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Can I use two different strings of solar panels on my MPPT80-600 charge controller and what would happen if I do?

It is never a good idea to mix and match solar panels because the MPPT80 only has a single power tracker, so the MPPT algorithm continuously adjusts the operating points in an attempt to find the maximum power point of the array, which means the unit is going to use the sum of both strings and will derate the value of the bigger string. 
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