Hello Perl Monks, The same question was asked here:

http://stackoverflow.com/questions/40414018/perl-program-to-look-for-k-mer-with-specific-sequence

but seems like it wasn't answered correctly or wasn't finished.

I need to build upon a previous program that I've written and find the first 1000 unique, k-mers of length 23 that end with GG from a Fasta file.

The first 20 lines of the Fasta file look like this: 
 > >2L type=chromosome_arm; loc=2L:1..23011544; ID=2L;  dbxref=REFSEQ:
+NT_033779,GB:AE014134; MD5=bfdfb99d39fa5174dae1e2ecd8a231cd; length=2
+3011544; release=r5.54; species=Dmel;
CGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTGCCTCTCAT
TTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCGAGAGTAGT
GCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATGGTGGCGGA
TGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAATAAATTCA
TTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGAGAGTAGTG
CCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTATATTACCG
CAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGCAGCGGAGATATT
TAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGCCAACATAT
TGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTTTACCGCAA
ACCCAAATCGACAATGCACGACAGAGGAAGCAGAACAGATATTTAGATTG
CCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCG
AGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATG
GTGGCGGATGAACGAGATGATAATATATTCAAGTTGCCGCTAATCAGAAA
TAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGA
GAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTA
TATTACCGCAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGCAGCG
GAGATATTTAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGC
CAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTT
TACCGCAAACCCAAATCGACAATGCACGACAGAGGAAGCAGAACAGATAT

[download]
And the expected outcome should be in this format: 
 >crispr_1
GGGTGGAGCTCCCGAAATGCAGG
>crispr_2
TTAATAAATATTGACACAGCGGG
>crispr_3
ATCGTGGGGCGTTTTGTGAAAGG
>crispr_4
AGTTTTTCACATAATCAGACAGG
>crispr_5
GTGTTGGATGAGTGTCCTCTGGG
>crispr_6
ATAGGTTGGTTGTTTTAAAAGGG
>crispr_7
AAATTTTTGTTGCCACTGAATGG
>crispr_8
AAGTTTCGAACTACGATGGTTGG
>crispr_9
CATGCTTTGTGGAAATAAGTCGG
>crispr_10
CACAGTGGGTGTTTGCACCTCGG
.....and so on

[download]
It should be the first 1000 unique sequences.

This is what I have so far: 
#!/usr/bin/perl
use warnings;
use strict;
my %windowSeqCount = (); 
my $sequenceRef = loadSequence("input.fasta");

#writing to a new file
open (UNIQUEKMERS,">",output.fasta') or die $!;

my $windowSize = 23; 
my $stepSize = 1; 
for(
my $windowStart = 0 ;
$windowStart <= ( length($$sequenceRef) - $windowSize );
$windowStart += $stepSize 
)
{
my $windowSeq = substr ( $$sequenceRef, $windowStart, $windowSize);
$windowSeqCount{$windowSeq}++ if $windowSeq =~ /GG$/; 
}

for (keys %windowSeqCount){
print UNIQUEKMERS $_, "\t", $windowSeqCount{$_}, "\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]
I know my current print section is incorrect and that it will find 23 length sequences ending with GG and store them in a hash with the number of occurences as values.
I can't seem to figure what I need to include in my code to find just the first 1000 unique sequences of length 23 ending in GG in the expected format.
Any help would be greatly appreciated!! Thank you!!!

In reply to program to look for specific K-mer sequence by pearllearner315

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