Alignment output of ClustDB. The BAC AC148340 (len1 = 105618 bp) is approximately contained in the BAC AC148483 (len2 = 298559 bp). The alignment has length aln = 105638 including 20 gaps in AC148340 and 9 gaps in AC148483. Its displayed part shows five clusters of mismatches surrounded by long perfect matches so that the number of errors does not exceed 10 in each window of size 40. Therefore, ClustDB does not look for improvements by introducing gaps and reports 69 errors, i.e. 16 errors more than the exact alignment computes. Note that each cluster of mismatches can be realigned with two gaps.