Probably you can clone the products into a plasmid vector and then sequence them with a single primer from the plasmid. (Obviously, you can't sequence with any primer mix intended for PCR, since it contains primers for both strands and will produce the mixed sequence of both strands and be unreadable.)

I think that the best choice is sequence the 16s with universal primers, and then blast.

Hope be helpfull

Probably you can clone the products into a plasmid vector and then sequence them with a single primer from the plasmid. (Obviously, you can't sequence with any primer mix intended for PCR, since it contains primers for both strands and will produce the mixed sequence of both strands and be unreadable.)

I don't support using Roche kits for research purpose. They keep lots of things confidential, which make them better for services. You should go with 16S Universal primers and sequence after successful cloning.

You can clone the PCR product into TA cloning vectors and use M13 Universal primers for sequencing. Then sequence data obtained will be useful in identifying the other organisms present.

Align complete genome of Neisseria gonorrhoeae (in KEGG you find three different genomes) and check conserved regions. Good luck!

Sneha, depending on the kit you are using, there is information in the package insert about the target sequence, although not at the primer sequence level, as you might wish. If using AMPLICOR CT/NG Test, the PI states that it uses the biotinylated primers SS01 and SS02 to define a sequence of approximately 201 nucleotides within the M·Ngo PII gene of N. gonorrhoeae.

Please dísregard opinion that Roche is good for services only. Roche Applied Science products specifically designed for research are excellent. The kit you are using (for specimens out of the validated types) is intended for diagnostics, primarily. Nevertheless it is extensively used in clinical studies. To this purpose, the specificity for gonococcal Neisseria species, given by primers, is enhanced by hybridization of the amplicon to a target-specific probe in a microplate. However, the specifcity declared by the manufacturer for different prevalence rates is of 97.9%, not 100. Plase be informed that primers sequence is covered by a patent. From public information SS01 and SS02 referred to as SEQ ID NO:5: - (i) SEQUENCE CHARACTERISTICS: #pairs (A) LENGTH: 23 base (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear - (ii) MOLECULE TYPE: DNA (genomic) - (xi) SEQUENCE DESCRIPTION: SEQ ID NO:5: # 23TGGC GAC