I have been working with Salk mutant lines obtained from ABRC,and have
identified a mutant I'm interested.But PCR analysis using T-DNA border and
genomic flanking primers showed insertion site was not as Salk center
predicted.So I designed a tail-PCR to recover the flanking sequence myself.
I obtained 300bp dna fragment with 200bp LB sequence and 100bp flanking
sequence.But when I run blast with the 100bp sequence , result showed this
fragment belong to no species,neither arabidopsis nor T-DNA ect.....
Could anyone give me some advice about this phenomena?Is this a common
problem of failed Tail-PCR?
Any advice will be appreciated