06 Honda Civic battery died I jumped it but now when ever I drive it all the dashboard lights flash?

After I got it started it works every time I try now but all my dash lights flash for a few minutes then they turn off but a light by my pedals flashes non stop anyone know what I can do to stop it.

What is the trim code for your 06 Civic? Lx, Ex, Gx, Dx, Si or Hybrid? I would start to check the fuses first since the vehicle had a jump start. Was it in a "Reverse polarity" connection by chance and the correction was made prior to the jump start? What do you mean a light is flashing by the pedals? Any after market accessories were install?

Check fuse #3 (10A) and #10 (7.5A) in the under dash fuse box and the mega fuse #1 (100A) in the under hood fuse/relay box or check them all in both boxes. The fuse(s) may blown due to the surging voltage or incorrect jump start.

Have the battery load test, check out the battery cable/terminals and the alternator/ charging system check out. Replace if failing the tests. The ELD (Electric Load Detector) unit may have failed. Any code in the PCM? (Engine computer/controller)

Edit: Update the information of what you'll find out and I'll be back to help. E mail me if you prefer. HTH