Dependence of accuracy and confidence of alignments versus the core shift c. A, B - evolutional distance of 30PAM; C, D - evolutional distance of 120PAM. A, C - console length r = 100%; B, D - console length r = 200%. The accuracy and confidence of the global (Glb.Accur., Glb.Conf.) and local (Lcl. Accur., Lcl.Conf.) alignments at the console length making 100% and 200% of the length of cores and at evolutional distances between the cores 30PAM and 120PAM. The parameter c (see its definition in subsection 2.1.1) determines the core shift value. The plots for accuracy and confidence are compatible at evolutional distance of 30PAM.