I really do want an array of one value, a 4 in this case. My original line was my @PromoterLenghts = ($PromoterMinLength .. $PromoterMaxLength); the min and max values were user entered.
Its most likely that I have made some kind of stupid mistake/typo in the code but I can't see what it is.
Try setting the @PromoterLenghts array to (2,3) and see what happens. Oh and delete any old permute.txt or output files that were generated on previous runs first.