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use strict;
use warnings;
...
3851 A A G G T T A A C C
3854 A A G G T T A A C C
3871 A A G G T T A A G G

Column :0
4 A    2 T    2 C    2 G
...
4 A    2 T    2 C    2 G
Column :2
4 A    4 G    2 T