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Comparison with Drosophila and Anopheles databases gave similar results, with estimates of sequences possessing no similarity of 44.7 and 45.9%, respectively.
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Loci, most difficult to assess with respect to the copy number upon gel-sizing (i.e. containing short repeats of 20 bp size or less, namely VNTR 19, 20 and 24) were sequenced to verify estimates of sequence divergence.
Interestingly, none of the pathways with either elevated or diminished pathway level transcript CV showed significantly different estimates of sequence polymorphism in comparison to randomly generated pathways (Table S5)[52].
This would produce upwardly biased estimates of sequence divergence.
We excluded these substitutions from our estimates of sequence divergence between ancestral and descendant repeat element copies, producing refined estimates of sequence divergence.
This would produce upwardly biased estimates of sequence divergence from consensus.
Estimates of sequence diversity are highest in the Yukon River and Kuskokwim River drainages near the Bering Sea.
These suboptimal alignments may lead to less accurate estimates of sequence divergence.
However, the availability of protein domains and their corresponding nucleotide sequences linked to estimates of sequence evolutionary rates is lacking.
We also constructed Neighbor-joining trees [ 39] of the amino acid sequences using MEGA4 [ 40] and Poisson-corrected estimates of sequence divergence.
The resulting estimates of sequence divergence were then used to obtain dates of divergence based on extrapolation from the strain HS-SOPE comparisons.
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