DTW(X,Y) can work on vectors of non-equal length. It will repeat elements in either X or Y so that the comparison is of the same length.
To find out what those indices are, you can use the version:
[D, IX, IY] = DTW(X,Y)
This returns two index vectors, IX and IY, of equal length. In this way you can determine which elements of X are paired with Y. See the second version documentation for dtw (link)
