MFEprimer-3.0 Primer Quality Reports (2023-12-20 17:31:28)

Primer ID                      Sequence (5'-->3')                    Length     GC      Tm      Dg        Binding Number
                                                                      (bp)      (%)    (°C)  (kcal/mol)   Plus     Minus

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.




Descriptions of [ 2 ] potential amplicons

AmpID HitID                                            Size       FpTm       RpTm       FpDg       RpDg  ProductTm        Ta
                                                       (bp)       (°C)       (°C)   kcal/mol   kcal/mol       (°C)       (°C)

1     chrY                                              112      62.64      61.89     -25.44     -25.26      76.85      57.46
2     chrX                                              106      61.86      62.15     -25.52     -25.23      76.36      57.11



Amplicon details


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

    Size = 112 bp, GC content = 43.75%, Tm = 76.85 °C, Ta = 57.46 °C
    F: Tm = 62.64 °C, Delta G = -25.44 kcal/mol, Start = 6869846, End = 6869869
    R: Tm = 61.89 °C, Delta G = -25.26 kcal/mol, Start = 6869934, End = 6869958
    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 = 43.40%, Tm = 76.36 °C, Ta = 57.11 °C
    F: Tm = 61.86 °C, Delta G = -25.52 kcal/mol, Start = 11296873, End = 11296896
    R: Tm = 62.15 °C, Delta G = -25.23 kcal/mol, Start = 11296955, End = 11296979
    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

            Primer file: primer.fa
               Database: hg38.fa
                 Kvalue: 9
               MisMatch: 0
         Tm cutoff (°C): 50.00
 Amplicon min size (bp): 0
 Amplicon max size (bp): 500
                    SNP: 
Monovalent cations [mM]: 50.00
  Divalent cations [mM]: 1.50
             dNTPs [mM]: 0.25
  Annealing oligos [nM]: 50.00



Cite

Kun Wang, Haiwei Li, Yue Xu, Qianzhi Shao, Jianming Yi, Ruichao Wang, Wanshi Cai, Xingyi Hang, 
Chenggang Zhang, Haoyang Cai, Wubin Qu, MFEprimer-3.0: quality control for PCR primers, 
Nucleic Acids Research, Volume 47, Issue W1, 02 July 2019, Pages W610-W613, 
https://doi.org/10.1093/nar/gkz351



Web & Contact

https://www.mfeprimer.com
Wubin Qu <quwubin@gmail.com>



Total time used: 580.53294ms.