Turn the problem on its head and try it this way:

sub gen;
sub gen{
    return @_[1..$#_] if $_[0] == 1;
    map{
        my $p=$_;
        map{ $p . $_ } gen( $_[0]-1, @_[1..$#_] )
    } @_[1..$#_]
}

my %seqs = ...;
my @patterns = gen( 7, qw[A C G T] );

my %counts;

for my $seq ( values %seqs ) {
    ++$counts{ substr $seq, $_, 7 } for 0 .. length( $seq )-7;
}

print "$_ ::= $counts{ $_ }" for @patterns;
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In my experiments on a 49 million base pairs sequence:

[ 0:15:31.00] C:\test\humanGenome>..\junk999 chr21.fa
16384 patterns.
49092500 base pairs
Using custom indexing found 35106546 matches; took 34.536852 seconds
Using custom index2 found 35106546 matches; took 31.354438 seconds
Simple search found 35106546 matches; took 2970.517883 seconds
[download]