Please select the Task here:   Go to Javascript version
Detection: Pick primers anywhere in the Sequence using targets and regions.
Cloning: Pick primers exactly at the border of included region.
Sequencing: Pick primers for sequencing along the sequence using targets and regions
Primer List: Pick a list of primers along the sequence using targets and regions
Primer Check: Check a primer provided in left primer input

Sequence Id: Mispriming/Repeat Library:
  A name to identify your output.   Or N-out undesirable sequence (vector, ALUs, LINEs...)
To upload or save any sequence from your local computer, choose here:
Paste source sequence below:
  5'->3', as ACGTNacgtn -- other letters treated as N -- numbers and blanks ignored FASTA format ok.
Pick left primer
or use left primer below.
Pick hybridization probe
(internal oligo) or use oligo below.
Pick right primer or use right primer
below (5'->3' on opposite strand).

Excluded Regions:  >
E.g. 401,7 68,3 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68. Or mark the source sequence with < and >: e.g. ...ATCT<CCCC>TCAT.. forbids primers in the central CCCC.
Targets:  ]
E.g. 50,2 requires primers to surround the 2 bases at positions 50 and 51. Or mark the source sequence with
[ and ]: e.g. ...ATCT[CCCC]TCAT.. means that primers must flank the central CCCC.
Included Region:  }
E.g. 20,400: only pick primers in the 400 base region starting at position 20. Or use { and } in the
source sequence to mark the beginning and end of the included region:
e.g. in ATC{TTC...TCT}AT the included region is TTC...TCT.

Please select special settings here:  
To upload or save a settings file from your local computer, choose here:
Product Size Ranges  
Primer Size Min: Opt: Max:
Primer Tm Min: Opt: Max:      Max Tm Difference:
Primer GC% Min: Opt: Max:
Salt Concentration: Fix the prime end of the primer
Annealing Oligo Concentration: Select which end of the primer is fixed and which end can be extended or shortened by Primer3Plus fo find optimal primers.
(Not the concentration of oligos in the reaction mix
but of those annealing to template.)

General Sequencing Conditions

Lead Bp: Space between primer binding site and the start of readable sequencing
Spacing Bp: Space between the primers on one DNA strand
Accuracy Bp: Space in which Primer3Plus picks the optimal primer
Pick Reverse Primers Pick also primers on the reverse DNA strand
Interval Bp: Space between primers on the forward and the reverse strand