Comintern contains python scripts to compute common intervals between two linear genomes. It can also be applied to find common intervals between any two sequences, wether or not they represent genomes, provided they are encoded in a genome format.
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Thomas Schmidt, Jens Stoye
Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences
Lecture Notes in Computer Science Volume 3109, 2004, pp 347-358