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I was using multAlin for multiple aligning a set of sequences. The output I and came across included the following documentation (English corrected):

Consensus symbols:
! is any of IV
$ is any of LM
% is any of FY
# is any of NDQEBZ

I understand what it says but I don't know how to interpret it further. What impact does this have on the sequence alignment?

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  • $\begingroup$ I find your post incomprehensible and am voting to close. However if you are having a problem with a software program I suggest you consult the documentation, the website or the support community. $\endgroup$ – David Aug 18 '18 at 19:14
  • $\begingroup$ Hi, this is the description: ! is anyone of IV $ is anyone of LM % is anyone of FY # is anyone of NDQEBZ I have emailed them for help, and even follow up on that email, but i did not get a reply at all. I really hope some bioinformatics expert can help me here. Thank you $\endgroup$ – Skyd4ncer Aug 20 '18 at 3:07
  • $\begingroup$ I have edited your question in a readable manner, which I would recommend if you post here again — the clearer you explain your problem, the more likely you are to get an answer. I have also answered your question, including sample output, that you would have done well to include in your question. $\endgroup$ – David Aug 20 '18 at 15:13
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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.

                  51                                                 100
          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

Multiple alginment

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.

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