I am trying to design oligos to make synthetic D loop structure. I am not sure how to align 3 DNA oligos to check for D look. I want to use this synthetic D loop for homologous recombination purpose. I am trying to align oligos by NCBI align or EBI clustralw, but this is not providing satisfactory image. please let me know if you have and appropriate method to check 3 strand DNA structure alignment. thank you in advance.