Why don't my de novo assembled contigs not have continuous ensembl blat alignments with a closely related reference genome? For example, I have a certain stretch of my contig with 100% identity, and then a new alignment begins after 10 bases (of the subject), and I get a score of say 99% and then another one with 97% identity. These hits point to the same locus of the reference. How can I have the entire stretch represented in one alignment, with gaps inserted if required, even if the identity goes down? That would help me in comparing the entire contig at once with the reference.