*2.5. Identification of Repeat Sequences in P. vulgaris Mitogenome*

Three kinds of repeats—SSRs, tandem repeats and dispersed repeats—were detected in the *P. vulgaris* mitogenome. The SSRs were detected using the web-based microsatellite identification tool MISA-web (https://webblast.ipk-gatersleben.de/misa/) [47] according to the methods of previous studies [9,26] with a motif size of one to six nucleotides and thresholds of eight, four, four, three, three, and three, respectively. Tandem repeats were identified using the online tool Tandem Repeats Finder 4.09 with default settings (http://tandem.bu.edu/trf/trf.html) [48]. AB-BLAST 3.0 was utilized to identify and locate dispersed repeats with the following parameters: M = 1, N = −3, Q = 3, R = 3, kap, span, <sup>B</sup> <sup>=</sup> <sup>1</sup> <sup>×</sup> <sup>10</sup><sup>9</sup> and W <sup>=</sup> 7, which have been proven as effective in many studies [8,9,49]. The BLAST hits with e-values < 1 and identities > 80% were considered as disperse repeats. The number of dispersed

repeats was calculated for seven size intervals (30–49, 50–69, 70–99, 100–149, 150–199, 200–999 and ≥1000 bp). Partly or wholly overlapping repeats were considered as a single repeat unit.
