a new record begins as the following:

>>>scopid1	scopid2

where scopid1 and scopid2 are the SCOP ids of the two domains whose alignment
is contained in this record

the sequence data for scopid1 (amino acid letters and hyphens for gaps) begins 
following the line:
>scopid1	scopid2	1

the sequence data for scopid2 begins following the line:
>scopid1	scopid2	2

the specification of which residues are considered to be the conserved core
(better matching 50%) are listed after the line:
>scopid1	scopid2	3

It is a list of numbers separated by spaces corresponding to positions in the
above strings (note that the strings will be the same length--they will be
padded with hyphens to represent terminal gaps when they occur)