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# First time
next unless defined %{$matches{$fasta_id}};         # False
...
# Second time
next unless defined %{$matches{$fasta_id}};         # Now true!!
last unless defined @{$matches{$fasta_id}{$site}};

# First time
next unless defined %{$matches{$fasta_id}};         # False -> next
...
# Second time
next unless defined %{$matches{$fasta_id}};         # Still false
last unless defined @{$matches{$fasta_id}{$site}};