Abstract: This work aims to extend the application range of MISA (MIcroSAtellite identification tool). The authors adjusted important parameters of MISA to find their effects on analysis results, and attempted to apply MISA to analyze other sequence types. Five different types of sequences of Beta vulgaris were collected and analyzed to find out appropriate parameters for each sequence type, and to clarify the effects of different parameters on analysis results. Among the five types of sequences, four were collected from public database and one was obtained from the early work of the research team. MISA was found to be able to analyze all these five sequence types of B. vulgaris sequences with appropriate analyzing parameters and sequence format. The max length of the sequence library was restricted by the redundant sequence removing tools, and affected redundant sequence processing, including both time consumption and analysis results. The length of detectable repeat units affected the amount of mined sites and the designing of primers. The length range of the sequence library did not disturb MISA analysis. About 8000 SSR sites were mined from the five types of B. vulgaris sequences using MISA tool with adjusted parameters. These results implied that MISA could be applied to analyzing different sequence types. Two parameters, the limit of sequence max length in the sequence pool and the length of detectable repeat units, should be adjusted. It is suggested that the sequences should be as long as possible under the permission of hardware and software, the length of repeat units should be adjusted according to the research purpose.