What steps will reproduce the problem? 1. The dataset and steps to reproduce was privately sent to avaron. It involves reading a custom alphabet with only 4 elements.

What is the expected output? What do you see instead? The same cost as if the dataset was encoded as DNA sequences.

Please use labels and text to provide additional information. Observed in the development revision 2331 and released 2318.

Fixed in build_4_0_2337.