Remarkably, although 16 tRNA genes have been lost, the mt genome size of S. magnus (13,818) is comparable to those of Leptotrombidium deliense (13,731) and L. akamushi (13,698) [ 10, 27] which is due to a larger LNR and more intergenic spacer regions.
Only factors with P < 0.05 binding to 60 or more distinct intergenic regions were considered.
A related problem is that of the evolutionary forces acting on regulatory sites and, more generally, intergenic regions.
Hence, the SIDD scores serve to separate the clearly divergent (less stable) and the convergent (more stable) intergenic regions.
As protein-coding regions in the genomes are conserved in related species more than intergenic regions, EST-based markers are useful for comparative mapping between them.
There are many more short intergenic regions than the long ones, which typically leads to the pattern described by the authors.
An additional outcome from this analysis is the high overlap between 3′-UTR and 3′-downstream (183) and between 5′ -UTR and 5′ -upstream (135), which indicates that many PS signals at the more distant intergenic regions are actually coming from its contained UTR region.
This effect was more pronounced in intergenic regions, while coding regions showed a more equal log2 ratio distribution across GC bins.
Because SNPs were only 1.8 times more located in intergenic regions and introns compared with coding regions, we conclude that point mutations are more frequent in coding DNA than indels leading to frame shifts immediately.
The poly A- 3' EST maps more to the intergenic regions than poly A+ and bimorphic 3' ESTs.
