Select genome, assembly & dbSNP
--Select genome--
Human
Mouse
--Select genome assembly--
hg38
hg19
hg18
--Select dbSNP build--
snp146
snp144
snp142
snp141
snp138
Select primer type
BSP Primer
BSP-COBRA Primer
MSP Primer
MSRE Primer
PyroSeq Primer
Upload Target region file
Upload target BED file :
Example target bed file
Upload Primer3 parameter file
Upload Primer3 parameter file :
Primer3 full parameter file
Compatible with Primer3web Version 4.0.0
Provide Restriction enzyme list(s)
Provide enzyme list :
Upload enzyme list file :
Example Type-II enzyme list
Min. RE cutsites
:
Parameters for primer selection
Pick left primer, or use left primer below:
Pick hybridization probe or use oligo below:
Pick right primer, or use right primer below:
Product Size Ranges
:
Primer pair to return
:
Targets
:
Included Region
:
Product size
:
Min:
Opt:
Max:
Primer Tm
:
Min:
Opt:
Max:
Primer size
:
Min:
Opt:
Max:
Product CpGs
:
CpG in primer
:
Primer non-CpG 'C's
:
Primer Poly T
:
Primer Poly X:
Parameters for PyroSeq primer selection
Window size
:
Overlap size
:
PyroSeq primer size :
Min:
Opt:
Max:
PyroSeq primer Tm :
Min:
Opt:
Max:
PyroSeq Product CpGs
:
CpG in PyroSeq primer
:
PyroSeq Primer non-CpG 'C's
:
PyroSeq Primer Poly T
:
PyroSeq Primer Poly X:
Parameters for Hyb Oligo (Internal Oligo) selection
Hyb Proble Size :
Min:
Opt:
Max:
Hyb Probe Tm :
Min:
Opt:
Max:
Hyb Probe GC% :
Min:
Opt:
Max:
Parameters for MSP primers
3'CpG constraint
:
Max Tm difference
:
Product length difference
:
Min:
Max:
Provide custom primer selection criteria table
Custom primer selection quality matrix :
Example primer selection matrix
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