Hm, somehow I missed that. Given the extra bit of data you supplied, I might recommend the use of List::MoreUtil's firstidx and lastidx functions. The fact that it's XS ought to help with the speed.

# 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;
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