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Table 4 Criteria for visual inspection of intergenic regions in Streptococcus pyogenes NZ311

From: Non-coding RNA detection methods combined to improve usability, reproducibility and precision

  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
  1. 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.