Abstract：Abstract SSR primers with dinucleotide repeat sequences are prone to continuous multi-peak, which influences the accurate collection of fingerprints. In order to improve the accuracy and automation of fingerprint analysis of such primers, an algorithm for the collection of fingerprints with continuous multi-peak was developed, and interactions between the continuous multi-peak algorithm and algorithms for other peaks including adjacent peak filtration, N+1 peak recognition, high-low peak filtration and diploid filtration were tested. Results demonstrated that the continuous multi-peak algorithm improved the accuracy and efficiency of fingerprint reading for SSR primers with dinucleotide repeat sequences, increased the accuracy of peak identification and location, and facilitated the estimation of peak height to truly reflect primer amplification. The error recognition probability of the continuous multi-peak peak was reduced from 50% to less than 1%, the recognition accuracy was increased from 2~4 bp to less than 1 bp, and the overall analysis time was shortened by more than 30%. By adjusting parameters, the intercoordination between the continuous multi-peak algorithm and algorithms for other peaks was guaranteed. The continuous multi-peak algorithm solves the identification and location of continuous multi-peak and the estimation of peak height, improves the efficacy of fingerprint collection of SSR primers with dinucleotide repeat sequences, eliminates the restriction in the application of SSR primers with dinucleotide repeat sequences that have the highest polymorphism in genomes and the most widely application, and provides important technical support for the better application of SSR primers in practice.
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