Examples for chimeric contigs in the non-barcoded assembly of unmasked sequences from a 48-BAC pool (non-bc). Coloured curves represent the coverage by reads from different BACs as identified by barcodes. BAC names and their read fraction in the whole non-bc contig are given in the same colour above the curves. Grey curves depict the 20mer frequency. Below the diagrams, the nucleotide identities to the corresponding contigs from the barcoded assemblies are given (rc = reverse complement). Red arrows indicate the points where the non-bc contigs are misassembled. (A, B, C) non-repetitive contig parts are joined by known repetitive elements (blue bars).(D) non-repetitive contig parts are joined at an unknown low complexity repeat without increased kmer frequency.