Computer generated sequence alignment became a conventional tool in bioinformatics. SIM is one of the methods for determining similarity between two sequences through a pair-wise sequence alignment. However, most of the conventional tools lack the ability of incorporating biological properties into the alignment result which often leads to incorrect alignment. In this paper, we used a pair-wise alignment system called SIM that incorporates biological properties into the algorithm so that it can

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... suggest an appropriate sequence alignment based on the given nucleotide base pairs. SIM indicated nucleotide sequences alignments and suggested massive rearrangements of extra chromosomal, which can be extrapolated to total genome rearrangements.