compmage: the chromosome "splitting" (which is kind of a misnomer) takes place during the creation of the gametes - before fertilization.
Here's a link to a pretty good, and relatively easy to understand, explanation. IOW, you don't have to worry about lining up base pairs - what gets separated are the two pairs of chromosomes. The chromatids aren't actually cut up. (See also "crossing over").
[This message has been edited by Quetzal, 06-20-2002]