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my @new = split ('>', $joi1);
...
my @new;
..
foreach (@new) {

use warnings;
use strict;
...
    grep {$_ < 1 || $num[$_] >= 10 || $alp[$_ - 1] ne $alp[$_ - 0]} 0 
+.. $#num;
print (join ('  ', @alp[@keep]), "\n");
print (join (' ', map {sprintf '%2d', $_} @num[@keep]), "\n");

A  G  C  T  T  T  C  G  G  C  A  A  T  G  C  T  G  C  C  C  C  C  A  T
+  C  T  T  T  C  G  T  A  G  C  T  G  A  A  A  A  T  C
23 43 45 65 76 54 34 54 65 45 56 87 56 23 43 23 45 65 45 76 78 34 12 3
+2 65 23 25 12 23 34 45 56 54 43 32 65 43 12 34 75 76 45