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;
[download]

Step 1: What exactly is it you don't like? (CRLF in the middle of your print)

Step 2: Where in the code does it do that? (Somewhere between printing the text of the line and printing the IN or OUT, conveniently, this is on the same line so you don't have to look very far.)

Step 3: Consider what it is doing there. Add debug prints to make clear what your variables are at that point. (There's a \n before your \tIN... and the $column[$number] is the thing before the \t... print "-=)$column[$number](=-";? Well, that will prove that you've got a CRLF in there.)

Step 4: Understand. The CRLF is in your string because every line of your file ends with a CRLF, of course!

Step 5: Fix it. chomp was made for this.