Figure 3
User interface for reviewing results of designed marker candidates. A. Circular viewer. The circular viewer presents a maximum of 60 primer pairs per page. Outer circle represents the forward primers, while inner circle the reverse primers. Each of four different nucleotides are denoted with different colors; red-A, green-T, blue-G and yellow-C. Mismatched nucleotides are highlighted using larger circles over matched ones. The pane on left upper corner display overall positional information for primers designed under selected parameters. Tm values for forward and reverse primers are depicted with red and blue circles, respectively, within minimum-to-maximum range, and accurate Tm values can be checked by selecting one of the primer pair candidates. Individual primer pairs of user’s interest can be selectively re-displayed using right button of the mouse over the circular viewer (the pane on left lower corner). B. Primer viewer. This viewer presents detailed information of selected primer pairs with aligned gene structure, corresponding genic sequence alignment, PCR product size and primer sequences. It also provides the results of eHT-PCR analyses.