I am using jackhmmer to cluster a set of protein sequences into groups. I am taking my 273 sequences, removing one and using that as the query against the 272 remaining sequences. Any hits which are found from the first query are removed from the pool for subsequent queries. The alignments jackhmmer produces however are multiple hit so more than one local alignment can be found in the target sequence and be included in the multiple alignment. Ideally I would like it to be aligned only once given that the same sequence is being aligned to itself multiple times. I've included an example alignment to help explain. A lot of the protein sequences are remotely related thus I thought jackhmmer would be more sensitive than a simple blastp and muscle alignment.