How to find SSR location i.e whether it is in CDS, or UTR

Question

[majeedaasim]

I have identified a set of SSR containing sequences from my transcriptome assembled denovo. I used ORF predictor to predict ORFs from SSR containing sequences. Now I would like to see whether my SSRs are in ORF, 5'UTR or 3'UTR and their relative frequency.

Is there anyway do it?

THanks

[Abhishek]

Did you find any answer to this? please share. Thanks

[Kristoffer Vitting-Seerup]

Just to be sure you mean "simple sequence repeat" right?

Answer 1

[lakhujanivijay]

How did you identified them? Tools generally output the locations as well from which the SSR's were identified.

[majeedaasim]

I identified them using MISA. I have the locations of my SSRs. But the point is how can I relate them to start and stop codons after finding ORFs using ORF predicting tool so that I may know whether it is within CDS or outside. I have a large set of sequences so it is cumbersome to inspect it manually. Is there any tool which can corelate the SSR star/stop positions with the predicted ORF start/stop positions.

Thanks