Fig. 6. Schematic representation of individual gene trans-splicing.

Each alignment start position observed was plotted at the corresponding genomic position with the number of supporting reads. The dots are colored according to the legend on the right, with red indicating a majority of SL reads, green a majority of endogenous hairpin reads and blue reads with no evidence for either. Dotted vertical lines indicate the position of a putative start codon. nlp-36 displayed a single SL1 trans-spliced site. M60.4 presents two trans-splicing sites indicative of two alternative promoters with distinct SL1/2 ratios. The Y37E3.7/Y37E3.8 operon with typical SL1 and SL2 preference. lev-11 gene distal promoter carries an endogenous hairpin while the proximal promoter is mainly SL1.