Abstract:
This invention relates to antisense oligonucleotides which modulate the expression of the ribonucleotide reductase or the secA genes in microorganisms. This invention is also related to methods of using such oligonucleotides in inhibiting the growth of microorganisms. These antisense oligonucleotides are particularly useful in treating pathological conditions in mammals which are mediated by the growth of microorganisms.

Description:
REFERENCE TO RELATED APPLICATIONS 
     This application claims benefit of U.S. Provisional Application Serial No. 60/052,160, filed Jul. 10, 1997, which application is incorporated herein by reference in its entirety. 
    
    
     BACKGROUND OF THE INVENTION 
     1. Field of the Invention 
     This invention relates to antisense oligonucleotides which modulate the activity of the ribonucleotide reductase genes and the secA genes in microorganisms. This invention is also related to methods of using such compounds in inhibiting the growth of microorganisms. 
     These antisense oligonucleotides are particularly useful in treating pathological conditions in mammals which are mediated by the growth of microorganisms. Accordingly, this invention also relates to pharmaceutical compositions comprising a pharmaceutically acceptable excipient and an effective amount of a compound of this invention. 
     These antisense oligonucleotides may also be used as anti-microbial agents for agricultural applications such as crop protection. 
     2. References 
     The following publications, patent applications and patents are cited in this application as superscript numbers: 
     1. Nordlund and Eklund “Structure and function of the  Escherichia coli  ribonucleotide reductase protein R2 ”, J. Mol. Biol. ( 1993) 232:123-164; 
     2. Carlson et al., “Primary structure of the  Escherichia coli  ribonucleoside diphosphate reductase operon”,  PNAS USA  (1984) 81:4294-4297; 
     3. Nilsson et al., “Nucleotide sequence of the gene coding for the large subunit of ribonucleotide reductase of  Escherichia coli  Correction”,  Nucleic Acids Research  (1988) 16:4174; 
     4. P. Reichard, “The anaerobic ribonucleotide reductase from  Escherichia coli”, J. Biol. Chem . (1993) 268:8383-8386; 
     5. Nordlund et al.,  Nature  (1990) 345:593-598; 
     6. der Blaauwen et al., “Inhibition of preprotein translocation and reversion of the membrane inserted state of secA by a carboxyl terminus binding Mab”,  Biochemistry  (1997) 36:9159-9168; 
     7. McNicholas et al., “Dual regulation of  Escherichia coli  secA translation by distinct upstream elements”,  J. Mol. Biol . (1997) 265:128-141; 
     8. U.S. Pat. No. 5,294,533; 
     9. Gasparro et al., “Photoactivatable antisense DNA: Suppression of ampicillin resistance in normally resistant  Escherichia coli”, Antisense Research and Development  (1991) 1:117-140; 
     10. White et al., “Inhibition of the multiple antibiotic resistance (mar) operon in  Escherichia coli  by antisense DNA analogs”,  Antimicrobial Agents and Chemotherapy  (1997) 41:2699-2704; 
     11. Nielsen et al.,  Science  (1991) 354:1497; 
     12. Good and Nielsen, “Inhibition of translation and bacterial growth by peptide nucleic acid targeted to ribosomal RNA”,  PNAS USA  (1998) 95:2073-2076; 
     13. Buchardt, deceased, et al., U.S. Pat. No. 5,766,855; 
     14. Buchardt, deceased, et al., U.S. Pat. No. 5,719,262; 
     15. U.S. Pat. No. 5,034,506; 
     16. Altschul, et al., “Basic local alignment search tool”,  J. Mol. Biol . (1990) 215:403-10; 
     17. Devereux. et al., “A comprehensive set of sequence analysis programs for the VAX”,  Nucleic Acids Res . (1984) 12:387-395; 
     18. Sambrook et al.,  Molecular Cloning: A Laboratory Manual , Cold Spring Harbor Laboratory, New York (1989, 1992); 
     19. Ausubel et al.,  Current Protocols in Molecular Biology , John Wiley and Sons, Baltimore Md. (1989); 
     20. Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor Mich. (1995); 
     21. Vega et al.,  Gene Targeting , CRC Press, Ann Arbor Mich. (1995); 
     22 . Vectors: A Survey of Molecular Cloning Vectors and Their Uses , Butterworths, Boston Mass. (1988) 
     23. U.S. Pat. No. 5,023,252, issued June 11, 1991 
     24. Felgner et al., U.S. Pat. No. 5,580,859. 
     25. U.S. Pat. No. 5,011,472 
     26 . Remington&#39;s Pharmaceutical Sciences , Mace Publishing Company, Philadelphia Pa. 17 th  ed. (1985); 
     27. Perbal,  A Practical Guide to Molecular Cloning , John Wiley &amp; Sons, New York (1988). 
     28 . PCR Protocols: A Guide To Methods And Applications , Academic Press, San Diego, Calif. (1990). 
     29. Dower, W. J.,  Nucleic Acids Res . (1988) 16:6127; 
     30. Neuman et al.,  EMBO J . (1982) 1:841; 
     31. Taketo A.,  Biochim Biophys. Acta  (1988) 949:318; 
     32. Miller J. H.  Experiments in Molecular Genetics , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1972); 
     33. Horwitz J. P.,  J. Med. Chem . (1964) 7:574; 
     34. Mann et al.,  Biochem .(1991) 30:1939; 
     35. Olsvik, et al.,  Acta Pathol. Microbiol. Immunol. Scand . [B] (1982) 90:319; 
     36. Laemmli, U. K.,  Nature  (1970) 227:680; 
     37. Choy et al.,  Cancer Res .(1988) 48:2029; 
     38. Wright and Anazodo,  Cancer J . (1988) 8:185-189; 
     39. Chan et al.,  Biochemistry  (1993) 32:12835-12840; 
     40. Carpentier P. L.,  Microbiology  4 th  ed. W.B.Saunders Company (1977); and 
     41. Wright et al.,  Adv. Enzyme Regul . (1981) 19:105-127. 
     All of the above publications, patent applications and patents are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent application or patent was specifically and individually indicated to be incorporated by reference in its entirety. 
     3. State of the Art 
     Ribonucleotide reductase catalyzes the de novo production of deoxyribonucleotides. The enzyme reduces the four main ribonucleotides to the corresponding deoxyribonucleotides required for DNA synthesis and repair (Wright et al. 41 ). 
     In mammalian and bacterial cells, de novo production of deoxyribonucleotides by ribonucleotide reductase is usually highly regulated on different levels in order to produce the correct amount of deoxyribonucleotides for DNA synthesis. In the DNA viruses, the metabolism of the host cell is directed towards production of viral DNA by virus encoded ribonucleotide reductases (Nordlund and Eklund 1 ). 
     Mammalian cells and many DNA viruses and prokaryotes, have a heterodimeric iron-containing ribonucleotide reductase enzyme of the α 2 β 2  type. For example, ribonucleotide reductase from  E. coli  is a multi-subunit α 2 β 2  enzyme where the two homo-dimeric proteins are denoted R1 and R2. The larger α 2  protein, R1, contains the binding sites for substrate and allosteric effectors and also the redox-active cysteine residues. Protein R1 has a molecular mass of 2×86,000 where each subunit contains 761 residues. The smaller β 2  protein, denoted R2, contains the dinuclear ferric center and a stable free tyrosyl radical necessary for the enzymatic activity. The R2 protein has a molecular mass of 2×43,500, where each subunit contains 375 amino acid residues (Nordlund and Eklund 1 ). 
     The nucleotide sequence of the  E. coli  K-12 DNA comprising the operon for the structural genes of the subunits of ribonucleotide reductase has been determined. The DNA sequence includes a total length of 8557 nucleotides. An open reading frame between nucleotides 3506 and 5834 has been identified as the nrdA gene. An open reading frame between nucleotides 6012 and 7139 encoding a 375-amino acid polypeptide has been identified as the nrdB gene (Carlson et al. 2 , and Nilsson et al. 3 ). The sequences of the nrdA and nrdB genes for  E. coli  are shown in FIGS. 1 and 2. 
     In  E. coli , the synthesis of ribonucleotide reductase is controlled at the level of transcription. The nrdA and nrdB genes direct the synthesis of a 3.2 kilobase polycistronic mRNA. Perturbations in DNA replication, either a shift up in growth conditions or an inhibition of DNA synthesis leads to increased synthesis of nrd MRNA (Carlson et al. 2 ). 
     A separate anaerobic ribonucleotide reductase has also been identified from  E.coli . The anaerobic  E. coli  reductase has a molecular mass of 145 kD and is a homodimer. The gene for the anaerobic reductase (nrdD) has been cloned and sequenced (P. Reichard 4 ). 
     The ribonucleotide reductase R2 genomic or cDNA sequences are known for several other species such as bacteriophage T4, clam, mouse,  Saccharomyces cerevisiae , vaccinia, herpes simplex virus types 1 and 2, varicella and Epstein-Barr virus (Nordlund et al. 5 ). The sequence of the nrdE and nrdF which code for the ribonucleotide reductase genes of  S. typhimurium  are shown in FIG.  3 . The sequence of the ribonucleotide reductase gene of  Lactococcus lactis  is shown in FIG.  4 . 
     The secA gene of  E. coli  encodes for one component of a multi-component system for the secretion of proteins across the inner membrane of  E. coli  (der Blaauwen et al. 6 ). The complete system consists of the SecB protein, a cytosolic chaperone, the SecA protein, the translocation ATPase and the heterotrimeric integral membrane SecY/SecE/SecG complex, which along with SecA serves as the preprotein channel. SecA protein plays a central role in the secretion process by binding the preprotein, secB protein, anionic phospholipids and SecY/SecE/SecG protein. These interactions allow SecA to recognize soluble preprotein and recruit it to translocation sites in the inner membrane. Once such protein translocation complexes have assembled; further steps require an ATP-driven cycle of insertion and de-insertion of secA protein with the inner membrane, where each cycle appears to be coupled to the translocation of a segment of the preprotein. 
     SecA is the only component of the secretion apparatus that has been shown to be regulated. SecA is the second gene in the geneX-secA operon and its translation varies over a tenfold range depending on the status of protein secretion in the cell. During protein-export proficient conditions secA auto-represses its translation by binding to a site that overlaps the secA ribosome-binding site of genes-secA RNA. SecA protein can also dissociate a preformed 30 S-tRNA MET -genes-secA RNA ternary complex in vitro. However, during a protein export block secA translation increases substantially although the mechanism responsible for this regulatory response has not been elucidated (McNicholas et al. 7 ). The sequence of the secA gene of  E. coli  is shown in FIG.  5 . 
     The secA gene sequence has been identified for a number of other species including  Mycobacterium bovis  (FIG.  6 ),  Mycobacterium tuberculosis  (FIG.  7 ),  Staphylococcus aureus  (FIG.  8 ),  Staphylococcus carnosus  (FIG.  9 ),  Bacillus subtilis, Bacillus firnus, Listeria monocytogenes, Mycobacterium smegmatis, Borrelia burgdorferi, P. sativum, S. griseus , and Synechoccus sp. 
     Antibiotics are important pharmaceuticals for the treatment of infectious diseases in a variety of animals including man. The tremendous utility and efficacy of antibiotics results from the interruption of bacterial (prokaryotic) cell growth with minimal damage or side effects to the eukaryotic host harboring the pathogenic organisms. In general, antibiotics destroy bacteria by interfering with the DNA replication, DNA to RNA transcription, translation (that is RNA to protein) or cell wall synthesis. 
     Although bacterial antibiotic resistance has been recognized since the advent of antimicrobial agents, the consequence of the emergence of resistant microorganisms, such resistance was historically controlled by the continued availability of effective alternative drugs. Now, drug resistance has emerged as a serious medical problem in the community, leading to increasing morbidity and mortality. The problem is worsened by the growing number of pathogens resistant to multiple, structurally unrelated drugs. The situation has become so desperate that antibiotics once removed from use because of toxic effects may be prescribed in an attempt to deal with the otherwise untreatable drug resistant bacteria. 
     Antisense oligonucleotides have been used to decrease the expression of specific genes by inhibiting transcription or translation of the desired gene and thereby achieving a phenotypic effect based upon the expression of that gene (Wright and Anazado 38 ). For example, antisense RNA is important in plasmid DNA copy number control, in development of bacteriophage P22. Antisense RNA&#39;s have been used experimentally to specifically inhibit in vitro translation of mRNA coding specifically from Drosophila hsp23, to inhibit Rous sarcoma virus replication and to inhibit 3T3 cell proliferation when directed toward the oncogene c-fos. Furthermore, it is not necessary to use the entire antisense MRNA since a short antisense oligonucleotide can inhibit gene expression. This is seen in the inhibition of chloramphenicol acetyltransferase gene expression and in the inhibition of specific antiviral activity to vesicular stomatitus virus by inhibiting the N-protein initiation site. Antisense oligonucleotides directed to the macromolecular synthesis operon of bacteria, containing the rpsU gene, the rpoD gene and the dnaG gene have been used for the detection of bacteria. (U.S. Pat. No. 5,294,533 8 ). Furthermore, photoactivatable antisense DNA complementary to a segment of the P-lactamase gene has been used to suppress ampicillin resistance in normally resistant  E. coli  (Gasparro et al. 9 ). Antisense DNA analogs have also been used to inhibit the multiple antibiotic resistant (mar) operon in  Escherichia coli  (White et al. 10 ). 
     Accordingly, there is a need to develop antisense oligonucleotides which will act to inhibit the growth of microorganisms. 
     SUMMARY OF THE INVENTION 
     This invention is directed to antisense oligonucleotides which modulate the expression of the ribonucleotide reductase and secA genes in microorganisms and pharmaceutical compositions comprising such antisense oligonucleotides. This invention is also related to methods of using such antisense oligonucleotides for inhibiting the growth of microorganisms. 
     Accordingly, in one of its composition aspects, this invention is directed to an antisense oligonucleotide, which oligonucleotide is nuclease resistant and comprises from about 3 to about 50 nucleotides, which nucleotides are complementary to the ribonucleotide reductase gene or the secA gene of a microorganism. The antisense oligonucleotide may have one or more phosphorothioate internucleotide linkages. 
     In another of its composition aspects, this invention is directed to an antisense oligonucleotide comprising from about 3 to about 50 nucleotides which is capable of binding to the ribonucleotide reductase gene or the secA gene of a microorganism, wherein the oligonucleotide comprises all or part of a sequence selected from the group consisting of SEQ ID NO:22; SEQ ID NO:43; SEQ ID NO:62; SEQ ID NO:74; SEQ ID NO:75; SEQ ID NO:76; SEQ ID NO:143; SEQ ID NO:145; SEQ ID NO:152; SEQ ID NO:164; SEQ ID NO:176; SEQ ID NO:186; SEQ ID NO:188; SEQ ID NO:189; SEQ ID NO: 191; SEQ ID NO: 192; SEQ ID NO:195; SEQ ID NO:197; SEQ ID NO:206; SEQ ID NO:212; SEQ ID NO:220; SEQ ID NO:229; SEQ ID NO:235; SEQ ID NO:254; SEQ ID NO:261; SEQ ID NO:262; SEQ ID NO:263; SEQ ID NO:264; and SEQ ID NO:265. 
     In still another of its composition aspects, this invention is directed to a pharmaceutical composition comprising a pharmaceutically acceptable excipient and an effective amount of an antisense oligonucleotide, which oligonucleotide is nuclease resistant and comprises from about 3 to about 50 nucleotides, which nucleotides are complementary to the ribonucleotide reductase gene or the secA gene of a microorganism. The oligonucleotide may be modified, for example, the oligonucleotide may have one or more phosphorothioate internucleotide linkages. 
     In one of its method aspects, this invention is directed to a method for inhibiting the expression of the ribonucleotide reductase gene in a microorganism having a ribonucleotide reductase gene comprising, administering to said microorganism or to a cell infected with said microorganism an effective amount of an antisense oligonucleotide comprising from at least about 3 nucleotides which are complementary to the ribonucleotide reductase gene of the microorganism under conditions such that the expression of the ribonucleotide reductase gene is inhibited. 
     In another of its method aspects, this invention is directed to a method for inhibiting the expression of the secA gene in a microorganism having a secA gene, comprising administering to said microorganism an effective amount of an antisense oligonucleotide comprising from at least about 3 nucleotides which are complementary to the secA gene of the microorganism under conditions such that expression of the secA gene is inhibited. 
     In one of its method aspects, this invention is directed to a method for inhibiting the growth of a microorganism encoding a ribonucleotide reductase gene or a secA gene, which method comprises administering to said microorganism or a cell infected with said microorganism an effective amount of an antisense oligonucleotide comprising from at least about 3 nucleotides which are complementary to either the ribonucleotide reductase gene or the secA gene of the microorganism under conditions such that the growth of the microorganism is inhibited. Preferably, the antisense oligonucleotide is selected from the group consisting of SEQ ID NO:22; SEQ ID NO:43; SEQ ID NO:62; SEQ ID NO:74; SEQ ID NO:75; SEQ ID NO:76; SEQ ID NO:143; SEQ ID NO:145; SEQ ID NO:152; SEQ ID NO:164; SEQ ID NO:176; SEQ ID NO:186; SEQ ID NO:188; SEQ ID NO:189; SEQ ID NO:191; SEQ ID NO:192; SEQ ID NO:195; SEQ ID NO:197; SEQ ID NO:206; SEQ ID NO:212; SEQ ID NO:220; SEQ ID NO:229; SEQ ID NO:235; SEQ ID NO:254; SEQ ID NO:261; SEQ ID NO:262; SEQ ID NO:263; SEQ ID NO:264; and SEQ ID NO:265. 
     In another of its method aspects, this invention is directed to a method for treating a mammalian pathologic condition mediated by a microorganism, which method comprises identifying a mammal having a pathologic condition mediated by a microorganism having a ribonucleotide reductase gene or a secA gene and administering to said mammal an effective amount of an antisense oligonucleotide comprising from at least about 3 nucleotides which are complementary to either the ribonucleotide reductase gene or the secA gene of the microorganism under conditions such that the growth of the microorganism is inhibited. 
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS 
     FIG. 1 is the sequence of the  E. coli  nrdA gene encoding the ribonucleotide reductase R1 subunit [SEQ ID NO:1]. 
     FIG. 2 is the sequence of the  E. coli  nrdB gene encoding the ribonucleotide reductase R2 subunit [SEQ ID NO:2]. The nrdB gene is encoded by nucleotides 7668 to 8798 of SEQ ID NO:2. 
     FIG. 3 is the sequence of the  S. typhimurium  nrdE and nrdF genes encoding the ribonucleotide reductase subunits [SEQ ID NO:3]. The nrdE gene is encoded by nucleotides 836 to 2980 and the nrdF gene is encoded by nucleotides 2991 to 3950 of SEQ ID NO:3. 
     FIG. 4 is the sequence of the  Lactococcus lactis  nrdEF operon encoding ribonucleotide reductase [SEQ ID NO:4]. 
     FIG. 5 is the sequence of the  E. coli  secA gene [SEQ ID NO:5]. 
     FIG. 6 is the sequence of the  Mycobacterium bovis  secA gene [SEQ ID NO:6]. 
     FIG. 7 is the sequence of the  Mycobacterium tuberculosis  secA gene [SEQ ID NO:7]. 
     FIG. 8 is the sequence of the  Staphylococcus aureus  secA gene [SEQ ID NO:8]. 
     FIG. 9 is the sequence of the  Staphylococcus carnosus  secA gene [SEQ ID NO:9]. 
     FIG. 10 is the sequence of the bovine herpes virus ribonucleotide reductase small subunit gene [SEQ ID NO:10]. 
     FIG. 11 is the sequence of the Herpes simplex virus type 1 UL39 gene encoding ribonucleotide reductase 1 [SEQ ID NO:11]. 
     FIG. 12 is the sequence of the Herpes simplex type 2 ribonucleotide reductase gene [SEQ ID NO:12]. The ribonucleotide reductase gene is encoded by nucleotides 419 to 3853 of SEQ ID NO:12. 
     FIG. 13 is the sequence of the equine herpes virus 4 ribonucleotide reductase large subunit and small subunit [SEQ ID NO:13]. The large subunit is encoded by nucleotides 77 to 2446 and the small subunit by nucleotides 2485-3447 of SEQ ID NO:13. 
     FIG. 14 is a photograph of a Western blot of a polyacrylamide gel of the cellular protein from  E. coli  cells carrying a plasmid containing the mouse ribonucleotide reductase R2 gene after treatment with either 20 μM or 200 μM of oligonucleotide AS-II-626-20. 
     FIG. 15 is a graph of the inhibition of  E. coli  growth after treatment of  E. coli  cells with ribonculeotide reductase antisense oligonucleotides. 
     FIG. 16 is a graph of the number of colony forming units/ml of  E. coli  cells after treatment with ribonucleotide reductase antisense oligonucleotides. 
     FIG. 17 is a photograph of a Western blot of a polyacrylamide gel of cellular protein from  E. coli  cells after treatment with secA antisense oligonucleotides. 
     FIGS. 18 a  and  18   b  are graphs of the number of colony forming units/ml of  E. coli  cells after treatment with secA antisense oligonucleotides. 
     FIGS. 19 a-g  are graphs of growth curves of  E. coli  K12 after treatment with antisense oligonucleotides. FIG. 19 a  shows the growth after treatment with 16 μM or 80 μM of antisense ES799 [SEQ ID NO:195]. FIG. 19 b  shows the growth after treatment with 20 AM of antisense ES1739 [SEQ ID NO:229]. FIG. 19 c  shows the growth after treatment with 80 μM of antisense ES851 [SEQ ID NO:197]. FIG. 19 d  shows the growth after treatment with 80 μM of antisense ES553 [SEQ ID NO:188]. FIG. 19 e  shows the growth after treatment with 80 μM of antisense ES646 [SEQ ID NO:191]. FIG. 19 f  shows the growth after treatment with 80 μM of antisense ES1845 [SEQ ID NO:235]. FIG. 19 g  shows the growth after treatment with 80 μM of antisense ES2537 [SEQ ID NO:254]. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     The present invention provides compounds that inhibit the growth of microbes by inhibiting the expression of a ribonucleotide reductase protein or the secA protein. Without being limited to any theory, the compounds inhibit the expression of the ribonucleotide reductase or the secA protein by inhibiting the transcription of the gene or the translation of the mRNA to protein. Such compounds include antisense oligonucleotides. 
     Definitions 
     As used herein, the following terms have the following meanings: 
     The term “antisense oligonucleotide” as used herein means a nucleotide sequence that is complementary to the MRNA for the desired gene. Preferably, the antisense oligonucleotide is complementary to the MRNA for ribonucleotide reductase or secA. 
     The term “oligonucleotide” refers to an oligomer or polymer of nucleotide or nucleoside monomers consisting of naturally occurring bases, sugars, and inter-sugar (backbone) linkages. The term also includes modified or substituted oligomers comprising non-naturally occurring monomers or portions thereof, which function similarly. Such modified or substituted oligomers may be preferred over naturally occurring forms because of the properties such as enhanced cellular uptake, or increased stability in the presence of nucleases. The term also includes chimeric oligonucleotides which contain two or more chemically distinct regions. For example, chimeric oligonucleotides may contain at least one region of modified nucleotides that confer beneficial properties (e.g. increased nuclease resistance, increased uptake into cells) or two or more oligonucleotides of the invention may be joined to form a chimeric oligonucleotide. 
     The antisense oligonucleotides of the present invention may be ribonucleic or deoxyribonucleic acids and may contain naturally occurring or synthetic monomeric bases, including adenine, guanine, cytosine, thymine and uracil. The oligonucleotides may also contain modified bases such as xanthine, hypoxanthine, 2-aminoadenine, 6-methyl, 2-propyl and other alkyl adenines, 5-halo uracil, 5-halo cytosine, 6-aza uracil, 6-aza cytosine and 6-aza thymine, pseudo uracil, 4-thiouracil, 8-halo adenine, 8-aminoadenine, 8-thiol adenine, 8-thiolalkyl adenines, 8-hydroxyl adenine and other 8-substituted adenines, 8-halo guanines, 8-amino guanine, 8-thiol guanine, 8-thioalkyl guanines, 8-hydroxyl guanine and other 8-substituted guanines, other aza and deaza uracils, thymidines, cytosines or guanines, 5-trifluoromethyl uracil and 5-trifluoro cytosine. 
     The antisense oligonucleotides of the invention may also comprise modified phosphorus oxygen heteroatoms in the phosphate backbone, short chain alkyl or cycloalkyl intersugar linkages or short chain heteroatom or heterocyclic intersugar linkages. For example, the antisense oligonucleotides may contain methyl phosphonates, phosphorothioates, phosphorodithioates, phosphotriesters, and morpholino oligomers. In one embodiment of the invention, the antisense oligonucleotides comprise phosphorothioate bonds linking between the four to six 3′-terminus nucleotides. In another embodiment, the phosphorothioate bonds link all the nucleotides. The antisense oligonucleotides may also have sugar mimetics. 
     The antisense oligonucleotides of the invention may also comprise nucleotide analogues wherein the structure of the nucleotide is fundamentally altered. An example of such an oligonucleotide analogue is a peptide nucleic acid (PNA) wherein the deoxyribose (or ribose) phosphate backbone in DNA (or RNA) is replaced with a polyamide backbone which is similar to that found in peptides (Nielsen et al. 11 ; Good and Nielsen 12 ; Buchardt, deceased, et al. 13 , U.S. Pat. No. 5,766,855; Buchardt, deceased, et al. 14 , U.S. Pat. No. 5,719,262). PNA analogues have been shown to be resistant to degradation by enzymes and to have extended lives in vivo and in vitro. PNAs also bind more strongly to a complementary DNA sequence than to a naturally occurring nucleic acid molecule due to the lack of charge repulsion between the PNA strand and the DNA strand. 
     The oligonucleotides of the present invention may also include other nucleotides comprising polymer backbones, cyclic backbones, or acyclic backbones. For example, the nucleotides may comprise morpholino backbone structures (U.S. Pat. No. 5,034,506 15 ). 
     The oligonucleotides of the present invention are “nuclease resistant” when they have either been modified such that they are not susceptible to degradation by DNA and RNA nucleases or alternatively they have been placed in a delivery vehicle which in itself protects the oligonucleotide from DNA or RNA nucleases. Nuclease resistant oligonucleotides include, for example, methyl phosphonates, phosphorothioates, phosphorodithioates, phosphotriesters, and morpholino oligomers. Suitable delivery vehicles for conferring nuclease resistance include, for example liposomes. 
     The oligonucleotides of the present invention may also contain groups, such as groups for improving the pharmacokinetic properties of an oligonucleotides, or groups for improving the pharmacodynamic properties of an oligonucleotide. Preferably, the oligonucleotides do not contain reporter groups or labels, such as fluorescent dyes or radioactive labels. 
     The antisense oligonucleotides may be complementary to the complete ribonucleotide reductase or secA gene including the introns. Preferably, the antisense oligonucleotides are complimentary to the mRNA region from the ribonucleotide reductase gene or the secA gene. 
     The antisense oligonucleotides may be selected from the sequence complementary to the ribonucletide reductase or secA genes such that the sequence exhibits the least likelihood of showing duplex formation, hair-pin formation, and homooligomer/sequence repeats but has a high to moderate potential to bind to the ribonucleotides reductase gene or the secA gene sequence and contains a GC clamp. These properties may be determined using the computer modeling program OLIGO Primer Analysis Software, Version 5.0 (distributed by National Biosciences, Inc., Plymouth, Minn.). This computer program allows the determination of a qualitative estimation of these five parameters. 
     Alternatively, the antisense oligonucleotides may also be selected on the basis that the sequence is highly conserved for either the ribonucleotide reductase or the secA genes between two or more microbial species. These properties may be determined using the BLASTN program (Altschul, et al. 16 ) of the University of Wisconsin Computer group (GCG) software (Devereux J. et al. 17 ) with the National Center for Biotechnology Information (NCBI) databases. 
     The antisense oligonucleotides generally comprise from at least about 3 nucleotides or nucleotide analogs, preferably from about 3 to about 50 nucleotides or nucleotide analogs, more preferably, from about 7 to about 35 nucleotides or nucleotide analogs, most preferably from about 15 to about 25 nucleotide or nucleotide analogs. 
     Preferably, the antisense oligonucleotides comprise from 3 to about 50 nucleotides or nucleotide analogs, more preferably from 20 to about 50 nucleotides or nucleotide analogs and further comprise all or part of the sequences set forth in Tables 1, 2, 3, and 4 (below). Preferably, the oligonucleotides complementary to the ribonucleotide reductase gene comprise SEQ ID NOS.: 14 to 157 as shown in Tables 1 and 2. Preferably, the antisense oligonucleotides complementary to the secA gene comprise the SEQ ID NOS.: 158 to 265 as shown in Tables 3 and 4. 
     
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Antisense oligonucleotides that target the  Escherichia coli   
               
               
                 K12 ribonucleotide reductase large subunit (R1) 
               
             
          
           
               
                   
                   
                   
                   
                 ΔG 
               
               
                 SEQ 
                   
                   
                 Tm 
                 (kcal/ 
               
               
                 ID No.: 
                 Name 
                 Sequence 5′→3′ 
                 (° C.) 
                 mol) 
               
               
                   
               
             
          
           
               
                 14 
                 ER1-16 
                 CCGTCGCGCTTTGTCACCAG 
                 61.1 
                 −43.0 
               
               
                 15 
                 ER1-24 
                 CTGTGCTACCGTCGCGCTTT 
                 57.8 
                 −42.0 
               
               
                 16 
                 ER1-33 
                 TGATGCGCTCTGTGCTACCG 
                 57.2 
                 −40.2 
               
               
                 17 
                 ER1-44 
                 TTTGTCGAGATTGAT GCGCT 
                 53.3 
                 −38.7 
               
               
                 18 
                 ER1-58 
                 AGAACGCGATGGATTTTGTC 
                 51.7 
                 −38.4 
               
               
                 19 
                 ER1-71 
                 TGCCGCCCAATCCAGAACGC 
                 64.6 
                 −46.0 
               
               
                 20 
                 ER1-79 
                 AGTCCTTCTGCCGCCCAATC 
                 57.7 
                 −42.2 
               
               
                 21 
                 ER1-128 
                 AAACTGAATGTGGGAGCGCA 
                 55.5 
                 −39.8 
               
               
                 22 
                 ER1-169 
                 ATAATGGTTTCGTGGATGTC 
                 55.5 
                 −35.4 
               
               
                 23 
                 ER1-180 
                 CGGCAGCCTTGATAATGGTT 
                 54.2 
                 −40.6 
               
               
                 24 
                 ER1-218 
                 ATACTGATAATCCGGCGCAT 
                 51.4 
                 −39.4 
               
               
                 25 
                 ER1-252 
                 TACGCAGGTGGAAGATCGCC 
                 57.3 
                 −41.4 
               
               
                 26 
                 ER1-294 
                 GGTCGTACAGCGCAGGCGGC 
                 64.4 
                 −45.9 
               
               
                 27 
                 ER1-320 
                 GCCCATCTCGACCATTTTCA 
                 54.7 
                 −39.7 
               
               
                 28 
                 ER1-330 
                 TATCGTATTTGCCCATCTCG 
                 50.4 
                 −38.1 
               
               
                 29 
                 ER1-423 
                 CGGCAGCATAAGAGAAGGTC 
                 51.6 
                 −38.5 
               
               
                 30 
                 ER1-439 
                 CCTTCCAGCTGCTTAACGGC 
                 56.4 
                 −41.9 
               
               
                 31 
                 ER1-450 
                 CCAGATATTTGCCTTCCAGC 
                 51.5 
                 −38.8 
               
               
                 32 
                 ER1-479 
                 ATAGATTTCGCCGGTCACGC 
                 56.4 
                 −41.8 
               
               
                 33 
                 ER1-495 
                 GGAACTGGGCGCTCTCATAG 
                 53.9 
                 −39.7 
               
               
                 34 
                 ER1-504 
                 GAATATAAAGGAACTGGGCG 
                 48.5 
                 −38.0 
               
               
                 35 
                 ER1-518 
                 GCACGCGGCAACTAGAATAT 
                 52.2 
                 −39.4 
               
               
                 36 
                 ER1-529 
                 TTCGAGAACAAGCACGCGGC 
                 60.8 
                 −43.3 
               
               
                 37 
                 ER1-543 
                 TTTCACGCGGGTAGTTCGAG 
                 55.2 
                 −40.5 
               
               
                 38 
                 ER1-566 
                 ACGCTTCACATATTGCAGGC 
                 52.2 
                 −38.7 
               
               
                 39 
                 ER1-584 
                 GGAAACCGCGTCGTAAAAAC 
                 53.9 
                 −40.8 
               
               
                 40 
                 ER1-592 
                 TTAAATGTGGAAACCGCGTC 
                 52.7 
                 −39.3 
               
               
                 41 
                 ER1-617 
                 CATGATTGGCGTCGGCAGCG 
                 64.0 
                 −44.9 
               
               
                 42 
                 ER1-628 
                 CGCACGCCGGACATGATTGG 
                 63.8 
                 −44.6 
               
               
                 43 
                 ER1-640 
                 CGAGTCGGGGTACGCACGCC 
                 64.2 
                 −45.8 
               
               
                 44 
                 ER1-667 
                 TCGATCAGTACGCAGGAGCT 
                 52.4 
                 −38.1 
               
               
                 45 
                 ER1-680 
                 GCTGTCACCGCACTCGATCA 
                 56.9 
                 −39.1 
               
               
                 46 
                 ER1-689 
                 GGAATCCAGGCTGTCACCGC 
                 59.0 
                 −41.9 
               
               
                 47 
                 ER1-704 
                 GGAGGTGGCGTTGATGGAAT 
                 56.0 
                 −40.6 
               
               
                 48 
                 ER1-716 
                 AACAATCGCGCTGGAGGTGG 
                 59.5 
                 −42.7 
               
               
                 49 
                 ER1-778 
                 CTACCCAGCGCACGAATACG 
                 55.7 
                 −40.9 
               
               
                 50 
                 ER1-817 
                 ATGCAGCCGGTATGGAACGC 
                 59.4 
                 −43.1 
               
               
                 51 
                 ER1-829 
                 TTGTAGAACGGAATGCAGCC 
                 52.8 
                 −38.8 
               
               
                 52 
                 ER1-846 
                 CCGCTGTCTGGAAATGTTTG 
                 53.1 
                 −38.6 
               
               
                 53 
                 ER1-855 
                 AGGATTTCACCGCTGTCTGG 
                 54.0 
                 −39.2 
               
               
                 54 
                 ER1-874 
                 CGCACACCGCCCTGAGAGCA 
                 63.9 
                 −44.0 
               
               
                 55 
                 ER1-907 
                 CACATCGGGTAGAACAGCGT 
                 52.5 
                 −38.1 
               
               
                 56 
                 ER1-925 
                 CTTTCCACTTCCAGATGCCA 
                 52.5 
                 −38.1 
               
               
                 57 
                 ER1-964 
                 TTGCCTTCCACACCACGGTT 
                 57.5 
                 −40.8 
               
               
                 58 
                 ER1-971 
                 CACGCGGTTGCCTTCCACAC 
                 60.8 
                 −42.5 
               
               
                 59 
                 ER1-981 
                 CCATATGACGCACGCGGTTG 
                 59.4 
                 −42.1 
               
               
                 60 
                 ER1-1034 
                 TTCACCTTTCAGCAGACGGG 
                 55.0 
                 −39.6 
               
               
                 61 
                 ER1-1055 
                 CGGGCTGAACAGGGTGATAT 
                 53.8 
                 −39.6 
               
               
                 62 
                 ER1-1059 
                 CGGACGGGCTGAACAGGGTG 
                 62.1 
                 −43.7 
               
               
                 63 
                 ER1-1061 
                 GTCGGACGGGCTGAACAGGG 
                 61.2 
                 −43.4 
               
               
                 64 
                 ER1-1106 
                 AAACTCTTCCTGATCGGCGA 
                 53.8 
                 −39.7 
               
               
                 65 
                 ER1-1148 
                 GCGGATGCTGTCGTCTTTCT 
                 54.3 
                 −39.4 
               
               
                 66 
                 ER1-1155 
                 GCTGCTTGCGGATGCTGTCG 
                 61.3 
                 −43.0 
               
               
                 67 
                 ER1-1166 
                 GGCTTTCACACGCTGCTTGC 
                 58.2 
                 −41.4 
               
               
                 68 
                 ER1-1173 
                 GCTCAACGGCTTTCACACGC 
                 58.0 
                 −41.3 
               
               
                 69 
                 ER1-1212 
                 GACCGGTAGACGCACGTTCC 
                 56.7 
                 −40.8 
               
               
                 70 
                 ER1-1255 
                 GGGCTATGGGTATTGCAGTG 
                 52.1 
                 −38.7 
               
               
                 71 
                 ER1-1259 
                 AAACGGGCTATGGGTATTGC 
                 53.3 
                 −40.7 
               
               
                 72 
                 ER1-1265 
                 CGGATCAAACGGGCTATGGG 
                 58.7 
                 −43.4 
               
               
                 73 
                 ER1-1311 
                 GGGCTATCTCCAGGCACAGG 
                 55.9 
                 −40.7 
               
               
                 74 
                 ER1-1315 
                 GGCAGGGCTATCTCCAGGCA 
                 58.7 
                 −42.5 
               
               
                 75 
                 ER1-1320 
                 TGGTCGGCAGGGCTATCTCC 
                 58.6 
                 −42.4 
               
               
                 76 
                 ER1-1326 
                 GCGGTTTGGTCGGCAGGGCT 
                 64.9 
                 −47.0 
               
               
                 77 
                 ER1-1330 
                 TTCAGCGGTTTGGTCGGCAG 
                 60.5 
                 −43.1 
               
               
                 78 
                 ER1-1336 
                 ACGTCGTTCAGCGGTTTGGT 
                 56.8 
                 −40.9 
               
               
                 79 
                 ER1-1356 
                 TTTCACCGTTCTCGTCGTTG 
                 53.5 
                 −38.5 
               
               
                 80 
                 ER1-1364 
                 CAGCGCGATTTCACCGTTCT 
                 57.5 
                 −41.7 
               
               
                 81 
                 ER1-1370 
                 CGTACACAGCGCGATTTCAC 
                 54.2 
                 −38.9 
               
               
                 82 
                 ER1-1379 
                 AGCAGACAGCGTACACAGCG 
                 54.0 
                 −38.2 
               
               
                 83 
                 ER1-1388 
                 CAGGTTGAAAGCAGACAGCG 
                 53.4 
                 −38.4 
               
               
                 84 
                 ER1-1397 
                 AATTGCGCCCAGGTTGAAAG 
                 56.5 
                 −41.9 
               
               
                 85 
                 ER1-1407 
                 CCAGGTTATTAATTGCGCCC 
                 53.8 
                 −41.3 
               
               
                 86 
                 ER1-1428 
                 TTGCCAGCTCTTCCAGTTCA 
                 53.3 
                 −38.2 
               
               
                 87 
                 ER1-1438 
                 ACCGCCAGAATTGCCAGCTC 
                 58.8 
                 −42.5 
               
               
                 88 
                 ER1-1451 
                 GTCAAGTGCACGAACCGCCA 
                 59.1 
                 −41.0 
               
               
                 89 
                 ER1-1463 
                 ATCCAGCAGCGCGTCAAGTG 
                 58.5 
                 −41.2 
               
               
                 90 
                 ER1-1468 
                 TGATAATCCAGCAGCGCGTC 
                 56.1 
                 −40.4 
               
               
                 91 
                 ER1-1535 
                 GATCACACCAATACCCAGCG 
                 52.6 
                 −38.1 
               
               
                 92 
                 ER1-1561 
                 TCGTTCGCCAGGTAGTAAGC 
                 52.2 
                 −39.0 
               
               
                 93 
                 ER1-1570 
                 CGTTTACCGTCGTTCGCCAG 
                 57.9 
                 −42.2 
               
               
                 94 
                 ER1-1584 
                 TGCCGTCGGAGTAGCGTTTA 
                 55.8 
                 −41.0 
               
               
                 95 
                 ER1-1605 
                 TATGCGTCAGGTTGTTGGCG 
                 56.8 
                 −40.5 
               
               
                 96 
                 ER1-1614 
                 CGAAGGTTTTATGCGTCAGG 
                 52.5 
                 −39.3 
               
               
                 97 
                 ER1-1688 
                 GTTAAACCACGGGCACGCGC 
                 62.0 
                 −45.0 
               
               
                 98 
                 ER1-1705 
                 TTCGCGTAAGTGGTTTCGTT 
                 52.6 
                 −39.3 
               
               
                 99 
                 ER1-1731 
                 TATAGGTATCGATCGGCAGG 
                 49.5 
                 −38.0 
               
               
                 100 
                 ER1-1777 
                 CAGTCGTAATGCAGCGGCTC 
                 55.8 
                 −40.2 
               
               
                 101 
                 ER1-1789 
                 CGCAGAGCTTCCCAGTCGTA 
                 55.4 
                 −40.0 
               
               
                 102 
                 ER1-1839 
                 TCAGAGCAGAAAGCGTGGAG 
                 53.0 
                 −38.1 
               
               
                 103 
                 ER1-1849 
                 TCGGACGGCATCAGAGCAGA 
                 58.9 
                 −40.9 
               
               
                 104 
                 ER1-1874 
                 GGCGTTAGAGATCTGCGAAG 
                 51.8 
                 −38.7 
               
               
                 105 
                 ER1-1916 
                 TTTGATGCTGACGTAACCGC 
                 53.7 
                 −39.0 
               
               
                 106 
                 ER1-1923 
                 TCGACGCTTTGATGCTGACG 
                 57.1 
                 −40.2 
               
               
                 107 
                 ER1-1944 
                 CCTGGCGCAAAATACCGTCT 
                 56.5 
                 −42.0 
               
               
                 108 
                 ER1-1957 
                 TAGTCCGGCACCACCTGGCG 
                 62.5 
                 −44.2 
               
               
                 109 
                 ER1-1968 
                 GCAGGTGCTCGTAGTCCGGC 
                 59.3 
                 −42.4 
               
               
                 110 
                 ER1-1974 
                 CGTCGTGCAGGTGCTCGTAG 
                 56.7 
                 −39.9 
               
               
                 111 
                 ER1-1983 
                 GCTCATAGGCGTCGTGCAGG 
                 58.0 
                 −41.4 
               
               
                 112 
                 ER1-1992 
                 CCCACAGCAGCTCATAGGCG 
                 58.0 
                 −41.5 
               
               
                 113 
                 ER1-2000 
                 CGGCATTTCCCACAGCAGCT 
                 59.7 
                 −42.8 
               
               
                 114 
                 ER1-2010 
                 CATCGTTACCCGGCATTTCC 
                 56.5 
                 −41.9 
               
               
                 115 
                 ER1-2083 
                 GGATCGTAGTTGGTGTTGGC 
                 51.8 
                 −39.9 
               
               
                 116 
                 ER1-2112 
                 TCGGCACTTTTCCTGACGGG 
                 59.5 
                 −42.8 
               
               
                 117 
                 ER1-2145 
                 AGGCGGTGAGCAGGTCTTTC 
                 55.7 
                 −40.5 
               
               
                 118 
                 ER1-2154 
                 CGAATTTGTAGGCGGTGAGC 
                 54.8 
                 −40.5 
               
               
                 119 
                 ER1-2166 
                 GTGTTTTGACCCCGAATTTG 
                 51.9 
                 −38.6 
               
               
                 120 
                 ER1-2211 
                 CGTCTTGTGCGTCTTCAGCG 
                 56.8 
                 −40.0 
               
               
                 121 
                 ER1-2262 
                 TCTTACATGCGCCGCTTTCG 
                 58.6 
                 −42.8 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Antisense oligonucleotides that target the  Escherichia coli   
               
               
                 K12 ribonucleotide reductase small subunit (R2) 
               
             
          
           
               
                   
                   
                   
                   
                 ΔG 
               
               
                 SEQ 
                   
                   
                 Tm 
                 (kcal/ 
               
               
                 ID No.: 
                 Name 
                 Sequence 5′→3′ 
                 (° C.) 
                 mol) 
               
               
                   
               
               
                 122 
                 ER2-50 
                 CGGCTGACCAAAGAACATCG 
                 55.5 
                 −40.0 
               
               
                 123 
                 ER2-60 
                 CCACGTTGACCGGCTGACCA 
                 61.2 
                 −42.2 
               
               
                 124 
                 ER2-67 
                 TAGCGAGCCACGTTGACCGG 
                 60.6 
                 −43.2 
               
               
                 125 
                 ER2-134 
                 CGGACGCCAGAAGAAAGAGA 
                 54.4 
                 −39.8 
               
               
                 126 
                 ER2-144 
                 CAACTTCTTCCGGACGCCAG 
                 57.0 
                 −41.3 
               
               
                 127 
                 ER2-168 
                 AATCTATACGGTCGCGGGAG 
                 53.4 
                 −40.5 
               
               
                 128 
                 ER2-198 
                 TGTGTTTTTCGTGCTCCGGC 
                 58.3 
                 −41.6 
               
               
                 129 
                 ER2-273 
                 GCAATAGCGCCACGTTCGGG 
                 62.1 
                 −45.2 
               
               
                 130 
                 ER2-284 
                 AGAAATAAGCGGCAATAGCG 
                 51.8 
                 −40.3 
               
               
                 131 
                 ER2-290 
                 CGGAATAGAAATAAGCGGCA 
                 52.4 
                 −40.3 
               
               
                 132 
                 ER2-307 
                 ACCCAGGTTTCCAGTTCCGG 
                 57.4 
                 −42.0 
               
               
                 133 
                 ER2-350 
                 ATAGGAACGGGAATGAATCG 
                 50.7 
                 −38.8 
               
               
                 134 
                 ER2-441 
                 TCCCTTCCGCACGTTTCTGG 
                 59.5 
                 −42.8 
               
               
                 135 
                 ER2-498 
                 CGCCCAGCAGATGCCAGTAG 
                 58.0 
                 −41.5 
               
               
                 136 
                 ER2-505 
                 GTACCTTCGCCCAGCAGATG 
                 54.6 
                 −39.7 
               
               
                 137 
                 ER2-544 
                 CGCAGGCTAACGGTCACAGT 
                 55.2 
                 −39.7 
               
               
                 138 
                 ER2-557 
                 TTTCTTCAGCTCGCGCAGGC 
                 60.2 
                 −43.4 
               
               
                 139 
                 ER2-640 
                 GCAAATGCGAAGGAACAAGC 
                 54.9 
                 −40.4 
               
               
                 140 
                 ER2-655 
                 ATCAATTCGCGTTCTGCAAA 
                 53.4 
                 −39.3 
               
               
                 141 
                 ER2-680 
                 GCGAATAATTTTGGCGTTGC 
                 54.9 
                 −41.6 
               
               
                 142 
                 ER2-692 
                 GCGGGCAATCAGGCGAATAA 
                 59.5 
                 −44.0 
               
               
                 143 
                 ER2-704 
                 CAGGGCTTCGTCGCGGGCAA 
                 66.8 
                 −47.8 
               
               
                 144 
                 ER2-714 
                 CGGTCAGGTGCAGGGCTTCG 
                 62.3 
                 −44.0 
               
               
                 145 
                 ER2-724 
                 TGCTGGGTGCCGGTCAGGTG 
                 63.6 
                 −43.5 
               
               
                 146 
                 ER2-728 
                 CATATGCTGGGTGCCGGTCA 
                 58.8 
                 −41.4 
               
               
                 147 
                 ER2-778 
                 GCAATTTCCGCCATCTCAGG 
                 56.8 
                 −41.5 
               
               
                 148 
                 ER2-796 
                 TCCTGCTTACACTCTTCGGC 
                 52.1 
                 −38.3 
               
               
                 149 
                 ER2-848 
                 ATCCGCCCAGTCTTTCTCCT 
                 54.2 
                 −40.4 
               
               
                 150 
                 ER2-857 
                 GAACAGATAATCCGCCCAGT 
                 50.7 
                 −38.1 
               
               
                 151 
                 ER2-976 
                 GGGTTGGAGCGCGTCTGGAA 
                 61.8 
                 −44.0 
               
               
                 152 
                 ER2-983 
                 CGGGATCGGGTTGGAGCGCG 
                 68.1 
                 −49.1 
               
               
                 153 
                 ER2-985 
                 CACGGGATCGGGTTGGAGCG 
                 64.0 
                 −45.6 
               
               
                 154 
                 ER2-1045 
                 CTGACTTCCACTTCCTGCGG 
                 54.6 
                 −39.9 
               
               
                 155 
                 ER2-1063 
                 TGCCCGACCAGATAAGAACT 
                 51.3 
                 −38.2 
               
               
                 156 
                 ER2-1076 
                 TTCCGAGTCAATCTGCCCGA 
                 57.8 
                 −41.2 
               
               
                 157 
                 ER2-1092 
                 AATCGTCGGTGTCCACTTCC 
                 53.6 
                 −38.8 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Antisense Sequences that Target  Escherichia coli  SecA 
               
             
          
           
               
                   
                   
                   
                   
                 ΔG 
               
               
                 SEQ 
                   
                   
                 Tm 
                 (kcal/ 
               
               
                 ID No.: 
                 Name 
                 Sequence 5′→3′ 
                 (° C.) 
                 mol) 
               
               
                   
               
             
          
           
               
                 158 
                 ES56 
                 GACCACTTTGCGCATCCGGC 
                 62.1 
                 −44.2 
               
               
                 159 
                 ES62 
                 GATGTTGACCACTTTGCGCA 
                 54.3 
                 −38.3 
               
               
                 160 
                 ES85 
                 ATCTCCGGTTCCATGGCATT 
                 55.5 
                 −40.8 
               
               
                 161 
                 ES92 
                 TTTTTCCATCTCCGGTTCCA 
                 54.3 
                 −40.1 
               
               
                 162 
                 ES116 
                 CCCTTTCAGTTCTTCGTCGG 
                 53.8 
                 −39.8 
               
               
                 163 
                 ES124 
                 GCGGTTTTCCCTTTCAGTTC 
                 52.9 
                 −39.9 
               
               
                 164 
                 ES129 
                 ACTCTGCGGTTTTCCCTTTC 
                 52.5 
                 −39.6 
               
               
                 165 
                 ES153 
                 CGCCTTTTTCCAGACGTGCA 
                 58.4 
                 −41.9 
               
               
                 166 
                 ES158 
                 CACTTCGCCTTTTTCCAGAC 
                 51.5 
                 −38.4 
               
               
                 167 
                 ES165 
                 TTTCCAGCACTTCGCCTTTT 
                 54.1 
                 −40.5 
               
               
                 168 
                 ES170 
                 CAGATTTTCCAGCACTTCGC 
                 52.5 
                 −38.6 
               
               
                 169 
                 ES206 
                 ACTTGCCTCACGTACCACGG 
                 54.9 
                 −39.5 
               
               
                 170 
                 ES215 
                 GACGCGCTTACTTGCCTCAC 
                 55.0 
                 −40.1 
               
               
                 171 
                 ES230 
                 GTGACGCATACCAAAGACGC 
                 53.1 
                 −38.5 
               
               
                 172 
                 ES264 
                 TAAGAACCATACCGCCGAGT 
                 51.5 
                 −39.1 
               
               
                 173 
                 ES286 
                 ATTTCGGCGATGCAGCGTTC 
                 59.7 
                 −43.4 
               
               
                 174 
                 ES303 
                 TTCCTTCACCGGTACGCATT 
                 54.5 
                 −40.3 
               
               
                 175 
                 ES307 
                 GTTTTTCCTTCACCGGTACG 
                 51.4 
                 −38.9 
               
               
                 176 
                 ES320 
                 CGTTGCGGTCAGGGTTTTTC 
                 56.8 
                 −41.6 
               
               
                 177 
                 ES336 
                 TCAGGTAAGCAGGCAGCGTT 
                 55.0 
                 −40.2 
               
               
                 178 
                 ES351 
                 TACCGGTTAGTGCGTTCAGG 
                 52.8 
                 −39.2 
               
               
                 179 
                 ES392 
                 TTGCGCCAGGTAGTCGTTGA 
                 56.5 
                 −40.4 
               
               
                 180 
                 ES398 
                 GTCACGTTGCGCCAGGTAGT 
                 55.0 
                 −39.5 
               
               
                 181 
                 ES418 
                 AGCGGACGGTTGTTTTCGGC 
                 60.8 
                 −44.5 
               
               
                 182 
                 ES429 
                 GGAATTCAAACAGCGGACGG 
                 56.7 
                 −41.5 
               
               
                 183 
                 ES436 
                 AGGCCAAGGAATTCAAACAG 
                 51.0 
                 −38.4 
               
               
                 184 
                 ES448 
                 ATACCGACAGTCAGGCCAAG 
                 51.6 
                 −38.0 
               
               
                 185 
                 ES485 
                 TTCGCGCTTTGCCGGTGCTG 
                 65.8 
                 −46.9 
               
               
                 186 
                 ES531 
                 AGCCGTATTCGTTGTTCGTA 
                 50.1 
                 −37.9 
               
               
                 187 
                 ES544 
                 CGCAGGTAGTCAAAGCCGTA 
                 53.1 
                 −39.5 
               
               
                 188 
                 ES553 
                 ATGTTGTCGCGCAGGTAGTC 
                 52.6 
                 −38.1 
               
               
                 189 
                 ES556 
                 GCCATGTTGTCGCGCAGGTA 
                 59.2 
                 −41.7 
               
               
                 190 
                 ES617 
                 GTCCACTTCGTCCACCAGCG 
                 57.7 
                 −40.4 
               
               
                 191 
                 ES646 
                 GGTGTACGCGCTTCATCGAT 
                 55.0 
                 −40.0 
               
               
                 192 
                 ES647 
                 CGGTGTACGCGCTTCATCGA 
                 59.3 
                 −42.1 
               
               
                 193 
                 ES695 
                 GCGTTTATACATTTCCGAGC 
                 49.5 
                 −38.4 
               
               
                 194 
                 ES724 
                 CGGATCAGGTGCGGAATAAT 
                 53.9 
                 −40.4 
               
               
                 195 
                 ES799 
                 TTCACCTGGCGAGATTTTTC 
                 51.8 
                 −38.6 
               
               
                 196 
                 ES824 
                 CAGCACCAGACCACGTTCGG 
                 58.6 
                 −40.7 
               
               
                 197 
                 ES851 
                 GCCCTCTTTCACCAGCAGTT 
                 53.3 
                 −39.1 
               
               
                 198 
                 ES866 
                 CCCTTCATCCATGATGCCCT 
                 55.9 
                 −40.6 
               
               
                 199 
                 ES889 
                 TTGGCCGGAGAGTACAGAGA 
                 52.2 
                 −38.1 
               
               
                 200 
                 ES898 
                 AGCATGATGTTGGCCGGAGA 
                 57.6 
                 −40.9 
               
               
                 201 
                 ES922 
                 AGCGCCGCCGTTACGTGGTG 
                 64.6 
                 −46.5 
               
               
                 202 
                 ES950 
                 GTCACGGGTAAACAGCGCAT 
                 54.9 
                 −40.0 
               
               
                 203 
                 ES1068 
                 CACCTTCTTTCGCTTCCACA 
                 52.8 
                 −38.4 
               
               
                 204 
                 ES1097 
                 CAGCGTTTGGTTTTCGTTCT 
                 52.1 
                 −38.9 
               
               
                 205 
                 ES1109 
                 GGTGATCGAAGCCAGCGTTT 
                 56.5 
                 −41.2 
               
               
                 206 
                 ES1128 
                 GACGGAAGTAGTTCTGGAAG 
                 45.5 
                 −35.0 
               
               
                 207 
                 ES1147 
                 CCCGCCAGTTTTTCATACAG 
                 52.3 
                 −39.2 
               
               
                 208 
                 ES1152 
                 TCATCCCCGCCAGTTTTTCA 
                 57.5 
                 −41.6 
               
               
                 209 
                 ES1218 
                 GAACAACGACGGTATCCAGC 
                 52.0 
                 −38.2 
               
               
                 210 
                 ES1328 
                 GCCTTTCGCAGTACGTTCTT 
                 51.4 
                 −38.9 
               
               
                 211 
                 ES1350 
                 TAGTACCCACCAGCACCGGC 
                 57.1 
                 −41.4 
               
               
                 212 
                 ES1398 
                 CGGCTTTGGTCAGTTCGTTT 
                 54.3 
                 −40.1 
               
               
                 213 
                 ES1410 
                 TGTGCTTAATACCGGCTTTG 
                 50.8 
                 −38.6 
               
               
                 214 
                 ES1439 
                 GTTGGCGTGGAATTTGGCGT 
                 59.3 
                 −43.0 
               
               
                 215 
                 ES1462 
                 GCCTGAGCAACAATCGCCGC 
                 62.4 
                 −44.5 
               
               
                 216 
                 ES1515 
                 CTGTACCACGACCCGCCATA 
                 55.6 
                 −40.3 
               
               
                 217 
                 ES1518 
                 TATCTGTACCACGACCCGCC 
                 54.7 
                 −40.0 
               
               
                 218 
                 ES1545 
                 CTGCCTGCCAGCTACCACCG 
                 60.2 
                 −42.9 
               
               
                 219 
                 ES1563 
                 TTTCCAGCGCGGCAACTTCT 
                 59.4 
                 −43.4 
               
               
                 220 
                 ES1581 
                 TTTGCTCTGCGGTCGGATTT 
                 57.0 
                 −41.8 
               
               
                 221 
                 ES1589 
                 TTTTTCAATTTGCTCTGCGG 
                 53.2 
                 −39.8 
               
               
                 222 
                 ES1624 
                 ACCGCATCGTGACGTACCTG 
                 55.7 
                 −39.6 
               
               
                 223 
                 ES1629 
                 CCAGTACCGCATCGTGACGT 
                 55.7 
                 −39.6 
               
               
                 224 
                 ES1633 
                 GCTTCCAGTACCGCATCGTG 
                 55.5 
                 −40.0 
               
               
                 225 
                 ES1655 
                 ACCGATGATATGCAGGCCAC 
                 54.6 
                 −39.6 
               
               
                 226 
                 ES1712 
                 ACGACCAGAACGACCGCGCA 
                 63.3 
                 −44.1 
               
               
                 227 
                 ES1718 
                 CCCCTGACGACCAGAACGAC 
                 56.6 
                 −40.1 
               
               
                 228 
                 ES1722 
                 CATCCCCCTGACGACCAGAA 
                 56.9 
                 −40.4 
               
               
                 229 
                 ES1739 
                 GAAACGGGAAGAACCAGCAT 
                 53.1 
                 −39.5 
               
               
                 230 
                 ES1748 
                 CGACAGGTAGAAACGGGAAG 
                 51.4 
                 −38.6 
               
               
                 231 
                 ES1781 
                 GGAAGCAAAAATACGCATCA 
                 50.6 
                 −38.2 
               
               
                 232 
                 ES1785 
                 GGTCGGAAGCAAAAATACGC 
                 53.9 
                 −40.9 
               
               
                 233 
                 ES1794 
                 CGGATACTCGGTCGGAAGCA 
                 57.3 
                 −41.7 
               
               
                 234 
                 ES1814 
                 ACCCAGTTTACGCATCATGC 
                 52.5 
                 −38.5 
               
               
                 235 
                 ES1845 
                 ACGGGTGTTCAATGGCTTCG 
                 57.1 
                 −41.2 
               
               
                 236 
                 ES1861 
                 ATCGCTTTAGTCACCCACGG 
                 54.1 
                 −40.0 
               
               
                 237 
                 ES1888 
                 CTTTCAACTTTACGCTGGGC 
                 51.9 
                 −39.3 
               
               
                 238 
                 ES1892 
                 ACGGCTTTCAACTTTACGCT 
                 51.1 
                 −39.2 
               
               
                 239 
                 ES2007 
                 TGGTTTCGCTCACATCGCTG 
                 57.0 
                 −40.0 
               
               
                 240 
                 ES2054 
                 GTAGGCATCAATGGTCGCTT 
                 51.7 
                 −38.5 
               
               
                 241 
                 ES2084 
                 CCACATTTCTTCCAGCGACT 
                 51.7 
                 −38.0 
               
               
                 242 
                 ES2087 
                 ATCCCACATTTCTTCCAGCG 
                 53.9 
                 −39.7 
               
               
                 243 
                 ES2191 
                 TCACGCAGCGTCTCTTCATG 
                 54.7 
                 −38.2 
               
               
                 244 
                 ES2275 
                 CCTTTCTCGAAGTGACGCAT 
                 51.9 
                 −38.2 
               
               
                 245 
                 ES2306 
                 CCACAGGGAGTCAAGCGTTT 
                 54.1 
                 −39.3 
               
               
                 246 
                 ES2325 
                 TCGCTGCCAGGTGCTCTTTC 
                 57.7 
                 −41.1 
               
               
                 247 
                 ES2330 
                 GTCCATCGCTGCCAGGTGCT 
                 59.7 
                 −41.9 
               
               
                 248 
                 ES2339 
                 ACGCAGATAGTCCATCGCTG 
                 52.7 
                 −38.4 
               
               
                 249 
                 ES2381 
                 CTTCGGATCTTTCTGTGCGT 
                 51.9 
                 −38.2 
               
               
                 250 
                 ES2395 
                 CGTTTGTATTCCTGCTTCGG 
                 52.5 
                 −39.4 
               
               
                 251 
                 ES2422 
                 ATCGCTGCAAACATGGAGAA 
                 53.1 
                 −38.5 
               
               
                 252 
                 ES2520 
                 CCATACGACGCTGTTGTTCC 
                 52.9 
                 −38.5 
               
               
                 253 
                 ES2525 
                 GGCTTCCATACGACGCTGTT 
                 54.2 
                 −40.0 
               
               
                 254 
                 ES2537 
                 CGCTAAACGCTCGGCTTCCA 
                 59.9 
                 −44.1 
               
               
                 255 
                 ES2555 
                 GCTAAGCTGCTGCATTTGCG 
                 56.2 
                 −41.3 
               
               
                 256 
                 ES2619 
                 CTACTTTGCGCTCTCCGGTT 
                 53.8 
                 −40.4 
               
               
                 257 
                 ES2626 
                 TTACGTCCTACTTTGCGCTC 
                 50.0 
                 −38.0 
               
               
                 258 
                 ES2646 
                 AACCGCACGGGCAAGGATCG 
                 63.6 
                 −45.9 
               
               
                 259 
                 ES2651 
                 ACCAGAACCGCACGGGCAAG 
                 61.7 
                 −44.0 
               
               
                 260 
                 ES2656 
                 TTTTTACCAGAACCGCACGG 
                 55.1 
                 −41.0 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
               
             
           
               
                 TABLE 4 
               
             
             
               
                   
               
               
                 Antisense Sequences that Target  E. coli   
               
               
                 SecA based on Conserved Sequences 
               
             
          
           
               
                   
                   
                   
                   
                 ΔG 
               
               
                 SEQ 
                   
                   
                 Tm 
                 (kcal/ 
               
               
                 ID No.: 
                 Name 
                 Sequence 5′→3′ 
                 (° C.) 
                 mol) 
               
               
                   
               
               
                 261 
                 ES386 
                 CAGGTAGTCGTTGACGGTAA 
                 47.7 
                 −35.7 
               
               
                 262 
                 ES388 
                 CAGGTAGTCGTTGACGGT 
                 45.0 
                 −32.9 
               
               
                 263 
                 ES1126 
                 CGGAAGTAGTTCTGGAAGGT 
                 47.6 
                 −36.5 
               
               
                 264 
                 ES1702 
                 CGACCGCGCAACTGGTTATC 
                 57.8 
                 −41.9 
               
               
                 265 
                 ES2644 
                 CCGCACGGGCAAGGATCGTT 
                 63.6 
                 −45.9 
               
               
                   
               
             
          
         
       
     
     In Tables 1, 2, 3, and 4, the “Tm” is the melting temperature of an oligonucleotide duplex calculated according to the nearest-neighbor thermodynamic values. At this temperature 50% of nucleic acid molecules are in duplex and 50% are denatured. The “ΔG” is the free energy of the oligonucleotide, which is a measurement of an oligonucleotide duplex stability. 
     The following sequences have been determined to be conserved among species: 
     ES386 [SEQ ID NO:261] is conserved among  Escherichia coli  and  Mycobacterium tuberculosis;    
     ES388 [SEQ ID NO:262] is conserved among  Escherichia coli; Mycobacterium tuberculosis ; and  Mycobacterium bovis;    
     ES553 [SEQ ID NO:188] is conserved among  Escherichia coli, Mycobacterium tuberculosis, Mycobacterium bovis, Streptomyces coelicolor ; and  Streptomyces lividans;    
     ES556 [SEQ ID NO:189] is conserved among  Escherichia coli, Mycobacterium tuberculosis, Mycobacterium bovis, Streptomyces coelicolor ; and  Streptomyces lividans ; and Synechoccus sp.; and 
     ES646 [SEQ ID NO:191] is conserved among  Escherichia coli  and  Staphylococcus carnosus;    
     ES1 126 [SEQ ID NO:263] is conserved among  Escherichia coli  and  Rhodobacter capsulatus  SecA genes. 
     ES2644 [SEQ ID NO:265] is conserved among  Escherichia coli  SecA gene, MutA (A:T to C:G transversion), and tyrosine-specific transport protein (tyrP) gene. 
     The term “alkyl” refers to monovalent alkyl groups preferably having from 1 to 20 carbon atoms and more preferably 1 to 6 carbon atoms. This term is exemplified by groups such as methyl, ethyl, n-propyl, iso-propyl, n-butyl, iso-butyl, n-hexyl, and the like. 
     The term “aryl” refers to an unsaturated aromatic carbocyclic group of from 6 to 14 carbon atoms having a single ring (e.g., phenyl) or multiple condensed (fused) rings (e.g., naphthyl or anthryl). Preferred aryls include phenyl, naphthyl and the like. 
     The term “cycloalkyl” refers to cyclic alkyl groups of from 3 to 20 carbon atoms having a single cyclic ring or multiple condensed rings. Such cycloalkyl groups include, by way of example, single ring structures such as cyclopropyl, cyclobutyl, cyclopentyl, cyclooctyl, and the like, or multiple ring structures such as adamantanyl, and the like. 
     The term “halo” or “halogen” refers to fluoro, chloro, bromo and iodo and preferably is either fluoro or chloro. 
     The term “thiol” refers to the grou —SH. 
     As to any of the above groups which contain one or more substituents, it is understood, of course, that such groups do not contain any substitution or substitution patterns which are sterically impractical and/or synthetically non-feasible. In addition, the compounds of this invention include all stereochemical isomers arising from the substitution of these compounds. 
     The term “pharmaceutically acceptable salt” refers to salts which retain the biological effectiveness and properties of the antisense oligonucleotides of this invention and which are not biologically or otherwise undesirable. In many cases, the antisense oligonucleotides of this invention are capable of forming acid and/or base salts by virtue of the presence of amino and/or carboxyl groups or groups similar thereto. 
     Pharmaceutically acceptable base addition salts can be prepared from inorganic and organic bases. Salts derived from inorganic bases, include by way of example only, sodium, potassium, lithium, ammonium, calcium and magnesium salts. Salts derived from organic bases include, but are not limited to, salts of primary, secondary and tertiary amines, such as alkyl amines, dialkyl amines, trialkyl amines, substituted alkyl amines, di(substituted alkyl) amines, tri(substituted alkyl) amines, alkenyl amines, dialkenyl amines, trialkenyl amines, substituted alkenyl amines, di(substituted alkenyl) amines, tri(substituted alkenyl) amines, cycloalkyl amines, di(cycloalkyl) amines, tri(cycloalkyl) amines, substituted cycloalkyl amines, disubstituted cycloalkyl amine, trisubstituted cycloalkyl amines, cycloalkenyl amines, di(cycloalkenyl) amines, tri(cycloalkenyl) amines, substituted cycloalkenyl amines, disubstituted cycloalkenyl amine, trisubstituted cycloalkenyl amines, aryl amines, diaryl amines, triaryl amines, heteroaryl amines, diheteroaryl amines, triheteroaryl amines, heterocyclic amines, diheterocyclic amines, triheterocyclic amines, mixed di- and tri-amines where at least two of the substituents on the amine are different and are selected from the group consisting of alkyl, substituted alkyl, alkenyl, substituted alkenyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, heteroaryl, heterocyclic, and the like. Also included are amines where the two or three substituents, together with the amino nitrogen, form a heterocyclic or heteroaryl group. 
     Examples of suitable amines include, by way of example only, isopropylamine, trimethyl amine, diethyl amine, tri(iso-propyl) amine, tri(n-propyl) amine, ethanolamine, 2-dimethylaminoethanol, tromethamine, lysine, arginine, histidine, caffeine, procaine, hydrabamine, choline, betaine, ethylenediamine, glucosamine, N-alkylglucamines, theobromine, purines, piperazine, piperidine, morpholine, N-ethylpiperidine, and the like. It should also be understood that other carboxylic acid derivatives would be useful in the practice of this invention, for example, carboxylic acid amides, including carboxamides, lower alkyl carboxamides, dialkyl carboxamides, and the like. 
     Pharmaceutically acceptable acid addition salts may be prepared from inorganic and organic acids. Salts derived from inorganic acids include hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Salts derived from organic acids include acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluene-sulfonic acid, salicylic acid, and the like. 
     The term “ribonucleotide reductase gene” or the “ribonucleoside diphosphate reductase gene” refers to any gene which encodes a protein that either reduces the four main ribonucleotides to the corresponding deoxyribonucleotides involved in DNA synthesis or encodes a subunit of a multimeric enzyme which reduces the four main ribonucleotides to the corresponding deoxyribonucleotides. Without being limiting, examples of ribonucleotide reductase genes from bacteria include the  E. coli  nrdA, nrdB and nrd D genes; the  S. typhimurium  nrdE and nrdF genes; and the  Lactococcus lactis  nrdEF gene. Examples of the ribonucleotide reductase genes from viruses include the herpes simplex type 1 and 2 ribonucleotide reductases and the bovine and equine herpes simplex ribonucleotide reductases. 
     The term “secA” refers to an oligonucleotide sequence which encodes a protein having similar properties as those expressed by the  E. coli  secA gene. Without being limiting, examples of secA genes from bacteria include the  Mycobacterium bovis  secA gene; the  Mycobacterium tuberculosis  secA gene, the  Staphylococcus aureus  secA gene and the  Staphylococcus carnosus  secA gene. 
     The term “microorganism” means a bacteria, fungi or virus having either a ribonucleotide reductase or secA gene. Specifically excluded from this definition is the material parasite, plasmodium. 
     The term “bacteria” refers to any bacteria encoding either a ribonucleotide reductase gene or a secA gene, including  Escherichi coli, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium smegmatis, Salmonella typhimurium, Thermoplasma acidophilum, Pyrococcusfuriosus, Bacillus subtilis, Bacillus firmus, Lactococcus lactis, Staphylococcus aureus, Staphylococcus carnosus, Listeria monocytogenes, Borrelia burgdorferi, P. sativum, S. griseus , and Synechoccus sp. 
     The term “virus” refers to any virus having a ribonucleotide reductase gene. Preferably the virus will be a DNA virus. Examples of suitable viruses include various herpes viruses (such as herpes simplex types 1 and 2, varicella-herpes zoster, cytomegalovirus and Epstein-Barr virus) and the various hepatitis viruses. 
     The term “complementary to” means that the antisense oligonucleotide sequence is capable of binding to the target sequence, ie the ribonucleotide reductase gene or the secA gene. Preferably the antisense oligonucleotide sequence has at least about 75% identity with the target sequence, preferably at least about 90% identity and most preferably at least about 95% identity with the target sequence allowing for gaps or mismatches of several bases. Identity can be determined, for example, by using the BLASTN program of the University of Wisconsin Computer Group (GCG) software. 
     The term “inhibiting growth” means a reduction in the growth of the bacteria or viruses of at least 25%, more preferably of at least 50% and most preferably of at least 75%. The reduction in growth can be determined for bacteria by a measuring the optical density of a liquid bacteria culture with a spectrophotometer or by counting the number of colony forming units/ml (CFU/ml) upon plating on culture plates. The reduction in growth can be determined for viruses by measuring the number of plaque forming units/ml upon plating on susceptible cells. 
     Preparation of the Antisense Oligonucleotides 
     The antisense oligonucleotides of the present invention may be prepared by conventional and well-known techniques. For example, the oligonucleotides may be prepared using solid-phase synthesis and in particular using commercially available equipment such as the equipment available from Applied Biosystems Canada Inc., Mississauga, Canada. The oligonucleotides may also be prepared by enzymatic digestion of the naturally occurring ribonucleotide reductase or secA gene by methods known in the art. 
     Isolation and Purification of the Antisense Oligonucleotides 
     Isolation and purification of the antisense oligonucleotides described herein can be effected, if desired, by any suitable separation or purification such as, for example, filtration, extraction, crystallization, column chromatography, thin-layer chromatography, thick-layer chromatography, preparative low or high-pressure liquid chromatography or a combination of these procedures. However, other equivalent separation or isolation procedures could, of course, also be used. 
     The invention contemplates a method of evaluating if an antisense oligonucleotide inhibits the growth of a microbe having a ribonucleotide reductase or secA gene. The method comprises selecting the microbe/microorganism having a ribonucleotide reductase or secA gene, administering the antisense oligonucleotide; and comparing the growth of the treated microbe with the growth of an untreated microorganism. 
     In order for the antisense oligonucleotide to effectively interrupt the expression of the ribonucleotide reductase or secA gene, the antisense oligonucleotide enters the microorganism&#39;s cell, in the case of fungal or bacterial cells or enter the mammalian cell having the virus target. 
     Although oligonucleotides are taken up by bacterial cells, some modification of the oligonucleotides may help facilitate or regulate said uptake. Thus, a carier molecule, for example an amino acid, can be linked to the oligonucleotide. For example, bacteria have multiple transport systems for the recognition and uptake of molecules of leucine. The addition of this amino acid to the oligonucleotide may facilitate the uptake of the oligonucleotide in the bacteria and not substantially interfere with the activity of the antisense oligonucleotide in the bacterial cell. 
     Other methods are contemplated for facilitating the uptake of the antisense oligonucleotide into bacteria. For example, the addition of other amino acids or peptides or primary amines to the 3′ or 5′ termini of the antisense oligonucleotide may enable utilization of specific transport systems. Addition of lactose to the oligonucleotide by a covalent linkage may also be used to enable transport of the antisense oligonucleotide by lactose permease. Other sugar transport systems are also known to be functional in bacteria and can be utilized in this invention. 
     With regard to inhibiting the expression of ribonucleotide reductase in DNA viruses, the antisense oligonucleotide is preferably introduced into the cell infected with the DNA virus. The antisense oligonucleotides may be delivered using vectors or liposomes. 
     An expression vector comprising the antisense oligonucleotide sequence may be constructed having regard to the sequence of the oligonucleotide and using procedures known in the art. The vectors may be selected from plasmids or benign viral vectors depending on the eukaryotic cell and the DNA virus. Phagemids are a specific example of beneficial vectors because they can be used either as plasmids or a bacteriophage vectors. Examples of other vectors include viruses such as bacteriiophages, baculoviruses and retroviruses, DNA viruses, liposomes and other recombination vectors. 
     Vectors can be constructed by those skilled in the art to contain all the expression elements required to achieve the desired transcription of the antisense oligonucleotide sequences. Therefore, the invention provides vectors comprising a transcription control sequence operatively linked to a sequence which encodes an antisense oligonucleotide. Suitable transcription and translation elements may be derived from a variety of sources, including bacterial, fungal, viral, mammalian or insect genes. Selection of appropriate elements is dependent on the host cell chosen. 
     Reporter genes may be included in the vector. Suitable reporter genes include β-galactosidase (e.g. lacZ), chloramphenicol, acetyl-transferase, firefly luciferase, or an immunoglobulin or portion thereof. Transcription of the antisense oligonucleotide may be monitored by monitoring for the expression of the reporter gene. 
     The vectors can be introduced into cells or tissues by any one of a variety of known methods within the art. Such methods can be found generally described in Sambrook et al. 18 ; Ausubel et al. 19 ; Chang et al. 20 ; Vega et al. 21 ; and Vectors: A Survey of Molecular Cloning Vectors and Their Uses 22  and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. 
     Introduction of nucleic acids by infection offers several advantages. Higher efficiency and specificity for tissue type can be obtained. Viruses typically infect and propagate in specific cell types. Thus, the virus&#39; specificity may be used to target the vector to specific cell types in vivo or within a tissue or mixed culture of cells. Viral vectors can also be modified with specific receptors or ligands to alter target specificity through receptor mediated events. 
     Pharmaceutical Formulations 
     When employed as pharmaceuticals, the antisense oligonucleotides are usually administered in the form of pharmaceutical compositions. These compounds can be administered by a variety of routes including oral, rectal, transdermal, subcutaneous, intravenous, intramuscular, and intranasal. These compounds are effective as both injectable and oral compositions. Such compositions are prepared in a manner well known in the pharmaceutical art and comprise at least one active compound. 
     This invention also includes pharmaceutical compositions which contain, as the active ingredient, one or more of the antisense oligonucleotides associated with pharmaceutically acceptable carriers. In making the compositions of this invention, the active ingredient is usually mixed with an excipient, diluted by an excipient or enclosed within such a carrier which can be in the form of a capsule, sachet, paper or other container. When the excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier or medium for the active ingredient. Thus, the compositions can be in the form of tablets, pills, powders, lozenges, sachets, cachets, elixirs, suspensions, emulsions, solutions, syrups, aerosols (as a solid or in a liquid medium), ointments containing, for example, up to 10% by weight of the active compound, soft and hard gelatin capsules, suppositories, sterile injectable solutions, and sterile packaged powders. 
     In preparing a formulation, it may be necessary to mill the active compound to provide the appropriate particle size prior to combining with the other ingredients. If the active compound is substantially insoluble, it ordinarily is milled to a particle size of less than 200 mesh. If the active compound is substantially water soluble, the particle size is normally adjusted by milling to provide a substantially uniform distribution in the formulation, e.g. about 40 mesh. 
     Some examples of suitable excipients include lactose, dextrose, sucrose, sorbitol, mannitol, starches, gum acacia, calcium phosphate, alginates, tragacanth, gelatin, calcium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, sterile water, syrup, and methyl cellulose. The formulations can additionally include: lubricating agents such as talc, magnesium stearate, and mineral oil; wetting agents; emulsifying and suspending agents; preserving agents such as methyl- and propylhydroxy-benzoates; sweetening agents; and flavoring agents. The compositions of the invention can be formulated so as to provide quick, sustained or delayed release of the active ingredient after administration to the patient by employing procedures known in the art. 
     The compositions are preferably formulated in a unit dosage form, each dosage containing from about 5 to about 100 mg, more usually about 10 to about 30 mg, of the active ingredient. The term “unit dosage forms” refers to physically discrete units suitable as unitary dosages for human subjects and other mammals, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect, in association with a suitable pharmaceutical excipient. Preferably, the antisense oligonucleotide is employed at no more than about 20 weight percent of the pharmaceutical composition, more preferably no more than about 15 weight percent, with the balance being pharmaceutically inert carrier(s). 
     The antisense oligonucleotide is effective over a wide dosage range and is generally administered in a pharmaceutically effective amount. It, will be understood, however, that the amount of the antisense oligonucleotide actually administered will be determined by a physician, in the light of the relevant circumstances, including the condition to be treated, the chosen route of administration, the actual compound administered, the age, weight, and response of the individual patient, the severity of the patient&#39;s symptoms, and the like. 
     For preparing solid compositions such as tablets, the principal active ingredient/antisense oligonucleotide is mixed with a pharmaceutical excipient to form a solid preformulation composition containing a homogeneous mixture of a compound of the present invention. When referring to these preformulation compositions as homogeneous, it is meant that the active ingredient is dispersed evenly throughout the composition so that the composition may be readily subdivided into equally effective unit dosage forms such as tablets, pills and capsules. This solid preformulation is then subdivided into unit dosage forms of the type described above containing from, for example, 0.1 to about 500 mg of the active ingredient of the present invention. 
     The tablets or pills of the present invention may be coated or otherwise compounded to provide a dosage form affording the advantage of prolonged action. For example, the tablet or pill can comprise an inner dosage and an outer dosage component, the latter being in the form of an envelope over the former. The two components can be separated by an enteric layer which serves to resist disintegration in the stomach and permit the inner component to pass intact into the duodenum or to be delayed in release. A variety of materials can be used for such enteric layers or coatings, such materials including a number of polymeric acids and mixtures of polymeric acids with such materials as shellac, cetyl alcohol, and cellulose acetate. 
     The liquid forms in which the novel compositions of the present invention may be incorporated for administration orally or by injection include aqueous solutions, suitably flavored syrups, aqueous or oil suspensions, and flavored emulsions with edible oils such as corn oil, cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as elixirs and similar pharmaceutical vehicles. 
     Compositions for inhalation or insufflation include solutions and suspensions in pharmaceutically acceptable, aqueous or organic solvents, or mixtures thereof, and powders. The liquid or solid compositions may contain suitable pharmaceutically acceptable excipients as described supra. Preferably the compositions are administered by the oral or nasal respiratory route for local or systemic effect. Compositions in preferably pharmaceutically acceptable solvents may be nebulized by use of inert gases. Nebulized solutions may be inhaled directly from the nebulizing device or the nebulizing device may be attached to a face mask tent, or intermittent positive pressure breathing machine. Solution, suspension, or powder compositions may be administered, preferably orally or nasally, from devices which deliver the formulation in an appropriate manner. 
     The following formulation examples illustrate representative pharmaceutical compositions of the present invention. 
     FORMULATION EXAMPLE 1 
     Hard gelatin capsules containing the following ingredients are prepared: 
     
       
         
               
               
               
             
               
               
               
             
           
               
                   
                   
               
               
                   
                   
                 Quantity 
               
               
                   
                 Ingredient 
                 (mg/capsule) 
               
               
                   
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 Active Ingredient 
                 30.0 
               
               
                   
                 Starch 
                 305.0 
               
               
                   
                 Magnesium stearate 
                 5.0 
               
               
                   
                   
               
             
          
         
       
     
     The above ingredients are mixed and filled into hard gelatin capsules in 340 mg quantities. 
     FORMULATION EXAMPLE 2 
     A tablet formula is prepared using the ingredients below: 
     
       
         
               
               
               
             
               
               
               
             
           
               
                   
                   
               
               
                   
                   
                 Quantity 
               
               
                   
                 Ingredient 
                 (mg/tablet) 
               
               
                   
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 Active Ingredient 
                 25.0 
               
               
                   
                 Cellulose, microcrystalline 
                 200.0 
               
               
                   
                 Colloidal silicon dioxide 
                 10.0 
               
               
                   
                 Stearic acid 
                 5.0 
               
               
                   
                   
               
             
          
         
       
     
     The components are blended and compressed to form tablets, each weighing 240 mg. 
     FORMULATION EXAMPLE 3 
     A dry powder inhaler formulation is prepared containing the following components: 
     
       
         
               
               
               
             
           
               
                   
                   
               
               
                   
                 Ingredient 
                 Weight % 
               
               
                   
                   
               
             
             
               
                   
                 Active Ingredient 
                 5 
               
               
                   
                 Lactose 
                 95 
               
               
                   
                   
               
             
          
         
       
     
     The active ingredient is mixed with the lactose and the mixture is added to a dry powder inhaling appliance. 
     FORMULATION EXAMPLE 4 
     Tablets, each containing 30 mg of active ingredient, are prepared as follows: 
     
       
         
               
               
               
             
           
               
                   
                   
               
               
                   
                   
                 Quantity 
               
               
                   
                 Ingredient 
                 (mg/tablet) 
               
               
                   
                   
               
             
             
               
                   
                 Active Ingredient 
                 30.0 mg 
               
               
                   
                 Starch 
                 45.0 mg 
               
               
                   
                 Microcrystalline cellulose 
                 35.0 mg 
               
               
                   
                 Polyvinylpyrrolidone 
                  4.0 mg 
               
               
                   
                 (as 10% solution in sterile water) 
               
               
                   
                 Sodium carboxymethyl starch 
                  4.5 mg 
               
               
                   
                 Magnesium stearate 
                  0.5 mg 
               
               
                   
                 Talc 
                  1.0 mg 
               
               
                   
                 Total 
                  120 mg 
               
               
                   
                   
               
             
          
         
       
     
     The active ingredient, starch and cellulose are passed through a No. 20 mesh U.S. sieve and mixed thoroughly. The solution of polyvinylpyrrolidone is mixed with the resultant powders, which are then passed through a 16 mesh U.S. sieve. The granules so produced are dried at 50° to 60° C. and passed through a 16 mesh U.S. sieve. The sodium carboxymethyl starch, magnesium stearate, and talc, previously passed through a No. 30 mesh U.S. sieve, are then added to the granules which, after mixing, are compressed on a tablet machine to yield tablets each weighing 120 mg. 
     FORMULATION EXAMPLE 5 
     Capsules, each containing 40 mg of medicament are made as follows: 
     
       
         
               
               
               
             
           
               
                   
                   
               
               
                   
                   
                 Quantity 
               
               
                   
                 Ingredient 
                 (mg/capsule) 
               
               
                   
                   
               
             
             
               
                   
                 Active Ingredient 
                  40.0 mg 
               
               
                   
                 Starch 
                 109.0 mg 
               
               
                   
                 Magnesium stearate 
                  1.0 mg 
               
               
                   
                 Total 
                 150.0 mg 
               
               
                   
                   
               
             
          
         
       
     
     The active ingredient, starch, and magnesium stearate are blended, passed through a No. 20 mesh U.S. sieve, and filled into hard gelatin capsules in 150 mg quantities. 
     FORMULATION EXAMPLE 6 
     Suppositories, each containing 25 mg of active ingredient are made as follows: 
     
       
         
               
               
               
             
           
               
                   
                   
               
               
                   
                 Ingredient 
                 Amount 
               
               
                   
                   
               
             
             
               
                   
                 Active Ingredient 
                   25 mg 
               
               
                   
                 Saturated fatty acid glycerides to 
                 2,000 mg 
               
               
                   
                   
               
             
          
         
       
     
     The active ingredient is passed through a No. 60 mesh U.S. sieve and suspended in the saturated fatty acid glycerides previously melted using the minimum heat necessary. The mixture is then poured into a suppository mold of nominal 2.0 g capacity and allowed to cool. 
     FORMULATION EXAMPLE 7 
     Suspensions, each containing 50 mg of medicament per 5.0 mL dose are made as follows: 
     
       
         
               
               
               
             
               
               
               
               
             
               
               
               
             
               
               
               
               
             
           
               
                   
                   
               
               
                   
                 Ingredient 
                 Amount 
               
               
                   
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 Active Ingredient 
                 50.0 
                 mg 
               
               
                   
                 Xanthan gum 
                 4.0 
                 mg 
               
               
                   
                 Sodium carboxymethyl cellulose (11%) 
                 50.0 
                 mg 
               
               
                   
                 Microcrystalline cellulose (89%) 
               
               
                   
                 Sucrose 
                 1.75 
                 g 
               
               
                   
                 Sodium benzoate 
                 10.0 
                 mg 
               
             
          
           
               
                   
                 Flavor and Color 
                 q.v. 
               
             
          
           
               
                   
                 Purified water to 
                 5.0 
                 mL 
               
               
                   
                   
               
             
          
         
       
     
     The active ingredient, sucrose and xanthan gum are blended, passed through a No. 10 mesh U.S. sieve, and then mixed with a previously made solution of the microcrystalline cellulose and sodium carboxymethyl cellulose in water. The sodium benzoate, flavor, and color are diluted with some of the water and added with stirring. Sufficient water is then added to produce the required volume. 
     FORMULATION EXAMPLE 8 
     
       
         
               
               
               
             
           
               
                   
                   
               
               
                   
                   
                 Quantity 
               
               
                   
                 Ingredient 
                 (mg/capsule) 
               
               
                   
                   
               
             
             
               
                   
                 Active Ingredient 
                  15.0 mg 
               
               
                   
                 Starch 
                 407.0 mg 
               
               
                   
                 Magnesium stearate 
                  3.0 mg 
               
               
                   
                 Total 
                 425.0 mg 
               
               
                   
                   
               
             
          
         
       
     
     The active ingredient, starch, and magnesium stearate are blended, passed through a No. 20 mesh U.S. sieve, and filled into hard gelatin capsules in 425.0 mg quantities. 
     FORMULATION EXAMPLE 9 
     A formulation may be prepared as follows: 
     
       
         
               
               
               
             
               
               
               
               
             
           
               
                   
                   
               
               
                   
                 Ingredient 
                 Quantity 
               
               
                   
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 Active Ingredient 
                 5.0 
                 mg 
               
               
                   
                 Corn Oil 
                 1.0 
                 mL 
               
               
                   
                   
               
             
          
         
       
     
     A topical formulation may be prepared as follows: 
     
       
         
               
               
               
             
               
               
               
               
             
           
               
                   
                   
               
               
                   
                 Ingredient 
                 Quantity 
               
               
                   
                   
               
             
             
               
                   
               
             
          
           
               
                   
                 Active Ingredient 
                 1-10 
                 g 
               
               
                   
                 Emulsifying Wax 
                 30 
                 g 
               
               
                   
                 Liquid Paraffin 
                 20 
                 g 
               
               
                   
                 White Soft Paraffin 
                 to 100 
                 g 
               
               
                   
                   
               
             
          
         
       
     
     The white soft paraffin is heated until molten. The liquid paraffin and emulsifying wax are incorporated and stirred until dissolved. The active ingredient is added and stirring is continued until dispersed. The mixture is then cooled until solid. 
     Another preferred formulation employed in the methods of the present invention employs transdermal delivery devices (“patches”). Such transdermal patches may be used to provide continuous or discontinuous infusion of the antisense oligonucleotides of the present invention in controlled amounts. The construction and use of transdermal patches for the delivery of pharmaceutical agents is well known in the art. See, for example, U.S. Pat. No. 5,023,252 23 , herein incorporated by reference. Such patches may be constructed for continuous, pulsatile, or on demand delivery of pharmaceutical agents. 
     Another preferred method of delivery involves “shotgun” delivery of the naked antisense oligonucleotides across the dermal layer. The delivery of “naked” antisense oligonucleotides is well known in the art. See, for example, Felgner et al., U.S. Pat. No. 5,580,859 24 . It is contemplated that the antisense oligonucleotides may be packaged in a lipid vesicle before “shotgun” delivery of the antisense oligonucleotide. 
     Frequently, it will be desirable or necessary to introduce the pharmaceutical composition to the brain, either directly or indirectly. Direct techniques usually involve placement of a drug delivery catheter into the host&#39;s ventricular system to bypass the blood-brain barrier. One such implantable delivery system used for the transport of biological factors to specific anatomical regions of the body is described in U.S. Pat. No. 5,011,472 25  which is herein incorporated by reference. 
     Indirect techniques, which are generally preferred, usually involve formulating the compositions to provide for drug latentiation by the conversion of hydrophilic drugs into lipid-soluble drugs. Latentiation is generally achieved through blocking of the hydroxy, carbonyl, sulfate, and primary amine groups present on the drug to render the drug more lipid soluble and amenable to transportation across the blood-brain barrier. Alternatively, the delivery of hydrophilic drugs may be enhanced by intra-arterial infusion of hypertonic solutions which can transiently open the blood-brain barrier. 
     Other suitable formulations for use in the present invention can be found in  Remington&#39;s Pharmaceutical Sciences   6 . 
     The antisense oligonucleotides or the pharmaceutical composition comprising the antisense oligonucleotides may be packaged into convenient kits providing the necessary materials packaged into suitable containers. 
     Utility 
     The antisense oligonucleotides of the present invention may be used for a variety of purposes. They may be used to inhibit the expression of the ribonucleotide reductase gene in a microorganism, resulting in the inhibition of growth of that microorganism. They may be used to inhibit the expression of the secA gene in a microorganism, resulting in the inhibition of growth of that microorganism. The oligonucleotides may be used as hybridization probes to detect the presence of the ribonucleotide reductase gene or the secA gene in the microorganism. When so used the oligonucleotides may be labeled with a suitable detectable group (a radioisotope, a ligand, another member of a specific binding pair, for example, biotin). The oligonucleotides may also be used to determine the presence of a particular microorganism in a biological sample. Finally, the oligonucleotides may be used as molecular wight markers. 
     In order to further illustrate the present invention and advantages thereof, the following specific examples are given but are not meant to limit the scope of the claims in any way. 
     EXAMPLES 
     In the examples below, all temperatures are in degrees Celsius (unless otherwise indicated) and all percentages are weight percentages (also unless otherwise indicated). 
     In the examples below, the following abbreviations have the following meanings. If an abbreviation is not defined, it has its generally accepted meaning: 
     μM=micromolar 
     mM=millimolar 
     M=molar 
     ml=milliliter 
     μl=microliter 
     mg=milligram 
     μg=microgram 
     IPTG=isopropyl-β-D-thiogalactoside 
     PAGE=polyacrylamide gel electrophoresis 
     PVDF=polyvinylidene difluoride 
     rpm=revolutions per minute 
     OD=optical density 
     CFU=colony forming units 
     ΔG=free energy, a measurement of oligonucleotide duplex stability 
     kcal=kilocalories 
     General Methods in Molecular Biology 
     Standard molecular biology techniques known in the art and not specifically described were generally followed as in Sambrook et al. 18 ; Ausubel et al. 19 ; and Perbal 27 . 
     The antisense oligonucleotides in Tables 1, 2 and 3 were selected from the sequence complementary to the ribonucleotide reductase or secA genes of  E. coli  such that the sequence exhibited the least likelihood of showing one or more of duplex formation, hair-pin formation, and homooligomer/sequence repeats but had a high to moderate potential to bind to the ribonucleotide reductase gene or the secA gene sequence. These properties were determined using the computer modeling program OLIGO Primer Analysis Software, Version 5.0 (distributed by National Biosciences, Inc., Plymouth, Minn.). 
     The antisense oligonucleotides in Table 4 were selected on the basis that the sequence is highly conserved for the secA genes between two or more microbial species. This property was determined using the BLASTN program (Altschul, et al. 16 ) of the University of Wisconsin Computer group (GCG) software (Devereux J. et al. 17 ) with the National Center for Biotechnology Information (NCBI) databases. 
     Phosphorothioate oligonucleotides comprising the desired sequences were specially ordered either from Boston BioSystems, Bedford Mass.; Canadian Life Technologies, Burlington, Canada; Dalton Chemical Laboratories, Inc., North York, Canada; Hybridon, Inc., Milford Mass.; Oligos Etc., or Oligos Therapeutics, Inc., Wilsonvill Oreg.; or TriLink Bio Technologies, San Diego, Calif. Antisense oligonucleotides may also be made by methods known in the art. 
     Polymerase chain reaction (PCR) was carried out generally as in  PCR Protocols: A Guide To Methods And Applications   28 . 
     Example 1 
     Inhibition of Mouse Ribonucleotide Reductase Small Subunit (R2) Expression in  Escherichia coli  by Antisense Oligonucleotide AS-II-626-20 
     Competent BL21 (DE3) cells carrying a plasmid containing the mouse ribonucleotide reductase R2 gene were used. (Mann et al. 34 ) The antisense oligonucleotide, AS-II-626-20, GGCTAAATCGCTCCACCAAG [SEQ ID NO:266] is specifically complementary to the mouse ribonucleotide reductase R2 gene. Approximately 10 10  bacteria/ml were electroporated using a Cell Porator (Gibco BRL, Burlington, Canada) in micro electro-chambers (0.4 cm between the electrodes) at a pulse of 2.4 kV, 4 kΩ with either 20 μM or 200 μM of antisense oligonucleotide AS-II-626-20, following methods described by the manufacturer (Dower W. J. 29 ; Neuman et; and Taketo, A. 31 ). Control populations were subjected to electroporation but without the antisense oligonucleotide AS-II-626-20. 
     The bacterial cells were then transferred to Luria-Bertani broth (Miller J. H. 32 ) containing 50 μg/ml of ampicillin and 0.4 mM of isopropyl β-D-thiogalactoside (IPTG) (expression inducer) (Horwitz J. P. 33 ) to grow at 30° C. on a shaker at 250 rotations per minute (rpm) for 5 hours. 
     The cells were harvested by centrifugation and treated with 2×sample loading buffer (100 mM Tris[hydroxymethyl′aminomethane, pH 6.8, 200 mM dithiothrietol, 4% sodium dodecyl sulfate, 20% glycerol and 0.015% bromophenol blue) and sonicated (Olsvik, et al. 35 ) for 15 seconds. The supernatants were resolved by polyacrylamide gel electrophoresis (PAGE) (Laemmli U.K. 36 ). 
     The ribonucleotide reductase R2 expression was detected by Western blot. The protein gel was blotted onto polyvinylidene difuoride (PVDF) protein sequencing membrane. (Choy et al. 37 ). The presence of the mouse ribonucleotide reductase was detected with a rabbit anti-mouse R2 subunit antibody (Chan et al. 39 ). The presence of the antibody bound to the ribonucleotide reducatase was detected using a second goat anti-rabbit immunoglobulin linked with horseradish peroxidase (Amersham Life Sciences, Oakville Canada). 
     The upper panel of FIG. 14 is a photograph of the Western Blot results. The lower panel of FIG. 14 is a photograph of the membrane stained with India ink to indicate the level of protein loaded in each lane. 
     It is clear that administration of either 20 μM or 200 μM AS-II-626-20 resulted in a marked reduction of mouse ribonucleotide reductase gene expression in the  E. coli  cells. 
     Example 2 
     Inhibition of Bacteria  Escherichia coli  K12 Growth by Antisense Oligonucleotides ER1-169 and ER2-724 Targeting  E. coli  Ribonucleotide Reductase Large Subunit (R1) and Small Subunit (R2) 
       E. coli  cells were electroporated by the method set forth in Example 1 with ER1-169 [SEQ ID NO:22] or ER2-724 [SEQ ID NO:145] at the concentrations shown in FIG. 15, while the control cells received oligonucleotide AS-II-626-20 [SEQ ID NO:266] (targeting mouse ribonucleotide reductase small subunit). 
     The  E. coli  cells were then transferred to fresh Luria-Bertani broth (Miller J. H. 32 ) to grow at 30° C. on a shaker at 250 rpm for 3 hours. The flasks for the test and the control each contained the same number of bacteria per ml at the start of the experiment. The optical density at 590 nm (OD 590 ) of the cultures was measured at the start and at the end of the 3 hours. The inhibition of  E. coli  growth was calculated by comparing the increase in OD 590  values at the start and the end of the 3 hours of the oligonucleotide-treated cultures to the increase of the control cultures at the start and at the end of the 3 hours. (Carpentier P.L. 40 ) 
     The results indicate that ER1-169 [SEQ ID NO:22] and ER2-724 [SEQ ID NO:145] inhibited the growth of  E. coli.    
     Example 3 
     Killing of  Escherichia coli  K12 by Antisense Oligonucleotides Targeting the Ribonucleotide Reductase Large Subunit (R1) or the Small Subunit (R2) 
       E. coli  cells (approximately 2×10 9  were incubated with 20 μM of each of the phosphorothioate oligonucleotides set forth in FIG. 12 on ice for 45 minutes. A control without oligonucleotides was also incubated for each experiment. Cells were heat shocked by placing them in a 42° C. bath for 45 seconds. (Sambrook J. et al. 18 ) 
     Luria-Bertani (LB) broth (Miller J. H. 32  ) was added and the samples were incubated at room temperature for 30 minutes. Dilutions of treated and untreated bacteria were incubated overnight at 37° C. on culture plates containing LB medium, and the number of colonies was counted. 
     The number of killed bacteria was calculated by subtracting the surviving colony forming units (CFU/ml) of the oligonucleotide-treated bacteria from the CFU/ml of the control. FIG. 16 shows the number of bacteria killed by treatment with the antisense sequences: ER1-640 [SEQ ID NO:43]; ER1-1059 [SEQ ID NO:62]; ER1-1320 [SEQ ID NO:75]; ER1-1315 [SEQ ID NO:74]; ER1-1326 [SEQ ID NO:76]; ER2-704 [SEQ ID NO:143] and ER2-983 [SEQ ID NO:152]. 
     The results from FIG. 16 show that antisense oligonucleotides complementary to either the R1 or R2 subunit of ribonucleotide reductase are effective as anti-bacterial agents. 
     Example 4 
     Inhibition of the secA Protein Expression in  Escherichia coli  Following Treatment with Antisense Phosphorothioate Oligonucleotides 
       E. coli  cells were heat shock transformed by the method set forth in Example 3 above with the 80 μM of each of the antisense phosphorothioate oligonucleotides set forth in FIG.  17 . 
     Luria-Bertani broth was then added to the treated  E. coli  cells and they were allowed to grow at 30° C. on a shaker at 250 rpm for 3 hours. 
     Approximately the same quantity of treated and untreated bacteria, based on optical density, were washed in phosphate buffered saline, suspended in 2×Laemmli sample buffer (Laemmli U. K. 36 ), heated for 5 minutes at 95° C. and subjected to SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). 
     The gel was blotted onto polyvinylidene difluoride protein sequencing membrane by the methods set forth in Example 1. A rabbit polyclonal SecA antiserum (der Blaauwen et al. 6 ) was used to detect the expression of the  E. coli  secA gene. The presence of bound rabbit antibody was detected using a goat anti-rabbit immunoglobulin (Amersham Life Sciences, Oakville, Canada). 
     FIG. 17 is a photograph of the Western Blot of  E. coli  cells treated with oligonucleotides ES799 [SEQ ID NO:195] (lane 1); ES1845 [SEQ ID NO:235] (lane 2); and the control (lane 3). When compared to the control, lane 3, the ES799 [SEQ ID NO:195] and ES1845 [SEQ ID NO:235] oligonucleotides clearly decreased the SecA protein levels in the treated  E. coli  cells. The top band in the FIG. 17 represents SecA. Non-specific background bands appear below the SecA protein band. 
     It has been found that the antisense oligonucleotides are effective inhibitors of SecA expression in  E. coli.    
     Example 5 
     Killing of  Escherichia coli  K12 by Antisense secA Oligonucleotides 
       E. coli  cells were heat shock transformed by the method described in Example 3 above with either 100 μM or 20 μM of the antisense phosphorothioate oligonucleotides set forth in FIGS. 18 a  and  18 b 
     Luria-Bertani (LB) broth (Miller J. H. 32 ) was added and the bacterial samples were incubated at room temperature for 30 minutes. Dilutions of treated and untreated bacteria were incubated overnight at 37° C. on culture plates containing LB medium, and the number of colonies was counted. 
     The number of killed bacteria was calculated by subtracting the surviving colony forming units (CFU/ml) of the oligonucleotide-treated bacteria from the CFU/ml of the control. FIGS. 18 a  and  18   b  show the number of bacteria killed by treatment with the various antisense sequences. Accordingly, antisense oligonucleotides complementary to the secA gene act to inhibit the growth of  E. coli.    
     Example 6 
     Effect of Antisense Oligonucleotides on  Escherichia coli  K12 Growth 
       E. coli  cells were heat shock transformed by the method described in Example 3 with either 16 μM, 20 μM or 80 μM of each of the antisense phosphorothioate oligonucleotides set forth in FIGS. 19 a-g.    
     Equal numbers of the treated  E. coli  cells were then transferred to flasks containing fresh Luria-Bertani broth to grow at 30° C. on a shaker at 250 rpm. The number of bacteria per flask was determined by the turbidity of the cultures at OD 620  taken each hour (Carpentier P.L. 40 ). 
     FIGS. 19 a-g  show the rate of growth of the  E. coli  in each of the flasks after treatment with the various oligonucleotides. When growth curves of the treated and untreated cultures were statistically analyzed, the growth of the antisense treated cultures was found to be significantly inhibited when compared to the control cultures. The statistical p values are found in the FIGURES. 
     
       
         
           
             265 
           
           
             1 
             2286 
             DNA 
             Escherichia coli 
           
            1
atgaatcaga atctgctggt gacaaagcgc gacggtagca cagagcgcat caatctcgac     60
aaaatccatc gcgttctgga ttgggcggca gaaggactgc ataacgtttc gatttcccag    120
gtcgagctgc gctcccacat tcagttttat gacggtatca agacctctga catccacgaa    180
accattatca aggctgccgc agacctgatc tcccgtgatg cgccggatta tcagtatctc    240
gccgcgcgcc tggcgatctt ccacctgcgt aaaaaagcct acggccagtt tgagccgcct    300
gcgctgtacg accacgtggt gaaaatggtc gagatgggca aatacgataa tcatctgctg    360
gaagactaca cggaagaaga gttcaagcag atggacacct ttatcgatca cgaccgtgat    420
atgaccttct cttatgctgc cgttaagcag ctggaaggca aatatctggt acagaaccgc    480
gtgaccggcg aaatctatga gagcgcccag ttcctttata ttctagttgc cgcgtgcttg    540
ttctcgaact acccgcgtga aacgcgcctg caatatgtga agcgttttta cgacgcggtt    600
tccacattta aaatttcgct gccgacgcca atcatgtccg gcgtgcgtac cccgactcgt    660
cagttcagct cctgcgtact gatcgagtgc ggtgacagcc tggattccat caacgccacc    720
tccagcgcga ttgttaaata cgtttcccag cgtgccggga tcggcatcaa cgccgggcgt    780
attcgtgcgc tgggtagccc gattcgcggt ggtgaagcgt tccataccgg ctgcattccg    840
ttctacaaac atttccagac agcggtgaaa tcctgctctc agggcggtgt gcgcggcggt    900
gcggcaacgc tgttctaccc gatgtggcat ctggaagtgg aaagcctgct ggtgttgaaa    960
aacaaccgtg gtgtggaagg caaccgcgtg cgtcatatgg actacggggt acaaatcaac   1020
aaactgatgt atacccgtct gctgaaaggt gaagatatca ccctgttcag cccgtccgac   1080
gtaccggggc tgtacgacgc gttcttcgcc gatcaggaag agtttgaacg tctgtatacc   1140
aaatatgaga aagacgacag catccgcaag cagcgtgtga aagccgttga gctgttctcg   1200
ctgatgatgc aggaacgtgc gtctaccggt cgtatctata ttcagaacgt tgaccactgc   1260
aatacccata gcccgtttga tccggccatc gcgccagtgc gtcagtctaa cctgtgcctg   1320
gagatagccc tgccgaccaa accgctgaac gacgtcaacg acgagaacgg tgaaatcgcg   1380
ctgtgtacgc tgtctgcttt caacctgggc gcaattaata acctggatga actggaagag   1440
ctggcaattc tggcggttcg tgcacttgac gcgctgctgg attatcagga ttacccgatc   1500
ccggccgcca aacgtggagc gatgggtcgt cgtacgctgg gtattggtgt gatcaacttc   1560
gcttactacc tggcgaacga cggtaaacgc tactccgacg gcagcgccaa caacctgacg   1620
cataaaacct tcgaagccat tcagtattac ctgctgaaag cctctaatga gctggcgaaa   1680
gagcaaggcg cgtgcccgtg gtttaacgaa accacttacg cgaaagggat cctgccgatc   1740
gatacctata agaaagatct ggataccatc gctaatgagc cgctgcatta cgactgggaa   1800
gctctgcgtg agtcaatcaa aacgcacggt ctgcgtaact ccacgctttc tgctctgatg   1860
ccgtccgaga cttcttcgca gatctctaac gccactaacg gtattgaacc gccgcgcggt   1920
tacgtcagca tcaaagcgtc gaaagacggt attttgcgcc aggtggtgcc ggactacgag   1980
cacctgcacg acgcctatga gctgctgtgg gaaatgccgg gtaacgatgg ttatctgcaa   2040
ctggtgggta tcatgcagaa atttatcgat cagtcgatct ctgccaacac caactacgat   2100
ccgtcacgct tcccgtcagg aaaagtgccg atgcagcagt tgctgaaaga cctgctcacc   2160
gcctacaaat tcggggtcaa aacactgtat tatcagaaca cccgtgacgg cgctgaagac   2220
gcacaagacg atctggtgcc gtcaatccag gacgatggct gcgaaagcgg cgcatgtaag   2280
atctga                                                              2286
 
           
             2 
             1560 
             DNA 
             Escherichia coli 
           
            2
ctggtgccgt caatccagga cgatggctgc gaaagcggcg catgtaagat ctgatattga     60
gatgccggat gcggcgtaaa cgccttatcc ggcctacggc tcggtttgta ggcctgataa    120
gacgcgccag cgtcgcatca ggctccgggt gccggatgca gcgtgaacgc cttatccggc    180
ctacggctcg gatttgtagg cctgataaga cgcgccagcg tcgcatcagg cacaggatgc    240
ggcgtaaaat gccttatccg gcattaaact cccaacagga cacactcatg gcatatacca    300
ccttttcaca gacgaaaaat gatcagctca aagaaccgat gttctttggt cagccggtca    360
acgtggctcg ctacgatcag caaaaatatg acatcttcga aaagctgatc gaaaagcagc    420
tctctttctt ctggcgtccg gaagaagttg acgtctcccg cgaccgtata gattaccagg    480
cgctgccgga gcacgaaaaa cacatcttta tcagcaacct gaaatatcag acgctgctgg    540
attccattca gggtcgtagc ccgaacgtgg cgctattgcc gcttatttct attccggaac    600
tggaaacctg ggtcgaaacc tgggcgttct cagaaacgat tcattcccgt tcctatactc    660
atatcattcg taatatcgtt aacgatccgt ctgttgtgtt tgacgatatc gtcaccaacg    720
agcagatcca gaaacgtgcg gaagggatct ccagctatta cgatgagctg atcgaaatga    780
ccagctactg gcatctgctg ggcgaaggta cccacaccgt taacggtaaa actgtgaccg    840
ttagcctgcg cgagctgaag aaaaaactgt atctctgcct gatgagcgtt aacgcgctgg    900
aagcgattcg tttctacgtc agctttgctt gttccttcgc atttgcagaa cgcgaattga    960
tggaaggcaa cgccaaaatt attcgcctga ttgcccgcga cgaagccctg cacctgaccg   1020
gcacccagca tatgctgaat ctgctgcgca gcggcgcgga cgatcctgag atggcggaaa   1080
ttgccgaaga gtgtaagcag gagtgctatg acctgtttgt tcaggcagct caacaggaga   1140
aagactgggc ggattatctg ttccgcgacg gttcgatgat tggtctgaat aaagacattc   1200
tctgccagta cgttgaatac atcaccaata tccgtatgca ggcagtcggt ttggatctgc   1260
cgttccagac gcgctccaac ccgatcccgt ggatcaacac ttggctggtg tctgataacg   1320
tgcaggttgc tccgcaggaa gtggaagtca gttcttatct ggtcgggcag attgactcgg   1380
aagtggacac cgacgatttg agtaacttcc agctctgatg gcccgcgtta ccctgcgcat   1440
cactggcaca caactgctgt gccaggatga acacccttcc cttctggcgg cgctggaatc   1500
ccacaatgtg gcggttgagt accagtgtcg cgaaggttac tgcggctcct gtcgcacacg   1560
 
           
             3 
             4594 
             DNA 
             Salmonella typhimurium 
           
            3
gtgaacgtcg atctggtgcc ggatgcagcg gatacgctcc gggcgcaagg atttcgtcaa     60
ttaccggtgg tgatggcggg cgatttgagc tggtctggct tccgcccgga catgattaac    120
cgtctgcacc cgacacccca cgcggcaaac gcatgagcgc gctcgtctac ttctccagca    180
gctctgaaaa tacgcaccgc tttatgcagc gtctggggct gcctgccacg cgtattccgc    240
tcaatgagcg ggagcgaatt caggtagacg aaccgtacat tctggttgtg ccgtcatacg    300
gcggcggcgg gatggccggt gcggtgccgc gacaggtgat ccgcttttta aatgatgaac    360
acaaccgggc gcgcattcgc ggcgttatcg cctccggtaa tcgcaatttc ggcgatgcct    420
ggggatgcgc tggcgatgtg atagcacaaa aatgcggcgt cccctggctg taccgctttg    480
agctcatggg cacacaacgc gacatcgata atgtccgaaa aggagtaaat gaattttggc    540
aacaactacc ccggagcgcg taatgcagga aaccatggat taccacgccc tgaacgcgat    600
gctgaatctt tacgataaag caggccatat tcagttcgac aaggaccagc aggcgatcga    660
cgccttcttt gccacccacg tccgcccgca ttccgtgacg tttgccagcc agcatgaacg    720
tctggggacg ctggttcggg aagggtatta cgatgacgcc gtcctcgcgc gttacgaccg    780
cgccttcgtc cttcgcctgt tcgagcacgc ccatgccagc ggctttcgct tccagacgtt    840
tcttggcgcc tggaagttct ataccagtta cacgctgaaa accttcgacg gcaaacgtta    900
tctggaacac tttgaagatc gggtgacaat ggtggcgttg acgctggcgc agggtgacga    960
aacgctggcc acccaactga ccgatgaaat gctttctggt cgctttcagc ccgctacccc   1020
gactttttta aattgcggca aacagcagcg tggggaactg gtctcctgct tcctgctccg   1080
tatcgaagac aacatggagt cgatcgggcg ggcggtgaat tcggcgctgc aactctccaa   1140
acgcggcggc ggcgtcgcgt ttttactctc caatctgcgc gaggcgggcg cgccgatcaa   1200
acgcattgag aatcagtctt ccggcgtgat cccggtgatg aaaatgctgg aagacgcgtt   1260
ttcgtatgcc aaccaacttg gcgcgcgcca gggggccggc gcggtttatc tccatgcgca   1320
ccatccggat attctgcgtt ttctggatac caaacgagaa aacgctgacg aaaaaatccg   1380
gatcaaaacg ctctctctcg gcgtggtgat cccggatatc accttccggc tggcgaaaga   1440
aaacgcgcaa atggcgctct tttcgcccta tgacatacaa cgacgctacg gcaaaccgtt   1500
tggcgatatc gccattagcg aacggtacga tgaattaatt gccgatccgc acgtgcgcaa   1560
aacctatatt aacgcccgtg acttttttca aacactggcg gagattcagt tcgaatccgg   1620
gtatccctac atcatgtttg aagatacggt aaaccgcgcg aatcccattg ctggtcgcat   1680
taatatgagc aacctgtgct cagaaatttt acaggtcaat agcgcttccc gttacgacga   1740
taaccttgac tatacccaca tcgggcatga catctcctgc aatctcggct cgctgaatat   1800
cgctcacgtc atggattcac cggacattgg ccgtaccgta gaaaccgcta ttcgcggcct   1860
gacggcggtg tcggacatga gccatatacg cagcgtgccc tcaatagccg ccggtaatgc   1920
cgcctctcat gccatcggtc tgggccagat gaatctgcat ggctatctgg cgagggaagg   1980
tattgcctac ggttcgccgg aggcgttgga tttcaccaat ctctattttt acaccattac   2040
ctggcatgcc gtgcatactt caatgcggct agcccgcgaa cgcggcaaaa ccttcgccgg   2100
atttgcgcag tcgcgctatg ccagcggcga ctattttacg cagtatttac aggacgactg   2160
gcaaccgaaa acagcgaaag tcagggcgct atttgcccgc agcggcatta cgctgcccac   2220
acgagaaatg tggctaaagc tgcgcgacga tgtgatgcgc tatggcatct ataaccaaaa   2280
tttgcaggcg gtgccgccga ccggttcgat ttcttacatt aatcatgcga cctccagcat   2340
tcatccgatt gtggccaaaa ttgagattcg caaagagggc aaaaccgggc gtgtgtatta   2400
ccccgcgccg tttatgacca atgaaaacct ggacatgtat caggatgctt acgatatcgg   2460
tccggaaaaa attattgata cctatgccga ggccacgcgc cacgtcgatc aagggctgtc   2520
gctcaccctg tttttccccg ataccgccac gacccgcgat atcaacaagg cgcagatcta   2580
tgcctggcga aaaggtatta agtccctgta ttacatccgg cttcgccagt tggcgctgga   2640
aggtactgaa attgaaggct gcgtatcctg cgcgctataa ggaaagccat atgaaattat   2700
ctcgtattag cgccatcaac tggaacaaga tccaggacga caaagatctg gaggtatgga   2760
accggctgac cagtaacttc tggctgccgg aaaaagtgcc gttatcgaat gatattccgg   2820
cctggcagac gctgagcgcc gccgaacagc agctcaccat tcgcgtgttt acgggactta   2880
cgctgctcga cactatccag aacatcgcag gcgcgccgtc gttaatggca gatgccatca   2940
cgccgcatga agaggcagtg ctgtcgaaca tcagctttat ggaagcggta cacgcccgct   3000
cttacagttc tattttctcc acgctgtgcc agacgaaaga ggttgatgcc gcctacgcct   3060
ggagcgaaga aaacccaccg cttcagcgta aggcgcagat tattttagct cattacgtca   3120
gcgatgaacc gctaaagaaa aagattgcca gcgtcttttt agagtctttt ctgttctatt   3180
ccggcttctg gttgccgatg tatttctcca gccgcggtaa gctcacgaac actgccgacc   3240
tgattcgttt aatcattcgc gatgaagcgg ttcacggtta ttatattggc tataagtatc   3300
agatagcgct acaaaaacta tcggcaatcg agcgtgaaga gttaaagctt ttcgcgctgg   3360
atttgttgat ggaactgtac gacaacgaaa tccgctacac agaagcgtta tatgcggaaa   3420
ccggctgggt taacgacgtc aaagccttct tgtgctacaa cgccaataaa gccttaatga   3480
acctgggtta tgaggcgtta tttccgccgg agatggcaga cgtgaatccc gcaatccttg   3540
ccgcgctctc gccgaatgcc gacgaaaacc atgatttctt ttccggctca ggttcatctt   3600
atgtgatggg gaaaacagtc gaaaccgaag acgaagactg gaatttttaa ccttacgggc   3660
atgggaaata acgttacatt tcccatgcct ttatttcaag caatagggag tcaaatcgcg   3720
caaatattac aacatgtcct acactcaata cgagtgacat tattcacctg gattccccca   3780
attcaggtgg atttttgctg gttgttccaa aaaatatctc ttcctcccca ttcgcgttca   3840
gcccttatat catgggaaat cacagccgat agcacctcgc aatattcatg ccagaagcaa   3900
attcagggtt gtctcagatt ctgagtatgt tagggtagaa aaaggtaact atttctatca   3960
ggtaacatat cgacataagt aaataacagg aatcattcta ttgcatggca attaaattag   4020
aagtgaagaa tctgtataaa atatttggag agcatccgca gcgtgccttc aaatatattg   4080
aaaagggact atcgaaagag caaatactgg aaaaaacggg gctatcgctt ggcgttaaag   4140
acgccagtct ggccattgaa gaaggcgaga tatttgtcat catgggatta tccggctcgg   4200
gtaaatccac aatggtacgc cttctcaatc gcctgattga acccacccgc ggacaggtac   4260
tgattgacgg cgttgatatt gccaaaatat cagacgctga gcttcgcgag gtgcgcagga   4320
aaaagattgc gatggtcttc cagtcatttg cgctcatgcc gcatatgacc gtgctggata   4380
atacggcatt cggtatggaa ttagcgggca tcgcggcgca agagcgtcgc gaaaaagcgc   4440
tggacgcctt gcgtcaggtg gggcttgaga attacgctca cgcctacccg gatgaacttt   4500
ccggtgggat gcgtcagcgt gttgggcttg cccgcgcgct ggcaatcaac cctgatatct   4560
tattaatgga tgaagcgttt tccgccctcg atcc                               4594
 
           
             4 
             1033 
             DNA 
             Lactococcus lactis 
           
            4
gaattcttat tttccctagc tttggattta ttctcacttc ctatgatctt ttattctcga     60
ttattatttt tgctttggca attattatca tttttcgaca taaaacaaac ctcaaaagaa    120
tcaaaaatca ttgtgaatcc cttgtcccct ttggtttaaa cttatcgaga caaaaagaaa    180
aatagcacaa tatattgtgt tgtttttctt tttttacata atttaacact atatctagta    240
tctttaattt gactagatat tttttttacg ctaaataaga ctataaaaac tcgagaaaaa    300
gtcaaggact ttttactccc gtctaaaaaa tatattggcc caaaaggaga tttaaaatgg    360
ttacagttta ttctaaaaac aattgtatgc aatgcaaaat ggtcaaaaaa tggctttctg    420
aacacgaaat tgcatttaac gaaatcaata ttgatgaaca gcctgaattt gtcgaaaaag    480
taattgaaat gggttttcga gctgctcctg taatcacaaa agatgatttc gccttttctg    540
gtttccgtcc ttctgaatta gcaaagttgg cttaatatga aacttgctta tttcagtgtg    600
actggacaaa cgcgtcgttt tgtttctaaa acagacttgc cgaatgtcga aattacacct    660
gacgatgatt tagagatgga cgagcctttc cttttgataa ctccctctta tgctgaagaa    720
tcaccaaccg tttctaaatc aatagacgtt atggactcgg tttttgactt tatggcttat    780
aatgataatt ataaacattg tcgtggaatt atcggcactg gaaatcgtaa ttttgctggc    840
atctatattt ttaccgctaa agaagtttca gcaaaatatc aaattccact tttatatgat    900
tttgagttta atggtacgcc agctgatgtt gctgctgttg aaaaactcgc tgcacagctt    960
gatcaaggag cgaaagtcac ctttaaaaat ccgctgtgat tttttatggc ttcaccctat   1020
ttgagtgaag ctt                                                      1033
 
           
             5 
             3811 
             DNA 
             Escherichia coli 
           
            5
cagctgtact ggcataacga catttatact gtcgtataaa attcgactgg caaatctggc     60
actctctccg gccaggtgaa ccagtcgttt ttttttgaat tttataagag ctataaaaaa    120
cggtgcgaac gctgttttct taagcacttt tccgcacaac ttatcttcat tcgtgctgtg    180
gactgcaggc tttaatgata agatttgtgc gctaaatacg tttgaatatg atcgggatgg    240
caataacgtg agtggaatac tgacgcgctg gcgacagttt ggtaaacgct acttctggcc    300
gcatctctta ttagggatgg ttgcggcgag tttaggtttg cctgcgctca gcaacgccgc    360
cgaaccaaac gcgcccgcaa aagcgacaac ccgcaaccac gagccttcag ccaaagttaa    420
ctttggtcaa ttggccttgc tggaagcgaa cacacgccgc ccgaattcga actattccgt    480
tgattactgg catcaacatg ccattcgcac ggtaatccgt catctttctt tcgcaatggc    540
accgcaaaca ctgcccgttg ctgaagaatc tttgcctctt caggcgcaac atcttgcatt    600
actggatacg ctcagcgcgc tgctgaccca ggaaggcacg ccgtctgaaa agggttatcg    660
cattgattat gcgcatttta ccccacaagc aaaattcagc acgcccgtct ggataagcca    720
ggcgcaaggc atccgtgctg gccctcaacg cctcacctaa caacaataaa cctttacttc    780
attttattaa ctccgcaacg cggggcgttt gagattttat tatgctaatc aaattgttaa    840
ctaaagtttt cggtagtcgt aacgatcgca ccctgcgccg gatgcgcaaa gtggtcaaca    900
tcatcaatgc catggaaccg gagatggaaa aactctccga cgaagaactg aaagggaaaa    960
ccgcagagtt tcgtgcacgt ctggaaaaag gcgaagtgct ggaaaatctg atcccggaag   1020
ctttcgccgt ggtacgtgag gcaagtaagc gcgtctttgg tatgcgtcac ttcgacgttc   1080
agttactcgg cggtatggtt cttaacgaac gctgcatcgc cgaaatgcgt accggtgaag   1140
gaaaaaccct gaccgcaacc ctccctcctt acctgaacgc actaaccggt aaaggcgtgc   1200
acgtagttac cgtcaacgac tacctggcgc aacgtgacgc cgaaaacaac cgtccgctgt   1260
ttgaattcct tggcctgact gtcggtatca acctgccggg catgccagca ccggcaaagc   1320
gcgaagctta cgcagctgac atcacttacg gtaccaacaa cgaatacggc tttgactacc   1380
tgcgcgacaa catggcgttc agccctgaag aacgtgtaca gcgtaaactg cactatgcgc   1440
tggtggacga agtggactcc atcctgatcg atgaagcgcg tacaccgctg atcatttccg   1500
gcccggcaga agacagctcg gaaatgtata aacgcgtgaa taaaattatt ccgcacctga   1560
tccgtcagga aaaagaagac tccgaaacct tccagggcga aggccacttc tcggtggacg   1620
aaaaatctcg ccaggtgaac ctgaccgaac gtggtctggt gctgattgaa gaactgctgg   1680
tgaaagaggg catcatggat gaaggggagt ctctgtactc tccggccaac atcatgctga   1740
tgcaccacgt aacggcggcg ctgcgcgctc atgcgctgtt tacccgtgac gtcgactaca   1800
tcgttaaaga tggtgaagtt atcatcgttg acgaacacac cggtcgtacc atgcagggcc   1860
gtcgctggtc cgatggtctg caccaggctg tggaagcgaa agaaggtgtg cagatccaga   1920
acgaaaacca aacgctggct tcgatcacct tccagaacta cttccgtctg tatgaaaaac   1980
tggcggggat gaccggtact gctgataccg aagctttcga atttagctca atctacaagc   2040
tggataccgt cgttgttccg accaaccgtc caatgattcg taaagatctg ccggacctgg   2100
tctacatgac tgaagcggaa aaaattcagg cgatcattga agatatcaaa gaacgtactg   2160
cgaaaggcca gccggtgctg gtgggtacta tctccatcga aaaatcggag ctggtgtcaa   2220
acgaactgac caaagccggt attaagcaca acgtcctgaa cgccaaattc cacgccaacg   2280
aagcggcgat tgttgctcag gcaggttatc cggctgcggt gactatcgcg accaatatgg   2340
cgggtcgtgg tacagatatt gtgctcggtg gtagctggca ggcagaagtt gccgcgctgg   2400
aaaatccgac cgcagagcaa attgaaaaaa ttaaagccga ctggcaggta cgtcacgatg   2460
cggtactgga agcaggtggc ctgcatatca tcggtaccga gcgtcacgaa tcccgtcgta   2520
tcgataacca gttgcgcggt cgttctggtc gtcaggggga tgctggttct tcccgtttct   2580
acctgtcgat ggaagatgcg ctgatgcgta tttttgcttc cgaccgagta tccggcatga   2640
tgcgtaaact gggtatgaag ccaggcgaag ccattgaaca cccgtgggtg actaaagcga   2700
ttgccaacgc ccagcgtaaa gttgaaagcc gtaacttcga cattcgtaag caactgctgg   2760
aatatgatga cgtggctaac gatcagcgtc gcgccattta ctcccagcgt aacgaactgt   2820
tggatgtcag cgatgtgagc gaaaccatta acagcattcg tgaagatgtg ttcaaagcga   2880
ccattgatgc ctacattcca ccacagtcgc tggaagaaat gtgggatatt ccggggctgc   2940
aggaacgtct gaagaacgat ttcgacctcg atttgccaat tgccgagtgg ctggataaag   3000
aaccagaact gcatgaagag acgctgcgtg acggcattct ggcgcagtcc atcgaagtgt   3060
atcagcgtaa agaagaagtg gttggtgctg agatgatgcg tcacttcgag aaaggcgtca   3120
tgctgcaaac gcttgactcc ctgtggaaag agcacctggc agcgatggac tatctgcgtc   3180
agggtatcca cctgcgtggc tacgcacaga aagatccgaa gcaggaatac aaacgtgaat   3240
cgttctccat gtttgcagcg atgctggagt cgttgaaata tgaagttatc agtacgctga   3300
gcaaagttca ggtacgtatg cctgaagagg ttgaggagct ggaacaacag cgtcgtatgg   3360
aagccgagcg tttagcgcaa atgcagcagc ttagccatca ggatgacgac tctgcagccg   3420
cagctgcact ggcggcgcaa accggagagc gcaaagtagg acgtaacgat ccttgcccgt   3480
gcggttctgg taaaaaatac aagcagtgcc atggccgcct gcaataaaag ctaactgttg   3540
aagtaaaagg cgcaggattc tgcgcctttt ttataggttt aagacaatga aaaagctgca   3600
aattgcggta ggtattattc gcaacgagaa caatgaaatc tttataacgc gtcgcgcagc   3660
agatgcgcac atggcgaata aactggagtt tcccggcggt aaaattgaaa tgggtgaaac   3720
gccggaacag gcggtggtgc gtgaacttca ggaagaagtc gggattaccc cccaacattt   3780
ttcgctattt gaaaaactgg aatatgaatt c                                  3811
 
           
             6 
             4045 
             DNA 
             Mycobacterium bovis 
           
            6
gatctacggc agaactcgtc gcttggagcg ttcgaccgac catctacctg ttcgacgtcg     60
aactcgacca ctgaacgtaa tcgccgccag cgcaagtcct gtcagcgcgt ggagatcacc    120
gcgcgtgggc gagggccggt ggtgcgaggt gaggcctgcg ccgacagctt ctatgccgcg    180
cttgaatcag cggtcgtcaa actggagagc gtgcgccgcg gtaaggatcg ccgcaaggtg    240
cactacggcg acaaaacccc ggtttcgctg gccgaggcga ccgcggtggt gccagcgccg    300
gagaacggct tcaacaccag accagccgag gcacacgatc acgacggtgc cgtcgtcgag    360
cgggagcctg ggcggatcgt tcgcaccaaa gaacacccgg ccaagccgat gtcggtcgat    420
gacgcgctct accagatgga gctggttgga cacgacttct tcttgttcta cgacaaggac    480
accgaacggc cgtcggtggt ctaccgccgg cacgcctacg actacggctt gatccgtctg    540
gcgtgatcgg cggcgcgcgc cgctcgtcac ctaccatggg agtcgcctta tctaaagact    600
cctacacatg cggggacata gctgtgctgt cgaagttgct gcgccttggc gaaggtcgca    660
tggtcaagcg cctcaagaag gtggcggact atgtcggcac tttgtccgac gatgtcgaga    720
aactcaccga cgccgagctg agggcgaaaa ccgacgagtt caagcggcgg ctggccgacc    780
agaaaaaccc agaaaccctc gacgacctgt tgcccgaggc cttcgccgtg gcccgcgagg    840
ccgcctggcg ggtgctggac cagcggccgt tcgacgtgca ggtgatgggt gcggccgccc    900
tgcacctggg caacgttgcc gagatgaaga ccggtgaagg caagaccctg acctgtgtgt    960
tgcccgctta cctcaatgcg ctggccggca acggcgtgca catcgtcacc gtcaacgact   1020
acctggctaa acgcgacagt gagtggatgg gccgcgtgca ccgcttcctc gggcttcagg   1080
tcggggtgat tttcgccacc atgacacccg atgaacgccg ggtggcctat aacgccgaca   1140
tcacctacgg caccaataac gagtttgggt tcgactacct gcgcgacaac atggcgcact   1200
cactggatga tctggtgcag cgcgggcacc attacgccat tgtcgacgag gtcgattcca   1260
tcctgatcga cgaggcccgc accccgctga tcatctccgg tcccgccgac ggcctccaac   1320
tggtacaccg agttcgccgg ttggcgccgc tgatggaaaa ggacgtccac tacgaggtcg   1380
atctacgcaa acgcaccgtc ggcgtgcacg agaagggtgt ggaattcgtc gaagaccagc   1440
tcggcatcga caacctgtac gaggccgcca actcgccgtt ggtcagctat ctcaacaacg   1500
ctctgaaggc caaagagctg ttcagccgcg acaaggacta catcgtccgc gatggtgagg   1560
tgctcatcgt cgacgagttc accggccggg tgctgatcgg ccgccgctac aacgagggca   1620
tcgaccaggc catcgaggcc aaggagcacg tcgagatcaa ggccgagaac cagacgctgg   1680
ccaccatcac gctgcagaac tacttccggc tctacgacaa gctcgccggc atgaccggca   1740
ccgcccagac ggaggcggcc gagctgcacg agatctacaa gctgggcgtg gtcagcatcc   1800
cgaccaacat gccgatgatc cgtgaagacc agtccgacct gatctacaag accgaggagg   1860
ccaagtacat cgcggtggtc gacgacgtcg ccgagcgcta cgcgaaggga cagccggtgc   1920
tgatcggcac caccagcgtg gagcgctcgg agtatctgtc gcggcagttc accaagcggc   1980
gcatcccgca caatgtgctc aacgccaagt accacgagca agaggcgacc atcatcgcgg   2040
tggcgggccg ccgcggcggc gtcaccgtcg ccaccaacat ggccggtcgc ggcaccgaca   2100
ttgtgctggg cggcaacgtc gactttctca ccgatcagcg gctgcgcgaa cggcctggat   2160
ccggtggaga cgcccgagga gtacgaggcg gcctggcact ccgaactgcc catcgtcaaa   2220
gaggaagcca gcaaggaggc caaggaagta atcgaggccg gcggctgtac gtgctgggca   2280
ccgagcggcc acgagtcgcg gcggatcgac aaccagttgc gtggccggtc cggccgccag   2340
gggaccccgg ggagtcgcgc ttctatttgt cgctgggtga cgagctgatg cgccgcttca   2400
atggcgcggc cttggagacc ttgttgacca ggctgaacct gcccgacgac gtgccgatcg   2460
aagccaagat ggtcacccgg gccatcaaga gcgcccagac ccaggtcgag cagcagaact   2520
ttgaggtccg caagaacgtc ctcaaatacg acgaggtgat gaaccagcag cgcaaggtca   2580
tctacgccga gcgccggcgc atcctcgaag gcgaaaacct caaggaccag gcgctggaca   2640
tggtccgcga tgtcatcacc gcctacgtcg acggcgcgac cggcgaaggc tatgccgaag   2700
attgggatct ggacgcgttg tggacggcac tcaaaaccct ctatccggag gggatcaccg   2760
ccgactcgct gacccgcaag gaccacgaat tcgagcgcga cgatctcacc cgcgaggagt   2820
tgctggaggc actactcaag gacgccgaac gtgcctatgc cgcacgggaa gccgaactcg   2880
aggaaatcgc cggcgagggt gcgatgcgcc agctggaacg caacgtgctg ctcaacgtca   2940
tagaccgtaa gtggcgtgaa cacctctacg agatggacta cctcaaggag ggtatcgggc   3000
tgcgcgcgat ggcgcacggc gatccgttgg tcgagtacca gcgtgagggc tacgacatgt   3060
tcatggccat gctcgacggc atgaaagagg aatcggtcgg cttcctgttc aacgtcaccg   3120
tggaggcggt ccccgccccg ccggttgccc cggctgccga acccgcagag cttgccgaat   3180
tcgccgccgc ggccgcagcc gcgggcagca acgcagcgcg gtcgatggtg gcgcgcgcga   3240
aagagctcca agtgcattac gcgccaaggg tgttgccagc gagtcgcccg ctttgaccta   3300
ttccggtccc gcggaggatg gctcggctca ggtgcagcgc aacggcggtg gagcccacaa   3360
gacgccggcc ggagtgccgg ccggtgctag ccggcgcgag cggcgcgaac gcgcccgccg   3420
acaaggccgc ggcgccaagc cgccgaaatc ggtcaagaag cgttagcgcg taggttgcag   3480
atgggtgtat cggtttctca gttcccagaa gtcacttccc ggcacacccc ggccccggcg   3540
cgcatgcaca tttcgttgca cggcgggcaa ggggttcgct aatctcaccc gttcgtcgac   3600
cttcgtcggc gtcggttctg ctggtagcgg ggttcggcgc tttcctggcg tttctcgact   3660
cgacaatcgt caacatcgcg ttcccggata tccagcgttc cttcccgtcc tacgacatcg   3720
ggagcctgtc ctggattctg aacggctata acatgctctt cgccgccttc atggttgcgg   3780
ccggcaggtt ggccgatttg ctgggccgca gacgacattc ctgtccggtg tgctggtgtt   3840
caccattgcg tccgggctgt gcgccgtcgc cggcagtgtc gagcagttgg tggcgttccg   3900
ggtgctgcag ggcatcgggg ctgcgatact cgtgcctcgt tcgctcgcac tggtcgttga   3960
gggcttcgac cgggccgccg cgcgcacgct atcggcctgt ggggtgcggc ggcagcgatc   4020
cactagttct agagcggcgc accgc                                         4045
 
           
             7 
             1433 
             DNA 
             Mycobacterium tuberculosis 
           
            7
tcaaacacca gaccagaagg aggcaacacg atcacggacg gtgccgttcg tcgagcggga     60
gcctggggcg gatcgttcgc accaaagaac aacccggcca cgccgatgtc ggtcgatgac    120
gcgctctacc agatggagct ggttggacac gacttcttct tgttctacga caaggacacc    180
gaacggccgt cggtggtcta ccgccggcac gcctacgact acggcttgat ccgtctggcg    240
tcatcggcgg cgcgcgccgc gtcgtcacct accatgggag tcgccttatc taaagactcc    300
tacacatgcg gggacatagc tgtgctgtcg aagttgctgc gccttggcga aggtcgcatg    360
gtcaagcgcc tcaagaaggt ggccgactat gtcggcactt tgtccgacga tgtcgagaaa    420
ctcaccgacg ccgagctgag ggcgaaaacc gacgagttca agcaggctgg ccgaccagaa    480
aaacccagaa accctcgacg acctgttgcc cgaggccttc accgtgcccc gcgagacccg    540
cctgccgggt gctggaccaa cgaccgttcg acgtgcaggt gatgggtacg accgccctgc    600
acctgggcga cgttgccgag atgtagaccg gtgaaggcaa gaccctgacc tgtgttttac    660
ccgcttacct caatgccctg gccgccaacg gcgtgcacgt agttaccgtc aacgactacc    720
tggctaaacg cgacagtgag tggatgggcc gcgtgcaccg cttcctcggg cttcaggtcg    780
gggtgatttt ggccaccatg acacccgatg aacgccgggt ggcctataac gccgacatca    840
cctacggcac caataacgag tttgggttcg actacctgcg cgacaacatg gcgcactcac    900
tggatgatct ggtgcagcgc gggcaccatt acgccattgt cgacgaaggt cgattccatc    960
ctgatcgacg agggcggggc ccccccccca tctccgcccg gggcgcccgc ctccaactgg   1020
ttcaccgagt tcgcccggtt ggcgtgccgc ggctggtttt ggacgtccac tacgaggtcg   1080
atctacgcaa acgcaccgtc ggcgtgcacg agaagggtgt ggaattcgtc gaagaccagc   1140
tcggcatcga caacctgtac gagaccgcca actcgccgtt ggtcagctat ctcaacaacg   1200
ctctgaaggc caaagagctg ttcagccgcg acaaggacta catcgtccgc gatggtgagg   1260
tgctcatcgt cgacgagttc accggccggg tgctgatcgg ccgccgctac aacgagggca   1320
tgcaccaggc catcgaggcc aaggagcacg tcgagatcaa ggccgagaac cagacgctgg   1380
ccaccatcac gctgcagaac tacttccggc tctaggagaa gctcgccggg atg          1433
 
           
             8 
             3124 
             DNA 
             Staphylococcus aureus 
           
            8
tggcttgatt caaactagtg aacaataaat taagtttaaa gcacttgtgt ttttgcacaa     60
gtttttttat actccaaaag caaattatga ctatttcata gttcgataat gtaatttgtt    120
gaatgaaaca tagtgactat gctaatgtta atggatgtat atatttgaat gttaagttaa    180
taatagtatg tcagtctatt gtatagtccg agtcgaaaat cgtaaaatat ttataatata    240
atttattagg aagtataatt gcgtattgag aatatattta ttagtgataa acttgttgac    300
aacagaatgt gaatgaagta tgtcataaat atatttatat tgattctaca aatgagtaaa    360
taagtataat tttctaacta taaatgataa gatatattgt tgtaggccaa acagtttttt    420
agctaaagga gcgaacgaaa tgggattttt atcaaaaatt cttgatggca ataataaaga    480
aattaaacag ttaggtaaac ttgctgataa agtaatcgct ttagaagaaa aaacggcaat    540
tttaactgat gaagaaattc gtaataaaac gaaacaattc caaacagaat tagctgacat    600
tgataatgtc aaaaagcaaa atgattattt acataaaatt ttaccagaag catatgcact    660
tgttagagaa ggctctaaac gtgtattcaa tatgacacca tataaagttc aaattatggg    720
tggtattgca attcataaag gtgatatcgc tgagatgaga acaggtgaag gtaaaacatt    780
aacagcgaca atgccaacat acttaaatgc attagctggt agaggtgttc acgttattac    840
agtcaatgaa tacttatcaa gtgttcaaag tgaagaaatg gctgagttat ataacttctt    900
aggtttgact gtcggattaa acttaaacag taagacgaca gaggaaaaac gtgaagcata    960
cgcacaagac attacttaca gtactaataa tgagctaggt tttgattact tacgagataa   1020
catggtgaat tattctgaag atagggtaat gcgtccatta cattttgcaa tcattgatga   1080
ggtggactca attttaatcg acgaggcacg tacgccatta attatttctg gtgaagctga   1140
aaagtcaacg tcactttata cacaagcaaa tgtttttgcg aaaatgttaa aacaggacga   1200
tgattataaa tacgatgaaa aaacgaaagc tgtacattta acagaacaag gtgcggataa   1260
agctgaacgt atgttcaaag ttgaaaactt atatgatgta caaaatgttg atgttattag   1320
tcatatcaac acagctttac gtgcgcacgt tacattacaa cgtgacgtag actatatggt   1380
tgttgatggc gaagtattaa ttgtcgatca atttacagga cgtacaatgc caggccgtcg   1440
tttctcggaa ggtttacacc aagctattga agcgaaggaa ggcgttcaaa ttcaaaatga   1500
atctaaaact atggcgtcta ttacattcca aaactatttc agaatgtaca ataaacttgc   1560
gggtatgaca ggtacagcta aaactgaaga agaagaattt agaaatattt ataacatgac   1620
agtaactcaa attccgacaa ataaacctgt gcaacgtaac gataagtctg atttaattta   1680
cattagccaa aaaggtaaat ttgatgcagt agtagaagat gttgttgaaa aacacaaggc   1740
agggcaacca gtgctattag gtactgttgc agttgagact tctgaatata tttcaaattt   1800
acttaaaaaa cgtggtatcc gtcatgatgt gttaaatgcg aaaaatcatg aacgtgaagc   1860
tgaaattgtt gcaggcgctg gacaaaaagg tgccgttact attgccacta acatggctgg   1920
tcggggtaca gatatcaaat taggtgaagg cgtagaggaa ttaggcggtt tagcagtaat   1980
aggtacagag cgacatgaat ctcgtcgtat tgatgaccag ttacgtggtc gttctggacg   2040
tcaaggtgat aaaggggata gtcgcttcta tttatcatta caagatgaat taatgattcg   2100
ttttggttct gaacgtttac agaaaatgat gagccgacta ggtttagatg actctacacc   2160
aattgaatca aaaatggtat caagagctgt tgaatcagca caaaaacgtg tagaaggtaa   2220
taacttcgac gcgcgtaaac gtatcttaga atacgatgaa gtattacgta aacaacgtga   2280
aattatctat aacgaaagaa atagtattat tgatgaagaa gacagctctc aagttgtaga   2340
tgcaatgcta cgttcaacgt tacaacgtag tatcaattac tatattaata cagcagatga   2400
cgagcctgaa tatcaaccat tcatcgacta cattaatgac atcttcttac aagaaggtga   2460
cattacagag gatgatatca aaggtaaaga tgctgaagat attttcgaag tcgtttgggc   2520
taagattgaa gcagcatatc aaagtcaaaa agatatctta gaagaacaaa tgaatgagtt   2580
tgagcgtatg attttacttc gttctattga tagccattgg actgatcata tcgacacaat   2640
ggatcaatta cgtcaaggta ttcacttacg ttcttatgca caacaaaatc cattacgtga   2700
ctatcaaaat gaaggtcatg aattatttga tatcatgatg caaaatattg aagaagatac   2760
ttgtaaattc attttaaaat ctgtagtaca agttgaagat aatattgaac gtgaaaaaac   2820
aacagagttt ggtgaagcga agcacgtttc agctgaagat ggtaaagaaa aagtgaaacc   2880
gaaaccaatc gttaaaggcg atcaagttgg tcgtaacgat gattgtccat gtggtagtgg   2940
taaaaaattc aaaaattgcc atggaaaata aatgatataa aataactcct tccaattaaa   3000
cacctatagt ttgtgttatg ggaggagtct ttttatttta caagcgttaa atactttaaa   3060
aaatgtgaag aagttgttaa acgttgttat gtacttagtt ttaaaaaatc ggtttaggca   3120
tatg                                                                3124
 
           
             9 
             3589 
             DNA 
             Staphylococcus carnosus 
           
            9
cttgaacgtt acttcactaa tgtgccgaat gtgaatgcac atgtaaaagt gaaaacttat     60
gcaaattcta gcacaaaatc gaagttacaa ttccgcttaa tgacgtgaca cttcgtgcag    120
aagaaagaaa cgatgattta tgctggaatt gacaagatca ctaacaaatt agaatgtcaa    180
gttcgtaaat acaaaacacg tgtcaatcgt aagaaacgta aagaaagcga acatgaacca    240
ttcccagcaa ctccggaaac tccgccggaa acagctgttg atcatgataa agatgatgaa    300
attgaaatca tccgttctaa acaattcagc ttgaaaccaa tggattctga agaagcggta    360
ttacaaatgg atttacttgg tactgatttc ttcatcttca atgaccgtga aactgatggt    420
acaagcattg tttaccgccg taaagacgga aaatatggtt tgattgaaac tgttgaaaaa    480
ctaatatgtg atatttgaaa gggctcttgc tgcattttct gctgcaagag tttctttttt    540
tgagaaagcc cttattaaga tttgattaat aaaaatacaa ttgattgatt tacacggggt    600
gtccatgtca aaataagagg gatgtattaa gttcataatt gtaatgtgag ctccgatgag    660
tgagcggcat atgattatga tatccatgtg gcacatgatg ttaacaaaaa gagaatgaaa    720
ctgtgagaag tacatcttga taaacacaac taggcagttt attaaaaaat aatgaacagt    780
atcctatgag tttttaagta taaattaagc catataaatg gtaagataaa ttgttgtaag    840
ccaaacagtt tttataccaa aggagcgaac agaatgggtt ttttaacaaa aattgttgac    900
ggcaataaga gagaaatcaa acgcctaagt aagcaagctg acaaagtaat ctcattagaa    960
gaagaaatgt caattcttac tgatgaagaa attagaaata aaacaaaagc attccaagaa   1020
agattgcaag cagaagaaca tgtaagcaaa caagataaaa ttttagaaga aatattacct   1080
gaagcatttg cgcttgtccg tgaaggagct aaacgtgtat ttaatatgac accttatcca   1140
gttcaaatca tgggtggtat cgccattcat aatggtgaca tttcagaaat gagaacaggt   1200
gaaggtaaaa cattaactgc aacgatgccg acttatttaa acgccttagc agcacgtggt   1260
gtgcatgtta ttacagtcaa tgaatacttg gcaagttctc aaagagaaga aatggccgag   1320
ttatataatt tccttggttt atcagtcgga ttgaacttga acagcttatc aacagaacaa   1380
aagcgtgaag cttataatgc agatattacg tatagtacaa ataatgaatt aggcttcgac   1440
tatttacgcg ataacatggt gaattattca gaagaacgtg ttatgcgtcc gcttcatttc   1500
gctatcattg atgaggtcga ctctatttta atcgatgaag cgcgtacacc attgattatt   1560
tcaggggaag ctgaaaaatc aacatctctt tatacacaag caaatgtttt cgctaaaatg   1620
ttaaaagcag aagatgatta taattatgat gaaaaaacaa aatcagtaca attaacagat   1680
caaggtgctg ataaagctga acgtatgttc aagttagata acttatatga tttgaaaaac   1740
gttgatatta tcacgcatat caatacagca ttacgtgcta actatacatt gcaacgcgat   1800
gtagattaca tggttgtaga tggagaagta ttgattgtcg accaatttac aggtcgaaca   1860
atgccaggtc gtcgattctc tgaaggactt caccaagcga ttgaggctaa agaaggggtt   1920
caaattcaaa atgaatctaa aacaatggct tctatcacat tccaaaacta cttccgtatg   1980
tataataaat tagccggtat gacaggtact gctaaaacag aggaagaaga attccgtaac   2040
atttataata tgacagttac acaaattcca acgaaccgtc ctgttcaacg tgaagataga   2100
cctgacttga ttttcatcag ccaaaaaggc aagttcgatg ctgttgttga agatgttgtt   2160
gaaaaacata aaaaaggcca accaattctt ttaggtactg tagcggttga aacaagtgaa   2220
tacatttcac aactattgaa aaaacgcggt gtgcgtcatg atgtcttaaa cgctaaaaac   2280
catgaacgcg aagctgaaat cgtatctaca gcaggtcaaa aaggtgcagt cacaatcgca   2340
acaaacatgg ctggtcgtgg taccgatatt aaattaggcg aaggtgttga agaattaggc   2400
ggccttgctg ttattggtac agaacgtcat gaatcacgcc gtatcgatga tcagttgcgt   2460
ggtcgttctg gacgacaagg tgaccgcgga gaaagccgtt tctatttatc attacaagat   2520
gagttgatgg tacgtttcgg ttctgaacgt ctgcaaaaaa tgatgggccg attaggtatg   2580
gatgactcta caccgattga atcaaaaatg gtatctcgag ctgttgaatc tgcacaaaaa   2640
cgtgttgaag gtaacaactt cgatgcacgt aaacgtatct tagaatacga tgaagtttta   2700
cgtaaacaac gtgaaatcat ttatggtgaa cgtaataata ttatcgattc agaatcaagt   2760
tctgaattag tcattacaat gatacgctct acattagatc gtgcaatcag ttattatgta   2820
aatgaagaat tggaagaaat tgactatgcg ccgtttatta attttgtgga agatgttttc   2880
ttdcacgaag gtgaagtcaa agaagatgaa atcaaaggta aaggtaaaga tcgtgaggat   2940
attttcgata cagtatgggc taaaattgaa aaagcttatg aagcacaaaa agccaatata   3000
cccgaccaat tcaatgaatt cgaacgtatg attttattac gttctattga tggaagatgg   3060
acagaccata tcgatacaat ggatcaatta cgtcaaggta tccatttacg ttcatacggt   3120
caacaaaacc cacttcgcga ctatcaaaat gaagggcacc aactatttga tacaatgatg   3180
gtcaatattg aagaagacgt cagcaaatat atcttgaaat caattatcac agtagatgat   3240
gatattgaac gtgataaagc aaaagaatat caaggacaac atgtatcagc tgaagatgga   3300
aaagaaaaag taaaaccgca accagttgtt aaagataatc acatcggaag aaatgatcct   3360
tgtccatgcg gcagcggtaa aaagtataaa aattgctgcg gtaaatagta agttgtatta   3420
ggaccactgt taaatagctt taagagagat gctcaattga aattgggtta tctttctaag   3480
ggctgtcagc ggtctttttt caatccaaca aaaatatgga tatatgctaa aataatagag   3540
taatctggaa aattaaactg gaattggaga gatatgaaaa tggaattat               3589
 
           
             10 
             1242 
             DNA 
             Bovine herpes virus 
           
            10
cagtcaatgt cgctcttcgt gaccgagcca atggacggaa aggtgcccgc ctcccagatc     60
atgaacctcc tagtgtacgc ctataagaag ggccttaaga cggggctcta ctactgcaag    120
atccgcaagg ccaccaacaa cggcgtcttc acgggcggcg acctcgtgtg ctctgggtgc    180
cacctgtagc gacgcgcgcc gagcgcgatg gccgaggcgg cggacgcggc gaccctcacg    240
cgtaaataca aatactttta cgagaccgag tgccccgacc tagatcactt gcggtcgctc    300
agcgtcgcaa accgctggct ggagaccgag tttcccctag cggacgacgc caaggacgtg    360
gcgcggctca gcggcgccga gctggagttt taccgctttc tgttcgcgtt cctctcggcc    420
gccgatgacc tcgtgaacgt caacctcggg gacctgtccg agctgttcac ccaaaaagac    480
atcctgcatt actatatcga gcaggagtcc atcgaagtgg tgcactcgcg ggtgtacagc    540
gccatacagc tgctgctctt tagaaacgac gcggtggcgc gcgcgggcta cgtagagggc    600
gccctcggcg acccggcggt ccggcgcaag gtggactggc tcgagcggcg cgtggccgcg    660
gcagagtcgg tggccgaaaa gtacgtgctc atgattctaa tcgagggcat ttttttctcc    720
tcctcgtttg cggcgattgc ctacctgcgc acccacaacc ttttcgtcgt gacgtgccaa    780
accaacgacc tcatcagccg cgacgaagcc gtgcacacgg ccgcgtcgtg ctgcatcttc    840
gacaactacc tcggcgggga gcggccgccg ccggcccgca tctacgagct gttccgcgaa    900
gcgtggaaat tgagcgcgag tttatttggt tgcgcgccgc gcggcagtca tatacttgac    960
gtggaggcta tttctgcgta cgtcgagtac agcgcggacc gcctgctcgc tgctatccag   1020
ctgcctcctc tgtttggcac cccgcctcct gggaccgatt ttcctttggc cctgatgact   1080
gccgagaagc acacgaactt ctttgagcgc cgcagcacca actacacagg caccgtaatc   1140
aacgacctgt agggcacccc cgctgccctg ccagagcgcc ccgcctttcc tcctccttct   1200
cacccccacg ccgcgaataa aaaatgttcc atgtcaacga aa                      1242
 
           
             11 
             3518 
             DNA 
             Herpes simplex virus 1 
           
            11
tcgagcccgc cgaaacccgc cgcgtctgtt gaaatggcca gccgcccagc cgcatcctct     60
cccgtcgaag cgcgggcccc ggttggggga caggaggccg gcggccccag cgcagccacc    120
cagggggagg ccgccggggc ccctctcgcc cacggccacc acgtgtactg ccagcgagtc    180
aatggcgtga tggtgctttc cgacaagacg cccgggtccg cgtcctaccg catcagcgat    240
agcaactttg tccaatgtgg ttccaactgc accatgatca tcgacggaga cgtggtgcgc    300
gggcgccccc aggacccggg ggccgcggca tcccccgctc ccttcgttgc ggtgacaaac    360
atcggagccg gcagcgacgg cgggaccgcc gtcgtggcat tcgggggaac cccacgtcgc    420
tcggcgggga cgtctaccgg tacccagacg gccgacgtcc ccaccgaggc ccttgggggc    480
ccccctcctc ctccccgctt caccctgggt ggcggctgtt gttcctgtcg cgacacacgg    540
cgccgctctg cggtattcgg gggggagggg gatccagtcg gccccgcgga gttcgtctcg    600
gacgaccggt cgtccgattc cgactcggat gactcggagg acacggactc ggagacgctg    660
tcacacgcct cctcggacgt gtccggcggg gccacgtacg acgacgccct tgactccgat    720
tcgtcatcgg atgactccct gcagatagat ggccccgtgt gtcgcccgtg gagcaatgac    780
accgcgcccc tggatgtttg ccccgggacc cccggcccgg gcgccgacgc cggtggtccc    840
tcagcggtag acccacacgc gccgacgcca gaggccggcg ctggtcttgc ggccgatccc    900
gccgtggccc gggaagacgc ggaggggctt tcggaccccc ggccacgtct gggaacgggc    960
acggcctacc ccgtccccct ggaactcacg cccgagaacg cggaggccgt ggcgcgcttt   1020
ctgggagatg ccgtgaaccg cgaacccgcg ctcatgctgg agtacttttg ccggtgcgcc   1080
cgcgaggaaa ccaagcgtgt cccccccagg acattcggca gcccccctcg cctcacggag   1140
gacgactttg ggcttctcaa ctacgcgctc gtggagatgc agcgcctgtg tctggacgtt   1200
cctccggtcc cgccgaacgc atacatgccc tattatctca gggagtatgt gacgcggctg   1260
gtcaacgggt tcaagccgct ggtgagccgg tccgctcgcc tttaccgcat cctgggggtt   1320
ctggtgcacc tgcggatccg gacccgggag gcctcctttg aggagtggct gcgatccaag   1380
gaagtggccc tggattttgg cctgacggaa aggcttcgcg agcacgaagc ccagctggtg   1440
atcctggccc aggctctgga ccattacgac tgtctgatcc acagcacacc gcacacgctg   1500
gtcgagcggg ggctgcaatc ggccctgaag tatgaggagt tttacctaaa gcgttttggc   1560
gggcactaca tggagtccgt cttccagatg tacacccgca tcgccggctt tttggcctgc   1620
cgggccacgc gcggcatgcg ccacatcgcc ctggggcgag aggggtcgtg gtgggaaatg   1680
ttcaagttct ttttccaccg cctctacgac caccagatcg taccgtcgac ccccgccatg   1740
ctgaacctgg ggacccgcaa ctactacacc tccagctgct acctggtaaa cccccaggcc   1800
accacaaaca aggcgaccct gcgggccatc accagcaacg tcagtgccat cctcgcccgc   1860
aacgggggca tcgggctatg cgtgcaggcg tttaacgact ccggccccgg gaccgccagc   1920
gtcatgcccg ccctcaaggt ccttgactcg ctggtggcgg cgcacaacaa agagagcgcg   1980
cgtccgaccg gcgcgtgcgt gtacctggag ccgtggcaca ccgacgtgcg ggccgtgctc   2040
cggatgaagg gggtcctcgc cggcgaagag gcccagcgct gcgacaatat cttcagcgcc   2100
ctctggatgc cagacctgtt tttcaagcgc ctgattcgcc acctggacgg cgagaagaac   2160
gtcacatgga ccctgttcga ccgggacacc agcatgtcgc tcgccgactt tcacggggag   2220
gagttcgaga agctctacca gcacctcgag gtcatggggt tcggcgagca gatacccatc   2280
caggagctgg cctatggcat tgtgcgcagt gcggccacga ccgggagccc cttcgtcatg   2340
ttcaaagacg cggtgaaccg ccactacatc tacgacaccc agggggcggc catcgccggc   2400
tccaacctct gcaccgagat cgtccatccg gcctccaagc gatccagtgg ggtctgcaac   2460
ctgggaagcg tgaatctggc ccgatgcgtc tccaggcaga cgtttgactt tgggcggctc   2520
cgcgacgccg tgcaggcgtg cgtgctgatg gtgaacatca tgatcgacag cacgctacaa   2580
cccacgcccc agtgcacccg cggcaacgac aacctgcggt ccatgggaat cggcatgcag   2640
ggcctgcaca cggcctgcct gaagctgggg ctggatctgg agtctgccga atttcaggac   2700
ctgaacaaac acatcgccga ggtgatgctg ctgtcggcga tgaagaccag caacgcgctg   2760
tgcgttcgcg gggcccgtcc cttcaaccac tttaagcgca gcatgtatcg cgccggccgc   2820
tttcactggg agcgctttcc ggacgcccgg ccgcggtacg agggcgagtg ggagatgcta   2880
cgccagagca tgatgaaaca cggcctgcgc aacagccagt ttgtcgcgct gatgcccacc   2940
gccgcctcgg cgcagatctc ggacgtcagc gagggctttg cccccctgtt caccaacctg   3000
ttcagcaagg tgacccggga cggcgagacg ctgcgcccca acacgctcct gctaaaggaa   3060
ctggaacgca cgtttagcgg gaagcgcctc ctggaggtga tggacagtct cgacgccaag   3120
cagtggtccg tgccgcaggc gctcccgtgc ctggagccca cccaccccct ccggcgattc   3180
aagaccgcgt ttgactacga ccagaagttg ctgatcgacc tgtgtgcgga ccgcgccccc   3240
tacgtcgacc atagccaatc catgaccctg tatgtcacgg agaaggcgga cgggaccctc   3300
ccagcctcca ccctggtccg ccttctggtc cacgcatata agcgcggact aaaaacaggg   3360
atgtactact gcaaggttcg caaggcgacc aacagcgggg tctttggcgg cgacgacaac   3420
attgtctgca tgagctgcgc gctgtgaccg acaaaccccc tccgcgccag gcccgccgcc   3480
actgtcgtcg ccgtcccaag ctctcccctg ctgccatg                           3518
 
           
             12 
             5956 
             DNA 
             Herpes simplex virus 2 
           
            12
gtgtgtttgg cgtgtgtctc tgaaatggcg gaaacccaca tgcaaatggg attcatggac     60
acgttacacc cccctgactc aggagatagg catatcctcc ttagattgac tcagcacacg    120
atcgcacccc acccctgtgt gccggggata aaagccaacg cgcgcggtct gggttaccac    180
aacaggtggg tgcttcgggg acttgacggt cgccactctc ctgcgagccc tcacgtcttc    240
gcccaccgat tcctgttgcg ttcctgtcgg ccggtgctgt cctgtcgaca gattgttggc    300
gactgcccgg gtgattcgtc ggccggtgcg tcctttcggt cgtaccgccc accccgcctc    360
ccacgggccc gccgctgttt ccgttcatcg cgtccgagcc accgtcacct tggttccaat    420
ggccaaccgc cctgccgcat ccgccctcgc cggagcgcgg tctccgtccg aacgacagga    480
accccgggag cccgaggtcg ccccccctgg cggcgaccac gtgttttgca ggaaagtcag    540
cggcgtgatg gtgctttcca gcgatccccc cggccccgcg gcctaccgca ttagcgacag    600
cagctttgtt caatgcggct ccaactgcag tatgataatc gacggagacg tggcgcgcgg    660
tcatttgcgt gacctcgagg gcgctacgtc caccggcgcc ttcgtcgcga tctcaaacgt    720
cgcagccggc ggggatggcc gaaccgccgt cgtggcgctc ggcggaacct cgggcccgtc    780
cgcgactaca tccgtgggga cccagacgtc cggggagttc ctccacggga acccaaggac    840
ccccgaaccc caaggacccc aggctgtccc cccgccccct cctcccccct ttccatgggg    900
ccacgagtgc tgcgcccgtc gcgatgccag gggcggcgcc gagaaggacg tcggggccgc    960
ggagtcatgg tcagacggcc cgtcgtccga ctccgaaacg gaggactcgg actcctcgga   1020
cgaggatacg ggctcgggtt cggagacgct gtctcgatcc tcttcgatct gggccgcagg   1080
ggcgactgac gacgatgaca gcgactccga ctcgcggtcg gacgactccg tgcagcccga   1140
cgttgtcgtt cgtcgcagat ggagcgacgg ccctgccccc gtggcctttc ccaagccccg   1200
gcgccccggc gactcccccg gaaaccccgg cctgggcgcc ggcaccgggc cgggctccgc   1260
gacggacccg cgcgcgtcgg ccgactccga ttccgcggcc cacgccgccg caccccaggc   1320
ggacgtggcg ccggttctgg acagccagcc cactgtggga acggaccccg gctacccagt   1380
ccccctagaa ctcacgcccg agaacgcgga ggcggtggcg cggtttctgg gggacgccgt   1440
cgaccgcgag cccgcgctca tgctggagta cttctgtcgg tgcgcccgcg aggagagcaa   1500
gcgcgtgccc ccacgaacct tcggcagcgc cccccgcctc acggaggacg actttgggct   1560
cctgaactac gcgctcgctg agatgcgacg cctgtgcctg gaccttcccc cggtcccccc   1620
caacgcatac acgccctatc atctgaggga gtatgcgacg cggctggtta acgggttcaa   1680
acccctggtg cggcggtccg cccgcctgta tcgcatcctg gggattctgg ttcacctgcg   1740
catccgtacc cgggaggcct cctttgagga atggatgcgc tccaaggagg tggacctgga   1800
cttcgggctg acggaaaggc ttcgcgaaca cgaggcccag ctaatgatcc tggcccaggc   1860
cctgaacccc tacgactgtc tgatccacag caccccgaac acgctcgtcg agcgggggct   1920
gcagtcggcg ctgaagtacg aagagtttta cctcaagcgc ttcggcgggc actacatgga   1980
gtccgtcttc cagatgtaca cccgcatcgc cgggttcctg gcgtgccggg cgacccgcgg   2040
catgcgccac atcgccctgg ggcgacaggg gtcgtggtgg gaaatgttca agttcttttt   2100
ccaccgcctc tacgaccacc agatcgtgcc gtccaccccc gccatgctga acctcggaac   2160
ccgcaactac tacacgtcca gctgatacct ggtaaacccc caggccacca ctaaccaggc   2220
caccctccgg gccatcaccg gcaacgtgag cgccatcctc gcccgcaacg ggggcatcgg   2280
gctgtgcatg caggcgttca acgacgccag ccccggcacc gccagcatca tgccggccct   2340
gaaggtcctg gactccctgg tggcggcgca caacaaacag agcacgcgcc ccaccggggc   2400
gtgcgtgtac ctggaaccct ggcacagcga cgttcgggcc gtgctcagaa tgaagggcgt   2460
cctcgccggc gaggaggccc agcgctgcga caacatcttc agcgccctct ggatgccgga   2520
cctgttcttc aagcgcctga tccgccacct cgacggcgag aaaaacgtca cctggtccct   2580
gttcgaccgg gacaccagca tgtcgctcgc cgactttcac ggcgaggagt tcgagaagct   2640
gtacgagcac ctcgaggcca tggggttcgg cgaaacgatc cccatccagg acctggcgta   2700
cgccatcgtg cgcagcgcgg ccaccaccgg aagccccttc atcatgttta aggacgcggt   2760
aaacagccac tacatctacg acacgcaagg ggcggccatt gccggctcca acctctgcac   2820
ggagatcgtc cacccgtcct ccaaacgctc cagcggggtc tgcaacctgg gcagcgtgaa   2880
tctggcccga tgcgtctccc ggcggacgtt cgattttggc atgctccgcg acgccgtgca   2940
ggcgtgcgtg ctaatggtta atatcatgat agacagcacg ctgcagccga cgccccagtg   3000
cgcccgcggc cacgacaacc tgcggtccat gggcattggc atgcagggcc tgcacacggc   3060
gtgcctgaag atgggcctgg atctggagtc ggccgagttc cgggacctga acacacacat   3120
cgccgaggtg atgctgctcg cggccatgaa gaccagtaac gcgctgtgcg ttcgcggggc   3180
gcgtcccttc agccacttta agcgcagcat gtaccgggcc ggccgctttc actgggagcg   3240
cttttcgaac gccagcccgc ggtacgaggg cgagtgggag atgctacgcc agagcatgat   3300
gaaacacggc ctgcgcaaca gccagttcat cgcgctcatg cccaccgccg cctcggccca   3360
gatctcggac gtcagccagg gctttgcccc cctgttcacc aacctgttca gcaaggtgac   3420
cagggacggc gagacgctgc gccccaacac gctcttgctg aaggaactcg agcgcacgtt   3480
cggcgggaag cggctcctgg acgcgatgga cgggctcgag gccaagcagt ggtctgtggc   3540
ccaggccctg ccttgcctgg accccgccca ccccctccgg cggttcaaga cggccttcga   3600
ctacgaccag gaactgctga tcgacctgtg tgcagaccgc gccccctatg ttgatcacag   3660
ccaatccatg actctgtatg tcacagagaa ggcggacggg acgctccccg cctccaccct   3720
ggtccgcctt ctcgtccacg catataagcg cggcctgaag acggggatgt actactgcaa   3780
ggttcgcaag gcgaccaaca gcggggtgtt cgccggcgac gacaacatcg tctgcacaag   3840
ctgcgcgctg taagcaacag cgctccgatc ggggtcaggc gtcgctctcg gtcccgcata   3900
tcgccatgga tcccgccgtc tcccccgcga gcaccgaccc cctagatacc cacgcgtcgg   3960
gggccggggc ggccccgatt ccggtgtgcc ccacccccga gcggtacttc tacacctccc   4020
agtgccccga catcaaccac cttcgctccc tcagcatcct gaaccgctgg ctggagaccg   4080
agctcgtgtt cgtcggggac gaggaggacg tctccaagct ctccgagggc gagctcggct   4140
tctaccgctt tctgtttgcc ttcctgtcgg ccgcggacga cctggtgacg gaaaacctgg   4200
gcggcctctc cggcctcttc gaacagaagg acattcttca ctactacgtg gagcaggaat   4260
gcatcgaggt cgtccactcc cgcgtctaca acatcatcca gctggtgctc tttcacaaca   4320
acgaccaggc gcgccgcgcc tatgtggccc gcaccatcaa ccacccggcc attcgcgtca   4380
aggtggactg gctggaggcg cgggtgcggg aatgcgactc gatcccggag aagttcatcc   4440
tcatgatcct catcgagggc gtcttttttg ccgcctcgtt cgccgccatc gcgtacctgc   4500
gcaccaacaa cctcctgcgg gtcacctgcc agtcgaacga cctcatcagc cgccacgagg   4560
ccgtgcatac gacagcctcg tgctacatct acaacaacta cctcgggggc cacgccaagc   4620
ccgaggcggc gcgcgtgtac cggctgtttc gggaggcggt ggatatcgag atcgggttca   4680
tccgatccca ggccccgacg gacagctcta tcctgagtcc gggggccctg gcggccatcg   4740
agaactacgt gcgattcagc gcggatcgcc tgctgggcct gatccatatg cagcccctgt   4800
attccgcccc cgcccccgac gccagctttc ccctcagcct catgtccacc gacaaacaca   4860
ccaacttctt cgagtgccgc agcacctcgt acgccggggc cgtcgtcaac gatctgtgag   4920
ggtctgggcg cccttgtagc gatgtctaac cgaaataaag gggtcgaaac ggactgttgg   4980
gtctccggtg tgattattac gcaggggagg ggggtggcgg ctggggaaag ggaaggaacg   5040
cccgaaacca gagaaaagga ccaaaaggga aacgcgtcca accgataaat caagcgccga   5100
ccagaacccc gagatgcata ataacaaacg attttattac tcttattatt aacaggtcgg   5160
gcatcgggag gggatggggg cgcgcgtttc ctccgttccg gctactcgtc ccagaattta   5220
gccaggacgt ccttgtaaaa cgcgggcggg ggcgcgtggg cccacacctg cgccagaaac   5280
cggtcggcga tgtccggggc ggtgatatga cgagtcacga tggagcgcgc taaatcttcg   5340
tcgcggaggt cctgatagat gggcagtctt tttagaagag tccagggtcc ccgctccttg   5400
gggctgataa gcgatatgac gtacttgacg tatctgtgct ccaccagctc ggcgatggtc   5460
atcggatcgg gcagccagtc cagggcctcc ggggcgtcgt ggatgacgtg gcggcgacgt   5520
ccggcgacat agccgcggtg ttccgcgacc cgctgcgcgt tggggacctg cacgagctcg   5580
ggcggggtga gtatctccga ggaggacgac cgggcgccgt cgcgcggccc accggcgacg   5640
tccgggggct ggaggggggg gtcttcttcg tagtcgtcct cgcccgcgat ctgttgggcc   5700
agaatttcgg tccacgagat gcgcgtctcg aggccgaccg gggccgcggt cagcgtaggc   5760
atgctctcca gggagcgcga gttggcgcgc tcccgccggg ccgcccggcg ggcctgggat   5820
cggctcgggg cggtccagtg acactcgcgc agcacgtcct cgacggacgc gtaggtgtta   5880
ttggggtgca ggtctgtgtg gcagcggacg aacagcgcca ggaactgcgg gtaactcatc   5940
ttgaagtacc ctgcag                                                   5956
 
           
             13 
             3678 
             DNA 
             Equine herpesvirus 4 
           
            13
aaaccactgt tctttacact ttatgctcta gtttttggta atagtgtctt ggaacacttt     60
taccctaaac gaaattatgg ctttggattt tttgagcacc gactgtccac tggggattgt    120
ttccgatatt atatccaacg tgaataccat caaagagtat ggatattcca gcgaattatc    180
aacaacgctg gcacctcgcc cgtctcgaga acaggtgtta gagtatatca ccagagtcgt    240
ggataaactc aagccgctgt gcagagtcga cgaacgcctt tacattgcgt gcggggagct    300
tgtacaccta cgaattaaag cacgcaacac agacctgaaa tattggctaa aatcgtctga    360
gattgatctt agcgatgtcg tggaacaggc catattggaa cacattgact ttgttcagaa    420
aaccctcaac tcgtttgaaa catcggaata ccgagatttg tgttcattag gcctgcaatc    480
tgcgctaaag tatgaagaaa tgtatttagc caaaatgcga ggcggacgtc tagagtccat    540
ggggcaattt tttcttagac ttgcaactac tgctacgcac tatactatgg aacaaccagc    600
aatggctcgc gtgttggtta gcggtgaggt tggctggaca tatattttca gagccttttt    660
tactgcgcta gccggacagg ttgtcattcc ggccacgcca attatgctgt ttggtgggag    720
agactgtggg tctatggcca gctgttattt gctaaacccc agggtaacag atatgaactc    780
tgcaattccg gctcttatgg aagaggttgg acccattttg tgcaaccgag gaggaattgg    840
actgtcttta cagaggttta acactccacc cacagaaggt tgttcacggg gtgtcatggc    900
tctcctaaag ctactagact ctatgaccat ggccattaac agcgacggtg aaagaccaac    960
aggagtgtgt gtttatttcg aaccctggca cgcagacatc cgcgccattt taaatatgcg   1020
cggaatgctg gccagagacg aaactgtgcg ctgcgacaac atctttgctt gtatgtggac   1080
cccagacctg ttttttgacc gctatcaacg gtacgtcgat ggagaaagcg gcataatgtg   1140
gactctgttt gatgatactg catcgcacct ctgccatatg tacggaaatg atttcacacg   1200
ggaatatgag cgcctggagc ggtgtggatt tgggatagac gctattccca tacaggacat   1260
ggcctttatc atagttagaa gtgctgtaat gacaggaagc ccatttttga tgtttaaaga   1320
cgcgtgcaac aggcactacc actttgacat gcggcagaga ggtgcgataa tggggtctaa   1380
tctatgcaca gaaattatcc agcatgccga cgaaacccaa aacggggtgt gtaatctagc   1440
cagcatcaac ctcccaaaat gtctagccct tccacctcca aatattgcag gtgtgccata   1500
ttttgacttc gccgctctgg gccgcgctgc cgcaactgcc acaatttttg tcaatgcgat   1560
gatgtgtgcc agcacatatc caactgttaa atcccagaaa ggcgttgaag aaaaccggtc   1620
gctgggactt ggaattcagg ggctacatac cacgtttttg atgctggacc tggatatggc   1680
atctccagag gcgcaccaac taaacaagca aatagcagaa aggctgttat tgaactctat   1740
gaaggccagc gcaacgctct gcaagctggg tatgcaaccc tttaaagggt ttgaagacag   1800
caagtacagt cggggggaac taccctttga tgcctaccca aatgtaacac taacaaaccg   1860
caacgcctgg cgtagacttc gcactgacat aaaacaatac ggcttgtaca attctcagtt   1920
tgtagcctat atgccaacag tatcttcgtc acaggttacc gagagcagcg aggggttttc   1980
tcctgtttac acaaacctgt ttagcaaagt tactgctacc ggggaagtac tcaggcccaa   2040
tgtactgcta atgcgcacca tcagaagtat ttttccacag gaatgcgcgc gcttacaagc   2100
gctatctacg ctagaagctg cgaaatggtc agttgtggga gcgtttggtg atttgccagt   2160
tggtcacccc ctcagtaagt ttaaaacagc atttgagtac gaccagacta tgctaattaa   2220
catgtgtgct gacagggctg cgtttgtgga ccagagccaa tccatgtctt tgtttataac   2280
tgagcctgct gacggaaaac tccccgcctc cagaattatg aatcttttgg tccacgcata   2340
taaacgcgga cttaaaacag gcatgtacta ctgcaaaatc aagaaggcaa caaacaacgg   2400
agtctttgtt ggcggagacc tagtctgcac cagctgcagc ttgtagggca gcctcgccat   2460
tttgcccagg gcgggaaaat aattatggcc ctcgaaaact ctaaaaaaac agattttgct   2520
gacgagttat tgataaatgc gtatttctat acgccggaat gtcccgatat tgaacaccta   2580
cgcttgttga gcgttgccaa ccgctggctg gatacggacc ttccaatttc tgatgacctc   2640
aaggacgttg ctaaactcgc gccagccgag cgagagtttt accggttttt gtttgccttt   2700
ttatctgctg ctgacgactt ggtaaattta aacctgggag atttatccgc actatttact   2760
caaaaggaca ttcttcacta ctacattgag caagagtcta ttgaagtaac gcactccaga   2820
gtatatagcg ctatacagct tatgttgttt ggaaacgacg caacagcgcg cgctaggtat   2880
gtcgcatctg ttgtcaaaga cgtggccata gacctaaagg tatcttggtt gcaagcaaag   2940
gtgcgagaat gcaaatctgt ggcggaaaag tatattttga tgatattaat agagggcgtt   3000
ttcttcgcgt cgtcctttcc gtccatcgca tatcttcgca cccacaatct ctttgtggta   3060
acctgtcaaa gtaatgattt aattagccgc gacgaagcaa ttcacaccaa cgcctcgtgc   3120
tgtatctaca acaactacct tgggcgtttt gaaaagccag ctccaacgag gatttatgcg   3180
ctgttttctg aggccgtaaa catcgagtgt gaatttttgc tttcccatgc ccccaaaagc   3240
agccacctgt tggacattga agccatcata tgctacgtac gctatagcgc ggacaggctt   3300
ttgggggaaa ttggactatc tccgctgttt aatgctccca aacccccacc aagcttcccc   3360
ctagctttca tgactgtgga aaaacatacc aacttttttg aaaggcgaag caccgcatac   3420
tcgggaactc ttataaacga tctgtaatgt aaaaataaaa actaattttg attcacttat   3480
ttgtcttgtt tgcgtgttgg atgtacgcga tttaaaaaaa tactgagaaa agatactccc   3540
gatttaactt tatttaagac cattgtcttc ggtgtccaca gtcatcccag tagttaacca   3600
acacagtgtt gtaatcagtg ggggtgggaa tgtggttcca aaacatatta gcaagctctc   3660
tgacaatttc gtgttcgg                                                 3678
 
           
             14 
             20 
             DNA 
             Escherichia coli 
           
            14
ccgtcgcgct ttgtcaccag                                                 20
 
           
             15 
             20 
             DNA 
             Escherichia coli 
           
            15
ctgtgctacc gtcgcgcttt                                                 20
 
           
             16 
             20 
             DNA 
             Escherichia coli 
           
            16
tgatgcgctc tgtgctaccg                                                 20
 
           
             17 
             20 
             DNA 
             Escherichia coli 
           
            17
tttgtcgaga ttgatgcgct                                                 20
 
           
             18 
             20 
             DNA 
             Escherichia coli 
           
            18
agaacgcgat ggattttgtc                                                 20
 
           
             19 
             20 
             DNA 
             Escherichia coli 
           
            19
tgccgcccaa tccagaacgc                                                 20
 
           
             20 
             20 
             DNA 
             Escherichia coli 
           
            20
agtccttctg ccgcccaatc                                                 20
 
           
             21 
             20 
             DNA 
             Escherichia coli 
           
            21
aaactgaatg tgggagcgca                                                 20
 
           
             22 
             20 
             DNA 
             Escherichia coli 
           
            22
ataatggttt cgtggatgtc                                                 20
 
           
             23 
             20 
             DNA 
             Escherichia coli 
           
            23
cggcagcctt gataatggtt                                                 20
 
           
             24 
             20 
             DNA 
             Escherichia coli 
           
            24
atactgataa tccggcgcat                                                 20
 
           
             25 
             20 
             DNA 
             Escherichia coli 
           
            25
tacgcaggtg gaagatcgcc                                                 20
 
           
             26 
             20 
             DNA 
             Escherichia coli 
           
            26
ggtcgtacag cgcaggcggc                                                 20
 
           
             27 
             20 
             DNA 
             Escherichia coli 
           
            27
gcccatctcg accattttca                                                 20
 
           
             28 
             20 
             DNA 
             Escherichia coli 
           
            28
tatcgtattt gcccatctcg                                                 20
 
           
             29 
             20 
             DNA 
             Escherichia coli 
           
            29
cggcagcata agagaaggtc                                                 20
 
           
             30 
             20 
             DNA 
             Escherichia coli 
           
            30
ccttccagct gcttaacggc                                                 20
 
           
             31 
             20 
             DNA 
             Escherichia coli 
           
            31
ccagatattt gccttccagc                                                 20
 
           
             32 
             20 
             DNA 
             Escherichia coli 
           
            32
atagatttcg ccggtcacgc                                                 20
 
           
             33 
             20 
             DNA 
             Escherichia coli 
           
            33
ggaactgggc gctctcatag                                                 20
 
           
             34 
             20 
             DNA 
             Escherichia coli 
           
            34
gaatataaag gaactgggcg                                                 20
 
           
             35 
             20 
             DNA 
             Escherichia coli 
           
            35
gcacgcggca actagaatat                                                 20
 
           
             36 
             20 
             DNA 
             Escherichia coli 
           
            36
ttcgagaaca agcacgcggc                                                 20
 
           
             37 
             20 
             DNA 
             Escherichia coli 
           
            37
tttcacgcgg gtagttcgag                                                 20
 
           
             38 
             20 
             DNA 
             Escherichia coli 
           
            38
acgcttcaca tattgcaggc                                                 20
 
           
             39 
             20 
             DNA 
             Escherichia coli 
           
            39
ggaaaccgcg tcgtaaaaac                                                 20
 
           
             40 
             20 
             DNA 
             Escherichia coli 
           
            40
ttaaatgtgg aaaccgcgtc                                                 20
 
           
             41 
             20 
             DNA 
             Escherichia coli 
           
            41
catgattggc gtcggcagcg                                                 20
 
           
             42 
             20 
             DNA 
             Escherichia coli 
           
            42
cgcacgccgg acatgattgg                                                 20
 
           
             43 
             20 
             DNA 
             Escherichia coli 
           
            43
cgagtcgggg tacgcacgcc                                                 20
 
           
             44 
             20 
             DNA 
             Escherichia coli 
           
            44
tcgatcagta cgcaggagct                                                 20
 
           
             45 
             20 
             DNA 
             Escherichia coli 
           
            45
gctgtcaccg cactcgatca                                                 20
 
           
             46 
             20 
             DNA 
             Escherichia coli 
           
            46
ggaatccagg ctgtcaccgc                                                 20
 
           
             47 
             20 
             DNA 
             Escherichia coli 
           
            47
ggaggtggcg ttgatggaat                                                 20
 
           
             48 
             20 
             DNA 
             Escherichia coli 
           
            48
aacaatcgcg ctggaggtgg                                                 20
 
           
             49 
             20 
             DNA 
             Escherichia coli 
           
            49
ctacccagcg cacgaatacg                                                 20
 
           
             50 
             20 
             DNA 
             Escherichia coli 
           
            50
atgcagccgg tatggaacgc                                                 20
 
           
             51 
             20 
             DNA 
             Escherichia coli 
           
            51
ttgtagaacg gaatgcagcc                                                 20
 
           
             52 
             20 
             DNA 
             Escherichia coli 
           
            52
ccgctgtctg gaaatgtttg                                                 20
 
           
             53 
             20 
             DNA 
             Escherichia coli 
           
            53
aggatttcac cgctgtctgg                                                 20
 
           
             54 
             20 
             DNA 
             Escherichia coli 
           
            54
cgcacaccgc cctgagagca                                                 20
 
           
             55 
             20 
             DNA 
             Escherichia coli 
           
            55
cacatcgggt agaacagcgt                                                 20
 
           
             56 
             20 
             DNA 
             Escherichia coli 
           
            56
ctttccactt ccagatgcca                                                 20
 
           
             57 
             20 
             DNA 
             Escherichia coli 
           
            57
ttgccttcca caccacggtt                                                 20
 
           
             58 
             20 
             DNA 
             Escherichia coli 
           
            58
cacgcggttg ccttccacac                                                 20
 
           
             59 
             20 
             DNA 
             Escherichia coli 
           
            59
ccatatgacg cacgcggttg                                                 20
 
           
             60 
             20 
             DNA 
             Escherichia coli 
           
            60
ttcacctttc agcagacggg                                                 20
 
           
             61 
             20 
             DNA 
             Escherichia coli 
           
            61
cgggctgaac agggtgatat                                                 20
 
           
             62 
             20 
             DNA 
             Escherichia coli 
           
            62
cggacgggct gaacagggtg                                                 20
 
           
             63 
             20 
             DNA 
             Escherichia coli 
           
            63
gtcggacggg ctgaacaggg                                                 20
 
           
             64 
             20 
             DNA 
             Escherichia coli 
           
            64
aaactcttcc tgatcggcga                                                 20
 
           
             65 
             20 
             DNA 
             Escherichia coli 
           
            65
gcggatgctg tcgtctttct                                                 20
 
           
             66 
             20 
             DNA 
             Escherichia coli 
           
            66
gctgcttgcg gatgctgtcg                                                 20
 
           
             67 
             20 
             DNA 
             Escherichia coli 
           
            67
ggctttcaca cgctgcttgc                                                 20
 
           
             68 
             20 
             DNA 
             Escherichia coli 
           
            68
gctcaacggc tttcacacgc                                                 20
 
           
             69 
             20 
             DNA 
             Escherichia coli 
           
            69
gaccggtaga cgcacgttcc                                                 20
 
           
             70 
             20 
             DNA 
             Escherichia coli 
           
            70
gggctatggg tattgcagtg                                                 20
 
           
             71 
             20 
             DNA 
             Escherichia coli 
           
            71
aaacgggcta tgggtattgc                                                 20
 
           
             72 
             20 
             DNA 
             Escherichia coli 
           
            72
cggatcaaac gggctatggg                                                 20
 
           
             73 
             20 
             DNA 
             Escherichia coli 
           
            73
gggctatctc caggcacagg                                                 20
 
           
             74 
             20 
             DNA 
             Escherichia coli 
           
            74
ggcagggcta tctccaggca                                                 20
 
           
             75 
             20 
             DNA 
             Escherichia coli 
           
            75
tggtcggcag ggctatctcc                                                 20
 
           
             76 
             20 
             DNA 
             Escherichia coli 
           
            76
gcggtttggt cggcagggct                                                 20
 
           
             77 
             20 
             DNA 
             Escherichia coli 
           
            77
ttcagcggtt tggtcggcag                                                 20
 
           
             78 
             20 
             DNA 
             Escherichia coli 
           
            78
acgtcgttca gcggtttggt                                                 20
 
           
             79 
             20 
             DNA 
             Escherichia coli 
           
            79
tttcaccgtt ctcgtcgttg                                                 20
 
           
             80 
             20 
             DNA 
             Escherichia coli 
           
            80
cagcgcgatt tcaccgttct                                                 20
 
           
             81 
             20 
             DNA 
             Escherichia coli 
           
            81
cgtacacagc gcgatttcac                                                 20
 
           
             82 
             20 
             DNA 
             Escherichia coli 
           
            82
agcagacagc gtacacagcg                                                 20
 
           
             83 
             20 
             DNA 
             Escherichia coli 
           
            83
caggttgaaa gcagacagcg                                                 20
 
           
             84 
             20 
             DNA 
             Escherichia coli 
           
            84
aattgcgccc aggttgaaag                                                 20
 
           
             85 
             20 
             DNA 
             Escherichia coli 
           
            85
ccaggttatt aattgcgccc                                                 20
 
           
             86 
             20 
             DNA 
             Escherichia coli 
           
            86
ttgccagctc ttccagttca                                                 20
 
           
             87 
             20 
             DNA 
             Escherichia coli 
           
            87
accgccagaa ttgccagctc                                                 20
 
           
             88 
             20 
             DNA 
             Escherichia coli 
           
            88
gtcaagtgca cgaaccgcca                                                 20
 
           
             89 
             20 
             DNA 
             Escherichia coli 
           
            89
atccagcagc gcgtcaagtg                                                 20
 
           
             90 
             20 
             DNA 
             Escherichia coli 
           
            90
tgataatcca gcagcgcgtc                                                 20
 
           
             91 
             20 
             DNA 
             Escherichia coli 
           
            91
gatcacacca atacccagcg                                                 20
 
           
             92 
             20 
             DNA 
             Escherichia coli 
           
            92
tcgttcgcca ggtagtaagc                                                 20
 
           
             93 
             20 
             DNA 
             Escherichia coli 
           
            93
cgtttaccgt cgttcgccag                                                 20
 
           
             94 
             20 
             DNA 
             Escherichia coli 
           
            94
tgccgtcgga gtagcgttta                                                 20
 
           
             95 
             20 
             DNA 
             Escherichia coli 
           
            95
tatgcgtcag gttgttggcg                                                 20
 
           
             96 
             20 
             DNA 
             Escherichia coli 
           
            96
cgaaggtttt atgcgtcagg                                                 20
 
           
             97 
             20 
             DNA 
             Escherichia coli 
           
            97
gttaaaccac gggcacgcgc                                                 20
 
           
             98 
             20 
             DNA 
             Escherichia coli 
           
            98
ttcgcgtaag tggtttcgtt                                                 20
 
           
             99 
             20 
             DNA 
             Escherichia coli 
           
            99
tataggtatc gatcggcagg                                                 20
 
           
             100 
             20 
             DNA 
             Escherichia coli 
           
            100
cagtcgtaat gcagcggctc                                                 20
 
           
             101 
             20 
             DNA 
             Escherichia coli 
           
            101
cgcagagctt cccagtcgta                                                 20
 
           
             102 
             20 
             DNA 
             Escherichia coli 
           
            102
tcagagcaga aagcgtggag                                                 20
 
           
             103 
             20 
             DNA 
             Escherichia coli 
           
            103
tcggacggca tcagagcaga                                                 20
 
           
             104 
             20 
             DNA 
             Escherichia coli 
           
            104
ggcgttagag atctgcgaag                                                 20
 
           
             105 
             20 
             DNA 
             Escherichia coli 
           
            105
tttgatgctg acgtaaccgc                                                 20
 
           
             106 
             20 
             DNA 
             Escherichia coli 
           
            106
tcgacgcttt gatgctgacg                                                 20
 
           
             107 
             20 
             DNA 
             Escherichia coli 
           
            107
cctggcgcaa aataccgtct                                                 20
 
           
             108 
             20 
             DNA 
             Escherichia coli 
           
            108
tagtccggca ccacctggcg                                                 20
 
           
             109 
             20 
             DNA 
             Escherichia coli 
           
            109
gcaggtgctc gtagtccggc                                                 20
 
           
             110 
             20 
             DNA 
             Escherichia coli 
           
            110
cgtcgtgcag gtgctcgtag                                                 20
 
           
             111 
             20 
             DNA 
             Escherichia coli 
           
            111
gctcataggc gtcgtgcagg                                                 20
 
           
             112 
             20 
             DNA 
             Escherichia coli 
           
            112
cccacagcag ctcataggcg                                                 20
 
           
             113 
             20 
             DNA 
             Escherichia coli 
           
            113
cggcatttcc cacagcagct                                                 20
 
           
             114 
             20 
             DNA 
             Escherichia coli 
           
            114
catcgttacc cggcatttcc                                                 20
 
           
             115 
             20 
             DNA 
             Escherichia coli 
           
            115
ggatcgtagt tggtgttggc                                                 20
 
           
             116 
             20 
             DNA 
             Escherichia coli 
           
            116
tcggcacttt tcctgacggg                                                 20
 
           
             117 
             20 
             DNA 
             Escherichia coli 
           
            117
aggcggtgag caggtctttc                                                 20
 
           
             118 
             20 
             DNA 
             Escherichia coli 
           
            118
cgaatttgta ggcggtgagc                                                 20
 
           
             119 
             20 
             DNA 
             Escherichia coli 
           
            119
gtgttttgac cccgaatttg                                                 20
 
           
             120 
             20 
             DNA 
             Escherichia coli 
           
            120
cgtcttgtgc gtcttcagcg                                                 20
 
           
             121 
             20 
             DNA 
             Escherichia coli 
           
            121
tcttacatgc gccgctttcg                                                 20
 
           
             122 
             20 
             DNA 
             Escherichia coli 
           
            122
cggctgacca aagaacatcg                                                 20
 
           
             123 
             20 
             DNA 
             Escherichia coli 
           
            123
ccacgttgac cggctgacca                                                 20
 
           
             124 
             20 
             DNA 
             Escherichia coli 
           
            124
tagcgagcca cgttgaccgg                                                 20
 
           
             125 
             20 
             DNA 
             Escherichia coli 
           
            125
cggacgccag aagaaagaga                                                 20
 
           
             126 
             20 
             DNA 
             Escherichia coli 
           
            126
caacttcttc cggacgccag                                                 20
 
           
             127 
             20 
             DNA 
             Escherichia coli 
           
            127
aatctatacg gtcgcgggag                                                 20
 
           
             128 
             20 
             DNA 
             Escherichia coli 
           
            128
tgtgtttttc gtgctccggc                                                 20
 
           
             129 
             20 
             DNA 
             Escherichia coli 
           
            129
gcaatagcgc cacgttcggg                                                 20
 
           
             130 
             20 
             DNA 
             Escherichia coli 
           
            130
agaaataagc ggcaatagcg                                                 20
 
           
             131 
             20 
             DNA 
             Escherichia coli 
           
            131
cggaatagaa ataagcggca                                                 20
 
           
             132 
             20 
             DNA 
             Escherichia coli 
           
            132
acccaggttt ccagttccgg                                                 20
 
           
             133 
             20 
             DNA 
             Escherichia coli 
           
            133
ataggaacgg gaatgaatcg                                                 20
 
           
             134 
             20 
             DNA 
             Escherichia coli 
           
            134
tcccttccgc acgtttctgg                                                 20
 
           
             135 
             20 
             DNA 
             Escherichia coli 
           
            135
cgcccagcag atgccagtag                                                 20
 
           
             136 
             20 
             DNA 
             Escherichia coli 
           
            136
gtaccttcgc ccagcagatg                                                 20
 
           
             137 
             20 
             DNA 
             Escherichia coli 
           
            137
cgcaggctaa cggtcacagt                                                 20
 
           
             138 
             20 
             DNA 
             Escherichia coli 
           
            138
tttcttcagc tcgcgcaggc                                                 20
 
           
             139 
             20 
             DNA 
             Escherichia coli 
           
            139
gcaaatgcga aggaacaagc                                                 20
 
           
             140 
             20 
             DNA 
             Escherichia coli 
           
            140
atcaattcgc gttctgcaaa                                                 20
 
           
             141 
             20 
             DNA 
             Escherichia coli 
           
            141
gcgaataatt ttggcgttgc                                                 20
 
           
             142 
             20 
             DNA 
             Escherichia coli 
           
            142
gcgggcaatc aggcgaataa                                                 20
 
           
             143 
             20 
             DNA 
             Escherichia coli 
           
            143
cagggcttcg tcgcgggcaa                                                 20
 
           
             144 
             20 
             DNA 
             Escherichia coli 
           
            144
cggtcaggtg cagggcttcg                                                 20
 
           
             145 
             20 
             DNA 
             Escherichia coli 
           
            145
tgctgggtgc cggtcaggtg                                                 20
 
           
             146 
             20 
             DNA 
             Escherichia coli 
           
            146
catatgctgg gtgccggtca                                                 20
 
           
             147 
             20 
             DNA 
             Escherichia coli 
           
            147
gcaatttccg ccatctcagg                                                 20
 
           
             148 
             20 
             DNA 
             Escherichia coli 
           
            148
tcctgcttac actcttcggc                                                 20
 
           
             149 
             20 
             DNA 
             Escherichia coli 
           
            149
atccgcccag tctttctcct                                                 20
 
           
             150 
             20 
             DNA 
             Escherichia coli 
           
            150
gaacagataa tccgcccagt                                                 20
 
           
             151 
             20 
             DNA 
             Escherichia coli 
           
            151
gggttggagc gcgtctggaa                                                 20
 
           
             152 
             20 
             DNA 
             Escherichia coli 
           
            152
cgggatcggg ttggagcgcg                                                 20
 
           
             153 
             20 
             DNA 
             Escherichia coli 
           
            153
cacgggatcg ggttggagcg                                                 20
 
           
             154 
             20 
             DNA 
             Escherichia coli 
           
            154
ctgacttcca cttcctgcgg                                                 20
 
           
             155 
             20 
             DNA 
             Escherichia coli 
           
            155
tgcccgacca gataagaact                                                 20
 
           
             156 
             20 
             DNA 
             Escherichia coli 
           
            156
ttccgagtca atctgcccga                                                 20
 
           
             157 
             20 
             DNA 
             Escherichia coli 
           
            157
aatcgtcggt gtccacttcc                                                 20
 
           
             158 
             20 
             DNA 
             Escherichia coli 
           
            158
gaccactttg cgcatccggc                                                 20
 
           
             159 
             20 
             DNA 
             Escherichia coli 
           
            159
gatgttgacc actttgcgca                                                 20
 
           
             160 
             20 
             DNA 
             Escherichia coli 
           
            160
atctccggtt ccatggcatt                                                 20
 
           
             161 
             20 
             DNA 
             Escherichia coli 
           
            161
tttttccatc tccggttcca                                                 20
 
           
             162 
             20 
             DNA 
             Escherichia coli 
           
            162
ccctttcagt tcttcgtcgg                                                 20
 
           
             163 
             20 
             DNA 
             Escherichia coli 
           
            163
gcggttttcc ctttcagttc                                                 20
 
           
             164 
             20 
             DNA 
             Escherichia coli 
           
            164
actctgcggt tttccctttc                                                 20
 
           
             165 
             20 
             DNA 
             Escherichia coli 
           
            165
cgcctttttc cagacgtgca                                                 20
 
           
             166 
             20 
             DNA 
             Escherichia coli 
           
            166
cacttcgcct ttttccagac                                                 20
 
           
             167 
             20 
             DNA 
             Escherichia coli 
           
            167
tttccagcac ttcgcctttt                                                 20
 
           
             168 
             20 
             DNA 
             Escherichia coli 
           
            168
cagattttcc agcacttcgc                                                 20
 
           
             169 
             20 
             DNA 
             Escherichia coli 
           
            169
acttgcctca cgtaccacgg                                                 20
 
           
             170 
             20 
             DNA 
             Escherichia coli 
           
            170
gacgcgctta cttgcctcac                                                 20
 
           
             171 
             20 
             DNA 
             Escherichia coli 
           
            171
gtgacgcata ccaaagacgc                                                 20
 
           
             172 
             20 
             DNA 
             Escherichia coli 
           
            172
taagaaccat accgccgagt                                                 20
 
           
             173 
             20 
             DNA 
             Escherichia coli 
           
            173
atttcggcga tgcagcgttc                                                 20
 
           
             174 
             20 
             DNA 
             Escherichia coli 
           
            174
ttccttcacc ggtacgcatt                                                 20
 
           
             175 
             20 
             DNA 
             Escherichia coli 
           
            175
gtttttcctt caccggtacg                                                 20
 
           
             176 
             20 
             DNA 
             Escherichia coli 
           
            176
cgttgcggtc agggtttttc                                                 20
 
           
             177 
             20 
             DNA 
             Escherichia coli 
           
            177
tcaggtaagc aggcagcgtt                                                 20
 
           
             178 
             20 
             DNA 
             Escherichia coli 
           
            178
taccggttag tgcgttcagg                                                 20
 
           
             179 
             20 
             DNA 
             Escherichia coli 
           
            179
ttgcgccagg tagtcgttga                                                 20
 
           
             180 
             20 
             DNA 
             Escherichia coli 
           
            180
gtcacgttgc gccaggtagt                                                 20
 
           
             181 
             20 
             DNA 
             Escherichia coli 
           
            181
agcggacggt tgttttcggc                                                 20
 
           
             182 
             20 
             DNA 
             Escherichia coli 
           
            182
ggaattcaaa cagcggacgg                                                 20
 
           
             183 
             20 
             DNA 
             Escherichia coli 
           
            183
aggccaagga attcaaacag                                                 20
 
           
             184 
             20 
             DNA 
             Escherichia coli 
           
            184
ataccgacag tcaggccaag                                                 20
 
           
             185 
             20 
             DNA 
             Escherichia coli 
           
            185
ttcgcgcttt gccggtgctg                                                 20
 
           
             186 
             20 
             DNA 
             Escherichia coli 
           
            186
agccgtattc gttgttcgta                                                 20
 
           
             187 
             20 
             DNA 
             Escherichia coli 
           
            187
cgcaggtagt caaagccgta                                                 20
 
           
             188 
             20 
             DNA 
             Escherichia coli 
           
            188
atgttgtcgc gcaggtagtc                                                 20
 
           
             189 
             20 
             DNA 
             Escherichia coli 
           
            189
gccatgttgt cgcgcaggta                                                 20
 
           
             190 
             20 
             DNA 
             Escherichia coli 
           
            190
gtccacttcg tccaccagcg                                                 20
 
           
             191 
             20 
             DNA 
             Escherichia coli 
           
            191
ggtgtacgcg cttcatcgat                                                 20
 
           
             192 
             20 
             DNA 
             Escherichia coli 
           
            192
cggtgtacgc gcttcatcga                                                 20
 
           
             193 
             20 
             DNA 
             Escherichia coli 
           
            193
gcgtttatac atttccgagc                                                 20
 
           
             194 
             20 
             DNA 
             Escherichia coli 
           
            194
cggatcaggt gcggaataat                                                 20
 
           
             195 
             20 
             DNA 
             Escherichia coli 
           
            195
ttcacctggc gagatttttc                                                 20
 
           
             196 
             20 
             DNA 
             Escherichia coli 
           
            196
cagcaccaga ccacgttcgg                                                 20
 
           
             197 
             20 
             DNA 
             Escherichia coli 
           
            197
gccctctttc accagcagtt                                                 20
 
           
             198 
             20 
             DNA 
             Escherichia coli 
           
            198
cccttcatcc atgatgccct                                                 20
 
           
             199 
             20 
             DNA 
             Escherichia coli 
           
            199
ttggccggag agtacagaga                                                 20
 
           
             200 
             20 
             DNA 
             Escherichia coli 
           
            200
agcatgatgt tggccggaga                                                 20
 
           
             201 
             20 
             DNA 
             Escherichia coli 
           
            201
agcgccgccg ttacgtggtg                                                 20
 
           
             202 
             20 
             DNA 
             Escherichia coli 
           
            202
gtcacgggta aacagcgcat                                                 20
 
           
             203 
             20 
             DNA 
             Escherichia coli 
           
            203
caccttcttt cgcttccaca                                                 20
 
           
             204 
             20 
             DNA 
             Escherichia coli 
           
            204
cagcgtttgg ttttcgttct                                                 20
 
           
             205 
             20 
             DNA 
             Escherichia coli 
           
            205
ggtgatcgaa gccagcgttt                                                 20
 
           
             206 
             20 
             DNA 
             Escherichia coli 
           
            206
gacggaagta gttctggaag                                                 20
 
           
             207 
             20 
             DNA 
             Escherichia coli 
           
            207
cccgccagtt tttcatacag                                                 20
 
           
             208 
             20 
             DNA 
             Escherichia coli 
           
            208
tcatccccgc cagtttttca                                                 20
 
           
             209 
             20 
             DNA 
             Escherichia coli 
           
            209
gaacaacgac ggtatccagc                                                 20
 
           
             210 
             20 
             DNA 
             Escherichia coli 
           
            210
gcctttcgca gtacgttctt                                                 20
 
           
             211 
             20 
             DNA 
             Escherichia coli 
           
            211
tagtacccac cagcaccggc                                                 20
 
           
             212 
             20 
             DNA 
             Escherichia coli 
           
            212
cggctttggt cagttcgttt                                                 20
 
           
             213 
             20 
             DNA 
             Escherichia coli 
           
            213
tgtgcttaat accggctttg                                                 20
 
           
             214 
             20 
             DNA 
             Escherichia coli 
           
            214
gttggcgtgg aatttggcgt                                                 20
 
           
             215 
             20 
             DNA 
             Escherichia coli 
           
            215
gcctgagcaa caatcgccgc                                                 20
 
           
             216 
             20 
             DNA 
             Escherichia coli 
           
            216
ctgtaccacg acccgccata                                                 20
 
           
             217 
             20 
             DNA 
             Escherichia coli 
           
            217
tatctgtacc acgacccgcc                                                 20
 
           
             218 
             20 
             DNA 
             Escherichia coli 
           
            218
ctgcctgcca gctaccaccg                                                 20
 
           
             219 
             20 
             DNA 
             Escherichia coli 
           
            219
tttccagcgc ggcaacttct                                                 20
 
           
             220 
             20 
             DNA 
             Escherichia coli 
           
            220
tttgctctgc ggtcggattt                                                 20
 
           
             221 
             20 
             DNA 
             Escherichia coli 
           
            221
tttttcaatt tgctctgcgg                                                 20
 
           
             222 
             20 
             DNA 
             Escherichia coli 
           
            222
accgcatcgt gacgtacctg                                                 20
 
           
             223 
             20 
             DNA 
             Escherichia coli 
           
            223
ccagtaccgc atcgtgacgt                                                 20
 
           
             224 
             20 
             DNA 
             Escherichia coli 
           
            224
gcttccagta ccgcatcgtg                                                 20
 
           
             225 
             20 
             DNA 
             Escherichia coli 
           
            225
accgatgata tgcaggccac                                                 20
 
           
             226 
             20 
             DNA 
             Escherichia coli 
           
            226
acgaccagaa cgaccgcgca                                                 20
 
           
             227 
             20 
             DNA 
             Escherichia coli 
           
            227
cccctgacga ccagaacgac                                                 20
 
           
             228 
             20 
             DNA 
             Escherichia coli 
           
            228
catccccctg acgaccagaa                                                 20
 
           
             229 
             20 
             DNA 
             Escherichia coli 
           
            229
gaaacgggaa gaaccagcat                                                 20
 
           
             230 
             20 
             DNA 
             Escherichia coli 
           
            230
cgacaggtag aaacgggaag                                                 20
 
           
             231 
             20 
             DNA 
             Escherichia coli 
           
            231
ggaagcaaaa atacgcatca                                                 20
 
           
             232 
             20 
             DNA 
             Escherichia coli 
           
            232
ggtcggaagc aaaaatacgc                                                 20
 
           
             233 
             20 
             DNA 
             Escherichia coli 
           
            233
cggatactcg gtcggaagca                                                 20
 
           
             234 
             20 
             DNA 
             Escherichia coli 
           
            234
acccagttta cgcatcatgc                                                 20
 
           
             235 
             20 
             DNA 
             Escherichia coli 
           
            235
acgggtgttc aatggcttcg                                                 20
 
           
             236 
             20 
             DNA 
             Escherichia coli 
           
            236
atcgctttag tcacccacgg                                                 20
 
           
             237 
             20 
             DNA 
             Escherichia coli 
           
            237
ctttcaactt tacgctgggc                                                 20
 
           
             238 
             20 
             DNA 
             Escherichia coli 
           
            238
acggctttca actttacgct                                                 20
 
           
             239 
             20 
             DNA 
             Escherichia coli 
           
            239
tggtttcgct cacatcgctg                                                 20
 
           
             240 
             20 
             DNA 
             Escherichia coli 
           
            240
gtaggcatca atggtcgctt                                                 20
 
           
             241 
             20 
             DNA 
             Escherichia coli 
           
            241
ccacatttct tccagcgact                                                 20
 
           
             242 
             20 
             DNA 
             Escherichia coli 
           
            242
atcccacatt tcttccagcg                                                 20
 
           
             243 
             20 
             DNA 
             Escherichia coli 
           
            243
tcacgcagcg tctcttcatg                                                 20
 
           
             244 
             20 
             DNA 
             Escherichia coli 
           
            244
cctttctcga agtgacgcat                                                 20
 
           
             245 
             20 
             DNA 
             Escherichia coli 
           
            245
ccacagggag tcaagcgttt                                                 20
 
           
             246 
             20 
             DNA 
             Escherichia coli 
           
            246
tcgctgccag gtgctctttc                                                 20
 
           
             247 
             20 
             DNA 
             Escherichia coli 
           
            247
gtccatcgct gccaggtgct                                                 20
 
           
             248 
             20 
             DNA 
             Escherichia coli 
           
            248
acgcagatag tccatcgctg                                                 20
 
           
             249 
             20 
             DNA 
             Escherichia coli 
           
            249
cttcggatct ttctgtgcgt                                                 20
 
           
             250 
             20 
             DNA 
             Escherichia coli 
           
            250
cgtttgtatt cctgcttcgg                                                 20
 
           
             251 
             20 
             DNA 
             Escherichia coli 
           
            251
atcgctgcaa acatggagaa                                                 20
 
           
             252 
             20 
             DNA 
             Escherichia coli 
           
            252
ccatacgacg ctgttgttcc                                                 20
 
           
             253 
             20 
             DNA 
             Escherichia coli 
           
            253
ggcttccata cgacgctgtt                                                 20
 
           
             254 
             20 
             DNA 
             Escherichia coli 
           
            254
cgctaaacgc tcggcttcca                                                 20
 
           
             255 
             20 
             DNA 
             Escherichia coli 
           
            255
gctaagctgc tgcatttgcg                                                 20
 
           
             256 
             20 
             DNA 
             Escherichia coli 
           
            256
ctactttgcg ctctccggtt                                                 20
 
           
             257 
             20 
             DNA 
             Escherichia coli 
           
            257
ttacgtccta ctttgcgctc                                                 20
 
           
             258 
             20 
             DNA 
             Escherichia coli 
           
            258
aaccgcacgg gcaaggatcg                                                 20
 
           
             259 
             20 
             DNA 
             Escherichia coli 
           
            259
accagaaccg cacgggcaag                                                 20
 
           
             260 
             20 
             DNA 
             Escherichia coli 
           
            260
tttttaccag aaccgcacgg                                                 20
 
           
             261 
             20 
             DNA 
             Escherichia coli 
           
            261
caggtagtcg ttgacggtaa                                                 20
 
           
             262 
             18 
             DNA 
             Escherichia coli 
           
            262
caggtagtcg ttgacggt                                                   18
 
           
             263 
             20 
             DNA 
             Escherichia coli 
           
            263
cggaagtagt tctggaaggt                                                 20
 
           
             264 
             20 
             DNA 
             Escherichia coli 
           
            264
cgaccgcgca actggttatc                                                 20
 
           
             265 
             20 
             DNA 
             Escherichia coli 
           
            265
ccgcacgggc aaggatcgtt                                                 20