Dear JohnGG, Thank you for your reply and suggestions. The sample data which i provided only has 4 sequences whereas in reality i have files which have greater than 25,000 sequences. In that situation I guess I might have to use loops to do the checking. Kindly let me know if I am thinking in the right direction.

In reply to Re^2: Comparing array of aligned sequences by newtoperlprog
in thread Comparing array of aligned sequences by newtoperlprog

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