# DREME 4.12.0 # command: dreme -v 1 -oc /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HAA1/dreme_out -png -dna -p /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HAA1/seqs-centered -n /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HAA1/seqs-shuffled # positives: 836 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HAA1/seqs-centered (Sat Jan 18 18:19:56 PST 2020) # negatives: 836 from /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HAA1/seqs-shuffled (Sat Jan 18 18:19:56 PST 2020) # host: kali.stanford.edu # when: Sat Jan 18 18:35:52 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 0.296 C 0.208 G 0.202 T 0.294 MOTIF SRGTTCGA DREME-1 # Word RC Word Pos Neg P-value E-value # BEST SRGTTCGA TCGAACYS 118 4 2.7e-032 9.1e-028 # CGGTTCGA TCGAACCG 43 0 6.5e-014 2.2e-009 # GGGTTCGA TCGAACCC 47 1 9.2e-014 3.1e-009 # GAGTTCGA TCGAACTC 14 1 4.7e-004 1.6e+001 # CAGTTCGA TCGAACTG 14 2 2.0e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 118 E= 9.1e-028 0.000000 0.483051 0.516949 0.000000 0.237288 0.000000 0.762712 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 AYCCRTAC DREME-2 # Word RC Word Pos Neg P-value E-value # BEST AYCCRTAC GTAYGGRT 105 5 4.1e-027 1.4e-022 # ACCCATAC GTATGGGT 54 3 9.7e-014 3.3e-009 # ATCCGTAC GTACGGAT 34 0 4.1e-011 1.4e-006 # ACCCGTAC GTACGGGT 15 0 2.9e-005 9.7e-001 # ATCCATAC GTATGGAT 14 2 2.0e-003 6.8e+001 letter-probability matrix: alength= 4 w= 8 nsites= 122 E= 1.4e-022 1.000000 0.000000 0.000000 0.000000 0.000000 0.581967 0.000000 0.418033 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.573770 0.000000 0.426230 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 CTBGGCCA DREME-3 # Word RC Word Pos Neg P-value E-value # BEST CTBGGCCA TGGCCVAG 71 3 8.6e-019 2.9e-014 # CTCGGCCA TGGCCGAG 36 1 1.9e-010 6.5e-006 # CTTGGCCA TGGCCAAG 23 1 1.3e-006 4.4e-002 # CTGGGCCA TGGCCCAG 12 1 1.7e-003 5.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 2.9e-014 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.507042 0.169014 0.323944 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 GCCWTAAC DREME-4 # Word RC Word Pos Neg P-value E-value # BEST GCCWTAAC GTTAWGGC 57 1 7.9e-017 2.7e-012 # GCCTTAAC GTTAAGGC 43 1 1.5e-012 5.1e-008 # GCCATAAC GTTATGGC 15 0 2.9e-005 9.6e-001 letter-probability matrix: alength= 4 w= 8 nsites= 58 E= 2.7e-012 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.258621 0.000000 0.000000 0.741379 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 MOTIF GCKCTACC DREME-5 # Word RC Word Pos Neg P-value E-value # BEST GCKCTACC GGTAGMGC 49 3 2.7e-012 9.2e-008 # GCGCTACC GGTAGCGC 34 2 7.2e-009 2.4e-004 # GCTCTACC GGTAGAGC 15 1 2.5e-004 8.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 49 E= 9.2e-008 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.693878 0.306122 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 ACTARACC DREME-6 # Word RC Word Pos Neg P-value E-value # BEST ACTARACC GGTYTAGT 41 1 6.1e-012 2.0e-007 # ACTAGACC GGTCTAGT 25 0 2.5e-008 8.3e-004 # ACTAAACC GGTTTAGT 16 1 1.3e-004 4.3e+000 letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 2.0e-007 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 0.390244 0.000000 0.609756 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 MOTIF CCCAHACA DREME-7 # Word RC Word Pos Neg P-value E-value # BEST CCCAHACA TGTDTGGG 59 9 9.1e-011 3.0e-006 # CCCACACA TGTGTGGG 31 6 1.7e-005 5.7e-001 # CCCAAACA TGTTTGGG 20 3 2.2e-004 7.5e+000 # CCCATACA TGTATGGG 9 0 1.9e-003 6.4e+001 letter-probability matrix: alength= 4 w= 8 nsites= 83 E= 3.0e-006 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 0.240964 0.650602 0.000000 0.108434 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 CGCCASAC DREME-8 # Word RC Word Pos Neg P-value E-value # BEST CGCCASAC GTSTGGCG 32 0 1.7e-010 5.8e-006 # CGCCACAC GTGTGGCG 21 0 4.2e-007 1.4e-002 # CGCCAGAC GTCTGGCG 11 0 4.7e-004 1.6e+001 letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 5.8e-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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.656250 0.343750 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF ATCKTGAG DREME-9 # Word RC Word Pos Neg P-value E-value # BEST ATCKTGAG CTCAMGAT 30 0 7.1e-010 2.4e-005 # ATCGTGAG CTCACGAT 20 0 8.5e-007 2.8e-002 # ATCTTGAG CTCAAGAT 10 0 9.5e-004 3.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 2.4e-005 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 0.666667 0.333333 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 AGAARA DREME-10 # Word RC Word Pos Neg P-value E-value # BEST AGAARA TYTTCT 245 142 1.4e-009 4.7e-005 # AGAAGA TCTTCT 79 32 2.3e-006 7.8e-002 # AGAAAA TTTTCT 190 118 3.5e-006 1.2e-001 letter-probability matrix: alength= 4 w= 6 nsites= 300 E= 4.7e-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 0.723333 0.000000 0.276667 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CYTGCGC DREME-11 # Word RC Word Pos Neg P-value E-value # BEST CYTGCGC GCGCARG 45 6 5.8e-009 1.9e-004 # CTTGCGC GCGCAAG 29 3 1.0e-006 3.5e-002 # CCTGCGC GCGCAGG 16 3 2.1e-003 7.0e+001 letter-probability matrix: alength= 4 w= 7 nsites= 49 E= 1.9e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.326531 0.000000 0.673469 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF CCDTGCA DREME-12 # Word RC Word Pos Neg P-value E-value # BEST CCDTGCA TGCAHGG 60 13 5.8e-009 1.9e-004 # CCGTGCA TGCACGG 26 4 2.6e-005 8.5e-001 # CCATGCA TGCATGG 20 5 1.9e-003 6.3e+001 # CCTTGCA TGCAAGG 19 5 3.1e-003 1.0e+002 letter-probability matrix: alength= 4 w= 7 nsites= 64 E= 1.9e-004 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.312500 0.000000 0.390625 0.296875 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGTTGCCA DREME-13 # Word RC Word Pos Neg P-value E-value # BEST CGTTGCCA TGGCAACG 26 0 1.2e-008 4.0e-004 # CGTTGCCA TGGCAACG 26 0 1.2e-008 4.0e-004 letter-probability matrix: alength= 4 w= 8 nsites= 26 E= 4.0e-004 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 0.000000 1.000000 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 ATGWGATA DREME-14 # Word RC Word Pos Neg P-value E-value # BEST ATGWGATA TATCWCAT 33 2 1.4e-008 4.5e-004 # ATGTGATA TATCACAT 18 1 3.5e-005 1.2e+000 # ATGAGATA TATCTCAT 16 1 1.3e-004 4.2e+000 letter-probability matrix: alength= 4 w= 8 nsites= 34 E= 4.5e-004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.470588 0.000000 0.000000 0.529412 0.000000 0.000000 1.000000 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 GATTWGAA DREME-15 # Word RC Word Pos Neg P-value E-value # BEST GATTWGAA TTCWAATC 40 5 2.7e-008 8.9e-004 # GATTAGAA TTCTAATC 25 1 3.4e-007 1.1e-002 # GATTTGAA TTCAAATC 15 4 9.3e-003 3.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 8.9e-004 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 0.000000 1.000000 0.625000 0.000000 0.000000 0.375000 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 AGTGGTTA DREME-16 # Word RC Word Pos Neg P-value E-value # BEST AGTGGTTA TAACCACT 31 2 5.1e-008 1.7e-003 # AGTGGTTA TAACCACT 31 2 5.1e-008 1.7e-003 letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 1.7e-003 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 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 MOTIF AYTGCGCC DREME-17 # Word RC Word Pos Neg P-value E-value # BEST AYTGCGCC GGCGCART 27 1 8.9e-008 2.9e-003 # ATTGCGCC GGCGCAAT 13 0 1.2e-004 3.8e+000 # ACTGCGCC GGCGCAGT 14 1 4.7e-004 1.5e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.9e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.518519 0.000000 0.481481 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF TGACCGMA DREME-18 # Word RC Word Pos Neg P-value E-value # BEST TGACCGMA TKCGGTCA 22 0 2.1e-007 6.8e-003 # TGACCGAA TTCGGTCA 14 0 5.8e-005 1.9e+000 # TGACCGCA TGCGGTCA 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 6.8e-003 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.636364 0.363636 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF ARTCATAC DREME-19 # Word RC Word Pos Neg P-value E-value # BEST ARTCATAC GTATGAYT 28 2 3.6e-007 1.2e-002 # AGTCATAC GTATGACT 15 1 2.5e-004 8.0e+000 # AATCATAC GTATGATT 13 1 8.8e-004 2.9e+001 letter-probability matrix: alength= 4 w= 8 nsites= 28 E= 1.2e-002 1.000000 0.000000 0.000000 0.000000 0.464286 0.000000 0.535714 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GGGGWTCA DREME-20 # Word RC Word Pos Neg P-value E-value # BEST GGGGWTCA TGAWCCCC 21 0 4.2e-007 1.4e-002 # GGGGATCA TGATCCCC 11 0 4.7e-004 1.5e+001 # GGGGTTCA TGAACCCC 10 0 9.5e-004 3.1e+001 letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 1.4e-002 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 1.000000 0.000000 0.523810 0.000000 0.000000 0.476190 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 CKTTGGGC DREME-21 # Word RC Word Pos Neg P-value E-value # BEST CKTTGGGC GCCCAAMG 27 2 6.8e-007 2.2e-002 # CTTTGGGC GCCCAAAG 11 0 4.7e-004 1.5e+001 # CGTTGGGC GCCCAACG 16 2 6.2e-004 2.0e+001 letter-probability matrix: alength= 4 w= 8 nsites= 27 E= 2.2e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.592593 0.407407 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 MOTIF GCATGSGA DREME-22 # Word RC Word Pos Neg P-value E-value # BEST GCATGSGA TCSCATGC 20 0 8.5e-007 2.8e-002 # GCATGGGA TCCCATGC 11 0 4.7e-004 1.5e+001 # GCATGCGA TCGCATGC 9 0 1.9e-003 6.2e+001 letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 2.8e-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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.450000 0.550000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF GAAAHAAA DREME-23 # Word RC Word Pos Neg P-value E-value # BEST GAAAHAAA TTTDTTTC 76 29 1.2e-006 4.1e-002 # GAAAAAAA TTTTTTTC 39 15 6.3e-004 2.0e+001 # GAAATAAA TTTATTTC 21 7 5.9e-003 1.9e+002 # GAAACAAA TTTGTTTC 20 7 9.1e-003 3.0e+002 letter-probability matrix: alength= 4 w= 8 nsites= 82 E= 4.1e-002 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 0.487805 0.243902 0.000000 0.268293 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 MOTIF CGGTMTCC DREME-24 # Word RC Word Pos Neg P-value E-value # BEST CGGTMTCC GGAKACCG 23 1 1.3e-006 4.2e-002 # CGGTCTCC GGAGACCG 15 1 2.5e-004 8.0e+000 # CGGTATCC GGATACCG 8 0 3.8e-003 1.3e+002 letter-probability matrix: alength= 4 w= 8 nsites= 23 E= 4.2e-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 0.347826 0.652174 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 # Stopping reason: E-value threshold exceeded # Running time: 125.44 seconds