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MySites in SharePoint everyday for few seconds(15-30) showing site not found and after that everything is fine..site is up and running. I checked all the WFE to check any errors in event log and I cannot see any errors....Any idea how i can troubleshoot this issue?

A: 

I'm not sure why this happens, but I think you just need some type of warmup script that runs in the morning:

  1. What is a SharePoint warmup script?
  2. Warm up your SharePoint servers
Kit Menke
what this has to do with warmup scripts? users were able to see their mysites but in the middle of the day we are seeing this for few seconds its showing site not found....I doubt warm up scripts would help in this as they are to warmup sharepoint and to reduce slowness...
TLLL
I suggested warmup scripts because it seemed easy to implement and might help you keep your sites up in the short term. Have you looked at the Trace log (generally in C:\Program Files\Common Files\Microsoft Shared\Web Server Extensions\12\LOGS)?
Kit Menke