Production of working drafts of BAC sequences from assemblies of 454 sequences. The relative order of sequence contigs can be inferred through (a.) identification of target site duplications (TSD) of transposable element sequences located at the edges of contigs or (b.) sequence alignment with a known reference transposable element. The latter only works reliably for elements that occur only once on the BAC analysed. c. For BAC 604D5, information from the order of genes in the orthologous region of the rice genome was used as well as the structure and organisation of transposable elements. d. Five contigs from BAC 509D2 could be arranged in two supercontigs whose linear orientaion to each other is unknown. Regions covered by 454 sequencing contigs are indicated as grey bars underneath the maps in c. and d.. Genes are depicted as black and transposable elements as white boxes. Transcriptional orientations of genes are indicated by arrows. TSD used to infer contig order are indicated. Gaps that were closed through alignment to reference transposon sequences are indicated by a curly bracket. Gaps that could be closed with low-quality 454 sequences are indicated by upward arrows. Question marks indicate a gap of unknown size between. Numbers above genes correspond to gene descriptions in Table 5.