Binoy, according to producer instruction, Metaphor agarose is similar in properties to PA gel. It provides twice the resolution capabilities of the finest  normal agarose. DNA fragments differing in size by 2% can be separated. But, it is still not enough to see difference of 2 bp for 200 bp product (1%).

Binoy, Metaphor Agarose gel in theory can separate bands with 2% difference in length. For 200 bp fragment - >=4bp. For 2bp difference you should use PA gel or capillary electrophoresis.   Ordinary agarose is not suitable for such task.

SSR considered bi-allelic marker it showed one or two alleles on gel, so polyacrylamide gel is good choice. 

you can run your PCR product on polyacrylamide gel  8% . this concentration allowed you to separate bands from 40bp to 600bp .

8% Gel

ddH2O

10X TBE

80% Glycerol

30% Acrylamide

APS

TEMED

Even if you'd be able to separate alleles of the same locus differing in 2 bp (1 bp is not considered as a microsatellite motif) by any agarose type or PAGE, you'd have a sizing problem, i.e. to determine the exact size of alleles of neighboring samples/lanes which might lead to mismatching. This will further lead you to derive a wrong conclusion about inter-sample similarities/dissimilarities which will cause misinterpretation of allelic frequencies and population structure. I would certainly opt for capillary electrophoresis.

Hi, I think you shoul be use fragment analyser like capilary electrophoresis for separate 2-4 bp differences beetween different pcr products. In contrary you can not do that with any agorose and polyacrilamide gels. 

I agree with all that that small difference bp is not possible to be discriminated with high-resolution agarose like metaphor. I would also advise to use DNA fragment analyzers based on capilary electrophoresis.  

Hi. Ofcourse Metaphore has been used in several works based on SSR markers and it is very safe gel but PG is not safe.