substr( $dna, $start + 1, $finish - $start, "X" x ( $finish - $start ) );


##</code><code>##

my $dna;
open DNA, "<dna.file" or die $!;
foreach (<DNA>) {
    chomp;
    $dna .= $_;
}
close DNA;

open POS, "<positions.input" or die $!;
foreach (<POS>) {
    chomp;
    my ($start, $finish) = split /\s+/;
    substr( $dna, $start + 1, $finish - $start, "X" x ( $finish - $start ) );
    print $dna, "\n";
}
close POS;