I am really new to perl and am taking a course on it. I wrote the following program for an assignment and am getting the incorrect output. I'm getting over a million lines while the expected output is closer to 250,000. The last 12 nts need to be unique to the genome. I have a feeling it's due to my regex. Any advice would be greatly appreciated. Thankyou.

 #!/usr/bin/perl
 use strict;
 use warnings;

my %windowSeqScore = ();                

my $input_file = '/scratch/Drosophila/dmel-all-chromosome-r6.02.fasta'
+;

my $sequenceRef = loadSequence($input_file);

my $output_file = 'unique12KmersEndingGG.fasta';
open (KMERS,">", $output_file) or die $!;

my $windowSize = 21;                    
my $stepSize = 1;                       

for ( my $windowStart = 0 ; $windowStart <= ( length ( $$sequenceRef )
+ - $windowSize );
                $windowStart += $stepSize ) {
        my $windowSeq = substr ( $$sequenceRef, $windowStart, $windowS
+ize);

       if ($windowSeq =~ /([ATCG]{10}GG$)/) {
                $windowSeqScore{$windowSeq}++;
        }
}

my $count = 0;                          

for (keys %windowSeqScore){             
        $count ++;                    
        if ($windowSeqScore{$_} == 1 ) {
        print KMERS ">crispr_$count", "\n", $_, "\n";
       }
}
sub loadSequence {
        my ($sequenceFile) = @_;        
        my $sequence = "";              
        unless ( open( FASTA, "<", $sequenceFile ) ) {
                die $!;
        }
        while (<FASTA>){                
                my $line = $_;          
                chomp ($line);          
                if ($line !~ /^>/ ) {   
                $sequence .= $line;     
                }
        }
        return \$sequence;
}
[download]

This is some of the output I'm getting

 >crispr_1
ACAACAATAATGCGACGATGG
>crispr_2
TCCGAAGTCTGCCACTTTAGG
>crispr_3
TGATTCCCGATGCAGTGGGGG
>crispr_4
GTGGGACGACTGGACAAGTGG
>crispr_5
GCCGAAGGAACAACACACAGG
>crispr_7
CAAAGTCACTGTCTACGCAGG
>crispr_8
ATCATTTGCTACCAGAAATGG
>crispr_9
ATCCTGCCTGGCAGCCGGAGG
>crispr_10
CCCTTGATCATGATAAATGGG
>crispr_11
AACAACTAACTCATTTTGTGG
>crispr_12
TTCCCAGCGGGGAAAAAATGG
>crispr_13
TCAAGAAAGATTTCCAAAAGG
>crispr_14
CCATGCGAGAAATCGCGCAGG
>crispr_15
GCTGCTCAAACTGGAACTTGG
[download]

this is some of the expected output I should be getting

 >crispr_1
TTTAGACTCCCCTTGTACAGG
>crispr_2
TCTTCAGTCTCCAGTCTCCGG
>crispr_3
TTGCGTTGCGGAGCATACTGG
>crispr_4
TGCCACCAGTGGTTCCAAGGG
>crispr_5
TTATGTTTGTACGAGGGGGGG
>crispr_6
TCTCTTTGGTTTACGGATGGG
>crispr_7
TTGGCAAGGAGACGGTCCTGG
>crispr_8
TGAATTAAAGCTTGCGCGAGG
>crispr_9
GGAAGAGGCATCAACGAGGGG
>crispr_10
TGCAGCGGCCTAACAAGGCGG
>crispr_11
CTGCCCGATCCTAACTCCAGG
>crispr_12
ATATATGTTTGACCGTCGGGG
>crispr_13
GGAAACAAAAGCCTATGCGGG
>crispr_14
TGCGATCAGGTGTATCCGAGG
[download]