Sequence comparison by dotter between the chimeric contigs (y-axis) shown in Figure 4 and the corresponding contigs from the assembly of masked sequences (masked in regions with 20mer frequencies >36, m36; x-axis). (A) The two contig parts of c24, wrongly assembled at the TA-repeat are separated in m36 forming three non-chimeric contigs. (B) The misassemblies at the LTRs in c31 are not observed in the m36 assembly. (C) The misassembly at the LTR in c83 is not present in the m36 assembly. The short section from 555O10 is contained in a chimeric contig of the masked assembly (m36_c286). (D) Contig c35 is also chimeric in the masked assembly (m36_c41) with the same read fractions and >99% nucleotide identity.