The best replacement for southern blot is pcr.

The best alternatives to southern blot are rated as following:
★★★★★  pcr
★★★★  northern blot
★★★  western blot
★★  dot blot
★  microarray
★  gel electrophoresis
  electrophoresis

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No companions for southern blot have been suggested so far.
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southern blot
pcr
northern blot