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I'm working on the simple sequence repeat (SSR). I found just one region (about 21 bp) with an SSR motif in a given gene. This gene has multiple transcripts, with the same SSR motif located in various positions of different transcripts. Could you please help me understand how this happened?

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Because of Alternative Splicing, suppose an exon occurs neither the first nor the last, then the same exon will come at various positions in different transcripts of the same gene. Thus, if your SSR of interest exists in that exon, you will find the same SSR located in the various positions of different transcripts.

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