*4.5. Detection Physical Counterparts of Basic Monomer and Proposed HOR Units*

RE identifies consensus sequences of the most abundant repetitive elements in the genome. However, these consensuses are only virtual assemblies of short reads originating from many different interspersed loci. To reveal the sequences' physical counterparts and sequence variation within the selected repetitive elements that are proposed to be HOR units, primers were designed based on the consensus sequences (supplementary data 3). PCRs were performed in 25 µL reactions and contained

1× TopBio Plain PP Master Mix (TopBio, Vestec, Czech Republic), each primer at 0.2 mM and 10 to 50 ng of genomic DNA. The cycling conditions were as follows: 4 min at 95 ◦C followed by 35 cycles of 95 ◦C for 30 s, sequence-specific annealing temperature for 30 s and 72 ◦C for 2.5 min, and a final extension at 72 ◦C for 10 min. The PCR results were verified on a 1% agarose gel (Figure 4). The PCR products of clusters were excised from the gels, cloned and sequenced at GATC Biotech (Konstanz, Germany) according to standard protocols.
