@seq = ('acgt','actg','cggt','cggt', 'actg', 'actg');
@num = ('1234','2345','3244','3455', '5230', '100000' );

for( 0..$#seq ){
   $struct{$seq[$_]}->[0] += $num[$_]
   and
   $struct{$seq[$_]}->[1]++
}

for( keys %struct ){
  print "$_\t", $struct{$_}->[0] / $struct{$_}->[1], $/
}

__END__

STDOUT:

acgt    1234
cggt    3349.5
actg    35858.3333333333
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