>atc:AGR_pTi_39_1-45_FD cctttcaagtcatagaacaccggggcatgtacaacttggggaagg
>atc:AGR_pTi_47_1-45_FD ccttacaggtcattgagcacagaggaatgttcaatttagggaaac
>atc:AGR_pTi_39_1-45_F      cctttcaagtcatagaacaccggggcatgtacaacttggggaagg
>atc:AGR_pTi_47_1-45_F      ccttacaggtcattgagcacagaggaatgttcaatttagggaaac
>atc:AGR_pTi_39_1-45_RD cctttcaagtcatagaacaccggggcatgtacaacttggggaagg
>atc:AGR_pTi_47_1-45_RD ccttacaggtcattgagcacagaggaatgttcaatttagggaaac
>atc:AGR_pTi_39_1-45_R  cctttcaagtcatagaacaccggggcatgtacaacttggggaagg

##</code><code>##

# my code so far

#!/usr/bin/perl -w
                                                                                                                     
open (FILEHANDLE, $ARGV[0]) or die "unable to open file";
open (OUTFILE, ">$ARGV[1]") or die;                                                                                                                     
my $line;
my @array;                                                                                                                     
my @seqs;
                                                                                                                     
while (<FILEHANDLE>)
{
    $line = $_;
    chomp ($line);                                                                                                                     
                                                                                                                     
    if ($line =~ /(\S+)(\s+)(\w+)/)   {                                                                                                                     
            push @seqs, "$3 ";                                                                                                                     
    }                                                                                                                                                                                                                                          
}
                                                                                                                     
foreach my $item (@seqs)   {
    unless ($seen{$item})   {
          $seen{$item} = 1;
          push (@uniq, $item);
          push @uniq, "\n";
 }                                                                                                                                                                                                                                          
    else {                                                                                                                     
          push (@duplicates, $item);
          push @duplicates, "\n";                                                                                                                     
    }
}
                                                                                                                     
print @uniq;                                                                                                                     
print OUTFILE "@duplicates\n";                                                                                                                     
close FILEHANDLE;
close OUTFILE;
exit;