Patent Publication Number: US-2005125160-A1

Title: Modifying the control of gene expression behavior by the deletion of connectrons and by the design and addition of synthetic connectrons in prokaryotic, archea and eukaryotic genomes

Description:
REFERENCE TO RELATED APPLICATION  
      The present application includes the subject of Provisional Application Ser. No. 60/393,558 filed Jul. 5, 2002  
      The present application is a continuation in part of U.S. patent application Ser. No. 09/866,925 filed May 30, 2001 entitled ALGORITHMIC DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES  
      The present application is also related to U.S. patent application Ser. No. 10/339,666 filed Jan. 10, 2003 entitled SIMULATION OF GENE EXPRESSION CONTROL USING CONNECTRONS, INTERFERENCE RNAS (IRNAS) AND SMALL TEMPORAL RNAS (STRNAS) IN PROKARYOTIC, ARCHEA AND EUKARYOTIC GENOMES  
      The present application is also related to U.S. patent application Ser. No. 10/364,516 filed Feb. 12, 2003 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  ESCHERICHIA COLI  K-12 MG1655 COMPLETE GENOME  
      The present application is also related to U.S. patent application Ser. No. 10/364,412 filed Feb. 12, 2003 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  SACCHAROMYCES CEREVISIAE  COMPLETE GENOME  
      The present application is also related to U.S. patent application Ser. No. 10/299,056 filed Nov. 19, 2002 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  HALOBACTERIUM  SP. NRC-1 COMPLETE GENOME  
      The present application is also related to U.S. patent application Ser. No. 10/367,832 filed Feb. 19, 2003 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  PSEUDOMONAS AERUGINOSA  PA01, COMPLETE GENOME  
      The present application is also related to U.S. patent application Ser. No. 10/287,818 filed Nov. 5, 2002 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  VIBRIO CHOLERAE  CHROMOSOME I, COMPLETE CHROMOSOME  
      The present application is also related to U.S. patent application Ser. No. 10/305,275 filed Nov. 27, 2002 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE  AEROPYRUM PERNIX  K1 COMPLETE GENOME  
    
    
     INTRODUCTION  
      The connectron structure of a genome determines sets of four DNA sequences of minimum length of 15-bases (C1 and C2 which are in the 3′UTR of a gene, Ti which is on the 5′-side and T2 which is on the 3′-side of a set of genes). The connectrons in a genome control the expression of sets of genes. Each native genome has a particular set of connectrons that control the expression of sets of genes in many different ways. The gene expression behavior can be changed by deleting existing connectrons and by adding new connectrons that have been designed to achieve specific new gene expression patterns. This patent application describes the invention of methods for deleting connectrons as well as the invention of four classes of synthetic and designed connectrons that can be used to modify the connectron behavior of a genome. In addition this application describes the invention of four methods that implement synthetic connectrons with differing proportions of novelty.  
     DEFINITIONS  
      Double Stranded DNA  
      Watson and Crick showed in 1953 that DNA naturally forms a double-stranded helix. A typical double stranded sequence is  
                                      5′-TAGAGGACTACCAC-3′                           3′-ATCTCCTCATGGTG-5′          
 
      Hydrogen Bond  
      The force between a hydrogen atom and another heavier atom such as Oxygen (O), Nitrogen (N), Phosphorus (P), or Sulfur (S).  
      Positive Strand  
      The positive strand is normally represented 5′ to 3′ running left to right as in  
                                      5′-TAGAGGACTACCAC-3′              
 
      Negative Strand  
      The negative strand is normally represented 5′ to 3′ running right to left as in  
                                      3′-ATCTCCTCATGGTG-5′              
 
      Single Stranded RNA  
      Either the positive or the negative strand of the double-stranded DNA can be transcribed by the polymerase. In RNA U replaces T.  
                                          RNA of positive   5′-UAGAGGAGUACCAC-3′               strand sequence                       RNA of negative   5′-GUGGUACUCCUCUA-3′           strand sequence          
 
      Antisense RNA  
      The antisense strand of any RNA sequence is the complement sequence  
                                          RNA sequence   5′-UAGAGGAGUACCAC-3′                           Antisense RNA sequence   3′-AUCUCCUCAUGGUG-5′          
 
      Triple Strand Helix  
      The RNA sequence of a RNA/DNA triple-strand complex is the same as the positive strand of the DNA  
                                          DNA positive strand   5′-TAGAGGAGTACCAC-3′                           DNA negative strand   3′-ATCTCCTCATGGTG-5′                       RNA strand   5′-UAGAGGAGUACCAC-3′          
 
      Promoter  
      Any region of DNA, that binds proteins which engage the polymerase transcription mechanism.  
      TATA Box  
      A region near the 3′ end of a promoter with the sequence TATA.  
      mRNA  
      The RNA produced from the DNA by the polymerase as a result of transcription  
      Start of Transcription  
      The 3′ end of a promoter where the polymerase mechanism begins to transcribe DNA into mRNA.  
      Exon  
      Any region of mRNA which is used to code for proteins  
      Intron  
      Any region of mRNA lying between two exons which is not used to code for proteins. The introns are edited out of the initial RNA transcript to form the mature mRNA.  
      3′ UTR  
      The untranslated 3′ end of an mRNA is beyond the end of the last exon. A stop codon in the mRNA causes the ribosome to stop the translation of mRNA into protein.  
      End of Translation  
      The 3′ end of the 3′-most exon.  
      Translated Region  
      Any collection of exons and introns.  
      Gene  
      Any DNA region that codes for a protein. Introns do not occur in prokaryotic genes and they sometime fail to occur in eukaryotic genes. A typical model of a gene is  
                                  |&lt;-----Promoter------&gt;|                         |&lt;−TATA Box−&gt;|                         |&lt;−Beginning of Translation           | ------------Translated Region----------------&gt;|                         End of Translation−&gt;|                 |&lt;−Exon−&gt;|&lt;−Intron−&gt;|&lt;−Exon−&gt;|&lt;−Intron−&gt;|&lt;−Exon−&gt;|&lt;−3′UTR−&gt;|       + strand -----------------------------------------------------------       − strand -----------------------------------------------------------       |&lt;---------------------------------Gene-----------------------------&gt;|                  
 
      Positive Strand Gene  
      Any gene in which the features run 5′ to 3′ on the positive strand  
      Negative Strand Gene  
      Any gene in which the features run 5′ to 3′ on the negative strand  
      C1 Sequence  
      Any positive or negative strand DNA sequence of 15 bases or more. The C2 sequence must occur in the same chromosome as the C1 sequence.  
      C2 Sequence  
      Any positive or negative strand DNA sequence of 15 bases or more. The C1 sequence must occur in the same chromosome as the C2 sequence.  
      C1/C2  
      Any positive or negative strand DNA sequence of 40 or more bases such that the C1 sequence is adjacent to the C2 sequence  
      T1 Sequence  
      Any positive or negative strand DNA sequence of 15 bases or more that is on the same chromosome as the T2 sequence. The T1 and T2 sequences must be between about 1 kb and 105 kb apart.  
      T2 Sequence  
      Any positive or negative strand DNA sequence of 15 bases or more that is on the same chromosome as the T1 sequence. The T2 and T1 sequences must be between about 1 kb and 105 kb apart.  
      Last Exon Gap or Gap-Distance  
      The number of bases between the end of transcription and the beginning of the C1/C2 sequence. In prokaryotes and single-celled eukaryotes this gap can range from no bases to 500 bases. In multi-celled eukaryotes the gap can be as large as 10,000 bases.  
      Poly-Adenylation Signal  
      A number of Adenosine (A) bases are added to the mRNA at the end of the 3′UTR.  
      Possible Connectron  
      Any set of T1, T2 and C1/C2 sequences such that the C1 sequence is identical to the T1 sequence and the C2 sequence is identical to the T2 sequence. The promoter of some gene causes the mRNA of the gene to be expressed. The mRNA is edited to eliminate the introns. The whole mRNA including the 3′UTR can move about in the cell or the nucleus of the cell. The C1/C2 RNA that is part of the 3′UTR moves to the T1 and T2 DNA sequences. A triple-stranded complex of the DNA and the RNA forms such that the C1 sequence forms hydrogen bonds with the T1 sequence and the C2 sequence forms hydrogen bonds with the T2 sequence. Because the C1 sequence is adjacent to the C2 sequence, the T1 sequence is brought physically close to the T2 sequence. This produces a loop of between about 1 kb and 105 kb in the DNA. Histone proteins reduce the length of the DNA by binding 200 bases. Histone/DNA complexes form six-fold symmetry chromatin assemblies. The diameter of the chromatin assemblies is approximately 30 nm.  
      Real Connectron  
      Any Possible Connectron which is within the Gap-Distance of some gene  
      Homologous connectron  
      The T1 sequence and the T2 sequence are on the same chromosome as the C1/C2 sequence  
      Heterologous Connectron  
      The T1 sequence and the T2 sequence are on a chromosome different from chromosome of the C1/C2 sequence  
      Permanent Connectron  
      Any C1/C2 sequence, which is 3′ UTR to some gene that is not surrounded by any T1 and T2 sequence pairs  
      Transient Connectron  
      Any C1/C2 sequence, which is 3′ UTR to some gene that is surrounded by one or more T1 and T2 sequence pairs  
      One-Shot or Self-Limiting Connectron  
      Any C1/C2 sequence which is 3′UTR to some gene that is surrounded by the T1 and T2 sequences such that C1=T1 and C2=T2  
      Geneless Connectron  
      Any C1/C2 sequence that is not 3′UTR to some gene but is surrounded by some T1 and T2. A promoter may lie 5′ to the C1/C2 sequence.  
      Bi-Directionality of Connectron Excitation  
      A C1/C2 short loop on one strand selects a T1-T2 long loop pair on the same or the opposite strand. The C1/C2 short loop has a complementary C1′/C2′ sequence on the opposite strand. Similarly the T1-T2 long loop pair has a complementary long loop pair T1′-T2′. Wherever a C1/C2, T1-T2 tetrad exists there is a complementary C1′/C2′, T1′-T2′ tetrad. The C1/C2 short loop can be transcribed as a 3′UTR to a gene on the same strand. The C1′/C2′ short loop which is on the strand opposite to the C1/C2 short loop can also can be transcribed as a 3′UTR to a gene on the same strand. There are four possible models of action  
                                                          T1   T2   gene - C1/C2                         + strand ---------------------------------------------------------------           − strand ---------------------------------------------------------------                             T1   T2                         + strand ----------------------------------------------------------------           − strand ----------------------------------------------------------------                         C2/C1 - gene                         + strand ----------------------------------------------------------------           − strand ----------------------------------------------------------------                                 T2′   T1′   C2′/C1′ - gene                         gene - C1′ /C2′                         + strand ----------------------------------------------------------------           − strand ----------------------------------------------------------------                             T2′   T1′                      
 
      Of course, the short loops and the long loops do not have to be on the same chromosome.  
      Hierarchy of Connectron Action  
      When a C1/C2 is expressed it forms a T1-T2 loop by forming a connectron. The C1/C2 sequence does not have to be on the same chromosome as the T1 and T2 sequences. This provides a way of causing interaction between chromosomes. When the T1-T2 loop forms, any genes in that loop region which had been expressing C1/C2 sequences in their 3′UTRs, now cease expressing the C1/C2 sequences. The connectrons formed by these C1/C2 sequences will cease to exist after some time thus opening up the genes inside the respective T1-T2 loops to expression. The hierarchy of connectron action is alternates between repression and expression. The connectron hierarchies can be of any depth.  
      One-to-Many Connectron Action  
      One C1/C2 sequence can form connectrons in many different places on many different chromosomes. The only requirement is that C1=T1 and C2=T2. This makes it possible for one expression event to control the expression of many genes on different chromosomes.  
      Many-to-One Connectron Action  
      C1/C2s that come from many different places on many different chromosomes can form a connectron for a specific T1-T2 sequence pair. The only requirement is that C1=T1 and C2=T2. This makes it possible for many different expression events to control the expression of one set of genes on a particular chromosome.  
      Many-to-Many Connectron Action  
      The arrangement of C1/C2s and T1-T2s across chromosomes can form a complex web of gene expression control relationships.  
      Percentage of the Genome Regulated by Connectrons  
      Since the connectrons for a sequenced genome can be calculated, the percentage of the genome that is open to connectron regulation can be known.  
      Emergent Property  
      The network of connectrons in any genome emerges from a knowledge of the complete DNA sequence of the genome. Because both the C1/C2 sequences and the T1-T2 sequences can be any place in the genome, the whole genomic sequence must be known before all the connectrons can be determined.  
      Paradigm Shift  
      For the past fifty years since the discovery by Watson and Crick of the double-helical nature of DNA, the reigning paradigm for scientific discovery has been the study of one gene and its effects on the behavior of a cell. The advent of genomic sequencing and this invention of connectrons that emerge from the whole genome will produce a shift in the way scientists view biological systems and the way they formulate and execute experiments. The many-to-many relationships between the connectrons mean that there are many ways in which the expression of a set of genes can be modulated. The multiplicity of control pathways produces a system stability that makes it possible for biological systems to be stable for long periods of evolutionary time. The thinking that goes into formulating scientific experiments will have to change to accommodate the changes in understanding that will be induced by the application and extension of this patent application.  
      Sequence Element  
      The double-stranded sequence of either a C1, a C2, a T1 or a T2 of some connectron.  
      Native Sequence Element  
      Any sequence element of a connectron which is a constitutive part of the native genome.  
      Native Connectron  
      Any connectron in which all four (i.e. the C1, C2, T1 and T2 sequence) sequence elements are constitutive parts of the native genome.  
      Synthetic Sequence Element  
      Any sequence element that has been added into a genome at some particular place. The actual sequence of bases may occur in one or more places in the genome. The synthetic aspect is that an instance has been placed into the genome at a specific place by design.  
      Copied Sequence Element  
      Any sequence element that has been copied from one place in a genome to another place in that genome.  
      Unique Sequence Element  
      Any double-stranded DNA sequence element for which there is only one pair of instances. Such a pair of instances can be used to implement the C1 and T1 synthetic sequence elements of a connectron or the C2 and T2 synthetic sequence elements of a connectron.  
      Extracted Sequence  
      Any sequence element that is moved from one place in a genome to another place in the same genome. The moved sequence element can be unique or non-unique.  
      Synthetic Connectron  
      Any connectron in which one or more of the sequence elements in a native connectron are substituted by synthetic sequence elements.  
      Designed Connectron  
      Any connectron that does not exist in the native genome.  
      RNA-Based Connectron  
      Any connectron in which the C1 and C2 elements are generated as RNA in the 3′UTR of some gene.  
      DBP  
      A multi-domain zinc-finger DNA Binding Protein that binds to a specific DNA double-stranded sequence.  
      Protein-Based Synthetic Connectron  
      Any synthetic connectron in which the C1 and C2 elements are generated by a DBP.  
      PNA  
      A Peptide Nucleic Acid is a molecular construct patented and supplied by Boehringer-Mannheim. The A, T, G, C base portions of are the same as an RNA but the ribose ring has been replaced by a peptide-like configuration of atoms.  
      PNA-Based Synthetic Connectron  
      Any synthetic connectron in which the C1 and C2 elements are generated by a sequence of Peptide Nucleic Acid (PNA) bases.  
      Generalized Synthetic Connectron  
      Any synthetic connectron in which the C1 and C2 elements are generated by two linked double-strand DNA binding elements.  
      Individual Connectron State  
      A binary representation of whether the C1-C2 elements are bound to the cognate T1 and T2 elements. A 0 means that the connectron is not formed. A 1 means that the connectron is formed and hence the expression of the genes between the T1 and T2 elements are turned off.  
      Genomic Connectron State  
      The collection of all the individual native and synthetic connectron states in a genome. The individual connectron states are ordered along each chromosome and plasmid by the position of the T1 element.  
      Connectron Simulation  
      The temporal transitions of the genomic connectron states as the individual connectron states interact with each other.  
     Content of the CD  
      The Sequence Listing Part is incorporated herein by reference. The material contained on this compact disc attached hereto was created on Jun. 30, 2003,  
      synthetic.sequences has 13,770 bytes  
     BRIEF DESCRIPTION OF THE OBJECTS OF THE INVENTION  
      The basic methods patent application provides the methods for determining the structure of the native connectrons in a variety of genomes. Since the original conceptualization of connectrons followed from the work that we did on the design of zinc-finger DNA Binding Proteins (DBPs), U.S. Pat. No. 6,205,404, it has always been the applicant&#39;s intention to use these designed proteins to modify genomic connectron behavior.  
      An object of this invention is to provide a method for utilizing the genomic simulation of connectron behavior to facilitate the optimization of design decisions related to deleting connectrons from a genome or adding connectrons to a genome.  
      An object of this invention is to provide a method for utilizing the genomic simulation by computer of connectron behavior to facilitate the optimization by computer of design decisions related to deleting connectrons from a genome or adding connectrons to a genome.  
      An object of this invention is to provide a method for modifying the connectron behavior of a genome by deleting and adding connectrons.  
      An object of the invention is to provide a method for creating new connectrons in a genome by copying one or more double-stranded DNA sequence elements from one place in the genome to another place in the genome or by extracting a double-stranded DNA sequence element from one place in the genome and moving it to another place in the genome or by introducing a new unique pair of double-stranded DNA sequence elements into the genome at specific places.  
      An object of the invention if to provide a method for creating new connectrons in a genome by copying, extracting or adding unique DNA elements in addition to using either DBPs, PNAs or a linked pair of generalized DNA binding elements to implement the C1 and C2 elements of the new connectron.  
     DESCRIPTION OF THE TABLES  
      Table 1  
      The 10 possible ways of deleting a connectron  
      Table 2  
      The 15 possible synthetic connectrons defined by combinations of native and synthetic elements  
      Table 3  
      The 4 possible synthetic connectrons defined by combinations of native and synthetic DNA elements and synthetic DBP elements  
      Table 4  
      The 4 possible synthetic connectrons defined by combinations of native and synthetic DNA elements and synthetic PNA elements  
      Table 5  
      The 4 possible synthetic connectrons defined by combinations of native and synthetic DNA elements and a pair of linked double-strand DNA binding elements  
      Table 6  
      The 2 possible ways of implementing a single synthetic element in a synthetic connectron  
      Table 7  
      The 14 possible ways of implementing a pair of synthetic elements in a synthetic connectron  
      Table 8  
      The 41 possible ways of implementing three synthetic elements in a synthetic connectron  
      Table 9  
      The 25 possible ways of implementing four synthetic elements in a synthetic connectron  
     DESCRIPTION OF THE INVENTION  
      The simulation of the connectron behavior of a genome provides a powerful way of understanding how individual connectrons interact with each other. From the more than 100 genomes whose connectron structure we have determined, it is clear that a given C1-C2 may generate many different connectrons—the one-to-many connectron action mode. Similarly it is clear that a given connectron may be generated by the expression of many different instances of the C1-C2 signal—the many-to-one connectron action mode. The temporal interaction of these one-to-many and many-to-one modes of connectron control of gene expression can best be understood by doing a genomic connectron simulation and looking at the results. This is especially important when determining when and where to delete connectrons from a native genome or add new connectrons to a native genome. Genomic connectron simulation is the subject of a related patent application.  
      Although there are instances in different genomes of a C1-C2 generating only one connectron, much more frequently a given C1-C2 will generate several connectrons. When only one connectron is generated by a given C1-C2, a decision to delete the connectron or to add another connectron using the same or different C1 or C2 elements will have no side effects as long as the T1 and T2 elements are only used by this connectron. This is the relative infrequent example of one-to-one. Much more frequently, deleting or changing a given C1 or C2 may have multiple consequences and serious behavioral side effects. Modification of genomic connectron control of gene expression will inevitably involve compromises, design decisions, and—worst of all—patch-ups. Consider an example in which a given C1-C2 generates two connectrons. For some reason we desire to delete one of the two connectrons. A patch-up can be achieved by finding some other way to generate the second connectron. This could be achieved by adding one or more synthetic connectron elements to generate the second connectron as a synthetic connectron.  
      If there are no side effects of a design decision then that is the optimum. If there are side effects, the genomic simulation of connectron behavior makes it possible to evaluate the genomic behavioral consequences of the design and implementation decisions.  
      The deletion of a connectron as shown in table 1 can occur in 10 different ways ranging from deleting or modifying just one sequence element to deleting or modifying all four sequence elements. Anything that destroys the sequence recognition of the T1 by the C1 or the T2 by the C2 will have the effect of deleting the connectron.  
      Any or all of the four elements (C1, C2, T1 and T2) of a native connectron can be replaced with synthetic elements to form a synthetic connectron. Table 2 gives the 15 possible types of synthetic connectrons. A designed connectron can be introduced into a genome to either (1) control the expression of a set of genes already controlled by other native connectrons, or (2) control the expression of a newly selected set of genes. Using DNA sequences, a designed connectron be made from any of the 15 combinations of native and synthetic elements in Table 2. If the C1 and C2 elements of a connectron are generated by a zinc-finger DBP then the 4 combinations of synthetic and designed connectrons in table 3 are possible. If the C1 and C2 elements of a connectron are generated by a PNA then the 4 combinations of synthetic and designed connectrons in table 4 are possible. If the C1 and C2 elements of a connectron are generated by a linked pair of DNA binding elements then the 4 combinations of synthetic and designed connectrons in table 5 are possible. The DNA binding elements G1 and G2 can be proteins or any other molecular material that recognizes the DNA sequences of the T1 and T2 elements.  
      The implementation of the synthetic elements of a designed connectron can be achieved in several different ways. In table 2 from one to four of the sequence elements of a connectron can be substituted by a synthetic sequence element. There are three different ways of creating a synthetic sequence element. An existing sequence element somewhere in the genome can be copied into a new location. An existing sequence element can be extracted from one location in the genome and placed in another position in the genome. A new pair of sequence elements not otherwise present in the genome can be created. One instance of this new, unique sequence element must be a C1 or a C2. If the first instance is a C1 then the second instance of this new, unique sequence element must be a T1. Similarly, if the first instance is a C2 then the second instance of this new, unique sequence element must be a T2. Table 6 shows that there are only two ways of generating a synthetic connectron when only one synthetic sequence element is used. Implementing a new, unique sequence element is not possible because these sequence elements must come in pairs. Table 7 shows that there are 14 ways of implementing a pair of synthetic sequence elements to form a synthetic connectron. Table 8 shows that there are 41 ways of implementing three synthetic sequence elements to form a synthetic connectron. Table 9 shows that there are 25 ways of implementing four synthetic sequence elements to form a synthetic connectron.  
    
    
     EXAMPLES  
      Tables 1 thru 9 provide a large combinatorial number of ways of deleting connectrons from a genome and of adding connectrons to a genome. We give one example of deleting one connectron from a single genome and five examples of a connectron to four different genomes. It is clear that many other variations would be obvious to someone skilled in the art.  
     Deletion of a Transient Connectron from One Chromosome to Itself  
      Connectron 13 is an example of a transient connectron in the  S. cerevisiae  genome. As per table 1, this connectron can be deleted by either deleting or modifying any one or all four of the connectron elements. The C1 and the C2 identifiers are 36 while the T1 identifier is 39 and the T2 identifier is 111. When this connectron is deleted, all the properties stated below disappear.  
      The original connectron 13 is described as  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  13   1   36   36   1   39   111   transient                  
 
      The C1/C2 source of the transient connectron 13 is represented in table 1 as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  CPT   36   1   1   12.572   12.788   .217   OS−&gt; ||||||||||||||||||                  
 
      The “Type” descriptor of this transient C1/C2 connectron source is “CPT”. The letter “P” indicates that the C1/C2 connectron source occurs on the positive strand of the double-stranded DNA of the genome. The letter “N” in this place would indicate a C1/C2 connectron source on the negative strand of the genomic DNA. The letter “T” in this descriptor indicates a “transient” connectron. Similarly, the letter “P” would indicate a permanent connectron that is shown in a later example. The “Start”, “Stop” and “Length” descriptors throughout these examples are given in kilo-bases (KB).  
      The T1-T2 target of the transient connectron 13 as shown in table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TP   39   1   1   12.572   12.807   .236             *−+++++++++++++++++++*                   TN   40   8   1   12.908   12.964   .057             *−++++++++++++++++++++*               CNT   41   1   1   12.908   12.964   .057          −−&gt;  |||||||||||||||||||||               CPT   42   1   1   12.908   12.964   .057          −−&gt;  |||||||||||||||||||||               TP   43   1   1   12.922   12.964   .043             *−+++++++++++++++++++++*               CNT   44   1   1   12.966   12.986   .021          −−&gt;  ||||||||||||||||||||||               CPT   45   8   1   12.966   12.986   .021          −−&gt;  ||||||||||||||||||||||               TP   46   1   1   12.966   12.986   .021             *−++++++++++++++++++++++*               TN   47   1   1   13.027   13.159   .133             *−+++++++++++++++++++++++*               CNT   48   1   1   13.028   13.099   .072         OS−&gt;  ||||||||||||||||||||||||               TP   49   1   1   13.028   13.099   .072             *−++++++++++++++++++++++++*               CPT   50   1   1   13.053   13.124   .072         OS−&gt;  |||||||||||||||||||||||||               TP   51   1   1   13.102   13.159   .058             *−+++++++++++++++++++++++++*               CNT   52   1   1   13.105   13.246   .142          −&gt;  ||||||||||||||||||||||||||               CPT   53   1   1   13.130   13.246   .117          −&gt;  ||||||||||||||||||||||||||               TN   54   1   1   13.176   13.194   .019             *−++++++++++++++++++++++++++*               TN   55   1   1   13.196   13.231   .036             *−+++++++++++++++++++++++++++**               TP   56   1   1   13.211   13.246   .036             *−+++++++++++++++++++++++++++++               CPT   57   1   1   13.253   13.290   .038          −−&gt;  |||||||||||||||||||||||||||||               TN   58   1   1   13.253   13.290   .038             *−+++++++++++++++++++++++++++++               TP   59   1   1   13.255   13.285   .031             *−+++++++++++++++++++++++++++++               CNT   60   1   1   13.255   13.290   .036          −−&gt;  |||||||||||||||||||||||||||||               CPT   61   8   1   13.295   13.315   .021          −−&gt;  |||||||||||||||||||||||||||||               TN   62   8   1   13.295   13.317   .023             *−+++++++++++++++++++++++++++++               CNT   63   8   1   13.340   13.379   .040          −−&gt;  |||||||||||||||||||||||||||||               CPT   64   8   1   13.341   13.380   .040          −−&gt;  |||||||||||||||||||||||||||||               GG   65   1   1   13.364   13.744   .381   Group0004   |||||||||||||||||||||||||||||               CPT   66   1   1   13.387   13.405   .019          −−&gt;  |||||||||||||||||||||||||||||               TN   67   8   1   13.387   13.413   .027             *−+++++++++++++++++++++++++++++               TP   68   1   1   13.444   13.460   .017             *−+++++++++++++++++++++++++++++               CPT   69   8   1   13.566   13.582   .017          −−&gt;  |||||||||||||||||||||||||||||               TN   70   8   1   13.574   13.591   .018             *−+++++++++++++++++++++++++++++               CPT   71   8   1   13.585   13.599   .016          −−&gt;  |||||||||||||||||||||||||||||               TN   72   1   1   13.656   13.681   .026             *−+++++++++++++++++++++++++++++               TP   73   1   1   13.656   13.706   .051             *−+++++++++++++++++++++++++++++               TN   74   9   1   13.704   13.726   .023             *−+++++++++++++++++++++++++++++               CPT   75   1   1   13.709   13.726   .018          −−&gt;  |||||||||||||||||||||||||||||               TN   76   1   1   13.734   13.750   .017             *−+++++++++++++++++++++++++++++               CPT   77   1   1   13.734   13.782   .049          −−&gt;  |||||||||||||||||||||||||||||               TP   78   1   1   13.734   13.782   .049             *−+++++++++++++++++++++++++++++               TN   79   1   1   13.768   13.782   .015             *−+++++++++++++++++++++++++++++               CPT   80   1   1   13.815   13.858   .044          −−&gt;  |||||||||||||||||||||||||||||               TN   81   1   1   13.840   13.858   .019             *−+++++++++++++++++++++++++++++               CPT   82   1   1   14.422   14.460   .039          −−&gt;  |||||||||||||||||||||||||||||               CPT   83   1   1   14.941   14.962   .022          −−&gt;  |||||||||||||||||||||||||||||               CPT   84   1   1   14.966   14.993   .028          −−&gt;  |||||||||||||||||||||||||||||               CPT   85   1   1   14.997   15.018   .022          −−&gt;  |||||||||||||||||||||||||||||               TP   86   1   1   15.795   15.816   .022             *−+++++++++++++++++++++++++++++               TP   87   1   1   15.996   16.020   .025             *−++*||||||||||||||||||||||||||               TP   88   1   1   16.874   16.898   .025             *−++−++++++++++++++++++++++++++               CNT   89   1   1   20.136   20.151   .016          −−&gt;  || ||||||||||||||||||||||||||               CNT   90   1   1   20.157   20.176   .020          −−&gt;  || ||||||||||||||||||||||||||               GG   91   1   1   21.526   21.852   .327   Group0005   || ||||||||||||||||||||||||||               CPT   92   1   1   22.257   22.304   .048          −−&gt;  || ||||||||||||||||||||||||||               CNT   93   1   1   22.275   22.304   .030          −−&gt;  || ||||||||||||||||||||||||||               CNT   94   1   1   22.307   22.322   .016          −−&gt;  || ||||||||||||||||||||||||||               CPT   95   1   1   22.307   22.322   .016          −−&gt;  || ||||||||||||||||||||||||||               CNT   96   1   1   22.324   22.338   .015          −−&gt;  || ||||||||||||||||||||||||||               CNT   97   1   1   22.351   22.367   .017          −−&gt;  || ||||||||||||||||||||||||||               CPT   98   8   1   22.351   22.367   .017          −−&gt;  || ||||||||||||||||||||||||||               CNT   99   1   1   22.376   22.392   .017          −−&gt;  || ||||||||||||||||||||||||||               CPT   100   8   1   22.376   22.392   .017          −−&gt;  || ||||||||||||||||||||||||||               TN   101   1   1   23.300   23.324   .025             *−++*||||||||||||||||||||||||||               CPT   102   8   1   23.683   23.716   .034          −−&gt;  |||||||||||||||||||||||||||||               GG   103   1   1   24.001   27.969   3.969   Group0006   |||||||||||||||||||||||||||||               TN   104   1   1   24.119   24.431   .313             *−++++**|||||||||||||||||||||||               CPT   105   1   1   24.283   24.352   .070         OS−&gt;  ||||  |||||||||||||||||||||||               TP   106   1   1   24.287   24.431   .145             *−++++−−+|||||||||||||||||||||               TN   107   1   1   24.433   24.514   .082             *−++++−−*−*||||||||||||||||||||               TN   108   1   1   24.516   24.603   .088             *−++++−−−−−*|||||||||||||||||||               TN   109   8   1   24.605   24.703   .099             *−++++−−−−−−**|||||||||||||||||               TN   110   1   1   24.743   24.854   .112             *−++++−−−−−−−−*||||||||||||||||               TP   111   1   1   24.863   25.001   .039             *−++++−−−−−−−−−+*++*+*|||||||||                  
 
      The “Type” descriptor of the Ti (Id number 39) is “TP” showing that is T1 target is on the positive strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 111) also has the type descriptor “TP”.  
      The T1-T2 loop diagram above can be read by tracing the path from the * of the T1 to the right to the appropriate *, then by tracing a path down the diagram to the first *, then by tracing a path left to the * of the T2. When horizontal lines (indicated by −) intersect with other vertical lines (indicated by |) then the symbol at that point is changed to a +. When the T1-T2 loop does not contain an groups of genes then the vertical symbol (indicated by | or +) is changed to @ as shown below  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  TN   xx   1   1   278.386   279.148   .763   *---*       XX   xx   1   1   278.387   278.416   .030   *  @       XX   xx   1   1   278.421   278.450   .030   *  @       TP   xx   1   1   278.452   278.892   .441   *---*                  
 
      Group0004 (Id number 65) has the type descriptor “GG”. The same is true for Group0006 (Id number 103).  
      Group0004 through Group0006 are described in table 2 as  
                                                               Chro-                           COG —     mo-       Gene Name   Id   some   Direction   Start   Stop   Length                                                            YAL064C-A   —   1   negative   13.364   13.744   .381       Group0005       YAL064W   —   1   positive   21.526   21.852   .327       Group0006       FL09   —   1   negative   24.001   27.969   3.969                  
 
      All of the data for the transient connectron 13 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   13   transient                                                         Chro-                       Control       mo-   C1/       Sequences -   Direction   some   C2_Id   Start   Stop   Length                   positive   1   36   12.572   12.788   .217                                             Trigger Gene -   Name   COG_Id   Start   Stop   Length                   YAL064W-B   —   12.047   12.427   .381                                                         Chro-                       Target       mo-       Sequences -   Direction   some       Start   Stop   Length                           T1_Id           positive   1   39   12.572   12.807   .236                   T2_Id                   111   24.863   25.001   .020                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0004   YAL064C-A   —   positive   13.364   13.744   .381       2   1   Group0005   YAL064W   —   positive   21.526   21.852   .327       3   1   Group0006   FL09   —   positive   24.001   27.969   3.969                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   1   41   negative   12.964   12.908   .057       2   1   42   positive   12.908   12.964   .057       3   1   44   negative   12.986   12.966   .021       4   1   45   positive   12.966   12.986   .021       5   1   48   negative   13.099   13.028   .072       6   1   50   positive   13.053   13.124   .072       7   1   52   negative   13.246   13.105   .142       8   1   53   positive   13.130   13.246   .117       9   1   57   positive   13.253   13.290   .038       10   1   60   negative   13.290   13.255   .036       11   1   61   positive   13.295   13.315   .021       12   1   63   negative   13.379   13.340   .040       13   1   64   positive   13.341   13.380   .040       14   1   66   positive   13.387   13.405   .019       15   1   69   positive   13.566   13.582   .017       16   1   71   positive   13.585   13.599   .016       17   1   75   positive   13.709   13.726   .018       18   1   77   positive   13.734   13.782   .049       19   1   80   positive   13.815   13.858   .044       20   1   82   positive   14.422   14.460   .039       21   1   83   positive   14.941   14.962   .022       22   1   84   positive   14.966   14.993   .028       23   1   85   positive   14.997   15.018   .022       24   1   89   negative   20.151   20.136   .016       25   1   90   negative   20.176   20.157   .020       26   1   92   positive   22.257   22.304   .048       27   1   93   negative   22.304   22.275   .030       28   1   94   negative   22.322   22.307   .016       29   1   95   positive   22.307   22.322   .016       30   1   96   negative   22.338   22.324   .015       31   1   97   negative   22.367   22.351   .017       32   1   98   positive   22.351   22.367   .017       33   1   99   negative   22.392   22.376   .017       34   1   100   positive   22.376   22.392   .017       35   1   102   positive   23.683   23.716   .034       36   1   105   positive   24.283   24.352   .070                  
 
      The verbose description of the transient connectron 13 is:  
      In the  Saccharomyces cerevisiae  complete genome the transient connectron number 13 is generated by the control sequence (C1/C2) whose identifier number is 36. This control sequence is on the positive strand of the genomic DNA of chromosome 1. The genomic start and stop positions of this control sequence are 12.572 KB and 12.788 KB with a length of 0.217 KB. Expression of the RNA for this connectron is triggered by the promotion of the gene whose name is YAL064W-B. The genomic start and stop positions of this gene are 12.047 KB and 12.427 KB and with a length of 0.381 KB. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the positive strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 39. The genomic start and stop positions of this initiating target sequence are 12.572 KB and 12.807 KB with a length of 0.236 KB. The identifier number of the terminating target sequence (T2) is 111. The genomic start and stop positions of this terminating target sequence are 24.863 KB and 25.001 KB with a length of 0.020 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name YAL064C-A. The genomic start and stop positions of this gene are 13.364 KB and 13.744 KB with a length of 0.381 KB. (2) The gene that has the name YAL064W. The genomic start and stop positions of this gene are 21.526 KB and 21.852 KB with a length of 0.327 KB. (3) The gene that has the name FLO9. The genomic start and stop positions of this gene are 24.001 KB and 27.969 KB with a length of 3.969 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 41 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 12.964 KB and 12.908 KB with a length of 0.057 KB. (2) The connectron that has the identifier 42 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 12.908 KB and 12.964 KB with a length of 0.057 KB. (3) The connectron that has the identifier 44 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 12.986 KB and 12.966 KB with a length of 0.021 KB. (4) The connectron that has the identifier 45 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 12.966 KB and 12.986 KB with a length of 0.021 KB. (5) The connectron that has the identifier 48 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 13.099 KB and 13.028 KB with a length of 0.072 KB. (6) The connectron that has the identifier 50 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.053 KB and 13.124 KB with a length of 0.072 KB. (7) The connectron that has the identifier 52 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 13.246 KB and 13.105 KB with a length of 0.142 KB. (8) The connectron that has the identifier 53 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.130 KB and 13.246 KB with a length of 0.117 KB. (9) The connectron that has the identifier 57 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.253 KB and 13.290 KB with a length of 0.038 KB. (10) The connectron that has the identifier 60 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 13.290 KB and 13.255 KB with a length of 0.036 KB. (11) The connectron that has the identifier 61 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.295 KB and 13.315 KB with a length of 0.021 KB. (12) The connectron that has the identifier 63 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 13.379 KB and 13.340 KB with a length of 0.040 KB. (13) The connectron that has the identifier 64 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.341 KB and 13.380 KB with a length of 0.040 KB. (14) The connectron that has the identifier 66 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.387 KB and 13.405 KB with a length of 0.019 KB. (15) The connectron that has the identifier 69 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.566 KB and 13.582 KB with a length of 0.017 KB. (16) The connectron that has the identifier 71 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.585 KB and 13.599 KB with a length of 0.016 KB. (17) The connectron that has the identifier 75 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.709 KB and 13.726 KB with a length of 0.018 KB. (18) The connectron that has the identifier 77 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.734 KB and 13.782 KB with a length of 0.049 KB. (19) The connectron that has the identifier 80 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 13.815 KB and 13.858 KB with a length of 0.044 KB. (20) The connectron that has the identifier 82 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 14.422 KB and 14.460 KB with a length of 0.039 KB. (21) The connectron that has the identifier 83 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 14.941 KB and 14.962 KB with a length of 0.022 KB. (22) The connectron that has the identifier 84 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 14.966 KB and 14.993 KB with a length of 0.028 KB. (23) The connectron that has the identifier 85 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 14.997 KB and 15.018 KB with a length of 0.022 KB. (24) The connectron that has the identifier 89 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 20.151 KB and 20.136 KB with a length of 0.016 KB. (25) The connectron that has the identifier 90 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 20.176 KB and 20.157 KB with a length of 0.020 KB. (26) The connectron that has the identifier 92 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 22.257 KB and 22.304 KB with a length of 0.048 KB. (27) The connectron that has the identifier 93 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 22.304 KB and 22.275 KB with a length of 0.030 KB. (28) The connectron that has the identifier 94 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 22.322 KB and 22.307 KB with a length of 0.016 KB. (29) The connectron that has the identifier 95 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 22.307 KB and 22.322 KB with a length of 0.016 KB. (30) The connectron that has the identifier 96 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 22.338 KB and 22.324 KB with a length of 0.015 KB. (31) The connectron that has the identifier 97 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 22.367 KB and 22.351 KB with a length of 0.017 KB. (32) The connectron that has the identifier 98 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 22.351 KB and 22.367 KB with a length of 0.017 KB. (33) The connectron that has the identifier 99 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 22.392 KB and 22.376 KB with a length of 0.017 KB. (34) The connectron that has the identifier 100 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 22.376 KB and 22.392 KB with a length of 0.017 KB. (35) The connectron that has the identifier 102 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 23.683 KB and 23.716 KB with a length of 0.034 KB. (36) The connectron that has the identifier 105 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 24.283 KB and 24.352 KB with a length of 0.070 KB.  
     Addition of a Synthetic Connectron of Type 2 from Table 2  
      A synthetic connectron of type 2 in which the C1 and C2 are synthetic elements, the T1 is a synthetic element and the T2 is a natural element can be introduced into the  E. coli  genome by modifying the DNA double-strand sequences at 4626.130 kb through 4626.166 kb for a length of 0.036 kb and by modifying the DNA double-strand sequence at 705.150 kb through 705.203 kb for a length of 0.054 kb.  
      Connectron 62521 is an example of a synthetic transient connectron. It is described as  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  62521   1   4651a   4651a   1   811a   975   transient                  
 
      The C1/C2 source of the transient connectron 62521 is represented in Table 1 as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  CPT   4651a   1   1   4626.130   4626.166   .037   ||| || | |||| || |  ||                  
 
      The “Type” descriptor of this transient C1/C2 connectron source is “CPT”. The letter “P” indicates that the C1/C2 connectron source occurs on the positive strand of the double-stranded DNA of the genome. The letter “N” in this place would indicate a C1/C2 connectron source on the negative strand of the genomic DNA. The letter “T” in this descriptor indicates a “transient” connectron. Similarly, the letter “P” would indicate a permanent connectron that is shown in a later example. The “Start”, “Stop” and “Length” descriptors throughout these examples are given in kilo-bases (KB).  
      The T1-T2 target of the transient connectron 62521 as shown in Table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TN   811a   1   1   705.150   705.203   .054             *−*                   TP   812   1   1   705.122   705.141   .020             *−+               GG   813   1   1   705.316   706.980   1.665   Group0150   |               TN   814   1   1   707.013   707.028   .016             *−+               TP   815   1   1   707.014   707.028   .015             *−+               CPT   816   1   1   707.055   707.109   .055          −−&gt;  |               TN   817   1   1   707.055   707.109   .055             *−+               TP   818   1   1   707.055   707.109   .055             *−+               CPT   819   1   1   707.112   707.162   .051         OS−&gt;  |               TN   820   1   1   707.112   707.162   .051             *−+               TP   821   1   1   707.112   707.162   .051             *−+               GG   822   1   1   707.557   710.688   3.131   Group0151   |               CNT   823   1   1   710.633   710.647   .015         OS−&gt;  |               TN   824   1   1   710.633   710.647   .015             *−+               CNT   825   1   1   710.652   710.666   .015          −−&gt;  |               GG   826   1   1   710.828   712.755   1.927   Group0152   |               TN   827   1   1   712.281   712.296   .016             *−+               GG   828   1   1   712.781   714.421   1.641   Group0153   |               TN   829   1   1   714.481   714.518   .038             *−+               CPT   830   1   1   714.481   714.519   .039         OS−&gt;  |               TP   831   1   1   714.482   714.519   .038             *−+               CPT   832   1   1   714.524   714.540   .017          −−&gt;  |               TN   833   1   1   714.524   714.540   .017             *−+               TP   834   1   1   714.524   714.540   .017             *−+               CNT   835   1   1   714.543   714.593   .051         OS−&gt;  |               TN   836   1   1   714.543   714.593   .051             *−+               TP   837   1   1   714.543   714.593   .051             *−+               CPT   838   1   1   714.544   714.606   .063         OS−&gt;  |               GG   839   1   1   714.635   715.928   1.293   Group0154   |               GN   840   1   1   715.170   715.532   .363   ybfg        |               TN   841   1   1   716.085   716.103   .019             *−+               TP   842   1   1   716.085   716.103   .019             *−+               GG   843   1   1   716.169   724.202   8.033   Group0155   |               CNT   844   1   1   720.278   720.296   .019          −−&gt;  |               GN   845   1   1   720.279   724.202   3.924   kdpe        |               TP   846   1   1   721.769   721.783   .015             *−+               TN   847   1   1   721.812   721.827   .016             *−+               GG   848   1   1   724.211   727.955   3.744   Group0156   |               TP   849   1   1   726.665   726.679   .015             *−+               GG   850   1   1   728.357   733.325   4.968   Group0157   |               GP   851   1   1   728.806   733.325   4.520   rhsc        |               CPT   852   1   1   729.408   729.446   .039          −−&gt;  |               TP   853   1   1   730.270   730.284   .015             *−+               CPT   854   1   1   730.443   730.457   .015          −−&gt;  |               CPT   855   1   1   730.468   730.482   .015          −−&gt;  |               CPT   856   1   1   730.484   730.507   .024          −−&gt;  |               CPT   857   1   1   731.251   731.290   .040          −−&gt;  |               TP   858   1   1   731.475   731.508   .034             *−+               TP   859   1   1   731.512   731.562   .051             *−+               TP   860   1   1   731.564   731.693   .130             *−+               TP   861   1   1   731.698   731.755   .058             *−+               TP   862   1   1   731.757   731.819   .063             *−+               TP   863   1   1   731.821   731.903   .083             *−+               TP   864   1   1   731.906   732.033   .128             *−+               CPT   865   1   1   731.994   732.016   .023          −−&gt;  |               CPT   866   1   1   732.019   732.034   .016          −−&gt;  |               TP   867   1   1   732.035   732.050   .016             *−+               TP   868   1   1   732.052   732.179   .128             *−+               CPT   869   1   1   732.065   732.179   .115         OS−&gt;  |               CPT   870   1   1   732.198   732.212   .015          −−&gt;  |               TP   871   1   1   732.198   732.212   .015             *−|               CPT   872   1   1   732.214   732.233   .020          −−&gt;  |               TP   873   1   1   732.214   732.233   .020             *−+               CPT   874   1   1   732.235   732.283   .049          −−&gt;  |               TP   875   1   1   732.235   732.283   .049             *−+               CPT   876   1   1   732.306   732.326   .021          −−&gt;  |               TP   877   1   1   732.306   732.326   .021             *−+               CPT   878   1   1   732.328   732.452   .125          −−&gt;  |               TP   879   1   1   732.328   732.482   .155             *−+               CPT   880   1   1   732.454   732.482   .029          −−&gt;  |               CPT   881   1   1   732.488   732.519   .032          −−&gt;  |               TN   882   1   1   733.330   733.344   .015             *−+               TP   883   1   1   733.330   733.344   .015             *−+               TP   884   1   1   733.371   733.513   .143             *−+               GG   885   1   1   733.443   735.442   2.000   Group0158   |               TP   886   1   1   733.515   733.564   .050             *−+               TP   887   1   1   733.569   733.626   .058             *−+               TP   888   1   1   733.628   733.645   .018             *−+               TP   889   1   1   733.647   733.696   .050             *−+               TP   890   1   1   733.698   733.774   .077             *−+               TP   891   1   1   733.776   733.904   .129             *−+               CPT   892   1   1   733.865   733.887   .023         OS−&gt;  |               CPT   893   1   1   733.890   733.905   .016          −−&gt;  |               TP   894   1   1   733.906   734.050   .145             *−+               CPT   895   1   1   733.936   734.050   .115          −−&gt;  |               TP   896   1   1   734.052   734.075   .024             *−+               CPT   897   1   1   734.052   734.139   .088          −−&gt;  |               TP   898   1   1   734.084   734.139   .056             *−+               TP   899   1   1   734.149   734.179   .031             *−+               CPT   900   1   1   734.164   734.321   .158          −−&gt;  |               TP   901   1   1   734.192   734.321   .130             *−+               TP   902   1   1   734.323   734.378   .056             *−+               CPT   903   1   1   734.323   734.381   .059          −−&gt;  |               CPT   904   1   1   735.525   735.569   .045          −−&gt;  |               TP   905   1   1   735.525   735.569   .045             *−+               CPT   906   1   1   735.606   735.703   .098          −−&gt;  |               TP   907   1   1   735.606   735.703   .098             *−+               TP   908   1   1   735.707   735.721   .015             *−+               CPT   909   1   1   735.707   735.728   .022          −−&gt;  |               TP   910   1   1   735.749   735.803   .055             *−+               CPT   911   1   1   735.807   735.964   .158         OS−&gt;  |               TP   912   1   1   735.814   735.895   .082             *−+               TP   913   1   1   735.905   735.934   .030             *−+               TP   914   1   1   735.938   736.083   .146             *−+               CPT   915   1   1   735.986   736.083   .098         OS−&gt;  |               TP   916   1   1   736.152   736.173   .022             *−+               TP   917   1   1   736.187   736.217   .031             *−+               TP   918   1   1   736.219   736.265   .047             *−+               TP   919   1   1   736.288   736.334   .047             *−+               GG   920   1   1   736.327   737.184   .858   Group0159   |               TP   921   1   1   736.349   736.469   .121             *−+               TP   922   1   1   736.516   736.628   .113             *−+               TP   923   1   1   736.630   736.645   .016             *−+               TP   924   1   1   736.654   736.792   .139             *−+               TN   925   1   1   736.654   736.809   .156             *−+               TN   926   1   1   736.816   736.832   .017             *−+               CPT   927   1   1   737.017   737.032   .016          −−&gt;  |               CPT   928   1   1   737.035   737.057   .023          −−&gt;  |               TN   929   1   1   737.168   737.188   .021             *−++               TP   930   1   1   737.196   737.290   .095             *−+               CPT   931   1   1   737.261   737.275   .015          −−&gt;  |               CPT   932   1   1   737.278   737.292   .015          −−&gt;  |               TP   933   1   1   737.292   737.393   .102             *−+               GG   934   1   1   737.315   738.076   .762   Group0160   |               TP   935   1   1   737.411   737.475   .065             *−+               TP   936   1   1   737.479   737.557   .079             *−+               TP   937   1   1   737.580   737.597   .018             *−+               TP   938   1   1   737.605   737.626   .022             *−+               TP   939   1   1   737.633   737.648   .016             *−+               TP   940   1   1   737.653   737.679   .027             *−+               TP   941   1   1   737.683   737.752   .070             *−+               TP   942   1   1   737.798   737.822   .025             *−+               TP   943   1   1   737.828   737.895   .068             *−+               TP   944   1   1   737.897   737.931   .035             *−+               CPT   945   1   1   737.930   737.967   .038          −−&gt;  |               TP   946   1   1   737.936   737.967   .032             *−+               TP   947   1   1   737.970   737.988   .019             *−+               TN   948   1   1   737.990   738.015   .026             *−+               TP   949   1   1   737.990   738.015   .026             *−+               TN   950   1   1   738.019   738.051   .033             *−+               TP   951   1   1   738.019   738.051   .033             *−++               TP   952   1   1   738.053   738.074   .022             *−+               TN   953   1   1   738.058   738.074   .017             *−+               TN   954   1   1   738.107   738.126   .020             *−+               GG   955   1   1   738.224   740.148   1.925   Group0161   |               TN   956   1   1   740.172   740.213   .042             *−+               CNT   957   1   1   740.172   740.290   .119         OS−&gt;  |               CPT   958   1   1   740.172   740.290   .119         OS−&gt;  |               TP   959   1   1   740.173   740.213   .041             *−+               TP   960   1   1   740.216   740.241   .026             *−+               TN   961   1   1   740.216   740.288   .073             *−+               TP   962   1   1   740.244   740.288   .045             *−+               GG   963   1   1   740.298   757.628   17.330   Group0162   |               GP   964   1   1   742.816   745.122   2.307   ybgj        |               CPT   965   1   1   744.643   744.657   .015          −−&gt;  |               CPT   966   1   1   744.664   744.678   .015          −−&gt;  |               GP   967   1   1   754.400   756.896   2.497   sdhc        |               CPT   968   1   1   755.680   755.714   .035          −−&gt;  |               GP   969   1   1   756.912   757.628   .717   sdhb        |               TN   970   1   1   757.626   757.712   .087             *−+               CPT   971   1   1   757.628   757.712   .085         OS−&gt;  |               TP   972   1   1   757.629   757.712   .084             *−+               GG   973   1   1   757.687   760.730   3.044   Group0163   |               CPT   974   1   1   757.717   757.736   .020          −−&gt;  |               TN   975   1   1   757.718   757.753   .036             *−+                  
 
      The “Type” descriptor of the T1 (Id number 811a) is “TN” showing that is T1 target is on the negative strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 975) also has the type descriptor “TN”.  
      The T1-T2 loop diagram above can be read by tracing the path from the * of the T1 to the right to the appropriate *, then by tracing a path down the diagram to the first *, then by tracing a path left to the * of the T2. When horizontal lines (indicated by −) intersect with other vertical lines (indicated by |) then the symbol at that point is changed to a +. When the T1-T2 loop does not contain an groups of genes then the vertical symbol (indicated by | or +) is chanted to @ as shown below  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  TN   xx   1   1   278.386   279.148   .763   *---*       XX   xx   1   1   278.387   278.416   .030   *  @       XX   xx   1   1   278.421   278.450   .030   *  @       TP   xx   1   1   278.452   278.892   .441   *---*                  
 
      Group0150 through Group0163 are described in Table 2 as  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0150                                   glns   COG0008   b   1   positive   705.316   706.980   1.665       Group0151       ybfm   —   b   1   positive   707.557   708.963   1.407       ybfn   —   b   1   positive   709.013   709.339   .327       fur   COG0735   b   1   negative   709.423   709.869   .447       flda   COG0716   b   1   negative   710.158   710.688   .531       Group0152       ybfe   —   b   1   negative   710.828   711.190   .363       ybff   COG0596   b   1   negative   711.261   712.025   .765       seqa   COG3057   b   1   positive   712.210   712.755   .546       Group0153       pgm   COG0033   b   1   positive   712.781   714.421   1.641       Group0154       ybfp   —   b   1   positive   714.635   715.129   .495       ybfg   —   b   1   negative   715.170   715.532   .363       ybfh   —   b   1   negative   715.611   715.928   .318       Group0155       pote   COG0531   b   1   negative   716.169   719.683   3.515       kdpe   COG0745   b   1   negative   720.279   724.202   3.924       Group0156       kdpb   COG2216   b   1   negative   724.211   726.259   2.049       kdpa   COG2060   b   1   negative   726.282   727.955   1.674       Group0157       ybfa   —   b   1   positive   728.357   728.563   .207       rhsc   —   b   1   positive   728.806   733.325   4.520       Group0158       b0703   COG3209   b   1   positive   733.443   735.442   2.000       Group0159       ybfl   —   b   1   positive   736.327   737.184   .858       Group0160       ybfd   —   b   1   positive   737.315   738.076   .762       Group0161       ybga   COG3272   b   1   positive   738.224   740.148   1.925       Group0162       ybgh   COG3104   b   1   negative   740.298   741.779   1.482       ybgi   COG0327   b   1   positive   742.050   742.793   .744       ybgj   COG2049   b   1   positive   742.816   745.122   2.307       nei   COG0266   b   1   positive   745.158   745.949   .792       abrb   —   b   1   negative   745.946   747.037   1.092       ybgo   —   b   1   negative   747.144   748.930   1.787       ybgq   —   b   1   negative   748.945   751.401   2.457       ybgd   —   b   1   negative   751.452   752.018   .567       glta   COG0372   b   1   negative   752.408   753.691   1.284       sdhc   COG2009   b   1   positive   754.400   756.896   2.497       sdhb   COG0479   b   1   positive   756.912   757.628   .717       Group0163       b0725   —   b   1   positive   757.687   760.730   3.044                  
 
      All of the data for the transient connectron 62521 are pulled together in the following table that is the “terse” description of the connectron  
                                          Connectron Relationships -   Global_Id   Type                   62521   transient                                                         Chro-                       Control   Direc-   mo-   C1/       Sequences -   tion   some   C2_Id   Start   Stop   Length                   positive   1   4651a   4626.130   4626.166   .036                                             Trigger                           Gene -   Name   COG_Id   Start   Stop   Length                   sms       4623.481   4626.116   2.636                                                         Chro-                       Target   Direc-   mo-       Sequences -   tion   some       Start   Stop   Length                           T1_Id           negative   1   811a   705.150   705.203   .054                   T2_Id                   975   757.753   757.718   .036                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0150   gins   COG0008   positive   705.316   706.980   1.665       2   1   Group0151   ybfm   —   positive   707.557   710.688   3.131       3   1   Group0151   ybfn   —   positive   709.013   709.339   .327       4   1   Group0151   fur   COG0735   negative   709.869   709.423   .447       5   1   Group0151   flda   COG0716   negative   710.688   710.158   .531       6   1   Group0152   ybfe   —   positive   710.828   712.755   1.927       7   1   Group0152   ybff   COG0596   negative   712.025   711.261   .765       8   1   Group0152   seqa   COG3057   positive   712.210   712.755   .546       9   1   Group0153   pgm   COG0033   positive   712.781   714.421   1.641       10   1   Group0154   ybfp   —   positive   714.635   715.928   1.293       11   1   Group0154   ybfg   —   negative   715.532   715.170   .363       12   1   Group0154   ybfh   —   negative   715.928   715.611   .318       13   1   Group0155   pote   COG0531   positive   716.169   724.202   8.033       14   1   Group0155   kdpe   COG0745   negative   724.202   720.279   3.924       15   1   Group0156   kdpb   COG2216   positive   724.211   727.955   3.744       16   1   Group0156   kdpa   COG2060   negative   727.955   726.282   1.674       17   1   Group0157   ybfa   —   positive   728.357   733.325   4.968       18   1   Group0157   rhsc   —   positive   728.806   733.325   4.520       19   1   Group0158   b0703   COG3209   positive   733.443   735.442   2.000       20   1   Group0159   ybfl   —   positive   736.327   737.184   .858       21   1   Group0160   ybfd   —   positive   737.315   738.076   .762       22   1   Group0161   ybga   COG3272   positive   738.224   740.148   1.925       23   1   Group0162   ybgh   COG3104   positive   740.298   757.628   17.330       24   1   Group0162   ybgi   COG0327   positive   742.050   742.793   .744       25   1   Group0162   ybgj   COG2049   positive   742.816   745.122   2.307       26   1   Group0162   nei   COG0266   positive   745.158   745.949   .792       27   1   Group0162   abrb   —   negative   747.037   745.946   1.092       28   1   Group0162   ybgo   —   negative   748.930   747.144   1.787       29   1   Group0162   ybgq   —   negative   751.401   748.945   2.457       30   1   Group0162   ybgd   —   negative   752.018   751.452   .567       31   1   Group0162   glta   COG0372   negative   753.691   752.408   1.284       32   1   Group0162   sdhc   COG2009   positive   754.400   756.896   2.497       33   1   Group0162   sdhb   COG0479   positive   756.912   757.628   .717       34   1   Group0163   b0725   —   positive   757.687   760.730   3.044                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   1   816   positive   707.055   707.109   .055       2   1   819   positive   707.112   707.162   .051       3   1   823   negative   710.647   710.633   .015       4   1   825   negative   710.666   710.652   .015       5   1   830   positive   714.481   714.519   .039       6   1   832   positive   714.524   714.540   .017       7   1   835   negative   714.593   714.543   .051       8   1   838   positive   714.544   714.606   .063       9   1   844   negative   720.296   720.278   .019       10   1   852   positive   729.408   729.446   .039       11   1   854   positive   730.443   730.457   .015       12   1   855   positive   730.468   730.482   .015       13   1   856   positive   730.484   730.507   .024       14   1   857   positive   731.251   731.290   .040       15   1   865   positive   731.994   732.016   .023       16   1   866   positive   732.019   732.034   .016       17   1   869   positive   732.065   732.179   .115       18   1   870   positive   732.198   732.212   .015       19   1   872   positive   732.214   732.233   .020       20   1   874   positive   732.235   732.283   .049       21   1   876   positive   732.306   732.326   .021       22   1   878   positive   732.328   732.452   .125       23   1   880   positive   732.454   732.482   .029       24   1   881   positive   732.488   732.519   .032       25   1   892   positive   733.865   733.887   .023       26   1   893   positive   733.890   733.905   .016       27   1   895   positive   733.936   734.050   .115       28   1   897   positive   734.052   734.139   .088       29   1   900   positive   734.164   734.321   .158       30   1   903   positive   734.323   734.381   .059       31   1   904   positive   735.525   735.569   .045       32   1   906   positive   735.606   735.703   .098       33   1   909   positive   735.707   735.728   .022       34   1   911   positive   735.807   735.964   .158       35   1   915   positive   735.986   736.083   .098       36   1   927   positive   737.017   737.032   .016       37   1   928   positive   737.035   737.057   .023       38   1   931   positive   737.261   737.275   .015       39   1   932   positive   737.278   737.292   .015       40   1   945   positive   737.930   737.967   .038       41   1   957   negative   740.290   740.172   .119       42   1   958   positive   740.172   740.290   .119       43   1   965   positive   744.643   744.657   .015       44   1   966   positive   744.664   744.678   .015       45   1   968   positive   755.680   755.714   .035       46   1   971   positive   757.628   757.712   .085       47   1   974   positive   757.717   757.736   .020                  
 
      The verbose description of the synthetic connectron 62521 is:  
      In the  Escherichia coli  K-12 MG1655 complete genome the transient connectron number 62521 is generated by the control sequence (C1/C2) whose identifier number is 4651a. This control sequence is on the positive strand of the genomic DNA of chromosome 1. The genomic start and stop positions of this control sequence are 4626.130 KB and 4626.166 KB with a length of 0.036 KB. Expression of the RNA for this connectron is triggered by the promotion of the gene whose name is sms. The genomic start and stop positions of this gene are 4623.481 KB and 4626.116 KB and with a length of 2.636 KB. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the negative strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 811a. The genomic start and stop positions of this initiating target sequence are 705.150 KB and 705.203 KB with a length of 0.054 KB. The identifier number of the terminating target sequence (T2) is 975. The genomic start and stop positions of this terminating target sequence are 757.753 KB and 757.718 KB with a length of 0.036 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name glns and with a COG identifier of COG0008. The genomic start and stop positions of this gene are 705.316 KB and 706.980 KB with a length of 1.665 KB. (2) The gene that has the name ybfm. The genomic start and stop positions of this gene are 707.557 KB and 710.688 KB with a length of 3.131 KB. (3) The gene that has the name ybfn. The genomic start and stop positions of this gene are 709.013 KB and 709.339 KB with a length of 0.327 KB. (4) The gene that has the name fur and with a COG identifier of COG0735. The genomic start and stop positions of this gene are 709.869 KB and 709.432 KB with a length of 0.447 KB. (5) The gene that has the name flda and with a COG identifier of COG0716. The genomic start and stop positions of this gene are 710.688 KB and 710.158 KB with a length of 0.531 KB. (6) The gene that has the name ybfe. The genomic start and stop positions of this gene are 710.828 KB and 712.755 KB with a length of 1.927 KB. (7) The gene that has the name ybff and with a COG identifier of COG0596. The genomic start and stop positions of this gene are 712.025 KB and 711.261 KB with a length of 0.765 KB. (8) The gene that has the name seqa and with a COG identifier of COG3057. The genomic start and stop positions of this gene are 712.210 KB and 712.755 KB with a length of 0.546 KB. (9) The gene that has the name pgm and with a COG identifier of COG0033. The genomic start and stop positions of this gene are 712.781 KB and 714.421 KB with a length of 1.641 KB. (10) The gene that has the name ybfp. The genomic start and stop positions of this gene are 714.635 KB and 715.928 KB with a length of 1.293 KB. (11) The gene that has the name ybfg. The genomic start and stop positions of this gene are 715.532 KB and 715.170 KB with a length of 0.363 KB. (12) The gene that has the name ybfh. The genomic start and stop positions of this gene are 715.928 KB and 715.611 KB with a length of 0.318 KB. (13) The gene that has the name pote and with a COG identifier of COG0531. The genomic start and stop positions of this gene are 716.169 KB and 724.202 KB with a length of 8.033 KB. (14) The gene that has the name kdpe and with a COG identifier of COG0745. The genomic start and stop positions of this gene are 724.202 KB and 720.279 KB with a length of 3.924 KB. (15) The gene that has the name kdpb and with a COG identifier of COG2216. The genomic start and stop positions of this gene are 724.211 KB and 727.955 KB with a length of 3.744 KG. (16) The gene that has the name kdpa and with a COG identifier of COG2060. The genomic start and stop positions of this gene are 727.955 KB and 726.282 KB with a length of 1.674 KB. (17) The gene that has the name ybfa. The genomic start and stop positions of this gene are 728.357 KB and 733.325 KB with a length of 4.968 KB. (18) The gene that has the name rhsc. The genomic start and stop positions of this gene are 728.806 KOB and 733.325 KB with a length of 4.520 KB. (19) The gene that has the name b0703 and with a COG identifier of COG3209. The genomic start and stop positions of this gene are 733.443 KB and 735.442 KB with a length of 2.000 KB. (20) The gene that has the name ybfl. The genomic start and stop positions of this gene are 736.327 KB and 737.184 KB with a length of 0.858 KB. (21) The gene that has the name ybfd. The genomic start and stop positions of this gene are 737.315 KB and 738.076 KB with a length of 0.762 KB. (22) The gene that has the name ybga and with a COG identifier of COG3272. The genomic start and stop positions of this gene are 738.224 KB and 740.148 KB with a length of 1.925 KB. (23) The gene that has the name ybgh and with a COG identifier of COG3104. The genomic start and stop positions of this gene are 740.298 KB and 757.628 KB with a length of 17.330 KB. (24) The gene that has the name ybgi and with a COG identifier of COG0327. The genomic start and stop positions of this gene are 742.050 KB and 742.793 KB with a length of 0.744 KB. (25) The gene that has the name ybgj and with a COG identifier of COG2049. The genomic start and stop positions of this gene are 742.816 KB and 745.122 KB with a length of 2.307 KB. (26) The gene that has the name nei and with a COG identifier of COG0266. The genomic start and stop positions of this gene are 745.158 KB and 745.949 KB with a length of 0.792 KB. (27) The gene that has the name abrb. The genomic start and stop positions of this gene are 747.037 KB and 745.946 KB with a length of 1.092 KB. (28) The gene that has the name ybgo. The genomic start and stop positions of this gene are 748.930 KB and 747.144 KB with a length of 1.787 KB. (29) The gene that has the name ybgq. The genomic start and stop positions of this gene are 751.410 KB and 748.945 KB with a length of 2.457 KB. (30) The gene that has the name ybgd. The genomic start and stop positions of this gene are 752.018 KB and 751.452 KB with a length of 0.567 KB. (31) The gene that has the name glta and with a COG identifier of COG0372. The genomic start and stop positions of this gene are 753.691 KB and 752.408 KB with a length of 1.284 KB. (32) The gene that has the name sdhc and with a COG identifier of COG2009. The genomic start and stop positions of this gene are 754.400 KB and 756.896 KB with a length of 2.497 KB. (33) The gene that has the name sdhb and with a COG identifier of COG0479. The genomic start and stop positions of this gene are 756.912 KB and 757.628 KB with a length of 0.717 KB. (34) The gene that has the name b0725. The genomic start and stop positions of this gene are 757.687 KB and 760.730 KB with a length of 3.044 KB.  
      This connection controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 816 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 707.055 KB and 707.109 KB with a length of 0.055 KB. (2) The connectron that has the identifier 819 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 707.112 KB and 707.162 KB with a length of 0.051 KB. (3) The connectron that has the identifier 823 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 710.647 KB and 710.633 KB with a length of 0.015 KB. (4) The connectron that has the identifier 825 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 710.666 KB and 710.652 KB with a length of 0.015 KB. (5) The connectron that has the identifier 830 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 714.481 KB and 714.519 KB with a length of 0.039 KB. (6) The connectron that has the identifier 832 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 714.524 KB and 714.540 KB with a length of 0.017 KB. (7) The connectron that has the identifier 835 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 714.593 KB and 714.543 KB with a length of 0.051 KB. (8) The connectron that has the identifier 838 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 714.544 KB and 714.606 KB with a length of 0.063 KB. (9) The connectron that has the identifier 844 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 720.296 KB and 720.278 KB with a length of 0.019 KB. (10) The connectron that has the identifier 852 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 729.408 KB and 729.446 KB with a length of 0.039 KB. (11) The connectron that has the identifier 854 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 730.443 KB and 730.457 KB with a length of 0.015 KB. (12) The connectron that has the identifier 855 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 730.468 KB and 730.482 KB with a length of 0.015 KB. (13) The connectron that has the identifier 856 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 730.484 KB and 730.507 KB with a length of 0.024 KB. (14) The connectron that has the identifier 857 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 731.251 KB and 731.290 KB with a length of 0.040 KB. (15) The connectron that has the identifier 865 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 731.994 KB and 732.016 KB with a length of 0.023 KB. The connectron that has the identifier 866 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.019 KB and 732.034 KB with a length of 0.016 KB. (17) The connectron that has the identifier 869 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.065 KB and 732.179 KB with a length of 0.115 KB. (18) The connectron that has the identifier 870 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.198 KB and 732.212 KB with a length of 0.015 KB. (19) The connectron that has the identifier 872 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.214 KB and 732.233 KB with a length of 0.020 KB. (20) The connectron that has the identifier 874 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.235 KB and 732.283 KB with a length of 0.049 KB. (21) The connectron that has the identifier 876 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.306 KB and 732.326 KB with a length of 0.021 KB. (22) The connectron that has the identifier 878 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.328 KB and 732.452 KB with a length of 0.125 KB. (23) The connectron that has the identifier 880 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.454 KB and 732.482 KB with a length of 0.029 KB. (24) The connectron that has the identifier 881 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.488 KB and 732.519 KB with a length of 0.032 KB. (25) The connectron that has the identifier 892 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 733.865 KB and 733.887 KB with a length of 0.023 KB. (26) The connectron that has the identifier 893 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 733.890 KB and 733.905 KB with a length of 0.016 KB. (27) The connectron that has the identifier 895 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 733.936 KB and 734.050 KB with a length of 0.115 KB. (28) The connectron that has the identifier 897 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.052 KB and 734.139 KB with a length of 0.088 KB. (29) The connectron that has the identifier 900 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.164 KB and 734.321 KB with a length of 0.158 KB. (30) The connectron that has the identifier 903 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.323 KB and 734.381 KB with a length of 0.059 KB. (31) The connectron that has the identifier 904 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.525 KB and 735.569 KB with a length of 0.045 KB. (32) The connectron that has the identifier 906 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.606 KB and 735.703 KB with a length of 0.098 KB. (33) The connectron that has the identifier 909 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.707 KB and 735,728 KB with a length of 0.022 KB. (34) The connectron that has the identifier 911 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.807 KB and 735.964 KB with a length of 0.158 KB. (35) The connectron that has the identifier 915 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.986 KB and 736.083 KB with a length of 0.098 KB. (36) The connectron that has the identifier 927 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.017 KB and 737.032 KB with a length of 0.016 KB. (37) The connectron that has the identifier 928 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.035 KB and 737.057 KB with a length of 0.023 KB. (38) The connectron that has the identifier 931 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.261 KB and 737.275 KB with a length of 0.015 KB. (39) The connectron that has the identifier 932 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.278 KB and 737.292 KB with a length of 0.015 KB. (40) The connectron that has the identifier 945 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.930 KB and 737.967 KB with a length of 0.038 KB. (41) The connectron that has the identifier 957 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 740.290 KB and 740.172 KB with a length of 0.119 KB. (42) The connectron that has the identifier 958 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 740.172 KB and 740.290 KB with a length of 0.119 KB. (43) The connectron that has the identifier 965 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 744.643 KB and 744.657 KB with a length of 0.015 KB. (44) The connectron that has the identifier 966 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 744.664 KB and 744.678 KB with a length of 0.015 KB. (45) The connectron that has the identifier 968 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 755.680 KB and 755.714 KB with a length of 0.035 KB. (46) The connectron that has the identifier 971 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 757.628 KB and 757.712 KB with a length of 0.085 KB. (47) The connectron that has the identifier 974 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 757.717 KB and 757.736 KB with a length of 0.020 KB.  
     Addition of a Synthetic Connectron of Type 4 from Table 2  
      A synthetic connectron of type 4 in which the C1 and C2 are synthetic elements and the T1 and T2 are natural elements can be introduced into the  E. coli  genome by modifying the DNA double-strand sequences at 4626.130 kb through 4626.166 kb for a length of 0.036 kb.  
      Connectron 62520 is an example of a synthetic transient connectron. It is described as  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  62520   1   4651a   4651a   1   809   975   transient                  
 
      The C1/C2 source of the transient connectron 62520 is represented in Table 1 as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  CPT   4651a   1   1   4626.130   4626.166   .036   ||| || | |||| || |  ||                  
 
      The “Type” descriptor of this transient C1/C2 connectron source is “CPT”. The letter “P” indicates that the C1/C2 connectron source occurs on the positive strand of the double-stranded DNA of the genome. The letter “N” in this place would indicate a C1/C2 connectron source on the negative strand of the genomic DNA. The letter “T” in this descriptor indicates a “transient” connectron. Similarly, the letter “P” would indicate a permanent connectron that is shown in a later example. The “Start”, “Stop” and “Length” descriptors throughout these examples are given in kilo-bases (KB).  
      The T1-T2 target of the transient connectron 62520 as shown in Table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TN   809   1   1   698.713   698.766   .054             *−+++*+++**++*+++++−+++++++++++                   GG   810   1   1   698.797   705.113   6.316   Group0149   ||||||||||| ||||| |||||||||||               TN   811   1   1   705.121   705.141   .021             *−++*++++++++**++++*+++++*+++++               TP   812   1   1   705.122   705.141   .020             *−++−+++++++++−++++++++++−+++++               GG   813   1   1   705.316   706.980   1.665   Group0150   || ||||||||| |||||||||| |||||               TN   814   1   1   707.013   707.028   .016             *−++*+++++++++*++++++++++*++++*               TP   815   1   1   707.014   707.028   .015             *−++++++++++++++++++++++++++++−               CPT   816   1   1   707.055   707.109   .055          −−&gt;  ||||||||||||||||||||||||||||               TN   817   1   1   707.055   707.109   .055             *−+++++++++*+*++++++++*+*+++++*               TP   818   1   1   707.055   707.109   .055             *−+++++++++−+−++++++++−+−++++++               CPT   819   1   1   707.112   707.162   .051         OS−&gt;  ||||||||| | |||||||| | ||||||               TN   820   1   1   707.112   707.162   .051             *−++++*++++*+*+++++*+**+*+*+*++               TP   821   1   1   707.112   707.162   .051             *−++++−++++++++++++−+−++++−+−++               GG   822   1   1   707.557   710.688   3.131   Group0151   |||| |||||||||||| | |||| | ||               CNT   823   1   1   710.633   710.647   .015         OS−&gt;  |||| |||||||||||| | |||| | ||               TN   824   1   1   710.633   710.647   .015             *−++++−*||||||||||| | |||| | ||               CNT   825   1   1   710.652   710.666   .015          −−&gt;  ||||  ||||||||||| | |||| | ||               GG   826   1   1   710.828   712.755   1.927   Group0152   ||||  ||||||||||| | |||| | ||               TN   827   1   1   712.281   712.296   .016             *−++++−−+++++++++++−+−++++−+−++               GG   828   1   1   712.781   714.421   1.641   Group0153   ||||  ||||||||||| | |||| | ||               TN   829   1   1   714.481   714.518   .038             *−++++**+++*+++++++*+*++++*+***               CPT   830   1   1   714.481   714.519   .039         OS−&gt;  ||||||||| |||||||||||||||||               TP   831   1   1   714.482   714.519   .038             *−+++++++++−+++++++++++++++++−−               CPT   832   1   1   714.524   714.540   .017          −−&gt;  ||||||||| |||||||||||||||||               TN   833   1   1   714.524   714.540   .017             *−+++++++++*+*+++++++++++++++**               TP   834   1   1   714.524   714.540   .017             *−+++++++++++−+++++++++++++++++               CNT   835   1   1   714.543   714.593   .051         OS−&gt;  ||||||||||| |||||||||||||||||               TN   836   1   1   714.543   714.593   .051             *−++*+++++++**++++++++*++++++++               TP   837   1   1   714.543   714.593   .051             *−++−+++++++−+++++++++−++++++++               CPT   838   1   1   714.544   714.606   .063         OS−&gt;  || ||||||| ||||||||| ||||||||               GG   839   1   1   714.635   715.928   1.293   Group0154   || ||||||| ||||||||| ||||||||               GN   840   1   1   715.170   715.532   .363   ybfg        || ||||||| ||||||||| ||||||||               TN   841   1   1   716.085   716.103   .019             *−++*+++++++*||||||||| ||||||||               TP   842   1   1   716.085   716.103   .019             *−++++++++++++++++++++*++++++++               GG   843   1   1   716.169   724.202   8.033   Group0155   |||||||||||||||||||||||||||||               CNT   844   1   1   720.278   720.296   .019          −−&gt;  |||||||||||||||||||||||||||||               GN   845   1   1   720.279   724.202   3.924   kdpe        |||||||||||||||||||||||||||||               TP   846   1   1   721.769   721.783   .015             *−+++++++++++++++++++++++++++++               TN   847   1   1   721.812   721.827   .016             *−+++++++++++++++++++++++++++++               GG   848   1   1   724.211   727.955   3.744   Group0156   |||||||||||||||||||||||||||||               TP   849   1   1   726.665   726.679   .015             *−+++++++++++++++++++++++++++++               GG   850   1   1   728.357   733.325   4.968   Group0157   |||||||||||||||||||||||||||||               GP   851   1   1   728.806   733.325   4.520   rhsc        |||||||||||||||||||||||||||||               CPT   852   1   1   729.408   729.446   .039          −−&gt;  |||||||||||||||||||||||||||||               TP   853   1   1   730.270   730.284   .015             *−+++++++++++++++++++++++++++++               CPT   854   1   1   730.443   730.457   .015          −−&gt;  |||||||||||||||||||||||||||||               CPT   855   1   1   730.468   730.482   .015          −−&gt;  |||||||||||||||||||||||||||||               CPT   856   1   1   730.484   730.507   .024          −−&gt;  |||||||||||||||||||||||||||||               CPT   857   1   1   731.251   731.290   .040          −−&gt;  |||||||||||||||||||||||||||||               TP   858   1   1   731.475   731.508   .034             *−+++++++++++++++++++++++++++++               TP   859   1   1   731.512   731.562   .051             *−+++++++++++++++++++++++++++++               TP   860   1   1   731.564   731.693   .130             *−+++++++++++++++++++++++++++++               TP   861   1   1   731.698   731.755   .058             *−+++++++++++++++++++++++++++++               TP   862   1   1   731.757   731.819   .063             *−+++++++++++++++++++++++++++++               TP   863   1   1   731.821   731.903   .083             *−+++++++++++++++++++++++++++++               TP   864   1   1   731.906   732.033   .128             *−+++++++++++++++++++++++++++++               CPT   865   1   1   731.994   732.016   .023          −−&gt;  |||||||||||||||||||||||||||||               CPT   866   1   1   732.019   732.034   .016          −−&gt;  |||||||||||||||||||||||||||||               TP   867   1   1   732.035   732.050   .016             *−+++++++++++++++++++++++++++++               TP   868   1   1   732.052   732.179   .128             *−+++++++++++++++++++++++++++++               CPT   869   1   1   732.065   732.179   .115         OS−&gt;   ||||||||||||||||||||||||||||               CPT   870   1   1   732.198   732.212   .015          −−&gt;   ||||||||||||||||||||||||||||               TP   871   1   1   732.198   732.212   .015             *−*||||||||||||||||||||||||||||               CPT   872   1   1   732.214   732.233   .020          −−&gt;  |||||||||||||||||||||||||||||               TP   873   1   1   732.214   732.233   .020             *−+++++++++++++++++++++++++++++               CPT   874   1   1   732.235   732.283   .049          −−&gt;  |||||||||||||||||||||||||||||               TP   875   1   1   732.235   732.283   .049             *−+++++++++++++++++++++++++++++               CPT   876   1   1   732.306   732.326   .021          −−&gt;  |||||||||||||||||||||||||||||               TP   877   1   1   732.306   732.326   .021             *−+++++++++++++++++++++++++++++               CPT   878   1   1   732.328   732.452   .125          −−&gt;  |||||||||||||||||||||||||||||               TP   879   1   1   732.328   732.482   .155             *−+++++++++++++++++++++++++++++               CPT   880   1   1   732.454   732.482   .029          −−&gt;  |||||||||||||||||||||||||||||               CPT   881   1   1   732.488   732.519   .032          −−&gt;  |||||||||||||||||||||||||||||               TN   882   1   1   733.330   733.344   .015             *−+++++++++++++++++++++++++++++               TP   883   1   1   733.330   733.344   .015             *−+++++++++++++++++++++++++++++               TP   884   1   1   733.371   733.513   .143             *−+++++++++++++++++++++++++++++               GG   885   1   1   733.443   735.442   2.000   Group0158   |||||||||||||||||||||||||||||               TP   886   1   1   733.515   733.564   .050             *−+++++++++++++++++++++++++++++               TP   887   1   1   733.569   733.626   .058             *−+++++++++++++++++++++++++++++               TP   888   1   1   733.628   733.645   .018             *−+++++++++++++++++++++++++++++               TP   889   1   1   733.647   733.696   .050             *−+++++++++++++++++++++++++++++               TP   890   1   1   733.698   733.774   .077             *−+++++++++++++++++++++++++++++               TP   891   1   1   733.776   733.904   .129             *−+++++++++++++++++++++++++++++               CPT   892   1   1   733.865   733.887   .023         OS−&gt;  ||||||||||||||||||||||||||||               CPT   893   1   1   733.890   733.905   .016          −−&gt;  |||||||||||||||||||||||||||||               TP   894   1   1   733.906   734.050   .145             *−+*+++++++++++++++++++++++++++               CPT   895   1   1   733.936   734.050   .115          −−&gt;  | |||||||||||||||||||||||||||               TP   896   1   1   734.052   734.075   .024             *−+−+++++++++++++++++++++++++++               CPT   897   1   1   734.052   734.139   .088          −−&gt;  | |||||||||||||||||||||||||||               TP   898   1   1   734.084   734.139   .056             *−*−+++++++++++++++++++++++++++               TP   899   1   1   734.149   734.179   .031             *−−−+++++++++++++++++++++++++++               CPT   900   1   1   734.164   734.321   .158          −−&gt;    |||||||||||||||||||||||||||               TP   901   1   1   734.192   734.321   .130             *−−−+++++++++++++++++++++++++++               TP   902   1   1   734.323   734.378   .056             *−−−+++++++++++++++++++++++++++               CPT   903   1   1   734.323   734.381   .059          −−&gt;    |||||||||||||||||||||||||||               CPT   904   1   1   735.525   735.569   .045          −−&gt;    |||||||||||||||||||||||||||               TP   905   1   1   735.525   735.569   .045             *−* |||||||||||||||||||||||||||               CPT   906   1   1   735.606   735.703   .098          −−&gt;  | |||||||||||||||||||||||||||               TP   907   1   1   735.606   735.703   .098             *−+*+++++++++++++++++++++++++++               TP   908   1   1   735.707   735.721   .015             *−+++++++++++++++++++++++++++++               CPT   909   1   1   735.707   735.728   .022          −−&gt;  |||||||||||||||||||||||||||||               TP   910   1   1   735.749   735.803   .055             *−+++++++++++++++++++++++++++++               CPT   911   1   1   735.807   735.964   .158         OS−&gt;  |||||||||||||||||||||||||||||               TP   912   1   1   735.814   735.895   .082             *−+++++++++++++++++++++++++++++               TP   913   1   1   735.905   735.934   .030             *−+++++++++++++++++++++++++++++               TP   914   1   1   735.938   736.083   .146             *−+++++++++++++++++++++++++++++               CPT   915   1   1   735.986   736.083   .098         OS−&gt;  |||||||||||||||||||||||||||||               TP   916   1   1   736.152   736.173   .022             *−+++++++++++++++++++++++++++++               TP   917   1   1   736.187   736.217   .031             *−+++++++++++++++++++++++++++++               TP   918   1   1   736.219   736.265   .047             *−+++++++++++++++++++++++++++++               TP   919   1   1   736.288   736.334   .047             *−+++++++++++++++++++++++++++++               GG   920   1   1   736.327   737.184   .858   Group0159   |||||||||||||||||||||||||||||               TP   921   1   1   736.349   736.469   .221             *−+++++++++++++++++++++++++++++               TP   922   1   1   736.516   736.628   .113             *−+++++++++++++++++++++++++++++               TP   923   1   1   736.630   736.645   .016             *−+++++++++++++++++++++++++++++               TP   924   1   1   736.654   736.792   .139             *−+++++++++++++++++++++++++++++               TN   925   1   1   736.654   736.809   .156             *−+++++++++++++++++++++++++++++               TN   926   1   1   736.816   736.832   .017             *−+++++++++++++++++++++++++++++               CPT   927   1   1   737.017   737.032   .016          −−&gt;  |||||||||||||||||||||||||||||               CPT   928   1   1   737.035   737.057   .023          −−&gt;  |||||||||||||||||||||||||||||               TN   929   1   1   737.168   737.188   .021             *−+++++++++++++++++++++++++++++               TP   930   1   1   737.196   737.290   .095             *−**+++++++++++++++++++++++++++               CPT   931   1   1   737.261   737.275   .015          −−&gt;    |||||||||||||||||||||||||||               CPT   932   1   1   737.278   737.292   .015          −−&gt;    |||||||||||||||||||||||||||               TP   933   1   1   737.292   737.393   .102             *−−−+++++++++++++++++++++++++++               GG   934   1   1   737.315   738.076   .762   Group0160     |||||||||||||||||||||||||||               TP   935   1   1   737.411   737.475   .065             *−−−+++++++++++++++++++++++++++               TP   936   1   1   737.479   737.557   .079             *−−−+++++++++++++++++++++++++++               TP   937   1   1   737.580   737.597   .018             *−−−+++++++++++++++++++++++++++               TP   938   1   1   737.605   737.626   .022             *−−−+++++++++++++++++++++++++++               TP   939   1   1   737.633   737.648   .016             *−−−+++++++++++++++++++++++++++               TP   940   1   1   737.653   737.679   .027             *−−−+++++++++++++++++++++++++++               TP   941   1   1   737.683   737.752   .070             *−−−+++++++++++++++++++++++++++               TP   942   1   1   737.798   737.822   .025             *−−−+++++++++++++++++++++++++++               TP   943   1   1   737.828   737.895   .068             *−−−+++++++++++++++++++++++++++               TP   944   1   1   737.897   737.931   .035             *−−−+++++++++++++++++++++++++++               CPT   945   1   1   737.930   737.967   .038          −−&gt;    |||||||||||||||||||||||||||               TP   946   1   1   737.936   737.967   .032             *−−−+++++++++++++++++++++++++++               TP   947   1   1   737.970   737.988   .019             *−−−+++++++++++++++++++++++++++               TN   948   1   1   737.990   738.015   .026             *−−−+++++++++++++++++++++++++++               TP   949   1   1   737.990   738.015   .026             *−−−+++++++++++++++++++++++++++               TN   950   1   1   738.019   738.051   .033             *−−−+++++++++++++++++++++++++++               TP   951   1   1   738.019   738.051   .033             *−−−+++++++++++++++++++++++++++               TP   952   1   1   738.053   738.074   .022             *−−−+++++++++++++++++++++++++++               TN   953   1   1   738.058   738.074   .017             *−−−+++++++++++++++++++++++++++               TN   954   1   1   738.107   738.126   .020             *−−−+++++++++++++++++++++++++++               GG   955   1   1   738.224   740.148   1.925   Group0161     |||||||||||||||||||||||||||               TN   956   1   1   740.172   740.213   .042             *−**++++*++++*+++*++++++*++++++               CNT   957   1   1   740.172   740.290   .119         OS−&gt;  |||||| |||| ||| |||||| ||||||               CPT   958   1   1   740.172   740.290   .119         OS−&gt;  |||||| |||| ||| |||||| ||||||               TP   959   1   1   740.173   740.213   .041             *−++++++*++++*+++**+++++*++++++               TP   960   1   1   740.216   740.241   .026             *−++++++++++++++++−++++++++++++               TN   961   1   1   740.216   740.288   .073             *−+++*++++++++**++−++++++++++++               TP   962   1   1   740.244   740.288   .045             *−+++−++++++++−−++*+++**+++++++               GG   963   1   1   740.298   757.628   17.330   Group0162   ||| ||||||||  ||||||  |||||||               GP   964   1   1   742.816   745.122   2.307   ybgj        ||| ||||||||  ||||||  |||||||               CPT   965   1   1   744.643   744.657   .015          −−&gt;  ||| ||||||||  ||||||  |||||||               CPT   966   1   1   744.664   744.678   .015          −−&gt;  ||| ||||||||  ||||||  |||||||               GP   967   1   1   754.400   756.896   2.497   sdhc        ||| ||||||||  ||||||  |||||||               CPT   968   1   1   755.680   755.714   .035          −−&gt;  ||| ||||||||  ||||||  |||||||               GP   969   1   1   756.912   757.628   .717   sdhb        ||| ||||||||  ||||||  |||||||               TN   970   1   1   757.626   757.712   .087             *−*+**+++*++++***+++++**+++*+++               CPT   971   1   1   757.628   757.712   .085         OS−&gt;   | |||| |||||| |||||||||| |||               TP   972   1   1   757.629   757.712   .084             *−−+−+++*−++++++−+*++++++++−+++               GG   973   1   1   757.687   760.730   3.044   Group0163    | |||  |||||| | |||||||| |||               CPT   974   1   1   757.717   757.736   .020          −−&gt;   | |||  |||||| | |||||||| |||               TN   975   1   1   757.718   757.753   .036             *−*+*+++***+++++*+−+*++++++−+++                  
 
      The “Type” descriptor of the T1 (Id number 809) is “TN” showing that is T1 target is on the negative strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 975) also has the type descriptor “TN”.  
      The T1-T2 loop diagram above can be read by tracing the path from the * of the T1 to the right to the appropriate *, then by tracing a path down the diagram to the first *, then by tracing a path left to the * of the T2. When horizontal lines (indicated by −) intersect with other vertical lines (indicated by |) then the symbol at that point is changed to a +. When the T1-T2 loop does not contain an groups of genes then the vertical symbol (indicated by | or +) is changed to @ as shown below  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  TN   xx   1   1   278.386   279.148   .763   *---*       XX   xx   1   1   278.387   278.416   .030   *  @       XX   xx   1   1   278.421   278.450   .030   *  @       TP   xx   1   1   278.452   278.892   .441   *---*                  
 
      Group0149 through Group0163 are described in Table 2 as  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0149                                   nagd   COG0647   b   1   negative   698.797   699.549   .753       nagc   COG1940   b   1   negative   699.597   700.817   1.221       naga   COG1820   b   1   negative   700.826   701.974   1.149       nagb   COG0363   b   1   negative   702.034   702.834   .801       nage   COG1264   b   1   positive   703.167   705.113   1.947       Group0150       gins   COG0008   b   1   positive   705.316   706.980   1.665       Group0151       ybfm   —   b   1   positive   707.557   708.963   1.407       ybfn   —   b   1   positive   709.013   709.339   .327       fur   COG0735   b   1   negative   709.423   709.869   .447       flda   COG0716   b   1   negative   710.158   710.688   .531       Group0152       ybfe   —   b   1   negative   710.828   711.190   .363       ybff   COG0596   b   1   negative   711.261   712.025   .765       seqa   COG3057   b   1   positive   712.210   712.755   .546       Group0153       pgm   COG0033   b   1   positive   712.781   714.421   1.641       Group0154       ybfp   —   b   1   positive   714.635   715.129   .495       ybfg   —   b   1   negative   715.170   715.532   .363       ybfh   —   b   1   negative   715.611   715.928   .318       Group0155       pote   COG0531   b   1   negative   716.169   719.683   3.515       kdpe   COG0745   b   1   negative   720.279   724.202   3.924       Group0156       kdpb   COG2216   b   1   negative   724.211   726.259   2.049       kdpa   COG2060   b   1   negative   726.282   727.955   1.674       Group0157       ybfa   —   b   1   positive   728.357   728.563   .207       rhsc   —   b   1   positive   728.806   733.325   4.520       Group0158       b0703   COG3209   b   1   positive   733.443   735.442   2.000       Group0159       ybfl   —   b   1   positive   736.327   737.184   .858       Group0160       ybfd   —   b   1   positive   737.315   738.076   .762       Group0161       ybga   COG3272   b   1   positive   738.224   740.148   1.925       Group0162       ybgh   COG3104   b   1   negative   740.298   741.779   1.482       ybgi   COG0327   b   1   positive   742.050   742.793   .744       ybgj   COG2049   b   1   positive   742.816   745.122   2.307       nei   COG0266   b   1   positive   745.158   745.949   .792       abrb   —   b   1   negative   745.946   747.037   1.092       ybgo   —   b   1   negative   747.144   748.930   1.787       ybgq   —   b   1   negative   748.945   751.401   2.457       ybgd   —   b   1   negative   751.452   752.018   .567       glta   COG0372   b   1   negative   752.408   753.691   1.284       sdhc   COG2009   b   1   positive   754.400   756.896   2.497       sdhb   COG0479   b   1   positive   756.912   757.628   .717       Group0163       b0725   —   b   1   positive   757.687   760.730   3.044                  
 
      All of the data for the transient connectron 62520 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   62520   transient                                                         Chro-                       Control       mo-   C1/       Sequences -   Direction   some   C2_Id   Start   Stop   Length                   positive   1   4651a   4626.130   4626.166   .036                                             Trigger Gene -   Name   COG_Id   Start   Stop   Length                   sms       4623.481   4626.116   2.636                                                         Chro-                       Target       mo-       Sequences   Direction   some       Start   Stop   Length                           T1_Id           negative   1   809   698.766   698.713   .054                   T2_Id                   975   757.753   757.718   .036                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0149   nagd   COG0647   positive   698.797   705.113   6.316       2   1   Group0149   nagc   COG1940   negative   700.817   699.597   1.221       3   1   Group0149   naga   COG1820   negative   701.974   700.826   1.149       4   1   Group0149   nagb   COG0363   negative   702.834   702.034   .801       5   1   Group0149   nage   COG1264   positive   703.167   705.113   1.947       6   1   Group0150   gins   COG0008   positive   705.316   706.980   1.665       7   1   Group0151   ybfm   —   positive   707.557   710.688   3.131       8   1   Group0151   ybfn   —   positive   709.013   709.339   .327       9   1   Group0151   fur   COG0735   negative   709.869   709.423   .447       10   1   Group0151   flda   COG0716   negative   710.688   710.158   .531       11   1   Group0152   ybfe   —   positive   710.828   712.755   1.927       12   1   Group0152   ybff   COG0596   negative   712.025   711.261   .765       13   1   Group0152   seqa   COG3057   positive   712.210   712.755   .546       14   1   Group0153   pgm   COG0033   positive   712.781   714.421   1.641       15   1   Group0154   ybfp   —   positive   714.635   715.928   1.293       16   1   Group0154   ybfg   —   negative   715.532   715.170   .363       17   1   Group0154   ybfh   —   negative   715.928   715.611   .318       18   1   Group0155   pote   COG0531   positive   716.169   724.202   8.033       19   1   Group0155   kdpe   COG0745   negative   724.202   720.279   3.924       20   1   Group0156   kdpb   COG2216   positive   724.211   727.955   3.744       21   1   Group0156   kdpa   COG2060   negative   727.955   726.282   1.674       22   1   Group0157   ybfa   —   positive   728.357   733.325   4.968       23   1   Group0157   rhsc   —   positive   728.806   733.325   4.520       24   1   Group0158   b0703   COG3209   positive   733.443   735.442   2.000       25   1   Group0159   ybfl   —   positive   736.327   737.184   .858       26   1   Group0160   ybfd   —   positive   737.315   738.076   .762       27   1   Group0161   ybga   COG3272   positive   738.224   740.148   1.925       28   1   Group0162   ybgh   COG3104   positive   740.298   757.628   17.330       29   1   Group0162   ybgi   COG0327   positive   742.050   742.793   .744       30   1   Group0162   ybgj   COG2049   positive   742.816   745.122   2.307       31   1   Group0162   nei   COG0266   positive   745.158   745.949   .792       32   1   Group0162   abrb   —   negative   747.037   745.946   1.092       33   1   Group0162   ybgo   —   negative   748.930   747.144   1.787       34   1   Group0162   ybgq   —   negative   751.401   748.945   2.457       35   1   Group0162   ybgd   —   negative   752.018   751.452   .567       36   1   Group0162   glta   COG0372   negative   753.691   752.408   1.284       37   1   Group0162   sdhc   COG2009   positive   754.400   756.896   2.497       38   1   Group0162   sdhb   COG0479   positive   756.912   757.628   .717       39   1   Group0163   b0725   —   positive   757.687   760.730   3.044                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/   Direc-       Id   some   C2_Id   tion   Start   Stop   Length               1   1   816   positive   707.055   707.109   .055       2   1   819   positive   707.112   707.162   .051       3   1   823   negative   710.647   710.633   .015       4   1   825   negative   710.666   710.652   .015       5   1   830   positive   714.481   714.519   .039       6   1   832   positive   714.524   714.540   .017       7   1   835   negative   714.593   714.543   .051       8   1   838   positive   714.544   714.606   .063       9   1   844   negative   720.296   720.278   .019       10   1   852   positive   729.408   729.446   .039       11   1   854   positive   730.443   730.457   .015       12   1   855   positive   730.468   730.482   .015       13   1   856   positive   730.484   730.507   .024       14   1   857   positive   731.251   731.290   .040       15   1   865   positive   731.994   732.016   .023       16   1   866   positive   732.019   732.034   .016       17   1   869   positive   732.065   732.179   .115       18   1   870   positive   732.198   732.212   .015       19   1   872   positive   732.214   732.233   .020       20   1   874   positive   732.235   732.283   .049       21   1   876   positive   732.306   732.326   .021       22   1   878   positive   732.328   732.452   .125       23   1   880   positive   732.454   732.482   .029       24   1   881   positive   732.488   732.519   .032       25   1   892   positive   733.865   733.887   .023       26   1   893   positive   733.890   733.905   .016       27   1   895   positive   733.936   734.050   .115       28   1   897   positive   734.052   734.139   .088       29   1   900   positive   734.164   734.321   .158       30   1   903   positive   734.323   734.381   .059       31   1   904   positive   735.525   735.569   .045       32   1   906   positive   735.606   735.703   .098       33   1   909   positive   735.707   735.728   .022       34   1   911   positive   735.807   735.964   .158       35   1   915   positive   735.986   736.083   .098       36   1   927   positive   737.017   737.032   .016       37   1   928   positive   737.035   737.057   .023       38   1   931   positive   737.261   737.275   .015       39   1   932   positive   737.278   737.292   .015       40   1   945   positive   737.930   737.967   .038       41   1   957   negative   740.290   740.172   .119       42   1   958   positive   740.172   740.290   .119       43   1   965   positive   744.643   744.657   .015       44   1   966   positive   744.664   744.678   .015       45   1   968   positive   755.680   755.714   .035       46   1   971   positive   757.628   757.712   .085       47   1   974   positive   757.717   757.736   .020                  
 
      The verbose description of the synthetic connectron 62520 is:  
      In the  Escherichia coli  K-12 MG1655 complete genome the transient connectron number 62520 is generated by the control sequence (C1/C2) whose identifier number is 4651a. This control sequence is on the positive strand of the genomic DNA of chromosome 1. The genomic start and stop positions of this control sequence are 4626.130 KB and 4626.166 KB with a length of 0.036 KB. Expression of the RNA for this connectron is triggered by the promotion of the gene whose name is sms. The genomic start and stop positions of this gene are 4623.481 KB and 4626.116 KB and with a length of 2.636 KB. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the negative strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 809. The genomic start and stop positions of this initiating target sequence are 698.766 KB and 698.713 KB with a length of 0.054 KB. The identifier number of the terminating target sequence (T2) is 975. The genomic start and stop positions of this terminating target sequence are 757.753 KB and 757.718 KB with a length of 0.036 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name nagd and with a COG identifier of COG0647. The genomic start and stop positions of this gene are 698.797 KB and 705.113 KB with a length of 6.316 KB. (2) The gene that has the name nagc and with a COG identifier of COG1940. The genomic start and stop positions of this gene are 700.817 KB and 699.597 KB with a length of 1.221 KB. (3) The gene that has the name naga and with a COG identifier of COG1820. The genomic start and stop positions of this gene are 701.974 KB and 700.826 KB with a length of 1.149 KB. (4) The gene that has the name nagb and with a COG identifier of COG0363. The genomic start and stop positions of this gene are 702.834 KB and 702.034 KB with a length of 0.801 KB. (5) The gene that has the name nage and with a COG identifier of COG1264. The genomic start and stop positions of this gene are 703.167 KB and 705.113 KB with a length of 1.947 KB. (6) The gene that has the name gins and with a COG identifier of COG0008. The genomic start and stop positions of this gene are 705.316 KB and 706.980 KB with a length of 1.665 KB. (7) The gene that has the name ybfm. The genomic start and stop positions of this gene are 707.557 KB and 710.688 KB with a length of 3.131 KB. (8) The gene that has the name ybfn. The genomic start and stop positions of this gene are 709.013 KB and 709.339 KB with a length of 0.327 KB. (9) The gene that has the name fur and with a COG identifier of COG0735. The genomic start and stop positions of this gene are 709.869 KB and 709.423 KB with a length of 0.447 KB. (10) The gene that has the name flda and with a COG identifier of COG0716. The genomic start and stop positions of this gene are 710.688 KB and 710.158 KB with a length of 0.531 KB. (11) The gene that has the name ybfe. The genomic start and stop positions of this gene are 710.828 KB and 712.755 KB with a length of 1.927 KB. (12) The gene that has the name ybff and with a COG identifier of COG0596. The genomic start and stop positions of this gene are 712.025 KB and 711.261 KB with a length of 0.765 KB. (13) The gene that has the name seqa and with a COG identifier of COG3057. The genomic start and stop positions of this gene are 712.210 KB and 712.755 KB with a length of 0.546 KB. (14) The gene that has the name pgm and with a COG identifier of COG0033. The genomic start and stop positions of this gene are 712.781 KB and 714.421 KB with a length of 1.641 KB. (15) The gene that has the name ybfp. The genomic start and stop positions of this gene are 714.635 KB and 715.928 KB with a length of 1.293 KB. (16) The gene that has the name ybfg. The genomic start and stop positions of this gene are 715.532 KB and 715.170 KB with a length of 0.363 KB. (17) The gene that has the name ybfh. The genomic start and stop positions of this gene are 715.928 KB and 715.611 KB with a length of 0.318 KB. (18) The gene that has the name pote and with a COG identifier of COG0531. The genomic start and stop positions of this gene are 716.169 KB and 724.202 KB with a length of 8.033 KB. (19) The gene that has the name kdpe and with a COG identifier of COG0745. The genomic start and stop positions of this gene are 724.202 KB and 720.279 KB with a length of 3.924 KB. (20) The gene that has the name kdpb and with a COG identifier of COG2216. The genomic start and stop positions of this gene are 724.211 KB and 727.955 KB with a length of 3.744 KB. (21) The gene that has the name kdpa and with a COG identifier of COG2060. The genomic start and stop positions of this gene are 727.955 KB and 726.282 KB with a length of 1.674 KB. (22) The gene that has the name ybfa. The genomic start and stop positions of this gene are 728.357 KB and 733.325 KB with a length of 4.968 KB. (23) The gene that has the name rhsc. The genomic start and stop positions of this gene are 728.806 KB and 733.325 KB with a length of 4.520 KB. (24) The gene that has the name b0703 and with a COG identifier of COG3209. The genomic start and stop positions of this gene are 733.443 KB and 735.442 KB with a length of 2.000 KB. (25) The gene that has the name ybfl. The genomic start and stop positions of this gene are 736.327 KB and 737.184 KB with a length of 0.858 KB. (26) The gene that has the name ybfd. The genomic start and stop positions of this gene are 737.315 KB and 738.076 KB with a length of 0.762 KB. (27) The gene that has the name ybga and with a COG identifier of COG3272. The genomic start and stop positions of this gene are 738.224 KB and 740.148 KB with a length of 1.925 KB. (28) The gene that has the name ybgh and with a COG identifier of COG3104. The genomic start and stop positions of this gene are 740.298 KB and 757.628 KB with a length of 17.330 KB. (29) The gene that has the name ybgi and with a COG identifier of COG0327. The genomic start and stop positions of this gene are 742.050 KB and 742.793 KB with a length of 0.744 KB. (30) The gene that has the name ybgj and with a COG identifier of COG2049. The genomic start and stop positions of this gene are 742.816 KB and 745.122 KB with a length of 2.307 KB. (31) The gene that has the name nei and with a COG identifier of COG0266. The genomic start and stop positions of this gene are 745.158 KB and 745.949 KB with a length of 0.792 KB. (32) The gene that has the name abrb. The genomic start and stop positions of this gene are 747.037 KB and 745.946 KB with a length of 1.092 KB. (33) The gene that has the name ybgo. The genomic start and stop positions of this gene are 748.930 KB and 747.144 KB with a length of 1.787 KB. (34) The gene that has the name ybgq. The genomic start and stop positions of this gene are 751.401 KB and 748.945 KB with a length of 2.457 KB. (35) The gene that has the name ybgd. The genomic start and stop positions of this gene are 752.018 KB and 751.452 KB with a length of 0.567 KB. (36) The gene that has the name glta and with a COG identifier of COG0372. The genomic start and stop positions of this gene are 753.691 KB and 752.408 KB with a length of 1.284 KB. (37) The gene that has the name sdhc and with a COG identifier of COG2009. The genomic start and stop positions of this gene are 754.400 KB and 756.896 KB with a length of 2.497 KB. (38) The gene that has the name sdhb and with a COG identifier of COG0479. The genomic start and stop positions of this gene are 756.912 KB and 757.628 KB with a length of 0.717 KB. (39) The gene that has the name b0725. The genomic start and stop positions of this gene are 757.687 KB and 760.730 KB with a length of 3.044 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 816 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 707.055 KB and 707.109 KB with a length of 0.055 KB. (2) The connectron that has the identifier 819 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 707.112 KB and 707.162 KB with a length of 0.051 KB. (3) The connectron that has the identifier 823 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 710.647 KB and 710.633 KB with a length of 0.015 KB. (4) The connectron that has the identifier 825 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 710.666 KB and 710.652 KB with a length of 0.015 KB. (5) The connectron that has the identifier 830 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 714.481 KB and 714.519 KB with a length of 0.039 KB. (6) The connectron that has the identifier 832 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 714.524 KB and 714.540 KB with a length of 0.017 KB. (7) The connectron that has the identifier 835 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 714.593 KB and 714.543 KB with a length of 0.051 KB. (8) The connectron that has the identifier 838 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 714.544 KB and 714.606 KB with a length of 0.063 KB. (9) The connectron that has the identifier 844 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 720.296 KB and 720.278 KB with a length of 0.019 KB. (10) The connectron that has the identifier 852 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 729.408 KB and 729.446 KB with a length of 0.039 KB. (11) The connectron that has the identifier 854 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 730.443 KB and 730.457 KB with a length of 0.015 KB. (12) The connectron that has the identifier 855 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 730.468 KB and 730.482 KB with a length of 0.015 KB. (13) The connectron that has the identifier 856 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 730.484 KB and 730.507 KB with a length of 0.024 KB. (14) The connectron that has the identifier 857 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 731.251 KB and 731.290 KB with a length of 0.040 KB. (15) The connectron that has the identifier 865 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 731.994 KB and 732.016 KB with a length of 0.023 KB. (16) The connectron that has the identifier 866 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.019 KB and 732.034 KB with a length of 0.016 KB. (17) The connectron that has the identifier 869 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.065 KB and 732.179 KB with a length of 0.115 KB. (18) The connectron that has the identifier 870 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.198 KB and 732.212 KB with a length of 0.015 KB. (19) The connectron that has the identifier 872 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.214 KB and 732.233 KB with a length of 0.020 KB. (20) The connectron that has the identifier 874 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.235 KB and 732.283 KB with a length of 0.049 KB. (21) The connectron that has the identifier 876 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.306 KB and 732.326 KB with a length of 0.021 KB. (22) The connectron that has the identifier 878 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.328 KB and 732.452 KB with a length of 0.125 KB. (23) The connectron that has the identifier 880 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.454 KB and 732.482 KB with a length of 0.029 KB. (24) The connectron that has the identifier 881 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 732.488 KB and 732.519 KB with a length of 0.032 KB. (25) The connectron that has the identifier 892 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 733.865 KB and 733.887 KB with a length of 0.023 KB. (26) The connectron that has the identifier 893 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 733.890 KB and 733.905 KB with a length of 0.016 KB. (27) The connectron that has the identifier 895 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 733.936 KB and 734.050 KB with a length of 0.115 KB. (28) The connectron that has the identifier 897 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.052 KB and 734.139 KB with a length of 0.088 KB. (29) The connectron that has the identifier 900 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.164 KB and 734.321 KB with a length of 0.158 KB. (30) The connectron that has the identifier 903 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.323 KB and 734.381 KB with a length of 0.059 KB. (31) The connectron that has the identifier 904 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.525 KB and 735.569 KB with a length of 0.045 KB. (32) The connectron that has the identifier 906 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.606 KB and 735.703 KB with a length of 0.098 KB. (33) The connectron that has the identifier 909 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.707 KB and 735.728 KB with a length of 0.022 KB. (34) The connectron that has the identifier 911 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.807 KB and 735.964 KB with a length of 0.158 KB. (35) The connectron that has the identifier 915 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 735.986 KB and 736.083 KB with a length of 0.098 KB. (36) The connectron that has the identifier 927 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.017 KB and 737.032 KB with a length of 0.016 KB. (37) The connectron that has the identifier 928 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.035 KB and 737.057 KB with a length of 0.023 KB. (38) The connectron that has the identifier 931 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.261 KB and 737.275 KB with a length of 0.015 KB. (39) The connectron that has the identifier 932 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.278 KB and 737.292 KB with a length of 0.015 KB. (40) The connectron that has the identifier 945 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 737.930 KB and 737.967 KB with a length of 0.038 KB. (41) The connectron that has the identifier 957 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 740.290 KB and 740.172 KB with a length of 0.119 KB. (42) The connectron that has the identifier 958 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 740.172 KB and 740.290 KB with a length of 0.119 KB. (43) The connectron that has the identifier 965 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 744.643 KB and 744.657 KB with a length of 0.015 KB. (44) The connectron that has the identifier 966 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 744.664 KB and 744.678 KB with a length of 0.015 KB. (45) The connectron that has the identifier 968 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 755.680 KB and 755.714 KB with a length of 0.035 KB. (46) The connectron that has the identifier 971 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 757.628 KB and 757.712 KB with a length of 0.085 KB. (47) The connectron that has the identifier 974 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 757.717 KB and 757.736 KB with a length of 0.020 KB.  
     Addition of a Synthetic Transient Connectron Between Chromosomes—Type 7 from Table 2  
      A synthetic virtual connectron of type 7 in which the C1 is a synthetic element and C2 is a natural element, the T1 is a natural element and the T2 is a synthetic element can be introduced into the  S. cerevisiae  genome by modifying the DNA double-strand sequence at 221.330 kb through 221.345 kb on chromosome 2 for a length of 0.016 kb and by modifying the DNA double-strand sequence at 488.140 kb through 488.297 on chromosome 5 for a length of 0.158 kb.  
      To create this example of a synthetic connectron of type 7 the T2 sequence for natural connectron 3558 (old position 497.581 kb through 498.091 kb) was copied into the new position stated above.  
      Connectron 75273 is an example of a transient connectron. It is described as  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_ld   T2_Id   Connectron_Type                  75273   2   792a   793   5   4749   4824a   transient                  
 
      The C1/C2 source of the transient connectron 75273 is represented in table 1 as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  CPT   792a   22   2   221.330   221.345   .016   --&gt;       CPT   793   22   2   221.346   221.361   .016   --&gt;                  
 
      The “Type” descriptor of this transient C1/C2 connectron source is “CPT”. The letter “P” indicates that the C1/C2 connectron source occurs on the positive strand of the double-stranded DNA of the genome. The letter “N” in this place would indicate a C1/C2 connectron source on the negative strand of the genomic DNA. The letter “T” in this descriptor indicates a “transient” connectron. Similarly, the letter “P” would indicate a permanent connectron that is shown in a later example. The “Start”, “Stop” and “Length” descriptors throughout these examples are given in kilo-bases (KB). The symbol OS-&gt; occurs because there is another connectron formed by this C1/C2 that happens to be a one-shot connectron.  
      The T1-T2 target of the transient connectron 75273 as shown in table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TN   4749   59   5   448.454   448.992   .539             *−*                   TP   4750   68   5   448.454   448.992   .539             *−+               CNT   4751   64   5   448.454   448.992   .539          −−&gt;  |               TP   4752   63   5   449.003   449.315   .313             *−+               TN   4753   65   5   449.003   449.315   .313             *−+               CNT   4754   60   5   449.003   449.315   .313         OS−&gt;  |               CNT   4755   5   5   449.317   449.482   .166         OS−&gt;  |               TN   4756   5   5   449.317   449.482   .166             *−+               TP   4757   64   5   449.317   449.482   .148             *−+               GG   4758   59   5   449.470   449.574   .105   Group0615   |               CPT   4759   70   5   449.490   449.563   .074          −−&gt;  |               TN   4760   70   5   449.490   449.563   .074             *−+               TP   4761   67   5   449.490   449.558   .069             *−+               CNT   4762   70   5   449.490   449.563   .074          −−&gt;  |               TN   4763   59   5   449.575   449.603   .029             *−+               TP   4764   59   5   449.575   449.603   .029             *−+               GG   4765   59   5   450.558   453.230   2.672   Group0616   |               TP   4766   59   5   452.176   452.190   .015             *−+               GG   4767   59   5   453.454   454.914   1.461   Group0617   |               CNT   4768   20   5   453.909   453.923   .015          −−&gt;  |               CNT   4769   20   5   453.928   453.942   .015          −−&gt;  |               TP   4770   59   5   454.644   454.658   .015             *−+               GG   4771   59   5   455.141   457.600   2.460   Group0618   |               TN   4772   66   5   456.316   456.331   .016             *−+               GG   4773   59   5   457.801   460.218   2.418   Group0619   |               TN   4774   66   5   460.340   460.355   .016             *−+               GG   4775   59   5   460.521   466.020   5.500   Group0620   |               GP   4776   59   5   462.580   462.861   .282   LSM5        |               TN   4777   59   5   463.743   463.758   .016             *−+               TP   4778   59   5   463.743   463.758   .016             *−+               CPT   4779   61   5   463.990   464.004   .015          −−&gt;  |               CPT   4780   61   5   464.010   464.024   .015          −−&gt;  |               TP   4781   59   5   465.739   465.754   .016             *−|               GG   4782   59   5   466.203   468.811   2.609   Group0621   |               GP   4783   59   5   468.365   468.811   .447   SPI1        |               TP   4784   69   5   469.451   469.518   .059             *−+               CNT   4785   67   5   469.451   469.530   .080         OS−&gt;  |               GG   4786   59   5   469.452   469.525   .074   Group0622   |               TN   4787   59   5   469.452   469.532   .081             *−+               CPT   4788   67   5   469.452   469.531   .080          −−&gt;  |               GG   4789   59   5   469.681   472.419   2.739   Group0623   |               TN   4790   20   5   471.772   471.786   .015             *−+               TP   4791   20   5   471.772   471.786   .015             *−+               GG   4792   59   5   472.652   482.843   10.192   Group0624   |               GP   4793   59   5   475.015   476.223   1.209   OXA1        |               TP   4794   63   5   476.803   476.817   .015             *−+               CPT   4795   60   5   478.412   478.426   .015          −−&gt;  |               CPT   4796   60   5   478.436   478.450   .015          −−&gt;  |               CNT   4797   47   5   481.782   481.812   .031          −−&gt;  |               TN   4798   20   5   482.192   482.206   .015             *−+               CNT   4799   67   5   482.676   482.690   .015          −−&gt;  |               CNT   4800   67   5   482.701   482.715   .015          −−&gt;  |               GG   4801   59   5   483.320   487.188   3.869   Group0625   |               GP   4802   59   5   484.783   487.188   2.406   SEC34       |               CNT   4803   61   5   485.099   485.113   .015          −−&gt;  |               CNT   4804   61   5   485.119   485.134   .016          −−&gt;  |               TN   4805   64   5   487.041   487.056   .016             *−+               GG   4806   59   5   487.326   487.397   .072   Group0626   |               CPT   4807   61   5   487.375   487.397   .023          −−&gt;  |               CPT   4808   61   5   487.400   487.415   .016          −−&gt;  |               CNT   4809   34   5   487.830   487.848   .019         OS−&gt;  |               CPT   4810   62   5   487.830   487.848   .019         OS−&gt;  |               TP   4811   60   5   487.830   487.848   .019             *−+               TN   4812   59   5   487.830   487.848   .019             *−+               CNT   4813   34   5   487.850   488.016   .167         OS−&gt;  |               CPT   4814   5   5   487.850   488.016   .167         OS−&gt;  |               TP   4815   5   5   487.850   488.016   .167             *−+               TN   4816   64   5   487.850   488.016   .167             *−+               CNT   4817   47   5   488.024   488.137   .114         OS−&gt;  |               CPT   4818   47   5   488.024   488.068   .045          −−&gt;  |               TN   4819   34   5   488.024   488.067   .044             *−+               TP   4820   34   5   488.024   488.067   .044             *−+               CPT   4821   69   5   488.069   488.137   .069         OS−&gt;  |               TN   4822   67   5   488.069   488.122   .054             *−+               TP   4823   59   5   488.069   488.085   .017             *−+               TP   4824   5   5   488.094   488.137   .044             *−+               TN   4824a   5   5   488.140   488.297   .158             *−*                  
 
      The “Type” descriptor of the Ti (Id number 4749) is “TN” showing that is T1 target is on the negative strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 4824a) also has the type descriptor “TN”.  
      The T1-T2 loop diagram above can be read by tracing the path from the * of the T1 to the right to the appropriate *, then by tracing a path down the diagram to the first *, then by tracing a path left to the * of the T2. When horizontal lines (indicated by −) intersect with other vertical lines (indicated by |) then the symbol at that point is changed to a +. When the T1-T2 loop does not contain an groups of genes then the vertical symbol (indicated by | or +) is changed to @ as shown below  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  TN   xx   1   1   278.386   279.148   .763   *---*       XX   xx   1   1   278.387   278.416   .030   *  @       XX   xx   1   1   278.421   278.450   .030   *  @       TP   xx   1   1   278.452   278.892   .441   *---*                  
 
      Group0615 (Id number 4758) has the type descriptor “GG”. The same is true for Group0626 (Id number 4806).  
      Group0615 through Group0626 are described in table 2 as  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0615                                   YER138W-A   —       5   positive   449.470   449.574   .105       Group0616       YER139C   —       5   negative   450.558   451.238   .681       YER140W   —       5   positive   451.560   453.230   1.671       Group0617       COX15   COG1612   O   5   positive   453.454   454.914   1.461       Group0618       MAG1   COG0122   L   5   negative   455.141   456.031   .891       DDI1   —       5   positive   456.314   457.600   1.287       Group0619       UBP5   —       5   negative   457.801   460.218   2.418       Group0620       FTR1   COG0672   P   5   negative   460.521   461.735   1.215       LSM5   COG1958   K   5   positive   462.580   462.861   .282       YER147C   —       5   negative   462.963   464.837   1.875       SPT15   COG2101   K   5   positive   465.298   466.020   .723       Group0621       PEA2   —       5   negative   466.203   467.465   1.263       SPI1   —       5   positive   468.365   468.811   .447       Group0622                   5   positive   469.452   469.525   .074       Group0623       UBP3   —       5   negative   469.681   472.419   2.739       Group0624       YER152C   COG1167   K   5   negative   472.652   473.983   1.332       PET122   —       5   negative   474.036   474.800   .765       OXA1   COG0706   N   5   positive   475.015   476.223   1.209       BEM2   —       5   negative   476.340   482.843   6.504       Group0625       YER156C   —       5   negative   483.320   484.336   1.017       SEC34   —       5   positive   484.783   487.188   2.406       Group0626                   5   positive   487.326   487.397   .072                  
 
      All of the data for the transient connectron 75273 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   75273   transient                                                         Chro-                       Control       mo-   C1/       Sequences -   Direction   some   C2_Id   Start   Stop   Length                   positive   2   792a   221.330   221.345   .016           positive   2   793   221.346   221.361   .016                                             Trigger Gene -   Name   COG_Id   Start   Stop   Length                   YBL005W-B   —   221.293   226.561   5.269                                                         Chro-                       Target       mo-       Sequences -   Direction   some       Start   Stop   Length                           T1_Id           negative   5   4749   448.992   448.454   .539                   T2_Id                   4824a   488.140   488.297   .158                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   5   Group0615   YER138W-A   —   positive   449.470   449.574   .105       2   5   Group0616   YER139C   —   positive   450.558   453.230   2.673       3   5   Group0616   YER140W   —   positive   451.560   453.230   1.671       4   5   Group0617   COX15   COG1612   positive   453.454   454.914   1.461       5   5   Group0618   MAG1   COG0122   positive   455.141   457.600   2.459       6   5   Group0618   DDI1   —   positive   456.314   457.600   1.287       7   5   Group0619   UBP5   —   positive   457.801   460.218   2.418       8   5   Group0620   FTR1   COG0672   positive   460.521   466.020   5.499       9   5   Group0620   LSM5   COG1958   positive   462.580   462.861   .282       10   5   Group0620   YER147C   —   negative   464.837   462.963   1.875       11   5   Group0620   SPT15   COG2101   positive   465.298   466.020   .723       12   5   Group0621   PEA2   —   positive   466.203   468.811   2.608       13   5   Group0621   SPI1   —   positive   468.365   468.811   .447       14   5   Group0622           positive   469.452   469.525   .074       15   5   Group0623   UBP3   —   positive   469.681   472.419   2.739       16   5   Group0624   YER152C   COG1167   positive   472.652   482.843   10.191       17   5   Group0624   PET122   —   negative   474.800   474.036   .765       18   5   Group0624   OXA1   COG0706   positive   475.015   476.223   1.209       19   5   Group0624   BEM2   —   negative   482.843   476.340   6.504       20   5   Group0625   YER156C   —   positive   483.320   487.188   3.868       21   5   Group0625   SEC34   —   positive   484.783   487.188   2.406       22   5   Group0626           positive   487.326   487.397   .072                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   5   4751   negative   448.992   448.454   .539       2   5   4754   negative   449.315   449.003   .313       3   5   4755   negative   449.482   449.317   .166       4   5   4759   positive   449.490   449.563   .074       5   5   4762   negative   449.563   449.490   .074       6   5   4768   negative   453.923   453.909   .015       7   5   4769   negative   453.942   453.928   .015       8   5   4779   positive   463.990   464.004   .015       9   5   4780   positive   464.010   464.024   .015       10   5   4785   negative   469.530   469.451   .080       11   5   4788   positive   469.452   469.531   .080       12   5   4795   positive   478.412   478.426   .015       13   5   4796   positive   478.436   478.450   .015       14   5   4797   negative   481.812   481.782   .031       15   5   4799   negative   482.690   482.676   .015       16   5   4800   negative   482.715   482.701   .015       17   5   4803   negative   485.113   485.099   .015       18   5   4804   negative   485.134   485.119   .016       19   5   4807   positive   487.375   487.397   .023       20   5   4808   positive   487.400   487.415   .016       21   5   4809   negative   487.848   487.830   .019       22   5   4810   positive   487.830   487.848   .019       23   5   4813   negative   488.016   487.850   .167       24   5   4814   positive   487.850   488.016   .167       25   5   4817   negative   488.137   488.024   .114       26   5   4818   positive   488.024   488.068   .045       27   5   4821   positive   488.069   488.137   .069                  
 
      The verbose description of the transient connectron 75273 is:  
      In the  Saccharomyces cerevisiae  complete genome the transient connectron number 75273 is generated by the control sequence C1 whose identifier number is 792a. This control sequence is on the positive strand of the genomic DNA of chromosome 2. The genomic start and stop positions of this control sequence are 221.330 KB and 221.345 KB with a length of 0.016 KB and by the control sequence C2 whose identifier number is 793. This control sequence is on the positive strand of the genomic DNA of chromosome 2. The genomic start and stop positions of this control sequence are 221.346 KB and 221.361 KB with a length of 0.016 KB. Expression of the RNA for this connectron is triggered by the promotion of the gene whose name is YBL005W-B. The genomic start and stop positions of this gene are 221.293 KB and 226.561 KB and with a length of 5.269 KB. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the negative strand of the genomic DNA on chromosome 5. The identifier number of the initiating target sequence (T1) is 4749. The genomic start and stop positions of this initiating target sequence are 448.992 KB and 448.454 KB with a length of 0.022 KB. The identifier number of the terminating target sequence (T2) is 4824a. The genomic start and stop positions of this terminating target sequence are 488.140 KB and 488.297 KB with a length of 0.158 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name YER138W-A. The genomic start and stop positions of this gene are 449.470 KB and 449.574 KB with a length of 0.105 KB. (2) The gene that has the name YER139C. The genomic start and stop positions of this gene are 450.558 KB and 453.230 KB with a length of 2.672 KB. (3) The gene that has the name YER140W. The genomic start and stop positions of this gene are 451.560 KB and 453.230 KB with a length of 1.671 KB. (4) The gene that has the name COX15 and with a COG identifier of COG1612. The genomic start and stop positions of this gene are 453.454 KB and 454.914 KB with a length of 1.461 KB. (5) The gene that has the name MAGi and with a COG identifier of COG0122. The genomic start and stop positions of this gene are 455.141 KB and 457.600 KB with a length of 2.459 KB. (6) The gene that has the name DDI1. The genomic start and stop positions of this gene are 456.314 KB and 457.600 KB with a length of 1.287 KB. (7) The gene that has the name UBP5. The genomic start and stop positions of this gene are 457.801 KB and 460.218 KB with a length of 2.418 KB. (8) The gene that has the name FTR1 and with a COG identifier of COG0672. The genomic start and stop positions of this gene are 460.521 KB and 466.020 KB with a length of 5.499 KB. (9) The gene that has the name LSM5 and with a COG identifier of COG1958. The genomic start and stop positions of this gene are 462.580 KB and 462.861 KB with a length of 0.282 KB. (10) The gene that has the name YER147C. The genomic start and stop positions of this gene are 464.837 KB and 462.963 KB with a length of 1.875 KB. (11) The gene that has the name SPT15 and with a COG identifier of COG2101. The genomic start and stop positions of this gene are 465.298 KB and 466.020 KB with a length of 0.723 KB. (12) The gene that has the name PEA2. The genomic start and stop positions of this gene are 466.203 KB and 468.811 KB with a length of 2.608 KB. (13) The gene that has the name SPI1. The genomic start and stop positions of this gene are 468.365 KB and 468.811 KB with a length of 0.447 KB. (14) The gene that has the name No_Name. The genomic start and stop positions of this gene are 469.452 KB and 469.525 KB with a length of 0.074 KB. (15) The gene that has the name UBP3. The genomic start and stop positions of this gene are 469.681 KB and 472.419 KB with a length of 2.739 KB. (16) The gene that has the name YER152C and with a COG identifier of COG1167. The genomic start and stop positions of this gene are 472.652 KB and 482.843 KB with a length of 10.191 KB. (17) The gene that has the name PET122. The genomic start and stop positions of this gene are 474.800 KB and 474.036 KB with a length of 0.765 KB. (18) The gene that has the name OXA1 and with a COG identifier of COG0706. The genomic start and stop positions of this gene are 475.015 KB and 476.223 KB with a length of 1.209 KB. (19) The gene that has the name BEM2. The genomic start and stop positions of this gene are 482.843 KB and 476.340 KB with a length of 6.504 KB. (20) The gene that has the name YER156C. The genomic start and stop positions of this gene are 483.320 KB and 487.188 KB with a length of 3.868 KB. (21) The gene that has the name SEC34. The genomic start and stop positions of this gene are 484.783 KB and 487.188 KB with a length of 2.406 KB. (22) The gene that has the name No_Name. The genomic start and stop positions of this gene are 487.326 KB and 487.397 KB with a length of 0.072 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 4751 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 448.992 KB and 448.454 KB with a length of 0.539 KB. (2) The connectron that has the identifier 4754 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 449.315 KB and 449.003 KB with a length of 0.313 KB. (3) The connectron that has the identifier 4755 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 449.482 KB and 449.317 KB with a length of 0.166 KB. (4) The connectron that has the identifier 4759 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 449.490 KB and 449.563 KB with a length of 0.074 KB. (5) The connectron that has the identifier 4762 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 449.563 KB and 449.490 KB with a length of 0.074 KB. (6) The connectron that has the identifier 4768 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 453.923 KB and 453.909 KB with a length of 0.015 KB. (7) The connectron that has the identifier 4769 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 453.942 KB and 453.928 KB with a length of 0.015 KB. (8) The connectron that has the identifier 4779 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 463.990 KB and 464.004 KB with a length of 0.015 KB. (9) The connectron that has the identifier 4780 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 464.010 KB and 464.024 KB with a length of 0.015 KB. (10) The connectron that has the identifier 4785 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 469.530 KB and 469.451 KB with a length of 0.080 KB. (11) The connectron that has the identifier 4788 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 469.452 KB and 469.531 KB with a length of 0.080 KB. (12) The connectron that has the identifier 4795 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 478.412 KB and 478.426 KB with a length of 0.015 KB. (13) The connectron that has the identifier 4796 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 478.436 KB and 478.450 KB with a length of 0.015 KB. (14) The connectron that has the identifier 4797 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 481.812 KB and 481.782 KB with a length of 0.031 KB. (15) The connectron that has the identifier 4799 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 482.690 KB and 482.676 KB with a length of 0.015 KB. (16) The connectron that has the identifier 4800 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 482.715 KB and 482.701 KB with a length of 0.015 KB. (17) The connectron that has the identifier 4803 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 485.113 KB and 485.099 KB with a length of 0.015 KB. (18) The connectron that has the identifier 4804 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 485.134 KB and 485.119 KB with a length of 0.016 KB. (19) The connectron that has the identifier 4807 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 487.375 KB and 487.397 KB with a length of 0.023 KB. (20) The connectron that has the identifier 4808 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 487.400 KB and 487.415 KB with a length of 0.016 KB. (21) The connectron that has the identifier 4809 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 487.848 KB and 487.830 KB with a length of 0.019 KB. (22) The connectron that has the identifier 4810 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 487.830 KB and 487.848 KB with a length of 0.019 KB. (23) The connectron that has the identifier 4813 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 488.016 KB and 487.850 KB with a length of 0.167 KB. (24) The connectron that has the identifier 4814 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 487.850 KB and 488.016 KB with a length of 0.022 KB. (25) The connectron that has the identifier 4817 is on chromosome 5 in the negative direction. The genomic start and stop positions of this connectron are 488.137 KB and 488.024 KB with a length of 0.114 KB. (26) The connectron that has the identifier 4818 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 488.024 KB and 488.068 KB with a length of 0.045 KB. (27) The connectron that has the identifier 4821 is on chromosome 5 in the positive direction. The genomic start and stop positions of this connectron are 488.069 KB and 488.137 KB with a length of 0.069 KB.  
     Addition of a Synthetic Connectron of Type 14 from Table 2  
      A synthetic virtual connectron of type 14 in which the C1 and C2 are natural elements, the T1 is a synthetic element and the T2 is a natual element can be introduced into the  Halobacterium  sp. genome by modifying the DNA double-strand sequences at 734.750 kb through 734.942 kb for a length of 0.193 kb.  
      To create this example of a synthetic connectron of type 15 the T1 sequence for natural connectron 6627 (old position 733.018 kb through 733.210 kb) was copied into the new position stated above.  
      Connectron 7341 is an example of a transient connectron. It is described as  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  2587   1   6612   6612   1   6627   6852   transient                  
 
      The C1/C2 source of the transient connectron 7341 is represented in Table 1 as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  CPT   6612   1   1   732.401   732.534   .134         OS−&gt;  |||||||||||||||||||||||||||||                  
 
      The “Type” descriptor of this transient C1/C2 connectron source is “CPT”. The letter “P” indicates that the C1/C2 connectron source occurs on the positive strand of the double-stranded DNA of the genome. The letter “N” in this place would indicate a C1/C2 connectron source on the negative strand of the genomic DNA. The letter “T” in this descriptor indicates a “transient” connectron. Similarly, the letter “P” would indicate a permanent connectron that is shown in a later example. The “Start”, “Stop” and “Length” descriptors throughout these examples are given in kilo-bases (KB). The symbol OS-&gt; occurs because there is another connectron formed by this C1/C2 that happens to be a one-shot connectron.  
      The T1-T2 target of the transient connectron 7341 as shown in Table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TP   6644a   1   1   734.750   734.942   .193             *−*                   GG   6646   1   1   735.009   735.881   .873   Group0493   |               CNT   6647   1   1   735.364   735.378   .015         OS−&gt;  |               TN   6648   1   1   735.364   735.378   .015             *−+               CNT   6649   1   1   735.389   735.403   .015          −−&gt;  |               CNT   6650   1   1   735.753   735.767   .015          −−&gt;  |               CNT   6651   1   1   735.775   735.789   .015          −−&gt;  |               GG   6652   1   1   735.910   737.544   1.634   Group0494   |               TN   6653   1   1   735.969   735.984   .016             *−+               TN   6654   1   1   736.126   736.140   .015             *−+               CPT   6655   1   1   736.325   736.339   .015          −−&gt;  |               TN   6656   1   1   736.327   736.342   .016             *−+               CPT   6657   1   1   736.345   736.359   .015          −−&gt;  |               TP   6658   1   1   736.903   736.917   .015             *−+               TN   6659   1   1   737.233   737.247   .015             *−+               TP   6660   1   1   737.271   737.285   .015             *−+               TN   6661   1   1   737.331   737.346   .016             *−+               GG   6662   1   1   737.643   737.972   .330   Group0495   |               TN   6663   1   1   737.752   737.766   .015             *−+               CNT   6664   1   1   737.752   737.782   .031          −−&gt;  |               TP   6665   1   1   737.761   737.775   .015             *−+               TN   6666   1   1   738.049   738.063   .015             *−+               GG   6667   1   1   738.107   739.835   1.728   Group0496   |               TN   6668   1   1   738.122   738.136   .015             *−+               TP   6669   1   1   738.122   738.136   .015             *−+               TP   6670   1   1   738.425   738.439   .015             *−+               TP   6671   1   1   738.503   738.517   .015             *−+               CNT   6672   1   1   738.517   738.562   .046          −−&gt;  |               TN   6673   1   1   738.544   738.559   .016             *−+               TN   6674   1   1   738.862   738.878   .017             *−+               TP   6675   1   1   738.862   738.878   .017             *−+               CNT   6676   1   1   738.975   738.989   .015          −−&gt;  |               CNT   6677   1   1   738.992   739.007   .016          −−&gt;  |               TN   6678   1   1   739.107   739.122   .016             *−+               GN   6679   1   1   739.248   739.835   .588   cheC1       |               TP   6680   1   1   739.435   739.449   .015             *−+               TN   6681   1   1   739.685   739.707   .023             *−+               TN   6682   1   1   739.761   739.775   .015             *−+               GG   6683   1   1   739.838   741.844   2.007   Group0497   |               TN   6684   1   1   739.849   739.863   .015             *−+               TP   6685   1   1   740.345   740.360   .016             *−+               TN   6686   1   1   740.362   740.376   .015             *−+               TP   6687   1   1   740.611   740.625   .015             *−+               TN   6688   1   1   741.100   741.116   .017             *−+               TP   6689   1   1   741.101   741.132   .032             *−+               TN   6690   1   1   741.218   741.232   .015             *−+               CNT   6691   1   1   741.352   741.368   .017          −−&gt;  |               TP   6692   1   1   741.354   741.376   .023             *−+               TN   6693   1   1   741.354   741.380   .027             *−+               CNT   6694   1   1   741.374   741.388   .015          −−&gt;  |               TN   6695   1   1   741.401   741.417   .017             *−+               CNT   6696   1   1   741.519   741.533   .015          −−&gt;  |               CNT   6697   1   1   741.538   741.552   .015          −−&gt;  |               TN   6698   1   1   741.538   741.552   .015             *−+               TN   6699   1   1   741.561   741.575   .015             *−+               GG   6700   1   1   741.846   743.248   1.403   Group0498   |               TN   6701   1   1   741.924   741.942   .019             *−+               TN   6702   1   1   742.194   742.208   .015             *−+               TP   6703   1   1   742.618   742.632   .015             *−+               TN   6704   1   1   742.943   742.957   .015             *−+               GG   6705   1   1   743.295   743.831   .537   Group0499   |               TP   6706   1   1   743.730   743.748   .019             *−+               GG   6707   1   1   743.896   744.489   .594   Group0500   |               TN   6708   1   1   743.916   743.930   .015             *−+               GG   6709   1   1   744.606   745.511   .906   Group0501   |               TN   6710   1   1   744.950   744.964   .015             *−+               TN   6711   1   1   745.047   745.061   .015             *−+               GG   6712   1   1   745.648   746.763   1.116   Group0502   |               CPT   6713   1   1   745.865   745.879   .015          −−&gt;  |               TN   6714   1   1   745.865   745.879   .015             *−+               CPT   6715   1   1   745.888   745.902   .015          −−&gt;  |               CPT   6716   1   1   746.140   746.155   .016          −−&gt;  |               TN   6717   1   1   746.153   746.175   .023             *−+               TP   6718   1   1   746.157   746.175   .019             *−+               CPT   6719   1   1   746.162   746.176   .015          −−&gt;  |               TN   6720   1   1   746.229   746.243   .015             *−+               CNT   6721   1   1   746.229   746.259   .031          −−&gt;  |               TN   6722   1   1   746.271   746.285   .015             *−+               TP   6723   1   1   746.356   746.380   .025             *−+               TN   6724   1   1   746.361   746.380   .020             *−+               TN   6725   1   1   746.386   746.400   .015             *−+               CPT   6726   1   1   746.453   746.467   .015          −−&gt;  |               TN   6727   1   1   746.453   746.472   .020             *−+               TP   6728   1   1   746.457   746.475   .019             *−+               CPT   6729   1   1   746.469   746.483   .015          −−&gt;  |               TP   6730   1   1   746.528   746.545   .018             *−+               TN   6731   1   1   746.532   746.556   .025             *−+               GG   6732   1   1   746.843   748.851   2.008   Group0503   |               CNT   6733   1   1   746.905   746.919   .015          −−&gt;  |               CNT   6734   1   1   746.927   746.941   .015          −−&gt;  |               GN   6735   1   1   747.151   748.605   1.455   VNG0983C    |               TN   6736   1   1   747.260   747.274   .015             *−+               TP   6737   1   1   747.475   747.489   .015             *−+               TN   6738   1   1   747.547   747.571   .025             *−+               TN   6739   1   1   747.934   747.948   .015             *−+               TP   6740   1   1   747.936   747.950   .015             *−+               TN   6741   1   1   748.130   748.144   .015             *−+               TP   6742   1   1   749.157   749.172   .016             *−+               TN   6743   1   1   749.375   749.389   .015             *−+               GG   6744   1   1   749.392   759.277   9.885   Group0504   |               CNT   6745   1   1   759.509   759.552   .044          −−&gt;  |               TP   6746   1   1   759.509   760.014   .506             *−+               TN   6747   1   1   759.528   760.031   .504             *−+               GG   6748   1   1   759.667   762.487   2.820   Group0505   |               GP   6749   1   1   760.682   762.487   1.806   boa4        |               CPT   6750   1   1   760.774   760.789   .016          −−&gt;  |               CPT   6751   1   1   760.798   760.814   .017          −−&gt;  |               TN   6752   1   1   760.875   760.889   .015             *−+               CPT   6753   1   1   760.878   760.892   .015          −−&gt;  |               CPT   6754   1   1   760.897   760.912   .016          −−&gt;  |               CPT   6755   1   1   761.496   761.510   .015          −−&gt;  |               CPT   6756   1   1   761.516   761.533   .018          −−&gt;  |               CPT   6757   1   1   761.542   761.557   .016          −−&gt;  |               TN   6758   1   1   761.542   761.557   .016             *−+               CPT   6759   1   1   761.576   761.597   .022          −−&gt;  |               CPT   6760   1   1   761.601   761.617   .017          −−&gt;  |               TN   6761   1   1   761.754   761.768   .015             *−+               CPT   6762   1   1   761.933   761.950   .018          −−&gt;  |               TP   6763   1   1   761.933   761.950   .018             *−+               CPT   6764   1   1   761.953   761.968   .016          −−&gt;  |               TN   6765   1   1   762.423   762.437   .015             *−+               GG   6766   1   1   762.609   764.612   2.004   Group0506   |               TN   6767   1   1   762.874   762.900   .027             *−+               TN   6768   1   1   762.946   762.960   .015             *−+               TN   6769   1   1   763.108   763.122   .015             *−+               TN   6770   1   1   763.273   763.304   .032             *−+               CPT   6771   1   1   763.283   763.304   .022          −−&gt;  |               TN   6772   1   1   763.306   763.320   .015             *−+               CPT   6773   1   1   763.306   763.321   .016          −−&gt;  |               CPT   6774   1   1   763.346   763.360   .015          −−&gt;  |               TN   6775   1   1   763.351   763.365   .015             *−+               TP   6776   1   1   763.351   763.365   .015             *−+               CPT   6777   1   1   763.362   763.376   .015          −−&gt;  |               TP   6778   1   1   763.391   763.407   .017             *−+               TN   6779   1   1   763.843   763.857   .015             *−+               TP   6780   1   1   763.843   763.857   .015             *−+               CNT   6781   1   1   763.965   763.986   .022          −−&gt;  |               CPT   6782   1   1   763.965   763.995   .031          −−&gt;  |               CNT   6783   1   1   763.990   764.011   .022          −−&gt;  |               CPT   6784   1   1   764.000   764.015   .016          −−&gt;  |               CNT   6785   1   1   764.075   764.089   .015          −−&gt;  |               CNT   6786   1   1   764.093   764.108   .016          −−&gt;  |               CPT   6787   1   1   764.156   764.171   .016          −−&gt;  |               CNT   6788   1   1   764.156   764.177   .022         OS−&gt;  |               TN   6789   1   1   764.156   764.177   .022             *−+               CNT   6790   1   1   764.181   764.195   .015          −−&gt;  |               TP   6791   1   1   764.181   764.201   .021             *−+               CPT   6792   1   1   764.181   764.204   .024          −−&gt;  |               CPT   6793   1   1   764.213   764.227   .013          −−&gt;  |               TP   6794   1   1   764.309   764.328   .020             *−+               TN   6795   1   1   764.312   764.326   .015             *−+               TN   6796   1   1   764.383   764.397   .015             *−+               TP   6797   1   1   764.530   764.545   .016             *−+               TN   6798   1   1   764.530   764.548   .019             *−+               GG   6799   1   1   764.619   765.629   1.011   Group0507   |               CPT   6800   1   1   764.791   764.808   .018          −−&gt;  |               CNT   6801   1   1   764.794   764.813   .020         OS−&gt;  |               TN   6802   1   1   764.794   764.832   .039             *−+               CPT   6803   1   1   764.810   764.826   .017          −−&gt;  |               CNT   6804   1   1   764.818   764.832   .015          −−&gt;  |               CPT   6805   1   1   764.831   764.853   .023          −−&gt;  |               CPT   6806   1   1   764.856   764.870   .015          −−&gt;  |               CNT   6807   1   1   764.984   764.998   .015         OS−&gt;  |               TN   6808   1   1   764.984   765.014   .031             *−+               CNT   6809   1   1   765.000   765.014   .015          −−&gt;  |               TN   6810   1   1   765.075   765.089   .015             *−+               CNT   6811   1   1   765.431   765.446   .016          −−&gt;  |               CNT   6812   1   1   765.456   765.473   .018          −−&gt;  |               CNT   6813   1   1   765.479   765.494   .016          −−&gt;  |               TN   6814   1   1   765.508   765.523   .016             *−+               TP   6815   1   1   765.573   765.587   .015             *−+               GG   6816   1   1   765.775   766.044   .270   Group0508   |               TN   6817   1   1   765.822   765.837   .016             *−+               TP   6818   1   1   766.162   766.176   .015             *−+               TN   6819   1   1   766.432   766.447   .016             *−+               GG   6820   1   1   766.603   766.812   .210   Group0509   |               CNT   6821   1   1   766.635   766.653   .019         OS−&gt;  |               TN   6822   1   1   766.635   766.653   .019             *−+               CNT   6823   1   1   766.655   766.675   .021          −−&gt;  |               TN   6824   1   1   766.863   766.878   .016             *−+               GG   6825   1   1   766.955   768.538   1.584   Group0510   |               TN   6826   1   1   767.682   767.700   .019             *−+               TP   6827   1   1   767.831   767.845   .015             *−+               TN   6828   1   1   768.028   768.048   .021             *−+               TP   6829   1   1   768.033   768.049   .017             *−+               TN   6830   1   1   768.377   768.391   .015             *−+               GG   6831   1   1   768.965   769.882   .918   Group0511   |               TN   6832   1   1   769.502   769.516   .015             *−+               TN   6833   1   1   769.541   769.555   .015             *−+               TP   6834   1   1   769.559   769.573   .015             *−+               GG   6833   1   1   769.965   770.189   .225   Group0512   |               TN   6836   1   1   770.120   770.134   .015             *−+               GG   6837   1   1   770.194   770.406   .213   Group0513   |               CPT   6838   1   1   770.226   770.240   .015          −−&gt;  |               CPT   6839   1   1   770.251   770.265   .015          −−&gt;  |               TP   6840   1   1   770.251   770.268   .018             *−+               CPT   6841   1   1   770.347   770.363   .017          −−&gt;  |               CPT   6842   1   1   770.365   770.379   .015          −−&gt;  |               GG   6843   1   1   770.516   771.546   1.030   Group0514   |               TN   6844   1   1   771.564   772.071   .508             *−+               CNT   6845   1   1   771.564   772.086   .523          −−&gt;  |               TP   6846   1   1   771.583   772.084   .502             *−+               GG   6847   1   1   771.722   771.925   .204   Group0515   |               TN   6848   1   1   772.963   772.977   .015             *−+               TP   6849   1   1   773.358   773.387   .030             *−+               GG   6850   1   1   773.360   773.950   .591   Group0516   |               CPT   6851   1   1   773.399   773.483   .085         OS−&gt;  |               TP   6852   1   1   773.399   773.483   .085             *−*                  
 
      The “Type” descriptor of the T1 (Id number 6644a) is “TP” showing that is T1 target is on the negative strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 6852) also has the type descriptor “TP”.  
      The T1-T2 loop diagram above can be read by tracing the path from the * of the T1 to the right to the appropriate *, then by tracing a path down the diagram to the first *, then by tracing a path left to the * of the T2. When horizontal lines (indicated by −) intersect with other vertical lines (indicated by |) then the symbol at that point is changed to a +. When the T1-T2 loop does not contain an groups of genes then the vertical symbol (indicated by | or +) is changed to @ as shown below  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  TN   xx   1   1   278.386   279.148   .763   *---*       XX   xx   1   1   278.387   278.416   .030   *  @       XX   xx   1   1   278.421   278.450   .030   *  @       TP   xx   1   1   278.452   278.892   .441   *---*                  
 
      Group0493 (Id number 6646) has the type descriptor “GG”. The same is true for the group headers through to Group0516 (Id number 6847).  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0493                                   VNG0964C   COG2469   S   1   positive   735.009   735.881   .873       Group0494       VNG0965C   COG2469   S   1   negative   735.910   736.773   .864       cheR   COG1352   N   1   negative   736.840   737.544   .705       Group0495       cheD   COG1871   N   1   negative   737.643   737.972   .330       Group0496       VNG0969H   COG1776   N   1   negative   738.107   739.246   1.140       cheC1   COG1776   N   1   negative   739.248   739.835   .588       Group0497       cheA   COG0643   N   1   negative   739.838   741.844   2.007       Group0498       cheB   COG2201   N   1   negative   741.846   743.248   1.403       Group0499       cheW1   COG0835   N   1   negative   743.295   743.831   .537       Group0500       VNG0978H           1   negative   743.896   744.489   .594       Group0501       VNG0979H           1   positive   744.606   745.511   .906       Group0502       VNG0981C   COG0436   E   1   positive   745.648   746.763   1.116       Group0503       VNG0982C   COG1873   S   1   positive   746.843   747.133   .291       VNG0983C   COG0618   R   1   negative   747.151   748.605   1.455       tRNA-Lys           1   positive   748.778   748.851   .074       Group0504       VNG0985H           1   positive   749.392   751.398   2.007       VNG0986H           1   positive   752.276   752.803   .528       VNG0987H           1   positive   753.131   753.547   .417       VNG0988H           1   positive   754.149   754.391   .243       VNG0989C   COG0582   L   1   negative   754.459   755.481   1.023       VNG0990H           1   positive   756.010   756.183   .174       VNG0991H           1   negative   756.675   757.016   .342       VNG0992H           1   negative   757.409   758.119   .711       VNG0993H           1   positive   758.465   759.277   .813       Group0505       VNG0994H           1   negative   759.667   759.870   .204       VNG0995H           1   positive   760.365   760.553   .189       boa4   COG3413   R   1   positive   760.682   762.487   1.806       Group0506       acs2   COG0365   I   1   positive   762.609   764.612   2.004       Group0507       yajO2   COG0667   C   1   negative   764.619   765.629   1.011       Group0508       VNG0999H           1   negative   765.775   766.044   .270       Group0509       VNG1000H   COG3205   S   1   positive   766.603   766.812   .210       Group0510       guaB   COG0516   F   1   negative   766.955   768.538   1.584       Group0511       VNG1002H           1   positive   768.965   769.882   .918       Group0512       VNG1003H           1   positive   769.965   770.189   .225       Group0513       VNG1005H           1   negative   770.194   770.406   .213       Group0514       tRNA-Trp           1   positive   770.516   770.691   .176       VNG1006H           1   positive   770.827   771.546   .720       Group0515       VNG1007H           1   negative   771.722   771.925   .204       Group0516       flaAla   COG1681   N   1   positive   773.360   773.950   .591                  
 
      All of the data for the transient connectron 7341 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   7341   transient                                                         Chro-                       Control       mo-   C1/       Sequences -   Direction   some   C2_Id   Start   Stop   Length                   positive   1   6612   732.401   732.534   .134                                             Trigger Gene -   Name   COG_Id   Start   Stop   Length                   flaBl   COG1681   731.799   732.380   .582                                                         Chro-                       Target       mo-       Sequences -   Direction   some       Start   Stop   Length                           T1_Id           positive   1   6644a   734.750   734.942   .193                   T2_Id                   6852   773.399   773.483   .085                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0493   VNG0964C   COG2469   positive   735.009   735.881   .873       2   1   Group0494   VNG0965C   COG2469   positive   735.910   737.544   1.634       3   1   Group0494   cheR   COG1352   negative   737.544   736.840   .705       4   1   Group0495   cheD   COG1871   positive   737.643   737.972   .330       5   1   Group0496   VNG0969H   COG1776   positive   738.107   739.835   1.728       6   1   Group0496   cheC1   COG1776   negative   739.835   739.248   .588       7   1   Group0497   cheA   COG0643   positive   739.838   741.844   2.007       8   1   Group0498   cheB   COG2201   positive   741.846   743.248   1.403       9   1   Group0499   cheW1   COG0835   positive   743.295   743.831   .537       10   1   Group0500   VNG0978H       positive   743.896   744.489   .594       11   1   Group0501   VNG0979H       positive   744.606   745.511   .906       12   1   Group0502   VNG0981C   COG0436   positive   745.648   746.763   1.116       13   1   Group0503   VNG0982C   COG1873   positive   746.843   748.851   2.008       14   1   Group0503   VNG0983C   COG0618   negative   748.605   747.151   1.455       15   1   Group0504   VNG0985H       positive   749.392   759.277   9.885       16   1   Group0504   VNG0986H       positive   752.276   752.803   .528       17   1   Group0504   VNG0987H       positive   753.131   753.547   .417       18   1   Group0504   VNG0988H       positive   754.149   754.391   .243       19   1   Group0504   VNG0989C   COG0582   negative   755.481   754.459   1.023       20   1   Group0504   VNG0990H       positive   756.010   756.183   .174       21   1   Group0504   VNG0991H       negative   757.016   756.675   .342       22   1   Group0504   VNG0992H       negative   758.119   757.409   .711       23   1   Group0504   VNG0993H       positive   758.465   759.277   .813       24   1   Group0505   VNG0994H       positive   759.667   762.487   2.820       25   1   Group0505   VNG0995H       positive   760.365   760.553   .189       26   1   Group0505   boa4   COG3413   positive   760.682   762.487   1.806       27   1   Group0506   acs2   COG0365   positive   762.609   764.612   2.004       28   1   Group0507   yajO2   COG0667   positive   764.619   765.629   1.011       29   1   Group0508   VNG0999H       positive   765.775   766.044   .270       30   1   Group0509   VNG1000H   COG3205   positive   766.603   766.812   .210       31   1   Group0510   guaB   COG0516   positive   766.955   768.538   1.584       32   1   Group0511   VNG1002H       positive   768.965   769.882   .918       33   1   Group0512   VNG1003H       positive   769.965   770.189   .225       34   1   Group0513   VNG1005H       positive   770.194   770.406   .213       35   1   Group0514   tRNA-Trp       positive   770.516   771.546   1.030       36   1   Group0514   VNG1006H       positive   770.827   771.546   .720       37   1   Group0515   VNG1007H       positive   771.722   771.925   .204       38   1   Group0516   flaAla   COG1681   positive   773.360   773.950   .591                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   1   6644   positive   734.735   734.749   .015       2   1   6647   negative   735.378   735.364   .015       3   1   6649   negative   735.403   735.389   .015       4   1   6650   negative   735.767   735.753   .015       5   1   6651   negative   735.789   735.775   .015       6   1   6655   positive   736.325   736.339   .015       7   1   6657   positive   736.345   736.359   .015       8   1   6664   negative   737.782   737.752   .031       9   1   6672   negative   738.562   738.517   .046       10   1   6676   negative   738.989   738.975   .015       11   1   6677   negative   739.007   738.992   .016       12   1   6691   negative   741.368   741.352   .017       13   1   6694   negative   741.388   741.374   .015       14   1   6696   negative   741.533   741.519   .015       15   1   6697   negative   741.552   741.538   .015       16   1   6713   positive   745.865   745.879   .015       17   1   6715   positive   745.888   745.902   .015       18   1   6716   positive   746.140   746.155   .016       19   1   6719   positive   746.162   746.176   .015       20   1   6721   negative   746.259   746.229   .031       21   1   6726   positive   746.453   746.467   .015       22   1   6729   positive   746.469   746.483   .015       23   1   6733   negative   746.919   746.905   .015       24   1   6734   negative   746.941   746.927   .015       25   1   6745   negative   759.552   759.509   .044       26   1   6750   positive   760.774   760.789   .016       27   1   6751   positive   760.798   760.814   .017       28   1   6753   positive   760.878   760.892   .015       29   1   6754   positive   760.897   760.912   .016       30   1   6755   positive   761.496   761.510   .015       31   1   6756   positive   761.516   761.533   .018       32   1   6757   positive   761.542   761.557   .016       33   1   6759   positive   761.576   761.597   .022       34   1   6760   positive   761.601   761.617   .017       35   1   6762   positive   761.933   761.950   .018       36   1   6764   positive   761.953   761.968   .016       37   1   6771   positive   763.283   763.304   .022       38   1   6773   positive   763.306   763.321   .016       39   1   6774   positive   763.346   763.360   .015       40   1   6777   positive   763.362   763.376   .015       41   1   6781   negative   763.986   763.965   .022       42   1   6782   positive   763.965   763.995   .031       43   1   6783   negative   764.011   763.990   .022       44   1   6784   positive   764.000   764.015   .016       45   1   6785   negative   764.089   764.075   .015       46   1   6786   negative   764.108   764.093   .016       47   1   6787   positive   764.156   764.171   .016       48   1   6788   negative   764.177   764.156   .022       49   1   6790   negative   764.195   764.181   .015       50   1   6792   positive   764.181   764.204   .024       51   1   6793   positive   764.213   764.227   .015       52   1   6800   positive   764.791   764.808   .018       53   1   6801   negative   764.813   764.794   .020       54   1   6803   positive   764.810   764.826   .017       55   1   6804   negative   764.832   764.818   .015       56   1   6805   positive   764.831   764.853   .023       57   1   6806   positive   764.856   764.870   .015       58   1   6807   negative   764.998   764.984   .015       59   1   6809   negative   765.014   765.000   .015       60   1   6811   negative   765.446   765.431   .016       61   1   6812   negative   765.473   765.456   .018       62   1   6813   negative   765.494   765.479   .016       63   1   6821   negative   766.653   766.635   .019       64   1   6823   negative   766.675   766.655   .021       65   1   6838   positive   770.226   770.240   .015       66   1   6839   positive   770.251   770.265   .015       67   1   6841   positive   770.347   770.363   .017       68   1   6842   positive   770.365   770.379   .015       69   1   6845   negative   772.086   771.564   .523       70   1   6851   positive   773.399   773.483   .085                  
 
      The verbose description of the transient connectron 7341 is:  
      In the  Halobacterium  sp. NRC-1 complete genome the transient connectron number 7341 is generated by the control sequence (C1/C2) whose identifier number is 6612. This control sequence is on the positive strand of the genomic DNA of chromosome 1. The genomic start and stop positions of this control sequence are 732.401 KB and 732.534 KB with a length of 0.134 KB. Expression of the RNA for this connectron is triggered by the promotion of the gene whose name is flaB1 and whose COG (Cluster of  Orthologous  Genes) identifier is COG1681. The genomic start and stop positions of this gene are 731.799 KB and 732.380 KB and with a length of 0.582 KB. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the positive strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 6644a. The genomic start and stop positions of this initiating target sequence are 734.750 KB and 734.942 KB with a length of 0.193 KB. The identifier number of the terminating target sequence (T2) is 6852. The genomic start and stop positions of this terminating target sequence are 773.399 KB and 773.483 KB with a length of 0.085 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name VNG0964C and with a COG identifier of COG2469. The genomic start and stop positions of this gene are 735.009 KB and 735.881 KB with a length of 0.873 KB. (2) The gene that has the name VNG0965C and with a COG identifier of COG2469. The genomic start and stop positions of this gene are 735.910 KB and 737.544 KB with a length of 1.634 KB. (3) The gene that has the name cheR and with a COG identifier of COG1352. The genomic start and stop positions of this gene are 737.544 KB and 736.840 KB with a length of 0.705 KB. (4) The gene that has the name cheD and with a COG identifier of COG1871. The genomic start and stop positions of this gene are 737.643 KB and 737.972 KB with a length of 0.330 KB. (5) The gene that has the name VNG0969H and with a COG identifier of COG1776. The genomic start and stop positions of this gene are 738.107 KB and 739.835 KB with a length of 1.728 KB. (6) The gene that has the name cheC1 and with a COG identifier of COG1776. The genomic start and stop positions of this gene are 739.835 KB and 739.248 KB with a length of 0.588 KB. (7) The gene that has the name cheA and with a COG identifier of COG0643. The genomic start and stop positions of this gene are 739.838 KB and 741.844 KB with a length of 2.007 KB. (8) The gene that has the name cheB and with a COG identifier of COG2201. The genomic start and stop positions of this gene are 741.846 KB and 743.248 KB with a length of 1.403 KB. (9) The gene that has the name cheW1 and with a COG identifier of COG0835. The genomic start and stop positions of this gene are 743.295 KB and 743.831 KB with a length of 0.537 KB. (10) The gene that has the name VNG0978H. The genomic start and stop positions of this gene are 743.896 KB and 744.489 KB with a length of 0.594 KB. (11) The gene that has the name VNG0979H. The genomic start and stop positions of this gene are 744.606 KB and 745.511 KB with a length of 0.906 KB. (12) The gene that has the name VNG0981C and with a COG identifier of COG0436. The genomic start and stop positions of this gene are 745.648 KB and 746.763 KB with a length of 1.116 KB. (13) The gene that has the name VNG0982C and with a COG identifier of COG1873. The genomic start and stop positions of this gene are 746.843 KB and 748.851 KB with a length of 2.008 KB. (14) The gene that has the name VNG0983C and with a COG identifier of COG0618. The genomic start and stop positions of this gene are 748.605 KB and 747.151 KB with a length of 1.455 KB. (15) The gene that has the name VNG0985H. The genomic start and stop positions of this gene are 749.392 KB and 759.277 KB with a length of 9.885 KB. (16) The gene that has the name VNG0986H. The genomic start and stop positions of this gene are 752.276 KB and 752.803 KB with a length of 0.528 KB. (17) The gene that has the name VNG0987H. The genomic start and stop positions of this gene are 753.131 KB and 753.547 KB with a length of 0.417 KB. (18) The gene that has the name VNG0988H. The genomic start and stop positions of this gene are 754.149 KB and 754.391 KB with a length of 0.243 KB. (19) The gene that has the name VNG0989C and with a COG identifier of COG0582. The genomic start and stop positions of this gene are 755.481 KB and 754.459 KB with a length of 1.023 KB. (20) The gene that has the name VNG0990H. The genomic start and stop positions of this gene are 756.010 KB and 756.183 KB with a length of 0.174 KB. (21) The gene that has the name VNG0991H. The genomic start and stop positions of this gene are 757.016 KB and 756.675 KB with a length of 0.342 KB. (22) The gene that has the name VNG0992H. The genomic start and stop positions of this gene are 758.119 KB and 757.409 KB with a length of 0.711 KB. (23) The gene that has the name VNG0993H. The genomic start and stop positions of this gene are 758.465 KB and 759.277 KB with a length of 0.813 KB. (24) The gene that has the name VNG0994H. The genomic start and stop positions of this gene are 759.667 KB and 762.487 KB with a length of 2.820 KB. (25) The gene that has the name VNG0995H. The genomic start and stop positions of this gene are 760.365 KB and 760.553 KB with a length of 0.189 KB. (26) The gene that has the name boa4 and with a COG identifier of COG3413. The genomic start and stop positions of this gene are 760.682 KB and 762.487 KB with a length of 1.806 KB. (27) The gene that has the name acs2 and with a COG identifier of COG0365. The genomic start and stop positions of this gene are 762.609 KB and 764.612 KB with a length of 2.004 KB. (28) The gene that has the name yajO2 and with a COG identifier of COG0667. The genomic start and stop positions of this gene are 764.619 KB and 765.629 KB with a length of 1.011 KB. (29) The gene that has the name VNG0999H. The genomic start and stop positions of this gene are 765.775 KB and 766.044 KB with a length of 0.270 KB. (30) The gene that has the name VNG1000H and with a COG identifier of COG3205. The genomic start and stop positions of this gene are 766.603 KB and 766.812 KB with a length of 0.210 KB. (31) The gene that has the name guaB and with a COG identifier of COG0516. The genomic start and stop positions of this gene are 766.955 KB and 768.538 KB with a length of 1.584 KB. (32) The gene that has the name VNG1002H. The genomic start and stop positions of this gene are 768.965 KB and 769.882 KB with a length of 0.918 KB. (33) The gene that has the name VNG1003H. The genomic start and stop positions of this gene are 769.965 KB and 770.189 KB with a length of 0.225 KB. (34) The gene that has the name VNG1005H. The genomic start and stop positions of this gene are 770.194 KB and 770.406 KB with a length of 0.213 KB. (35) The gene that has the name tRNA-Trp. The genomic start and stop positions of this gene are 770.516 KB and 771.546 KB with a length of 1.030 KB. (36) The gene that has the name VNG1006H. The genomic start and stop positions of this gene are 770.827 KB and 771.546 KB with a length of 0.720 KB. (37) The gene that has the name VNG1007H. The genomic start and stop positions of this gene are 771.722 KB and 771.925 KB with a length of 0.204 KB. (38) The gene that has the name flaA1a and with a COG identifier of COG1681. The genomic start and stop positions of this gene are 773.360 KB and 773.950 KB with a length of 0.591 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 6644 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 734.735 KB and 734.749 KB with a length of 0.015 KB. (2) The connectron that has the identifier 6647 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 735.378 KB and 735.364 KB with a length of 0.015 KB. (3) The connectron that has the identifier 6649 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 735.403 KB and 735.389 KB with a length of 0.015 KB. (4) The connectron that has the identifier 6650 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 735.767 KB and 735.753 KB with a length of 0.015 KB. (5) The connectron that has the identifier 6651 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 735.789 KB and 735.775 KB with a length of 0.015 KB. (6) The connectron that has the identifier 6655 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 736.325 KB and 736.339 KB with a length of 0.015 KB. (7) The connectron that has the identifier 6657 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 736.345 KB and 736.359 KB with a length of 0.015 KB. (8) The connectron that has the identifier 6664 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 737.782 KB and 737.752 KB with a length of 0.031 KB. (9) The connectron that has the identifier 6672 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 738.562 KB and 738.517 KB with a length of 0.046 KB. (10) The connectron that has the identifier 6676 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 738.989 KB and 738.975 KB with a length of 0.015 KB. (11) The connectron that has the identifier 6677 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 739.007 KB and 738.992 KB with a length of 0.016 KB. (12) The connectron that has the identifier 6691 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 741.368 KB and 741.352 KB with a length of 0.017 KB. (13) The connectron that has the identifier 6694 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 741.388 KB and 741.374 KB with a length of 0.015 KB. (14) The connectron that has the identifier 6696 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 741.533 KB and 741.519 KB with a length of 0.015 KB. (15) The connectron that has the identifier 6697 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 741.552 KB and 741.538 KB with a length of 0.015 KB. (16) The connectron that has the identifier 6713 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 745.865 KB and 745.879 KB with a length of 0.015 KB. (17) The connectron that has the identifier 6715 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 745.888 KB and 745.902 KB with a length of 0.015 KB. (18) The connectron that has the identifier 6716 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 746.140 KB and 746.155 KB with a length of 0.016 KB. (19) The connectron that has the identifier 6719 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 746.162 KB and 746.176 KB with a length of 0.015 KB. (20) The connectron that has the identifier 6721 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 746.259 KB and 746.229 KB with a length of 0.031 KB. (21) The connectron that has the identifier 6726 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 746.453 KB and 746.467 KB with a length of 0.015 KB. (22) The connectron that has the identifier 6729 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 746.469 KB and 746.483 KB with a length of 0.015 KB. (23) The connectron that has the identifier 6733 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 746.919 KB and 746.905 KB with a length of 0.015 KB. (24) The connectron that has the identifier 6734 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 746.941 KB and 746.927 KB with a length of 0.015 KB. (25) The connectron that has the identifier 6745 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 759.552 KB and 759.509 KB with a length of 0.044 KB. (26) The connectron that has the identifier 6750 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 760.774 KB and 760.789 KB with a length of 0.016 KB. (27) The connectron that has the identifier 6751 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 760.798 KB and 760.814 KB with a length of 0.017 KB. (28) The connectron that has the identifier 6753 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 760.878 KB and 760.892 KB with a length of 0.015 KB. (29) The connectron that has the identifier 6754 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 760.897 KB and 760.912 KB with a length of 0.016 KB. (30) The connectron that has the identifier 6755 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.496 KB and 761.510 KB with a length of 0.015 KB. (31) The connectron that has the identifier 6756 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.516 KB and 761.533 KB with a length of 0.018 KB. (32) The connectron that has the identifier 6757 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.542 KB and 761.557 KB with a length of 0.016 KB. (33) The connectron that has the identifier 6759 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.576 KB and 761.597 KB with a length of 0.022 KB. (34) The connectron that has the identifier 6760 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.601 KB and 761.617 KB with a length of 0.017 KB. (35) The connectron that has the identifier 6762 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.933 KB and 761.950 KB with a length of 0.018 KB. (36) The connectron that has the identifier 6764 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 761.953 KB and 761.968 KB with a length of 0.016 KB. (37) The connectron that has the identifier 6771 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 763.283 KB and 763.304 KB with a length of 0.022 KB. (38) The connectron that has the identifier 6773 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 763.306 KB and 763.321 KB with a length of 0.016 KB. (39) The connectron that has the identifier 6774 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 763.346 KB and 763.360 KB with a length of 0.015 KB. (40) The connectron that has the identifier 6777 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 763.362 KB and 763.376 KB with a length of 0.015 KB. (41) The connectron that has the identifier 6781 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 763.986 KB and 763.965 KB with a length of 0.022 KB. (42) The connectron that has the identifier 6782 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 763.965 KB and 763.995 KB with a length of 0.031 KB. (43) The connectron that has the identifier 6783 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.011 KB and 763.990 KB with a length of 0.022 KB. (44) The connectron that has the identifier 6784 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.000 KB and 764.015 KB with a length of 0.016 KB. (45) The connectron that has the identifier 6785 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.089 KB and 764.075 KB with a length of 0.015 KB. (46) The connectron that has the identifier 6786 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.108 KB and 764.093 KB with a length of 0.016 KB. (47) The connectron that has the identifier 6787 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.156 KB and 764.171 KB with a length of 0.016 KB. (48) The connectron that has the identifier 6788 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.177 KB and 764.156 KB with a length of 0.022 KB. (49) The connectron that has the identifier 6790 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.195 KB and 764.181 KB with a length of 0.015 KB. (50) The connectron that has the identifier 6792 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.181 KB and 764.204 KB with a length of 0.024 KB. (51) The connectron that has the identifier 6793 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.213 KB and 764.227 KB with a length of 0.015 KB. (52) The connectron that has the identifier 6800 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.791 KB and 764.808 KB with a length of 0.018 KB. (53) The connectron that has the identifier 6801 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.813 KB and 764.794 KB with a length of 0.020 KB. (54) The connectron that has the identifier 6803 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.810 KB and 764.826 KB with a length of 0.017 KB. (55) The connectron that has the identifier 6804 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.832 KB and 764.818 KB with a length of 0.015 KB. (56) The connectron that has the identifier 6805 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.831 KB and 764.853 KB with a length of 0.023 KB. (57) The connectron that has the identifier 6806 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 764.856 KB and 764.870 KB with a length of 0.015 KB. (58) The connectron that has the identifier 6807 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 764.998 KB and 764.984 KB with a length of 0.015 KB. (59) The connectron that has the identifier 6809 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 765.014 KB and 765.000 KB with a length of 0.015 KB. (60) The connectron that has the identifier 6811 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 765.446 KB and 765.431 KB with a length of 0.016 KB. (61) The connectron that has the identifier 6812 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 765.473 KB and 765.456 KB with a length of 0.018 KB. (62) The connectron that has the identifier 6813 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 765.494 KB and 765.479 KB with a length of 0.016 KB. (63) The connectron that has the identifier 6821 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 766.653 KB and 766.635 KB with a length of 0.019 KB. (64) The connectron that has the identifier 6823 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 766.675 KB and 766.655 KB with a length of 0.021 KB. (65) The connectron that has the identifier 6838 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 770.226 KB and 770.240 KB with a length of 0.015 KB. (66) The connectron that has the identifier 6839 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 770.251 KB and 770.265 KB with a length of 0.015 KB. (67) The connectron that has the identifier 6841 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 770.347 KB and 770.363 KB with a length of 0.017 KB. (68) The connectron that has the identifier 6842 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 770.365 KB and 770.379 KB with a length of 0.015 KB. (69) The connectron that has the identifier 6845 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 772.086 KB and 771.564 KB with a length of 0.523 KB. (70) The connectron that has the identifier 6851 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 773.399 KB and 773.483 KB with a length of 0.085 KB.  
     Addition of a Synthetic Virtual Connectron of Type 15 from Table 2  
      A synthetic virtual connectron of type 15 in which the C1 and C2 are natural elements, the T1 is a natural element and the T2 is a synthetic element can be introduced into the  P. aeruginosa  genome by modifying the DNA double-strand sequences at 4838.155 kb through 4838.323kb for a length of 0.169 kb.  
      To create this example of a synthetic connectron of type 14 the T2 sequence for natural connectron 23295 (old position 4848.679 kb through 4939.847 kb) was copied into the new position stated above.  
      Connectron 28739 is an example of a synthetic transient connectron. It is described as  
                                                                   C1/C2           T1-T2               Global_id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  28739   1   53464   53464   1   53531   53569   transient                  
 
      The C1/C2 source of the transient connectron 28739 is represented in table 1 as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  CPT   53464   1   1   4832.718   4832.838   .121          −−&gt;  |||||||||||||||||||||||||||||                  
 
      The “Type” descriptor of this transient C1/C2 connectron source is “CPT”. The letter “P” indicates that the C1/C2 connectron source occurs on the positive strand of the double-stranded DNA of the genome. The letter “N” in this place would indicate a C1/C2 connectron source on the negative strand of the genomic DNA. The letter “T” in this descriptor indicates a “transient” connectron. Similarly, the letter “P” would indicate a permanent connectron that is shown in a later example. The “Start”, “Stop” and “Length” descriptors throughout these examples are given in kilo-bases (KB).  
      The T1-T2 target of the transient connectron 28739 as shown in table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TP   53531   1   1   4836.528   4836.721   .194             *−*                   CPT   53532   1   1   4836.728   4836.746   .019         OS−&gt;  |               TP   53533   1   1   4836.728   4836.746   .019             *−+               TN   53534   1   1   4836.728   4836.779   .052             *−+               CPT   53535   1   1   4836.748   4836.779   .032         OS−&gt;  |               TP   53536   1   1   4836.748   4836.779   .032             *−+               CPT   53537   1   1   4836.781   4836.821   .041         OS−&gt;  |               TP   53538   1   1   4836.781   4836.821   .041             *−+               TN   53539   1   1   4836.781   4836.918   .138             *−+               TP   53540   1   1   4836.840   4836.855   .016             *−+               CPT   53541   1   1   4836.877   4836.918   .042         OS−&gt;  |               TP   53542   1   1   4836.877   4836.918   .042             *−+               TP   53543   1   1   4836.940   4836.957   .018             *−+               CPT   53544   1   1   4836.940   4836.982   .043         OS−&gt;  |               CPT   53545   1   1   4836.990   4837.123   .134         OS−&gt;  |               TP   53546   1   1   4836.990   4837.123   .134             *−+               TN   53547   1   1   4836.990   4837.153   .164             *−+               CPT   53548   1   1   4837.126   4837.148   .023          −−&gt;  |               TP   53549   1   1   4837.129   4837.153   .025             *−+               TP   53549a   1   1   4838.155   4838.323   .169             *−*                  
 
      The “Type” descriptor of the T1 (Id number 53531) is “TP” showing that is T1 target is on the positive strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 53549a) also has the type descriptor “TP”.  
      The T1-T2 loop diagram above can be read by tracing the path from the * of the T1 to the right to the appropriate *, then by tracing a path down the diagram to the first *, then by tracing a path left to the * of the T2. When horizontal lines (indicated by −) intersect with other vertical lines (indicated by |) then the symbol at that point is changed to a +. When the T1-T2 loop does not contain an groups of genes then the vertical symbol (indicated by | or +) is changed to @ as shown below  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                  TN   xx   1   1   278.386   279.148   .763   *---*       XX   xx   1   1   278.387   278.416   .030   *  @       XX   xx   1   1   278.421   278.450   .030   *  @       TP   xx   1   1   278.452   278.892   .441   *---*                  
 
      Since this synthetic connectron is a virtual connectron there are no gene groups that are controlled by the existence of this connectron. Instead the expression of the C1/C2 sources of six one-shot connectrons (type designator “CPT” for Id numbers 53532, 53535, 53537, 53541, 53544, and 53544) and one transient connectron (type designator “CPT” for Id numbers 53548) are controlled by this connectron.  
      All of the data for the transient connectron 28739 are pulled together in the following table that is the “terse” description of the connectron.  
                                                          Connectron Relationships -   Global_Id   Type                           28739   transient                                                             Chro-                       Control   Direc-   mo-   C1/       Sequences -   tion   some   C2_Id   Start   Stop   Length                   posi-   1   53464   4832.718   4832.838   .121           tive                                             Trigger Gene -   Name   COG_Id   Start   Stop   Length                   pctC   COG0840   4831.371   4833.269   1.899                                                         Chro-                       Target   Direc-   mo-       Sequences -   tion   some       Start   Stop   Length                           T1_Id           posi-   1   53531   4836.528   4836.721   .194           tive                   T2_Id                   53549a   4838.155   4838.323   .169                         Controlled Genes                                 none                             Controlled Connectrons                                             Chro-                           Local —     mo-   C1/   Direc-       Id   some   C2_Id   tion   Start   Stop   Length               1   1   53532   positive   4836.728   4836.746   .019       2   1   53535   positive   4836.748   4836.779   .032       3   1   53537   positive   4836.781   4836.821   .041       4   1   53541   positive   4836.877   4836.918   .042       5   1   53544   positive   4836.940   4836.982   .043       6   1   53545   positive   4836.990   4837.123   .134       7   1   53548   positive   4837.126   4837.148   .023       8   1   53551   positive   4837.419   4837.448   .030       9   1   53552   positive   4837.572   4837.622   .051       10   1   53554   positive   4837.962   4837.999   .038       11   1   53557   positive   4838.217   4838.258   .042       12   1   53559   positive   4838.295   4838.362   .068       13   1   53563   positive   4838.457   4838.476   .020       14   1   53564   positive   4838.478   4838.645   .168       15   1   53567   positive   4838.654   4838.847   .194                  
 
      The verbose description of the transient connectron 28739 is:  
      In the  Pseudomonas aeruginosa  PA01, complete genome the transient connectron number 23295 is generated by the control sequence (C1/C2) whose identifier number is 53464. This control sequence is on the positive strand of the genomic DNA of chromosome 1. The genomic start and stop positions of this control sequence are 4832.718 KB and 4832.838 KB with a length of 0.121 KB. Expression of the RNA for this connectron is triggered by the promotion of the gene whose name is pctc and whose COG (Cluster of Orthologous Genes) identifier is COG0840. The genomic start and stop positions of this gene are 4831.371 KB and 4833.269 KB and with a length of 1.899 KB. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the positive strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 53531. The genomic start and stop positions of this initiating target sequence are 4836.528 KB and 4836.721 KB with a length of 0.194 KB. The identifier number of the terminating target sequence (T2) is 53569. The genomic start and stop positions of this terminating target sequence are 4838.155 KB and 4838.323 KB with a length of 0.169 KB.  
      This connectron controls the modulation of the expression of the following gene(s): none  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 53532 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4836.728 KB and 4836.746 KB with a length of 0.019 KB. (2) The connectron that has the identifier 53535 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4836.748 KB and 4836.779 KB with a length of 0.032 KB. (3) The connectron that has the identifier 53537 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4836.781 KB and 4836.821 KB with a length of 0.041 KB. (4) The connectron that has the identifier 53541 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4836.877 KB and 4836.918 KB with a length of 0.042 KB. (5) The connectron that has the identifier 53544 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4836.940 KB and 4836.982 KB with a length of 0.043 KB. (6) The connectron that has the identifier 53545 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4836.990 KB and 4837.123 KB with a length of 0.134 KB. (7) The connectron that has the identifier 53548 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4837.126 KB and 4837.148 KB with a length of 0.023 KB. (8) The connectron that has the identifier 53551 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4837.419 KB and 4837.448 KB with a length of 0.030 KB. (9) The connectron that has the identifier 53552 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4837.572 KB and 4837.622 KB with a length of 0.051 KB. (10) The connectron that has the identifier 53554 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4837.962 KB and 4837.999 KB with a length of 0.038 KB. (11) The connectron that has the identifier 53557 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4838.217 KB and 4838.258 KB with a length of 0.042 KB. (12) The connectron that has the identifier 53559 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4838.295 KB and 4838.362 KB with a length of 0.068 KB. (13) The connectron that has the identifier 53563 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4838.457 KB and 4838.476 KB with a length of 0.020 KB. (14) The connectron that has the identifier 53564 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4838.478 KB and 4838.645 KB with a length of 0.168 KB. (15) The connectron that has the identifier 53567 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 4838.654 KB and 4838.847 KB with a length of 0.194 KB.  
     Synthetic Connectron Formed by a DBP  
      A synthetic connectron can be introduced into the  V. cholerae  genome by introducing a 12-domain zinc-finger protein that recognizes the sequence  
                                      tccccatgag catagatatg cagqtaggcq gcaagt              
 
      Connectron 7580 is an example of a synthetic transient connectron.  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  7580   1   Synthetic   DBP   1   607   646   synthetic                  
 
      The T1-T2 target of the transient connectron 7580 as shown in Table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TN   607   1   1   952.642   952.777   .136             *−++++*+++*+++++++*+*++++**++++                   TP   608   1   1   952.648   952.777   .130             *−++++−+++−*+++*+*−++*++++−++++               GG   609   1   1   952.846   954.393   1.548   Group0127   |||| |||  ||| |  || |||| ||||               TN   610   1   1   954.486   954.587   .102             *−++++*+++*−+++−+−*+*−++*+**+++               TP   611   1   1   954.486   954.587   .102             *−+++++++++**++*+*++−**+−++−+*+               CNT   612   1   1   954.497   954.589   .093         OS−&gt;  |||||||||| ||||||| | | || | |               CPT   613   1   1   954.503   954.520   .018          −−&gt;  |||||||||| ||||||| | | || | |               CPT   614   1   1   954.522   954.588   .067          −−&gt;  |||||||||| ||||||| | | || | |               TP   615   1   1   954.601   954.658   .058             *−++++++++++*+++++++*+*+*++*++−+−*               TN   616   1   1   954.602   954.658   .057             *−+++++++++++++++++*+++++*+***−               CNT   617   1   1   954.616   954.658   .043          −−&gt;  ||||||||||||||||| ||||| || |               CPT   618   1   1   954.624   954.639   .016          −−&gt;  ||||||||||||||||| ||||| || |               CPT   619   1   1   954.641   954.658   .018          −−&gt;  ||||||||||||||||| ||||| || |               GG   620   1   1   954.684   958.635   3.951   Group0128   ||||||||||||||||| ||||| || |               GP   621   1   1   955.956   956.342   .387   VC0897      ||||||||||||||||| ||||| || |               CPT   622   1   1   956.873   956.887   .015          −−&gt;  ||||||||||||||||| ||||| || |               CPT   623   1   1   956.896   956.910   .015          −−&gt;  ||||||||||||||||| ||||| || |               TN   624   1   1   958.089   958.103   .015             *−+*||||||||||||||| ||||| || |               GG   625   1   1   958.840   972.992   14.152   Group0129   | ||||||||||||||| ||||| || |               GP   626   1   1   971.304   972.992   1.689   VC0911      | ||||||||||||||| ||||| || |               TP   627   1   1   973.170   973.250   .081             *−+*||||||||||||||| ||||| || |               GG   628   1   1   973.171   973.763   .592   Group0130   ||||||||||||||||| ||||| || |               CPT   629   1   1   973.339   973.434   .096         OS−&gt;  ||||||||||||||||| ||||| || |               CPT   630   1   1   973.508   973.603   .096         OS−&gt;  ||||||||||||||||| ||||| || |               TP   631   1   1   973.693   973.773   .081             *−+*||||||||||||||| ||||| || |               GG   632   1   1   973.767   996.501   22.734   Group0131   | ||||||||||||||| ||||| || |               GP   633   1   1   974.049   978.217   4.169   VC0913      | ||||||||||||||| ||||| || |               CPT   634   1   1   977.711   977.725   .015          −−&gt;  | ||||||||||||||| ||||| || |               CPT   635   1   1   977.732   977.746   .015          −−&gt;  | ||||||||||||||| ||||| || |               GP   636   1   1   986.166   990.921   4.756   VC0923      | ||||||||||||||| ||||| || |               CPT   637   1   1   986.862   986.877   .016          −−&gt;  | ||||||||||||||| ||||| || |               CPT   638   1   1   986.885   986.899   .015          −−&gt;  | ||||||||||||||| ||||| || |               TN   639   1   1   996.556   996.577   .022             *−+**|||||||||||||| ||||| || |               TP   640   1   1   996.556   996.577   .022             *−++−+++*++++++++++*||||| || |               GG   641   1   1   996.656   1005.792   9.136   Group0132   || ||| |||||||||||||||| || |               GP   642   1   1   1002.462   1005.792   3.331   VC0937      || ||| |||||||||||||||| || |               TP   643   1   1   1005.810   1005.874   .065             *−++*+++*++*+*+++++++++++*++*+*               CNT   644   1   1   1005.810   1005.921   .112         OS−&gt;  ||||||||| | |||||||||||||||||               CPT   645   1   1   1005.810   1005.926   .117          −−&gt;  ||||||||| | |||||||||||||||||               TN   646   1   1   1005.810   1005.926   .117             *−++++*++++*+*+++++++++*+++*+++                  
 
      Group0127 through Group0132 are described in Table 2 as  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0127                                   VC0894   COG0607   P   1   positive   952.846   954.393   1.548       Group0128       VC0895           1   negative   954.684   954.860   .177       VC0896   COG0583   K   1   positive   955.014   955.934   .921       VC0897   COG2363   S   1   positive   955.956   956.342   .387       VC0898   COG0258   L   1   negative   956.372   957.223   .852       VC0899   COG1611   R   1   negative   957.262   958.635   1.374       Group0129       VC0900   COG2199   T   1   negative   958.840   960.414   1.575       VC0901   COG0457   R   1   negative   960.516   962.777   2.262       VC0902   COG0780   R   1   negative   962.792   963.655   .864       VC0903           1   positive   963.686   964.282   .597       VC0904           1   positive   964.284   965.060   .777       VC0905   COG1464   M   1   negative   965.193   966.020   .828       VC0906   COG2011   R   1   negative   966.039   967.740   1.702       VC0908   COG0241   E   1   positive   967.976   968.536   .561       VC0909   COG1609   K   1   positive   968.601   969.551   .951       VC0910   COG1263   G   1   positive   969.788   971.224   1.437       VC0911   COG0366   G   1   positive   971.304   972.992   1.689       Group0130       tRNA-Tyr-2           1   positive   973.171   973.255   .085       tRNA-Tyr-3           1   positive   973.340   973.424   .085       tRNA-Tyr-4           1   positive   973.509   973.593   .085       tRNA-Tyr-5           1   positive   973.679   973.763   .085       Group0131       VC0912           1   positive   973.767   973.862   .096       VC0913   COG0845   Q   1   positive   974.049   978.217   4.169       VC0915           1   positive   978.272   978.382   .111       VC0916   COG0394   T   1   positive   978.644   979.144   .501       VC0917   COG0381   M   1   positive   979.457   980.575   1.119       VC0918   COG0677   M   1   positive   980.595   986.155   5.561       VC0923   COG1045   E   1   positive   986.166   990.921   4.756       VC0928           1   positive   991.117   991.932   .816       VC0929           1   negative   992.138   993.364   1.227       VC0930           1   positive   993.628   996.501   2.874       Group0132       VC0931   COG3307   M   1   negative   996.656   997.972   1.317       VC0932           1   negative   998.148   998.752   .605       VC0934   COG2148   M   1   positive   999.242   1000.639   1.398       VC0935           1   positive   1000.710   1001.906   1.197       VC0936   COG1596   M   1   positive   1001.910   1002.437   .528       VC0937   COG3206   N   1   positive   1002.462   1005.792   3.331                  
 
      All of the data for the transient connectron 7580 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   7580   synthetic                 Control Sequences - Synthetic DNA Binding       Protein that recognizes the sequence       tccccatgag catagatatg caggtaggcg gcaagt                                                         Chro-                       Target       mo-       Sequences -   Direction   some       Start   Stop   Length                           T1_Id                   negative   1   607   952.777   952.642   .136                   T2_Id                   646   1005.926   1005.810   .117                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0127   VC0894   COG0607   positive   952.846   954.393   1.548       2   1   Group0128   VC0895       positive   954.684   958.635   3.951       3   1   Group0128   VC0896   COG0583   positive   955.014   955.934   .921       4   1   Group0128   VC0897   COG2363   positive   955.956   956.342   .387       5   1   Group0128   VC0898   COG0258   negative   957.223   956.372   .852       6   1   Group0128   VC0899   COG1611   negative   958.635   957.262   1.374       7   1   Group0129   VC0900   COG2199   positive   958.840   972.992   14.152       8   1   Group0129   VC0901   COG0457   negative   962.777   960.516   2.262       9   1   Group0129   VC0902   COG0780   negative   963.655   962.792   .864       10   1   Group0129   VC0903       positive   963.686   964.282   .597       11   1   Group0129   VC0904       positive   964.284   965.060   .777       12   1   Group0129   VC0905   COG1464   negative   966.020   965.193   .828       13   1   Group0129   VC0906   COG2011   negative   967.740   966.039   1.702       14   1   Group0129   VC0908   COG0241   positive   967.976   968.536   .561       15   1   Group0129   VC0909   COG1609   positive   968.601   969.551   .951       16   1   Group0129   VC0910   COG1263   positive   969.788   971.224   1.437       17   1   Group0129   VC0911   COG0366   positive   971.304   972.992   1.689       18   1   Group0130   tRNA-Tyr-       positive   973.171   973.763   .592       19   1   Group0131   VC0912       positive   973.767   996.501   22.734       20   1   Group0131   VC0913   COG0845   positive   974.049   978.217   4.169       21   1   Group0131   VC0915       positive   978.272   978.382   .111       22   1   Group0131   VC0916   COG0394   positive   978.644   979.144   .501       23   1   Group0131   VC0917   COG0381   positive   979.457   980.575   1.119       24   1   Group0131   VC0918   COG0677   positive   980.595   986.155   5.561       25   1   Group0131   VC0923   COG1045   positive   986.166   990.921   4.756       26   1   Group0131   VC0928       positive   991.117   991.932   .816       27   1   Group0131   VC0929       negative   993.364   992.138   1.227       28   1   Group0131   VC0930       positive   993.628   996.501   2.874       29   1   Group0132   VC0931   COG3307   positive   996.656   1005.792   9.136       30   1   Group0132   VC0932       negative   998.752   998.148   .605       31   1   Group0132   VC0934   COG2148   positive   999.242   1000.639   1.398       32   1   Group0132   VC0935       positive   1000.710   1001.906   1.197       33   1   Group0132   VC0936   COG1596   positive   1001.910   1002.437   .528       34   1   Group0132   VC0937   COG3206   positive   1002.462   1005.792   3.331                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   1   612   negative   954.589   954.497   .093       2   1   613   positive   954.503   954.520   .018       3   1   614   positive   954.522   954.588   .067       4   1   617   negative   954.658   954.616   .043       5   1   618   positive   954.624   954.639   .016       6   1   619   positive   954.641   954.658   .018       7   1   622   positive   956.873   956.887   .015       8   1   623   positive   956.896   956.910   .015       9   1   629   positive   973.339   973.434   .096       10   1   630   positive   973.508   973.603   .096       11   1   634   positive   977.711   977.725   .015       12   1   635   positive   977.732   977.746   .015       13   1   637   positive   986.862   986.877   .016       14   1   638   positive   986.885   986.899   .015       15   1   644   negative   1005.921   1005.810   .112       16   1   645   positive   1005.810   1005.926   .117                  
 
      The verbose description of the synthetic connectron 7580 is:  
      In the  Vibrio cholerae  chromosome I, complete chromosome the synthetic connectron number 7580 is generated by a synthetic DNA binding protein that recognizes the sequence tccccatgagcatagatatgcaggtaggcggcaagt. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the negative strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 607. The genomic start and stop positions of this initiating target sequence are 952.777 KB and 952.642 KB with a length of 0.136 KB. The identifier number of the terminating target sequence (T2) is 646. The genomic start and stop positions of this terminating target sequence are 1005.926 KB and 1005.810 KB with a length of 0.117 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name VC0894 and with a COG identifier of COG0607. The genomic start and stop positions of this gene are 952.846 KB and 954.393 KB with a length of 1.548 KB. (2) The gene that has the name VC0895. The genomic start and stop positions of this gene are 954.684 KB and 958.635 KB with a length of 3.951 KB. (3) The gene that has the name VC0896 and with a COG identifier of COG0583. The genomic start and stop positions of this gene are 955.014 KB and 955.934 KB with a length of 0.921 KB. (4) The gene that has the name VC0897 and with a COG identifier of COG2363. The genomic start and stop positions of this gene are 955.956 KB and 956.342 KB with a length of 0.387 KB. (5) The gene that has the name VC0898 and with a COG identifier of COG0258. The genomic start and stop positions of this gene are 957.223 KB and 956.372 KB with a length of 0.852 KB. (6) The gene that has the name VC0899 and with a COG identifier of COG1611. The genomic start and stop positions of this gene are 958.635 KB and 957.262 KB with a length of 1.374 KB. (7) The gene that has the name VC0900 and with a COG identifier of COG2199. The genomic start and stop positions of this gene are 958.840 KB and 972.992 KB with a length of 14.152 KB. (8) The gene that has the name VC0901 and with a COG identifier of COG0457. The genomic start and stop positions of this gene are 962.777 KB and 960.516 KB with a length of 2.262 KB. (9) The gene that has the name VC0902 and with a COG identifier of COG0780. The genomic start and stop positions of this gene are 963.655 KB and 962.792 KB with a length of 0.864 KB. (10) The gene that has the name VC0903. The genomic start and stop positions of this gene are 963.686 KB and 964.282 KB with a length of 0.597 KB. (11) The gene that has the name VC0904. The genomic start and stop positions of this gene are 964.284 KB and 965.060 KB with a length of 0.777 KB. (12) The gene that has the name VC0905 and with a COG identifier of COG1464. The genomic start and stop positions of this gene are 966.020 KB and 965.193 KB with a length of 0.828 KB. (13) The gene that has the name VC0906 and with a COG identifier of COG2011. The genomic start and stop positions of this gene are 967.740 KB and 966.039 KB with a length of 1.702 KB. (14) The gene that has the name VC0908 and with a COG identifier of COG0241. The genomic start and stop positions of this gene are 967.976 KB and 968.536 KB with a length of 0.561 KB. (15) The gene that has the name VC0909 and with a COG identifier of COG1609. The genomic start and stop positions of this gene are 968.601 KB and 969.551 KB with a length of 0.951 KB. (16) The gene that has the name VC0910 and with a COG identifier of COG1263. The genomic start and stop positions of this gene are 969.788 KB and 971.224 KB with a length of 1.437 KB. (17) The gene that has the name VC0911 and with a COG identifier of COG0366. The genomic start and stop positions of this gene are 971.304 KB and 972.992 KB with a length of 1.689 KB. (18) The gene that has the name tRNA-Tyr-. The genomic start and stop positions of this gene are 973.171 KB and 973.763 KB with a length of 0.592 KB. (19) The gene that has the name VC0912. The genomic start and stop positions of this gene are 973.767 KB and 996.501 KB with a length of 22.734 KB. (20) The gene that has the name VC0913 and with a COG identifier of COG0845. The genomic start and stop positions of this gene are 974.049 KB and 978.217 KB with a length of 4.169 KB. (21) The gene that has the name VC0915. The genomic start and stop positions of this gene are 978.272 KB and 978.382 KB with a length of 0.111 KB. (22) The gene that has the name VC0916 and with a COG identifier of COG0394. The genomic start and stop positions of this gene are 978.644 KB and 979.144 KB with a length of 0.501 KB. (23) The gene that has the name VC0917 and with a COG identifier of COG0381. The genomic start and stop positions of this gene are 979.457 KB and 980.575 KB with a length of 1.119 KB. (24) The gene that has the name VC0918 and with a COG identifier of COG0677. The genomic start and stop positions of this gene are 980.595 KB and 986.155 KB with a length of 5.561 KB. (25) The gene that has the name VC0923 and with a COG identifier of COG1045. The genomic start and stop positions of this gene are 986.166 KB and 990.921 KB with a length of 4.756 KB. (26) The gene that has the name VC0928. The genomic start and stop positions of this gene are 991.117 KB and 991.932 KB with a length of 0.816 KB. (27) The gene that has the name VC0929. The genomic start and stop positions of this gene are 993.364 KB and 992.138 KB with a length of 1.227 KB. (28) The gene that has the name VC0930. The genomic start and stop positions of this gene are 993.628 KB and 996.501 KB with a length of 2.874 KB. (29) The gene that has the name VC0931 and with a COG identifier of COG3307. The genomic start and stop positions of this gene are 996.656 KB and 1005.792 KB with a length of 9.136 KB. (30) The gene that has the name VC0932. The genomic start and stop positions of this gene are 998.752 KB and 998.148 KB with a length of 0.605 KB. (31) The gene that has the name VC0934 and with a COG identifier of COG2148. The genomic start and stop positions of this gene are 999.242 KB and 1000.639 KB with a length of 1.398 KB. (32) The gene that has the name VC0935. The genomic start and stop positions of this gene are 1000.710 KB and 1001.906 KB with a length of 1.197 KB. (33) The gene that has the name VC0936 and with a COG identifier of COG1596. The genomic start and stop positions of this gene are 1001.910 KB and 1002.437 KB with a length of 0.528 KB. (34) The gene that has the name VC0937 and with a COG identifier of COG3206. The genomic start and stop positions of this gene are 1002.462 KB and 1005.792 KB with a length of 3.331 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 612 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 954.589 KB and 954.497 KB with a length of 0.093 KB. (2) The connectron that has the identifier 613 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.503 KB and 954.520 KB with a length of 0.018 KB. (3) The connectron that has the identifier 614 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.522 KB and 954.588 KB with a length of 0.067 KB. (4) The connectron that has the identifier 617 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 954.658 KB and 954.616 KB with a length of 0.043 KB. (5) The connectron that has the identifier 618 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.624 KB and 954.639 KB with a length of 0.016 KB. (6) The connectron that has the identifier 619 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.641 KB and 954.658 KB with a length of 0.018 KB. (7) The connectron that has the identifier 622 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 956.873 KB and 956.887 KB with a length of 0.015 KB. (8) The connectron that has the identifier 623 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 956.896 KB and 956.910 KB with a length of 0.015 KB. (9) The connectron that has the identifier 629 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 973.339 KB and 973.434 KB with a length of 0.096 KB. (10) The connectron that has the identifier 630 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 973.508 KB and 973.603 KB with a length of 0.096 KB. (11) The connectron that has the identifier 634 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 977.711 KB and 977.725 KB with a length of 0.015 KB. (12) The connectron that has the identifier 635 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 977.732 KB and 977.746 KB with a length of 0.015 KB. (13) The connectron that has the identifier 637 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 986.862 KB and 986.877 KB with a length of 0.016 KB. (14) The connectron that has the identifier 638 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 986.885 KB and 986.899 KB with a length of 0.015 KB. (15) The connectron that has the identifier 644 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 1005.921 KB and 1005.810 KB with a length of 0.112 KB. (16) The connectron that has the identifier 645 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 1005.810 KB and 1005.926 KB with a length of 0.117 KB.  
     Synthetic Connectron Formed by a PNA  
      A synthetic connectron can be introduced into the  V. cholerae  genome by introducing a PNA that recognizes the sequence  
                                      tccccatgag catagatatg caggtaggcg gcaagt              
 
      Connectron 7581 is an example of a synthetic transient connectron.  
                                                                   C1/C2           T1-T2               Global_Id   Chromosome   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  7581   1   Synthetic   PNA   1   607   646   synthetic                  
 
      The T1-T2 target of the transient connectron 7581 as shown in Table 1 is represented as  
                                                           Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                    TN   607   1   1   952.642   952.777   .136             *−++++*+++*+++++++*+*++++**++++                   TP   608   1   1   952.648   952.777   .130             *−++++−+++−*+++*+*−++*++++−++++               GG   609   1   1   952.846   954.393   1.548   Group0127   |||| |||  ||| |  || |||| ||||               TN   610   1   1   954.486   954.587   .102             *−++++*+++*−+++−+−*+*−++*+**+++               TP   611   1   1   954.486   954.587   .102             *−+++++++++**++*+*++−**+−++−+*+               CNT   612   1   1   954.497   954.589   .093         OS−&gt;  |||||||||| ||||||| | | || | |               CPT   613   1   1   954.503   954.520   .018          −−&gt;  |||||||||| ||||||| | | || | |               CPT   614   1   1   954.522   954.588   .067          −−&gt;  |||||||||| ||||||| | | || | |               TP   615   1   1   954.601   954.658   .058             *−++++++++++*+++++++*+*+*++*++−+−*               TN   616   1   1   954.602   954.658   .057             *−+++++++++++++++++*+++++*+***−               CNT   617   1   1   954.616   954.658   .043          −−&gt;  ||||||||||||||||| ||||| || |               CPT   618   1   1   954.624   954.639   .016          −−&gt;  ||||||||||||||||| ||||| || |               CPT   619   1   1   954.641   954.658   .018          −−&gt;  ||||||||||||||||| ||||| || |               GG   620   1   1   954.684   958.635   3.951   Group0128   ||||||||||||||||| ||||| || |               GP   621   1   1   955.956   956.342   .387   VC0897      ||||||||||||||||| ||||| || |               CPT   622   1   1   956.873   956.887   .015          −−&gt;  ||||||||||||||||| ||||| || |               CPT   623   1   1   956.896   956.910   .015          −−&gt;  ||||||||||||||||| ||||| || |               TN   624   1   1   958.089   958.103   .015             *−+*||||||||||||||| ||||| || |               GG   625   1   1   958.840   972.992   14.152   Group0129   | ||||||||||||||| ||||| || |               GP   626   1   1   971.304   972.992   1.689   VC0911      | ||||||||||||||| ||||| || |               TP   627   1   1   973.170   973.250   .081             *−+*||||||||||||||| ||||| || |               GG   628   1   1   973.171   973.763   .592   Group0130   ||||||||||||||||| ||||| || |               CPT   629   1   1   973.339   973.434   .096         OS−&gt;  ||||||||||||||||| ||||| || |               CPT   630   1   1   973.508   973.603   .096         OS−&gt;  ||||||||||||||||| ||||| || |               TP   631   1   1   973.693   973.773   .081             *−+*||||||||||||||| ||||| || |               GG   632   1   1   973.767   996.501   22.734   Group0131   | ||||||||||||||| ||||| || |               GP   633   1   1   974.049   978.217   4.169   VC0913      | ||||||||||||||| ||||| || |               CPT   634   1   1   977.711   977.725   .015          −−&gt;  | ||||||||||||||| ||||| || |               CPT   635   1   1   977.732   977.746   .015          −−&gt;  | ||||||||||||||| ||||| || |               GP   636   1   1   986.166   990.921   4.756   VC0923      | ||||||||||||||| ||||| || |               CPT   637   1   1   986.862   986.877   .016          −−&gt;  | ||||||||||||||| ||||| || |               CPT   638   1   1   986.885   986.899   .015          −−&gt;  | ||||||||||||||| ||||| || |               TN   639   1   1   996.556   996.577   .022             *−+**|||||||||||||| ||||| || |               TP   640   1   1   996.556   996.577   .022             *−++−+++*++++++++++*||||| || |               GG   641   1   1   996.656   1005.792   9.136   Group0132   || ||| |||||||||||||||| || |               GP   642   1   1   1002.462   1005.792   3.331   VC0937      || ||| |||||||||||||||| || |               TP   643   1   1   1005.810   1005.874   .065             *−++*+++*++*+*+++++++++++*++*+*               CNT   644   1   1   1005.810   1005.921   .112         OS−&gt;  ||||||||| | |||||||||||||||||               CPT   645   1   1   1005.810   1005.926   .117          −−&gt;  ||||||||| | |||||||||||||||||               TN   646   1   1   1005.810   1005.926   .117             *−++++*++++*+*+++++++++*+++*+++                  
 
      Group0127 through Group0132 are described in Table 2 as  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0127                                   VC0894   COG0607   P   1   positive   952.846   954.393   1.548       Group0128       VC0895           1   negative   954.684   954.860   .177       VC0896   COG0583   K   1   positive   955.014   955.934   .921       VC0897   COG2363   S   1   positive   955.956   956.342   .387       VC0898   COG0258   L   1   negative   956.372   957.223   .852       VC0899   COG1611   R   1   negative   957.262   958.635   1.374       Group0129       VC0900   COG2199   T   1   negative   958.840   960.414   1.575       VC0901   COG0457   R   1   negative   960.516   962.777   2.262       VC0902   COG0780   R   1   negative   962.792   963.655   .864       VC0903           1   positive   963.686   964.282   .597       VC0904           1   positive   964.284   965.060   .777       VC0905   COG1464   M   1   negative   965.193   966.020   .828       VC0906   COG2011   R   1   negative   966.039   967.740   1.702       VC0908   COG0241   E   1   positive   967.976   968.536   .561       VC0909   COG1609   K   1   positive   968.601   969.551   .951       VC0910   COG1263   G   1   positive   969.788   971.224   1.437       VC0911   COG0366   G   1   positive   971.304   972.992   1.689       Group0130       tRNA-Tyr-2           1   positive   973.171   973.255   .085       tRNA-Tyr-3           1   positive   973.340   973.424   .085       tRNA-Tyr-4           1   positive   973.509   973.593   .085       tRNA-Tyr-5           1   positive   973.679   973.763   .085       Group0131       VC0912           1   positive   973.767   973.862   .096       VC0913   COG0845   Q   1   positive   974.049   978.217   4.169       VC0915           1   positive   978.272   978.382   .111       VC0916   COG0394   T   1   positive   978.644   979.144   .501       VC0917   COG0381   M   1   positive   979.457   980.575   1.119       VC0918   COG0677   M   1   positive   980.595   986.155   5.561       VC0923   COG1045   E   1   positive   986.166   990.921   4.756       VC0928           1   positive   991.117   991.932   .816       VC0929           1   negative   992.138   993.364   1.227       VC0930           1   positive   993.628   996.501   2.874       Group0132       VC0931   COG3307   M   1   negative   996.656   997.972   1.317       VC0932           1   negative   998.148   998.752   .605       VC0934   COG2148   M   1   positive   999.242   1000.639   1.398       VC0935           1   positive   1000.710   1001.906   1.197       VC0936   COG1596   M   1   positive   1001.910   1002.437   .528       VC0937   COG3206   N   1   positive   1002.462   1005.792   3.331                  
 
      All of the data for the transient connectron 7581 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   7581   synthetic                 Control Sequences - Synthetic PNA that       recognizes the sequence       tccccatgag catagatatg caggtaggcg gcaagt                                                         Chro-                       Target       mo-       Sequences -   Direction   some       Start   Stop   Length                           T1_Id                   negative   1   607   952.777   952.642   .136                   T2_Id                   646   1005.926   1005.810   .117                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0127   VC0894   COG0607   positive   952.846   954.393   1.548       2   1   Group0128   VC0895       positive   954.684   958.635   3.951       3   1   Group0128   VC0896   COG0583   positive   955.014   955.934   .921       4   1   Group0128   VC0897   COG2363   positive   955.956   956.342   .387       5   1   Group0128   VC0898   COG0258   negative   957.223   956.372   .852       6   1   Group0128   VC0899   COG1611   negative   958.635   957.262   1.374       7   1   Group0129   VC0900   COG2199   positive   958.840   972.992   14.152       8   1   Group0129   VC0901   COG0457   negative   962.777   960.516   2.262       9   1   Group0129   VC0902   COG0780   negative   963.655   962.792   .864       10   1   Group0129   VC0903       positive   963.686   964.282   .597       11   1   Group0129   VC0904       positive   964.284   965.060   .777       12   1   Group0129   VC0905   COG1464   negative   966.020   965.193   .828       13   1   Group0129   VC0906   COG2011   negative   967.740   966.039   1.702       14   1   Group0129   VC0908   COG0241   positive   967.976   968.536   .561       15   1   Group0129   VC0909   COG1609   positive   968.601   969.551   .951       16   1   Group0129   VC0910   COG1263   positive   969.788   971.224   1.437       17   1   Group0129   VC0911   COG0366   positive   971.304   972.992   1.689       18   1   Group0130   tRNA-Tyr-       positive   973.171   973.763   .592       19   1   Group0131   VC0912       positive   973.767   996.501   22.734       20   1   Group0131   VC0913   COG0845   positive   974.049   978.217   4.169       21   1   Group0131   VC0915       positive   978.272   978.382   .111       22   1   Group0131   VC0916   COG0394   positive   978.644   979.144   .501       23   1   Group0131   VC0917   COG0381   positive   979.457   980.575   1.119       24   1   Group0131   VC0918   COG0677   positive   980.595   986.155   5.561       25   1   Group0131   VC0923   COG1045   positive   986.166   990.921   4.756       26   1   Group0131   VC0928       positive   991.117   991.932   .816       27   1   Group0131   VC0929       negative   993.364   992.138   1.227       28   1   Group0131   VC0930       positive   993.628   996.501   2.874       29   1   Group0132   VC0931   COG3307   positive   996.656   1005.792   9.136       30   1   Group0132   VC0932       negative   998.752   998.148   .605       31   1   Group0132   VC0934   COG2148   positive   999.242   1000.639   1.398       32   1   Group0132   VC0935       positive   1000.710   1001.906   1.197       33   1   Group0132   VC0936   COG1596   positive   1001.910   1002.437   .528       34   1   Group0132   VC0937   COG3206   positive   1002.462   1005.792   3.331                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   1   612   negative   954.589   954.497   .093       2   1   613   positive   954.503   954.520   .018       3   1   614   positive   954.522   954.588   .067       4   1   617   negative   954.658   954.616   .043       5   1   618   positive   954.624   954.639   .016       6   1   619   positive   954.641   954.658   .018       7   1   622   positive   956.873   956.887   .015       8   1   623   positive   956.896   956.910   .015       9   1   629   positive   973.339   973.434   .096       10   1   630   positive   973.508   973.603   .096       11   1   634   positive   977.711   977.725   .015       12   1   635   positive   977.732   977.746   .015       13   1   637   positive   986.862   986.877   .016       14   1   638   positive   986.885   986.899   .015       15   1   644   negative   1005.921   1005.810   .112       16   1   645   positive   1005.810   1005.926   .117                  
 
      The verbose description of the synthetic connectron 7581 is:  
      In the  Vibrio cholerae  chromosome I, complete chromosome the synthetic connectron number 7580 is generated by a synthetic PNA that recognizes the sequence tccccatgagcatagatatgcaggtaggcggcaagt. This connectron causes stabilization of a loop of DNA. The target sequences (T1-T2) are on the negative strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 607. The genomic start and stop positions of this initiating target sequence are 952.777 KB and 952.642 KB with a length of 0.136 KB. The identifier number of the terminating target sequence (T2) is 646. The genomic start and stop positions of this terminating target sequence are 1005.926 KB and 1005.810 KB with a length of 0.117 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name VC0894 and with a COG identifier of COG0607. The genomic start and stop positions of this gene are 952.846 KB and 954.393 KB with a length of 1.548 KB. (2) The gene that has the name VC0895. The genomic start and stop positions of this gene are 954.684 KB and 958.635 KB with a length of 3.951 KB. (3) The gene that has the name VC0896 and with a COG identifier of COG0583. The genomic start and stop positions of this gene are 955.014 KB and 955.934 KB with a length of 0.921 KB. (4) The gene that has the name VC0897 and with a COG identifier of COG2363. The genomic start and stop positions of this gene are 955.956 KB and 956.342 KB with a length of 0.387 KB. (5) The gene that has the name VC0898 and with a COG identifier of COG0258. The genomic start and stop positions of this gene are 957.223 KB and 956.372 KB with a length of 0.852 KB. (6) The gene that has the name VC0899 and with a COG identifier of COG1611. The genomic start and stop positions of this gene are 958.635 KB and 957.262 KB with a length of 1.374 KB. (7) The gene that has the name VC0900 and with a COG identifier of COG2199. The genomic start and stop positions of this gene are 958.840 KB and 972.992 KB with a length of 14.152 KB. (8) The gene that has the name VC0901 and with a COG identifier of COG0457. The genomic start and stop positions of this gene are 962.777 KB and 960.516 KB with a length of 2.262 KB. (9) The gene that has the name VC0902 and with a COG identifier of COG0780. The genomic start and stop positions of this gene are 963.655 KB and 962.792 KB with a length of 0.864 KB. (10) The gene that has the name VC0903. The genomic start and stop positions of this gene are 963.686 KB and 964.282 KB with a length of 0.597 KB. (11) The gene that has the name VC0904. The genomic start and stop positions of this gene are 964.284 KB and 965.060 KB with a length of 0.777 KB. (12) The gene that has the name VC0905 and with a COG identifier of COG1464. The genomic start and stop positions of this gene are 966.020 KB and 965.193 KB with a length of 0.828 KB. (13) The gene that has the name VC0906 and with a COG identifier of COG2011. The genomic start and stop positions of this gene are 967.740 KB and 966.039 KB with a length of 1.702 KB. (14) The gene that has the name VC0908 and with a COG identifier of COG0241. The genomic start and stop positions of this gene are 967.976 KB and 968.536 KB with a length of 0.561 KB. (15) The gene that has the name VC0909 and with a COG identifier of COG1609. The genomic start and stop positions of this gene are 968.601 KB and 969.551 KB with a length of 0.951 KB. (16) The gene that has the name VC0910 and with a COG identifier of COG1263. The genomic start and stop positions of this gene are 969.788 KB and 971.224 KB with a length of 1.437 KB. (17) The gene that has the name VC0911 and with a COG identifier of COG0366. The genomic start and stop positions of this gene are 971.304 KB and 972.992 KB with a length of 1.689 KB. (18) The gene that has the name tRNA-Tyr-. The genomic start and stop positions of this gene are 973.171 KB and 973.763 KB with a length of 0.592 KB. (19) The gene that has the name VC0912. The genomic start and stop positions of this gene are 973.767 KB and 996.501 KB with a length of 22.734 KB. (20) The gene that has the name VC0913 and with a COG identifier of COG0845. The genomic start and stop positions of this gene are 974.049 KB and 978.217 KB with a length of 4.169 KB. (21) The gene that has the name VC0915. The genomic start and stop positions of this gene are 978.272 KB and 978.382 KB with a length of 0.111 KB. (22) The gene that has the name VC0916 and with a COG identifier of COG0394. The genomic start and stop positions of this gene are 978.644 KB and 979.144 KB with a length of 0.501 KB. (23) The gene that has the name VC0917 and with a COG identifier of COG0381. The genomic start and stop positions of this gene are 979.457 KB and 980.575 KB with a length of 1.119 KB. (24) The gene that has the name VC0918 and with a COG identifier of COG0677. The genomic start and stop positions of this gene are 980.595 KB and 986.155 KB with a length of 5.561 KB. (25) The gene that has the name VC0923 and with a COG identifier of COG1045. The genomic start and stop positions of this gene are 986.166 KB and 990.921 KB with a length of 4.756 KB. (26) The gene that has the name VC0928. The genomic start and stop positions of this gene are 991.117 KB and 991.932 KB with a length of 0.816 KB. (27) The gene that has the name VC0929. The genomic start and stop positions of this gene are 993.364 KB and 992.138 KB with a length of 1.227 KB. (28) The gene that has the name VC0930. The genomic start and stop positions of this gene are 993.628 KB and 996.501 KB with a length of 2.874 KB. (29) The gene that has the name VC0931 and with a COG identifier of COG3307. The genomic start and stop positions of this gene are 996.656 KB and 1005.792 KB with a length of 9.136 KB. (30) The gene that has the name VC0932. The genomic start and stop positions of this gene are 998.752 KB and 998.148 KB with a length of 0.605 KB. (31) The gene that has the name VC0934 and with a COG identifier of COG2148. The genomic start and stop positions of this gene are 999.242 KB and 1000.639 KB with a length of 1.398 KB. (32) The gene that has the name VC0935. The genomic start and stop positions of this gene are 1000.710 KB and 1001.906 KB with a length of 1.197 KB. (33) The gene that has the name VC0936 and with a COG identifier of COG1596. The genomic start and stop positions of this gene are 1001.910 KB and 1002.437 KB with a length of 0.528 KB. (34) The gene that has the name VC0937 and with a COG identifier of COG3206. The genomic start and stop positions of this gene are 1002.462 KB and 1005.792 KB with a length of 3.331 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 612 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 954.589 KB and 954.497 KB with a length of 0.093 KB. (2) The connectron that has the identifier 613 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.503 KB and 954.520 KB with a length of 0.018 KB. (3) The connectron that has the identifier 614 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.522 KB and 954.588 KB with a length of 0.067 KB. (4) The connectron that has the identifier 617 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 954.658 KB and 954.616 KB with a length of 0.043 KB. (5) The connectron that has the identifier 618 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.624 KB and 954.639 KB with a length of 0.016 KB. (6) The connectron that has the identifier 619 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 954.641 KB and 954.658 KB with a length of 0.018 KB. (7) The connectron that has the identifier 622 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 956.873 KB and 956.887 KB with a length of 0.015 KB. (8) The connectron that has the identifier 623 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 956.896 KB and 956.910 KB with a length of 0.015 KB. (9) The connectron that has the identifier 629 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 973.339 KB and 973.434 KB with a length of 0.096 KB. (10) The connectron that has the identifier 630 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 973.508 KB and 973.603 KB with a length of 0.096 KB. (11) The connectron that has the identifier 634 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 977.711 KB and 977.725 KB with a length of 0.015 KB. (12) The connectron that has the identifier 635 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 977.732 KB and 977.746 KB with a length of 0.015 KB. (13) The connectron that has the identifier 637 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 986.862 KB and 986.877 KB with a length of 0.016 KB. (14) The connectron that has the identifier 638 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 986.885 KB and 986.899 KB with a length of 0.015 KB. (15) The connectron that has the identifier 644 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 1005.921 KB and 1005.810 KB with a length of 0.112 KB. (16) The connectron that has the identifier 645 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 1005.810 KB and 1005.926 KB with a length of 0.117 KB.  
     Synthetic Connectron Formed by a Pair of Linked DNA Binding Objects  
      A synthetic connectron can be introduced into the  A. pernix  genome by introducing a pair of linked DNA binding objects that recognize the sequences  
                                      G1 cccgacacaacctgc               and                       G2 cccggggttcccgag          
 
      Connectron 917 is an example of a synthetic transient connectron.  
                                                               Chro-                                   mo-   C1/C2           T1-T2       Global_Id   some   C1_Id   C2_Id   Chromosome   T1_Id   T2_Id   Connectron_Type                  917   1   G1   G2   1   218   295   synthetic                  
 
      The T1-T2 target of the transient connectron 917 as shown in Table 1 is represented as  
                                                               Type   Num   Jobno   Chr   Start   Stop   Length   GeneName                                                                        TN   218   1   1   284.008   284.071   .064       *−+*+−++*|||| |||  |                   TP   219   1   1   284.008   284.071   .064       −+++*|| |||| |||  |               CPT   220   1   1   284.009   284.071   .063         --&gt;     |||||| |||| |||  |               CNT   221   1   1   284.073   284.144   .072         --&gt;     |||||| |||| |||  |               CPT   222   1   1   284.073   284.145   .073         --&gt;     |||||| |||| |||  |               TP   223   1   1   284.073   284.160   .088       *−++++++*++++*|||  |               TN   224   1   1   284.073   284.251   .179       *−+++++++++++++++**+*               CNT   225   1   1   284.158   284.251   .094         --&gt;     |||||||||||||||||||               CPT   226   1   1   284.158   284.251   .094         --&gt;     |||||||||||||||||||               TP   227   1   1   284.162   284.251   .090       *−+++++++++++++++++++**               CPT   228   1   1   284.253   284.280   .028         --&gt;     |||||||||||||||||||||               TN   229   1   1   284.253   284.305   .053       *−+++++++++++++++++++++*               TP   230   1   1   284.253   284.316   .064       *−++++++++++++++++++++++**               CPT   231   1   1   284.283   284.305   .023         --&gt;     ||||||||||||||||||||||||               GG   232   1   1   284.391   287.510   3.120   Group0053     ||||||||||||||||||||||||               TN   233   1   1   286.094   286.108   .015       *−++++++++++++++++++++++++*               GG   234   1   1   287.521   291.639   4.118   Group0054     |||||||||||||||||||||||||               TP   235   1   1   288.611   288.625   .015       *−+++++*|||||||||||||||||||               GG   236   1   1   291.643   295.139   3.496   Group0055   ||||| |||||||||||||||||||               TP   237   1   1   295.230   295.259   .030       *−+++++*|||||||||||||||||||               GG   238   1   1   295.231   293.529   .298   Group0056     |||||||||||||||||||||||||               GP   239   1   1   295.342   295.518   .177   APES013     |||||||||||||||||||||||||               CPT   240   1   1   295.415   295.444   .030         --&gt;     |||||||||||||||||||||||||               TP   241   1   1   295.417   295.444   .028       *−+++++++++*+++++++++++++++*               GG   242   1   1   295.572   296.676   1.104   Group0057     ||||||||| ||||||||||||||||               TN   243   1   1   296.080   296.095   .016       *−+++++++++*||||||||||||||||               TN   244   1   1   296.913   296.927   .015       *−++++++++++++++++++++++++++*               GG   245   1   1   297.071   298.857   1.786   Group0058     |||||||||||||||||||||||||||               TP   246   1   1   298.617   298.631   .015       *−+++++++++++++++++++++++++++*               GG   247   1   1   298.856   305.941   7.085   Group0059     ||||||||||||||||||||||||||||               CNT   248   1   1   300.742   300.757   .016         --&gt;     ||||||||||||||||||||||||||||               CNT   249   1   1   300.767   300.781   .015         --&gt;     ||||||||||||||||||||||||||||               GN   250   1   1   301.243   303.153   1.911   APE0428     ||||||||||||||||||||||||||||               TN   251   1   1   301.733   301.748   .016       *−++++++++++++*+++++++++++++++*               GP   252   1   1   305.005   305.611   .607   APE0434     |||||||||||| ||||||||||||||||               CPT   253   1   1   305.334   305.348   .015         --&gt;     |||||||||||| ||||||||||||||||               CPT   254   1   1   305.358   305.372   .015         --&gt;     |||||||||||| ||||||||||||||||               CNT   255   1   1   305.552   305.566   .015         --&gt;     |||||||||||| ||||||||||||||||               TN   256   1   1   305.562   305.576   .015       *−++++++++++++*++++++++++++++++               CNT   257   1   1   305.568   305.582   .015         --&gt;     |||||||||||||||||||||||||||||               GG   258   1   1   306.121   308.859   2.738   Group0060     |||||||||||||||||||||||||||||               TP   259   1   1   307.532   307.547   .016       *−+++++++++++++++++++++++++++++               TN   260   1   1   307.814   307.828   .015       *−+++++++++++++++++++++++++++++               TN   261   1   1   308.559   308.573   .015       *−+++++++++++++++++++++++++++++               GG   262   1   1   308.989   312.190   3.201   Group0061     |||||||||||||||||||||||||||||               TN   263   1   1   311.735   311.750   .016       *−+++++++++++++++++++++++++++++               GG   264   1   1   312.215   313.258   1.043   Group0062     |||||||||||||||||||||||||||||               TP   265   1   1   312.894   312.909   .016       *−+++++++++++++++++++++++++++++               GG   266   1   1   313.378   315.728   2.350   Group0063     |||||||||||||||||||||||||||||               TN   267   1   1   314.051   314.065   .015       *−+++++++++++++++++++++++++++++               TN   268   1   1   314.826   314.840   .015       *−+++++++++++++++++++++++++++++               TN   269   1   1   315.511   315.525   .015       *−+++++++++++++++++++++++++++++               TP   270   1   1   315.747   315.761   .015       *−+++++++++++++++++++++++++++++               GG   271   1   1   315.792   318.996   3.204   Group0064     |||||||||||||||||||||||||||||               GP   272   1   1   317.638   318.996   1.359   APE0457     |||||||||||||||||||||||||||||               ONT   273   1   1   317.668   317.682   .015         --&gt;     |||||||||||||||||||||||||||||               TP   274   1   1   317.689   317.703   .015       *−+++++++++++++++++++++++++++++               CNT   275   1   1   317.690   317.704   .015         --&gt;     |||||||||||||||||||||||||||||               GG   276   1   1   318.432   318.914   .483   Group0065     |||||||||||||||||||||||||||||               CPT   277   1   1   319.097   319.127   .031         --&gt;     |||||||||||||||||||||||||||||               TN   278   1   1   319.122   319.137   .016       *−+++++++++++++++++++++++++++++               GG   279   1   1   319.335   319.673   .339   Group0066     |||||||||||||||||||||||||||||               TN   280   1   1   319.515   319.529   .015       *−+++++++++++++++++++++++++++++               TP   281   1   1   319.572   319.586   .015       *−+++++++++++++++++++++++++++++               GG   282   1   1   319.733   324.526   4.793   Group0067     |||||||||||||||||||||||||||||               CNT   283   1   1   320.484   320.513   .030         --&gt;     |||||||||||||||||||||||||||||               GN   284   1   1   320.700   322.241   1.542   APE0462     |||||||||||||||||||||||||||||               TN   285   1   1   323.674   323.688   .015       *−++++++++*||||||||||||||||||||               GG   286   1   1   324.030   324.335   .306   Group0068     |||||||| ||||||||||||||||||||               TN   287   1   1   324.137   324.151   .015       *−++++++++−++++++++++++++++++++               GG   288   1   1   324.606   325.575   .969   Group0069     |||||||| ||||||||||||||||||||               GP   289   1   1   325.141   325.575   .435   APE0469     |||||||| ||||||||||||||||||||               CNT   290   1   1   325.950   325.979   .030         --&gt;     |||||||| ||||||||||||||||||||               CPT   291   1   1   325.950   325.979   .030         --&gt;     |||||||| ||||||||||||||||||||               TN   292   1   1   325.959   325.975   .017       *−++++++++−+*++++++++++++++++++               GG   293   1   1   325.980   326.717   .738   Group0070     |||||||| | ||||||||||||||||||               CNT   294   1   1   326.716   326.878   .163        OS-&gt;     |||||||| | ||||||||||||||||||               TN   295   1   1   326.716   326.878   .163       *−+*+++++*−+−++++*|||||||||||||                  
 
      The “Type” descriptor of the T1 (Id number 218) is “TN” showing that is T1 target is on the negative strand of the double-stranded genomic DNA. Because the T1 and the T2 targets have to be on the same strand, the T2 target (Id number 295) also has the type descriptor “TN”.  
      Group0053 through Group0070 are described in Table 2 as  
                                                       Gene_Name   COG_Id   Chromosome   Direction   Start   Stop   Length                                                                Group0053                                   APE0413   COG0553   K   1   negative   284.391   287.510   3.120       Group0054       APE0414           1   negative   287.521   288.066   .546       APE0415   COG1483   R   1   negative   288.073   291.639   3.567       Group0055       APE0416   COG1743   L   1   negative   291.643   294.666   3.024       APE0417           1   positive   292.319   292.636   .318       APE0418           1   positive   294.690   295.139   .450       Group0056       tRNA-Thr           1   positive   295.231   295.325   .095       APES013           1   positive   295.342   295.518   .177       tRNA-Met           1   positive   295.405   295.529   .125       Group0057       APES014           1   negative   295.572   295.754   .183       APE0419           1   negative   295.891   296.676   .786       Group0058       APE0420           1   positive   297.071   298.113   1.043       APE0422           1   negative   297.448   297.993   .546       APE0423   COG0084   L   1   negative   298.099   298.857   .759       Group0059       APE0424           1   positive   298.856   299.269   .414       APE0425           1   negative   298.973   299.332   .360       APE0426   COG2246   S   1   positive   299.481   300.602   1.122       APE0427   COG1573   L   1   positive   300.649   301.296   .648       APE0428   COG1750   R   1   negative   301.243   303.153   1.911       APE0429           1   positive   303.244   303.786   .543       APE0430           1   negative   303.403   303.720   .318       APE0431           1   positive   303.833   304.911   1.079       APE0432           1   negative   304.284   304.688   .405       APE0434           1   positive   305.005   305.611   .607       APE0436   COG1093   J   1   negative   305.192   305.941   .750       Group0060       APES015   COG2051   J   1   negative   306.121   306.342   .222       APES016   COG1631   J   1   negative   306.359   306.550   .192       APE0437           1   negative   306.674   308.859   2.186       APE0439           1   positive   307.209   307.841   .633       Group0061       APES017           1   negative   308.989   309.186   .198       APE0442   COG1594   K   1   negative   309.201   309.515   .315       APES018           1   negative   309.642   309.842   .201       APE0443   COG1761   K   1   negative   309.915   310.223   .309       APE0444   COG3286   S   1   negative   310.227   310.832   .606       APE0445   COG1096   J   1   negative   310.912   312.190   1.279       Group0062       APE0447   COG1736   J   1   negative   312.215   313.237   1.023       APE0448           1   positive   312.650   313.258   .609       Group0063       APE0449   COG0197   J   1   negative   313.378   313.902   .525       APE0450   COG0303   H   1   positive   313.995   315.728   1.734       APE0451           1   negative   314.028   314.714   .687       Group0064       APES019           1   negative   315.792   315.986   .195       APE0452           1   negative   316.237   316.791   .555       APE0453           1   positive   316.247   317.576   1.330       APE0454   COG1489   G   1   negative   316.820   317.542   .723       APE0456           1   negative   317.632   318.099   .468       APE0457   COG0160   E   1   positive   317.638   318.996   1.359       Group0065       APE0458           1   negative   318.432   318.914   .483       Group0066       APE0459           1   negative   319.335   319.673   .339       Group0067       APE0460           1   positive   319.733   320.038   .306       APE0461   COG1591   L   1   positive   320.272   320.703   .432       APE0462   COG1855   R   1   negative   320.700   322.241   1.542       APE0463           1   positive   321.610   322.074   .465       APE0464           1   positive   322.317   323.228   .912       APE0465   COG0301   H   1   negative   323.288   324.526   1.239       Group0068       APE0466           1   positive   324.030   324.335   .306       Group0069       APE0468           1   positive   324.606   325.049   .444       APE0469   COG1318   K   1   positive   325.141   325.575   .435       Group0070       APE0470   COG1277   R   1   negative   325.980   326.717   .738                  
 
      All of the data for the transient connectron 917 are pulled together in the following table that is the “terse” description of the connectron.  
                                          Connectron Relationships -   Global_Id   Type                   917   synthetic                 Control Sequences - Synthetic Pair of Linked       DNA Binding Objects that recognize the sequences       G1 = cccgacacaacctgc and G2 = cccggggttcccgag                                                         Chro-                       Target       mo-       Sequences -   Direction   some       Start   Stop   Length                           T1_Id           negative   1   218   284.071   284.008   .064                   T2_Id                   295   326.878   326.716   .163                         Controlled Genes                                                 Local_Id   Chromosome   Group   Name   COG_Id   Direction   Start   Stop   Length               1   1   Group0053   APE0413   COG0553   positive   284.391   287.510   3.120       2   1   Group0054   APE0414       positive   287.521   291.639   4.118       3   1   Group0054   APE0415   COG1483   negative   291.639   288.073   3.567       4   1   Group0055   APE0416   COG1743   positive   291.643   295.139   3.496       5   1   Group0055   APE0417       positive   292.319   292.636   .318       6   1   Group0055   APE0418       positive   294.690   295.139   .450       7   1   Group0056   tRNA-Thr       positive   295.231   295.529   .298       8   1   Group0056   APES013       positive   295.342   295.518   .177       9   1   Group0057   APES014       positive   295.572   296.676   1.104       10   1   Group0057   APE0419       negative   296.676   295.891   .786       11   1   Group0058   APE0420       positive   297.071   298.857   1.786       12   1   Group0058   APE0422       negative   297.993   297.448   .546       13   1   Group0058   APE0423   COG0084   negative   298.857   298.099   .759       14   1   Group0059   APE0424       positive   298.856   305.941   7.085       15   1   Group0059   APE0425       negative   299.332   298.973   .360       16   1   Group0059   APE0426   COG2246   positive   299.481   300.602   1.122       17   1   Group0059   APE0427   COG1573   positive   300.649   301.296   .648       18   1   Group0059   APE0428   COG1750   negative   303.153   301.243   1.911       19   1   Group0059   APE0429       positive   303.244   303.786   .543       20   1   Group0059   APE0430       negative   303.720   303.403   .318       21   1   Group0059   APE0431       positive   303.833   304.911   1.079       22   1   Group0059   APE0432       negative   304.688   304.284   .405       23   1   Group0059   APE0434       positive   305.005   305.611   .607       24   1   Group0059   APE0436   COG1093   negative   305.941   305.192   .750       25   1   Group0060   APES015   COG2051   positive   306.121   308.859   2.738       26   1   Group0060   APES016   COG1631   negative   306.550   306.359   .192       27   1   Group0060   APE0437       negative   308.859   306.674   2.186       28   1   Group0060   APE0439       positive   307.209   307.841   .633       29   1   Group0061   APES017       positive   308.989   312.190   3.201       30   1   Group0061   APE0442   COG1594   negative   309.515   309.201   .315       31   1   Group0061   APES018       negative   309.842   309.642   .201       32   1   Group0061   APE0443   COG1761   negative   310.223   309.915   .309       33   1   Group0061   APE0444   COG3286   negative   310.832   310.227   .606       34   1   Group0061   APE0445   COG1096   negative   312.190   310.912   1.279       35   1   Group0062   APE0447   COG1736   positive   312.215   313.258   1.043       36   1   Group0062   APE0448       positive   312.650   313.258   .609       37   1   Group0063   APE0449   COG0197   positive   313.378   315.728   2.350       38   1   Group0063   APE0450   COG0303   positive   313.995   315.728   1.734       39   1   Group0063   APE0451       negative   314.714   314.028   .687       40   1   Group0064   APES019       positive   315.792   318.996   3.204       41   1   Group0064   APE0452       negative   316.791   316.237   .555       42   1   Group0064   APE0453       positive   316.247   317.576   1.330       43   1   Group0064   APE0454   COG1489   negative   317.542   316.820   .723       44   1   Group0064   APE0456       negative   318.099   317.632   .468       45   1   Group0064   APE0457   COG0160   positive   317.638   318.996   1.359       46   1   Group0065   APE0458       positive   318.432   318.914   .483       47   1   Group0066   APE0459       positive   319.335   319.673   .339       48   1   Group0067   APE0460       positive   319.733   324.526   4.793       49   1   Group0067   APE0461   COG1591   positive   320.272   320.703   .432       50   1   Group0067   APE0462   COG1855   negative   322.241   320.700   1.542       51   1   Group0067   APE0463       positive   321.610   322.074   .465       52   1   Group0067   APE0464       positive   322.317   323.228   .912       53   1   Group0067   APE0465   COG0301   negative   324.526   323.288   1.239       54   1   Group0068   APE0466       positive   324.030   324.335   .306       55   1   Group0069   APE0468       positive   324.606   325.575   .969       56   1   Group0069   APE0469   COG1318   positive   325.141   325.575   .435       57   1   Group0070   APE0470   COG1277   positive   325.980   326.717   .738                         Controlled Connectrons                                             Chro-                           Local —     mo-   C1/       Id   some   C2_Id   Direction   Start   Stop   Length               1   1   220   positive   284.009   284.071   .063       2   1   221   negative   284.144   284.073   .072       3   1   222   positive   284.073   284.145   .073       4   1   225   negative   284.251   284.158   .094       5   1   226   positive   284.158   284.251   .094       6   1   228   positive   284.253   284.280   .028       7   1   231   positive   284.283   284.305   .023       8   1   240   positive   295.415   295.444   .030       9   1   248   negative   300.757   300.742   .016       10   1   249   negative   300.781   300.767   .015       11   1   253   positive   305.334   305.348   .015       12   1   254   positive   305.358   305.372   .015       13   1   255   negative   305.566   305.552   .015       14   1   257   negative   305.582   305.568   .015       15   1   273   negative   317.682   317.668   .015       16   1   275   negative   317.704   317.690   .015       17   1   277   positive   319.097   319.127   .031       18   1   283   negative   320.513   320.484   .030       19   1   290   negative   325.979   325.950   .030       20   1   291   positive   325.950   325.979   .030       21   1   294   negative   326.878   326.716   .163                  
 
      The verbose description of the transient connectron 917 is:  
      In the  Aeropyrum pernix  K1 complete genome the synthetic connectron number 917 is generated by a synthetic pair of linked DNA binding objects that recognizes the sequences G1=cccgacacaacctgc and G2=cccggggttcccgag. The target sequences (T1-T2) are on the negative strand of the genomic DNA on chromosome 1. The identifier number of the initiating target sequence (T1) is 218. The genomic start and stop positions of this initiating target sequence are 284.071 KB and 284.008 KB with a length of 0.064 KB. The identifier number of the terminating target sequence (T2) is 295. The genomic start and stop positions of this terminating target sequence are 326.878 KB and 326.716 KB with a length of 0.163 KB.  
      This connectron controls the modulation of the expression of the following gene(s): (1) The gene that has the name APE0413 and with a COG identifier of COG0553. The genomic start and stop positions of this gene are 284.391 KB and 287.510 KB with a length of 3.120 KB. (2) The gene that has the name APE0414. The genomic start and stop positions of this gene are 287.521 KB and 291.639 KB with a length of 4.118 KB. (3) The gene that has the name APE0415 and with a COG identifier of COG1483. The genomic start and stop positions of this gene are 291.639 KB and 288.073 KB with a length of 3.567 KB. (4) The gene that has the name APE0416 and with a COG identifier of COG1743. The genomic start and stop positions of this gene are 291.643 KB and 295.139 KB with a length of 3.496 KB. (5) The gene that has the name APE0417. The genomic start and stop positions of this gene are 292.319 KB and 292.636 KB with a length of 0.318 KB. (6) The gene that has the name APE0418. The genomic start and stop positions of this gene are 294.690 KB and 295.139 KB with a length of 0.450 KB. (7) The gene that has the name tRNA-Thr. The genomic start and stop positions of this gene are 295.231 KB and 295.529 KB with a length of 0.298 KB. (8) The gene that has the name APES013. The genomic start and stop positions of this gene are 295.342 KB and 295.518 KB with a length of 0.177 KB. (9) The gene that has the name APES014. The genomic start and stop positions of this gene are 295.572 KB and 296.676 KB with a length of 1.104 KB. (10) The gene that has the name APE0419. The genomic start and stop positions of this gene are 296.676 KB and 295.891 KB with a length of 0.786 KB. (11) The gene that has the name APE0420. The genomic start and stop positions of this gene are 297.071 KB and 298.857 KB with a length of 1.786 KB. (12) The gene that has the name APE0422. The genomic start and stop positions of this gene are 297.993 KB and 297.448 KB with a length of 0.546 KB. (13) The gene that has the name APE0423 and with a COG identifier of COG0084. The genomic start and stop positions of this gene are 298.857 KB and 298.099 KB with a length of 0.759 KB. (14) The gene that has the name APE0424. The genomic start and stop positions of this gene are 298.856 KB and 305.941 KB with a length of 7.085 KB. (15) The gene that has the name APE0425. The genomic start and stop positions of this gene are 299.332 KB and 298.973 KB with a length of 0.360 KB. (16) The gene that has the name APE0426 and with a COG identifier of COG2246. The genomic start and stop positions of this gene are 299.481 KB and 300.602 KB with a length of 1.122 KB. (17) The gene that has the name APE0427 and with a COG identifier of COG1573. The genomic start and stop positions of this gene are 300.649 KB and 301.296 KB with a length of 0.648 KB. (18) The gene that has the name APE0428 and with a COG identifier of COG1750. The genomic start and stop positions of this gene are 303.153 KB and 301.243 KB with a length of 1.911 KB. (19) The gene that has the name APE0429. The genomic start and stop positions of this gene are 303.244 KB and 303.786 KB with a length of 0.543 KB. (20) The gene that has the name APE0430. The genomic start and stop positions of this gene are 303.720 KB and 303.403 KB with a length of 0.318 KB. (21) The gene that has the name APE0431. The genomic start and stop positions of this gene are 303.833 KB and 304.911 KB with a length of 1.079 KB. (22) The gene that has the name APE0432. The genomic start and stop positions of this gene are 304.688 KB and 304.284 KB with a length of 0.405 KB. (23) The gene that has the name APE0434. The genomic start and stop positions of this gene are 305.005 KB and 305.611 KB with a length of 0.607 KB. (24) The gene that has the name APE0436 and with a COG identifier of COG1093. The genomic start and stop positions of this gene are 305.941 KB and 305.192 KB with a length of 0.750 KB. (25) The gene that has the name APES015 and with a COG identifier of COG2051. The genomic start and stop positions of this gene are 306.121 KB and 308.859 KB with a length of 2.738 KB. (26) The gene that has the name APES016 and with a COG identifier of COG1631. The genomic start and stop positions of this gene are 306.550 KB and 306.359 KB with a length of 0.192 KB. (27) The gene that has the name APE0437. The genomic start and stop positions of this gene are 308.859 KB and 306.674 KB with a length of 2.186 KB. (28) The gene that has the name APE0439. The genomic start and stop positions of this gene are 307.209 KB and 307.841 KB with a length of 0.633 KB. (29) The gene that has the name APES017. The genomic start and stop positions of this gene are 308.989 KB and 312.190 KB with a length of 3.201 KB. (30) The gene that has the name APE0442 and with a COG identifier of COG1594. The genomic start and stop positions of this gene are 309.515 KB and 309.201 KB with a length of 0.315 KB. (31) The gene that has the name APES018. The genomic start and stop positions of this gene are 309.842 KB and 309.642 KB with a length of 0.201 KB. (32) The gene that has the name APE0443 and with a COG identifier of COG1761. The genomic start and stop positions of this gene are 310.223 KB and 309.915 KB with a length of 0.309 KB. (33) The gene that has the name APE0444 and with a COG identifier of COG3286. The genomic start and stop positions of this gene are 310.832 KB and 310.227 KB with a length of 0.606 KB. (34) The gene that has the name APE0445 and with a COG identifier of COG1096. The genomic start and stop positions of this gene are 312.190 KB and 310.912 KB with a length of 1.279 KB. (35) The gene that has the name APE0447 and with a COG identifier of COG1736. The genomic start and stop positions of this gene are 312.215 KB and 313.258 KB with a length of 1.043 KB. (36) The gene that has the name APE0448. The genomic start and stop positions of this gene are 312.650 KB and 313.258 KB with a length of 0.609 KB. (37) The gene that has the name APE0449 and with a COG identifier of COG0197. The genomic start and stop positions of this gene are 313.378 KB and 315.728 KB with a length of 2.350 KB. (38) The gene that has the name APE0450 and with a COG identifier of COG0303. The genomic start and stop positions of this gene are 313.995 KB and 315.728 KB with a length of 1.734 KB. (39) The gene that has the name APE0451. The genomic start and stop positions of this gene are 314.714 KB and 314.028 KB with a length of 0.687 KB. (40) The gene that has the name APES019. The genomic start and stop positions of this gene are 315.792 KB and 318.996 KB with a length of 3.204 KB. (41) The gene that has the name APE0452. The genomic start and stop positions of this gene are 316.791 KB and 316.237 KB with a length of 0.555 KB. (42) The gene that has the name APE0453. The genomic start and stop positions of this gene are 316.247 KB and 317.576 KB with a length of 1.330 KB. (43) The gene that has the name APE0454 and with a COG identifier of COG1489. The genomic start and stop positions of this gene are 317.542 KB and 316.820 KB with a length of 0.723 KB. (44) The gene that has the name APE0456. The genomic start and stop positions of this gene are 318.099 KB and 317.632 KB with a length of 0.468 KB. (45) The gene that has the name APE0457 and with a COG identifier of COG0160. The genomic start and stop positions of this gene are 317.638 KB and 318.996 KB with a length of 1.359 KB. (46) The gene that has the name APE0458. The genomic start and stop positions of this gene are 318.432 KB and 318.914 KB with a length of 0.483 KB. (47) The gene that has the name APE0459. The genomic start and stop positions of this gene are 319.335 KB and 319.673 KB with a length of 0.339 KB. (48) The gene that has the name APE0460. The genomic start and stop positions of this gene are 319.733 KB and 324.526 KB with a length of 4.793 KB. (49) The gene that has the name APE0461 and with a COG identifier of COG1591. The genomic start and stop positions of this gene are 320.272 KB and 320.703 KB with a length of 0.432 KB. (50) The gene that has the name APE0462 and with a COG identifier of COG1855. The genomic start and stop positions of this gene are 322.241 KB and 320.700 KB with a length of 1.542 KB. (51) The gene that has the name APE0463. The genomic start and stop positions of this gene are 321.610 KB and 322.074 KB with a length of 0.465 KB. (52) The gene that has the name APE0464. The genomic start and stop positions of this gene are 322.317 KB and 323.228 KB with a length of 0.912 KB. (53) The gene that has the name APE0465 and with a COG identifier of COG0301. The genomic start and stop positions of this gene are 324.526 KB and 323.288 KB with a length of 1.239 KB. (54) The gene that has the name APE0466. The genomic start and stop positions of this gene are 324.030 KB and 324.335 KB with a length of 0.306 KB. (55) The gene that has the name APE0468. The genomic start and stop positions of this gene are 324.606 KB and 325.575 KB with a length of 0.969 KB. (56) The gene that has the name APE0469 and with a COG identifier of COG1318. The genomic start and stop positions of this gene are 325.141 KB and 325.575 KB with a length of 0.435 KB. (57) The gene that has the name APE0470 and with a COG identifier of COG1277. The genomic start and stop positions of this gene are 325.980 KB and 326.717 KB with a length of 0.738 KB.  
      This connectron controls the turning off of the expression of the following connectron(s): (1) The connectron that has the identifier 220 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 284.009 KB and 284.071 KB with a length of 0.063 KB. (2) The connectron that has the identifier 221 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 284.144 KB and 284.073 KB with a length of 0.072 KB. (3) The connectron that has the identifier 222 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 284.073 KB and 284.145 KB with a length of 0.073 KB. (4) The connectron that has the identifier 225 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 284.251 KB and 284.158 KB with a length of 0.094 KB. (5) The connectron that has the identifier 226 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 284.158 KB and 284.251 KB with a length of 0.094 KB. (6) The connectron that has the identifier 228 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 284.253 KB and 284.280 KB with a length of 0.028 KB. (7) The connectron that has the identifier 231 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 284.283 KB and 284.305 KB with a length of 0.023 KB. (8) The connectron that has the identifier 240 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 295.415 KB and 295.444 KB with a length of 0.030 KB. (9) The connectron that has the identifier 248 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 300.757 KB and 300.742 KB with a length of 0.016 KB. (10) The connectron that has the identifier 249 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 300.781 KB and 300.767 KB with a length of 0.015 KB. (11) The connectron that has the identifier 253 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 305.334 KB and 305.348 KB with a length of 0.015 KB. (12) The connectron that has the identifier 254 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 305.358 KB and 305.372 KB with a length of 0.015 KB. (13) The connectron that has the identifier 255 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 305.566 KB and 305.552 KB with a length of 0.015 KB. (14) The connectron that has the identifier 257 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 305.582 KB and 305.568 KB with a length of 0.015 KB. (15) The connectron that has the identifier 273 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 317.682 KB and 317.668 KB with a length of 0.015 KB. (16) The connectron that has the identifier 275 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 317.704 KB and 317.690 KB with a length of 0.015 KB. (17) The connectron that has the identifier 277 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 319.097 KB and 319.127 KB with a length of 0.031 KB. (18) The connectron that has the identifier 283 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 320.513 KB and 320.484 KB with a length of 0.030 KB. (19) The connectron that has the identifier 290 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 325.979 KB and 325.950 KB with a length of 0.030 KB. (20) The connectron that has the identifier 291 is on chromosome 1 in the positive direction. The genomic start and stop positions of this connectron are 325.950 KB and 325.979 KB with a length of 0.030 KB. (21) The connectron that has the identifier 294 is on chromosome 1 in the negative direction. The genomic start and stop positions of this connectron are 326.878 KB and 326.716 KB with a length of 0.163 KB.