c:\@Work\Perl\monks>perl -wMstrict -MData::Dump -le
"my $line =
   'AAAATTTTCCCCGGGGAAAGGxAAAACCCCTTTTGGGGAAAGGxAAAATTTTCCCCGGGGAAAGG'
   ;
 ;;
 my (%unique_data, $count);
 while ($line =~ m{ (.{9} [ATCG]{10} GG) }xmsg) {
   print qq{>crispr_@{[ ++$count ]} '$1'} unless $unique_data{$1}++;
   }
 ;;
 dd \%unique_data;
"
>crispr_1 'AAAATTTTCCCCGGGGAAAGG'
>crispr_2 'AAAACCCCTTTTGGGGAAAGG'
{ "AAAACCCCTTTTGGGGAAAGG" => 1, "AAAATTTTCCCCGGGGAAAGG" => 2 }