Patent Publication Number: US-8993239-B2

Title: Nucleic acid beacons for fluorescent in-situ hybridization and chip technology

Description:
The present invention relates to beacons for fluorescent in-situ hybridisation and chip technology. 
     BACKGROUND/PRIOR ART 
     Since the wide-spread success of the polymerase chain reaction (PCR) technology, microbiology laboratories are waiting for the application of molecular biology to routine microbiology. This has been held back by an inherent and fundamental problem of molecular biology. Because of its precision, you need to know which tools (probes) to choose. The prerequisite is, that a request has to be specified with respect to organisms to be detected. In clinical samples, however, you do not know which of the over 2000 clinically relevant pathogens is the causative agent of an infection. A rational approach solves the problem
         Focus must be made on 95% of problem causing organisms   If it is known where the sample was taken, and clinical data is present, the number of organisms can be reduced to between 2 and 16.   The number of organisms to cover the 95-percentile in most clinical samples is in the order of 100       

     This rationale makes it economically feasible to run a DNA-probe based assay on a routine basis. 
     Grouping of micro-organisms and the very rapid testing for presence/absence of specific or a range of micro-organisms is also of relevance in other fields of microbiological testing: Blood banks, Pharmaceutical industry, Cosmetic industry and the Food industry. Frequently the same organisms are of relevance throughout the disciplines and reaction conditions therefor need to be standardised for all probes. 
     The detection of ribosomal RNA via Fluorescent in-situ Hybridisation (FISH) or utilising chip technology represents an efficient way of utilising sensitivity and specificity of DNA-probes without having to use an enzymatic amplification step. FISH relies on two approaches to the in-situ detection of targets generating a signal strong enough to be detected with standard measuring devices such as an epifluorescence microscope:
         1. Identical molecules are present within a cell in sufficient numbers to bind one specific oligonucletide or nucleotide analogue probe with one fluorophor each.   2. Large probes carrying a plurality of fluorophores e.g. labelled cosmids.       

     FISH technology for the identification of micro-organisms in their respective environments is well known in the art. Application of FISH for the detection of pathogens is of especial interest to the clinical microbiology and infectiology, where FISH excels in speed and cost efficiency. 
     Detecting rRNA with chip technology also relieves from the necessity to amplify the target. Total rRNA is extracted from a sample and placed on a chip. Specific probes are concentrated on a small surface area and attract respective rRNA-molecules to give specific presence/absence signals. In order to make such chips economically viable they need to be used repeatedly with as little manipulations as possible. Furthermore the standardisation of probe characteristics is paramount for the generation of reproducible results. 
     In order to gain acceptance in a routine environment probes must be designed in such a way that all probes for one disease state can be run simultaneously under identical conditions in or on one vessel (chips, micro-fluidic devices or micro titre plates). In the design of the probes and to make the probes economically viable, it must be taken into account that one probe may be of relevance to different disease states. Therefor, not only one set of probes but all probes must work under identical hybridisation conditions. Sequence and length of the working probes must be tested accordingly. 
     The selection and definition of a working probe cannot be performed by simple sequence comparison and determination of a theoretical T m -value. Depending on the algorithm applied a wide set of values are obtained giving no guidance to the choice of probe sequence suitable for standardised hybridisation conditions. 
     The choice of algorithm and factors influencing the quality of a probe is discussed widely in the art (1-7). Further guidance may be sought comparing sequences and actual position in the three dimensional structure of the ribosome. In an attempt to rationalise the design of probes Behrens et al (8) investigated the correlation between hybridisation sites and actual accessibility with the help of the 3 Å three dimensional model of the ribosome. Their findings demonstrated that the SDS used in in-situ procedures has a predominant denaturing effect, not captured by algorithms predicting secondary structures. 
     A further problem in both FISH and chip technology is that the procedure calls for a stringent wash step to remove unbound probes, requiring additional handling steps, reagents and time. The success of a hybridisation may depend largely on the skill and precision applied to the washing step. However, routine applications call for minimal steps and hands-on time, most importantly they must be independent from individual skills. 
     One solution to the reduction of steps would be the application of fluorescence resonance energy transfer (“FRET”) in an oligo-nucleotide or nucleotide analogue hairpin formation (molecular beacon). Several approaches to the development of beacons are known in the art and generalised descriptions to their construction are freely available (13). Beacons are widely used in real time PCR, where they anneal in solution to an increasing number of templates generated by amplifying enzymes (15). Only few attempts have been made to generate beacons for the detection/identification of bacteria on membranes (14). One successful beacon was constructed to detect  E. coli  in whole cells with a peptide nucleic acid (PNA) probe. The corresponding DNA-probe failed to give adequate performance (16). The production of further PNA-beacons is limited due to the poor solubility of PNA based oligonucleotides as laid down in design recommendations (17). 
     Patent CA 2176266/EP 0745690 gives guidance to the construction of universal stems for real time PCR (9). Surprisingly, these recommendations do not render working beacons when combined with probes designed to identify micro-organisms in-situ. Real time PCR is performed in solution while both ISH (in-situ hybridisation) and chips require fixed targets. Their thermodynamic details were not compatible with in-situ hybridisation and FRET requirements. Thus, universally working stems could not be predicted for applications with fixed targets. It was therefore necessary to empirically search for specific beacons fitting individual oligo-nucleotide or nucleotide analogues in order to accomplish a plurality of beacons working under identical ISH specifications. 
     In the selection of ISH-beacons care has to be taken that the stem does not hinder the delicate balance of hybridising towards RNA entwined in large protein/RNA complexes such as ribosomes. The accessibility of binding sites is widely discussed in the art and is summarised in (1). 
     Further limitations in the design of a beacon probe are given by the size of pores generated in the cell wall during the ISH procedure. Adding the same stem to different probes results in distinctly individual beacons. A plurality of probes already form hairpin loops and the addition of a stem does not result in a “beacon” formation. In addition, simply adding bases to form complementary pairs may increase the T m  to such an extent that the hairpin is thermodynamically preferred rather than the hybrid formation. Special stems have to be devised that pull the sequence into beacon formation while maintaining the T m  at or below that of the hybrid. The teachings with respect to the design of beacons (13) show that the increase of the stem length by one base pair increases the T m  by 5° C. and that the T m  of the stem should be 10° C. higher than the T m  of the hybridising sequence. 
     FISH with single microorganisms, such as bacteria, based upon specific rRNA sequences, may be difficult due to sterical hindrance of the rRNA in the ribosome. In other words, a beacon forming a hairpin may poorly anneal to the embedded rRNA target sequence. 
     It is therefore the subject of the present invention to provide molecular beacons which overcome the above described disadvantages at least partially. The solution provided in the present invention and preferred embodiments thereof are described in the claims. 
     Subject of the present invention is a nucleic acid capable of forming a hybrid with a target nucleic acid sequence and capable of forming a stem-loop structure if no hybrid is formed with the target sequence, said nucleic acid comprising
     (a) a nucleic acid portion comprising
       (a1) a sequence complementary to the target nucleic acid sequence,   (a2) a pair of two complementary sequences capable of forming a stem,   
       (b) an effector and an inhibitor, wherein the inhibitor inhibits the effector when the nucleic acid forms a stem-loop structure, and wherein the effector is active when the nucleic acid is not forming a stem-loop structure.   

     The nucleic acid of the present invention capable of forming a hybrid with a target nucleic acid sequence and capable of forming a stem-loop structure if no hybrid is formed with the target sequence is also referred herein as “beacon”, “molecular beacon”, “hairpin”, or “hairpin loop”, wherein the “open” form (no stem is formed) as well as the “closed” form (the beacon forms a stem) is included. The open form includes a beacon not forming a hybrid with a target sequence and a beacon forming a hybrid with the target sequence. 
     In particular, the two complementary sequences (a2) are flanking the sequence (a1), i.e. the first sequence (a2) is attached at the 3′ end of the sequence (a1) and the second sequence (a2) is attached at the 5′ end of the sequence (a1). 
     The hybrid of the sequence (a1)) with the target sequence is also referred herein as “hybrid with the cognate sequence” or as “cognate hybrid”. 
     In the present invention, the effector may be attached at one of the two complementary sequences capable of forming a stem, whereas the inhibitor may be attached at the other of the two complementary sequences, so that the inhibitor essentially inhibits the effector activity when a stem is formed, and that the effector is active when the hairpin is open. Preferably, the effector is attached at the 5′ end or the 3′ end of the beacon, respectively, or at a position which is 1, 2, 3, 4, or 5 nucleotides distant to the 5′ end or the 3′ end, respectively. The inhibitor is preferably attached at the other end not covered by the effector, i.e. at the 3′ end or the 5′ end, respectively, or at a position which is 1, 2, 3, 4, or 5 nucleotides distant to the 3′ end or the 5′ end, respectively. 
     The design of the hairpin loops disclosed herein therefore differs fundamentally from beacons well known in the art. 
     Hybridisation of the beacon of the present invention with target sequence may take place under conditions where the loop is open. A beacon which is not forming a stem when hybridizing is capable of annealing to a target rRNA sequence, for instance, and can therefor achieve successful hybridisation. 
     This goal is for instance achieved by a T m  of the beacon (i.e. the T m  of the stem) which is essentially equal to or lower than the T m  of the cognate hybrid (i.e. the hybrid of the beacon with the target sequence). Thus, hybridisation with the target sequence takes place when the stem is open, for instance if hybridisation takes place under essentially Mg 2+  free conditions. 
     “Essentially equal T m ” of the cognate hybrid and the stem of the beacon refers to melting temperatures differing in less than 5° C., preferably less than 3° C., more preferably less than 2° C., more preferably less than 1° C., more preferably less than 0.5° C., even more preferably less than 0.2° C., most preferably less than 0.1° C. 
     In order to achieve an inhibition of the effector by the inhibitor, both of which form part of the beacon, in those beacon molecules not hybridising with the target sequence, stem formation must be induced after the hybridisation reaction. This may for instance be achieved by a beacon having a ΔG&lt;0, so the hairpin will form spontaneously. Further, stem formation may be introduced by washing with a Mg 2+  containing buffer as described herein. 
     In particular, the hairpin loops are constructed in such a way that under standardised hybridisation conditions (e.g. under essentially Mg 2+  free conditions) the beacon stem is open so that possible sterical limitations do not hinder the hybridisation process. For instance, sterical limitations may be present when the target sequence is a rRNA sequence. If the effector is a fluorophor, the fluorophor will not be quenched by the close proximity of ribosomal proteins. 
     Suitable conditions for induction of stem formation after hybridisation include an Mg 2+  containing buffer, for instance containing about 1 to about 20 mM Mg 2+ , more particular about 5 to about 15 mM Mg 2+ , even more particular about 8 to about 12 mM Mg 2+ , most particular about 10 mM Mg 2+ . The buffer may have a pH&gt;8. 
     Furthermore, the beacons function in their entirety and cannot be dissected into stem and loop as nearest neighbour and stacking effect have a profound influence in their thermodynamic properties. Preferred beacons of the present invention are summarised in Table 1. They clearly show that the preferred stem sequence is independent from the ΔG, T m , GC content or length of the sequence chosen to identify a species. 
     In the present invention, the thermodynamic specifications for the individual construction of beacons suitable for standardised conditions are set: The Gibbs energy (ΔG) for the formation of the beacon has to be designed in such a way that
         The beacon will form spontaneously (ΔG&lt;0) in the absence of a cognate target sequence under hybridisation conditions.   The ΔG of the cognate hybrid is significantly lower (i.e. is more negative) than the ΔG of the beacon.   The respective ΔG of the beacon is lower than a mismatch or non-cognate sequence.   The T m  for the formation of the beacon has to be designed in such a way that the T m  of the beacon is lower than or essentially at the T m  of the hybrid.       

     It is preferred that the ΔG of the cognate hybrid is in the range of about −17 to about −25 kcal/mol, preferably about −18 to about −24 kcal/mol, more preferably about −19 to about −23 kcal/mol, most preferably about −20 to about −22 kcal/mol under hybridisation conditions. 
     It is also preferred that the ΔG of the cognate hybrids under hybridisation conditions do not vary more than 5 kcal/mol, preferably no more than 3 kcal/mol, more preferably 2 kcal/mol and most preferably 1 kcal/mol. 
     Occasionally cognate sequences may form spontaneous hairpin loops, where one arm only needs to be supplemented to achieve the beacon formation. If the target sequence is a rRNA sequence, this, however renders the effector, e.g. the fluorophor, in very close proximity to potentially quenching proteins of the ribosome. In a preferred configuration the stem is extended. In order to conform with said thermodynamic specifications as described herein even with an extended stem a method was devised to keep both the T m  and ΔG within the specifications. According to the present invention, this can be achieved by the introduction of at least one non-matched nucleotide or nucleotide analogue. In the present invention, introduction of at least one non-matched nucleotide may be enhanced by the introduction of an additional nucleotide or nucleotide analogue, so that the two complementary sequences have a different length, and the stem becomes “bended” (see for example position 36 in SEQ ID NO:1), or/and may be achieved by a replacement of a matching nucleotide or nucleotide analogue by a non-matching nucleotide or nucleotide analogue (see for example position 5 in SEQ ID NO: 7). Thus, in the present invention, the “complementary sequences capable of forming a stem” may also include at least one non-matched nucleotide, preferably 1, 2, 3, 4 or 5 non-matched nucleotides. 
     As can be seen from Table 2 none of the sequences disclosed here could be devised as PNA-beacons due to the said limitations in the construction of PNA-oligonucleotides. The major limitation being in the oligonucleotide length required to have both sufficient specificity and a stem length sufficient to ensure the re-folding of the loop when not hybridised. It is therefore necessary to devise DNA-beacons that are able to hybridise with sufficient affinity and speed to enable the in-situ identification of micro-organisms. 
     The beacon of the present invention is not a PNA beacon. The backbone of the beacon is preferably a nucleic acid backbone. The beacon may comprise a nucleic acid analogue such as a deoxyribonucleotide analogue or a ribonucleotide analogue in the nucleic acid portion or/and in the linker if a linker is present. This analogue is preferably a nucleotide analogue modified at the sugar moiety, the base or/and the phosphate groups. The nucleotide analogue is preferably not a PNA building block. 
     Following the said 95-percentile in clinical samples, pathogens can be grouped into disease related groups. Probes towards these organisms must work simultaneously under the said conditions, especially if all probes are to be utilised on one chip. The chip application calls for a stringent standardisation of both the cognate and stem characteristics. If a combination of more than one probe is employed, i.e. at least two probes, all probes have to be designed to work on the same slide/chip simultaneously. 
     Another subject of the present invention is a combination comprising at least 2, preferably at least 10, at least 20, at least 30, at least 40, or at least 50 beacons. The combination may comprise but is not limited to all of the beacons of Table 1, preferably at the maximum 100, at the maximum 80, at the maximum 70, at the maximum 60, at the maximum 50, at the maximum 40, at the maximum 30 or at the maximum 20 beacons. 
     In a combination of the present invention, the beacons may have the same or different target sequences. It is preferred that the target sequences of individual beacons are different. 
     In a combination of beacons of the present invention, the ΔG difference of the individual beacons of the hybrid of the sequences of (a2) or/and the hybrid of the sequence of (a1) with a target sequence may be at the maximum about 4 kcal/mol, preferably at the maximum about 3 kcal/mol, more preferably at the maximum about 2 kcal/mol, and most preferably at the maximum about 1 kcal/mol with respect to the cognate sequence. 
     In a combination, the T m  values of individual beacons with respect to its respective cognate sequence may differ at the maximum by about 3° C., preferably at the maximum about 2° C., more preferably at the maximum about 1° C. 
     It is preferred that in the combination of the present invention the individual nucleic acids function uniformly. “Functioning uniformly” means that successful hybridisation can be achieved with different nucleic acids probes of the present invention under the same hybridisation conditions, for instance under standardised hybridisation conditions. In other words, uniformly functioning nucleic acids of the present invention do not require individual optimisation of the hybridisation conditions. 
     Depending on the disease state certain pathogens most frequently are the causative agents and can thus be compiled into diagnostic groups. Addition or omission of certain pathogens may be required depending on regional epidemiology in order to reach the 95-percentile. The preferred listing of Table 1 covers the requirements of Europe and most of North America. 
     Yet another aspect of the present invention is a kit or chip which may contain at least two beacons of Table 1 required to detect the listed organisms optionally together with the required hybridisation reagents, Preferably, the chip or kit contains at least 10, at least 20, at least 30, at least 40, or at least 50 beacons. The kit or chip may contain at the maximum all of the beacons of Table 1, preferably at the maximum 100, at the maximum 80, at the maximum 70, at the maximum 60, at the maximum 50, at the maximum 40, at the maximum 30 or at the maximum 20 beacons. 
     List of groupings and resulting kits for the detection, enumeration and identification of the listed organisms is compiled in Table 1. 
     The beacons can be applied to assays designed to be performed in tubes, microtitre plates, filtered microtitre wells, slides and chips. The detection can be made with fluorescence, time resolved fluorescence, with a plurality of fluorophores and utilising electrochemical enzymes. 
     In the preferred embodiment for FISH the assay is performed on glass slides designed to hold and separate several samples. 
     Another subject of the present invention is a hybridisation method comprising
     (a) contacting at least one nucleic acid of any of the present invention or a combination of nucleic acids of the present invention with a biological sample,   (b) hybridising the nucleic acid or the combination of nucleic acid of (a) with the sample under conditions where the stem of the nucleic is open, e.g. hybridising with a buffer which is essentially free of Mg 2+ , and   (c) inducing conditions which allow for stem formation in those nucleic acid molecules of (a) not forming a hybrid with the sample, e.g. washing with a Magnesium containing buffer, for instance at pH&gt;8 or/and at room temperature.   

     The sample may be any sample of biological origin, such as a clinical or food sample, suspected of comprising a nucleic acid to be detected by the beacon. The sample may be a sample comprising microorganisms, such as bacteria, yeasts and molds, in particular Gram positive or/and Gram negative bacteria. 
     Also employed in the hybridisation method of the present invention can be a kit or chip as described herein. 
     “Essentially free of Mg 2+ ” refers to a Mg 2+  concentration of less than 1 mM, preferably less than 0.1 mM, more preferably less than 0.05 mM, most preferably less than 0.01 mM. 
     The buffer in step (c) may contain about 1 to about 20 mM Mg 2+ , more particular about 5 to about 15 mM Mg 2+ , even more particular about 8 to about 12 mM Mg 2+ , most particular about 10 mM Mg 2+ . 
     Any suitable hybridisation protocol comprising application of an essentially Mg 2+  free solution and a Mg 2+  containing solution as indicated above may be applied. For instance, the following protocol may be used: Aliquots of clinical samples are applied to defined fields on the slides. Preferably a defined quantity of 10 μl is applied and dried.
     1. The samples are the heat fixed to the slides.   2. Gram positive organisms are subjected to a Lysozyme/Lysostaphin digestion following well published specifications. In a preferred embodiment the digestion is run for 7 minutes at 46° C. in a humidified chamber.   3. Pores are then formed for instance by immersing the slide 100% methanol or ethanol for several minutes. In a preferred embodiment the methanol or ethanol is ice cold and the immersion time is 7 minutes for Gram negative organisms and 3 minutes for Gram positive organisms.   4. The slide is then dried on a slide warmer, for instance at 55° C.   5. The beacons are dissolved in a hybridisation buffer (which may be essentially free of Mg 2+ ) and then applied to each field of the slide while on the slide warmer.   6. The slide is placed in a hybridisation chamber, humidified with hybridisation buffer. In a preferred embodiment the slide is covered with a hydrophobic cover slip and placed on a covered slide warmer at 46° C. for 12 minutes.   7. The slide is then washed with a Magnesium containing buffer, for instance at pH&gt;8 or/and at room temperature. The buffer main contain about 1 to about 20 mM Mg 2+ , more particular about 5 to about 15 mM Mg 2+ , even more particular about 8 to about 12 mM Mg 2+ , most particular 10 mM Mg 2+     8. The slide is then dried and may be mounted with mounting fluid and can be read under an epifluorescence microscope at a total magnification of for instance 400×, 600×, or 1000×.   

     Should other vessels be used for the hybridisation, the detection may be via flow-cytometry or automated fluorescence reader well known in the art. 
     Yet another embodiment of the present invention relates to Chip applications of the beacons of the present invention. For Chip applications the beacons need to be covalently attached to a carrier surface. To facilitate this, the 3′-terminal base of the designed beacons may be either biotinylated or linked via a hetero-bifunctional reagent to an enzyme using methods well known in the art of protein and nucleic acid chemistry. Biotinylated beacons may then be added to Streptavidin coated chips as can be obtained freely from commercial sources (19). In this application the respective biotinylated hairpin loops can be attached to plurality of distinct fields of one chip, for instance at least 10, at least 50, at least 100, at least 200, or at least 500 fields, or at the maximum 500, at the maximum 400 or at the maximum 300 fields. Total RNA can be extracted from samples using commercially available kits (20) and can be applied to the chip under hybridising conditions. After hybridisation the chip can be briefly washed with a magnesium containing buffer, for instance at pH&gt;8. Fluorescence on a field marks the presence of specific target sequence, for instance a specific RNA indicating the presence of a respective organism in the sample. 
     In order to open hybridisation assays to large scale routine applications it is necessary to analyse a plurality of samples sequentially on one reusable chip. The design of the chip must allow large scale production, efficient quality control and long shelf live. 
     In order to meet these specifications, in another embodiment of the present invention, a beacon of the present invention is covalently attached to an enzyme exerting a signal by catalysing a specific reaction. In particular, the enzyme may exert an electrochemical signal. Suitable enzymes comprise, but are not limited to tyrosinase, peroxidase, sulfite oxidase, alkaline phosphatase, glucose oxydase, guanine oxidase. In a preferred embodiment the enzyme is recombinantly derived from a genomic sequence of a thermo- or hyperthermophylic organism to render it stable under hybridisation conditions and elevated temperatures (21). The enzyme may be attached to the beacon at one end of the beacon molecule. At the other end of the molecule, an inhibitor may be attached which is capable of inhibiting the enzyme activity. When no cognate sequence to said hairpin loops is present the inhibitor inhibits the enzyme and no signal is generated. In the presence of a cognate sequence the loop will remain unfolded with the inhibitor well removed from the enzyme and the enzyme will produce an electrochemical signal which can be detected by devices well described in the art. A linker may be employed for the attachment of the enzyme or/and the inhibitor, in particular for the attachment of the inhibitor. 
     In a further preferred embodiment glucose oxidase is attached to one end of the said hairpin loops and a glucose oxidase inhibitor, such as an adenine nucleotide or adenine nucleotide analogue is attached to the other end of the hairpin loop. Adenine nucleotides are known inhibitors of glucose oxidase (22, 23). A linker may be employed for the attachment of the glucose oxidase or/and the glucose oxidase inhibitor, in particular for the attachment of the glucose oxidase inhibitor. When no cognate sequence to said hairpin loops is present the inhibitor, in particular the adenine nucleotide inhibits the enzyme and no signal is generated. In the presence of a cognate sequence the loop will remain unfolded with the inhibitor well removed from the enzyme and the enzyme will produce an electrochemical signal which can be detected by devices well described in the art. 
     To perform such an assay a large plurality of sequences with identical characteristics (Table I) have been developed, which may be applied to defined positions on the detecting device (chip) respectively. Total RNA is extracted from a sample utilising extraction procedure and kits readily available on the market (20) and placed on the chip under hybridisation conditions. After the hybridisation the chip is washed with substrate buffer at 46° C. and the signal is read. At the end of the cycle all hybridised RNA is washed off with hybridisation buffer at elevated temperature. Preferably the wash temperature is chosen 10° C. above the respective T m . In a preferred embodiment the chip is washed at 60° C. with hybridisation buffer. The temperature may then dropped to 46° C. to equilibrate for the next analytical cycle. 
    
    
     LEGENDS 
     Table 1 describes beacon sequences of the present invention. Abbreviations: R&amp;G: a red or/and a green fluorescent dye may be attached to the beacon, such as Cy3 or FITC or a derivative thereof. 
     Table 2 describes that PNA beacons are not suitable in the present invention. Calculations were performed with the sequences of Table 1 assuming the beacon to be a PNA beacon. In contrast to DNA beacons, all of the following five criteria have to be fulfilled: GC content&lt;60%, &lt;3 bases selfcomplementary, 4 purines in a row, length of maximal 18, inverse sequence palindromes or repeats or hairpins. “Yes” (“No”) in Table 2 indicates that the criterion is fulfilled (not fulfilled). The column “Final” indicates if a PNA beacon is suitable in the present invention (“Yes”) or not (“No”). “No” in final indicates that one of the five criteria is not met. “Yes” would indicate that all criteria are met. All sequences of Table 2 are judged to be “No”. Thus, no one of the sequences of Table 1 would be suitable in a PNA beacon. 
     REFERENCES 
     
         
         1. Sebastian Behrens, Caroline Ruhland, João Inácio, Harald Huber, A. Fonseca, I. Spencer-Martins, Bernhard M. Fuchs, and Rudolf Amann, In Situ Accessibility of Small-Subunit rRNA of Members of the Domains Bacteria, Archaea, and Eucarya to Cy3-Labeled Oligonucletide or nucleotide analogue Probes, Applied and Environmental Microbiology, March 2003, p. 1748-1758, Vol. 69, No. 3 
         2. Wallace, R. B.; Shaffer, J.; Murphy, R. F.; Bonner, J.; Hirose, T.; Itakura, K. Nucleic Acids Res. 6, 3543 (1979). 
         3. Howley, P. M; Israel, M. F.; Iaw, M-F.; Martin, M. A. J. Biol. Chem. 254, 4876.
       The equations for RNA are:
 
 Tm =79.8+18.5 log  M+ 58.4( XG+XC )+11.8( XG+XC )2−820 /L− 0.35 F  
   And for DNA-RNA hybrids:
 
 Tm =79.8+18.5 log  M+ 58.4( XG+XC )+11.8( XG+XC )2−820 /L− 0.50 F  
   
     
         4. Breslauer, K. J.; Frank, R.; Bl{hacek over (s)}ker, H.; Marky, L. A. Proc. Natl. Acad. Sci. USA 83, 3746-3750 (1986). For RNA see: Freier, S. M.; Kierzek, R.; Jaeger, J. A.; Sugimoto, N.; Caruthers, M. H.; Neilson, T.; Turner, D. H. Proc. Natl. Acad. Sci. 83, 9373-9377 (1986). 
         5. Rychlik, W.; Spencer, W. J.; Rhoads, R. E. (1990) Nucl. Acids Res. 18 (21), 6409-6412. 
         6. Owczarzy R., You Y., Moreira B. G., Manthey J. A., Huang L., Behlke M. A., Walder J. A. (2004) Effects of Sodium Ions on DNA Duplex Oligomers: Improved Predictions of Melting Temperatures, Biochemistry, 43:3537-3554. 
         7. Sebastian Behrens, 1  Bernhard M. Fuchs, 1  Florian Mueller, 2  and Rudolf Amann 1  Appl Environ Microbiol. 2003 August; 69(8): 4935-4941. 
         8. HYBRIDIZATION PROBES FOR NUCLEIC ACID DETECTION—UNIVERSAL STEMS document view Patent number: CA2176266 Publication date: 1996 Nov. 13,/EP0745690 (A2) 
         9. Tyagi, S., D. P. Bratu, and F. R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16:49-53. 
         10. Tyagi, S., and F. R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308. 
         11. Schofield, P., A. N. Pell, and D. O. Krause. 1997. Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria. Appl. Environ. Microbiol. 63:1143-1147. 
         12. www.molecular-beacons.org 
         13. Molecular Beacons: Trial of a Fluorescence-Based Solution by Hybridization Technique for Ecological Studies with Ruminal Bacteria PETER SCHOFIELD, ALICE N. PELL, *AND DENIS O. KRAUSE† APPLIED AND ENVIRONMENTAL MICROBIOLOGY, March 1997, p. 1143-1147 
         14. Steven Park, May Wong, Salvatore A. E. Marras, Emily W. Cross, Timothy E. Kiehn, Vishnu Chaturvedi, Sanjay Tyagi, and David S. Perlin Journal of Clinical Microbiology, August 2000, p. 2829-2836, Vol. 38, No. 8; Rapid Identification of  Candida dubliniensis  Using a Species-Specific Molecular Beacon 
         15. Chuanwu Xi, Michal Balberg, Stephen A. Boppart, and Lutgarde Raskin APPLIED AND ENVIRONMENTAL MICROBIOLOGY, September 2003, p. 5673-5678 Vol. 69, No. 9 Use of DNA and Peptide Nucleic Acid Molecular Beacons for Detection and Quantification of rRNA in Solution and in Whole Cells 
         16. Guidelines for Sequence Design of PNA Oligomers wvvw.appliedbiosystems.com/support/seqguide.cfm 
         17. Tijssen, P. Hybridization with nucleic acid probes. part I. Theory and nucleic acid preparation, p. 268. Elsevier Science Publishers B.V., Amsterdam. 
         18. Nanogen, www.nanogen.com 
         19. Qiagene, www.Qiagene.com 
         20. Microbiology and Molecular Biology Reviews, March 2001, p. 1-43, Vol. 65, No. 1 Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability, Claire Vieille and Gregory J. Zeikus 
         21. ELECTROCHEMICAL SENSORS FOR ENVIRONMENTAL MONITORING: A REVIEW OF RECENT TECHNOLOGY by JOSEPH WANG Department of Chemistry and Biochemistry, New Mexico State University Las Cruces, N. Mex. 88003 
         22. Brenda, www.brenda.uni-koeln.de 
       
    
     
       
         
           
               
               
               
               
               
               
               
               
             
               
                   
                 TABLE I 
               
               
                   
                   
               
             
            
               
                   
                   
                   
                   
                   
                   
                   
                 Fuchs score 
               
               
                   
                 Loop Diagostics 
                   
                   
                   
                   
                 Position on 
                 1 = high; VI = 
               
               
                   
                 Code number 
                   
                 Target organism 
                 Beacon name 
                 RNA 
                 rRNA ( Ecoli ) 
                 no/low signal 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                 L-01-1 
                 -10 
                 R&amp;G  Acinetobacter   
                 B-Acibact-1 
                 16S rRNA 
                 652-669 
                 650-667 V 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-2 
                 -10 
                 R&amp;G  Acinatobacter baumanii   
                 B-Acinbaum-2 
                 16S rRNA 
                 67-86 
                 66-83 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-3 
                 -10 
                 R&amp;G  Actinomyces  spp. 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-4 
                 -10 
                 R&amp;G  Aspergillus  spp 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-5 
                 -10 
                 
                   Aspergillus flavus 
                 
                 Aspfla 
                 18s 
                 NA 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-6 
                 -10 
                 
                   Aspergillus fumigatus 
                 
                 Aspfum 
                 18s 
                 NA 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-7 
                 -10 
                 
                   Aspergillus niger 
                 
                 Aspnig 
                 18s 
                 NA 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-8 
                 -10 
                 
                   Aspergillus terreus 
                 
                 Aspter 
                 18s 
                 NA 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-9 
                 -10 
                 R&amp;G  Bacteroides / Prevotella   
                 B-BacPrev 
                 16S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-10 
                 -10 
                 R&amp;G  Borrelia burgdorferi   
                 B-Borrburg 
                 16S rRNA 
                 39-58 
                 38-54 = II; 48-65 = 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 II 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-11 
                 -10 
                 R&amp;G  Bordetella pertussis   
                 B-Borper 
                 23S rRNA 
                 1768-1785 
                 1768-1786 = IV 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-12 
                 -10 
                 R&amp;G  Burkholderia cepacia   
                 B-Burcep-complex-1 
                 16S 
                 425-449 
                 431-448 = III 
               
               
                   
                   
                 -50 
                 complex = Option I 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-13 
                 -10 
                 R&amp;G  Burkholderia cepacia   
                 B-Burcep-complex- 
                 16S 
                 404-383 
                 387-403 = IV 
               
               
                   
                   
                 -50 
                 complex, two beacons = 
                 2a 
               
               
                   
                   
                 -100 
                 Option II 
               
               
                   
                   
               
               
                   
                 L- 
                   
                   
                 B-Burcep-compl-2b 
                 16S 
                 446-433 
                 431-448 = III 
               
               
                   
                   
               
               
                   
                 L-01-14 
                 -10 
                 R&amp;G  Burkholderia cepacia   
                 B-Burcep-pure 
                 16S 
                 441-460 
                 440-456 = I 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-15 
                 -10 
                 R&amp;G  Burkholderia pyrrocinia / 
                 B-Burstabpyramb 
                 16S 
                 407-424 
                 413-429 = II 
               
               
                   
                   
                 -50 
                   stabilis / ambifaria   
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-16 
                 -10 
                 R&amp;G  Burkholderia dolosa / anthina   
                 B-Burdolant 
                 16S 
                 474-458 
                 443-460 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-17 
                 -10 
                 R&amp;G  Burkholderia multivorans   
                 B-Burmult 
                 16S 
                 475-463 
                 455-473 = VI 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-18 
                 -10 
                 R&amp;G  Burkholderia   
                 B-Bur-vietceno 
                 16S 
                 475-458 
                 455-473 = VI 
               
               
                   
                   
                   
                   cenocepacia / vietnamiensis   
               
               
                   
                   
               
               
                   
                 L-01-19 
                 -10 
                 R&amp;G  Campylobacter  (pathogenic 
                 Ctherm 
                 23S 
                 1419 
               
               
                   
                   
                 -50 
                 
                   thermophiles 
                 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-20 
                 -10 
                 R&amp;G  Campylobacter lari   
                 Clari 
                 16S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-21 
                 -10 
                 R&amp;G  Campylobacter jejuni   
                 Cpjej 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-22 
                 -10 
                 R&amp;G Cp.  upsaliensis   
                 Cpups 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-23 
                 -10 
                 R&amp;G Cp  coli   
                 Cpcoli 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-24 
                 -10 
                 R&amp;G Cp  coli -comp 
                 Cpcolicomp 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-25 
                 -10 
                 R&amp;G  Chlamydia   
                 S-G-Chla-0232-A- 
               
               
                   
                   
                 -50 
                   
                 18 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-26 
                 -10 
                 R&amp;G Chlamydiaceae 
                 S-F-Chlae-0574-a- 
               
               
                   
                   
                 -50 
                   
                 A-18 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-27 
                 -10 
                 R&amp;G Chlamydiales 
                 S-O-Chls-0523-a-A- 
               
               
                   
                   
                 -50 
                   
                 18b 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-28 
                 -10 
                 R&amp;G  Chlamydophila   
                 S-G-Chlph-0583-a- 
               
               
                   
                   
                 -50 
                   
                 A-18 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-29 
                 -10 
                 R&amp;G  Chlamydia pneumoniae   
                 B-Chlapneu 
                 16S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-36 
                 -10 
                 R&amp;G “ Chlamydia psittaci ” group 
                 S-S-Cps-1414-a-A- 
               
               
                   
                   
                 -50 
                   
                 18 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-31 
                 -10 
                 R&amp;G Subgroup of the 
                 Bn9658 
               
               
                   
                   
                 -50 
                 Parachlamydiaceae 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-32 
                 -10 
                 R&amp;G  Chlamydia  ssp. 
                 ChlamyA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-33 
                 -10 
                 R&amp;G  Chlamydia trachomatis   
                 ChltraA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-34 
                 -10 
                 R&amp;G  Canda albicans   
                 Can-alb-2 
                 18S 
                 314-295 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-35 
                 -10 
                 R&amp;G  Canda krusei   
                 Cankru-2 
                 18S 
                 146-169 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-36 
                 -10 
                 R&amp;G  Candida dubliniensis   
                 Can-dub-2 
                 18S 
                 187-206 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-37 
                 -10 
                 R&amp;G  Candida glabrata   
                 Can-gla-2 
                 18S 
                 379-363 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-38 
                 -10 
                 R&amp;G  Candida parapsilosis   
                 Can-para-2 
                 18S 
                 310-291 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-39 
                 -10 
                 R&amp;G  Candida  spp 
                 Can-spp-2 
                 18S 
                 366-347 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-40 
                 -10 
                 R&amp;G  Candida tropicales   
                 Can-trop-3 
                 18S 
                 64-84 
                 NA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-41 
                 -10 
                 
                   Candida lusitaniae 
                 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-42 
                 -10 
                 R&amp;G  Citrobacter freundii   
                 B-cifreu 
                 23S rRNA 
                 542-559 
                 547-564 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-43 
                 -10 
                 R&amp;G  Clostridium botulinum   
                 B-Clobot 
                 16S rRNA 
                 173-194 
                 173-190IV, 181-198 = 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 II 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-44 
                 -10 
                 
                   Clostridium difficile 
                 
                 B-Clodiff 
                 16S rRNA 
                 73-51 
                 38-54 = II; 55-72 = 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 III 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-45 
                 -10 
                 R&amp;G  Clostridium  spp 
                 B-Clospp 
                 16S rRNA 
                 52-35 
                 48-65 = II; 38-54 = 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 II 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-46 
                 -10 
                 R&amp;G  Clostridium perfringens   
                 B-Cloper-Cp2-10 
                 16S rRNA 
                 212-189 
                 199-215 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-47 
                 -10 
                 R&amp;G  Clostridium perfringens   
                 B-Cloper-Cp2-18 
                 16S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-48 
                 -10 
                 
                   Clostridium tetani 
                 
                 B-Clotet 
                 16S rRNA 
                 114-95  
                 91-108 = II; 102-118 = 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 III 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-49 
                 -10 
                 
                   Cryptococcus neoformans 
                 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-50 
                 -10 
                 R&amp;G Enterobacteriaceae 
                 B-EBAC-1791 
                 23S rRNA 
                 1811-1791 
                 1787-1804 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-51 
                 -10 
                 R&amp;G Enterobacteriaceae 
                 B-Entero-1247 
                 16S rRNA 
                 1264-1247 
                 1248-1265 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-52 
                 -10 
                 R&amp;G Enterobacteriaceae 
                 B-Entero + 182 
                 16S rRNA 
                 Sbjct: 201-182 
                 199-215 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-53 
                 -10 
                 R&amp;G  Enterococci   
                 B-Entcoc 
                 16S rRNA 
                 242-225 
                 218-235 = I; 236-252 = 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 II 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-54 
                 -10 
                 R&amp;G  Enterococcus faecalis   
                 B-Ent-alis 
                 16S rRNA 
                 129-146 
                 127-144 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-55 
                 -10 
                 R&amp;G  Enterococcus faecium   
                 B-Ent-ium 
                 16S rRNA 
                 192-212 
                 191-209 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-56 
                 -10 
                 R&amp;G  Escherichia coli   
                 B-Ecol-On 1 
                 16S rRNA 
                 75-95 
                 66-83 = II; 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 73-90 = IV 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-57 
                 -10 
                 R&amp;G Eu-bacteria 
                 Eub 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-58 
                 -10 
                 R&amp;G  Fusarium  spp 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-59 
                 -10 
                 R&amp;G  Gardnerella vaginalis   
                 Garvag 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-60 
                 -10 
                 R&amp;G  Haemophilus influenzae   
                 B-Haeinf-2 
                 16S rRNA 
                 189-167 
                 173-190 = IV; 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 181-198 = II 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-61 
                 -10 
                 R&amp;G  Haemophilus influenzae   
                 B-Haeinf-3 
                 16S rRNA 
                 183-162 
                 163-180 = IV 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-62 
                 -10 
                 R&amp;G  Klebsiella pneumoniae   
                 b-Klepne-2 
                 16S rRNA 
                 445-465 
                 443*460 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-63 
                 -10 
                 R&amp;G  Klebsiella oxytoca   
                 B-Kleboxy 
                 16S rRNA 
                 467-444 
                 446-463 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-64 
                 -10 
                 R&amp;G  Lactobacillus brevis   
                 B-Lacbrev 
                 16S rRNA 
                 84-63 
                 63-80 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-65 
                 -10 
                 R&amp;G  Mycobacterium avium   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-66 
                 -10 
                 R&amp;G  Mycobacterium bovis   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-67 
                 -10 
                 R&amp;G  Mycobacterium chelonae   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-68 
                 -10 
                 R&amp;G  Mycobacterium fortuitum   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-69 
                 -10 
                 R&amp;G  Mycobacterium gordonae   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-70 
                 -10 
                 R&amp;G  Mycobacterium intracellulare   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-71 
                 -10 
                 R&amp;G  Mycobacterium kansasii   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-72 
                 -10 
                 R&amp;G  Mycobacterium malmoense   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-73 
                 -10 
                 R&amp;G  Mycobacterium smegmatis   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-74 
                 -10 
                 R&amp;G  Mycobacterium tuberculosis   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-75 
                 -10 
                 R&amp;G  Mycobacterium xenopi   
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-76 
                 -10 
                 R&amp;G  Legionella pneumophila   
                 B-Legpne 
                 16S rRNA 
                 633-616 
                 614-631 = IV 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-77 
                 -10 
                 R&amp;G  Listeria monocytogenes   
                 Lismon 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-78 
                 -10 
                 R&amp;G  Mycoplasma hominis   
                 Mychom 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-79 
                   
                 R&amp;G  Nocardia  spp. 
               
               
                   
                   
               
               
                   
                 L-01-80 
                 -10 
                 R&amp;G  Proteus mirabili / vulgaris   
                 B-Protmivi 
                 23S rRNA 
                 1835-1818 
                 1823-1839 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-81 
                 -10 
                 R&amp;G Pneumoscystis-1 
                 Pcp-1 
                 18S 
                 1155 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-82 
                 -10 
                 R&amp;G Pneumocystis-2 
                 Pcp-2 
                 18S 
                  845 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-83 
                   
                 R&amp;G  Propionibacterium acnes   
               
               
                   
                   
               
               
                   
                 L-01-84 
                   
                 R&amp;G  Propionibacterium  spp 
               
               
                   
                   
                   
                 (other than Psaer) 
               
               
                   
                   
               
               
                   
                 L-01-85 
                 -10 
                 R&amp;G  Pseudomonas aeruginosa   
                 B-Psaer C 
                 23S rRNA 
                 1526-1508 
                 1509-1526 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-86 
                 -10 
                 R&amp;G  Pseudomonas  spp 
                 Psspp 
                 16S rRNA 
                 79-59 
                 60-077 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-87 
                 -10 
                 R&amp;G Salmonellen 
                 Sal 23S 331 
                 23S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-88 
                 -10 
                 R&amp;G Salmonellen 331 Komp 
                 Komp Sal 23S 331 
                 23S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-89 
                 -10 
                 R&amp;G Salmonellen 
                 Sal 23S 1705 
                 23S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-90 
                 -10 
                 R&amp;G Salmonellen 
                 Sal 23S 1705 Komp 
                 23S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-91 
                 -10 
                 R&amp;G Salmonellen 
                 Sal 23S 544 
                 23S rRNA 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-92 
                 -10 
                 R&amp;G  Salmonella   
                 B-Sal 1686 
                 23S rRNA 
                 1705-1686 
                 1696-1713 = I; 
               
               
                   
                   
                 -50 
                   
                   
                   
                   
                 1678-1695 = III 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-93 
                 -10 
                 R&amp;G  Serratia  spp 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-94 
                 -10 
                 R&amp;G  Serratia marcescens   
                 B-Sermarc 
                 16S rRNA 
                 637-656 
                 639-656 = VI 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-95 
                 -10 
                 R&amp;G  Staphylococcus aureus   
                 B-Staphau 
                 16S rRNA 
                  75-52; 
                 55-72 = III 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-96 
                 -10 
                 R&amp;G Staphylococci 
                 B-Staphspp-2 
                 16S rRNA 
                 769-751 
                 756-773 = IV 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-97 
                 -10 
                 R&amp;G  Stenotrophomonas maltofilia   
                 Stemal-2 
                 16S rRNA 
                 592-612 
                 614-631 = IV 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-98 
                 -10 
                 R&amp;G  Streptococcus agalactiae   
                 B-Straga-2 
                 16S rRNA 
                 416-396 
                 396-412 = IV 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-99 
                 -10 
                 R&amp;G Streptococci 
                 B-Strept-2 
                 16S rRNA 
                 459-439 
                 440-456 = I 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-100 
                 -10 
                 R&amp;G  Streptococcus pneumoniae   
                 B-Strepne-2 
                 16S rRNA 
                 202-178 
                 181-198 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-101 
                 -10 
                 R&amp;G  Streptococcus pyogenes   
                 B-Strpyo-C 
                 16S rRNA 
                 196-217 
                 199-215 = II 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-102 
                 -10 
                 R&amp;G  Ureaplasma urealyticum   
                 Ureure 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-103 
                 -10 
                 R&amp;G Urogenital-Peptostreptococci 
                 Pepure 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
               
                   
                 L-01-104 
                 -10 
                 R&amp;G  Yersinia enterocolitica   
                 Yerent 
               
               
                   
                   
                 -50 
               
               
                   
                   
                 -100 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                   
                   
                 delta Gs 
               
               
                 Loop Diagostics 
                   
                   
                   
                   
                   
                 AT 
                   
                 target: 
               
               
                 Code number 
                   
                 SEQ. ID. NO: 
                 Sequence 5′-3′ 
                   
                 Length 
                 Content 
                 GC content 
                 −21 +/− 2 kcal/mol 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 L-01-1 
                 -10 
                 Beacon 
                 1 
                 TGCCGGATT  ACC ATC CTC TCC CAT   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −21.9 
               
               
                   
                   
                   
                   
                   ACT CTA  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 2 
                 ACC ATC CTC TCC CAT ACT CTA 
                 Beacon 
                 39 
                   
                   
                 54% 
                 ΔG = −0.48 
               
               
                   
                 -100 
                 Target 
                 3 
                 TAG AGT ATG GGA GAG GAT GGT 
               
               
                   
               
               
                 L-01-2 
                 -10 
                 Beacon 
                 4 
                 GCGCG TC CGG TAG CAA GCT ACC TTC 
                 Probe/target 
                 20 
                 9 
                 11 
                 55% 
                 ΔG = −22.1 
               
               
                   
                   
                   
                   
                 CGCGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 5 
                 TC CGG TAG CAA GCT ACC TTC 
                 Beacon 
                 30 
                 9 
                 21 
                 70% 
                 ΔG = −0.94 
               
               
                   
                 -100 
                 Target 
                 6 
                 GAA GGT AGC TTG CTA CCG GA 
               
               
                   
               
               
                 L-01-3 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-4 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-5 
                 -10 
                 Beacon 
                 7 
                 CCGCCGGCGT AC AGA GTT CGT GGT 
                 Probe/target 
                 20 
                 9 
                 11 
                 55% 
                 ΔG = −21.5 
               
               
                   
                   
                   
                   
                 GTC TCC TCGCCCAGCGG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 8 
                 AC AGA GTT CGT GGT GTC TCC 
                 Beacon 
                 41 
                 12 
                 29 
                 71% 
                 ΔG = −0.19 
               
               
                   
                 -100 
                 Target 
                 9 
                 GGA GAC ACC ACG AAC TCT GT 
               
               
                   
               
               
                 L-01-6 
                 -10 
                 Beacon 
                 10 
                 cgtc gcc tac aga gca ggt gac g 
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 ΔG = −20.6 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 11 
                 gcc tac aga gca ggt gac 
                 Beacon 
                 23 
                 8 
                 15 
                 65% 
                 ΔG = −0.86 
               
               
                   
                 -100 
                 Target 
                 12 
                 gtc acc tgc tct gta ggc 
               
               
                   
               
               
                 L-01-7 
                 -10 
                 Beacon 
                 13 
                 ctctga a ctg att gca ttc aat caa ctc agag 
                 Probe/target 
                 25 
                 16 
                 9 
                 36% 
                 ΔG = −21.4 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 14 
                 a ctg att gca ttc aat caa ctc aga 
                 Beacon 
                 32 
                 19 
                 13 
                 41% 
                 ΔG = −0.18 
               
               
                   
                 -100 
                 Target 
                 15 
                 tct gag ttg att gaa tgc aat cag t 
               
               
                   
               
               
                 L-01-8 
                 -10 
                 Beacon 
                 16 
                 TCCGTC tga ttg caa aga atc aca ctc aga 
                 Probe/target 
                 24 
                 15 
                 9 
                 38% 
                 ΔG = −20.9 
               
               
                   
                   
                   
                   
                 GACGGA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 17 
                 tga ttg caa aga atc aca ctc aga 
                 Beacon 
                 36 
                 19 
                 17 
                 47% 
                 ΔG = −0.63 
               
               
                   
                 -100 
                 Target 
                 18 
                 tct gag tgt gat tct ttg caa tca 
               
               
                   
               
               
                 L-01-9 
                 -10 
                 Beacon 
                 19 
                 GCCGCCGGCAT CCA ATG TGG GGG 
                 Probe/target 
                 17 
                 6 
                 11 
                 59% 
                 ΔG = −20.1 
               
               
                   
                   
                   
                   
                 ACC TTC TAGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 20 
                 CCA ATG TGG GGG ACC TTC 
                 Beacon 
                 39 
                   
                   
                 74% 
                 ΔG = −0.70 
               
               
                   
                 -100 
                 Target 
                 21 
                 GAA GGT CCC CCA CAT TGG 
               
               
                   
               
               
                 L-01-10 
                 -10 
                 Beacon 
                 22 
                 TGCCGGATT  CA TGC TTA AGA CGC ACT   
                 Probe/target 
                 20 
                 9 
                 11 
                 50% 
                 ΔG = −20.9 
               
               
                   
                   
                   
                   
                   GCC  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 23 
                 CA TGC TTA AGA CGC ACT GCC 
                 Beacon 
                 39 
                   
                   
                 56% 
                 ΔG = −0.59 
               
               
                   
                 -100 
                 Target 
                 24 
                 GGC AGT GCG TCT TAA GCA TG 
               
               
                   
               
               
                 L-01-11 
                 -10 
                 Beacon 
                 25 
                 TGCCGGATT  CAG CAC TCT GCA AAG   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −20.5 
               
               
                   
                   
                   
                   
                   ACG AAA  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 26 
                 CAG CAC TCT GCA AAG ACG AAA 
                 Beacon 
                 40 
                   
                   
                 53% 
                 ΔG = −0.48 
               
               
                   
                 -100 
                 Target 
                 27 
                 TTT CGT CTT TGC AGA GTG CTG 
               
               
                   
               
               
                 L-01-12 
                 -10 
                 Beacon 
                 28 
                 ACCGCTC  TTT CTT TCC GGA CAA AAG   
                 Probe/target 
                 24 
                 15 
                 9 
                 38% 
                 ΔG = −20.9 
               
               
                   
                   
                   
                   
                   TGC TTT  GAGCGGCT 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 29 
                 TTT CTT TCC GGA CAA AAG TGC TTT 
                 Beacon 
                 39 
                   
                   
                 51% 
                 ΔG = −0.92 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 30 
                 AAA GCA CTT TTG TCC GGA AAG AAA 
               
               
                   
               
               
                 L-01-13 
                 -10 
                 Beacon 
                 31 
                 CGCCTTC  AGA ACC AAG GAT TTC TTT   
                 Probe/target 
                 22 
                 12 
                 10 
                 45% 
                 ΔG = −20.5 
               
               
                   
                   
                   
                   
                   CCG G  GAAGGCG 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 32 
                 AGA ACC AAG GAT TTC TTT CCG G 
                 Beacon 
                   
                   
                   
                   
                 ΔG = −1.07 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 33 
                 CCG GAA AGA AAT CCT TGG TTC T 
                   
                 36 
                   
                   
                 56% 
               
               
                   
               
               
                 L- 
                   
                 Beacon 
                 34 
                 ACGCA  AGAGCCAAGGTTTTCTTTCCG   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −20.2 
               
               
                   
                   
                   
                   
                 CTTGCGT 
                 Hybrid 
               
               
                   
                   
                 probe 
                 35 
                 AGA GCC AAG GTT TTC TTT CCG 
                 Beacon 
                 34 
                   
                   
                 50% 
                 ΔG = −1.05 
               
               
                   
                   
                 sequence 
               
               
                   
                   
                 Target 
                 36 
                 CGG AAA GAA AAC CTT GGC TCT 
               
               
                   
               
               
                 L-01-14 
                 -10 
                 Beacon 
                 37 
                 ACGCTC  G TCA TCC CCC GGC CAT   
                 Probe/target 
                 16 
                 5 
                 11 
                 69% 
                 ΔG = −20.1 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 38 
                 G TCA TCC CCC GGC CAT 
                 Beacon 
                 28 
                   
                   
                 68% 
                 ΔG = −1.00 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 39 
                 ATG GCC GGG GGA TGA C 
               
               
                   
               
               
                 L-01-15 
                 -10 
                 Beacon 
                 40 
                 CGCTC  CGT CAT CCC CCG GCT ATA   
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 ΔG = −20.6 
               
               
                   
                   
                   
                   
                 GGAGCG 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 41 
                 CGT CAT CCC CCG GCT ATA 
                 Beacon 
                 29 
                   
                   
                 69% 
                 ΔG = −0.43 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 42 
                 TAT AGC CGG GGG ATG ACG 
               
               
                   
               
               
                 L-01-16 
                 -10 
                 Beacon 
                 43 
                 CCGCTC  GT CAT CCC CCG GCT GTA   
                 Probe/target 
                 17 
                 6 
                 11 
                 65% 
                 ΔG = −20.6 
               
               
                   
                   
                   
                   
                 GAGCGG 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 44 
                 GT CAT CCC CCG GCT GTA 
                 Beacon 
                 29 
                   
                   
                 72% 
                 ΔG = −0.43 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 45 
                 TAC AGC CGG GGG ATG AC 
               
               
                   
               
               
                 L-01-17 
                 -10 
                 Beacon 
                 46 
                 GCCGCCGGCGT  CGT CAT CCC CCG   
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 ΔG = −20.0 
               
               
                   
                   
                   
                   
                   ATC GTA  TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 47 
                 CGT CAT CCC CCG ATC GTA 
                 Beacon 
                 41 
                   
                   
                 73% 
                 ΔG = −1.11 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 48 
                 TAC GAT CGG GGG ATG ACG 
               
               
                   
               
               
                 L-01-18 
                 -10 
                 Beacon 
                 49 
                 GCCGCCGGCGT  CGT CAT CCC CCG ACT   
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 ΔG = −20.3 
               
               
                   
                   
                   
                   
                   GTA  TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                   
                 probe 
                 50 
                 CGT CAT CCC CCG ACT GTA 
                 Beacon 
                 41 
                   
                   
                 76% 
                 ΔG = −1.11 
               
               
                   
                   
                 sequence 
               
               
                   
                   
                 Target 
                 51 
                 TAC AGT CGG GGG ATG ACG 
               
               
                   
               
               
                 L-01-19 
                 -10 
                 Beacon 
               
               
                   
                 -50 
                 Probe 
                 52 
                 GCC CTA AGC GTC CTT CCA 
               
               
                   
                 -100 
                 Target 
               
               
                   
               
               
                 L-01-20 
                 -10 
                 Beacon 
                 53 
                 ACGCTC  GAA GTG TAA GCA ACT AAA T   
                 Probe/target 
                 19 
                 13 
                 6 
                 32% 
                 −14 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 54 
                 GAA GTG TAA GCA ACT AAA T 
                 Beacon 
                 31 
                   
                   
                 45% 
                 −0.78 
               
               
                   
                 -100 
                 Target 
                 55 
                 A TTT AGT TGC TTA CAC TTC 
               
               
                   
               
               
                 L-01-21 
                 -10 
                 Beacon 
                 56 
                 ACGCTC A GC TAA CCA CTT ATA CCG   
                 Probe/target 
                 18 
                 10 
                 8 
                 44% 
                 −17.3 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 57 
                 AGC TAA CCA CTT ATA CCG 
                 Beacon 
                 30 
                   
                   
                 53% 
                 −0.67 
               
               
                   
                 -100 
                 Target 
                 58 
                 CGG TAT AAG TGG TTA GCT 
               
               
                   
               
               
                 L-01-22 
                 -10 
                 Beacon 
                 59 
                 CCGCTC  CGT GTG TCG CCC TAG GCG   
                 Probe/target 
                 20 
                 7 
                 13 
                 65% 
                 −25.4 
               
               
                   
                   
                   
                   
                   TA  GAGCGG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 60 
                 CGT GTG TCG CCC TAG GCG TA 
                 Beacon 
                 32 
                   
                   
                 72% 
                 −0.84 
               
               
                   
                 -100 
                 Target 
                 61 
                 TA CGC CTA GGG CGA CAC ACG 
               
               
                   
               
               
                 L-01-23 
                 -10 
                 Beacon 
                 62 
                 CCGCTC  TCG ATG GCA TCA GGG GTT   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 −20.7 
               
               
                   
                   
                   
                   
                 GAGCGG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 63 
                 TCG ATG GCA TCA GGG GTT 
                 Beacon 
                 30 
                   
                   
                 67% 
                 −0.82 
               
               
                   
                 -100 
                 Target 
                 64 
                 AAC CCC TGA TGC CAT CGA 
               
               
                   
               
               
                 L-01-24 
                 -10 
                 Beacon 
                 65 
                 not required, competitor is not labelled 
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 −22.0 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 66 
                 TCG ACG GCA TCA GGG GTT 
                 Beacon 
               
               
                   
                 -100 
                 Target 
                 67 
                 AAC CCC TGA TGC CGT CGA 
               
               
                   
               
               
                 L-01-25 
                 -10 
                 Beacon 
                 68 
                 ACGCCGGCGT  TAG CTG ATA TCA CAT   
                 Probe/target 
                 18 
                 12 
                 6 
                 33% 
                 −14.4 
               
               
                   
                   
                   
                   
                   AGA  TCGCCCAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 69 
                 TAG CTG ATA TCA CAT AGA 
                 Beacon 
                 39 
                   
                   
                 59% 
                 −0.06 
               
               
                   
                 -100 
                 Target 
                 70 
                 TCT ATG TGA TAT CAG CTA 
               
               
                   
               
               
                 L-01-26 
                 -10 
                 Beacon 
                 71 
                 TCCGCCGGCGT  CTT TCC GCC TAC ACG   
                 Probe/target 
                 18 
                 6 
                 12 
                 67% 
                 −22.0 
               
               
                   
                   
                   
                   
                   CCC  TCGCCCAGCGGA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 72 
                 CTT TCC GCC TAC ACG CCC 
                 Beacon 
                 41 
                   
                   
                 73% 
                 −1.22 
               
               
                   
                 -100 
                 Target 
                 73 
                 GGG CGT GTA GGC GGA AAG 
               
               
                   
               
               
                 L-01-27 
                 -10 
                 Beacon 
                 74 
                 TCCGCCGGCGT  CCT CCG TAT TAC CGC   
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 −20.5 
               
               
                   
                   
                   
                   
                   AGC  TCGCCCAGCGGA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 75 
                 CCT CCG TAT TAC CGC AGC 
                 Beacon 
                 41 
                   
                   
                 71% 
                 −1.22 
               
               
                   
                 -100 
                 Target 
                 76 
                 GCT GCG GTA ATA CGG AGG 
               
               
                   
               
               
                 L-01-28 
                 -10 
                 Beacon 
                 77 
                 ACGCCGGCGT  CTA ACT TTC CTT TCC   
                 Probe/target 
                 18 
                 9 
                 9 
                 50% 
                 −17.3 
               
               
                   
                   
                   
                   
                   GCC  TCGCCCAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 78 
                 CTA ACT TTC CTT TCC GCC 
                 Beacon 
                 39 
                   
                   
                 64% 
                 −0.06 
               
               
                   
                 -100 
                 Target 
                 79 
                 GGC GGA AAG GAA AGT TAG 
               
               
                   
               
               
                 L-01-29 
                 -10 
                 Beacon 
                 80 
                 TCCACCGGCGT  CTC TTC CTC AAC CGA   
                 Probe/target 
                 18 
                 9 
                 9 
                 50% 
                 −16.4 
               
               
                   
                   
                   
                   
                   AAG  TCGCCCAGTGGA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 81 
                 CTC TTC CTC AAC CGA AAG 
                 Beacon 
                 41 
                   
                   
                 61% 
               
               
                   
                 -100 
                 Target 
                 82 
                 CTT TCG GTT GAG GAA GAG 
               
               
                   
               
               
                 L-01-30 
                 -10 
                 Beacon 
                 83 
                 TCAGCCGGCGT  AAG GCA AAA CCA ACT   
                 Probe/target 
                 18 
                 9 
                 9 
                 50% 
                 −18.8 
               
               
                   
                   
                   
                   
                   CCC  TCGCCCAGCTGA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 84 
                 AAG GCA AAA CCA ACT CCC 
                 Beacon 
                 41 
                   
                   
                 61% 
                 −0.02 
               
               
                   
                 -100 
                 Target 
                 85 
                 GGG AGT TGG TTT TGC CTT 
               
               
                   
               
               
                 L-01-31 
                 -10 
                 Beacon 
                 86 
                 CCGCCGGCGT  TCC GTT TTC TCC GCC   
                 Probe/target 
                 18 
                 8 
                 10 
                 50% 
                 −19.7 
               
               
                   
                   
                   
                   
                   TAC  TCGCCCAGCGG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 87 
                 TCC GTT TTC TCC GCC TAC 
                 Beacon 
                 39 
                   
                   
                 69% 
                 −0.40 
               
               
                   
                 -100 
                 Target 
                 88 
                 GTA GGC GGA GAA AAC GGA 
               
               
                   
               
               
                 L-01-32 
                 -10 
                 Beacon 
                 89 
                 TCCGCCGGCGT  GCT CCC CTT GCT TTC   
                 Probe/target 
                 18 
                 6 
                 12 
                 61% 
                 −21.7 
               
               
                   
                   
                   
                   
                   GCG  TCGCCCAGCGGA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 90 
                 GCT CCC CTT GCT TTC GCG 
                 Beacon 
                 42 
                   
                   
                 69% 
                 −1.22 
               
               
                   
                 -100 
                 Target 
                 91 
                 CGC GAA AGC AAG GGG AGC 
               
               
                   
               
               
                 L-01-33 
                 -10 
                 Beacon 
                 92 
                 ACGCTC  TCG GAT GCC CAA ATA TCG   
                 Probe/target 
                 18 
                 9 
                 9 
                 50% 
                 −18.4 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 93 
                 TCG GAT GCC CAA ATA TCG 
                 Beacon 
                 30 
                   
                   
                 57% 
                 −0.44 
               
               
                   
                 -100 
                 Target 
                 94 
                 CGA TAT TTG GGC ATC CGA 
               
               
                   
               
               
                 L-01-34 
                 -10 
                 Beacon 
                 95 
                 GG aa tgg cta ccc aga agg aaa CCATTCC 
                 Probe/target 
                 20 
                 11 
                 9 
                 45% 
                 ΔG = −19.7 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 96 
                 aa tgg cta ccc aga agg aaa 
                 Beacon 
                 29 
                   
                 15 
                 52% 
                 ΔG = −0.57 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 97 
                 ttt cct tct ggg tag cca tt 
               
               
                   
               
               
                 L-01-35 
                 -10 
                 Beacon 
                 98 
                 CCGCTC tgt att agc tct aga ttt cca cgg 
                 Probe/target 
                 24 
                 15 
                 9 
                 38% 
                 ΔG = −21.9 
               
               
                   
                   
                   
                   
                 GAGCGG 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 99 
                 tgt att agc tct aga ttt cca cgg 
                 Beacon 
                 36 
                   
                 19 
                 53% 
                 ΔG = −0.56 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 100 
                 ccg tgg aaa tct aga gct aat aca 
               
               
                   
               
               
                 L-01-36 
                 -10 
                 Beacon 
                 101 
                 GTTTGcc ccg aaa gag taa ctt gca 
                 Probe/target 
                 20 
                 10 
                 10 
                 50% 
                 ΔG = −19.8 
               
               
                   
                   
                   
                   
                 GGCAAAC 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 102 
                 cc ccg aaa gag taa ctt gca 
                 Beacon 
                 32 
                   
                 16 
                 50% 
                 ΔG = −0.55 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 103 
                 tgc aag tta ctc ttt cgg gg 
               
               
                   
               
               
                 L-01-37 
                 -10 
                 Beacon 
                 104 
                 GCCGCCGGCGT gg cca ccc agg ccc aaa 
                 Probe/target 
                 17 
                 5 
                 12 
                 71% 
                 ΔG = −22.5 
               
               
                   
                   
                   
                   
                 TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 105 
                 gg cca ccc agg ccc aaa 
                 Beacon 
                 40 
                   
                 32 
                 80% 
                 ΔG = −2.30 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 106 
                 ttt ggg cct ggg tgg cc 
               
               
                   
               
               
                 L-01-38 
                 -10 
                 Beacon 
                 107 
                 GCCGCCGGCGT gc caa aaa ggc tag cca 
                 Probe/target 
                 20 
                 10 
                 10 
                 50% 
                 ΔG = −20.9 
               
               
                   
                   
                   
                   
                 gaa TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 108 
                 gc caa aaa ggc tag cca gaa 
                 Beacon 
                 43 
                   
                 30 
                 70% 
                 ΔG = −1.76 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 109 
                 ttc tgg cta gcc ttt ttg gc 
               
               
                   
               
               
                 L-01-39 
                 -10 
                 Beacon 
                 110 
                 ACGC gct tgg ctg gcc ggt c GCGT 
                 Probe/target 
                 16 
                 4 
                 12 
                 75% 
                 ΔG = −21.1 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 111 
                 g acc ggc cag cca agc 
                 Beacon 
                 24 
                   
                 18 
                 75% 
                 ΔG = −0.90 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 112 
                 gct tgg ctg gcc ggt c 
               
               
                   
               
               
                 L-01-40 
                 -10 
                 Beacon 
                 113 
                 ACCGCCGGCGT tac gca tca gaa aga tgg 
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −20.7 
               
               
                   
                   
                   
                   
                 acc TCGCCCAGCGGT 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 114 
                 tac gca tca gaa aga tgg acc 
                 Beacon 
                 44 
                   
                 28 
                 64% 
                 ΔG = −1.03 
               
               
                   
                   
                 sequence 
               
               
                   
                 -100 
                 Target 
                 115 
                 GGT CCA TCT TTC TGA TGC GTA 
               
               
                   
               
               
                 L-01-41 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-42 
                 -10 
                 Beacon 
                 116 
                 TGCCGGATT  CTAC TTG TTA GGT GAC   
                 Probe/target 
                 21 
                 10 
                 11 
                 48% 
                 ΔG = −20.4 
               
               
                   
                   
                   
                   
                   TGC GT  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 117 
                 C TAC TTG TTA GGT GAC TGC GT 
                 Beacon 
                 40 
                   
                   
                 53% 
                 ΔG = −0.48 
               
               
                   
                 -100 
                 Target 
                 118 
                 AC GCA GTC ACC TAA CAA GTA G 
               
               
                   
               
               
                 L-01-43 
                 -10 
                 Beacon 
                 119 
                 TCTTG TAG T GC CGT TTC ATG CGA 
                 Probe/target 
                 22 
                 12 
                 10 
                 45% 
                 ΔG = −20.7 
               
               
                   
                   
                   
                   
                 AAC TAC AA GA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 120 
                 GC CGT TTC ATG CGA AAC TAC AA 
                 Beacon 
                 33 
                   
                   
                 42% 
                 ΔG = −0.79 
               
               
                   
                 -100 
                 Target 
                 121 
                 TT GTA GTT TCG CAT GAA ACG GC 
               
               
                   
               
               
                 L-01-44 
                 -10 
                 Beacon 
                 122 
                 GCCGCCGGCGT CGAAG TAA ATC GCT 
                 Probe/target 
                 23 
                 13 
                 10 
                 43% 
                 ΔG = −20.8 
               
               
                   
                   
                   
                   
                 CAA CTT GCA TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 123 
                 CGA AGT AAA TCG CTC AAC TTG CA 
                 Beacon 
                 46 
                   
                 30 
                 65% 
                 ΔG = −1.33 
               
               
                   
                 -100 
                 Target 
                 124 
                 TGC AAG TTG AGC GAT TTA CTT CG 
               
               
                   
               
               
                 L-01-45 
                 -10 
                 Beacon 
                 125 
                 CGCTCA CAC CCG TCC GCC GCT AAT 
                 Probe/target 
                 18 
                 6 
                 12 
                 67% 
                 ΔG = −22.0 
               
               
                   
                   
                   
                   
                 GAGCG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 126 
                 CAC CCG TCC GCC GCT AAT 
                 Beacon 
                 29 
                   
                   
                 69% 
                 ΔG = −0.39 
               
               
                   
                 -100 
                 Target 
                 127 
                 ATT AGC GGC GGA CGG GTG 
               
               
                   
               
               
                 L-01-46 
                 -10 
                 Beacon 
                 128 
                 GCCGCCGGCGT  G ATT GCT CCT TTG   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −20.9 
               
               
                   
                   
                   
                   
                   GTT GAA TGA TG  TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 129 
                 G ATT GCT CCT TTG GTT GAA TGA TG 
                 Beacon 
                 44 
                   
                   
                 68% 
                 ΔG = −1.22 
               
               
                   
                 -100 
                 Target 
                 130 
                 CA TCA TTC AAC CAA AGG AGC AAT C 
               
               
                   
               
               
                 L-01-47 
                 -10 
                 Beacon 
                 131 
                 ACGCTC  GGT TGA ATG ATG ATG CCA T   
                 Probe/target 
                 19 
                 10 
                 9 
                 42% 
                 ΔG = −21.2 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 132 
                 GGT TGA ATG ATG ATG CCA TCT TT 
               
               
                   
                 -100 
                 Target 
                 133 
                 AA AGA TGG CAT CAT CAT TCA ACC 
                 Beacon 
                 31 
                   
                   
                 52% 
                 ΔG = −0.16 
               
               
                   
               
               
                 L-01-48 
                 -10 
                 Beacon 
                 134 
                 GCGGAC CT GTG TTA CTC ACC CGT 
                 Probe/target 
                 20 
                 8 
                 12 
                 42% 
                 ΔG = −21.6 
               
               
                   
                   
                   
                   
                 CCG C 
                 Hybrid 
               
               
                   
                 -50 
                 probe 
                 135 
                 CT GTG TTA CTC ACC CGT CCG 
               
               
                   
                 -100 
                 Target 
                 136 
                 CGG ACG GGT GAG TAA CAC AG 
                 Beacon 
                 27 
                   
                 18 
                 52% 
                 ΔG = −1.15 
               
               
                   
               
               
                 L-01-49 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-50 
                 -10 
                 Beacon 
                 137 
                 TGCCGGATT   TT CGT GTT TGC ACA GTG   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −21.1 
               
               
                   
                   
                   
                   
                   CTG T  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 138 
                 TT CGT GTT TGC ACA GTG CTG T 
                 Beacon 
                 40 
                   
                   
                 53% 
                 ΔG = −0.48 
               
               
                   
                 -100 
                 Target 
                 139 
                 A CAG CAC TGT GCA AAC ACG AA 
               
               
                   
               
               
                 L-01-51 
                 -10 
                 Beacon 
                 140 
                 TGCCGGATT  TCT CGC GAG GTC GCT   
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 ΔG = −21.0 
               
               
                   
                   
                   
                   
                   TCT  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 141 
                 TCT CGC GAG GTC GCT TCT 
               
               
                   
                 -100 
                 Target 
                 142 
                 AGA AGC GAC CTC GCG AGA 
                 Beacon 
                   
                   
                   
                   
                 ΔG = −0.80 
               
               
                   
               
               
                 L-01-52 
                 -10 
                 Beacon 
                 143 
                 TGCCGGATT  CCC CCW CTT TGG TCT   
                 Probe/target 
                 20 
                 8 
                 12 
                 60% 
                 ΔG = −20.4 
               
               
                   
                   
                   
                   
                   TGC GA  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 144 
                 CCC CCW CTT TGG TCT TGC GA 
               
               
                   
                 -100 
                 Target 
                 145 
                 TC GCA AGA CCA AAG WGG GGG 
                 Beacon 
                 39 
                   
                   
                 59% 
                 ΔG = −0.59 
               
               
                   
               
               
                 L-01-53 
                 -10 
                 Beacon 
                 146 
                 TGCCGGATT  ATC CAT CAG CGA CAC   
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 ΔG = −20.5 
               
               
                   
                   
                   
                   
                   CCG  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 147 
                 ATC CAT CAG CGA CAC CCG 
               
               
                   
                 -100 
                 Target 
                 148 
                 CGG GTG TCG CTG ATG GAT 
                 Beacon 
                 38 
                   
                   
                 58% 
                 ΔG = −0.80 
               
               
                   
               
               
                 L-01-54 
                 -10 
                 Beacon 
                 149 
                 TGCCGGATT  CCC TCT GAT GGG TAG   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 ΔG = −19.2 
               
               
                   
                   
                   
                   
                   GTT  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 150 
                 CCC TCT GAT GGG TAG GTT 
               
               
                   
                 -100 
                 Target 
                 151 
                 AAC CTA CCC ATC AGA GGG 
                 Beacon 
                 37 
                   
                   
                 57% 
                 ΔG = −0.80 
               
               
                   
               
               
                 L-01-55 
                 -10 
                 Beacon 
                 152 
                 GCCGCCGGCGT  TTC AAA TCA AAA CCA   
                 Probe/target 
                 24 
                 15 
                 9 
                 38% 
                 ΔG = −20.0 
               
               
                   
                   
                   
                   
                   TGC GGT TTC  TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 153 
                 TTC AAA TCA AAA CCA TGC GGT TTC 
               
               
                   
                 -100 
                 Target 
                 154 
                 GAA ACC GCA TGG TTT TGA TTT GAA 
                 Beacon 
                 47 
                   
                   
                 62% 
                 ΔG = −9.42 
               
               
                   
               
               
                 L-01-56 
                 -10 
                 Beacon 
                 155 
                 TGCCGGATT  GGA AGA AGC TTG CTT   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −20.3 
               
               
                   
                   
                   
                   
                   CTT TGC  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 156 
                 GGA AGA AGC TTG CTT CTT TGC 
               
               
                   
                 -100 
                 Target 
                 157 
                 GCA AAG AAG CAA GCT TCT TCC 
                 Beacon 
                 40 
                   
                   
                 53% 
                 ΔG = −1.80 
               
               
                   
               
               
                 L-01-57 
                 -10 
                 Beacon 
                 158 
                 CGCTC  GCT GCC TCC CGT AGG AGT   
                 Probe/target 
                 18 
                 6 
                 12 
                 67% 
                 −23.5 
               
               
                   
                   
                   
                   
                 GAGCG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 159 
                 GCT GCC TCC CGT AGG AGT 
                 Beacon 
                 28 
                   
                   
                 71% 
                 −0.94 
               
               
                   
                 -100 
                 Target 
                 160 
                 ACT CCT ACG GGA GGC AGC 
               
               
                   
               
               
                 L-01-58 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-59- 
                 10 
                 Beacon 
                 161 
                 ACGCTC  CAC CAT GAA GCA ACC CGT   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 −19.5 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 162 
                 CAC CAT GAA GCA ACC CGT 
                 Beacon 
                 30 
                   
                   
                 60% 
                 −0.50 
               
               
                   
                 -100 
                 Target 
                 163 
                 ACG GGT TGC TTC ATG GTG 
               
               
                   
               
               
                 L-01-60 
                 -10 
                 Beacon 
                 164 
                 ACCCGCTA  TT CCG ATA ATA CGC GGT   
                 Probe/target 
                 23 
                 13 
                 10 
                 43% 
                 ΔG = −21.4 
               
               
                   
                   
                   
                   
                   ATT AGC  GGGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 165 
                 TT CCG ATA ATA CGC GGT ATT AGC 
               
               
                   
                 -100 
                 Target 
                 166 
                 GCT AAT ACC GCG TAT TAT CGG AA 
                 Beacon 
                 35 
                   
                   
                 51% 
                 ΔG = −1.18 
               
               
                   
               
               
                 L-01-61 
                 -10 
                 Beacon 
                 167 
                 CGGTGCTC  TA ATA CGC GGT ATT AGC   
                 Probe/target 
                 22 
                 12 
                 10 
                 45% 
                 αG = −20.3 
               
               
                   
                   
                   
                   
                   GAC AG  AGAGCACCG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 168 
                 TA ATA CGC GGT ATT AGC GAC AG 
               
               
                   
                 -100 
                 Target 
                 169 
                 CT GTC GCT AAT ACC GCG TAT AT 
                 Beacon 
                 39 
                   
                   
                 56% 
                 ΔG = −1.76 
               
               
                   
               
               
                 L-01-62 
                 -10 
                 Beacon 
                 170 
                 ACGCCGGCGT AGG TTA TTA ACC TCA 
                 Probe/target 
                 21 
                 12 
                 9 
                 43% 
                 ΔG = −19.8 
               
               
                   
                   
                   
                   
                 TCG CCT TCGCCCAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 171 
                 AGG TTA TTA ACC TCA TCG CCT 
               
               
                   
                 -100 
                 Target 
                 172 
                 AGG CGA TGA GGT TAA TAA CCT 
                 Beacon 
                 40 
                   
                   
                 63% 
                 ΔG = −0.92 
               
               
                   
               
               
                 L-01-63 
                 -10 
                 Beacon 
                 173 
                 GGAAGGGATAT AGG TTA TTA ACC TCA 
                 Probe/target 
                 24 
                 13 
                 11 
                 46% 
                 ΔG = −20.7 
               
               
                   
                   
                   
                   
                 CTC CCT TCC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 174 
                 AGG TTA TTA ACC TCA CTC CCT TCC 
               
               
                   
                 -100 
                 Target 
                 175 
                 GGA AGG GAG TGA GGT TAA TAA CCT 
                 Beacon 
                 35 
                   
                 16 
                 46% 
                 ΔG = −1.02 
               
               
                   
               
               
                 L-01-64 
                 -10 
                 Beacon 
                 176 
                 CGC TCAT TCA ACG GAA GCT CGT TCG 
                 Probe/target 
                 22 
                 11 
                 11 
                 50% 
                 ΔG = −21.5 
               
               
                   
                   
                   
                   
                 ATGAGCG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 177 
                 TCAT TCA ACG GAA GCT CGT TCG 
               
               
                   
                 -100 
                 Target 
                 178 
                 CGAAC GAGCTTCCGT TGAATGA 
                 Beacon 
                 31 
                   
                   
                 48% 
                 ΔG = −0.95 
               
               
                   
               
               
                 L-01-65 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-66 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-67 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-68 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-69 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-70 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-71 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-72 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-73 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-74 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-75 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-76 
                 -10 
                 Beacon 
                 179 
                 TGCCGGATT  ATC TGA CCG TCC CAG   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 ΔG = −19.9 
               
               
                   
                   
                   
                   
                   GTT  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 180 
                 ATC TGA CCG TCC CAG GTT 
               
               
                   
                 -100 
                 Target 
                 181 
                 AAC CTG GGA CGG TCA GAT 
                 Beacon 
                 37 
                   
                   
                 57% 
                 ΔG = −0.80 
               
               
                   
               
               
                 L-01-77 
                 -10 
                 Beacon 
                 182 
                 ACGCTC  ATA AGA TGT GGC GCA TGC   
                 Probe/target 
                 18 
                 9 
                 9 
                 50% 
                 −19.3 
               
               
                   
                   
                   
                   
                 GAGCT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 183 
                 ATA AGA TGT GGC GCA TGC 
                 Beacon 
                 30 
                   
                   
                 57% 
                 −0.64 
               
               
                   
                 -100 
                 Target 
                 184 
                 GCA TGC GCC ACA TCT TAT 
               
               
                   
               
               
                 L-01-78 
                 -10 
                 Beacon 
                   
                 to be determined 
                   
                   
                 0 
                   
                   
                 −19.0 
               
               
                   
                 -50 
                 Probe 
                 185 
                 ATT GCT AAC CTC GCT CGA 
                   
                   
                   
                   
                   
                 −0.40 
               
               
                   
                 -100 
                 Target 
                 186 
                 TCG AGC GAG GTT AGC AAT 
               
               
                   
               
               
                 L-01-79 
                   
                   
                   
                   
                   
                   
                 0 
               
               
                   
               
               
                 L-01-80 
                 -10 
                 Beacon 
                 187 
                 GGC GTC ACA CCG G AT ACG 
                 Probe/target 
                 18 
                 6 
                 12 
                 67% 
                 ΔG = −20.8 
               
               
                   
                   
                   
                   
                 TAGTGCTACGCC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 188 
                 GGC GTC ACA CCG G AT ACG 
               
               
                   
                 -100 
                 Target 
                 189 
                 CCGT ATC CGG TGT GAC GCC 
                 Beacon 
                 30 
                   
                   
                 63% 
                 ΔG = −0.84 
               
               
                   
               
               
                 L-01-81 
                 -10 
                 Beacon 
                 190 
                 ACTC  GGC TTC ATG CCA ACA GTC   
                 Probe/target 
                 21 
                 11 
                 10 
                 57% 
                 −20.2 
               
               
                   
                   
                   
                   
                 
                   GAGT 
                 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 191 
                 GGC TTC ATG CCA ACA GTC 
                 Beacon 
                 25 
                   
                   
                 56% 
                 −0.45 
               
               
                   
                 -100 
                 Target 
                 192 
                 GAC TGT TGG CAT GAA GCC 
               
               
                   
               
               
                 L-01-82 
                 -10 
                 Beacon 
                 193 
                 GACAC  CAT AAG ATG CCG AGC GAG   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 −19.2 
               
               
                   
                   
                   
                   
                 GTGTC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 194 
                 CAT AAG ATG CCG AGC GAG 
                 Beacon 
                 28 
                   
                   
                 57% 
                 −0.11 
               
               
                   
                 -100 
                 Target 
                 195 
                 CTC GCT CGG CAT CTT ATG 
               
               
                   
               
               
                 L-01-83 
                   
                   
                   
                   
                   
                 0 
               
               
                   
               
               
                 L-01-84 
                   
                   
                   
                   
                   
                 0 
               
               
                   
               
               
                 L-01-85 
                 -10 
                 Beacon 
                 196 
                 ACCGCCGGCGT  A AGA CGA CTC GTC   
                 Probe/target 
                 20 
                 10 
                 10 
                 50% 
                 ΔG = −20.3 
               
               
                   
                   
                   
                   
                   ATC ACC T  TCGCCCAGCGGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 197 
                 A AGA CGA CTC GTC ATC ACC T 
                   
                 42 
                   
                   
                 67% 
                 ΔG = −1.13 
               
               
                   
                 -100 
                 Target 
                 198 
                 A GGT GAT GAC GAGTCG TCT T 
                 Beacon 
               
               
                   
               
               
                 L-01-86 
                 -10 
                 Beacon 
                 199 
                 GCCGCCGGCGT  GGC AGA TTC CTA   
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −21.2 
               
               
                   
                   
                   
                   
                   GGC ATT ACT  TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 200 
                 GGC AGA TTC CTA GGC ATT ACT 
               
               
                   
                 -100 
                 Target 
                 201 
                 AGT AAT GCC TAG GAA TCT GCC 
                 Beacon 
                 44 
                   
                 30 
                 68% 
                 ΔG = −1.65 
               
               
                   
               
               
                 L-01-87 
                 -10 
                 Beacon 
                 202 
                 AGCTC  TGC GCT TTT GTG TAC GGG   
                 Probe/target 
                 21 
                 10 
                 11 
                 57% 
                 −25.3 
               
               
                   
                   
                   
                   
                   GCT  GAGCT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 203 
                 TGC GCT TTT GTG TAC GGG GCT 
                 Beacon 
                 31 
                   
                   
                 58% 
                 −0.34 
               
               
                   
                 -100 
                 Target 
                 204 
                 AGC CCC GTA CAC AAA AGC GCA 
               
               
                   
               
               
                 L-01-88 
                 −10 
                 Beacon 
                   
                 not required, competitor is not labelled 
                 Probe/target 
                 18 
                 7 
                 11 
                 61% 
                 −18.8 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 205 
                 G TGCA TTT GTG TAC GGG GC 
                 Beacon 
               
               
                   
                 -100 
                 Target 
                 206 
                 AGC CCC GTA CAC AAA AGC GCA 
               
               
                   
               
               
                 L-01-89 
                 -10 
                 Beacon 
                 207 
                 CGCTC  CTT CAC CTA CGT GTC AGC G   
                 Probe/target 
                 19 
                 8 
                 11 
                 58% 
                 −21.1 
               
               
                   
                   
                   
                   
                 GAGCG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 208 
                 CTT CAC CTA CGT GTC AGC G 
                 Beacon 
                 29 
                   
                   
                 66% 
                 −0.78 
               
               
                   
                 -100 
                 Target 
                 209 
                 C GCT GAC ACG TAG GTG AAG 
               
               
                   
               
               
                 L-01-90 
                 -10 
                 Beacon 
                   
                 not required, competitor is not labelled 
                 Probe/target 
                 20 
                 10 
                 10 
                 50% 
                 −9.6 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 −50 
                 Probe 
                 210 
                 T CAC CTA CAT ATC AGC GTG C 
                 Beacon 
                   
                   
                   
                   
                 −0.26 
               
               
                   
                 −100 
                 Target 
                 211 
                 C GCT GAC ACG TAG GTG AAG A 
               
               
                   
               
               
                 L-01-91 
                 -10 
                 Beacon 
                   
                 ? 
                 Probe/target 
                 18 
                 9 
                 9 
                 50% 
               
               
                   
                   
                   
                   
                   
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 212 
                 GTT TAC CTG TGT GAC TGC 
                 Beacon 
               
               
                   
                 -100 
                 Target 
                   
                 0 
               
               
                   
               
               
                 L-01-92 
                 -10 
                 Beacon 
                 213 
                 TGCCGGATT  CTT CAC CTA CGT GTC   
                 Probe/target 
                 19 
                 8 
                 11 
                 58% 
                 ΔG = −21.1 
               
               
                   
                   
                   
                   
                   AGC G  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 214 
                 CTT CAC CTA CGT GTC AGC G 
               
               
                   
                 -100 
                 Target 
                 215 
                 C GCT GAC ACG TAG GTG AAG 
                 Beacon 
                 38 
                   
                   
                 58% 
                 ΔG = −0.69 
               
               
                   
               
               
                 L-01-93 
                 -10 
                   
                   
                   
                   
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-94 
                 -10 
                 Beacon 
                 216 
                 GCCGCCGGCGT CG AGA CTC TAG CTT 
                 Probe/target 
                 20 
                 9 
                 11 
                 55% 
                 ΔG = −21.8 
               
               
                   
                   
                   
                   
                 GCC AGT TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 217 
                 CG AGA CTC TAG CTT GCC AGT 
               
               
                   
                 -100 
                 Target 
                 218 
                 ACT GGC AAG CTA GAG TCT CG 
                 Beacon 
                 43 
                   
                   
                 72% 
                 ΔG = −1.76 
               
               
                   
               
               
                 L-01-95 
                 -10 
                 Beacon 
                 219 
                 TGCCGGATT  TTC TCG TCC GTT CGC   
                 Probe/target 
                 24 
                 10 
                 14 
                 58% 
                 ΔG = −20.7 
               
               
                   
                   
                   
                   
                   TCG ACT TGC  AATCCCGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 220 
                 TTC TCG TCC GTT CGC TCG ACT TGC 
               
               
                   
                 -100 
                 Target 
                 221 
                 GCA AGT CGA GCG AAC GGA CGA GAA 
                 Beacon 
                 43 
                   
                   
                 58% 
                 ΔG = −0.22 
               
               
                   
               
               
                 L-01-96 
                 -10 
                 Beacon 
                 222 
                 GCAAC TT TCG CAC ATC AGC GTC AGT 
                 Probe/target 
                 21 
                 11 
                 10 
                 48% 
                 ΔG = −20.9 
               
               
                   
                   
                   
                   
                 T GC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 223 
                 TT TCG CAC ATC AGC GTC AGT T 
               
               
                   
                 -100 
                 Target 
                 224 
                 A ACT GAC GCT GAT GTG CGA AA 
                 Beacon 
                 28 
                   
                   
                 54% 
                 ΔG = −0.84 
               
               
                   
               
               
                 L-01-97 
                 -10 
                 Beacon 
                 225 
                 CCC TCT ACC ACA CTC TAG TCG GGT 
                 Probe/target 
                 21 
                 9 
                 12 
                 52% 
                 ΔG = −21.2 
               
               
                   
                   
                   
                   
                 AGA GGG 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 226 
                 CCC TCT ACC ACA CTC TAG TCG 
               
               
                   
                 -100 
                 Target 
                 227 
                 CGA CTA GAG TGT GGT AGA GGG 
                 Beacon 
                 30 
                   
                   
                 57% 
                 ΔG = −1.63 
               
               
                   
               
               
                 L-01-98 
                 -10 
                 Beacon 
                 228 
                 GCCGCCGGCGT  ACT CCT ACC AAC GTT   
                 Probe/target 
                 21 
                 10 
                 11 
                 48% 
                 ΔG = −20.5 
               
               
                   
                   
                   
                   
                   CTT CTC  TCGCCCAGCGGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 229 
                 ACT CCT ACC AAC GTT CTT CTC 
               
               
                   
                 -100 
                 Target 
                 230 
                 GAG AAG AAC GTT GGT AGG AGT 
                 Beacon 
                 45 
                   
                   
                 67% 
                 ΔG = −0.79 
               
               
                   
               
               
                 L-01-99 
                 -10 
                 Beacon 
                 231 
                 GGCCTTC GCC GTC CCT TTC TGG TTA 
                 Probe/target 
                 21 
                 10 
                 11 
                 52% 
                 ΔG = −22.3 
               
               
                   
                   
                   
                   
                 GTT GAAGGCC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 232 
                 GCC GTC CCT TTC TGG TTA GTT 
               
               
                   
                 -100 
                 Target 
                 233 
                 AAC TAA CCA GAA AGG GAC GGC 
                 Beacon 
                 35 
                   
                   
                 60% 
                 ΔG = −1.15 
               
               
                   
               
               
                 L-01-100 
                 -10 
                 Beacon 
                 234 
                 GCGT TAA GCA AAT GTC ATG CAA CAT 
                 Probe/target 
                 25 
                 17 
                 8 
                 32% 
                 ΔG = −20.4 
               
               
                   
                   
                   
                   
                 CTA CTTAACGC 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 235 
                 T TAA GCA AAT GTC ATG CAA CAT CTA 
               
               
                   
                 -100 
                 Target 
                 236 
                 TAG ATG TTG CAT GAC ATT TGC TTA A 
                 Beacon 
                 38 
                   
                   
                 39% 
                 ΔG = −0.64 
               
               
                   
               
               
                 L-01-101 
                 -10 
                 Beacon 
                 237 
                 TGCCTTC  GAG CAA TTG CCC CTT TTA   
                 Probe/target 
                 24 
                 15 
                 9 
                 38% 
                 ΔG = −20.0 
               
               
                   
                   
                   
                   
                   AAT TAC  GAAGGCA 
                 Hybrid 
               
               
                   
                 -50 
                 Probe seq 
                 238 
                 GAG CAA TTG CCC CTT TTA AAT TAC 
               
               
                   
                 -100 
                 Target 
                 239 
                 GTA ATT TAA AAG GGG CAA TTG CTC 
                 Beacon 
                 38 
                   
                   
                 45% 
                 ΔG = −1.01 
               
               
                   
               
               
                 L-01-102 
                 -10 
                 Beacon 
                 240 
                 ACGCTC  GTT CCC CAA CTC CCT ACT   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 −20.2 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 241 
                 GTT CCC CAA CTC CCT ACT 
                 Beacon 
                 30 
                   
                   
                 60% 
                 −0.78 
               
               
                   
                 -100 
                 Target 
                 242 
                 AGT AGG GAG TTG GGG AAC 
               
               
                   
               
               
                 L-01-103 
                 -10 
                 Beacon 
                 243 
                 ACTC  CCC CTT GTG TAA GGC AGG   
                 Probe/target 
                 24 
                 13 
                 11 
                 54% 
                 −21.4 
               
               
                   
                   
                   
                   
                 
                   GAGT 
                 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 244 
                 CCC CTT GTG TAA GGC AGG 
                 Beacon 
                 28 
                   
                   
                 54% 
                 −0.61 
               
               
                   
                 -100 
                 Target 
                 245 
                 CCT GCC TTA CAC AAG GGG 
               
               
                   
               
               
                 L-01-104 
                 -10 
                 Beacon 
                 246 
                 ACGCTC  CCC ACT TTG GTC CGA AGA   
                 Probe/target 
                 18 
                 8 
                 10 
                 56% 
                 −19.6 
               
               
                   
                   
                   
                   
                 GAGCGT 
                 Hybrid 
               
               
                   
                 -50 
                 Probe 
                 247 
                 CCC ACT TTG GTC CGA AGA 
                 Beacon 
                 30 
                   
                   
                 60% 
                 −0.66 
               
               
                   
                 -100 
                 Target 
                 248 
                 TCT TCG GAC CAA AGT GGG 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 Loop 
                 Tm 
                 Td 
                   
                   
                 Probe match 
                 Probe match 
               
               
                 Diagostics 
                 target: 
                 (Suggs et 
                   
                 Probe match direct hits I 
                 direct hits II 
                 direct hits III 
               
               
                 Code number 
                 71 +/− 3° C. 
                 al) 48-60 
                 RNA Blast hits 
                 (16S only) 
                 (16S only) 
                 (16S only) 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 L-01-1 
                 -10 
                 71.6 
                 62 
                 41 
                   Acinetobacter  (651/1392) 
                 Moraxellaceae 
                 unclassified_Moraxellaceae 
               
               
                   
                   
                   
                   
                   
                   
                 (665/2068) 
                 (6/31) 
               
               
                   
                 -50 
                 65.9 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-2 
                 -10 
                 72.2 
                 62 
                 Acinetobacter_baumannii_X81667 
                 Moraxellaceae (23/2142) 
               
               
                   
                 -50 
                 69.8 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-3 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-4 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-5 
                 -10 
                 70.8 
                 62 
               
               
                   
                 -50 
                 63.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-6 
                 -10 
                 70.0 
                 58 
               
               
                   
                 -50 
                 67.8 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-7 
                 -10 
                 69.4 
                 68 
               
               
                   
                 -50 
                 63.1 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-8 
                 -10 
                 68.9 
                 66 
               
               
                   
                 -50 
                 66.6 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-9 
                 -10 
                 68.6 
                 56 
               
               
                   
                 -50 
                 66.0 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-10 
                 -10 
                 70.2 
                 62 
                 34  B burgdorferi /100  Borrelia   
                 89  B burgdorferi/245    Borrelia   
               
               
                   
                 -50 
                 66.7 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-11 
                 -10 
                 68.8 
                 62 
                   B. pertussis. Parapertussis , 
                 0 
                 0 
                 0 
               
               
                   
                 -50 
                 65.9 
                   
                 B_bronchiseptica, Bordetella_avium 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-12 
                 -10 
                 69.6 
                 66 
                   
                 Burkholderiaceae (1867/2900) 
               
               
                   
                 -50 
                 68.0 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-13 
                 -10 
                 69.0 
                 64 
                   
                 Burkholderiaceae (78/2900) 
               
               
                   
                 -50 
                 69.0 
               
               
                   
                 -100 
               
               
                   
               
               
                 L- 
                   
                 68.8 
                 62 
                   
                 Burkholderiaceae (3/2900) 
               
               
                   
                   
                 69.0 
               
               
                   
               
               
                 L-01-14 
                 -10 
                 69.6 
                 54 
                   
                 Burkholderiaceae (23/2900) 
               
               
                   
                 -50 
                 69.9 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-15 
                 -10 
                 70.5 
                 58 
                   
                 Burkholderiaceae (67/2900).  B   
               
               
                   
                 -50 
                 65.3 
                   
                   
                 
                   pyrrocinea 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-16 
                 -10 
                 70.5 
                 56 
                   
                 Burkholderiaceae (23/2900) 
               
               
                   
                 -50 
                 65.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-17 
                 -10 
                 69.0 
                 58 
                   
                 Burkholderiaceae (1/2900) 
               
               
                   
                 -50 
                 67.1 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-18 
                 -10 
                 69.6 
                 58 
                   
                 Burkholderiaceaei (143/2900) 
               
               
                   
                   
                 67.1 
               
               
                   
               
               
                 L-01-19 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-20 
                 -10 
                 57 
                 50 
               
               
                   
                 -50 
                 68.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-21 
                 -10 
                 63.6 
                 52 
               
               
                   
                 -50 
                 67.4 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-22 
                 -10 
                 77.8 
                 66 
               
               
                   
                 -50 
                 68.5 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-23 
                 -10 
                 70.1 
                 56 
               
               
                   
                 -50 
                 68.0 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-24 
                 -10 
                 72.7 
                 58 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-25 
                 -10 
                 57.7 
                 48 
               
               
                   
                 -50 
                 62.7 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-26 
                 -10 
                 72.6 
                 60 
               
               
                   
                 -50 
                 67.8 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-27 
                 -10 
                 69.8 
                 58 
               
               
                   
                 -50 
                 67.8 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-28 
                 -10 
                 63.6 
                 54 
               
               
                   
                 -50 
                 62.7 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-29 
                 -10 
                 61.9 
                 54 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-30 
                 -10 
                 67.3 
                 54 
               
               
                   
                 -50 
                 62.5 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-31 
                 -10 
                 68.2 
                 56 
               
               
                   
                 -50 
                 64.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-32 
                 -10 
                 72.2 
                 60 
               
               
                   
                 -50 
                 67.8 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-33 
                 -10 
                 65.8 
                 54 
               
               
                   
                 -50 
                 65.7 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-34 
                 -10 
                 68.3 
                 58 
                 26/26 @ 40 
               
               
                   
                 -50 
                 66.2 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-35 
                 -10 
                 70.8 
                 66 
                 1/3 @48 others non clinical speces 
               
               
                   
                 -50 
                 66.4 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-36 
                 -10 
                 68.2° 
                 60 
                 7/7 @ 40 
               
               
                   
                 -50 
                 65.9 C 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-37 
                 -10 
                 74.0 C 
                 58 
                 8/11 @34; 3 non-clinical 
               
               
                   
                 -50 
                 69.5 C 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-38 
                 -10 
                 70.2 C 
                 60 
                 17/24 @ 40; 3 C fennica; 
               
               
                   
                 -50 
                 69.9 C 
                   
                 1 C solomi; 1 C spp; 2 uncultured 
               
               
                   
                 -100 
                   
                   
                 eukaryotic genes 
               
               
                   
               
               
                 L-01-39 
                 -10 
                 71.5 C 
                 56 
                 51/55 @40 
               
               
                   
                 -50 
                 70.0 C 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-40 
                 -10 
                 69.5° C. 
                 62 
                 4/11@42 
               
               
                   
                 -50 
                 66.9° C. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-41 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-42 
                 -10 
                 69.0 
                 64 
                 only  Citrobacter freundii  and 
                 0 
                 0 
                 0 
               
               
                   
                 -50 
                 65.9 
                   
                   Pseudomonas aeruginosa  @full score 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-43 
                 -10 
                 69.4 
                 64 
               
               
                   
                 -50 
                 65.6 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-44 
                 -10 
                 69.4 
                 66 
                 Only C-diff @ full score 
                 Clostridium_difficile_X73450 
                 Clostridiaceae 
               
               
                   
                 -50 
                 68.0 
                   
                   
                   
                 (18/8924) 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-45 
                 -10 
                 73.1 
                 60 
               
               
                   
                 -50 
                 65.2 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-46 
                 -10 
                 69.1 
                 62 
                 Only  Clostridium perfringens   
                 Clostridiaceae (49/7851) 
               
               
                   
                 -50 
                 67.6 
                   
                 with full score 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-47 
                 -10 
                 69.3 
                 56 
                 Only  Clostridium perfringens   
                 Clostridiaceae (49/7851) 
               
               
                   
                 -50 
                   
                   
                 with full score 
               
               
                   
                 -100 
                 63.6 
               
               
                   
               
               
                 L-01-48 
                 -10 
                 71.3 
                 64 
                 Only  Clostridium tetani  with 
                 Clostridiaceae (1/8924) 
               
               
                   
                 -50 
                   
                   
                 full score 
               
               
                   
                 -100 
                 70.9 
               
               
                   
               
               
                 L-01-49 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-50 
                 -10 
                 70.2 
                 62 
                 92 Enterobacteriaceae 
                 0 
                 0 
                 0 
               
               
                   
                 -50 
                 65.9 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-51 
                 -10 
                 70.7 
                 58 
                 101 Enterobacteriaceae 
                 Enterobacteriaceae (1857/5527) 
               
               
                   
                 -50 
                   
                   
                   
                 including; Proteus (24/90); 
               
               
                   
                 -100 
                 68.2 
                   
                   
                 Providencia (17/35) 
               
               
                   
               
               
                 L-01-52 
                 -10 
                 69.7 
                 64 
                 101 Enterobacteriaceae 
                 Enterobacteriaceae (2663/5527) 
               
               
                   
                 -50 
                   
                   
                   
                 without Proteus&amp;Providencia 
               
               
                   
                 -100 
                 66.7 
               
               
                   
               
               
                 L-01-53 
                 -10 
                 69.5 
                 58 
                 18 Enterococci 
                 genus  Enterococcus  (425/847) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 68.2 
               
               
                   
               
               
                 L-01-54 
                 -10 
                 67.7 
                 56 
                 only  E. faecalis  with full sore 
                   Enterococcus  (193/803) the 
               
               
                   
                 -50 
                   
                   
                   
                 other 600 are mostly 
               
               
                   
                 -100 
                 68.2 
                   
                   
                 unclassified E, no  faecalis   
               
               
                   
               
               
                 L-01-55 
                 -10 
                 67.7 
                 66 
                 5  faecium  and 1  faecalis  at 
                 64/157 are  faecium  only 1 
                 0 
                 0 
               
               
                   
                 -50 
                   
                   
                 full score 
                 
                   faecalis 
                 
               
               
                   
                 -100 
                 64.0 
               
               
                   
               
               
                 L-01-56 
                 -10 
                 68.8 
                 62 
                 18  E. coli  &amp; EHEC/39 total rest 
                 0 
                 0 
                 0 
               
               
                   
                 -50 
                   
                   
                 is only Haemophilus_parasuis, 
               
               
                   
                 -100 
                 67.2 
                   
                   Mannheimia alucosida . 
               
               
                   
               
               
                 L-01-57 
                 -10 
                 75.1 
                 60 
               
               
                   
                 -50 
                 67.7 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-58 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-59 
                 -10 
                 68 
                 56 
               
               
                   
                 -50 
                 66.2 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-60 
                 -10 
                 70.6 
                 66 
                 Haemophilus_influenzae_F_U32708 
                 Pasteurellaceae (283/2293) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 69.1 
               
               
                   
               
               
                 L-01-61 
                 -10 
                 69.2 
                 64 
                 Haemophilus_influenzae_F_U32708 
                 Pasteurellaceae (278/2293) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 T 70.9 
               
               
                   
               
               
                 L-01-62 
                 -10 
                 68.1 
                 60 
                 Klebsiella_pneumoniae_Y17656 
                 Enterobacteriaceae (32/5830) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 66.1 
               
               
                   
               
               
                 L-01-63 
                 -10 
                 69.3 
                 70 
                 Klebsiella_oxytoca_Y17655 
                 Enterobacteriaceae (20/6874) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 68.3 
               
               
                   
               
               
                 L-01-64 
                 -10 
                 70.4 
                 66 
                 Lactobacillus_brevis_X61134 
                 Lactobacillaceae (38/2674) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 66.6 
               
               
                   
               
               
                 L-01-65 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-66 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-67 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-68 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-69 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-70 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-71 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-72 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-73 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-74 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-75 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-76 
                 -10 
                 69.2 
                 56 
                 Only  Legionella  with full score 
                 78  Legionella  only 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 68.2 
               
               
                   
               
               
                 L-01-77 
                 -10 
                 67.5 
                 54 
               
               
                   
                 -50 
                 67.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-78 
                 -10 
                 67.1 
                 0 
               
               
                   
                 -50 
                 64.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-79 
                   
                 0 
               
               
                   
               
               
                 L-01-80 
                 -10 
                 70.4 
                 60 
                 Proteus 23s sequence not found in 
                 0 
                 0 
                 0 
               
               
                   
                 -50 
                   
                   
                 data base; nearest hit is  E. coli   
               
               
                   
                 -100 
                 66.2 
                   
                 with a score of 28 (out of 36) 
               
               
                   
               
               
                 L-01-81 
                 -10 
                 69 
                 62 
               
               
                   
                 -50 
                 65.5 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-82 
                 -10 
                 67.5 
               
               
                   
                 -50 
                 63.2 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-83 
                   
                 0 
               
               
                   
               
               
                 L-01-84 
                   
                 0 
               
               
                   
               
               
                 L-01-85 
                 -10 
                 69.1 
                 60 
               
               
                   
                 -50 
                 67.4 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-86 
                 -10 
                 70.5 
                 62 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 69.4 
               
               
                   
               
               
                 L-01-87 
                 -10 
                 77.6 
                 64 
               
               
                   
                 -50 
                 64.1 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-88 
                 -10 
                 66.4 
                 58 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-89 
                 -10 
                 70.8 
                 60 
               
               
                   
                 -50 
                 68.0 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-90 
                 -10 
                 46 
                 60 
               
               
                   
                 -50 
                 64.0 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-91 
                 -10 
                   
                 54 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-92 
                 -10 
                 70.4 
                 60 
                 9  Salmonella , 1  Y enterolytica , no 
                 0 
                 0 
                 0 
               
               
                   
                 -50 
                   
                   
                 other hit 
               
               
                   
                 -100 
                 67.4 
               
               
                   
               
               
                 L-01-93 
                 -10 
                   
                 0 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-94 
                 -10 
                 71.6 
                 62 
                 Serratia_marcescens_AF124042 
                 opened, click to collapse genus 
               
               
                   
                 -50 
                   
                   
                   
                   Serratia  (249/544) (hits/total 
               
               
                   
                 -100 
                 69.9 
                   
                   
                 searched) 
               
               
                   
               
               
                 L-01-95 
                 -10 
                 69.9 
                 76 
                 12 Stapg  aureus  w full score, 
                 77 out of 171 (Staur catches 78/ 
               
               
                   
                 -50 
                   
                   
                 no others 
                 269 and is therefore less specific 
               
               
                   
                 -100 
                 64.0 
               
               
                   
               
               
                 L-01-96 
                 -10 
                 70.2 
                 62 
                   
                 Staphylococcaceae 
               
               
                   
                 -50 
                   
                   
                   
                 (1230/2473) 
               
               
                   
                 -100 
                 Tm = 
               
               
                   
                   
                 66.4 Å° C. 
               
               
                   
               
               
                 L-01-97 
                 -10 
                 70.5 
                 66 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 70.8 
               
               
                   
               
               
                 L-01-98 
                 -10 
                 69.1 
                 64 
                   Streptococcus agalactiae , 
                 Streptococcaceae (96/7045) 
               
               
                   
                 -50 
                   
                   
                   Streptococcus difficile  @ full score 
               
               
                   
                 -100 
                 65.7 
               
               
                   
               
               
                 L-01-99 
                 -10 
                 72.7 
                 64 
                 Streptococcus_criae_X58316 
                 Lactobacillales (337/12134) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 69.9 
               
               
                   
               
               
                 L-01-100 
                 -10 
                 68.4 
                 66 
                 Streptococcus_mitis_D38482 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 65.9 
               
               
                   
               
               
                 L-01-101 
                 -10 
                 67.9 
                 66 
                 Streptococcus_pyogenes_AF076028 
                 Streptococcaceae (95/7045) 
               
               
                   
                 -50 
               
               
                   
                 -100 
                 67.7 
               
               
                   
               
               
                 L-01-102 
                 -10 
                 69.1 
                 56 
               
               
                   
                 -50 
                 68.3 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-103 
                 -10 
                 71.8 
                 70 
               
               
                   
                 -50 
                 67.5 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-104 
                 -10 
                 68.1 
                 56 
               
               
                   
                 -50 
                 67.0 
               
               
                   
                 -100 
               
               
                   
               
            
           
           
               
               
            
               
                 Loop Diagostics 
                   
               
               
                 Code number 
                 Reference for cognate sequence 
               
               
                   
               
            
           
           
               
               
               
            
               
                 L-01-1 
                 -10 
                 Wagner M., Erhart R., Manz W., Amann R., Lemmer H., Wedi D. and Schleifer K.-H. (1994). Appl. Environ. Microbiol. 60: 
               
               
                   
                 -50 
                 792-800. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-2 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-3 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-4 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-5 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-6 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-7 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-8 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-9 
                 -10 
                 See also Pat. 4,977,251 11.12.1990: DNA Sonden für die Detektion von  Bacteroides  Spezies (expired) Manz W., et al.. 
               
               
                   
                 -50 
                 (1996). Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum 
               
               
                   
                 -100 
                   cytophaga - flavobacter - bacteroides  in the natural environment. Microbiol. 142: 1097-1106. 
               
               
                   
               
               
                 L-01-10 
                 -10 
                 Hammer et al, Microbiology (2001), 147, 1425-1436. 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-11 
                 -10 
                 Jürgen Bohnert, Barbara Hübner, Konrad Botzenhart, Int. J. Hyg. Environ. Health 203, 77-82 (2000) 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-12 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-13 
                 -10 
                 New: according to Govan this should cover,  B. pyrocina ,  stabilis ,  multivorans ,  cepacia ,  ambiforia   
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L- 
                   
                 New: according to Govan this should cover,  B. dolosa ,  cenocepacia ,  vietnamensis ,  anthina   
               
               
                   
               
               
                 L-01-14 
                 -10 
                 New: only  B. cepacia  and  tropicalis   
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-15 
                 -10 
                 New, catches  B pyrocina ,  stabilis  and  ambifaria   
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-16 
                 -10 
                 New: according to Govan this should cover,  B. doloda anthinia   
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-17 
                 -10 
                 New: according to Govan this should cover,  B. multivorans   
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-18 
                 -10 
                 New: according to Govan this should cover,  B. cenocepacia  and  vietnamiensis   
               
               
                   
               
               
                 L-01-19 
                 -10 
                 Popped presentation in Jena, slides available, and Sven Poppert, Andreas Essig, Reinhard Marre, Michael Wagner, and 
               
               
                   
                 -50 
                 Matthias Horn. 2002. Detection and differentiation of chlamydiae by fluorescence in situ hybridization (FISH). Appl. Environ. 
               
               
                   
                 -100 
                 Microbial: 68; 4081-4089 
               
               
                   
               
               
                 L-01-20 
                 -10 
                 Poppert presentation in Jena, slides available, and Sven Poppert, Andreas Essig, Reinhard Marre, Michael Wagner, and 
               
               
                   
                 -50 
                 Mathias Horn. 2002. Detection and differentiation of chlamydiae by fluorescence in situ hybridization (FISH). Appl. Environ. 
               
               
                   
                 -100 
                 Microbial: 68; 4081-4089 
               
               
                   
               
               
                 L-01-21 
                 -10 
                 Poppert presentation in Jena, slides available, and Sven Poppert, Andreas Essig, Reinhard Marre, Michael Wagner, and 
               
               
                   
                 -50 
                 Matthias Horn. 2002. Detection and differentiation of chlamydiae by fluorescence in situ hybridization (FISH). Appl. Environ. 
               
               
                   
                 -100 
                 Microbial: 68; 4081-4089 
               
               
                   
               
               
                 L-01-22 
                 -10 
                 Poppert presentation in Jena, slides available, and Sven Poppert, Andreas Essig, Reinhard Marre, Michael Wagner, and 
               
               
                   
                 -50 
                 Mdtthias Horn. 2002. Detection and differentiation of chlamydiae by fluorescence in situ hybridization (FISH). Appl. Environ. 
               
               
                   
                 -100 
                 Microbial: 68; 4081-4089 
               
               
                   
               
               
                 L-01-23 
                 -10 
                 Poppert presentation in Jena, slides available, and Sven Poppert, Andreas Essig, Reinhard Marre, Michael Wagner, and 
               
               
                   
                 -50 
                 Matthias Horn. 2002. Detection and differentiation of chlamydiae by fluorescence in situ hybridization (FISH). Appl. Environ. 
               
               
                   
                 -100 
                 Microbial: 68; 4081-4089 
               
               
                   
               
               
                 L-01-24 
                 -10 
                 Poppert presentation in Jena, slides available, and Sven Popped, Andreas Essig, Reinhard Marre, Michael Wagner, and 
               
               
                   
                 -50 
                 Matthias Horn. 2002. Detection and differentiation of chlamydiae by fluorescence in situ hybridization (FISH). Appl. Environ. 
               
               
                   
                 -100 
                 Microbial: 68; 4081-4089 
               
               
                   
               
               
                 L-01-25 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-26 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-27 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-28 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-29 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-30 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-31 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-32 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-33 
                 -10 
                 Applied and Environmental Microbiology, August 2002, p. 4081-4089, Vol. 68, No. 8 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-34 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-35 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-36 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-37 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-38 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-39 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-40 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-41 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-42 
                 -10 
                 INAUGURAL-DISSERTATION, Qiang Fang, zu Tübingen, C:\Aktenkoffer\paper\FISH\23s-probe for  Salmonella .pdf 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-43 
                 -10 
                 derived from Meier H., Amann R., Ludwig W. and Schleifer K.-H. (1999). Specific oligonucleotide probes for in situ 
               
               
                   
                 -50 
                 detection . . . Syst. Appl. Microbiol. 22: 186-196. This detects Firmicutes. TGG AAG ATT CCC TAC TGC crap. Clavel T., 
               
               
                   
                 -100 
                 Borrmann D., Braune A., Doré J. and Blaut M. (2006). Occurrence and activity of human intestinal bacteria that activate 
               
               
                   
                   
                 dietary lignans. Anaerobe: In press, 5′-CTC GGA CAT TAC TGC CCG CG-3′ 
               
               
                   
               
               
                 L-01-44 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-45 
                 -10 
                 derived from Meier H., Amann R., Ludwig W. and Schleifer K. -H. (1999). Specific oligonucleotide probes for in situ 
               
               
                   
                 -50 
                 detection . . . Syst. Appl. Microbial. 22: 186-196. This detects Firmicutes. TGG AAG ATT CCC TAC TGC crap. Clavel T., 
               
               
                   
                 -100 
                 Borrmann D., Braune A., Doré J. and Blaut M. (2006). Occurrence and activity of human intestinal bacteria that activate 
               
               
                   
                   
                 dietary lignans. Anaerobe: In press, 5′-CTC GGA CAT TAC TGC CCG CG-3′ 
               
               
                   
               
               
                 L-01-46 
                 -10 
                 Rönner S. G. E. and Stackebrandt E. (1994). Identification of  Clostridium perfringens  by 16S and 23S rRNA oligonucleotide 
               
               
                   
                 -50 
                 probes. Syst. Appl. Microbial. 17: 425-432. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-47 
                 -10 
                 Rönner S. G. E. and Stackebrandt E. (1994). Identification of  Clostridium perfringens  by 16S and 23S rRNA oligonucleotide 
               
               
                   
                 -50 
                 probes. Syst. Appl. Microbial. 17: 425-432. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-48 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-49 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-50 
                 -10 
                 derived from Jürgen Bohnert, Barbara Hübner, Konrad Botzenhart Int. J. Hyg. Environ. Health 203, 77-82 (2000) 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-51 
                 -10 
                 derived from Ootsubo M., Shimizu T., Tanaka R., Sawabe T., Tajima K., Yoshimizu M., Ezura Y., Ezaki T. and Oyaizu H. 
               
               
                   
                 -50 
                 (2002). Oligonucleotide probe for detecting Enterobacteriaceae by in situ hybridization. J. Appl. Microbiol. 93: 60-68. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-52 
                 -10 
                 derived from Kempf V. A., Trebesius K. and Autenrieth I. B. (2000). Fluorescent in situ hybridization allows rapid 
               
               
                   
                 -50 
                 identification of microorganisms in blood cultures. J. Clin. Microbiol. 38: 830-838. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-53 
                 -10 
                 derived from: Wang R., Beggs M., Robertson L. and Cerniglia C. (2002). Design and evaluation of oligonucleotide-microarray 
               
               
                   
                 -50 
                 method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213: 175-182. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-54 
                 -10 
                 derived from Behr T., Koob C., Schedl M., Mehlen A., Meier H., Knopp D., Frahm E., Obst U., Schleifer K., Niessner R. and 
               
               
                   
                 -50 
                 Ludwig W. (2000). A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse 
               
               
                   
                 -100 
                 hybridization. Syst. Appl. Microbiol. 23: 563-572. 
               
               
                   
               
               
                 L-01-55 
                 -10 
                 NEW, started from the Wang sequence and moved towards 5′ step by step and ran BLASTs 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-56 
                 -10 
                 derived from: Wang R., Beggs M., Robertson L. and Cemiglia C. (2002). Design and evaluation of oligonucleotide-microarray 
               
               
                   
                 -50 
                 method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213: 175-182. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-57 
                 -10 
                 Amman review 1995 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-58 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-59 
                 -10 
                 Compare sequence: Patent 5654418 05.08.1997 von Sheiness (Becton Dickinson and Company): Nucleic acid probes 
               
               
                   
                 -50 
                 useful for detecting microorganisms associated with vaginal infections. Verfahren zur Detektion von von Mikroorganismen diemit 
               
               
                   
                 -100 
                 vaginalen Krankheiten assoziiert sind, z.  B. Gardnerella vaginalis ,  Trichomonas vaginalis  und  Candida albicans . Beispiel 
               
               
                   
                   
                 für ein Krankheitsbild und den entsprechenden Sondensatz. 
               
               
                   
               
               
                 L-01-60 
                 -10 
                 New 6 base over-lap w Haeinf-1 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-61 
                 -10 
                 New, no over-lap 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-62 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-63 
                 -10 
                 NEW 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-64 
                 -10 
                 derived from Blasco L., Ferrer S. and Pardo I. (2003). Development of specific fluorescent oligonucleotide probes for in situ 
               
               
                   
                 -50 
                 identification of wine lactic acid bacteria. FEMS Microbiol. Lett. 225: 115-123. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-65 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-66 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-67 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-68 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-69 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-70 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-71 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-72 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-73 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-74 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-75 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-76 
                 -10 
                 Dorothee Grimm, 1 Hilde Merkert, 1 Wolfgang Ludwig, 2 Karl-Heinz Schleifer, 2 Jörg Hacker, 1 and Bettina C. Brand1* Appl 
               
               
                   
                 -50 
                 Environ Microbiol. 1998 July; 64(7): 2686-2690. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-77 
                 -10 
                 Wang, R. -F., Cao, W. -W. and Johnson, M. G. (1991). Development of a 16S rRNA-based oligomer probe specific for 
               
               
                   
                 -50 
                   Listeria monocytogenes . Appl. Environ. Microbiol. 57, 3666-3670. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-78 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-79 
               
               
                   
               
               
                 L-01-80 
                 -10 
                 derived from INAUGURAL-DISSERTATION, Qiang Fang, zu Tübingen, C:\Aktenkoffer\paper\FISH\23s-probe for 
               
               
                   
                 -50 
                   Salmonella .pdf 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-81 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-82 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-83 
               
               
                   
               
               
                 L-01-84 
               
               
                   
               
               
                 L-01-85 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-86 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-87 
                 -10 
                   Salmonella  spp. in foods by fluorescent in situ hybridization with 23S rRNA probes: a comparison with conventional culture 
               
               
                   
                 -50 
                 methods. J Food Prot. 2003 May; 66(5)723-31 *Fang Q, Brockmann 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-88 
                 -10 
                   Salmonella  spp. in foods by fluorescent in situ hybridization with 23S rRNA probes: a comparison with conventional culture 
               
               
                   
                 -50 
                 methods. J Food Prot. 2003 May; 66(5)723-31 *Fang Q, Brockmann 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-89 
                 -10 
                   Salmonella  spp. in foods by fluorescent in situ hybridization with 23S rRNA probes: a comparison with conventional culture 
               
               
                   
                 -50 
                 methods. J Food Prot. 2003 May; 66(5)723-31 *Fang Q, Brockmann 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-90 
                 -10 
                   Salmonella  spp. in foods by fluorescent in situ hybridization with 23S rRNA probes: a comparison with conventional culture 
               
               
                   
                 -50 
                 methods. J Food Prot. 2003 May; 66(5)723-31 *Fang Q, Brockmann 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-91 
                 -10 
                   Salmonella  spp. in foods by fluorescent in situ hybridization with 23S rRNA probes: a comparison with conventional culture 
               
               
                   
                 -50 
                 methods. J Food Prot. 2003 May; 66(5)723-31 *Fang Q, Brockmann 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-92 
                 -10 
                   Salmonella  spp. in foods by fluorescent in situ hybridization with 235 rRNA probes: a comparison with conventional culture 
               
               
                   
                 -50 
                 methods. J Food Prot. 2003 May; 66(5)723-31 *Fang Q, Brockmann 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-93 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-94 
                 -10 
                 new 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-95 
                 -10 
                 derived from Urakawa H., Fantroussi, S. E., Smidt, H., Smoot, J. C., Tribou, E. H., Kelly, J. J., Noble, P. A., Stahl, D. A. 
               
               
                   
                 -50 
                 (2003). Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Envir. Microbiol. 69: 
               
               
                   
                 -100 
                 2848-2856. 
               
               
                   
               
               
                 L-01-96 
                 -10 
                 derived from Urakawa H., Fantroussi, S. E., Smidt, H., Smoot, J. C., Tribou, E. H., Kelly, J. J., Noble, P. A., Stahl, D. A. 
               
               
                   
                 -50 
                 (2003). Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays. Appl. Envir. Microbiol. 69: 
               
               
                   
                 -100 
                 2848-2856. 
               
               
                   
               
               
                 L-01-97 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-98 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-99 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-100 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-101 
                 -10 
                 New 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-102 
                 -10 
                 Compare sequence: Pat. 5,728,522 17.03.1998 von Del Vecchio (Research Corporation Technologies): Oligonucleotides 
               
               
                   
                 -50 
                 and nucleic acids for the detection of  Ureaplasma urealyticum . Test für die PCR-Detektion von  Ureaplasma urealyticum   
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-103 
                 -10 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-104 
                 -10 
                 Compare for sequences: Pat. 5,593,831 14.01.1997 von Shah (Amoco Corporation): Nucleic acid probes for the detection 
               
               
                   
                 -50 
                 of  Yersinia enterocolitica : Nukleinsäure Sonden, die an die rRNA von  Y. enterocolitica  binden nicht aber an die rRNA von 
               
               
                   
                 -100 
                 non- Yersinia enterocolitica  für die Detektion von  Yersinia enterocolitica  in Nahrungsmitteln und anderen Proben. Karlheinz 
               
               
                   
                   
                 Trebesius et al., Journal of Clinical Microbiology, September 1998, p. 2557-2564, Vol. 36, No. 9 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
             
               
                   
                 TABLE 2 
               
             
            
               
                   
                   
               
               
                   
                 PNA-suitable? 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                   
                   
                   
                 length inverse 
                   
               
               
                   
                   
                   
                   
                   
                   
                   
                   
                   
                 seq., (max 
               
               
                 Loop 
                   
                   
                   
                   
                   
                   
                 on &lt;3- 
                 on 4 
                 palindromes/ 
               
               
                 Diagostics 
                 Target 
                   
                   
                   
                 GC 
                 on GC 
                 base self 
                 purins 
                 18) repeats/ 
               
               
                 Code number 
                 organism 
                 Sequence 5′-3′ 
                   
                 Length 
                 content 
                 content 
                 complem. 
                 in a row 
                 hairpin 
                 Final 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                 L-01-1 
                 -10 
                 
                   Acinetobacter 
                 
                 TGCCGGATT  ACC ATC CTC TCC CAT   
                 Beacon 
                 39 
                   
                 54% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   ACT CTA  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 ACC ATC CTC TCC CAT ACT CTA 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                 yes 
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TAG AGT ATG GGA GAG GAT GGT 
               
               
                   
               
               
                 L-01-2 
                 -10 
                 
                   Acinatobacter 
                 
                 GCGCG TC CGG TAG CAA GCT ACC 
                 Beacon 
                 30 
                 21 
                 70% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   baumanii 
                 
                 TTC CGCGC 
               
               
                   
                 -50 
                   
                 TC CGG TAG CAA GCT ACC TTC 
                 Probe/target Hybrid 
                 20 
                 11 
                 55% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GAA GGT AGC TTG CTA CCG GA 
               
               
                   
               
               
                 L-01-3 
                 -10 
                 
                   Actinomyces 
                 
               
               
                   
                 -50 
                 spp. 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-4 
                 -10 
                   Aspergillus  spp 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-5 
                 -10 
                 
                   Aspergillus 
                 
                 CCGCCGGCGT AC AGA GTT CGT GGT 
                 Beacon 
                 41 
                 29 
                 71% 
                 no 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   flavus 
                 
                 GTC TCC TCGCCCAGCGG 
               
               
                   
                 -50 
                   
                 AC AGA GTT CGT GGT GTC TCC 
                 Probe/target Hybrid 
                 20 
                 11 
                 55% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GGA GAC ACC ACG AAC TCT GT 
               
               
                   
               
               
                 L-01-6 
                 -10 
                 
                   Aspergillus 
                 
                 cgtc gcc tac aga gca ggt gac g 
                 Beacon 
                 23 
                 15 
                 65% 
                 no 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -50 
                 
                   fumigatus 
                 
                 gcc tac aga gca ggt gac 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 gtc acc tgc tct gta ggc 
               
               
                   
               
               
                 L-01-7 
                 -10 
                 
                   Aspergillus 
                 
                 ctctga a ctg att gca ttc aat caa 
                 Beacon 
                 32 
                 13 
                 41% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   niger 
                 
                 ctc agag 
               
               
                   
                 -50 
                   
                 a ctg att gca ttc aat caa ctc aga 
                 Probe/target Hybrid 
                 25 
                 9 
                 36% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 tct gag ttg att gaa tgc aat cag t 
               
               
                   
               
               
                 L-01-8 
                 -10 
                 
                   Appergillus 
                 
                 TCCGTC tga ttg caa aga atc aca ctc 
                 Beacon 
                 36 
                 17 
                 47% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   terreus 
                 
                 aga GACGGA 
               
               
                   
                 -50 
                   
                 tga ttg caa aga atc aca ctc aga 
                 Probe/target Hybrid 
                 24 
                 9 
                 38% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 tct gag tgt gat tct ttg caa tca 
               
               
                   
               
               
                 L-01-9 
                 -10 
                   Bacteroides / 
                 GCCGCCGGCAT CCA ATG TGG GGG 
                 Beacon 
                 39 
                   
                 74% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   Prevotella 
                 
                 ACC TTC TAGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 CCA ATG TGG GGG ACC TTC 
                 Probe/target Hybrid 
                 17 
                 11 
                 59% 
                 yes 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GAA GGT CCC CCA CAT TGG 
               
               
                   
               
               
                 L-01-10 
                 -10 
                 
                   Borrelia 
                 
                 TGCCGGATT  CA TGC TTA AGA CGC   
                 Beacon 
                 39 
                   
                 56% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   burgdorferi 
                 
                   ACT GCC  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 CA TGC TTA AGA CGC ACT GCC 
                 Probe/target Hybrid 
                 20 
                 11 
                 50% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GGC AGT GCG TCT TAA GCA TG 
               
               
                   
               
               
                 L-01-11 
                 -10 
                 
                   Bordetella 
                 
                 TGCCGGATT  CAG CAC TCT GCA AAG   
                 Beacon 
                 40 
                   
                 53% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   pertussis 
                 
                   ACG AAA  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 CAG CAC TCT GCA AAG ACG AAA 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TTT CGT CTT TGC AGA GTG CTG 
               
               
                   
               
               
                 L-01-12 
                 -10 
                 
                   Burkholderia 
                 
                 ACCGCTC  TTT CTT TCC GGA CAA AAG   
                 Beacon 
                 39 
                   
                 51% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   cepacia 
                 
                   TGC TTT  GAGCGGCT 
               
               
                   
                 -50 
                 complex = 
                 TTT CTT TCC GGA CAA AAG TGC TTT 
                 Probe/target Hybrid 
                 24 
                 9 
                 38% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                 Option I 
                 AAA GCA CTT TTG TCC GGA AAG AAA 
               
               
                   
               
               
                 L-01-13 
                 -10 
                 
                   Burkholderia 
                 
                 CGCCTTC  AGA ACC AAG GAT TTC   
                 Beacon 
                 36 
                   
                 56% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   cepacia 
                 
                   TTT CCG G  GAAGGCG 
               
               
                   
                 -50 
                 complex, two 
                 AGA ACC AAG GAT TTC TTT CCG G 
                 Probe/target Hybrid 
                 22 
                 10 
                 45% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                 beacons = 
                 CCG GAA AGA AAT CCT TGG TTC T 
               
               
                   
                   
                 Option II 
               
               
                   
               
               
                 L- 
                   
                   
                 ACGCA  AGAGCCAAGGTTTTCTTTCCG   
                 Beacon 
                 34 
                   
                 50% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 CTTGCGT 
               
               
                   
                   
                   
                 AGA GCC AAG GTT TTC TTT CCG 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 CGG AAA GAA AAC CTT GGC TCT 
               
               
                   
               
               
                 L-01-14 
                 -10 
                 
                   Burkholderia 
                 
                 ACGCTC  G TCA TCC CCC GGC CAT   
                 Beacon 
                 28 
                   
                 68% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   cepacia 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 G TCA TCC CCC GGC CAT 
                 Probe/target Hybrid 
                 16 
                 11 
                 69% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 ATG GCC GGG GGA TGA C 
               
               
                   
               
               
                 L-01-15 
                 -10 
                 
                   Burkholderia 
                 
                 CGCTC  CGT CAT CCC CCG GCT ATA   
                 Beacon 
                 29 
                   
                 69% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                   pyrrocinia / 
                 GGAGCG 
               
               
                   
                 -50 
                   stabilis / ambifaria   
                 CGT CAT CCC CCG GCT ATA 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 TAT AGC CGG GGG ATG ACG 
               
               
                   
               
               
                 L-01-16 
                 -10 
                 
                   Burkholderia 
                 
                 CCGCTC  GT CAT CCC CCG GCT GTA   
                 Beacon 
                 29 
                   
                 72% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                   dolosa / anthina   
                 GAGCGG 
               
               
                   
                 -50 
                   
                 GT CAT CCC CCG GCT GTA 
                 Probe/target Hybrid 
                 17 
                 11 
                 65% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 TAC AGC CGG GGG ATG AC 
               
               
                   
               
               
                 L-01-17 
                 -10 
                 
                   Burkholderia 
                 
                 GCCGCCGGCGT  CGT CAT CCC CCG   
                 Beacon 
                 41 
                   
                 73% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   multivorans 
                 
                   ATC GTA  TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 CGT CAT CCC CCG ATC GTA 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 TAC GAT CGG GGG ATG ACG 
               
               
                   
               
               
                 L-01-18 
                 -10 
                 
                   Burkholderia 
                 
                 GCCGCCGGCGT  CGT CAT CCC CCG   
                 Beacon 
                 41 
                   
                 76% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                   cenocepacia / 
                   ACT GTA  TCGCCCAGCGGC 
               
               
                   
                   
                 
                   vietnamiensis 
                 
                 CGT CAT CCC CCG ACT GTA 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                   
                   
                 TAC AGT CGG GGG ATG ACG 
               
               
                   
               
               
                 L-01-19 
                 -10 
                 
                   Campylobacter 
                 
                 GCC CTA AGC GTC CTT CCA 
                   
                 18 
                 11 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -50 
                 (pathogenic 
               
               
                   
                 -100 
                 thermophiles 
               
               
                   
               
               
                 L-01-20 
                 -10 
                 
                   Campylobacterlari 
                 
                 ACGCTC  GAA GTG TAA GCA ACT AAA   
                 Beacon 
                 31 
                   
                 45% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 T GAGCGT 
               
               
                   
                 -50 
                   
                 GAA GTG TAA GCA ACT AAA T 
                 Probe/target Hybrid 
                 19 
                 6 
                 32% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 A TTT AGT TGC TTA CAC TTC 
               
               
                   
               
               
                 L-01-21 
                 -10 
                 
                   Campylobacter 
                 
                 ACGCTC A GC TAA CCA CTT ATA CCG   
                 Beacon 
                 30 
                   
                 53% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   jejuni 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 AGC TAA CCA CTT ATA CCG 
                 Probe/target Hybrid 
                 18 
                 8 
                 44% 
                 yes 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CGG TAT AAG TGG TTA GCT 
               
               
                   
               
               
                 L-01-22 
                 -10 
                 
                   Cp. upsaliensis 
                 
                 CCGCTC  CGT GTG TCG CCC TAG GCG   
                 Beacon 
                 32 
                   
                 72% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   TA  GAGCGG 
               
               
                   
                 -50 
                   
                 CGT GTG TCG CCC TAG GCG TA 
                 Probe/target Hybrid 
                 20 
                 13 
                 65% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TA CGC CTA GGG CGA CAC ACG 
               
               
                   
               
               
                 L-01-23 
                 -10 
                 
                   Cp coli 
                 
                 CCGCTC  TCG ATG GCA TCA GGG GTT   
                 Beacon 
                 30 
                   
                 67% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                 GAGCGG 
               
               
                   
                 -50 
                   
                 TCG ATG GCA TCA GGG GTT 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AAC CCC TGA TGC CAT CGA 
               
               
                   
               
               
                 L-01-24 
                 -10 
                   Cp coli -comp 
                 not required, competitor is 
                 Beacon 
               
               
                   
                   
                   
                 not labelled 
               
               
                   
                 -50 
                   
                 TCG ACG GCA TCA GGG GTT 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AAC CCC TGA TGC CGT CGA 
               
               
                   
               
               
                 L-01-25 
                 -10 
                 
                   Chlamydia 
                 
                 ACGCCGGCGT  TAG CTG ATA TCA CAT   
                 Beacon 
                 39 
                   
                 59% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                   AGA  TCGCCCAGCGT 
               
               
                   
                 -50 
                   
                 TAG CTG ATA TCA CAT AGA 
                 Probe/target Hybrid 
                 18 
                 6 
                 33% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 TCT ATG TGA TAT CAG CTA 
               
               
                   
               
               
                 L-01-26 
                 -10 
                 
                   Chlamydiaceae 
                 
                 TCCGCCGGCGT  CTT TCC GCC TAC   
                 Beacon 
                 41 
                   
                 73% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   ACG CCC  TCGCCCAGCGGA 
               
               
                   
                 -50 
                   
                 CTT TCC GCC TAC ACG CCC 
                 Probe/target Hybrid 
                 18 
                 12 
                 67% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GGG CGT GTA GGC GGA AAG 
               
               
                   
               
               
                 L-01-27 
                 -10 
                 
                   Chlamydiales 
                 
                 TCCGCCGGCGT  CCT CCG TAT TAC   
                 Beacon 
                 41 
                   
                 71% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   CGC AGC  TCGCCCAGCGGA 
               
               
                   
                 -50 
                   
                 CCT CCG TAT TAC CGC AGC 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GCT GCG GTA ATA CGG AGG 
               
               
                   
               
               
                 L-01-28 
                 -10 
                 
                   Chlamydophila 
                 
                 ACGCCGGCGT  CTA ACT TTC CTT TCC   
                 Beacon 
                 39 
                   
                 64% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   GCC  TCGCCCAGCGT 
               
               
                   
                 -50 
                   
                 CTA ACT TTC CTT TCC GCC 
                 Probe/target Hybrid 
                 18 
                 9 
                 50% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GGC GGA AAG GAA AGT TAG 
               
               
                   
               
               
                 L-01-29 
                 -10 
                 
                   Chlamydia 
                 
                 TCCACCGGCGT  CTC TTC CTC AAC   
                 Beacon 
                 41 
                   
                 61% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   pneumoniae 
                 
                   CGA AAG  TCGCCCAGTGGA 
               
               
                   
                 -50 
                   
                 CTC TTC CTC AAC CGA AAG 
                 Probe/target Hybrid 
                 18 
                 9 
                 50% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CTT TCG GTT GAG GAA GAG 
               
               
                   
               
               
                 L-01-30 
                 -10 
                 “ Chlamydia   
                 TCAGCCGGCGT  AAG GCA AAA CCA   
                 Beacon 
                 41 
                   
                 61% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   psittaci ” group 
                   ACT CCC  TCGCCCAGCTGA 
               
               
                   
                 -50 
                   
                 AAG GCA AAA CCA ACT CCC 
                 Probe/target Hybrid 
                 18 
                 9 
                 50% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GGG AGT TGG TTT TGC CTT 
               
               
                   
               
               
                 L-01-31 
                 -10 
                 Subgroup of the 
                 CCGCCGGCGT  TCC GTT TTC TCC GCC   
                 Beacon 
                 39 
                   
                 69% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 Parachlamydiaceae 
                   TAC  TCGCCCAGCGG 
               
               
                   
                 -50 
                   
                 TCC GTT TTC TCC GCC TAC 
                 Probe/target Hybrid 
                 18 
                 10 
                 50% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GTA GGC GGA GAA AAC GGA 
               
               
                   
               
               
                 L-01-32 
                 -10 
                   Chlamydia  ssp. 
                 TCCGCCGGCGT  GCT CCC CTT GCT   
                 Beacon 
                 42 
                   
                 69% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   TTC GCG  TCGCCCAGCGGA 
               
               
                   
                 -50 
                   
                 GCT CCC CTT GCT TTC GCG 
                 Probe/target Hybrid 
                 18 
                 12 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CGC GAA AGC AAG GGG AGC 
               
               
                   
               
               
                 L-01-33 
                 -10 
                 
                   Chlamydia 
                 
                 ACGCTC  TCG GAT GCC CAA ATA TCG   
                 Beacon 
                 30 
                   
                 57% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   trachomatis 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 TCG GAT GCC CAA ATA TCG 
                 Probe/target Hybrid 
                 18 
                 9 
                 50% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CGA TAT TTG GGC ATC CGA 
               
               
                   
               
               
                 L-01-34 
                 -10 
                 
                   Canda albicans 
                 
                 GG aa tgg cta ccc aga agg aaa 
                 Beacon 
                 29 
                 15 
                 52% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 CCATTCC 
               
               
                   
                 -50 
                   
                 aa tgg cta ccc aga agg aaa 
                 Probe/target Hybrid 
                 20 
                 9 
                 45% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 ttt cct tct ggg tag cca tt 
               
               
                   
               
               
                 L-01-35 
                 -10 
                 
                   Canda krusei 
                 
                 CCGCTC tgt att agc tct aga ttt 
                 Beacon 
                 36 
                 19 
                 53% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 cca cgg GAGCGG 
               
               
                   
                 -50 
                   
                 tgt att agc tct aga ttt cca cgg 
                 Probe/target Hybrid 
                 24 
                 9 
                 38% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 ccg tgg aaa tct aga gct aat aca 
               
               
                   
               
               
                 L-01-36 
                 -10 
                 
                   Candida 
                 
                 GTTTGcc ccg aaa gag taa ctt gca 
                 Beacon 
                 32 
                 16 
                 50% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   dubliniensis 
                 
                 GGCAAAC 
               
               
                   
                 -50 
                   
                 cc ccg aaa gag taa ctt gca 
                 Probe/target Hybrid 
                 20 
                 10 
                 50% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 tgc aag tta ctc ttt cgg gg 
               
               
                   
               
               
                 L-01-37 
                 -10 
                 
                   Candida 
                 
                 GCCGCCGGCGT gg cca ccc agg ccc aaa 
                 Beacon 
                 40 
                 32 
                 80% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   glabrata 
                 
                 TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 gg cca ccc agg ccc aaa 
                 Probe/target Hybrid 
                 17 
                 12 
                 71% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 ttt ggg cct ggg tgg cc 
               
               
                   
               
               
                 L-01-38 
                 -10 
                 
                   Candida 
                 
                 GCCGCCGGCGT gc caa aaa ggc tag cca 
                 Beacon 
                 43 
                 30 
                 70% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   Parapsilosis 
                 
                 gaa TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 gc caa aaa ggc tag cca gaa 
                 Probe/target Hybrid 
                 20 
                 10 
                 50% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 ttc tgg cta gcc ttt ttg gc 
               
               
                   
               
               
                 L-01-39 
                 -10 
                   Candida  spp 
                 ACGC gct tgg ctg gcc ggt c GCGT 
                 Beacon 
               
               
                   
                 -50 
                   
                 g acc ggc cag cca agc 
                 Probe/target Hybrid 
                 16 
                 12 
                 75% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 gct tgg ctg gcc ggt c 
                   
                 24 
                 18 
                 75% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
               
               
                 L-01-40 
                 -10 
                 
                   Candida 
                 
                 ACCGCCGGCGT tac gca tca gaa aga tgg 
                 Beacon 
                 44 
                 28 
                 64% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   tropicales 
                 
                 acc TCGCCCAGCGGT 
               
               
                   
                 -50 
                   
                 tac gca tca gaa aga tgg acc 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                   
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GGT CCA TCT TTC TGA TGC GTA 
               
               
                   
               
               
                 L-01-41 
                 -10 
                 
                   Candida 
                 
                   
                 Beacon 
               
               
                   
                 -50 
                 
                   lusitaniae 
                 
                   
                 Probe/target Hybrid 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-42 
                 -10 
                 
                   Citrobacter 
                 
                 TGCCGGATT  C TAC TTG TTA GGT   
                 Beacon 
                 40 
                   
                 53% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   freundii 
                 
                   GAC TGC GT  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 C TAC TTG TTA GGT GAC TGC GT 
                 Probe/target Hybrid 
                 21 
                 11 
                 48% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 AC GCA GTC ACC TAA CAA GTA G 
               
               
                   
               
               
                 L-01-43 
                 -10 
                 
                   Clostridium 
                 
                 TCTTG TAG T GC CGT TTC ATG CGA 
                 Beacon 
                 33 
                   
                 42% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   botulinum 
                 
                 AAC TAC AA GA 
               
               
                   
                 -50 
                   
                 GC CGT TTC ATG CGA AAC TAC AA 
                 Probe/target Hybrid 
                 22 
                 10 
                 45% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TT GTA GTT TCG CAT GAA ACG GC 
               
               
                   
               
               
                 L-01-44 
                 -10 
                 
                   Clostridium 
                 
                 GCCGCCGGCGT CGAAG TAA ATC 
                 Beacon 
                 46 
                 30 
                 65% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   difficile 
                 
                 GCT CAA CTT GCA TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 CGA AGT AAA TCG CTC AAC TTG CA 
                 Probe/target Hybrid 
                 23 
                 10 
                 43% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TGC AAG TTG AGC GAT TTA CTT CG 
               
               
                   
               
               
                 L-01-45 
                 -10 
                   Clostridium  spp 
                 CGCTCA CAC CCG TCC GCC GCT AAT 
                 Beacon 
                 29 
                   
                 69% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                 GAGCG 
               
               
                   
                 -50 
                   
                 CAC CCG TCC GCC GCT AAT 
                 Probe/target Hybrid 
                 18 
                 12 
                 67% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 ATT AGC GGC GGA CGG GTG 
               
               
                   
               
               
                 L-01-46 
                 -10 
                 
                   Clostridium 
                 
                 GCCGCCGGCGT  G ATT GCT CCT TTG   
                 Beacon 
                 44 
                   
                 68% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   perfringens 
                 
                   GTT GAA TGA TG  TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 G ATT GCT CCT TTG GTT GAA TGA TG 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 CA TCA TTC AAC CAA AGG AGC AAT C 
               
               
                   
               
               
                 L-01-47 
                 -10 
                 
                   Clostridium 
                 
                 ACGCTC  GGT TGA ATG ATG ATG CCA   
                 Beacon 
                 31 
                   
                 52% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   perfringens 
                 
                   T  GAGCGT 
               
               
                   
                 -50 
                   
                 GGT TGA ATG ATG ATG CCA TCT TT 
                 Probe/target Hybrid 
                 19 
                 9 
                 42% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 AA AGA TGG CAT CAT CAT TCA ACC 
               
               
                   
               
               
                 L-01-48 
                 -10 
                 
                   Clostridium 
                 
                 GCGGAC CT GTG TTA CTC ACC CGT 
                 Beacon 
                 27 
                 18 
                 52% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   tetani 
                 
                 CCG C 
               
               
                   
                 -50 
                   
                 CT GTG TTA CTC ACC CGT CCG 
                 Probe/target Hybrid 
                 20 
                 12 
                 42% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 CGG ACG GGT GAG TAA CAC AG 
               
               
                   
               
               
                 L-01-49 
                 -10 
                 
                   Cryptococcus 
                 
                   
                 Beacon 
               
               
                   
                 -50 
                 
                   neoformans 
                 
                   
                 Probe/target Hybrid 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-50 
                 -10 
                 Enterobacteriaceae 
                 TGCCGGATT  TT CGT GTT TGC ACA   
                 Beacon 
                 40 
                   
                 53% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                   GTG CTG T  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 TT CGT GTT TGC ACA GTG CTG T 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 A CAG CAC TGT GCA AAC ACG AA 
               
               
                   
               
               
                 L-01-51 
                 -10 
                 Enterobacteriaceae 
                 TGCCGGATT  TCT CGC GAG GTC GCT   
                 Beacon 
                 27 
                 16 
                 59% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   TCT  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 TCT CGC GAG GTC GCT TCT 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AGA AGC GAC CTC GCG AGA 
               
               
                   
               
               
                 L-01-52 
                 -10 
                 Enterobacteriaceae 
                 TGCCGGATT  CCC CCW CTT TGG TCT   
                 Beacon 
                 39 
                   
                 59% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   TGC GA  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 CCC CCW CTT TGG TCT TGC GA 
                 Probe/target Hybrid 
                 20 
                 12 
                 60% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TC GCA AGA CCA AAG WGG GGG 
               
               
                   
               
               
                 L-01-53 
                 -10 
                 Enterococci 
                 TGCCGGATT  ATC CAT CAG CGA CAC   
                 Beacon 
                 38 
                   
                 58% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   CCG  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 ATC CAT CAG CGA CAC CCG 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CGG GTG TCG CTG ATG GAT 
               
               
                   
               
               
                 L-01-54 
                 -10 
                 
                   Enterococcus 
                 
                 TGCCGGATT  CCC TCT GAT GGG TAG   
                 Beacon 
                 37 
                   
                 57% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   faecalis 
                 
                   GTT  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 CCC TCT GAT GGG TAG GTT 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AAC CTA CCC ATC AGA GGG 
               
               
                   
               
               
                 L-01-55 
                 -10 
                 
                   Enterococcus 
                 
                 GCCGCCGGCGT  TTC AAA TCA AAA   
                 Beacon 
                 47 
                   
                 62% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   faecium 
                 
                   CCA TGC GGT TTC  TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 TTC AAA TCA AAA CCA TGC GGT TTC 
                 Probe/target Hybrid 
                 24 
                 9 
                 38% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GAA ACC GCA TGG TTT TGA TTT GAA 
               
               
                   
               
               
                 L-01-56 
                 -10 
                 
                   Escherichia coil 
                 
                 TGCCGGATT  GGA AGA AGC TTG CTT   
                 Beacon 
                 40 
                   
                 53% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                   CTT TGC  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 GGA AGA AGC TTG CTT CTT TGC 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GCA AAG AAG GAA GCT TCT TCC 
               
               
                   
               
               
                 L-01-57 
                 -10 
                 Eu-bacteria 
                 CGCTC  GCT GCC TCC CGT AGG AGT   
                 Beacon 
                 28 
                   
                 71% 
                 no 
                   
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                 GAGCG 
               
               
                   
                 -50 
                   
                 GCT GCC TCC CGT AGG AGT 
                 Probe/target Hybrid 
                 18 
                 12 
                 67% 
                 no 
                 no 
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 ACT CCT ACG GGA GGC AGC 
               
               
                   
               
               
                 L-01-58 
                 -10 
                   Fusarium  spp 
               
               
                   
                 -50 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-59 
                 -10 
                 
                   Gardnerella 
                 
                 ACGCTC  CAC CAT GAA GCA ACC CGT   
                 Beacon 
                 30 
                   
                 60% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   vaginalis 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 CAC CAT GAA GCA ACC CGT 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 ACG GGT TGC TTC ATG GTG 
               
               
                   
               
               
                 L-01-60 
                 -10 
                 
                   Haemophilus 
                 
                 ACCCGCTA  TT CCG ATA ATA CGC   
                 Beacon 
                 35 
                   
                 51% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   influenzae 
                 
                   GGT ATT AGC  GGGT 
               
               
                   
                 -50 
                   
                 TT CCG ATA ATA CGC GGT ATT AGC 
                 Probe/target Hybrid 
                 23 
                 10 
                 43% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GCT AAT ACC GCG TAT TAT CGG AA 
               
               
                   
               
               
                 L-01-61 
                 -10 
                 
                   Haemophilus 
                 
                 CGGTGCTC  TA ATA CGC GGT ATT   
                 Beacon 
                 39 
                   
                 56% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   influenzae 
                 
                   AGC GAC AG  AGAGCACCG 
               
               
                   
                 -50 
                   
                 TA ATA CGC GGT ATT AGC GAC AG 
                 Probe/target Hybrid 
                 22 
                 10 
                 45% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 CT GTC GCT AAT ACC GCG TAT AT 
               
               
                   
               
               
                 L-01-62 
                 -10 
                 
                   Klebsiella 
                 
                 ACGCCGGCGT AGG TTA TTA ACC 
                 Beacon 
                 40 
                   
                 63% 
                   
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   pneumoniae 
                 
                 TCA TCG CCT TCGCCCAGCGT 
               
               
                   
                 -50 
                   
                 AGG TTA TTA ACC TCA TCG CCT 
                 Probe/target Hybrid 
                 21 
                 9 
                 43% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 AGG CGA TGA GGT TAA TAA CCT 
               
               
                   
               
               
                 L-01-63 
                 -10 
                 
                   Klebsiella 
                 
                 GGAAGGGATAT AGG TTA TTA ACC 
                 Beacon 
                 35 
                 16 
                 46% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   oxytoca 
                 
                 TCA CTC CCT TCC 
               
               
                   
                 -50 
                   
                 AGG TTA TTA ACC TCA CTC CCT TCC 
                 Probe/target Hybrid 
                 24 
                 111 
                 46% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GGA AGG GAG TGA GGT TAA TAA CCT 
               
               
                   
               
               
                 L-01-64 
                 -10 
                 
                   Lactobacillus 
                 
                 CGC TCAT TCA ACG GAA GCT CGT 
                 Beacon 
                 31 
                   
                 48% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   brevis 
                 
                 TCG ATGAGCG 
               
               
                   
                 -50 
                   
                 TCAT TCA ACG GAA GCT CGT TCG 
                 Probe/target Hybrid 
                 22 
                 11 
                 50% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 CGAAC GAGCTTCCGT TGAATGA 
               
               
                   
               
               
                 L-01-65 
                 -10 
                 
                   Mycobacterium 
                 
                   
                 Beacon 
               
               
                   
                 -50 
                 
                   avium 
                 
                   
                 Probe/target Hybrid 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-66 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   bovis 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-67 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   chelonae 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-68 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   fortuitum 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-69 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   gordonae 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-70 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 intracellulare 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-71 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   kansasil 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-72 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   malmoense 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-73 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   smegmatis 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-74 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   tuberculosis 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-75 
                 -10 
                 
                   Mycobacterium 
                 
               
               
                   
                 -50 
                 
                   xenopi 
                 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-76 
                 -10 
                 
                   Legionella 
                 
                 TGCCGGATT  ATC TGA CCG TCC CAG   
                 Beacon 
                 37 
                   
                 57% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   pneumophila 
                 
                   GTT  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 ATC TGA CCG TCC CAG GTT 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AAC CTG GGA CGG TCA GAT 
               
               
                   
               
               
                 L-01-77 
                 -10 
                 
                   Listeria 
                 
                 ACGCTC  ATA AGA TGT GGC GCA TGC   
                 Beacon 
                 30 
                   
                 57% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   monocytogenes 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 ATA AGA TGT GGC GCA TGC 
                 Probe/target Hybrid 
                 18 
                 9 
                 50% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 GCA TGC GCC ACA TCT TAT 
               
               
                   
               
               
                 L-01-78 
                 -10 
                 
                   Mycoplasma 
                 
                 TBD 
                 Beacon 
               
               
                   
                 -50 
                 
                   hominis 
                 
                 ATT GCT AAC CTC GCT CGA 
                 Probe/target Hybrid 
               
               
                   
                 -100 
                   
                 TCG AGC GAG GTT AGC AAT 
               
               
                   
               
               
                 L-01-79 
                   
                   Nocardia  spp. 
                   
                 Beacon 
               
               
                   
                   
                   
                   
                 Probe/target Hybrid 
               
               
                   
               
               
                 L-01-80 
                 -10 
                 
                   Proteus 
                 
                 GGC GTC ACA CCG G AT ACG 
                 Beacon 
                 30 
                   
                 63% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   mirabill / vulgaris   
                 TAGTGCTACGCC 
               
               
                   
                 -50 
                   
                 GGC GTC ACA CCG G AT ACG 
                 Probe/target Hybrid 
                 18 
                 12 
                 67% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CCGT ATC CGG TGT GAC GCC 
               
               
                   
               
               
                 L-01-81 
                 -10 
                   Pneumoscystis -1 
                 ACTC  GGC TTC ATG CCA ACA GTC   
                 Beacon 
                 25 
                   
                 56% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 
                   GAGT 
                 
               
               
                   
                 -50 
                   
                 GGC TTC ATG CCA ACA GTC 
                 Probe/target Hybrid 
                 21 
                 10 
                 57% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GAC TGT TGG CAT GAA GCC 
               
               
                   
               
               
                 L-01-82 
                 -10 
                   Pneumocystis -2 
                 GACAC  CAT AAG ATG CCG AGC GAG   
                 Beacon 
                 28 
                   
                 57% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                 GTGTC 
               
               
                   
                 -50 
                   
                 CAT AAG ATG CCG AGC GAG 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 CTC GCT CGG CAT CTT ATG 
               
               
                   
               
               
                 L-01-83 
                   
                 
                   Propionibacterium 
                 
               
               
                   
                   
                 
                   acnes 
                 
               
               
                   
               
               
                 L-01-84 
                   
                 
                   Propionibacterium 
                 
               
               
                   
                   
                 spp (other 
               
               
                   
                   
                 than Psaer) 
               
               
                   
               
               
                 L-01-85 
                 -10 
                 
                   Pseudomonas 
                 
                 ACCGCCGGCGT  A AGA CGA CTC GTC   
                 Beacon 
                 42 
                   
                 67% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   aeruginosa 
                 
                   ATC ACC T  TCGCCCAGCGGT 
               
               
                   
                 -50 
                   
                 A AGA CGA CTC GTC ATC ACC T 
                 Probe/target Hybrid 
                 20 
                 10 
                 50% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 A GGT GAT GAC GAGTCG TCT T 
               
               
                   
               
               
                 L-01-86 
                 -10 
                 
                   Pseudomonas 
                 
                 GCCGCCGGCGT  GGC AGA TTC CTA   
                 Beacon 
                 44 
                 30 
                 68% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 spp 
                   GGC ATT ACT  TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 GGC AGA TTC CTA GGC ATT ACT 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 AGT AAT GCC TAG GAA TCT GCC 
               
               
                   
               
               
                 L-01-87 
                 -10 
                 
                   Salmonellen 
                 
                 AGCTC  TGC GCT TTT GTG TAC GGG   
                 Beacon 
                 31 
                   
                 58% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                   GCT  GAGCT 
               
               
                   
                 -50 
                   
                 TGC GCT TTT GTG TAC GGG GCT 
                 Probe/target Hybrid 
                 21 
                 11 
                 57% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 AGC CCC GTA CAC AAA AGC GCA 
               
               
                   
               
               
                 L-01-88 
                 -10 
                 
                   Salmonellen 
                 
                 not required, competitor 
                 Beacon 
               
               
                   
                   
                 331 Komp 
                 is not labelled 
               
               
                   
                 -50 
                   
                 G TGCA TTT GTG TAC GGG GC 
                 Probe/target Hybrid 
                 18 
                 11 
                 61% 
                 no 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AGC CCC GTA CAC AAA AGC GCA 
               
               
                   
               
               
                 L-01-89 
                 -10 
                 
                   Salmonellen 
                 
                 CGCTC  CTT CAC CTA CGT GTC AGC G   
                 Beacon 
                 29 
                   
                 66% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 GAGCG 
               
               
                   
                 -50 
                   
                 CTT CAC CTA CGT GTC AGC G 
                 Probe/target Hybrid 
                 19 
                 11 
                 58% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 C GCT GAC ACG TAG GTG AAG 
               
               
                   
               
               
                 L-01-90 
                 -10 
                 
                   Salmonellen 
                 
                 not required, competitor 
                 Beacon 
               
               
                   
                   
                   
                 is not labelled 
               
               
                   
                 -50 
                   
                 T CAC CTA CAT ATC AGC GTG C 
                 Probe/target Hybrid 
                 20 
                 10 
                 50% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 C GCT GAC ACG TAG GTG AAG A 
               
               
                   
               
               
                 L-01-91 
                 -10 
                 
                   Salmonellen 
                 
                   
                 Beacon 
               
               
                   
                 -50 
                   
                   
                 Probe/target Hybrid 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-92 
                 -10 
                 
                   Salmonella 
                 
                 TGCCGGATT  CTT CAC CTA CGT GTC   
                 Beacon 
                 38 
                   
                 58% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                   AGC G  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 CTT CAC CTA CGT GTC AGC G 
                 Probe/target Hybrid 
                 19 
                 11 
                 58% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 C GCT GAC ACG TAG GTG AAG 
               
               
                   
               
               
                 L-01-93 
                 -10 
                   Serratia  spp 
                   
                 Beacon 
               
               
                   
                 -50 
                   
                   
                 Probe/target Hybrid 
               
               
                   
                 -100 
               
               
                   
               
               
                 L-01-94 
                 -10 
                 
                   Serratia 
                 
                 GCCGCCGGCGT CG AGA CTC TAG 
                 Beacon 
                 43 
                   
                 72% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   marcesceris 
                 
                 CTT GCC AGT TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 CG AGA CTC TAG CTT GCC AGT 
                 Probe/target Hybrid 
                 20 
                 11 
                 55% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 ACT GGC AAG CTA GAG TCT CG 
               
               
                   
               
               
                 L-01-95 
                 -10 
                 
                   Staphylococcus 
                 
                 TGCCGGATT  TTC TCG TCC GTT CGC   
                 Beacon 
                 43 
                   
                 158% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   aureus 
                 
                   TCG ACT TGC  AATCCCGGCA 
               
               
                   
                 -50 
                   
                 TTC TCG TCC GTT CGC TCG ACT TGC 
                 Probe/target Hybrid 
                 24 
                 14 
                 58% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GCA AGT CGA GCG AAC GGA CGA GAA 
               
               
                   
               
               
                 L-01-96 
                 -10 
                 Staphylococci 
                 GCAAC TT TCG CAC ATC AGC GTC 
                 Beacon 
                 281 
                   
                 54% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                   
                 AGT T GC 
               
               
                   
                 -50 
                   
                 TT TCG CAC ATC AGC GTC AGT T 
                 Probe/target Hybrid 
                 21 
                 10 
                 48% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 A ACT GAC GCT GAT GTG CGA AA 
               
               
                   
               
               
                 L-01-97 
                 -10 
                 
                   Stenotrophomonas 
                 
                 CCC TCT ACC ACA CTC TAG TCG GGT 
                 Beacon 
                 30 
                   
                 57% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   maltofilia 
                 
                 AGA GGG 
               
               
                   
                 -50 
                   
                 CCC TCT ACC ACA CTC TAG TCG 
                 Probe/target Hybrid 
                 21 
                 12 
                 52% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 CGA CTA GAG TGT GGT AGA GGG 
               
               
                   
               
               
                 L-01-98 
                 -10 
                 
                   Streptococcus 
                 
                 GCCGCCGGCGT  ACT CCT ACC AAC   
                 Beacon 
                 45 
                   
                 67% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   agalactiae 
                 
                   GTT CTT CTC  TCGCCCAGCGGC 
               
               
                   
                 -50 
                   
                 ACT CCT ACC AAC GTT CTT CTC 
                 Probe/target Hybrid 
                 21 
                 11 
                 48% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GAG AAG AAC GTT GGT AGG AGT 
               
               
                   
               
               
                 L-01-99 
                 -10 
                 Streptococci 
                 GGCCTTC GCC GTC CCT TTC TGG 
                 Beacon 
                 35 
                   
                 60% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                   
                 TTA GTT GAAGGCC 
               
               
                   
                 -50 
                   
                 GCC GTC CCT TTC TGG TTA GTT 
                 Probe/target Hybrid 
                 21 
                 11 
                 52% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 AAC TAA CCA GAA AGG GAC GGC 
               
               
                   
               
               
                 L-01-100 
                 -10 
                 
                   Streptococcus 
                 
                 GCGT TAA GCA AAT GTC ATG CAA CAT 
                 Beacon 
                 38 
                   
                 39% 
                 yes 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   pneumoniae 
                 
                 CTA CTTAACGC 
               
               
                   
                 -50 
                   
                 T TAA GCA AAT GTC ATG CAA CAT CTA 
                 Probe/target Hybrid 
                 25 
                 8 
                 32% 
                 yes 
                   
                 yes 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 TAG ATG TTG CAT GAC ATT TGC TTA A 
               
               
                   
               
               
                 L-01-101 
                 -10 
                 
                   Streptococcus 
                 
                 TGCCTTC  GAG CAA TTG CCC CTT TTA   
                 Beacon 
                 38 
                   
                 45% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   pyogenes 
                 
                   AAT TAC  GAAGGCA 
               
               
                   
                 -50 
                   
                 GAG CAA TTG CCC CTT TTA AAT TAC 
                 Probe/target Hybrid 
                 24 
                 9 
                 38% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 GTA ATT TAA AAG GGG CAA TTG CTC 
               
               
                   
               
               
                 L-01-102 
                 -10 
                 
                   Ureaplasma 
                 
                 ACGCTC  GTT CCC CAA CTC CCT ACT   
                 Beacon 
                 30 
                   
                 60% 
                 no 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 
                   urealyticum 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 GTT CCC CAA CTC CCT ACT 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 AGT AGG GAG TTG GGG AAC 
               
               
                   
               
               
                 L-01-103 
                 -10 
                 Urogenital- 
                 ACTC  CCC CTT GTG TM GGC AGG   
                 Beacon 
                 28 
                   
                 54% 
                 yes 
                 no 
                 no 
                 no 
                 no 
               
               
                   
                   
                 Peptostreptococci 
                 
                   GAGT 
                 
               
               
                   
                 -50 
                   
                 CCC CTT GTG TAA GGC AGG 
                 Probe/target Hybrid 
                 24 
                 11 
                 54% 
                 yes 
                   
                 no 
                 no 
                 no 
               
               
                   
                 -100 
                   
                 CCT GCC TTA CAC AAG GGG 
               
               
                   
               
               
                 L-01-104 
                 -10 
                 
                   Yersinia 
                 
                 ACGCTC  CCC ACT TTG GTC CGA AGA   
                 Beacon 
                 30 
                   
                 60% 
                 no 
                 no 
                 yes 
                 no 
                 no 
               
               
                   
                   
                 
                   enterocolitica 
                 
                 GAGCGT 
               
               
                   
                 -50 
                   
                 CCC ACT TTG GTC CGA AGA 
                 Probe/target Hybrid 
                 18 
                 10 
                 56% 
                 yes 
                   
                 no 
                 yes 
                 no 
               
               
                   
                 -100 
                   
                 TCT TCG GAC CAA AGT GGG 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 List of Beacon probes that work under identical conditions as in 
               
               
                 Table 1 and possess very similar physicochemical conditions 
               
            
           
           
               
               
               
            
               
                 Target organism 
                 Beacon name 
                 Sequence 5′-3′ 
               
               
                   
               
               
                   Acinetobacter  spp. 
                 B-Acibact-1 
                 TGCCGGTT 
               
               
                   
                   
                 
                   TTAGGCCAGATGGCTGCC 
                 
               
               
                   
                   
                 AATCCCGGCA 
               
               
                   
               
               
                   Aspergillus fumigatus , 
                 Aspfum 
                 CCGG  CCC CCG AGA GGT   
               
               
                   
                   
                   GAT ACA T  GCCGG 
               
               
                   
               
               
                   Aspergillus niger , 
                 Aspnig 
                 CCGGC  AAT TAC AAT GCG   
               
               
                   
                   
                   GAC TCC GAA G  CCGG 
               
               
                   
               
               
                   Klebsiella pneumoniae , 
                 B;Klepne-2 
                 ACGCCGGCGT  AGG TTA   
               
               
                   
                   
                   TTA ACC TCA TCG  CCT 
               
               
                   
                   
                 TCGCCCAGCGT 
               
               
                   
               
               
                   Mycobacterium avium  Complex, 
                 B.Mycav 
                 CCC  GGT GTT GAT ATA   
               
               
                   
                   
                   AGG CAG GTG  CCGGG 
               
               
                   
               
               
                   Mycobacterium chelonae , 
                 B-Mchel 
                 CCCGG  CA TGA AGT GTG   
               
               
                   
                   
                   TGG TCC TAT  CCGGG 
               
               
                   
               
               
                   Mycobacterium fortuitum , 
                 B-Mfort 
                 CCCGG  TGA AGC GCG   
               
               
                   
                   
                 TGG TCA TAT TC CCGGG 
               
               
                   
               
               
                   Mycobacterium gordonae , 
                 B-Mgord 
                 CCCGG  TGT GTC CTG TGG   
               
               
                   
                   
                   TCC TAT TC  CCGGG 
               
               
                   
               
               
                   Mycobacterium intracellulare , 
                 B-Mintra 
                 CCCGG  AC ATG CGT CTA   
               
               
                   
                   
                   AAG GTC CTA  CCGGG 
               
               
                   
               
               
                   Mycobacterium kansasii / gastri , 
                 B-Mkan 
                 CCCGG  TA GAG CTG AGA   
               
               
                   
                   
                   CGT ATC GAT C  CGGG 
               
               
                   
               
               
                   Mycobacterium malmoense , 
                 B-Mmalm 
                 CCG  CG CCA CTG AAA   
               
               
                   
                   
                   CGC CCT ATT  CGCGG 
               
               
                   
               
               
                   Mycobacterium smegmatis , 
                 B-Msmeg 
                 CCCGG  CAC GTC GAG   
               
               
                   
                   
                   GGC TCT GAC  CCGGG 
               
               
                   
               
               
                 
                   Mycobacterium tuberculosis 
                 
                 B-Mtb-compl 
                 CCA  CCG GAG AGG AAA   
               
               
                 complex, 
                   
                   AGG AGG  TGG 
               
               
                   
               
               
                   Mycobacterium xenopi , 
                 B-Mxen 
                 CCGCG  C CGC TAC CAA   
               
               
                   
                   
                   ACG CTT TC  GCGG 
               
               
                   
               
               
                   Shigella  (some  E. coli ), 
                 B-Shig 
                 CCGGG  tca ccc tgt atc gca   
               
               
                   
                   
                   cac ct  CCCGG 
               
               
                   
               
               
                   Staphylococcus aureus , 
                 B-Staphau 
                 TGCCGGATT  TTC TCG TCC   
               
               
                   
                   
                 
                   GTT CGC TCG ACT TGC 
                 
               
               
                   
                   
                 AATCCCGGCA 
               
               
                   
               
               
                   Streptococcus agalactiae , 
                 B-Straga-2 
                 GCCGCCGGCGT  ACT CCT   
               
               
                   
                   
                 
                   ACC AAC GTT CTT CTC 
                 
               
               
                   
                   
                 TCGCCCAGCGGC 
               
               
                   
               
               
                   Streptococcus pyogenes , 
                 B-Strpyo-C 
                 TGCCTTC  GAG CAA TTG   
               
               
                   
                   
                 
                   CCC CTT TTA AAT TAC 
                 
               
               
                   
                   
                 GAAGGCA 
               
               
                   
               
               
                   Citrobacter freundii , 
                 Citfreu-WI 
                 CCCGGT  CGC TTC ATT   
               
               
                   
                   
                 
                   ACG CTA TGT ATC C 
                 
               
               
                   
                   
                 ACCGGG 
               
               
                   
               
               
                   Streptococcus pyogenes , 
                 B-Strpyo-D 
                 CGCTC  GAG CAA TTG CCC   
               
               
                   
                   
                   CTT TTA AAT TAC  GAGCG 
               
               
                   
               
               
                   Streptococcus pneumoniae , 
                 B-Strepne-2 
                 CCGT  TAA GCA AAT GTC   
               
               
                   
                   
                 
                   ATG CAA CAT CTA CTTA 
                 
               
               
                   
                   
                 ACGG 
               
               
                   
               
               
                 Streptococci, F111 
                 B-Strept-2 
                 CGCCTTC  GCC GTC CCT   
               
               
                   
                   
                 TTC TGG TTA GTT 
               
               
                   
                   
                 GAAGGCG 
               
               
                   
               
               
                   Streptococcus agalactiae , 
                 B-Straga-3 
                 CCGCT  ACT CCT ACC AAC   
               
               
                   
                   
                   GTT CTT CTC  AGCGG 
               
               
                   
               
               
                   Serratia marcescens , 
                 B-Sermarc 
                 CCGCTC  CG AGA CTC TAG   
               
               
                   
                   
                   CTT GCC AGT  GAGCGG 
               
               
                   
               
               
                   Pseudomonas  spp., 
                 B-Psspp 
                 CGCTC  GGC AGA TTC CTA   
               
               
                   
                   
                   GGC ATT ACT  GAGCG 
               
               
                   
               
               
                 Staphylococci, 
                 B-Staphspp-2 
                 CCAAC  TT TCG CAC ATC   
               
               
                   
                   
                   AGC GTC AGT T  GG 
               
               
                   
               
               
                   Salmonella , 
                 B-Sal 1686 
                 CGCTC  CTT CAC CTA CGT   
               
               
                   
                   
                   GTC AGC G  GAGCG 
               
               
                   
               
               
                   Pseudomonas aeruginosa , 
                 B-Psaer D 
                 CCCGG  A AGA CGA CTC   
               
               
                   
                   
                   GTC ATC AGC T  CCGGG 
               
               
                   
               
               
                   Legionella pneumophila , 
                 B-Legpne 
                 CC GG  ATC TGA CCG TCC   
               
               
                   
                   
                   CAG GTT  CC GG 
               
               
                   
               
               
                   Klebsiella oxytoca , 
                 B-Kleboxy 
                 CCGAGGT  AGG TTA TTA   
               
               
                   
                   
                 
                   ACC TCA CTC CCT TCC 
                 
               
               
                   
                   
                 TCGG 
               
               
                   
               
               
                   Staphylococcus aureus , 
                 B-Staur-W1 
                 CCCCT  CAA GCT TCT CGT   
               
               
                   
                   
                   CCG TTC G  A GGGG 
               
               
                   
               
               
                   Listeria monocytogenes , 
                 Lismon 
                 CCTA  GCA TGC GCC ACA   
               
               
                   
                   
                   TCT TAT CA  GCTAGG 
               
               
                   
               
               
                   Klebsiella pneumoniae , 
                 B-Klepne-3 
                 CAGGCTT  AGG TTA TTA   
               
               
                   
                   
                   ACC TCA TCG CCT  G 
               
               
                   
               
               
                   Haemophilus influenzae , 
                 B-Haeinf 
                 CCCGG  CC GCA CTT TCA   
               
               
                   
                   
                   TCT TCC GAT  CCGGG 
               
               
                   
               
               
                   Burkholderia  spp., 
                 B-Burk. Spp 
                 CCCGG  CCA GTC ACC AAT   
               
               
                   
                   
                   GCA GTT CC  CCGGG 
               
               
                   
               
               
                   Burkholderia cepatia  &amp;  Burkholderia   
                 B-Burcep-cen WI 
                 CCT  GCC TA TGT ATT CAG   
               
               
                   cenocepatia , 
                   
                   CCA TGG  CAGG 
               
               
                   
               
               
                   Burkholderia malii  &amp;  Burkholderia   
                 B-Burpseumal WI 
                 GGGCC  T CGC CTC ACT   
               
               
                   pseudomalei , 
                   
                   AGA CCT ATG  CCGGG 
               
               
                   
               
               
                   Burkholderia vietnamensis , 
                 B-Burviet WI 
                 CCCGG  T CGC TTC TCT   
               
               
                   
                   
                   GGA CCT ATG  CCGGG 
               
               
                   
               
               
                   Burkholderia multivorans , 
                 B-Burmult WI 
                 CCCGG  CTT CAC CCT TCC   
               
               
                   
                   
                   AGC GCA  CCGGG 
               
               
                   
               
               
                   Burkholderia gladioli , 
                 B-Burgla WI 
                 CCA GC GG TAC GGT CAC   
               
               
                   
                   
                   TGT TAA ACT  GCTGG 
               
               
                   
               
               
                   Acinetobacter  spp, 
                 B-Acibact-2 
                 CCGTAG  ACC ATC CTC   
               
               
                   
                   
                   TCC CAT ACT CTA  CGG 
               
               
                   
               
               
                   Acinetobacter baumanii , 
                 B-Acinbaum-3 
                 C  CG CTA GGT CCG GTA   
               
               
                   
                   
                   GCA AGC  GG 
               
               
                   
               
               
                   Aspergillus flavus , 
                 B-Aspfla-3 
                 CGGCC  TAC ATT CCG GGA   
               
               
                   
                   
                   GCC TTT G  GCCG 
               
               
                   
               
               
                   Aspergillus terreus , 
                 Aspter 
                 CCGAT  CAG ACA CCC CGC   
               
               
                   
                   
                   CCC ATA  GATCGG 
               
               
                   
               
               
                   Bacteroides / Prevotella , 
                 B-BacPrev 
                 CCGCG  GT GTC TCA GTT   
               
               
                   
                   
                   CCA ATG TGG G  CGCGG 
               
               
                   
               
               
                 
                   Borrelia 
                 
                 B-Borrcompl 
                 CCCGG  GGT AAC AGA TAA   
               
               
                   burgdorferi  +  garinii  +  afzelii  +  valaisiana , 
                   
                   CAA GGG TTG  CCCGGG 
               
               
                   
               
               
                   Bordetella pertussis , 
                 B-Borper 
                 CCGGG  CTC CCC ACA CTT   
               
               
                   
                   
                   TCG TGC A  CCCGG 
               
               
                   
               
               
                   Escherichia coli , 
                 B-Ecol-II 
                 CCG  GCA AAG AAG CAA   
               
               
                   
                   
                   GCT TCT TCC  CCGG 
               
               
                   
               
               
                   Gardnerella vaginalis , 
                 Garvag 
                 CCGCTC  CAC CAT GAA   
               
               
                   
                   
                   GCA ACC CGT  GAGCGG 
               
               
                   
               
               
                 Eu-bacteria, 
                 B-Eub-338 
                 CCGCGT  GCT GCC TCC   
               
               
                   
                   
                   CGT AGG AGT  CGCGG 
               
               
                   
               
               
                   Enterococcus faecium , 
                 B-Encoc-ium 
                 C  TTC AAA TCA AAA CCA   
               
               
                   
                   
                   TGC GGT TTC  ATTTGAAG 
               
               
                   
               
               
                   Stenotrophomonas maltophilia , 
                 B-Stemal-2 
                 CCCGGA  CCC TCT ACC   
               
               
                   
                   
                   ACA CTC TAG TCG  CCGGG 
               
               
                   
               
               
                   Enterococcus faecalis , 
                 B-Encoc-alis-1 
                 CAACCA  CCC TCT GAT   
               
               
                   
                   
                   GGG TAG GTT  G 
               
               
                   
               
               
                 Enterococci, 
                 B-Entcoc 
                 CCCGG  C ATC CAT CAG   
               
               
                   
                   
                   CGA CAC CCG CCG  GG 
               
               
                   
               
               
                 Enterobacteriaceae, 
                 B-Entero-1247 
                 CCCGG  TCT CGC GAG GTC   
               
               
                   
                   
                   GCT TCT  CCGGG 
               
               
                   
               
               
                   Clostridium perfringens , 
                 B-Cloper-Cp2-10 
                 GCATCA  G ATT GCT CCT   
               
               
                   
                   
                   TTG GTT GAA TGA TG  C 
               
               
                   
               
               
                   Clostridium  spp., 
                 B-Clospp 
                 CCC  GG TAC CGT CAT TAT   
               
               
                   
                   
                   CGT CCC  CCGGG 
               
               
                   
               
               
                   Chlamydia trachomatis , 
                 ChltraA 
                 CCGC  TCG GAT GCC CAA   
               
               
                   
                   
                   ATA TCG C GG 
               
               
                   
               
               
                   Candida dubliniensis , 
                 B-Can-dub 
                 CCCGG  C CCG AAA GAG   
               
               
                   
                   
                   TAA CTT GCA AAA  CCGGG 
               
               
                   
               
               
                   Candida glabrata , 
                 B-Cangla 
                 CCCGG  AGG CAA GGG   
               
               
                   
                   
                   GCG CAA AA  CCGGG 
               
               
                   
               
               
                   Candida krusei , ( Issatchenkia   
                 B-Cankru 
                 CCGTGA  CCT GCA GCA   
               
               
                   orientalis ) 
                   
                   AGA ACC GAT  CACGG 
               
               
                   
               
               
                   Candida lusitaniae , ( Clavispora   
                 B. Canlus 
                 CACT  G CCG ACT CAG ACC   
               
               
                   lusitaniae ) 
                   
                   ACG AAA  GCAGTG 
               
               
                   
               
               
                   Candida albicans , 
                 B-Canalb-3 
                 CCGCG  TT TAC ACA GAC   
               
               
                   
                   
                   CCG GGT CAT  CGCGG 
               
               
                   
               
               
                   Candida tropicalis , 
                 B-Cantrop 
                 CCTCGG  AC ATT CCA ACG   
               
               
                   
                   
                   CAA TTC TCCTAC  CGAGG 
               
               
                   
               
               
                   Candida parapsilosis , 
                 B-Can-para 
                 CCCGG  CAC ATT TCT TTG   
               
               
                   
                   
                   CAC TTA TCC TAC  CCGGG 
               
               
                   
               
               
                   Chlamydia pneumoniae , 
                 B-Chlapneu 
                 CCGGG  CTC TTC CTC AAC   
               
               
                   
                   
                   CGA AAG GT  CCCGG 
               
               
                   
               
               
                   Chlamydia psittaci  group, 
                 B-S-S-Cps-1414-a-A-18 
                 CCGG  AAG GCA AAA CCA   
               
               
                   
                   
                   ACT CCC AT  CCGG 
               
               
                   
               
               
                   Campylobacter  (pathogenic 
                 B-Ctherm 
                 CCCGG  GCC CTA AGC GTC   
               
               
                   thermophiles ), 
                   
                   CTT CCA  CCGGG 
               
               
                   
               
               
                   Campylobacter coli , 
                 B-Cpcoli 
                 CGCTC  TCG ATG GCA TCA   
               
               
                   
                   
                   GGG GTT  GAGCG 
               
               
                   
               
               
                   Campylobacter lari , 
                 Clari 
                 CCCGG  CCC GAA GTG TTA   
               
               
                   
                   
                   GCA ACT AAA TC  GCCGGG 
               
               
                   
               
               
                   Campylobacter jejuni , 
                 B-Cjj 
                 CCGGG  TA AGC TAA CCA   
               
               
                   
                   
                   CAC CTT ATA CCG  CCCGG 
               
               
                   
               
               
                   Campylobacter upsaliensis , 
                 B-Cpups 
                 CCCGGGC  CGT GTG TCG   
               
               
                   
                   
                 
                   CCC TAG GCG TA 
                 
               
               
                   
                   
                 GCCCGGG 
               
               
                   
               
               
                   Pneumocystis carinii , 
                 B-Pncari 
                 CCCTGC  TA TCC AGT AAC   
               
               
                   
                   
                   TGA AAC CGA TGC  AGGG 
               
               
                   
               
               
                   Mycoplasma pneumoniae , 
                 B-Myplapn 
                 CCTCCG  TGA TAG CTG   
               
               
                   
                   
                   TTT CCA ACT ACC GGA  GG 
               
               
                   
               
               
                   Cryptococcus neoformans , 
                 B-Cryneo 
                 CCTGG  TAT GAT TCA CCA   
               
               
                   
                   
                   TAG AGG GCC  AGG 
               
               
                   
               
               
                 EHEC, 
                 B-EHEC 
                 CCCG  GT CAC CCC ATA   
               
               
                   
                   
                   AAA GAG GCT  CCGGG 
               
               
                   
               
               
                   Neisseria meningitidis , 
                 B-Neimeng 
                 CACCG  TTA TCC CCC ACT   
               
               
                   
                   
                   ACT CGG  TG 
               
               
                   
               
               
                   Neisseria gonorrhoeae , 
                 B-Neigon 
                 CCCGG  ACC CCG CCA   
               
               
                   
                   
                   ACC AGC TAA  CCGGG 
               
               
                   
               
               
                   Clostridium difficile , 
                 B-Clodiff 
                 CGGGT  CGA AGT AAA TCG   
               
               
                   
                   
                   CTC AAC TTG CA  CCCG 
               
               
                   
               
               
                   Clostridium botulinum , 
                 B-Clobot 
                 CG TT  GC CGT TTC ATG   
               
               
                   
                   
                   CGA AAC TAC AA  CG 
               
               
                   
               
               
                   Clostridium tetani , 
                 B-Clotet 
                 CCGG AA  CT GTG TTA CTC   
               
               
                   
                   
                   ACC CGT CCG  G 
               
               
                   
               
               
                   Peptostreptococcus anaerobius , 
                 B-Pepan 
                 CCGGC  CTT TGA TAT ATC   
               
               
                   
                   
                   TAC GAT GCC G  G 
               
               
                   
               
               
                   Peptostreptococcus magnus , 
                 B-pepmag 
                 CCGC  CTA ATC CGA AAT   
               
               
                   
                   
                   GAA TTC TGG CG  G 
               
               
                   
               
               
                   Peptostreptococcus magnus , 
                 B-pepmag 
                 CCGCC  ATG TGT TTC TAC   
               
               
                   
                   
                   GAT TTT ATG CGG  CGG 
               
               
                   
               
               
                   Peptostreptococcus micros , 
                 B-Pepmic 
                 CCCGG  ACT TTC ATT TCA   
               
               
                   
                   
                   TTT CCA TTC CCG  GG 
               
               
                   
               
               
                   Enterococcus faecalis , 
                 B-Encoc-alis-2 
                 CCATCG  GCA CTC GGG   
               
               
                   
                   
                   AGG AAA GAA G  CGATGG 
               
               
                   
               
               
                   Enterococcus faecium , 
                 B-entfae-1 
                 CGC  CCA TGC GGT TTT   
               
               
                   
                   
                   GAT TGT TAT AC  GGGCG 
               
               
                   
               
               
                   Enterococcus casseliflavus , 
                 B-Entcas 
                 CCGCG  CAA GGG ACG   
               
               
                   
                   
                 
                   AAC ATT TTA CTC TC 
                 
               
               
                   
                   
                 GCGG 
               
               
                   
               
               
                   Enterococcus gallinarum , 
                 B-entfae-2 
                 CCGCG  CAA GGG ATG   
               
               
                   
                   
                   AAC GTT CTA CTC  GCGG 
               
               
                   
               
               
                   Candida albicans , 
                 B-Canalb-2 
                 CCCGG  TTT CCT TCT GGG   
               
               
                   
                   
                   TAG CCA TT  CCGGG 
               
               
                   
               
               
                   Morganella morganii  ( Proteus   
                 B. Mormorg 
                 CCGG  CAA GAC TCT AGC   
               
               
                   morganii ), 
                   
                   TGA CCA GTA TC  GCCGG 
               
               
                   
               
               
                   Proteus mirabilis , 
                 B-Protmir 
                 CG  CCGATA GTG CAA GGT   
               
               
                   
                   
                   CCG AAG  CGGCG 
               
               
                   
               
               
                   Proteus vulgaris , 
                 B-Protvul 
                 CCG  CCG TAG ACG TCA   
               
               
                   
                   
                   TGC GGT A  GGCGG 
               
               
                   
               
               
                   Treponema pallidum , 
                 B-Trepal 
                 CCCGG  TCC GCC ACT CTA   
               
               
                   
                   
                   GAG AAA CG  CCGGG 
               
               
                   
               
               
                   Trichonomas vaginalis , 
                 B-Trivag 
                 CCCGG  GAA TGG CGT   
               
               
                   
                   
                   GCC TCT GAT GA  CCGGG 
               
               
                   
               
               
                   Micrococci , 
                 B-Micoc 
                 CCCGG  ACC TCA CAG TAT   
               
               
                   
                   
                   CGC AAC C  GGG 
               
               
                   
               
               
                   Lactobacillus brevis , 
                 B-Lacbrev 
                 CGG  CCG CGG GAT CAT   
               
               
                   
                   
                   CCA GAA  GGCCG 
               
               
                   
               
               
                   Yersinia enterocolitica , 
                 B-Yerent 
                 CCCGG  ATC TCT GCT AAA   
               
               
                   
                   
                   TTC CGT GGA TG  CCGGG 
               
               
                   
               
               
                   Bacillus cereus , 
                 B-Baccer 
                 CCATAC  CAC TCT GCT   
               
               
                   
                   
                   CCC GAA GG  TATGG 
               
               
                   
               
               
                   Vibrio cholerae , 
                 B-Vibchol 
                 CTGAT  GCA TAT CCG GTA   
               
               
                   
                   
                   GCG CAA G  CATCAG 
               
               
                   
               
               
                   Vibrio parahaemolyticus , 
                 B-Vibpara 
                 CCCGG  TGC AGC TAT TAA   
               
               
                   
                   
                   CTA CAC TAC C  CCGGG 
               
               
                   
               
               
                   Cryptosporidium  spp., 
                 B-Crypt 
                 CCGTA  CAT AAG GTG CTG   
               
               
                   
                   
                   AAG GAG TAA G  TACGG 
               
               
                   
               
               
                   Coxiella burnetii , 
                 B-Cox 
                 CCGGG  ACC CTT GAG AAT   
               
               
                   
                   
                   TTC TTC CCC  GG 
               
               
                   
               
               
                   Bartonella  spp., 
                 B-Bart 
                 CCG  GCA CAA ATT TCT   
               
               
                   
                   
                 
                   CTG TGT TAT TCC G 
                 
               
               
                   
                   
                 CCGG 
               
               
                   
               
               
                   Enterobacter sakazakii , 
                 B-Entsak 
                 CCCGG  TCT CTG CAG GAT   
               
               
                   
                   
                   TCT CTG GAT G  CCGGG 
               
               
                   
               
               
                   Enterobacter cloacae , 
                 B-Entclo 
               
               
                   
               
               
                   Enterobacter aerogenes , 
                 B-Entaer 
               
               
                   
               
               
                   Ehrlichia  spp., 
                 B-Ehrlich 
                 CCGC  GCT AAT CTA ACG   
               
               
                   
                   
                   TAG GCT CAT C  GCGG 
               
               
                   
               
               
                   Rickettsia  spp., 
                 B-Rickspp 
                 CCGCG  CAC TCA CTC GGT   
               
               
                   
                   
                   ATT GCT GGA T  CGCGG 
               
               
                   
               
               
                   Rickettsia  spotted fever complex, 
                 B-Rickspot 
                 CTA  GCC CCA ATT AGT   
               
               
                   
                   
                   CCG TTC G  GCTAG 
               
               
                   
               
               
                   Rickettsia typhi  complex, 
                 B-Ricktyph 
                 CG  CCC GTC TGC CAC   
               
               
                   
                   
                   TAA TTA ACT A  GGGCG 
               
               
                   
               
               
                   Leishmania  spp., 
                 B-Leisch 
                 CCCGG  AAA AGG CGT TAC   
               
               
                   
                   
                   GGC CGG  G 
               
               
                   
               
               
                   Toxoplasma gondii , 
                 B-Toxgan 
                 CCGGC  TCC AGG GGA   
               
               
                   
                   
                   AGA GGC ATG  CCGG 
               
               
                   
               
               
                 Yeast spp., 
                 B-Yeast 
                 CCCG  GGT ATT TAC ATT   
               
               
                   
                   
                 
                   GTA CTC ATT CCA A 
                 
               
               
                   
                   
                 CCGGG 
               
               
                   
               
               
                   Francisella tularensis , 
                 B-Frantul 
                 CCAT  GCG ACA GCC CGA   
               
               
                   
                   
                   AAG CCA  GCATGG 
               
               
                   
               
               
                   Lactobacillus  spp. A, 
                 B-lactspp-A 
                 CCC  GGA GTT CCA CTG   
               
               
                   
                   
                   TCC TCT TC  CCGGG 
               
               
                   
               
               
                   Lactobacillus  spp. B, 
                 B-lactspp-B 
                 CCCGG  ATC AGT CTC TCA   
               
               
                   
                   
                   ACT CGG C  CGGG 
               
               
                   
               
               
                   Burkholderia cepacia  complex 
                 B-Bcc 
                 CCC 
               
               
                   
                   
                 
                   GGTTGGCAACCCTCTGTTCC 
                 
               
               
                   
                   
                 CCGGG 
               
               
                   
               
               
                   Staphylococcus aureus , 
                 B-Staur-3 
                 CCT  G CAA GCT TCT   
               
               
                   
                   
                 
                   CGT CCG TTC GC 
                 
               
               
                   
                   
                 AGG 
               
               
                   
               
               
                 
                   Burkholderia ambifaria 
                 
                 B-Burkamp 
                 pending due to lack of 23S 
               
               
                   
                   
                 sequences 
               
               
                   
               
               
                 
                   Burkholderia antina 
                 
                 B-Burkant 
                 pending due to lack of 23S 
               
               
                   
                   
                 sequences 
               
               
                   
               
               
                 
                   Burkholderia dolosa 
                 
                 B-Burkdol 
                 pending due to lack of 23S 
               
               
                   
                   
                 sequences 
               
               
                   
               
               
                 
                   Burkholderia pyrrocinia 
                 
                 B-Burkpyrr 
                 pending due to lack of 23S 
               
               
                   
                   
                 sequences 
               
               
                   
               
               
                 
                   Burkholderia stabilis 
                 
                 B-Burkstab 
                 pending due to lack of 23S 
               
               
                   
                   
                 sequences 
               
               
                   
               
               
                 Lactobacilli, 
               
               
                   
               
               
                   Candida  spp, 
                 see Yeast 
               
               
                   
               
               
                 Lactobacilli, 
               
               
                   
               
               
                   Staphylococcus corosus , 
               
               
                   
               
               
                   Staphylococcus aureus , 
                 B-Staur 
                 CCCCT  CAA GCT TCT   
               
               
                   
                   
                 
                   CGT CCG TTC G 
                 
               
               
                   
                   
                 AGGGG 
               
               
                   
               
               
                 Eu-bacteria, 
                 B-Eub-338 
                 CCGCGT  GCT GCC TCC   
               
               
                   
                   
                   CGT AGG AGT  CGCGG 
               
               
                   
               
               
                 Eu-bacteria, 
                 B-Eub-338 
                 CCGCGT  GCT GCC TCC   
               
               
                   
                   
                   CGT AGG AGT  CGCGG 
               
               
                   
               
               
                 Eu-bacteria, 
                 B-Eub-338 
                 CCGCGT  GCT GCC TCC   
               
               
                   
                   
                   CGT AGG AGT  CGCGG 
               
               
                   
               
               
                 Eu-bacteria, 
                 B-Eub-338 
                 CCGCGT  GCT GCC TCC   
               
               
                   
                   
                   CGT AGG AGT  CGCGG