Massive genome rearrangement processes are known to occur during the sexual reproduction of the ciliate Oxytricha trifallax making it an ideal model organism to study gene rearrangements. During these processes a transcriptionally active somatic nucleus (macronucleus) is developed from a copy of its germline nucleus (micronucleus). In the micronucleus, macronuclear genes are found divided into potentially scrambled and inverted segments. Some regions between consecutive macronuclear destined segments of one gene contain multiple layers of segments from other genes. This nesting of gene segments significantly contributes to the complexity of the DNA recombination. Mathematical notions to measure the nesting of gene segments have been developed. Through computational analysis, we have identified all occurrences of interleaving segments and 137 instances of 2 to 4 levels of nested genes have been detected in the recently sequenced genome of O. trifallax.