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.......    .......   ......
GATTACGAGTGGCGCTCGTGTAACGGCA
GATTACG    GCGCTCG   AACGGCA

.........       .......
GATTACGAGTGGCGCTCGTGTAACGGCA
GATTACG
  TTACGAG       CGTGTAA

             GCTCGTG
  ..................
GATTACGAGTGGCGCTCGTGTAACGGCA
   TACGAGT
        GTGGCGC

          ..            ..     
GATTACGAGTGGCGCTCGTGTAACGGCA
          GG            GG

#!/usr/bin/perl -w
use strict;
...

   }