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The content of this paper addresses the issue of how to perform analysis of a cross domain reference architecture. The cross domain reference architecture is designed based on the domains requirements and features modeling. The definition of a cross domain reference architecture is based on well known concepts from software architecture description, service orientation and product line. We apply a method based on change scenarios to analyze variability at the architectural level. In order to handle complexity in analysis we propose categories of change scenarios to be derived from each problem domain and we provide informal guidelines for each step of the analysis method.