Anonymous Monk,
So my earlier assumption that you wanted to throw away non sequence lines was correct. I believe you can avoid an array all together. 
#!/usr/bin/perl
use strict;
use warnings;

my $file = $ARGV[0] || 'default';
open (DNA, '<', $file) or die "Unable to open $file for reading : $!";
my %seq;

while ( <DNA> ) {
    my $dna = <DNA>;
    my $pairs = "a2" x ((length $dna) / 2);
    $seq{$_}++ for unpack $pairs , $dna;
}
print "$_ : $seq{$_}\n" for keys %seq;

[download]
Cheers - L~R

In reply to Re: Re: Re: input record separator help by Limbic~Region
in thread input record separator help by Anonymous Monk

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