During sequence analysis one of my Chrysaora sp. shows 83% identity with Cyanea sp. Query cover value is 99%. I am sure it is Chrysaora sp. Why this sequence couldn’t show any similarity with any other Chrysaora sp. Is any mistake in my sequence?
Riyas,
I assume this is Sanger sequencing given the length. The first thing you need to do is check on the sequence quality. Are there N's in the sequence you got, that would suggest sequencing problems. Ultimately, it is critical to look at the actual sequencing traces and look for the strength of the peaks, whether there are competing peaks or changes in peak spacing etc. that might suggest a problem.
Dear Riyas
May be abecause of Ns in your sequence. So it need to finalaized before you analyze.
There are no Ns in the 533bp sequence you blasted. But I agree with Prescott 100% - you need to check the traces you got back from the Sanger sequencing. Depending on how you asked for the results to be presented to you, you may have just taken the consesus sequence generated by the sequencer, which won't take into account any polymorphisms, peak saturation, and overall quality of sequencing.
You can also check your primers...!!! are there any SNPs in your primer sequence?
If there are than it might not bind on the required position. Design new set of primers.
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