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The point is to see the common and the diverging elements.
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Although TinT performs a subsequent stringent quality-check of detected fragmented elements, miss-annotations, especially if old and thus highly diverged elements are involved, cannot be completely excluded.
Importantly, average methylation was significantly lower for both the red and green clade elements, compared to black clade elements, supporting the notion that phylogenetically older and more uniform elements tend to be more highly methylated than younger and diverged elements.
To identify more diverged elements, we used the 157 high confidence elements identified through this iterative search as initial queries for a second search with less stringent search parameters.
To rule out the possibility that our similarity searches could not detect highly diverged elements we analyzed all the sequences to try to identify repeats de novo through a clustering approach.
Although our methods are apparently very good at identifying high copy number elements and moderate-to-low copy number families with high similarity, they will necessarily be inadequate for identifying very low copy number families and older highly diverged elements in a genome.
Only short and/or highly diverged element fragments are not identifiable by our search strategy as seen, for example, for the previously identified rooA fragments in D. melanogaster.
Reproductive barriers are prerequisites for the evolution of diverging genetic elements, which convey an ecological separation (Mallet 2007; Giraud et al. 2010).
Furthermore, they allow us to propose diverged sequence elements that may contribute to the differences in the recombinational landscape in the two species.
Six other splice sites were either in close proximity (within 5 codons) or bordering diverged inserted elements.
There might also be "leakage" because of partially diverged regulatory elements, resulting in cross-responsiveness on cellular or environmental stimuli.
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