🚀 go-pugleaf

I think you are getting to technical in a field that is more abstract. 
The position of genetic loci are not measured in base pairs, the are
positioned on a genetic map of each chromosome.  Thus, each gene is
positioned only with respect to other genes.  The distances between genes
are expressed in centi-Morgans (after the great geneticist Thomas Morgan)
and these distances are not actual physical lengths, rather they represent
recombination frequencies between genes.

The position of genes are not necessarily important for their function. 
There is no obvious reason why genes are where they are.   Alleles are on
the same genetic locus by definition.  An allele is really the same gene! 
It is a slight variation of a gene product.  For example, at a single hair
color locus the genes for blonde or brown hair are allelic.  You have one
or the other, but not both.  The actual proteins that these genes encode
are probably slight variations of each other.  Crossing over has nothing
to do with alleles.  Just think of it this way.  If genes did not have
alleles, we would all be identical, as in twins.  Do you understand? 
Humans have all the same genes at the same loci, that is what makes us
human.  However, we have many different combinations of alleles at most
loci, thus we are all a bit different.  Alleles generally are regulated
the same way, by the same promoter sequences.  The differences between two
alleles are really quite small and may only represent a single base-pair
change that may change one amino acid.

Good luck with your studies.

Greg Dressler
Howard Hughes Med. Inst.
Univ. of Michigan, Ann Arbor