shRNA Design - (Jun/09/2006 )

I've tried to design shRNA to target Collagen XVI in mouse with Invitrogens Block-it RNAi Designer. But when I do Blast search on these targets it also shows homologies to other sequences on other chromosomes. However these homologies are not for the full length of the target sequence but for e.g. 16 of 21 nucleotides.
I'm pretty new to the whole field and now not sure what consequences this could have if I would choose these targets.
It would be very nice if somebody could help me.

Sometimes it is hard to avoid partial homology of a siRNA target with other sequences. It is OK if the matches are at the 5' end of the target. 3' portion of the target (or 5' end of the siRNA guide strand) offers critical sequence specificity and should not have homology with other sequence.