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The genome sequence information is essential to understand the function of extensive arrangements of genes. It is significant to combine all sequence information in a precise database to provide an efficient manner of sequence similarity search. The complete genome analysis, which is one of the essential steps to know their characteristics, is very important. Complete genome analysis is depends on matrix frequency of sequence residue calculation and CGR analysis. In this study, we select rice as the specimen for complete genome analysis. Rice is one of the most essential cereal crops providing food for more than half of the world’s population.