G'day oxydeepu,

"I hope the question is clear."

There is no question. You haven't ask one. You've only provided a specification. You seem to want someone here to do your work for you for free.

You did exactly the same with:

• Sorting the numbers: A little tricky.
• Hexamer combination from 3mers.
• Format a Dumper module output file.
• Compare elements of a line in a file

Please read "Do Your Own Work" in How (Not) To Ask A Question as well as How do I post a question effectively?. Come back when you're prepared to show some effort yourself. This is not a code writing service.