Bioinformatics encompass storing, analyzing and interpreting the biological data. Most of the challenges for Machine Learning methods like Cellular Automata is to furnish the functional information with the corresponding biological sequences. In eukaryotes DNA is divided into introns and exons. The introns will be removed to make the coding region by a process called splicing. By indentifying a splice site we can easily specify the DNA sequence category (Donor/Accepter/Neither).Splicing sites play an important role in understanding the genes. A class of CA which can handle fuzzy logic is employed with modified clonal algorithm is proposed to identify the splicing site. This classifier is tested with Irvine Primate Splice Junction Database. It is compared with NNspIICE, GENIO, HSPL and SPIICE VIEW. The reported accuracy and efficiency of prediction is quite promising.