My problem seems to be resolved. I used dephosphorylated vector in ligation because of the non-complete restriction efficiency to avoid self-ligated clones (There are two different RE sites in this cloning). But I didn't know that our oligos came without phosphate groups at ends. Therefore I made a new restriction digestion without dephosphorylation of the vectror. So, I got appropriate number of colonies relative to controll.
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