The aim of this paper is to present a new approach, called 'Hybrid Chromosome Model' (HXM), which allows both the extraction of regions of similarity between two sequences, and the compartimentation of a set of DNA sequences. The principle of the method consists in compacting a set of sequences (split into fragments of fixed length) into a 'hybrid chromosome', which results from the stacking of the whole sequence fragments. We have illustrated our approach on the 32 subtelomeres of Saccharomyces cerevisae. The compartimentation of these chromosome extremities into common regions of similarity has been carried out. The approach HXM is a fast and efficient tool for mapping entire genomes and for extracting ancient duplications within or between genomes.