Specificity result

Done Task link: 52cb28d4-e881-45ff-bf58-8200134c7a98 (remember for later use)

Primer list

*PBN and MBN: primer binding number to the plus and minus strand.
Primer ID Sequence (5' → 3') Size (bp) GC (%) Tm (°C) ΔG (kcal/mol) PBN* MBN*
1 CCCTGGGCTCTGTAAAGAATAGTG 24 50.00 61.23 -24.52 16338 16595
2 ATCAGAGCTTAAACTGGGAAGCTG 24 45.83 61.41 -24.59 38955 38976

Hairpin list (0)

No hairpins found.

Dimer list (0)

No dimers found.

Histogram of size of 2 potential amplicons


Description of 2 potential amplicons

Amp ID Product Name Fp x Rp Product Size (bp) Fp Tm (°C) Rp Tm (°C) Fp ΔG (kcal/mol) Rp ΔG (kcal/mol)
 1 chrY 2 x 1 112 62.64 61.89 -25.44 -25.26
 2 chrX 1 x 2 106 61.86 62.15 -25.52 -25.23

Amplicon details

Amp 1: 2 + 1 ==> chrY:6869846-6869958

Size = 112 bp, GC content = 43.75%
F: Tm = 62.64 °C, ΔG = -25.44 kcal/mol
R: Tm = 61.89 °C, ΔG = -25.26 kcal/mol
Binding sites: 6869847(24/24) ... 6869958(24/24)

>>>2
   1                       24
5' ATCAGAGCTTAAACTGGGAAGCTG 3'
   ::::::::::::::::::::::::                                                        6869958
5' ATCAGAGCTTAAACTGGGAAGCTGatggtaggaactgta...gatgaagaatccaccCACTATTCTTTACAGAGCCCAGGG 3'
   6869847                                                  ::::::::::::::::::::::::
                                                         3' CACTATTCTTTACAGAGCCCAGGG 5'
                                                           24                      1
                                                                                   1<<<


>Amp_1 2 + 1 ==> chrY:6869846-6869958 
ATCAGAGCTTAAACTGGGAAGCTGatggtaggaactgtaaaattgggaccacttgagaaaccactttatttgggatgaag
aatccaccCACTATTCTTTACAGAGCCCAGGG
Amp 2: 1 + 2 ==> chrX:11296873-11296979

Size = 106 bp, GC content = 43.4%
F: Tm = 61.86 °C, ΔG = -25.52 kcal/mol
R: Tm = 62.15 °C, ΔG = -25.23 kcal/mol
Binding sites: 11296874(24/24) ... 11296979(24/24)

>>>1
   1                       24
5' CCCTGGGCTCTGTAAAGAATAGTG 3'
   ::::::::::::::::::::::::                                                        11296979
5' CCCTGGGCTCTGTAAAGAATAGTGtgttgattctttatc...tacagttcctaccacCAGCTTCCCAGTTTAAGCTCTGAT 3'
   11296874                                                 ::::::::::::::::::::::::
                                                         3' CAGCTTCCCAGTTTAAGCTCTGAT 5'
                                                           24                      1
                                                                                   2<<<


>Amp_2 1 + 2 ==> chrX:11296873-11296979 
CCCTGGGCTCTGTAAAGAATAGTGtgttgattctttatcccagatgtttctcaagtggtcctgattttacagttcctacc
acCAGCTTCCCAGTTTAAGCTCTGAT

Parameters

Database hg38.fa
Kvalue 9
Mismatch 0
Product Min Size (bp) 0
Product Max Size (bp) 500
Tm (°C) 50
Concentration of monovalent cations (mM) 50
Concentration of divalent cations (mM) 1.5
Concentration of dNTPs (mM) 0.25
Concentration of annealing oligos (nM) 50