BatchPrimer3
a high-throughput web tool for picking PCR and sequencing primers
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Choose primer type:
Generic primers
SSR screening and primers
Hybridization oligos
SNP (allele) flanking primers
Single base extension (SBE) primers and SNP (allele) flanking primers
Single base extension (SBE) primers
Allele-specific primers and allele-flanking primers
Allele-specific primers
Tetra-primer ARMS-PCR primers
Sequencing primers
Design pairs of generic primers for any DNA sequences.
Reset the entire form
User's e-mail
(results will be sent to the user)
(Optional)
Input Sequences:
Upload sequence file in FASTA format
:
OR
copy/paste
source sequences
in FASTA format.
Example sequences
Clear sequence only
Pick left primer or use the left primer
Pick right primer or use the right primer
Mispriming/repeat library
:
NONE
Arabidopsis
Brachypodium
Brassica
Glycine
Gramineae
Hordeum
Lotus
Oryza
Sorghum
Solanum
Triticum
Zea
Wheat
General Settings for Generic Primers
Product Size
Min:
Opt:
(0 for no Opt)
Max:
Number To Return:
Max 3' Stability:
Max Mispriming:
Pair Max Mispriming:
Primer Size
Min:
Opt:
Max:
Primer Tm
Min:
Opt:
Max:
Max Tm Difference:
Product Tm
Min:
Opt:
Max:
Primer GC%
Min:
Opt:
Max:
Max Self Complementarity:
Max 3' Self Complementarity:
Max #N's:
Max Poly-X:
Inside Target Penalty:
Outside Target Penalty:
Set Inside Target Penalty to allow primers inside a target.
CG Clamp:
Salt Concentration:
Annealing Oligo Concentration:
(Not the concentration of oligos in the reaction mix but of those annealing to template.)
Liberal Base
Penalty Weights for Generic Primers
Tm
Lt:
Gt:
Size
Lt:
Gt:
GC%
Lt:
Gt:
Self Complementarity
3' Self Complementarity
#N's
Mispriming
Sequence Quality
End Sequence Quality
Position Penalty
End Stability
Penalty Weights for Generic Primer Pairs
Product Size
Lt:
Gt:
Product Tm
Lt:
Gt:
Tm Difference
Any Complementarity
3' Complementarity
Pair Mispriming
Primer Penalty Weight
Hyb Oligo Penalty Weight