I think you should think about what do you really want to find?
 the first match and a mapping from that on?
 the longest math and a mapping from that on?
 the most matches and a mapping between those?
 the best mapping (define "best")
To give examples for each of my points, I use these arrays
a b c d e f g h i j k l m
z b y d e x h i j k w v m
how would that map?
 this would find the first match at "b" and result in
abcdefghijklm
zbydexhijkwvm
 this would find the longest match at "h i j k" and result in something like
a bcdefghijklm
z bydexhijkwv m
 this would find
abcdef ghijkl m
zbydex hijkw vm
 I have no idea about that
From what I recall from my studies, at least the "mostmatches" sounds to me like a problem that has a complexity O(n)=n**2.
You will have to compare each possible mapping, score it and compare the scores to decide which fits your needs best.
Nontrivial, i think
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