SSR Analysis

SSR Analysis Online Inquiry

CD Genomics as one of the providers of Simple Sequence Repeats (SSR), we use bioinformatics methods to help you perform SSR analysis and SSR primer design quickly and accurately. If we are fortunate to cooperate, we will provide you with a high-quality data analysis platform, a fast analysis cycle and a high-quality result report.

Introduction of SSR Analysis

Simple Sequence Repeats (SSR), also known as short tandem repeats (STR) or microsatellites, are simple repeats evenly distributed in the genome of eukaryotes, and it consists of tandem repeats of 2 to 6 nucleotides. Because the number of repetitions of repeat units is highly variable and abundant among individuals, the application of simple repeat sequence tags is very extensive. Simple repetitive sequence sites are usually amplified by PCR, and the amplified products are analyzed by electrophoresis, and alleles are separated according to size for detection.

The principle of SSR markers-due to the variation in the number of repeat units at a single microsatellite locus, the variation in the length of individual amplification products produces length polymorphism, which is called simple sequence repeat length polymorphism (SSLP), and each amplification site represents a pair of alleles at this locus. Because the number of SSR repeats varies greatly, SSR markers can reveal much higher polymorphism than restriction endonuclease fragment length polymorphism (RFLP). Apply bioinformatics analysis methods to analyze the sequencing data of multiple mixed samples to obtain polymorphic SSR sequences and design SSR primers.

Fig 2. PAGE results from the PCR amplification of 23 SSR primer pairs at a 60 °C annealing temperature. Fig 1. PAGE results from the PCR amplification of 23 SSR primer pairs at a 60 °C annealing temperature. (Huabai X, Pujuan Z, et al. 2018)

Application of SSR Analysis

Genetic cross breeding.

Draw a chromosome genetic map.

Conservation and utilization of germplasm resources.

Genome association analysis.

DNA fingerprinting and variety identification.

Quantitative trait loci (QTL) analysis.

Genetic diversity analysis.

Advantages of SSR Analysis

SSR technology has the following advantages:

Rich in quantity, covering the entire genome, revealing high polymorphisms.

It has the characteristics of multiple alleles and provides a high amount of information.

In the Mendelian way of inheritance, homozygous and heterozygous can be identified.

The experiment is reproducible and the results are reliable. Each site is determined by the designed primer sequence, which is convenient for different laboratories to communicate and cooperate with each other to develop primers.

CD Genomics Analysis Pipeline

Fig 3. Pipeline of SSR Analysis. - CD GenomicsFig 2. Pipeline of Simple Sequence Repeats analysis.

Bioinformatics Analysis Content

1. Sequencing data statistics 2. Data quality control
3. High quality data acquisition 4. SSR screening results
5. SSRs motif calling 6. SSRs clustering analysis
7. SSRs polymorphism evaluation 8. SSRs primer design

For Simple Sequence Repeats analysis, the customized information analysis content can be negotiated and determined according to the needs of customers. If you have any needs, please click online inquiry.

Turnaround Time

Fig 4. SSR Analysis turnaround time - CD Genomics.

About one to two weeks, it is also related to the number of samples and the quality of sequencing data.

Bioinformatics-Analysis, a division of CD Genomics, staffed by highly experienced biological scientists in data analysis. For SSR analysis, if you have any questions, please feel free to contact us and see how we can help you address your problems.


  1. Huabai X, Pujuan Z, et al. Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear[J]. Bmc Genomics, 2018, 19(1):473.
* For Research Use Only. Not for use in diagnostic procedures.
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