Short-range scaffold accuracy assessment via Validated Fosmid Regions. First, validated Fosmid regions (VFRs) were identified (86 in bird and 56 in snake, see text). Then VFRs were divided into non-overlapping 1,000 nt fragments and pairs of 100 nt ‘tags’ were extracted from ends of each fragment and searched (using BLAST) against all scaffolds from each assembly. A summary score for each assembly was calculated as the product of a) the number of pairs of tags that both matched the same scaffold in an assembly (at any distance apart) and b) the percentage of only the uniquely matching tag pairs that matched at the expected distance (± 2 nt). Theoretical maximum scores, which assume that all tag-pairs would map uniquely to a single scaffold, are indicated by red dashed line (988 for bird and 350 for snake).