select the part of the sequence you want to delete | right-click the selection | Edit Selection () | Delete the text in the dialog | Replace
The selection shown in the dialog will be replaced by the text you enter. If you delete the text, the selection will be replaced by an empty text, i.e. deleted.
To delete entire columns:
select the part of the alignment you want to delete | right-click the selection | Delete columns
The selection may cover one or more sequences, but the Delete columns function will always apply to the entire alignment.