index.pl

#!/usr/bin/perl
use strict;
use warnings;

my $target="ATcgAGCGTTTCG";

print $target."\n";
$target=uc("ATcgAGCGTTTCG");


my @pos;
@pos[0]=0;
for(my $i=1; $i<=3; $i++){
        @pos[$i] = index($target,"CG",@pos[$i-1]) + 1;
        print "$i\t@pos[$i]\n";
}