Maximum length constraint

[anands-repo]

Is there a maximum length limitation to the aligning reads? When I try to align sequences with length approximately 30,000, I always see that only around the first 16500 bases are aligned even though the two sequences are very similar.

Actually, it could be a limitation on the maximum alignment score that may be stored. The alignment score seems limited to 32767. Maybe signed 16 bit integers are used for storing alignment scores ...