$hu_aln and $hd_aln contain Bio::SimpleAlign objects. If you read the linked documentation, you may find that one of the methods of that class gives you access to the data you need. It doesn't support a default stringification, so you can't print the object directly and get what you expect. (I don't know what you expect, so I can't tell you which method is likely to help.)

In reply to Re^3: Problem with getting the right object by chromatic
in thread Problem with getting the right object by lomSpace

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