use feature ":5.14";
use warnings FATAL => qw(all);
use strict;
use Data::Dump qw(dump pp);

my @positions;
for(split /\n/, <<'END') 
1 ACAC
2 AGAC
3 AGTC
4 ACCA
END
 {push @positions, [split/ /] unless /[GT]/;
 }

say "With bases: ", dump(@positions);

$_ = $_->[0] for @positions;
say "Without bases: ", dump(@positions);