In a text representation of an alignment, all CA-atoms of the residues that are at the same position in different sequences form a position of the alignment (i.e., the first letters of the sequences form one position, the second ones — another position, etc.).
Difference of distance between corresponding atoms is used as the measure of similarity of the disposition.
For any two positions included into geometrical core, the distances between CA atoms of those positions in all structures may differ not more than the value of the parameter "Distance spreading".
Algorithm: Sergei Spirin, Andrei Alexeevski, Boris Nagaev
Programming: Boris Nagaev (computation), Sergei Spirin (web-interface)