Do you need to sequence the whole 3645 bases or just the coding sequences?

If just the coding sequences and it is split into exons then an answer would need the positions ( therefore sizes) of all of the exons

I would use one primer per ~700 bp. Usually the primers fall off after 700-100 bps

Paul Rutland Yes sir, actually I have to sequence the entire 3645 bps. I was confused whether if I have to use one set of primer or either one forward or one reverse every ~850bp.

Sajede Rasouli Hi. Thanks for replying! So, either forward or reverse primer for every 700bps or one set (both forward and reverse) every 700bps?

In that case I agree with Sajede Rasouli . You will get no sequence under the primer or for the next 30 bases so at the very least the 2 end sequences will have to be done forwards and reverse. Also you will need to allow for this in all the forward primers which will nedd to overlap with the expected sequence bu about 60 bases so if you think you can get 700 sequenced nases the next primer should be at about base 640. Some high GC or very high AT regions may need shorter sequencing but whether you need both directions depends on the quality of the template and its sequence so I would sequence forwards and only do the reverse at the ends or when the sequence looks poor if money is an issue. Many people will claim to get 900 bases per sequence but signal strength is stronger and reading is easier with shorter reads and if you are sequencing off one long template then you will see the extra bases when things go well

Paul Rutland I understand. Thank you sir for your help!