Unfortunately, the pictures in that link are wrong. That is a pretty common mistake in herper genetics web pages.
I prefer the Genetics Home Reference, which can be freely downloaded. http://ghr.nlm.nih.gov/handbook
I just wish that when the GHR showed an X-shaped chromosome, they had made it clear that the chromosome is in the process of dividing into two rod-shaped chromosomes.
Here is a more accurate version (IMO) of the text in the "HOW DOES ALL THIS WORK?" section of http://ball-pythons.net/forums/showthread.php?t=52847:
HOW DOES ALL THIS WORK?
Picture a pair of shoestrings. Hold them up side-by-side. Now picture each shoestring run through colored balls, like a string of beads.
There are two chromosomes. Each string of beads represents the DNA strand in a single rod-shaped chromosome.
Each bead represents a single gene or allele.
A bead in one string and the corresponding bead in the other string represent a pair of genes/alleles located at a specific locus.