My biologist friend isn't patient enough to ELI5, but AFAIU don't genes realign through the natural course of replication? That is, there is no specific, canonical sequence at large scales, neither between two individuals nor even two cells, even if the complete set of base pairs[1] is otherwise identical (i.e. no mutations).

I realize that the magnitude of this natural shuffling, even during meiosis, is nowhere near like what happens when sequencing DNA[2], but (assuming I'm correct) it's helpful to realize that this problem of deciphering the "correct" sequence reflects something intrinsic to the operation of the machinery; that this applies even when the relevant macro sequences are all genes that directly code for phenotypes as traditionally understood; and that gene sequencing works precisely because many (most?) genes are relatively tolerant to being spliced in at random locations in the strand. (Which is different than saying all locations--or even any two locations--produce identical results.)

[1] I refrain from saying "complete set of genes" because I imagine for some genes location at both the micro- and macro-scale is everything. AFAIU the term gene is sometimes better understood as more a description of the result of possibly non-local sequences which maintain reproductive affinity than an identification of a specifically adjoining sequence of base pairs.

[2] Or is it?