Aligning a query against a suffix tree. Aligning the query ATAT against the suffix tree for ATATCAT$. The path from the root to each leaf encodes a sequence that occurs in the reference at the label of that leaf. The blue path shows the extent of the alignment in the tree. The query occurs at position 1 with a alignment length of 4. For l ≥ 2, MUMmerGPU will print the red nodes as alignments with an alignment length equal to 2, the sequence depth of the lowest common ancestor between the red nodes and the blue node.
Schatz et al. BMC Bioinformatics 2007 8:474 doi:10.1186/1471-2105-8-474