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CI (Φ11), dnaA (Φ12), and amidase (Φ13) are phage genes that were used as endogenous controls. The deletion of Φ11 int makes prophage Φ11 immovable on its host genome (indicated by an asterisk) though integrases of Φ12 and Φ13 remain the same. Phage-cured strain RN4220 was used for positive control.
