trouble reading output of clustal omega

Question

[virus_n00b]

I am using clustal omega provided by (( for performing MSA. I have given some sequences as input and got output as shown below.

CLUSTAL O(1.2.1) multiple sequence alignment


variant9       ------------------------------------------------------------
variant7       ------------------------------------------------------------
variant8       ----ECAB----------AAAAACAAAAGAAFAAAAE--CEEAAECBEA-ABAAFAABCC
variant5       -------------EAAAAAAAAAAAAAEGAAAACAA------------------------
variant6       -------------EAAAAAAAAAAAAAEGAAAACAA------------------------
variant2       -----------------EEAAAAAAA----------------------------------
variant1       EAEAABEAAAAAAEEABCAAAAAAACBAAAAAACCAAB----------------------
variant3       --FAHCDDAGHFHHHBFDDAAGAABCAAGDBFGCCDEHGBDHEAFCFFGGHGAHHABHCC
variant4       --FAHCDDAGHFHHHBFDDAAGAABCAAGDBFGCCDEHGADHEAFCFFGGHGAFHABHCC
variant10      --FAHCDDAGHFHHHBFDDAAGAABCAAGDBFGCCDEHGBDHEAFCFFGGHGAFHABHCC


variant9       ----EAAAAA----AAAAAAAAAABAAAAAAAAAAAAAAAAAAAABAAAAAAAAAACAAA
variant7       ----EAAAAA----AAAAAAAAEAEAAAAAAAAAAAAAAAAAAAABAAAAAAAAAACAAA
variant8       AACFBAFCACCAAFBECCABDABABGCAAFBAC--EBAFAGBBAAABAHDEECGBACAAE
variant5       --------------AA--AAACAAAAC----AC--CBABAB------AAAACACAACAAA
variant6       --------------AA--AAACAAAAC----AC--CBABAB------AAAACACAACAAA
variant2       --------AAAAAEAF--AAAAAAAAAAAAAA-------AAAAAABAAAAAAAAAACAAA
variant1       --------------AB--AAAAAAEACABCAEA--------------AAAABACAACAAA
variant3       CBFFEGFCDCACGEBF--GEDEDAEACCFCFFC--CGFFABAHFHHDHHAFGFCDACHGE
variant4       CBFFEGFCDCACGEAF--GEBEDAEACCFCFFC--CGFBABAHFHHDHHAFGFCDACHGE
variant10      CBFFEGFCDCACGEBF--GEBEDAEACCFCFFC--CGFBABAHFHHDHHAFGFCDACHGE
                                 .    * ..                            ** . 

variant9       AAAAAAAAAAAAAAA---AAAAABAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABA
variant7       AAAAAAAAAAAAAAA---AAAAABBAAAAAAAAAAAAAAAAAAAAAAAAAAAAEAAAAAA
variant8       --------------------AAACAAAEBEABBAB--AAGEFACGAEEAACGAABE----
variant5       AAAA--BACABBAAABEBADBAACAAAAAAAAAAAEAA--------EEEACAA------A
variant6       AAAA--BACABBAAABEBADBAACAAAAAAAAAAAEAA--------EEEACAA------A
variant2       AAAAAAAAAAAAAAA---AAAAABBAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABAAA
variant1       BAAABABACAABGAA---A-AAACFAAAEAAAAAAEAAAA---------AAAA-------
variant3       ---EHDFCCDD---------------EBEB-DEEFGAHBB---------DEHE-------
variant4       ---EHDFCCDD---------------EBEB-DEEFEAAAA---------AABA-------
variant10      ---EHDFCCDD---------------EBEB-DEEFEAABA---------CCDA-------


variant9       AABAAAAAAAAAABAAAAAAAEAABACCDAAABCBFAAEEBAABABHBEABAGADFC-AC
variant7       AAAAAAAAAAAAAAAAAAAAAEAABACCDAABAABFAAEEBAABABHBEABAGADBC-AC
variant8       -EBBFAEABAAECAACAACA----BBCAB-----------------------------BE
variant5       EABAAAAAAAAACAADAAAA--------AAAAAAAECAAGAHBBDEHEGAGEGACFB-AA
variant6       EABAAAAAAAAACAADAAAA--------AAAAAAAECAAGAHBBDEHEGAGEGACFB-AA
variant2       AAAAAAAAAAAAAAAAAAAAAEAABACCDAABAABFAAEEBAABABHBEABAGADFC-AC
variant1       ---------AAACAAAAAAAAAAAAACABAA--------GAHBBDEHGGAGEGBCFB-AA
variant3       ---------GAGEGACFB--------------------------------AAGAAFFBEH
variant4       ---------AAAAAAAAAAAAAAA---------------------BBAAAAAAAAFAAAC
variant10      ---------AABCBFAAEEBAABA---------------------BHBEABAGADFC-AC
                        .*                                                 

variant9       AGADCECAAHAEEBF------------------
variant7       AGADCECACHAEEBF------------------
variant8       CAAEFACFHADAADAAAAEEHH-----------
variant5       GAAFFBEHHHHDCEFDGGBGHHEDHDDBHHHDF
variant6       GAAFFBEHHHGDDEFDGGBGHHEDHDDBHHHDF
variant2       AGADCECACHAEEBF------------------
variant1       GAAFFBEHHHGDCEFDGGBGHHEDHDHBHHHDF
variant3       --------HHGDCEFDGHBGHHEDHDDBHHHDF
variant4       CAAAAACCBAAACA-------------------
variant10      AGADCECCAHAEEBF------------------

I know that the '*' implies that all the matching characters but am confused in what the '.' implies. Are there any better methods than clustal omega for MSA?

[GenoMax]

In MSA, a . represents a semi-conserved residue (* represents conserved residue).

This alignment does not look great. Were the starting sequences of similar length (and known to be related)? Just by eye it appears that there may be a couple of groups. Did you make a simple tree?