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for my $href ( @AoH ) {
  for my $role ( sort keys %$href ) {
...
+ . "\n";
}

for my $href ( @AoH ) {
  for my $key ( sort keys %$href ){
...
    $index += 3 while ( ($index + 3) < $href->{$key} );
    print "$key $href->{$key} " . substr($sequences{$key}, $index, 3) 
+. "\n";
}