# Patent

## Title
Genetic fingerprinting and identification method

## Abstract

The present disclosure provides methods for molecular fingerprinting for the characterization and identification of organisms. More specifically, in one aspect the present invention provides a method of identifying an organism in a sample by embedding fingerprint bands from any amplification based fingerprinting method within a DNA sequence so that small differences in size are resolvable. Fingerprint output is provided in a text file format that can then be analyzed by bioinformatics tools.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application claims the benefit of U.S. Provisional Application No. 61/235,999, filed Aug. 21, 2009, which is incorporated by reference herein in its entirety.


FIELD OF THE INVENTION
This invention relates to the field of molecular biology and more specifically to methods for molecular fingerprinting for the characterization and identification of organisms.
BACKGROUND OF THE INVENTION
Central to the field of microbiology is the ability to positively identify microorganisms at the level of genus, species, or serotype. Correct identification is not only an essential tool in the laboratory, but it plays a significant role in the control of microbial contamination in the processing of food stuffs, the production of agricultural products, and the monitoring of environmental media, such as ground water. Of greatest concern is the detection and control of pathogenic microorganisms. Typically, pathogen identification has relied on methods for distinguishing phenotypic aspects, such as growth or motility characteristics, and for immunological and serological characteristics. Selective growth procedures and immunological methods are the traditional methods of choice for bacterial identification and these can be effective for the presumptive detection of a large number of species within a particular genus. However, these methods are time consuming and are subject to error. Selective growth methods require culturing and subculturing in selective media, followed by subjective analysis by an experienced investigator. Immunological detection (e.g., ELISA) is more rapid and specific, however, it still requires growth of a significant population of organisms and isolation of the relevant antigens. For these reasons, interest has turned to detection of bacterial pathogens based on nucleic acid sequence.
Nucleic acid polymorphism provides a means to identify species, serotypes, strains, varieties, breeds, or individuals based on differences in their genetic make up. Nucleic acid polymorphism can be caused by nucleotide substitution, insertion, or deletion. The ability to determine genetic polymorphism has widespread application in areas such as genome mapping, genetic linkage studies, medical diagnosis, epidemiological studies, forensics, and agriculture. Several methods have been developed to compare homogenous segments of DNA to determine if polymorphism exists.
One method for determining genetic polymorphism uses primers of an arbitrary sequence to amplify DNA by the polymerase chain reaction (PCR) (Williams et al., Nucleic Acids Res. 18:6531-35 (1990); U.S. Pat. No. 5,126,239, incorporated herein by reference). Because the primers are not designed to amplify a specific sequence, the technique is called random amplification of polymorphic DNA (RAPD) or arbitrarily primed PCR (APPCR). The primers used are at least seven nucleotides in length. Under the proper conditions, differences as small as a single nucleotide can affect the binding of the primer to the template DNA, thus resulting in differences in the distribution of amplification products produced between genomes.
Another method for identifying and mapping genetic polymorphisms has been termed amplified fragment length polymorphism (AFLP; U.S. Pat. No. 5,874,215, incorporated herein by reference). AFLP combines the use of restriction enzymes with the use of PCR. Briefly, restriction fragments are produced by the digestion of genomic DNA with a single or a pair of restriction enzymes. If a pair of enzymes is used, enzymes are paired based on differences in the frequency of restriction sites in the genome, such that one of the restriction enzymes is a “frequent cutter” while the remaining enzyme is a “rare cutter.” The use of two enzymes results in the production of single and double digestion fragments. Next, double stranded synthetic oligonucleotide adaptors of 10-30 bases are ligated onto the fragments generated. Primers are then designed based on the sequence of the adapters and the restriction site. When pairs of restriction enzymes are used, nucleotides extending into the restriction sites are added to the 3′ end of the primers such that only fragments generated due to the action of both enzymes (double cut fragments) are amplified. Using this method, any polymorphism present at or near the restriction site will affect the binding of the primer and thus the distribution of the amplification products. In addition, any differences in the nucleotide sequence in the area flanked by the primers will also be detected. AFLP allows for the simultaneous co-amplification of multiple fragments.
A further method is Direct Linear Analysis (DLA), which analyzes individual DNA molecules bound with sequence-specific tags (see Chan et al., Genome Res. 14:1137-46 (2004); U.S. Pat. No. 6,263,286, incorporated herein by reference). The method is intended to identify repetitive information in DNA, which is moved past at least one station, at which labelled units of DNA interact with the station to produce a DNA-dependent impulse. Because the extended objects are similar, or preferably identical, and comprise a similar, or preferably identical, pattern of labelled units, a characteristic signature of interactions is repeated as each extended object moves past a station or a plurality of stations. This repetitive information is extracted from the overall raw data by means of an autocorrelation function and is then used to determine structural information about the DNA.
Another method is amplification of repetitive elements (REP-PCR). This technique is based on families of repetitive DNA sequences present throughout the genome of diverse bacterial species (reviewed by Versalovic et al., Methods Mol. Cell. Biol. 5:25-40 (1994)). Repetitive extragenic palindromic (REP) sequences are thought to play an important role in the organization of the bacterial genome. Genomic organization is believed to be shaped by selection and the differential dispersion of these elements within the genome of closely related bacterial strains can be used to discriminate between strains (see, e.g., Louws et al., Appl. Environ. Micro. 60:2286-95 (1994)). REP-PCR utilizes oligonucleotide primers complementary to these repetitive sequences to amplify the variably sized DNA fragments lying between them. The resulting products are separated by electrophoresis to establish the DNA “fingerprint” for each strain.
The output data of these fingerprinting systems generally is measured by assigning band sizes, though these assignments are somewhat imprecise depending on the sizing ladder used for the comparison. In addition, the output data can be difficult to compare between laboratories and often relies on the use of expensive proprietary software programs (such as BioNumerics, Applied Maths, Austin, Tex.) to handle the data.
SUMMARY OF THE INVENTION
Applicants have solved the aforementioned problems by embedding the fingerprint bands from any amplification based fingerprinting method within a DNA sequence so that small differences in size are resolvable. Fingerprint output is provided in a text file format that can then be analyzed by powerful, freeware bioinformatics tools.
One aspect is for a method of identifying an organism in a sample comprising: (a) providing a sample comprising said organism, said organism comprising at least one nucleic acid; (b) combining said sample or the at least one nucleic acid therefrom with an amplification mix comprising at least one labeled oligonucleotide primer; (c) generating at least one labeled amplification product from the at least one nucleic acid of said organism using a nucleotide amplification technique employing said at least one labeled oligonucleotide primer; (d) combining said at least one labeled amplification product with products of a DNA sequencing reaction to create a separation mix; and (e) separating said separation mix on the basis of oligonucleotide length in a fluorescent DNA sequencing instrument to generate a sequence embedded fingerprint pattern for said organism.
In some aspects, the method comprises after step (e) the further steps of: (f) comparing said sequence embedded fingerprint pattern for said organism to a database containing sequence embedded fingerprint patterns for known organisms; and (g) identifying said organism as a function of said comparison to said database.
Another aspect is for an isolated polynucleotide comprising the nucleic acid sequence set forth in SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5.
Other objects and advantages will become apparent to those skilled in the art upon reference to the detailed description that hereinafter follows.
SUMMARY OF THE SEQUENCES
SEQ ID NOs:1-4 and 25 are the nucleotide sequences of oligonucleotide primers useful in the present invention. Each primer can be employed alone or in conjunction with one or more other primers. For example, SEQ ID NOs:1-4 can be employed together to create the FB1D1 primer mix, while SEQ ID NO:25 can be employed alone as the FP5 primer.
SEQ ID NOS:5-7, 13, and 14 are the nucleotide sequences resulting from operating the method of the present invention with negative control PCR reactions obtained using the FB1D1 primer set.
SEQ ID NOS:8-12 are the nucleotide sequences resulting from operating the method of the present invention with PCR reactions obtained using the FB1D1 primer set and Saccharomyces cerevisiae DNA.
SEQ ID NOS:15-19 are the nucleotide sequences resulting from operating the method of the present invention with PCR reactions obtained using the FB1D1 primer set and Salmonella enterica DNA.
SEQ ID NOS:20-24 are the nucleotide sequences resulting from operating the method of the present invention with PCR reactions obtained using the FB1D1 primer set and Staphylococcus aureus DNA.
SEQ ID NOS:26-30 are the nucleotide sequences resulting from operating the method of the present invention with negative control PCR reactions obtained using the FP5 primer.
SEQ ID NOS:31-35 are the nucleotide sequences resulting from operating the method of the present invention with PCR reactions obtained using the FP5 primer and Staphylococcus aureus DNA.
SEQ ID NOS:36-40 are the nucleotide sequences resulting from operating the method of the present invention with PCR reactions obtained using the FP5 primer and Salmonella enterica DNA.
SEQ ID NOS:41-45 are the nucleotide sequences resulting from operating the method of the present invention with PCR reactions obtained using the FP5 primer and Saccharomyces cerevisiae DNA.
SEQ ID NO:46 is the consensus nucleotide sequence obtained from a sequence comparison of SEQ ID NOS:21-23.
SEQ ID NO:47 is the consensus nucleotide sequence obtained from a sequence comparison of SEQ ID NOS:33-35.
SEQ ID NO:48 is the consensus nucleotide sequence obtained from a sequence comparison of SEQ ID NOS:9-11.
SEQ ID NO:49 is the consensus nucleotide sequence obtained from a sequence comparison of SEQ ID NOS:41, 43, and 45.
SEQ ID NO:50 is the consensus nucleotide sequence obtained from a sequence comparison of SEQ ID NOS:17-19.
SEQ ID NO:51 is the consensus nucleotide sequence obtained from a sequence comparison of SEQ ID NOS:36-38.
The sequences conform with 37 C.F.R. §§1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. 1.822.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1A shows a phylogram generated from a Clustal W alignment of all sequence reads from primer mix FB1D1 of Example 1.
FIG. 1B shows a phylogram generated from a Clustal W alignment of all sequence reads from single primer FP5 of Example 1.



DETAILED DESCRIPTION
Applicants specifically incorporate the entire contents of all cited references in this disclosure. Further, when an amount, concentration, or other value or parameter is given as either a range, preferred range, or a list of upper preferable values and lower preferable values, this is to be understood as specifically disclosing all ranges formed from any pair of any upper range limit or preferred value and any lower range limit or preferred value, regardless of whether ranges are separately disclosed. Where a range of numerical values is recited herein, unless otherwise stated, the range is intended to include the endpoints thereof, and all integers and fractions within the range. It is not intended that the scope of the invention be limited to the specific values recited when defining a range.
The term “comprising” is intended to include embodiments encompassed by the terms “consisting essentially of” and “consisting of.” Similarly, the term “consisting essentially of” is intended to include embodiments encompassed by the term “consisting of.”
The term “oligonucleotide” as used herein refers to a molecule comprised of two or more deoxyribonucleotides or ribonucleotides.
The term “primer” as used herein refers to an oligonucleotide of any arbitrary sequence, whether occurring naturally, as in a purified restriction digest, or produced synthetically, that is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product which is complementary to a nucleic acid strand is induced, i.e., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH. It is preferable that primers are sequences that do not form a secondary structure by base pairing with other copies of the primer or sequences that form a “hair pin” configuration. The sequence conveniently can be generated by computer or selected at random from a gene bank. The primer is preferably single stranded for maximum efficiency in amplification, but may alternatively be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxyribonucleotide.
In the present disclosure, primers used for amplification based fingerprint methods are labelled with a fluor. Following generation of the fingerprint products by amplification, the fingerprint amplicons are comingled with the product of a previously performed DNA sequencing reaction. The comingled products are then run to produce a DNA sequence from a fluorescent DNA sequencing instrument. The sequence output is perturbed at positions where the fingerprint products are migrating with like-sized DNA sequencing fragments. The perturbations result in an altered DNA sequence output from the instrument. These alterations are reproducible, and comparison of the output sequences can be used to characterize and/or identify the organism whose DNA was subject to the fingerprinting method.
The nucleic acids to be analyzed by a process described herein may be DNA or RNA, and the DNA or RNA may be double stranded or single stranded. Any source of nucleic acid, in purified or nonpurified form, can be utilized as the starting nucleic acid. For example, the nucleic acid may be from a natural DNA or RNA from any source, including virus, bacteria, and higher organisms such as plants, animals, and microbes or from cloned DNA or RNA. Additionally, the nucleic acid may constitute the entire nucleic acid or may be a fraction of a complex mixture of nucleic acids. Preferably, the nucleic acid is deoxyribonucleic acid.
Processes described herein are applicable to any nucleic acid-containing starting material, including foods and allied products, vaccines and milk infected with a virus or a bacterium, whole blood, blood serum, buffy coat, urine, feces, liquor cerebrospinalis, sperm, saliva, tissues, and cell cultures (such as mammalian cell cultures and bacterial cultures). The processes are also applicable to relatively pure input materials, such as the product of a PCR or the product to be purified further of another process for recovering nucleic acids.
The step of generating an amplified nucleic acid product can be performed by, for example, RAPD PCR, AFLP PCR, REP-PCR, or DLA. Using RAPD as an example, the choice of nucleic acid polymerase used in the extension reaction, depends on the nature of the template. For DNA template strands, suitable commercially available DNA polymerase includes DNA polymerase obtained from the thermophilic bacterium Thermus aquaticus (Taq polymerase) or other thermostable polymerases. Structural variants and modified forms of this and other DNA polymerases would also be expected to be useful in the process of the present invention. For RNA templates, reverse transcriptase is an example of a DNA polymerase that would also be expected to be useful. In the presence of the nucleoside triphosphate substrates, natural or analogues, the polymerase extends the length of the primer in the 3′ direction. The sequence of the extension product will generally be complementary to the corresponding sequence of the template strand.
The nucleoside triphosphate substrates are employed as described in PCR Protocols, A Guide to Methods and Applications, M. A. Innis, D. H. Gelfand, J.-J. Sninsky and T. J. White, eds. pp. 3-12, Academic Press (1989), which is incorporated by reference, and U.S. Pat. Nos. 4,683,195 and 4,683,202, both incorporated by reference. The substrates can be modified for a variety of experimental purposes in ways known to those skilled in the art. As an example, at least one of the natural nucleoside triphosphate substrates may be replaced by a mobility-shifting analogue as taught in U.S. Pat. No. 4,879,214, which is incorporated by reference.
Specifically, U.S. Pat. No. 4,683,202 to Mullis is directed to a process for amplifying any desired specific nucleic acid sequence contained in a nucleic acid or mixture thereof. The process of Mullis comprises treating separate complementary strands of the nucleic acid with a molar excess of two oligonucleotide primers, and extending the primers to form complementary primer extension products, which act as templates for synthesizing the desired nucleic acid sequence. The primers of Mullis are designed to be sufficiently complementary to different strands of each specific sequence to be amplified. The steps of the reaction may be carried out stepwise or simultaneously and can be repeated as often as desired.
In one embodiment, at least one primer of greater than seven nucleotides is provided. Primers can be synthesized by standard techniques known to those skilled in the art. In some embodiments, at least one primer of nine to ten nucleotides in length is employed. Conveniently, one primer is employed. The at least one primer is labelled, preferably with a fluorophore, which can be, for example, dR6G, dR110, dTAMRA, dROX, VIC, NED, PET, LIZ, 6-FAM, TAMRA, DyeMer488/615, DyeMer488/630, PE-TexasRed, ECD, Alexa Fluor 610RPE, FITC, Oregon Green 488, or Qdot525. Other fluorophores can also be employed.
In some embodiments, a nucleic acid is contacted with at least one oligonucleotide primer as described herein. The extension product is dissociated from the complementary random nucleic acid on which it was synthesized to produce a single-stranded molecule; and the random nucleic acid segment is amplified by contacting the single-stranded extension product with a primer from above under conditions as, for example, disclosed in PCR Protocols and U.S. Pat. No. 4,683,202 such that an amplification extension product is synthesized using the single strand produced (i.e., the dissociated extension product) as a template.
The comingled products are then run to produce a DNA sequence from a fluorescent DNA sequencing instrument. The sequence output is perturbed at positions where the fingerprint products are migrating with like-sized DNA sequencing fragments. The perturbations result in an altered DNA sequence output from the instrument. These alterations are reproducible, and comparison of the output sequences can be used to characterize and/or identify the organism whose DNA was subject to the fingerprinting method using powerful freeware sequence analysis tools such as BLAST and Clustal W.
A process disclosed herein can be used to construct a nucleic acid ‘fingerprint’. Such fingerprints are specific to individual organisms and can be applied to problems of identification or distinguishing of individual organisms. Such a fingerprint would be constructed using multiple polymorphisms generated by different primers and detected by the present invention, just as the polymorphisms are used to create a fingerprint in Jeffreys, A. J., “Individual-Specific ‘Fingerprints’ of Human DNA”, Nature 316:76-79 (1985), which is incorporated herein by reference. That is, genomes are compared for the presence of absence of polymorphisms.
In some embodiments, the steps of generating amplification products and producing an amplification profile after mixing the amplifications products with the oligonucleotide size ladder can be repeated at different stringency conditions as compared to that of a first pass through the process to generate a different amplification profile as compared to that generated by the first pass. Multiple repetitions are of course possible.
EXAMPLES
The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the preferred features of this invention, and without departing from the spirit and scope thereof, can make various changes and modification of the invention to adapt it to various uses and conditions.
Example 1
The hypothesis that labeled amplification based fingerprinting products could be detected and reproducibly placed within a DNA sequence by means of the invention was tested using Random amplification of polymorphic DNA (RAPD) fingerprinting to generate the fingerprinting products. PCR was performed using a mix of four primers labeled at the 5′ end with a FAM fluor, collectively known as primer mix FB1D1 and single primer FP5 (see Table 1).







TABLE 1





Primers















FB1D1 primer mix








1.
5' FAM-CGCTTCGCGTTTTAAAAACCGACATGAGTACAATAC



(SEQ ID NO: 1)


 


2.
5' FAM-CGCTTCGCGTTTTAAAAACCGACATGAGTACAATCC



(SEQ ID NO: 2)


 


3.
5' FAM-CGCTTCGCGTTTTAAAAACCGACATGAGTACAATGC



(SEQ ID NO: 3)


 


4.
5' FAM-CGCTTCGCGTTTTAAAAACCGACATGAGTACAATTC



(SEQ ID NO: 4)


 







FP5 primer








5.
5' FAM-ATCCGGCATATCTCGACATTCCTGATTACAATCC



(SEQ ID NO: 25)









For primer mix FB1D1, each primer was present in the reaction at 0.25 μM concentration in the presence of other components necessary for performing polymerase chain reaction (nucleotides, polymerase, buffer) in a total reaction volume of 30 μl; for single primer FP5, it was present in the reaction at 0.1 μM concentration in a total reaction volume of 30 μl, in the presence of the other components required by polymerase chain reaction.

Reactions were run either with or without (negative controls) the addition of purified microbial DNA from three diverse organisms (one yeast, one gram positive bacterium and one gram negative bacterium (Table 2)) at a concentration of 30 ng per reaction. Five replicates each were run for the negative control and each of the microbial DNA's.







TABLE 2





Microbial species analyzed
















1. Salmonella enterica (serovar Minnesota) MR595
ATCC 49284D


2. Staphylococcus aureus Mu3
ATCC 700698D-5


3. Saccharomyces cerevisiae S288C
ATCC 204508D-5









PCR was carried out using a 2 minute hold at 95° C. followed by 10 cycles of 15 seconds at 95° C., 5 minutes at 40° C. and 1 minute at 70° C., followed by 30 cycles of 95° C. for 15 seconds and 3 minutes at 70° C.
PCR reaction products were cleaned up as appropriate for DNA sequence reactions prior to loading on a capillary electrophoresis sequence apparatus, at which time the PCR products are recovered in a 15 μl volume of H2O.
A 2 μl aliquot of the PCR product is then added to 20 μl of deionized water. A commercial sequence standard (hsp 60, Applied Biosystems, Foster City, Calif.) is prepared as follows. A 1 μl aliquot of the sequence standard is mixed with 9 μl of formamide (HiDi, Applied Biosystems). 1.5 μl of the diluted PCR product is then added to the 10 μl sequence standard/formamide solution. Samples are then mixed, denatured as for a standard sequencing reaction and loaded on to an Applied Biosystems 3730 DNA sequencer and run using standard DNA sequencing conditions. The output sequence files are then analyzed using standard DNA sequence analysis tools.
In order to test the ability of this invention to characterize an organism as belonging to a group (characterization) the sequences were examined using the Clustal W program (European Bioinformatics Institute web server). Two sets of alignments of sequences produced from primer mix FB1D1 and single primer FP5 of Example 1 are shown in Tables 3A and 3B and the resulting phylograms are shown in FIGS. 1A and 1B. As hypothesized, the perturbations of the sequence due to the comingling of the PCR products from the RAPD fingerprinting reaction were detected as changes in the sequence output from the instrument. Clustal W alignments show that the replicate samples from a single organism cluster together and are separate from the clusters for non-identical microorganisms.







TABLE 3A





CLUSTAL 2.0.11 multiple sequence alignment of all sequence reads from


primer mix FB1D1 of Example 1.

















SEQ ID NO: 5
-------------GTTGNT-CNNCTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
46


FB1D1-neg-control-4




SEQ ID NO: 6
--------------------TCNCNGCTGACAATGCTGCTGCTGCTTCNCCTCNNNGTCT
40


FB1D1-neg-control-5




SEQ ID NO: 7
--------GTNNNGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCNNTGTCT
52


FB1D1-neg-control-2




SEQ ID NO: 8
------------TGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCT
48


FB1D1-S. cerevisiae-5




SEQ ID NO: 9
-----CTGNTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCT
55


FB1D1-S. cerevisiae-1




SEQ ID NO: 10
----NCNGNNNNNGNTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCNCTGTCT
56


FB1D1-S. cerevisiae-3




SEQ ID NO: 11
-----CTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
55


FB1D1-S. cerevisiae-2




SEQ ID NO: 12
-------------GTTGNT--CNCNGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCT
45


FB1D1-S. cerevisiae-4




SEQ ID NO: 13
--------GNTANGTTGCTNCTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
52


FB1D1-neg-control-1




SEQ ID NO: 14
GNTNNCTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
60


FB1D1-neg-control-3




SEQ ID NO: 15
------CNGNNNTGTTNCTCNN-CTGCTGACAATGCTGCTGNNGNNNCNCCTCNCTGTCT
53


FB1D1-S. enterica-5




SEQ ID NO: 16
------CNGNNNNGTTGCTNCTACTGCTGACAATGCTGCTGNNGNNNCNCCTCNCTGTCT
54


FB1D1-S. enterica-4




SEQ ID NO: 17
------CNGNNANGTTNNTCNN--NGCTGACAATGCTGCTGCNGCTTCNCCTCNCTGTCT
52


FB1D1-S. enterica-2




SEQ ID NO: 18
-------------GTTNNTCNN--NGCTGACAATGCTGCTGCNGCTTCTCCTCNCTGTCT
45


FB1D1-S. enterica-3




SEQ ID NO: 19
-------------GTTGCTNCTACTGCTGANAATGCTGCTGCTGCTTCTCCTCNCTGTCT
47


FB1D1-S. enterica-1




SEQ ID NO: 20
----------------GNTCNC--NGNNGANNATGNTGCTGCTGCTTNNNGNNNCTGTCT
42


FB1D1-S. aureus-4




SEQ ID NO: 21
---------TNNGTTGNTCTAC--NGNTGACNATGCTGCTGCTGCTTNNNNNNNCTGTCT
49


FB1D1-S. aureus-2




SEQ ID NO: 22
------CNGTTATGTTGCTCTC--NGCTGACNATGCTGCTGCTGCTTCNNGNNNCTGTCT
52


FB1D1-S. aureus-3




SEQ ID NO: 23
-------------GTTGNTCNN--NGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCT
45


FB1D1-S. aureus-1




SEQ ID NO: 24
------CNGNNANGTTGNTCNN--NGCTGANNN-GCTGCTGCTGCTTCNNGTNNCTGTCT
51


FB1D1-S. aureus-5
            *  **    * *****  *            ****




           



 


FB1D1-neg-control-4
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
106


FB1D1-neg-control-5
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
100


FB1D1-neg-control-2
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
112


FB1D1-S. cerevisiae-5
CCACTTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCNGAGNGNTA
108


FB1D1-S. cerevisiae-1
CCACTTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCNGAGNGCTA
115


FB1D1-S. cerevisiae-3
CCACTTCCTTGAACAATGCGCCGTCNTGCTTCTTTTGCCTCCCGCTGCTCCNNANNGNTA
116


FB1D1-S. cerevisiae-2
CCACTTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCNGAGNGNTA
115


FB1D1-S. cerevisiae-4
CCACTTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCANAGNGCTA
105


FB1D1-neg-control-1
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
112


FB1D1-neg-control-3
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
120


FB1D1-S. enterica-5
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
113


FB1D1-S. enterica-4
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
114


FB1D1-S. enterica-2
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
112


FB1D1-S. enterica-3
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
105


FB1D1-S. enterica-1
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
107


FB1D1-S. aureus-4
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
102


FB1D1-S. aureus-2
CCACTTCCTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
109


FB1D1-S. aureus-3
CCACTTCCTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
112


FB1D1-S. aureus-1
CCACTTCCTTGAACANTGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
105


FB1D1-S. aureus-5
CCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTA
111



*************** ** **** * *************************  *  * **



 


FB1D1-neg-control-4
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
166


FB1D1-neg-control-5
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
160


FB1D1-neg-control-2
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
172


FB1D1-S. cerevisiae-5
GGCCGCAGATCANAACCACCACAGTCAATATCACCACCTTCNTCTTATAGATTCGGAATC
168


FB1D1-S. cerevisiae-1
GGCCGCAGATCAGAACCACCACAGNCAATATCACCACCNNCNNCTTATAGATTCGGAATC
175


FB1D1-S. cerevisiae-3
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
176


FB1D1-S. cerevisiae-2
GGCCGCAGATCAGAACCACCACAGNCAATATCACCACCNTCNNCTTATANATTCGGAATC
175


FB1D1-S. cerevisiae-4
GGCCGCAGATCANAACCACCACAGNCAATATCACCACCNTCNNCTTATAGATTCGGAATC
165


FB1D1-neg-control-1
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
172


FB1D1-neg-control-3
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
180


FB1D1-S. enterica-5
GGCCGCAGATCAGAACCACCACAGTCAATATCACCNCCTTCCTCTTATAGATTCGGAATC
173


FB1D1-S. enterica-4
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
174


FB1D1-S. enterica-2
GGCCGCAGATCANAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
172


FB1D1-S. enterica-3
GGCCGCAGATCANAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
165


FB1D1-S. enterica-1
GGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATC
167


FB1D1-S. aureus-4
NGNCNNAGATCAGAACCACCACAGTCANNNTCNCCNCCTTCCTCTTATAGATTCGGAATC
162


FB1D1-S. aureus-2
NGNNNNAGATCAGAACCACCACAGNCNNNNTNACCNCCTTCCTCTTATAGATTCGGAATC
169


FB1D1-S. aureus-3
GGNCNNAGATCAGAACCACCACAGNCNNTATCNCCNCCTTCCTCTTATAGATTCGGAATC
172


FB1D1-S. aureus-1
NGNCNNAGATCAGAACCACCACAGNCNNNNTCNCCNCCTTCCTCTTATAGATTCGGAATC
165


FB1D1-S. aureus-5
GGCCGCAGATCAGAACCACCACAGTCNATATCACCNCCTTCCTCTTATAGATTCGGAATC
171



 *    ****** *********** *    *  ** **  *  ****** ********** 



 


FB1D1-neg-control-4
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
226


FB1D1-neg-control-5
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
220


FB1D1-neg-control-2
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
232


FB1D1-S. cerevisiae-5
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
228


FB1D1-S. cerevisiae-1
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
235


FB1D1-S. cerevisiae-3
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
236


FB1D1-S. cerevisiae-2
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
235


FB1D1-S. cerevisiae-4
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
225


FB1D1-neg-control-1
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
232


FB1D1-neg-control-3
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
240


FB1D1-S. enterica-5
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNGNNNNNNAGCTGANGAGC
233


FB1D1-S. enterica-4
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNNNNNNNNAGCTGANGANC
234


FB1D1-S. enterica-2
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNNNNNGNNAGCTGANGANC
232


FB1D1-S. enterica-3
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNNNNNNNGAGCTGAGGAGC
225


FB1D1-S. enterica-1
TCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNGCAGGCGAGCTGAGGAGC
227


FB1D1-S. aureus-4
TCATGATAGGGNNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGANGAGC
222


FB1D1-S. aureus-2
TCATGATAGGGNNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCNAGCTGANGAGC
229


FB1D1-S. aureus-3
TCATGATAGGGNNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGANGAGC
232


FB1D1-S. aureus-1
TCATGATAGGGGNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
225


FB1D1-S. aureus-5
TCATGATAGGGGCTCANCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGC
231



***********  **  ************************        ****** ** *



 


FB1D1-neg-control-4
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGNNNNGNNNNNNNNCGTG
286


FB1D1-neg-control-5
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGNNNNNNNNNNNNCGTG
280


FB1D1-neg-control-2
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAANANNTCGTG
292


FB1D1-S. cerevisiae-5
AATTGCAGGTGATATGATGTGCTCGGCTCNNNGGGCGNGGN-NNNNNNNNNNANGNCNNG
287


FB1D1-S. cerevisiae-1
AATTGCNGGTGATATGATGTGCTCGGCTCNNNGGGNNNGGN-GNNNNNNNNANGNCNNG-
293


FB1D1-S. cerevisiae-3
AATTGCAGGTGATATGATGTGCTCGGCTCANGGGGNNNNNN-NNNNNNNNNNNNNNNNNG
295


FB1D1-S. cerevisiae-2
AATTGCAGGTGATATGATGTGCTCGGCTCANNGGGCNNNNN-NNNNNNNNNNNNNNNNTG
294


FB1D1-S. cerevisiae-4
AATTGCAGGTGATATGATGTGCTCGGCTCNNNGGGCGNNNN-NNNNNNNNNNNNNNCNNG
284


FB1D1-neg-control-1
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCNNNGAGNAGGANGTCGTG
292


FB1D1-neg-control-3
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCNGNNNNNGNNAGGAAGAAGTCGTG
300


FB1D1-S. enterica-5
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAAGAAGNNNNN
293


FB1D1-S. enterica-4
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGANANGAANAAGTNNNN
294


FB1D1-S. enterica-2
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGNNNNNNAAGNNNNN
292


FB1D1-S. enterica-3
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCNGGNNAGGAAGAAGNNNNN
285


FB1D1-S. enterica-1
AATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCNGNNNNGNNNGAAGTCNNG
287


FB1D1-S. aureus-4
ANTTGCAGGNGNNNNNNTGTGCTCGGCTCAAGAAGCGGGCCCNGNNNNNANNAAGTCGTG
282


FB1D1-S. aureus-2
ANTTGCAGGNGNNNGNNTGTGCTCGGCTCAAGANGCGGGNCCGGANAGGAAGAAGTCGTG
289


FB1D1-S. aureus-3
AATTGCAGGTGNNNNNATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAAGAAGTCGTG
292


FB1D1-S. aureus-1
ANTTGCAGGTGNNNNNATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAAGAAGTCGTG
285


FB1D1-S. aureus-5
AATTGCAGGTGNNNNNNNGTGCTCGGCTCAAGAAGCGGGCCNNGNNNNNNNNNAGTCGTG
291



* **** ** * *********** *



 


FB1D1-neg-control-4
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGAATGN
345


FB1D1-neg-control-5
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGAANGN
339


FB1D1-neg-control-2
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGAATGN
351


FB1D1-S. cerevisiae-5
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCGGGNGGNATGN
346


FB1D1-S. cerevisiae-1
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCNNNNGGNNNGT
352


FB1D1-S. cerevisiae-3
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGNNGGN
354


FB1D1-S. cerevisiae-2
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGNNGGN
353


FB1D1-S. cerevisiae-4
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGNNNNGN
343


FB1D1-neg-control-1
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGNNNGN
351


FB1D1-neg-control-3
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCNNCTGGANTNN
359


FB1D1-S. enterica-5
NCGGGGGCTAATTATTGGCAAAACGAGCTCTTGTTNNNNNNNNNNNNNNGNNNNNNNNNN
353


FB1D1-S. enterica-4
NCNNGG-CTAATTATTGGCAAAACGAGCTCTTGTTNNNNNNNNNNNNNNGNNNNNNNNNN
353


FB1D1-S. enterica-2
NNNNNN-NTAATTATTGGCAAAACGAGCTCTTGTTNNNNNNNNNNNNNNGNNNNNNNNNN
351


FB1D1-S. enterica-3
NNNNNN-NTAATTATTGGCAAAACGAGCTCTTGTTGTANNNNNNNNNNNGNNNNNNNNNN
344


FB1D1-S. enterica-1
NCGNGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTANNNNNNNNNNNGNNNNNNNNNN
346


FB1D1-S. aureus-4
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGANNNGGGGGGGGGGN
341


FB1D1-S. aureus-2
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGNNNNNNNNNNNNNNN
348


FB1D1-S. aureus-3
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGNAAACNTNGNNNGGGGGGGGNNNN
351


FB1D1-S. aureus-1
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATNGNNNNNNNNNNNNNNN
344


FB1D1-S. aureus-5
CCGGGG-CTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGANNNNNNNNNNNNNN
350



        ***************************



 


FB1D1-neg-control-4
CNCTAATNNNNNNNTCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
405


FB1D1-neg-control-5
CNCTAANNNNNNAT-CAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
398


FB1D1-neg-control-2
CNCTAANNNNNNNN-NAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
410


FB1D1-S. cerevisiae-5
NNNNNANGNNNNNN-NNNNNNGNNNNNNGGNATGATGGTTGCTCAGAGGCAGGAGAAGAG
405


FB1D1-S. cerevisiae-1
NNNNNNNGGNGNNN-GANNNTGNNNNNNGGNATGATGGTTGCTCAGAGGCAGGAGAAGAG
411


FB1D1-S. cerevisiae-3
NNNNNATGGNGNNN-NNNNNTGCCNNNNNGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
413


FB1D1-S. cerevisiae-2
NNNNNATGGNGNNN-GNNNNTGNNNNNNGGGATGATGGTTGCTCAGAGGCAGGAGAAGAG
412


FB1D1-S. cerevisiae-4
NNNNNANGGNGNNN-NNNNGTGNNNNNNGGNATGATGGTTGCTCAGAGGCAGGAGAAGAG
402


FB1D1-neg-control-1
NACTNANNNNNNNN-CAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
410


FB1D1-neg-control-3
NNNNNATGGCGAAT-CAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
418


FB1D1-S. enterica-5
NNACNNNNGGNNNNNCAATATTCCNTANNGCATGATGGTTGCTCAGAGGCANNNNNNNAG
413


FB1D1-S. enterica-4
NNNCTNNNNNNGNNCNA-TATTCCNTAANGCATGATGGTTGCTCAGAGGCAGGNNNNNAN
412


FB1D1-S. enterica-2
NA--CTANNGNNGNNCAATATTCCNTANNGCATGATGGTTGCTCAGAGGCAGNNNNNNAG
409


FB1D1-S. enterica-3
NA--CTNNNNGNGNNCAATATTCCNTANNGCATGATGGTTGCTCAGAGGCAGNNNNNNAG
402


FB1D1-S. enterica-1
NC--TANNGNNNNATCNATATTCCNTAANGCATGATGGTTGCTCAGAGGCANGNNNNA-G
403


FB1D1-S. aureus-4
NNN-NNNNNNNA--TCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
398


FB1D1-S. aureus-2
NNN-NNNNNNNNA-TCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
406


FB1D1-S. aureus-3
NNN-NNNNNNNNA-TCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
409


FB1D1-S. aureus-1
NNN-NNNNNNNNGNNCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
403


FB1D1-S. aureus-5
NNN-NNNNNNNNNNNCNATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAG
409



                             * ********************



 


FB1D1-neg-control-4
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
465


FB1D1-neg-control-5
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
458


FB1D1-neg-control-2
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
470


FB1D1-S. cerevisiae-5
CAACGAATACGATCCTATNAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
465


FB1D1-S. cerevisiae-1
CAACGAATACGATCCTATNAAAGATAAAACATAAATAAACNGTCTTGATTATATTCTGGG
471


FB1D1-S. cerevisiae-3
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
473


FB1D1-S. cerevisiae-2
CAACGAATACNATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
472


FB1D1-S. cerevisiae-4
CAACGAATACGATCCTATNAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
462


FB1D1-neg-control-1
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
470


FB1D1-neg-control-3
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
478


FB1D1-S. enterica-5
CAANNNNNNCGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
473


FB1D1-S. enterica-4
CAANNNNNNCGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
472


FB1D1-S. enterica-2
CAACNNANNCNATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
469


FB1D1-S. enterica-3
CAANNNANNCGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
462


FB1D1-S. enterica-1
CAACNAANACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
463


FB1D1-S. aureus-4
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
458


FB1D1-S. aureus-2
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
466


FB1D1-S. aureus-3
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
469


FB1D1-S. aureus-1
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
463


FB1D1-S. aureus-5
CAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
469



         * ******* ********************* *******************



 


FB1D1-neg-control-4
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-TA
524


FB1D1-neg-control-5
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-TA
517


FB1D1-neg-control-2
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-TA
529


FB1D1-S. cerevisiae-5
TATTAAANNCNCNGNCNGAACAAATATATGCTTTGTNNNNNNTNNNGCCTTNNNNNN-GN
524


FB1D1-S. cerevisiae-1
TATTAAANNCNNNGNNAGAACAAATATATGCTTTNNNNNNNNTCNNGNCNNNNNNNN-NN
530


FB1D1-S. cerevisiae-3
TATTAAAGNCNCAGNCAGAACAAATATATGCTTTGTNNCTNNNCNTGCCTTCTTNNN-NN
532


FB1D1-S. cerevisiae-2
TATTAAANNNNNNGNCAGAACAAATATATGCTTTGNNNNNTNNCNTGNNNNCNNNNG-GN
531


FB1D1-S. cerevisiae-4
TATTAAANNNNNNGTCAGAACAAATATATGCTTTGTNNNNNNNCNNNCCTTCTNNNN-GN
521


FB1D1-neg-control-1
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCATTAC
530


FB1D1-neg-control-3
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCNNNNNNGT-TA
537


FB1D1-S. enterica-5
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCAN-NN
532


FB1D1-S. enterica-4
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCAT-NN
531


FB1D1-S. enterica-2
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCAN-NN
528


FB1D1-S. enterica-3
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCAT-NN
521


FB1D1-S. enterica-1
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTNCNNGCCTTCTTCAT-NN
522


FB1D1-S. aureus-4
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-TN
517


FB1D1-S. aureus-2
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCNT-TA
525


FB1D1-S. aureus-3
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-TA
528


FB1D1-S. aureus-1
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-NN
522


FB1D1-S. aureus-5
TATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCAT-TA
528



*******          *****************



 


FB1D1-neg-control-4
CCAANNGNNTNNNCNNNNNNNNNNAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
584


FB1D1-neg-control-5
CCNANNNNNNNNNNNNNNNNNNTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
577


FB1D1-neg-control-2
CCAACTGCTTNNNCGGCCNCNTTNAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
589


FB1D1-S. cerevisiae-5
NNNNNNNNNNNNNCGGCCANNNNNNNAGAACTTGTGNNNNNATAAGAAGATATTTTATTC
584


FB1D1-S. cerevisiae-1
NNNNNNNNNNNNNNGGCCACATTAAGAGAACTTGTNNNNNNNTAAGAAGATATTTTATTC
590


FB1D1-S. cerevisiae-3
NNNNNNNNNNNNNNGGCCACNNNNNNAGAACTTGNGGNGNNATAAGAAGATATTTTATTC
592


FB1D1-S. cerevisiae-2
NNNNNNNNNNNNNNGGCCNCNNNNNGAGAACTTGTNNNNNNNTAAGAAGATATTTTATTC
591


FB1D1-S. cerevisiae-4
NNNNNNNNNNNNNNGGCCNNNNNNNGAGAACTTGTNNNNNNNTAAGAAGATATTTTATTC
581


FB1D1-neg-control-1
NNNNNNNNNNCGCGGGCNNNNNNAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
590


FB1D1-neg-control-3
CNNNNTGNTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
597


FB1D1-S. enterica-5
NNNACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
592


FB1D1-S. enterica-4
NNNNNTGCTTCCGCGGNNACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
591


FB1D1-S. enterica-2
NNNANNGCTNNNNNGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
588


FB1D1-S. enterica-3
NNNNNTGNTTCCGCGGNCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
581


FB1D1-S. enterica-1
NNNNNNGNTTCCGCGNNNNCATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTC
582


FB1D1-S. aureus-4
NNNNNNGNTNCNGCGGCCACATTAAGAGAACTTGNGNTAAGATAAGAAGATATTTTATTC
577


FB1D1-S. aureus-2
CCAACTGCTTCCGCGGCCACATTAAGAGAACTTGNGNTAAGATAAGAAGATATTTTATTC
585


FB1D1-S. aureus-3
CCAACTGCTTCCGCGGCCACATTAAGAGAACTTGNGGTAAGATAAGAAGATATTTTATTC
588


FB1D1-S. aureus-1
NNNNNTGCTTCCGCGGCCACATTAAGAGAACTTGGGGTAAGATAAGAAGATATTTTATTC
582


FB1D1-S. aureus-5
NNNNCNGCNNNNNNGNCCACATTAAGAGAACTTGNGGTAAGATAAGAAGATATTTTATTC
588



                          ********        ******************



 


FB1D1-neg-control-4
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
644


FB1D1-neg-control-5
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
637


FB1D1-neg-control-2
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
649


FB1D1-S. cerevisiae-5
GNTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
644


FB1D1-S. cerevisiae-1
GNTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
650


FB1D1-S. cerevisiae-3
GNTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
652


FB1D1-S. cerevisiae-2
GNNCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
651


FB1D1-S. cerevisiae-4
GNTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
641


FB1D1-neg-control-1
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
650


FB1D1-neg-control-3
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
657


FB1D1-S. enterica-5
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTNNNNNNNAGGCGGTTAATTG
652


FB1D1-S. enterica-4
GTTCTGCTGACTTGCTGGATGTCGGGAAATANTCTGCATTNNANNNNAGGCGGTTAATTG
651


FB1D1-S. enterica-2
GTTCTGCTGACTTGCTGGATGTCGGGAAATANTCTGCATTTNNNNNNAGGCGGTTAATTG
648


FB1D1-S. enterica-3
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTNNNNNNAGGCGGTTAATTG
641


FB1D1-S. enterica-1
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTNNNNNGAGGCGGTTAATTG
642


FB1D1-S. aureus-4
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
637


FB1D1-S. aureus-2
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
645


FB1D1-S. aureus-3
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
648


FB1D1-S. aureus-1
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
642


FB1D1-S. aureus-5
GTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTG
648



*  **************************** ********       *************



 


FB1D1-neg-control-4
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
704


FB1D1-neg-control-5
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
697


FB1D1-neg-control-2
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
709


FB1D1-S. cerevisiae-5
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
704


FB1D1-S. cerevisiae-1
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
710


FB1D1-S. cerevisiae-3
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
712


FB1D1-S. cerevisiae-2
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
711


FB1D1-S. cerevisiae-4
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
701


FB1D1-neg-control-1
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
710


FB1D1-neg-control-3
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
717


FB1D1-S. enterica-5
CANATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
712


FB1D1-S. enterica-4
CANATATAATTGGTAGTGAAAAGGGNCNNTGCTATGGTCACCGTGAAGCGAGTACAGCAG
711


FB1D1-S. enterica-2
CANATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
708


FB1D1-S. enterica-3
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
701


FB1D1-S. enterica-1
CAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
702


FB1D1-S. aureus-4
CAGATATAATTGGTAGTGAAAAGGNGNNTTGCTATGGTCACCGTGAAGNGAGTACAGCAG
697


FB1D1-S. aureus-2
CAGATATAATTGGTAGTGAAAAGGNGCGTTGCTATGGTCACCGTGAAGNGAGTACAGCAG
705


FB1D1-S. aureus-3
CAGATATAATTGGTAGTGAAAAGGNNNNTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
708


FB1D1-S. aureus-1
CAGATATAATTGGTAGTGAAAAGGNNNNTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
702


FB1D1-S. aureus-5
CAGATATAATTGGTAGTGAAAAGGNNNNTTGCTATGGTCACCGTGAAGCGAGTACAGCAG
708



** *********************     ******************* ***********



 


FB1D1-neg-control-4
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
764


FB1D1-neg-control-5
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
757


FB1D1-neg-control-2
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGNTTTAGTCG
769


FB1D1-S. cerevisiae-5
CACAAGAATGTGTGCCGNTCTCAGTTAATATTGTTTGAATATGGNAACCTGTTTTAGTCG
764


FB1D1-S. cerevisiae-1
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTNTGAATATGGTAACCTGNTTTAGTCG
770


FB1D1-S. cerevisiae-3
CACAAGANNGTGTGCCGTTCTCAGTTAATATNGNNNGAATATGGTAACCTGNTTTAGTCG
772


FB1D1-S. cerevisiae-2
CACANGANNGTGTGCCGTTCTCAGTTAATATTGNTTGAATATGGTAACCTGTTTTAGTCG
771


FB1D1-S. cerevisiae-4
CACAANANNGNGTGCCGTTCTCAGTTNNNNNNGTTTGAATATGGTAACCTGTTTTAGTCG
761


FB1D1-neg-control-1
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
770


FB1D1-neg-control-3
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
777


FB1D1-S. enterica-5
CACAAGAATGTGNGCCGTTCTCNNNNNNTATTGTTTGAATATNNNNACCTGTTTTAGTCG
772


FB1D1-S. enterica-4
CACAAGAATGTGNGCCGTTCTCNNNNNNTATTGTTTGAATATGNNNACCTGNTTTAGTCG
771


FB1D1-S. enterica-2
CACAAGAATGNGTGCCGTTCTCNGNNNNTATTGTTTGAATATGGNAACCTGTTTTAGTCG
768


FB1D1-S. enterica-3
CACAAGAATGTGTGCCGTTCTCNNNNNNTATTGTTTGAATATGGNAACCTGTTTTAGTCG
761


FB1D1-S. enterica-1
CACAAGAATGTGTGCCGTTCTCNNNNNNTATTGTTTGAATATGGTAACCTGTTTTAGTCG
762


FB1D1-S. aureus-4
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
757


FB1D1-S. aureus-2
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
765


FB1D1-S. aureus-3
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
768


FB1D1-S. aureus-1
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
762


FB1D1-S. aureus-5
CACAAGAATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCG
768



****  *  * * **** ****          *   ******    ***** ********



 


FB1D1-neg-control-4
GTTTAAAGGTAAGAAGANCTAACCAAAAACAAC-ACTGCAGTGACTG--ANNGTAGTATT
821


FB1D1-neg-control-5
GTTTAAAGGNAAGAAGATCTAACCAAAAACAAC-ACTGCAGTGACTG--ATTG-------
807


FB1D1-neg-control-2
GTTTAAAGGTAAGAAGATCTAACCNAAAACAAC-ACTGCAGTGACTG--ATT--------
818


FB1D1-S. cerevisiae-5
GTTTAAAGGTAAGAAGATCTAACCNAAAACAAN-NNNNNNNGNCNNN--NNGNNGNNNNN
821


FB1D1-S. cerevisiae-1
GTTTAAAGGTAAGAAGATCTAACCAAAAACAAC-ACTGCNNGNCNGN--NNNNNNGGNNN
827


FB1D1-S. cerevisiae-3
GTTTAAAGGTAAGAAGANCTAACCAAAAACAAC-ACTGCNNNNNNNN--NNGGGGGNNNN
829


FB1D1-S. cerevisiae-2
GTTTAAAGGTAAGAAGANCTAACCNAAAACAAC-ACTGCNNNNNNGN--GGGGGGNNNNN
828


FB1D1-S. cerevisiae-4
GTTTAAAGGNAAGAAGATCTAACCAAAAACAAC-ACTGCANTGNCNG--NGNNGGNNNNN
818


FB1D1-neg-control-1
GTTTAAAGGTAAGAAGATCTAACCNAAAACAAC-ACTGCAGTGACTG--A----------
817


FB1D1-neg-control-3
GTTTAAAGGTAAGAAGATCTANNNNNNNNNNNNCACTGCAGNGACTG--ANNGNAGTATT
835


FB1D1-S. enterica-5
GTTTAANNNNNNNNNNNTCTAACCNAAAAC-AACACTGCAGNGACTG--ANNGTAGTATT
829


FB1D1-S. enterica-4
GTTTAANNNNNNNNNNNTCTAACNNAAAAC-AACACTGCNGNGACTG--ANTGNNNNATT
828


FB1D1-S. enterica-2
GNTTAANNNNNNNNNNNTCTAACCAAAAAC-AACACTGNNGNGACTG--ANTGTAGTATT
825


FB1D1-S. enterica-3
GTTTAAANGNNNNNNNT-CTAACCNAAAAC-AACACTGCAGTGACNG--ANNNNNGTANT
817


FB1D1-S. enterica-1
GTTTAANNNNNNNNNNNTCTAACCAAAAAC-AACACTGCAGNGGNNNGGNNNGTAGTATT
821


FB1D1-S. aureus-4
GTTTAAAGGTAAGAAGATCTAACCAAAAAC-AACACTGNNNNGNNNG--ATTGTAGNNNN
814


FB1D1-S. aureus-2
GTTTAAAGGTAAGAAGATCTAACCAAAAAC-AACACNGCAGTGACTG--ATTGNNGNNNN
822


FB1D1-S. aureus-3
GNTTAAAGGTAAGAAGATCTAACNNAAANNCAACACTGCANNGACTG--NNNNNNNNNAT
826


FB1D1-S. aureus-1
GTTTAAAGGTNAGAAGATCTAACCAAAAAC-AACACTGCAGNGACTG--ATTGTAGTATT
819


FB1D1-S. aureus-5
GTTTAAAGGTAAGAAGATCTAACCAAAANC-AACACTGCAGTGACNG--NNNNGNNGNAT
825



* ****            ***



 


FB1D1-neg-control-4
------------------------------------------------------------



FB1D1-neg-control-5
------------------------------------------------------------



FB1D1-neg-control-2
------------------------------------------------------------



FB1D1-S. cerevisiae-5
NNNNNNTT--A--CTTNNNNNNNATTTTGGNNGNA--AACATCAACGG-NNNNNNTCAAC
874


FB1D1-S. cerevisiae-1
NNNNNNNNTTA--CTNNNNNNNNATTTTGGNN-TA--AACATCAACGG-NNNNNNNCANC
881


FB1D1-S. cerevisiae-3
NNNNNNNTT-A--CTNNNNGNNNNTTNNNGGNGNA--AACATCNACGN-NNNNNNNCAAC
883


FB1D1-S. cerevisiae-2
NNNNNNNNT-A--CTTNNNNNNNNNNNNNNNNNN----ACATCNNCGN-NNNNNNNCAAC
880


FB1D1-S. cerevisiae-4
NNNNNNNNNTA--CTTANNNNNNNNNNNNNNGGNGTAAACATCAACGN-NNNNNTCNACC
875


FB1D1-neg-control-1
------------------------------------------------------------



FB1D1-neg-control-3
TATTTTTTT-A--CTTAATCTNNATTTTGGTGNAA---ACATCNACGG-CNN--------
880


FB1D1-S. enterica-5
TATTTTTNNNN--CNNNNNCTTNANTTT-GGTGTA--AACATCAACGG-CGCACTT----
879


FB1D1-S. enterica-4
TATTTTTTTAC--NNNNNNNNNNNTTT--GGTGTA--AACATCAACGG-CGCACTTCNN-
880


FB1D1-S. enterica-2
TATTTTNNNNN--NNNNNCTTAATTTT--GGTGNA--AACATCNACGG-CGCACTTCAAC
878


FB1D1-S. enterica-3
TATTTTTTTAC--TNNNNNNNNNNNNTTTGGTGNA--AACATCAACGG-CGCACTTC---
869


FB1D1-S. enterica-1
TATTTTNNNNN--NNNNNNCTTAATTTT-GGNGNA--AACATCNACGG-CGCACNTNNN-
874


FB1D1-S. aureus-4
NANNNNNTTT--ACNTAATCNTANTTTT-GGTGNA--AACATCAACGG-CGCACTTCAAC
868


FB1D1-S. aureus-2
NNNNNTTTTTT-ANNTNATCTTAATTTT-GGTGTA--AACATCNACGG-CGCACTTCAA-
876


FB1D1-S. aureus-3
TNNNNNNTTTTTACTTAATCTTAATTTT-GGTGTA--AACATCAACNGGCGCACTTN---
880


FB1D1-S. aureus-1
TATTTTTNNN---NNNNNNCTNNATTTT-GGTGTA--AACATCAACGG-CGCACNN----
868


FB1D1-S. aureus-5
TTATTTTTNN--NNNNNNNNTTAATTTT-GGNGNA--AACATCAACGG-CGCACTTCN--
877
















TABLE 3B





CLUSTAL 2.0.11 multiple sequence alignment of all sequence


reads from single primer FP5 of Example 1.

















SEQ ID NO: 26
-----------NNNNNNNATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
49


FP5-neg-control-4




SEQ ID NO: 27
---------NNNNTTNNNATTACTGTTAATGNTGCTACTACTGCTGACAATGCTGCTGCT
51


FP5-neg-control-5




SEQ ID NO: 28
---------NNGNNNNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
51


FP5-neg-control-3




SEQ ID NO: 29
--------NCTGGTNNNNNNNACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


FP5-neg-control-2




SEQ ID NO: 30
--------NCNGNNNATGANTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


FP5-neg-control-1




SEQ ID NO: 31
--------NCCNGNNNNNNNTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


FP5-S. aureus-4




SEQ ID NO: 32
--------------------TACTGTTAATGTTGNNNCNNNNGCTGACAATGCTGCTGCT
40


FP5-S. aureus-5




SEQ ID NO: 33
-NNNGCNGCCNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
59


FP5-S. aureus-2




SEQ ID NO: 34
------NNNCTGGTTNTGANTACTGNNNNNGTTGCTACTACTGCTGACAATGCTGCTGCT
54


FP5-S. aureus-3




SEQ ID NO: 35
-----NNNNCTGGTTNTGANTACTGTTAANGTTGCTACTACTGCTGACAATGCTGCTGCT
55


FP5-S. aureus-1




SEQ ID NO: 36
------------NTTNTGATTACTGTTNNNNNTGCTACTACTGCTGACAATGCTGCTGCT
48


FP5-S. enterica-2




SEQ ID NO: 37
-----NNNNNNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
55


FP5-S. enterica-3




SEQ ID NO: 38
---------CTGNNNNTGATTACTGTNNNNGTTGCTACTACTGCTGACAATGCTGCTGCT
51


FP5-S. enterica-1




SEQ ID NO: 39
--NNNNNNCCTGGTNATGANTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
58


FP5-S. enterica-4




SEQ ID NO: 40
-------------NNNNNATTNCTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
47


FP5-S. enterica-5




SEQ ID NO: 41
-------------NNNNNATNNCTGTTNATGTTGCTNCTACTGCTGACAATGCTGCTGCT
47


FP5-S. cerevisiae-3




SEQ ID NO: 42
------------NTTNNGATTACTGTTAATNNTNNTNCTACTGCTGACAATGCTGCTGCT
48


FP5-S. cerevisiae-5




SEQ ID NO: 43
NNNTGNNGCCTGNTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
60


FP5-S. cerevisiae-2




SEQ ID NO: 44
--------CCTGGTTANGANTACTGNTNNNGNTGCTACTACTGCTGACAATGCTGCTGCT
52


FP5-S. cerevisiae-4




SEQ ID NO: 45
--------CCTGNNNNNGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


FP5-S. cerevisiae-1





         ***       *    *    ******************



 


FP5-neg-control-4
GCTTCNCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
109


FP5-neg-control-5
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
111


FP5-neg-control-3
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
111


FP5-neg-control-2
GCTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112


FP5-neg-control-1
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112


FP5-S. aureus-4
GCTTCTCCTCNNTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112


FP5-S. aureus-5
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
100


FP5-S. aureus-2
GCTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
119


FP5-S. aureus-3
GCTTCTCNTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
114


FP5-S. aureus-1
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
115


FP5-S. enterica-2
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
108


FP5-S. enterica-3
GCTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
115


FP5-S. enterica-1
GCTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
111


FP5-S. enterica-4
GCTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
118


FP5-S. enterica-5
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
107


FP5-S. cerevisiae-3
GCTTCTCCTCNNTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
107


FP5-S. cerevisiae-5
GCTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
108


FP5-S. cerevisiae-2
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
120


FP5-S. cerevisiae-4
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112


FP5-S. cerevisiae-1
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112



***** * * * ************************************************



 


FP5-neg-control-4
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
169


FP5-neg-control-5
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
171


FP5-neg-control-3
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
171


FP5-neg-control-2
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172


FP5-neg-control-1
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172


FP5-S. aureus-4
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172


FP5-S. aureus-5
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
160


FP5-S. aureus-2
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
179


FP5-S. aureus-3
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
174


FP5-S. aureus-1
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
175


FP5-S. enterica-2
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
168


FP5-S. enterica-3
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
175


FP5-S. enterica-1
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
171


FP5-S. enterica-4
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
178


FP5-S. enterica-5
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
167


FP5-S. cerevisiae-3
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
167


FP5-S. cerevisiae-5
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
168


FP5-S. cerevisiae-2
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
180


FP5-S. cerevisiae-4
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172


FP5-S. cerevisiae-1
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172



************************************************************



 


FP5-neg-control-4
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
229


FP5-neg-control-5
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
231


FP5-neg-control-3
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
231


FP5-neg-control-2
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232


FP5-neg-control-1
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232


FP5-S. aureus-4
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232


FP5-S. aureus-5
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
220


FP5-S. aureus-2
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
239


FP5-S. aureus-3
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
234


FP5-S. aureus-1
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
235


FP5-S. enterica-2
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
228


FP5-S. enterica-3
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
235


FP5-S. enterica-1
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
231


FP5-S. enterica-4
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
238


FP5-S. enterica-5
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
227


FP5-S. cerevisiae-3
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
227


FP5-S. cerevisiae-5
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
228


FP5-S. cerevisiae-2
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
240


FP5-S. cerevisiae-4
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232


FP5-S. cerevisiae-1
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232



************************************************************



 


FP5-neg-control-4
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
289


FP5-neg-control-5
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
291


FP5-neg-control-3
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
291


FP5-neg-control-2
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292


FP5-neg-control-1
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292


FP5-S. aureus-4
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292


FP5-S. aureus-5
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
280


FP5-S. aureus-2
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
299


FP5-S. aureus-3
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
294


FP5-S. aureus-1
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
295


FP5-S. enterica-2
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
288


FP5-S. enterica-3
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
295


FP5-S. enterica-1
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
291


FP5-S. enterica-4
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
298


FP5-S. enterica-5
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
287


FP5-S. cerevisiae-3
CAGGCGAGCTGAGGAGNNNTTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
287


FP5-S. cerevisiae-5
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
288


FP5-S. cerevisiae-2
CAGGCGAGCTGAGGAGCANTTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
300


FP5-S. cerevisiae-4
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292


FP5-S. cerevisiae-1
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292



****************   *****************************************



 


FP5-neg-control-4
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
349


FP5-neg-control-5
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
351


FP5-neg-control-3
GAGAGGAANAAGNCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
351


FP5-neg-control-2
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
352


FP5-neg-control-1
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
352


FP5-S. aureus-4
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
352


FP5-S. aureus-5
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
340


FP5-S. aureus-2
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
359


FP5-S. aureus-3
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
354


FP5-S. aureus-1
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACCAGCTCTTGTTGTAAACNTT
355


FP5-S. enterica-2
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
348


FP5-S. enterica-3
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
355


FP5-S. enterica-1
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
351


FP5-S. enterica-4
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
358


FP5-S. enterica-5
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATT
347


FP5-S. cerevisiae-3
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
347


FP5-S. cerevisiae-5
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
348


FP5-S. cerevisiae-2
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
360


FP5-S. cerevisiae-4
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACNTN
352


FP5-S. cerevisiae-1
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
352



******** *** ******************************************** *



 


FP5-neg-control-4
GATCCAACTGGAANNNNNNNNNNGGNNNNNNNNNNNNNCATAAGGCATGATGGTTGCTCA
409


FP5-neg-control-5
GATCCAACTGGANNGNNNNNNATGGNNNNNNNNNNNTCCATAAGGCATGATGGTTGCTCA
411


FP5-neg-control-3
GATCCAACTGGAANNNNNNNNNTGNNNNNNNNNNNTTCCATAAGGCATGATGGTTGCTCA
411


FP5-neg-control-2
GATCCAACTGGNANGNCACNNNNGNNNNNNNAATATTCCATAAGGCATGATGGTTGCTCA
412


FP5-neg-control-1
GATCCAACTGGAATGTCACTAANGGNNNNNNNATATTCCATAAGGCATGATGGTTGCTCA
412


FP5-S. aureus-4
GATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCA
412


FP5-S. aureus-5
GATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCA
400


FP5-S. aureus-2
GATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCA
419


FP5-S. aureus-3
GATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCA
414


FP5-S. aureus-1
GNTNCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCA
415


FP5-S. enterica-2
GATCCAACTGGAATGTCACTAANNNNNNNNNNATATTCCATAAGGCATGATGGTTGCTCA
408


FP5-S. enterica-3
GATCCAACTGGAATGTCACTAANNNNNNNNNNNTATTCCATAAGGCATGATGGTTGCTCA
415


FP5-S. enterica-1
GATCCAACTGGAATGTCACTAANNNNNNNNAN-TATTCCATAAGGCATGATGGTTGCTCA
410


FP5-S. enterica-4
GATCCAACTGGAATGTCACTAANNNNNNNNAA-TATTCCATAAGGCATGATGGTTGCTCA
417


FP5-S. enterica-5
GATCCAACTGGAATGTCACTAANNNNNNNNNAATATTCCATAAGGCATGATGGTTGCTCA
407


FP5-S. cerevisiae-3
NNNNNNNNTGGNATGTCACTAATGGCGAATNNNNANNNNNTAAGGNNTGATGGTTGCTCA
407


FP5-S. cerevisiae-5
NNNNNNNNNGGAATGTCACTAATGGCGAATCNNNNNNNCNTAAGGNNNGNTGGTTGCTCA
408


FP5-S. cerevisiae-2
NNNNNNNNNNNNANGTCACTAATGGCGAANNNNNANNNNNTAAGGNNTGATGGTTGCTCA
420


FP5-S. cerevisiae-4
NNNNNNNNNGGAATGTCACTAATGGCGAATNNNNNNNNNNTAAGGCATGATGGTTGCTCA
412


FP5-S. cerevisiae-1
NNNNNNNNNGGAATGTCACTAATGGCGAANNNNNNNNNNNTAAGGNATGATGGTTGCTCA
412



                                        *****   * **********



 


FP5-neg-control-4
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
469


FP5-neg-control-5
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
471


FP5-neg-control-3
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
471


FP5-neg-control-2
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
472


FP5-neg-control-1
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
472


FP5-S. aureus-4
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
472


FP5-S. aureus-5
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
460


FP5-S. aureus-2
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
479


FP5-S. aureus-3
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
474


FP5-S. aureus-1
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
475


FP5-S. enterica-2
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
468


FP5-S. enterica-3
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
475


FP5-S. enterica-1
GAGGCNGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
470


FP5-S. enterica-4
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
477


FP5-S. enterica-5
GAGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCT
467


FP5-S. cerevisiae-3
GAGGCAGGAGAAGAGCNNNGNATACNNNNNTATAAAAGATAAAACATAAATAAACAGTCT
467


FP5-S. cerevisiae-5
GAGGCAGGAGAAGAGCNNNGNATACGNNNNTATAAAAGATAAAACATAAATAAACAGTCT
468


FP5-S. cerevisiae-2
GAGGCAGGAGAAGAGNNNNGNATACNNNNNNATAAAAGATAAAACATAAATAAACAGTCT
480


FP5-S. cerevisiae-4
GAGGCAGGAGAAGAGCAACGAATACNNNNNNATAAAAGATAAAACATAAATAAACAGTCT
472


FP5-S. cerevisiae-1
GAGGCAGGAGAAGAGCAACGAATACGANGCNNTAAAAGATAAAACATAAATAAACAGTCT
472



***** *********    * ****       ****************************



 


FP5-neg-control-4
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
529


FP5-neg-control-5
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
531


FP5-neg-control-3
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
531


FP5-neg-control-2
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532


FP5-neg-control-1
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532


FP5-S. aureus-4
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532


FP5-S. aureus-5
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
520


FP5-S. aureus-2
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
539


FP5-S. aureus-3
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
534


FP5-S. aureus-1
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
535


FP5-S. enterica-2
TGATTATATTCTGGGTATTAAAGCCACAANNNNNNNNNNNNTNTGCTTTGTATCTTTNNN
528


FP5-S. enterica-3
TGATTATATTCTGGGTATTAAAGCCACANNNNNNNNNNNNNTATGCTTTGTATCTTNNNN
535


FP5-S. enterica-1
TGATTATATTCTGGGTATTAAAGCCACANNNNNNNNNGANNTATGCTTTGTATCTTNNNN
530


FP5-S. enterica-4
TGATTATATTCTGGGTATTAAAGCCACAANGNGNNNNNANNTATGCTTTGTATCTTNNNN
537


FP5-S. enterica-5
TGATTATATTCTGGGTATTAAAGCCACANNNNNNNNNGANNTATGCTTTGTATCTTTTCT
527


FP5-S. cerevisiae-3
TGATTATATTCTGGGTATTAAAGCCNCAATCNNANNAAATATATGCTTTGTATCTTTTCT
527


FP5-S. cerevisiae-5
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
528


FP5-S. cerevisiae-2
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
540


FP5-S. cerevisiae-4
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532


FP5-S. cerevisiae-1
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532



************************* **             * *************



 


FP5-neg-control-4
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTANNAGAACTTGTGGTAAGATAAG
589


FP5-neg-control-5
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
591


FP5-neg-control-3
TGCCTTCTTCATTACCAACTGNTTCCGCGGNCACNTTAAGAGAACTTGTGGTAAGATAAG
591


FP5-neg-control-2
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
592


FP5-neg-control-1
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
592


FP5-S. aureus-4
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
592


FP5-S. aureus-5
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
580


FP5-S. aureus-2
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
599


FP5-S. aureus-3
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
594


FP5-S. aureus-1
TGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
595


FP5-S. enterica-2
NGCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAN
588


FP5-S. enterica-3
NGNCNTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
595


FP5-S. enterica-1
NGNCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
590


FP5-S. enterica-4
NNNCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAN
597


FP5-S. enterica-5
TGNCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
587


FP5-S. cerevisiae-3
TGCCTNNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
587


FP5-S. cerevisiae-5
TGCCTNNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGNAAGATAAG
588


FP5-S. cerevisiae-2
TGCCTNNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
600


FP5-S. cerevisiae-4
TGCCTTNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGNTAAGATAAG
592


FP5-S. cerevisiae-1
TGCCTTNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
592



   *                   ******* *** ***  **********  *******



 


FP5-neg-control-4
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
649


FP5-neg-control-5
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
651


FP5-neg-control-3
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
651


FP5-neg-control-2
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
652


FP5-neg-control-1
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
652


FP5-S. aureus-4
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
652


FP5-S. aureus-5
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
640


FP5-S. aureus-2
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
659


FP5-S. aureus-3
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
654


FP5-S. aureus-1
AAGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
655


FP5-S. enterica-2
AANATATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
648


FP5-S. enterica-3
AAGATATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
655


FP5-S. enterica-1
AAGATATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
650


FP5-S. enterica-4
ANNANNTTTTATTCGNNNNGNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
657


FP5-S. enterica-5
AAGATATTTTATTCGNNCNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAA
647


FP5-S. cerevisiae-3
AAGATATTTTATTCNNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
647


FP5-S. cerevisiae-5
AAGATATTTTATTCNNNNNNNTNNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
648


FP5-S. cerevisiae-2
AAGATATTTTATTCGNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
660


FP5-S. cerevisiae-4
AAGATATTTTATTCNNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
652


FP5-S. cerevisiae-1
AAGATATTTTATTCGNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
652



*  *  ********       *       *******************************



 


FP5-neg-control-4
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
709


FP5-neg-control-5
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
711


FP5-neg-control-3
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
711


FP5-neg-control-2
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
712


FP5-neg-control-1
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
712


FP5-S. aureus-4
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
712


FP5-S. aureus-5
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
700


FP5-S. aureus-2
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
719


FP5-S. aureus-3
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
714


FP5-S. aureus-1
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
715


FP5-S. enterica-2
GAGGCGGTTAATTGCAGATATAATTNNNNNNNNNNNNGGTCGTTGCTATGGTCACCGTGA
708


FP5-S. enterica-3
GAGGCGGTTAATTGCAGATATAATTGGNNNNNNNNNNGNTCGTTGCTATGGTCACCGTGA
715


FP5-S. enterica-1
GAGGCGGTTAATTGCAGATATAATTGGNNGTNNNNNNGNNCGTTGCTATGGTCACCGTGA
710


FP5-S. enterica-4
GAGGCGGNTAATTGCAGATATAATTGGNNGTNNNNNNGGTCGTTGCTATGGTCACCGTGA
717


FP5-S. enterica-5
GAGGCGGTTAATTGCAGATATAATTGGNNGTNNNNNNGGTCGTTGCTATGGTCACCGTGA
707


FP5-S. cerevisiae-3
GAGGCGGTTAANTGCAGATATAATTGNNNNNNNNNNNGGTCGTTGCTATGGTCACCGTGA
707


FP5-S. cerevisiae-5
GAGGCGGTTAANTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
708


FP5-S. cerevisiae-2
GANGCGGNTAANTGNANATATNATTGGNNGNGAAA-------------------------
695


FP5-S. cerevisiae-4
GAGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
712


FP5-S. cerevisiae-1
GAGGCGGTTNNNTGNAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
712



** **** *   ** * **** ***



 


FP5-neg-control-4
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGTTAATATTGNTTGAATATGGTA
769


FP5-neg-control-5
AGCGAGTACAGCAGCACAAGAATGTGTGCCGNTCTCAGTTAATATTGTTTGAATATGGTA
771


FP5-neg-control-3
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGTTAATATTGNTTGAATATGGTA
771


FP5-neg-control-2
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGTTAATATTGNTTGAATATGGNA
772


FP5-neg-control-1
AGCGAGTACAGCAGCACAAGAATGNGTGCCGTTCTCAGTTAATATTGTTTGAATATGGNA
772


FP5-S. aureus-4
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGTNNGNNNNNNNNGAATATGGTA
772


FP5-S. aureus-5
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNNNNNNNNNNGAATATGGTA
760


FP5-S. aureus-2
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNNNNNNNNNNGAATATGGTA
779


FP5-S. aureus-3
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNGNANNNNNNGAATATGGTA
774


FP5-S. aureus-1
AGCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNNNNNNNNNNGAATATGGTA
775


FP5-S. enterica-2
AGCGAGTNNNGCNNNNNNAGANTGNGNGGNNGNNNNNNNNNATATTGNTTGAATATGGNN
768


FP5-S. enterica-3
AGCGAGTACAGCAGCACAAGAATGTGTGNNNNNNNNNNNNAATATTGNTTGAATATGGTA
775


FP5-S. enterica-1
AGCGAGTACNNCAGCACAAGAATGTGTGNNNNNNNNNNNTAATATNGTTTGAATATGGTA
770


FP5-S. enterica-4
AGCGAGTACAGCAGCACAAGAATGTGTGNNGNNNNNNNNTAATATTGTTTGAATATGGTA
777


FP5-S. enterica-5
AGCGAGTACAGCAGCACAAGAATGTGTNNNNNNNNNNNNTAATATTGTTTGAATATGGTA
767


FP5-S. cerevisiae-3
AGCGAGTACAGCNNNNNNNNNATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTA
767


FP5-S. cerevisiae-5
AGCGAGTACNNNGNNNNNNNNATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTA
768


FP5-S. cerevisiae-2
------------------------------------------------------------



FP5-S. cerevisiae-4
AGCGAGTACNNNNNNNNNNNNATGTGTGCCGTTCTCAGTTAATATTGNNTGAATATGGTA
772


FP5-S. cerevisiae-1
AGCGAGTACAGCNGNNNNNNNATGTGTGCCGTTCTCAGTTAATATTGTTTGAATANGGNN
772


 


FP5-neg-control-4
ACCTGTTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGTGACTG
829


FP5-neg-control-5
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGTGACTG
831


FP5-neg-control-3
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGTGACTG
831


FP5-neg-control-2
ACCTGNTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGNGACTG
832


FP5-neg-control-1
ACCTGNTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGTGACTG
832


FP5-S. aureus-4
ACCTGNTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAACNNNNNNGCAGTGACTG
832


FP5-S. aureus-5
ACCTGNTTTAGTCGGNTTAAAGGNAAGAAGANCTAACCAAAAACNNN-------------
807


FP5-S. aureus-2
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAANNNNNNTGCAGTGACTG
839


FP5-S. aureus-3
ACCTGTTTTAGTCGGTTTANANNNNAGAAGATCTAACCNNAAAA----------------
818


FP5-S. aureus-1
ACCTGNTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCAAANACANN-------------
822


FP5-S. enterica-2
NCCTGNTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGTGACTG
828


FP5-S. enterica-3
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCNAAAACNACACTGCAGTGACTG
835


FP5-S. enterica-1
ACCTGTTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGTGACNN
830


FP5-S. enterica-4
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGTGACTG
837


FP5-S. enterica-5
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGTGACTG
827


FP5-S. cerevisiae-3
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGANCTAACCAAAAACAACACTGCAGTGACTG
827


FP5-S. cerevisiae-5
ACCTGTTTTAGTCGGTTTAAAGGTAAGANNANNTAACCAAAAACAACACTGCAGTGACTG
828


FP5-S. cerevisiae-2
------------------------------------------------------------



FP5-S. cerevisiae-4
ACCTGTTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGNGACTG
832


FP5-S. cerevisiae-1
NNNNGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGNGACTG
832


 


FP5-neg-control-4
ATTGNAGTANTTATTTTTNNACT-------------------------------------
852


FP5-neg-control-5
ATTGTAGTANTTATTTTTTTACTTAATCTTAANNNNNNG---------------------
870


FP5-neg-control-3
ATTGNAGTATTTNNNNNTNN----------------------------------------
851


FP5-neg-control-2
ATTGNANNATTTATTTNNNNNCNNNNTCNTNNNNNNNGNGTAAACATCNACGGCGCACTT
892


FP5-neg-control-1
ATTGTAGTATTTATTTTTTTACNNNNNCTTAANNNNNNNGNANACNTCAACGGCGCACTT
892


FP5-S. aureus-4
ATTGNNG-----------------------------------------------------
839


FP5-S. aureus-5
------------------------------------------------------------



FP5-S. aureus-2
ANNGNAGTATTTATTTTTTTACTTAA----------------------------------
865


FP5-S. aureus-3
------------------------------------------------------------



FP5-S. aureus-1
------------------------------------------------------------



FP5-S. enterica-2
ATTGTAGNANNNNNNN--------------------------------------------
844


FP5-S. enterica-3
ATTGNAGTATNNNNNN--------------------------------------------
851


FP5-S. enterica-1
NNNNNAGTATNNNNNNTTTTACTTANNNNNAATTNTGGTGTAAACATCANCGGCGCACTT
890


FP5-S. enterica-4
ATTGTAGTANNNNNNNTTTTACTTAATCTTAATTTTGG----------------------
875


FP5-S. enterica-5
ATTGNNGNANN-------------------------------------------------
838


FP5-S. cerevisiae-3
ATTGNAGNANTTATTTTTTTACTTAATCTTAANTTNNG----------------------
865


FP5-S. cerevisiae-5
ATNGNAGTATTTATTTTTTTACTTAATCTTAATTTNGNNGNAAACATCANCGGNNNGNTT
888


FP5-S. cerevisiae-2
------------------------------------------------------------



FP5-S. cerevisiae-4
ATTGNAGTATTTATTTTTTTACTTAATCTTAATTTTGGGGN-------------------
873


FP5-S. cerevisiae-1
ATTGTAGTATTTATTTTNNNNNNNNATCTT------------------------------
862









In order to test the ability of the invention to provide a means of identification by comparison to a database, the first three sequence embedded fingerprints (Numbers 1-3) generated for each microorganism were used to produce a consensus fingerprint sequence for that organism (Tables 4-6). These consensus sequences were then used to create a BLAST database (NCBI BLAST web server). The fifth sequence embedded fingerprint (number 5) for each organism was used to query the database. The resultant blast scores (Tables 7-9) show that the comparison of BLAST program identifies each microorganisms sequence embedded fingerprint as belonging to the correct species (highest total score).







TABLE 4A





CLUSTAL 2.0.11 muultiple sequence alignment


First three Staphylococcus aureus MU3 sequence embedded fingerprints by primer mix 


FB1D1 were aligned and used to generate a consensus sequence

















SEQ ID NO: 46
-------GTTGCTCT-CNGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCTCCACTTC



consensus




SEQ ID NO: 22
CNGTTATGTTGCTCT-CNGCTGACNATGCTGCTGCTGCTTCNNGNNNCTGTCTCCACTTC
59


FB1D1 S. aureus 3




SEQ ID NO: 21
----TNNGTTGNTCTACNGNTGACNATGCTGCTGCTGCTTNNNNNNNCTGTCTCCACTTC
56


FB1D1 S. aureus 2




SEQ ID NO: 23
-------GTTGNTCN-NNGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCTCCACTTC
52


FB1D1 S. aureus 1





       **** **   ** ******************** ** ****************



 


consensus
CTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTANGNCNNA



FB1D1 S. aureus 3
CTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTAGGNCNNA
119


FB1D1 S. aureus 2
CTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTANGNNNNA
116


FB1D1 S. aureus 1
CTTGAACANTGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTANGNCNNA
112



******** ** ***************************************** ** ***



 


consensus
CATCAGAACCACCACAGNCNNTNTCNCCNCCTTCCTCTTATAGATTCGGAATCTCATGAT



FB1D1 S. aureus 3
GATCAGAACCACCACAGNCNNTATCNCCNCCTTCCTCTTATAGATTCGGAATCTCATGAT
179


FB1D1 S. aureus 2
GATCAGAACCACCACAGNCNNNNTNACCNCCTTCCTCTTATAGATTCGGAATCTCATGAT
176


FB1D1 S. aureus 1
GATCAGAACCACCACAGNCNNNNTCNCCNCCTTCCTCTTATAGATTCGGAATCTCATGAT
172



*********************  *  **********************************



 


consensus
AGGGNNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGANGAGCANTTGCA



FB1D1 S. aureus 3
AGGGNNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGANGAGCAATTGCA
239


FB1D1 S. aureus 2
AGGGNNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCNAGCTGANGAGCANTTGCA
236


FB1D1 S. aureus 1
AGGGGNTCNNCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGCANTTGCA
232



**** ************************************ ****** ***** *****



 


consensus
GGTGNNNNNATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAAGAAGTCGTGCCGGGGC



FB1D1 S. aureus 3
GGTGNNNNNATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAAGAAGTCGTGCCGGGGC
299


FB1D1 S. aureus 2
GGNGNNNGNNTGTGCTCGGCTCAAGANGCGGGNCCGGANAGGAAGAAGTCGTGCCGGGGC
296


FB1D1 S. aureus 1
GGTGNNNNNATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAGGAAGAAGTCGTGCCGGGGC
292



** **** * **************** ***** ***** *********************



 


consensus
TAATTATTGGCAAAACGAGCTCTTGTTGTAAACATNGNNNNNNNNNNNNNNNNNNNNNNN



FB1D1 S. aureus 3
TAATTATTGGCAAAACGAGCTCTTGTTGNAAACNTNGNNNGGGGGGGGNNNNNNNNNNNN
359


FB1D1 S. aureus 2
TAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGNNNNNNNNNNNNNNNNNNNNNNN
356


FB1D1 S. aureus 1
TAATTATTGGCAAAACGAGCTCTTGTTGTAAACATNGNNNNNNNNNNNNNNNNNNNNNNN
352



**************************** **** * ****        ************



 


consensus
NNN-ATCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAATA



FB1D1 S. aureus 3
NNN-ATCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAATA
418


FB1D1 S. aureus 2
NNN-ATCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAATA
415


FB1D1 S. aureus 1
NNNGNNCAATATTCCATAAGGCATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAATA
412



***   ******************************************************



 


consensus
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC



FB1D1 S. aureus 3
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC
478


FB1D1 S. aureus 2
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC
475


FB1D1 S. aureus 1
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC
472



************************************************************



 


consensus
CACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCATTACCAACTGCTT



FB1D1 S. aureus 3
CACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCATTACCAACTGCTT
538


FB1D1 S. aureus 2
CACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCNTTACCAACTGCTT
535


FB1D1 S. aureus 1
CACAATCAGAACAAATATATGCTTTGTATCTTTTCTTGCCTTCTTCATNNNNNNNTGCTT
532



********************************************** *       *****



 


consensus
CCGCGGCCACATTAAGAGAACTTGNGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA



FB1D1 S. aureus 3
CCGCGGCCACATTAAGAGAACTTGNGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA
598


FB1D1 S. aureus 2
CCGCGGCCACATTAAGAGAACTTGNGNTAAGATAAGAAGATATTTTATTCGTTCTGCTGA
595


FB1D1 S. aureus 1
CCGCGGCCACATTAAGAGAACTTGGGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA
592



************************ * *********************************



 


consensus
CTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATAAT



FB1D1 S. aureus 3
CTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATAAT
658


FB1D1 S. aureus 2
CTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATAAT
655


FB1D1 S. aureus 1
CTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATAAT
652



************************************************************



 


consensus
TGGTAGTGAAAAGGNNNNTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG



FB1D1 S. aureus 3
TGGTAGTGAAAAGGNNNNTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG
718


FB1D1 S. aureus 2
TGGTAGTGAAAAGGNGCGTTGCTATGGTCACCGTGAAGNGAGTACAGCAGCACAAGAATG
715


FB1D1 S. aureus 1
TGGTAGTGAAAAGGNNNNTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG
712



***************   ******************** *********************



 


consensus
TGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCGGNTTAAAGGT



FB1D1 S. aureus 3
TGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCGGNTTAAAGGT
778


FB1D1 S. aureus 2
TGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCGGTTTAAAGGT
775


FB1D1 S. aureus 1
TGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTAACCTGTTTTAGTCGGTTTAAAGGT
772


 


consensus
AAGAAGATCTAACCAAAAAC-AACACTGCAGNGACTGATTGNNGNN-TTNNNNNTTTTTT



FB1D1 S. aureus 3
AAGAAGATCTAACNNAAANNCAACACTGCANNGACTGNNNNNNNNNATTNNNNNNTTTTT
838


FB1D1 S. aureus 2
AAGAAGATCTAACCAAAAAC-AACACNGCAGTGACTGATTGNNGNN-NNNNNNNTTTTTT
833


FB1D1 S. aureus 1
NAGAAGATCTAACCAAAAAC-AACACTGCAGNGACTGATTGTAGTA---TTTATTTTTNN
828



 ************  ***   ***** ***  *****                  ***



 


consensus
ACTTAATCTTAATTTTGGTGTAAACATCAACGG-CGCAC-----



FB1D1 S. aureus 3
ACTTAATCTTAATTTTGGTGTAAACATCAACNGGCGCACTTN--
880


FB1D1 S. aureus 2
ANNTNATCTTAATTTTGGTGTAAACATCNACGG-CGCACTTCAA
876


FB1D1 S. aureus 1
NNNNNNNCTNNATTTTGGTGTAAACATCAACGG-CGCACNN---
868



       **  ***************** ** * *****
















TABLE 4B





CLUSTAL 2.0.11 multiple sequence alignment


First three Staphylococcus aureus MU3 sequence embedded fingerprints by primer


FP5 were aligned and used to generate a consensus sequence

















SEQ ID NO: 47
-----NNNCTGGTTNTGANTACTGTTAANGTTGCTACTACTGCTGACAATGCTGCTGCTG
55


Consensus




SEQ ID NO: 33
NNNGCNGCCNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTG
60


FP5-S. aureus-2




SEQ ID NO: 35
----NNNNCTGGTTNTGANTACTGTTAANGTTGCTACTACTGCTGACAATGCTGCTGCTG
56


FP5-S. aureus-1




SEQ ID ND: 34
-----NNNCTGGTTNTGANTACTGNNNNNGTTGCTACTACTGCTGACAATGCTGCTGCTG
55


FP5-S. aureus-3





     *  * ******** *****     *******************************



 


Consensus
CTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCG
115


FP5-S. aureus-2
CTTCTCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCG
120


FP5-S. aureus-1
CTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCG
116


FP5-S. aureus-3
CTTCTCNTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCG
115



****** * ***************************************************



 


Consensus
CTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTC
175


FP5-S. aureus-2
CTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTC
180


FP5-S. aureus-1
CTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTC
176


FP5-S. aureus-3
CTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTC
175



************************************************************



 


Consensus
TTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGC
235


FP5-S. aureus-2
TTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGC
240


FP5-S. aureus-1
TTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGC
236


FP5-S. aureus-3
TTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGC
235



************************************************************



 


Consensus
AGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGG
295


FP5-S. aureus-2
AGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGG
300


FP5-S. aureus-1
AGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGG
296


FP5-S. aureus-3
AGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGG
295



************************************************************



 


Consensus
AGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTG
355


FP5-S. aureus-2
AGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTG
360


FP5-S. aureus-1
AGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACNTTG
356


FP5-S. aureus-3
AGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTG
355



******************************************************** ***



 


Consensus
ATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCAG
415


FP5-S. aureus-2
ATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCAG
420


FP5-S. aureus-1
NTNCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCAG
416


FP5-S. aureus-3
ATCCAACTGGAATGTCACTAATGGCGAATCAATATTCCATAAGGCATGATGGTTGCTCAG
415



 * *********************************************************



 


Consensus
AGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTT
475


FP5-S. aureus-2
AGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTT
480


FP5-S. aureus-1
AGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTT
476


FP5-S. aureus-3
AGGCAGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTT
475



************************************************************



 


Consensus
GATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTT
535


FP5-S. aureus-2
GATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTT
540


FP5-S. aureus-1
GATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTT
536


FP5-S. aureus-3
GATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCTT
535



************************************************************



 


Consensus
GCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGA
595


FP5-S. aureus-2
GCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGA
600


FP5-S. aureus-1
GCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGA
596


FP5-S. aureus-3
GCCTTCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGA
595



************************************************************



 


Consensus
AGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAG
655


FP5-S. aureus-2
AGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAG
660


FP5-S. aureus-1
AGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAG
656


FP5-S. aureus-3
AGATATTTTATTCGTTCTGCTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAG
655



************************************************************



 


Consensus
AGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAA
715


FP5-S. aureus-2
AGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAA
720


FP5-S. aureus-1
AGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAA
716


FP5-S. aureus-3
AGGCGGTTAATTGCAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAA
715



************************************************************



 


Consensus
GCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNNNNNNNNNNGAATATGGTAA
775


FP5-S. aureus-2
GCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNNNNNNNNNNGAATATGGTAA
780


FP5-S. aureus-1
GCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNNNNNNNNNNGAATATGGTAA
776


FP5-S. aureus-3
GCGAGTACAGCAGCACAAGAATGTGTGCCGTTCTCAGNNNGNANNNNNNGAATATGGTAA
775



**************************************** * *****************



 


Consensus
CCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAANN----------------
819


FP5-S. aureus-2
CCTGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAANNNNNNTGCAGTGACTGA
840


FP5-S. aureus-1
CCTGNTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCAAANACANN--------------
822


FP5-S. aureus-3
CCTGTTTTAGTCGGTTTANANNNNAGAAGATCTAACCNNAAAA-----------------
818



**** ********* *** *    *************  * *
















TABLE 5A





CLUSTAL 2.0.11 multiple sequence alignment


First Three Saccharomyces cerevisiae S288C sequence embedded fingerprints by primer mix


FB1D1 were aligned and used to generate a consensus sequence

















SEQ ID NO: 48
 CTGNTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCTCCAC



Consensus




SEQ ID NO: 10
NCNGNNNNNGNTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCNCTGTCTCCAC
60


FB1D1 S. cerevisiae 3




SEQ ID NO: 11
-CTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCTCCAC
59


FB1D1 S. cerevisiae 2




SEQ ID NO: 9
-CTGNTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCTCCAC
59


FB1D1 S. cerevisiae 1





 * *     * ********************************* **** **********



 


Consensus
TTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCNGAGNGNTAGGCC



FB1D1 S. cervisiae 3
TTCCTTGAACAATGCGCCGTCNTGCTTCTTTTGCCTCCCGCTGCTCCNNANNGNTAGGCC
120


FB1D1 S. cervisiae 2
TTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCNGAGNGNTAGGCC
119


FB1D1 S. cervisiae 1
TTCCTTGAACAATGCGCCGNCNTGCTTCTTTTGCCTCCCGCTGCTCCNGAGNGCTAGGCC
119



******************* **************************** * ** ******



 


Consensus
GCAGATCAGAACCACCACAGNCAATATCACCACCNTCNNCTTATAGATTCGGAATCTCAT



FB1D1 S. cervisiae 3
GCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATCTCAT
180


FB1D1 S. cervisiae 2
GCAGATCAGAACCACCACAGNCAATATCACCACCNTCNNCTTATANATTCGGAATCTCAT
179


FB1D1 S. cervisiae 1
GCAGATCAGAACCACCACAGNCAATATCACCACCNNCNNCTTATAGATTCGGAATCTCAT
179



******************** *************  *  ****** **************



 


Consensus
GATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGCAATT



FB1D1 S. cervisiae 3
GATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGCAATT
240


FB1D1 S. cervisiae 2
GATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGCAATT
239


FB1D1 S. cervisiae 1
GATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGCGAGCTGAGGAGCAATT
239



************************************************************



 


Consensus
GCAGGTGATATGATGTGCTCGGCTCANNGGGNNNNNNNNNNNNNNNNNNNNNNTGCCGGG



FB1D1 S. cervisiae 3
GCAGGTGATATGATGTGCTCGGCTCANGGGGNNNNNNNNNNNNNNNNNNNNNNNGCCGGG
300


FB1D1 S. cervisiae 2
GCAGGTGATATGATGTGCTCGGCTCANNGGGCNNNNNNNNNNNNNNNNNNNNNTGCCGGG
299


FB1D1 S. cervisiae 1
GCNGGTGATATGATGTGCTCGGCTCNNNGGGNNNGGNGNNNNNNNNANGNCNN-GCCGGG
298



** ********************** * *** **  * ******** * * ** ******



 


Consensus
GCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGNNGGNNNNNNA



FB1D1 S. cervisiae 3
GCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGNNGGNNNNNNA
360


FB1D1 S. cervisiae 2
GCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCAACTGGNNGGNNNNNNA
359


FB1D1 S. cervisiae 1
GCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCCNNNNGGNNNGTNNNNNN
358



*******************************************    **** * *****



 


Consensus
TGGNGNNNGNNNNTGNCNNNNGGCATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAA



FB1D1 S. cervisiae 3
TGGNGNNNNNNNNTGCCNNNNNGCATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAA
420


FB1D1 S. cervisiae 2
TGGNGNNNGNNNNTGNNNNNNGGGATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAA
419


FB1D1 S. cervisiae 1
NGGNGNNNGANNNTGNNNNNNGGNATGATGGTTGCTCAGAGGCAGGAGAAGAGCAACGAA
418



 *******  *****  **** * *  *********************************



 


Consensus
TACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAA



FB1D1 S. cervisiae 3
TACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAA
480


FB1D1 S. cervisiae 2
TACNATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAA
479


FB1D1 S. cervisiae 1
TACGATCCTATNAAAGATAAAACATAAATAAACNGTCTTGATTATATTCTGGGTATTAAA
478



*** ******* ********************* **************************



 


Consensus
NNCNNNGNCAGAACAAATATATGCTTTGNNNNNNNNCNTGNCNNCNNNNNNNNNNNNNNN



FB1D1 S. cervisiae 3
GNCNCAGNCAGAACAAATATATGCTTTGTNNCTNNNCNTGCCTTCTTNNNNNNNNNNNNN
540


FB1D1 S. cervisiae 2
NNNNNNGNCAGAACAAATATATGCTTTGNNNNNTNNCNTGNNNNCNNNNGGNNNNNNNNN
539


FB1D1 S. cervisiae 1
NNCNNNGNNAGAACAAATATATGCTTTNNNNNNNNTCNNGNCNNNNNNNNNNNNNNNNNN
538



 * *  ** ******************  **   * ** *       **  *********



 


Consensus
NNNNNNGGCCACNNNNNGAGAACTTGTNNNNNNNTAAGAAGATATTTTATTCGNTCTGCT



FB1D1 S. cervisiae 3
NNNNNNGGCCACNNNNNNAGAACTTGNGGNGNNATAAGAAGATATTTTATTCGNTCTGCT
600


FB1D1 S. cervisiae 2
NNNNNNGGCCNCNNNNNGAGAACTTGTNNNNNNNTAAGAAGATATTTTATTCGNNCTGCT
599


FB1D1 S. cervisiae 1
NNNNNNGGCCACATTAAGAGAACTTGTNNNNNNNTAAGAAGATATTTTATTCGNTCTGCT
598



********** *      ********   * ** ******************** ***** 



 


Consensus
GACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATA



FB1D1 S. cervisiae 3
GACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATA
660


FB1D1 S. cervisiae 2
GACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATA
659


FB1D1 S. cervisiae 1
GACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGCGGTTAATTGCAGATATA
658



************************************************************



 


Consensus
ATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAN



FB1D1 S. cervisiae 3
ATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAN
720


FB1D1 S. cervisiae 2
ATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACANGAN
719


FB1D1 S. cervisiae 1
ATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAA
718



******************************************************** **



 


Consensus
NGTGTGCCGTTCTCAGTTAATATTGNNTGAATATGGTAACCTGNTTTAGTCGGTTTAAAG



FB1D1 S. cervisiae 3
NGTGTGCCGTTCTCAGTTAATATNGNNNGAATATGGTAACCTGNTTTAGTCGGTTTAAAG
780


FB1D1 S. cervisiae 2
NGTGTGCCGTTCTCAGTTAATATTGNTTGAATATGGTAACCTGTTTTAGTCGGTTTAAAG
779


FB1D1 S. cervisiae 1
TGTGTGCCGTTCTCAGTTAATATTGTNTGAATATGGTAACCTGNTTTAGTCGGTTTAAAG
778



 ********************** *   *************** ****************



 


Consensus
GTAAGAAGANCTAACCAAAAACAACACTGCNNNNNNGNNNGGGGGNNNNNNNNNNNNTAC



FB1D1 S. cervisiae 3
GTAAGAAGANCTAACCAAAAACAACACTGCNNNNNNNNNNGGGGGNNNNNNNNNNNTTAC
840


FB1D1 S. cervisiae 2
GTAAGAAGANCTAACCNAAAACAACACTGCNNNNNNGNGGGGGGNNNNNNNNNNNNNTAC
839


FB1D1 S. cervisiae 1
GTAAGAAGATCTAACCAAAAACAACACTGCNNGNCNGNNNNNNNGGNNNNNNNNNNNTTA
838



********* ****** *************** * * *        ********** *



 


Consensus
TNNNNNNNNNTTNNNGGNGNAAACATCNACGNNNNNNNNCAACCAATN



FB1D1 S. cervisiae 3
TNNNNGNNNNTTNNNGGNGNAAACATCNACGNNNNNNNNCAACCNATNNN
890


FB1D1 S. cervisiae 2
TTNNNNNNNNNNNNNNNNNN--ACATCNNCGNNNNNNNNCAACCAATAN-
886


FB1D1 S. cervisiae 1
CTNNNNNNNNATTTTGGNNTAAACATCAACGGNNNNNNNCANCCANNN--
886



  *** ****       *    *****  ** ********* **
















TABLE 5B





CLUSTAL 2.0.11 multiple sequence alignment


First Three Saccharomyces cerevisiae S288C sequence embedded fingerprints


by primer FP5 were aligned and used to generate a consensus sequence

















SEQ ID NO: 49
--------CCTGNNNNNGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


Consensus




SEQ ID NO: 45
--------CCTGNNNNNGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


FP5-S. cerevisiae-1




SEQ ID NO: 43
NNNTGNNGCCTGNTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
60


FP5-S. cerevisiae-2




SEQ ID NO: 41
-------------NNNNNATNNCTGTTNATGTTGCTNCTACTGCTGACAATGCTGCTGCT
47


FP5-S. cerevisiae-3





               *  **  ***** ******** ***********************



 


Consensus
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112


FP5-S. cerevisiae-1
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
112


FP5-S. cerevisiae-2
GCTTCTCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
120


FP5-S. cerevisiae-3
GCTTCTCCTCNNTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCC
107



*********** ************************************************



 


Consensus
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172


FP5-S. cerevisiae-1
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
172


FP5-S. cerevisiae-2
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
180


FP5-S. cerevisiae-3
GCTGCTCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCT
167



************************************************************



 


Consensus
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232


FP5-S. cerevisiae-1
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
232


FP5-S. cerevisiae-2
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
240


FP5-S. cerevisiae-3
CTTATAGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTG
227



************************************************************



 


Consensus
CAGGCGAGCTGAGGAGCANTTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292


FP5-S. cerevisiae-1
CAGGCGAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
292


FP5-S. cerevisiae-2
CAGGCGAGCTGAGGAGCANTTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
300


FP5-S. cerevisiae-3
CAGGCGAGCTGAGGAGNNNTTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCG
287



****************   *****************************************



 


Consensus
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
352


FP5-S. cerevisiae-1
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
352


FP5-S. cerevisiae-2
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
360


FP5-S. cerevisiae-3
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATN
347



************************************************************



 


Consensus
NNNNNNNNNGGNATGTCACTAATGGCGAANNNNNANNNNNTAAGGNNTGATGGTTGCTCA
412


FP5-S. cerevisiae-1
NNNNNNNNNGGAATGTCACTAATGGCGAANNNNNNNNNNNTAAGGNATGATGGTTGCTCA
412


FP5-S. cerevisiae-2
NNNNNNNNNNNNANGTCACTAATGGCGAANNNNNANNNNNTAAGGNNTGATGGTTGCTCA
420


FP5-S. cerevisiae-3
NNNNNNNNTGGNATGTCACTAATGGCGAATNNNNANNNNNTAAGGNNTGATGGTTGCTCA
407



********    * *************** **** *********** *************



 


Consensus
GAGGCAGGAGAAGAGCNNNGNATACNNNNNNATAAAAGATAAAACATAAATAAACAGTCT
472


FP5-S. cerevisiae-1
GAGGCAGGAGAAGAGCAACGAATACGANGCNNTAAAAGATAAAACATAAATAAACAGTCT
472


FP5-S. cerevisiae-2
GAGGCAGGAGAAGAGNNNNGNATACNNNNNNATAAAAGATAAAACATAAATAAACAGTCT
480


FP5-S. cerevisiae-3
GAGGCAGGAGAAGAGCNNNGNATACNNNNNTATAAAAGATAAAACATAAATAAACAGTCT
467



***************    * ****  *    ****************************



 


Consensus
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532


FP5-S. cerevisiae-1
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
532


FP5-S. cerevisiae-2
TGATTATATTCTGGGTATTAAAGCCACAATCAGAACAAATATATGCTTTGTATCTTTTCT
540


FP5-S. cerevisiae-3
TGATTATATTCTGGGTATTAAAGCCNCAATCNNANNAAATATATGCTTTGTATCTTTTCT
527



************************* *****  *  ************************



 


Consensus
TGCCTNNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
592


FP5-S. cerevisiae-1
TGCCTTNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
592


FP5-S. cerevisiae-2
TGCCTNNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
600


FP5-S. cerevisiae-3
TGCCTNNNNNNNNNNNNNNNNNNTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAG
587



***** ******************************************************



 


Consensus
AAGATATTTTATTCGNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
652


FP5-S. cerevisiae-1
AAGATATTTTATTCGNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
652


FP5-S. cerevisiae-2
AAGATATTTTATTCGNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
660


FP5-S. cerevisiae-3
AAGATATTTTATTCNNNNNNNTGNNNNNNTGGATGTCGGGAAATATTCTGCATTTGATAA
647



************** *********************************************



 


Consensus
GAGGCGGTTAANTGNAGATATAATTGGNNGNGAAA-------------------------
687


FP5-S. cerevisiae-1
GAGGCGGTTNNNTGNAGATATAATTGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGA
712


FP5-S. cerevisiae-2
GANGCGGNTAANTGNANATATNATTGGNNGNGAAA-------------------------
695


FP5-S. cerevisiae-3
GAGGCGGTTAANTGCAGATATAATTGNNNNNNNNNNNGGTCGTTGCTATGGTCACCGTGA
707



** **** *  *** * **** ****



 


Consensus
------------------------------------------------------------



FP5-S. cerevisiae-1
AGCGAGTACAGCNGNNNNNNNATGTGTGCCGTTCTCAGTTAATATTGTTTGAATANGGNN
772


FP5-S. cerevisiae-2
------------------------------------------------------------



FP5-S. cerevisiae-3
AGCGAGTACAGCNNNNNNNNNATGTGTGCCGTTCTCAGTTAATATTGTTTGAATATGGTA
767


 


Consensus
------------------------------------------------------------



FP5-S. cerevisiae-1
NNNNGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGNGACTG
832


FP5-S. cerevisiae-2
------------------------------------------------------------



FP5-S. cerevisiae-3
ACCTGTTTTAGTCGGTTTAAAGGTAAGAAGANCTAACCAAAAACAACACTGCAGTGACTG
827


 


Consensus
--------------------------------------



FP5-S. cerevisiae-1
ATTGTAGTATTTATTTTNNNNNNNNATCTT--------
862


FP5-S. cerevisiae-2
--------------------------------------



FP5-S. cerevisiae-3
ATTGNAGNANTTATTTTTTTACTTAATCTTAANTTNNG
865
















TABLE 6A





CLUSTAL 2.0.11 multiple sequence alignment


First Three Salmonella enterica MR595 sequence embedded fingerprints by primer


mix FB1D1 were aligned and used to generate a consensus sequence

















SEQ ID NO: 50
GCTGACAATGCTGCTGCNGCTTCTCCTCNCTGTCTCCACTT



Consensus




SEQ ID NO: 18
-------GTTNNTCNNN--GCTGACAATGCTGCTGCNGCTTCTCCTCNCTGTCTCCACTT
51


FB1D1 S. enterica 3




SEQ ID NO: 17
CNGNNANGTTNNTCNNN--GCTGACAATGCTGCTGCNGCTTCNCCTCNCTGTCTCCACTT
58


FB1D1 S. enterica 2




SEQ ID NO: 19
-------GTTGCTNCTACTGCTGANAATGCTGCTGCTGCTTCTCCTCNCTGTCTCCACTT
53


FB1D1 S. enterica 1
       ***  *      ***** *********** ***** *****************




       



 


Consensus
CCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTAGGCCGC



FB1D1 S. enterica 3
CCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTAGGCCGC
111


FB1D1 S. enterica 2
CCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTAGGCCGC
118


FB1D1 S. enterica 1
CCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTAGGCCGC
113



************************************************************



 


Consensus
AGATCANAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATCTCATGA



FB1D1 S. enterica 3
AGATCANAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATCTCATGA
171


FB1D1 S. enterica 2
AGATCANAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATCTCATGA
178


FB1D1 S. enterica 1
AGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTATAGATTCGGAATCTCATGA
173



****** *****************************************************



 


Consensus
TAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNNNNNNNGAGCTGAGGAGCAATTGC



FB1D1 S. enterica 3
TAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNNNNNNNGAGCTGAGGAGCAATTGC
231


FB1D1 S. enterica 2
TAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNNNNNGNNAGCTGANGANCAATTGC
238


FB1D1 S. enterica 1
TAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTNGCAGGCGAGCTGAGGAGCAATTGC
233



************************************  ******   **    *******



 


Consensus
AGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCNGGNNNGNNNGAAGNNNNNNNNNNN



FB1D1 S. enterica 3
AGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCNGGNNAGGAAGAAGNNNNNNNNNNN
291


FB1D1 S. enterica 2
AGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGNNNNNNAAGNNNNNNNNNNN
298


FB1D1 S. enterica 1
AGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCNGNNNNGNNNGAAGTCNNGNCGNGG
293



********************************** *          ***  ** *  *



 


Consensus
NTAATTATTGGCAAAACGAGCTCTTGTTGTANNNNNNNNNNNGNNNNNNNNNNNACTNNN



FB1D1 S. enterica 3
NTAATTATTGGCAAAACGAGCTCTTGTTGTANNNNNNNNNNNGNNNNNNNNNNNACTNNN
351


FB1D1 S. enterica 2
NTAATTATTGGCAAAACGAGCTCTTGTTNNNNNNNNNNNNNNGNNNNNNNNNNNACTANN
358


FB1D1 S. enterica 1
CTAATTATTGGCAAAACGAGCTCTTGTTGTANNNNNNNNNNNGNNNNNNNNNNNCTANNG
353



 ***************************   ***********************    *



 


Consensus
NNNGNNCAATATTCCNTANNGCATGATGGTTGCTCAGAGGCAGNNNNNNAGCAANNNANN



FB1D1 S. enterica 3
NGNGNNCAATATTCCNTANNGCATGATGGTTGCTCAGAGGCAGNNNNNNAGCAANNNANN
411


FB1D1 S. enterica 2
GNNGNNCAATATTCCNTANNGCATGATGGTTGCTCAGAGGCAGNNNNNNAGCAACNNANN
418


FB1D1 S. enterica 1
NNNNATCNATATTCCNTAANGCATGATGGTTGCTCAGAGGCANGNNNN-AGCAACNAANA
412



  *   * ********** ***********************  **** **** * **



 


Consensus
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC



FB1D1 S. enterica 3
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC
471


FB1D1 S. enterica 2
CNATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC
478


FB1D1 S. enterica 1
CGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGGTATTAAAGC
472



* **********************************************************



 


Consensus
CACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCATNNNNNNNNGNTT



FB1D1 S. enterica 3
CACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCATNNNNNNNTGNTT
531


FB1D1 S. enterica 2
CACAATCAGAACAAATATATGCTTTGTATCTTNNNNNGCCTTCTTCANNNNNNANNGCTN
538


FB1D1 S. enterica 1
CACAATCAGAACAAATATATGCTTTGTATCTTTNCNNGCCTTCTTCATNNNNNNNNGNTT
532



******************************** * ************ ***** * * *



 


Consensus
CCGCGGNCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA



FB1D1 S. enterica 3
CCGCGGNCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA
591


FB1D1 S. enterica 2
NNNNGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA
598


FB1D1 S. enterica 1
CCGCGNNNNCATTAAGAGAACTTGTGGTAAGATAAGAAGATATTTTATTCGTTCTGCTGA
592



    *    ***************************************************



 


Consensus
CTTGCTGGATGTCGGGAAATATTCTGCATTTNNNNNNAGGCGGTTAATTGCAGATATAAT



FB1D1 S. enterica 3
CTTGCTGGATGTCGGGAAATATTCTGCATTTNNNNNNAGGCGGTTAATTGCAGATATAAT
651


FB1D1 S. enterica 2
CTTGCTGGATGTCGGGAAATANTCTGCATTTNNNNNNAGGCGGTTAATTGCANATATAAT
658


FB1D1 S. enterica 1
CTTGCTGGATGTCGGGAAATATTCTGCATTTNNNNNGAGGCGGTTAATTGCAGATATAAT
652



********************* ************** *************** *******



 


Consensus
TGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG



FB1D1 S. enterica 3
TGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG
711


FB1D1 S. enterica 2
TGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG
718


FB1D1 S. enterica 1
TGGTAGTGAAAAGGGTCGTTGCTATGGTCACCGTGAAGCGAGTACAGCAGCACAAGAATG
712



************************************************************



 


Consensus
TGTGCCGTTCTCNNNNNNTATTGTTTGAATATGGNAACCTGTTTTAGTCGGTTTAAANNN



FB1D1 S. enterica 3
TGTGCCGTTCTCNNNNNNTATTGTTTGAATATGGNAACCTGTTTTAGTCGGTTTAAANGN
771


FB1D1 S. enterica 2
NGTGCCGTTCTCNGNNNNTATTGTTTGAATATGGNAACCTGTTTTAGTCGGNTTAANNNN
778


FB1D1 S. enterica 1
TGTGCCGTTCTCNNNNNNTATTGTTTGAATATGGTAACCTGTTTTAGTCGGTTTAANNNN
772



 ************ ******************** **************** **** * *



 


Consensus
NNNNNNNTCTAACCNAAAACAACACTGCAGNGACNG--ANNGTAGTATTTATTTTNNNNN



FB1D1 S. enterica 3
NNNNNNT-CTAACCNAAAACAACACTGCAGTGACNG--ANNNNNGTANTTATTTTTTTAC
828


FB1D1 S. enterica 2
NNNNNNNTCTAACCAAAAACAACACTGNNGNGACTG--ANTGTAGTATTTATTTTNNNNN
836


FB1D1 S. enterica 1
NNNNNNNTCTAACCAAAAACAACACTGCAGNGGNNNGGNNNGTAGTATTTATTTTNNNNN
832



******  ****** ************  * *       *    *** ******* 



 


Consensus
NNNNNNCTTAATTTT-GGTGNAAACATCNACGGCGCACTTC



FB1D1 S. enterica 3
TNNNNNNNNNNNNTTTGGTGNAAACATCAACGGCGCACTTC--------
869


FB1D1 S. enterica 2
NNNNN-CTTAATTTT-GGTGNAAACATCNACGGCGCACTTCAACCANNN
883


FB1D1 S. enterica 1
NNNNNNCTTAATTTT-GGNGNAAACATCNACGGCGCACNTNNN------
874



 ****        *  ** ********* ********* *

















TABLE 6B





CLUSTAL 2.0.11 multiple sequence alignment



First Three Salmonella enterica MR595 sequence embedded fingerprints by



primer FP5 were aligned and used to generate a consensus sequence

















SEQ ID NO: 51
------GNTTNTGATTACTGTTNNNGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
54


Consensus




SEQ ID NO: 38
----CTGNNNNTGATTACTGTNNNNGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
56


FP5-S. enterica-1




SEQ ID NO: 37
NNNNNNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
60


FP5-S. enterica-3




SEQ ID NO: 36
-------NTTNTGATTACTGTTNNNNNTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
53


FP5-S. enterica-2





          ***********      *********************************



 


Consensus
TCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGC
114


FP5-S. enterica-1
TCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGC
116


FP5-S. enterica-3
TCCTNNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGC
120


FP5-S. enterica-2
TCCTCNCTGTCTCCACTTCCTTGAACAATGCGCCGTCATGCTTCTTTTGCCTCCCGCTGC
113



**** *******************************************************



 


Consensus
TCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTAT
174


FP5-S. enterica-1
TCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTAT
176


FP5-S. enterica-3
TCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTAT
180


FP5-S. enterica-2
TCCAGAAAGCTAGGCCGCAGATCAGAACCACCACAGTCAATATCACCACCTTCCTCTTAT
173



************************************************************



 


Consensus
AGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGC
234


FP5-S. enterica-1
AGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGC
236


FP5-S. enterica-3
AGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGC
240


FP5-S. enterica-2
AGATTCGGAATCTCATGATAGGGGCTCAGCCTCTGTGCGAGTGGAGAGAAGTTTGCAGGC
233



************************************************************



 


Consensus
GAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAG
294


FP5-S. enterica-1
GAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAG
296


FP5-S. enterica-3
GAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAG
300


FP5-S. enterica-2
GAGCTGAGGAGCAATTGCAGGTGATATGATGTGCTCGGCTCAAGAAGCGGGCCCGGAGAG
293



************************************************************



 


Consensus
GAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCC
354


FP5-S. enterica-1
GAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCC
356


FP5-S. enterica-3
GAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCC
360


FP5-S. enterica-2
GAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACATTGATCC
353



************************************************************



 


Consensus
AACTGGAATGTCACTAANNNNNNNNNNT-ATTCCATAAGGCATGATGGTTGCTCAGAGGC
413


FP5-S. enterica-1
AACTGGAATGTCACTAANNNNNNNNANT-ATTCCATAAGGCATGATGGTTGCTCAGAGGC
415


FP5-S. enterica-3
AACTGGAATGTCACTAANNNNNNNNNNNTATTCCATAAGGCATGATGGTTGCTCAGAGGC
420


FP5-S. enterica-2
AACTGGAATGTCACTAANNNNNNNNNNATATTCCATAAGGCATGATGGTTGCTCAGAGGC
413



************************* *  *******************************



 


Consensus
AGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATT
473


FP5-S. enterica-1
NGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATT
475


FP5-S. enterica-3
AGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATT
480


FP5-S. enterica-2
AGGAGAAGAGCAACGAATACGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATT
473



 ***********************************************************



 


Consensus
ATATTCTGGGTATTAAAGCCACANNNNNNNNNNNNNTATGCTTTGTATCTTNNNNNGNCT
533


FP5-S. enterica-1
ATATTCTGGGTATTAAAGCCACANNNNNNNNNGANNTATGCTTTGTATCTTNNNNNGNCT
535


FP5-S. enterica-3
ATATTCTGGGTATTAAAGCCACANNNNNNNNNNNNNTATGCTTTGTATCTTNNNNNGNCN
540


FP5-S. enterica-2
ATATTCTGGGTATTAAAGCCACAANNNNNNNNNNNNTNTGCTTTGTATCTTTNNNNGCCT
533



*********************** ********  *** ************* ***** *



 


Consensus
TCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGAT
593


FP5-S. enterica-1
TCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGAT
595


FP5-S. enterica-3
TCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAAGAAGAT
600


FP5-S. enterica-2
TCTTCATTACCAACTGCTTCCGCGGCCACATTAAGAGAACTTGTGGTAAGATAANAANAT
593



****************************************************** ** **



 


Consensus
ATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGC
653


FP5-S. enterica-1
ATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGC
655


FP5-S. enterica-3
ATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGC
660


FP5-S. enterica-2
ATTTTATTCNNNNNNNTGACTTGCTGGATGTCGGGAAATATTCTGCATTTGATAAGAGGC
653



************************************************************



 


Consensus
GGTTAATTGCAGATATAATTGGNNNNNNNNNNGNTCGTTGCTATGGTCACCGTGAAGCGA
713


FP5-S. enterica-1
GGTTAATTGCAGATATAATTGGNNGTNNNNNNGNNCGTTGCTATGGTCACCGTGAAGCGA
715


FP5-S. enterica-3
GGTTAATTGCAGATATAATTGGNNNNNNNNNNGNTCGTTGCTATGGTCACCGTGAAGCGA
720


FP5-S. enterica-2
GGTTAATTGCAGATATAATTNNNNNNNNNNNNGGTCGTTGCTATGGTCACCGTGAAGCGA
713



********************  **  *******  *************************



 


Consensus
GTACNGCAGCACAAGAATGTGTGNNNNNNNNNNNNAATATTGNTTGAATATGGTAACCTG
773


FP5-S. enterica-1
GTACNNCAGCACAAGAATGTGTGNNNNNNNNNNNTAATATNGTTTGAATATGGTAACCTG
775


FP5-S. enterica-3
GTACAGCAGCACAAGAATGTGTGNNNNNNNNNNNNAATATTGNTTGAATATGGTAACCTG
780


FP5-S. enterica-2
GTNNNGCNNNNNNAGANTGNGNGGNNGNNNNNNNNNATATTGNTTGAATATGGNNNCCTG
773



**    *      *** ** * * ** *******  **** * **********   ****



 


Consensus
TTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGTGACTGATTGN
833


FP5-S. enterica-1
TTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCAAAAACAACACTGCAGTGACNNNNNNN
835


FP5-S. enterica-3
TTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCNAAAACNACACTGCAGTGACTGATTGN
840


FP5-S. enterica-2
NTTTAGTCGGNTTAAAGGTAAGAAGATCTAACCNAAAACAACACTGCAGTGACTGATTGT
833



 ********* ********************** ***** *************



 


Consensus
AGTATNNNNNN-------------------------------------------------
844


FP5-S. enterica-1
AGTATNNNNNNTTTTACTTANNNNNAATTNTGGTGTAAACATCANCGGCGCACTTCNACC
895


FP5-S. enterica-3
AGTATNNNNNN-------------------------------------------------
851


FP5-S. enterica-2
AGNANNNNNNN-------------------------------------------------
844



** * ******



 


Consensus
------------------------------



FP5-S. enterica-1
NATACTCCAATGNTTTATCCATCGACATGN
925


FP5-S. enterica-3
------------------------------



FP5-S. enterica-2
------------------------------
















TABLE 7







Staphylococcus aureus MU3 sequence embedded fingerprint #5 was run as query


sequence. Using BLASTN, low complexity filter on, with values of +2 for a match


and −3 for a mismatch against the consensus sequence for all three organisms.


Sequences producing significant alignments:













Accession
Description
Max score
Total score
Query coverage
E value
Max ident Links










by primer mix FB1D1:













25817
Staphalococcus aureus MU3
922
989
91%
0.0
92%


25816
Salmonella enterica MR595
892
892
97%
0.0
85%


25815
Saccharomyces cervisiae S288C
820
820
89%
0.0
84%







by single primer FP5:













8382
Staphalococcus aureus MU3
1355 
1355
99%
0.0
98%


8381
Salmonella enterica MR595
1128 
1128
99%
0.0
89%


8383
Saccharomyces cervisiae S288C
940
940
83%
0.0
88%
















TABLE 8







Saccharomyces cerevisiae S288C MU3 sequence embedded fingerprint #5 was run as


query sequence. Using BLASTN, low complexity filter on, with values of +2 for a


match and −3 for a mismatch against the consensus sequences for all three


organisms


Sequences producing significant alignments:













Accession
Description
Max score
Total score
Query coverage
E value
Max ident Links










by primer mix FB1D1:













36125
Saccharomyces cervisiae S288C
594
963
82%
8e−174
96%


36126
Salmonella enterica MR595
439
756
79%
4e−127
93%


36127
Staphalococcus aureus MU3
459
736
75%
4e−133
100%







by single primer FP5:













39539
Saccharomyces cervisiae S288C
928
928
73%
0.0
96%


39538
Staphalococcus aureus MU3
1088 
1088
87%
0.0
87%


39537
Salmonella enterica MR595
971
971
90%
0.0
84%
















TABLE 9







Salmonella enterica MR595 sequence embedded fingerprint #5 was run as query


sequence. Using BLASTN, low complexity filter on, with values of +2 for a match


and −3 for a mismatch against the consensus sequence for all three organisms.


Sequences producing significant alignments:













Accession
Description
Max score
Total score
Query coverage
E value
Max ident Links










by primer mix FB1D1:













49678
Salmonella enterica MR595
928
928
97%
0.0
92%


49679
Staphalococcus aureus MU3
760
830
91%
0.0
84%


49677
Saccharomyces cervisiae S288C
607
607
91%
1e−177
75%







by single primer FP5:













20645
Salmonella enterica MR595
1229 
1229
98%
0.0
96%


20646
Staphalococcus aureus MU3
1220 
1220
95%
0.0
92%


20647
Saccharomyces cervisiae S288C
888
888
79%
0.0
88%

## Claims

1. A method of generating a sequence embedded fingerprint pattern for identifying an organism in a sample comprising:
(a) providing a sample comprising said organism, said organism comprising at least one nucleic acid;
(b) combining said sample or the at least one nucleic acid therefrom with an amplification mix comprising at least one labeled oligonucleotide primer;
(c) generating at least one labeled amplification product from the at least one nucleic acid of said organism using a nucleotide amplification technique employing said at least one labeled oligonucleotide primer;
(d) combining said at least one labeled amplification product with products from a previously performed DNA sequencing reaction of a known organism to create a separation mix; and
(e) separating said separation mix on the basis of oligonucleotide length in a fluorescent DNA sequencing instrument to generate a sequence embedded fingerprint pattern for said organism, wherein the sequence embedded fingerprint pattern is generated by perturbing sequence output at positions where fingerprint products are migrating with like-sized DNA sequence fragments.

2. The method of claim 1, comprising after step (e) the further steps of:
(f) comparing said sequence embedded fingerprint pattern for said organism to a database containing sequence embedded fingerprint patterns for known organisms; and
(g) identifying said organism as a function of said comparison to said database.

3. The method of claim 1, wherein said organism is a microorganism.

4. The method of claim 1, wherein said organism is unknown.

5. The method of claim 1, wherein said nucleotide amplification technique is a random amplification of polymorphic DNA (RAPD) polymerase chain reaction (PCR).

6. The method of claim 1, wherein said at least one nucleic acid is DNA.

7. The method of claim 1, comprising after step (e) the further step of repeating steps (c)-(e) at different stringency conditions as compared to that of a first pass through steps (c)-(e) to generate a different amplification profile as compared to that generated by the first pass through steps (c)-(e).

8. The method of claim 1, wherein step (e) is performed by capillary gel electrophoresis.

9. The method of claim 1, wherein steps (b)-(c) are performed by one or more primers comprising nucleic acid sequences selected from the group consisting of SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:25, and a combination thereof.