Programa alineamiento

			#!/usr/bin/perl -w
			use strict;
			 
			my @query1;
			my @subject1;
			my $query2;
			my $subject2;
			my $i=0;
			while (){
			if ($query2=~ m/Query\s+\d+\s+\(S+)\s+\d+/){
			@query1=split (//,$1);
			}
			 
			if ($subject2=~ m/Sbjct\s+\(d+)\s+\(S+)\s+\d+/){
			@subject1=split(//,$3);
			}
			 
			if ($query2[$i] eq "*" ){
			if ($subject2[$i] eq "C" || $subject2[$i] eq "c"){
			print "posicion",$i+$2,"\n";
			}
			}
			$i=$i+1;
			}