Screenshot of Jalview visualization of alignment on dataset BB40040. Jalview screenshots of two different regions of the reference multiple alignment of dataset BB40040, featuring our consistent partial columns for smin = 2 shown in colour. The local similarities detected by NLD that are responsible for the 0 TC score are shown as the yellow-green coloured sites enclosed in the red dotted region. This is a (rare) example where a local similarity involving up to 18 sequences turns out to be biologically wrong. The offset on the columns resulting from the wrong alignment of the last sequence is sufficient to induce at least one mistake per column along a large part of the core region.