Fig. 2.

Alignment performance using segments from human transcriptome, tested for different values of L, to align 40 million reads of length 101 (first sample in SwitchTx dataset, see section 3). Performance is shown in terms of the number of multimapped reads (red solid line) and unmapped reads (blue solid line), compared to the number of multimapped reads (red dotted line) and unmapped reads (blue dotted line) when aligning using the transcriptome