Fig. 2. AssemblyLIGN sequence alignment of the three fragments amplified from Chinese Spring derived nullisomic-tetrasomic lines (N4BT4D and N4DT4B) using gwm538F and gwm538R primers. Fragments are labeled by size in nucleotides. Nucleotide positions are indicated at top of the figure. Primer sequences for gwm538F, gwm538R and gwm538snpF1 are included for comparison. Black arrows indicate SNPs (in bold text) occurring outside the microsatellite region. The SNP indicated at Position 18 was designed as a mismatch to all three fragments (see results) and does not ‘naturally’ occur there. Period ‘.’ characters are used as pads to allow justification for the alignment of different size fragments.