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Disclosed herein are isolated nucleic acid molecules that may be used as an internal positive controls in probe-based nucleic acid assays such as TaqMan® based assays. Also disclosed are probes comprising the isolated nucleic acid molecule of the present invention. The probes may comprise a reporter molecule and a quencher molecule. Also disclosed are assays which comprise using the probe of the present invention. The probes may be used to distinguish false negative results from true negative results in assays for a target nucleic acid molecule. The probe may be used in conjunction with probe-based nucleic acid assays for the detection of an organism such as one belonging to Bacillus, Mycobacterium, Francisella, Brucella, Clostridium, Yersinia, Variola, Orthopox, or Burkholderia.