In either case, it writes the implied sequence such that the output file can be used immediately as the input file for other sequence mapping or comparison programs. In the table of back-translations options, the codons are written in order of their preference in the codon frequency table. All of the codons and their preferences are included to help you look critically at the alternative oligonucleotides that you might want to synthesize. For instance, if for one amino acid the codon preference is not strong, you could consider making a mixture that contains all of the different possibilities. Pro Trp UCC 0.37 UUC 0.76 UCC 0.37 CAG 0.86 CCG 0.77 UGG 1.00 UCU 0.
Composition counts trinucleotides from any set of sequences.
No checking is done to see that your codon frequency table and your translation table agree. The most ambiguous back-translated sequence comes from the translation table. The most probable back-translated sequence comes from the codon frequency table. The table of codon choices also comes from the codon frequency table. These codes are not capable of correctly representing sets of codons where more than one of the bases is incompletely permuted.