stssearchs reads in one or more sequences to be searched. For each pair of primers, it looks for matches between a the primers and the query sequence in either orientation.
Any matches found will be reported. Only one primer need match for it to be reported..
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The primers file consists of three columns separated by tabs or spaces.
The first column is the name of the primer pair.
The second column is the sequence of the first primer.
The third column is the sequence of the second primer.
The output file consists of one line per match. This consists of:
If you want something that only reports matches of both primer pairs and can find mismatches, use primersearch.