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The ND5 locus was more highly resolving than COI as it showed more sequence variation: nucleotide diversity and average number of nucleotide differences (k) were 3.2 and 2.9 times higher for ND5, respectively (Table 3).
Interestingly, the enzymes of proteasome-lacking organisms exhibit more sequence variation, only matched by Nitrospirae exponents.
The C2AB region is highly conserved whereas the N-terminal portion has much more sequence variation.
The C2AB region is highly conserved whereas the N-terminal portion has a little more sequence variation.
Interestingly, the PCA based on the normalized values showed that there is more sequence variation between gene features than between chromosomes.
Regardless of mechanism, Rhox2 paralogues show significantly more sequence variation than Rhox3 and 4, which may affect the evolutionary trajectories of these genes.
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In contrast, the Pribnow box is recognizable but less conserved, indicating more sequence variations among promoters.
In future, sequencing the whole length of GTR2 in B. napus is needed to identify more sequence variations responsible for GS, because InDels may also exist in the promoter, terminator, or intron regions.
We were able to show that CC founder strains contained significantly more sequence variations in cis-regulatory elements in any of the studied tissues and cell lines than did nonfounder strains.
mRNA-Seq is a powerful tool to develop SNPs but has some limitations for detecting more extensive sequence variation.
However, at the limit of somatic mutation detection with real time PCR technologies, sequencing by Sanger is not suitable as a confirmatory method and validation of results may require a more quantitative sequence variation assay.
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