Fig. 5.
Alignment examples–shown here are four examples where Pairagon finds the correct alignment and GMap does not. (a) GMap adds two bases of the initial microexon to the second exon and leaves the rest unaligned. (b) GMap does not align the final base. (c) GMap incorrectly marks the left side of an intron. (d) GMap marks an insertion as an intron.