HI, thank you very much and sorry I did not read the rules (I did now), I posted my message a bit in a rush. Anyway I tried your suggestions, but still there are some problems with it. For example:

open my $fh_in , '<', 'test1.txt' or die "Can not open file test1.txt:
+ $!";
open my $fh_out, '>', 'test2.txt' or die "Can not open file test2.txt:
+ $!";
while (<$fh_in>) {
    s/\s+/\t/g;    
    print $fh_out "$_\n";
}
close $fh_out;
close $fh_in;
[download]

The code does the job but still there is a problem in the 5th column since there is not always an entry. This is an example of my text file:

MGI:1918918                    381629                         0610007C
+21Rik             5            syntenic            51374             
+             C2orf28                   2p23.3                    B
MGI:1918917                    71667                          0610007L
+01Rik             5            syntenic F          55069             
+             C7orf42                   7q11.21                   C
MGI:1923501                    76251                          0610007P
+08Rik             13           syntenic B3         375748            
+             C9orf102                  9q22.32                   M
MGI:1915571                    58520                          0610007P
+14Rik             12           syntenic            11161             
+             C14orf1                   14q24.3                   B
[download]

In the lines with no entry in the 5 th column there should be second TAB. I currently work with an if(...){then....} I hope it is clearer now, Thanks Martin

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