The Parts Of My Dual Extrusion Print Aren't Lined Up Right

MakerBot executes an alignment script on every MakerBot Replicator 2X before shipping to make sure the nozzles are lined up correctly. However, if plastic coming from the two extruders does not appear to be aligned correctly along the X or Y planes during dual extrusion prints, you can run the alignment script again at home. During this script you will print some test extrusions and give your MakerBot Replicator 2X feedback so that it knows exactly where the two nozzles are in relation to each other.  

How do I use the alignment script?One of my nozzles is higher up than the other

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