Figure 3.

Examples of protein-coding and tRNA gene annotations (green arrows) by GeSeq with high-quality settings visualized by SeqBuilder.v13.0.0 (DNASTAR, Madison, WI, USA). The coordinates of the chloroplast protein-coding genes psbZ and psbC (only 3΄ end shown) as annotated by BLATx exactly match to their corresponding profile HMM hits (orange arrows). The tRNA gene trnS which is annotated in-between the two protein-coding genes by BLATn is confirmed by both de novo tRNA predictors tRNAscan-SE and Aragorn (light and dark gray arrows, respectively). See Supplementary Figure S2B and (C) for the corresponding GenBank file excerpt.