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