A text file with a single line consisting of ~155e6 characters, all 0's and N's, is read in as a scalar variable. Each character is assigned to a single element of an array

As a scalar, your 155e6 file will require ~ 150 MegaBytes of memory.

As an array, 1 char per element, it will require ~ 10 GigaBytes of memory. Assuming you have that available.

But for your stated goal:

The goal: change all elements of the @info array that lie outside of my intervals to N's.

There is no need to go through the time and memory costly process of spliting your string to an array. And no need to iterate over 155 million characters one at a time.

You can easily and quickly overwrite the characters outside your ranges with 'N's, in-place in the scalar:

open( SEQ, 
    "/Users/logancurtis-whitchurch/Dropbox/thesis_folder/consensus_fil
+es/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 stri
+ng to 'N'
substr( $bigScalar, $lastEnd, length( $bigScalar ) ) =~ tr[\x00-\xff][
+N];

## do something with $bigScalar
...
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