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Microsatellites are found in taxonomically different organisms,and such repeats are related with genomic structure,function and certain diseases.To characterize microsatellites for macaques,we searched and compared SSRs with 1–6 bp nucleotide motifs in rhesus,cynomolgus and pigtailed macaque.A total of 1395671,1284929 and 1266348 perfect SSRs were mined,respectively.The most frequent perfect SSRs were mononucleotide SSRs.The most GC-content was in dinucleotide SSRs and the least was in the mononucleotide SSRs.Chromosome size was positively correlated with SSR number and negatively correlated with the relative frequency and density of SSRs.The GC content of chromosome SSRs were negatively correlated with relative frequency of SSRs and GC content of chromosome sequences.The features of microsatellite distribution in assembled genomes of the three species were greatly similar,which revealed that the distributional pattern of microsatellites is probably conservative in genus Macaca.The degenerated number of repeat motifs was found to be different in pentanucleotide and hexanucleotide repeats.Species-specific motifs for each macaque were significantly underrepresented.Overall,SSR frequencies of each chromosome in rhesus macaque were higher than in cynomolgus macaque.The maximum repeat times of mono-to pentanucleotide repeats in cynomolgus macaque was more than other two macaques.These results emphasize the genetic diversity and phylogenetic relationship of genus Macaca species.Our data will be beneficial for comparative genome mapping,understanding the distribution of SSRs and genome structure between these animal models,and provide a foundation for further development and identification of more macaque-specific SSRs.