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Such a low similarity between mouse and vole Oct4 proteins contrasts with much higher nucleotide homology (87%) between Oct4 genes in these species.
A possible explanation for this observation is that much higher nucleotide substitution rates for RNA viruses permit more rapid adaptation, greatly increasing the chances of successfully invading a new host population (21, 22 ).
When controlling for differences in sampling by comparing nucleotide diversity for CDEII to that estimated from TEs in the same strains using TE data from [ 14], I still see much higher nucleotide diversity in CDEII (Table 2 Figure 1).
Previous studies indicated that these markers not only showed high insertion polymorphism, but also can be efficiently converted into SNP markers for high-throughput genetic or diversity mapping due to much higher nucleotide polymorphism in the junction sites as compared to the gene regions [ 11].
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Also, the average nucleotide heterozygosity at the hsp82 locus was 0.0016, compared to a much higher average nucleotide difference of 0.024 among mmr-b copies within an isolate, suggesting multiple copies homogenized by concerted evolution rather than allelic variation.
If a portion of the sex chromosomes is substantially diverged, we expected much higher average nucleotide diversity per site in one sex (females for female heterogamy) in genomic windows spanning this diverged region.
As expected, these extreme differences in divergence and polymorphism between the two V1R genes are reflected in much higher (∼ten-fold) nucleotide diversity and nucleotide polymorphism in Vmn1r71 compared to Vmn1r67 (Fig. 1).
The number of tri-nucleotide SSRs was much higher than di-nucleotide SSRs.
Phylogenetic analysis of the sequences at the 5' and 3' termini of RNA11 of 94 group A RV strains identified two regions in the 3' arm that showed both much higher levels of nucleotide variation than the surrounding sequences and also strong evidence of co-variation (Fig. 1).
Therefore, the likelihood that an amino acid appears repeatedly and in isolation, is much higher than for nucleotides.
But if we compare performance of the initial PWM with those of the optimized di-nucleotide PWM we can see that the OFr is much lower (i.e. specificity is much higher) for the di-nucleotide matrix with similar sensitivity.
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