Interaction between frames and between residues, and other small mistakes

I have just realized that the presence of a hidden stop in frame 1 may prevent the presence of a hidden stop in frame 2, and vice-versa. Therefore, the probabilities are not independent.

Also, the presence of a stop between two amino-acids may prevent (or facilitate) the presence of another stop between the neighbouring ones.

Also, our method is not taking everything into account: For the same pair of aminoacids, in some cases we may be at one single-point mutation of forming a stop codon, sometimes at two, three, etc.

Thus, I am going to switch to another analysis method, taking into account single-point mutations.

BUT ATTENTION: The very different probabilities for different aminoacid pairs are still unexplained. Especially, the large amount of aminoacid pairs with significantly lower probability of having hidden stops codons is unexplained. The new analysis will probably mix all the data, and we may lose this detail.

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