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 111 E= 1.3e-019 1.000000 0.000000 0.000000 0.000000 0.000000 0.558559 0.000000 0.441441 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.549550 0.000000 0.450450 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 GGTTCRA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 105 11 5.0e-022 1.6e-017 # GGTTCGA TCGAACC 76 3 2.3e-020 7.5e-016 # GGTTCAA TTGAACC 29 8 3.3e-004 1.1e+001 letter-probability matrix: alength= 4 w= 7 nsites= 105 E= 1.6e-017 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 0.276190 0.000000 0.723810 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACTBGGCC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST ACTBGGCC GGCCVAGT 64 1 4.8e-019 1.6e-014 # ACTTGGCC GGCCAAGT 32 0 1.7e-010 5.5e-006 # ACTCGGCC GGCCGAGT 30 0 7.0e-010 2.3e-005 # ACTGGGCC GGCCCAGT 12 1 1.6e-003 5.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 64 E= 1.6e-014 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 0.406250 0.187500 0.406250 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 BTAAGGCG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST BTAAGGCG CGCCTTAV 70 3 1.5e-018 5.0e-014 # TTAAGGCG CGCCTTAA 41 2 6.6e-011 2.1e-006 # CTAAGGCG CGCCTTAG 17 1 6.7e-005 2.2e+000 # GTAAGGCG CGCCTTAC 12 0 2.3e-004 7.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 70 E= 5.0e-014 0.000000 0.242857 0.171429 0.585714 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 0.000000 0.000000 1.000000 0.000000 MOTIF TGGCGYA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST TGGCGYA TRCGCCA 53 2 1.8e-014 5.9e-010 # TGGCGCA TGCGCCA 30 1 1.1e-008 3.7e-004 # TGGCGTA TACGCCA 23 1 1.3e-006 4.2e-002 letter-probability matrix: alength= 4 w= 7 nsites= 53 E= 5.9e-010 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 0.566038 0.000000 0.433962 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 49 1 2.1e-014 6.9e-010 # GCGCTACC GGTAGCGC 32 1 2.9e-009 9.4e-005 # GCTCTACC GGTAGAGC 17 0 7.0e-006 2.3e-001 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 6.9e-010 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.653061 0.346939 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 CRCCCA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 140 50 1.2e-012 3.8e-008 # CACCCA TGGGTG 100 33 5.1e-010 1.7e-005 # CGCCCA TGGGCG 45 18 3.5e-004 1.1e+001 letter-probability matrix: alength= 4 w= 6 nsites= 234 E= 3.8e-008 0.000000 1.000000 0.000000 0.000000 0.794872 0.000000 0.205128 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 CTARACCA DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CTARACCA TGGTYTAG 40 1 1.2e-011 3.7e-007 # CTAGACCA TGGTCTAG 26 0 1.2e-008 3.8e-004 # CTAAACCA TGGTTTAG 14 1 4.6e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 3.7e-007 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.350000 0.000000 0.650000 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 ARAAAWA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ARAAAWA TWTTTYT 248 138 6.2e-011 2.0e-006 # AGAAAAA TTTTTCT 93 29 6.2e-010 2.0e-005 # AAAAAAA TTTTTTT 123 68 1.4e-005 4.3e-001 # AAAAATA TATTTTT 83 44 2.0e-004 6.3e+000 # AGAAATA TATTTCT 37 19 1.0e-002 3.2e+002 letter-probability matrix: alength= 4 w= 7 nsites= 321 E= 2.0e-006 1.000000 0.000000 0.000000 0.000000 0.641745 0.000000 0.358255 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 0.660436 0.000000 0.000000 0.339564 1.000000 0.000000 0.000000 0.000000 MOTIF ATGGCAWC DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 44 3 7.1e-011 2.3e-006 # ATGGCATC GATGCCAT 18 0 3.5e-006 1.1e-001 # ATGGCAAC GTTGCCAT 26 3 6.4e-006 2.0e-001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.3e-006 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 0.590909 0.000000 0.000000 0.409091 0.000000 1.000000 0.000000 0.000000 MOTIF GGYTATCA DREME-11 # Word RC Word Pos Neg P-value E-value # BEST GGYTATCA TGATARCC 32 1 2.9e-009 9.2e-005 # GGCTATCA TGATAGCC 17 0 7.0e-006 2.2e-001 # GGTTATCA TGATAACC 15 1 2.4e-004 7.7e+000 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 9.2e-005 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.531250 0.000000 0.468750 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 TAGTRTA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST TAGTRTA TAYACTA 59 13 9.4e-009 3.0e-004 # TAGTGTA TACACTA 36 7 3.4e-006 1.1e-001 # TAGTATA TATACTA 23 6 1.1e-003 3.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 60 E= 3.0e-004 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 0.383333 0.000000 0.616667 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CCGTGSA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CCGTGSA TSCACGG 43 6 1.8e-008 5.8e-004 # CCGTGGA TCCACGG 22 2 1.6e-005 5.0e-001 # CCGTGCA TGCACGG 22 4 2.4e-004 7.6e+000 letter-probability matrix: alength= 4 w= 7 nsites= 44 E= 5.8e-004 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GTCAKAC DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GTCAKAC GTMTGAC 38 4 1.9e-008 6.1e-004 # GTCATAC GTATGAC 24 3 2.1e-005 6.7e-001 # GTCAGAC GTCTGAC 14 1 4.6e-004 1.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 38 E= 6.1e-004 0.000000 0.000000 1.000000 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 0.368421 0.631579 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TTGAARA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TTGAARA TYTTCAA 90 35 1.6e-007 5.0e-003 # TTGAAGA TCTTCAA 35 10 1.0e-004 3.2e+000 # TTGAAAA TTTTCAA 58 25 1.3e-004 4.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 96 E= 5.0e-003 0.000000 0.000000 0.000000 1.000000 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 0.625000 0.000000 0.375000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTGYTAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGTGYTAA TTARCACG 25 1 3.4e-007 1.0e-002 # CGTGTTAA TTAACACG 14 1 4.6e-004 1.5e+001 # CGTGCTAA TTAGCACG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.0e-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 0.440000 0.000000 0.560000 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 ACTGAGCT DREME-17 # Word RC Word Pos Neg P-value E-value # BEST ACTGAGCT AGCTCAGT 23 1 1.3e-006 4.0e-002 # ACTGAGCT AGCTCAGT 23 1 1.3e-006 4.0e-002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.0e-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 # Stopping reason: E-value threshold exceeded # Running time: 84.47 seconds