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Phalaenopsis has few sequence resources.
Sequences which covered more than 70% overlap between forward and reverse sequences were considered (except a few sequence of matK where coverage was less than 50%).
We find it striking that there appear to be so few sequence regions with either consistently low or high branch lengths across all four species.
Intuitively, this can be understood by considering that polymorphisms can often be confused with fixed differences between species when single, or few, sequence comparisons are used to measure divergence.
Recent reports demonstrate that even after several billion fragments are sequenced, almost a quarter of the human bisulfite genome is represented by just a few sequence traces, and more than a third of all CpG dinucleotides are unanalyzed [4].
It remains to be seen whether any of these apparently Pae-specific genomic regions, discussed below, are also conserved in other P. syringae pathovars of woody hosts for which few sequence data are currently available.
The shift of mismatch motifs by a few sequence positions about the middle base of the probe and the effect of flanking mismatches adjacent to triples with a central mismatch can be neglected to a good approximation.
For many species, none or very few sequence data are available.
With this comprehensive update in place, we anticipate very few sequence changes in the future.
Consequently, the most distant homologs detected by HHpred often have few sequence motifs conserved.
On the other hand, many miRNA are represented by only a few sequence reads.
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