The comparative analysis of the multilocus spectra obtained on the basis of use as primers in polymerase chain reaction of fragments of long terminal repeats (LTR) of endogenous retroviruses – SIRE-1, PawS5, BARE-1, BERV-K1 and BERV β-3 – in a number of breeds of cattle, sheep and horses was carried out. We compared the obtained multilocus spectra with homologous sequences from the reference genomes of cattle, sheep, horses, represented in GenBank, and miRNAs databases. It was discovered that the complexity of the resulting multilocus spectra could be related to the frequency of homologous sites to primers in the genomes of the studied species, the functional significance of the genomic elements that are associated with them and the comparative “oldness” of endogenous retroviruses. The most significant interbreed differences in cattle and sheep were detected in the spectra of PawS5 and BERV β-3 primers, in horses – in SIRE-1 and PawS5 spectra.
