Please tell me how to efficiently remove bases that are out of the codon frame as follows. Protein: [N-ter]- S D C V E I L T N C A -[C-ter]
Nucleotide: [5']- G TCA GAC TGC GTA GAA ATT CTT ACA AAT TGT GCA GA -[3']
I aligned the nucleotide sequences based on the amino acid alignment with the backtrans option of Trimal. However, the extra bases cause misalignment of nucleotide sequences, so I am looking for ways to remove the out-of-frame bases.