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I am extracting a property of a signal which I represent with either a 0 for absent or 1 for present. This property is extracted for each data point in a time series and in the end I am left with a binary sequence for each signal. These sequences are somewhat similar, since their origin is related, but they are different signals (not just a delayed version of each other). I am currently using cross-correlation to estimate a "delay" between them, but I just read that cross-correlation is mostly suited for delayed versions of the same signal. I would like to know what alternatives I could use.

You can get an example of the data here:

https://www.dropbox.com/s/64uci3juok0qrd2/states.mat

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