Structural element tripod showing success for DoPloCompare. The structural element Tripod . (A) The desired secondary structure for which the algorithm tries to design a sequence, the element is composed of four stems, three of which with terminal hairpin, surrounding a multibranch loop. (B) The exact solution found when using the modified RNAinverse with DoPloCompare distance. (C) The closest secondary structure the algorithm returns after 500 iterations, when using the original RNAinverse with base-pairing distance.