FSA alignment of BALIBASE set BB11001. The figure shows a segment of the FSA alignment of BB11001. Core block columns (yellow) that agree with the reference alignment are indicated by asterisks. Columns marked exclamatory are core block columns that have been split into two by FSA. Measures that consider columns in the test alignment as units, such as CSF, may assign this alignment a perfect score, and measures that consider pairs of sequences, such as SPS, may assign it a high score despite this problem, which is common in FSA and DIALIGN. Measures that are more sensitive to this type of problem include CS, which treats a reference column as a unit, and ‘gappiness‘, which can be defined as the average fraction of gapped sequences per column.