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View SSRs Roya

MISA – MIcroSAtellite identification tool

This tool allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases.

In order to design primers flanking the microsatellite loci, two perl scripts serve as interface modules for the program-to-program data interchange between MISA and the primer modelling software Primer3 (Whitehead Institute). For installation instructions of Primer3 see


Supplemental perl tools:

Get – perl script useful for pre-preprocessing sequences (invocation without parameters is explaining the syntax)

Get Primer 3 interface modules – perl scripts allowing the interaction with Primer3


Sequence source file: “454AllContigsOnel.seq”

Definement of microsatellites (unit size / minimum number of repeats):

(2/6) (3/5) (4/5) (5/5) (6/5)

Maximal number of bases interrupting 2 SSRs in a compound microsatellite: 100

Results of Microsatellite Search

Total number of sequences examined: 45244

Total size of examined sequences (bp): 14771588

Total number of identified SSRs: 1077

Number of SSR containing sequences: 895

Number of sequences containing more than 1 SSR: 118

Number of SSRs present in compound formation: 135