Tiling primer design for whole genome

[SwathiNadendla]

Hi Team,
I am working on development of primers for Newcastle disease virus whole genome. I have tried to include different genotypes together in the input fasta file under 200 sequences the coverage was good but it excluded most of the references and considered only a few. Is it common and the primers would work I am concerned with one particular class of the virus as it's more diverse had to downsize sequences to get all genotypes

Looking forward for discussions.

Thankyou,
Swathi.