The symmetry relationships between pairs of connectrons Reference to Related Applications The present application includes the subject of Provisional Application Serial No. 60/455, 563 filed March 19,2003 The present application is a continuation in part of US Patent Application Serial Number 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. (referred to as"basic methods patent application") This present application is related to PCT application PCT/US01/16471 filed May 31,2001 and 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 US Patent Application Serial Number 10/339,666 filed January 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 US Patent Application Serial Number 10/364, 516 filed February 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 US Patent Application Serial Number 10/364,412 filed February 12,2003 entitled DETERMINATION OF FLANKING DNA SEQUENCES THAT CONTROL THE EXPRESSION OF SETS OF GENES IN THE SACCHAROMYCES CEREVISIAE COMPLETE GENOME Introduction The connectron structure of a genome determines sets of four DNA sequences of minimum length of 15-bases (Cl and C2 which are in the 3'UTR of a gene or pseudogene, and T1 and T2 which bracket a set of genes or pseudogenes). The connectrons in a genome control the expression of sets of genes. This patent application describes new types of connectrons as well as how pairs of equivalent and non-equivalent RNA sequences can bind to double-stranded DNA to form a variety of connectrons.

Definitions Previous definitions of connectron structure are included by reference.

Connectrome-All the connectrons in a given genome.

Dominant Direction-The DNA sequence of a chromosome or a genome from the 5'end to the 3'end of the positive strand.

Anti-Dominant Direction-The DNA sequence of a chromosome or a genome from the 5'end to the 3'end of the negative strand.

C1/C2 Polarity-The direction of the binding of the RNA of a connectron in the major groove of the double-stranded DNA in the dominant direction or the anti-dominant direction.

Uni-Polar C1/C2-The binding of the RNA of a connectron such that either (1) both the Cl sequence and the C2 sequence bind in the dominant direction or (2) both the Cl sequence and the C2 sequence bind in the anti-dominant direction.

Bi-Polar C1/C2-The binding of the RNA of a connectron such that either (1) the Cl sequence binds in the dominant direction and the C2 sequence binds in the anti-dominant direction or (2) the Cl sequence binds in the anti-dominant direction and the C2 sequence binds in the dominant direction.

Reverse Complement-Going away from a given point, the same sequence occurs on opposite strands. In the example below the sequence GCATCC in the dominant direction of the positive strand occurs somewhere else in the genome in the anti- dominant direction of the negative strand Positive Strand 5'-GCATCCGTGTAAT ATTACACGGATGC-3' Negative Strand 3'-CGTAGGCACATTA TAATGTGCCTACG-5' Equivalent Sequences-Two sequences such that the second sequence is in the reverse complement of the first sequence First sequence 5'-GCATCCGTGTAAT-3' (A) Second sequence 5'-ATTACACGGATGC-3' (A') If the first sequence is called A then the second sequence is called A' Symmetric Lower-Upper Pair of Connectrons-The binding of two equivalent uni-polar RNA C1/C2 sequence pairs to double- stranded DNA.

Asymmetric Lower-Upper Pair of Connectrons-The binding of two non-equivalent uni-polar RNA C1/C2 sequence pairs to double-stranded DNA.

Symmetric Left-Right Pair of Connectrons-The binding of two equivalent bi-polar RNA C1/C2 sequence pairs to double- stranded DNA.

Asymmetric Left-Right Pair of Connectrons-The binding of two non-equivalent bi-polar RNA C1/C2 sequence pairs to double- stranded DNA.

Connectron Lifetime-A time that varies directly with the length of the shorter of the two triple-stranded generalized

Hoogsteen helices formed by the binding of the Cl and C2 RNA connectron sequences to the major groove of the double- stranded DNA.

Connectron Pair Lifetime-A time that varies directly with the product of the lifetimes of the two connectrons in the pair.

Specificity of a Pair of Connectrons-The number of similar or different C1/C2 sources needed to form the pair of connectrons.

Symmetric Connectron Specificity-The specificity of a pair of connectrons formed with equivalent uni-polar or bi-polar RNA sequences.

Asymmetric Connectron Specificity-The specificity of a pair of connectrons formed with non-equivalent uni-polar or bi- polar RNA sequences.

Competitive Mode of Behavior in the Formation of a Connectron Pair-The situation where two different genes produce the same uni-polar or bi-polar C1/C2 sequences of the same or different lengths that bind to the major groove of the double- stranded DNA to form a connectron pair.

Cooperative Mode of Behavior in the Formation of a Connectron Pair-The situation where two different genes produce different uni-polar or bi-polar C1/C2 sequences of the same or different lengths that bind to the major groove of the double- stranded DNA to form a connectron pair such that the connectron pair could only be formed from the two different C1/C2 sequences.

Prior Art Included by reference.

Brief Description of the Objects of the Invention The basic methods patent application provides the methods for determining the structure of the connectrons in a variety of prokaryotic, Archeal and eukaryotic genomes.

An object of this invention is to provide a method for identifying a one or more new classs of connectrons that bind to the major groove of double-stranded DNA in two directions.

An object of this invention is to provide a method for designing a new class of connectrons that bind to the major groove of double-stranded DNA in two directions.

An object of this invention is to provide a method for identifying the relationship between a pair of connectrons in a genome.

An object of this invention is to provide a method for designing the relationship between a pair of connectrons in a genome.

An object of this invention is to provide a method for identifying the relationship between an existing pair of connectrons in a genome that act in competitive mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.

An object of this invention is to provide a method for designing a new synthetic pair of connectrons in a genome that

act in competitive mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.

An object of this invention is to provide a method for identifying the relationship between an existing pair of connectrons in a genome that act in cooperative mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.

An object of this invention is to provide a method for designing a new synthetic pair of connectrons in a genome that act in cooperative mode such that with respect to the individual connectrons there is an increased lifetime of connectron control of a set of genes.

Description of the Drawings and Tables Figure 1 Shows how (a) a lower connectron and (b) an upper connectron, form (c) an lower-upper connectron pair Figure 2 Shows how (a) a left connectron and (b) a right connectron, form (c) a left-right connectron pair Figure 3 Shows (a) a symmetric lower-upper connectron pair, (b) an asymmetric lower-upper connectron pair Figure 4 Shows (a) a symmetric left-right connectron pair, (b) an asymmetric left-right connectron pair Figure 5 Shows (a) Concise representation of an asymmetric lower-upper connectron pair and (b) detailed representation of a asymmetric lower-upper connectron pair Figure 6 Shows (a) Concise representation of an asymmetric left-right connectron pair and (b) detailed representation of a asymmetric left-right connectron pair Figure 7 Shows the four variations of symmetric lower-upper connectron pairs- (a) dominant-dominant, (b) anti-dominant-dominant, (c) dominant-anti- dominant, and (d) anti-dominant-dominant Figure 8 Shows the four variations of symmetric left-right connectron pairs- (a) dominant-dominant, (b) anti-dominant-dominant, (c) dominant-anti- dominant, and (d) anti-dominant-dominant Figure 9 Shows the four variations of asymmetric lower-upper connectron pairs- (a) dominant-dominant, (b) anti-dominant-dominant, (c) dominant-anti- dominant, and (d) anti-dominant-dominant Figure 10 Shows the four variations of asymmetric left-right connectron pairs- (a) dominant-dominant, (b) anti-dominant-dominant, (c) dominant-anti- dominant, and (d) anti-dominant-dominant Figure 11 Shows (a) the competitive blocking of symmetric lower-upper long-lived connectrons, (b) the competitive blocking of symmetric left-right long- lived connectrons, and (c) the relative timing

windows for competitive blocking of symmetric long- lived connectrons Figure 12 Shows (a) the competitive blocking of asymmetric lower-upper long-lived connectrons, (b) the competitive blocking of asymmetric lower-upper long- lived connectrons, (c) the competitive blocking of asymmetric left-right long-lived connectrons, and (d) the competitive blocking of asymmetric left- right long-lived connectrons Figure 13 Shows (a) the timing windows for competitive blocking of asymmetric long-lived connectrons Figure 14 Shows (a) a fully symmetric connectron tetrad, (b) non-competitive blocking effect by a left short- lived connectrons of a long-lived cooperative connectron pair, (c) non-competitive blocking effect by a right short-lived connectrons of a long-lived cooperative connectron pair, and (d) the timing windows for non-competitive blocking of asymmetric long-lived connectrons Description of the Invention The basic methods patent application for the determination of connectron structure defines the DNA and RNA sequence components that make up a connectron, as well as presenting examples of different sorts of connectrons from many different types of genomes. The computer algorithm presented in that patent application shows how to find connectrons in a particular genome. The genomic patent applications utilize the power of this computer algorithm to determine all of the connectrons in a particular genome. Although the basic methods patent application identifies permanent, transient and one-shot connectrons, the view presented is that of a single connectron. This patent application presents the relationships among pairs of connectrons. This invention will allow us to organize the connectrons in a genome and show how pairs of connectrons work together to produce new gene

expression regulation properties. In particular, this invention will allow us to show how different C1/C2 connectron sequences from different gene expression events can cooperate to form a pair of long-lived connectrons. The ability to form very specific and cooperative conjunctive events makes it possible for biological systems to form arbitrarily complex control procedures that may very well be needed for cellular differentiation and the development of a complete multi-celled organism from a single cell.

A connectron forms a loop in a piece of double-stranded DNA.

As shown in figure la the DNA runs from the 5'end shown on the lower left in a counter-clockwise direction to the 3'end shown on the lower right. The RNA generated by the promotion and transcription of some gene or pseudo-gene somewhere in the genome binds to two distinct double-stranded DNA sequences to form two distinct triple-stranded generalized Hoogsteen helices. In figure la the first triple-stranded (generalized Hoogsteen) helix is called A and the second helix is called B.

The A helix forms along the major groove of the DNA in the 5' to 3'direction. Similarly the B helix in figure la forms along the major groove of the DNA in the 5'to 3'direction.

The A-B pair of triple-stranded helices occupy the lower position in the X-shape formed by the loop. Hence in figure la the connectron is described as a"lower connectron". In figure 1b both the A and B helices form in the 5'to 3' direction, but they occupy the upper position in the X-shape formed by the loop. Hence in figure 1b the connectron is described as an"upper connectron". In figure Ic the lower and upper connectrons are shown binding simultaneously.

In figure 2a the A helix forms along the major groove of the DNA in the 5'to 3'direction but the B helix forms along the

major groove of the DNA by binding along the major groove of the double helix in the 3'to 5'direction. The importance of this connectron is that the RNA switches strands as it moves from A-helix binding to B-helix binding. This is true in all left and right connectrons. The A-B pair of helices in figure 2a occupy the left position in the X-shape formed by the loop.

Hence in figure 2a the connectron is described as a"left connectron". In figure 2b the A triple-strand helix forms along the major groove of the DNA in the 3'to 5'direction, so this connectron is given the designation A-B and is described as a"right connectron". In figure 2c the left and right connectrons are shown binding simultaneously.

In figure 3a the pair of lower and upper connectrons have the same sequences (i. e. A and B) hence this pair of connectrons is called a"symmetric lower-upper connectron pair". In figure 3b the lower connectron has the sequence A-B and the upper connectron has the sequence C-D hence this pair of connectrons is called an"asymmetric lower-upper connectron pair".

In figure 4a the pair of left and right connectrons have the same sequences (i. e. A and B) hence this pair of connectrons is called a"symmetric left-right connectron pair". In figure 4b the left connectron has the sequence A-B and the right connectron has the sequence C-D, where C is not equal to A and/or D is not equal to B hence this pair of connectrons is called an"asymmetric left-right connectron pair".

Figure 5a-a re-statement of figure 3b-is a concise representation of an asymmetric lower-upper connectron pair.

Figure 5b is a detailed representation of the same asymmetric lower-upper connectron pair showing the sequence relationships

between the RNA strand and the two DNA strands. The equivalence of the RNA-strand sequence and the 5'to 3'DNA- strand sequence means that the RNA-strand sequence will share the hydrogen bonds to the 3'to 5'DNA-strand sequence.

Figure 6a-a re-statement of figure 4b-is a concise representation of an asymmetric left-right connectron pair.

Figure 6b is a detailed representation of the same asymmetric left-right connectron pair showing the sequence relationships between the RNA strand and the two DNA strands. The equivalence of the RNA-strand sequence and the 5'to 3'DNA- strand sequence for the first triple helix of each of these connectrons means that the RNA-strand sequence will share the hydrogen bonds to the 3'to 5'DNA-strand sequence.

Similarly, the equivalence of the RNA-strand sequence and the 3'to 5'DNA-strand sequence for the second triple helix of each of these connectrons means that the RNA-strand sequence will share the hydrogen bonds to the 5'to 3'DNA-strand sequence.

Figure 7a shows the lower and upper connectrons both binding in the dominant direction with the sequence A-B hence this pair of connectrons is called a"dominant-dominant symmetric lower-upper connectron pair". Figure 7b shows the lower and upper connectrons both binding in the anti-dominant direction with the sequence B'-A'thence this pair of connectrons is called an"anti-dominant-anti-dominant symmetric lower-upper connectron pair". In figure 7c the lower connectron binds in the dominant direction with the sequence A-B and the upper connectron binds in the anti-dominant direction with the sequence B'-A'hence this pair of connectrons is called a "dominant-anti-dominant symmetric lower-upper connectron pair". In figure 7d the lower connectron binds in the anti-

dominant direction with the sequence B'A'and the upper connectron binds in the dominant direction with the sequence A-B. In figure 7 each of the four sequence pairs is different, hence there are four different types of symmetric lower-upper connectron pairs.

Figure 8a shows the left and right connectrons both binding in the dominant direction with the sequences A-B hence this pair of connectrons is called a"dominant-dominant symmetric left-right connectron pair". Figure 8b shows the lower and upper connectrons both binding in the anti-dominant direction with the sequence B'-A'hence this pair of connectrons is called an"anti-dominant-anti-dominant symmetric left-right connectron pair". In figure 8c the left connectron binds in the dominant direction with the sequence A-B and the right connectron binds in the anti-dominant direction with the sequence B'-A'hence this pair of connectrons is called a "dominant-anti-dominant symmetric left-right connectron pair". In figure 8d the left connectron binds in the anti- dominant direction with the sequence B'-A'and the right connectron binds in the dominant direction with the sequence A-B hence this pair of connectrons is called an"anti-dominant - dominant symmetric left-right connectron pair". In figure 8 each of the four sequence pairs is different, hence there are four different types of symmetric left-right connectron pairs.

Figure 9a shows the lower and upper connectrons both binding in the dominant direction but the sequences of the two connectrons are different. The lower connectron has the sequence are A-B and the upper connectron has the sequence C-D hence this pair of connectrons is called a"dominant- dominant asymmetric lower-upper connectron pair". In figure 9b the lower connectron binds in the dominant direction with

the sequence B'-A'and the upper connectron binds in the anti- dominant direction with the sequence D'-C'hence this pair of connectrons is called an"anti-dominant-anti-dominant asymmetric lower-upper connectron pair". In figure 9c the lower connectron binds in the dominant direction with the sequence A-B and the upper connectron binds in the anti- dominant direction with the sequence D'-C'hence this pair of connectrons is called a"dominant-anti-dominant asymmetric lower-upper connectron pair". In figure 9d the lower connectron binds in the anti-dominant direction with the sequence B'-A'and the upper connectron binds in the dominant direction with the sequence C-D hence this pair of connectrons is called an"anti-dominant-dominant asymmetric lower-upper connectron pair". In figure 9 each of the four sequence pairs is different, hence there are four different types of asymmetric lower-upper connectron pairs.

Figure 10a shows the left and right connectrons both binding in the dominant direction but the sequences of the two connectrons are different. The left connectron has the sequence A-B and the right connectron has the sequence C-D hence this pair of connectrons is called a"dominant- dominant asymmetric left-right connectron pair". In figure 10b the left connectron binds in the anti-dominant direction with the sequence B'-A'and the right connectron binds in the anti-dominant direction with the sequence D'-C'hence this pair of connectrons is called an'anti-dominant-anti- dominant asymmetric left-right connectron pair". In figure 10c the left connectron binds in the dominant direction with the sequence A-B and the right connectron binds in the anti- dominant direction with the sequence D'-C'hence this pair of connectrons is called a"dominant-anti-dominant asymmetric left-right connectron. In figure 10d the left connectron

binds in the anti-dominant direction with the sequence B'-A' and the right connectron binds in the dominant direction with the sequence C-D hence this pair of connectrons is called an "anti-dominant-dominant asymmetric left-right connectron.

In figure 10 each of the four sequence pairs is different, hence there are four different types of asymmetric left-right connectron pairs.

The lifetime of a single connectrons is easy to understand.

Consider a single connectron as shown in figure la. For the sake of example let the A triple-strand (generalized Hoogsteen) helix be the minimum length of 15 bases and let the B triple-strand helix be some long length, for example 100 bases. Remember that the RNA-DNA structure of the connectrons is immersed in a bath of water at 37 degrees Celsius. Thermal motion will cause the A triple-strand helix to dissolve into the RNA and DNA components much more rapidly than the much longer B triple-strand helix, so the lifetime of the connectrons varies directly with the length of the shorter of the two triple-strand helices. If the length of the A and B helices are the same then the lifetime of the connectron varies directly with the length of either helix.

Now think about the lifetime of a pair of connectrons as shown in figure Ic. For the sake of simplicity, assume that the A and B helices are the same length. In order for the loop to open up, at least one lower helix and one upper helix has to dissolve at the same time. Either or both of the two lower helices can dissolve at the same time but as long as the upper pair of helices is not dissolved, the loop will stay closed.

The same is true for the reverse-either of both of the two upper helices can dissolve at the same time but as long as the two lower helices stay intact, the loop stays closed.

Physical chemistry is replete with two-part binding events like this. The general description of such events is that the lifetime varies directly with the product of the two binding energies. In the case of a pair of lower-upper connectrons, the lifetime varies directly as the product of the shorter of the lower helices and the shorter of the upper helices. Of course, the same thing is true for the left-right connectron pairs shown in figure 2c.

Whatever the binding energy of an RNA strand is with respect to its cognate double-stranded DNA sequence, whenever a sequence pair (for example A-B or B'-A') can form a pair of connectrons, the binding energy of the pair of connectrons is the product of the binding energy of the each connectron.

When two different sequence pairs (for example A-B and B'-A' as shown in figure 7) form a pair of connectrons then the pair of connectrons can be formed as one of the four following combinations Figure 5a lower (A-B) and upper (A-B) Figure 5b lower (B'-A') and upper (B'-A') Figure 5c lower (A-B) and upper (B'-A') Figure 5d lower (B'-A') and upper (A-B) In principle, A-B and B'-A'could be produced by the expression of two different genes. Because the pair of connectrons can form in four different ways, the two genes causing the production of the two different RNAs are competing for control of the formation of the connectron pair.

The left-right connectron pairs in figure 8 have the same properties as the lower-upper connectron pairs in figure 7. In principle, A-B and B'-A'could be produced by the expression

of two different genes. Because the pair of connectrons can form in four different ways, the two genes causing the production of the two different RNAs are competing for control of the formation of the connectron pair.

When two different sequence pairs (for example A-B and C-D) form a pair of connectrons then the pair of connectrons can be formed in only one way as shown in figure 9a. A-B and C-D can be produced by the expression of two different genes. Because the pair of connectrons can form in only one way, the two genes causing the production of the'two different RNAs are cooperating for control of the formation of the connectron pair. The same cooperative behavior is also true of the sequence combinations in figures 9b, 9c and 9d.

Like figures 7 and 8 (that describe symmetric connectron pairs), figures 9 and 10 (that describe asymmetric connectron pairs) share the same properties. When two different sequence pairs (for example A-B and C-D) form a pair of connectrons then the pair of connectrons can be formed in only one way as shown in figure 10a. A-B and C-D can be produced by the expression of two different genes. Because the pair of connectrons can form in only one way, the two genes causing the production of the two different RNAs are cooperating for control of the formation of the connectron pair. The same cooperative behavior is also true of the sequence combinations in figures lOb, 10c and 10d.

In figures 7 and 8 (that describe symmetric connectron pairs) the connectron pair constructs produce competition whereas in figures 9 and 10 (that describe asymmetric connectron pairs) the connectron pair constructs produce cooperation. Figures 7

and 8 are symmetric constructs whereas figures 9 and 10 are asymmetric constructs.

Whereas in figure 7 the sequence along the DNA the X-shape of the crossing (i. e. either the/sequence or the \ sequence) is the sequence A-B, in figure 8 the same elements are reverse- complements.

The algorithm described in the basic methods patent application finds all of the uni-polar the connectrons in a genome. This patent application describes connectrons in terms of their symmetry properties (i. e. uni-polar, bi-polar, lower, upper, left, right, symmetric, asymmetric). The original algorithm has been modified and the connectron structure of the genomes recomputed to find both the uni-polar and bi-polar connectrons. The modification of the basic connectron determination algorithm to identify the left-right connectrons required only a half dozen lines of code change which is at or below the level of resolution of the flow charts presented in the basic methods patent application. The utility of this patent application is that we have shown that pairs of connectrons both compete and cooperate by forming in the same place (i. e. the X-shaped loop interaction region) to produce lifetimes that vary directly with the product of the lifetimes of the individual connectrons.

Figure lla shows how one source (A-B) of the C1/C2 RNA that forms a lower-upper connectron pair with a relatively short product lifetime can temporally compete with another source of a much longer C1/C2 RNA which could form a much longer-lived symmetric connectron pair. Figure llb shows how one source (A-B) of the C1/C2 RNA that forms a left-right connectron pair with a relatively short product lifetime can temporally

compete with another source of a much longer C1/C2 RNA which could form a much longer-lived symmetric connectron pair. As shown in figure llc, the shorter A-B connectron pair only has to last throughout the expression window of the longer connectron pair in order to prevent the longer-lived connectron pair from forming. After the short-lived A-B connectron pair expires, the loop is effectively open.

Figure 12a shows how a short-lived lower connectron can block the formation of a much longer-lived asymmetric connectron pair. Figure 12b shows how a short-lived upper connectron can block the formation of a much longer-lived asymmetric connectron pair. Figure 12c shows how a short-lived left connectron can block the formation of a much longer-lived asymmetric connectron pair. Figure 12d shows how a short-lived right connectron can block the formation of a much longer- lived asymmetric connectron pair.

Figure 13a shows the timing windows for the competitive blocking of an asymmetric long-lived connectron pairs as shown in figures 12a and 12c. Figure 13b shows the timing windows for the competitive blocking of an asymmetric long-lived connectron pair pairs as shown in figures 12b and 12d.

Figure 14a shows how, in-principle, four connectrons could form at a given site. Clearly not all four of these connectrons can form at this site at the same time because each connectron occupies two of the four target (T1 or T2) sites. The lower A-B and upper C-D pair can form at the same time or the left A-C'and right D'-B pair can form at the same time. Figure 14b shows how a short-lived left connectron A-C' can block the formation of a much longer-lived cooperative connectron pair A-B and C-D. Figure 14c shows how a short-

lived right connectron D'-B can block the formation of a much longer-lived cooperative connectron pair A-B and C-D. Figure 14d shows the timing chart for this type of temporal blocking.

Figures llc, 13a and 14d show three distinctly different types of temporal blocking. To someone skilled in the art it would be obvious that it does not matter whether the lower-upper or left-right connectrons are used for either the blocking or blocked connectrons-as long as the relative patterns are maintained.

The utility of the connectron pairs shown in figures 1 to 14 is that they form the primitives of a language that can build arbitrarily large and complex patterns of structural and temporal connectron control of gene expression. These language primitives can be used to analyze patterns of connectron control of gene expression in all types of genomes (i. e. prokaryotic, Archeal and eukaryotic). These language primitives can also be used to create new patterns of connectron control of gene expression in all types of genomes.

These same primitives will help us to understand how cells differentiate from each other in terms of their gene expression and how a single cell develops into a complete organism.

Although figures 1 to 14 function in the first instance to describe the relationships between the control sequences (i. e. the Cls and C2s) produced by the same or different gene expressions and the target sequences (i. e. the T1s and the T2s) in a pair of connectrons, these same figures can also function as the basis for the design of new synthetic pairs of connectrons. For example, the target sequences (A-B) that form the symmetric connectron pair shown in figure 3a could be modified by changing the upper connectron T1 sequence from A

to C and the upper connectron T2 sequence from B to D to form the asymmetric connectron pair shown in figure 3b. The C1/C2 sequences C-D could then be inserted in the 3'UTR of some gene so the A-B and C-D connectron pair would be formed only when two genes expressed. This modification of the upper connectron sequences is an example of how all the connectron pair properties in figures 1 to 14 could be instantiated either by de-novo sequence placement or by partial modification of existing sequences and relationships. Anyone skilled in the art should be able to convert the descriptions of connectron-pair properties in figures 1 to 14 into design specifications thereby opening up the control of gene expression to a whole range of new possibilities.

The utility of pairs of connectrons (a) whether existing or designed or (b) whether competitive or cooperative is that the lifetime of a single connectron whether it is short or long is multiplied by the existence of an adjacent connectron of similar or different lifetime properties. While the product of the lifetimes of two 15-base connectrons is a modest 225, the product of the lifetimes of two 100-base connectrons would provide an impressive 10,000. Long-lived connectron pairs provide the possibility of turning off a set of genes for extended periods of time. In the examples that follow, Nature has used sequence matches that vary in this range.

Examples Figures 1 to 14 provide a large number of ways of describing and designing connectron pairs in a genome. We give examples of the description of symmetric and asymmetric connectron pairs in six classes of genomes (prokaryotic, Archeal, single- celled eukaryotic, multi-celled eukaryotic, mammalian and plant). We also give two examples of the design of an asymmetric connectron pair in a single-celled eukaryote and a mammal. It is clear that many other variations of'symmetric and asymmetric connectron pairs could be described or designed by someone skilled in the art.

Description of a symmetric lower-upper connectron pair in E. coli E. coli is a prokaryotic organism. A single connectron has been selected from the E. coli connectrome to illustrate the properties of a lower-upper connectron pair. Because the connectron is very long it can be split into two connectrons , that then bind as a pair. In this and each of the following examples, a header indicates the function of each data field.

Because of print-page limitations, the"sequence of match" field has been moved to the left side of each example.

The connectron 1434 has a C1-T1 binding length of 182 bases and a C2-T2 binding length of 171 bases. The shorter of the two matches of 171 bases is then halved with the first half becoming the A and the second half becoming the B in figure 3a producing a producted connectron pair lifetime of 7225.

genome Connectron id chromosome contig (. groups) id type CP = control element on positive strand CN = control element on negative strand TP = target element on positive strand TN = target element on negative strand match start match stop type Connectron | = lower/upper I/r = left/right source of Connectron I = gene I = pseudogene length of match sequence of match ) )) eco 1434 1 1 7435 CP 4505. 026 4505. 207 1/u g 182 CTGTAGATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGG TGTTTTGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAA CCAGATCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGA AAGTACTGCCGAATTAGCCCATTTGTGTTCTC eco 1434 1 1 508 TN 279. 155 279. 336 1/u g 182 CTGTAGATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGG TGTTTTGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAA CCAGATCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGA AAGTACTGCCGAATTAGCCCATTTGTGTTCTC eco. 1434 1 1 7435 CP 4505. 031 4505. 201 1/u g 171 GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAACCAGA TCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGAAAGTA CTGCCGAATTAGCCCATTTGT eco 1434 1 1 472 TN 270. 811 270. 981 1/u g 171 GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAACCAGA TCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGAAAGTA CTGCCGAATTAGCCCATTTGT Can form an AB symmetric pair of 1/u Connectrons with a lifetime = X 85 = 171 GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAACCAGA TCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGAAAGTA CTGCCGAATTAGCCCATTTGT 171 GATTCAATCTGTCAATGCAACACCCCTTTCAATTATCTCTTTCGGTGTTT TGAACTTCAGTGTCTTTCTCGGTCTGTTGTTTAGCTGAGCAGCAACCAGA TCTAGTTCATGTTGAGTATATTGGGCAAGACATGTCTTTTTAGGAAAGTA CTGCCGAATTAGCCCATTTGT

279. 279. 239 279. 252 279. 336---270. 811 270. 270. 981 /\ /\ 279. 155 270. 981 \/ \ \// \ \// 279. 239 270. 897 \/ X /\ 270. 895 279. 252 //\ \ //\ \ /\ 270. 811 279. 336 /\ Description of a symmetric lower-upper connectron pair in S. tokodaii S. tokodaii is a Archeal organism. In this and the following examples, the header does not show all the cases for a given data field.

The connectron 4240 has a C1-T1 binding length of 67 bases. and a C2-T2 binding length of 85 bases. The effective match of 52 bases is then halved with the first half becoming the A and the second half becoming the B in figure 3a producing a producted connectron pair lifetime of 676. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I sto 4240 1 1 3986 CN 1178. 996 1179. 062 1/u g 67 TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA AACTACCGGGTACATGA sto 4240 1 1 447 TP 61. 903 61. 969 1/u g 67 TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA AACTACCGGGTACATGA

sto 4240 1 1 3986 CN 1178. 963 1179. 047 1/u g 85 TTGTAATATTATATCAGTTTACTTCTAATATACTGTACCCCCTTCAAGTA AGCCTCATTTAAGGGAGTTTTCTCCCTTGAATAAA sto 4240 1 1 646 TP 123. 599 123. 683 1/u g 85 TTGTAATATTATATCAGTTTACTTCTAATATACTGTACCCCCTTCAAGTA AGCCTCATTTAaGGGAGTTTTCTCCCTTGAATAaA AGCCTCATTTAAGGGAGTTTTCTCCCTTGAATAAA Can form an AB symmetric pair of 1/u Connectrons with a lifetime = 26 X 26 = 52 TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA AA 52 TGTACCCCCTTCAAGTAAGCCTCATTTAAGGGAGTTTTCTCCCTTGAATA AA 61. 903 61. 928 61. 944 61. 969---123. 599 123. 624 123. 658 123. 683 /\ /\ 61. 903 123. 683 \/ \ \// \ 61. 928 *. 123. 658 \/ X /\ 123. 624 *. 61. 944 //\ \ //\ \ /\ 123. 599 61. 969 /\ Description of a symmetric lower-upper connectron pair in S. cerevisiae The connectron 385 has a C1-T1 binding length of 117 and a C2- T2 binding length also of 117 bases. Since the two matches are equal, the 117 bases are then halved with the first half becoming the A and the second half becoming the B in figure 3a producing a producted connectron pair lifetime of 3364.

S. cerevisiae is a single-celled eukaryotic organism.

genome Connectron id chromosome contig (. id type match start match stop type of Connectron source of Connectron length of match sequence of match I yst 385 15 15 28455 CP 975. 950 976. 066 1/u g 117 TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA ATAGGATCAATGAATAT yst 385 1 1 419 TN 165. 888 166. 004 1/u g 117 TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA ATAGGATCAATGAATAT yst 385 15 15 28455 CP 975. 950 976. 066 1/u g 117 TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA ATAGGATCAATGAATAT yst 385 1 1 355 TN 160. 257 160. 373 1/u g 117 TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA ATAGGATCAATGAATAT Can form an AB symmetric pair of 1/u Connectrons with a lifetime 58 3364 117 TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA ATAGGATCAATGAATAT 117 TTACTAGTATATTATCATATACGGTGTTAGAAGATGACGCAAATGATGAG AAATAGTCATCTAAATTAGTGGAAGCTGAAACGCAAGGATTGATAATGTA ATAGGATCAATGAATAT 165. 888 165. 945 165. 947 166. 004---160. 257 160. 314 160. 316 160. 373 /''\ /\ 165u888 160. 373 \/ \ \// \ \// 165. 945 316 \/ X /\ 160. 314 *. 165. 947 //\ \ //\ /\ 160. 257 166. 004 ,/\

Description of a symmetric lower-upper connectron pair in C. elegans C. elegans is a 1,000-celled eukaryotic organism.

The connectron 55 has a C1-T1 binding length of 68 and a C2-T2 binding length also of 68 bases. The effective match of 43 bases is then halved with the first half becoming the A and the second half becoming the B in figure 3a producing a producted connectron pair lifetime of 441. genome Connectron id chromosome contig (. groups) id I match start match stop type of Connectron source length of match sequence of match I I I I I I I I I I I I wrm 55 1 1 380 CN 221. 205 221. 272 GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCATCTGCAAG GATAAACTCGCATGTCGA wrm 55 1 1 433 TN 250. 979 251. 046 68 GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCATCTGCAAG GATAAACTCGCATGTCGA wrm 55 1 1 380 CN 221. 180 221. 247 1/u 68 GAGCTCGCAACACCGGCCGAGCAGCGGGAATTGCTTCGTCAAATGATCGA CGGAGGGCTTTTGGCCAT wrm 55 1 1 354 TN 214. 904 214. 971 1/u 68 GAGCTCGCAACACCGGCCGAGCAGCGGGAATTGCTTCGTCAAATGATCGA CGGAGGGCTTTTGGCCAT Can form an AB symmetric pair of 1/u Connectrons with a lifetime = 21 X 21 = 43 GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCAT 43 GGGAATTGCTTCGTCAAATGATCGACGGAGGGCTTTTGGCCAT

250. 979 250. 999 251. 026 251. 046---214. 904 214. 924 214. 951 214. 971 /''\ /\ 250. 979 214. 971 \/ \ \// \ \// 250. 999 214. 951 \/ X /\ 214. 924 251. 026 //\ \ //\ \ /\ 214. 904 251. 046 /\ I typeDescription of a symmetric lower-upper connectron pair in H. sapiens H. sapiens is a multi-celled eukaryotic organism-a mammal.

The connectron 1211 has a C1-T1 binding length of 58 bases and a C2-T2 binding length also of 58 bases. Since the two matches are equal, 58 is then halved with the first half becoming the A and the second half becoming the B in figure 3a producing a producted connectron pair lifetime of 841. genome Connectron id chromosome I (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I I I I I I hsd 1211 4 1 1331 CP 16. 381 16. 438 1/u g GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT AAAGATCA hsd 1211 4 1 1542 TP 500. 217 500. 274 1/u g 58 GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT AAAGATCA hsd 1211 4 1 1331 CP 16. 381 16. 438 1/u g 58

GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT AAAGATCA hsd 1211 4 1 1559 TP 504. 937 504. 994 1/u g 58 GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT AAAGATCA Can form an AB symmetric pair of 1/u Connectrons with a lifetime = 29 X 29 = 58 GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT AAAGATCA 58 GGTGAGTACCTTTCTATGAAGGTGATAAGGATCCACTGAGTCTTCCATAT AAAGATCA 500. 217 500. 245 500. 246 500. 274---504. 937 504. 965 504. 966 504. 994 /\ /\ 500. 217 504. 994 \/ \ \// \\1/ 500. 245 *. 504. 966 \/ X /\ 504. 965 *. 500. 246 //\ \ //\ \ \ 504. 937 500. 274 /\ Description of a symmetric lower-upper connectron pair in A. thaliana A. thaliana is a multi-celled eukaryotic organism-a plant.

The connectron 3 has a C1-T1 binding length of 94 bases and a C2-T2 binding length of 79 bases. The shorter of the two matches of 79 bases is then halved with the first half becoming the A and the second half becoming the B in figure 5a producing a producted connectron pair lifetime of 1521.

genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I 1 I I I I I I I ath 3 29822 CN 21590. 870 21590. 960 1/u g 94 TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT ATCCAATAATTAATTATGGCCAAATCCAAGTTCTAGAGTTTTCT ath 3 7951 TP 3780. 765 3780. 858 1/u g 94 TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT ATCCAATAATTAATTATGGCCAAATCCAAGTTCTAGAGTTTTCT ath 3 29822 CN 21590. 870 21590. 950 1/u g 79 TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT ATCCAATAATTAATTATGGCCAAATCCAA ath 3 7985 TP 3785. 281 3785. 359 1/u g 79 TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT ATCCAATAATTAATTATGGCCAAATCCAA Can form an AB symmetric pair of 1/u Connectrons with a lifetime = 39 X 39 = 79 TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT ATCCAATAATTAATTATGGCCAAATCCAA 79 TGTTGAAAGTTAAACTTGATTTTGAATCAAGTTTAATTATTGGATCAATT ATCCAATAATTAATTATGGCCAAATCCAA 3780. 765 3780. 803 3780. 820 3780. 858---3785. 281 3785. 319 3785. 321 3785. 359 /'\ /\ 3780. 765 3785. 359 \/ \\// \\// 3780. 803 3785. 321 \/ X /\ 3785. 319 *. 3780. 820 //\ \ //\ \ /\ 3785. 281 3780. 858 /\

Description of an asymmetric lower-upper connectron pair in E. coli The connectron 14918 has a C1-T1 binding length of 27 bases and a C2-T2 binding length of 35 bases. The shorter of the two matches at 27 bases produces the lifetime for this connectron. The connectron 15118 has a Cl-T1 binding length of 20 bases and a C2-T2 binding length of 22 bases. The shorter of the two matches at 20 bases produces the lifetime for this connectron. The lifetime of this pair of anti- dominant-dominant connectrons as shown in figure 9d is 540. genome I id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match ! eco 14918 1 1 7316 CN 4454. 807 4454. 833 1/u g 27 AAATGCCGGATGCGGCGTGAACGCCTT eco 14918 1 1 6955 TN 4242. 757 4242. 783 1/u g 27 AAATGCCGGATGCGGCGTGAACGCCTT eco 14918 1 1 7316 CN 4454. 810 4454. 844 1/u g 35 TGCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC eco 14918 1 1 6937 TN 4233. 017 4233. 051 1/u g 35 TGCCGGATGCGGCGTGAACGCCTTATCCGGCCTAC eco 15118 1 1 1544 CP 831. 575 831. 594 1/u g 20 TGTAGGCCGGATAAGGCGTT eco 15118 1 1 6939 TP 4232. 999 4233. 018 1/u g 20 TGTAGGCCGGATAAGGCGTT eco 15118 1 1 1544 CP 831. 596 831. 617 1/u g 22 ACGCCGCATCCGGCATTTCACA

eco 15118 1 1 6957 TP 4242. 783 4242. 804 1/u g 22 ACGCCGCATCCGGCATTTCACA ACGCCGCATCCGGCATTTCACA Found L/U AD AB-CD Connectron pair for 14918 and 15118 with a lifetime = 27 X 20 = . 000. 001 4242. 757 4242. 783 4233. 017 4233. 051---4232. 999 4233. 018 4242. 783 4242. 804 /'\ /\ 4242. 757 4233. 051 \/ \ \// \ \// 4242. 783 *. 4233. 017 \/ X /\ 4233. 018 *. 4242. 783 //\ //\ /\ 4232. 999 4242. 804 /\ Description of an asymmetric lower-upper connectron pair in S. tokodaii The connectron 6416 has a C1-T1 binding length of 59 bases and a C2-T2 binding length of 60 bases. The shorter of the two matches at 59 bases produces the lifetime for this connectron.

The connectron 6477 has a C1-T1 binding length of 189 bases and a C2-T2 binding length of 36 bases. The shorter of the two matches at 36 bases produces the lifetime for this connectron. The lifetime of this pair of dominant-anti- dominant connectrons as shown in figure 9d is 2124. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match ) sto 6416 1 1 3245 CP 1036. 523 1036. 581 1/u g 59

ACTCCCAGTGAGGGATAGGGGTAACGGACTGAAGACCCAGCCCGTGGTCT ACCGCTGGA sto 6416 1 1 3439 TP 1079. 594 1079. 652 1/u g 59 ACTCCCAGTGAGGGATAGGGGTAACGGACTGAAGACCCAGCCCGTGGTCT ACCGCTGGA sto 6416 1 1 3250 CP 1036. 635 1036. 694 1/u g 60 ATGAAGGTGGTAAACCACAAACCTATGAACCGCCCTAAGGGAACCCTCGC CCTTTAGGGC sto 6416 1 1 3714 TP 1146. 360 1146. 419 1/u g 60 ATGAAGGTGGTAAACCACAAACCTATGAACCGCCCTAAGGGAACCCTCGC CCTTTAGGGC CCTTTAGGGC sto 6477 1 1 618 CN 120. 361 120. 549 1/u g 189 CTATCCCTCACCAAGAGTTGCCCTCTGCTCTTGGCTCTTGGGGACTCGGG GATATGTAGTTCTGTGCGGGGACACATATCTTCAGTATGCCCACCTTTGT GGGCTTCCCCGCACTTTATTAATAGTTTTAAGCTAAGATTAAAAACTTTA CCCCGCCTTAAAAGGCGAGGCTTGCCCCGCGTTTTGTCA sto 6477 1 1 3709 TN 1146. 169 1146. 357 1/u g 189 CTATCCCTCACCAAGAGTTGCCCTCTGCTCTTGGCTCTTGGGGACTCGGG GATATGTAGTTCTGTGCGGGGACACATATCTTCAGTATGCCCACCTTTGT GGGCTTCCCCGCACTTTATTAATAGTTTTAAGCTAAGATTAAARACTTTA CCCCGCCTTAAAAGGCGAGGCTTGCCCCGCGTTTTGTCA sto 6477 1 1 622 CN 120. 590 120. 625 1/u g 36 CACCCACCCCGCTCCGTTCGTCCAGCGGTAGACCAC sto 6477 1 1 3446 TN 1079. 651 1079. 686 1/u g 36 CACCCACCCCGCTCCGTTCGTCCAGCGGTAGACCAC Found L/U DA AB-CD Connectron pair for 6416 and 6477 with a lifetime = 59 X 36 = . 001. 003 1079. 594 1079. 652 1146. 360 1146. 419---1146. 169 1146. 357 1079. 651 1079. 686 /'\ /\ 1079. 594 1146. 419 \/ \ \// \\// 1079. 652 1146. 360 \/ X /\ 1146. 357 1079. 651 //\ //\ \ /\ 1146. 169 1079. 686 \

Description of an asymmetric lower-upper connectron pair in S. cerevisiae The connectron 3814 has a C1-T1 binding length of 72 bases and a C2-T2 binding length of 72 bases. The either of the two matches at 72 bases produces the lifetime for this connectron. The connectron 3847 has a C1-T1 binding length of 81 bases and a C2-T2 binding length of 89 bases. The shorter of the two matches at 81 bases produces the lifetime for this connectron.

The lifetime of this pair of anti-dominant-dominant connectrons as shown in figure 9d is 5832. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I 1 I I I I yst 3814 13 13 23498 CP 362. 701 362. 772 1/u g 72 ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT TTTATATGTTTCATTATCCTAT yst 3814 2 2 1896 TN 265. 267 265. 338 1/u g 72 ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT TTTATATGTTTCATTATCCTAT yst 3814 13 13 23498 CP 362. 701 362. 772 1/u g 72 ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT TTTATATGTTTCATTATCCTAT yst 3814 2 2 1495 TN 226. 820 226. 891 1/u g ATGGAATCTATATTTCTACATACTAATATTACGATTATTCCTCATTCCGT TTTATATGTTTCATTATCCTAT TTTATATGTTTCATTATCCTAT yst 3847 13 13 23551 CN 372. 772 372. 852 1/u g 81 AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT ATAGATTCCATTTTGAGGATTCCTATATCCT yst 3847 2 2 1496 TP 226. 739 226. 819 1/u g 81 AAACATATAAAACGGAATGAGGAATAATCGTAATATTAGTATGTAGAAAT ATAGATTCCATTTTGAGGATTCCTATATCCT

yst 3847 13 13 23551 CN 372. 836 372. 924 1/u g 89 GAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTA ATATTATAGCCTTTATCAACAATGGAATCCCAACAATTA yst 3847 2 2 1923 TP 265. 340 265. 428 1/u g 89 GAGGATTCCTATATCCTCGAGGAGAACTTCTAGTATATTCTGTATACCTA ATATTATAGCCTTTATCAACAATGGAATCCCAACAATTA Found L/U AD AB-CD Connectron pair for 3814 and 3847 with a lifetime = 5832 . 002. 001 265. 267 265. 338 226. 820 226. 891---226. 739 226. 819 265. 340 265. 428 /\ /\ 265. 267 226. 891 \/ \ \ 265. 338 *. 226. 820 \/ X /\ 226. 819 *. 265. 340 //\ \ //\ \ /\ 226. 739 265. 428 /\ Description of an asymmetric lower-upper connectron pair in C. elegans The connectron 23175 has a C1-T1 binding length of 15 bases and a C2-T2 binding length of 18 bases. The shorter of the two matches at 15 bases produces the lifetime for this connectron. The connectron 23179 has a C1-T1 binding length of 16 bases and a C2-T2 binding length of 19 bases. The shorter of the two matches at 16 bases produces the lifetime for this connectron. The lifetime of this pair of dominant- anti-dominant connectrons as shown in figure 9c is 240.

genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I I I I I I wrm 23175 4 2 22854 CP 708. 778 708. 792 1/u g 15 TGGTCTGCTAAATCG wrm 23175 4 2 21925 TP 415. 203 415. 217 1/u g 15 TGGTCTGCTAAATCG wrm 23175 4 2 22854 CP 708. 793 708. 810 1/u g 18 AAACTTGTAGTTTGTAGT wrm 23175 4 2 22166 TP 486. 479 486. 496 1/u g 18 AAACTTGTAGTTTGTAGT AAACTTGTAGTTTGTAGT wrm 23179 4 2 24763 CN 1373. 569 1373. 584 1/u g 16 ATTTAGCAGACCCAAA wrm 23179 4 2 22165 TN 486. 461 486. 476 1/u g 16 ATTTAGCAGACCCAAA wrm 23179 4 2 24763 CN 1373. 554 1373. 572 1/u g 19 AAACTACAAATTTCGATTT wrm 23179 4 2 21926 TN 415. 212 230 1/u g 19 AAACTACARATTTcGATTT AAACTACAAATTTCGATTT Found L/U DA AB-CD Connectron pair for 23175 and 23179 with a lifetime = 15 X 16 = . 005. 003 415. 203 415. 217 486. 479 486. 496---486. 461 486. 476 415. 212 415. 230 /\ /\ 415. 203 486. 496 \/ \ \// \ 415. 217 *. 486. 479 \/ X /\ 486. 476 212 //\ \ //\ \ /\ 486. 461 415. 230 /\

415.Description of an asymmetric lower-upper connectron pair in H. sapiens The connectron 383992 has a C1-T1 binding length of 39 bases and a C2-T2 binding length of 41 bases. The shorter of the two matches at 39 bases produces the lifetime for this connectron. The connectron 383993 has a C1-T1 binding length of 40 bases and a C2-T2 binding length of 34 bases. The shorter of the two matches at 34 bases produces the lifetime for this connectron. The lifetime of this pair of dominant- anti-dominant connectrons as shown in figure 9c is 1326. genome Connectron id chromosome contig I groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I 1 I I I I hsd 383992 920 19 756303 CP 21789. 055 21789. 092 u/d g 39 AGCCCGAGCCCCACCTCTCCCTTAGGGACCTCCGCCCAC hsd 383992 920 19 756563 TP 21820. 715 21820. 754 u/d g 39 AGCCCGAGCCCCACCTCTCCCTTAGGGACCTCCGCCCAC hsd 383992 920 19 756303 CP 21789. 080 21789. 121 u/d g 41 ACCTCCGCCCACCCTACCCTCAAGCCAGGATGCCCGGAGCG hsd 383992 920 19 756615 TP 21827. 379 21827. 420 u/d g 41 ACCTCCGCCCACCCTACCCTCAAGCCAGGATGCCCGGAGCG ACCTCC6CCCACCCTACCCTCAAGCCAGGATGCCCGGAGCG hsd 383993 920 19 756433 CN 21808. 781 21808. 820 u/d g 40 CCTAAGGGAGAGGTGGGGCTCGGGCTGAATCCCTCGTTGG hsd 383993 920 19 756614 TN 21827. 338 21827. 377 u/d g 40 CCTAAGGGAGAGGTGGGGCTCGGGCTGAATCCCTCGTTGG hsd 383993 920 19 756433 CN 21808. 740 21808. 773 u/d g 34 GCTCCGGGCATCCTGGCTTGAGGGTAGAGTGGGC hsd 383993 920 19 756564 TN 21820. 748 21820. 781 u/d g 34 GCTCCGGGCATCCTGGCTTGAGGGTAGAGTGGGC

Found pair for 383992 and 383993 with a lifetime = 39 X 34 = 1326 0. 006 0. 002 21820. 715 21820. 754 21827. 379 21827. 420---21827. 338 21827. 377 21820. 748 21820. 781 /% /% 21820. 7 21827. 420 b/ % % 21820. 754 21827. 379 / X /% 21827. 377 21820. 748 //% //% % /% 21827. 338 21820. 781 /% Description of an asymmetric lower-upper connectron pair in A. thaliana The connectron 188312 has a C1-T1 binding length of 20 bases and a C2-T2 binding length of 30 bases. The shorter of the two matches at 20 bases produces the lifetime for this connectron. The connectron 188397 has a C1-T1 binding length of 30 bases and a C2-T2 binding length of 16 bases. The shorter of the two matches at 16 bases produces the lifetime for this connectron. The lifetime of this pair of dominant- anti-dominant connectrons as shown in figure 9c is 340. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I I 1 1 1 I ath 188312 18 4 269631 CP 5320. 517 5320. 536 u/d g 20

TTGTAGACGTATGGTGGTGG ath 188312 18 4 269507 TP 5311. 160 5311. 179 u/d g 20 TTGTAGACGTATGGTGGTGG ath 188312 18 4 269631 CP 5320. 519 5320. 548 u/d g 30 GTAGACGTATGGTGGTGGTGGAGACTTGTA ath 188312 18 4 269890 TP 5340. 361 5340. 390 u/d g 30 GTAGACGTATGGTGGTGGTGGAGACTTGTA GTAGACGTATGGTGGTGGTGGAGACTTGTA ath 188397 18 4 269741 CN 5324. 883 5324. 921 u/d g 39 GCTCTCCACCACCACCATACTACAGTCCATCTCCAAAGG ath 188397 18 4 269881 TN 5340. 322 5340. 360 u/d g 39 GCTCTCCACCACCACCATACTACAGTCCATCTCCAAAGG ath 188397 18 4 269741 CN 5324. 867 5324. 882 u/d g 16 CCACCATACGTCTACA ath 188397 18 4 269509 TN 5311. 176 5311. 191 u/d g 16 CCACCATACGTCTACA CCACCATACGTCTACA Found L/U Connectron pair for 188312 and 188397 with a lifetime = 20 X 16 = 320 0. 003 0. 001 5311. 160 5311. 179 5340. 361 5340. 390---5340. 322 5340. 360 5311. 176 5311. 191 J.. /\ 5311. 160 5340. 390 \/ \ \// \ \// 5311. 179 5340. 361 \/ X /\ 5340. 360 5311. 176 //\ \ //\ \ \ 5340. 322 5311. 191 /\ Description of an asymmetric left-right connectron pair in E. coli The connectron 3707 has a C1-T1 binding length of 21 bases and a C2-T2 binding length of 19 bases. The shorter of the two matches at 19 bases produces the lifetime for this connectron.

The connectron 3763 has a C1-T1 binding length of 42 bases and a C2-T2 binding length of 37 bases. The shorter of the two matches at 37 bases produces the lifetime for this connectron.

The lifetime of this pair of dominant-dominant connectrons as shown in figure 10a is 703. genome Connectron id chromosome i (. groups) id t match start match stop type of Connectron source of Connectron length match sequence of match I I I I 1 I l I I 1 I I eco 3707 1 1 3906 CN 2338. 350 2338. 370 1/r g 21 AACGCCTTATCCGGCCTACGG eco 3707 1 1 689 TP 374. 169 374. 189 1/r g 21 AACGCCTTATCCGGCCTACGG eco 3707 1 1 3906 CN 2338. 380 2338. 398 1/r g 19 GTAGGCCTGATAAGACGCG eco 3707 1 1 707 TN 376. 619 376. 637 1/r g 19 GTAGGCCTGATAAGACGCG GTAGGCCTGATAAGACGCG eco 3763 1 1 709 CP 376. 712 376. 753 1lu g 42 GTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTCGTGC eco 3763 1 1 690 TN 374. 152 374. 193 1/r g 42 GTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCAGTCGTGC eco 3763 1 1 709 CP 376. 717 376. 753 1/r g 37 CCGGATAAGGCGTTCACGCCGCATCCGGCAGTCGTGC eco 3763 1 1 706 TP 376. 617 376. 653 1/r g 37 CCGGATAAGGCGTTCACGCCGCATCCGGCAGTCGTGC CCGGATAAGGCGTTCACGCCGCATCCGGCAGTCGTGC Found L/R DD AB-CD Connectron pair for 3707 and 3763 with X 37 = . 004. 002

374. 169 374. 189 376. 619 376. 637---374. 152 374. 193 376. 617 376. 653 /\ /\ 376. 637 374. 152 \/ \/ \ \// 376. 619 193 \ \// ) X ( //\ 374. 189/* 376. 617 //\ \ /\ /\ 374. 169 376. 653 /\ Description of an asymmetric left-right connectron pair in S. cerevisiae The connectron 6834 has a C1-T1 binding length of 105 bases and a C2-T2 binding length of 38 bases. The shorter of the two matches at 38 bases produces the lifetime for this connectron. The connectron 6944 has a C1-T1 binding length of 152 bases and a C2-T2 binding length of 143 bases. The shorter of the two matches at 143 bases produces the lifetime for this connectron. The lifetime of this pair of dominant- anti-dominant connectrons as shown in figure 10c is 5434. genome Connectron id chromosome contig (. id type match start match stop type of Connectron source of Connectron length of match sequence of match t) yst 6834 7 7 10928 CN 111. 321 111. 425 1/r g 105 CGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTG GAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAAC ATATA yst 6834 3 3 2988 TP 84. 359 84. 463 ihr g 105

CGGTGTTAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTG GAAGCTGAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAAC ATATA yst 6834 7 7 10945 CN 111. 449 111. 486 ihr g 38 TCATCTACTAACTAGTATTTACGTTACTAGTATATTAT yst 6834 3 3 3500 TN 168. 765 168. 802 1/r g 38 TCATCTACTAACTAGTATTTACGTTACTAGTATATTAT TCATCTACTAACTAGTATTTACGTTACTAGTATATTAT yst 6944 4 4 5116 CN 645. 641 645. 792 1/r g 152 TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAA AA yst 6944 3 3 2991 TP 84. 315 84. 466 1/r g 152 TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAACATATAA AA yst 6944 4 4 5116 CN 645. 641 645. 783 1/r g 143 TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAA yst 6944 3 3 3496 TN 168. 762 168. 904 1/r g 143 TCATCTACTAACTAGTATTTACGTTACTAGTATATTATCATATACGGTGT TAGAAGATGACGCAAATGATGAGAAATAGTCATCTAAATTAGTGGAAGCT GABACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAA GAAACGCAAGGATTGATAATGTAATAGGATCAATGAATATTAA Found L/R DA AB-CD Connectron pair for 6834 and 6944 with a lifetime = X 143 = . 003. 003 84. 359 84. 463 168. 765 168. 802---84. 315 84. 466 168. 762 168. 904 l.. /\ 168. 802 84. 315 \/ \/ \\// 168. 765 466 \ \// ) X ( //\ 84. 463/* 168. 762 //\ /\ /\ 84. 359 168. 904 /\

Description of an asymmetric left-right connectron pair in C. elegans The connectron 40849 has a C1-T1 binding length of 34 bases and a C2-T2 binding length of 34 bases. The either of the two matches at 34 bases produces the lifetime for this connectron.

The connectron 40850 has a C1-T1 binding length of 48 bases and a C2-T2 binding length of 39 bases. The shorter of the two matches at 39 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant- dominant connectrons as shown in figure 10d is 1326. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I 1 wrm 40849 6 2 51392 CN 13819. 470 13819. 500 1/r g 34 ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT wrm 40849 6 2 51379 TN 13817. 594 13817. 630 1/r g 34 ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT wrm 40849 6 2 51392 CN 13819. 470 13819. 500 1/r g 34 ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT wrm 40849 6 2 51400 TP 13820. 550 13820. 583 1/r g 34 ACCGARCCCAACGGCCCTCTTTAGGGCCACAAAT ACCGAACCCAACGGCCCTCTTTAGGGCCACAAAT wrm 40850 6 2 51410 CN 13820. 791 13820. 840 1/r g 48 CAACACACCTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGTT wrm 40850 6 2 51379 TN 13817. 583 13817. 630 1/r g 48 CAACACACCTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGTT wrm 40850 6 2 51410 CN 13820. 800 13820. 840 1/r g 39 CTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGT wrm 40850 6 2 51400 TP 13820. 550 13820. 584 1/r g 39 CTAACCGAACCCAACGGCCCTCTTTAGGGCCACAAATGT CTAACCGRRCCCRACGGCCCTCTTTAGGGCCACRAATGT

Found L/R AD AB-CD Connectron pair for 40849 and 40850 with a lifetime = 34 X 39 = 1326 . 003. 003 13817. 595 13817. 628 13820. 550 13820. 583---13817. 584 13817. 631 13820. 547 13820. 585 / /\ 13820. 583 13817. 584 \/ \/ \ \// 13820. 631 \ ) X ( //\ 13817. 628/* 547 //\ /\ /\ 13817. 595 13820. 585 /\ Description of an asymmetric left-right connectron pair in H. sapiens The connectron 67620 has a C1-T1 binding length of 38 bases and a C2-T2 binding length of 33 bases. The shorter of the two matches at 33 bases produces the lifetime for this connectron. The connectron 67621 has a C1-T1 binding length of 41 bases and a C2-T2 binding length of 42 bases. The shorter of the two matches at 41 bases produces the lifetime for this connectron. The lifetime of this pair of dominant- anti-dominant connectrons as shown in figure 10c is 1353. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match I I I I I I I I I I I l hsd 67620 100 1 96091 CN 1705. 996 1706. 033 1/r g 38 GTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC hsd 67620 60 1 78101 TP 218. 397 218. 434 1/r g 38

GTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGC hsd 67620 100 1 96101 CN 1705. 970 1706. 002 1/r g 33 AGGTCAGGAGATCGAGACCATCCTGGCTAACAC hsd 67620 60 1 78110 TN 234. 341 234. 373 1/r g 33 AGGTCAGGAGATCGAGACCATCCTGGCTAACAC AGGTCAGGAGATCGAGACCATCCTGGCTAACAC hsd 67621 100 1 98781 CN 3142. 085 3142. 125 1lu g 41 CGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC hsd 67621 60 1 78101 TP 218. 395 218. 435 1/r g 41 CGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCC hsd 67621 100 1 98781 CN 3142. 052 3142. 093 1/r g 42 GAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAAC hsd 67621 60 1 78110 TN 234. 340 234. 381 1/r g 42 GAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAAC GAGGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAAC Found L/R DA AB-CD Connectron pair for 67620 and 67621 with a lifetime = 33 X 41 = 0. 001 0. 001 218. 397 218. 434 234. 341 234. 373---218. 395 218. 435 234. 340 234. 381 /\ /\ 234. 373 218. 395 \/ \/ \ \// 234. 341 435 \ \// ) X ( //\ 218. 434/* 234. 340 //\ \ /\ /\ 218. 397 234. 381 /\ Description of an asymmetric left-right connectron pair in A. thaliana The connectron 5 has a C1-T1 binding length of 28 bases and a C2-T2 binding length of 35 bases. The shorter of the two matches at 28 bases produces the lifetime for this connectron.

The connectron 6 has a C1-T1 binding length of 37 bases and a

C2-T2 binding length of 68 bases. The shorter of the two matches at 37 bases produces the lifetime for this connectron.

The lifetime of this pair of anti-dominant-dominant connectrons as shown in figure 10d is 1036. genome Connectron id chromosome contig (. groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match ! ath 5 15 3 102175 CN 12540. 150 12540. 174 1/r g 28 ATCATCAATGAACTCATTTGGCTAAGGT ath 5 15 3 102902 TN 13558. 720 13558. 750 1/r g 28 ATCATCAATGAACTCATTTGGCTAAGGT ath 5 15 3 102176 CN 12540. 184 12540. 220 1/r g 35 ACATTCATTAGTTCTGGAACGTGAATCAAGCAATG ath 5 15 3 103090 TP 13634. 210 13634. 240 1/r g 35 ACATTCATTAGTTCTGGAACGTGAATCAAGCAATG ACATTCATTAGTTCTGGAACGTGAATCAAGCAATG ath 6 15 3 103067 CP 13626. 660 13626. 700 1/r g 37 ATGCATCATCAATGAACTCATTTGGCTAAGGTGAAGG ath 6 15 3 102902 TN 13558. 713 13558. 750 1/r g 37 ATGCATCATCAATGAACTCATTTGGCTAAGGTGAAGG ath 6 15 3 103067 CP 13626. 624 13626. 691 1/r g 68 TTTAACATTCATTAGTTCTGGAACGTGAATCAAGCAATGCATCATCAATG AACTCATTTGGCTAAGGT ath 6 15 3 103090 TP 13634. 202 13634. 270 1/r g 68 TTTAACATTCATTAGTTCTGGAACGTGAATCAAGCAATGCATCATCAATG AACTCATTTGGCTAAGGT Found L/R AD AB-CD Connectron pair for 5 and 6 with a lifetime = 28 X 37 = 1036 . 005. 004

13558. 718 13558.745 13634.206 13634. 240---13558. 714 13558.750 13634.202 13634.269 <BR> <BR> <BR> <BR> <BR> <BR> /\<BR> <BR> <BR> /\ 13634. 240 * * 13558.714 \/ \/ \ \// 13634.206 \ * * l13558. 750 \ \// ) X ( //\ \ 13558. 745/* * \13634. 202 //\ \ /\ /\ 13558. 718 * * 13634.269 /\ Design of an asymmetric lower-upper connectron pair in S. cerevisiae There are many ways to design a pair of connectrons. In this example we have chosen to replace the Cl source and the T1 target of the upper naturally occuring connectron with another sequence. Design of a connectron pair can be accomplished by anyone skilled the art by modifying and/or replacing any of the sources and targets in the four positions of either a lower-upper or a left-right connectron pair. A totally synthetic pair of dominant-anti-dominant connectrons could also be designed de-novo.

The connectron 5441 has a C1-T1 binding length of 82 bases and a C2-T2 binding length of 35 bases. The shorter of the two matches at 34 bases produces the lifetime for this connectron.

The connectron 5500 has a C1-T1 binding length of 16 bases and a C2-T2 binding length of 16 bases. Either of the two matches at 16 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant-dominant connectrons as shown in figure 9c is 544.

genome I id chromosome ) (. id type match start match stop type of Connectron source of Connectron length of match sequence of match !)) yst 5441 3 3 2944 CP 84. 84. 193 1/u g 82 ATACGTTTGAAGAAATCACTTTATGGATTGAAACAAAGTGGAGCGRACTG GTACGAAACTATCAAATCATACCTGATAAAAC yst 5441 3 3 2901 TP 82. 743 82. 824 1/u g 82 ATACGTTTGAAGAAATCACTTTATGGATTGAAACAAAGTGGAGCGAACTG GTACGAAACTATCAAATCATACCTGATAAAAC yst 5441 3 3 2965 CP 84. 195 84. 228 1/u g 34 GAAACGTGACGGTACTCATAAAGCTAGATTTGTT yst 5441 3 3 3529 TP 169. 327 169. 360 1/u g 34 GAAACGTGACGGTACTCATABAGCTAGATTTGTT GAAACGTGACGGTACTCATAAAGCTAGATTTGTT yst 5500 3 3 3387 CN 151. 534 151. 549 1/u g 16 TAATTGTTGGGATTCC yst 5500 3 3 3526 TN 169. 308 169. 323 1/u g 16 TAATTGTTGGGATTCC yst 5500 3 3 3387 CN 151. 516 151. 531 1/u g 16 AAAGGCTATAATATTA yst 5500 3 3 2905 TN 82. 825 82. 840 1/u g 16 AAAGGCTATAATATTA Found L/U DA AB-CD Connectron pair for 5441 and 5500 with a lifetime = 34 X 16 = . 001. 004 82. 743 82. 824 169. 327 169. 360---169. 308 169. 323 82. 825 82. 840 /''\ /\ 82. 743 169. 360 \/ \ \ \// 82. 824 169. 327 \/ X /\ 169. 323 82. 825 //\ \ //\ \ /\ 169. 308 82. 840 /\ Design of an asymmetric lower-upper connectron pair in H. sapiens There are many ways to design a pair of connectrons. In this example we have chosen to replace the Cl source and the T1 target of the right naturally occuring connectron with another sequence. Design of a connectron pair can be accomplished by anyone skilled the art by modifying and/or replacing any of the sources and targets in the four positions of either a lower-upper or a left-right connectron pair. A totally synthetic pair of anti-dominant-dominant connectrons could also be designed de-novo.

The connectron 395760 has a C1-T1 binding length of 32 bases and a C2-T2 binding length of 32 bases. Either of the two matches at 32 bases produces the lifetime for this connectron.

The connectron 395762 has a C1-T1 binding length of 40 bases and a C2-T2 binding length of 39 bases. The shorter of the two matches at 39 bases produces the lifetime for this connectron. The lifetime of this pair of anti-dominant- dominant connectrons as shown in figure 10c is 1248. genome Connectron id chromosome contig l groups) id type match start match stop type of Connectron source of Connectron length of match sequence of match 8 hsd 395760 920 19 747775 CP 17572. 332 17572. 363 1/r g 32 CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA hsd 395760 922 19 765474 TN 27988. 178 27988. 209 1/r g 32 CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA hsd 395760 920 19 747777 CP 17572. 369 17572. 400 ihr g 32

l l I (.CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA hsd 395760 922 19 765567 TP 28004.852 28004.883 1/r g 32 CCAGCCCCTCCTCCCTCAGACCCAGGAGTCCA hsd 395762 920 19 747819 CP 17573. 447 17573. 486 1/r g 40 CCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGACCCC hsd 395762 922 19 765474 TN 27988. 176 27988.215 1/r g 40 CCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGACCCC hsd 395762 920 19 747823 CP 17573.520 17573. 557 1/r g 39 GGCCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGGT hsd 395762 922 19 765567 TP 28004. 848 28004.887 1/r g 39 GGCCCCAGCCCCTCCTCCCTCAGACCCAGGAGTCCAGGT Found L/R AD AB-CD Connectron pair for 395760 and 395762 with a lifetime = 32 X 39 = 1248 0.006 0. 004 27988.178 27988.209 28004. 852 28004. 883---27988. 176 27988.215 28004.848 28004.887 <BR> <BR> <BR> <BR> <BR> <BR> <BR> <BR> <BR> /%<BR> <BR> <BR> <BR> % 28004.883 * * 27988.176 % / <BR> <BR> % / <BR> <BR> <BR> <BR> % % / / 28004. 852 % * * /27988. 215 % %// ) X ( //% % 27988. 209/* * % 28004. 848 / / % % /% /% 27988. 178 * * 28004.887 /%