I am using the Arduino Mega schematic found here and it's mostly clear, but there are a few resistors floating in the middle and I'm not quite sure what they're for or where they go:
Does anyone know what these are and where they go?
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Those are unused resistors in resistor arrays. The arrays have 4 resistors side by side in a single package. Not all of the elements are always needed, but they have to be in the schematic anyway since they exist in real life.