# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MOT1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MOT1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MOT1/seqs-shuffled # positives: 870 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MOT1/seqs-centered (Sat Jan 18 08:04:05 PST 2020) # negatives: 870 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MOT1/seqs-shuffled (Sat Jan 18 08:04:05 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 08:18:27 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 0.279 C 0.218 G 0.225 T 0.278 MOTIF GGTTCRA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGTTCRA TYGAACC 140 17 1.3e-027 4.8e-023 # GGTTCGA TCGAACC 101 5 8.0e-026 2.9e-021 # GGTTCAA TTGAACC 41 12 3.2e-005 1.2e+000 letter-probability matrix: alength= 4 w= 7 nsites= 142 E= 4.8e-023 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 0.288732 0.000000 0.711268 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CTYGGCCA DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CTYGGCCA TGGCCRAG 55 1 3.4e-016 1.2e-011 # CTCGGCCA TGGCCGAG 30 0 7.2e-010 2.6e-005 # CTTGGCCA TGGCCAAG 25 1 3.4e-007 1.2e-002 letter-probability matrix: alength= 4 w= 8 nsites= 55 E= 1.2e-011 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.545455 0.000000 0.454545 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 CCTTAVC DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CCTTAVC GBTAAGG 100 21 1.2e-014 4.3e-010 # CCTTAAC GTTAAGG 40 7 3.9e-007 1.4e-002 # CCTTAGC GCTAAGG 30 6 3.0e-005 1.1e+000 # CCTTACC GGTAAGG 30 8 2.1e-004 7.4e+000 letter-probability matrix: alength= 4 w= 7 nsites= 100 E= 4.3e-010 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 0.400000 0.300000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GTGRTAR DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GTGRTAR YTAYCAC 110 29 1.7e-013 6.2e-009 # GTGATAG CTATCAC 37 8 6.0e-006 2.2e-001 # GTGGTAA TTACCAC 34 9 7.1e-005 2.5e+000 # GTGATAA TTATCAC 21 5 1.2e-003 4.2e+001 # GTGGTAG CTACCAC 20 7 9.1e-003 3.3e+002 letter-probability matrix: alength= 4 w= 7 nsites= 115 E= 6.2e-009 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.504348 0.000000 0.495652 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.478261 0.000000 0.521739 0.000000 MOTIF AAGARA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AAGARA TYTCTT 238 138 3.5e-009 1.2e-004 # AAGAAA TTTCTT 166 101 9.6e-006 3.4e-001 # AAGAGA TCTCTT 87 43 3.9e-005 1.4e+000 letter-probability matrix: alength= 4 w= 6 nsites= 280 E= 1.2e-004 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 0.667857 0.000000 0.332143 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ACGGTR DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACGGTR YACCGT 104 39 6.9e-009 2.4e-004 # ACGGTG CACCGT 68 24 1.4e-006 4.9e-002 # ACGGTA TACCGT 39 15 6.3e-004 2.2e+001 letter-probability matrix: alength= 4 w= 6 nsites= 111 E= 2.4e-004 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 0.378378 0.000000 0.621622 0.000000 MOTIF ATCTTYTG DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATCTTYTG CARAAGAT 35 3 2.5e-008 8.8e-004 # ATCTTCTG CAGAAGAT 23 2 8.6e-006 3.0e-001 # ATCTTTTG CAAAAGAT 12 1 1.7e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 35 E= 8.8e-004 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.657143 0.000000 0.342857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ATCKTGAG DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 31 2 5.2e-008 1.8e-003 # ATCGTGAG CTCACGAT 20 1 9.5e-006 3.3e-001 # ATCTTGAG CTCAAGAT 11 1 3.1e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.8e-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 0.645161 0.354839 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 AAMAATA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST AAMAATA TATTKTT 75 25 1.3e-007 4.6e-003 # AACAATA TATTGTT 27 6 1.4e-004 5.0e+000 # AAAAATA TATTTTT 48 19 2.0e-004 7.1e+000 letter-probability matrix: alength= 4 w= 7 nsites= 78 E= 4.6e-003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.641026 0.358974 0.000000 0.000000 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 MOTIF AGAATKGG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGAATKGG CCMATTCT 26 1 1.8e-007 6.1e-003 # AGAATGGG CCCATTCT 19 1 1.8e-005 6.4e-001 # AGAATTGG CCAATTCT 7 0 7.7e-003 2.7e+002 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 6.1e-003 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.730769 0.269231 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF CAKACGCG DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CAKACGCG CGCGTMTG 26 1 1.8e-007 6.1e-003 # CATACGCG CGCGTATG 13 0 1.2e-004 4.1e+000 # CAGACGCG CGCGTCTG 13 1 8.8e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 6.1e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 0.000000 0.000000 1.000000 0.000000 MOTIF AGACCACR DREME-12 # Word RC Word Pos Neg P-value E-value # BEST AGACCACR YGTGGTCT 22 0 2.1e-007 7.3e-003 # AGACCACG CGTGGTCT 12 0 2.3e-004 8.2e+000 # AGACCACA TGTGGTCT 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 7.3e-003 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.454545 0.000000 0.545455 0.000000 MOTIF CATCCRTA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CATCCRTA TAYGGATG 25 1 3.4e-007 1.2e-002 # CATCCGTA TACGGATG 15 1 2.5e-004 8.6e+000 # CATCCATA TATGGATG 10 0 9.5e-004 3.3e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.2e-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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GCTTY DREME-14 # Word RC Word Pos Neg P-value E-value # BEST GCTTY RAAGC 355 258 7.0e-007 2.4e-002 # GCTTC GAAGC 161 111 5.9e-004 2.1e+001 # GCTTT AAAGC 230 176 1.3e-003 4.6e+001 letter-probability matrix: alength= 4 w= 5 nsites= 430 E= 2.4e-002 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 0.000000 0.000000 1.000000 0.000000 0.420930 0.000000 0.579070 MOTIF TAGTGTAR DREME-15 # Word RC Word Pos Neg P-value E-value # BEST TAGTGTAR YTACACTA 29 3 1.1e-006 3.6e-002 # TAGTGTAA TTACACTA 17 2 3.4e-004 1.2e+001 # TAGTGTAG CTACACTA 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.6e-002 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.586207 0.000000 0.413793 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 83.64 seconds