I guess this is not homework as the source data is presented as two synchronised arrays not a file to read or array of arrays. If it is homework then I recon the OP already did some work to get from a file of data to two arrays.

My output disagrees with the OP's (is actg == acgt ??) and you would be better storing the source data in an array of arrays. I have dumped out the hash of hash I build to collate the data so you can see clearly what is going on. Data::Dumper is fantastic when you are developing any sort of interesting data structure.

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

#e.g.

my @sequence = ('acgt','actg','cggt','cggt');
my @numbers = ('1234','2345','3244','3455');

my %collated;
for (0..$#sequence) {
    $collated{$sequence[$_]}{total}+=$numbers[$_];
    $collated{$sequence[$_]}{number}++;
}

print Dumper(\%collated);

for (sort keys %collated) {
    print "sequence: $_ = ";
    print ( $collated{$_}{total} / $collated{$_}{number} ) , "\n";
}
__END__


# my output

$VAR1 = {
          'acgt' => {
                      'number' => 1,
                      'total' => 1234
                    },
          'cggt' => {
                      'number' => 2,
                      'total' => 6699
                    },
          'actg' => {
                      'number' => 1,
                      'total' => 2345
                    }
        };

sequence: acgt = 1234
sequence: actg = 2345
sequence: cggt = 3349.5
[download]

Cheers,
R.