case 1:

1. From the first select area, all the strains of Mycoplasma hyopneumoniae are selected
2. From the second select area, the non-target species likely to be in the sample are chosen; other genomes from genus of mycoplasma
3. E-mail address is provided in case the job will take long time
4. Optional PCR conditions are not modified
5. ButtonPICK PRIMERS is clicked
6. Following interim page is displayed: RUN1
   The request ID is your queries specific ID. By this ID you may find later your results from page http://bioinfo.ut.ee/multimprimer3/results?flag=ID by substituting 'ID' with specified request ID
7. Next, by clicking the button CHECK RESULTS further page is displayed: RUN2
8. After that, if you inserted email address, you may close the window and wait for the email notifying that results have been finished; otherwise you can bookmark this page or remember the request ID and come back later.
9. From the RESULT page you can get designed PCR primers. Requested number of primers (you can change this number from page http://bioinfo.ut.ee/multimprimer3/primerdesign.php, by default this is one) are designed for each consensus sequence formed from copies of repetitive sequence (MultimPrimer3 looks for three different repetitive sequences). Primers are not scored, this means all designed primers are suggested to work at equal level.

case 2:

User has FASTA files with copies of repetitive sequence from species of Mycoplasma hyopneumoniae. He/she wants detection primers for all thouse sequences. He/she suspects that the repetitive sequence may be homologous with other members of genus mycoplasma which may also occur in the sample. Hereby, all species of mycoplasma in list of non-target genomes are selected.
1. Fasta format sequences are pasted to the textarea
2. Thereafter non-target species are selected, human genome is not required
3. Next, you can follow the previous example from point 3