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I need to find the flanking region

Hi, I have some coordinates (like: chr5:83033623-83213540, chr6:116440663-116774122, chr9:66226352-66300177) I need to find the flanking region that is inside the these Regions.Please help me,Thanks.

sequence
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written by hosin • hosin

Could you please clarify what you need? To me, it seems a logical contradiction to "find flanking region that is inside these regions". Also, although your post does not state, the tag you used imply you want to extract sequences from a reference genome using these flanking regions, is this correct? Like you already asked on How I can find flanking regions ?

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written by h.mon h.mon

Thanks for answer, Actuallly I have some coordinates (like: chr5:83033623-83213540, chr6:116440663-116774122, chr9:66226352-66300177). I have to design primers for further quantitative real-time PCR (QPCR) confirmation, about these coordinates .QPCR primers need to be on the flanking region. can you help me?

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written by hosin • hosin

Hi hosein_salehi6, you have been asking this same question for some weeks now. You always ask about extracting sequences from coordinates (and you had been given several good answers to this question), but in reality you want to design RT-PCR primers. This is known as a XY-problem, and it seems it is a recursive one.

To design the primers, use Primer-BLAST, and check these tutorials:

How To Create Real-Time PCR Primers Using Primer-BLAST

A Step-by-Step Guide to Designing qPCR Primers

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written by h.mon h.mon

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