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## your original code
@{$sets{$fasta_id}[$setscounter]{$sitekey}} = grep {
     $_ >= $lowerlimit and $_ <= $upperlimit
}  @{$matches{$fasta_id}{$sitekey}};

@{$sets{$fasta_id}[$setscounter]{$sitekey}} = ();
foreach ( sort @{$matches{$fasta_id}{$sitekey}} ) {
...
    next if $_ < $lowerlimit;
    push @{$sets{$fasta_id}[$setscounter]{$sitekey}}, $_;
}