Counting / Sorting by matches to an oligo

I tried to “misuse” the trim.seqs command to count how many of my sequences (in this case actually an alignment of sequences from various sources) have a match with a specified oligo (my intention is to test various potential primers). I supplied the oligo sequence as a barcode in the .oligos file. However this does not seem to work - only very few sequences are assigned to this group although many more have the oligo sequence, as a quick check in BioEdit showed. I assume mothur uses certain criteria to limit where it looks for the barcode sequence? Is there another way to do this?

To explain: silva has very nice tools to assess the coverage of oligos and primers for 16S (TestProbe, TestPrime)- I’d like to have a similar ability with regards to funcitonal genes, using alignments I maintain myself. I guess I could use ARB, but I don’t have a Linux machine handy at all my work places, so a Windows alternative would be nice…

I think what you might want is the pcr.seqs command - check that out and let us know whether you have any questions.