I changed my code a bit, but now it prints in this way:

5 Q CAA OUT16 Q CAG OUT

21 Q CAA OUT

74 Q CAA OUT

80 Q CAG OUT

82 Q CAG OUT

84 Q CAG OUT

85 Q CAG OUT

89 Q CAG

IN

90 Q CAG

IN

91 Q CAG

IN

92 Q CAG

IN

93 Q CAA

IN

94 Q CAG

IN

95 Q CAG

IN

96 Q CAG

IN

98 Q CAG OUT

99 Q CAG OUT

100 Q CAG OUT

I would like to get:

My OUTPUT FILE:

5 Q CAA OUT

16 Q CAG OUT

21 Q CAA OUT

74 Q CAA OUT

80 Q CAG OUT

82 Q CAG OUT

84 Q CAG OUT

85 Q CAG OUT

89 Q CAG IN

90 Q CAG IN

91 Q CAG IN

92 Q CAG IN

93 Q CAA IN

94 Q CAG IN

95 Q CAG IN

96 Q CAG IN

98 Q CAG OUT

99 Q CAG OUT

100 Q CAG OUT

Here is my code:

use strict; 
use warnings;

open(FILE, "<", "Q.txt");

my @column=(<FILE>);    #get the lines from the standard input into an
+ array
my $file;
chomp $file;                 
    my $number=0;
        while($number <= $#column) {       #go through the array from 
+0 to the last element
         my $j;
         my $count=0;
              foreach ($j=$number; $j < $#column; $j++) {    #select t
+he numbers from the beginning of the line in the current and next ele
+ment
    
                my $d=($column[$j]=~/(\d+)/)[0] - ($column[$j+1]=~/(\d
++)/)[0]; #difference
                last if abs($d)!= 1;       #if differ more than 1 - le
+ave  
     
                 $count+=$d;       #accumulate the difference
  
    }     
             if(abs($count)>=7) {
             chomp($column[$_]);
               $column[$_]=$column[$_]. "\tIN\n" for $number..$j;     
+  #IN if >8
              $number=$j+1;  
             } 
                if (abs($count)<8) {
                chomp($column[$number]);
                   $column[$number] = $column[$number]."\tOUT\n";     
+  #OUT if < 8
                   $number++;
                 }
    }

print for @column;
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