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Repeat sequence analyses in the chloroplast genome

CL Changhong Li
YZ Yongqi Zheng
PH Ping Huang
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Simple sequence repeats (SSRs) on the cp genome were mined using MISA software (MicroSAtellite, https://pgrc.ipk-gatersleben.de/misa/). The minimal repeat units were set as mono-12, dimer-6, trimer-5, tetramer-5, pentamer-4 and hexamer-4, and Primer 3 was used for designing primer pairs in the flanking region of each candidate locus94. Tandem repeat sequences were analyzed by Tandem Repeats Finder95, the alignment parameters were set at recommended values (Match-2, Mismatch-7, Delta-7), and the minimum alignment score and maximum period size were set as 80 and 500, respectively. Palindromic repeat sequences, dispersed repeat sequences (including the forward repeats and inverse repeats) and complement repeats were analyzed by REPuter (https://bibiserv.cebitec.uni-bielefeld.de/reputerl)96, and the minimum repeat size and maximum base mismatch were set as 30 and 3, respectively.

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