Hi,

I have identified some tandem repeat loci from the reference assembled genome of a fungal species, and now I want to screen for loci located near conserved regions. How can I determine the conserved regions?

There are three other genome assembly data available for this fungal species in the NCBI database. Can I align them to search for conserved regions? However, these genome assembly data are very large, and they include hundreds of scaffolds and no assembled chromosomes. What tool should I use for the alignment?