Fig 3. The sequencing of cloned amplicons from different perfect transcript-derived (I) (CaTMS1055) and compound genomic (II) (CaGMS1156) microsatellite markers showing FLP between ICC4958 and PI489777 and their multiple sequence alignment (C and D) validated the presence of expected microsatellite repeat-motifs which corresponded well with our in silico prediction of expansion and contraction of a number of microsatellite repeat-units.

The fragment sizes (bp) of the amplified polymorphic alleles are indicated. M: 50 bp DNA ladder size standard. The identities of two markers with their detailed information are provided in the S2 Table.