- As arrows or boxes in the sequence views:
- Linear and circular view of sequences () / ().
- Alignments ().
- Graphical view of sequence lists ().
- BLAST views (only the query sequence at the top can have annotations) ().
- Cloning editor ().
- Primer designer (both for single sequences and alignments) () / ().
- Contig/mapping view ().
- In the table of annotations ().
- In the text view of sequences ()
In all the views except the text view (), annotations can be added, modified and deleted. This is described in the following sections.