# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-shuffled # positives: 867 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-centered (Sat Jan 18 01:42:00 PST 2020) # negatives: 867 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/seqs-shuffled (Sat Jan 18 01:42:00 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 01:56:39 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 0.310 C 0.196 G 0.186 T 0.308 MOTIF GGWTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GGWTCGA TCGAWCC 124 12 1.3e-026 4.3e-022 # GGTTCGA TCGAACC 104 8 5.9e-024 1.9e-019 # GGATCGA TCGATCC 32 4 7.8e-007 2.5e-002 letter-probability matrix: alength= 4 w= 7 nsites= 124 E= 4.3e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.209677 0.000000 0.000000 0.790323 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 CCRTACAY DREME-2 # Word RC Word Pos Neg P-value E-value # BEST CCRTACAY RTGTAYGG 87 4 1.4e-022 4.6e-018 # CCGTACAT ATGTACGG 29 0 1.5e-009 4.8e-005 # CCATACAT ATGTATGG 33 1 1.5e-009 5.0e-005 # CCGTACAC GTGTACGG 17 0 7.0e-006 2.3e-001 # CCATACAC GTGTATGG 14 3 6.2e-003 2.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 99 E= 4.6e-018 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.515152 0.000000 0.484848 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.323232 0.000000 0.676768 MOTIF AGTGGTWA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTWA TWACCACT 72 3 4.5e-019 1.5e-014 # AGTGGTTA TAACCACT 49 2 3.1e-013 1.0e-008 # AGTGGTAA TTACCACT 23 1 1.3e-006 4.2e-002 letter-probability matrix: alength= 4 w= 8 nsites= 72 E= 1.5e-014 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 0.319444 0.000000 0.000000 0.680556 1.000000 0.000000 0.000000 0.000000 MOTIF CAACTKGG DREME-4 # Word RC Word Pos Neg P-value E-value # BEST CAACTKGG CCMAGTTG 54 2 1.0e-014 3.3e-010 # CAACTTGG CCAAGTTG 41 1 6.2e-012 2.0e-007 # CAACTGGG CCCAGTTG 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 54 E= 3.3e-010 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.240741 0.759259 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 MOTIF ARAAAAR DREME-5 # Word RC Word Pos Neg P-value E-value # BEST ARAAAAR YTTTTYT 283 151 1.4e-013 4.5e-009 # AAAAAAA TTTTTTT 146 76 3.0e-007 9.6e-003 # AAAAAAG CTTTTTT 101 53 3.2e-005 1.0e+000 # AGAAAAA TTTTTCT 96 51 6.7e-005 2.2e+000 # AGAAAAG CTTTTCT 48 23 1.7e-003 5.4e+001 letter-probability matrix: alength= 4 w= 7 nsites= 350 E= 4.5e-009 1.000000 0.000000 0.000000 0.000000 0.622857 0.000000 0.377143 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 0.622857 0.000000 0.377143 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 46 1 1.9e-013 6.1e-009 # GCGCTACC GGTAGCGC 33 0 8.5e-011 2.7e-006 # GCTCTACC GGTAGAGC 13 1 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 46 E= 6.1e-009 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.717391 0.282609 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 CGCSTTA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CGCSTTA TAASGCG 65 11 3.8e-011 1.2e-006 # CGCCTTA TAAGGCG 47 6 1.8e-009 5.7e-005 # CGCGTTA TAACGCG 18 5 5.1e-003 1.6e+002 letter-probability matrix: alength= 4 w= 7 nsites= 65 E= 1.2e-006 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 0.723077 0.276923 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 CGTWGCC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGTWGCC GGCWACG 34 0 4.2e-011 1.3e-006 # CGTTGCC GGCAACG 27 0 6.1e-009 1.9e-004 # CGTAGCC GGCTACG 7 0 7.7e-003 2.5e+002 letter-probability matrix: alength= 4 w= 7 nsites= 34 E= 1.3e-006 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.205882 0.000000 0.000000 0.794118 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 CRCCCA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST CRCCCA TGGGYG 123 50 2.5e-009 8.0e-005 # CACCCA TGGGTG 87 39 5.5e-006 1.8e-001 # CGCCCA TGGGCG 41 12 3.2e-005 1.0e+000 letter-probability matrix: alength= 4 w= 6 nsites= 194 E= 8.0e-005 0.000000 1.000000 0.000000 0.000000 0.778351 0.000000 0.221649 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 ACCACTYG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST ACCACTYG CRAGTGGT 29 1 2.3e-008 7.3e-004 # ACCACTTG CAAGTGGT 19 1 1.8e-005 5.8e-001 # ACCACTCG CGAGTGGT 10 0 9.5e-004 3.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 7.3e-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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.344828 0.000000 0.655172 0.000000 0.000000 1.000000 0.000000 MOTIF CCGATGAW DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCGATGAW WTCATCGG 25 0 2.5e-008 7.9e-004 # CCGATGAA TTCATCGG 14 0 5.8e-005 1.8e+000 # CCGATGAT ATCATCGG 11 0 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 7.9e-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 1.000000 0.000000 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 0.560000 0.000000 0.000000 0.440000 MOTIF GMTTAACA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST GMTTAACA TGTTAAKC 30 2 9.9e-008 3.1e-003 # GCTTAACA TGTTAAGC 17 0 7.0e-006 2.2e-001 # GATTAACA TGTTAATC 13 2 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.1e-003 0.000000 0.000000 1.000000 0.000000 0.433333 0.566667 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GGTCTCY DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GGTCTCY RGAGACC 37 5 1.6e-007 5.2e-003 # GGTCTCC GGAGACC 22 3 7.1e-005 2.2e+000 # GGTCTCT AGAGACC 15 2 1.1e-003 3.5e+001 letter-probability matrix: alength= 4 w= 7 nsites= 46 E= 5.2e-003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.478261 0.000000 0.521739 MOTIF AGACCACR DREME-14 # Word RC Word Pos Neg P-value E-value # BEST AGACCACR YGTGGTCT 25 1 3.4e-007 1.1e-002 # AGACCACG CGTGGTCT 14 1 4.7e-004 1.5e+001 # AGACCACA TGTGGTCT 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 0.000000 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 0.440000 0.000000 0.560000 0.000000 MOTIF AGTCAKAC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST AGTCAKAC GTMTGACT 30 3 5.7e-007 1.8e-002 # AGTCAGAC GTCTGACT 14 1 4.7e-004 1.5e+001 # AGTCATAC GTATGACT 16 2 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 1.8e-002 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.466667 0.533333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CGGTGAAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CGGTGAAA TTTCACCG 20 0 8.5e-007 2.7e-002 # CGGTGAAA TTTCACCG 20 0 8.5e-007 2.7e-002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.7e-002 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 # Stopping reason: E-value threshold exceeded # Running time: 89.08 seconds