Alternating thirds usually refers to moving up a scale (or group of notes) by skipping a single note before moving on in the pattern.
For example, if playing in the key of C, the note pattern is:
C D E F G A B C D E...
An alternating thirds pattern could play through those notes in that order, but also playing the note that is 2 notes away (this distance is called a third). It would look like this (I will put parentheses around the sets of thirds so it is easier to see):
(C E) (D F) (E G) (F A) (G B) (A C) (B D) (C E)
You can see that the first note in every pair is the next note in the scale, but the note played before the next pair is a *third* away from the note just played.
It makes more sense to see it on an instrument
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