*4.3. Satellite DNA Clusters Screening for Tandem Repeats*

All genomically abundant clusters containing at least 0.01% of the input reads were examined manually to select those that potentially possess tandemly organized DNA. Primary selection of the clusters was performed based on their form (Figure 2A). Contigs of each selected cluster were analyzed using the following publicly available online tools: (i) the YASS genomic similarity tool, which enables searches of more fuzzy repeats for potential tandem organization (http://bioinfo.lifl.fr/yass/yass. php) [54], with each contig compared against itself and visualized by dot plots (Figure 2B); (ii) BLAST was used to confirm that the cluster belongs to the CficCl-61-40 satDNA family (supplementary data 1); and (iii) primers were designed from the consensus sequence for PCR conformation of the typical tandem array structure (Figure 2C). Each search was performed for each of the analyzed species.
