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Last update on 04. Mar 2022 .
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Design Primers


ARB_NT/Probes/Design Primers



Searches for primer pairs within the given physical and biological ranges

  1. select a species (ARB_NT <INFO button>)
  2. open 'PRIMER DESIGN' window
  3. specify search parameters
  4. press 'GO' (will open ´Primer Design RESULT´).


This initializes the values left and right position and the primer distance with (hopefully) reasonable defaults.

Search parameters  

Left/right position

specifies the ranges (where the primer shall reside) using a START position and a given NUMBER OF BASES.
The actual sequence data of the currently selected species is examined and the end position of the primer range is set dynamically, such that the range contains the specified number of bases.

Primer length

Specifies a lower and upper limit for the number of bases the reported primers shall contain.

Primer distance

Specifies the minimum and maximum wanted distance (in number of bases) between the left and right primer of the reported primer pairs. Optional parameters (ignored if 0).

G+C ratio / temperature

Specifies minima and maxima for G+C-ratio and temperature of the reported primers.

Min. dist to next match of primer

If a value above zero is specified, the search accepts primers matching at additional positions, if the distance betweeen the selected position and additional positions is greater than the specified value.
A value of zero or below forces all primers to be well-defined (i.e. to match only once).
Example: primerposition   100
         min.dist          50
         2nd occurrence    30 => distance 70 => primer remains in list
         3rd occurrence   140 => distance 40 => primer is removed from list

Expand IUPAC codes

If option is checked, all possibilities of IUPAC codes are permutated when testing for primer matches.
When unchecked, primers containing IUPAC codes will not be considered.

Max. number of results

Limits the number of reported results.

G+C- / temperature-factor

Allows to weight the impact of G+C vs. temperature while scoring the reported results.


all specified positions are from range [0 .. N-1], i.e. when you use a position from EDIT4, you need to subtract 1



Wolfram Foerster 2001






ARB will crash if you use Primer Design without taking care about the estimated memory needed (lower right corner).



No bugs known