MFE
primer
3.1
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Specificity
* Primer sequences (<= 50)
(example)
Number of primer sequences should <= 50, degenerate primers should <= 2. Otherwise, please use the
local command-line version.
* Background Database
UCSC - Homo sapien - hg19 - Genome
UCSC - Anolis carolinensis - anoCar1 - Genome
UCSC - Anolis carolinensis - anoCar2 - Genome
UCSC - Anopheles gambiae v. MOZ2 - anoGam1 - Genome
UCSC - Apis mellifera - apiMel1 - Genome
UCSC - Apis mellifera - apiMel2 - Genome
UCSC - Aplysia californica - aplCal1 - Genome
UCSC - Apteryx australis - aptMan1 - Genome
UCSC - Aquila chrysaetos canadensis - aquChr2 - Genome
UCSC - Balaenoptera acutorostrata scammoni - balAcu1 - Genome
UCSC - Bison bison - bisBis1 - Genome
UCSC - Bos taurus - bosTau2 - Genome
UCSC - Bos taurus - bosTau3 - Genome
UCSC - Bos taurus - bosTau4 - Genome
UCSC - Bos taurus - bosTau6 - Genome
UCSC - Bos taurus - bosTau7 - Genome
UCSC - Bos taurus - bosTau8 - Genome
UCSC - Branchiostoma floridae - braFlo1 - Genome
UCSC - Caenorhabditis japonica - caeJap1 - Genome
UCSC - Caenorhabditis brenneri (PB2801) - caePb1 - Genome
UCSC - Caenorhabditis brenneri (PB2801) - caePb2 - Genome
UCSC - Caenorhabditis remanei - caeRem2 - Genome
UCSC - Caenorhabditis remanei - caeRem3 - Genome
UCSC - Callithrix jacchus - calJac1 - Genome
UCSC - Callithrix jacchus - calJac3 - Genome
UCSC - Callorhinchus milii - calMil1 - Genome
UCSC - Canis familiaris - canFam1 - Genome
UCSC - Canis familiaris - canFam3 - Genome
UCSC - Cavia porcellus - cavPor3 - Genome
UCSC - Caenorhabditis briggsae - cb3 - Genome
UCSC - Caenorhabditis elegans - ce10 - Genome
UCSC - Caenorhabditis elegans - ce11 - Genome
UCSC - Caenorhabditis elegans - ce2 - Genome
UCSC - Caenorhabditis elegans - ce4 - Genome
UCSC - Caenorhabditis elegans - ce6 - Genome
UCSC - Ceratotherium simum - cerSim1 - Genome
UCSC - Chlorocebus sabaeus - chlSab2 - Genome
UCSC - Choloepus hoffmanni - choHof1 - Genome
Painted turtle genomic DNA from UCSC chrPic1
UCSC - Ciona intestinalis (sea squirt) - ci1 - Genome
UCSC - Ciona intestinalis (sea squirt) - ci2 - Genome
UCSC - Ciona intestinalis (sea squirt) - ci3 - Genome
UCSC - Cricetulus griseus - criGri1 - Genome
UCSC - Cricetulus griseus - criGriChoV1 - Genome
UCSC - Danio rerio - danRer10 - Genome
UCSC - Danio rerio - danRer11 - Genome
UCSC - Danio rerio - danRer3 - Genome
UCSC - Danio rerio - danRer4 - Genome
UCSC - Danio rerio - danRer5 - Genome
UCSC - Danio rerio - danRer6 - Genome
UCSC - Danio rerio - danRer7 - Genome
UCSC - Dasypus novemcinctus - dasNov3 - Genome
UCSC - Dipodomys ordii - dipOrd1 - Genome
UCSC - Drosophila melanogaster - dm1 - Genome
UCSC - Drosophila melanogaster - dm2 - Genome
UCSC - Drosophila melanogaster - dm3 - Genome
UCSC - Drosophila melanogaster - dm6 - Genome
UCSC - Drosophila pseudoobscura - dp2 - Genome
UCSC - Drosophila pseudoobscura - dp3 - Genome
UCSC - Drosophila ananassae - droAna1 - Genome
UCSC - Drosophila ananassae - droAna2 - Genome
UCSC - Drosophila erecta - droEre1 - Genome
UCSC - Drosophila grimshawi - droGri1 - Genome
UCSC - Drosophila mojavensis - droMoj1 - Genome
UCSC - Drosophila mojavensis - droMoj2 - Genome
UCSC - Drosophila persimilis - droPer1 - Genome
UCSC - Drosophila sechellia - droSec1 - Genome
UCSC - Drosophila simulans - droSim1 - Genome
UCSC - Drosophila virilis - droVir1 - Genome
UCSC - Drosophila virilis - droVir2 - Genome
UCSC - Drosophila yakuba - droYak1 - Genome
UCSC - Drosophila yakuba - droYak2 - Genome
UCSC - Filoviridae ebolavirus - eboVir3 - Genome
UCSC - Echinops telfairi - echTel1 - Genome
UCSC - Echinops telfairi - echTel2 - Genome
UCSC - Equus caballus - equCab1 - Genome
UCSC - Equus caballus - equCab2 - Genome
UCSC - Erinaceus europaeus - eriEur1 - Genome
UCSC - Erinaceus europaeus - eriEur2 - Genome
UCSC - Felis catus - felCat3 - Genome
UCSC - Felis catus - felCat4 - Genome
UCSC - Felis catus - felCat5 - Genome
UCSC - Felis catus - felCat8 - Genome
UCSC - Takifugu rubripes v3.0 - fr1 - Genome
UCSC - Takifugu rubripes v4.0 - fr2 - Genome
UCSC - Takifugu rubripes v5.0 - fr3 - Genome
UCSC - Gadus morhua - gadMor1 - Genome
UCSC - Gallus gallus v1.0 - galGal2 - Genome
UCSC - Gallus gallus v2.1 - galGal3 - Genome
UCSC - Gallus gallus - galGal4 - Genome
UCSC - Gallus gallus - galGal5 - Genome
UCSC - Galeopterus variegatus - balAcu1 - Genome
UCSC - Gasterosteus aculeatus - gasAcu1 - Genome
UCSC - Geospiza fortis - geoFor1 - Genome
UCSC - Gorilla gorilla gorilla - gorGor3 - Genome
UCSC - Gorilla gorilla gorilla - gorGor4 - Genome
UCSC - Gorilla gorilla gorilla - gorGor5 - Genome
UCSC - Heterocephalus glaber - hetGla1 - Genome
UCSC - Heterocephalus glaber - hetGla2 - Genome
UCSC - Homo sapien - hg16 - Genome
UCSC - Homo sapien - hg18 - Genome
UCSC - Homo sapien - hg38 - Genome
UCSC - Latimeria chalumnae - latCha1 - Genome
UCSC - Loxodonta africana - loxAfr3 - Genome
UCSC - Notamacropus eugenii - macEug2 - Genome
UCSC - Macaca fascicularis - macFas5 - Genome
UCSC - Manis pentadactyla - manPen1 - Genome
UCSC - Meleagris gallopavo - melGal1 - Genome
UCSC - Meleagris gallopavo - melGal5 - Genome
UCSC - Melopsittacus undulatus - melUnd1 - Genome
UCSC - Microcebus murinus - micMur1 - Genome
UCSC - Microcebus murinus - micMur2 - Genome
UCSC - Mus musculus - mm39 - Genome
UCSC - Mus musculus - mm10 - Genome
UCSC - Mus musculus - mm7 - Genome
UCSC - Mus musculus - mm8 - Genome
UCSC - Mus musculus - mm9 - Genome
UCSC - Monodelphis domestica - monDom4 - Genome
UCSC - Monodelphis domestica - monDom5 - Genome
UCSC - Mustela putorius furo - musFur1 - Genome
UCSC - Myotis lucifugus - myoLuc2 - Genome
UCSC - Nanorana parkeri - nanPar1 - Genome
UCSC - Nasalis larvatus - nasLar1 - Genome
UCSC - Nomascus leucogenys - nomLeu1 - Genome
UCSC - Nomascus leucogenys - nomLeu2 - Genome
UCSC - Nomascus leucogenys - nomLeu3 - Genome
UCSC - Ochotona princeps - ochPri2 - Genome
UCSC - Ochotona princeps - ochPri3 - Genome
UCSC - Oreochromis niloticus - oreNil2 - Genome
UCSC - Ornithorhynchus anatinus - ornAna1 - Genome
UCSC - Ornithorhynchus anatinus - ornAna2 - Genome
UCSC - Oryctolagus cuniculus - oryCun2 - Genome
UCSC - Oryzias latipes - oryLat2 - Genome
UCSC - Otolemur garnettii - otoGar3 - Genome
UCSC - Ovis aries - oviAri1 - Genome
UCSC - Ovis aries - oviAri3 - Genome
UCSC - Pan paniscus - panPan1 - Genome
UCSC - Pan paniscus - panPan2 - Genome
UCSC - Pan troglodytes - panTro1 - Genome
UCSC - Pan troglodytes - panTro2 - Genome
UCSC - Pan troglodytes - panTro3 - Genome
UCSC - Pan troglodytes - panTro4 - Genome
UCSC - Pan troglodytes - panTro5 - Genome
UCSC - Papio anubis - papAnu2 - Genome
UCSC - Papio hamadryas - papHam1 - Genome
UCSC - Petromyzon marinus - petMar1 - Genome
UCSC - Petromyzon marinus - petMar2 - Genome
UCSC - Pongo abelii - ponAbe2 - Genome
UCSC - Pristionchus pacificus (5.0) - priPac1 - Genome
UCSC - Procavia capensis - proCap1 - Genome
UCSC - Pteropus vampyrus - pteVam1 - Genome
UCSC - Rhesus macaque - rheMac2 - Genome
UCSC - Rhesus macaque - rheMac3 - Genome
UCSC - Rhesus macaque - rheMac8 - Genome
UCSC - Rhinopithecus roxellana - rhiRox1 - Genome
UCSC - Rattus norvegicus - rn4 - Genome
UCSC - Rattus norvegicus - rn5 - Genome
UCSC - Rattus norvegicus - rn6 - Genome
UCSC - Saccharomyces cerevisiae - sacCer1 - Genome
UCSC - Saccharomyces cerevisiae - sacCer2 - Genome
UCSC - Saccharomyces cerevisiae - sacCer3 - Genome
UCSC - Saimiri boliviensis - saiBol1 - Genome
UCSC - Sarcophilus harrisii - sarHar1 - Genome
UCSC - Sorex araneus - sorAra1 - Genome
UCSC - Sorex araneus - sorAra2 - Genome
UCSC - Spermophilus tridecemlineatus - speTri2 - Genome
UCSC - Strongylocentrotus purpuratus - strPur1 - Genome
UCSC - Strongylocentrotus purpuratus - strPur2 - Genome
UCSC - Sus scrofa - susScr11 - Genome
UCSC - Sus scrofa - susScr2 - Genome
UCSC - Sus scrofa - susScr3 - Genome
UCSC - Taeniopygia guttata - taeGut1 - Genome
UCSC - Taeniopygia guttata - taeGut2 - Genome
UCSC - Tarsius syrichta - tarSyr1 - Genome
UCSC - Tarsius syrichta - tarSyr2 - Genome
UCSC - Tetraodon nigroviridis - tetNig1 - Genome
UCSC - Tetraodon nigroviridis - tetNig2 - Genome
UCSC - Trichechus manatus latirostris - triMan1 - Genome
UCSC - Tupaia belangeri - tupBel1 - Genome
UCSC - Tursiops truncatus - turTru2 - Genome
UCSC - Vicugna pacos - vicPac1 - Genome
UCSC - Vicugna pacos - vicPac2 - Genome
UCSC - Xenopus laevis - xenLae2 - Genome
UCSC - Xenopus tropicalis - xenTro1 - Genome
UCSC - Xenopus tropicalis - xenTro2 - Genome
UCSC - Xenopus tropicalis - xenTro3 - Genome
UCSC - Xenopus tropicalis - xenTro7 - Genome
UCSC - Xenopus tropicalis - xenTro9 - Genome
Fragaria vesca v2.0.a1 pseudomolecules
HBV https://www.ncbi.nlm.nih.gov/nuccore ("Hepatitis B virus"[Organism] OR HBV[All Fields]) AND "Hepatitis B
HOMD 16S rRNA RefSeq V13.2
HPV (human papillomavirus reference genomes) https://pave.niaid.nih.gov/#explore/reference_genomes/human_genomes
Human GRCh37 RNA
Human GRCh38 RNA
Mouse GRCm38 RNA
Mycobacterium tuberculosis H37Rv complete genome
Pantodon buchholzi mitochondrial DNA (complete genome) https://www.ncbi.nlm.nih.gov/nuccore/15430523?report=fasta,
Potato Genome Sequence (DM_v4.04_pseudomolecules)
Prunus persica v2.0.a1 scaffolds
Pseudomonas Genomic DNA (pgd_r_16_2)
Phaseolus vulgaris v2.1 genome
Phaseolus vulgaris v2.1 transcript
Rice Genome release 7
UNITE Includes singletons set as RefS (version 7.1)
UNITE Includes global and 97% singletons (version 7.1)
SILVA-NR99 type strains
Staphylococcus aureus subsp. aureus USA300_FPR3757 ( complete genome)
Arabidopsis thaliana Genome (TAIR10)
Arabidopsis transcriptome (cDNA, TAIR10)
UNITE public 22.08.2016
Zea mays (AGPv4) http://www.maizegdb.org/;
Drosophila melanogaster genome (fruit fly assembly Release 6 plus ISO1 MT)
Drosophila melanogaster RNA (fruit fly assembly Release 6 plus ISO1 MT)
Rattus norvegicus RNA (Norway rat assembly Rnor_6.0)
Danio rerio RNA (zebrafish assembly GRCz11)
Danio rerio genome (zebrafish assembly GRCz11)
Danio rerio RNA (zebrafish assembly GRCz11)
Apis mellifera RNA (honey bee assembly Amel_4.5)
Apis mellifera genome (honey bee assembly Amel_4.5)
Apis mellifera RNA (honey bee assembly Amel_4.5)
Caenorhabditis elegans (assembly WBcel235) RNA
Sus scrofa (pig) representative genome Sscrofa11.1
Sus scrofa (pig) RNA Sscrofa11.1
Escherichia coli str. K-12 substr. MG1655 (reference genome)
Saccharomyces cerevisiae S288C (assembly R64) (reference genome)
Salmonella enterica subsp. enterica serovar Typhi str. CT18 (genome)
Klebsiella pneumoniae subsp. pneumoniae HS11286 genome
Riemerella anatipestifer representative genome
Crassostrea virginica genome (assembly C_virginica-3.0)
Crassostrea virginica RNA (assembly C_virginica-3.0)
C.chinense(assembly Chinense.v1.2.Total)
Capsicum_annuum(assembly Capsicum_annuum_UCD10X_v.1.0)
Capsicum_annuum(assembly Annuum.v1.6.Total)
C. baccatum(assembly Baccatum.v1.2.Total)
Bubalus bubalis (water buffalo)-All 4 genomes for species
Fragaria_x_ananassa_Genome_v1.0_FAN_r1.1_scaffolds.fasta
Sorghum bicolor (assembly Sorghum_bicolor_NCBIv3)
Bovine coronavirus(viruses)
Myxococcus xanthus DK 1622, complete genome
Haloferax volcanii(Representative genome Haloferax volcanii DS2)
Chlamydia trachomatis(Reference genome Chlamydia trachomatis 434/Bu)
Neisseria gonorrhoeae(Reference genome Neisseria gonorrhoeae FA 1090)
Corynebacterium kutscheri
Streptococcus pneumoniae(Reference genome: Streptococcus pneumoniae R6)
Mycoplasma pulmonis(Representative genome Mycoplasma pulmonis UAB CTIP)
Bos_taurus_UMD_3.1.1 assembly for Bos taurus
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2(genome)
Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 (genome)
Moraxella catarrhalis(All 106 genomes for species)
Spirodela polyrhiza (assembly ASM198140v1)
Bacillus cereus(Reference genome Bacillus cereus ATCC 14579)
Pelodiscus sinensis (assembly PelSin_1.0)
Physcomitrella patens (assembly Phypa V3)
Trichomonas vaginalis G3 (assembly ASM282v1)
Solanum lycopersicum (assembly SL3.0)
Solanum tuberosum (assembly SolTub_3.0)
Castor canadensis (assembly C.can genome v1.0)
Vaccinia virus WR (complete genome)
African swine fever virus
Clostridium perfringens (Representative genome Clostridium perfringens ATCC 13124)
Stenotrophomonas maltophilia K279a (complete genome)
longan (Dimocarpus longan Lour.)
Oryza sativa Japonica (IRGSP-1.0)
Oryza sativa Japonica (cDNA)
Leishmania KDNA
Oilseed rape (Brassica napus L.)
Alphavirus (nucleotide)
BosGru_v2.0_genomic
Araport11_genes (cdna)
Medicago truncatula (assembly MedtrA17_4.0)
Oreochromis niloticus (Refseq mRNA)
Manihot esculenta (assembly Manihot esculenta v6)
Moniliophthora perniciosa FA553 (assembly ASM18302v1)
Moniliophthora roreri (assembly ASM146670v1)
Macaca_fascicularis (RNA)
Hepacivirus (HCV data set)
Triticum aestivum (bread wheat assembly iwgsc_refseqv1.0)
SARS-CoV-2 (11750 sequences, update 2020-09-02)
SARS-CoV-2 (random 2000 sequences, from NCBI Virus, update 2023-11-17)
NCBI Virus (143747 complete nucleotides, update 2020-04-07)
Plasmodium species / Genome (release 47)
Plasmodium species / mRNA (release 47)
Brassica napus / No2127 genome
Brassica napus / Shengli genome
Brassica napus / Tapidor genome
Brassica napus / ZS11 genome
Brassica napus / Westar genome
Brassica napus / Zheyou7 genome
Brassica napus / Quinta genome
Brassica napus / Gangan genome
Apostasia shenzhenica (assembly ASM278626v1)
Phalaenopsis equestris (assembly ASM126359v1)
Dendrobium catenatum (assembly ASM160598v2)
Enterovirus (328 genome assemblies)
Aspergillus niger (16 genomes)
Influenza Virus
Mouse mRNA (mm10 refMrna from ucsc)
Pekin duck (Anas platyrhynchos (mallard), GCF_015476345.1)
Glycine max (soybean), GCF_000004515.6, Williams 82, Mar 10, 2021
dog genome, Oct. 2020 (Dog10K_Boxer_Tasha/canFam6)
Spinacia oleracea (spinach) GCA_020520425.1 2021-10-20
Allow mismatch at the 3' end
No
Yes
Accurate but slow, new in version 3.0.
T
m
Min
°C
Minimum T
m
value required for the binding stability between primer and its binding sites.
Size (bp)
From
To
Product size: 0 (min) - 100000 (max).
Concentration of monovalent cations (usually KCl)
mM
Concentration of divalent cations (usually MgCl
2
)
mM
Concentration of dNTPs
mM
Annealing oligo concentration
nM
Run
MFEprimer-3.1
Featured
New Server
New
Primer Design
Specificity analysis
Dimer analysis
Hairpin analysis
Old Versions
MFEprimer-3.0
MFEprimer-2.0
Contact
Bugs? contact Wubin Qu <quwubin@gmail.com>