If only a single region is
selected the following columns of information are available:
Standard PCR output table
- Sequence - the primer's sequence.
- Score - measures how much the properties of the primer (or primer pair) deviates from the optimal solution in terms of the chosen parameters and tolerances. The higher the score, the better the solution. The scale is from 0 to 100.
- Region - the interval of the template sequence covered by the primer
- Self annealing - the maximum self annealing score of the primer in units of hydrogen bonds
- Self annealing alignment - a visualization of the highest maximum scoring self annealing alignment
- Self end annealing - the maximum score of consecutive end base-pairings allowed between the ends of two copies of the same molecule in units of hydrogen bonds
- GC content - the fraction of G and C nucleotides in the primer
- Melting temperature of the primer-template complex
- Secondary structure score - the score of the optimal secondary DNA structure found for the primer. Secondary structures are scored by adding the number of hydrogen bonds in the structure, and 2 extra hydrogen bonds are added for each stacking base-pair in the structure
- Secondary structure - a visualization of the optimal DNA structure found for the primer
If both a forward and a reverse region are selected a table of primer pairs is shown, where the above columns (excluding the score) are represented twice, once for the forward primer (designated by the letter F) and once for the reverse primer (designated by the letter R).
Before these, and following the score of the primer pair, are the following columns pertaining to primer pair-information available:
- Pair annealing - the number of hydrogen bonds found in the optimal alignment of the forward and the reverse primer in a primer pair
- Pair annealing alignment - a visualization of the optimal alignment of the forward and the reverse primer in a primer pair.
- Pair end annealing - the maximum score of consecutive end base-pairings found between the ends of the two primers in the primer pair, in units of hydrogen bonds
- Fragment length - the length (number of nucleotides) of the PCR fragment generated by the primer pair