\textbf{Extremely small negative gap length for \textit{in silico} map of scaffold 81.}
 Two XMAP alignments for \textit{in silico} map of sequence scaffold 81 are shown. Consensus genome maps (blue with molecule map coverage shown in dark blue) align to the \textit{in silico} maps of scaffolds (green with contigs overlaid as translucent colored squares). Sequence scaffolds 79-83 were placed within ChLG 5 and sequence scaffolds 99-103 were placed with ChLG 7 by the \textit{T. castaneum} genetic map. (A) Half of the \textit{in silico} map of sequence scaffold 81 aligns with its assigned ChLG (black arrow). (B) The other half aligns with ChLG 7 (red arrow) producing a negative gap length smaller than -20 kb. The alignment that places sequence scaffold 81 with ChLG 7 disagrees with the genetic map and was manually rejected for Tcas5.2.