Certain species of ciliates undergo massive genome rearrangements during the development of a somatic macronucleus from a germline micronucleus, and are used as model organisms to study DNA rearrangement. Recent sequencing of the 0. trifallax germline genome allows for the detailed study of scrambled patterns genome-wide. We present a mathematical framework to describe the order and orientation of scrambled segments (the macronuclear-destined sequences, or MDSs). For example, we catalog all germline loci with odd/even patterns that partition MDSs (an example would be 1-3-4-2-4-6, etc.) and many elaborate variations. We have observed that occurrences of such patterns can explain approximately 82% of all scrambled loci. We also study the complexity of the remaining highly scrambled cases, some of which contain nested occurrences of such patterns. .