Putative Simple Sequence Repeats (SSRs) in the Camellia Genomes
The tea plant genome of shuchazao (version 2) were scanned with the MIcroSAtellite identification tool (MISA) to identify putative perfect mono-, di-, tri-, tetra-, penta-, and hexanucleotide simple sequence repeats. The minimum sizes for the putative SSRs are: 10 repeats for mononucleotides, 6 repeats for dinucleotides, 5 repeats for trinucleotides, 5 repeats for tetranucleotides, 5 repeats for pentanucleotides, and 5 repeats for hexanucleotides. The polymorphic status of SSRs among 18 tea plant species were evaluated using CandiSSR (version 20170708).
This page allows the display of the putative SSRs filtered by type and/or polymorphic status. If you are interested in finding the locations where a repeated motif is found, the bottom form can be used to conduct a search by motif.
Select SSR type:
OR Enter a SSR motif to search for (i.e., AT, CTG, TTGT):
Only show SSRs with polymorphic status?
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PolySSR filters:
| missing rate | (e.g., 0.05) | |
| standard deviation | (e.g., 0.50) | |
| primer transferability | (e.g., 0.99) | |
| (Instructions: please see CandiSSR paper for parameter details ) | ||
Results for types of SSRs in tea plant genome searched are listed below:
| SSRID | ScaffoId | SSR type | SSR | Size(bp) | Start | End | Polymorphic? |
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Download all searched genomic SSRs：
Download upstream 100 bp of searched PolySSRs： Go to primer design?
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