I am willing to bet your grep is the slowest bit, but have you profiled the code? Anyhow, assuming the grep bit is your bottleneck: 

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

[download]

Depending on your data, you may gain some performance by using a sorted array instead: 

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

[download]

This will only have an advantage if sort is sufficiently fast and there are many elements above $upperlimit, so this suggestion comes with an extreme case of "know thy data".

<–radiant.matrix–>
Ramblings and references
The Code that can be seen is not the true Code
I haven't found a problem yet that can't be solved by a well-placed trebuchet

In reply to Re: Help tightening up a subroutine please by radiantmatrix
in thread Help tightening up a subroutine please by mdunnbass

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