GeneDesign's Short Sequence Removal module allows you to alter a nucleotide sequence without changing its first frame translation by changing whole codons around the target sequence. This is exactly like the Silent Site Removal module except that the user is allowed to define the sequence to be removed.
You must provide two nucleotide sequences - a longer one as the main sequence, and a shorter one (at least 2 bp) to be removed from the first sequence. You have the option of defining an organism. If you do, the codons that are more optimal for expression in that organism will be considered first when altering sequence. If you do not select an organism, every codon replacement will be random.