#!/usr/bin/env perl

use strict;
use warnings;
use autodie;

my ($fasta_in, $fasta_out) = qw{
    pm_1205271_bio_fasta_extract_dummy_in.fasta
    pm_1205271_bio_fasta_extract_dummy_out.fasta
};

my $re = qr[(.{10}GG)\z];

{
    open my $in_fh, '<', $fasta_in;
    open my $out_fh, '>', $fasta_out;

    local $/ = "\n>";

    while (<$in_fh>) {
        chomp;
        substr $_, 0, 1, '' if $. == 1;
        my ($head, $seq) = split /\n/;
        next unless $seq =~ $re;
        next if index($seq, $1) < length($seq) - length($1);
        print $out_fh ">$head\n$seq\n";
    }
}

##</code><code>##

$ cat pm_1205271_bio_fasta_extract_dummy_in.fasta
>1: not wanted - too short
xxxGG
>2: wanted - exact match
xxxxxxxxxxGG
>3: not wanted - not unique
xxxxxxxxxxGGxxxxxxxxxxGG
>4: wanted - unique (but only just)
xxxxxxxxxGGxxxxxxxxxxGG
>5: not wanted - no GG at end
xxxxxxxxxxGGx
>6: not wanted - no match at all
xxxxxxxxxxAA
>7: wanted - match unique
yyyyyyyyyyGGxxxxxxxxxxGG
$ pm_1205271_bio_fasta_extract.pl
$ cat pm_1205271_bio_fasta_extract_dummy_out.fasta
>2: wanted - exact match
xxxxxxxxxxGG
>4: wanted - unique (but only just)
xxxxxxxxxGGxxxxxxxxxxGG
>7: wanted - match unique
yyyyyyyyyyGGxxxxxxxxxxGG