[Bio-software] cross_match - multiple matches?

[ehs]

I have been trying to cross_match some sequences against themselves to try to
cluster sequences. However, cross_match only returns one match per sequence,
when I know there should be multiple matches for many of them.

Does anyone out there know if there is a flag which reports back ALL of the
matches found by crossmatch, rather than just the best match?

Thanks

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