Try this:

my %bighash;
my $motif;
my $score;
my $hoa;  # formerly %hoa
my $tag;

while ( <DATA> )
{
  chomp;
  my @aoa;
  if ( /^TAG/ )
  {
    $tag = (split(/: /,$_))[1];
    die "No tag!" unless $tag;
    $bighash{ $tag } = $hoa = +{};
  }
  elsif(/^MOTIF/)
  {
     ($motif,$score)=(split (/[\s,]/,$_))[1,3]; 
      push @{$hoa->{$motif}}, $score;
  }
  elsif(/^\d,-\d+,[ATCG]*$/)
  {
      @aoa = split(/,/,$_); 
      push @{$hoa->{$motif}}, [ @aoa ];
  }
  #print Dumper $hoa ;
}               # -----  end while  -----
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Note that I turned %hoa into $hoa; I think it's easier to work with hashrefs in this case.