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Table 7 Comparison of conservation scores between highest scoring k-mers and position weight matrices (PWM) for 20 known regulatory elements in S. cerevisiae, obtained when comparing S. cerevisiae and S. bayanus

From: Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

Name Sequence Score PWM consensus Score
Bas1 AAGAGTCA 93.8* [AG][AG]NANGAGTCA 80.9
Cbf1 CACGTGA 421.3* [AG][AG]TCACGTG 406.5
Fkh1/2 TAAACAA 110.3 GTAAACAA[AT] 114.1*
Gcn4 TGACTCA 93.4 [AG][AG]TGA[CG]TCA 135.4*
Gcr1 TGGAAGC 82.7* [AG]GCTTCCT CG]T 42.7
Hap4 CCAATCA 104.2* G[AG][AG]CCAATCA 96.6
Ino4 CATGTGA 91.2* CAT[CG]TGAAAA 61.1
Mbp1 ACGCGTC 204.1 ACGCGTNA[AG]N 210.2*
Msn2/4 AAAGGGG 140.1 A[AG]GGGG 169.7*
PAC GCGATGAG 404.6 GCGATGAGNT 520.3*
Pdr3 CCGCGGA 76.9 [CG]NNTCCG[CT]GGAA 102.5*
Rap1 TGGGTGT 103.8 [AG]TGTN[CT]GG[AG]TG 253.2*
Reb1 CGGGTAA Inf [CG]CGGGTAA[CT] Inf
Rpn4 TTTGCCACC 218.6 GGTGGCAAAA 259.4*
RRPE AAAAATTT 509.9* TGAAAAATTT 388.80
Ste12 TGAAACA 81.4 ANNNTGAAACA 100.0*
Sum1/Ndt80 TGACACA 135.4* [AG][CT]G[AT]CA[CG][AT]AA[AT] 100.0
Swi4 CGCGAAA 224.1* NNNNC[AG]CGAAAA 116.6
Ume6 TAGCCGCC 377.2 TCGGCGGC[AT]A 410.0*
Xbp1 CCTCGAG 86.7 GCCTCGA[AG]G[AC]G[AG] 141.7*
  1. *Indicates which regulatory element representation (k-mer or weight matrix) obtained the highest conservation score. Inf corresponds to very large conservation scores, obtained when taking the negative natural logarithm of near-zero hypergeometric p-values.
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