An introductory video on the analysis of dot plots and protein alignments, presented by GEP Virtual TA Rae Lucas, is now available on the GEP’s YouTube Channel. The dot plots and protein alignments presented in this video were generated from Gene Model Checker, with our reference organism being Drosophila melanogaster. We begin with an overview of protein alignments and how we interpret their various features, along with what this means for our aligned gene sequence. We then move on to reading and analyzing dot plots, a feature that correlates with protein alignments. A major feature of the dot plot includes word size, which may be manipulated by the user to increase or decrease sensitivity of the plot; we discuss this in brief and when we might use this before looking at common patterns that may appear in our plots. Such patterns discussed include repeating sequences, short tandem repeats, and inversions.