Fragment sizes smaller than expected - (Mar/09/2016 )

Hi I was wondering if somebody could help me please.

I have created primers for plasmid groucho wt a40 DNA, optimised their annealing temperature and when loaded onto a 1% agarose gel expect to get a fragment size of 900bp and have been getting that result.

However when I took this DNA from a transgenic Drosophila and ran it alongside the plasmid DNA... where the plasmid DNA gave me a band of size 900bp the genomic dna taken from the Drosophila only gave me a band of 100bp... why is this when my expected fragment size is 900bp???

Thanks

Primer binding in the drosophila is different?