I cannot think of anything cheaper than sequencing these days. If you're looking for an alternative, though, you can try qPCR or dot blotting-hybridization.

Based on my experience with repeats during genome finishing, I would argue that the possible solutions depend heavily on the approximate number of repeats.

If you expect less than 15 copies, sequencing might be the cheapest solution.

Another possibilitiy is a simple gel electrophoresis, although you might need to use either a polyacrylamide gel for optimal resolution or a capillary system like the Bioanalyzer from Agilent. Once again, if you have more than ~15-25 repeats, you might not be able to get the exact number.

One thing to keep in mind: If you amplify a region like that with PCR, you will end up with chimerical products (basically a ladder). That might help you to determine the size of the largest product, but that could already be shorter than the original. Things like that are still quite a challenge.

In my opinion sequencing will be the cheapest method. The cost of your research work depends upon the number of samples and size of the PCR fragment. In addition to this sequencing of amplified fragment reveals the difference in the number of repeats i different samples used. Good luck

Before anything, you dears all have my sincerely thanks for your perfect and interesting answers,

Also dear christian, Its necessary to tell you that number of copy is variable between 11 to 14, I think. Anyway, according to condition It would be better using of sequencing. However many thanks for your next guides about using of ladder and DNA markers in gel electrophoresis as a alternate method. Hope for cheap and routine next generation sequencing everywhere in the world for research and clinical purposes.

Finally many thanks to your time.

My dear friend,

If you are working with mammal samples, try about using Allelic ladders. This will be the best option.