MP-Ref: Multiplex PCR Primer Design for Reference Genomes

Done Task link: e7cd1164-3441-4a50-8c76-1862ef09f6aa (remember for later use)

Coverage report

total size: 28071 bp, cov size: 28071, 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 chr5 70924941 70953012 28071 28071 100.00 0 0.00

Primer list

tube: 2, primers: 42, product size range (bp): 702 - 1000, download primers.

Tube 1
ID TemplateID FpTm (°G) RpTm (°G) FpSize (bp) RpSize (bp) AmpSize (bp) AmpGC (%)
T1P1 chr5:70924941-70925441 60.08 60.02 23 23 984 54.07
T1P2 chr5:70926378-70926878 59.31 60.22 22 22 984 45.12
T1P3 chr5:70927684-70928184 59.37 60.03 22 22 846 48.11
T1P4 chr5:70929104-70929604 60.16 60.09 22 22 973 49.33
T1P5 chr5:70930645-70931145 60.75 60.42 22 22 849 37.81
T1P6 chr5:70931990-70932490 59.51 60.03 22 22 1000 42.50
T1P7 chr5:70933633-70934133 59.77 60.63 22 22 934 40.58
T1P8 chr5:70934777-70935277 59.51 60.61 23 22 930 47.74
T1P9 chr5:70936063-70936563 60.03 59.77 22 22 985 38.17
T1P10 chr5:70937301-70937801 60.03 60.16 22 22 702 40.88
T1P11 chr5:70938479-70938979 60.29 61.13 22 21 999 35.54
T1P12 chr5:70939807-70940307 60.61 59.83 22 22 908 41.08
T1P13 chr5:70941190-70941690 60.76 60.49 22 22 925 37.30
T1P14 chr5:70942802-70943302 59.90 59.90 20 20 960 39.69
T1P15 chr5:70944197-70944697 60.04 59.89 20 21 895 37.88
T1P16 chr5:70945322-70945822 60.03 59.63 22 23 886 40.18
T1P17 chr5:70946830-70947330 59.19 60.29 23 22 825 44.61
T1P18 chr5:70948246-70948746 59.38 59.58 22 22 847 39.67
T1P19 chr5:70949531-70950031 59.76 60.49 22 22 745 40.27
T1P20 chr5:70950572-70951072 59.45 59.76 22 22 816 48.77
T1P21 chr5:70951952-70952452 60.24 59.51 21 23 998 36.77
Tube 2
ID TemplateID FpTm (°G) RpTm (°G) FpSize (bp) RpSize (bp) AmpSize (bp) AmpGC (%)
T2P1 chr5:70925680-70926180 60.10 59.56 21 22 922 48.70
T2P2 chr5:70927127-70927627 59.83 60.24 22 21 999 46.05
T2P3 chr5:70928392-70928892 60.36 60.16 22 22 805 43.48
T2P4 chr5:70929799-70930299 60.16 60.56 22 22 914 41.25
T2P5 chr5:70931408-70931908 59.44 59.05 22 22 978 40.49
T2P6 chr5:70932891-70933391 60.34 59.96 23 23 906 37.97
T2P7 chr5:70934163-70934663 60.02 59.16 22 22 856 38.79
T2P8 chr5:70935539-70936039 60.29 59.90 22 22 806 38.96
T2P9 chr5:70936689-70937189 59.90 59.62 20 20 989 47.22
T2P10 chr5:70937835-70938335 60.02 60.15 23 23 935 38.82
T2P11 chr5:70939306-70939806 60.49 60.50 24 24 991 38.04
T2P12 chr5:70940630-70941130 59.96 59.97 22 22 843 42.94
T2P13 chr5:70942049-70942549 60.50 60.16 22 22 848 38.09
T2P14 chr5:70943569-70944069 59.84 59.58 22 23 852 39.20
T2P15 chr5:70944719-70945219 59.77 60.02 25 23 863 40.32
T2P16 chr5:70946069-70946569 60.33 60.08 23 23 957 34.80
T2P17 chr5:70947594-70948094 59.68 60.41 20 20 721 41.75
T2P18 chr5:70948802-70949302 59.45 59.77 22 22 882 39.23
T2P19 chr5:70950076-70950576 60.03 59.37 22 22 991 46.32
T2P20 chr5:70951105-70951605 59.69 59.82 20 21 947 43.08
T2P21 chr5:70952467-70952967 59.96 60.26 21 20 970 37.63

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) 500
Product Max Size (bp) 1000
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 0
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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