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Essentiall you define the data using timeseries:
ts1 = timeseries(data1); ts2 = timeseries(data2);
And then synchronize:
[ts1 ts2] = synchronize(ts1,ts2,'union');
This may be overly simplistic for what you are trying to do, but you can try it and comment back with what is and is not working more specifically.
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