MP-Ref: Multiplex PCR Primer Design for Reference Genomes

Done Task link: af0f0fc7-4468-4885-bf2e-85b6841699fd (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): 196 - 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 60.49 59.96 22 22 212 44.81

Parameters

Target Database hg38.fa
Validation method ngs
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) 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) 350
Min Off-targets 0
Max Off-targets 0
Minimum Diffierent Bases 50
SNP Skip Size 9
InDel Skip Size 15
Background Database 1 canFam6.fa
Background Database 2 GCF_000005845.2_ASM584v2_genomic.fna
Min Amplicon Count on Background Genomes 0
Max Amplicon Count on Background Genomes 0
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