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 ...
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 ...