Contig assembly in different genomes of the same species

Question

[MAPK]

Hi All, I was using PRICE tool (http://derisilab.ucsf.edu/software/price/) to assemble a contig with a seed sequence( ~200bp) in genomes of the same species. I was able to extend the seed sequence in one genome up to 3600 bp, but could not extend it from other genomes of the same species. This contig is expected to be found in all genomes I am analyzing, but looks like either assembly or the sequence coverage of the genome is the reason why it is not assembled from all genomes. What could be the reasons/factors that affect the assembly of the contiguous sequence using a seed sequence where one genome has the extended/assembled contig and the other do not?