Jute (Corchorus spp.) is the second most important fibre producing plant in India. The study on jute at the molecular level till date is very limited. Simple sequence repeats (SSRs) are useful tools as molecular markers in genetic studies. Recently with rapid advancement of sequencing and documentation in public data base has enabled scientists in hassle free data mining. Development of high throughput method for detection of SSRs has given a new dimension in their use as molecular markers. In the present study, 826 EST sequences of Corchorus capsularis and 30 EST sequences of Corchorus olitorius, downloaded from National Center for Biotechnology Information (NCBI) and were analyzed through bioinformatic tools like UniVec, trimest, CAP3, and MISA. Several microsatellite markers were identified for these two species of jute which would be further helpful for genetic mapping. The study of functional domain markers (FDM) can provide information of functional property of microsatellite markers and predicted protein domains. The functional domains designed from SSR-FDMs will help to analyze molecular markers that have functional importance and should also facilitate the analysis of genetic diversity in plants.
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