Figure 5

MegaBlast analysis showing sequence identity to WGS reads using the BES CG816569 from H51D13 in octaploid-like contig 9077. Sequence analysis only partly supported the inference that the contig was a product of four coalesced regions. Shown is an alignment of 301–477 bp of the BES "H51D13_Build4MTP8A23_gi89261445_4" against 7.3 million reads with repeat masking that gave 3 identical matches among 9–10 homeologous sequences. Cluster 1 was composed of traces ending in 340, 924 and 694 that shared T rather than C at position 330 (circled). Cluster 2 was composed of clones ending in 666 and 123 and shared T rather than C at position 375. Cluster 3 was composed of clones ending in 694, 224, 642, 287 and 026 that shared GG at position 385. The homeologs clustered into 3 separate sets, one less than the number expected for an octaploid-like region in an inbreeding species.