for my $role (sort keys %$href ){
  my $key;
  if (!exists $sequences{$key}){ # line 33
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While $key is declared it is uninitialized which is what Perl is complaining about when it tells you: "use of uninitialized value in exists at sample.pl line 33". Changing each mention of $key to $role gives

12345 21 GCT
12345 42 CAG
67891 32 GCA
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I can't tell if that is what you were expecting. I would consider choosing a better name for $href.