Untested: 
if (my @matches = $sequence[1] =~ m/^(.*)$reg(.*)$/i) {
    @{ $aligned[$posCount] }[ 0 .. $numInsertionDeletes - 1 ] = @match
+es;
}

[download]

In reply to Re: Need a Method to add recursion to my regex by choroba
in thread Need a Method to add recursion to my regex by vivomancer

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