It wouldn't show those as being similar. Any apparent similarity is an accident of the alphabet being used - all my sentences are composed of the same 26 letters, so they're all "similar" in a very broad sense, but they are all also very different from each other when you look at the details.
Just as in algebra and sentences, in genomes the order of operations matters. You get two different answers for both those problems because A) the parts are in a different order, and; B) the algebraic order of operations insures it in those cases. And just like those algebraic expressions are "instructions", so is the genome - it's a set of instructions for doing something. And as the "reader" travels along the genome, the order in which it encounters the "instructions" matters very much.
Think of an example like this: suppose you have two segments, one that reads AGVLUR, and a second that reads LRGVAU (which I just made up out of thin air). Both those segments are composed of exactly the same parts, just as your algebraic expressions have the same numbers and the same operations, just in a different order. And just like your expressions, the order matters - they have the same parts, but the products are likely going to be completely different because the order of operations is different in either case. So even though they're made up of the same parts, position and order are critical, and the two segments will not match each other at all for comparative purposes. That's why scientists try very hard to align the segments they want to compare, to insure that they get the best comparison possible.
And just like those algebraic expressions are "instructions", so is the genome - it's a set of instructions for doing something.
Does the genome support conditional operations and recursives?
This is where your whole theory goes to pot and you do not see it. Yes indeed the sequence of amino acids does indeed have bearing on the protein produced. However a protein like anything else is more than the sum of its parts and these 'scientists' should be ashamed to claim otherwise. Proteins are very specific, that is why the human body needs 100,000 of them to function. Every single amino acid in a protein contributes to how the protein folds and what shape it takes. This is very important since the shape is often the function of the protein. In attacking viruses and bacteria the shape enables the destruction of invaders. Shape is so important that the mere changing of the shape of a protein can result in death. That is what happens with mad cow disease.