A  83    GLU       A  90    GLU^?     
A 163    ARG       A  83    ARG^?     
A 222    ARG       A   5    ARG^?

A 229    ALA       A 115    ALA~?     
A 257    ALA       A 118    ALA~?     
A 328    ASP       A  95    ASP~?

A  83    GLU       A  90    GLU^?     
A 163    ARG       A  83    ARG^?     
A 222    ARG       A   5    ARG^?

A  83    GLU       B  90    GLU^?     
A 163    ARG       B  83    ARG^?     
A 222    ARG       B  5     ARG^?      
     

##</code><code>##

#!/usr/bin/perl

open (FILE, 'bodo.txt');
open (OUTFILE, '>output.txt') or die "die";

$/ = "

";

$i=0;
$j=0;
$k=0;
$l=0;
$m=0;
$n=0;

while ($line = <FILE>) {
chomp;

($i_new, $j_new, $k_new) = (split /\s+/,$line) [ -2,-8,-14 ] ; #assign each number to a variable
($l_new, $m_new, $n_new) = (split /\s+/,$line) [ -5,-11,-17 ] ; # assign each number to a variable

if ($i==$i_new && $j==$j_new && $k==$k_new && $l==$l_new && $m==$m_new && $n==$n_new){
#do nothing
}
else {
print OUTFILE $line;
}

$i=$i_new;
$j=$j_new;
$k=$k_new;
$l=$l_new;
$m=$m_new;
$n=$n_new;

}
close (FILE);
close (OUTFILE);
exit;