# for clarity...
my $result;
my $src = $matches{$fasta_id}{$sitekey};

# Use a slice and firstidx/lastidx to copy the range of values
@newArray = @$src[ 
   (firstidx {$_ >= $lowerlimit} @$src )..(lastidx {$_ <= $upperlimit} @$src)
];

$result = \@newArray;