$threshold = "N" # see description above
for($i=1;$i<=6;$i++) {
my $pattern = "." x $i;
while ($sequence_string =~ /($pattern)\1{$threshold,}/g) { .... }
}

##</code><code>##

while ($sequence_string =~ /(.)\1{$threshold,}|(.{2,3}?)\2{$threshold,}|(.{4,6}?)\3{$threshold,}/g)

##</code><code>##

$i = 1;
while ($i < $genome_length)
{
   for ($j=1;$j<=6;$j++)
   {
      # run regexp looking for motifs of length $j
      # starting at position $i
   }
   $i = (end of previous match + 1)
}