microsatellite query

[NGS_New_User]

Hello wise people!

I have approx 10,000 microsatellites that I obtained from some assembled dna of a non-model organism. I selected a subset of the microsatellites including 50bp of the right and left flanking sites.
My intent is to use this subset as a query to search in sequenced dna data from a number of sample populations and see if I can find similar sequences in the different popns.

I am trying to think of a way to do this, does anyone know of a program/software (or a combination of different programs) that can achieve this? For those who use CLC gwb, any ideas?
I was thinking of mapping each popn to the microsatellite+flanking seqs (use the microsatellite seqs as reference), extracting a consensus sequence, then aligning that sequence back to the microsatellite seq. Is that a good way or what?
Please help...

[vivek_]

Out of curiosity, can you please tell me how you identified the microsatellite regions? Any specific tool or method?

[NGS_New_User]

Out of curiosity, can you please tell me how you identified the microsatellite regions? Any specific tool or method?

I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.

[JackieBadger]

How large is your subset that you want to investigate?

[vivek_]

I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.

Thanks for that. TRF seems to have been used in the 1000 genomes analysis as well.

[NGS_New_User]

How large is your subset that you want to investigate?

I am first starting with a small group ie 10 sequences, each sequence is approx 150bp (ie the left flank region + repeat motif + right flanking region). The size of one of the popns that I want to search in is approx 1.8million sequences.