(en)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 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.

1.ApplicationNumber: US-201313914987-A
1.PublishNumber: US-2013274458-A1
2.Date Publish: 20131017
3.Inventor: BURNS FRANK R.
PENG XUAN

4.Inventor Harmonized: BURNS FRANK R(US)
PENG XUAN(US)

5.Country: US
6.Claims:
(en)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 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.

7.Description:
(en)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 FB1 D1 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 FB1 D1 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 FB1 D1 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 FB1 D1 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 FB1 D1 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 FB1 D1 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 FB1 D1, 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 H 2 O.
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 FB1 D1 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
FB1D1-neg-control-4
-------------GTTGNT-CNNCTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
46

SEQ ID NO: 6
FB1D1-neg-control-5
--------------------TCNCNGCTGACAATGCTGCTGCTGCTTCNCCTCNNNGTCT
40

SEQ ID NO: 7
FB1D1-neg-control-2
--------GTNNNGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCNNTGTCT
52

SEQ ID NO: 8
FB1D1- S. cerevisiae -5
------------TGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCT
48

SEQ ID NO: 9
FB1D1- S. cerevisiae -1
-----CTGNTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCT
55

SEQ ID NO: 10
FB1D1- S. cerevisiae -3
----NCNGNNNNNGNTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCNCTGTCT
56

SEQ ID NO: 11
FB1D1- S. cerevisiae -2
-----CTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
55

SEQ ID NO: 12
FB1D1- S. cerevisiae -4
-------------GTTGNT--CNCNGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCT
45

SEQ ID NO: 13
FB1D1-neg-control-1
--------GNTANGTTGCTNCTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
52

SEQ ID NO: 14
FB1D1-neg-control-3
GNTNNCTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCT
60

SEQ ID NO: 15
FB1D1- S. enterica -5
------CNGNNNTGTTNCTCNN-CTGCTGACAATGCTGCTGNNGNNNCNCCTCNCTGTCT
53

SEQ ID NO: 16
FB1D1- S. enterica -4
------CNGNNNNGTTGCTNCTACTGCTGACAATGCTGCTGNNGNNNCNCCTCNCTGTCT
54

SEQ ID NO: 17
FB1D1- S. enterica -2
------CNGNNANGTTNNTCNN--NGCTGACAATGCTGCTGCNGCTTCNCCTCNCTGTCT
52

SEQ ID NO: 18
FB1D1- S. enterica -3
-------------GTTNNTCNN--NGCTGACAATGCTGCTGCNGCTTCTCCTCNCTGTCT
45

SEQ ID NO: 19
FB1D1- S. enterica -1
-------------GTTGCTNCTACTGCTGANAATGCTGCTGCTGCTTCTCCTCNCTGTCT
47

SEQ ID NO: 20
FB1D1- S. aureus -4
----------------GNTCNC--NGNNGANNATGNTGCTGCTGCTTNNNGNNNCTGTCT
42

SEQ ID NO: 21
FB1D1- S. aureus -2
---------TNNGTTGNTCTAC--NGNTGACNATGCTGCTGCTGCTTNNNNNNNCTGTCT
49

SEQ ID NO: 22
FB1D1- S. aureus -3
------CNGTTATGTTGCTCTC--NGCTGACNATGCTGCTGCTGCTTCNNGNNNCTGTCT
52

SEQ ID NO: 23
FB1D1- S. aureus -1
-------------GTTGNTCNN--NGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCT
45

SEQ ID NO: 24
FB1D1- S. aureus -5
------CNGNNANGTTGNTCNN--NGCTGANNN-GCTGCTGCTGCTTCNNGTNNCTGTCT
51






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




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
NGNNNNAGATCAGAACCACCAGAGNCNNNNTNACCNCCTTCCTCTTATAGATTCGGAATC
169

FB1D1- S. aureus -3
GGNCNNAGATCAGAACCACCACAGNCNNTATCNCCNCCTTCCTCTTATAGATTCGGAATC
172

FB1D1- S. aureus -1
NGNCNNAGATCAGAACCAGCACAGNCNNNNTCNCCNCCTTCCTCTTATAGATTCGGAATC
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

FS1D1- 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
NNNNNNNNNCGATCCTATAAAAGATAAAACATAAATAAACAGTCTTGATTATATTCTGGG
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
TATTAAAGCCACAATCAGAACANATATATGCTTTGTATCTTTNCNNGCCTTCTTCAT-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--AfTGNNGNNNN
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 FP5-neg-control-4
-----------NNNNNNNATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
49

SEQ ID NO: 27 FP5-neg-control-5
---------NNNNTTNNNATTACTGTTAATGNTGCTACTACTGCTGACAATGCTGCTGCT
51

SEQ ID NO: 28 FP5-neg-control-3
---------NNGNNNNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
51

SEQ ID NO: 29 FP5-neg-control-2
--------NCTGGTNNNNNNNACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52

SEQ ID NO: 30 FP5-neg-control-1
--------NCNGNNNATGANTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52

SEQ ID NO: 31 FP5- S. aureus -4
--------NCCNGNNNNNNNTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52

SEQ ID NO: 32 FP5- S. aureus -5
--------------------TACTGTTAATGTTGNNNCNNNNGCTGACAATGCTGCTGCT
40

SEQ ID NO: 33 FP5- S. aureus -2
-NNNGCNGCCNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
59

SEQ ID NO: 34 FP5- S. aureus -3
------NNNCTGGTTNTGANTACTGNNNNNGTTGCTACTACTGCTGACAATGCTGCTGCT
54

SEQ ID NO: 35 FP5- S. aureus -1
-----NNNNCTGGTTNTGANTACTGTTAANGTTGCTACTACTGCTGACAATGCTGCTGCT
55

SEQ ID NO: 36 FP5- S. enterica -2
------------NTTNTGATTACTGTTNNNNNTGCTACTACTGCTGACAATGCTGCTGCT
48

SEQ ID NO: 37 FP5- S. enterica -3
-----NNNNNNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
55

SEQ ID NO: 38 FP5- S. enterica -1
---------CTGNNNNTGATTACTGTNNNNGTTGCTACTACTGCTGACAATGCTGCTGCT
51

SEQ ID NO: 39 FP5- S. enterica -4
--NNNNNNCCTGGTNATGANTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
58

SEQ ID NO: 40 FP5- S. enterica -5
-------------NNNNNATTNCTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
47

SEQ ID NO: 41 FP5- S. cerevisiae -3
-------------NNNNNATNNCTGTTNATGTTGCTNCTACTGCTGACAATGCTGCTGCT
47

SEQ ID NO: 42 FP5- S. cerevisiae -5
------------NTTNNGATTACTGTTAATNNTNNTNCTACTGCTGACAATGCTGCTGCT
48

SEQ ID NO: 43 FP5- S. cerevisiae -2
NNNTGNNGCCTGNTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
60

SEQ ID NO: 44 FP5- S. cerevisiae -4
--------CCTGGTTANGANTACTGNTNNNGNTGCTACTACTGCTGACAATGCTGCTGCT
52

SEQ ID NO: 45 FP5- S. cerevisiae -1
--------CCTGNNNNNGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52


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




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
GAGAGGAAGAAGTCGTGCCGGGGCTAATTATTGGCAAAACGAGCTCTTGTTGTAAACNTT
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


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




FP-neg-control-4
GATCCAACTGGAANNNNNNNNNNGGNNNNNNNNNNNNNCATAAGGCATGATGGTTGCTCA
409

FP5-neg-control-5
GATCCAACTGGANNGNNNNNNATGGNNNNNNNNNNNTCCATAAGGCATGATGGTTGCTCA
411

FP5-neg-control-3
GATCCAACTGGAANNNNNNNNNTGNNNNNNNNNNNTTCCATAAGGCATGATGGTTGCTCA
411

FP5-neg-control-2
GATCCAACTGGNANGNCACNNNNGNNNNNNMAATATTCCATAAGGCATGATGGTTGCTCA
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

FPS- 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 multiple 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 consensus
-------GTTGCTCT-CNGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCTCCACTTC


SEQ ID NO: 22 FB1D1 S. aureus 3
CNGTTATGTTGCTCT-CNGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCTCCACTTC
59

SEQ ID NO: 21 FB1D1 S. aureus 2
----TNNGTTGNTCTACNGNTGACNATGCTGCTGCTGCTTNNNNNNNCTGTCTCCACTTC
56

SEQ ID NO: 23 FB1D1 S. aureus 1
-------GTTGNTCN-NNGCTGACNATGCTGCTGCTGCTTNNNGNNNCTGTCTCCACTTC
52


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




consensus
CTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTANGNCNNA


FB1D1 S. aureus 3
CTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTAGGNCNNA
119

FB1D1 S. aureus 2
CTTGAACAATGNGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTANGNNNNA
116

FB1D1 S. aureus 1
CTTGAACANTGCGCCGTCATGCTTCTTTTGCCTCCCGCTGCTCCAGAAAGCTANGNCNNA
112


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




consensus
GATCAGAACCACCACAGNCNNTNTCNCCNCCTTCCTCTTATAGATTCGGAATCTCATGAT


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
TGGTAGTGAAAAGGNGCGTTGCTATGGTCACCGTGAAGNGAGTACAGGAGCACAAGAATG
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 Consensus
-----NNNCTGGTTNTGANTACTGTTAANGTTGCTACTACTGCTGACAATGCTGCTGCTG
55

SEQ ID NO: 33 FP5- S. aureus -2
NNNGCNGCCNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTG
60

SEQ ID NO: 35 FP5- S. aureus -1
----NNNNCTGGTTNTGANTACTGTTAANGTTGCTACTACTGCTGACAATGCTGCTGCTG
56

SEQ ID NO: 34 FP5- S. aureus -3
-----NNNCTGGTTNTGANTACTGNNNNNGTTGCTACTACTGCTGACAATGCTGCTGCTG
55


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




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
GCGAGTACAGGAGCACAAGAATGTGTGCCGTTCTCAGNNNGNANNNNNNGAATATGGTAA
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 Consensus
CTGNTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCTCCAC


SEQ ID NO: 10 FB1D1 S. cervisiae 3
NCNGNNNNNGNTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCNCTGTCTCCAC
60

SEQ ID NO: 11 FB1D1 S. cervisiae 2
-CTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCNCCTCNCTGTCTCCAC
59

SEQ ID NO: 9 FB1D1 S. cervisiae 1
-CTGNTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTCTCCTCACTGTCTCCAC
59


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




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 Consensus
--------CCTGNNNNNGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52

SEQ ID NO: 45 FP5- S. cerevisiae -1
--------CCTGNNNNNGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
52

SEQ ID NO: 43 FP5- S. cerevisiae -2
NNNTGNNGCCTGNTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCT
60

SEQ ID NO: 41 FP5- S. cerevisiae -3
-------------NNNNNATNNCTGTTNATGTTGCTNCTACTGCTGACAATGCTGCTGCT
47


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




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
NNNNGTTTTAGTCGGTTTAAAGGTAAGAAGATCTAACCAAAAAGAACACTGCAGNGACTG
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 Consensus
GCTGACAATGCTGCTGCNGCTTCTCCTCNCTGTCTCCACTT


SEQ ID NO: 18 FB1D1 S. enterica 3
-------GTTNNTCNNN--GCTGACAATGCTGCTGCNGCTTCTCCTCNCTGTCTCCACTT
51

SEQ ID NO: 17 FB1D1 S. enterica 2
CNGNNANGTTNNTCNNN--GCTGACAATGCTGCTGCNGCTTCNCCTCNCTGTCTCCACTT
58

SEQ ID NO: 19 FB1D1 S. enterica 1
-------GTTGCTNCTACTGCTGANAATGCTGCTGCTGCTTCTCCTCNCTGTCTCCACTT
53


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




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 Consensus
------GNTTNTGATTACTGTTNNNGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
54

SEQ ID NO: 38 FP5- S. enterica -1
----CTGNNNNTGATTACTGTNNNNGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
56

SEQ ID NO: 37 FP5- S. enterica -3
NNNNNNGGTTNTGATTACTGTTAATGTTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
60

SEQ ID NO: 36 FP5- S. enterica -2
-------NTTNTGATTACTGTTNNNNNTGCTACTACTGCTGACAATGCTGCTGCTGCTTC
53


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




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.









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





Sequences producing significant alignments:

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









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





Sequences producing significant alignments:

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.









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





Sequences producing significant alignments:

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%