A subordinate clause is a group of words that have at least a subject and a verb and that can not stand on its own as a sentence because it does not express a complete thought.
In the sentence, there is a subordinate clause and an independent clause. The independent clause is "Joe's term paper was late" because it expresses a complete thought, and the subordinate clause is "Although the assignment was given early" because it does not express a complete thought: it can not be alone, it needs to be next to another clause to make sense.
