######
agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactg
   |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---ttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactg
gttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagac
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
gttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagac
agataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggt
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
agataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggt
aacggtgcgggctgacgcgtacaggaaacacagaaaaaag
||||||||||||||||||||||||||||||||||||||||
aacggtgcgggctgacgcgtacaggaaacacagaaaaaag
######
agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactg
                                                                                
--------------------------------------------------------------------------------
gttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagac
                                                                                
--------------------------------------------------------------------------------
agataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggt
                                                                               |
------------------------------------------------------------------------------nt
aacggtgcgggctgacgcgtacaggaaacacagaaaaaag
     |      |      |                    
-----t------t------t-------------------n
######
--------------------------------------------------------------------------------
                                                                                
ttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactggtt
--------------------------------------------------------------------------------
                                                                                
acctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagacaga
---------------------------------------------------------------------------nt---
                                                                            |   
taaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaac
--t------t------t---------nc---------
  |      |      |          |         
ggtgcgggctgacgcgtacaggaaacacagaaaaaag
######
nttttnc
 ||||  
ntttt-n
# wildcards are represented by n
