# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/seqs-shuffled # positives: 759 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/seqs-centered (Sun Jan 19 02:10:25 PST 2020) # negatives: 759 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/seqs-shuffled (Sun Jan 19 02:10:26 PST 2020) # host: kali.stanford.edu # when: Sun Jan 19 02:25:43 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 0.300 C 0.201 G 0.196 T 0.303 MOTIF GRVTCGAA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST GRVTCGAA TTCGABYC 110 6 8.2e-028 2.6e-023 # GAATCGAA TTCGATTC 29 0 1.4e-009 4.5e-005 # GGATCGAA TTCGATCC 25 1 3.3e-007 1.1e-002 # GAGTCGAA TTCGACTC 20 1 9.4e-006 3.0e-001 # GGCTCGAA TTCGAGCC 15 2 1.1e-003 3.6e+001 # GGGTCGAA TTCGACCC 13 2 3.6e-003 1.1e+002 # GACTCGAA TTCGAGTC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 111 E= 2.6e-023 0.000000 0.000000 1.000000 0.000000 0.513514 0.000000 0.486486 0.000000 0.495495 0.207207 0.297297 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AGTGGTW DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTW WACCACT 111 13 2.4e-022 7.6e-018 # AGTGGTT AACCACT 82 7 1.7e-018 5.5e-014 # AGTGGTA TACCACT 46 6 3.0e-009 9.6e-005 letter-probability matrix: alength= 4 w= 7 nsites= 131 E= 7.6e-018 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 0.351145 0.000000 0.000000 0.648855 MOTIF TGTAYGGR DREME-3 # Word RC Word Pos Neg P-value E-value # BEST TGTAYGGR YCCRTACA 85 8 1.4e-018 4.6e-014 # TGTATGGG CCCATACA 37 3 6.6e-009 2.1e-004 # TGTACGGA TCCGTACA 34 2 6.9e-009 2.2e-004 # TGTATGGA TCCATACA 14 2 2.0e-003 6.3e+001 # TGTACGGG CCCGTACA 10 1 5.7e-003 1.8e+002 letter-probability matrix: alength= 4 w= 8 nsites= 98 E= 4.6e-014 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 0.469388 0.000000 0.530612 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.520408 0.000000 0.479592 0.000000 MOTIF AACTKGGC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST AACTKGGC GCCMAGTT 52 2 3.6e-014 1.1e-009 # AACTTGGC GCCAAGTT 39 1 2.3e-011 7.3e-007 # AACTGGGC GCCCAGTT 13 1 8.8e-004 2.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 52 E= 1.1e-009 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 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF AARAAAWA DREME-5 # Word RC Word Pos Neg P-value E-value # BEST AARAAAWA TWTTTYTT 169 66 1.1e-013 3.4e-009 # AAGAAAAA TTTTTCTT 52 13 3.5e-007 1.1e-002 # AAAAAATA TATTTTTT 63 23 5.4e-006 1.7e-001 # AAGAAATA TATTTCTT 21 4 4.1e-004 1.3e+001 # AAAAAAAA TTTTTTTT 66 39 4.1e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 196 E= 3.4e-009 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.663265 0.000000 0.336735 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 0.576531 0.000000 0.000000 0.423469 1.000000 0.000000 0.000000 0.000000 MOTIF GCKCTACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 42 2 3.3e-011 1.0e-006 # GCGCTACC GGTAGCGC 30 2 9.5e-008 3.0e-003 # GCTCTACC GGTAGAGC 12 0 2.3e-004 7.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 42 E= 1.0e-006 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.714286 0.285714 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 ATGGCAWC DREME-7 # Word RC Word Pos Neg P-value E-value # BEST ATGGCAWC GWTGCCAT 44 3 7.0e-011 2.2e-006 # ATGGCATC GATGCCAT 18 0 3.4e-006 1.1e-001 # ATGGCAAC GTTGCCAT 26 3 6.4e-006 2.0e-001 letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 2.2e-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 ACCCAVAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST ACCCAVAC GTBTGGGT 46 6 3.0e-009 9.4e-005 # ACCCAAAC GTTTGGGT 13 0 1.2e-004 3.6e+000 # ACCCAGAC GTCTGGGT 12 0 2.3e-004 7.3e+000 # ACCCACAC GTGTGGGT 25 6 3.9e-004 1.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 89 E= 9.4e-005 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.146067 0.719101 0.134831 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GYGGTCTA DREME-9 # Word RC Word Pos Neg P-value E-value # BEST GYGGTCTA TAGACCRC 34 2 6.9e-009 2.2e-004 # GTGGTCTA TAGACCAC 23 1 1.3e-006 4.0e-002 # GCGGTCTA TAGACCGC 11 1 3.1e-003 9.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 2.2e-004 0.000000 0.000000 1.000000 0.000000 0.000000 0.323529 0.000000 0.676471 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 1.000000 0.000000 0.000000 0.000000 MOTIF AGAYCGGG DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGAYCGGG CCCGRTCT 30 1 1.1e-008 3.5e-004 # AGATCGGG CCCGATCT 17 1 6.7e-005 2.1e+000 # AGACCGGG CCCGGTCT 13 0 1.2e-004 3.6e+000 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.5e-004 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 0.433333 0.000000 0.566667 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 1.000000 0.000000 MOTIF CCTTAAMC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CCTTAAMC GKTTAAGG 34 3 4.5e-008 1.4e-003 # CCTTAACC GGTTAAGG 23 2 8.4e-006 2.6e-001 # CCTTAAAC GTTTAAGG 11 1 3.1e-003 9.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 1.4e-003 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 1.000000 0.000000 0.000000 0.000000 0.323529 0.676471 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ACACTATA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST ACACTATA TATAGTGT 24 0 5.0e-008 1.5e-003 # ACACTATA TATAGTGT 24 0 5.0e-008 1.5e-003 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 1.5e-003 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 0.000000 0.000000 1.000000 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 GCGCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST GCGCCA TGGCGC 51 11 8.1e-008 2.5e-003 # GCGCCA TGGCGC 51 11 8.1e-008 2.5e-003 letter-probability matrix: alength= 4 w= 6 nsites= 51 E= 2.5e-003 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 1.000000 0.000000 0.000000 0.000000 MOTIF CTATCACR DREME-14 # Word RC Word Pos Neg P-value E-value # BEST CTATCACR YGTGATAG 33 3 8.5e-008 2.6e-003 # CTATCACG CGTGATAG 16 0 1.4e-005 4.3e-001 # CTATCACA TGTGATAG 17 3 1.2e-003 3.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 33 E= 2.6e-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 0.000000 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 CASACGC DREME-15 # Word RC Word Pos Neg P-value E-value # BEST CASACGC GCGTSTG 35 4 1.2e-007 3.8e-003 # CACACGC GCGTGTG 18 2 1.9e-004 5.7e+000 # CAGACGC GCGTCTG 17 2 3.4e-004 1.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 35 E= 3.8e-003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.514286 0.485714 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 MOTIF CRTGCTAA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST CRTGCTAA TTAGCAYG 22 0 2.0e-007 6.3e-003 # CGTGCTAA TTAGCACG 12 0 2.3e-004 7.2e+000 # CATGCTAA TTAGCATG 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.3e-003 0.000000 1.000000 0.000000 0.000000 0.454545 0.000000 0.545455 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 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 CGCGGGSA DREME-17 # Word RC Word Pos Neg P-value E-value # BEST CGCGGGSA TSCCCGCG 25 1 3.3e-007 1.0e-002 # CGCGGGGA TCCCCGCG 13 0 1.2e-004 3.6e+000 # CGCGGGCA TGCCCGCG 12 1 1.6e-003 5.1e+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 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 1.000000 0.000000 0.000000 0.480000 0.520000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AAAGCRTG DREME-18 # Word RC Word Pos Neg P-value E-value # BEST AAAGCRTG CAYGCTTT 24 1 6.5e-007 2.0e-002 # AAAGCGTG CACGCTTT 13 0 1.2e-004 3.6e+000 # AAAGCATG CATGCTTT 11 1 3.1e-003 9.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 24 E= 2.0e-002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.458333 0.000000 0.541667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 MOTIF TAKCTCA DREME-19 # Word RC Word Pos Neg P-value E-value # BEST TAKCTCA TGAGMTA 47 11 6.6e-007 2.0e-002 # TAGCTCA TGAGCTA 22 3 7.0e-005 2.1e+000 # TATCTCA TGAGATA 25 8 2.1e-003 6.3e+001 letter-probability matrix: alength= 4 w= 7 nsites= 50 E= 2.0e-002 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.440000 0.560000 0.000000 1.000000 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 GGCCMAAC DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GGCCMAAC GTTKGGCC 27 2 6.6e-007 2.0e-002 # GGCCCAAC GTTGGGCC 14 1 4.6e-004 1.4e+001 # GGCCAAAC GTTTGGCC 13 1 8.8e-004 2.7e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.0e-002 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 0.481481 0.518519 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 MOTIF CTKCGGTC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CTKCGGTC GACCGMAG 20 0 8.4e-007 2.6e-002 # CTTCGGTC GACCGAAG 11 0 4.7e-004 1.4e+001 # CTGCGGTC GACCGCAG 9 0 1.9e-003 5.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.450000 0.550000 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 1.000000 0.000000 0.000000 MOTIF GAYCTCCA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GAYCTCCA TGGAGRTC 20 0 8.4e-007 2.6e-002 # GATCTCCA TGGAGATC 12 0 2.3e-004 7.1e+000 # GACCTCCA TGGAGGTC 8 0 3.8e-003 1.2e+002 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-002 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF TCCGTGSA DREME-23 # Word RC Word Pos Neg P-value E-value # BEST TCCGTGSA TSCACGGA 20 0 8.4e-007 2.6e-002 # TCCGTGCA TGCACGGA 10 0 9.5e-004 2.9e+001 # TCCGTGGA TCCACGGA 10 0 9.5e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.6e-002 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 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 CCAAMAGA DREME-24 # Word RC Word Pos Neg P-value E-value # BEST CCAAMAGA TCTKTTGG 29 3 1.0e-006 3.1e-002 # CCAACAGA TCTGTTGG 15 1 2.4e-004 7.4e+000 # CCAAAAGA TCTTTTGG 14 2 2.0e-003 6.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.1e-002 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 0.482759 0.517241 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 MOTIF TCTAATCW DREME-25 # Word RC Word Pos Neg P-value E-value # BEST TCTAATCW WGATTAGA 29 3 1.0e-006 3.1e-002 # TCTAATCT AGATTAGA 14 0 5.7e-005 1.7e+000 # TCTAATCA TGATTAGA 15 3 3.6e-003 1.1e+002 letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 3.1e-002 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.517241 0.000000 0.000000 0.482759 # Stopping reason: E-value threshold exceeded # Running time: 117.13 seconds