MP-Ref: Multiplex PCR Primer Design for Reference Genomes

Done Task link: 7b52d2ed-e160-4750-b3e3-61b58610cbff (remember for later use)

Coverage report

total size: 3 bp, cov size: 3, cov rate: 100.00%, miss size: 0, miss rate: 0.00%, download coverage report.

Chrom Start End Size (bp) CovSize (bp) CovRate (%) MissSize (bp) MissRate (%)
1 chrM 1000 1001 1 1 100.00 0 0.00
2 chrM 2000 2001 1 1 100.00 0 0.00
3 chrM 3000 3001 1 1 100.00 0 0.00

Primer list

tube: 3, primers: 3, product size range (bp): 182 - 196, download primers.

Tube 1
ID TemplateID FpTm (°G) RpTm (°G) FpSize (bp) RpSize (bp) AmpSize (bp) AmpGC (%)
T1P1 chrM:920-1001 59.64 59.54 24 25 182 45.60
Tube 2
ID TemplateID FpTm (°G) RpTm (°G) FpSize (bp) RpSize (bp) AmpSize (bp) AmpGC (%)
T2P1 chrM:1920-2001 59.83 59.74 20 20 196 45.41
Tube 3
ID TemplateID FpTm (°G) RpTm (°G) FpSize (bp) RpSize (bp) AmpSize (bp) AmpGC (%)
T3P1 chrM:2920-3001 60.42 60.74 22 22 195 44.62

Parameters

Target Database hg38.fa
Validation method sanger
Product Size Min Difference 0
Primer Min Size (bp) 16
Primer Opt Size (bp) 22
Primer Max Size (bp) 32
Primer Min GC (%) 20
Primer Opt GC (%) 50
Primer Max GC (%) 82
Primer Min Tm (°C) 58
Primer Opt Tm (°C) 60
Primer Max Tm (°C) 62
Product Min Size (bp) 160
Product Max Size (bp) 200
Product Min GC (%) 25
Product Opt GC (%) 50
Product Max GC (%) 78
Dimer ΔG (kcal/mol) -3.50
Hairpin Score 5
Non-specific Amplicon Tm (°C) 47
Non-specific Amplicon Min Size (bp) 0
Non-specific Amplicon Max Size (bp) 300
Min Off-targets 0
Max Off-targets 10
Minimum Diffierent Bases 50
SNP Skip Size 9
InDel Skip Size 15
Background Database 1 -
Background Database 2 -
Min Amplicon Count on Background Genomes 0
Max Amplicon Count on Background Genomes 0
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