I'm not a 100% clear on what you're trying to achieve but this sounds like a good use case for xcorr. You can look at the usage with the xcorr(x, y, maxlag) syntax. You can skip the second argument in the call to xcorr to calculate auto-correlation.
If it suits your use case, you can perform a max operation on the output from xcorr to identify the lag which gives the highest correlation value. Here's an example of that in the 2D case although the same principles will apply in the 1D case as well: Align two images using cross-correlation
