Cyclone V flashing LEDs and clock (Verilog)

You're doing the right thing - dividing down the clock with a counter.

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if i wanted to use the PLL but i didn't wanted to use a Quartus MegaFunction

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If you want to instantiate a PLL I strongly recommend you use the MegaFunction/MegaCore Wizards. You can instantiate them in other ways. However, with little/no experience you should use the tools that are there to prevent you making mistakes.

Note: in Cyclone V the lowest frequency you can generate from the PLL is 5MHz. So, to flash that LED - in a manner in which you can see it flashing - you will still need the counter.

Cheers,

Alex