my $mask_input = <INPUT>;

...

my $lastEnd = 1;

while ( <INTERVAL> ) {
    
    my (undef, $start, $end) = split '\s', $_; 

    ## change everything from the end of the last range
    ## to the start of this range to 'N'
    substr( $mask_input, $lastEnd, $start ) =~ tr[\x00-\xff][N];
    $lastEnd = $end;
    
}

...
	
print OUT "$mask_input";

##</code><code>##

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";