I have identified SSR from some function gene sequence. Further I have done blast N to check sequence similarity which give 90 % query coverage but the part of sequence containing SSR is not lie in alignment with other sequence found in blast analysis. In that case how to proceed for PCR .
Ibrahim Celik
Coverage and identity depend on target sequences. target sequence might be homolog gene. Thus, You do not expect 100% coverage. Also if the target sequence is EST, ESTs are not complete sequences. You do not worry about blast results. Just design PCR primers and perform PCR. maybe later on you can sequence the PCR fragment for verification.
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