the labels I have are not the same as the ones in the dye set installed in our genetic analyzer. And the company I want to order from does not have the same labels. I think they should be the same for the analysis?
That dye Tags will definitely depend upon the Instrument that you will use to analyze your experimental PCR samples. So choose as per Instrument capacity in your lab or Institute/University.
In case you are analyzing (Fragment analysis) the PCR products in your inhouse facility, you may consult the equipment manual. In case you are outsourcing the fragment analysis part, you need to consult your service provider. Moreover, you don't really need to label SSR primers individually. You may put an M13 tag in the 5` of the forward primer and use a common labelled primer for labelling of fragments. For details kindly consult the paper, Schuelke M. 2000 An economic method for the fluorescent labelling of PCR fragments. Nat. Biotechnol. 18, 233–234
If you are labeling not for accurate genotyping but also for multiplexing, then it is possible to use 4-5 different dyes using ABI DNA analyzers. If you still want to increase the fold of multiplexing you may consider using the same dye for SSRs of distinctly different amplicon lengths - for example one SSR with amplicon size of 200 bp and another SSR with 400 or still longer PCR products. This way one can go up to 8-10 SSR multiplexing for a single genotype.
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