Hi mdunnbass,

First of all, before you do anything else, put the following 2 lines at the top of your program:

use strict;
use warnings;
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Now run your program, and get the output:

Global symbol "@fastarray" requires explicit package name at x line 5.
Global symbol "$setscounter" requires explicit package name at x line 
+6.
Global symbol "%matches" requires explicit package name at x line 7.
Global symbol "@fastarray" requires explicit package name at x line 7.
Global symbol "$site" requires explicit package name at x line 8.
Global symbol "%matches" requires explicit package name at x line 8.
Global symbol "@fastarray" requires explicit package name at x line 8.
Global symbol "%matches" requires explicit package name at x line 9.
Global symbol "@fastarray" requires explicit package name at x line 9.
Global symbol "$site" requires explicit package name at x line 9.
Global symbol "$i" requires explicit package name at x line 10.
Global symbol "$i" requires explicit package name at x line 11.
Global symbol "%matches" requires explicit package name at x line 11.
Global symbol "@fastarray" requires explicit package name at x line 11
+.
Global symbol "$site" requires explicit package name at x line 11.
Global symbol "$lowerlimit" requires explicit package name at x line 1
+2.
Global symbol "%matches" requires explicit package name at x line 13.
Global symbol "@fastarray" requires explicit package name at x line 13
+.
Global symbol "$site" requires explicit package name at x line 13.
# ... etc. ...
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Now go and fix those problems; declare each symbol in the outermost scope that they are needed.  For example:

my @fastarray;
my @fastarray;
my $setscounter;
my %matches;
my $site;
my %sets;
                                                                      
+          
FASTA: for (my $h=0;$h<(@fastarray);$h++) {
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You shouldn't ever have to declare the same variable twice (otherwise, it's like using a whole different variable).

That should give you some clues about where your problem is.

Update:  added more my declarations at the outer-most scope; the other variables can all be declared where they are first used (eg. my $upperlimit = my $span + $lowerlimit;).