I think you should think about what do you really want to find?

1. the first match and a mapping from that on?
2. the longest math and a mapping from that on?
3. the most matches and a mapping between those?
4. 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?

1. this would find the first match at "b" and result in
   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
   
2. this would find the longest match at "h i j k" and result in something like
   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
   
3. this would find
   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
   
4. I have no idea about that From what I recall from my studies, at least the "most-matches" 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.

   Non-trivial, i think