| More docs on the ARB website. See also index of helppages. Last update on 24. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary
- Design Primers

Related topics:

- Primer Design/IUPAC codes

# Primer Design/Search Parameters

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_NT/ETC/Primer Design

## DESCRIPTION

### left/right position: specifies the start of primer ranges (leftmost base position) [right.min > left.min]

### left/right number of bases specifies how many bases a primer range includes

### primer length: number of bases within a primer [length > 0]

### primer distance: min/max number of bases between leftmost base in left primer and rightmost base in right primer

### G+C ratio: range of GC-ratio of primers in percent (countG+countC / countBases * 100)

### temperature: range of temperature of primers (4*(countG+countC) + 2*(countA+countT))

    minimal distance to next match of primer:
    if a primer is found again outside this range it is ignored
    example: primerpos        100
             min.dist          50
             2nd occurrence    30 => primer remains in list
             3rd occurrence   140 => primer is removed from list

### expand IUPAC-codes: switches expansion of IUPAC-codes on/off example: TTRC is expanded to TTAC and TTGC

### maximal number of results: how many possible pairs you want ?

### G+C-factor / temperature-factor: weight of GC / temperature while evaluation of possible primerpairs

## NOTES

### written by Wolfram Foerster 2001

## EXAMPLES

### None

## WARNINGS

### None

## BUGS

### No bugs known