Align Check command

I am a new member of the forum, and relatively new to Mothur. I recently used the align check command with my data, and would like to try to understand the results. How do I know if my alignment is “good” vs. “bad” using the data I get with the align check command?

It’s pretty relative. In general, a pound sign is an indication of a bad base pairing; however, even E. coli has something like 20 #'s in it so well-aligned sequences are expected to have #s too. An early idea was to use these data as a starting point for looking at sequences in ARB to see if one can improve the alignment of the query or reference sequence.