MP-Ref: Multiplex PCR Primer Design for Reference Genomes

Done Task link: fa320f27-b518-450a-8b5e-199e5f06eab5 (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: 1, primers: 3, product size range (bp): 166 - 290, download primers.

Tube 1
ID TemplateID FpTm (°G) RpTm (°G) FpSize (bp) RpSize (bp) AmpSize (bp) AmpGC (%)
T1P1 chrM:1000-1001 60.04 59.54 21 22 290 43.45
T1P2 chrM:2000-2001 59.83 59.74 20 20 196 45.41
T1P3 chrM:3000-3001 60.88 59.96 22 22 166 46.39

Parameters

Target Database hg38.fa
Validation method gel
Product Size Min Difference 20
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) 300
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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