Our genetic code considers codons as nonoverlapping chunks, but one can imagine an alien genetic code that allows codons to overlap. For example, an RNA sequence ...AGCCGUUCACUAGUCUCAUC... may be read according to an overlapping triplet genetic code as:
AGCCG UUC UCA CAC ACUwhich would translate to Phe-Ser-His-Thr... (FSHT...) using terrestrial codon assignments. Alternatively, the overlap may be two nucleotides, giving:
AGCCG UUC CAC CUA AGUwhich (with terrestrial assignments) would translate to Phe-His-Leu-Ser... (FHLS...).
Genetic codes of different fixed lengths can also use overlapping codons. For example, the previous RNA read according to an overlapping duplet code might be broken up as:
AGCCG UU UC CA ACNote that translation in your in-vitro system (unlike natural translation) can initiate anywhere in the RNA (see IN-VITRO-TRANSLATION).
In the absence of experimental results, any of these possibilities (and many more) may be right. However, you can exclude many of them by assuming them to be true and showing that doing so leads to a contradiction, for example a codon that codes for one amino acid in one context and another in a different context.