Complex repeat sequences, such as those found in D21S11, can contain variable repeat blocks in which the order is switched around for alleles that are the same length. For example, the STR locus D21S11 has four alleles that are all 210bp when amplified with the Profiler Plus™ kit (Appendix I). While these alleles would be sized based on overall length to be 'allele 30', they contain repeat blocks of 4-6-CR-12, 5-6-CR-11, 6-5-CR-11, and 6-6-CR-10 for the pattern [TCTA]-[TCTG]-constant region (CR)-[TCTA]. In such cases, variant alleles would only be detectable with complete sequence analysis.
It is important to realize that from an operational point of view internal allele variation is not significant. In the end a match is being made against many loci not just one, such as D21S11, with possible internal sequence variation.
Most of the STR loci used in human identity testing have not exhibited internal sequence variation (see Appendix I), particularly the simple repeat loci TPOX, CSF1PO, D5S818, D16S539, TH01, D18S51, and D7S820. Remember that we are essentially binning alleles based on measured size anyway with STR typing since sequence analysis of individual alleles is too time consuming and would rarely reveal additional information because STR variation is primarily size-based.
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