It would be helpful to have several test cases with actual input and actual matching output for each case.

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1188439

use strict;
use warnings;

$_ = join('', grep /^[\sACGT]+$/, <DATA>) =~ tr/ACGT//cdr;

my $count = 0;

while( /(?=(.{21}GG))/g and $count < 1000 )
  {
  /(?=$1).+$1/ or print ">crispr_@{[++$count]}\n$1\n";
  }

__DATA__
 > >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;
CCTCTCATTTTCTCTCCCATATTATAGGGAGAAATATGATCGCGTATGCG
AGAGTAGTGCCAACATATTGTGCTCTTTGATTTTTTGGCAACCCAAAATG
TAAATTCATTGCAACGTTAAATACAGCACAATATATGATCGCGTATGCGA
GAGTAGTGCCAACATATTGTGCTAATGAGTGCCTCTCGTTCTCTGTCTTA
TATTACCGCAAACCCAAAAAGACAATACACGACAGAGAGAGAGAGCAGCG
GAGATATTTAGATTGCCTATTAAATATGATCGCGTATGCGAGAGTAGTGC
CAACATATTGTGCTCTCTATATAATGACTGCCTCTCATTCTGTCTTATTT
TACCGCAAACCCAAATCGACAATGCACGACAGAGGAAGCAGAACAGATAT
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