You're definitely right that there are a number of simple-ish ways to represent the data, but in a tradition regression model the 102nd attribute being the lett

You're definitely right that there are a number of simple-ish ways to represent the data, but in a tradition regression model the 102nd attribute being the letter A could mean something totally different than the 103rd attribute equaling A. So therefore the authors had a challenge having sequences that are different lengths. In the past, one possible workaround that people have done with some success is taking some fixed length summary (say, the proportion of As, Cs, Gs, and Ts). Then you can control the order and avoid having to consider a possibly intractable number of sub-sequence comparisons, but you also lose information that might be important.