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Self Assessment - CIS / tax free personal allowance

Hi
  • Approx earnings £29000
  • Approx tax paid (through cis system) £5700
  • Approx Expenses £3800
I am self employed and get paid through the cis system so pay 20% on all my earnings each month. 
When I complete my self assessment tax return, even with expenses, it shows I am due back £1600. I was under the impression even those self employed were entitled to £12500 tax free earnings each year. As I have paid 20% on all I have earnt this year, surely i am owed back the tax on the first £12500 earnings at the very least, before we even consider my expenses. Meaning my tax rebate should be a minimum of £2500???
How is the "tax-free personal allowance" accounted for in my scenario?
Many thanks in advance for all your help. 

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