I have a genomic regions sequenced from few accessions of a plant species. When I built a MSA of this region in different accessions. It looks like only the 4 genes present in this region are aligning. These four genes are less than 1 kb and the total genomic region is 16 kb. I know I have to provide more details to my query but does it look like something unusual (faster evolution) or it is normal that nongenic regions does not align in different accessions. If something is interesting then what I can do further.