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>perl -wMstrict -le
"use List::Util qw(reduce);
...
 print qq{'$cons'};
"
'..XX.XX.....X..'

my @seqs = qw(
  CTCG--ATCG-ATCG
...
  ATGC-A-TCG-ATCG
  ATGC--ATCG-ATCG
  );