Figure 6

Workflow for refining the SAT analyses on the consensus sequences and their respective primers pairs. The user can view the full details (Primers, SSRs, Alignment, Sequence) for each sequence and choose to manually validate the corresponding primer pairs (A). For sequences with "specific" primers, the first pair of primers found by ePrimer3 automatically get the "validated" status (B). For sequences without primers, SAT proposes to run ePrimer3 again, using modified analysis parameters, and the user decides whether or not to accept any newly detected primers into the database. Alternatively, a primer pair for each remaining sequence can be entered manually (C). For sequences with non-specific primers, SAT proposes to restart the sequence alignment using CAP3, within each subgroup redefined by the results of Blast and Graph9, with the option of keeping the newly formed consensus sequence (D).