chomp( my $mask_input = <INPUT> );
my $new_mask = 'N' x length $mask_input;

...

while ( <INTERVAL> ) {
    
    my ( undef, $start, $end ) = split;
    --$start;
    substr $new_mask, $start, $end - $start, substr $mask_input, $start, $end - $start;

}

...
	
print OUT "$new_mask\n";