This most frequently happens with FASTA format since it doesn’t declare what the data type is. When using drag and drop, Geneious tries to figure out what type of sequence it is looking at and use the correct import. If there are ambiguities in your nucleotide sequence Geneious may think it is protein sequence. To be certain that you’ve imported your data as the correct type though, use File→Import→From File... and choose the format and type from the list.
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