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?
You'd want to use a multiple sequence alignment program, such as Clustal. (http://www.clustal.org/)
You can also run ClustalW over the web at a number of places, such as http://www.ebi.ac.uk/Tools/msa/clustalw2/
I have had better results using cmalign from Infernal for 16S rRNA. It takes account of the conserved secondary structure.
http://infernal.janelia.org/ http://rdp.cme.msu.edu/misc/resources.jsp
The Clustal family of tools is by far the most common/popular. But, another option is T-coffee and its associated tools.
As well as ClustalW, T-Coffee and a number of other multiple sequence alignment tools are also available on the EMBL-EBI web site: http://www.ebi.ac.uk/Tools/msa/
There are lots of types of alignment programs Clustal, muscle, t-coffee, etc, that will do what you want them to do.
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.
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I just want to say that, by definition, all 16S sequences are homologous with one another. Sequences/features are, or are not, homologous. It is a purely binary state. When you are doing sequence alignment and identifying conserved regions you are identifying regions of high similarity or identity based on some metric. The entire sequence is homologous with the other sequences in the set because they are all descended from a common ancestor.