Fig. 5.

The chromosome 18 lcr16a duplication is flanked by 4 kb direct repeats. A modified UCSC genome browser representation of the lcr16a integration on chromosome 18 is shown. The core duplicon is flanked by ∼4 kb direct repeats (light blue bars; chr18_SD). Breakpoints of the flanking repeats are localized in the 3′ transduction (3′ TD—red bars) of an SVA_C element and directly downstream of an SVA_B element. The inset shows the complex junction at the 3′ lcr16a integration site involving, among others, the insertion of an unrelated DNA segment and the inversion of part of the SVA_C 3′ transduction. The marmoset alignment net is provided to illustrate the different origins of the sequences. The RepeatMasker track has been reduced to show SVA only.