I think some problems have come to your gel, e.g., temperature, concentration, agent...

Hi,

I had this issue when I tried to genotype/sequence ~800bp-1kb with a high fidelity polymerase so I changed my pcr conditions to low anneling temp for the first 10 cycles (about 5 less) then for the last 24 cycles I used the the primer specific temp. This gave me specific bands and good sequencing results

hope this helps, best of luck!