SSR Finder

Identify and analyze Simple Sequence Repeats (SSR) in nucleotide sequences for cassava molecular marker development

About SSR Markers

Simple Sequence Repeats (SSR), also known as microsatellites, are DNA sequences consisting of 1-6 nucleotide units that are repeated in the genome. Due to their high polymorphism, co-dominant inheritance, and wide distribution, SSRs have become important molecular marker tools in cassava genetic and breeding research.

The SSR Finder tool can help you:

  • Quickly identify all potential SSR loci from DNA sequences
  • Analyze the distribution of different types of SSRs
  • Provide basic data for molecular marker-assisted breeding
  • Support research on cassava genetic diversity, cultivar identification, and genetic map construction

How to Use SSR Finder

1. Enter a DNA sequence in FASTA format or upload a sequence file

2. Set SSR search parameters (such as repeat unit length, minimum repeat times, etc.)

3. Click the "Start Search" button, and the system will analyze the sequence and display the results

4. The results table can be exported to Excel or CSV format for further analysis

Example Sequence

You can use the following example sequence to test the SSR Finder functionality:

>Cassava_Example_Sequence ATGATGATGATGATGATGAAAAAAAAAAAACGCGCGCGCGCGCGCGCGCGCGGAAGAAGAAGAA GCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTCACACACACACACACACACACACATATATATATATA TATATAGCATGCATGCATGCATGCATGCATGAGAGAGAGAGAGAGAGAGATCTCTCTCTCTCTC TCTCTCATCATCATCATCATCAGCAGCAGCAGCAGCACAACAACAACAACAACAACAACAATGGTGG TGGTGGTGGTGGTGGCTACGATACTACGACTACGACTACGACAGCCCATAGATAGATAGATAGA TAGATAGATAGATAGATAGATTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGGGGGGCGGC GGCGGCGGCGGCGGCGGCGGCGGCGGCAAACAAACAAACAAACAAACAAACAAGTAGTAGTAGTAG TAGTTAGAGCTACCACCATCATCATCATCATCATCATCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCAT

SSR Analysis Results

Found 0 SSR loci

No. Sequence ID SSR Type Motif Repeat Count Start Position End Position Sequence Length