I have a FASTA file with multiple 16s sequences. I want to find the conserved regions between all of the sequences. I used blastn but it wouldn't compare the sequences with each other . . . Any suggestions on a specific program or online tool I could use ?
I will also be devil's advocate here and suggest that to truly understand what homologies you have between marker genes, such as 16S, you'll have to look at the sequences yourself -- after you run the alignment programs.
No alignment program is perfect (and I don't think we should expect them to be) and I argue that all alignments should be subsequently edited by eye. You'll be able to start identifying homologies (SNPs, DIPs, other polymorphisms, etc.), find regions that are misaligned, and identify specific regions within the 16S that are meaningful for your research.