The ubiquity of deep neural networks (DNNs) continues to rise, making them a crucial application class for hardware optimizations. However, detailed profiling and characterization of DNN training remains difficult as these applications often run for hours to days on real hardware. Prior works exploit the iterative nature of DNNs to profile a few training iterations. While such a strategy is sound for networks like convolutional neural networks (CNNs), where the nature of the computation is largely input independent, we observe in this work that this approach is sub-optimal for sequence-based neural networks (SQNNs) such as recurrent neural networks (RNNs). The amount and nature of computations in SQNNs can vary for each input, resulting in heterogeneity across iterations. Thus, arbitrarily selecting a few iterations is insufficient to accurately summarize the behavior of the entire training run. To tackle this challenge, we carefully study the factors that impact SQNN training iterations and identify input sequence length as the key determining factor for variations across iterations. We then use this observation to characterize all iterations of an SQNN training run (requiring no profiling or simulation of the application) and select representative iterations, which we term SeqPoints. We analyze two state-of-the-art SQNNs, DeepSpeech2 and Google's Neural Machine Translation (GNMT), and show that SeqPoints can represent their entire training runs accurately, resulting in geomean errors of only 0.11% and 0.53%, respectively, when projecting overall runtime and 0.13% and 1.50% when projecting speedups due to architectural changes. This high accuracy is achieved while reducing the time needed for profiling by 345x and 214x for the two networks compared to full training runs. As a result, SeqPoint can enable analysis of SQNN training runs in mere minutes instead of hours or days.