Resolution:
## Figure 2.
Exact matching versus inexact alignment. Illustration of how EXACTMATCH (top) and
Bowtie's aligner (bottom) proceed when there is no exact match for query 'ggta' but
there is a one-mismatch alignment when 'a' is replaced by 'g'. Boxed pairs of numbers
denote ranges of matrix rows beginning with the suffix observed up to that point.
A red X marks where the algorithm encounters an empty range and either aborts (as
in EXACTMATCH) or backtracks (as in the inexact algorithm). A green check marks where
the algorithm finds a nonempty range delimiting one or more occurrences of a reportable
alignment for the query.
Langmead |