Examples of repeat reconstruction from assembled 454 reads. (A) The complete rDNA coding region including genes for 18S, 5.8S and 25S rRNA and parts of the large intergenic spacer (IGS) was reconstructed as a single contig (CL2Contig6). The graph shows the read depth (number of assembled reads) along the contig sequence. (B) Reconstruction of the Ty3/gypsy retroelement Peabody, including most of its long terminal repeat (LTR) sequence and complete polyprotein-coding region (gag-pol). (C) A novel Ty1/copia element Ps-copia-1/751, reconstructed from ten overlapping contigs. The region devoid of stop codons encoding gag-pol was identified in frame +3. Yellow bars depict length and relative positions of the overlapping contigs, stop codons are represented by red vertical lines.