Thank you so much for your help, There is another question that I would like to know if I want to get out put with more details what should I do, cause In some part of my data I have similar coordinates which make problem with script they look like : 

__DATA__
chr1    101  105   X     X     -
chr1    101  105   X     X     -
chr1    101  105   X     X     -
chr1    101  105   X     X     -
chr1    102  108   X     X     -
chr1    106  111   X     X     -
chr1    106  111   X     X     -
chr1    112  113   X     X     -
chr1    113  115   X     X     -
chr2    114  118   X     X     -
chr2    114  118   X     X     -
chr2    114  118   X     X     -
chr2    114  118   X     X     -
chr2    119  121   X     X     -
chr2    120  123   X     X     -
chr3    125  130   X     X     -
chr3    125  130   X     X     -
chr3    131  132   X     X     -

then I want to get output like this :

output :

ID_1    chr1   101   105   4
ID_1    chr1   102   106   1
ID_1    chr1   106   111   2
ID_2    chr1   112   113   1
ID_3    chr1   113   115   1
ID_1    chr2   114   118   1
ID_2    chr2   119   123   1
ID_2    chr2   119   123   1
ID_1    chr3   125   130   2
ID_2    chr3   131   132   1

[download]
which it counts the number of similar coordinates as well and show them individually instead of total counting by merging them.

In reply to Re^2: Counting problem! by g-alone
in thread Help the counting! by g-alone

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