You can copy annotations from one sequence to other sequences in the same alignment or assembly document by right-clicking on the annotation and choosing Annotation → Copy to. This will give you the option of either transferring the annotation to the consensus sequence, reference sequence (if there is one), or any of the other sequences in the alignment or assembly. You can also use the associated options: Copy all x to... to copy all annotations of the currently selected annotation type on the selected sequence; and Copy all in selected region to... to copy all annotations in the selected sequence. In each case, the annotation(s) will be copied across regardless of the similarity between the sequences.
Using Transfer Annotations, you can copy annotations to the reference and/or consensus sequence of an alignment or assembly. This function can be accessed from the Annotate and Predict menu, or in the Live Annotate and Predict tab in the sequence viewer. To set a sequence as a reference sequence Ctrl-click on it and choose Set as reference sequence.
Annotations will only be transferred where the annotated sequence and the reference/consensus sequence have at least the specified minimum similarity. All transferred annotations will be annotated with a Transferred From qualifier indicating the names of the sequences the annotation came from (sorted in order of decreasing similarity), and a Transferred Similarity qualifier which indicates the percentage similarity of the most similar sequence the annotation was transferred from.
Annotations of the same type and covering the same interval that would be transferred from multiple sequences are merged together such that the name of the transferred annotation will consist of the names of all contributing annotations sorted in order of decreasing similarity. Similarly, if contributing annotations have different qualifier values, the resulting qualifier value will consist of all contributing qualifier values sorted in order of decreasing similarity.
The percentage similarity is the sum of the similarity values for each position as a fraction of the sum of the maximum similarity values of the bases/residues in each position. For example if one sequence is LLK and the other is LIK using the Blosum62 matrix, L/L scores 4, I/I scores 4, L/I scores 2, K/K scores 5. Therefore the total score is 4+2+5=11 out of a maximum of 4+maximum(4,4)+5=13 for a percentage similarity of 85%. Gaps (if allowed) are scored as the lowest value from the score matrix (e.g. -4 for Blosum62).
Translation properties on CDS annotations are not transferred to the destination sequence. Instead these are renamed to Transferred Translation. The Sequence View calculates and displays an Automatic Translation property on any CDS annotation without a translation. However, this is not a real annotation property that is visible when exported. To add a real Translation property to annotations, use Tools →Workflows → Set CDS Translation Property.