Abstract: Objective To develop a simple method identifying and illustrating clustered repeats in bacterial genomes, and to observe the patterns of clustered repeats in Salmonella genomes. Methods Bacterial genomes were cut into overlapped pieces of identical size with a sliding window strategy. Each piece of genome fragment was aligned against itself with BLAT integrated in PipMaker, which was further used to build collinearity figures. Collinearity figures were analyzed to identify the clustered repeats. Results With the new pipelineCRpred (Clustered Repeat Predicter), Salmonella typhimurium LT2 genome was screened,and in total 151clustered repeats were disclosed. Pattern analysis on these repeats indicated that there were five categories, including low-copy simple tandem repeats, high-copy simple tandem repeats, interspaced tandem repeats, reverse-complementary repeats, and interspaced reverse-complementary repeats. Nine repeat regions in LT2 genome were discovered whichcould not be simply classified into the 5 categories defined above. Conclusions A new, simple and intuitive strategywas proposed to identify and show clustered repeats in genomes, providing clues for CRISPR, VNTR and other repeat-related studies.

Key words: repeat sequence, Salmonella, Pipmaker, CRISPR, VNTR