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Genomic micro-satellites are the genomic regions consisting of short and repetitive DNA motifs. Micro-satellite region usually exposes intrinsic polymorphism in terms of the numbers of repetitive motifs, which is often described as a probability distribution of the numbers of repeats. In cancer genomics, for any micro-satellite region, it is considered as a micro-satellite instability (MSI) event, if the probability distribution sampled from tumor tissue is significantly different from the distribution sampled from the corresponding normal tissue. Since recent studies have emphasized the importance of micro-satellite instability events in cancer diagnosis and treatments, a series of computational approaches have been developed to detect MSI events from the sequencing data. However, the existing methods suffer an accuracy loss when clonal micro-satellites exist, which are recently observed in some TCGA/ICGC samples. For a …