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Recombination frequency is proportional to the size of the repeat: large (>1 kb) repeats recombine at high frequency, intermediate-sized (100 1000 nt) repeats recombine sporadically, and short (<100 nt) repeats are thought to recombine rarely, if ever [7], [12], [13].
Overall, we notice a trend that STRs of increased size of the repeat unit exhibit lower variation.
The 33 proteins were further classified depending on the content and relative size of the repeat domains.
Dividing the size of this region by the size of the repeat unit yielded the number of repeats in each locus.
In order to assess the size variation in these three SSRs, we designed primers that flank the repeat regions and scored the size of the repeat regions across the 143 accessions.
The expected occurrence of insertion into the repeat was calculated based on the size of the repeat compared to the size of the rest of the plasmid (minus the bla gene and the origin of replication).
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Written in Java, Lirex provides a user-friendly interface and allows users to specify LIR searching criteria, such as length of the region, as well as pattern and size of the repeats.
The identity and the size of the repeats were limited to no less than 90% (hamming distance equal to 3) and 30 bp in unit length, respectively.
Indeed, the basic view that nuclear aggregates formed by CUG expansions are intrinsically toxic and/or that toxicity severity is determined only by the size of the repeats and their concentration have been already challenged by various studies [6], [17] [19].
In case where recombination between the inverted repeats results in an inversion of the internal sequence, the recombination rate between the inverted repeats is positively related to the size of the repeats but negatively related to the distance between the repeats [52].
Recombination frequency seems to depend on the size of the repeats.
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