Additional file 5 — ChLGs before and after super scaffolding Alignments of Tcas5.0 and Tcas5.2 in silico maps to consensus genome maps for all ChLGs. Consensus genome maps (blue with molecule coverage shown in dark blue) aligned to the in silico maps (green with contigs overlaid as translucent colored squares). Alignment to both Tcas5.2 super scaffolds (top alignment) and Tcas5.0 scaffolds (bottom alignment) are shown.