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Genomes not only evolve at the level of nucleotide sequence, but also overall organization that include indels and rearrangement leading to sequence reorganization.
However, the effects of domestication and artificial selection are still mostly unknown at the level of nucleotide sequence variation.
In many cases, the level of nucleotide sequence identity of these transposons is unexpectedly high when considering the deep divergence of their host species (fig. 4).
The level of nucleotide sequence identity between the JE77 strain and No. 24/2010 was 93.4%, and that between JE77 and No. 50/2010 was 94.0%.
To align protein coding sequences (CDS) at the level of nucleotide sequence, we aligned sequences in protein space and project the aligned positions back to the nucleotide coordinates.
Of added benefit, this method is not dependent on the level of nucleotide sequence conservation in the promoter regions, which can vary extensively [ 5].
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In this study, we determined the binding sites of condensin on fission yeast (Schizosaccharomyces pombe) chromosomes at the level of nucleotide sequences using chromatin immunoprecipitation (ChIP) and ChIP sequencing (ChIP-seq).
Although the levels of nucleotide sequence variation between and within individual EHDV serotypes have not yet been fully explored, initial studies suggest that the same may be true for EHDV [15].
The levels of nucleotide sequence identity shared between the SH1211 and JXA1 strains for the other ORFs ranged from 94.9%to97.5%5%.
Evolutionary closeness of phages in this group is manifest at the levels of nucleotide sequence, protein sequence and genomic organization [ 13].
The gki, recP, and xpt loci exhibit the highest level of nucleotide sequence diversity.
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