open( SEQ, 
    "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/consensus_files/mask_files/mask."."$population".".chr.23.txt"
) or die "can't open masked file\n";

my $bigScalar = <SEQ>;
close SEQ;

open (INTERVAL, "<$filtered_sites") or die "can't open $filtered_sites";
my $lastEnd = 0;
while( <INTERVAL> ) {
    my( $start, $end ) = split "\t", $_;

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

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

## do something with $bigScalar
...