SEQUENCE_COMPARISON

Hello.

I am trying to use the command: SEQUENCE_COMPARISON, but I don´t understand the output, in the MATRIX_FILE. I mean, I don´t know what each number means ( which one is the score which I can use to compare different alignments)

For example, thix matrix is the result when I use : RR_FILE = '$(LIB)/gonnet.sim.mat' and my alignmet.

sequenceA 514.40 297.72 sequenceB 297.72 504.86

I suposse the score I have to compare is 297.72 (which changes in different alignments).

My problem is that I am using another aligment server, with the same parameters I use in Modeller , and it gives only the score 504.

Thanks in advance