The application of transposable element (TE) consensus/pHMM sequence models to genome annotation necessitates the use of alignment score thresholds to manage the level of false discovery. While the success of aligners such as Blast can be attributed, in part, to the development of rigorous sequence alignment statistics, TEs and nucleotide alignment in general pose challenges to their general applicability. We present the methods currently employed by Dfam to generate pHMM thresholds, and recent work to extend this to consensus sequences.