The sequence is numbered using the Kabat numbering scheme.
Using the Kabat numbered sequence, a control file is written for the Kabatman database program. This file requests the number of times the amino acid type found in your sequence occurs at that Kabat position in the database. It runs Kabatman on this control file and then parses the output to find residues which occur in less than 1% of the chains in the Kabat database. These data are reported to the user.
Note that the comparison is not species-specific; positions are compared with the residues found in all sequences in the Kabat data.
Species-specific comparisons can be performed in abYsis.