use strict;
use warnings;

use Data::Dumper;

my @seqFiles = glob q{spw961600_seq*};
my %counts;

foreach my $seqFile ( @seqFiles )
{
    my $seq = do {
       open my $seqFH, q{<}, $seqFile
          or die qq{open: < $seqFile: $!\n};
       local $/;
       <$seqFH>;
       };
    while ( $seq =~ m{(?=(..))}g )
    {
        $counts{ totals }->{ $1 } ++;
        $counts{ $seqFile }->{ $1 } ++;
    }
}

print Data::Dumper->Dumpxs( [ \ %counts ], [ qw{ *counts } ] );