Example of joining scaffolds where adjacent ends are alternative assemblies of the same region. (a) Using physical mapping techniques, scaffolds AAAB01008904 and AAAB0108851 are placed adjacent to one another on chromosome arm 2R. In the previous genome assembly, MOZ2, the scaffolds were placed with an arbitrary 10 kbp of gap between them. (b) After alignment of scaffolds using Exonerate and Dotter, it was clear that there was about 64 kbp of sequence overlap between the 3' end of AAAB01008904 and the 5' end of AAAB0108851. Based on BAC coverage of each scaffold and gaps in each of the scaffold sequences, we chose to keep the overlapping region from AAAB01008904 (base-pairs 1102797 to 1759265) and use it for the new chromosome assembly. (c) The corresponding overlapping region from AAAB0108851 (base-pairs 1 to 635373) was deemed to be an alternative assembly segment, with the rest of the scaffold kept as part of the chromosome assembly. The regions retained as parts of chromosome arm 2R were placed adjacent to each other with no inter- scaffold gap.