#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new( -file   => "dmel-all-chromosome-r6.18.fasta" ,
                           -format => 'fasta');
my $fasta;
while ( my $seq = $in->next_seq() ) {
	$fasta .= $seq->seq;
}

my %seen;

for my $i (0 .. length($fasta) - 21) {
	my $kmer =  substr $fasta, $i, 21;
	next unless substr($kmer, -2) eq 'GG';
	my $match = substr($kmer, -12);
	$seen{$match}{count}++;
	$seen{$match}{kmer} = $kmer;
}

my $crispr;
for my $key (keys %seen) {
	next unless $seen{$key}{count} == 1;
	print "crispr_", ++$crispr, "\n";
	print $seen{$key}{kmer}, "\n";	
}

__END__
*** ouput

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_126892
TTGCTTGGCACTAAGGCGGGG
crispr_126893
CACCAAAAAGGACTTGCGTGG
crispr_126894
GTGCCCCTCACTCATGCGGGG
crispr_126895
TAAAAAGCGACGCAGTATTGG
crispr_126896
CCGGATTTCTTCGTACAGGGG
crispr_126897
GGTGGCTATGCTATGGTACGG
crispr_126898
CTGCGTTGATGTTAGGTAGGG
crispr_126899
GCTGGGACCCGAATACGTAGG