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my @sets = (
  [qw( a c f g e h i )],      # X
  [qw( a b c d e f g h i )],  # Y
  [qw( a c d e f g h i )],    # Z
);

X  Y  Z
a  a  a
...
e     
h  h  h
i  i  i

my @idx = (
  [0, undef, 1, undef, undef, 2, 3, 4, 5, 6],  # X
  [0, 1, 2, 3, 4, 5, 6, undef, 7, 8],          # Y
  [0, undef, 1, 2, 3, 4, 5, undef, 6, 7],      # Z
);

my @sets = (
  [qw( a b c f g )],  # X
  [qw( a b d f g )],  # Y
  [qw( a b e f g )],  # Z
);

X  Y  Z
a  a  a
...
      e
f  f  f
g  g  g