The concept of shift error and the fraction of correctly aligned residues ( f
). Aligned and unaligned residues are indicated by uppercase and lowercase letters, respectively. Residues aligned in the reference alignment are in bold. The numbers above the reference alignment are the serial numbers of residues in the aligned span of the reference alignment. The shift errors (δ) are shown on the test alignment, where 'x' indicates that δ is not defined for the unaligned residue in the test alignment although it is aligned in the reference alignment. The two residues of the pair #5 are not considered at all for the shift error calculation since they are not aligned in the reference alignment. For this example, fcar(0) = 0/16, fcar(4) = 6/16, and fcar(8) = 12/16.