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
Input Sequences: (the maximum of 500 sequences at a time will be processed)
Upload sequence file in FASTA format
:
OR
copy/paste
source sequences
in FASTA format.
Example sequences
Clear sequence
>DB019K18_R1.ab1 TGCTGCCTGCGGTCGACTCTGAGGATCAACCGTCCCCCATCCCATTAAAG GAGATCCCACTACTGTACTGCGAGCTCGAAAAGTACTCCTACATGATATC ACATCAGAATCGCAACTGAGTACGGCGAATGCTACCCATGGACCGTCTAA GTTGGAGAGATCTCATATTCTCGTCGAAGAAGAAGAAGAAGAAGAAGATG CAAAAGAGCAGAAAGGAAAAGGCAGCGGGCAAAGTAAAAGGAGAACTTCA CGGGGTTTTGCATGGTGCACCGGCCATGGTTCATGTGTAGGCTGGCCCCC TATGCCTTTCTCTTTTTTTGTTGGTTTTCAAGACTGTCTTGTTGGTGAGA AGTGTAAATACGGAGTGCATGCGACGAGGTTTAGGCTCATGTTTATTCTC TGACGAAAGGTTTTGTTGAGCCATAAAAACCTGTCCCTGTGATGATCTCC GGAGTTCCTCACGCAAATCTGCAAAATAGGGCTTAGAAAGTAAAAGCCGT AAACAAGCAGTGCTGACTGAATCGAGAGAAAAAAAAAATAGGGCAGCGCT GAGCAGTGGGGAAACCCGGCCCAGCCCGGACCCACTCCATAAAGCTCGAT TTGTCGTACTGCTCGACCCACATCACCCCTGTTGCCT >DB025J05_R1.ab1 AGGATCCCCTATAGTCACCTTTGCTTTCACCAATAGCCCGATGCCACTCC AGCTGTATGTGTACACCATGCGTTAATGCCCTTTGGATAGTACGTACAGT GACCTAGATAAGGATTCTAAGTTTTTCCATCTGTGGTGGTCCGGTGATGA GTTAATTTTAGGACGTGTCGGCATGACCAGGCAACGTTTGCCTCTTCCAG AGTACAAGTACGTGGACACTCTCATGGTTATTTCATATACTTATTGGAGT ATAAGTACGTACGTAGACACACCCATCATTTAGGTTTTCAGGAGCACTGT CGTAGCCGCTGTCACCGGAGATTTTTGGTTCCCCTCGCCTCCGGCCGCCG CCTTGGCGCTGCGAGGTGGAAGAAACCTCAGTTTTTTTAAGATTATCCAG AAGTTTTTGCTTATATCGATTGGTTGGTTCTGATCGGCAACGCCATGATG GAGGGTGCGATGTCGTCACGAATAAAGGTACTTCGGTCTCTTCCTCTGTT GTGGTGGTGCCTCAACGGGCGTTGCTGCGGAGCCAGAATTTTTTAATCCC CGTGGATTTAGTATACCCGATCTTGTGGGATCTTGGGTTTGTGTACTCCC AGCGCGGATCTGTTGAGTTTTTGTTAGTGT >DB025J09_R1.ab1 AGGATCCATTTTCGCGCATTGATCGGACAGCTCAAGGAGCCTTGTTTCTA TGTTGGGTGGCGCTTCCGCTCCATATGGGGCGGGTTGGCATCCTTTTGCC ATTGTAGGTCTATGACGTAGATCTGACAAACAAGATCCGTTAGCACTTCA CGTTCTCCTGTTTTATTTGGATCTTCCGGTTAATGTTTTATGATCCAGAT CCGACAAATATGAGCCGTTCCCCAAACATGGTAATGGCTCAAACTGTAGA ACTTCAGCAGATCCTCTCATGTTAAATGGTCCTTCCTGTTAATTTCTGGA GAGTTCACATCCATTTGGCCGTTGTAGTGTGTAACGGTTTTGATCCGACA AATATGATCCATTCCTCACATCGGACGGCTCAAGGATAGCACTTTTAAGT GGCTCTTCCAATTAATTTGGTGATGGTTGAGTTTTGAATGCTTTGCCTTC ATTTGGAACCAAAAATAGCAAAGAGTCCTTTTTGTGTTCTATGGATTCAC TAAGCATGATATATGTAGGTTTATGCAGAATATTTGCTAGAGTTGGTCAT TATATATTTTTTCCATCCGACCGCAAACT >DB037E22_R1.ab1 TCGACTCTGAGGATCCATGTTGCTTACATATAGGGAGCTATCTAACCGTT GCTCTTGTAATTTCTTCAATCCAAATTTGGACATCTGTCTTAGTACTTGT TTGGCTTGGAGAAGACACTTGTCCCCGTAGTTTTTCTCTTGCAAAGACAC AAATGATTGATCCCAATTTCAACGCTGGAATAAAAAACCAGTACGTTTAG CGGCCGCGAATCGACGACACGATCGAGTAGGGCAACGACTAATAGAATAG AAAATTAGCAAAAAGGAAGATAGAGCTAGAAATTAAGCAAGCAAGCGCCG GACAGATCGAGCAAGTGCACCGCATCCGGCCAAGAGGGGTCACCACCACT CGACAGCCTAAGCATGTCACGCAAACGACTTGTCCTAGCTACGGCTCGGA GACTAATCAGGTTGAAAGCTCGAAGGGGATCTGAAAGTTTGAAGGAGACG GGATAGCGTCTGGACAGATTAATCAGGTGCGTTCTCCGACAGCTTCGTCT CAGGCTGTCAGCCGGCGTGTCAAATCCTAGCACTTCACTAATTTGCTCGG CGATCGTCGACGCACGCCGCCGCAGCACGACGCCTACGTGCACAGCTAGC GAGCGAGCGCCGGCACTGAACGTTTCAAGTTTCAACTCTACTATTC >DB044D14_R1.ab1 AGGATCCCCAGTTGTCGAGCCTTTCCATGGATTGGATCTGGCCCCTGGCA TCCTACTGCGGTCGTATCCGGCAGAAGCACCGTCGTGTGCCGTCGCGTCC TCCTACGCCCGTATCCCGCTGAATCGTCATCATGTGCCAGCGCGTCCTAC CCCACGCCACCACGTTGGTTCCCACGCAGCTAGGCCTTTCCATGGCCTGG ATCTAGCACCATGCATCCTCCCTACGACTGGATTCGGCGGAACCACCATC GCACACCACCATTGGACCTCATCTTAGTGCCGCCACCGAAGTTCATCTCG ACGTAGATCCAATTAGTTTTTTTCAGCAAATTAAGGCTTAGAACTAAAGT CCAAACATTAAAACTTGAAAAATTAAAATCTTCAAATCAAAGAGTAAAAA ATAAAAGTGGATAAAAATCAAAAGTCAAGAAACTGAAATTAAAGTAAGCC AAGAAAAGAAAAAAACTTTCGATAGCCATGTCGGAATTCGTCGGCCAACT CTTGTCCCGACGGTCTTTATCTCATTATTCAATCCTCTTTACCCTAAAAA GAGAGAGTAAAAGCGAGAACTGCGCGTAGCACATGTAGCAAGGCTCGCGG TGGAGCAGCCTGCCCGCATGAGTTCAAGTCCCACTACTACAAAACAGTGT ATATGTGACGAGTCATCAGTGACAGGCTTCATCAGTAACGGGCTTACCAC GCCCGTCACTGATGACACACCATCAGTGACGGGCGCGTGCTCACCCG >DB044D18_R1.ab1 TCGACTCTGAGGATCCGCACCATTCAATTTGTCTCTGGAGCAAGTGGCCA CACCTCACCGCCCCCTGATAAATCCCGGAAGAGAAATTGTCCGTCCAGCC TTTATAAAACCTGCAGTTCAGGATCGGATCCTCCGTCACCACCCTACCAT CATCAACGAATCCACCCCTGAGAAGTCCACCCCTCCACCACAACACCAAC AACAACAGATCGCCGCCATGTCCAGCTCCGGCGTCGACGGAGCGGCGAAC CCGGCGCTGGGGCCGGACACGGACGCGCCGGCCGGCGAGGGCCTGTCGCA GGCGCAGTTCGCGGCGGGGTGCTTCTGGAGCGTGGAGCTGGCGTACCAGC GGCTCCCCGGCGTGGCGCGCACGGAGGTGGGCTACTCGCAGGGGCACGTC GACGAGCCGACCTACCGCGGCGTCTGCGGCGGCGGCACGGGCCACGCCGA GGCTGTGCGCGTGCACTACGACCCCAAGGAGTGCCCCTACGCCGTGCTCC TCGACGTCTTCTGGGCCAAGCACAACCCCACCACGCTCAACAGACAGGTA CGCCGATGACTAGTGCTTTGATGTTTGACGTGCGTACTGCGCAGCGCCCA TGCCGTCGGCCTTGGCAACGGGGCCGCGCGTTCCGATCTTGACGCCGGCG TTGCAAGGTTCAATGAACCTGGCACGGGTTCGCTTCGGGGGCTGACTCGT TCTGAGCAAGTTGGTTCGGACCA
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