Two genes are on the same chromosome, separated by ~5kb. For some reason, when I go to the sequence page on Phytozome for each gene and search upstream or downstream of each of these genes, I'm completely unable to find the other in the place where it's supposed to be.
If I take the 7kb upstream flanking sequence of the downstream gene and MUSCLE it with the 7kb downstream flanking sequence of the upstream gene, there is not perfect alignment as would be expected. There's some alignment, better in some parts than others, very good in a highly conserved protein domain but there appear to be many indels and SNPs elsewhere.
What is going on? They should be the same. Is it possible that one gene only appears in the softmasked genome and one only appears in the hardmasked genome? What else could explain this? I was hoping to determine the whole sequence of this segment of the chromosome including both of those genes, but is that not possible in this case?
Can you tell us the two genes you are looking at so that we can replicate the behaviour?