Note alignment refers to the task of matching individual notes of two versions of the same symbolically encoded piece. Methods addressing this task commonly rely on sequence alignment algorithms such as Hidden Markov Models or Dynamic Time Warping (DTW) applied directly to note or onset sequences. While successful in many cases, such methods struggle with large mismatches between the versions. In this work, we learn note-wise representations from data augmented with various complex mismatch cases, e.g. repeats, skips, block insertions, and long trills. At the heart of our approach lies a transformer encoder network - TheGlueNote - which predicts pairwise note similarities for two 512 note subsequences. We postprocess the predicted similarities using flavors of weightedDTW and pitch-separated onsetDTW to retrieve note matches for two sequences of arbitrary length. Our approach performs on par with the state of the art in terms of note alignment accuracy, is considerably more robust to version mismatches, and works directly on any pair of MIDI files.