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Now it needs to be translated to programming terms. Computers use bits and bytes.
Programs work with variables and memory contents.

I'll let you do the translating to programming language from your project's terminology(jargon)
Do you have a java programming question?

If you want anyone to test your code, you need to post a complete program that compiles and executes.
A small program that shows the problem without any other stuff that is not related to the...

cossover phenomenon. given 2 dan strands
d nucleotides from d position i+1 go d 2nd strand.
d first i nucleotides of d 2nd strand

None of that has any meaing for me.

#3 in post#18

You'll have to translate from the jargon you used in post#13 to something related to java programming.

What is a String?

Please explain you question. I don't understand what you are asking.

By strand do you mean another linked list?
Change the links to point to the front of the new list and change the end of the new list to be back into the original list.
Draw it on a piece of paper...

I don't do any work out of the public. If you want help you'll have to post code here with your questions.
If you can isolate a particular problem to a small program that will help.

Use the linked list class's methods to get the nodes one by one and assign them to an array slot as you get them.

Can you explain what you are trying to do?
"print out in an array" makes no sense to me.
Do you want to extract nodes from a linked list and store them in an array?

Do you have any code that you are having problems with?
If so, post the code and ask questions about your problems.