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In a previous paper, the second and third named authors introduced the concept of the complete cycle index and discussed a relation with the complete weight enumerator in coding theory. In this paper, we introduce the concept of the complete joint cycle index and the average complete joint cycle index, and discuss a relation with the complete joint weight enumerator and the average complete joint weight enumerator, respectively, in coding theory. Moreover, the notion of the average intersection numbers is given, and we discuss a relation with the average intersection numbers in coding theory.