Removing subsequence is not intuitive to end users.
I would suggest opening up a new fasta, and let the user curate the result by deleting/changing bases that is incorrect, then export the fasta. Miscalled bases could contribute to mistranslation and what looks like mutation while it is not.
Maybe it would be better to basecall the ABI as accurate as possible first, by using tools like tracetuner
http://sourceforge.net/projects/tracetuner/ So that we could minimize manual correction of the base called.