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Short tandem repeats (STRs), or microsatellites, are the class of repeat sequences that have repeat units of up to 6 bp directly adjacent to each other. STRs are generally more polymorphic than other kinds of variation such as sequence copy number and single-nucleotide polymorphisms (Verstrepen et al., 2005). The length variability of STRs is associated with phenotypic variation in many species (Pearson et al., 2005; Sureshkumar et al., 2009; Castel et al., 2010; Whan et al., 2010). These disorders are commonly caused by repeat expansion. Analysing the variation of STRs, and particularly long STRs, is an important step to understand their variability across individuals and the mechanisms that lead to their instability.