Variable number of tandem repeals (VNTR) stands for a tandem repeat which has variation in length and the number of repeated segments between individuals. VNTRs are useful as molecule markers in many applications, such as DNA fingerprinting, genetic disease analysis and molecular typing of prokaryotes. It costs a large amount of money and time to identify these special loci by using traditional biological experiments. Here we develop a novel tool, VNTR analyzer, to identify and analyze VNTR in genome sequence by comparing genomic sequences of different strains. In this study, we demonstrate its ability to detect VNTRs by analyzing 3 bacterial species: Staphylococcus aureus, Xylella fastidiosa and Salmonella enterica. The results showed that our program could find VNTRs accurately in a short time. Moreover, the program provides biologists a colorful visualization tool for further analysis.