atac 0~20150903+r2013-8build2 (amd64 binary) in ubuntu kinetic

 atac computes a one-to-one pairwise alignment of large DNA sequences. It first
 finds the unique k-mers in each sequence, chains them to larger blocks, and
 fills in spaces between blocks. It was written primarily to transfer
 annotations between different assemblies of the human genome.
 .
 The output is a set of ungapped 'matches', and a set of gapped 'runs' formed
 from the matches. Each match or run associates one sequence with the other
 sequence. The association is 'unique', in that there is no other (sizeable)
 associations for either sequence. Thus, large repeats and duplications are not
 present in the output - they appear as unmapped regions.
 .
 Though the output is always pairwise, atac can cache intermediate results to
 speed a comparisons of multiple sequences.
 .
 This package is part of the Kmer suite.