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(ii) Evaluating only the top 15% most variable positions as estimated by the entropy calculation (It is more likely to identify a significant distribution at the most variable positions).
For the PKR-BD, most variable positions were detected in the ISDR (11 of 40, 27.5%), when compared with the remaining positions within the PKR-BD (5 of 26, 19.2%).
Although residue 86 is one of the most variable positions in the large subunit (up to 11 different amino acids across the 499 plant species; [26]), His86⇒Tyr86 replacement is very rare, considering that about 76% from 491 flowering species have His86, but only two species (<1%) have Tyr86 [15].
The most variable positions are outside the EF-hand domains, which are well conserved.
This proportion is the smallest for the highly conserved sites, and the highest for the most variable positions.
Resolution of EFs trees does not increase when the most variable positions are excluded from the alignments (supplementary figs. S2 and S3, Supplementary Material online).
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As the third codon position is the most variable codon position due to degeneracy of the genetic code, variation of G+C content at the third codon position (GC3) should have the greatest effect on OSC usage bias for frame +2.
It was shown earlier that selection may be operating in the protein coding regions on most variable synonymous positions to maintain a more stable and ordered mRNA secondary structures [30].
To simplify annotation of Prdm9 ZFAs in subsequent analyses, we used a one-letter code to identify each ZF repeat depending on the amino acid triads present at the most variable three positions, −1, 3, and 6, as well as additional alterations (Fig. 2A) (see Materials and Methods for detail).
Finally, following recent reports that most methylation variable positions are located outside of CpG-islands [19], we explored the genomic pattern of methylation variable positions in relation to CpG density.
Two types of core repeats are distinctive, based on six most exclusive variable positions.
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