If I use one set of primers to amplify DNA form one nematode (Primers were designed (on the basis of ITS-1 rDNA sequences for taxonomically close nematodes) to amplify another nematode of same genus, and I get amplification, sequence it. How can I say what part of DNA, I have amplified?
With other nematode of same genus, they got amplification of partial 18s,complete ITS1,5.8S,ITS2 and partial 28s. How can I know about these regions from my sequence?
Generall I do a multiple sequence alignment of your sequence with the known documented full sequence. It will show which are the probable location. Unless your sequence is a lot of repeat then maybe difficult.
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