I can only agree with amarquis. You are still far from clear.

I appreciate that English is not your native language (here's a friendly hint: sentences start with capital letters) but you're not making it easy for us to help you. In particular, you still haven't replied to the very first question that you were asked in an attempt to get you to clarify your problem:

What is a bp and how are you calculating it?

Presuming that 'bp' is the same as 'basepair', such information could possibly help us understand what you mean by, for example:

and if the next line has hits lying less than 200basepairs then add them to the first and go on unless and until you could not find any hits with in the 200basepairs gap.

Less than 200 'basepairs' from what? 'Go on' doing what? What is a '200 basepairs gap'?

In reply to Re^3: how to get clusters? by Not_a_Number
in thread how to get clusters? by sirna

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