The use of these symbols in output of the type shown below is purely presentational, to help you inspect the alignment and identify regions of partial conservation.
CCPC50 SEEGFK.YGE GILEVAEKNP DLTWTEADLI EYVTDPKPWL VKMTDDKGAK
CCRF2C TYPEFK.YKD SIVALGASG. .FAWTEEDIA TYVKDPGAFL KEKLDDKKAK
CCRF2S TQADFKGYGE GMKEAGAKG. .LAWDEEHFV QYVQDPTKFL KEYTGDAKAK
CCQF2R HKDNYA.YSE SYTEMKAKG. .LTWTEANLA AYVKNPKAFV LEKSGDPKAK
CCQF2P TFAGYS.YSP GYTVMGQKG. .HTWDDNALK AYLLDPKGYV QAKSGDPKAN
Consensus t...%k.Y.e g..e.gakg. .ltWt#..l. .Yv.#Pk.fl .ek.gD.kAk
This is quite independent of the logic (algorithm) of the program, which is indicated by the documentational comments:
Symbol comparison table: blosum62
Gap weight: 12
Gap length weight: 2
This also gives a reference to the original paper you should read to find more information about the program.
You would also be advised to read the Wikipedia entry on Multiple Sequence Alignment and on Sequence Alignment in general. I would mention that this is an old method (as the appearance of the site also indicates). If it gives useful results, fine. Otherwise you might try the more popular and more frequently updated Clustal, which is available online or as a standalone program.