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The compilation of all SSRs revealed that the proportion of SSR unit sizes was not evenly distributed.
We noted that the proportion of six different SSR unit sizes was not evenly distributed among perfect SSR groups.
For the purpose of polymorphic marker discovery, additional Class I SSRs were predicted using less stringent criteria: allowing for a SSR unit size of 2-5 bp, a minimum of 75% identity to the SSR unit and a minimum number of five repetitions.
SSRs were required to have a total length of ≥ 12 bp, SSR unit length ≥ 1-8 bp and 100% identical repetition of the SSR unit.
Analysis of SSR motifs revealed that the proportion of SSR unit sizes was not evenly distributed.
In contrast, the poly(A) sequence and the SSR unit caused a frameshift mutation in cemA of P. verticillata.
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In the imperfect and compound SSR categories, only mono-, di- and tri-nucleotide SSR units were present.
The numbers of SSR units varied greatly from two to > 35, and included perfect, compound and imperfect SSR units.
Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats.
SSR units flanking the 3' UTR of putative RTE-like conserved domains were visually identified.
SSR units at the 3' UTR, and TSD sequences at 5' and 3' flanking regions were visually identified.
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