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
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* |