deletion mutant in Cyanobacteria

[Farid jalali]

Hello,

I have designed a construct where a cloned cyanobacterial restriction 
fragment will be cut, a region of the fragment removed, and in its place 
a cassette conferring resistance to an antiobiotic will be placed. My 
question deals with the fact that the region I will remove is not the 
same size as the cassette. The species I work with undergoes homologous 
recombination quite readily, and I am wondering if removing a region 
from the construct that is larger than the genomic region is going to be 
a problem. 
I hope this doesn't sound to confusing. Any info would be greatly 
appreciated.

Thanks 

Farid Jalali
Department of Botany
Erindale College
University of Toronto