It looks like you need something like this: 

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

my $input_file  = '/scratch/Drosophila/dmel-all-chromosome-r6.02.fasta
+';
my $output_file = 'unique12KmersEndingGG.fasta';

open my $FASTA, '<', $input_file  or die "Cannot open '$input_file' be
+cause: $!";
open my $KMERS, '>', $output_file or die "Cannot open '$output_file' b
+ecause: $!";

my ( $count, %unique_data );

while ( my $line = <$FASTA> ) {
    next if $line =~ /^>/;
    while ( $line =~ / ( .{9} [ATCG]{10} G \K G ) /gsx ) {
        print $KMERS '>crispr_', ++$count "\n$1\n" unless $unique_data
+{ $1 }++;
        }
    }

[download]

In reply to Re: unique sequences by jwkrahn
in thread unique sequences by Anonymous Monk

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