Bioinformatic Analysis of Inherited Templates (BAIT) localizes unplaced scaffolds in late-version assemblies. Orphan scaffolds can be correctly oriented and localized relative to the rest of the genome by comparing template-strand inheritance. The orientation of an orphan scaffold is arbitrary, because it is not anchored to the rest of the genome, so it can be correctly oriented with respect its located chromosome, or misoriented. (a) For a single library where the unplaced scaffold GL456239.1 is WW, BAIT maps its potential location (shown in red) to both WW genomic regions (correctly oriented), and CC genomic regions (misoriented). If only one library is analyzed, all locations map with 100% concordance. Note that a WW scaffold will not locate to a WC chromosome, so chr8, chr14, chr16, chr18, and chr19 are 0% concordant. (b) BAIT iterates over a second library where GL456239.1 is CC. The results of the two libraries combined reduce the number of potential mapping locations from 17 to only 3 that map with 100% concordance. Because chr8, chr14, and chr16 are WC in this library also, these chromosomes map with 0% concordance. (c) BAIT iterates over a third library where GL456239.1 is WC, and thus maps to all chromosomes that are WC. The result of the three combined libraries reduces the number of potential mapping locations to 2: the centromeric tips of chr1 and chr4. (d) The combined results after iteration of all 62 libraries refine the location of GL456239.1 to the first 10 Mb of chr1 in the reverse orientation (with a concordance of 91%). The fragment was further refined to an unbridged gap occupying the first 3 Mb of chr1. Abbreviations: C, Crick; chr, chromosome; W, Watson.