Microsatellites or simple sequence repeats (SSRs) are tandemly repeated tracts of DNA composed of 1–6 base pair (bp) units. The perfect SRRs were searched and computed by using bioinformatics methods in the complete genomes of goat (Capra hircus) and Tibetan antelope (Pantholops hodgsonii), and their number, frequency, density and distribution of SSRs were comparative analyzed in the study. The total SSRs number detected in the goat and Tibetan antelope genomes were 920 300 and 913 059 loci respectively, which accounted for 5.56‰ and 5.39‰ of its whole genome length, respectively. The number, proportion, frequency and density of six SSRs repeat types were abided by the following pattern: mono- > di- > tri- > penta- > tetra- > hexa-nucleotide SSRs in the goat and Tibetan antelope genomes. There were significant differences compared among these characteristics of six SSRs repeat types, and no significant difference among these characteristics of the same SSRs repeat type. Tri- nucleotide SSRs was the most abundant type in the 5′-UTR (5′-Untranslated Regions) and exon area of goat genes, followed by the pattern: mono- > di- > tetra- > penta- > hexa-nucleotide SSRs; while mono- nucleotide SSRs was the most abundant type in its 3′-UTR (3′-Untranslated Regions) and intron area, followed by the pattern: di- > tetra- > tri- > penta- > hexa-nucleotide SSRs. The overall SSRs number was compared in all autosomes and X chromosome of goat, the largest SSRs number was found in chromosome 1 followed by chromosome 2, X, 6, 4 and 8, and the smaller SSRs number was in chromosome 25 and 28. There no significant difference in the SSRs frequency among all chromosomes in the goat (P > 0.05). The dominant SSRs motifs of all repeat type showed great similarity in the goat and Tibetan antelope genomes, which were consistent with the dominant SSRs motifs of different repeat type in the cattle and sheep genomes.
