Table 4.
Criteria for visual inspection of intergenic regions in Streptococcus pyogenes NZ311
| start | 1) BLAST vs Streptococci | 2) BLAST vs S. pyogenes | 3) DNA base stacking energy | 4) RNAfold | |
|---|---|---|---|---|---|
| 1 | 202790 | X | X | ||
| 2 | 216807 | X | X | X | |
| 3 | 273446 | X | X | X | |
| 4 | 308253 | X | X | X | |
| 5 | 349593 | X | X | X | |
| 6 | 362796 | X | X | ||
| 7 | 363720 | X | X | X | |
| 8 | 407642 | X | X | ||
| 9 | 506298 | X | X | X | |
| 10 | 512500 | X | X | X | |
| 11 | 554314 | X | X | X | |
| 12 | 568980 | X | X | X | |
| 13 | 806825 | X | X | ||
| 14 | 827250 | X | X | ||
| 15 | 949486 | X | X | ||
| 16 | 1201476 | X | X | ||
| 17 | 1487751 | X | X | X | |
| 18 | 1571435 | X | X | ||
| 19 | 1581266 | X | |||
| 20 | 1704825 | X | X | X | |
Criteria: 1) increased conservation shown by BLAST against selected Streptococci genomes (see the moses website for a List). 2) increased conservation shown by BLAST against all Streptococcus pyogenes substrains. 3) increased DNA base stacking energy profile or presence of two nearby peaks. 4) a peak in the RNAfold profile.