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Publication numberWO2008000632 A1
Publication typeApplication
Application numberPCT/EP2007/055943
Publication dateJan 3, 2008
Filing dateJun 15, 2007
Priority dateJun 29, 2006
Also published asCA2657975A1, CN101490262A, CN101490262B, EP2035561A1, EP2423315A1, EP2423315B1, US8812247, US20090286280, US20140377800
Publication numberPCT/2007/55943, PCT/EP/2007/055943, PCT/EP/2007/55943, PCT/EP/7/055943, PCT/EP/7/55943, PCT/EP2007/055943, PCT/EP2007/55943, PCT/EP2007055943, PCT/EP200755943, PCT/EP7/055943, PCT/EP7/55943, PCT/EP7055943, PCT/EP755943, WO 2008/000632 A1, WO 2008000632 A1, WO 2008000632A1, WO-A1-2008000632, WO2008/000632A1, WO2008000632 A1, WO2008000632A1
InventorsJohannes Andries Roubos, Van Noel Nicolaas Maria E Peij
ApplicantDsm Ip Assets Bv, Johannes Andries Roubos, Van Noel Nicolaas Maria E Peij
Export CitationBiBTeX, EndNote, RefMan
External Links: Patentscope, Espacenet
A method for achieving improved polypeptide expression
WO 2008000632 A1
Abstract
The present invention relates to methods of optimization of a protein coding sequences for expression in a given host cell. The methods apply genetic algorithms to optimise single codon fitness and/or codon pair fitness sequences coding for a predetermined amino acid sequence. In the algorithm generation of new sequence variants and subsequent selection of fitter variants is reiterated until the variant coding sequences reach a minimum value for single codon fitness and/or codon pair fitness. The invention also relates to a computer comprising a processor and memory, the processor being arranged to read from and write into the memory, the memory comprising data and instructions arranged to provide the processor with the capacity to perform the genetic algorithms for optimisation of single codon fitness and/or codon pair fitness. The invention further relates to nucleic acids comprising a coding sequence for a predetermined amino acid sequence, the coding sequence being optimised with respect to single codon fitness and/or codon pair fitness for a given host in the methods of the invention, to host cells comprising such nucleic acids and to methods for producing polypeptides and other fermentation products in which these host cells are used.
Claims  (OCR text may contain errors)
Claims
1. A method of optimization of a nucleotide coding sequence coding for a predetermined amino acid sequence, whereby the coding sequence is optimized for expression in a predetermined host cell, the method comprising: a) generating at least one original coding sequence that codes for the predetermined amino acid sequence; b) generating at least one newly generated coding sequence from this at least one original coding sequence by replacing in this at least one original coding sequence one or more codons by a synonymous codon; c) determining a fitness value of said at least one original coding sequence and a fitness value of said at least one newly generated coding sequence while using a fitness function that determines at least one of single codon fitness and codon pair fitness for the predetermined host cell; d) choosing one or more selected coding sequence amongst said at least one original coding sequence and said at least one newly generated coding sequence in accordance with a predetermined selection criterion such that the higher is said fitness value, the higher is a chance of being chosen; e) repeating actions b) through d) while treating said one or more selected coding sequence as one or more original coding sequence in actions b) through d) until a predetermined iteration stop criterion is fulfilled.
2. A method according to claim 1, wherein said predetermined selection criterion is such that said one or more selected coding sequence have a best fitness value according to a predetermined criterion.
3. A method according to claim 1 or 2, wherein said method comprises, after action e): f) selecting a best individual coding sequence amongst said one or more selected coding sequences where said best individual coding sequence has a better fitness value than other selected coding sequences.
4. A method according to any one of claims 1 - 3, wherein said predetermined iteration stop criterion is at least one of: (a) testing whether at least one of said selected coding sequences have a best fitness value above a predetermined threshold value;
(b) testing whether none of said selected coding sequences has a best fitness value below said predetermined threshold value; (c) testing whether at least one of said selected coding sequences has at least 30% of the codon pairs with associated positive codon pair weights for the predetermined host cell in said original coding sequence being transformed into codon pairs with associated negative weights; and, (d) testing whether at least one of said selected coding sequences has at least 30% of the codon pairs with associated positive weights above 0 for the predetermined host cell in said original coding sequence being transformed into codon pairs with associated weights below 0.
5. A method according to any one of claims 1 - 4, wherein said fitness function defines single codon fitness by means of:
fitc(g) = l00 - - rc s (c(k))\ - l00 where g symbolizes a coding sequence, \g\ its length, g(k) its k-th codon, rc fargef (c(k)) is a desired ratio of codon c(k) and r/ (c(k)) an actual ratio in the nucleotide coding sequence g.
6. A method according to any one of claims 1 - 4, wherein said fitness function defines codon pair fitness by means of: i Isl-i fitcp(g) =—- ∑w((c(k),c(k + \))
\ 8 \ ~*- k=\ where w((c(k), c(k + I)) is a weight of a codon pair in a coding sequence g, \g\ is length of said nucleotide coding sequence and c(k) is k-th codon in said coding sequence.
7. A method according to any one of claims 1 - 4, wherein said fitness function is defined by means of:
flhombi where i I Issll--ii fitcp(g) =-—- ∑w((c(k),c(k + ϊ))
fitsc ω = cpi is a real value greater than zero, fitcp(g) is codon pair fitness function, fitsc(g) is a single codon fitness function, w((c(k), c(k + I)) is a weight of a codon pair in a coding sequence g, \g\ is length of said coding sequence, c(k) is k-th codon in said sequence of codons, rtarget (c(k)) is a desired ratio of codon c(k) and rg (c(k)) an actual ratio in the coding sequence g.
8. A method according to claim 7, wherein cpi is between 10~4 and 0.5.
9. A method according to any one of claims 6 - 8, wherein said codon pair weights w are taken from a 61x61 codon pair matrix without stop codons, or a 61 x 64 codon pair matrix that includes stop-codons, and wherein said codon pair weights w are calculated on the basis of a computer-based method, using as input at least one of:
(a) a group of nucleotide sequences consisting of at least 200 coding sequences of a predetermined host;
(b) a group of nucleotide sequences consisting of at least 200 coding sequences of the species to which the predetermined host belongs;
(c) a group of nucleotide sequences consisting of at least 5% of the protein encoding nucleotide sequences in a genome sequence of the predetermined host; and, (d) a group of nucleotide sequences consisting of at least 5% of the protein encoding nucleotide sequences in a genome sequence of a genus related to the predetermined host.
10. A method according to claim 9, wherein said codon pair weights w are determined for at least 5%, 10%, 20%, 50%, and preferably 100% of the possible 61 x 64 codon pairs including the termination signal as stop codon.
11. A method according to claim 6 - 8, wherein said codon pair weights w are taken from a 61x61 codon pair matrix without stop codons, or a 61 x 64 codon pair matrix that includes stop- codons, and wherein said codon pair weights w are defined by means of:
n '((c c )) where the combined expected values exp ' ' J are defined by means of:
ck esyricl)
where r^ ^ck> denote the single codon ratio of Ck in the whole genome data set and nobs ((c, >c 7)) the occurrences of a pair (ci,q) in the highly expressed group, and wherein the highly expressed group are the genes whose mRNA's can be detected at a level of at least 20 copies per cell.
12. A method according any of the preceding claims where said original coding nucleotide sequence coding for predetermined amino acid sequence is selected from:
(a) a wild-type nucleotide sequence coding for said predetermined amino acid sequence
(b) a reverse translation of the predetermined amino acid sequence whereby a codon for an amino acid position in the predetermined amino acid sequence is randomly chosen from the synonymous codons coding for the amino acid; and, (c) a reverse translation of the predetermined amino acid sequence whereby a codon for an amino acid position in the predetermined amino acid sequence is chosen in accordance with a single-codon bias for the predetermined host cell or a species related to the host cell.
13. A method according to any of claims 1 - 12, wherein said predetermined host cell is a cell of a microorganism, preferably a microorganism of a genus selected from: Bacillus, Actinomycetis, Escherichia, Streptomyces, Aspergillus, Penicillium, Kluyveromyces, Saccharomyces.
14. A method according to any of claims 1 - 12, wherein said predetermined host cell is a cell of an animal or plant, preferably a cell of a cell line selected from CHO, BHK, NSO, COS, Vero, PER.C6™, HEK-293, Drosophila S2, Spodoptera Sf9 and Spodoptera Sf21.
15. A computer comprising a processor and memory, the processor being arranged to read from said memory and write into said memory, the memory comprising data and instructions arranged to provide said processor with the capacity to perform the method of any of the claims 1 - 14.
16. Computer program product comprising data and instructions and arranged to be loaded in a memory of a computer that also comprises a processor, the processor being arranged to read from said memory and write into said memory, the data and instructions being arranged to provide said processor with the capacity to perform the method of any of the claims 1 - 14.
17. Data carrier provided with a computer program product as claimed in claim 16.
18. A nucleic acid molecule comprising a coding sequence coding for a predetermined amino acid sequence, wherein the coding sequence is not a naturally occurring coding sequence and wherein, the coding sequence has afitcp(g) of at least below -0.1, and preferably below -0.2, and more preferably below -0.3 for a predetermined host cell.
19. A nucleic acid molecule comprising a coding sequence coding for a predetermined amino acid sequence, wherein the coding sequence is not a naturally occurring coding sequence and wherein, the coding sequence has afitcp(g) of at least below -0.1, and preferably below -0.2 for a predetermined host cell and afitSCι(g) of at least below 0.1 for a predetermined host cell.
20. A nucleic acid molecule according to claim 18 or 19, wherein the coding sequence is operably linked to expression control sequence that are capable of directing expression of the coding sequence in the predetermined host cell.
21. A host cell comprising a nucleic acid molecule as defined in claim 20.
22. A method for producing a polypeptide having the predetermined amino acid sequence, the method comprising culturing a host cell as defined in claim 21 under conditions conducive to the expression of the polypeptide and, optionally, recovery of the polypeptide.
23. A method for producing at least one of an intracellular and an extracellular metabolite, the method comprising culturing a host cell as defined in claim 21 under conditions conducive to the production of the metabolite, whereby preferably the polypeptide having the predetermined amino acid sequence is involved in the production of the metabolite.
Description  (OCR text may contain errors)

DSM IP Assets B.V. 2505 IWO

A method for achieving improved polypeptide expression

Field of the invention The present invention relates to a method for producing a polypeptide in a host cell, wherein the nucleotide sequences encoding the polypeptide have been modified with respect to their codon-usage, in particular the codon-pairs that are used, to obtain improved expression of the nucleotide sequence encoding the polypeptide and/or improved production of the polypeptide.

Background of the art

The present invention relates to improved methods for producing polypeptides. Numerous approaches have been applied in generating strains for protein over-expression and/or production. This includes, but is not limited to, making strains with multi-copies of the gene encoding the protein of interest (POI) and applying strong promoter sequences.

Each specific amino acid is encoded by a minimum of one codon and a maximum of six codons. Prior research has shown that codon usage in genes encoding the cell's polypeptides is biased among species (Kanaya, S, Y. Yamada, Y. Kudo and T. Ikemura (1999) Studies of codon usage and tRNA genes at 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238:143-155). Prior publications disclose optimization of codon use in a given host cell to improve polypeptide production (as example see WO 97/11086). More specifically, WO 03/70957 describes optimized codon use in filamentous fungi for producing plant polypeptides. In all these cases of 'classic' codon optimization, a native codon has been substituted by the most frequent codon from a reference set of genes, whereas the rate of codon translation for each amino acid is designed to be high (optimized).

More recently, in WO 03/85114 a harmonization of codon use was described which takes into effect the distribution of all codons in genes of the host organism, assuming that these effect protein folding. The availability of fully sequenced genomes of many organisms in recent years, e.g.

Bacillus subtilis (Kunst et al. 1997), Bacillus amiloliquefaciens, Aspergillus niger (Pel et al., 2007, Nat Biotech. 25: 221-231), Kluyvewmyces lactis, Sacchawmyces cerevisiae (http://www.ycastgcnomc.org/), various plant genomes, mouse, rat and human, has offered the possibility of analyzing different aspects of the gene sequences themselves in relation to their natural expression level (mRNA or protein level). A good example is codon usage (bias) analysis, and subsequent single-codon optimization. Note that single-codon optimization is herein understood to refer to codon optimization or codon harmonization techniques that focus on the optimization of codons as single independent entities, in contrast to codon-pair optimization, which is the topic of the current invention.

Whereas single-codon usage (bias) has been studied extensively before (for an overview, see Gustafsson et al., 2004, Trends Biotechnol. 22:346-353), there are only a few reports on codon pair usage and for optimization of codon-pairs.

The effect of a few specific codon-pairs on ribosomal frameshifts in E. coli has e.g. been investigated for the AGG-AGG codon-pair (Spanjaard and van Duin, 1988, Proc. Natl. Acad. Sci. USA 85:7967-7971; Gurvich et al., 2005, J. Bacteriol. 187:4023-432), and for UUU-YNN sites (Schwarz and Curran, 1997, Nucleic Acids Res. 25:2005-2011).

Gutman and Hatfield (1989, Proc. Natl. Acad. Sci USA 86:3699-3703) analyzed a larger set of sequences for all possible codon pairs for E. coli and found that codon pairs are directionally biased. In addition, they observed that highly underrepresented pairs are used almost used twice as frequently as overrepresented ones in highly expressed genes, whereas in poorly expressed genes overrepresented pairs are used more frequently. US 5,082,767 (Hatfield and Gutman, 1992) discloses a method for determining relative native codon pairing preferences in an organism and altering codon pairing of a gene of interest in accordance with said codon pairing preferences to change the translational kinetics of said gene in a predetermined manner, with examples for E. coli and S. cerevisiae. However, in their method, Hatfield and Gutman only optimize individual pairs of adjacent codons. Moreover, in their patent (US 5,082,767), it is claimed to increase translational kinetics of at least a portion of a gene by a modified sequence in which codon pairing is altered to increase the number of codon pairs that, in comparison to random codon pair usage, are the more abundant and yet more under-represented codon pairs in a organism. The present invention discloses a method to increase translation by a modified sequence in which codon pairing is altered to increase the number of codon pairs that, in comparison to random codon pair usage, are the more over-represented codon pairs in an organism. Moura et al. (2005, Genome Biology, 6:R28) analyzed the entire S. cerevisae ORFeome but did not find a statistically significant bias for about 47% of the codon pairs. The respective values differed from one species to another, resulting in "codon context maps" that can be regarded as "species-specific fingerprints" of the codon pair usage. Boycheva et al. (2003, Bioinformatics Jj)(8):987-998) identified two sets of codon pairs in E. coli referred to as hypothetically attenuating and hypothetically non-attenuating by looking for over- and under-represented codon pairs among genes with high and poor expression. However, they do not propose a method to apply this finding, nor gave any experimental prove for their hypothesis. Note that these groups are defined completely opposite to the ones defined by Gutman and Hatfield (1989, 1992, supra), who proposed a non-attenuating effect for highly underrepresented pairs in highly expressed genes.

Buchan, Aucott and Stanfield (2006, Nucleic Acids Research 34(3): 1015-1027) analyzed tRNA properties with respect to codon pair bias. As for the implications of biases in codon pair utilization, Irwin et al. (1995, J. Biol.

Chem. 270:22801-22806) demonstrated in E. coli that the rate of synthesis actually decreased substantially when replacing a highly underrepresented codon pair by a highly overrepresented one and increased when exchanging a slightly underrepresented codon pair for a more highly underrepresented. This is quite remarkable as it is rather the opposite of what one would expect given the influence of single codon bias on protein levels.

However, none of the above-cited art discloses how to optimize the codon-pair usage of a full-length codon sequence taking account of the fact that by definition codon pairs overlap and that therefore optimization of each individual codon pair affects the bias of the overlapping up- and downstream codon pairs. Moreover, none of the cited art discloses a method that combines optimization of both single codons as well as codon pairs. Codon pair optimization taking into account said codon pair overlapping and optional combination of said codon-pair optimization with single-codon optimization would greatly improve expression of the nucleotide sequence encoding the polypeptide of interest and/or improve production of said polypeptide.

There is thus still a need in the art for novel methods for optimization of coding sequences for improving the production a polypeptide in a host cell.

Summary of the invention

An object of the present invention is to provide a method for optimizing the coding sequence for efficient gene transcription and protein translation. To that effect, the invention provides a method of optimization of a nucleotide sequence encoding a predetermined amino acid sequence, whereby the coding sequence is optimized for expression in a predetermined host cell, the method comprising: (a) generating at least one original coding sequence that codes for the predetermined amino acid sequence; (b) generating at least one newly generated coding sequence from this at least one original coding sequence by replacing in this at least one original coding sequence one or more codons by a synonymous codon; (c) determining a fitness value of said at least one original coding sequence and a fitness value of said at least one newly generated coding sequence while using a fitness function that determines at least one of single codon fitness and codon pair fitness for the predetermined host cell; (d) choosing one or more selected coding sequence amongst said at least one original coding sequence and said at least one newly generated coding sequence in accordance with a predetermined selection criterion such that the higher is said fitness value, the higher is a chance of being chosen; and (e) repeating actions b) through d) while treating said one or more selected coding sequence as one or more original coding sequence in actions b) through d) until a predetermined iteration stop criterion is fulfilled.

In embodiments, the invention addresses aspects like single codon usage, codon harmonization, dinucleotide usage, and related to that codon-pair bias. The method can be performed by a computer program running on a computer that uses a mathematical algorithm for sequence analysis and sequence optimization that may be implemented in MATLAB (http ://www.mathworks. com/) .

In addition to positive codon optimization (e.g. for modulation of gene expression and protein production in a positive way), the invention also provides a method for adapting codons towards "bad" codon pairs (i.e. negative codon-pair optimization). The latter method is useful for control purposes as well as for modulating gene expression in a negative way.

Brief description of the drawings

It is observed that the present invention will be illustrated with reference to several figures which are only intended to illustrate the invention and not to limit its scope which is defined by the annexed claims and its equivalents. Figure 1 shows a computer arrangement on which the method of the invention can be performed.

Figure 2 shows a flow chart of an embodiment of the invention.

Figure 3 shows a distribution of codon pair bias values for 3,721 sense:sense codon pairs in different organisms. The numbers in the top right corner of each histogram are the standard deviations for the observed distribution; the mean values (not shown) are between -0.06 and - 0.01 for all organisms.

Figure 4 shows the correlation in codon pair bias of various organisms. The correlation coefficient is shown in the top right corner of each subplot. Figure 5 shows a codon bias map for A. niger. The bias values range from -0.67 to 0.54, where in other organisms they might even get slightly above +-0.9 (see also Figure 3). The highest intensities of black in these diagrams represent values of 0.9 (Figures 5 A and 5 C for the positive values, green in the original) and -0.9 (Figures 5B and 5D for the negative values, red in the original). In Figures 5 A and B the rows and columns are sorted according to the codons their alphabetical order. In Figures 5C and 5D the rows are sorted according to the alphabetical order of the third position nucleotide as first sorting criterion and the middle position nucleotide as second sorting criterion, and first position nucleotide as third sorting criterion.

Figure 6 shows a codon bias map for B. subtilus. The bias values range from -0.97 to 0.87, where in other organisms they might even get slightly above +-0.9 (see also Figure 3). The highest intensities of black in these diagrams represent values of 0.9 (Figure 6A for the positive values, green in the original) and -0.9 (Figure 6B for the negative values, red in the original).

Figure 7 shows a codon bias map for E. coli. The bias values range from -0.97 to 0.85, where in other organisms they might even get slightly above +-0.9 (see also Figure 3). The highest intensities of black in these diagrams represent values of 0.9 (Figure 7A for the positive values, green in the original) and -0.9 (Figure 7B for the negative values, red in the original).

Figure 8 shows a codon bias map for 479 highly transcribed genes of A. niger, analogous to the previous Figures 5-7. The highest intensities of black in these diagrams represent values of 0.9 (Figure 8A for the positive values, green in the original) and -0.9 (Figure 8B for the negative values, red in the original). The maximum bias value in this group is 0.91 the minimum is -1, i.e. some possible codon pairs do not occur at all, although their individual codons and the encoded amino acid pair do. This might be a result of the smaller size of 188,067 codon pairs, compared to 5,885,942 in the full genome. However, the main reason will be the real under representation of such pairs due to selection in highly expressed genes. Figure 9 shows a Scatter plot of bias in a group of 479 highly expressed genes (vertical axis) versus the bias in all genes (horizontal) of A. niger. All 3,721 codon pairs not involving stop codons are shown. Colours from light grey to black were assigned according to the absolute values of the z-scores in the overall genome, i.e. light dots in the plot do not have a significant bias in all genes), as were sizes according to the absolute z-scores in the highly expressed group, i.e. very small dots do not have a significant bias there (here |z-score|<1.9). The solid black line indicates where both bias values are equal; the dashed line shows the best linear approximation of the actual correlation (identified by principal component analysis); its slope is around 2.1.

Figure 10 Fitness values of the 4,584 A. niger genes compared to the logarithm of their transcription levels. The correlation coefficient is -0.62. Figure 11 shows single codon vs. codon pair optimization. The wild type

does not fit on this plot (it would be far to the right and above). It is clear that the cpi parameter determines a trade-off between single codon and codon pair fitness. The optimal gene is always the one with the lowest values for fitsc and fitcp. Given the position of the dots, it is therefore not clear for which value of cpi the best gene could be obtained, since we do not know yet whether single codon usage or codon pair usage is more important. Although, the examples provides strong evidence that codon pair fitness is very important in addition to single-codon fitness, which means that cpi should be chosen at least >0.

Figure 12 shows two diagrams that show the sequence quality of the first 20 (out of 499) codons of the aforementioned FUA (see also Example 2). The black dots indicate the desired codon ratios, whereas the x-marks show the actual ones (in the whole gene), connected via a dashed line. Single codon fitness can then be interpreted as the average of the lengths of these dashed lines (note that for codons where desired and actual ratio are equal, as for example TGG (which has no synonymous codons) on position 4 and 5, this "length" is zero; note also that "length" can never be negative). The black bars, in turn, show the weights of the pair formed by the two adjacent codons. The black dots (in the middle, below the bars) indicate the minimum weight of any codon pair that encodes the same dipeptide. The codon pair fitness is then the average height of these bars (note that height as used here can well be negative).

Figure 13 depicts the convergence of fitCOmbι using the described genetic algorithm approach of the invention for optimization of the amyB gene that results in SEQ ID NO. 6.

Figure 14 depicts, for reasons of explanation, a part of a single-codon distribution diagram, like one is shown for example in Figure 15. The two graphs indicate the single-codon usage for the two synonymous codons that code for phenylalanine: UUU (top) and UUC (bottom). The X- axis and Y- axis of both graphs goes from 0% to 100%. The grey histogram is a codon-usage histogram, normalized for each amino acid (group of synonymous codons), for a group of 250 highly expressed A. niger genes, where the genes are binned in groups having 0%, >0 - <10%, 10 - <20%, ... , 90 - <100%, 100%. For example, 50% of the highly-expressed genes fall in the group with 0% usage of the UUU codon, and consequently 100% usage of the UUC codon for coding phenylalanine. The white bar gives the codon-usage of gene A (WT amyB in this case) in similar bins as for the histogram; thus 100% in bin 20-30% (20% with 3/15 codons being UUU) for gene A, and consequently 100% in bin 80-<90% (80% with 12/15 being UUC). The black bar gives the statistics for gene B (the single-codon optimized variant for amyB in this case). In a similar way, one can create a matrix of 16 times 4 graphs, showing statistics for all 64 codons, see for example Figure 15. Figure 15 (parts 1 and 2) depicts the single-codon frequency for the single-codon optimized amyB gene (black) versus the wild-type amyB gene (white). The grey histogram depicts the statistics for 250 highly-expressed genes in A. niger. It is clear that certain codons, like the one for cysteine (UGU/UGC), histidine (CAU/CAC), tyrosine (UAU/UAC) and others were subject to real improvements.

Figure 16 (parts 1 and 2) depicts the single-codon frequency for an amyB gene that has been optimized with respect to both single-codon and codon-pairs (black) versus the wild-type amyB gene (white). The grey histogram depicts the statistics for 250 highly-expressed genes in

A. niger. It is clear that these graphs highly resemble the situation for the single-codon optimized gene depicted in Figure 15.

Figure 17 depicts a part of the full diagram (Figure 18) with single-codon and codon pair statistics for the WT amyB gene of A. niger. On the X-axis, one finds the subsequent codons in a gene starting at position 1 with the start-codon ATG. The black dot '.' indicates the target single-codon ratio for the codon at this position with respect to its synonymous codons. For ATG this is 1.0 (100%). The cross 'x' is the actual codon ratio it the shown gene; a dotted line shows the difference between the target ratio and the actual ratio. The codon-pair weight is a value between -1 and 1. The bar indicates the actual codon-pair weight of the adjacent codons, while the pentagram indicates the weight of the optimal achievable synonymous codon-pair (not taking into account the neighboring pairs). For example the first bar is -0.23 which is the weight for 'ATG-GTC, second is 0.66 being the weight for 'GTC -GCG'.

Figure 18 depicts the single codon and codon pair statistics for SEQ ID NO. 2 (WT AmyB).

Figure 19 depict the single codon and codon pair statistics for SEQ ID NO. 5 (single codon-optimized AmyB). Figure 20 depict the single codon and codon pair statistics for SEQ ID NO. 6 (single codon and codon pair optimized WT AmyB).

Figure 21 depicts a plasmid map of expression vector pGBFINFUA-1. Figure 21 also provides a representative map for plasmid pGBFINFUA-2 and pGB FINFU A-3. All clones originate from the pGBFIN-12 (described in WO99/32617) expression vector. Indicated are the glaA flanking regions relative to the variant sequences of the amyB promoter and the A. niger amyB cDNA sequence encoding alpha-amylase. The E. coli DNA can be removed by digestion with restriction enzyme Notl, prior to transformation of the A. niger strains.

Figure 22 depicts a schematic representation of integration through single homologous recombination. The expression vector comprises the selectable amdS marker, and the glaA promoter connected to the amyB gene. These features are flanked by homologous regions of the glaA locus (3' glaA and 3" glaA, respectively) to direct integration at the genomic glaA locus.

Figure 23 depicts alpha-amylase activity in culture broth for A. niger strains expressing three different constructs. Depicted is the alpha-amylase activity in culture broth of A. niger strains expressing a native amyB construct, wherein (1) the translation initiation sequence and the translation termination sequence were modified (pGBFINFUA-1), and (2) the translation initiation sequence, the translation termination sequence and the single-codon usage were modified (pGBFINFUA-2), and (3) the translation initiation sequence, the translation termination sequence and the single-codon usage and codon-pair usage were modified (pGBFINFUA-3) according a method of the invention. Alpha-amylase activities are depicted in relative units [AU], with the average of the 6 one-copy strains of the FUAl group of 10 strains at day 4 set at 100%. The ten transformants per group indicated are independently isolated and cultivated transformants.

Figure 24 (A and B) depicts the single-codon frequency for the single-codon optimization for Bacillus species. An explanation of the sub-graphs is given by Figure 14. The grey histogram presents the codon distribution for the 50 highest expressed genes in B. subtilis, see text. The black bars indicate the target single-codon frequency.

Figure 25 depicts the single codon and codon pair statistics for SEQ ID NO. 14 (1/3), SEQ ID NO. 17 (2/3) and SEQ ID NO. 14 (3/3), the sequenced optimized using codon pair + single codon (1/3), single-codon (2/3), and negative codon-pair + single codon optimization (3/3), respectively. See Figure 17 for an explanation of the graph.

Figure 26. E.coli/Bacillus shuttle vector pBHA-12. The multiple cloning sites (MCS) 1 and 2 are depicted.

Figure 27. An example of cloning of a gene in the E.coli/Bacillus shuttle vector pBHA- 12. The Figure shows the cloned part A and B (grey arrows) of the SEQ ID NO. 9. The cloning sites of the part IA are depicted: Ndel and BamHl, for the part IB Smal and Kpnl. The E.coli part was excised using PVMII. Detailed description of the invention

In addition to single codon bias, other structures in the nucleotide sequence are likely to influence protein expression as well, e.g. dinucleotides or repeats of certain short nucleotide sequences (codon usage after all can be interpreted as a pattern in tri-nucleotide sequences in line with the reading frame). This work presents a method for identifying a preference for certain codon pairs, i.e. whether codons appear in the gene as if they were selected according to the identified codon usage ratios, but then distributed randomly in the gene (with respect to the amino acid sequence), or whether some codons appear more often next to certain codons and less often next to others.

pair 1 pair 3 pair 5

ATG'GTT'GCATGGTGGTCT'... pair 2 pair 4 pair...

An analysis of codon pairs also covers other aspects, namely dinucleotide usage around the reading frame borders and a possible preference for certain single nucleotides next to a codon. The present invention discloses methods for generating a codon-pair bias table for a given host organism whereby either all identified ORFs of sequenced full genomes are used as input or selected groups of genes, e.g. highly expressed genes. The present invention discloses a method wherein a codon-pair bias table thus identified is subsequently applied for optimization of codon-pair distribution in a gene of interest (GOI) for improving the expression of the corresponding protein of interest (POI).

Single codon optimization offers a good starting point for improving expression levels of proteins of interest. Whereas others tried to overcome drawbacks resulting from the presence of rejected codons in the gene of interest by adaptation of the host organism, inserting additional copies of tRNA genes for tRNAs with low abundance (e.g. Stratagene BL-21 CodonPlus™ competent cells, Novagen Rosetta™ host strains, both E. coli), the present inventors have focused on the adaptation of the genes of interest themselves. Unwanted codons in a genetic sequence have been replaced by synonymous ones so that the single codon distribution of the resulting sequence was as close as possible to previously identified desired codon ratios.

This codon harmonization, however, still has a very large number of possible genes that are equally "optimal" since the overall codon distribution in an optimized gene is the selection criterion, so further desired properties of the codon sequence can easily be taken into account, for example the absence of certain enzyme's restriction sites or codon pairs known to cause frameshifts. One step further, one could optimize codon pair usage to a limited extent. But when optimizing codon pairs of a gene, e.g. towards the usage of the most abundant ones, the single codon usage of the resulting sequence might not be close to the optimum, since there might be preferred codon pairs consisting of underrepresented single codons, so a balance between single codon and codon pair optimization must be found. The present invention discloses methods that allow balancing both single codon and codon pair optimization. Codon pair optimization taking into account codon pair overlapping and optional combination of said codon-pair optimization with single-codon optimization greatly improve expression of the nucleotide sequence encoding the polypeptide of interest and/or improve production of said polypeptide. In the context of this invention, a nucleotide coding sequence or coding sequence is defined as a nucleotide sequence encoding a polypeptide. The boundaries of the coding sequence are generally determined by the start codon (usually ATG in eukaryotes, while it can be one of ATG, CTG, GTG, TTG in prokaryotes) located at the beginning of the open reading frame at the 5' end of the mRNA and a stop codon (generally one of TAA, TGA, TAG, although exceptions to this 'universal' coding exists) located just downstream of the open reading frame at the 3' end of the mRNA. A coding sequence can include, but is not limited to, DNA, cDNA, RNA, and recombinant nucleic acid (DNA, cDNA, RNA) sequences (note that it is well known in the art that Uracil, U, replaces the deoxynucleotide Thymine, T, in RNA). If the coding sequence is intended for expression in a eukaryotic cell, a polyadenylation signal and transcription termination sequence will usually be located 3' to the coding sequence. A coding sequence comprises a translational initiator coding sequence, and optionally a signal sequence, and optionally one or more intron sequences. Even though the terms "coding sequence" and "gene" strictly do not refer to the same entity, both term are frequently used interchangeably herein and the skilled person will understand from the context whether the term refers to a full gene or only its coding sequence.

Method and computer arrangement for single codon and/or codon pair adaptation

As for the single codon usage properties of highly expressed genes, a "manual" comparison of single codon ratios in all genes and a group of highly expressed ones has lead to some "desired codon ratios" for the improvement of genes with respect to their expression level.

Single codon adaptation of a gene can then be performed by: (1) calculating the actual ratios in the gene, repeatedly picking a codon (e.g. randomly) whose desired ratio is lower than the actual one and replacing it by a synonymous one with a too low ratio; or (2) calculating the desired number of each codon using the "desired codon ratios", making groups of synonymous codons, and repeatedly picking a codon (e.g. randomly) from a synonymous group coding for the pre-specified amino acid, for each position in the gene.; making multiple variants using method (1) and/or (2) and based on additional selection criteria picking the most relevant gene (e.g. wanted and unwanted restriction sites and/or folding energy). Yet this approach is not suitable for codon pair adaptation, firstly because visual inspection of bias data for all codon pairs is out of the question in view of the complexity and secondly because altering of one codon pair, which means replacing at least one of the two participating codons, will also affect at least one of the adjacent codon pairs, so "desired codon pair ratios" would be unachievable. Because of the constraints implied by this, a deterministic approach was considered too complex and not promising enough and a "genetic algorithm" approach was then chosen.

It is observed that the term "genetic algorithm" may be confusing in the sense that it seems to relate to genetic engineering. However, a "genetic algorithm" is an approach from computer science that is used to approximate solutions to multidimensional optimization problems (Michalewicz, Z., Genetic Algorithms + Data Structure = Evolution Programs, Springer Verlag 1994; David E. Goldberg. Genetic Algorithms in Search, Optimization and Machine Learning. Addison- Wesley, Reading MA, 1989; http://en.wikipedia.org/wiki/Genetic_algorithm). In the present invention, this approach is used in solving the optimization problem of selecting the "best" possible gene, i.e. coding sequence for a particular protein of interest. In this approach, each position in the gene, i.e. each codon can be considered one dimension, with the set of values being discrete and determined by the available synonymous codons.

Generally, in a genetic algorithm, at first a set of possible "solutions" to the problem is often generated randomly, or by variations on initial provided solutions (although many other methods approaches exist). This set is called "population"; its elements are "individuals" or "chromosomes", mostly represented by vectors (in the mathematical sense) containing coordinates for each dimension. Since genetic algorithms were modeled after processes involved in natural selection, much of the terminology is borrowed from genetics. However, since they are (unlike in this case) mostly applied in the field of computer science and to, but also some example to application of genetic algorithms in biological science problems have been presented, e.g. for protein secondary structure prediction (Armano et al. 2005 BMC Bioinformatics 1(6) Suppl. 4:S3); in silico metabolic network optimization (Patil et al. 2005 BMC Bioinformaiics. 23(6):308); clustering gene expression data (Di Gesu et al. 2005 BMC Bioinformatics.7(6):289). In the present case, a vector contains codons. From that population, new individuals are created by altering certain positions of an existing individual ("mutation") or by combining a part (i.e. certain coordinates) of an individual with another part (i.e. the coordinates for the other dimensions) from another individual ("crossover"). It is then examined how good these individuals are (since the new ones are also possible solutions to the initial optimization problem) and the better ("fittest") of the individuals are taken again as initial population for generating new individuals ("next generation"; e.g. , the best 10, 20, 30, 40, 50, 60% are kept, but many other possibilities exist to selecting a subset for offspring for obtaining a convergence toward fitter individuals, e.g. roulette wheel selecting, see Michalewicz, Z, 1994). When allowing the best individual from the initial population to be taken over to the next generation, it is ensured that with every population the quality of the possible solutions gets better or at least stays the same. It is then assumed that with a run of this algorithm for many generations (= iterations; some hundred to several thousand, depending on the complexity of the problem) one will get a solution close to the optimum. Genetic algorithms have been investigated closely in computer science, including properties such as optimal proportion of population size and number of generations, how to prevent the algorithm from getting stuck in local optima etc., but this should not matter much here now. For information on how to set these parameters for the actual optimization procedure, see the description implemented genetic algorithm in MATLAB in Example 2. This will be explained in detail with reference to Figure 2. Figure 2 shows a flow chart of a genetic algorithm for gene optimization. Such a genetic algorithm can be performed on a suitably programmed computer, an example of which will be shown in and explained first with reference to Figure 1. Figure 1 shows an overview of a computer arrangement that can be used to carry out the method according to the invention. The arrangement comprises a processor 1 for carrying out arithmetic operations.

Note that genetic algorithms are generally non-deterministic as they involve randomized steps (e.g. randomized selection criteria and/or randomized operator choice and/or randomized generation of potential solutions), however, exceptions exist that perform in a deterministic way. "Genetic algorithms" is a generic tool for those algorithms that deal with a group (called population) of potential solutions, which is by screening and/or selection and/or removal, and/or (re)introduction of (newly) generated solutions driven toward and optimal solution by using one or multiple objectives. Considering this definition, also methods described as evolutionary programming, evolutionary algorithms, classic genetic algorithms, real-coded genetic algorithms, simulated annealing, ant algorithms, and also Monte-Carlo and chemotaxis methods, belong to a similar class of algorithms, opposite to methods that are based on the convergence of a single potential solutions toward an optimal solution using a deterministic algorithm, like linear programming and gradient algorithms. Furthermore, a skilled person will understand from the context whether another original term refers to the same class of algorithms. Moreover, although a genetic algorithm is the preferred method, we do not exclude any other method than genetic algorithms for solving the single-codon and/or codon-pair optimization problem as described within this invention.

The processor 1 is connected to a plurality of memory components, including a hard disk 5,

Read Only Memory (ROM) 7, Electrically Erasable Programmable Read Only Memory (EEPROM) 9, and Random Access Memory (RAM) 11. Not all of these memory types need necessarily be provided. Moreover, these memory components need not be located physically close to the processor 1 but may be located remote from the processor 1.

The processor 1 is also connected to means for inputting instructions, data etc. by a user, like a keyboard 13, and a mouse 15. Other input means, such as a touch screen, a track ball and/or a voice converter, known to persons skilled in the art may be provided too.

A reading unit 17 connected to the processor 1 is provided. The reading unit 17 is arranged to read data from and possibly write data on a data carrier like a floppy disk 19 or a CDROM 21. Other data carriers may be tapes, DVD, memory sticks etc. as is known to persons skilled in the art. The processor 1 is also connected to a printer 23 for printing output data on paper, as well as to a display 3, for instance, a monitor or LCD (Liquid Crystal Display) screen, or any other type of display known to persons skilled in the art.

The processor 1 may be connected to a communication network 27, for instance, the Public Switched Telephone Network (PSTN), a Local Area Network (LAN), a Wide Area Network (WAN), etc. by means of I/O means 25. The processor 1 may be arranged to communicate with other communication arrangements through the network 27.

The data carrier 19, 21 may comprise a computer program product in the form of data and instructions arranged to provide the processor with the capacity to perform a method in accordance with the invention. However, such computer program product may, alternatively, be downloaded via the telecommunication network 27. The processor 1 may be implemented as stand alone system, or as a plurality of parallel operating processors each arranged to carry out subtasks of a larger computer program, or as one or more main processors with several sub-processors. Parts of the functionality of the invention may even be carried out by remote processors communicating with processor 1 through the network 27. Now the genetic algorithm of Figure 2 will be explained, as may be performed on processor 1 when it runs a computer program stored in its memory.

In action 32 the computer generates one or more genes that code for a predetermined protein. This can be done by taking data to that effect from a table stored in the memory of the computer. Such genes may e.g. be:

> ATG'GTT'GCA'TGG'TGG'TCT' ...

> ATG'GTA'GCA'TGG'TGG'TCA'...

> ...

For the purpose of the algorithm, these generated genes are termed "original genes". After action 32, the computer program performs one or more iteration loops by performing actions 34-40 one or more times.

In action 34, the computer program generates new genes by replacing one or more of the codons in the original gene(s) by synonymous codons such that the newly generated gene(s) still code for the predetermined protein (crossover & mutation process). To be able to do so, the memory of the computer stores a codon usage table which shows which codons code for which amino acids. (Note that deviations from the "universal code" exist and are taken into account if this is the case for the specified host organisms, see for example Laplaza et al, 2006, Enzyme and Microbial Technology, 3^:741-747). Knowing the sequence of amino acids in the protein, the computer program can select alternative codons from the table as are well known in the art. Using the example of action 32, the newly generated genes may be (indicated in bold): o ATG'GTT'GCA'TGG'TGG'TCT' ... o ATG'GTA'GCA'TGG'TGG'TCA'...

> ATG'GTT'GCA'TGG'TGG'TCA' ... o ATG'GTA'GCA'TGG'TGG'TCA'... > ATG'GTA'GCC'TGG'TGG'TCA' ...

In action 36, a quality value of all genes including the original and the newly generated genes is determined by the computer program using a fitness function which determines at least one of codon fitness and codon pair fitness. Examples of such fitness functions will be explained in detail below in the section "Performing codon pair optimization". In action 38, a number of genes showing a best fitness based on the fitness function are selected for taking part in the "breeding process" (crossover and mutation), and a number of genes showing worst fitness based on the fitness function are selected for removal from the population. These numbers may be predetermined numbers or depend on a predetermined amount of improvement of fitness. The selection of those genes might be deterministic, but generally a stochastic process is followed where the "fittest genes" having a higher change for being selected for breeding, and the opposite for deletion from the population. This method is called roulette -wheel selection.

The resulting selected genes for breeding may e.g. be (non-selected genes are shown with a deletion line):

ATG'GTT'GCA'TGG'TGG'TCT' ... *■ ATG 'GTA 'fiCA 'TGG 'TGG 'TC A '

ATG'GTT'GCA'TGG'TGG'TCA' ... — ATG 'GTA' GCA 'TGG 'TGG 'TCA' w ATG'GTA 'GCCTGG'TGG'TC A '

In action 40, the computer program tests whether one or multiple termination criteria are fulfilled. Often one of the termination criteria is a predetermined maximum number of iterations. Alternative criteria are checking if the fitness obtained by the selected genes is improved with at least a minimum threshold value relative to the fitness of the original genes, or checking if the fitness obtained by the selected genes is improved with at least a minimum threshold value relative to the fitness of the gene with had best fitness n iterations ago (preferably n is a value in <10,100> is chosen). If the overall termination coterie is not fulfilled the computer program jumps back to action 34 while treating the selected genes as "original genes". If, in action 40, the computer program establishes that the improvement is below the minimum threshold value further iteration of the actions 34-38 does not make much sense and the computer program continues with action 42.

It is to be understood that any other suitable iteration stop criterion, like the number of iterations performed, can be used in action 40 to leave the iteration actions 34-40 and continue with action 42.

In action 42, the gene with the best fitness amongst all selected genes is selected and presented to the user, e.g. via the monitor or via a printout by means of printer.

In the case of gene adaptation using a genetic algorithm, it has to be assured that the crossover is always performed at a reading frame position, because otherwise the resulting amino acid sequence might be changed when combining one nucleotide of one and two nucleotides of another codon. For better convergence, a modified mutation operator is proposed that for this mutation operator only those synonymous codon replacements have been allowed that result in at least one of better single codon or better codon pair usage. So an important question for codon pair optimization now is how to measure the quality of the individuals. This so-called fitness function can be regarded the central part of the genetic algorithm, since it is the actual function to be optimized. In the present invention, a preferred approach is to assign a real number (called weight) to each codon pair and take the average of the weights in a gene as its "fitness", thus resulting in a function to be minimized.

It the current description, the inventors describe the process of gene optimization as a minimization problem. This is a rather arbitrarily approach. Note that, if a function /were to be maximized, one could as well look for the minimum of -/, so this is no restriction to generality.

Hence, a method for determining codon pair weights has to be identified, where codon pairs considered good for expression level have a low weight and pairs considered bad a high one.

Identification of codon pair weights for gene adaptation

For identification of codon pair weights that relate to a higher transcription/expression level, and which may serve as input for adaptation of codon pair usage, the following methods may be applied, which are herein exemplified by A. niger, for which a transcription levels for most of the expressed genes are known, and for B. subtilis, for which data on transcription levels was available and also a set of 300 highly expressed genes.

In A. niger, where a complete ranking extracted from GeneChip data was available for the aforementioned set of 4,584 actually expressed genes (see Example 1), the mean codon pair weights of each gene (i.e. the equivalent of the fitcp{g) values) were calculated. Then the genes were sorted according to fitness values (ascending order) and expression level (descending order). Since highly expressed genes are supposed to have low codon pair fitness values, these two rankings would be equal when using ideal codon pair weights, so a comparison of these two rankings can give information about the quality of the weights used in the fitness function (where slightly more attention was given to the "correct" ranking of the highly expressed genes than to the ranking of the mediocre ones). Additionally, the correlation coefficient (covariance divided by the standard deviation of each variable) between ranking and average codon pair weights of the 4,584 genes was calculated. Several possible sets of weights may be used in the methods of the invention, including on or more selected from the group consisting of: (i) bias values from the whole genome; (ii) bias values from a group of highly expressed genes; (iii) bias with all the values that do not have a certain minimum z-score set to zero (whereby the z-score is determined as described in Example 1.1.4); (iv) bias values raised to the power of 2 or 3, 4, 5 or higher (to give highly preferred or rejected codons a lower/higher influence); (v) z-scores themselves; (vi) difference of bias values/z-scores from the highly expressed group and the full genome; and, (vii) combinations of one or more of (i) - (vi).

For the genetic algorithm, their negations have been used, since preferred codon pairs had been arbitrarily identified with positive values, whereas the genetic algorithm performs minimization. This applies to all the above-mentioned weights.

A more preferred weight matrix may be obtained - as described above - by calculating the codon pair "bias" in a highly expressed group using expected values calculated based on the codon ratios of the whole genome. Let rsf (ck ) still denote the single codon ratio of ct in the whole genome data set and n &h uc c \\ the occurrences of a pair (q,c/) in the highly expressed

group, then the calculation of the "combined expected values" "^"((ς,^)) corresponds to

combi / / w all / \ all / \ X 1 hieh / / \\ neV (.(C1 , C ^) = Tx (C1 ) Tx (Cj ) - 2^ n obs ((C k , Ci )) c^ ^syn{cl ) C1 esyiiCj ) and thus

Where w((ci,cj)) is defined as a weight of a codon pair (cuq) in a sequence g of codons.

Note that since the optimization function will look for a minimum average weight, the two terms of the numerator have been reversed compared to the equation for the bias values, but this does not affect the correlation with the expression levels other than that it changes the sign.

Unlike all other weight sets tested, codon pairs involving codons that are more underrepresented in the highly expressed group get a slight disadvantage here. Thus, these weights are the only ones that also reflect the different single codon bias of the highly expressed group and all genes. Using these weights carries the risk of rejecting some codon pairs that actually have a positive bias in the highly expressed group, but consist of (in the highly expressed group) rarely used codons. However, since our desired single codon ratios are usually not identical to those in the group of genes with high expression, but more "extreme" than these, single codon optimization would replace these underrepresented anyway, so we can consider the weights described above very convenient for codon pair optimization. Thus, although the codon pair weights also reflect single codon bias to a limited extend, for the optimization, single codon usage is regarded as a separate, additional issue. Optimization of single codons and codon pairs using a genetic algorithm

In the method of the invention preferably a computer arrangement programmed to perform a genetic algorithm as described herein above is used to perform codon pair adaptation or combined single codon and codon pair adaptation have been performed. Applying a genetic algorithm for single codon adaptation is also possible and not excluded from the invention, but here undesired codons can be replaced by synonymous codons without constraints with respect to neighboring codons and therefore using a genetic algorithm is not really necessary.

As for codon pairs, changing a single codon will usually alter the weight of two codon pairs, and therefore codon pair optimization is heavily constrained because a single codon change replacing an unwanted codon pair will always change another codon pair, and this is not necessarily a change for the better, and correcting a change for the worse in an adjacent codon pair will then again alter another pair, and so on.

For the mutation operator, only those alterations of the codon sequence have been allowed that did not change the encoded peptide sequence and that improved at least one of single codon fitness and codon pair fitness, i.e. before changing a codon the mutation operator looks for synonymous codons that are either underrepresented (according to the desired single codon ratios) or one where the two codon pairs it is involved in have better weights. It is selected randomly which one of the two types of mutation is performed. Performing the former

"mutation" operator on every single codon is sufficient for creating a single-codon-optimized gene without any use of the genetic algorithm.

The quality of a gene is determined considering two aspects, namely single codon "fitness" and codon pair "fitness". The latter is simply the average of the weights w((c(k), c(k+l)) of all codon pairs in a sequence g of codons (or gene). I.e., when g again symbolizes the sequence of codons, \g\ its length (in codons) and c(k) its k-th codon:

1 I Issll--ii fitcp(g) = - - ∑w((c(k),c(k + l))

S ~1 Jt=i

Single codon fitness is defined to be the difference of the actual codon ratios in the gene and the target codon ratios, normalized for the number of occurrences of every codon. Single codon ratios are defined and may be determined as described in Example 1.1.2 herein. Let r'"rget (c(k)) be the desired ratio (or frequency) of codon Ck and rs 8 c (c(k)) as before the actual ratio in the gene g, then the single codon fitness is defined as

IsI fit* (S) = ∑\Cge' (c(k)) - ri (c(k))\

S Jt=i Thus, fitsc can reach values in [0,1] with the optimal sequence being close to 0, whereas fitcp is limited by the weights, which here are also in [-1,1].

To optimize for both aspects, in an embodiment, a combined fitness function has been introduced:

fitcombi

cpi + fitsc(g)

Here, cpi, which stands for "codon pair importance", is a real value greater than zero and determines which of the two fitness functions has more influence on the combined fitness. With cpi close to zero, the denominator approaches zero when fitsc(g) gets better (i.e. also close to zero) and thus small changes in fit sc(g) influence fitCOmbι(g) more than small changes in fit cp(g), whereas with a high cpi slight improvements in fit cp(g) may have a larger effect on fitcombι(g) than medium improvements in fit sc(g). Note that fit combι values that are obtained using different values of cpi are not comparable (cpi close to 0 might result in fitcombi values close to -100, whereas is fitcomh usually between 0 and -1 for cpi > 0.2).

In an embodiment, a "penalty" is added if g contains certain unwanted sequences, e.g. restriction sites or sequences resulting in undesired secondary structures in mRNA. This may be useful when constructing synthetic genes, but in itself is unrelated to optimization of single codon and codon pair usage. A modified fitness function becomes:

fitcombl (g) = . r . . + P(g) cpι + fitsc (g)

where P(g) denotes a penalty function that creates a positive weight in case an unwanted sequence structure is part of gene g.

It is to be understood that in the embodiments of the invention herein the nucleotide and amino acid sequences may be theoretical sequences that exist only on e.g. paper or another preferably computer readable data carrier, or they may exist as a tangibly, physically created embodiment. In a first aspect the invention therefore relates to a method of optimization of a nucleotide coding sequence that codes for a predetermined amino acid sequence, whereby the coding sequence is optimized for expression in a predetermined host cell. The method preferably comprises the steps of: (a) generating at least one original coding sequence that codes for the predetermined amino acid sequence; (b) generating at least one newly generated coding sequence from this at least one original coding sequence by replacing in this at least one original coding sequence one or more codons by a synonymous codon; (c) determining a fitness value of said at least one original coding sequence and a fitness value of said at least one newly generated coding sequence while using a fitness function that determines at least one of single codon fitness and codon pair fitness for the predetermined host cell; (d) choosing one or more selected coding sequence amongst said at least one original gene and said at least one newly generated coding sequence in accordance with a predetermined selection criterion such that the higher is said fitness value, the higher is a chance of being chosen; and, (e) repeating actions b) through d) while treating said one or more selected coding sequence as one or more original coding sequence in actions b) through d) until a predetermined iteration stop criterion is fulfilled. According to an embodiment of the invention, the method preferably comprises the steps of: (a) generating at least one original coding sequence that codes for the predetermined amino acid sequence; (b) generating at least one newly generated coding sequence from this at least one original coding sequence by replacing in this at least one original coding sequence one or more codons by a synonymous codon; (c) determining a fitness value of said at least one original coding sequence and a fitness value of said at least one newly generated coding sequence while using a fitness function that determines codon pair fitness for the predetermined host cell; (d) choosing one or more selected coding sequence amongst said at least one original gene and said at least one newly generated coding sequence in accordance with a predetermined selection criterion such that the higher is said fitness value, the higher is a chance of being chosen; and, (e) repeating actions b) through d) while treating said one or more selected coding sequence as one or more original coding sequence in actions b) through d) until a predetermined iteration stop criterion is fulfilled.

According to another embodiment of the invention, the method preferably comprises the steps of: (a) generating at least one original coding sequence that codes for the predetermined amino acid sequence; (b) generating at least one newly generated coding sequence from this at least one original coding sequence by replacing in this at least one original coding sequence one or more codons by a synonymous codon; (c) determining a fitness value of said at least one original coding sequence and a fitness value of said at least one newly generated coding sequence while using a fitness function that comprises determining single codon fitness and codon pair fitness for the predetermined host cell; (d) choosing one or more selected coding sequence amongst said at least one original gene and said at least one newly generated coding sequence in accordance with a predetermined selection criterion such that the higher is said fitness value, the higher is a chance of being chosen; and, (e) repeating actions b) through d) while treating said one or more selected coding sequence as one or more original coding sequence in actions b) through d) until a predetermined iteration stop criterion is fulfilled.

In the methods preferably the predetermined selection criterion is such that said one or more selected coding sequence have a best fitness value according to a predetermined criterion. The methods according to the invention, may further comprises, after action e): selecting a best individual coding sequence amongst said one or more selected coding sequences where said best individual coding sequence has a better fitness value than other selected coding sequences. In the methods of the invention, the said predetermined iteration stop criterion preferably is at least one of: (a) testing whether at least one of said selected coding sequences have a best fitness value above a predetermined threshold value; (b) testing whether none of said selected coding sequences has a best fitness value below said predetermined threshold value; (c) testing whether at least one of said selected coding sequences has at least 30% of the codon pairs with associated positive codon pair weights for the predetermined host cell in said original coding sequence being transformed into codon pairs with associated negative weights; and, (d) testing whether at least one of said selected coding sequences has at least 10, 20, 30, 40, 50, 60, 70, 80 or 90% of the codon pairs with associated positive weights above 0 for the predetermined host cell in said original coding sequence being transformed into codon pairs with associated weights below 0.

In the methods of the invention the fitness function preferably defines single codon fitness by means of:

fitc(g) = l00 - - rc s (c(k))\ -l00

where g symbolizes a coding sequence, \g\ its length, g(k) its k-th codon, rc fargef (c(k)) is a desired ratio of codon c(k) (APPENDIX 2; CR vectors) and r/ (c(k)) an actual ratio in the nucleotide coding sequence g.

In the methods of the invention the fitness function preferably defines codon pair fitness by means of: i I Issll--ii fitcp(g) =-—- ∑w((c(k),c(k + ϊ))

where w((c(k), c(k + I)) is a weight of a codon pair in a coding sequence g, \g\ is length of said nucleotide coding sequence and c(k) is k-th codon in said coding sequence. More preferably, in the methods of the invention the fitness function is defined by means of:

ft ( Λ - ^ (g) cpι + βsc(g)

where

fitsc (g) = —

cpi is a real value greater or equal zero, fitcp(g) is codon pair fitness function, fitsc(g) is a single codon fitness function, w((c(k), c(k + I)) is a weight of a codon pair in a coding sequence g

(APPENDIX 3; CPW matrix), \g\ is length of said coding sequence, c(k) is k-th codon in said sequence of codons, r^rget (c(k)) is a desired ratio of codon c(k) and rfc (c(k)) an actual ratio in the coding sequence g. Preferably cpi is between 0 and 10, more preferably between 0 and 0.5 and most preferably about 0.2.

In the methods of the invention, the codon pair weights w (APPENDIX 3) may be taken from a 64x64 codon pair matrix including stop codons. Note that the weights for stop:sense pairs and stop: stop pairs are always zero. The codon pair weights w are preferably calculated on the basis of a computer-based method, using as input at least one of: (a) a genome sequence of the predetermined host cell for which at least 5, 10, 20 or 80% of the protein encoding nucleotide sequences are sequenced; (b) a genome sequence of a related species to the predetermined host cell for which at least 5, 10, 20 or 80% of the protein encoding nucleotide sequences are sequenced; (c) a group of nucleotide sequences consisting of at least 200 coding sequences of the predetermined host cell; and, (d) a group of nucleotide sequences consisting of at least 200 coding sequences of a species related to the predetermined host cell. A related species is herein understood to refer to a species of which the nucleotide sequence of the small subunit ribosomal RNA has at least 60, 70, 80, or 90% identity with the nucleotide sequence of the small subunit ribosomal RNA of the predetermined host cell (Wuyts et al., 2004, Nucleic Acids Res. 32: DlOl-D 103).

The codon pair weights w need not be determined for all of the possible 61x64 codon pairs including the termination signal as stop codon but may be determined for only a fraction thereof, e.g. for at least 5%, 10%, 20%, 50%, and preferably 100% of the possible 61x64 codon pairs including the termination signal as stop codon.

Selection highly expressed genes For calculation of the codon pair weight matrices and the single codon target ratio vectors one can apply a set of nucleotide sequences from the specified host cell itself, a set of nucleotide sequences from a related species, or a combination of both. The set A of nucleotide sequences is called the 'reference set all'. Most preferably this set contains the full set of open reading frames (ORFs) for an organism that is completely sequenced (>95%). In a preferred embodiment of the invention, a subset B is selected that contains a subset that is overrepresented with highly expressed genes or genes coding for highly expressed proteins. This set can be determined using measurements, and subsequent ranking, like a mRNA hybridization using array technology, e.g. arrays from Affymetrix, Nimblegen, Agilent or any other source for the reference set A. Other measurements can be RT-PCR, protein gels, MS-MS analysis, or any other measurement technique known by the person skilled in the art. Besides making a ranking on the basis of measurements, one can also apply bioinformatics tools to either predict directly a group of highly expressed genes, for example by selecting the most biased genes (Carbone et al, 2003), or by selecting genes known to be highly expressed in a wide range of organisms. Among these are, ribosomal proteins, glycolytic and TCA cycle genes involved in primary metabolism, genes involved in transcription and translation.

Preferably, the codon pair weights w are calculated on the basis of a computer-based method, using as input the group of highly expressed genes in the predetermined host cell. Highly expressed genes are herein understood to mean genes whose mRNA's can be detected at a level of at least 10, preferably 20, more preferably 50, more preferably 100, more preferably 500 and most preferably at least 1,000 copies per cell. For example, Gygi et al. measured -15,000 mRNA molecules per yeast cell. The abundance of specific mRNAs was determined to be in the range of 0.1-470 per cell (Gygi, S.P., Y. Rochon, B.R. Franza and R. Aebersold (1999). Correlation between protein and mRNA abundance in yeast. MoL CeL Biol. 19(3): 1720- 30) or a factor 10 lower: 0.01-50 per cell (by Akashi, H. (2003). Translational selection and yeast proteome evolution. Genetics 164(4): 1291-1303.).

Alternatively, the group of highly expressed genes in the predetermined host cell may be the group comprising the 1000, 500, 400, 300, or 200 or 100 most abundant mRNA's or proteins. The skilled person will recognize that for calculation of single-codon ratio's the group- size of highly expressed genes might be small, since at maximum only 64 target values are being specified. Here a reference set with high-expressed genes might be as low as 1 gene, but generally one considers 1% of the genome size a representive set of the highly expressed genes, see for example Carbone, A. et al. (2003) (Codon adaptation index as a measure of dominating codon bias. Bioinformatics. l_9(16):2005-15). For the calculation of a codon-pair weight matrix, usually a set of 200-500 reference genes fulfils, which corresponds with 2-7% of a bacterial genome (3000-15000 genes).

Another possibility is to derive a subset of presumably highly expressed genes from literature. For example, for Bacillus subtilis, being a model organism, quite some literature on single-codon bias exists. A good overview on the state-of-the-art for B. subtilis is given by the work of Kanaya et al. (1999). In our approach, see example 4, we group the data in a subset of highly-expressed groups on the basis of mRNA levels measured by Affymetrix technology, and compare these sequences with the whole set of genome ORFs. Other options that have been used in literature are protein expression data, and functional categorical groups of (expected) genes like ribosomal proteins, proteins involved in translation and transcription, sporulation, energy metabolism, and the flagellar system (Kanaya et al., 1999; Karlin and Mrazek, 2000).

Indeed one often finds, for example, high codon bias in the ribosomal proteins, as well as in the other named groups. However, generally not all genes in the latter groups show such behavior. Also, we do not know how ribosomal proteins react in low-growth production conditions. Therefore, a straightforward measurement technique to deriving a subset of highly expressed genes seems to be logic. Then we can choose transcriptomics (TX) and/or proteomics (PX) data. For both there are pros and cons. TX gives a rather complete picture for mRNA levels of genes in the full genome, while PX data might be biased by overrepresentation of water-soluble proteins. TX data is a direct measure for the available mRNA that is subject to translation, while protein is part of an accumulation process in which turnover also plays an important role. Anyway, TX and PX data are shown to correlate for the highly-expressed genes (Gygi et al, 1999). Another interesting work is the prediction of highly-expressed (PHX) genes by deviation from the average codon usage and similarity to ribosomal proteins, and those involved in translation and transcription processing factors, and to chaperone degradation proteins (Karlin and Mrazek, 2000). In particular for fast growing organisms, like Bacillus, E. coli, etc., major glycolytic genes and tricarboxylic acid cycle genes are found to belong to the above group. The method prediction compares well with known highly-expressed genes at mRNA data and protein expression.

The skilled person will appreciate that both the single codon weights and codon-pair weights w may be determined for modified host cells that have been modified with respect to the content and nature of their tRNA encoding genes, i.e. host cells comprising additional copies of existing tRNA genes, new (exogenous) tRNA genes, including non-natural tRNA genes, including genes encoding tuna's that have been modified to include non-natural amino-acids or other chemical compounds, as well as host cells in which one or more tRNA genes have been inactivated or deleted.

In the method of the invention, the original coding nucleotide sequence that codes for predetermined amino acid sequence may be selected from: (a) a wild-type nucleotide sequence that codes for the predetermined amino acid sequence; (b) a reverse translation of the predetermined amino acid sequence whereby a codon for an amino acid position in the predetermined amino acid sequence is randomly chosen from the synonymous codons coding for the amino acid; and, (c) a reverse translation of the predetermined amino acid sequence whereby a codon for an amino acid position in the predetermined amino acid sequence is chosen in accordance with a single-codon bias for the predetermined host cell or a species related to the host cell.

Host cells

In the methods of the invention the predetermined host may be any host cell or organism that is suitable for the production of a polypeptide of interest by means of expression of an optimized nucleotide coding sequence. The host cell may thus be a prokaryotic or a eukaryotic host cell. The host cell may be a host cell that is suitable for culture in liquid or on solid media. Alternatively, the host cell may be a cell that is part of a multicellular tissue or and multicellular organism such as a (transgenic) plant, animal or human.

The host cells may be microbial or non-microbial. Suitable non-microbial host cells include e.g. mammalian host cells such as Hamster cells: CHO (Chinese hamster ovary), BHK (Baby Hamster Kidney) cells, mouse cells (e.g. NSO), monkey cells such as COS or Vero; human cells such as PER.C6™ or HEK-293 cells; or insect cells such as Drosophila S2 and Spodoptera Sf9 or SfZl cells; or plant cells such as tobacco, tomato, potato, oilseed rape, cabbage, pea, wheat, corn, rice, Taxus species such as Taxus brevifolia, Arabidopsis species such as Arabidopsis thaliana, and Nicotiana species such as Nicotiana tabacum. Such non- microbial cells are particularly suitable for the production of mammalian or human proteins for use in mammalian or human therapy.

The host cell may also be microbial host cells such as bacterial or fungal cells. Suitable bacterial host cells include both Gram-positive and Gram-negative bacteria. Examples of suitable bacterial host cells include bacteria from the genera Bacillus, Actinomycetis, Escherichia, Streptomyces as well as lactic acid bacteria such as Lactobacillus, Streptococcus, Lactococcus, Oenococcus, Leuconostoc, Pediococcus, Carnobacterium, Propionibacterium, Enterococcus and Bifidobacterium. Particularly preferred are Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis, Escherichia coli, Streptomyces coelicolor, Streptomyces clavuligerus, and Lactobacillus plantarum, Lactococcus lactis.

Alternatively, the host cell may be a eukaryotic microorganism such as a yeast or a filamentous fungus. Preferred yeasts as host cells belong to the genera Saccharomyces, Kluyveromyces, Candida, Pichia, Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, and Yarrowia. Particularly preferred Debaromyces host cells include Saccharomyces cerevisiae, and Kluyveromyces lactis.

According to a more preferred embodiment, the host cell of the present invention is a cell of a filamentous fungus. "Filamentous fungi" include all filamentous forms of the subdivision Eumycota and Oomycota (as defined by Hawksworth et al., 1995, supra). The filamentous fungi are characterized by a mycelia wall composed of chitin, cellulose, glucan, chitosan, mannan, and other complex polysaccharides. Vegetative growth is by hyphal elongation and carbon catabolism is obligatory aerobic. Filamentous fungal genera of which strains may be used as host cells in the present invention include, but are not limited to, strains of the genera Acremonium, Aspergillus, Aureobasidium, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium, Piromyces, Schizophyllum, Chrysosporium, Talaromyces, Thermoascus, Thielavia, Tolypocladium, and Trichoderma. Preferably a filamentous fungus belonging to a species selected from the group consisting of Aspergillus niger, Aspergillus oryzae, Aspergillus sojae, Trichoderma reesei or Penicillium chrysogenum. Example of suitable host strains include: Aspergillus niger CBS 513.88 (Pel et al., 2007, Nat Biotech. 25: 221-231), Aspergillus oryzae ATCC 20423, IFO 4177, ATCC 1011, ATCC 9576, ATCC14488-14491, ATCC 11601, ATCC12892, P. chrysogenum CBS 455.95, Penicillium citrinum ATCC 38065, Penicillium chrysogenum P2, Acremonium chrysogenum ATCC 36225 or ATCC 48272, Trichoderma reesei ATCC 26921 or ATCC 56765 or ATCC 26921, Aspergillus sojae ATCCl 1906, Chrysosporium lucknowense ATCC44006 and derivatives thereof. The host cell may be a wild type filamentous fungus host cell or a variant, a mutant or a genetically modified filamentous fungus host cell. Such modified filamentous fungal host cells include e.g. host cells with reduced protease levels, such as the protease deficient strains as Aspergillus oryzae JaL 125 (described in WO 97/35956 or EP 429 490); the tripeptidyl- aminopeptidases-deficient A. niger strain as disclosed in WO 96/14404, or host cells with reduced production of the protease transcriptional activator (prtT; as described in WO 01/68864, US2004/0191864A1 and WO 2006/040312); host strains like the Aspergillus oryzae BECh2, wherein three TAKA amylase genes, two protease genes, as well as the ability to form the metabolites cyclopiazonic acid and kojic acid have been inactivated (BECh2 is described in WO 00/39322); filamentous fungal host cells comprising an elevated unfolded protein response (UPR) compared to the wild type cell to enhance production abilities of a polypeptide of interest (described in US2004/0186070A1, US2001/0034045 Al, WOO 1/72783 A2 and WO2005/123763); host cells with an oxalate deficient phenotype (described in WO2004/070022A2 and WO2000/50576); host cells with a reduced expression of an abundant endogenous polypeptide such as a glucoamylase, neutral alpha-amylase A, neutral alpha- amylase B, alpha- 1, 6-transglucosidase, proteases, cellobiohydrolase and/or oxalic acid hydrolase (as may be obtained by genetic modification according to the techniques described in US2004/0191864A1); host cells with an increased efficiency of homologous recombination (having deficient hdfA or hdfB gene as described in WO2005/095624); and host cells having any possible combination of these modifications .

In a method of the invention, the predetermined amino acid sequence may be an amino acid sequence (of a polypeptide of interest) that is heterologous to said predetermined host cell, or it may be an amino acid sequence (of a polypeptide of interest) that is homologous to said predetermined host cell.

The term "heterologous" when used with respect to a nucleic acid (DNA or RNA) or protein refers to a nucleic acid or protein that does not occur naturally as part of the organism, cell, genome or DNA or RNA sequence in which it is present, or that is found in a cell or location or locations in the genome or DNA or RNA sequence that differ from that in which it is found in nature. Heterologous nucleic acids or proteins are not endogenous to the cell into which it is introduced, but has been obtained from another cell or synthetically or recombinantly produced. Generally, though not necessarily, such nucleic acids encode proteins that are not normally produced by the cell in which the nucleic acid is expressed. Any nucleic acid or protein that one of skill in the art would recognize as heterologous or foreign to the cell in which it is expressed is herein encompassed by the term heterologous nucleic acid or protein. The term heterologous also applies to non-natural combinations of nucleic acid or amino acid sequences, i.e. combinations where at least two of the combined sequences are foreign with respect to each other. The term "homologous" when used to indicate the relation between a given (recombinant) nucleic acid or polypeptide molecule and a given host organism or host cell, is understood to mean that in nature the nucleic acid or polypeptide molecule is produced by a host cell or organisms of the same species, preferably of the same variety or strain. The predetermined amino acid sequence may be the sequence of any polypeptide of interest having a commercial or industrial applicability or utility. Thus, the polypeptide of interest may be an antibody or a portion thereof, an antigen, a clotting factor, an enzyme, a hormone or a hormone variant, a receptor or portions thereof, a regulatory protein, a structural protein, a reporter, or a transport protein, intracellular protein, protein involved in secretion process, protein involved in folding process, chaperone, peptide amino acid transporter, glycosylation factor, transcription factor. Preferably, the polypeptide of interest is secreted into the extracellular environment of the host cell by the classical secretion pathway, by a non- classical secretion pathway or by an alternative secretion pathway (described in WO 2006/040340). In case the polypeptide of interest is an enzyme it may e.g. be an oxidoreductase, transferase, hydrolase, lyase, isomerase, ligase, catalase, cellulase, chitinase, cutinase, deoxyribonuclease, dextranase, esterase. More preferred enzymes include e.g. carbohydrases, e.g. cellulases such as endoglucanases, β-glucanases, cellobiohydrolases or β-glucosidases, hemicellulases or pectinolytic enzymes such as xylanases, xylosidases, mannanases, galactanases, galactosidases, pectin methyl esterases, pectin lyases, pectate lyases, endopolygalacturonases, exopolygalacturonases rhamnogalacturonases, arabanases, arabinofuranosidases, arabinoxylan hydrolases, galacturonases, lyases, or amylolytic enzymes; hydrolase, isomerase, or ligase, phosphatases such as phytases, esterases such as lipases, proteolytic enzymes, oxidoreductases such as oxidases, transferases, or isomerases, phytases, aminopeptidases, carboxypeptidases, endo-proteases, metallo-proteases, serine -proteases, catalases, chitinases, cutinases, cyclodextrin glycosyltransferases, deoxyribonucleases, alpha- galactosidases, beta-galactosidases, glucoamylases, alpha-glucosidases, beta-glucosidases, haloperoxidases, invertases, laccases, mannosidase, mutanases, peroxidases, phospholipases, polyphenoloxidases, ribonucleases, transglutaminases, glucose oxidases, hexose oxidases, and monooxygenases. Several therapeutic proteins of interest include e.g. antibodies and fragment thereof, human insulin and analogs thereof, human lactoferrin and analogs thereof, human growth hormone, erythropoietin, tissue plasminogen activator (tPA) or insulinotropin. The polypeptide may be involved in the synthesis of a metabolite, preferably citric acid. Such polypeptides e.g. include: aconitate hydratase, aconitase hydroxylase, 6-phosphofructokinase, citrate synthase, carboxyphosphonoenolpyruvate phosphonomutase, glycolate reductase, glucose oxidase precursor goxC, nucleoside-diphosphate-sugar epimerase, glucose oxidase, Manganese- superoxide-dismutase, citrate lyase, ubiquinone reductase, carrier proteins, citrate transporter proteins, mitochondrial respiratory proteins and metal transporter proteins.

Computer, program and data carrier

In a further aspect the invention relates to a computer comprising a processor and memory, the processor being arranged to read from said memory and write into said memory, the memory comprising data and instructions arranged to provide said processor with the capacity to perform the method of the invention. In another aspect the invention relates to a computer program product comprising data and instructions and arranged to be loaded in a memory of a computer that also comprises a processor, the processor being arranged to read from said memory and write into said memory, the data and instructions being arranged to provide said processor with the capacity to perform the method of the invention. In yet another aspect the invention relates to a data carrier provided with a computer program product as defined above.

Nucleic acid molecules

In a further aspect the invention relates to a nucleic acid molecule comprising a coding sequence coding for a predetermined amino acid sequence. The coding sequence preferably is a nucleotide sequence that does not resemble a naturally occurring coding sequence. Rather the coding sequence in the nucleic acid molecule is a nucleotide sequence that is not found in nature but is an artificial, i.e. an engineered, man-made nucleotide sequence that was generated on the basis of the method for optimization of single codon and/or codon pair bias for a predetermined host cell in accordance with the methods defined herein and that was subsequently synthesized as a tangible nucleic acid molecule. Preferably, the coding sequence has a fitsc(g) of at least below 0.2, or more preferably below 0.1 and most preferably below 0.02 for a predetermined host cell. More preferably, the coding sequence has a fitcp(g) of at least below 0 for a predetermined host cell. Most preferably, the coding sequence has &fitcp(g) of at least below - 0.1 for a predetermined host cell, or more preferably at least below -0.2. Preferably the number of codon-pair in an optimized gene g contains at least 60, 70, 75, 80, 85% codon pairs and most preferably at least 90% codon pairs with associated negative codon-pairs for the specified host organisms The predetermined amino acid sequence encoded by the coding sequence may be any polypeptide of interest as herein defined above and also the predetermined host cell may be any host cell as defined above herein.

In the nucleic acid molecule, the coding sequence preferably is operably linked to an expression control sequence that are capable of directing expression of the coding sequence in the predetermined host cell. In the context of the invention, a control sequence is defined as a nucleotide sequence operatively associated to a coding sequence when present together and which include all components necessary or advantageous for expression of the nucleotide sequence encoding the polypeptide to be produced. Each control sequence may be native or foreign to the nucleotide sequence encoding the polypeptide to be produced. Such control sequences may include, but are not limited to, a leader sequence, a polyadenylation sequence, a propeptide sequence, a promoter, a translational initiator sequence, a translational initiator coding sequence, a translational transcription terminator and a transcription terminator sequence. The control sequences may be provided with linkers, e.g., for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the nucleotide sequence encoding a polypeptide.

Expression control sequences will usually minimally comprise a promoter. As used herein, the term "promoter" refers to a nucleic acid fragment that functions to control the transcription of one or more genes, located upstream with respect to the direction of transcription of the transcription initiation site of the gene, and is structurally identified by the presence of a binding site for DNA-dependent RNA polymerase, transcription initiation sites and any other DNA sequences, including, but not limited to transcription factor binding sites, repressor and activator protein binding sites, and any other sequences of nucleotides known to one of skill in the art to act directly or indirectly to regulate the amount of transcription from the promoter. A "constitutive" promoter is a promoter that is active under most environmental and developmental conditions. An "inducible" promoter is a promoter that is active under environmental or developmental regulation.

A DNA segment such as an expression control sequence is "operably linked" when it is placed into a functional relationship with another DNA segment. For example, a promoter or enhancer is operably linked to a coding sequence if it stimulates the transcription of the sequence. DNA for a signal sequence is operably linked to DNA encoding a polypeptide if it is expressed as a pre-protein that participates in the secretion of the polypeptide. Generally, DNA sequences that are operably linked are contiguous, and, in the case of a signal sequence, both contiguous and in reading phase. However, enhancers need not be contiguous with the coding sequences whose transcription they control. Linking is accomplished by ligation at convenient restriction sites or at adapters, linkers, or PCR fragments by means know in the art.

The selection of an appropriate promoter sequence generally depends upon the host cell selected for the expression of the DNA segment. Examples of suitable promoter sequences include prokaryotic, and eukaryotic promoters well known in the art (see, e.g. Sambrook and Russell, 2001, "Molecular Cloning: A Laboratory Manual (3rd edition), Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, New York). The transcriptional regulatory sequences typically include a heterologous enhancer or promoter that is recognized by the host. The selection of an appropriate promoter depends upon the host, but promoters such as the trp, lac and phage promoters, tRNA promoters and glycolytic enzyme promoters are known and available (see, e.g. Sambrook and Russell, 2001, supra). Examples of preferred inducible promoters that can be used are a starch-, copper-, oleic acid-inducible promoters. Preferred promoters for filamentous fungal host cells e.g. include the glucoamylase promoter of A. niger or the TAKA amylase promoter of A. oryzae and the promoters described in WO2005/100573. The nucleotide sequence of the invention may further comprise a signal sequence, or rather a signal peptide-coding region. A signal sequence codes for an amino acid sequence linked to the amino terminus of the polypeptide, which can direct the expressed polypeptide into the cell's secretory pathway. Signal sequences usually contain a hydrophobic core of about 4-15 amino acids, which is often immediately preceded by a basic amino acid. At the carboxyl- terminal end of the signal peptide there are a pair of small, uncharged amino acids separated by a single intervening amino acid that defines the signal peptide cleavage site, von Heijne, G. (1990) J. Membrane Biol. 115: 195-201. Despite their overall structural and functional similarities, native signal peptides do not have a consensus sequence. Suitable signal peptide- coding regions may be obtained from a glucoamylase or an amylase gene from an Aspergillus species, a lipase or proteinase gene from a Rhizomucor species, the gene for the alpha-factor from Saccharomyces cerevisiae, an amylase or a protease gene from a Bacillus species, or the calf pre-pro-chymosin gene. However, any signal peptide-coding region capable of directing the expressed protein into the secretory pathway of a host cell of choice may be used in the present invention. Preferred signal peptide coding regions for filamentous fungus host cells are the signal peptide coding region obtained from Aspergillus oryzae TAKA amylase gene (EP 238 023), Aspergillus niger neutral amylase gene, Aspergillus niger glucoamylase, the Rhizomucor miehei aspartic proteinase gene, the Humicola lanuginosa cellulase gene, Humicola insolens cellulase, Humicola insolens cutinase the Candida antarctica lipase B gene or the Rhizomucor miehei lipase gene and mutant, truncated, and hybrid signal sequence thereof. In a preferred embodiment of the invention the nucleotide sequence encoding the signal sequence is an integral part of the coding sequence that is optimized with respect to single codon and/or codon pair bias for the predetermined host.

In the nucleic acid molecule of the invention, the coding sequence is further preferably operably linked to a translational initiator sequence. In eukaryotes, the nucleotide consensus sequence (6-12 nucleotides) before the initiator ATG-codon is often called Kozak consensus sequence due to the initial work on this topic (Kozak, M. (1987): an analysis of 5'-noncoding sequences from 699 vertebrate messenger RNAs. Nucl. Acid Res. 15(20): 8125-47). The original Kozak consensus sequence CCCGCCGCCrCC(ATG)G, including a +4 nucleotide derived by Kozak is associated with the initiation of translation in higher eukaryotes. For prokaryote host cells the corresponding Shine-Delgarno sequence (AGGAGG) is preferably present in the 5'- untranslated region of prokaryotic mRNAs to serve as a translational start site for ribosomes.

In the context of this invention, the term "translational initiator sequence" is defined as the ten nucleotides immediately upstream of the initiator or start codon of the open reading frame of a DNA sequence coding for a polypeptide. The initiator or start codon encodes for the amino acid methionine. The initiator codon is typically ATG, but may also be any functional start codon such as GTG, TTG or CTG.

In a particularly preferred embodiment of the invention, the nucleic acid molecule comprises a coding sequence coding for a predetermined amino acid sequence that is to be expressed in a fungal host cell, i.e. the predetermined host cell is preferably a fungus of which filamentous fungi are most preferred. Nucleic acid molecules comprising coding sequences that are optimized for expression in fungi in accordance with the invention may further comprise the one or more of the following elements: 1) a fungal consensus translational initiator sequence; 2) a fungal translational initiator coding sequence; and 3) a fungal translational termination sequence.

A consensus fungal translational initiator sequence preferably is defined by the following sequences: 5'-mwChkyCAmv-3', using ambiguity codes for nucleotides: m (A/C); r (AJG); w (A/T); s (C/G); y (C/T); k (G/T); v (A/C/G); h (A/C/T); d (A/G/T); b (C/G/T); n (A/C/G/T). According to a more preferred embodiment, the sequences are: 5'-mwChkyCAAA-3'; 5'- mwChkyCAC A-3 ' or 5'-mwChkyCAAG-3'. Most preferably the translational initiation consensus sequence is 5'-CACCGTCAAA-3' or 5 '-CGCAGTCAAG-S ' .

In the context of this invention, the term "consensus translational initiator coding sequence" is defined herein as the nine nucleotides immediately downstream of the initiator codon of the open reading frame of a coding sequence (the initiator codon is typically ATG, but may also be any functional start codon such as GTG). A preferred fungal consensus translational initiator coding sequence has the following nucleotide sequence: 5'-GCTnCCyyC-3', using ambiguity codes for nucleotides y (C/T) and n (A/C/G/T). This leads to 16 variants for the translational initiator coding sequence of which 5'- GCT TCC TTC -3' is most preferred. Using a consensus translational initiator coding sequence, the following amino acids are allowed at the amino acid positions mentioned: alanine at +2, alanine, serine, proline, or threonine at +3, and phenylalanine, serine, leucine or proline at +4 position in the polypeptide that is encoded. Preferably in the present invention, the consensus translational initiator coding sequence is foreign to the nucleic acid sequence encoding the polypeptide to be produced, but the consensus translational initiator may be native to the fungal host cell.

In the context of this invention, the term "translational termination sequence" is defined as the four nucleotides starting from the translational stop codon at the 3 ' end of the open reading frame or coding sequence. Preferred fungal translational termination sequence include: 5'- TAAG-3', 5'- TAGA-3' and 5'-TAAA-3\ of which 5'-TAAA-3' is most preferred. A coding sequence coding for a predetermined amino acid sequence that is to be expressed in a fungal host cell is further preferably optimized with respect to single codon frequency such that at least one, two, three, four or five original codons, more preferably at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 50%, 75%, 80%, 85%, 90%, or 95% of the original codons have been exchanged with a synonymous codon, the synonymous codon encoding the same amino acid as the native codon and having a higher frequency in the codon usage as defined in the Table A than the original codon.

Table A: Optimal filamentous fungal codon frequency for synonymous codons in %.

A even more preferred coding sequence coding for a predetermined amino acid sequence that is to be expressed in a fungal host cell is further preferably optimized with respect to single codon frequency such that at least one, two, three, four or five original codons, more preferably at least 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 50%, 75%, 80%, 85%, 90%, or 95% of the original codons have been exchanged with a synonymous codon, the synonymous codon changing the codon frequency such that the value of the absolute difference between the percentage for said codon in said frequency and listed optimal percentage becomes smaller after modification, applying the following list of optimal percentages: cysteine encoded by TGC (100%); phenylalanine by TTC (100%); histidine by CAC (100%); lysine by AAG (100%); asparagine by AAC (100%); glutamine by CAG (100%); tyrosine by TAC (100%); alanine by GCT (38.0%) , GCC (50.7%), or GCG (11.3%); aspartate by GAC (63.2%); glutamate by GAG (74.2%); glycine by GGT (49.0%), GGC (35.9%), GGA (15.1%); isoleucine by ATT (26.7%), ATC (73.3%); leucine by TTG (12.7%), CTT (17.4%), CTC (38.7%), CTG (31.2%); proline by CCT (35.6%), CCC (64.4%); arginine by CGT (49.1%), CGC (50.9%); serine by TCT (20.8%), TCC (44.0%), TCG (14.4%), AGC (20.8%); threonine by ACT (29.7%), ACC (70.3%) and/or valine by GTT (27.4%), GTC (54.5%), GTG (18.1%); all other possible amino acid encoding codons (0%).

The above defined nucleic acid molecules comprising the coding sequences of the invention (for expression in a predetermined host cell) may further comprise the elements that are usually found in expression vectors such as a selectable marker, an origin of replication and/or sequences that facilitate integration, preferably through homologous recombination at a predetermined site in the genome. Such further elements are well known in the art and need no further specification herein.

In a further aspect the invention pertains to a host cell comprising a nucleic acid molecule as defined herein above. The host cell preferably is a host cell as herein defined above. In yet a further aspect the invention relates to a method for producing a polypeptide having the predetermined amino acid sequence. The method preferably comprises culturing a host cell comprising a nucleic acid molecule as defined herein above, under conditions conducive to the expression of the polypeptide and, optionally, recovery of the polypeptide.

In again a further aspect the invention relates to method for producing at least one of an intracellular and an extracellular metabolite. The method comprising culturing a host cell as defined in herein above under conditions conducive to the production of the metabolite. Preferably, in the host the polypeptide having the predetermined amino acid sequence (that is encoded by the nucleic acid molecule as defined above) is involved in the production of the metabolite. The metabolite (be it a primary or secondary metabolite, or both; be it intra-, extracellular or both) may be any fermentation product that may be produced in a fermentation process. Such fermentation products e.g. include amino acids such as lysine, glutamic acid, leucin, threonin, tryptophan; antibiotics, including e.g. ampicilline, bacitracin, cephalosporins, erythromycin, monensin, penicillins, streptomycin, tetracyclines, tylosin, macrolides, and quinolones; preferred antibiotics are cephalosporins and beta-lactams; lipids and fatty acids including e.g. poly unsaturated fatty acids (PUFAs); alkanol such as ethanol, propanol and butanol; polyols such as 1,3-propane-diol, butandiol, glycerol and xylitol; ketons such as aceton; amines, diamines, ethylene; isoprenoids such as carotenoids, carotene, astaxanthin, lycopene, lutein; acrylic acid, sterols such as cholesterol and ergosterol; vitamins including e.g. the vitamins A, B2 B12, C, D, E and K, and organic acids including e.g. glucaric acid, gluconic acid, glutaric acid, adipic acid, succinic acid, tartaric acid, oxalic acid, acetic acid, lactic acid, formic acid, malic acid, maleic acid, malonic acid, citric acid, fumaric acid, itaconic acid, levulinic acid, xylonic acid, aconitic acid, ascorbic acid, kojic acid, and comeric acid; a preferred organic acid is citric acid.

In this document and in its claims, the verb "to comprise" and its conjugations is used in its non-limiting sense to mean that items following the word are included, but items not specifically mentioned are not excluded. In addition, reference to an element by the indefinite article "a" or "an" does not exclude the possibility that more than one of the element is present, unless the context clearly requires that there be one and only one of the elements. The indefinite article "a" or "an" thus usually means "at least one". 

Examples

1. Example 1 : Analysis of codon pair bias 1.1 Material and methods 1.1.1 Data and software Codon pair analysis may be performed on coding sequences (CDS) in whole genome sequence data as well as partial groups derived of those (or a partial genome sequence, like for example cDNA/EST libraries, or even partial genome data from multiple genomes from related organisms). The tools used in the present invention read these data using FASTA files as input. The vast majority of all calculations have been performed in MATLAB 7.01 (The Math Works, Inc., www.mathworks .com), but for some detailed analyses of the obtained results Spotfire DecisionSite 8.0 (Spotfire, Inc., http://www.spotfire.com/products/decisionsite.cfm) was used.

For A. niger, a FASTA file with predicted cDNA sequences for the full genome of CBS513.88 (Pel et al, 2007, Nat Biotech. 25: 221-231) and a group of 479 highly expressed genes were used. Furthermore, since usually less than half of the > 14,000 genes in A. niger are expressed at the same time under pilot-scale fermentation conditions, data from 24 GeneChips obtained using such conditions was used to extract a second set of genes that includes only genes that are actually expressed within various experiments (taking only genes with at least 18 'present' calls into account, using Affymetrix MAS5.0 array analysis software; this set comprised 4,584 genes) and to rank them according to observed mRNA level (since no other data was available at that time), so a set of (presumably) highly expressed genes of any size can be identified easily. This second set was created to be able to rank the data according to their expression level.

For this analysis we have used transcription levels of the genes. Alternatively one can also apply quantitative protein expression data, e.g. by two-dimensional gel electrophoresis of the proteins and subsequent identification via mass spectrometry. However, generating protein expression on large sets of proteins is still quite time consuming in comparison with determination of mRNA levels (e.g. using genechips). Therefore, what is done here is to study the effect of codon bias on translation before translation has actually happened. Gygi et αl. (Yeast. MoI. CeI. Biol. 19(3): 1720-30) actually found a "correlation of protein and mRNA expression levels with codon bias" in E. coli, even although the correlation of mRNA and protein expression levels was rather rudimentary only. Hence, the term "expression level" will be used in this text when actually only the effect on the transcription level has been determined.

For Bacillus subtilis, an organism containing around 4,000 genes, a group of 300 highly expressed genes was available and has been analyzed. See Table 1.1 for an overview of the basic properties of the genomes of all organisms that have been taken into account in this study (however, not all of them will be described in detail).

In every analysis, (putative) genes that included one or more stop codons at another position than the end and sequences with a length not divisible by three (i.e. where a frameshift might have occurred during sequencing) have been ignored. Also the first five and the last five codons of every gene have not been taken into account because these sites might be involved in protein binding and releasing efficiency and therefore be subject to different selection pressures than the other parts of the sequence, so codon and codon pair bias there might not be representative. ORFs (ORF = open reading frame) shorter than 20 codons have also been omitted from the analysis. In Table 1.1 this is already taken into account.

Table 1.1 Nucleotide content of several organisms, including number of ORF's and genome size in Megabasepair (Mbp). nucleotide content name of organism # of ORFs * Mbp i A ! C ' G T

A. nidulans 7,782 10.61 24% 28% 26% I 22%

A. niger 13,962; 18.41 ; 24% 5 27% ; 26% : 22% A. oryzae 12,074 16,29 25% ! 26% i 26% 23%

B. amyloliquefaciens 4,449 3,54 26% 24% 27% : 23%

B. subtilis 4,104; 3.66 ; 30% . 20% ; 24% 26% E. coli K12 4,289 4.09 24% : 25% ! 27% 24%

K. lactis 5,336 7.52 : 32% 19% 21% ; 28%

P. chrysogenum 13,164; 17.54 i 24% 27% ; 25% 23% S. cerevisiae 6,449 9.01 33% ; 19% : 20% 28%

S. coelicolor 7,894 7.62 ; 14% 37% 35% i 13%

T. reesei 8,331; 1 1.45 : 23% ' 30% : 28% 20%

1.1.2 Expected occurrences of codon pairs

In order to analyze codon pair usage, first the occurrences of every single codon and every codon pair have been counted, below denoted by nobΛ(cι>c,)) , where obs stands for observed.

The double parenthesis are necessary to indicate that "observed number", i.e. nobs, is a function with just one argument, which itself is a pair (in that case: a pair of codons, i.e. (c;,c/)). The same applies to all functions on codon pairs defined below. The indices /, j and also k can be 1 to 64, indicating the number of the codon in the internal representation (according to their alphabetical order). (cι,cj) denoting a codon pair with a being the left codon (i.e. the 5' triplet of the 6- nucleotide sequence) and right q one {i.e. closer to the 3 '-end), as well as the number of occurrences ns a" (ck) for every codon ct (where the subscript sc stands for single codon and the superscript all indicates that the number refers to the full genome, as opposed to nfc (ck ) , which will be used to denote codon ratios in a single gene g; functions of codon pairs like nobs((cι>c,)) always refer to the number in the full genome or a larger group of genes). Single codon ratios (Note that in some papers these ratios are also called frequencies. However, codon frequencies may also refer to the number of occurrences of a codon divided by the total number of all codons) were then calculated

where syn(ck) denotes the set of codons that encode for the same amino acid as c* and are thus synonymous to c*. Thus, the value of the sum below the fraction bar equals the number of occurrences of the amino acid encoded by c/ in the whole proteome. See Appendix 1 for a concise list of the most important symbols and formulas used here.

To reveal whether certain alleged codon pair preferences are only the result of preferences of the individual codons, it is necessary to calculate expected values for every codon pair based on individual codon frequencies. These have been calculated using the formula

nZ"«cι,cj)) = rsf (cιyrsf(cjy ∑ nobs«cm,cj)

The superscript own is used to distinguish the values from those obtained using other methods mentioned later. In the last factor of this equation, the actual numbers of occurrences of all synonymous codon pairs are summed up. Thus, the expected amount of each codon pair is the product of the individual codon usage ratios and the number of occurrences of the respective amino acid pair.

Gutman and Hatfield (1989, Proc. Natl. Acad. Sci USA 86:3699-3703) proposed another method of calculating expected values. Their initial approach was to calculate the codon frequencies (i.e. the amount of codons in a gene g divided by the total number of codons in g, denoted \g\) for every gene individually, and then multiply these values pair wise and with the number of codon pairs in that sequence (which is |g|-l).

g≡ORFs \ 8 \ 8

In this equation "ghl" denotes Gutman and Hatfield method 1 (1989, supra). This results in expected codon pair values for each gene (the part after the sum operator in the equation above), which are then added up, resulting in final expected values that are by definition adjusted for possible deviations in single codon usage among different genes of the same genome, but do not take a possible bias in amino acid pair usage into account. This means that if certain amino acids tend to be next to each other more often than others, or, in other words, if the numbers of occurrences of the amino acid pairs are not similar to what they would be in randomized sequences with the same amino acid composition, the expected values would also be significantly different in that codon pairs encoding rather rarely used amino acid pairs would have too high expected values and those of more often used amino acid pairs too low ones.

Gutman and Hatfield (1989, supra) also proposed a method of normalizing their expected values for amino acid pair bias. Therefore, they simply compared the expected number of amino acid pairs according to their methods with the observed ones and scaled the expected values of all affected codon pairs accordingly to make the former match the latter:

Σ nobs((Cm> Cn)) cmesyn(c, )

<P ((C1 , C1 )) = n% ((C1 , C1 )) '-

∑ nshl((c c ))

≡ ≡ssyynn({cc )) <Ξ ιssyynn((cc:: ))

In this equation "gh2" denotes Gutman and Hatfield method 2 (1989, supra).

1.1.3 Calculating codon pair bias

The actual codon pair bias bias((chCj) should then result from the difference between the expected and actual (observed) numbers of the codon pairs (where any of these methods for the expected values can be used). The initial approach was to calculate it simply by

This way, the bias value would indicate how many percent more or less often than expected the codon pair is actually used (if multiplied by 100%, that is). For amino acid pairs not occurring in an analyzed set of genes, the bias value according to the formula would be 0/0 for all corresponding codon pairs. In that case, it is defined to be 0. The lower limit of the bias values would thus be -1, whereas there is no clear upper limit. This was considered somewhat impractical, so instead lobs ((c, ,c, )) - n ((c, 9c, )) bias ((C1 , c )) = ma*(nobs ((C1 9 C1 )), nexp ((C1 , C1 ))) was used, where max(a,b) denotes the greater of the two values a and b, which always results in a bias value in (-1,1). This means that the bias value can be -1, but not +1. The former happens when a certain codon pair is not used at all to encode for an amino acid pair that really occurs; the value +1 can not be reached because «exP((c,,cj)) would have to be 0 then, but this is only possible when wofa ((c,,c;))is 0, too.

The interpretation given above is still valid for bias values <0 (which means that «ofe((c,>c;)) <

so both formulas have the same result). If «ofe((c,,c;)) > «exp ((c,,c;))? the bias values (which are >0 then) indicate how many percent lower than the observed value the expected value is (i.e. in that case the baseline is changed).

1.1.4 Statistical significance of the bias

Gutman and Hatfield (1989, supra) used a χ2-test to determine the statistical significance of their results. This test is used to check how likely it is that certain observed results occurred by chance under a specific hypothesis. When examining codon pairs, this hypothesis would be that the codon pair usage is the result of a random selection of every codon independently. To test this hypothesis, a χ2-value is calculated

2 = y Kfa ((C M >O) ~ neXp (.(.Cn, ,Cn )))2 (cm,cπ )eCP nexp ((Cm > Cn )) (with CP denoting the set of all codon pairs not including a stop codon). The number of degrees of freedom is then 3720 (61*61-1). If codon pair selection were random, one would expect the χ2-value to be around 3720 (equal to the number of degrees of freedom) with a standard deviation equal to the square root of 2*degrees of freedom.

This way, the overall statistical significance of the observed bias can be tested. However, one can also deduce the statistical significance of the bias of individual codon pairs. As for the method of calculating expected values proposed earlier, the number of occurrences of a codon pair is considered to be the result of a sequence of independent yes/no experiments (yes: these two codons are selected for encoding the respective amino acid pair; no: another codon pair is selected), so it follows a binomial distribution, which can be approximated by a normal distribution if the set of analyzed genes is sufficiently large. This is considered a good approximation if n*p>4, where n stands for the number of experiments and p for the probability of "yes"., which is also the expected value. Therefore, for every codon pair a standard deviation can be calculated according to the formula

σ((cι ,cj)) = ^nexp(( ,Cj))- (\-r:»(cι)- r:»(Cj)) _

Then, the standard scores, also referred to as z-scores, can be calculated Z(Hc1 , c })) = ("Ofa ((g, » gj )) - " ((g, » gj )) σ((c, ,c}))

The absolute value of the z-score tells how many standard deviations away from the expected value the actual (observed) value is. Assuming a normal distribution, approximately 95% of all observations should be within two standard deviations from the expected value and >99% within three.

1.2 Results

1.2.1 Existence of codon pair bias

Using the above methods we have found that significant codon pair biases exist. For all investigated organisms, the χ2-test delivered χ2-values several times as high as the number of degrees of freedom and thus also many standard deviations above the expected value. As for the bias of individual codon pairs, the finding of Moura et al. that in yeast "about 47% of codon-pair contexts fall within the interval -3 to +3" standard deviations away from the expected values (although they calculated the expected values in a different way), which corresponds to the z- scores in our analysis, could be confirmed. Overall, there are significantly more codon pairs with rather high z-scores than there should be if codon pair usage were random. See Table 1.2: with a random selection, which would result approximately in a normal distribution, for example only about 5% of all codon pairs should have a z-score greater than 2 or less than -2, but in the whole genome of the selected four organisms, this actually applies to more than two thirds.

Table 1.2. Z-scores in different organisms

z-score >1 >2 >3 normal distribution 68.3% 5 .0 % 0 .3 % A. nidulans 86.1% 73.7% 60.4%

A. niger "8972%"" 79.1% "69.7%

A. oryzae 88.4% 76.7%, 65.1%

B. amyloliquefaciens 88.1% 76.4% 64.0%

B. subtilis 86.1%, I 72.0% 59.3%

E. coli K12 86.1% 74.8% 64.0%

K. lactis 82.6% 67.0% 53.4%

P. chrysogenum 89.3% 79.1% 69.0%

S. cerevisiae 82.7% 67.6% 52.1%

S. coelicolor 82.0%, 66.5%, 53.5%

T. reesei 89.0% 79.8% 71.0%

Note that these values are somewhat correlated with genome size (see Table 1.1 for a comparison), i.e. organism with larger genomes tend to have codon pairs with more extreme z- scores. Especially when analyzing smaller groups of genes (e.g. 479 highly expressed ones in A. niger), the values are lower (for this example: 65.1%, 37.2% and 19.7%, respectively), as smaller numbers of occurrences lead to higher standard deviations (compared to the expected values) and thus to less statistical significance of the results. This leads to the conclusion that codon pair usage is not the result of a random selection of the codons according to the single codon ratios. The distribution of the bias values themselves differs from one organism to another. This can be explained with reference to Figure 3 which shows the distribution of codon pair bias values for the 3,721 sense:sense codon pairs in different organisms. The numbers in the top right corner of each histogram in Figure 3 are the standard deviations for the observed distribution; the mean values (not shown) are between -0.06 and -0.01 for all organisms. In the histograms shown in Figure 3, one can see that out of the ten tested organisms, the bacteria E. coli, B. subtilus, B. amiloliquefaciens and S. coelicolor have the most extreme codon pair bias, whereas bias in the fungi A. niger, A. oryzae, A. terreus, A. nidulans, P. chrysogenum and yeasts S. cerevisiae and K. lactis, is less extreme.

Another interesting observation can be made when comparing codon pair bias of different organisms. Bias values from related organisms show a higher correlation than those from unrelated organisms. This is explained with reference to Figure 4. Figure 4 shows correlation in codon pair bias of various organisms. A correlation coefficient is shown in the top right corner of each subplot. In this analysis, the highest correlations could be observed between A. niger vs. P. chrysogenum, and A. niger vs. A. oryzae, the lowest, i.e. effectively no correlation could be observed between B. subtilis and S. coelicolor. Interestingly, no negative correlations have been observed. This means that although organisms with a high GC-content (like S. coelicolor) mostly prefer those codons that are the less used ones in AT-rich organisms (like S. cerevisiae or, although not extremely AT-rich, B. subtilis), there are no two organism where the preferred pairs of one organism were likely to be rejected in the other and vice versa. This could mean that although bias of almost every single codon is organism-dependent, there are several codon pairs that are preferred and/or rejected in almost every organism (e.g. because of their likeliness to cause frameshifts or tRNAs with not matching structure).

1.2.2 Patterns in codon pair bias

In order to visualize the observed codon pair bias, so-called maps can be drawn as has been done by Moura et al. (2005) (they refer to these maps as "codon context maps"). This can be most easily explained with reference to colored images that consist of colored rectangles for every codon pair, with the rows representing the first and the columns representing the second codon of the pair. Red colors indicate a negative and green ones a positive bias. White represents codon pairs that really have a bias equal 0 (which is the case for ATG-ATG, for example, since that is the only way to encode the amino acid pair Met-Met) and pairs incorporating a stop codon.

However, colored images cannot be part of the disclosure of a patent application. For black & white visualization, the image will be split in two images in this example. Figure 5A displays the positive codon pairs for A. niger, while Figure 5B displays the negative codon pairs for A. niger (see also Appendix 3, Table Cl). The more biased the codon-pair, the more black the corresponding rectangle. The bias values here range from -0.67 to 0.54, where in other organisms they might even get slightly above +/-0.9 (see also figure 3). The highest intensities of black (original green (top) and black (original red (bottom)) in these diagrams represent values of 0.9 and -0.9, respectively (not reached here; mostly, the absolute values of the maximum bias are slightly lower than those of the minimum bias. In addition, we refer to CPW matrix-tables in Appendix 3, which contain the numerical values of the bias of the codon pairs and we refer to Figure 5 as a black and white example of the colored image, whereby the skilled person may reconstruct a colored version using the numerical values from the tables in Appendix 3. The first approach to these codon pair maps was to have the rows and columns sorted according to their alphabetical order (as this is the order of their internal representation). What could be seen in that map was that the diagonals seemed to contain slightly more green than red spots, which indicates that many codons have a preference for the same codon as its neighbor. Furthermore, most neighboring columns were somewhat similar where neighboring rows were mostly not (data not shown) see Figures 5 A and 5B and Appendix 3, Table Cl. However most rows were similar to a row separated by three others, i.e. there was some similarity of every fourth row.

Since the common property of every fourth row is the last nucleotide of the first codon of the pairs, it is more preferred to sort rows sorted according to the alphabetical order of the third position as first sorting criterion and the middle position as second. What can then be seen in the map for A. niger (Figures 5C and D, and Appendix 3, Table Cl) is that bias seems to correlate indeed mainly with the last nucleotide of the first (5') and the first nucleotide of the second (3') codon, as most values of the respective blocks of 16*16 codon pairs have the same color. For example, a general rule that can be identified in Aspergillus is that codon pairs like xxT-Axx (x denoting any nucleotide, indicating that the one at the respective position is not important for the specified rule) are rejected (red block in the lower left corner), whereas the pattern xxA-Txx characterizes preferred codons (green block in the top right corner), again indicating that codon pair bias is directional. However, not all bias can be explained just with patterns in the two neighboring nucleotides in the "middle" of the codon pair. xxC-Axx codon pairs, for example (see second block from top on the very left), are not generally preferred or rejected, but there is a clear preference for pairs of the pattern xxC-AAx (note the four green columns on the left of the block just mentioned). Bias can also depend on not neighboring nucleotides (e.g. the strong rejection of CxA-Gxx pairs in B. subtilis; see Figures 6A and 6B and Appendix 3, Table C4). Unfortunately, codon pair bias cannot always be attributed to such "simple" patterns (see for example the rather chaotic map for E. coli in Figures 7A and B and Appendix 3, Table C5) - even when performing a cluster analysis using Spotfire DecisionSite 8.0 (http://www.spotfire.com/products/decisionsite.cfm) no general properties could be found (data not shown), i.e. the identified clusters consisted mostly of unrelated codons (i.e. no common nucleotides at the same position).

1.2.3 Relation of bias and expression level

Looking at the bias map for the genes with high expression level (or better: presumably high expression level, since they were identified by looking at transcription levels only) of A. niger (see Figure 8), the existence of larger groups, i.e. blocks in the diagram, is not as obvious (or, in other words, simple rules as described above might not exist at all). Yet since two thirds of all codon pairs occur 36 or less times in this group, and because of the on average much lower z-scores as mentioned above, one can attribute this to a large extent to random fluctuations.

Figure 9 shows a scatter plot of bias in a group of 479 highly expressed genes (vertical axis) versus the bias in all genes (horizontal) of A. niger. All 3,721 codon pairs not involving stop codons are shown.

Shading from light gray to black were assigned according to the absolute values of the z-scores in the overall genome, i.e. light dots in the plot do not have a significant bias in all genes), as were sizes according to the absolute z-scores in the highly expressed group, i.e. very small dots do not have a significant bias there (here |z-score|<1.9). The solid black line indicates where both bias values are equal; the dashed black line shows the best linear approximation of the actual correlation (identified by principal component analysis); its slope is around 2.1. When comparing the two bias values of each codon pair in the highly expressed group and in the full genome (see the scatter plot in Figure 9), one can see that for most pairs the bias in the highly transcribed group is more extreme, i.e. lower if it is below 0 and higher if it is positive, but there are some pairs where the bias values are quite different and even have a different sign. However, these are mostly codon pairs with a small number of occurrences in the top group, and most pairs where the bias is highly significant (blue, large circles) have similar biases in both groups (i.e. they are close to the blue line that indicates where both bias values are equal).

No specific patterns regarding similar bias differences of codons that share two of the three nucleotides could be found (neither for A. niger nor for B. subtilis), i.e. in plots of the bias difference analogous to the one above there were no larger groups with similar bias difference.

1.3. Details of the identification of codon pair weights for gene adaptation

Codon pair weight for adaptation can be determined now according the described methods (Appendix 1: Codon pair weights - method one sequence group (or genome)): 1. based on the full set of genes; based on a subset of 1.

2. being identified as the fraction of highly expressed genes.

In addition, we started a search to identify codon pair weights that clearly relate to a higher transcription level, which is required for a improved method for adaptation of codon pair usage, the following methods have been applied: In A. niger, where a complete ranking extracted from GeneChip data was available for the aforementioned set of 4,584 actually expressed genes (see "Data" in "Materials and Methods"), the mean codon pair weights of each gene (i.e. the equivalent of the fitcp(g) values) were calculated. Then the genes were sorted according to fitness values (ascending order) and expression level (descending order). Since highly expressed genes are supposed to have low codon pair fitness values, these two rankings would be equal when using ideal codon pair weights, so a comparison of these two rankings can give information about the quality of the weights used in the fitness function (where slightly more attention was given to the "correct" ranking of the highly expressed genes than to the ranking of the mediocre ones). Additionally, the correlation coefficient (covariance divided by the standard deviation of each variable) between ranking and average codon pair weights of the 4,584 genes was calculated.

Several possible sets of weights have been examined, including i. bias values from the whole genome, ii. bias values of the highly expressed group, iii. bias with all the values that do not have a certain minimum z-score set to zero iv. bias values raised to the power of 2 (and some other values) to give highly preferred or rejected codons a lower/higher influence v. combinations thereof vi. z-scores themselves vii. difference of bias values/z-scores from the highly expressed group and the full genome.

For the genetic algorithm (GA), their negations have been used, since preferred codon pairs had been identified with positive values (rather arbitrarily), but the GA performs minimization. This applies to all weights mentioned.

Out of these, the "best" weight matrix turned out to be a combination of item ii to iv, however, an even better one could be obtained - as described above - by calculating the codon pair "bias" in the highly expressed group using expected values calculated based on the codon ratios of the whole genome. Figure 10 shows the correlation that is observed. Unlike all other weight sets tested, codon pairs involving codons that are more underrepresented in the highly expressed group get a slight disadvantage here. Thus, these weights are the only ones that also reflect the different single codon bias of the highly expressed group and all genes. Using these weights carries the risk of rejecting some codon pairs that actually have a positive bias in the highly expressed group, but consist of (in the highly expressed group) rarely used codons. However, since our desired single codon ratios are usually not identical to those in the group of genes with high expression, but more "extreme" than these, single codon optimization would replace these underrepresented anyway, so we can consider the weights described above very convenient for codon pair optimization. Concluding, a potentially improved codon pair weight matrix for gene adaptation has been identified as described above. The equation is given in Appendix 1: Codon pair weights - method highly expressed group with reference group (or genome).

1.4. Single codon and codon pair optimization in silico 1.4.1 Material and methods

The developed MATLAB toolbox for analyzing and optimizing genes consists of several functions that have been organized in different directories according to their capacities. In order to use them, it is therefore necessary to make all of them known to the MATLAB environment. To do this, select "Set Path" from the File menu and then click "Add with subfolders" and select the path where the toolbox is installed (usually called "Matlab-bio"). Also add the location of FASTA and other files that should be analyzed. All individual MATLAB functions are briefly described in "contents.m" (type "help Matlab-bio" to display this file in the MATLAB environment and use "help" followed by a function's name to get detailed information about it). For gene optimization focusing on codon pair usage, the two important functions are "f ullanalysis" and "geneopt".

If the full genome of an organism you want to adapt a gene to is located in the file, say, "Aniger_ORF.fasta" and the identifiers of its highly expressed genes are in "an-high.txt" type "f ullanalysis ( ' Aniger_ORF . f asta ' , ' an-high . txt ' , ' an ' ) ; " and you will get (i) a codon pair bias map for the full genome, (ii) a codon pair bias map for the group of genes in the second file and (iii) several variables (i.e. sets of temporarily stored data) in the MATLAB workspace for further use. The third parameter of "fullanalysis" determines only how these variables are named and can be omitted if only one genome is to be analyzed at the same time. Among the mentioned variables are: (i) codon pair usage and bias data for the full genome (named "cpan" in this example), (ii) the same for the special group of genes specified by the second parameter (named "cpans") and (iii) structure with target single codon ratios and codon pair weights that can be used for the genetic algorithm. "fullanalysis ( xXyz_ORF . f asta' ) ; " will only show the codon pair bias map and store the bias data for the respective genome. Although the second parameter may be any file that includes gene identifiers (e.g. a set of genes with low expression or genes with a certain common function), it is always treated like a set of highly expressed genes regarding this (potential) parameter (named "optpαrαmforαn" in the example, which stands for the optimization parameter for the specified organism). Note that the single codon ratios here are simply calculated r ^ (ck) = 2 - rsc (ck) - rsc (ck ) ^ wnicn is an acceptable approximation. Target ratios might be as well identified by other methods that include the details of the single codon distribution (see main text) in order to further improve specification of desired ratios. In addition, target ratios may be left empty when no specific bias is found, in order to give the codon-pair algorithm more freedom in finding solutions with a higher codon-pair fitness. Several of such pre-determined single-codon target vectors are given in Appendix 1, for various host organisms.

To use pre-specified single-codon target ratio's for the genetic algorithm, change the field "cr" of the parameter by typing "optparamf oran . cr = [", then paste the single codon ratios (e.g. copied from an Excel sheet; note that they should be in alphabetical order of the codons), type "] ; " if the ratios are available as a 64-element row or "] ' ; " if they are copied from a column and press enter (note the additional single quotation mark or apostrophe following the closing bracket in the latter case). Unimportant codon ratios, i.e. codons where no specific target ratio is desired, may be assigned the "value" NaN (not a number) and they will be ignored when single codon fitness is calculated. To exclude certain short sequences from the optimized gene, set the parameter "rs" in the same way, where each sequence must be enclosed by single quotation marks and all sequences together must be enclosed in braces, e.g. (without the line break) "optparamf oran . rs = { ' CTGCAG ' ' GCGGCGCC ' } ; ". Finally, the field cpi of the parameter might be changed to give single codon optimization or codon pair optimization a higher importance in the combined fitness function (see the subsection "performing codon pair optimization" in "results and discussion"). The default value is 0.2. Set it to a lower value if the results of the experiments with codon pair optimized genes reveal little improvement of codon pair optimized genes compared to single codon optimized ones; in the opposite case, a higher cpi might be better.

The actual optimization of the gene using the genetic algorithm can then be performed using the function geneopt. The only parameters needed are the sequence to be optimized and the structure containing codon pair weights, target ratios and restriction sites as described above, so geneopt ( XMUVARNEQST* ' , optparamf oran) ; could for example be used to optimize the given (rather short) protein sequence for high expression in A. niger; the ' * ' is used to denote that the resulting genetic sequence should have a stop codon at the end (however, as the optimal stop signal in A. niger is believed to be the tetramer TAAA, this is not necessary). Note that the sequence to be optimized must again be enclosed in single quotation marks; if the sequence contains only the letters A, C, G, T or U and its length is a factor of 3, it is automatically regarded a nucleotide sequence. The genetic algorithm then runs for 1000 generations with a population size of 200, of which 80 each are kept for the generation (the 79 best and one randomly picked) and used to generate new individuals, where 40% of the new individuals are generated using crossover and 60% using the mutation operator. These default values turned out to be very convenient for the optimization, i.e. changes in these parameters will only, if at all, lead to very slightly "better" genes, but they can be changed as well, for example if significantly more or less calculation time should be spent on the optimization (an average run of geneopt with a gene of about 500 codons takes about 15 minutes on a 1.4 GHz Pentium M Processor), geneopt ( seq, optparamf oran, [ 50 750 5 0 0 . 6 ] ) will, for example, let the genetic algorithm calculate 750 generations of a population where 50 individuals are kept for each new generation and 250 are newly generated (5*50; i.e. 300 individuals are examined in each generation), only the best (and no randomly picked) individuals are kept and 60% of the recombinations are performed using the crossover operator. For more details on how to specify these parameters, type help geneopt and help genet icalgorithm. Note that although the procedure of generating codon pair weights from analyzing the corresponding FASTA files is shown and described here for A. niger and B. subtilis, just for these two organisms this is not necessary because these calculations have already been performed for previous gene optimizations. For easier use, the respective parameters for the genetic algorithms have been stored (type "load gadata for an" or "load gadata for bs", respectively; note that the parameters there are now just simply called an_param and bs_param.

1.4.2 Results

Figure 11 shows fitness values of five optimized versions each for different values of cpi (see legend of the diagram in Figure 11). The protein is a fungal α-amylase (FUA; also referred to as AmyB) that was optimized for the host A. niger (see Example 2). Additionally, the results of "pure" single codon optimization (black dots on the right) and codon pair optimization are shown (group top left). The optimized versions were obtained by running the genetic algorithm for around 1000 generations with a population size of 400, which took about 17 minutes for each run on a 1.4 GHz Pentium M. Note that pure single codon optimization and pure codon pair optimization took only about 60% of that time.

In Figurel 1 the wild type (fitsc(gfUa)=0Λ65,fitcp(gfua)=0.033) does not fit on this plot (it would be far to the right and above). The optimal gene is always the one with the lowest values for fitsc and fitcp. Given the position of the dots, it is therefore not clear for which value of cpi the most improved gene could be obtained, since we do not know yet whether single codon usage or codon pair usage is more important. However, a fare trade-off seems to appear in case of cpi = 0.2.

The improvement in single codon and codon pair usage can be visualized in so-called sequence quality plots proposed in this work. Figure 12 illustrates two diagrams which show the sequence quality of the first 20 (out of 499) codons of the aforementioned FUA (see also Example 2).

Note that these sequence quality diagrams not only depend on the sequence itself, but also on the set of weights and the desired single codon ratios and thus on the organism. Note also that it is possible to define target single codon ratios as "don't care" for those codons with low or no codon bias, i.e. the usage of a certain codon is not considered positive or negative for expression compared to its synonymous codons. In that case, only the blue x-mark is shown for the actual ratio of the respective codon in the gene and that particular position is ignored when calculating single codon fitness (see 1.4. Single codon and codon pair optimization in silico).

1.5 Conclusions

A significant correlation of codon pair usage and transcription levels has been established in a wide range of organisms. It was demonstrated that this bias cannot only be explained by dinucleotide bias around the reading frame site. Since possible explanations for preference or rejection of certain codon pairs all focus on the translation, it should be assumed that both are caused by natural selection acting at the same time on characteristics that affect translation and other characteristics that affect transcription in order to minimize the cell's efforts to produce enzymes or at least the more important of them.

Optimizing codon pair usage in polypeptide coding sequences can thus be considered for achieving improved overexpression, in addition to classic single-codon optimization or single codon harmonization, where only single codons frequencies are considered for optimization. Codon pair adaptation and single codon adaptation of the same gene interfere only slightly for the investigated fungal host class and the bacilli in this example, i.e. both can be performed at the same time and the result will have "better" single codon usage and "better" codon pair usage than the wild-type gene, and any of the two aspects can only be improved slightly when ignoring the other one.

To read the FASTA files and perform the analysis and optimization, user-friendly MATLAB functions have been designed. New methods of visualizing codon pair bias and codon pair usage of single genes have been introduced as well, see Example 2 and Example 4. The genetic algorithm designed for the optimization allows effective dealing with the constraints imposed by interdependence of adjacent codon pairs while the specially designed mutation operators that always improve one of the two aspects of sequence quality (single codon an codon pair fitness) help to circumvent the inefficiency usually accompanying genetic algorithms because of their trait of generating many bad possible solutions in the recombination step after the first few generations.

The proper codon pair usage influences enzyme production, which will be shown experimentally in the following examples. Codon pair optimized variants of three genes to be expressed in B. subtilis have been prepared, of which one each will be compared to a synthetic gene that has adapted single codon usage only and another one to a synthetic gene that has gone through the optimization process using the negation of the presumably positive weights, but still been optimized for single codon usage the same way as before, see Example 4 and Example 5. This way, the notion of Irwin et al. (1995) that underrepresented codons stimulate translation, which was rejected here, will also put to the test. For A. niger, a codon pair optimized version of the aforementioned amyB will be tested and compared to the wild-type and synthetic gene with single codon harmonization, see Examples 2 and 3.

2. Example 2: Use of a method of the invention for construction of improved DNA sequences for improving production of the Aspergillus niger fungal amylase enzyme in A. niger. Below, the method of the invention is applied to design novel nucleotide sequences for the

AmyB (FUA) gene of A. niger, which are optimized in single codon and / or codon pair usage for improved expression in A. niger. This method can be applied the same way for the improvement of codon use of any nucleotide sequence.

2.1 Introduction

A concept of single-codon optimization by means of codon-harmonization was previously developed by the applicants of this invention and reported in the main text (see also example 3). In this example we show how one applied the method of the invention to design a gene that were optimized for both single codon and codon pair usage. In this specific case weight matrices are applied that have been created by applying two subsets of 2% and 4% of highly expressed genes of the full A. niger genome that contains 14,000 genes. For the single-codon usage the algorithm has driven the solution to a gene with synonymous codon-frequencies as defined by Table B.I (= column 3 of Table 2.1), while for the codon-pair usage, it will optimized toward an optimal set of codon-pairs with a high frequency of them having associated negative weights (in Table C.2), being the codon-pairs that are overrepresented with respect to its expected values in the set of 4% highly expressed genes. Note that in case one does not have a defined list of highly expressed genes for a specified host, one can also (i) apply the weight matrices of a similar host organism, for example the P. chrysogenum matrices can be applied for A niger, or (ii) apply the full genome sequence data or a subset of it to derive good, but less optimal weight matrices.

2.2 Materials and Methods

2 .2.1 Wild-type amvB coding sequence encoding A. niger alpha-amylase AmvB

The DNA sequence of the amyB gene encoding the alpha-amylase protein was disclosed in J. Biochem. MoI. Biol. 37(4):429-438(2004) (Matsubara T., Ammar Y.B., Anindyawati T., Yamamoto S., Ito K., Iizuka M., Minamiura N. "Molecular cloning and determination of the nucleotide sequence of raw starch digesting alpha-amylase from Aspergillus awamori KT-I l.") and also can be retrieved from EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/index.html) under accession number AB083159. The genomic sequence of the native A. niger amyB gene is shown as SEQ ID NO. 1. The corresponding coding or cDNA sequence of amyB is shown as SEQ ID NO. 2. The translated sequence of SEQ ID NO. 2 is assigned as the SEQ ID NO. 3, representing the A. niger alpha-amylase protein AmyB. This sequence has also a 100% similarity with the A. oryzae alpha-amylase protein (Wirsel S., Lachmund A., Wildhardt G., Ruttkowski E., "Three alpha-amylase genes of Aspergillus oryzae exhibit identical intron-exon organization."; MoI. Microbiol. 3:3-14(1989, UniProt accession nr. P 10529, Pl 1763 or Q00250). Optimization according a method of the invention has been performed on the amyB cDNA sequence.

2.3 Design procedure The optimized coding nucleotide sequence SEQ ID NO 6 is the result of a run with the described software method. The applied parameters were: population size = 200; number of iterations = 1000; cpi = 0.20, CPW matrix = "Table C.2. CPW: Aspergillus niger - highly expressed sequences" and the CR matrix = "Table B.I column 4: CR table ANS: Aspergillus niger - highly expressed sequences". Moreover, a penalty value of +1 is added to fitcombι for each occurrence of a Pstl (CTGCAG) and Notl (GCGGCGCC) site.

Convergence of the solution toward a minimal value for fitCOmbι is shown in Figure 13. The obtained objective values for SEQ ID NO. 6 are given in Table 2.2, together with those for SEQ ID NO. 2 and SEQ ID NO. 5. Figure 14 explains the single codon statistics for these genes as is shown in Figure 15 and 16, and Table 2.2 gives the actual values for the codons in the three sequences. Figure 18-20 show both single-codon and codon pair statistics for the three gene variants. This type of graph is explained in detail in Figure 17 and its description. From these graphs it is clear that single-codon statistics are highly similar for SEQ ID NO. 5 and SEQ ID NO. 6. However, the method of the invention leads to a gene with an improved number of codon pairs with associated negative weights (wcp{g) < 0), 93% vs. 74%, and also a further reduction in fitcp from -0.18 to -0.34 indicating a more optimal usage of codon pairs having more negative weights associated with them.

Table 2.1 Codon optimization for amyB.

AA Codon Optimal amyB amyB amyB amyB codon w.t. w.t. SC sc & cp distribution [# [% optimized optimized

[%] codons] codons [# codons] [# codons ]

/AA]

A AIa GCT 38 5 11.9 16 18

AIa GCC 51 15 35.7 21 23

AIa GCA 0 12 28.6 0 0

Ala GCG 11 10 23.8 5 1

C Cys TGT 0 7 77.8 0 0

Cys TGC 100 2 22.2 9 9

D Asp GAT 36 20 47.6 15 15

Asp GAC 64 22 52.4 27 27

E GIu GAA 26 5 41.7 3 3

GIu GAG 74 7 58.3 9 9

F Phe TTT 0 3 20.0 0 0

Phe TTC 100 12 80.0 15 15

G GIy GGT 49 10 23.3 21 22 GIy GGC 35 18 41.9 15 15 GIy GGA 16 10 23.3 7 6 GIy GGG 0 5 11.6 0 0

H His CAT 0 3 42.9 0 0 His CAC 100 4 57.1 7 7

Ile ATT 27 7 25.0 7 7

Ile ATC 73 19 67.9 21 21

He ATA 0 2 7.1 0 0

K Lys_AAA 0 7 35.0 0 0 Lys AAG 100 13 65.0 20 20

L Leu TTA 0 1 2.7 0 0

Leu TTG 13 10 27.0 5 4 Leu CTT 17 4 10.8 6 7

Leu CTC 38 13 35.1 14 15

Leu CTA 0 3 8.1 0 0

Leu CTG 32 6 16.2 12 11

M MetATG 100 10 100.0 10 10

N AsnAAT 0 3 11.5 0 0

AsnAAC 100 23 88.5 26 26

P Pro CCT 36 6 27.3 8 8

Pro CCC 64 8 36.4 14 14

Pro CCA 0 3 13.6 0 0

Pro CCG 0 5 22.7 0 0

Q GIn CAA 0 5 25.0 0 0

GIn CAG 100 15 75.0 20 20

R Arg CGT 49 1 10.0 5 5

Arg CGC 51 2 20.0 5 5

Arg CGA 0 2 20.0 0 0

Arg CGG 0 2 20.0 0 0

Arg AGA 0 0 0.0 0 0

Arg AGG 0 3 8.1 0 0

S Ser TCT 21 4 10.8 8 8

Ser TCC 44 9 24.3 16 17

Ser TCA 0 4 10.8 0 0

Ser TCG 14 10 27.0 5 4

SerAGT 0 4 10.8 0 0

SerAGC 21 6 16.2 8 8

T Thr ACT 30 9 22.5 12 12

Thr ACC 70 13 32.5 28 28

Thr ACA 0 10 25.0 0 0

Thr ACG 0 8 20.0 0 0

V VaI GTT 27 5 16.1 8 9 VaI GTC 54 12 38.7 17 17

VaI GTA 0 4 12.9 0 0

VaI GTG 19 10 32.3 6 5

W Trp TGG 100 12 100.0 12 12

Y Tyr TAT 0 11 31.4 0 0

Tyr TAC 100 24 68.6 35 35

ible 2.2 Codon optimization for amyB.

Sequence Type Ih fit* Wrp 8) /*' cumbϊ

0 (rpi=02)

SEQ ID NO. 2 W T 0, 1652 0.0329 37 .3% 0.090

SEQ ID NO. 5 SC optimized 0, 0(46 -0.1765 73 .9% -0.862

SEQ ID NO. 6 SC f cp optimized 0, 0109 -0.3420 92 .6% -1 .621

All three sequences listed in Table 2.2 are coding sequences of which the translated sequence Is assigned a* SEQ (D , ->.

3. Example 3: Testing of the method of the invention for construction of improved DNA sequences for providing improved production of the Aspergillus niger fungal amylase enzyme in A. niger. The method of the invention is below applied to the improvement of single codon and codon pair use of the AmyB gene of A. niger. This method can be applied the same way for the improvement of codon use and improved expression of any nucleotide sequence.

3.1 Material and Methods 3.1.1 Strains

WT 1 : This A. niger strain is used as a wild-type strain. This strain is deposited at the CBS Institute under the deposit number CBS 513.88.

WT 2: This A. niger strain is a WT 1 strain comprising a deletion of the gene encoding glucoamylase (glaA). WT 2 was constructed by using the "MARKER-GENE FREE" approach as described in EP 0 635 574 Bl. In this patent it is extensively described how to delete glaA specific DNA sequences in the genome of CBS 513.88. The procedure resulted in a MARKER- GENE FREE AgIaA recombinant A. niger CBS 513.88 strain, possessing finally no foreign DNA sequences at all.

WT 3: This A. niger strain is a WT 2 strain comprising a mutation which results in an oxalate deficient A. niger strain. WT 3 was constructed by using the method as described in EP 1590444. In this patent application, it is extensively described how to screen for an oxalate deficient A. niger strain. Strain WT3 was constructed according to the methods of Examples 1 and 2 of EP 1590444, strain WT 3 is mutant strain 22 of EP 1590444 (designated FINAL in EP1590444).

WT 4: This A. niger strain is a WT 3 strain comprising the deletion of three genes encoding alpha-amylases (amyB, amyBl and amyBlϊ) in three subsequent steps. The construction of deletion vectors and genomic deletion of these three genes has been described in detail in WO2005095624. The vectors pDEL-AMYA, pDEL-AMYBI and pDEL-AMYBII, described in WO2005095624, have been used according the "MARKER-GENE FREE" approach as described in EP 0 635 574 Bl. The procedure described above resulted in an oxalate deficient, MARKER-GENE FREE AgIaA, AamyA, AamyBl and AamyBU amylase-negative recombinant A. niger CBS 513.88 strain, possessing finally no foreign DNA sequences at all. As such, WT 4 is more optimized for alpha-amylase expression compared to WTl.

3.1.2 A. niger shake flask fermentations A. niger strains were pre-cultured in 20 ml pre-culture medium as described in the

Examples: "A. niger shake flask fermentations" section of WO99/32617. After overnight growth, 10 ml of this culture was transferred to fermentation medium 1 (FMl) for alpha- amylase fermentations. Fermentation is performed in 500 ml flasks with baffle with 100 ml fermentation broth at 34°C and 170 rpm for the number of days indicated, generally as described in WO99/32617.

This FMl medium contains per liter: 52.570 g glucose, 8.5 g maltose, 25 g Caseinhydrolysate, 12.5 g Yeast extract, 1 g KH2PO4, 2 g K2SO4, 0.5 g MgSO4.7H2O, 0.03 g ZnC12, 80.02 g CaC12, 0.01 g MnSO4.4H2O, 0.3 g FeSO4.7H2O, 10 ml Pen-Strep (Invitrogen, cat. nr. 10378-016), 48 g MES, adjusted to pH 5.6 with 4 N H2SO4.

3.1.3 Fungal alpha-amylase activity

To determine the alpha-amylase activity in A. niger culture broth, the Megazyme cereal alpha-amylase kit is used (Megazyme, CERALPHA alpha amylase assay kit, catalogue, ref. K- CERA, year 2000-2001), according protocol of the supplier. The measured activity is based on hydrolysis of non-reducing-end blocked p-nitrophenyl maltoheptaoside in the presence of excess glucoamylase and α-glucosidase. The amount of formed p-nitrophenol is a measure for alpha-amylase activity present in a sample.

3.2 Construction of an Aspergillus expression construct for the wild-type amyB coding sequence encoding A. niger alpha-amylase AmyB

The DNA sequence of the wild-type amyB gene have been described under 2.2.1. For expression analysis in Aspergillus species of A. niger amyB constructs, the strong amyB promoter is applied for over-expression of the alpha amylase enzyme in A. niger using pGBFIN- based expression constructs (as described in WO99/32617). The translational initiation sequence of the amyB promoter including ATG start codon of PamyB is 5'-GGCATTTATG ATG-3' or 5'-GAAGGCATTT ATG-3', dependent on which ATG is selected as start codon. This translational initiation sequence of PamyB has been modified into 5'-CACCGTCAAA ATG-3' in all subsequent amyB expression constructs generated below. Appropriate restriction sites were introduced at both ends to allow cloning in an expression vector. The native amyB gene contains a 'TGA' stop codon. In all amyB constructs made below, the 5'-TGA-3' translational termination sequence was replaced by 5'-TAAA-3' followed by the 5' -TTAATT AA-3' of the Pad restriction site. At the 5 '-end an Xhol site was introduced and at the 3 '-end a Pad site. Therefore, a fragment comprising a modified genomic amyB promoter and amyB cDNA sequence was completely synthesized, cloned and the sequence was confirmed by sequence analysis.

This fragment comprising the alpha-amylase promoter with modified translational initiation sequence and amyB cDNA sequence with modified translational termination sequence was digested with Xhol and Pad and introduced in an Xhol and Pad digested pGBFIN-12 vector (construction and layout as described in WO99/32617), generating pGBFINFUA-1 (Figure 21). The sequence of the introduced PCR fragment was confirmed by sequence analysis and its sequence is presented in SEQ ID NO. 4.

3.3 Improvement of the single-codon usage for the alpha-amylase coding sequence amyB for expression in A. niger

A method of single-codon optimization is applied below for the improvement of codon use of the amyB gene of A. niger. The nucleotide coding sequence of the native amyB is shown as SEQ ID NO. 2. The codon use of the native amyB gene of A. niger and the synthetic optimized variant are given in Table 2.1 below. For the native and single-codon optimized synthetic amyB gene, the exact numbers for each codon are given as well as the distribution per amino acid. Additionally, the third column provides the proposed optimal distribution, which is the target for optimization. For the group 1 amino acids, there is only one possibility. Group 1 consists of methionine that is always encoded by ATG and tryptophane that is always encoded by TGG.

The group 2 amino acids are subject to optimization according to the extreme frequency of 0% or 100%, the strategy is clear. All codons for a group 2 AA are specifically changed into the optimal variant of the two possible codons. More specifically for cysteine, a codon, TGT is replaced by TGC; for phenylalanine, TTT by TTC; for histidine, CAT by CAC; for lysine, AAA by AAG, for asparagine, AAT by AAC; for glutamine, CAA by CAG; for tyrosine, TAT by TAC.

The group 3 amino acids can be encoded by several codons as indicated in Table 3.1; each codon being present in a preferred codon frequency: for alanine GCT, GCC, GCA, GCG; for aspartate, GAT, GAC; for glutamate, GAA, GAG; for glycine, GGT, GGC, GGA, GGG; for isoleucine, ATT, ATC, ATA; for leucine, TTA, TTG, CTT, CTC, CTA, CTG; for proline, CCT, CCC, CCA, CCG; for arginine, CGT, CGC, CGA, CGG, AGA, AGG; for serine, TCT, TCC, TCA, TCG, AGT, AGC; for threonine, ACT, ACC, ACA, ACG; for valine, GTT, GTC, GTA, GTG, are optimized according the following methodology: For the group 3 amino acids (AA) and their encoding codons, the calculation of the optimal occurrence of each possible codon within a given coding sequence is performed according to the following methodology: i. sum for each of the respective group 3 AA, the total number of residues encoded in the given sequence, see column Al (Table 3.1), ii. for each AA and codon encoding that AA, multiply the total number for that AA by the optimal codon distribution in Table 2.1, resulting in a raw codon distribution, which generally may contain decimal numbers, see column A2 (Table 3.2), iii. round off the values of the raw codon distribution (ii), by removing the digits, resulting in a rounded off codon distribution, see column A3 (Table 3.2), iv. sum for each of the AA, the total number of AA represented in the rounded off codon distribution (iii), see column A4 (Table 3.1), v. calculate the total missing number of residues for each of the respective AA in the rounded off codon distribution, by subtracting the total number of residues encoded in the given sequence (i) with the total number of AA represented in the rounded off codon distribution (iv), see column A5 (Table 3.1), vi. calculate for each codon, the decimal difference between the raw codon distribution (ii) and the rounded off codon distribution (iii) by subtraction, see column A6 (Table 3.2), vii. multiply for each codon, the decimal difference (vi) and the optimal codon distribution in table 1, giving a weight value for each codon, see column A7 (Table 3.2), viii. for each of the respective AA, select for the amount of missing residues (v), the respective amount of codons that have the highest weight value (vii), see column A8

(Table 3.2), ix. the calculation of the final optimal codon distribution within a given sequence encoding a polypeptide is calculated by summing the rounded off codon distribution (iii) and the selected amount of missing residues (viii) for each codon, see column A9 (Table 3.2).

Table 3.1

AA(i) I Al A4 A5

Ala 1 42 40 2

Asp 2 42 41 1

GIu 3 12 11 1

GIy 4 43 42 1 lie 5 28 27 1

Leu 6 37 35 2

Pro 7 22 21 1

Arg 8 10 9 1

Ser 9 37 35 2

Thr 10 40 40 0

VaI 11 31 29 2

Table 3.2

Subsequently, a completely new nucleotide coding sequence was created by random distribution of the proposed number of synonymous codons (Table 2.1) for each amino acid in the original amyB peptide. The synthetic amyB sequence, resulting from the process described above, is indicated in SEQ ID NO. 5. Secondary structures in the modified coding sequence were checked using the Clone Manager 7 program (Sci. Ed. Central: Scientific & Educational software, version 7.02) for possible occurrence of harmful secondary structures.

3.4 Optimization of the coding sequence according a the combined single-codon and codon- pair method of the invention for the alpha-amylase coding sequence amyB for expression in

A. niger

A method of the invention is applied for the improvement of the coding sequence of the amyB gene of A. niger. The optimized amyB sequence, resulting from the process described in

Example 2, is indicated in SEQ ID NO. 6. Secondary structures in the modified coding sequence were checked using the Clone Manager 7 program (Sci. Ed. Central: Scientific & Educational software, version 7.02) for possible occurrence of harmful secondary structures.

3.5 Construction of modified amyB expression vectors for expressing A. niger alpha-amylase ArnyB encoded by coding sequences described in examples 3.2 and 3.3

The DNA sequence of the Xhol - Pad fragment of pGBFINFUA-1 (Figure 21) is shown as SEQ ID NO. 4 and comprises the amyB promoter and wild- type amyB cDNA sequence with a modified translational initiation sequence and modified translation stop sequence. The DNA sequence comprising a variant of the translational initiation sequence of the alpha-amylase promoter combined with a codon optimized coding sequence for the alpha-amylase encoding amyB gene, as described in Example 1.2, is shown as SEQ ID NO. 7. The DNA sequence comprising a variant of the translational initiation sequence of the alpha-amylase promoter combined with an optimized coding sequence according the combined single-codon and codon- pair method of the invention for the alpha-amylase encoding amyB gene, as described in

Example 3.3, is shown as SEQ ID NO. 8.

For cloning these modified sequence variants in an expression vector, the two synthetic gene fragments were digested with Xhol and Pad and introduced in the large fragment of an

Xhol and Pad digested pGBFINFUA-1 vector (Figure 21), generating variant expression vectors. After checking the integration of the correct fragment, the variant expression constructs were named pGB FINFU A-2 and pGB FINFU A-3, as described below in Table 3.3.

Table 3.3: Modified expression constructs for alpha-amylase expression in A niger

The translated sequences of the amyB coding sequences of plasmid pGB FINFU A-I to pGB FINFU A- 3 are according to the amino acid sequence as depicted in SEQ ID NO 3, representing the wild-type A. niger alpha-amylase enzyme.

3.6 Expression in A. niger of modified pGBFINFUA- expression constructs of A. niger alpha- amylase

The pGBFINFUA- 1, -2 and -3 expression constructs, prepared as described above, were introduced in A. niger by transformation as described below and according to the strategy depicted in Figure 22. In order to introduce the three pGBFINFUA- 1, -2 and -3 vectors (Table 3.3) in WT 4, a transformation and subsequent selection of transformants was carried out as described in WO98/46772 and WO99/32617. In brief, linear DNA of the pGBFINFUA- constructs was isolated and used to transform A. niger. Transformants were selected on acetamide media and colony purified according standard procedures. Colonies were diagnosed for integration at the glaA locus and for copy number using PCR. Ten independent transformants of each of the pGBFINFUA- 1, -2 and -3 constructs with similar estimated copy numbers (low copy: 1-3) were selected and numbered using the name of the transforming plasmid, as for example FUA-I -1 (for the first pGBFINFUA-1 transformant) and FUA-3-1 (for the first pGBFINFUA-3 transformant), respectively. The selected FUA-strains and A. niger WT 4 were used to perform shake flask experiments in 100 ml of the medium and under conditions as described above. After 3 and 4 days of fermentation, samples were taken.

The production of alpha-amylase enzyme was measured in all three different A. niger FUA-transformants. As can be learned from Figure 23, optimization of the coding sequence according the method of the invention shows a higher improvement on expression of AmyB compared to the other method tested called single-codon optimization. These figures have been summarized in Table 3.4 below. Table 3.4. Relative average alpha-amylase activities of transformants with wild-type construct compared to those with modified amyB coding sequences (as concluded from Figure 23).

These results indicate clearly that the method of the invention can be applied to improve protein expression in a host, although the expression construct and host has already several other optimizations, such as for example a strong promoter, an improved translation initiation sequence, an improved translation stop sequence, an optimal single-codon usage and / or an improved host for protein expression.

4. Example 4: Design of improved DNA sequences for expression of three heterologous enzymes in Bacillus species: Bacillus subtilis and Bacillus amiloliquefaciens.

4.1. Introduction Example 4 describes the experiment design and application of a method of the invention described in this patent for (improved) expression of heterologous proteins in both Bacillus species, more specifically in this example Bacillus subtilis and Bacillus amiloliquefaciens. A preferred expression host is Bacillus amiloliquefaciens. The Bacillus subtilis genome was published in 1997 and other Bacillus species followed (Kunst, F. et al. 1997 '. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-56; Rey, M.W. et al. (2004). Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biology 5:R77; Rasko D.A. et al. (2005). Genomics of the Bacillus cereus group of organisms. FEMS Microbiology Reviews 29:303-329). In this example, the full sequence of B. subtilis was chosen as the basis for calculating single-codon frequencies and codon-pair weights. Comparison of GC-content and tRNAs provided a similar picture for the Bacillus species mentioned (vide supra). This is an indication that the same statistics are applicable for other related Bacillus species. Moreover, from example 1 (see also Figure 4), it was already clear that related species show similar codon-pair frequencies.

In Figure 4 (see also example 1), a codon-pair comparison plot, based on full genome statistics for B. subtilis vs. B. amyloliquefaciens can be found. A good correlation between both data sets is observed. Moreover, it seems that B. amyloliquefaciens is more versatile, since there is a subgroup of codon-pair combinations that is well accepted in B. amiloliquefaciens, while it has highly negative values for B. subtilis; the opposite is not observed.

4.2. Experiment design

Three proteins sequences were selected for expression in both Bacillus subtilis and Bacillus amiloliquefaciens: Protein 1: Xylose (glucose) isomerase xylA (EC.5.3.1.5) from Bacillus stearothermophilus;

Protein 2: Xylose (glucose) isomerase xylA (EC.5.3.1.5) from Streptomyces olivochromo genes; Protein 3: L-arabinose isomerase (EC 5.3.1.4) from Thermoanaerobacter mathranii. Table 4.1 Overview gene constructs; Protein 2 was chosen to further explore the codon-pair concept in broader sense.

Table 4.1 provides an overview of the methods applied to the 3 genes described above. For Protein 1, Protein 2 and Protein 3, the codon-pair optimization of the method of the invention is applied in addition to the single codon optimization developed before.

As a control, the effect of single codon optimization and negative codon pair optimization was tested experimentally by including 2 additional constructs for protein 2. One variant (SEQ. ID. 18) is designed where it is 'optimized' toward bad codon pairs (i.e. negative codon- pair optimization), and a second one with only single-codon optimization (SEQ. ID. 17). Protein 2 was chosen, since Streptomyces species show highly different codon-pair bias, see example 1 and Figure 4.

All designed B. amyloliquefaciens genes avoided the occurrence of Ndel (CATATG) and BamHl (GGATTC) restriction sites. Additionally, they contained a single restriction site for removing the E. coli part of the cloning vector pBHA12.

4.3. Single codon optimization

Single-codon optimized variants for Protein 1 and Protein 2 were designed using the method described in Example 3.3 for single-codon optimization, resulting in SEQ ID NO. 16 and SEQ ID NO. 17, respectively. The applied single-codon distribution table (Table 4.2) was determined using the 50 most-highly expressed genes as determined by 24 Affymetrix GeneChips for B. subtilus 168 using 6 independent fermentation time-series. All GeneChips were normalized with respect to their arithmetic mean. The expression list excludes those genes that were deliberately over expressed in strain engineering, and hence their measured expression level cannot be correlated with their codon usage.

Determination of single codon distribution table 4.2 is done by visual inspection of codon frequency histograms of 50, 100, 200, 400 highest expressed sequences and of all B. subtilis sequences. In case of a clear trend toward either 0% or 100% for the most highly expressed genes, an assignment of 0% and 100% was made, respectively. For the other codons that were not assigned, the average usage was calculated and normalized to the set of synonymous codons, by leaving out the assigned codons. The resulting target single-codon frequencies are given in Table 4.2, column 3.

Table 4.2 Codon-usage distribution for synthetic gene design on the basis of the 50 most highly- expressed genes and visual inspection of single codon usage histograms, e.g. Figure 24; Don' t care terms can be applied during codon-pair optimization to let the choice for those codons free, thus not taking into account single-codon optimization for these codons.

Single codon

Don't care = 0 distribution

% care = 1

A AIa GCT 50 0

AIa GCC 0 1

AIa GCA 50 0

AIa GCG 0 1

C Cys TGT 51 0

Cys TGC 49 0

D Asp GAT 63 1

Asp GAC 37 1

E GIu GAA 100 1

GIu GAG 0 1

F Phe TTT 55 0

Phe TTC 45 0

G GIy GGT 31 1

GIy GGC 34 1

GIy GGA 35 1

Gly_GGG 0 1 H His CAT 71 0

His CAC 29 0

I Ile ATT 60 0

Ile ATC 40 0

He ATA 0 1

K Lys AAA 100 1

Lys AAG 0 1

L Leu TTA 39 0

Leu TTG 24 0

Leu CTT 37 0

Leu CTC 0 1

Leu CTA 0 1

Leu CTG 0 1

M MetATG 100 1

N AsnAAT 45 0

AsnAAC 55 0

P Pro CCT 35 0

Pro CCC 0 1

Pro CCA 22 0

Pro CCG 43 0

Q GIn CAA 100 1

GIn CAG 0 1

R Arg CGT 38 0

Arg CGC 34 0

Arg CGA 0 1

Arg CGG 0 1 Arg AGA 28 0

Arg AGG 0 1

S Ser TCT 34 0

Ser TCC 0 1

Ser TCA 34 0

Ser TCG 0 1

SerAGT 0 1

SerAGC 32 0

T ThrACT 33 0

ThrACC 0 1

ThrACA 46 0

ThrACG 22 1

V VaI GTT 47 1

VaI GTC 0 1

VaI GTA 23 1

VaI GTG 30 1

W Trp TGG 100 1

Y Tyr TAT 62 0

Tyr TAC 38 0

Stop TGA 0 1

Stop TAG 0 1

Stop TAA 100 1 4.4. Codon pair optimization

Codon pair optimization was performed according the method of the invention. The optimized coding nucleotide sequences SEQ ID NO. 13-15 are the result of a run with the described software method. The applied parameters were: population size = 200; number of iterations = 1000; cpi = 0.20, CPW matrix = "Table C.4. CPW: Bacillus subtilis - highly expressed sequences" and the CR matrix = "Table B.I column 5: CR table BAS: Bacillus subtilis - highly expressed sequences" (also in Table 4.2) and 'don't care elements as in Table 4.2. Moreover, a penalty value of +1 is added to fitCOmbι for each occurrence of a N del (CATATG) and BamHl (GGATTC) restriction site. The optimized coding nucleotide sequences SEQ ID NO. 18 is the result of a run with the described software method. The applied parameters were: population size = 200; number of iterations = 1000; cpi = 0.20, CPW matrix = -1 times "Table C.4. CPW: Bacillus subtilis - highly expressed sequences" (for obtaining codon-pair optimization toward bad codon pairs) and the CR matrix = "Table B.I column 5: CR table BAS: Bacillus subtilis - highly expressed sequences" (also in Table 4.2) and 'don't care elements as in Table 4.2. Moreover, a penalty value of +1 is added to fit COmbι for each occurrence of a MM (CATATG) and BamHl (GGATTC) restriction site.

'Don't care' elements in Table 4.2 are chosen for those codons that do not show codon bias. This was done by visual inspection of the single-codon bias graph, see 4.3. The usage of such elements provides additional freedom to the codon-pair part of the optimization.

All optimizations converged toward a minimal value for fitCOmbι- The obtained objective values for SEQ ID NO. 13-15 and SEQ ID NO18 are given in Table 4.2, together with those for SEQ ID NO. 11, SEQ ID NO. 16 and SEQ ID NO. 17. From that data it is clear that single codon statistics are highly similar for SEQ ID NO. 16 and SEQ ID NO. 17 in comparison with SEQ ID NO. 14 and SEQ ID NO. 15. However, the method of the invention leads to a gene with an improved number of codon pairs with associated negative weights, indicating a more optimal usage of codon pairs having more negative weights associated with them, see Table 4.3.

'Optimizing' using maximization of fitcp leads to a gene with an increased number of codon pairs with associated positive weights, indicating an increased usage of codon pairs having more positive weights associated with them, thus bad influence on translation characteristics is expected. For SEQ ID NO. 18 (wcp(g) < 0) is 24 % vs. 85% for SEQ ID NO. 14, and also fitcp increased from 1.20 to -1.43. Table 4,3 Codon optimization; objective fitness values for genes for expression in B. suhύlis and 8. ainyhliquefaciens .

5. Example 5: Testing the method of the invention for expression of three heterologous enzymes in Bacillus subtilis and Bacillus amyloliquefaciens.

5.1 Introduction Example 5 describes the experiment and results of the expression of 3 heterologous genes with sequence variants of these in both Bacillus subtilis and Bacillus amiloliquefaciens hosts cells. Variants are made according the method of the invention, as described in Example 4.

5.2 Materials and Methods

5.2.1 Bacillus growth media

2*TY (per L): tryptone peptone 16 g, yeast extract Difco 1O g, NaCl 5 g.

5.2.2 Transformation of B. subtilis Media

2x SOJz.iz.en medium: 28 g K2HPO4; 12 g KH2PO4; 4 g (NH4)2SO4; 2.3 g Na3-citrate.2H2O; 0.4 g MgSO4 .7 H2O; H2O to 900 ml and adjust to pH 7.0-7.4 with 4N NaOH. Add H2O to 1 liter.

Autoclave 20 minutes at 1200C.

Ix Syizizen-ylus medium: add to 50 ml 2x Spizizen medium 50 ml milliQ;l ml 50% glucose and 100 μl casamino acids (20 μg/ml final concentration).

A single Bacillus colony (or an aliquot from a deep freeze vessel) from a non-selective 2xTY agar plate was inoculated in 10 ml 2xTY broth in a 100 ml shake flask. Cells were grown overnight in an incubator shaker at 370C and ± 250 rpm. The OD was measured at 600 nm and the culture was diluted with Ix Spizizen-plus medium till ODOOOKO. I . Cells were grown at 37°C and 250-300 rpm till the culture ODOOO is 0.4 - 0.6. The culture was diluted 1:1 with Ix Spizizen medium supplemented with 0.5% glucose (starvation medium) and it was incubated for 90 min at 37°C and 250-300 rpm. The culture was centrifuged at 4500 rpm in a tabletop centrifuge for

10 minutes. 90% of the supernatant was removed and pellet was suspended in rest volume. DNA

(1 - 5 μg in a maximum of 20 μl) was mixed with 0.5 ml competent cells in a universal and incubated for 1 hour at 37°C in a rotary shaking water bath under firm shaking (^5/6). Cells were plated (20 to 200 μl) on selective 2xTY agar plates containing 25-μg/ml kanamycin and incubated over night at 37°C.

5.2.3 Preparation of cell-free extract The pellet obtained from 1 ml culture was resuspended in buffer A containing 10 mM

Thris-HCl (pH 7.5), 10 mM EDTA, F50 mM NaCl, lmg/ml lysozyme and protease inhibitors (Complete EDTA-free protease inhibitor cocktail, Roche). The resuspended pellets were incubated for 30 min at 37°C, for protoplastation and subsequently sonicated as follows: 30 sec, 10 amplitude microns (3 cycles), with 15 sec. cooling between cycles. After sonification cell debris was spun down by centrifugation (10 min, 13000 rpm at 4°C), and the clear lysates were used for further analysis.

5.2.4 Selection of glucose isomerase and L-arabinose isomerase encoding genes and design of synthetic genes for expression in Bacillus amyloliquefaciens and Bacillus subtilis

Three enzymes selected are:

1. Bacillus stearothermophilus xylose isomerase (P54272 Swissprot); protein sequence SEQ ID NO. 9,

2. Streptomyces olivochromogenes xylose isomerase (P15587 Swissprot); protein SEQ ID NO. 10,

3. Thermoanaerobacter mathranii L-arabinose isomerase (AJ 582623.1 EMBL, and also US2003/012971A1), protein SEQ ID NO. 11, nucleotide SEQ ID NO. 12.

As seen above the selected enzymes have different microbial origin. With the aim to overproduce these enzymes in Bacillus subtilis or Bacillus amyloliquefaciens we have optimized the nucleotide sequence for each protein in such a way that it is suitable for expression in Bacillus species, see Example 4.

We have optimized the nucleotide sequences that encode the above mentioned enzymes. The sequences are listed in the sequence list under the SEQ ID NO. 13. {Bacillus stearothermophilus glucose (xylose) isomerase), SEQ ID NO. 14. {Streptomyces olivochromogenes glucose (xylose) isomerase), SEQ ID NO. 15. {Thermoanaerobacter mathranii L-arabinose isomerase). As a control, one variant with a single-codon optimization without codon-pair optimization, SEQ ID NO. 16-17, and one with single-codon optimization with "negative codon-pair optimization" SEQ ID NO. 18, were generated, see example 4 and Table 4.1.

5.3 Cloning of the glucose isomerase and L-arabinose isomerase encoding genes in the E.coli/Bacillus shuttle vector and transformation to Bacilli

For the expression of the selected genes in Bacilli we have used the pBHA12 E.coli/Bacillus shuffle vector (Figure 26). This vector is essentially derived from the expression vector pBHA-1 (EP 340878) in which a promoter derived from the amyQ gene of Bacillus amyloliquefaciens replaced the Hpall promoter. The pBHA12 plasmid contains two multiple cloning sites (Figure 26). All selected and optimized genes were made synthetically (DNA 2.0, Menlo Park, CA, U.S.A.) as two fragments (A and B). The A fragment corresponding to the 5' end of the gene was clone behind the amyQ promoter. Both fragments have been extended with specific restriction endonuclease sites in order to allow direct cloning in the multiple cloning sites 1 and 2 (see Figure 27). The 3' end of the fragment A and 5' end of the fragment B overlap by a unique restriction endonuclease site that allows excision of the E. coli part of the vector and back ligation prior to the transformation of Bacillus subtilis (CBS 363.94). During the procedure of cloning and transformation of B. subtilis, E. coli was used as an intermediate host. The two- step cloning approach in pBHA12 was chosen in order to avoid possible problems during cloning and propagation of the expression vectors in E. coli. In Table 5.1 the restriction enzyme recognition sites added to fragments A and B are listed as well as the unique restriction site that allows back ligation and as such reconstruction of an entire and functional gene. All the 5' ends of the A fragments contain Ndel site (recognition sequence CATATG) that allows cloning of genes as a fragment starting exactly at their respective start codon (ATG).

Table 5.1. The summary of the restriction endonuclease (RE) cloning sites that have been added to the gene fragments to facilitate the cloning in pBHA12.

The A and B fragments of 5 genes have been cloned in two steps in the MCSl and 2, respectively, as shown for the SEQ ID NO. 13 in Figure 27, using the standard molecular biology methods (Sambrook & Russell, Molecular Cloning: A Laboratory Manual, 3rd Ed., CSHL Press, Cold Spring Harbor, NY, 2001; and Ausubel et al, Current Protocols in Molecular Biology, Wiley InterScience, NY, 1995). The transformation was performed in the E.coli TOPlO (Invitrogen) or INVI lO (Invitrogen) in the case of using methylation sensitive restriction endonucleases in a further step. Several E. coli ampicilline resistant transformants for each expression construct were isolated using the mini or midi plasmid isolation kits (Macherey- Nagel and Sigma, respectively). The correct ligation of the corresponding A and B fragments in the pBHA12 vector was confirmed by restriction analysis. In the next step the pBHA12 plasmids that contained the A and B fragments of the genes were digested with the unique restriction endonuc lease (see Table 5.1) to excise the E. coli part of the vector. The Bacillus part of the vector that contained the interrupted gene was isolated from the agarose gel using gel extraction kit (Macherey-Nagel) and back ligated. The ligation mixture was transformed to B. subtilis CBS 363.94 strain by competent cell transformation. Several B. subtilis kanamycin resistant transformants for each expression construct were isolated using the mini or midi plasmid isolation kits (Macherey-Nagel and Sigma, respectively). The expression constructs were checked by restriction analysis for the correct pattern after the excision of the E. coli part and the back ligation of the Bacillus part of the pBHA12 vector. For each construct three B. subtilis transformants were selected for analysis of the cell free extract.

5.4 Detection of overproduced enzymes in Bacilli

Three B. subtilis transformants and three B. amyloliquefaciens transformants for each construct were used to analyze the cell free extract for the presence of the corresponding protein - glucose or L-arabinose isomerase. The 2xTY fermentation media were used to grow the strains. Samples (ImI) were taken at 24 hours of fermentation (in shake flask) and the cell free extract was prepared including protease inhibitors in the extraction buffer. 13μl of the cell free extract were analyzed on SDS-PAGE (Invitrogen). For several transformants a clear band corresponding to the expected Mw of the overexpressed protein was detected. A visual comparison of the bands is given in Table 5.2. It is clear that the method of the invention improved protein production for Bacillus stearothermophilus xylose isomerase, Streptomyces olivochromogenes xylose isomerase and Thermoanaerobacter mathranii L-arabinose isomerase, by using the codon-pair method, i.e. this results in improved protein production in comparison with either the WT reference gene or the single-codon optimized variants. Moreover, if negative codon-pair optimization was applied together with single-codon optimization, no product was detected.

Table 5.2 Overexpression of three heterologous genes in Bacilli. WT: Wild type; sc: single codon optimization; cp: codon pair optimization; cp": negative codon pair optimization.

REFERENCES

Boycheva, S., Chkodrov, G. & Ivanov, I. (2003). Codon pairs in the genome of Escherichia coli. Bioinformatics 19(8):987-998 Gurvich, O.L., Baranov, P.V., Gesteland, R.F., Atkins, J.F. (2005). Expression levels influence ribosomal frameshifting at the tandem rare arginine codons AGG AGG and AGA AGA. J. Bacteriol. 187:4023-4032.

Gustafsson, C, Govindarajan, S. & Minshull, J. (2004). Codon bias and heterologous protein expression. Trends Biotechnol. 22(7):346-353 Gutman, G. A. & Hatfield, G. W. (1989). Nonrandom utilization of codon pairs in Escherichia coli. PNAS 86:3699-3703

Gygi, S.P., Rochon, Y., Franza, B. R., & Aebersold, R. (1999). Correlation between protein and mRNA abundance in Yeast. MoI. CeI. Biol. 19(3):1720-30

Hatfield, G.W. & Gutman, G.A. (1992). Codon pair utilization. United States Patent No 5,082,767

Irwin, B., Heck, D. & Hatfield, G.W. (1995). Codon pair utilization biases influence translational elongation step times. J Biol Chem 270:22801-22806

Karlin et al. (2001). Characterization of highly expressed genes of four fast-growing bacteria. J. of Bacteriology 183(17):5025-39. Kunst, F. et al. (1997). The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256

Lithwick, G. & Margalit, H. (2003). Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res. 13(12): 2665-73.

Makrides, S. C. (1996). Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol. Rev. 60:512-538

Moura, G. et al. (2005). Comparative context analysis of codon pairs on an ORFeome scale. Genome Biology 2005, 6:R28

Nevalainen, K.M.H., Te'o, V.S.J. & Bergquist, P. L. (2005). Heterologous protein expression in filamentous fungi. Trends Biotechnol. 2005 23(9):468-474 Pel, H. J., et al. (2007). Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS513.88. Nat Biotech. 2007 25(2): 221-231

Punt, P.J., van Biezen, N., Conesa, A., Albers, A., Mangnus, J. & van den Hondel, C. (2005). Filamentous fungi as cell factories for heterologous protein production. Trends Biotechnol. 20(5):200-206

Rocha, E. P. C, A. Danchin and A. Viari (1999). Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis. NAR, 27(17):3567- 76.Boycheva, S., Chkodrov, G. & Ivanov, I. (2003). Codon pairs in the genome of Escherichia coli. Bioinformatics 19(8):987-998 Schwartz, S. & Curran, J.F. (1997). Analyses of frameshifting at UUU-pyrimidine sites. NAR 25(10):2005-2011

Spanjaard, R. A. & van Duin, J. (1988). Translation of the sequence AGG-AGG yields 50% ribosomal frameshift. PNAS 85:7967-7971

APPENDIX 1 : List of symbols and equations

Single codon:

Codons encoding the same amino acid: synicj

Number of occurrences of the codon C1 : nκ(c,)

Ratio of the codon ck (compared to its synonyms):

Codon pair:

(C1, C1)

Occurrences (observed number) of codon pair:

Expected number of this codon pair:

nZ"((ci,c})) = C(ci)-r::(c})- Σ n oJ(Cm,Cn))

Corresponding standard deviation: σ((Cj ,C])) = ]nexp ((C1 , C] )) (1 - rsf (c, ) if (c} ))

Corresponding standard score (z-score):

(( ΛΛ _(nobs((c1,cJ))- W6^p ((C1, C7)) z((c, 'Cj))- σ( J(,c,,cy ^)); Bias coefficient for a codon pair:

, c} )))

Combined "expected" values (for weights):

Codon pair weights - method one sequence group (or genome):

Codon pair weights - method highly expressed group with reference group (or genome):

APPENDIX 2: CR vectors

Table B.I: CR matrix values for the following organisms in columns: (1) AN: A. niger full genome - method: statistical distribution; (2) ANS: A. niger 250 highly-expressed genes - method: visual inspection, (3) AN d: A. niger care-don't care (0-1) vector; (4) BS: B. subtilis full genome - method: statistical distribution; (5) BSS: B. subtilis 50 highly-expressed genes - method: visual inspection, (6) BS d: B. subtilis care-don't care (0-1) vector; (7) EC: E. coli full genome 4298 seq; - method: statistical distribution; (8) ECS E. coli highly expressed group 100 seq from Carbone et al. (2003) - method: visual inspection; (9) EC d: E. coli care-don't care (0- 1) vector; (10) BA: B. amyloliquefaciens full genome - method: statistical distribution; (11) BAS: B. amyolliquefaciens 50 highly-expressed genes - method: visual inspection, (12) BS d: B. amyolliquefaciens care-don't care (0-1) vector; (13) SC: S. cerevisiae full genome - method: statistical distribution; (14) SCS: S. cerevisiae 200 highly-expressed genes - method: visual inspection, (15) SC_d: S. cerevisiae care-don't care (0-1) vector; (16) SCO: S. coelicolorA3(2) full genome - method: statistical distribution

Note: For fungal microorganisms, and more specific P. chrysogenum, A. Oryzae, A. terreus, A. nidulans, A. fumigatus, T. reesei, N. fischerii, the CR vector derived using the A. niger sequences applies. For yeast in general, and more specific K. lactis and S. pombe, the CR vector derived using the S. cerevisiae sequences applies. For Streptomyces species the CR vector derived using S. coelicolor A3 (2) applies.

1 2 3 4 5 6 7 8 9 10 11 12

AN ANS AN_d BS BSS BS d EC ECS EC d BA BAS BA d

1 AAA 33 0 1 71 100 1 75 81 0 69 100 1

2 AAC 58 100 1 43 55 0 73 100 0 66 50 0

3 AAG 67 100 1 29 0 1 25 19 0 31 0 1

4 AAT 42 0 1 57 45 0 66 0 0 76 50 0

5 ACA 21 0 1 41 46 0 14 0 0 29 30 0

6 ACC 35 70 1 16 0 1 42 57 1 21 0 1

7 ACG 22 0 1 26 22 1 26 0 0 38 40 0

8 ACT 23 30 1 17 33 0 18 43 1 13 30 0

9 AGA 13 0 1 27 28 0 5 0 0 14 20 0

10 AGC 18 21 1 22 32 0 27 28 1 22 30 0

11 AGG 12 0 1 10 0 1 3 0 0 7 0 1

12 AGT 13 0 1 11 0 1 16 0 0 9 0 1

13 ATA 14 0 1 14 0 1 9 0 0 15 0 1

14 ATC 52 73 1 35 40 0 41 72 1 42 40 0

15 ATG 100 100 1 100 100 1 100 100 0 100 100 1

16 ATT 34 27 1 51 60 0 51 28 1 44 60 0

17 CAA 40 0 1 53 100 1 36 17 0 42 60 0

18 CAC 51 100 1 32 29 0 42 81 0 41 40 0

19 CAG 60 100 1 47 0 1 64 83 0 58 40 0

20 CAT 49 0 1 68 71 0 58 19 0 59 60 0

21 CCA 22 0 1 20 22 0 20 14 0 11 0 1

22 CCC 29 64 1 10 0 1 13 0 0 17 0 1

23 CCG 24 0 1 41 43 0 49 86 0 52 60 0 CCT 25 36 1 29 35 0 17 0 0 20 40 0

CGA 15 0 1 10 0 1 7 0 0 12 0 1

CGC 25 51 1 19 34 0 38 34 0 32 40 0

CGG 18 0 1 15 0 1 10 0 0 20 0 1

CGT 16 49 1 18 38 0 36 66 0 15 40 0

CTA 10 0 1 5 0 1 4 0 0 4 0 1

CTC 24 38 1 11 0 1 10 0 0 17 0 1

CTG 25 32 1 23 0 1 47 100 0 28 20 0

CTT 17 17 1 23 37 0 11 0 0 21 30 0

GAA 42 26 1 69 100 1 69 80 0 66 40 0

GAC 49 64 1 36 37 1 37 64 1 44 40 0

GAG 58 74 1 31 0 1 31 20 0 34 60 0

GAT 51 36 1 64 63 1 63 36 1 56 60 0

GCA 21 0 1 29 50 0 22 30 0 18 30 0

GCC 32 51 1 20 0 1 27 0 0 26 0 1

GCG 21 11 1 25 0 1 34 23 0 38 30 0

GCT 26 38 1 26 50 0 17 47 0 18 40 0

GGA 24 16 1 32 35 1 12 0 0 26 30 0

GGC 32 35 1 33 34 1 39 42 1 41 40 0

GGG 19 0 1 16 0 1 15 0 0 17 0 1

GGT 25 49 1 19 31 1 34 58 1 16 30 0

GTA 11 0 1 21 23 1 16 29 0 16 25 0

GTC 35 54 1 24 0 1 21 0 0 32 25 0

GTG 30 19 1 26 30 1 36 19 0 28 25 0

GTT 24 27 1 29 47 1 26 53 0 23 25 0

TAA 27 100 1 62 100 1 59 100 0 41 100 1

TAC 58 100 1 34 38 0 42 76 1 59 50 0

TAG 31 0 1 22 0 1 32 0 0 21 0 1

TAT 42 0 1 66 62 0 58 24 1 16 50 0

TCA 13 0 1 24 34 0 13 0 0 16 30 0

TCC 23 44 1 12 0 1 14 31 1 16 0 1

TCG 17 14 1 10 0 1 14 0 0 61 40 0

TCT 17 21 1 21 34 0 15 41 1 100 30 0

TGA 42 0 1 16 0 1 9 0 0 39 20 0

TGC 59 100 1 54 49 0 55 100 0 17 30 0

TGG 100 100 1 100 100 1 100 100 0 41 0 1

TGT 41 0 1 46 51 0 45 0 0 14 0 1

TTA 6 0 1 21 39 0 14 0 0 59 0 1

TTC 65 100 1 30 45 0 41 77 1 69 40 0

TTG 18 13 1 16 24 0 13 0 0 66 100 1

TTT 35 0 1 70 55 0 59 23 1 31 60 0

AN ANS AN_d BA BAS BA d EC ECS EC d BS BSS BS d

1 2 3 4 5 6 7 8 9 10 11 12 Table B.I continued

13 14 15 16 17 18 19 20 21 22 23 24

SC SCS SC d SCO

1 AAA 59 21 1 5

2 AAC 40 75 1 96

3 AAG 41 79 1 95

4 AAT 60 25 1 4

5 ACA 31 6 1 2

6 ACC 21 40 1 65

7 ACG 14 2 1 31

8 ACT 34 52 1 2

9 AGA 47 76 1 1

10 AGC 11 3 1 25

11 AGG 21 3 1 4

12 AGT 16 4 1 3

13 ATA 28 0 1 2

14 ATC 26 48 1 96

15 ATG 100 100 1 100

16 ATT 46 58 1 2

17 CAA 69 90 1 5

18 CAC 36 59 1 93

19 CAG 31 10 1 95

20 CAT 64 41 1 7

21 CCA 41 74 1 2

22 CCC 16 5 1 41

23 CCG 13 0 1 54

24 CCT 31 23 1 2

25 CGA 7 0 1 3

26 CGC 6 1 1 47

27 CGG 4 0 1 39

28 CGT 14 25 1 6

29 CTA 14 9 1 0

30 CTC 6 0 1 36

31 CTG 11 5 1 60

32 CTT 13 3 1 2

33 GAA 70 85 1 15

34 GAC 35 51 1 95

35 GAG 30 15 1 85

36 GAT 65 49 1 5

37 GCA 30 2 1 4

38 GCC 22 33 1 58

39 GCG 11 0 1 36

40 GCT 37 64 1 2

41 GGA 23 0 1 7 GGC 20 8 1 64

GGG 12 1 1 19

GGT 45 95 1 10

GTA 22 0 1 3

GTC 20 39 1 55

GTG 19 8 1 40

GTT 39 54 1 2

TAA - 100 1 -

TAC 43 74 1 95

TAG - 0 1 -

TAT 57 26 1 5

TCA 21 8 1 2

TCC 16 32 1 41

TCG 10 5 1 28

TCT 26 48 1 1

TGA - 0 1 -

TGC 38 13 1 91

TGG 100 100 1 100

TGT 62 87 1 9

TTA 28 21 1 0

TTC 41 71 1 98

TTG 28 62 1 2

TTT 59 29 1 2

SC SCS 1 SCO

13 14 15 16 17 18 19 20 21 22 23 24

APPENDIX 3: CPW matrices

Table Cl: CPW matrix Aspergillus niger full genome (left codon indicated in column 2, right codon indicated in row 2). Host cell: A. niger, Sequence data: full A niger genome.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 062 037 038 034 -016 007 018 029 -019 -003 -014 011

2 AAC -017 -028 -023 -005 008 -025 -001 003 002 -030 017 -004

3 AAG -002 -020 -024 -005 -002 -004 -012 003 -014 -005 -018 -003

4 AAT 024 045 044 022 016 016 015 006 019 017 023 008

5 ACA 000 009 025 004 -025 004 014 020 -025 -001 -022 010

6 ACC -017 -035 -028 -007 011 -030 017 001 -008 -022 007 -002

7 ACG -018 001 -006 -005 000 021 -014 010 -025 015 -036 000

8 ACT 036 057 053 040 013 017 017 -022 003 027 015 020

9 AGA -001 005 006 -008 -018 019 010 011 -037 -017 -030 -015

10 AGC -028 -026 -026 -025 000 -006 004 003 -020 -031 -004 -021

11 AGG -031 008 -022 -032 -017 031 -025 001 -039 010 -052 -018

12 AGT 021 035 047 017 024 037 028 013 021 028 027 005

13 ATA 006 025 038 016 -021 003 008 004 -010 007 -007 017

14 ATC -027 -035 -031 -015 003 -030 -003 -004 014 -010 020 002

15 ATG 002 -006 -001 009 005 001 -010 004 -013 -014 -008 000

16 ATT 050 055 056 045 034 026 026 016 041 044 046 038

17 CAA 027 021 025 010 -015 -001 014 020 -007 -009 005 003

18 CAC -029 -025 -026 -018 -005 -022 001 -003 011 -025 032 -009

19 CAG -017 -008 -013 -011 -008 009 -009 -006 -008 -001 002 -001

20 CAT 023 044 046 009 008 018 015 004 042 029 050 022

21 CCA 010 016 024 001 -024 001 012 002 -012 013 -011 017

22 CCC -028 -036 -037 -015 009 -015 003 -004 -012 -017 005 -006

23 CCG -014 007 006 -009 -012 008 -014 000 -004 032 -006 014

24 CCT 038 046 048 026 009 018 016 -002 031 038 033 023

25 CGA 017 019 028 012 -019 006 016 017 -003 -014 001 003

26 CGC -024 -025 -026 -022 -007 -016 -016 003 001 -032 018 -027

27 CGG -022 013 001 -015 -026 015 -031 -011 -024 007 -019 -018

28 CGT 051 045 067 048 029 024 032 017 063 044 058 040

29 CTA 024 026 043 025 -003 003 033 027 024 012 018 025

30 CTC -023 -030 -020 -011 003 -024 009 -002 029 -017 033 -006

31 CTG -016 -012 -013 004 012 007 002 009 012 001 004 009

32 CTT 054 052 064 048 019 023 026 011 056 044 055 038

33 GAA 046 027 024 009 -009 006 009 017 -023 -016 -014 -012

34 GAC -018 -021 -028 -019 001 -013 -003 000 001 -031 005 -023

35 GAG -007 -007 -023 -019 -005 010 -022 -003 -019 -009 -031 -020

36 GAT 024 034 036 009 006 012 002 -001 020 019 027 001

37 GCA 008 009 015 000 -016 007 005 004 -019 007 -023 006

38 GCC -028 -036 -028 -023 010 -011 -004 -005 -005 -025 -001 -026 39 GCG -0 07 0 11 -0 06 -0 08 -0 16 0 15 -0 26 0 00 -0 18 0 28 -0 31 0 05

40 GCT 0 38 0 60 0 48 0 38 0 16 0 21 0 10 -0 12 0 18 0 31 0 22 0 13

41 GGA 0 03 -0 09 -0 11 -0 19 -0 21 0 07 -0 09 -0 05 -0 37 -0 20 -0 30 -0 28

42 GGC -0 12 -0 13 -0 19 -0 04 -0 10 -0 12 -0 11 -0 04 0 10 -0 25 0 15 -0 27

43 GGG -0 33 0 21 -0 17 -0 29 -0 15 0 34 -0 26 -0 02 -0 31 0 20 -0 52 -0 25

44 GGT 0 34 0 31 0 65 0 32 0 24 0 17 0 38 0 03 0 31 0 21 0 45 -0 02

45 GTA 0 22 0 30 0 38 0 09 -0 13 0 09 0 08 0 12 0 18 0 38 0 07 0 39

46 GTC -0 20 -0 34 -0 33 -0 24 0 14 -0 18 0 00 -0 18 0 18 -0 19 0 15 -0 11

47 GTG -0 01 0 03 -0 06 0 06 -0 01 0 09 -0 22 -0 12 0 03 0 16 -0 27 0 24

48 GTT 0 53 0 55 0 50 0 38 0 35 0 31 0 13 -0 03 0 43 0 37 0 24 0 28

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 18 -0 29 -0 24 -0 06 0 13 -0 23 0 00 0 01 0 15 -0 20 0 34 -0 06

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 33 0 44 0 41 0 24 0 18 0 14 0 05 0 05 0 32 0 33 0 31 0 21

53 TCA 0 01 0 22 0 29 -0 03 -0 33 0 02 0 05 -0 09 -0 18 0 11 -0 27 0 14

54 TCC -0 21 -0 30 -0 30 -0 07 0 07 -0 21 0 10 0 00 -0 01 -0 19 0 08 0 13

55 TCG -0 14 0 06 -0 02 -0 11 -0 09 0 00 -0 20 -0 09 -0 07 0 21 -0 21 0 10

56 TCT 0 44 0 55 0 56 0 37 0 03 0 15 0 17 -0 13 0 22 0 35 0 30 0 37

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 26 -0 19 -0 25 -0 23 -0 10 -0 10 -0 15 -0 07 -0 09 -0 10 -0 04 -0 26

59 TGG -0 09 0 02 0 05 -0 03 -0 03 0 15 -0 15 -0 04 -0 28 -0 01 -0 29 -0 22

60 TGT 0 27 0 43 0 61 0 31 0 16 0 25 0 14 0 08 0 39 0 47 0 37 0 32

61 TTA 0 31 0 39 0 41 0 20 -0 05 0 13 0 11 0 09 0 04 0 24 -0 01 0 13

62 TTC -0 18 -0 30 -0 27 -0 08 0 14 -0 24 0 05 -0 06 0 19 -0 09 0 20 0 02

63 TTG -0 17 -0 12 -0 26 -0 24 -0 17 -0 08 -0 34 -0 29 -0 08 0 08 -0 35 -0 12

64 TTT 0 54 0 58 0 61 0 46 0 25 0 19 0 09 0 08 0 40 0 41 0 29 0 29

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table Cl continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 14 0 21 0 19 0 31 -0 14 -0 07 0 16 -0 08 -0 11 -0 04 0 05 0 19

2 AAC 0.24 -0.17 -0.09 0.08 -0.02 -0.18 -0.11 0.10 0.05 -0.19 -0.05 0.08

3 AAG -0 04 -0 13 -0 08 -0 01 0 06 0 00 -0 06 0 08 0 03 -0 09 0 00 0 05

4 AAT 0 06 0 08 0 14 0 04 0 06 0 16 0 15 0 02 0 07 0 05 0 10 0 05

5 ACA -0 11 0 20 0 04 0 20 -0 07 0 01 0 05 0 00 -0 22 -0 02 0 00 0 05

6 ACC 0 11 -0 29 -0 14 -0 07 0 09 -0 12 0 08 0 20 0 19 0 02 0 11 0 21

7 ACG -0 16 0 12 -0 05 0 09 -0 06 -0 02 -0 19 -0 07 -0 03 0 10 -0 15 0 04

8 ACT 0 12 0 18 0 26 0 09 -0 01 -0 01 0 04 -0 02 -0 02 -0 16 -0 07 -0 19

9 AGA -0 31 0 19 0 06 0 09 -0 14 -0 05 -0 05 -0 15 -0 10 0 15 0 10 0 14

10 AGC -0 08 -0 09 -0 20 -0 09 0 00 -0 05 -0 09 -0 12 0 13 0 22 0 13 0 16

11 AGG -0 44 0 19 -0 09 -0 11 0 05 0 20 0 10 0 02 -0 15 0 27 -0 05 0 01

12 AGT -0 20 0 03 0 11 -0 02 -0 04 0 11 0 07 -0 12 0 04 0 07 -0 05 0 02 ATA -034 017 010 021 -014 011 007 -007 -020 -008 -002 -009

ATC 0 21 -0 25 -0 19 000 004 -018 -002 017 016 -009 0 21 019

ATG -0 09 0 01 0 00 003 004 -004 -003 004 -001 001 -0 02 002

ATT 0 24 0 19 0 32 016 -003 007 003 -001 003 -019 -0 03 -016

CAA -0 21 0 14 0 15 025 -016 002 022 -003 -015 002 0 10 014

CAC 0 21 -0 16 -0 13 -002 -014 -018 000 014 007 -001 0 06 015

CAG -0 09 -0 07 -0 09 -007 001 004 -006 -004 -011 004 0 00 -001

CAT -0 04 0 16 0 15 001 -006 014 015 -005 -007 -004 -0 03 -011

CCA -0 02 0 24 0 09 008 -005 011 021 008 -030 008 -0 03 010

CCC -0 06 -0 29 -0 20 -012 006 016 002 015 019 056 0 06 029

CCG -0 14 0 09 -0 04 005 -008 002 -007 -010 -008 018 -0 19 001

CCT 0 07 0 20 0 26 008 -012 -017 001 -019 -023 -017 -0 20 -025

CGA 0 07 0 28 0 18 025 -015 -011 -008 -004 -027 005 -0 23 -003

CGC -0 01 -0 23 -0 20 -014 007 007 -004 -007 023 020 0 23 031

CGG -0 33 0 18 -0 06 -003 007 030 017 005 -023 012 -0 14 -008

CGT 0 11 0 01 0 31 019 -008 -010 002 -009 -013 -022 -0 20 -020

CTA 0 03 0 25 0 24 032 -019 -015 -004 -010 -026 -008 -0 05 -006

CTC 0 06 -0 22 -0 08 -003 006 -003 017 023 014 -012 0 31 013

CTG 0 05 0 00 -0 02 006 002 -006 -012 005 015 009 0 15 009

CTT 0 21 0 25 0 39 020 -012 -013 004 -018 -023 -034 -0 04 -033

GAA -0 07 0 11 0 13 014 -005 007 017 000 000 009 0 10 016

GAC 0 10 0 00 -0 10 -003 -004 -015 -012 -003 016 -012 -0 02 -001

GAG -0 05 -0 01 -0 09 -014 001 003 -009 -007 -009 002 -0 09 -009

GAT -0 01 0 06 0 11 -008 010 022 009 -002 010 -002 -0 04 002

GCA 0 09 0 30 0 18 017 004 010 007 -002 -018 010 -0 10 -002

GCC 0 13 -0 27 -0 24 -028 021 000 004 014 028 020 0 15 020

GCG 0 01 0 23 0 02 008 -010 002 -024 -023 -009 006 -0 28 -007

GCT 0 12 0 18 0 24 -007 004 004 -002 -006 004 -013 -0 01 -026

GGA -0 11 0 21 0 02 007 000 017 -001 -001 -008 016 -0 05 004

GGC 0 12 -0 04 -0 14 -010 -005 -015 -014 -012 016 007 0 09 000

GGG -0 30 0 26 -0 08 -015 016 033 006 -004 -015 001 -0 20 -018

GGT 0 15 -0 13 0 26 -003 004 006 011 -002 011 -002 0 06 -015

GTA -0 04 0 30 0 22 020 -017 -002 -004 -016 -029 -004 -0 11 -021

GTC 0 13 -0 22 -0 18 -023 023 -002 010 019 033 011 0 27 015

GTG 0 02 0 19 -0 01 -006 001 003 -021 -008 014 010 -0 15 -007

GTT 0 14 0 22 0 25 000 001 000 004 -008 -005 -021 -0 02 -032

TAA 0 00 0 00 0 00 000 000 000 000 000 000 000 0 00 000

TAC 0 18 -0 17 -0 11 004 002 -015 -005 013 017 -002 0 17 015

TAG 0 00 0 00 0 00 000 000 000 000 000 000 000 0 00 000

TAT 0 08 0 13 0 18 005 -001 011 006 -004 -006 -015 -0 15 -015

TCA -0 24 0 20 0 04 007 000 018 014 012 -028 000 0 00 -002

TCC -0 01 -0 25 -0 11 003 013 -002 008 016 012 012 0 09 018

TCG -0 14 0 12 0 00 015 -012 005 -011 -012 -004 004 -0 14 -009

TCT 0 08 0 21 0 33 021 -008 -001 002 -009 -015 -021 -0 13 -027 57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 05 -0 01 -0 14 -0 17 0 04 -0 04 -0 06 -0 05 0 26 0 17 0 06 0 15

59 TGG -0 09 0 09 0 00 -0 09 0 05 0 00 -0 03 0 00 -0 02 0 06 -0 07 0 02

60 TGT -0 02 0 16 0 23 0 12 -0 06 0 15 0 09 -0 01 -0 13 -0 11 -0 27 -0 21

61 TTA -0 25 0 27 0 09 0 18 -0 18 -0 01 0 00 -0 20 -0 32 -0 01 -0 12 -0 15

62 TTC 0 30 -0 21 -0 13 -0 02 0 04 -0 20 -0 14 0 12 0 20 -0 11 0 11 -0 02

63 TTG -0 23 -0 12 -0 28 -0 26 0 15 0 27 -0 02 0 05 0 21 0 27 0 09 0 08

64 TTT 0 28 0 21 0 29 0 13 0 10 0 17 0 19 0 07 0 00 -0 09 -0 01 -0 07

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table 1 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA -0 14 0 13 0 00 0 25 -0 12 0 05 0 15 0 18 -0 15 -0 18 0 07 -0 04

2 AAC 0 02 -0 18 -0 06 -0 11 0 11 -0 20 -0 08 0 05 0 11 0 02 0 09 0 29

3 AAG 0 13 0 01 0 08 0 07 0 04 -0 06 -0 10 -0 04 0 10 0 09 -0 04 0 04

4 AAT -0 02 0 09 -0 06 0 17 -0 10 0 03 -0 01 0 06 -0 12 -0 17 -0 13 -0 20

5 ACA -0 01 0 23 0 14 0 44 -0 12 0 27 0 14 0 16 -0 10 -0 09 0 05 0 03

6 ACC 0 25 -0 06 0 20 0 08 0 13 -0 23 0 08 0 18 0 09 -0 11 0 11 0 17

7 ACG -0 01 0 05 -0 04 0 28 -0 07 0 15 -0 11 0 07 -0 06 -0 05 -0 19 -0 13

8 ACT -0 15 -0 16 -0 07 -0 22 -0 07 -0 10 -0 07 -0 11 0 00 0 15 0 04 0 04

9 AGA 0 00 0 26 -0 16 0 24 -0 18 0 25 0 11 0 06 -0 14 0 01 0 04 -0 04

10 AGC 0 06 0 20 0 02 0 02 0 23 0 30 0 19 0 09 -0 02 -0 05 0 03 0 14

11 AGG 0 19 0 37 0 21 0 37 -0 22 0 36 0 05 -0 09 -0 14 0 18 -0 22 -0 21

12 AGT -0 21 -0 08 -0 26 -0 05 -0 27 -0 08 -0 20 -0 16 -0 16 -0 14 -0 11 -0 22

13 ATA -0 12 0 32 0 08 0 17 -0 24 0 13 0 15 -0 06 0 03 0 17 0 25 0 22

14 ATC 0 07 -0 18 -0 01 -0 09 0 12 -0 18 0 08 0 17 0 14 -0 04 0 13 0 25

15 ATG 0 07 -0 01 0 06 0 06 0 00 0 00 -0 09 -0 07 0 03 0 00 -0 02 0 00

16 ATT -0 16 -0 11 -0 13 -0 11 -0 09 -0 15 -0 09 -0 12 -0 19 -0 21 -0 24 -0 19

17 CAA -0 03 0 13 0 03 0 15 -0 07 0 08 0 20 0 16 -0 18 -0 06 0 12 -0 08

18 CAC 0 02 -0 14 0 06 -0 23 0 19 -0 07 0 12 0 11 0 03 0 05 0 09 0 17

19 CAG -0 04 -0 06 0 00 -0 02 -0 04 0 00 -0 15 -0 10 0 01 0 12 0 02 -0 02

20 CAT -0.12 -0.09 -0.10 -0.14 -0.19 -0.08 -0.07 -0.13 -0.14 -0.02 0.00 -0.17

21 CCA -0 09 0 26 0 06 0 33 -0 08 0 28 0 13 0 14 -0 11 -0 04 0 06 0 00

22 CCC 0 00 0 08 0 07 -0 12 0 22 -0 05 0 33 0 21 -0 04 -0 09 -0 02 0 07

23 CCG 0 02 0 01 0 00 0 21 -0 09 0 19 -0 11 0 04 -0 03 -0 01 -0 11 -0 09

24 CCT -0 20 -0 15 -0 07 -0 34 -0 11 -0 12 -0 01 -0 24 0 06 0 15 0 18 0 02

25 CGA -0 29 0 09 -0 15 0 18 -0 31 0 04 -0 17 0 03 0 04 0 10 0 17 0 13

26 CGC 0 24 0 04 0 13 -0 02 0 25 0 18 0 18 0 27 0 02 -0 04 0 09 0 10

27 CGG 0 08 0 24 0 05 0 26 -0 01 0 33 -0 05 0 09 0 02 0 14 0 00 -0 08

28 CGT -0 18 -0 31 -0 17 -0 36 -0 29 -0 33 -0 26 -0 24 -0 06 -0 12 0 04 -0 12

29 CTA -0 32 -0 03 -0 18 0 05 -0 32 0 06 0 16 -0 07 -0 03 0 01 0 15 0 11

30 CTC 0 03 -0 25 0 17 -0 10 0 09 -0 31 0 19 0 09 0 06 -0 09 0 14 0 20 31 CTG 0 02 -0 15 -0 05 -0 04 0 16 0 10 -0 04 0 09 -O 10 -O 10 -O 11 -0 02

32 CTT -0 19 -0 12 -0 03 -0 25 -0 28 -0 30 -0 11 -0 32 0 00 -0 05 0 09 -0 02

33 GAA 0 07 0 27 0 06 0 26 -0 04 0 16 0 18 O 12 -O 14 -O 14 0 01 -O 10

34 GAC -0 03 -0 11 -0 09 -0 17 0 17 -0 04 -0 01 -0 02 O 13 0 06 0 08 O 19

35 GAG 0 06 0 07 0 01 0 02 -0 03 0 08 -0 17 -O 12 O 12 0 22 -0 02 -0 02

36 GAT 0 01 0 08 -0 08 0 07 -0 03 0 05 -0 06 -0 03 -0 05 -0 04 -O 12 -O 17

37 GCA -0 04 0 31 0 04 0 34 0 11 0 39 0 17 0 21 -0 07 -O 12 -0 08 -O 12

38 GCC 0 26 0 02 0 17 -0 06 0 23 0 00 0 08 O 15 O 10 -0 06 O 12 0 09

39 GCG 0 01 -0 05 -0 15 0 08 0 07 0 20 -0 26 0 01 0 00 0 02 -0 21 -O 12

40 GCT -0 04 -0 03 -0 02 -0 30 0 01 -0 04 -0 08 -O 14 0 05 0 30 0 04 -0 01

41 GGA -0 08 0 30 -0 08 0 16 0 02 0 39 0 07 O 18 -0 04 O 11 -0 05 0 01

42 GGC 0 12 0 01 0 10 -0 20 0 19 0 14 0 14 O 14 O 12 0 04 0 00 O 11

43 GGG 0 09 0 35 0 15 0 26 -0 12 0 32 -0 10 -O 12 0 02 0 28 -O 19 -O 17

44 GGT 0 07 -0 10 -0 04 -0 22 -0 08 -0 20 -0 16 -0 27 -0 05 -O 10 O 15 -O 19

45 GTA -0 14 0 21 -0 12 0 26 -0 13 0 21 0 16 -0 05 0 08 0 20 0 20 O 14

46 GTC 0 13 -0 12 0 07 -0 05 0 23 -0 08 0 11 0 06 0 22 -0 05 0 08 O 17

47 GTG -0 02 -0 13 -0 14 0 16 0 09 0 16 -0 15 -0 03 -0 05 0 07 -O 13 -O 17

48 GTT -0 06 -0 06 -0 02 -0 14 -0 08 -0 10 -0 10 -0 20 -0 07 -0 01 -O 15 -O 13

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 05 -0 17 0 03 -0 16 0 18 -0 15 0 02 O 12 O 10 -0 03 0 06 O 18

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 10 -0 11 -0 07 -0 02 -0 12 -0 16 -0 10 -O 13 -0 06 -0 05 -O 12 -O 14

53 TCA -0 07 0 32 -0 01 0 36 -0 11 0 28 0 26 O 10 -0 06 -0 03 O 13 O 12

54 TCC 0 14 -0 02 0 17 0 07 0 14 -0 19 0 16 O 13 0 03 -O 13 0 09 O 17

55 TCG -0 07 0 00 -0 09 0 15 -0 07 0 15 -O i l -0 03 -0 06 0 01 -0 12 -0 08

56 TCT -0 14 -0 12 -0 05 -0 25 -0 16 -0 12 0 02 -O 15 0 02 O 15 O 14 0 05

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 20 0 13 0 12 -0 05 0 29 0 27 O 17 O 17 0 09 0 04 0 03 O 12

59 TGG 0 15 0 08 0 17 0 17 -0 14 0 09 -0 05 -0 07 0 01 O 12 -0 01 -O 10

60 TGT -0 23 -0 16 -0 29 -0 09 -0 21 -0 16 -O 19 -0 23 -O 11 0 01 -0 04 -O 19

61 TTA -0 23 0 25 -0 14 0 19 -0 33 -0 01 -0 06 -0 20 0 04 O 13 O 16 O 11

62 TTC 0 01 -0 22 -0 08 -0 20 0 18 -0 21 -0 01 0 01 O 14 0 04 O 11 0 24

63 TTG 0 12 0 20 0 09 0 27 0 16 0 25 0 06 0 04 -0 03 O 14 -O 14 -O 14

64 TTT -0 07 0 11 0 09 0 18 0 01 0 00 O 11 0 01 -O 13 -0 20 -0 22 -0 21

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table Cl continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -0 27 -0 15 -0 04 0 06 -0 15 -0 15 -0 13 0 21 -0 26 -0 12 0 04 0 18

2 AAC 0 31 0 04 0 41 0 39 0 26 0 01 0 31 0 27 0 42 0 09 0 30 0 32

3 AAG 0 16 0 05 0 00 0 04 0 09 0 01 0 10 -0 03 0 22 -0 03 0 02 -0 02

4 AAT -0 23 -0 26 -0 35 -0 23 -0 23 -0 26 -0 29 -0 02 -0 13 -0 30 -0 23 -0 25 ACA -029 -007 001 006 -002 006 -001 034 -024 010 006 018

ACC 0 28 0 16 0 35 038 025 000 031 011 035 -0 07 021 0 18

ACG -0 08 0 01 -0 30 -001 002 001 -021 007 -009 0 06 -025 0 03

ACT -0 19 -0 17 -0 15 -027 -023 -020 -019 -028 -012 -0 14 -002 -0 27

AGA -0 16 0 15 0 01 004 -022 009 -019 008 -035 0 19 008 0 14

AGC 0 18 0 15 0 31 027 016 008 021 016 027 0 13 017 0 20

AGG 0 00 0 32 -0 08 -003 -002 028 -025 008 -021 0 25 -013 -0 13

AGT -0 09 -0 05 -0 23 -017 -029 -017 -032 -030 -031 -0 16 -031 -0 30

ATA -0 16 0 14 0 14 013 016 028 012 037 -028 0 22 019 0 22

ATC 0 28 0 04 0 33 035 017 006 025 015 043 0 04 024 0 35

ATG 0 02 0 02 -0 04 -001 001 -005 005 002 -004 0 01 000 0 00

ATT -0 23 -0 30 -0 30 -028 -028 -023 -028 -020 -016 -0 32 -026 -0 30

CAA -0 23 -0 10 0 04 -002 -018 -020 -016 011 -028 -0 11 006 0 08

CAC 0 30 0 03 0 33 027 021 -003 032 015 044 0 02 048 0 21

CAG 0 07 0 14 0 00 002 008 008 025 000 006 0 03 003 0 03

CAT -0 22 -0 11 -0 25 -016 -012 -016 -016 -004 -020 -0 23 -010 -0 28

CCA -0 25 0 01 0 11 -007 -011 002 -003 020 -027 0 05 004 0 12

CCC 0 25 0 03 0 28 020 016 004 020 -002 025 -0 09 018 0 16

CCG 0 03 0 13 -0 13 -003 000 016 -012 010 -007 0 17 -013 -0 05

CCT -0 16 0 01 -0 08 -028 -017 -007 -011 -022 -009 -0 06 002 -0 25

CGA -0 23 0 08 -0 07 008 -012 -005 -001 023 -025 0 03 001 0 16

CGC 0 14 -0 06 0 24 031 016 -001 021 013 023 0 11 011 0 31

CGG 0 02 0 17 -0 24 -006 006 025 018 014 -023 0 19 -015 -0 02

CGT -0 05 -0 23 -0 15 -026 -022 -019 -001 -044 -015 -0 28 -013 -0 27

CTA -0 26 -0 08 0 11 000 -019 -013 006 019 -025 -0 05 018 0 14

CTC 0 31 -0 02 0 40 029 024 010 035 016 033 -0 08 032 0 24

CTG -0 06 -0 06 -0 13 -009 -015 -005 -002 -012 -004 -0 03 -009 -0 01

CTT -0 14 -0 10 -0 13 -022 -023 001 -018 -023 -001 -0 18 003 -0 27

GAA -0 21 -0 14 -0 08 -006 -017 -013 -022 006 -026 -0 09 -001 0 01

GAC 0 32 0 17 0 38 039 029 013 021 026 036 0 28 025 0 30

GAG 0 14 0 19 -0 04 006 016 017 -002 004 004 0 18 -003 -0 02

GAT -0 16 -0 17 -0 34 -023 -018 -015 -031 -007 -019 -0 13 -025 -0 29

GCA -0 30 0 05 -0 02 -002 -011 001 000 017 -021 0 19 002 0 13

GCC 0 30 0 10 0 34 028 027 017 027 000 023 0 01 008 0 17

GCG 0 13 0 23 -0 23 014 015 014 -008 007 -004 0 26 -014 0 09

GCT -0 12 -0 13 -0 18 -040 -018 -011 -022 -037 -011 -0 15 -015 -0 30

GGA -0 06 0 23 0 10 008 -012 011 -009 009 -011 0 26 007 0 17

GGC 0 12 0 09 0 24 018 025 005 027 014 025 0 20 015 0 26

GGG 0 02 0 33 -0 12 001 028 042 028 021 -023 0 37 -020 -0 03

GGT -0 14 -0 27 -0 09 -040 -022 -018 -007 -054 -020 -0 32 -018 -0 39

GTA -0 25 -0 04 -0 01 000 -009 016 -008 037 -031 0 13 014 0 23

GTC 0 25 0 10 0 31 022 017 000 018 004 039 0 09 025 0 27

GTG 0 03 0 12 -0 08 -009 004 015 003 016 -009 0 15 -028 -0 09

GTT -0 15 -0 10 -0 25 -032 -022 -015 -031 -030 -001 -0 17 -014 -0 34 49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 35 0 03 0 34 0 33 0 17 -0 07 0 28 0 20 0 42 0 13 0 19 0 30

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 17 -0 24 -0 38 -0 19 -0 17 -0 17 -0 18 -0 03 -0 11 -0 23 -0 26 -0 25

53 TCA -0 24 0 02 0 14 0 03 0 00 0 17 -0 07 0 31 -0 27 0 09 0 12 0 18

54 TCC 0 17 -0 08 0 32 0 23 0 21 0 00 0 22 0 10 0 28 -0 07 0 19 0 21

55 TCG 0 07 0 09 -0 08 0 03 0 07 0 12 -0 06 0 23 -0 12 0 09 -0 11 0 06

56 TCT -0 26 -0 18 -0 19 -0 35 -0 24 -0 14 -0 18 -0 20 -0 10 -0 08 -0 05 -0 20

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 18 0 04 0 24 0 20 0 25 0 18 0 14 -0 03 0 19 0 21 0 17 0 29

59 TGG 0 02 0 11 -0 12 -0 04 -0 07 0 07 0 18 -0 14 -0 20 0 24 -0 12 -0 05

60 TGT -0 06 -0 15 -0 29 -0 22 -0 17 -0 03 -0 21 -0 26 -0 22 -0 21 -0 21 -0 31

61 TTA -0 11 0 15 0 13 0 03 0 00 0 17 -0 15 0 19 -0 28 0 20 0 11 0 07

62 TTC 0 40 0 12 0 38 0 35 0 30 0 21 0 32 0 16 0 45 0 06 0 30 0 29

63 TTG 0 09 0 17 -0 15 -0 05 -0 01 0 21 -0 16 0 08 -0 01 0 13 -0 14 -0 12

64 TTT -0 29 -0 33 -0 42 -0 36 -0 29 -0 28 -0 40 -0 27 -0 15 -0 30 -0 33 -0 31

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table Cl continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 25 0 00 -0 18 -0 32 -0 22 -0 04 -0 04 0 00 -0 37 -0 34 -0 29

2 AAC 0 00 -0 25 0 00 0 06 0 15 -0 09 -0 11 0 12 0 00 -0 19 -0 12 0 16

3 AAG 0 00 0 14 0 00 0 14 O i l 0 13 0 04 0 13 0 00 0 27 0 24 0 22

4 AAT 0 00 0 30 0 00 0 14 0 04 0 16 0 14 0 10 0 00 0 09 0 19 0 11

5 ACA 0 00 -0 14 0 00 -0 21 -0 25 -0 12 -0 06 -0 18 0 00 -0 14 -0 22 -0 14

6 ACC 0 00 -0 27 0 00 0 17 0 17 -0 22 -0 01 0 12 0 00 -0 23 -0 11 0 12

7 ACG 0 00 0 23 0 00 0 06 0 19 0 36 0 09 0 19 0 00 0 33 0 31 0 34

8 ACT 0 00 0 31 0 00 0 21 -0 07 0 02 -0 04 -0 07 0 00 0 03 0 17 -0 01

9 AGA 0 00 -0 05 0 00 -0 25 -0 05 0 25 0 15 0 09 0 00 -0 18 -0 18 -0 17

10 AGC 0 00 -0 23 0 00 -0 13 0 10 0 08 0 10 0 09 0 00 -0 21 -0 21 -0 14

11 AGG 0 00 0 44 0 00 -0 02 -0 05 0 43 0 12 0 19 0 00 0 39 0 21 0 05

12 AGT 0 00 0 30 0 00 0 02 0 21 0 44 0 38 0 34 0 00 0 15 0 21 0 16

13 ATA 0 00 -0 20 0 00 -0 31 -0 51 -0 32 -0 27 -0 37 0 00 -0 21 -0 26 -0 29

14 ATC 0 00 -0 27 0 00 0 12 0 17 -0 23 0 03 0 10 0 00 -0 10 -0 10 0 10

15 ATG 0 00 -0 01 0 00 0 02 0 08 0 07 0 02 0 00 0 00 -0 01 0 00 0 02

16 ATT 0 00 0 41 0 00 0 38 0 13 0 07 0 20 0 13 0 00 0 20 0 31 0 13

17 CAA 0 00 -0 07 0 00 -0 13 -0 19 -0 10 0 07 0 06 0 00 -0 22 -0 20 -0 24

18 CAC 0 00 -0 21 0 00 -0 02 0 11 -0 15 -0 06 0 05 0 00 -0 21 -0 15 0 08

19 CAG 0 00 0 13 0 00 0 00 -0 08 0 14 0 02 0 06 0 00 0 22 0 16 0 16

20 CAT 0 00 0 29 0 00 0 00 -0 07 0 09 0 02 0 04 0 00 0 17 0 19 0 06

21 CCA 0 00 -0 07 0 00 -0 09 -0 38 -0 15 -0 13 -0 17 0 00 -0 11 -0 18 -0 17

22 CCC 0 00 -0 17 0 00 0 23 0 15 -0 16 0 13 0 04 0 00 -0 08 -0 02 0 10 CCG 000 013 000 -016 -006 O 19 -008 001 000 026 006 021

CCT 000 011 000 009 -011 002 005 -O 12 000 -006 O 16 -009

CGA 000 -006 000 -016 -033 007 -O 17 003 000 -O 16 -O 16 -O 11

CGC 000 -016 000 000 004 -O 11 005 006 000 -O 14 -009 007

CGG 000 012 000 -020 -015 O 18 -024 -001 000 020 009 008

CGT 000 032 000 019 019 O 16 025 009 000 009 026 004

CTA 000 -018 000 -015 -034 -021 -008 -O 17 000 -O 14 -023 -020

CTC 000 -032 000 008 009 -034 O 13 -001 000 -023 -O 18 -009

CTG 000 013 000 003 007 O 14 005 O 12 000 021 O 15 O 19

CTT 000 019 000 016 -003 -006 006 -O 14 000 -O 10 007 -006

GAA 000 -012 000 -012 -012 -003 009 001 000 -017 -022 -022

GAC 000 -025 000 -011 013 -007 -023 -003 000 -022 -023 -O 15

GAG 000 020 000 -003 015 025 -001 O 12 000 023 021 008

GAT 000 032 000 012 014 028 O 12 020 000 029 030 O 16

GCA 000 -015 000 -024 -030 -007 -O 18 -024 000 -O 10 -009 -006

GCC 000 -022 000 011 024 -008 -003 007 000 -006 -O 11 -009

GCG 000 026 000 -014 012 031 -003 O 14 000 032 007 O 16

GCT 000 038 000 013 003 009 006 -007 000 006 O 18 -O 14

GGA 000 -014 000 -023 -012 O 17 002 -002 000 -002 -O 17 -022

GGC 000 -011 000 -004 001 -008 000 -O 14 000 -O 17 -O 16 -O 12

GGG 000 026 000 -027 001 038 000 000 000 032 009 -O 14

GGT 000 036 000 027 028 027 029 O 15 000 032 037 O 17

GTA 000 -024 000 -033 -043 -030 -030 -043 000 -029 -026 -O 18

GTC 000 -021 000 -002 014 -O 17 001 -001 000 -020 -O 12 002

GTG 000 028 000 -005 Oil 029 -009 -002 000 026 O 18 O 12

GTT 000 033 000 015 003 007 004 -O 10 000 O 17 O 14 000

TAA 000 000 000 000 000 000 000 000 000 000 000 000

TAC 000 -027 000 -003 022 -O 14 -O 17 -001 000 -O 17 -O 16 001

TAG 000 000 000 000 000 000 000 000 000 000 000 000

TAT 000 037 000 023 009 O 14 002 003 000 024 027 005

TCA 000 -013 000 -011 -043 -021 -O 15 -024 000 -O 15 -023 -O 18

TCC 000 -021 000 016 O 16 -023 O 10 000 000 -O 12 -001 O 18

TCG 000 020 000 -001 003 O 14 -O 15 000 000 030 O 11 023

TCT 000 028 000 018 -O 12 -O 13 -002 -025 000 005 026 -002

TGA 000 000 000 000 000 000 000 000 000 000 000 000

TGC 000 -015 000 -021 007 -O 19 -O 16 -009 000 -O 13 -O 16 -O 16

TGG 000 008 000 -010 002 O 12 004 000 000 008 000 -O 10

TGT 000 044 000 012 004 020 O 15 O 12 000 032 027 O 10

TTA 000 002 000 -023 -044 -013 -026 -029 000 -005 -026 -030

TTC 000 -024 000 004 O 12 -023 -004 000 000 -O 10 -O 12 -005

TTG 000 029 000 004 O 19 028 003 008 000 038 028 O 13

TTT 000 035 000 025 O 15 008 -003 -003 000 O 17 024 O 16

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60 Table Cl continued

61 62 63 64

TTA TTC TTG TTT

1 AAA -0 29 -0 15 -0 09 -0 02

2 AAC 0 33 -0 19 0 14 -0 10

3 AAG 0 24 0 02 0 12 0 14

4 AAT -0 04 0 21 0 14 0 34

5 ACA -0 41 -0 04 -0 13 -0 11

6 ACC 0 23 -0 17 0 08 -0 04

7 ACG 0 12 0 26 0 06 0 00

8 ACT -0 14 0 09 -0 10 0 21

9 AGA -0 35 0 27 0 01 0 01

10 AGC -0 16 -0 07 -0 14 -0 16

11 AGG -0 25 0 28 -0 19 -0 06

12 AGT -O i l 0 20 -0 07 0 24

13 ATA -0 42 -0 23 -0 18 -0 33

14 ATC 0 17 -0 21 0 18 0 14

15 ATG 0 22 0 02 0 15 -0 03

16 ATT 0 23 0 27 0 19 0 46

17 CAA -0 36 -0 11 -0 03 -0 07

18 CAC 0 26 -0 11 0 11 -0 10

19 CAG 0 12 0 06 0 14 0 09

20 CAT -0 04 0 09 0 04 0 18

21 CCA -0 32 0 01 -0 20 -0 17

22 CCC 0 04 -0 12 -0 04 0 09

23 CCG -0 17 0 12 -0 22 -0 09

24 CCT -0 17 0 06 -0 11 0 13

25 CGA -0 24 -0 06 -0 02 -0 07

26 CGC 0 03 -0 19 0 16 0 03

27 CGG -0 27 -0 13 -0 19 -0 20

28 CGT -0 05 0 14 0 24 0 40

29 CTA -0 28 -0 04 0 13 -0 14

30 CTC 0 20 -0 29 0 29 -0 01

31 CTG 0 34 0 15 0 23 0 17

32 CTT 0 00 -0 01 0 07 0 23

33 GAA -0 19 0 00 -0 08 -0 08

34 GAC 0 29 -0 10 -0 08 -0 33

35 GAG 0 23 0 08 -0 03 -0 09

36 GAT 0 10 0 24 0 03 0 25

37 GCA -0 26 0 02 -0 21 -0 20

38 GCC 0 13 -0 04 -0 08 -0 16

39 GCG 0 12 0 24 -0 23 -0 11

40 GCT -0 17 0 08 -0 15 0 10 GGA -0 26 0 03 -0 13 -0 15

GGC 0 00 -0 10 -0 09 -0 04

GGG -0 33 0 00 -0 37 -0 36

GGT 0 12 0 23 0 28 0 43

GTA -0 38 -0 13 -0 13 -0 25

GTC 0 23 -0 19 0 04 -0 11

GTG 0 26 0 28 -0 10 -0 17

GTT 0 22 0 20 0 06 0 34

TAA 0 00 0 00 0 00 0 00

TAC 0 25 -0 15 0 21 -0 11

TAG 0 00 0 00 0 00 0 00

TAT 0 18 0 21 0 15 0 25

TCA -0 39 -0 08 -0 13 -0 14

TCC 0 05 -0 12 0 08 0 06

TCG -0 01 0 14 -0 02 0 03

TCT -0 13 0 02 -0 05 0 10

TGA 0 00 0 00 0 00 0 00

TGC -0 10 -0 07 -0 13 -0 17

TGG 0 04 0 04 0 10 -0 06

TGT -0 09 0 19 0 01 0 15

TTA -0 39 -0 03 -0 14 -0 21

TTC 0 19 -0 24 0 00 -0 01

TTG 0 17 0 23 -0 05 0 03

TTT 0 28 0 29 0 15 0 56

TTA TTC TTG TTT

61 62 63 64

Table C.2: CPW matrix A. niger highly expressed sequences (left codon indicated in column 2, right codon indicated in row 2). Host cell: A. niger; Sequence data: full A. niger genome; Highly expressed group: 400 seqs.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 0 93 0 64 0 65 0 92 0 61 0 65 0 67 0 57 0 07 0 61 -0 09 0 75

2 AAC 0 44 -0 48 -0 42 0 49 0 57 -0 50 0 16 -0 33 0 33 -0 25 0 60 0 13

3 AAG 0 51 -0 42 -0 36 0 48 0 27 -0 46 0 43 -0 18 -0 23 -0 14 0 13 0 23

4 AAT 0 60 0 68 0 75 0 65 0 35 0 63 0 44 0 80 0 75 0 36 0 80 0 31

5 ACA 0 29 0 45 0 56 0 71 0 22 0 43 0 15 0 66 0 33 0 58 -0 14 0 28

6 ACC 0 34 -0 58 -0 53 0 45 0 33 -0 59 0 43 -0 46 0 31 -0 41 -0 20 0 15

7 ACG 0 25 -0 02 0 39 0 16 0 56 0 08 0 52 0 47 0 01 0 59 -0 30 0 57

8 ACT 0 50 0 81 0 48 0 48 0 66 0 10 0 60 0 20 -0 36 0 26 0 64 0 62

9 AGA 0 64 -0 07 0 01 0 27 0 56 0 27 0 63 0 29 -0 32 0 34 0 09 0 27

10 AGC 0 34 -0 39 -0 44 0 08 0 40 -0 34 0 33 -0 38 0 42 -0 39 -0 30 0 20

11 AGG -0 20 0 24 -0 29 0 17 -0 44 -0 33 -0 44 0 17 -0 04 0 58 0 72 0 33

12 AGT 0 78 0 56 0 79 0 51 0 28 0 58 0 54 0 45 0 49 0 71 0 89 0 75

13 ATA 0 02 0 86 0 62 0 58 0 44 0 61 0 53 0 74 0 41 0 68 0 69 0 50

14 ATC 0 12 -0 53 -0 44 0 29 0 52 -0 58 0 12 -0 03 0 38 -0 14 0 04 0 21

15 ATG 0 41 -0 21 -0 13 0 44 0 56 -0 25 0 28 -0 16 -0 08 -0 36 0 31 0 26

16 ATT 0 63 0 77 0 82 0 82 0 66 0 38 0 61 0 47 0 76 0 61 0 75 0 58

17 CAA 0 70 0 52 0 58 0 01 -0 25 0 44 0 03 0 57 -0 45 0 19 -0 06 0 53

18 CAC -0 13 -0 47 -0 47 -0 04 0 41 -0 55 -0 29 -0 05 0 02 -0 28 -0 31 0 16

19 CAG 0 29 -0 29 -0 37 0 18 0 45 -0 39 0 49 -0 27 0 15 -0 24 0 22 0 13

20 CAT 0 74 0 74 0 84 0 55 0 49 0 48 0 61 0 70 0 77 0 77 0 84 0 57

21 CCA 0 61 0 76 0 31 0 48 -0 33 0 31 0 04 0 41 0 32 0 29 0 28 0 66

22 CCC 0 57 -0 56 -0 62 0 12 0 38 -0 44 0 25 -0 31 -0 06 -0 51 -0 40 0 28

23 CCG 0 13 0 08 0 59 0 27 0 33 0 36 0 46 0 19 0 19 0 59 0 84 0 61

24 CCT 0 53 0 24 0 55 0 43 -0 13 -0 22 0 51 -0 16 0 80 -0 24 0 57 -0 18

25 CGA 0 73 0 37 0 77 0 77 -0 07 0 38 0 61 0 62 0 72 0 35 0 80 0 52

26 CGC 0 34 -0 49 -0 56 -0 03 0 51 -0 40 0 26 -0 29 -0 36 -0 47 -0 10 -0 08

27 CGG 0 20 0 32 0 58 0 48 0 14 0 48 0 11 0 34 0 58 0 51 0 25 0 40

28 CGT 0 77 -0 21 0 21 0 59 0 11 -0 48 0 09 0 08 0 66 0 48 0 78 0 53

29 CTA 0 80 0 47 0 71 0 91 -0 07 0 19 0 83 0 51 -0 26 0 12 0 45 0 38

30 CTC 0 20 -0 46 -0 49 0 14 0 40 -0 44 0 39 -0 07 0 28 -0 32 0 49 -0 25

31 CTG 0 42 -0 34 -0 22 0 38 0 61 -0 42 0 38 0 08 0 30 -0 24 -0 42 0 24

32 CTT 0 32 0 40 0 74 0 81 0 42 -0 04 0 43 -0 02 0 70 0 48 0 84 0 51

33 GAA 0 79 0 31 0 58 0 58 0 10 0 33 0 47 0 64 0 48 0 34 0 01 0 49

34 GAC 0 37 -0 42 -0 50 0 13 0 34 -0 47 0 46 -0 18 0 23 -0 39 0 50 -0 26

35 GAG 0 52 -0 37 -0 43 0 28 0 54 -0 43 0 33 -0 40 0 06 -0 38 0 22 0 09

36 GAT 0 66 0 42 0 66 0 42 -0 16 0 19 0 57 0 31 0 59 0 52 0 23 0 44

37 GCA 0 24 0 21 0 48 0 42 0 46 0 32 -0 10 0 43 0 20 0 17 -0 35 0 58

38 GCC 0 38 -0 61 -0 54 0 25 0 19 -0 47 0 11 -0 37 -0 08 -0 44 0 52 -0 14

39 GCG 0 66 0 26 0 42 0 30 0 50 0 42 0 54 0 24 0 06 0 53 0 63 0 73

40 GCT 0 38 0 66 0 32 0 78 0 49 -0 20 0 50 -0 27 -0 21 0 19 0 54 0 48

41 GGA 0 67 -0 01 -0 01 0 40 0 33 0 05 -0 03 -0 02 0 11 -0 36 0 53 0 02

42 GGC 0 11 -0 38 -0 51 0 33 0 52 -0 30 0 26 -0 05 -0 13 -0 48 -0 23 -0 13

43 GGG 0 72 0 53 0 61 0 64 0 64 0 44 0 70 0 57 0 83 0 66 0 91 0 57

44 GGT 0 48 -0 29 0 42 0 48 0 62 -0 53 0 57 -0 35 0 58 0 01 0 78 0 15

45 GTA 0 79 0 65 0 64 0 58 0 56 0 50 0 75 0 35 0 70 0 59 0 68 0 34

46 GTC 0 25 -0 60 -0 56 0 39 0 66 -0 55 0 32 -0 22 0 33 -0 33 -0 26 -0 02

47 GTG 0 63 0 21 0 37 0 71 0 32 -0 22 0 19 0 20 0 22 0 22 -0 23 0 67

48 GTT 0 60 0 51 0 54 0 64 0 72 0 01 0 56 0 05 0 83 0 41 0 69 0 75

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 34 -0 49 -0 45 0 39 0 49 -0 52 0 59 -0 31 -0 42 -0 25 0 68 0 08 51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 84 0 72 0 81 0 74 0 52 0 48 0 73 0 22 1 00 0 62 -0 17 0 80

53 TCA 0 40 0 60 0 66 -0 06 -0 64 0 33 -0 43 0 57 0 36 0 33 -0 63 0 36

54 TCC 0 42 -0 55 -0 57 0 35 0 69 -0 47 0 48 -0 28 0 05 -0 30 -0 28 0 13

55 TCG 0 18 -0 02 0 13 -0 09 0 13 0 02 0 29 0 24 0 39 0 30 0 07 0 43

56 TCT 0 70 0 75 0 64 0 74 0 50 0 02 0 21 -0 05 0 22 0 29 0 70 0 82

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 57 -0 33 -0 33 -0 17 0 20 -0 46 0 11 -0 31 -0 05 0 39 -0 52 0 41

59 TGG 0 19 -0 20 -0 06 0 43 0 63 -0 28 0 65 -0 34 -0 50 0 03 0 09 -0 12

60 TGT 0 20 0 74 0 42 0 50 0 67 0 41 0 81 0 64 0 42 0 77 1 00 0 38

61 TTA 0 85 0 85 0 45 0 51 0 49 0 69 0 36 0 69 0 41 0 53 0 16 0 56

62 TTC 0 18 -0 45 -0 35 0 42 0 33 -0 46 0 36 -0 18 0 46 -0 14 0 17 0 09

63 TTG -0 26 -0 02 0 10 -0 05 0 25 -0 21 -0 06 -0 22 0 42 0 30 0 59 0 17

64 TTT 0 70 0 82 0 82 0 77 0 53 0 49 0 54 0 62 -0 23 0 52 -0 27 0 76

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.2 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA 0 11 0 75 0 53 0 32 -0 36 -0 09 0 55 0 56 0 61 0 29 0 53 0 80

2 AAC 0 76 -0 39 -0 10 -0 08 0 35 -0 44 -0 46 0 40 0 62 -0 56 0 04 -0 15

3 AAG 0 63 -0 36 -0 16 0 17 0 47 -0 37 -0 26 0 55 0 53 -0 51 0 23 -0 08

4 AAT 0 18 0 60 0 19 0 53 0 79 0 61 0 63 0 15 0 79 0 55 0 77 0 16

5 ACA 0 70 0 59 0 37 0 47 -0 15 0 35 -0 17 0 49 0 03 0 05 0 73 0 16

6 ACC 0 31 -0 53 -0 41 -0 28 0 37 -0 53 -0 28 0 68 0 62 -0 54 -0 01 0 03

7 ACG -0 24 0 58 0 52 0 47 0 53 0 27 0 34 0 27 0 61 0 53 0 53 0 39

8 ACT 0 70 0 14 0 37 0 55 0 38 -0 25 -0 22 0 17 0 31 -0 51 0 57 -0 31

9 AGA 0 12 -0 39 0 10 0 62 -0 14 -0 26 0 06 0 25 0 50 0 30 0 31 0 02

10 AGC 0 64 -0 23 -0 26 -0 01 0 43 -0 05 -0 28 0 38 0 58 -0 16 0 15 -0 11

11 AGG -0 60 0 55 0 05 0 75 0 20 -0 39 0 47 0 65 0 15 0 63 0 76 -0 21

12 AGT 0 55 0 22 0 39 0 45 0 49 0 21 0 23 0 54 0 27 0 29 0 53 0 15

13 ATA -0 15 0 74 0 56 0 62 0 06 0 74 -0 04 0 84 -0 38 -0 07 0 88 0 46

14 ATC 0 58 -0 43 -0 31 -0 07 0 33 -0 52 -0 29 0 52 0 04 -0 39 0 25 0 09

15 ATG -0 07 -0 16 0 00 0 33 0 10 -0 26 -0 06 0 41 0 22 -0 41 0 28 0 43

16 ATT 0 84 0 48 0 57 0 28 0 07 0 24 0 34 0 42 0 63 -0 10 0 18 0 01

17 CAA 0 77 0 30 0 25 0 56 0 21 -0 19 0 44 0 28 -0 32 -0 05 -0 13 0 22

18 CAC 0 93 -0 49 -0 20 -0 10 -0 37 -0 52 -0 18 0 57 0 38 -0 55 0 39 -0 26

19 CAG -0 08 -0 32 -0 12 0 08 0 20 -0 17 -0 30 0 24 0 49 -0 29 0 43 -0 07

20 CAT 0 44 0 53 0 30 0 62 0 09 0 49 0 61 0 25 0 26 0 62 0 62 -0 08

21 CCA 0 62 0 22 0 65 0 57 0 39 0 66 0 68 0 66 0 17 0 26 -0 33 -0 08

22 CCC 0 17 -0 48 -0 42 -0 34 0 40 -0 57 -0 51 0 54 0 37 0 26 -0 08 -0 05

23 CCG 0 20 0 42 0 11 0 23 0 34 0 49 0 35 0 57 0 10 0 52 0 26 0 69

24 CCT -0 28 0 34 0 32 0 29 0 25 -0 46 -0 22 0 17 -0 45 -0 41 0 14 -0 39

25 CGA 0 66 0 44 0 48 0 57 0 73 0 57 0 49 0 49 0 69 0 64 0 41 -0 25

26 CGC 0 73 -0 09 -0 34 -0 07 0 26 -0 40 -0 45 0 57 0 52 -0 57 0 23 -0 20

27 CGG 0 24 0 40 0 36 0 48 0 46 0 51 0 71 0 71 -0 14 0 50 0 42 0 76

28 CGT -0 19 -0 61 0 00 -0 01 0 02 -0 55 -0 48 -0 18 0 44 -0 62 0 18 -0 29

29 CTA 0 33 0 80 0 47 0 57 -0 16 -0 38 0 48 0 37 -0 30 -0 21 0 48 0 05

30 CTC 0 65 -0 35 -0 18 -0 08 0 50 -0 38 -0 41 0 62 0 58 -0 48 0 35 -0 01

31 CTG 0 71 -0 40 -0 25 -0 05 0 34 -0 35 -0 20 0 32 0 62 -0 30 0 31 0 20

32 CTT 0 61 0 44 0 56 0 56 -0 24 -0 16 -0 10 0 39 -0 41 -0 46 0 50 -0 37

33 GAA -0 20 0 25 0 42 0 39 -0 16 -0 22 0 45 0 55 -0 17 0 49 0 73 0 27

34 GAC 0 59 -0 26 -0 31 -0 11 0 34 -0 43 -0 43 0 19 0 53 -0 54 0 27 -0 31

35 GAG 0 59 -0 33 -0 21 0 17 0 32 -0 38 -0 29 0 57 0 35 -0 46 0 29 -0 27 36 GAT 0 01 0 11 0 47 0 36 0 62 0 29 0 20 0 39 0 44 0 23 0 46 0 27

37 GCA 0 75 0 46 0 56 0 50 0 43 0 26 0 49 0 69 -0 08 0 53 0 38 0 41

38 GCC 0 52 -0 49 -0 39 -0 37 0 53 -0 39 -0 33 0 47 0 81 -0 34 0 54 0 01

39 GCG 0 91 0 69 0 47 0 55 0 54 0 05 0 01 0 68 0 25 0 55 0 38 0 30

40 GCT 0 33 -0 10 0 08 0 15 0 41 -0 51 -0 42 0 35 0 57 -0 60 0 40 -0 61

41 GGA 0 71 0 45 0 06 0 36 0 53 -0 03 0 15 0 44 -0 23 0 13 0 40 -0 13

42 GGC 0 63 -0 01 -0 11 0 04 0 24 -0 41 -0 40 0 37 0 05 -0 22 0 50 -0 15

43 GGG -0 41 0 59 0 72 0 76 0 53 0 34 0 46 0 65 0 40 0 55 0 49 0 37

44 GGT 0 78 -0 58 -0 20 0 00 0 41 -0 37 -0 26 0 42 0 61 -0 51 0 61 -0 42

45 GTA 0 18 0 82 0 78 0 69 0 41 0 34 0 56 0 39 0 44 0 39 0 57 0 61

46 GTC 0 80 -0 52 -0 40 -0 28 0 68 -0 49 -0 32 0 49 0 74 -0 41 0 62 0 13

47 GTG 0 69 0 39 0 30 0 55 0 18 0 05 -0 10 0 66 0 72 -0 05 0 37 -0 01

48 GTT 0 58 0 11 0 37 0 16 -0 19 -0 27 -0 04 0 27 0 39 -0 56 -0 01 -0 47

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 71 -0 34 -0 30 0 03 -0 15 -0 46 -0 21 0 28 0 35 -0 53 0 30 -0 05

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 29 0 48 0 69 0 32 0 24 0 55 0 47 0 53 0 66 0 27 0 41 0 32

53 TCA 0 52 0 09 0 50 0 54 0 42 0 59 0 19 0 33 -0 48 0 66 0 61 0 01

54 TCC 0 44 -0 54 -0 37 -0 23 0 30 -0 45 -0 45 0 09 0 55 -0 46 -0 16 -0 01

55 TCG 0 40 0 16 0 30 0 27 0 29 0 25 0 25 0 27 0 27 0 10 0 41 0 24

56 TCT 0 61 0 22 0 29 0 75 0 32 -0 45 -0 16 0 03 -0 02 -0 42 0 16 -0 35

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 44 0 12 -0 25 -0 36 0 02 -0 46 -0 27 0 43 0 37 -0 56 0 73 0 07

59 TGG -0 24 0 02 0 00 0 08 0 10 -0 26 -0 05 0 42 -0 12 -0 18 0 23 0 15

60 TGT 0 07 -0 10 0 56 0 52 -0 25 0 27 0 79 0 62 0 53 0 45 -0 07 0 10

61 TTA 0 23 0 90 0 78 0 51 -0 39 0 80 0 74 -0 08 0 48 0 47 -0 16 0 37

62 TTC 0 63 -0 30 -0 24 -0 21 0 41 -0 42 -0 39 0 35 0 17 -0 48 0 31 -0 14

63 TTG 0 50 -0 05 -0 12 -0 31 0 58 0 01 0 34 0 38 0 59 0 38 0 38 0 12

64 TTT 0 75 0 49 0 72 0 68 0 40 0 71 0 69 0 32 0 60 0 39 0 73 0 41

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.2 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA 0 29 0 27 0 75 0 72 0 56 0 49 0 73 0 55 0 35 0 35 0 37 0 19

2 AAC -0 07 -0 52 0 42 -0 45 -0 12 -0 36 -0 36 -0 10 0 19 -0 34 -0 29 0 30

3 AAG 0 60 -0 26 0 35 -0 47 0 09 -0 42 -0 18 -0 09 0 27 -0 24 -0 28 0 12

4 AAT 0 57 0 30 0 75 0 22 0 72 0 41 0 48 0 66 0 42 0 17 0 22 0 22

5 ACA 0 55 -0 33 0 52 0 81 -0 25 0 52 0 53 0 27 0 25 0 37 0 43 0 38

6 ACC 0 69 -0 38 0 27 -0 53 -0 45 -0 52 -0 30 -0 02 0 22 -0 42 -0 30 0 12

7 ACG 0 57 0 63 0 68 0 61 0 61 0 50 0 35 0 27 0 36 0 25 0 13 0 47

8 ACT 0 48 -0 37 0 41 -0 51 0 53 -0 31 -0 21 -0 01 0 39 -0 24 -0 38 0 08

9 AGA 0 63 0 22 0 29 0 45 0 29 -0 11 0 38 -0 30 0 31 0 42 0 46 0 62

10 AGC 0 32 -0 08 0 41 -0 34 0 71 0 18 0 30 -0 05 -0 19 0 02 0 04 0 41

11 AGG 0 70 -0 35 0 55 0 71 0 25 0 47 0 50 -0 17 0 09 -0 40 0 23 0 56

12 AGT 0 38 0 36 0 47 0 32 0 24 -0 07 -0 23 0 20 0 15 0 09 0 00 0 04

13 ATA 0 44 0 78 0 66 -0 20 -0 33 0 38 0 12 0 52 0 26 0 78 0 77 0 81

14 ATC 0 44 -0 37 0 44 -0 61 0 67 -0 33 -0 34 0 02 0 30 -0 10 -0 06 0 14

15 ATG 0 40 -0 26 0 37 -0 19 0 57 -0 18 -0 01 -0 30 0 13 -0 08 -0 08 0 09

16 ATT 0 67 0 02 0 31 0 01 0 36 -0 03 0 14 0 03 0 18 -0 34 -0 39 -0 02

17 CAA 0 59 0 60 0 42 0 06 0 46 0 40 0 37 0 28 0 23 0 31 0 45 0 27

18 CAC 0 60 -0 36 -0 01 -0 66 -0 26 -0 46 -0 41 -0 10 -0 12 -0 43 -0 22 0 35

19 CAG 0 50 -0 33 0 45 -0 51 0 66 -0 44 -0 28 -0 15 0 28 -0 21 -0 35 -0 06

20 CAT 0 65 0 66 0 47 0 23 -0 30 0 60 0 52 0 76 0 24 0 32 0 29 0 19 21 CCA 0 78 0 39 0 33 0 57 0 35 0 65 0 10 0 49 0 19 0 45 0 33 0 50

22 CCC 0 49 -0 31 0 55 -0 69 -0 29 -0 34 0 04 0 09 0 07 -0 32 -0 46 -0 17

23 CCG 0 66 0 42 0 53 0 71 0 50 0 49 0 24 -0 05 0 51 -0 09 0 45 0 45

24 CCT -0 22 -0 34 0 61 -0 64 0 43 -0 35 -0 41 -0 33 0 14 -0 31 -0 13 0 29

25 CGA 0 64 0 62 0 46 0 69 0 10 0 73 0 45 0 35 0 34 0 30 0 69 0 71

26 CGC -0 13 -0 45 0 37 -0 62 0 17 -0 30 -0 11 0 35 0 17 0 01 -0 22 0 20

27 CGG 0 19 0 63 0 76 0 60 0 53 0 78 0 62 0 58 0 56 0 36 0 46 0 20

28 CGT 0 48 -0 45 0 21 -0 69 -0 16 -0 63 -0 59 -0 47 0 09 -0 62 -0 64 -0 33

29 CTA 0 45 -0 51 -0 01 -0 25 -0 36 -0 30 0 52 0 55 0 73 0 29 0 39 0 17

30 CTC 0 69 -0 54 0 07 -0 65 0 70 -0 44 -0 18 -0 28 0 14 -0 29 -0 33 0 02

31 CTG 0 54 -0 22 0 52 -0 35 0 69 -0 18 -0 01 0 04 0 13 -0 10 -0 18 0 13

32 CTT 0 58 0 02 0 60 -0 33 0 33 -0 31 -0 24 -0 05 0 26 -0 34 -0 30 0 10

33 GAA 0 14 0 49 0 63 0 22 0 79 0 25 0 49 0 42 0 24 -0 08 0 30 0 22

34 GAC 0 52 -0 44 -0 15 -0 58 -0 09 -0 33 -0 10 -0 26 0 32 -0 05 -0 21 0 34

35 GAG 0 40 -0 32 0 39 -0 58 0 57 -0 42 -0 29 -0 34 0 34 -0 11 -0 34 0 05

36 GAT -0 09 0 44 0 66 0 30 0 61 0 06 0 02 -0 07 0 50 -0 29 -0 21 0 13

37 GCA 0 39 0 64 0 60 0 67 0 48 0 73 0 52 0 39 0 41 0 35 0 17 0 47

38 GCC 0 72 -0 34 0 49 -0 56 0 72 -0 36 -0 19 -0 23 0 42 -0 38 -0 25 -0 12

39 GCG 0 74 0 65 0 52 0 31 0 23 0 26 0 35 0 44 0 37 -0 08 0 36 0 34

40 GCT 0 59 -0 53 0 48 -0 65 0 62 -0 47 -0 36 -0 37 0 20 0 13 -0 44 0 09

41 GGA 0 71 0 14 0 62 -0 10 0 64 0 56 0 58 0 48 0 48 0 51 0 30 0 25

42 GGC 0 33 -0 35 0 60 -0 60 0 08 0 17 0 08 0 29 0 33 0 17 -0 18 0 37

43 GGG -0 13 0 81 0 81 0 15 0 45 0 35 0 72 0 62 0 59 0 41 0 64 0 65

44 GGT 0 65 -0 27 0 59 -0 64 -0 11 -0 64 -0 54 -0 47 -0 12 -0 58 -0 47 -0 26

45 GTA 0 77 0 16 0 91 0 66 0 78 0 56 0 62 0 46 0 75 0 71 0 70 0 48

46 GTC 0 57 -0 52 0 25 -0 62 0 28 -0 40 -0 23 -0 31 0 43 -0 28 -0 23 0 15

47 GTG 0 66 -0 03 0 52 0 45 0 78 0 06 0 15 0 07 0 36 0 19 0 15 0 50

48 GTT 0 78 -0 20 0 53 -0 25 -0 07 -0 37 -0 14 -0 10 0 01 -0 48 -0 47 0 07

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 57 -0 42 0 23 -0 54 0 38 -0 36 -0 24 -0 21 0 18 -0 28 -0 33 0 25

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 57 0 63 0 39 0 56 -0 11 0 22 -0 07 0 48 0 50 0 16 0 26 0 09

53 TCA -0 18 0 68 0 63 0 34 -0 55 0 24 0 46 0 46 0 54 0 27 0 11 -0 03

54 TCC 0 77 -0 48 0 14 -0 52 -0 21 -0 40 -0 30 -0 01 0 34 -0 54 -0 38 0 09

55 TCG 0 49 0 20 0 53 0 55 -0 54 0 34 0 10 0 32 0 42 0 20 0 18 0 19

56 TCT -0 02 -0 47 0 43 -0 55 0 42 -0 15 -0 30 -0 32 0 14 0 16 -0 20 0 26

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 82 0 05 0 73 -0 59 -0 22 -0 02 -0 04 0 34 0 09 0 02 -0 20 0 13

59 TGG 0 74 -0 28 0 61 -0 02 -0 43 -0 12 0 05 0 17 0 21 0 11 -0 12 -0 10

60 TGT 0 41 0 71 -0 19 -0 46 0 09 -0 05 -0 11 -0 09 0 24 0 32 0 16 -0 37

61 TTA 0 10 0 93 0 43 0 78 -0 05 0 48 0 40 1 00 0 43 0 23 0 85 0 81

62 TTC 0 67 -0 37 0 43 -0 61 0 04 -0 26 -0 35 -0 15 0 31 -0 17 -0 21 0 25

63 TTG 0 56 0 63 0 59 0 30 -0 13 -0 01 0 29 0 01 0 37 0 24 0 08 0 22

64 TTT 0 82 0 64 0 77 0 68 -0 50 0 64 0 68 0 45 0 03 -0 35 0 10 0 45

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.2 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA 0 41 0 43 0 35 0 59 -0 15 0 24 0 21 0 76 0 90 0 31 0 57 0 60

2 AAC 0 66 -0 30 0 33 -0 04 0 12 -0 32 0 53 -0 22 0 92 -0 40 0 38 -0 03

3 AAG 0 49 -0 43 0 52 -0 27 0 38 -0 14 0 85 -0 47 0 73 -0 42 0 29 -0 20

4 AAT -0 06 -0 11 0 24 -0 13 0 34 0 11 0 36 0 27 0 57 -0 07 0 14 0 15

5 ACA 0 53 0 45 0 57 0 54 0 64 0 46 0 45 0 53 0 06 0 55 0 37 0 69 ACC 030 -014 053 -014 019 -017 069 -046 077 -045 029 -031

ACG 024 -0 12 050 018 041 041 070 029 004 057 018 0 12

ACT -018 -0 47 005 -054 -003 -030 055 -061 024 -038 025 -0 30

AGA 016 0 27 050 047 018 063 082 021 042 054 035 0 45

AGC 059 0 14 058 -008 053 -005 071 -035 073 005 017 -0 12

AGG -034 0 09 082 044 057 049 081 039 -018 021 051 0 47

AGT 046 -0 26 024 005 035 016 053 -032 036 -016 -017 -0 09

ATA 060 0 70 079 077 016 086 083 083 -054 073 052 0 69

ATC 061 -0 06 062 -004 040 020 079 -044 072 -026 053 0 15

ATG 030 -0 24 038 -008 033 006 036 -033 058 -023 030 -0 11

ATT 029 -0 55 002 -044 -003 -021 039 -047 000 -045 007 -0 23

CAA -002 0 24 048 037 008 017 068 003 050 034 054 0 55

CAC 020 -0 34 032 -027 -004 -015 080 -044 045 -043 071 -0 35

CAG 033 -0 29 027 -033 032 -012 075 -045 057 -042 016 -0 29

CAT -042 0 39 043 045 001 016 052 027 092 -015 048 0 20

CCA 045 0 57 035 009 035 -007 -029 038 -025 057 054 0 55

CCC 057 -0 43 057 -029 009 -020 064 -057 012 -048 -008 -0 31

CCG 014 0 22 009 -017 056 049 064 053 068 043 042 0 12

CCT 053 -0 26 055 -044 012 005 060 -048 059 -028 011 -0 17

CGA 068 0 66 075 060 047 -017 053 070 078 013 047 0 58

CGC 022 -0 15 065 -015 044 010 060 -006 009 014 020 0 12

CGG 052 0 43 039 030 063 058 074 042 025 055 011 0 27

CGT 009 -0 69 -002 -066 -035 -043 045 -082 051 -073 -026 -0 46

CTA 053 -0 13 -023 -032 -039 -022 066 073 044 056 075 -0 22

CTC 048 -0 22 052 -007 013 005 078 -035 067 -038 038 -0 01

CTG 024 -0 28 020 -026 007 -007 065 -032 035 -035 011 -0 09

CTT 034 -0 45 045 -046 -032 -026 058 -058 -007 -033 018 -0 28

GAA 016 0 03 021 038 030 005 049 031 070 -016 034 0 34

GAC 060 -0 12 049 026 040 -016 069 -014 059 006 049 0 02

GAG 051 -0 29 044 -037 034 -015 077 -049 069 -031 037 -0 32

GAT 053 -0 42 009 -029 004 -017 006 -007 036 -036 015 -0 27

GCA 029 0 66 042 051 023 030 039 050 -022 051 037 0 53

GCC 061 -0 28 042 -006 054 023 075 -049 059 -041 034 -0 28

GCG 046 0 28 044 048 051 051 074 032 016 045 045 0 51

GCT 031 -0 53 012 -058 -005 -035 057 -064 007 -040 019 -0 36

GGA 014 0 38 050 042 045 046 080 031 078 050 063 0 23

GGC 051 0 36 075 011 049 028 075 008 064 047 054 0 28

GGG 061 0 78 084 046 060 083 089 078 073 073 074 0 77

GGT 039 -0 66 032 -067 -015 -033 063 -078 063 -066 -022 -0 69

GTA -011 -0 05 034 073 051 051 -021 089 066 039 046 0 70

GTC 043 -0 16 066 -020 022 -014 047 -053 067 -036 041 -0 04

GTG 059 0 14 058 021 050 037 071 055 075 022 039 0 38

GTT -013 -0 47 022 -053 002 -017 041 -056 057 -051 006 -0 50

TAA 000 0 00 000 000 000 000 000 000 000 000 000 0 00

TAC 066 -0 32 052 -024 041 -022 006 -022 077 -016 -010 0 15

TAG 000 0 00 000 000 000 000 000 000 000 000 000 0 00

TAT 045 -0 26 059 -013 038 -014 052 011 036 -004 020 -0 25

TCA 055 0 54 016 031 043 082 062 078 044 022 049 0 57

TCC 010 -0 39 053 -032 000 -037 052 -050 047 -054 010 -0 36

TCG 021 0 20 040 013 041 039 066 035 057 037 027 0 35

TCT 020 -0 44 026 -051 008 -042 006 -037 033 -009 033 -0 16

TGA 000 0 00 000 000 000 000 000 000 000 000 000 0 00

TGC 063 0 14 031 -043 041 026 016 -043 -017 035 058 0 23

TGG 035 0 00 000 -019 042 012 068 -045 -015 049 -017 -0 31

TGT 050 -0 23 025 -023 021 031 044 -040 066 -058 035 -0 46

TTA 068 0 70 070 045 092 095 -002 081 036 079 -014 1 00 62 TTC 0 77 -0 26 0 66 -0 24 0 46 0 06 0 80 -0 43 0 09 -0 35 0 45 0 01

63 TTG 0 55 0 29 0 45 0 27 0 47 0 47 0 78 0 00 0 23 0 34 0 33 0 01

64 TTT 0 19 -0 27 0 01 -0 17 0 06 -0 02 0 55 -0 29 0 74 -0 14 0 23 0 26

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.2 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 0 05 0 00 0 44 -0 60 0 47 0 21 0 51 0 00 0 06 -0 07 0 16

2 AAC 0 00 -0 38 0 00 0 11 0 51 -0 47 -0 17 -0 17 0 00 -0 39 -0 30 0 08

3 AAG 0 00 -0 27 0 00 0 43 0 32 -0 38 0 04 0 04 0 00 -0 17 0 03 0 25

4 AAT 0 00 0 47 0 00 0 74 0 47 0 66 0 45 0 43 0 00 0 58 0 72 0 65

5 ACA 0 00 0 10 0 00 0 36 0 29 0 26 0 35 0 18 0 00 0 31 -0 11 0 26

6 ACC 0 00 -0 54 0 00 0 41 0 29 -0 58 -0 30 -0 01 0 00 -0 44 -0 22 0 29

7 ACG 0 00 0 11 0 00 0 59 0 18 0 40 0 22 0 46 0 00 0 52 0 03 0 65

8 ACT 0 00 0 47 0 00 0 54 0 38 -0 12 0 33 -0 22 0 00 -0 19 0 53 -0 02

9 AGA 0 00 -0 27 0 00 -0 51 0 12 -0 31 0 72 -0 19 0 00 0 27 -0 66 -0 17

10 AGC 0 00 -0 45 0 00 0 29 -0 12 -0 28 0 22 -0 22 0 00 -0 11 -0 40 -0 06

11 AGG 0 00 0 71 0 00 0 46 0 18 -0 43 0 56 0 30 0 00 0 87 0 49 0 36

12 AGT 0 00 0 28 0 00 0 33 0 31 0 55 0 70 0 47 0 00 0 30 0 65 0 61

13 ATA 0 00 0 30 0 00 -0 42 -0 84 0 70 0 67 -0 57 0 00 0 40 0 58 -0 54

14 ATC 0 00 -0 41 0 00 0 35 0 64 -0 59 0 23 -0 05 0 00 -0 17 -0 32 -0 17

15 ATG 0 00 -0 22 0 00 0 45 0 34 -0 17 0 39 0 09 0 00 -0 11 0 00 0 21

16 ATT 0 00 0 55 0 00 0 47 0 69 0 41 0 48 0 48 0 00 0 51 0 62 0 25

17 CAA 0 00 0 06 0 00 -0 09 0 59 0 19 0 29 0 40 0 00 0 16 -0 04 -0 42

18 CAC 0 00 -0 47 0 00 0 35 0 17 -0 54 -0 01 -0 33 0 00 -0 50 -0 35 -0 04

19 CAG 0 00 -0 16 0 00 0 32 0 43 -0 42 -0 05 -0 08 0 00 -0 10 0 03 0 45

20 CAT 0 00 0 51 0 00 0 45 0 54 0 42 0 38 0 23 0 00 0 66 0 64 0 89

21 CCA 0 00 0 09 0 00 0 52 0 29 0 25 0 37 -0 05 0 00 0 26 0 45 0 38

22 CCC 0 00 -0 50 0 00 0 51 0 76 -0 59 0 33 -0 17 0 00 -0 42 -0 33 0 37

23 CCG 0 00 -0 02 0 00 0 23 -0 33 0 39 0 37 0 19 0 00 0 64 0 38 1 00

24 CCT 0 00 0 10 0 00 0 52 0 67 -0 12 0 17 -0 06 0 00 -0 45 -0 07 -0 07

25 CGA 0 00 -0 22 0 00 0 71 -0 43 0 17 0 26 0 67 0 00 0 45 0 55 0 08

26 CGC 0 00 -0 35 0 00 0 43 0 26 -0 53 -0 27 -0 36 0 00 -0 61 0 00 0 40

27 CGG 0 00 0 34 0 00 0 56 0 36 0 32 0 56 0 50 0 00 0 51 0 44 0 53

28 CGT 0 00 -0 39 0 00 0 50 0 26 -0 28 0 22 0 14 0 00 -0 08 -0 02 0 43

29 CTA 0 00 -0 15 0 00 0 61 0 59 -0 25 0 54 0 57 0 00 0 47 -0 11 1 00

30 CTC 0 00 -0 41 0 00 0 24 0 11 -0 46 0 27 -0 13 0 00 -0 42 -0 44 -0 11

31 CTG 0 00 -0 28 0 00 0 31 -0 10 -0 21 0 11 -0 15 0 00 -0 01 0 11 0 23

32 CTT 0 00 0 20 0 00 0 59 0 25 -0 18 0 03 -0 30 0 00 -0 51 0 32 0 36

33 GAA 0 00 -0 21 0 00 0 33 0 46 0 07 0 18 0 35 0 00 0 45 -0 13 0 26

34 GAC 0 00 -0 47 0 00 0 42 0 61 -0 44 -0 12 -0 32 0 00 -0 43 -0 33 0 00

35 GAG 0 00 -0 20 0 00 0 48 0 56 -0 40 0 20 -0 09 0 00 -0 38 0 10 0 36

36 GAT 0 00 0 30 0 00 0 56 0 68 0 20 0 44 0 29 0 00 0 62 0 52 0 25

37 GCA 0 00 0 13 0 00 0 38 -0 11 0 03 0 23 0 21 0 00 0 17 0 10 0 45

38 GCC 0 00 -0 59 0 00 0 38 0 57 -0 56 0 17 -0 13 0 00 -0 25 -0 33 -0 23

39 GCG 0 00 0 54 0 00 0 55 0 18 0 52 0 52 0 27 0 00 0 69 0 39 0 68

40 GCT 0 00 0 44 0 00 0 27 0 49 -0 32 0 26 -0 13 0 00 -0 26 0 27 -0 15

41 GGA 0 00 -0 25 0 00 0 03 0 23 -0 15 0 19 0 39 0 00 0 02 0 03 -0 26

42 GGC 0 00 -0 26 0 00 0 31 0 46 -0 37 0 38 -0 28 0 00 -0 22 -0 40 -0 07

43 GGG 0 00 0 56 0 00 0 12 0 33 0 61 0 40 0 37 0 00 0 68 0 70 0 29

44 GGT 0 00 -0 16 0 00 0 49 0 75 -0 32 0 51 0 06 0 00 -0 10 0 42 0 38

45 GTA 0 00 -0 30 0 00 0 58 0 11 0 08 -0 05 -0 52 0 00 0 43 0 45 0 22

46 GTC 0 00 -0 44 0 00 0 25 0 51 -0 55 0 22 -0 30 0 00 -0 50 -0 30 0 26 47 GTG 0 00 0 19 0 00 0 48 0 11 0 39 0 46 0 08 0 00 0 03 0 06 0 70

48 GTT 0 00 0 08 0 00 0 57 0 02 -0 27 0 43 0 16 0 00 0 24 0 42 0 52

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 00 -0 43 0 00 0 18 0 23 -0 40 0 04 -0 50 0 00 -0 43 -0 28 0 13

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 00 0 61 0 00 0 71 0 84 0 43 0 60 0 27 0 00 0 78 0 65 0 57

53 TCA 0 00 0 39 0 00 0 41 -0 19 -0 07 0 58 -0 10 0 00 0 34 0 21 0 32

54 TCC 0 00 -0 47 0 00 0 31 0 27 -0 52 0 47 -0 22 0 00 -0 48 -0 25 0 36

55 TCG 0 00 0 34 0 00 0 52 0 11 0 22 0 11 0 14 0 00 0 38 0 48 0 74

56 TCT 0 00 0 17 0 00 0 14 0 22 -0 48 0 02 -0 34 0 00 -0 40 0 12 0 28

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 00 -0 32 0 00 0 35 0 30 -0 47 -0 45 -0 47 0 00 -0 30 -0 25 -0 08

59 TGG 0 00 -0 19 0 00 0 38 -0 24 -0 13 0 28 0 17 0 00 0 11 0 00 -0 16

60 TGT 0 00 0 34 0 00 0 14 0 61 0 51 0 75 0 49 0 00 0 50 0 56 0 50

61 TTA 0 00 0 54 0 00 0 36 -0 20 0 56 0 41 0 49 0 00 0 83 0 55 0 72

62 TTC 0 00 -0 42 0 00 0 33 0 51 -0 49 0 38 -0 19 0 00 -0 08 -0 21 -0 35

63 TTG 0 00 0 20 0 00 0 09 0 43 0 31 0 43 0 25 0 00 0 79 0 54 0 25

64 TTT 0 00 0 68 0 00 0 77 0 65 0 27 0 43 -0 09 0 00 0 74 0 59 0 30

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT 49 50 51 52 53 54 55 56 57 58 59 60

Table C.2 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 72 0 34 0 10 0 50

2 AAC 0 79 -0 39 0 00 0 31

3 AAG 0 15 -0 27 0 34 0 39

4 AAT 0 46 0 65 0 37 0 45

5 ACA 0 00 0 14 0 08 0 37

6 ACC 0 89 -0 37 0 19 0 54

7 ACG 0 81 0 46 0 68 -0 10

8 ACT 0 82 -0 09 0 21 0 15

9 AGA 0 10 0 21 0 18 0 66

10 AGC 0 55 -0 12 -0 01 0 21

11 AGG 0 05 0 52 -0 18 0 71

12 AGT 0 42 0 37 0 20 0 66

13 ATA 0 29 0 42 0 71 0 42

14 ATC 0 50 -0 41 0 24 0 29

15 ATG 0 52 -0 16 0 35 0 45

16 ATT 0 85 0 54 0 20 0 53

17 CAA 0 05 0 11 -0 12 0 34

18 CAC 0 73 -0 37 0 05 0 07

19 CAG 0 70 -0 26 0 51 0 46

20 CAT 0 79 0 34 0 33 0 71

21 CCA -0 07 0 31 0 36 0 22

22 CCC 0 55 -0 51 -0 32 0 32

23 CCG 0 41 0 39 0 25 0 40

24 CCT 0 57 0 01 0 37 0 66

25 CGA 1 00 0 42 0 54 0 43

26 CGC -0 29 -0 44 0 11 -0 20

27 CGG 0 61 0 30 0 03 0 57

28 CGT 1 00 -0 37 0 02 0 46

29 CTA -0 64 -0 19 0 53 0 00

30 CTC 0 65 -0 44 0 10 0 18

31 CTG 0 68 -0 06 0 25 0 25 CTT 0 49 0 00 0 07 0 49

GAA 0 55 0 13 0 20 0 39

GAC 0 71 -0 41 0 19 -0 13

GAG 0 78 -0 28 0 22 0 43

GAT 0 87 0 44 0 37 0 78

GCA 0 50 0 46 0 13 0 26

GCC 0 82 -0 17 0 03 0 17

GCG 0 46 0 20 0 44 -0 07

GCT 0 49 -0 36 0 11 0 46

GGA 0 31 -0 14 0 18 0 36

GGC 0 76 -0 12 0 12 0 43

GGG 0 53 0 63 -0 05 0 35

GGT 0 94 -0 44 0 52 0 75

GTA 0 57 0 27 0 48 0 63

GTC 0 58 -0 43 0 26 0 29

GTG 0 93 0 10 0 30 0 35

GTT 0 59 0 22 0 39 0 51

TAA 0 00 0 00 0 00 0 00

TAC 0 87 -0 37 0 27 0 14

TAG 0 00 0 00 0 00 0 00

TAT 0 79 0 56 0 58 0 65

TCA 0 09 0 29 0 12 0 49

TCC 0 65 -0 32 0 19 0 39

TCG 0 62 -0 11 0 44 0 33

TCT -0 41 -0 32 0 27 0 27

TGA 0 00 0 00 0 00 0 00

TGC 0 30 -0 28 -0 18 0 20

TGG 0 77 -0 14 0 11 0 37

TGT -0 14 0 33 0 44 0 38

TTA 0 66 0 79 0 67 0 40

TTC 0 75 -0 37 0 13 0 34

TTG 0 59 0 40 0 33 0 39

TTT 0 77 0 63 0 50 0 80

TTA TTC TTG TTT

61 62 63 64

Table C.3: CPW matrix Bacillus subtilis full genome (left codon indicated in column 2, right codon indicated in row 2). Host cell: B. subtilis; Sequence data: full B. subtilis genome.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 002 -028 -011 004 -028 -013 -023 044 016 -039 -002 004

2 AAC -004 -022 001 -016 009 010 006 010 -017 -063 -038 -054

3 AAG 000 033 018 036 043 059 038 050 048 022 028 005

4 AAT -003 011 013 024 -008 -005 -020 029 061 057 056 032

5 ACA -022 -031 -027 -016 -013 -024 -013 -033 -045 -030 -051 -025

6 ACC 040 019 043 -013 042 010 061 -012 005 037 016 002

7 ACG -006 022 -020 004 -018 017 001 -031 -037 026 -022 -002

8 ACT 057 069 054 049 045 053 068 018 036 075 032 046

9 AGA -031 -031 -032 -018 -009 -030 -037 022 -044 -034 -059 -020

10 AGC -009 005 -015 -014 -007 -015 -010 -020 -031 -032 -059 -038

11 AGG 030 052 023 029 035 051 045 043 -007 044 -002 026

12 AGT 010 054 028 028 003 052 003 015 071 087 082 080

13 ATA -040 -015 -037 -008 024 -023 012 -014 -011 028 -043 006

14 ATC -015 -017 007 -029 -005 -013 015 -021 -044 -050 -047 -048

15 ATG 011 008 -021 -006 002 014 -010 -001 -031 -009 -032 -019

16 ATT 020 021 031 031 -002 003 -003 018 069 085 066 060

17 CAA -027 -043 -038 -026 -010 -046 -026 -002 -018 -040 -018 -017

18 CAC 014 -004 -004 -022 026 -008 010 010 -032 -052 -040 -044

19 CAG 047 058 040 052 031 041 016 033 050 065 029 063

20 CAT -006 001 002 015 -012 001 -009 011 061 066 062 047

21 CCA -034 -049 -045 -034 009 -033 011 -037 -051 -048 -051 -050

22 CCC 050 035 059 -009 055 025 069 -011 014 030 083 011

23 CCG -002 018 -013 -012 -031 -009 -003 -051 -022 037 039 007

24 CCT 031 049 033 039 049 045 067 028 055 080 054 058

25 CGA -047 -052 -032 -045 -008 -021 -016 001 -032 -055 017 -022

26 CGC 031 013 010 -010 015 -006 014 027 -013 -033 -015 -031

27 CGG 021 048 021 004 -025 024 -043 -004 038 045 031 046

28 CGT 042 061 051 050 024 059 017 036 089 090 090 085

29 CTA -036 -020 -043 -027 029 -036 028 -006 -037 -031 -047 -023

30 CTC 037 034 027 -002 034 -009 050 -011 -039 -038 -004 -033

31 CTG -010 003 -020 -013 -026 -018 -023 -041 009 045 010 039

32 CTT 067 061 068 055 056 044 061 031 054 074 060 068

33 GAA -009 -025 -006 -003 -020 -016 -021 028 008 -037 015 -015

34 GAC -005 -016 -005 -021 013 001 018 -007 -035 -065 -052 -058

35 GAG 020 040 017 032 036 057 016 035 034 023 050 014

36 GAT -001 007 014 018 -009 009 -015 013 072 077 072 056

37 GCA -029 -029 -024 -019 -021 -032 -007 -038 -046 -027 -039 -035

38 GCC 013 -010 005 -035 016 012 044 -031 -047 -023 006 -025

39 GCG -007 030 -015 004 -025 021 005 -026 -025 044 031 026

40 GCT 043 044 047 050 033 053 056 013 065 087 076 061

41 GGA -033 -038 -011 -024 -021 -023 -036 -014 -029 -045 -020 -026 42 GGC 0 30 0 27 0 21 0 11 0 10 0 07 0 14 -0 01 -0 27 -0 30 -0 36 -0 27

43 GGG -0 24 -0 01 -0 13 -0 16 0 10 0 34 0 10 0 22 0 07 0 10 0 21 -0 02

44 GGT 0 32 0 52 0 51 0 51 0 23 0 62 0 23 0 08 0 81 0 88 0 85 0 84

45 GTA -0 34 -0 34 -0 37 -0 22 -0 09 -0 23 -0 21 0 05 -0 28 -0 09 -0 40 0 00

46 GTC 0 00 0 01 0 43 -0 26 0 01 -0 26 0 03 -0 19 -0 55 -0 56 -0 38 -0 47

47 GTG -0 21 0 05 -0 29 -0 16 -0 25 -0 05 -0 17 0 02 0 22 0 55 0 19 0 42

48 GTT 0 56 0 49 0 49 0 53 0 41 0 36 0 41 0 13 0 68 0 87 0 76 0 66

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 01 -0 32 0 10 -0 20 -0 04 -0 03 -0 03 0 02 -0 36 -0 60 -0 49 -0 58

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 06 0 11 0 09 0 24 -0 05 0 20 -0 12 0 24 0 65 0 75 0 68 0 54

53 TCA -0 19 -0 22 -0 19 -0 22 -0 16 -0 27 -0 04 -0 44 -0 32 -0 23 -0 36 -0 16

54 TCC 0 25 0 06 0 37 -0 26 0 28 0 06 0 45 -0 15 -0 42 -0 22 0 29 -0 30

55 TCG -0 02 0 32 -0 14 -0 06 -0 05 0 08 0 24 -0 28 -0 03 0 58 0 22 0 20

56 TCT 0 15 0 27 0 24 0 24 0 23 0 31 0 51 -0 13 0 70 0 86 0 56 0 58

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 06 -0 09 -0 14 -0 15 0 21 -0 20 0 05 0 31 0 08 -0 39 -0 34 -0 12

59 TGG 0 13 0 06 -0 23 -0 04 -0 02 0 29 -0 19 0 15 -0 28 -0 20 0 04 -0 13

60 TGT 0 01 0 33 0 02 0 05 0 01 -0 26 -0 30 0 20 0 82 0 91 0 83 0 70

61 TTA -0 35 -0 36 -0 37 -0 35 -0 17 -0 33 -0 32 -0 33 -0 26 -0 16 -0 19 -0 21

62 TTC -0 09 0 02 0 02 -0 04 0 12 -0 18 0 29 -0 29 -0 54 -0 49 -0 58 -0 46

63 TTG -0 08 0 10 -0 22 -0 19 0 15 0 04 0 10 -0 18 0 00 0 43 0 11 0 16

64 TTT -0 02 0 03 0 14 -0 01 0 02 -0 16 0 00 0 05 0 49 0 80 0 50 0 57

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.3 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 36 -0 29 -0 14 0 22 0 07 0 14 0 15 0 35 0 07 0 35 0 19 0 45

2 AAC 0 17 0 01 0 04 0 06 0 09 0 02 0 32 0 17 0 20 0 17 0 19 0 12

3 AAG 0 01 0 32 0 38 0 29 -0 12 -0 37 -0 28 -0 41 -0 20 -0 31 -0 41 -0 42

4 AAT -0 25 -0 06 -0 03 0 05 -0 23 0 04 -0 02 -0 14 -0 26 -0 27 -0 11 0 06

5 ACA 0 16 0 23 0 04 0 36 0 02 0 09 -0 05 0 22 0 08 0 27 -0 03 0 05

6 ACC -0 05 -0 23 0 19 -0 52 0 00 -0 05 O i l -0 29 0 29 0 40 0 47 0 36

7 ACG -0 35 -0 19 -0 35 -0 37 0 05 0 18 0 30 0 24 -0 32 0 05 -0 24 -0 33

8 ACT 0 51 0 78 0 64 0 66 -0 34 -0 39 -0 08 -0 33 0 05 0 14 0 29 -0 09

9 AGA -0 14 -0 09 -0 11 0 11 0 21 0 23 -0 19 0 28 0 44 0 23 0 26 0 36

10 AGC -0 09 0 06 -0 21 -0 02 -0 20 -0 07 -0 20 -0 13 0 35 0 36 0 10 0 34

11 AGG -0 14 0 31 0 21 0 25 -0 13 -0 26 -0 40 -0 27 -0 29 -0 02 -0 33 -0 31

12 AGT -0 22 0 24 -0 06 -0 08 0 08 0 43 0 18 0 01 -0 21 -0 31 0 00 -0 07

13 ATA 0 02 0 68 0 56 0 72 -0 19 0 04 -0 09 0 01 -0 05 -0 13 -0 17 0 05

14 ATC -0 11 -0 24 -0 19 -0 26 0 31 0 38 0 38 0 24 0 20 0 11 0 28 0 32

15 ATG 0 09 0 02 0 00 -0 04 0 27 -0 04 -0 22 0 02 0 26 0 10 -0 11 -0 02

16 ATT 0 22 0 03 0 03 0 07 -0 23 -0 25 -0 10 -0 13 -0 21 -0 29 -0 12 -0 08 CAA -021 -033 -030 -014 064 076 070 074 069 073 087 081

CAC 0 26 0 05 0 05 005 015 000 017 000 -001 007 017 013

CAG 0 45 0 42 0 45 019 -031 -044 -048 -043 -040 -044 -046 -047

CAT 0 04 -0 03 -0 02 -006 -005 -003 -009 001 -010 -026 000 -002

CCA -0 02 -0 22 -0 32 007 058 054 065 064 040 071 087 065

CCC 0 42 0 15 0 36 006 -003 -035 034 -011 013 069 044 -002

CCG 0 12 -0 12 -0 18 -036 -024 -009 -014 -015 -040 -024 -022 -035

CCT 0 43 0 57 0 52 046 -008 -002 -009 -012 -005 008 023 003

CGA -0 15 -0 37 -0 38 -023 068 060 059 057 064 079 071 085

CGC 0 27 -0 05 0 18 008 -006 -029 -032 -031 028 -007 -012 001

CGG -0 05 -0 03 -0 15 -030 000 -014 -012 -025 017 -022 -023 -020

CGT 0 33 0 22 0 34 021 014 024 032 023 -024 -043 -032 -028

CTA -0 17 0 20 0 12 038 054 065 060 048 075 076 080 079

CTC -0 04 -0 10 -0 11 -024 021 037 044 017 022 -009 015 010

CTG 0 29 -0 25 -0 22 -021 -023 -014 -004 001 -025 -012 -032 -026

CTT 0 47 0 53 0 58 048 -025 -042 -023 -030 -020 -029 -018 -032

GAA -0 17 -0 20 -0 10 013 012 028 010 037 025 040 022 051

GAC 0 16 0 07 -0 02 -006 011 016 016 -006 032 021 010 -006

GAG 0 16 0 22 0 24 002 -006 -033 -029 -046 -037 -030 -042 -044

GAT -0 09 0 02 0 01 000 -006 011 -009 -006 -016 -018 -001 001

GCA 0 14 0 17 -0 05 032 005 022 -008 033 009 011 021 014

GCC -0 10 -0 22 -0 06 -041 -005 -008 012 -028 043 039 052 037

GCG -0 09 -0 12 -0 28 -034 -008 009 010 008 -034 -017 -033 -034

GCT 0 38 0 57 0 53 041 -016 -020 016 -012 004 -029 010 -016

GGA 0 10 0 01 -0 07 016 -014 003 -019 004 029 046 010 022

GGC 0 02 -0 07 -0 07 -015 019 010 007 001 041 036 010 011

GGG -0 26 0 17 -0 03 -022 -018 -027 -031 -039 -037 -026 -044 -038

GGT 0 13 0 21 0 30 013 038 029 038 039 009 -031 -010 -008

GTA 0 40 0 51 0 36 066 022 020 -017 029 043 028 034 038

GTC -0 14 -0 39 -0 37 -043 042 034 053 016 057 051 048 044

GTG 0 08 -0 04 -0 14 -018 017 004 -016 020 -003 -009 -041 -028

GTT 0 35 0 27 0 43 032 -032 -036 -029 -033 -023 -039 -012 -031

TAA 0 00 0 00 0 00 000 000 000 000 000 000 000 000 000

TAC -0 39 0 10 0 07 017 032 029 039 021 039 041 019 031

TAG 0 00 0 00 0 00 000 000 000 000 000 000 000 000 000

TAT -0 18 -0 10 -0 04 009 -023 -020 -007 -006 -023 -012 -016 000

TCA 0 05 0 17 0 08 022 005 017 017 026 -013 022 028 -007

TCC -0 09 -0 21 -0 10 -036 022 -012 036 002 017 021 054 032

TCG -0 24 -0 08 0 02 -038 007 017 030 -002 -037 -030 -018 -048

TCT 0 19 0 33 0 29 018 -028 -021 004 -014 -039 -040 003 -032

TGA 0 00 0 00 0 00 000 000 000 000 000 000 000 000 000

TGC 0 09 -0 01 -0 02 036 -020 -037 -022 -005 025 043 -008 031

TGG -0 17 0 09 0 00 -001 039 -006 -029 003 042 041 -023 004

TGT -0 38 -0 24 0 02 -007 051 020 013 031 -004 -031 -017 -010 61 TTA -0 24 -0 16 -0 22 0 02 0 40 0 51 0 31 0 24 0 69 0 61 0 81 0 64

62 TTC 0 26 0 13 0 25 0 18 -0 08 -0 07 0 28 -0 01 -0 08 -0 08 -0 16 -0 33

63 TTG -0 01 -0 05 -0 05 -0 28 0 07 0 10 -0 23 0 14 -0 04 0 19 -0 24 -0 14

64 TTT -0 01 -0 17 -0 10 -0 01 -0 10 0 13 0 02 -0 04 -0 02 -0 02 0 16 0 18

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.3 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA -0 37 0 05 -0 23 0 30 0 00 0 43 0 29 0 57 -0 09 -0 17 0 04 0 22

2 AAC -0 36 -0 39 -0 23 -0 43 -0 29 0 17 -0 15 -0 09 0 33 0 28 0 42 0 26

3 AAG -0 17 0 07 -0 44 -0 06 -0 53 -0 53 -0 69 -0 60 0 03 -0 02 0 29 -0 19

4 AAT 0 01 0 40 0 23 0 25 -0 33 -0 06 0 08 0 13 -0 29 -0 20 0 00 -0 16

5 ACA 0 15 0 29 0 43 0 25 0 27 0 08 0 27 0 21 -0 02 -0 08 -0 16 0 05

6 ACC -0 05 -0 31 -0 15 -0 32 0 20 0 21 0 33 0 06 0 41 0 39 0 29 0 04

7 ACG 0 45 0 49 0 47 0 55 -0 27 -0 33 -0 41 -0 47 0 27 0 43 0 33 0 12

8 ACT 0 57 0 28 0 47 -0 26 -0 22 0 44 0 62 0 01 -0 42 -0 37 -0 36 -0 35

9 AGA -0 30 0 06 -0 20 0 22 0 58 0 45 0 33 0 58 -0 13 -0 21 -0 23 0 16

10 AGC -0 36 -0 37 -0 41 -0 41 0 11 0 11 -0 08 0 14 0 43 0 35 0 25 0 37

11 AGG -0 27 -0 12 -0 39 0 04 -0 27 -0 55 -0 68 -0 51 0 04 0 15 -0 14 -0 05

12 AGT 0 40 0 84 0 70 0 78 -0 27 0 04 0 17 0 04 -0 52 -0 44 -0 47 -0 44

13 ATA -0 17 0 15 0 06 0 21 -0 24 0 07 0 26 0 31 -0 24 -0 22 -0 18 -0 13

14 ATC 0 10 -0 42 0 14 -0 26 0 15 0 29 0 37 0 25 0 28 0 31 0 39 0 39

15 ATG 0 45 0 26 0 15 0 21 0 14 -0 22 -0 43 -0 18 0 10 -0 05 -0 18 0 03

16 ATT 0 14 0 08 0 38 0 14 -0 06 -0 12 0 34 0 15 -0 19 -0 10 0 00 -0 21

17 CAA 0 49 0 73 0 68 0 78 0 43 0 81 0 82 0 85 0 14 0 02 -0 11 0 19

18 CAC -0 19 -0 53 -0 27 -0 46 0 10 0 21 0 31 0 11 0 27 0 36 0 14 0 12

19 CAG -0 39 -0 43 -0 52 -0 45 -0 36 -0 50 -0 58 -0 58 -0 03 0 04 -0 10 -0 19

20 CAT 0 10 0 25 0 13 0 13 0 03 0 10 0 26 0 26 -0 06 -0 14 -0 17 -0 06

21 CCA 0 60 0 67 0 73 0 60 0 53 0 69 0 77 0 72 0 25 0 07 -0 02 0 25

22 CCC -0 48 -0 62 -0 1 1 -0 57 0 21 0 19 0 61 0 40 0 25 0 08 -0 17 -0 17

23 CCG -0 12 -0 22 -0 15 -0 22 -0 26 -0 55 -0 33 -0 52 0 21 0 36 0 28 0 31

24 CCT 0 45 0 38 0 63 0 04 0 15 0 29 0 65 0 24 -0 33 -0 32 -0 34 -0 40

25 CGA 0 53 0 65 0 68 0 70 0 51 0 64 0 59 0 66 0 36 0 28 0 05 0 30

26 CGC 0 09 -0 51 -0 23 -0 51 0 10 0 09 -0 06 0 14 0 58 0 29 0 24 0 35

27 CGG -0 01 0 36 0 16 0 21 0 12 -0 37 -0 51 -0 41 -0 04 -0 04 -0 14 -0 06

28 CGT 0 85 0 76 0 85 0 48 -0 03 -0 30 -0 05 -0 11 -0 27 -0 34 -0 17 -0 33

29 CTA 0 85 0 82 0 76 0 72 0 15 0 72 0 78 0 70 0 19 0 24 -0 11 0 16

30 CTC 0 08 -0 32 0 07 -0 30 0 42 0 28 0 49 0 38 0 35 0 10 0 49 -0 06

31 CTG 0 10 -0 12 -0 18 -0 13 0 09 -0 32 -0 44 -0 31 0 30 0 39 0 05 0 27

32 CTT 0 10 -0 31 0 02 -0 21 0 06 -0 14 0 34 0 11 -0 35 -0 09 -0 38 -0 44

33 GAA -0 23 0 20 -0 11 0 33 0 29 0 48 0 27 0 58 -0 02 -0 07 -0 13 0 16

34 GAC -0 38 -0 54 -0 45 -0 51 0 27 0 28 0 32 0 25 0 36 0 39 0 25 0 25

35 GAG -0 13 -0 21 -0 49 -0 34 -0 39 -0 35 -0 60 -0 63 0 10 0 08 0 17 -0 23 36 GAT 0 16 0 49 0 33 0 39 0 04 0 06 0 17 0 10 -0 18 -0 18 -0 09 -0 13

37 GCA 0 17 0 19 0 36 0 26 0 16 0 15 0 24 0 24 0 00 -0 05 -0 02 0 14

38 GCC -0 01 -0 46 -0 18 -0 38 0 40 0 31 0 47 0 27 0 43 0 37 0 18 0 20

39 GCG 0 10 0 21 0 10 -0 01 -0 11 -0 39 -0 37 -0 48 0 13 0 24 0 14 0 21

40 GCT 0 68 0 64 0 73 0 22 0 03 0 15 0 53 0 03 -0 31 -0 36 -0 29 -0 35

41 GGA -0 11 -0 05 0 06 0 03 0 25 0 30 0 27 0 27 -0 14 -0 28 -0 04 0 06

42 GGC 0 00 -0 08 -0 16 -0 31 0 33 0 46 0 32 0 14 0 41 0 30 0 18 0 27

43 GGG -0 09 -0 13 -0 16 0 02 -0 17 -0 36 -0 53 -0 56 0 05 0 21 0 27 0 12

44 GGT 0 71 0 79 0 79 0 67 0 14 0 02 0 34 -0 20 -0 37 -0 38 -0 28 -0 28

45 GTA 0 32 0 32 0 30 0 37 0 14 0 22 0 30 0 51 -0 06 -0 12 -0 18 0 12

46 GTC 0 20 -0 32 0 18 -0 18 0 47 0 45 0 50 0 50 0 49 0 46 0 37 0 18

47 GTG 0 18 0 12 -0 07 0 00 -0 10 -0 37 -0 55 -0 42 0 18 0 27 0 14 0 25

48 GTT 0 21 0 01 0 16 -0 02 -0 05 -0 21 0 18 0 04 -0 35 -0 31 -0 27 -0 35

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 33 -0 42 -0 39 -0 40 0 05 0 34 0 42 0 36 0 29 0 29 0 19 0 16

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 11 0 32 0 08 0 29 -0 12 0 11 0 39 0 36 -0 18 -0 16 0 04 -0 06

53 TCA 0 24 0 28 0 26 0 39 -0 14 0 08 0 34 0 16 0 03 -0 07 -0 14 0 07

54 TCC -0 07 -0 45 -0 1 1 -0 41 0 12 0 27 0 51 0 17 0 55 0 46 0 34 0 30

55 TCG 0 39 0 37 0 23 0 10 -0 36 -0 38 -0 31 -0 47 0 26 0 33 0 21 0 18

56 TCT 0 40 0 60 0 65 0 35 -0 19 -0 16 0 41 -0 12 -0 25 -0 20 -0 15 -0 30

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 49 -0 53 -0 45 -0 47 0 13 0 27 -0 02 0 35 0 50 0 43 0 14 0 39

59 TGG 0 22 0 10 -0 08 0 36 -0 04 -0 28 -0 41 -0 17 0 08 0 16 -0 14 -0 08

60 TGT 0 84 0 83 0 64 0 77 -0 31 -0 21 0 00 0 03 -0 29 -0 36 -0 37 -0 31

61 TTA 0 49 0 64 0 43 0 65 0 15 0 55 0 58 0 66 0 03 0 10 -0 10 0 07

62 TTC -0 33 -0 50 -0 26 -0 53 -0 01 0 24 0 32 0 28 0 44 0 48 0 53 0 44

63 TTG -0 23 -0 25 -0 26 -0 25 -0 22 -0 32 -0 47 -0 35 0 27 0 23 0 11 0 15

64 TTT 0 43 0 42 0 38 0 43 -0 08 -0 06 0 37 0 39 -0 22 -0 18 -0 07 -0 17

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.3 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -0 18 0 02 -0 30 0 25 -0 07 -0 17 -0 30 0 17 -0 19 0 17 -0 21 0 47

2 AAC 0 15 0 03 0 20 0 26 -0 30 -0 31 -0 21 -0 24 0 09 0 19 0 30 0 33

3 AAG 0 26 0 49 0 08 0 24 0 21 0 37 0 25 0 42 -0 13 0 09 -0 27 -0 12

4 AAT -0 06 -0 26 -0 17 0 07 0 22 0 37 0 30 0 32 -0 25 -0 21 -0 23 0 09

5 ACA 0 06 0 06 0 07 -0 10 0 02 -0 11 -0 16 -0 11 0 22 0 23 0 26 0 28

6 ACC 0 12 0 20 0 37 -0 20 -0 31 -0 30 -0 27 -0 33 -0 12 -0 03 0 19 -0 34

7 ACG -0 03 0 40 0 25 -0 12 0 17 0 55 0 39 0 30 0 14 0 17 0 23 -0 20

8 ACT -0 28 -0 23 0 01 -0 40 0 04 0 16 0 28 -0 19 -0 40 -0 36 -0 15 -0 51

9 AGA -0 07 -0 01 -0 33 0 28 -0 26 -0 15 -0 38 0 19 0 21 0 19 -0 15 0 49

10 AGC 0 36 0 20 0 35 0 43 -0 38 -0 29 -0 33 -0 28 0 30 0 43 0 30 0 49

11 AGG -0 03 0 24 -0 22 0 20 -0 34 0 06 0 36 0 54 0 05 0 34 -0 29 0 07

12 AGT -0 10 -0 09 -0 21 -0 06 0 59 0 82 0 80 0 56 -0 37 -0 28 -0 44 -0 28

13 ATA 0 24 0 20 0 13 0 22 0 28 0 23 0 10 0 13 0 53 0 65 0 68 0 70 14 ATC 006 -022 024 005 -030 -048 -039 -047 -009 -O 11 O 16 -009

15 ATG 008 028 -018 -008 007 O 14 -032 005 013 O 12 -O 18 001

16 ATT 000 -030 001 005 051 045 051 041 -O 10 -022 -O 11 -001

17 CAA 011 001 002 O 16 -O 15 -O 19 -034 -O 17 -O 11 -004 -024 028

18 CAC 018 -029 O 15 -O 13 -032 -049 -037 -038 O 13 008 023 006

19 CAG -013 024 -O 17 -O 12 O 11 042 000 047 025 O 17 -O 18 -002

20 CAT 006 -O 13 -004 O 15 037 031 032 033 -O 11 -O 11 -020 021

21 CCA 036 020 047 -004 031 O 12 -001 -025 035 O 16 039 O 17

22 CCC -023 -027 O 10 -058 -056 -063 -031 -057 -001 -022 O 16 -031

23 CCG -006 036 026 -O 14 -007 021 024 004 035 037 036 -O 11

24 CCT -008 -O 11 -002 -028 025 033 043 -020 -025 -037 004 -047

25 CGA 047 057 020 022 022 O 12 005 031 047 O 12 -022 042

26 CGC 026 004 O 10 O 17 -041 -045 -022 -037 031 -003 020 029

27 CGG -022 O 18 -027 005 003 038 032 060 -005 O 19 -029 O 13

28 CGT -002 -024 -021 000 069 077 071 068 -039 -041 -039 -021

29 CTA 042 O 14 036 O 13 030 -009 -008 -O 17 O 11 -009 020 O 15

30 CTC 009 -022 024 -O 13 -042 -064 -048 -065 -O 10 -049 -O 13 -047

31 CTG 006 020 003 001 052 047 034 054 063 047 045 046

32 CTT -014 -040 -008 -029 -003 -025 005 -O 19 -026 -049 -034 -035

33 GAA -010 -001 -032 O 15 -009 -021 -022 O 14 -008 008 -029 032

34 GAC 018 005 O 17 O 13 -043 -048 -040 -042 027 034 032 026

35 GAG 019 052 O 14 026 028 031 O 18 044 009 026 -005 -O 16

36 GAT -004 -O 19 -008 003 039 050 050 042 -023 -007 -023 -005

37 GCA 000 -009 O 19 001 006 -004 -006 -O 16 026 020 026 023

38 GCC 007 O 17 032 -O 19 -041 -033 -024 -049 O 16 009 037 -O 10

39 GCG -019 032 O 11 -O 11 -001 030 006 O 13 O 17 027 021 -O 12

40 GCT -007 -O 17 O 10 -023 037 053 052 024 -036 -034 -003 -046

41 GGA 005 O 13 -021 O 19 O 17 025 024 056 038 049 041 050

42 GGC 010 003 O 19 -002 -054 -040 -038 -046 -004 003 008 -O 13

43 GGG -011 047 -003 009 O 17 052 059 079 023 044 038 006

44 GGT -022 -O 10 -025 -O 19 062 080 070 060 -051 -048 -045 -051

45 GTA 007 -008 002 007 021 025 -O 12 -002 043 048 049 058

46 GTC 017 007 046 004 -042 -058 -045 -061 -001 -O 16 -005 -020

47 GTG -012 028 -O 10 006 063 068 049 072 056 048 031 042

48 GTT 001 -034 -O 11 -020 030 047 040 O 12 -031 -050 -032 -035

49 TAA 000 000 000 000 000 000 000 000 000 000 000 000

50 TAC 010 O 11 002 000 -045 -045 -043 -034 025 039 023 044

51 TAG 000 000 000 000 000 000 000 000 000 000 000 000

52 TAT -003 -O 13 -O 11 O 18 033 039 047 045 -030 -O 17 -024 O 13

53 TCA -010 -O 14 -003 -020 -007 -O 13 000 -021 022 021 034 O 14

54 TCC 006 -O 14 044 -031 -O 14 -035 -O 12 -044 026 -002 054 -025

55 TCG -018 025 O 16 -O 13 O 11 038 O 17 009 O 19 021 021 -020

56 TCT -Oil -016 013 -031 044 058 056 023 -031 -040 009 -049

57 TGA 000 000 000 000 000 000 000 000 000 000 000 000

58 TGC 023 -001 000 036 -049 -038 -035 -O 17 033 039 037 058

59 TGG -006 029 -O 19 008 -023 009 000 032 006 033 -030 005

60 TGT -029 -005 -023 008 069 089 080 063 -046 -044 -036 -002

61 TTA 025 021 026 027 O 10 O 12 -O 17 -007 029 034 025 032

62 TTC 020 -005 045 O 16 -033 -044 -033 -040 033 025 056 008

63 TTG -O 15 031 -003 -O 13 039 048 034 057 048 033 005 -006

64 TTT 001 -028 -009 004 035 O 19 037 033 007 -031 -006 -007

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.3 continued 49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

AAA 000 -018 000 006 -O 19 023 -021 040 000 -009 -003 008

AAC 000 -008 000 -009 023 009 031 027 000 -029 -025 -025

AAG 000 011 000 008 034 039 O 18 027 000 O 17 007 -O 10

AAT 000 001 000 O 11 006 027 009 028 000 030 026 030

ACA 000 000 000 O 12 -O 12 -003 -001 006 000 005 000 000

ACC 000 on 000 -O 17 030 -009 -020 -013 000 -O 14 042 -001

ACG 000 -003 000 -007 021 024 039 O 18 000 005 O 10 053

ACT 000 -O 12 000 007 -032 -O 15 002 -038 000 -004 -037 -048

AGA 000 O 18 000 038 036 045 003 050 000 O 14 -O 16 044

AGC 000 -O 13 000 -O 18 023 024 -002 O 18 000 -031 -039 -029

AGG 000 023 000 026 025 035 -O 17 042 000 O 19 O 10 030

AGT 000 044 000 O 16 -022 021 -005 O 14 000 082 048 041

ATA 000 -024 000 -003 -O 12 -023 -038 -006 000 -030 -045 -021

ATC 000 038 000 025 035 033 045 040 000 022 028 020

ATG 000 -O 19 000 O 12 O 14 008 -007 005 000 -009 000 O 12

ATT 000 -O 15 000 -O 16 -O 16 -025 000 -032 000 -003 -001 -009

CAA 000 -027 000 -021 -O 18 -028 -039 -004 000 -035 -O 19 -021

CAC 000 028 000 009 024 -007 O 13 O 10 000 -021 -007 007

CAG 000 040 000 027 025 O 13 021 024 000 039 024 047

CAT 000 -008 000 -007 -008 -027 -002 -006 000 O 17 004 -008

CCA 000 -030 000 -O 18 -028 -O 17 -006 -039 000 -036 -038 -O 16

CCC 000 042 000 000 O 13 -O 16 028 023 000 -O 13 071 022

CCG 000 032 000 033 021 030 044 007 000 037 029 043

CCT 000 -O 15 000 -030 -021 -040 -024 -035 000 -O 19 -020 -033

CGA 000 -O 16 000 -020 025 003 -001 025 000 -005 O 15 -001

CGC 000 -025 000 -027 -006 -028 004 000 000 -054 -047 -056

CGG 000 034 000 024 024 051 -006 043 000 056 059 042

CGT 000 -O 14 000 -025 -042 -042 -050 -045 000 059 063 035

CTA 000 -037 000 -037 -028 -037 -047 -020 000 -050 -053 -051

CTC 000 026 000 O 17 022 028 034 021 000 028 028 -O 16

CTG 000 O 11 000 O 11 006 -005 -001 -002 000 029 O 18 060

CTT 000 -006 000 -O 13 -009 -029 -007 -044 000 -O 15 O 11 -O 11

GAA 000 -O 16 000 005 -007 008 -022 028 000 -O 15 000 -003

GAC 000 028 000 O 18 050 034 036 038 000 -024 -021 -O 11

GAG 000 O 13 000 005 028 050 O 15 029 000 O 18 000 029

GAT 000 -008 000 -O 12 -O 12 -O 15 -O 11 001 000 020 O 15 005

GCA 000 -004 000 O 15 000 -023 -008 -001 000 001 -O 11 000

GCC 000 008 000 -008 031 O 16 033 007 000 -039 O 11 -029

GCG 000 029 000 026 039 041 053 029 000 040 035 034

GCT 000 -025 000 -027 -041 -045 -025 -048 000 O 18 -024 -O 10

GGA 000 010 000 010 -005 079 007 042 000 013 027 031

GGC 000 -020 000 -O 17 022 O 11 O 18 O 17 000 -039 -046 -047

GGG 000 029 000 024 042 060 039 041 000 028 046 047

GGT 000 025 000 -O 10 -051 -O 11 -039 -041 000 076 070 063

GTA 000 -035 000 -008 -029 -032 -039 -027 000 001 -036 -033

GTC 000 048 000 021 041 036 044 044 000 -004 029 004

GTG 000 -O 10 000 -002 023 026 023 021 000 036 O 11 042

GTT 000 007 000 -O 12 -O 14 -040 -001 -037 000 -O 12 003 -021

TAA 000 000 000 000 000 000 000 000 000 000 000 000

TAC 000 000 000 005 029 008 005 O 18 000 -O 10 -005 -020

TAG 000 000 000 000 000 000 000 000 000 000 000 000

TAT 000 -002 000 -002 -009 -O 14 -001 009 000 007 003 O 11

TCA 000 O 18 000 030 008 -009 O 13 -O 10 000 026 O 10 032

TCC 000 -O 10 000 -029 -001 -O 13 O 14 -O 17 000 -040 020 -032 55 TCG 0 00 0 24 0 00 0 16 0 29 0 30 0 51 O 14 0 00 0 38 0 25 0 55

56 TCT 0 00 -0 08 0 00 -O i l -0 30 -0 27 -0 12 -0 40 0 00 0 12 0 10 -O 17

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 00 -0 08 0 00 -0 05 0 09 O 19 -0 28 0 25 0 00 -0 31 -0 32 -0 41

59 TGG 0 00 -0 10 0 00 0 06 O 15 0 32 -0 03 -0 01 0 00 0 06 0 00 -0 07

60 TGT 0 00 0 27 0 00 -0 03 -0 30 -O 17 -0 30 0 07 0 00 0 86 0 56 0 45

61 TTA 0 00 0 03 0 00 -O 15 -0 20 -0 20 -0 21 -0 05 0 00 -0 34 -0 29 -O 10

62 TTC 0 00 0 13 0 00 0 21 0 01 -0 05 0 04 -0 07 0 00 -0 09 -0 09 -O 19

63 TTG 0 00 0 22 0 00 O 17 O 17 O 12 0 27 -0 01 0 00 0 07 0 22 0 49

64 TTT 0 00 -0 06 0 00 -0 09 -O 11 -O 10 -0 05 -O 17 0 00 O 14 0 05 -0 01

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.3 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 34 -0 27 0 31 0 26

2 AAC 0 22 -0 27 0 24 -0 06

3 AAG 0 63 -0 10 0 72 -0 12

4 AAT -0 09 -0 13 -0 07 0 25

5 ACA 0 06 0 00 -0 22 0 16

6 ACC 0 12 -0 15 -0 08 -0 30

7 ACG 0 15 0 07 0 58 -0 10

8 ACT -0 11 0 13 -0 03 0 19

9 AGA 0 48 0 44 0 29 0 48

10 AGC 0 26 0 21 0 10 -0 01

11 AGG 0 46 0 29 0 68 0 29

12 AGT -0 27 0 38 -0 26 0 10

13 ATA -0 45 -0 39 -0 48 -0 10

14 ATC 0 35 0 21 0 49 0 28

15 ATG 0 74 -0 02 0 76 0 01

16 ATT -0 47 -0 32 -0 45 0 04

17 CAA 0 11 -0 12 0 14 -0 17

18 CAC 0 09 0 05 -0 11 0 17

19 CAG 0 66 0 27 0 68 0 16

20 CAT -0 31 0 02 -0 43 -0 09

21 CCA -0 22 -0 22 -0 18 -0 28

22 CCC 0 38 0 42 0 10 0 22

23 CCG 0 40 0 23 0 67 -0 04

24 CCT -0 27 0 15 0 01 0 05

25 CGA -0 24 -0 34 -0 22 -0 24

26 CGC 0 33 0 04 0 18 0 05

27 CGG 0 41 0 41 0 72 0 00

28 CGT -0 36 -0 40 -0 37 -0 45

29 CTA -0 49 -0 30 -0 57 -0 28

30 CTC 0 35 0 32 0 04 0 23

31 CTG 0 19 0 10 0 49 -0 19 CTT -0 05 0 25 -0 33 0 41

GAA 0 20 -0 04 0 02 0 03

GAC 0 12 0 20 0 07 0 18

GAG 0 52 0 22 0 58 -0 11

GAT -0 33 -0 10 -0 40 -0 10

GCA -0 05 0 18 -0 20 -0 02

GCC 0 35 0 26 0 14 0 05

GCG 0 21 0 34 0 56 -0 09

GCT -0 36 -0 08 -0 32 -0 19

GGA -0 01 0 10 -0 14 0 03

GGC 0 27 0 08 0 11 0 13

GGG 0 19 0 43 0 40 -0 02

GGT -0 40 -0 13 -0 46 -0 34

GTA -0 24 -0 36 -0 36 -0 25

GTC 0 53 0 32 0 42 0 29

GTG 0 14 0 17 0 45 -0 15

GTT -0 25 0 00 -0 24 0 09

TAA 0 00 0 00 0 00 0 00

TAC -0 07 0 08 -0 05 0 13

TAG 0 00 0 00 0 00 0 00

TAT -0 43 -0 21 -0 50 0 03

TCA -0 13 0 02 -0 20 0 01

TCC 0 09 -0 11 0 02 -0 24

TCG -0 17 0 10 0 56 -0 28

TCT -0 33 0 09 -0 09 0 09

TGA 0 00 0 00 0 00 0 00

TGC 0 23 0 13 0 09 0 10

TGG 0 70 0 01 0 83 -0 01

TGT -0 31 0 17 -0 33 -0 22

TTA -0 17 -0 09 -0 20 -0 15

TTC -0 22 -0 26 0 15 -0 14

TTG 0 24 -0 05 0 58 -0 24

TTT -0 44 -0 25 -0 36 0 30

TTA TTC TTG TTT

61 62 63 64 Table C.4: CPW matrix Bacillus subtilis highly expressed sequences (left codon indicated in column 2, right codon indicated in row 2). Host cell: B. subtilus; Sequence data: full B. subtilus genome; Highly expressed group: 415 seqs.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA -0 03 -0 38 -0 04 0 19 -0 34 0 00 -0 23 0 22 0 36 -0 17 0 48 0 25

2 AAC -0 30 -0 53 -0 05 -0 02 -0 18 0 39 0 03 -0 11 0 03 -0 69 0 26 0 06

3 AAG 0 03 0 24 0 17 0 48 0 59 0 79 0 50 0 58 0 82 0 26 0 88 -0 11

4 AAT 0 15 0 27 0 48 0 49 -0 10 0 19 -0 16 0 60 0 87 0 83 0 89 0 27

5 ACA -0 32 -0 46 -0 18 -0 09 -0 24 0 00 0 24 -0 59 -0 24 -0 49 -0 13 0 11

6 ACC 0 51 0 51 0 75 0 30 0 43 0 64 0 78 -0 31 0 23 0 79 1 00 0 09

7 ACG 0 14 -0 14 -0 14 0 32 -0 12 0 03 -0 08 -0 16 -0 21 0 32 0 25 0 33

8 ACT 0 44 0 35 0 10 0 68 0 50 1 00 0 89 -0 39 0 08 0 48 -0 52 1 00

9 AGA -0 18 -0 33 -0 19 0 35 -0 12 0 22 -0 28 0 11 0 10 -0 01 -0 25 -0 50

10 AGC -0 17 -0 10 0 12 0 14 -0 05 0 39 -0 23 -0 18 -0 39 -0 13 -0 36 -0 47

11 AGG 0 88 0 84 0 86 0 49 0 76 1 00 1 00 1 00 0 33 1 00 0 39 0 45

12 AGT -0 01 0 72 0 68 0 67 -0 20 0 47 0 05 -0 06 0 79 0 84 1 00 0 66

13 ATA 0 01 0 26 0 53 0 43 0 73 0 65 0 17 0 83 0 48 0 67 1 00 0 76

14 ATC -0 28 -0 44 0 07 -0 20 -0 08 0 29 0 20 -0 48 -0 09 -0 52 -0 30 -0 56

15 ATG 0 13 -0 27 -0 24 0 29 0 25 -0 06 -0 11 -0 27 -0 23 0 17 0 43 -0 25

16 ATT 0 15 0 09 0 12 0 42 -0 30 0 31 0 15 0 01 0 90 0 84 0 91 0 76

17 CAA -0 32 -0 54 -0 43 -0 08 -0 29 -0 25 -0 42 0 20 0 12 -0 46 0 49 0 33

18 CAC -0 14 -0 44 0 26 0 35 0 11 0 24 -0 19 -0 34 -0 37 -0 65 -0 31 -0 58

19 CAG 0 57 0 60 0 61 0 56 0 62 0 45 -0 02 0 45 0 61 0 84 0 29 0 88

20 CAT -0 04 -0 19 0 15 0 31 -0 09 0 35 -0 05 0 16 0 74 0 73 1 00 0 56

21 CCA -0 31 -0 64 -0 46 -0 17 -0 09 0 00 0 17 -0 64 -0 60 -0 66 -0 41 -0 31

22 CCC 0 69 0 39 1 00 0 84 1 00 0 58 1 00 0 58 0 56 1 00 1 00 0 38

23 CCG 0 07 0 09 -0 17 -0 09 -0 43 0 65 0 13 -0 61 -0 07 0 65 0 75 -0 21

24 CCT 0 06 0 30 0 39 0 51 0 38 0 47 0 77 0 74 0 73 0 47 1 00 0 81

25 CGA 0 16 -0 47 0 74 -0 42 0 20 0 41 0 48 0 71 -0 42 -0 31 1 00 -0 05

26 CGC -0 36 -0 41 -0 22 0 09 -0 02 0 04 -0 18 -0 08 -0 53 -0 41 0 45 -0 63

27 CGG 0 48 0 61 0 20 0 40 -0 05 0 46 -0 28 1 00 0 74 0 26 1 00 0 35

28 CGT -0 23 0 24 0 30 -0 20 -0 42 0 69 -0 40 -0 51 1 00 1 00 1 00 1 00

29 CTA -0 24 -0 30 -0 25 0 01 0 59 0 74 1 00 -0 04 -0 36 -0 52 0 29 0 58

30 CTC 0 47 0 09 0 29 0 35 0 46 0 30 0 31 -0 28 0 08 -0 38 0 37 -0 10

31 CTG -0 13 -0 29 0 03 -0 05 -0 30 -0 12 -0 31 -0 57 0 25 0 64 -0 03 0 65

32 CTT 0 47 0 54 0 72 0 69 0 49 0 62 0 81 -0 08 0 62 0 72 0 56 0 65

33 GAA -0 08 -0 35 0 05 0 13 -0 25 -0 09 -0 11 -0 07 0 26 -0 37 0 75 -0 08

34 GAC -0 23 -0 33 -0 02 -0 14 -0 10 0 29 0 32 -0 37 -0 08 -0 71 -0 04 -0 61

35 GAG 0 09 0 23 0 14 0 42 0 21 0 84 0 53 0 32 0 64 0 25 0 55 0 23

36 GAT 0 00 -0 03 0 41 0 34 -0 12 0 30 -0 01 0 10 0 85 0 78 0 83 0 76

37 GCA -0 29 -0 44 0 02 0 51 -0 41 -0 06 0 42 -0 57 -0 43 -0 29 0 47 -0 62

38 GCC 0 39 -0 31 0 43 0 04 0 58 0 64 0 72 0 04 -0 24 0 11 0 28 -0 08

39 GCG -0 23 -0 06 -0 22 -0 01 -0 29 0 15 0 10 -0 52 -0 31 0 39 0 58 0 14

40 GCT 0 19 -0 04 0 54 0 47 0 25 0 80 0 40 -0 17 0 94 0 95 0 85 0 39 41 GGA -0 14 -0 45 0 24 -0 16 -0 38 0 36 -0 38 -0 24 -0 10 -0 51 0 67 -0 28

42 GGC 0 12 -0 02 0 09 0 31 0 10 0 61 0 25 0 17 -0 05 -0 28 0 40 0 20

43 GGG -0 13 0 40 0 38 0 12 0 52 0 49 0 76 0 59 0 54 0 62 0 79 0 67

44 GGT -0 27 -0 19 0 37 0 68 -0 31 0 37 0 09 -0 52 0 93 1 00 1 00 0 70

45 GTA -0 45 -0 51 -0 19 -0 17 -0 32 -0 14 -0 39 -0 52 -0 30 -0 11 0 78 0 07

46 GTC 0 11 0 12 0 57 -0 11 -0 08 0 37 0 52 -0 24 -0 40 -0 51 0 84 -0 51

47 GTG -0 20 -0 26 -0 35 0 15 -0 19 0 18 -0 05 -0 01 0 58 0 35 0 51 0 12

48 GTT 0 52 0 20 0 52 0 69 0 46 0 71 0 39 -0 24 0 62 0 82 0 55 0 76

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 21 -0 66 -0 04 0 14 -0 43 0 42 0 23 -0 46 -0 31 -0 51 0 50 -0 68

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 03 0 37 0 28 0 46 0 36 0 54 -0 30 0 31 0 76 1 00 1 00 0 76

53 TCA -0 24 -0 49 0 29 0 22 0 12 -0 23 -0 11 -0 66 -0 36 -0 32 0 24 -0 53

54 TCC 0 59 -0 03 0 31 -0 34 0 41 0 36 0 49 -0 42 -0 54 -0 34 1 00 -0 28

55 TCG 0 20 0 56 -0 30 0 21 0 36 0 73 0 84 0 46 -0 07 1 00 -0 15 -0 05

56 TCT -0 15 -0 23 -0 07 0 16 -0 21 0 46 0 52 -0 25 0 79 1 00 1 00 0 31

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 17 -0 18 0 30 0 24 -0 05 1 00 -0 28 0 33 -0 44 -0 38 1 00 0 00

59 TGG 0 18 -0 22 -0 30 0 22 0 13 0 55 -0 33 -0 04 -0 35 -0 47 0 04 -0 31

60 TGT -0 09 -0 16 0 43 0 07 -0 21 -0 18 0 28 -0 18 1 00 1 00 1 00 1 00

61 TTA -0 33 -0 52 -0 32 -0 14 -0 19 0 40 -0 32 -0 48 -0 31 -0 11 0 46 0 04

62 TTC -0 38 -0 39 -0 06 0 49 -0 38 0 33 0 07 -0 19 -0 55 -0 62 -0 46 -0 54

63 TTG -0 23 -0 12 -0 18 0 00 0 27 0 23 0 09 -0 44 0 33 0 75 0 31 0 46

64 TTT 0 16 -0 12 0 34 0 11 0 13 -0 27 0 31 0 16 0 59 0 88 0 75 0 73

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.4 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA 0 42 -0 44 -0 15 0 14 -0 04 -0 12 0 37 0 57 0 04 0 46 0 21 0 20

2 AAC 0 66 -0 46 -0 33 0 09 -0 30 -0 15 0 04 -0 14 -0 24 0 53 -0 15 0 13

3 AAG 0 92 0 46 0 39 0 21 -0 19 -0 51 -0 33 -0 39 -0 04 0 84 -0 36 -0 49

4 AAT 0 54 -0 11 0 38 0 24 -0 01 -0 18 0 33 0 30 -0 08 -0 08 -0 08 0 36

5 ACA 0 70 -0 18 -0 12 0 23 -0 14 -0 28 0 06 0 24 -0 34 0 33 -0 11 0 04

6 ACC 0 08 0 08 0 38 -0 32 0 47 -0 33 0 45 0 63 0 51 0 66 0 93 0 68

7 ACG -0 42 -0 27 -0 26 -0 39 0 31 0 22 0 16 0 40 -0 51 0 59 0 00 -0 34

8 ACT 0 54 0 95 0 58 0 74 -0 47 -0 62 -0 34 -0 36 -0 61 0 66 0 58 0 04

9 AGA 0 41 -0 10 0 39 0 24 0 61 -0 29 0 20 0 15 0 48 1 00 -0 16 0 43

10 AGC 0 37 -0 19 0 01 -0 22 -0 16 -0 36 -0 18 0 36 0 14 0 70 0 07 0 24

11 AGG 0 35 0 57 0 61 0 60 0 70 0 57 0 38 0 16 0 53 1 00 0 18 0 38

12 AGT 0 17 0 54 0 23 0 12 0 73 0 43 0 44 0 30 0 37 0 34 0 32 -0 03

13 ATA 0 81 0 80 0 93 0 71 0 15 0 33 0 05 0 13 0 16 0 64 -0 08 0 11

14 ATC 0 15 -0 51 -0 36 -0 20 0 05 0 26 0 34 0 12 -0 20 0 64 0 07 0 44

15 ATG 0 55 -0 13 0 00 -0 03 0 19 -0 21 -0 17 0 13 -0 11 0 44 0 11 -0 18 ATT 066 -003 018 021 -022 -048 -004 019 -025 047 -019 -006

CAA 0 21 -049 -0 32 -0 14 059 090 082 061 056 0 81 089 0 83

CAC 1 00 -011 -0 14 -0 33 004 -057 009 -005 -021 1 00 004 -0 04

CAG 0 70 050 0 49 0 31 -026 -042 -053 -042 -050 0 04 -046 -0 49

CAT 0 56 -003 0 08 0 05 013 032 -016 018 -032 0 51 -007 0 18

CCA 0 75 -050 -0 23 0 08 -002 -037 079 090 012 1 00 100 0 13

CCC 1 00 100 0 63 1 00 035 -021 100 017 007 1 00 100 0 39

CCG 0 57 -038 -0 28 -0 43 -039 005 050 -012 -042 -0 17 -032 -0 47

CCT 1 00 056 0 60 0 64 -033 021 -015 -026 042 1 00 050 -0 13

CGA -0 20 -020 -0 24 -0 07 041 100 070 080 054 1 00 080 1 00

CGC 0 85 012 -0 24 -0 20 -023 -026 -043 -012 -033 0 55 -010 -0 11

CGG 0 04 010 -0 09 -0 27 037 049 026 000 016 1 00 064 0 26

CGT 0 67 -036 -0 20 -0 24 -062 -036 003 -029 -055 -0 03 -053 -0 63

CTA 1 00 018 -0 01 -0 01 042 100 100 056 067 1 00 086 1 00

CTC 0 46 -003 -0 13 -0 20 055 061 060 032 028 0 69 025 0 24

CTG 0 24 -040 -0 27 -0 22 -011 054 019 019 -030 0 86 -024 0 02

CTT 0 75 037 0 61 0 65 -047 -058 -022 -046 -036 0 42 -027 -0 60

GAA 0 35 -034 -0 14 0 10 027 063 013 037 035 0 91 038 0 46

GAC 0 53 -008 0 08 0 07 -029 -034 038 -016 -015 0 46 023 0 00

GAG 0 56 022 0 36 0 10 -019 -058 -038 -043 -028 -0 09 -053 -0 56

GAT 0 30 -007 -0 04 -0 08 013 023 -010 014 -005 0 49 -015 -0 06

GCA 0 59 -019 -0 22 0 34 -015 015 -025 035 -017 0 82 -007 -0 07

GCC 0 45 -008 0 23 -0 19 023 011 043 007 053 0 75 050 0 69

GCG 0 13 -035 -0 25 -0 39 002 -037 051 -003 -027 0 42 -028 -0 25

GCT 0 45 042 0 49 0 46 -042 -033 022 000 -015 0 79 015 -0 47

GGA 0 82 -003 0 24 0 15 -020 -054 -005 017 008 0 41 -016 0 09

GGC 0 35 -019 0 03 -0 02 -004 -006 022 013 024 0 64 001 0 39

GGG 0 54 039 0 25 -0 13 010 -033 001 005 -006 0 25 -041 -0 47

GGT 0 19 -043 -0 41 -0 07 011 008 -002 061 006 0 67 012 -0 12

GTA 0 62 015 0 35 0 74 014 -019 -014 029 -001 0 52 008 -0 04

GTC 0 57 -037 -0 34 -0 37 052 061 065 062 083 0 46 074 0 44

GTG 0 57 -011 -0 06 0 14 035 022 002 016 -002 0 46 -046 -0 32

GTT 0 35 -036 0 28 0 25 -044 -051 -037 -040 -024 0 18 003 -0 39

TAA 0 00 000 0 00 0 00 000 000 000 000 000 0 00 000 0 00

TAC -0 12 -043 -0 26 0 32 -012 -006 024 004 -025 0 37 029 0 02

TAG 0 00 000 0 00 0 00 000 000 000 000 000 0 00 000 0 00

TAT 0 30 -005 0 19 0 10 -004 005 -001 -003 -026 0 49 -017 0 21

TCA 0 76 006 -0 21 0 25 -021 -001 013 032 -020 0 12 016 -0 27

TCC 0 56 -026 -0 20 -0 35 078 -038 043 055 024 0 46 056 0 83

TCG 1 00 -019 0 37 -0 38 002 -031 028 028 004 0 32 -040 -0 48

TCT 0 17 -014 0 14 0 31 -053 -046 029 -032 -061 1 00 011 -0 40

TGA 0 00 000 0 00 0 00 000 000 000 000 000 0 00 000 0 00

TGC 0 49 -016 0 09 0 63 -022 -050 -037 -019 -023 0 32 016 -0 06

TGG -0 23 005 0 00 0 04 046 -029 -032 020 034 1 00 000 -0 35 60 TGT -0 18 -0 59 -0 10 0 40 0 69 0 39 0 36 0 70 0 61 0 17 -0 01 -0 35

61 TTA 0 90 -0 38 -0 20 0 07 0 37 0 55 0 12 0 22 0 50 0 64 0 78 0 34

62 TTC 0 59 -0 23 -0 16 0 02 -0 51 -0 58 -0 37 -0 41 -0 55 0 27 -0 36 -0 65

63 TTG 0 60 -0 28 0 06 -0 22 0 00 -0 13 -0 15 0 36 0 25 0 10 -0 20 0 23

64 TTT 0 23 0 02 0 09 -0 05 0 31 0 49 0 47 0 41 0 27 0 66 0 37 0 68

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.4 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA -0 20 -0 38 -0 04 -0 20 -0 17 0 49 0 50 0 26 -0 13 -0 26 -0 06 0 25

2 AAC -0 22 -0 55 0 04 -0 70 -0 61 0 17 -0 31 -0 46 0 13 -0 10 0 39 0 18

3 AAG 0 30 -0 03 0 07 -0 50 -0 39 -0 31 -0 66 -0 68 0 25 -0 12 0 38 -0 05

4 AAT 0 33 0 53 0 73 -0 20 0 33 0 29 0 25 0 03 -0 19 -0 27 -0 02 0 12

5 ACA 1 00 0 04 0 42 -0 02 0 36 0 37 0 17 -0 08 -0 20 0 05 0 05 0 20

6 ACC 0 19 0 43 0 75 0 13 0 34 0 56 0 45 -0 14 0 57 0 37 0 33 0 21

7 ACG 0 52 0 44 0 56 0 23 -0 36 -0 17 -0 23 -0 49 0 27 0 55 0 68 0 25

8 ACT 0 19 -0 47 1 00 -0 83 0 02 0 57 0 73 -0 02 -0 42 -0 67 -0 45 -0 43

9 AGA -0 34 -0 09 0 60 0 19 0 78 0 70 0 35 0 72 -0 07 -0 27 0 03 0 44

10 AGC 0 49 -0 60 -0 08 -0 33 0 09 0 30 -0 04 -0 24 0 34 0 31 0 40 0 50

11 AGG 1 00 0 73 -0 31 0 69 0 39 -0 08 -0 44 0 24 0 53 0 32 0 34 -0 26

12 AGT 0 45 0 49 0 32 0 71 0 01 0 78 0 07 -0 12 -0 51 -0 54 -0 51 -0 44

13 ATA -0 03 0 36 1 00 0 63 0 61 -0 04 0 59 0 67 0 43 0 56 0 46 0 15

14 ATC 0 07 -0 63 0 36 -0 62 0 07 0 36 0 48 -0 41 -0 10 -0 01 0 31 0 17

15 ATG 0 86 -0 13 0 41 -0 32 0 67 0 18 -0 40 -0 43 0 02 -0 12 -0 04 0 08

16 ATT 0 15 0 01 0 74 -0 39 0 22 -0 14 0 52 -0 02 -0 14 -0 20 -0 04 -0 08

17 CAA 0 34 0 54 0 90 0 38 0 59 0 94 0 91 0 86 0 04 0 21 -0 30 0 18

18 CAC 0 07 -0 54 -0 56 -0 71 0 18 0 82 0 15 -0 38 -0 11 0 23 0 26 0 08

19 CAG 0 32 -0 52 -0 58 -0 54 -0 46 -0 49 -0 44 -0 68 0 05 0 18 0 25 -0 29

20 CAT 0 77 0 36 0 44 0 15 0 40 0 65 0 50 0 46 0 14 -0 21 -0 23 0 05

21 CCA 0 45 -0 02 0 66 -0 32 1 00 0 64 0 58 0 66 0 08 0 05 -0 26 0 13

22 CCC 1 00 -0 77 1 00 0 38 1 00 0 23 0 82 0 64 0 46 0 53 0 32 0 82

23 CCG -0 30 0 34 0 27 -0 51 -0 43 -0 39 -0 20 -0 62 0 25 0 33 0 51 0 28

24 CCT 1 00 0 33 0 33 -0 35 0 19 0 29 0 61 0 05 -0 40 -0 39 -0 33 -0 45

25 CGA 1 00 0 73 1 00 0 70 0 41 0 74 0 39 0 63 0 54 0 18 0 79 0 44

26 CGC 0 20 -0 66 -0 12 -0 76 -0 27 -0 32 -0 38 -0 08 0 43 -0 13 0 10 0 22

27 CGG 1 00 0 51 0 36 0 81 0 27 0 36 -0 33 -0 22 0 50 0 30 0 34 0 37

28 CGT 1 00 0 29 0 44 -0 64 -0 55 -0 40 -0 05 -0 60 -0 52 -0 62 -0 63 -0 19

29 CTA 1 00 1 00 1 00 1 00 -0 26 0 10 0 86 0 86 0 03 0 33 -0 16 0 02

30 CTC 0 70 -0 11 0 26 -0 23 0 70 0 74 0 57 0 50 0 53 0 11 0 67 -0 12

31 CTG 0 72 -0 11 0 48 -0 27 0 44 -0 27 -0 22 -0 43 0 49 0 45 0 22 0 48

32 CTT -0 22 -0 72 0 13 -0 60 -0 11 -0 30 0 01 -0 50 -0 53 -0 40 -0 43 -0 54

33 GAA -0 02 -0 03 0 22 -0 03 0 24 0 33 0 33 0 50 -0 11 -0 27 -0 20 0 08

34 GAC -0 42 -0 74 -0 37 -0 67 0 23 0 26 0 31 0 02 0 05 0 29 0 24 0 17 35 GAG 0 22 -0 53 -0 21 -0 61 -0 48 -0 46 -0 50 -0 70 0 30 0 22 0 43 0 15

36 GAT 0 59 0 43 0 65 0 57 0 20 0 10 0 23 -0 10 -0 11 -0 31 0 06 0 07

37 GCA 0 87 -0 38 0 61 -0 19 0 26 0 19 0 36 -0 06 0 12 -0 07 0 20 0 20

38 GCC 0 83 0 11 0 47 -0 55 0 67 0 63 0 45 0 59 0 39 0 63 0 43 0 31

39 GCG 0 32 -0 17 0 67 -0 40 -0 04 -0 25 -0 37 -0 59 0 14 0 12 0 19 0 26

40 GCT 0 41 0 32 0 82 -0 54 -0 35 0 38 0 54 -0 16 -0 43 -0 56 -0 31 -0 27

41 GGA 0 26 -0 51 0 42 -0 48 0 61 0 43 0 41 -0 04 -0 11 -0 27 0 15 -0 03

42 GGC 0 33 -0 30 0 05 -0 57 -0 16 0 42 0 34 -0 12 0 34 0 12 0 20 0 35

43 GGG 0 39 0 15 0 26 0 24 0 50 0 23 -0 16 -0 45 0 40 0 33 0 66 0 36

44 GGT 0 82 0 58 0 89 -0 25 -0 35 -0 32 0 63 -0 65 -0 49 -0 59 -0 44 -0 05

45 GTA 0 58 -0 32 0 36 -0 19 -0 43 0 14 0 23 -0 17 -0 11 -0 15 -0 34 0 06

46 GTC 0 68 -0 46 0 81 -0 46 0 56 0 35 0 66 0 54 0 56 0 51 0 60 0 31

47 GTG 0 37 0 04 0 61 -0 09 0 41 -0 43 -0 51 -0 47 0 47 0 28 0 38 0 35

48 GTT 0 28 -0 40 0 47 -0 54 0 06 -0 20 0 58 -0 27 -0 47 -0 43 -0 30 -0 35

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 17 -0 63 -0 25 -0 70 -0 33 0 20 0 19 -0 23 0 16 0 42 0 29 -0 23

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 35 0 22 0 68 0 10 0 20 0 07 0 50 0 30 -0 15 -0 17 0 04 0 14

53 TCA 1 00 0 20 0 85 -0 04 0 34 -0 14 0 18 0 00 0 12 0 14 -0 02 0 21

54 TCC 1 00 -0 60 0 18 -0 40 -0 17 0 65 0 58 0 09 0 69 0 56 0 34 0 26

55 TCG 0 43 0 74 0 65 -0 17 -0 35 -0 11 -0 37 -0 50 0 60 0 89 0 49 0 19

56 TCT 0 72 -0 15 1 00 -0 39 -0 43 0 45 0 43 -0 29 -0 40 -0 49 -0 31 -0 34

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 15 -0 63 -0 30 -0 60 0 21 0 30 -0 32 -0 13 0 61 0 30 -0 19 0 52

59 TGG 0 69 -0 01 0 24 0 17 0 62 -0 41 -0 30 -0 16 0 05 -0 14 -0 09 0 09

60 TGT 1 00 1 00 1 00 1 00 0 04 0 15 0 60 -0 28 -0 20 -0 16 -0 43 -0 42

61 TTA 0 65 0 67 0 68 0 34 0 65 0 47 0 64 0 50 0 07 0 35 0 20 0 40

62 TTC -0 22 -0 60 -0 29 -0 77 -0 30 0 11 -0 27 -0 44 0 24 -0 15 0 64 0 36

63 TTG 1 00 -0 04 0 04 -0 24 -0 24 -0 31 -0 33 -0 45 0 42 0 30 0 37 0 34

64 TTT 0 64 0 66 0 85 0 61 0 46 0 40 0 58 0 41 -0 27 -0 27 0 23 0 09

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.4 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -0 24 -0 06 -0 31 0 08 0 09 -0 31 -0 15 -0 16 -0 44 0 20 -0 08 0 24

2 AAC -0 05 0 57 -0 13 -0 25 -0 42 -0 39 -0 10 -0 50 -0 35 0 11 0 04 -0 11

3 AAG 0 38 0 77 0 32 0 46 0 51 0 34 0 60 0 36 0 11 0 45 0 06 -0 08

4 AAT -0 08 0 20 -0 22 0 30 0 47 0 55 0 51 0 47 -0 02 0 15 -0 11 0 27

5 ACA 0 25 0 34 0 18 -0 32 0 00 0 00 0 02 -0 36 0 18 0 10 0 28 0 11

6 ACC 0 49 0 62 0 34 -0 09 -0 09 0 04 0 04 -0 41 0 24 0 11 0 55 -0 18

7 ACG -0 15 0 77 0 39 -0 21 0 38 0 57 0 89 0 29 0 15 0 06 0 55 -0 23

8 ACT -0 56 -0 31 0 10 -0 59 -0 26 -0 24 0 42 -0 63 -0 56 -0 21 -0 13 -0 58

9 AGA 0 13 0 58 -0 43 0 47 0 11 0 14 0 15 0 08 0 54 0 71 0 30 0 52 AGC 039 047 049 051 -052 -035 016 001 -013 061 047 047

AGG 0 58 043 0 55 068 -017 063 048 054 016 0 52 036 085

AGT -0 29 -013 -0 34 -034 068 078 085 060 -045 -0 05 -033 -042

ATA 0 73 046 0 50 092 081 072 029 079 100 0 86 078 074

ATC -0 18 -003 0 21 -035 -042 -051 -039 -067 -044 -0 19 012 -027

ATG 0 03 065 -0 05 -034 023 -003 010 -030 009 0 08 005 -015

ATT -0 15 -012 0 16 -007 070 058 077 033 024 -0 07 012 -016

CAA 0 07 023 0 01 -003 013 -037 -018 -050 -042 -0 06 -014 016

CAC 0 07 -003 0 19 004 -019 -053 005 -058 -029 -0 06 -007 -042

CAG -0 16 043 -0 04 -027 044 052 004 037 025 0 44 -006 004

CAT 0 13 -011 -0 16 001 031 026 061 031 -002 0 15 -009 052

CCA 0 09 038 0 43 -023 007 021 023 -056 018 0 38 031 -017

CCC 0 03 078 -0 03 -022 015 -035 073 -017 100 0 41 056 047

CCG 0 05 029 0 34 -024 005 021 050 -015 017 0 40 049 -019

CCT 0 00 -013 0 20 -053 -015 028 016 -050 -047 -0 41 009 -048

CGA 0 86 063 0 86 069 048 -007 075 078 059 0 85 038 044

CGC -0 17 040 -0 12 -007 -068 -044 018 -069 -038 -0 01 -018 -031

CGG 0 33 055 0 20 -012 092 056 069 086 062 0 62 -012 040

CGT -0 31 -021 -0 68 -047 030 062 046 -030 -066 -0 51 -055 -049

CTA 0 48 065 -0 19 012 048 -036 -021 -065 -025 0 16 015 -046

CTC 0 14 023 0 39 002 -038 -067 022 -068 -037 -0 33 055 -055

CTG 0 28 064 0 26 008 065 053 074 054 072 0 76 068 065

CTT -0 41 -045 -0 22 -050 -021 -046 027 -050 -042 -0 52 -034 -052

GAA -0 27 018 -0 33 -007 007 -039 018 -025 -024 0 16 -025 005

GAC 0 26 034 0 16 -022 -050 -057 000 -061 028 0 45 030 -016

GAG 0 45 078 0 36 027 042 041 071 049 004 0 37 046 -008

GAT 0 07 -002 -0 19 -008 055 064 079 039 -040 0 22 -012 -001

GCA -0 09 021 0 15 -018 018 -004 -005 -015 025 0 20 045 016

GCC 0 31 040 0 55 013 -041 -027 035 -054 045 0 55 058 013

GCG -0 04 058 0 23 -019 009 047 027 -017 014 0 40 019 -019

GCT -0 21 010 -0 24 -053 014 034 068 -025 -054 -0 38 000 -058

GGA 0 13 049 -0 21 015 050 035 030 064 016 0 73 066 062

GGC 0 10 007 0 18 -007 -063 -046 015 -057 -017 0 22 019 -036

GGG 0 37 070 0 38 038 037 066 086 068 019 0 58 062 -002

GGT -0 32 014 -0 56 -051 061 082 075 039 -059 -0 53 -037 -057

GTA 0 14 011 -0 38 -019 028 005 007 -030 038 0 11 066 046

GTC 0 26 044 0 50 003 -046 -057 -005 -064 -022 0 55 016 -034

GTG 0 35 060 -0 03 003 067 061 071 064 079 0 65 055 062

GTT -0 21 -034 -0 28 -026 037 042 073 -018 -051 -0 40 -036 -053

TAA 0 00 000 0 00 000 000 000 000 000 000 0 00 000 000

TAC -0 19 005 0 13 -032 -034 -055 -025 -060 012 0 20 000 003

TAG 0 00 000 0 00 000 000 000 000 000 000 0 00 000 000

TAT 0 06 019 -0 03 010 047 044 059 051 -015 -0 06 -015 019

TCA 0 25 -012 0 11 -034 048 -022 026 -038 -005 0 16 039 015 54 TCC 0 01 0 38 0 68 -0 42 -0 02 -0 45 0 51 -0 42 0 66 0 57 0 91 -0 14

55 TCG 0 42 0 74 0 49 0 23 0 11 0 70 0 53 0 03 0 14 0 78 0 46 -0 08

56 TCT -0 05 0 03 -0 18 -0 65 0 40 0 45 0 54 -0 45 -0 56 -0 48 0 14 -0 56

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 47 0 28 -0 35 0 24 -0 50 -0 45 -0 03 -0 15 -0 28 0 47 0 47 0 52

59 TGG -0 18 0 13 -0 10 0 26 0 05 -0 34 0 50 0 41 -0 18 0 54 -0 27 0 00

60 TGT 0 04 -0 23 -0 16 -0 09 1 00 0 74 0 64 0 52 -0 29 -0 48 -0 33 0 22

61 TTA 0 01 0 55 0 19 0 51 0 30 0 26 0 29 -0 07 -0 08 0 18 0 61 0 10

62 TTC -0 05 0 01 0 16 0 04 -0 38 -0 49 -0 39 -0 65 -0 17 0 04 0 57 -0 36

63 TTG -0 36 0 49 0 29 -0 05 0 62 0 53 0 75 0 71 0 27 0 62 0 45 0 25

64 TTT 0 11 0 13 -0 22 -0 01 0 44 0 43 0 65 0 35 0 00 -0 12 0 19 0 01

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.4 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 21 0 00 0 10 -0 35 0 10 -0 04 0 11 0 00 -0 23 -0 06 -0 19

2 AAC 0 00 -0 46 0 00 -0 15 -0 28 -0 12 0 68 -0 45 0 00 -0 52 -0 39 -0 41

3 AAG 0 00 -0 12 0 00 0 17 0 23 0 50 0 62 0 18 0 00 0 66 0 15 0 59

4 AAT 0 00 0 38 0 00 0 28 0 41 0 51 0 50 0 57 0 00 0 73 0 50 0 67

5 ACA 0 00 -0 04 0 00 0 19 -0 32 -0 18 0 18 0 01 0 00 -0 37 0 05 0 05

6 ACC 0 00 0 28 0 00 0 29 0 39 0 63 0 77 0 54 0 00 -0 25 0 40 1 00

7 ACG 0 00 -0 33 0 00 0 00 0 34 0 02 0 31 0 39 0 00 0 01 0 28 1 00

8 ACT 0 00 -0 58 0 00 0 35 -0 38 -0 32 0 07 -0 54 0 00 0 00 -0 50 -0 38

9 AGA 0 00 0 54 0 00 0 69 0 82 0 84 -0 19 0 70 0 00 0 43 -0 10 -0 03

10 AGC 0 00 -0 39 0 00 -0 17 -0 05 0 49 0 52 -0 03 0 00 0 27 -0 32 -0 32

11 AGG 0 00 0 37 0 00 1 00 1 00 1 00 -0 11 0 72 0 00 1 00 0 62 1 00

12 AGT 0 00 0 84 0 00 0 39 -0 18 1 00 -0 53 -0 28 0 00 1 00 0 71 0 35

13 ATA 0 00 0 80 0 00 -0 05 0 57 0 03 0 26 0 27 0 00 0 39 0 55 1 00

14 ATC 0 00 -0 05 0 00 0 33 0 28 0 22 0 25 0 02 0 00 0 59 0 40 -0 11

15 ATG 0 00 -0 21 0 00 0 15 0 03 -0 35 0 32 0 13 0 00 -0 18 0 00 0 26

16 ATT 0 00 -0 47 0 00 0 17 -0 10 -0 23 0 27 -0 44 0 00 -0 34 -0 30 -0 16

17 CAA 0 00 -0 36 0 00 -0 24 -0 09 0 00 -0 46 -0 41 0 00 -0 26 -0 29 -0 39

18 CAC 0 00 -0 01 0 00 -0 20 0 07 0 04 1 00 0 10 0 00 0 45 -0 12 -0 01

19 CAG 0 00 0 29 0 00 0 48 0 49 0 53 0 29 -0 26 0 00 0 54 0 42 0 44

20 CAT 0 00 0 00 0 00 0 12 -0 27 0 17 0 70 -0 10 0 00 -0 18 0 07 0 01

21 CCA 0 00 -0 56 0 00 -0 04 -0 14 0 53 0 70 -0 48 0 00 -0 52 -0 18 -0 40

22 CCC 0 00 0 66 0 00 1 00 0 18 0 50 -0 21 0 69 0 00 1 00 0 57 1 00

23 CCG 0 00 0 09 0 00 0 48 -0 01 0 59 0 35 -0 48 0 00 1 00 0 29 0 64

24 CCT 0 00 -0 53 0 00 -0 12 0 06 0 53 0 41 -0 43 0 00 -0 45 -0 32 -0 55

25 CGA 0 00 0 39 0 00 0 01 0 77 0 15 1 00 0 73 0 00 -0 33 0 27 -0 63

26 CGC 0 00 -0 42 0 00 -0 27 -0 30 1 00 1 00 -0 46 0 00 -0 68 -0 61 -0 53

27 CGG 0 00 0 44 0 00 0 50 0 57 0 48 0 67 0 84 0 00 1 00 0 78 0 44

28 CGT 0 00 -0 59 0 00 -0 53 -0 67 0 09 -0 51 -0 80 0 00 1 00 0 80 1 00 29 CTA 0 00 -0 48 0 00 -0 18 0 26 0 66 -0 41 -0 32 0 00 -0 41 -0 60 -0 51

30 CTC 0 00 0 14 0 00 0 31 0 02 1 00 0 81 0 44 0 00 0 25 0 18 1 00

31 CTG 0 00 0 33 0 00 -0 10 -0 18 0 37 0 65 -0 12 0 00 0 30 0 48 0 79

32 CTT 0 00 -0 59 0 00 -0 16 -0 21 -0 50 -0 19 -0 66 0 00 -0 52 0 23 0 36

33 GAA 0 00 -0 34 0 00 0 32 -0 16 0 21 -0 14 0 14 0 00 0 40 0 13 -0 25

34 GAC 0 00 -0 20 0 00 0 18 0 31 0 31 0 27 0 14 0 00 -0 51 -0 38 0 17

35 GAG 0 00 0 00 0 00 -0 09 0 22 0 47 0 33 0 45 0 00 -0 41 -0 22 0 49

36 GAT 0 00 -0 28 0 00 0 19 -0 06 -0 19 0 59 0 23 0 00 0 38 0 35 0 16

37 GCA 0 00 -0 09 0 00 0 14 0 04 -0 27 0 08 0 09 0 00 -0 41 -0 18 0 21

38 GCC 0 00 0 53 0 00 0 28 0 57 0 71 0 25 0 69 0 00 -0 05 0 28 0 36

39 GCG 0 00 -0 01 0 00 0 34 0 28 0 54 0 61 0 18 0 00 0 31 0 28 0 50

40 GCT 0 00 -0 50 0 00 -0 29 -0 26 -0 53 -0 36 -0 64 0 00 0 41 -0 23 -0 49

41 GGA 0 00 -0 10 0 00 0 12 0 04 0 72 0 38 0 21 0 00 0 48 0 34 0 62

42 GGC 0 00 -0 16 0 00 -0 10 0 47 0 17 0 59 0 08 0 00 -0 42 -0 47 -0 59

43 GGG 0 00 0 26 0 00 0 35 0 63 0 87 0 83 0 49 0 00 0 40 0 58 0 27

44 GGT 0 00 0 34 0 00 -0 24 -0 65 0 17 -0 17 -0 73 0 00 1 00 0 53 0 36

45 GTA 0 00 -0 64 0 00 -0 17 -0 38 -0 18 -0 07 -0 55 0 00 -0 32 -0 11 -0 37

46 GTC 0 00 0 59 0 00 0 53 0 61 0 79 0 28 0 60 0 00 -0 19 0 23 0 10

47 GTG 0 00 -0 08 0 00 0 41 0 18 0 50 0 46 0 29 0 00 0 51 0 15 0 70

48 GTT 0 00 -0 33 0 00 -0 03 -0 12 -0 23 0 26 -0 53 0 00 0 21 -0 21 -0 33

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 00 -0 13 0 00 0 21 0 41 -0 07 0 09 -0 44 0 00 -0 17 -0 09 -0 49

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 00 0 04 0 00 -0 08 -0 06 -0 13 -0 18 0 16 0 00 0 57 0 05 -0 04

53 TCA 0 00 -0 31 0 00 0 57 0 32 0 26 0 38 -0 19 0 00 -0 29 -0 03 0 43

54 TCC 0 00 -0 37 0 00 0 29 0 26 0 33 -0 12 0 02 0 00 0 14 1 00 0 48

55 TCG 0 00 0 50 0 00 0 64 0 69 0 72 0 64 0 29 0 00 0 45 0 40 1 00

56 TCT 0 00 -0 42 0 00 -0 19 -0 38 -0 35 0 47 -0 54 0 00 -0 38 -0 38 -0 49

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 00 0 13 0 00 -0 20 0 11 -0 18 -0 03 -0 01 0 00 -0 55 1 00 -0 26

59 TGG 0 00 0 20 0 00 -0 09 0 89 0 81 0 26 -0 31 0 00 -0 34 0 00 0 63

60 TGT 0 00 0 65 0 00 -0 12 -0 38 0 02 -0 20 0 08 0 00 1 00 -0 55 1 00

61 TTA 0 00 0 34 0 00 0 33 -0 29 -0 27 0 23 -0 31 0 00 -0 54 0 05 1 00

62 TTC 0 00 -0 57 0 00 -0 13 -0 46 0 07 -0 24 -0 57 0 00 -0 18 -0 52 -0 33

63 TTG 0 00 0 16 0 00 0 60 0 34 0 78 0 58 0 11 0 00 -0 27 -0 45 0 33

64 TTT 0 00 0 25 0 00 0 27 0 25 0 35 0 59 0 11 0 00 0 23 0 51 0 07

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.4 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 32 -0 44 0 42 0 38

2 AAC 0 12 -0 58 0 11 -0 10

3 AAG 0 70 -0 02 0 66 -0 03 AAT 0 32 -0 14 0 52 0 66

ACA 0 01 -0 33 -0 32 0 04

ACC 0 07 -0 04 0 36 0 34

ACG 0 30 -0 34 0 43 -0 06

ACT -0 34 0 30 0 04 0 56

AGA 0 43 0 31 0 27 0 68

AGC 0 42 -0 29 0 33 -0 13

AGG 0 53 0 53 1 00 0 67

AGT -0 12 0 36 0 19 0 39

ATA -0 10 -0 41 -0 35 0 42

ATC 0 05 -0 36 0 27 0 36

ATG 0 80 -0 41 0 86 0 33

ATT -0 41 -0 49 -0 30 0 35

CAA 0 16 -0 33 0 10 -0 05

CAC -0 40 -0 43 -0 25 0 18

CAG 0 67 0 06 0 63 0 27

CAT -0 37 -0 18 -0 43 0 19

CCA -0 04 -0 60 -0 42 -0 30

CCC 0 78 1 00 0 44 0 61

CCG 0 32 -0 08 0 71 0 01

CCT -0 09 0 22 0 04 0 35

CGA 0 55 -0 37 1 00 -0 15

CGC -0 05 -0 48 -0 30 -0 09

CGG 0 63 0 86 0 88 0 15

CGT -0 48 -0 71 -0 51 -0 12

CTA -0 47 -0 69 -0 49 -0 15

CTC 0 54 -0 18 -0 14 0 53

CTG 0 39 -0 31 0 50 -0 04

CTT -0 22 0 02 -0 19 0 66

GAA 0 37 -0 33 0 26 0 16

GAC 0 08 -0 38 0 00 0 34

GAG 0 46 0 14 0 67 0 09

GAT -0 09 -0 26 -0 41 0 14

GCA -0 09 -0 30 0 04 0 13

GCC 0 53 0 15 -0 07 0 20

GCG 0 10 -0 05 0 70 -0 16

GCT -0 40 -0 15 -0 12 0 16

GGA 0 17 -0 23 -0 01 0 35

GGC 0 18 -0 46 0 11 0 25

GGG 0 87 0 53 0 59 0 52

GGT -0 37 -0 50 -0 52 -0 23

GTA -0 37 -0 69 -0 34 -0 14

GTC 0 74 0 24 0 43 0 29

GTG 0 36 0 30 0 62 0 01 GTT -0 14 0 05 -0 15 0 30

TAA 0 00 0 00 0 00 0 00

TAC 0 08 -0 28 0 03 -0 11

TAG 0 00 0 00 0 00 0 00

TAT -0 22 -0 25 -0 50 0 32

TCA -0 43 0 07 0 21 -0 12

TCC 0 39 0 09 -0 30 0 51

TCG 0 35 0 17 0 50 -0 20

TCT -0 29 -0 49 0 02 0 39

TGA 0 00 0 00 0 00 0 00

TGC -0 17 -0 47 0 49 0 11

TGG 0 51 -0 18 0 63 0 11

TGT 0 51 0 23 -0 36 0 28

TTA 0 34 -0 22 0 49 0 16

TTC -0 41 -0 67 -0 23 -0 18

TTG 0 33 -0 49 0 71 -0 13

TTT -0 29 -0 05 -0 05 0 58

TTA TTC TTG TTT

61 62 63 64

Table C.5: CPW matrix Escherichia coli Kl 2 full genome (left codon indicated in column 2, right codon indicated in row T). Host cell: E. coli; Sequence data: full E. coli genome.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 0 19 0 01 -0 04 -0 10 -0 31 -0 06 -0 24 0 18 -0 03 0 08 0 20 0 07

2 AAC 0 13 0 09 0 01 0 25 0 38 -0 08 0 34 0 18 -0 32 -0 41 -0 33 -0 36

3 AAG -0 35 0 14 -0 17 0 17 0 15 0 53 0 47 0 58 -0 17 0 14 -0 12 -0 13

4 AAT -0 13 -0 10 -0 05 -0 24 0 04 -0 23 -0 04 -0 14 0 27 0 16 0 47 0 15

5 ACA -0 19 0 32 -0 21 -0 05 -0 52 0 20 -0 27 -0 07 -0 37 0 66 -0 54 0 43

6 ACC -0 21 -0 29 0 08 -0 19 0 01 -0 25 -0 17 -0 26 -0 10 -0 47 -0 06 -0 39

7 ACG 0 41 0 74 0 28 0 55 0 10 0 52 0 23 0 40 0 68 0 91 0 50 0 88

8 ACT 0 01 -0 36 0 20 0 00 0 37 0 11 0 24 0 28 0 83 0 87 0 93 0 85

9 AGA -0 41 0 01 -0 53 -0 59 -0 74 -0 22 -0 50 0 02 -0 85 0 41 -0 72 -0 59

10 AGC -0 21 -0 05 -0 22 -0 21 0 24 0 23 0 28 0 33 0 07 -0 10 -0 29 -0 27

11 AGG 0 11 0 43 -0 46 -0 05 -0 49 0 70 0 29 0 11 -0 67 0 51 -0 04 -0 31

12 AGT -0 28 -0 19 -0 42 -0 41 0 06 0 16 0 03 0 20 0 41 0 05 0 71 0 02

13 ATA -0 39 0 15 -0 34 -0 35 -0 45 -0 16 -0 23 -0 24 -0 74 -0 13 -0 70 0 02

14 ATC -0 03 -0 25 -0 12 0 06 0 50 -0 34 0 44 -0 32 0 07 -0 36 -0 46 -0 34

15 ATG 0 11 0 01 -0 27 -0 01 0 22 -0 04 -0 12 0 18 0 62 -0 03 0 28 -0 06

16 ATT 0 16 0 15 0 02 0 16 0 49 -0 02 0 38 -0 05 0 47 0 43 0 86 0 58

17 CAA -0 34 -0 34 -0 31 -0 35 -0 39 -0 27 -0 37 -0 25 0 08 -0 38 0 04 -0 45

18 CAC 0 17 -0 10 0 13 0 12 0 36 -0 19 0 38 -0 02 0 44 -0 36 0 10 -0 41

19 CAG 0 28 0 22 0 22 0 34 0 04 0 35 0 13 0 25 0 60 0 30 0 52 0 34

20 CAT -0 12 -0 13 -0 05 0 19 0 20 -0 13 0 10 -0 10 0 16 0 28 0 90 0 47

21 CCA -0 19 -0 16 0 11 -0 18 -0 56 -0 28 -0 44 -0 12 -0 35 0 25 0 31 0 39

22 CCC 0 13 -0 21 0 47 -0 38 -0 23 -0 04 0 11 -0 01 -0 59 -0 51 -0 52 -0 28

23 CCG -0 11 0 10 -0 06 0 22 -0 16 0 31 -0 08 0 10 0 72 0 56 0 75 0 59

24 CCT 0 39 -0 04 0 40 0 18 0 19 0 40 0 41 0 29 0 93 0 87 0 88 0 91

25 CGA -0 08 0 50 0 12 -0 19 -0 42 -0 10 0 03 -0 17 -0 33 0 25 -0 42 0 35

26 CGC 0 18 0 21 -0 07 -0 04 -0 08 -0 01 0 14 0 05 -0 10 -0 33 -0 28 -0 42

27 CGG 0 55 0 79 0 18 0 71 -0 41 0 60 0 20 0 25 0 05 0 79 0 02 0 43

28 CGT -0 07 -0 20 -0 30 -0 24 0 25 -0 11 0 34 -0 33 0 67 0 06 0 63 0 20

29 CTA -0 41 -0 01 -0 21 -0 18 -0 38 -0 10 -0 11 0 05 -0 51 -0 27 -0 54 -0 38

30 CTC 0 19 -0 50 -0 11 -0 55 0 25 -0 33 0 32 -0 35 -0 24 -0 06 -0 55 -0 24

31 CTG -0 09 0 29 0 06 0 14 0 00 0 09 -0 10 0 09 0 75 0 60 0 59 0 56

32 CTT 0 34 -0 26 -0 16 -0 43 0 43 0 22 0 55 0 09 0 39 -0 16 0 65 0 43

33 GAA 0 00 -0 14 0 18 -0 03 -0 21 -0 21 -0 24 0 11 0 09 -0 13 -0 15 -0 17

34 GAC 0.01 -0.03 0.01 0.25 0.21 -0.19 0.12 0.00 -0.68 -0.58 -0.71 -0.52

35 GAG -0 04 0 25 -0 21 0 20 0 05 0 87 0 03 0 56 0 06 0 07 0 01 -0 05 36 GAT -0 02 -0 20 0 05 0 18 0 25 -0 13 0 16 0 10 0 53 0 23 0 77 0 51

37 GCA -0 21 0 18 0 10 0 14 -0 44 -0 02 -0 44 0 01 -0 36 0 34 -0 52 0 27

38 GCC 0 12 -0 23 0 62 -0 26 -0 01 -0 11 -0 11 -0 12 -0 74 -0 65 -0 60 -0 65

39 GCG -0 09 0 44 -0 27 0 24 -0 19 0 34 -0 07 0 29 0 40 0 67 0 38 0 65

40 GCT 0 14 -0 41 0 37 -0 08 0 27 0 30 0 32 0 22 0 85 0 85 0 91 0 91

41 GGA -0 15 0 36 0 10 -0 31 -0 62 0 05 -0 54 -0 24 -0 72 -0 01 -0 52 -0 40

42 GGC 0 10 -0 01 0 02 -0 08 -0 01 -0 04 0 04 -0 01 -0 36 -0 31 -0 50 -0 34

43 GGG 0 24 0 72 0 33 0 15 -0 24 0 72 -0 05 0 05 0 07 0 63 0 46 0 16

44 GGT -0 16 -0 15 -0 11 -0 10 -0 19 0 58 -0 27 -0 25 0 50 0 05 0 76 0 32

45 GTA -0 27 0 15 0 21 -0 05 -0 22 0 22 -0 33 -0 05 -0 54 0 22 -0 29 0 09

46 GTC 0 29 0 03 0 67 -0 25 -0 03 -0 37 -0 10 -0 47 -0 59 -0 59 -0 68 -0 58

47 GTG -0 16 0 41 -0 30 0 05 0 10 0 26 -0 16 0 04 0 29 0 43 0 33 0 20

48 GTT 0 25 -0 31 -0 02 -0 08 0 44 0 23 0 44 0 11 0 58 0 46 0 84 0 58

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 11 -0 40 0 02 0 39 0 29 -0 43 0 41 -0 02 0 02 -0 48 0 11 -0 24

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 05 -0 16 0 12 0 55 0 52 -0 20 0 38 0 49 0 65 0 31 0 72 0 67

53 TCA -0.08 0.36 0.11 0.21 -0.56 -0.08 -0.43 -0.04 -0.23 0.62 -0.47 0.44

54 TCC 0 50 -0 12 0 56 0 25 -0 17 -0 38 -0 16 -0 39 -0 33 -0 58 -0 47 -0 53

55 TCG 0 05 0 53 0 06 0 38 -0 16 0 28 -0 14 0 39 0 67 0 75 0 65 0 70

56 TCT 0 45 -0 24 0 46 0 31 0 18 -0 07 0 28 -0 07 0 83 0 97 0 70 0 92

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 05 0 36 0 49 0 08 0 11 0 02 0 46 0 27 -0 15 0 22 -0 26 0 32

59 TGG 0 06 0 02 -0 16 -0 03 -0 21 0 27 -0 28 0 13 0 57 0 15 0 97 -0 09

60 TGT -0 14 -0 11 -0 22 -0 33 -0 16 -0 13 -0 24 -0 29 0 51 0 30 0 64 0 23

61 TTA -0 07 0 42 0 10 -0 15 -0 11 -0 33 -0 40 -0 15 -0 51 -0 47 -0 46 -0 59

62 TTC 0 01 0 03 0 12 0 22 0 49 -0 15 0 44 -0 23 -0 24 -0 25 -0 63 -0 11

63 TTG 0 20 0 55 0 14 0 08 0 30 0 38 0 12 0 31 0 34 0 23 0 23 -0 20

64 TTT -0 04 -0 10 0 04 -0 05 0 49 -0 25 0 35 -0 22 0 44 0 31 0 83 0 38

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.5 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 42 -0 08 0 05 0 20 0 14 0 12 0 20 0 12 0 16 0 04 0 07 0 10

2 AAC 0 54 0 11 0 22 0 31 0 48 -0 11 -0 02 0 09 0 10 0 30 -0 18 0 29

3 AAG -0 33 -0 03 -0 14 -0 02 -0 42 -0 26 -0 34 -0 30 -0 41 -0 29 -0 16 -0 11 AAT 004 -026 -021 -O 22 -008 -003 -O 19 003 001 -O 08 O 05 -003

ACA -045 039 -009 O 31 -039 021 O 12 006 -049 -O 25 -O 20 -038

ACC 038 -029 -009 -O 19 046 -004 021 024 052 O 61 O 68 058

ACG -001 061 -004 O 33 -045 -003 004 -007 -067 -O 29 -O 47 -039

ACT 034 -025 039 -O 13 003 -042 -029 -003 052 O 08 O 35 034

AGA -074 038 -Oil -O Ol -012 056 042 002 003 -O 33 O 21 -O 14

AGC 041 025 031 O 12 047 -020 -040 -021 035 O 51 O 07 053

AGG -072 024 -O 14 O 28 -047 040 -O 13 -003 -051 -O 42 -O 30 -O 19

AGT 013 004 -001 -O 13 049 O 19 -020 004 048 O 45 O 36 042

ATA -064 032 -O 13 O 30 -023 O 18 O 14 023 007 -O 44 O 23 -O 17

ATC 068 -020 -004 O 19 066 -008 O 12 025 030 -O 24 O Ol -006

ATG 006 -008 000 O 07 009 -O 12 -004 O 10 -O 14 O 06 O 05 -002

ATT 045 -014 005 -O 02 030 -O 10 -035 -O 11 O 14 -O 28 O 12 -026

CAA -048 -029 -006 -O 21 -031 007 023 -012 002 -O 23 -O 05 -026

CAC 055 015 040 O 16 068 000 O 11 009 039 O 44 O 22 023

CAG -008 024 003 O 20 -028 O 15 021 -007 -O 19 O 35 O 10 004

CAT 026 -011 -023 -O 17 -004 -002 -025 -005 -007 -O 21 -O 16 -030

CCA -0.35 0.03 -0.22 O .13 -0.45 -0.05 0.04 0.06 -0.37 O .18 -O .15 -0.11

CCC -051 -035 051 -O 28 075 044 059 021 065 O 16 O 74 O 11

CCG -017 028 -O 17 -O 08 -035 -009 -O 10 -O 14 -047 O 12 -O 02 009

CCT -001 003 063 O 25 067 041 066 005 O 18 -O 20 O 53 004

CGA -057 013 -047 -O 25 -033 035 029 -O 12 -037 -O 24 -O 06 -051

CGC 040 014 031 -O 03 068 001 -021 -O 10 024 O 11 -O 10 O 18

CGG -062 023 -061 -O 10 -040 039 -O 10 -001 024 O 40 O 83 006

CGT 046 007 025 -O 14 065 -002 -024 -003 O 13 O 36 -O 23 002

CTA -025 024 005 O 07 -071 -036 -029 -039 -040 -O 60 -O 41 -052

CTC 048 017 072 O 30 081 040 046 042 086 -O 10 O 72 042

CTG 013 021 -009 -O Ol -040 008 071 -009 006 O 17 O 10 O 17

CTT 027 -021 075 O 15 070 039 030 008 053 -O 30 O 49 -020

GAA -025 -004 020 O 18 007 025 033 O 16 036 -O 03 O 09 002

GAC 063 019 029 O 37 045 -007 -008 004 038 O 35 -O 09 042

GAG -032 -022 -031 O 06 -043 -033 -029 -029 -042 O 65 -O 24 -O 18

GAT 033 -026 -O 15 -O 10 -003 -O 19 -007 O 19 O 10 -O 23 -O 07 -O 11

GCA -033 024 -O 13 O 18 -032 022 O 14 O 14 -040 O 07 -O 35 -029

GCC 029 -002 036 -O 19 066 O 17 027 O 18 054 O 04 O 60 033

GCG -027 036 -031 -O 13 -042 -O 13 -O 17 -O 18 -043 O 31 -O 13 003

GCT 024 -027 059 O OO 057 -022 009 002 038 -O 05 O 19 028

GGA -061 061 -037 O 02 -035 -001 O 13 -029 -033 O 13 -O 20 O 10

GGC 034 027 O 19 O Ol 082 054 053 053 029 O 24 O Ol 044 43 GGG -0 47 -0 28 -0 43 -0 28 -0 73 0 10 -0 45 -0 50 -0 67 0 72 -0 52 -0 02

44 GGT 0 43 -0 01 0 30 -0 09 0 40 -0 32 -0 24 -0 19 0 39 0 64 0 10 0 33

45 GTA -0 04 0 52 -0 11 0 41 -0 34 0 07 -0 33 -0 10 -0 15 -0 09 -0 36 -0 12

46 GTC 0 26 0 02 0 30 -0 13 0 86 0 42 0 45 0 16 0 76 0 18 0 62 0 31

47 GTG -0 05 -0 01 -0 35 -0 20 -0 13 0 36 -0 20 -0 18 -0 19 0 28 -0 21 -0 01

48 GTT 0 47 -0 22 0 59 0 13 0 59 -0 31 -0 13 -0 07 0 42 -0 27 0 03 -0 30

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 44 -0 20 0 13 0 17 0 65 0 02 0 17 0 24 0 35 0 10 0 15 0 30

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 03 -0 19 -0 09 0 17 -0 03 -0 37 -0 27 0 25 0 18 -0 35 -0 19 -0 03

53 TCA -0 54 0 28 -0 33 0 17 -0 39 0 13 0 26 0 19 -0 45 -0 38 -0 33 -0 28

54 TCC 0 08 -0 28 0 22 -0 10 0 73 0 22 0 39 0 41 0 35 -0 16 0 42 -0 06

55 TCG -0 38 0 29 -0 43 -0 17 -0 49 0 11 0 01 -0 01 -0 62 -0 34 -0 31 -0 23

56 TCT -0 08 -0 21 0 41 -0 12 0 47 -0 32 0 33 0 12 0 14 -0 14 0 07 -0 14

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 13 0 27 0 19 0 10 0 48 -0 19 -0 28 -0 13 -0 02 0 43 -0 35 0 09

59 TGG -0 49 0 01 0 00 0 12 -0 09 0 08 0 05 -0 06 0 10 0 26 -0 06 -0 09

60 TGT -0.22 -0.10 -0.19 -0.24 0.71 0.32 -0.16 0.17 0.52 0.62 0.09 0.38

61 TTA -0 27 -0 06 -0 25 -0 20 -0 31 0 11 -0 24 0 03 0 09 -0 57 -0 21 -0 36

62 TTC 0 68 0 30 0 57 0 53 0 84 -0 35 -0 50 -0 08 0 26 -0 27 -0 45 -0 26

63 TTG -0 39 -0 05 -0 33 -0 40 -0 45 -0 17 -0 54 -0 27 -0 37 -0 45 -0 27 -0 40

64 TTT 0 18 -0 29 -0 30 -0 25 0 52 0 32 0 15 0 13 0 54 0 02 0 45 0 12

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.5 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA 0 27 0 06 0 16 0 21 0 20 -0 06 0 05 0 20 0 14 -0 10 -0 46 -0 14

2 AAC 0 10 -0 17 0 02 -0 16 0 66 -0 15 -0 09 0 00 0 03 -0 14 0 18 0 02

3 AAG -0 56 -0 25 -0 50 -0 27 -0 51 -0 23 -0 38 -0 06 0 61 0 56 0 41 0 42

4 AAT 0 10 0 12 0 12 0 34 0 04 -0 40 0 07 -0 30 -0 13 -0 13 0 02 0 19

5 ACA -0 18 0 21 0 02 0 38 -0 47 -0 15 0 25 -0 23 -0 19 0 26 -0 10 0 20

6 ACC -0 10 -0 12 0 19 0 08 0 53 0 38 0 54 0 46 0 01 -0 24 0 16 -0 15

7 ACG -0 46 -0 03 -0 30 -0 21 -0 72 -0 42 -0 53 -0 47 0 16 0 54 0 49 0 45

8 ACT 0 49 -0 06 0 81 0 17 0 35 0 14 0 42 0 31 -0 40 -0 49 0 07 0 01

9 AGA -0 54 0 30 -0 31 0 31 -0 13 0 30 0 43 -0 28 0 05 0 41 0 07 0 28

10 AGC 0 14 -0 09 -0 09 -0 12 0 66 0 16 0 06 0 32 -0 25 -0 16 -0 12 -0 26 AGG -063 020 -030 021 -070 -028 -018 -062 001 044 -019 -012

AGT 028 024 -015 032 062 030 019 018 -039 001 -020 -0 06

ATA -023 031 010 020 -031 -021 041 -033 006 047 011 0 33

ATC 069 -021 055 006 084 -059 031 -005 008 -042 030 0 15

ATG 021 -008 031 -009 005 -017 -002 019 -003 002 007 -0 01

ATT 050 -019 054 -008 062 -044 007 -030 -012 025 -011 -0 01

CAA -038 010 -031 -009 -016 -030 -021 -039 044 059 011 0 56

CAC 010 000 002 -004 080 029 019 014 013 -028 014 -0 16

CAG -043 029 -020 -009 -031 016 047 -032 -015 -017 -015 -0 26

CAT 024 -015 -019 013 -006 -026 -010 -042 -012 -008 -002 0 37

CCA -052 -020 -038 020 -036 021 018 018 -014 -006 -010 0 28

CCC -022 025 -016 031 057 061 074 042 050 -005 054 -0 31

CCG -011 -017 055 -020 -052 -006 -030 010 -013 016 021 0 11

CCT 050 039 056 035 036 054 061 030 -015 -039 010 -0 18

CGA -034 -005 -038 -004 -053 -027 -039 -030 026 061 027 0 45

CGC 037 002 027 001 081 051 012 045 013 -021 001 -0 22

CGG -056 021 -064 -006 -056 034 -025 -025 -026 064 008 0 26

CGT 0.30 -0.02 -0.10 0.01 0.56 0.25 -0.20 0.01 -0.13 -0.10 0.04 0 .17

CTA -054 -052 -054 -037 -046 -041 -016 -041 079 092 077 0 84

CTC 068 077 033 079 093 066 081 062 000 -068 047 -0 50

CTG 020 -006 028 -017 004 015 002 010 -030 024 -020 -0 12

CTT 069 052 058 056 050 022 069 025 -017 -001 -053 -0 49

GAA 030 024 011 019 029 030 -001 029 007 -004 -049 -0 27

GAC -001 -013 -009 -018 066 005 014 017 008 -004 015 -0 08

GAG -045 -019 -051 -034 -049 067 -031 -021 059 061 047 0 53

GAT 054 -005 023 025 028 -049 015 -015 -005 -014 -007 0 16

GCA -033 027 -008 027 -033 031 001 017 -026 026 -022 0 19

GCC 006 -002 002 004 073 052 052 052 017 -024 014 -0 30

GCG -044 015 -037 -020 -058 008 -042 -011 021 057 040 0 33

GCT 055 018 066 021 045 051 047 045 -039 -047 005 -0 27

GGA -063 -034 -054 -035 -029 042 004 -026 019 051 009 0 45

GGC 061 056 061 055 073 054 025 042 -007 -020 -013 -0 35

GGG -071 -036 -059 -046 -069 078 -051 -052 036 076 031 0 52

GGT 045 001 025 -017 064 084 -004 031 -013 010 005 0 10

GTA -008 -020 -004 -034 -004 000 -032 -025 -003 040 000 0 30

GTC 067 045 043 042 089 055 070 058 013 023 -001 -0 45

GTG 006 -012 -027 -025 -020 -003 -040 -004 025 055 023 0 23

GTT 042 013 058 012 056 017 040 028 -025 -011 -037 -0 33

TAA 000 000 000 000 000 000 000 000 000 000 000 0 00 50 TAC 0 31 -0 02 -0 06 0 10 0 76 0 07 0 22 0 31 0 06 -0 33 0 18 0 02

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 10 -0 26 0 01 0 15 0 15 -0 53 -0 13 -0 33 -0 10 -0 31 0 00 0 47

53 TCA -0 15 -0 08 -0 29 0 30 -0 57 -0 25 -0 11 -0 28 0 01 0 41 0 28 0 40

54 TCC -0 15 -0 23 0 04 0 01 0 66 0 38 0 51 0 41 0 48 -0 12 0 38 0 00

55 TCG -0 28 -0 19 -0 42 -0 07 -0 69 -0 33 -0 53 -0 44 0 42 0 67 0 68 0 62

56 TCT 0 68 0 10 0 75 0 24 0 26 0 22 0 20 -0 09 -0 17 -0 50 0 42 0 00

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 02 -0 13 -0 24 -0 14 0 73 -0 07 -0 24 0 04 0 06 -0 21 0 24 0 00

59 TGG -0 50 0 22 -0 40 0 00 -0 47 0 57 -0 11 0 22 -0 08 0 26 0 19 -0 13

60 TGT -0 10 0 42 -0 54 0 35 0 49 0 38 -0 07 0 05 -0 18 0 00 0 02 0 20

61 TTA 0 12 -0 29 -0 12 -0 20 0 00 -0 28 -0 04 -0 21 0 66 0 74 0 62 0 56

62 TTC 0 64 -0 42 0 23 -0 33 0 83 -0 66 -0 12 -0 29 0 26 -0 07 0 30 0 15

63 TTG -0 28 -0 21 -0 28 -0 28 -0 54 -0 44 -0 49 -0 43 0 84 0 90 0 83 0 69

64 TTT 0 64 0 22 0 54 0 34 0 63 -0 29 0 51 -0 14 -0 19 -0 06 -0 12 -0 04

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.5 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA 0 00 -0 15 -0 21 0 31 0 11 -0 16 -0 28 -0 01 0 29 -0 08 -0 22 0 18

2 AAC 0 41 -0 36 0 27 0 14 0 19 -0 21 0 36 -0 20 0 12 -0 36 0 07 -0 10

3 AAG 0 28 0 52 0 18 0 25 -0 05 0 41 0 17 0 68 -0 04 0 19 0 10 0 11

4 AAT 0 20 -0 34 0 13 -0 05 0 35 -0 04 0 56 0 10 0 35 -0 22 0 29 0 13

5 ACA -0 24 0 28 0 15 0 06 -0 43 0 26 -0 13 0 10 -0 15 0 37 0 25 0 33

6 ACC 0 02 -0 19 0 30 -0 11 -0 40 -0 04 -0 32 -0 20 -0 03 -0 01 0 19 -0 22

7 ACG -0 32 0 70 -0 19 0 22 0 20 0 48 0 24 0 43 -0 45 0 17 -0 27 0 06

8 ACT -0 06 -0 25 -0 08 -0 26 0 03 -0 30 0 67 0 11 0 04 -0 03 0 47 0 04

9 AGA -0 30 0 45 -0 02 0 09 -0 54 0 27 -0 14 0 33 -0 21 -0 02 0 14 0 07

10 AGC 0 17 -0 39 0 34 0 55 -0 15 -0 14 0 10 -0 16 -0 12 -0 16 -0 01 0 01

11 AGG -0 49 0 51 0 04 -0 23 -0 26 0 51 0 41 0 60 0 17 0 55 -0 10 -0 06

12 AGT 0 12 -0 14 0 03 0 01 0 04 0 20 0 29 0 09 0 45 0 40 0 37 0 37

13 ATA 0 21 0 00 0 40 0 33 0 26 0 39 0 05 0 31 0 40 0 03 0 43 0 19

14 ATC 0 45 -0 43 0 45 -0 19 0 64 -0 13 0 44 -0 13 0 53 -0 38 0 34 -0 13

15 ATG -0 05 0 52 -0 29 0 12 -0 14 -0 10 -0 36 0 43 0 29 0 08 -0 21 0 14

16 ATT 0 46 -0 41 0 30 -0 26 0 68 -0 22 0 59 -0 24 0 59 -0 39 0 14 -0 21

17 CAA 0 61 0 43 0 54 0 54 -0 04 0 34 -0 27 0 27 0 60 0 61 0 58 0 55 CAC 0 21 -0 34 0 14 -0 21 0 16 -0 35 0 05 -0 41 -0 24 -0 33 0 87 -0 36

CAG -0 32 0 21 -0 36 -0 19 -0 31 -0 08 -0 45 0 36 -0 31 -0 01 -0 27 -0 28

CAT 0 35 -0 11 0 10 -0 04 0 32 0 29 0 52 0 28 0 25 -0 15 0 04 -0 10

CCA 0 01 0 24 0 33 0 19 -0 41 -0 03 -0 09 0 15 -0 07 0 55 0 26 0 44

CCC -0 37 -0 46 0 06 -0 40 -0 47 -0 41 0 34 -0 35 0 05 -0 20 0 30 -0 29

CCG -0 25 0 76 0 09 0 34 -0 04 0 33 0 01 0 35 -0 42 0 31 -0 14 -0 06

CCT -0 29 -0 45 -0 38 -0 46 -0 22 -0 44 0 05 -0 08 -0 06 -0 08 0 40 -0 22

CGA 0 09 0 36 0 11 0 11 -0 11 0 57 0 17 0 54 -0 19 0 24 -0 07 0 40

CGC -0 04 -0 28 0 22 -0 07 -0 06 -0 21 0 01 -0 14 -0 27 -0 12 -0 15 -0 13

CGG -0 52 0 23 -0 49 -0 21 -0 45 0 52 0 16 0 55 -0 66 -0 19 -0 55 -0 21

CGT 0 25 0 24 0 14 0 00 -0 03 -0 01 0 17 -0 07 0 36 0 43 0 48 0 31

CTA 0 76 0 73 0 75 0 78 0 73 0 71 0 59 0 74 0 83 0 72 0 81 0 72

CTC 0 43 -0 34 0 42 0 11 -0 20 -0 59 -0 34 -0 54 0 71 0 39 0 75 0 47

CTG -0 43 0 48 -0 46 -0 12 0 01 0 23 -0 27 0 29 -0 29 -0 12 -0 49 -0 15

CTT 0 29 -0 33 0 33 -0 21 0 17 -0 39 -0 23 -0 08 0 64 0 31 0 73 0 37

GAA 0 02 -0 13 -0 25 0 09 -0 07 -0 13 -0 42 -0 16 0 21 -0 07 -0 33 0 02

GAC 0 29 -0 16 0 24 -0 02 0 15 -0 23 0 02 -0 28 0 16 -0 06 0 18 -0 16

GAG 0.32 0.51 0 .12 0.42 0.45 0.59 0.21 0.67 0.44 0.44 0.25 0.40

GAT 0 26 -0 25 0 01 -0 13 0 34 -0 04 0 59 0 10 0 29 -0 19 -0 01 -0 02

GCA -0 13 0 41 0 18 0 10 -0 25 -0 03 -0 21 -0 12 -0 16 0 42 0 25 0 38

GCC -0 17 -0 15 0 28 -0 18 -0 68 0 87 -0 56 -0 09 0 00 0 05 0 31 -0 12

GCG -0 33 0 70 -0 19 0 33 -0 06 0 26 0 05 0 19 -0 50 0 28 -0 32 0 01

GCT -0 20 -0 31 -0 13 -0 30 0 01 -0 15 0 21 -0 02 -0 23 0 08 0 43 -0 11

GGA 0 11 0 38 0 26 0 44 -0 01 0 65 0 54 0 71 0 41 0 63 0 63 0 62

GGC -0 46 0 96 -0 28 -0 11 -0 21 -0 38 -0 15 -0 37 -0 42 -0 14 -0 33 -0 27

GGG -0 12 0 44 -0 24 0 23 0 30 0 73 0 67 0 84 -0 03 0 60 0 31 0 32

GGT -0 05 0 04 -0 02 0 01 0 21 0 17 0 21 -0 07 0 13 0 24 0 20 0 12

GTA 0 24 0 46 0 14 0 41 0 26 0 42 -0 07 0 20 0 28 0 39 0 07 0 46

GTC 0 27 -0 35 0 13 -0 26 -0 04 -0 31 -0 43 -0 44 0 46 0 12 0 30 0 04

GTG -0 03 0 66 -0 34 0 20 0 32 0 46 -0 01 0 36 -0 13 -0 06 -0 48 -0 16

GTT 0 21 -0 37 0 23 -0 37 0 44 -0 26 0 06 -0 17 0 45 0 08 0 49 -0 04

TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

TAC 0 24 -0 33 0 25 -0 08 0 34 -0 31 0 24 -0 29 0 31 -0 12 0 34 -0 11

TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

TAT 0 24 -0 33 0 18 0 16 0 37 0 02 0 60 0 15 0 29 -0 35 0 11 -0 17

TCA -0 17 0 15 0 19 0 35 -0 28 0 41 0 21 0 30 -0 21 0 20 0 27 0 35

TCC -0 16 -0 07 0 38 -0 20 -0 09 -0 39 -0 36 -0 47 -0 20 -0 10 0 30 -0 11

TCG -0 27 0 64 -0 14 0 22 0 45 0 74 0 47 0 61 -0 52 0 02 -0 42 0 03

TCT -0 12 -0 39 -0 16 -0 33 0 41 -0 24 0 76 -0 31 -0 20 -0 07 0 44 -0 31 57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 05 -0 17 0 23 0 09 0 01 -0 04 0 08 -0 13 -0 18 0 02 -0 11 0 18

59 TGG -0 09 0 46 -0 25 0 10 -0 58 0 01 -0 08 0 46 -0 32 0 33 -0 08 0 12

60 TGT -0 08 -0 06 -0 04 -0 08 0 16 0 07 0 28 -0 06 0 12 -0 13 0 05 0 11

61 TTA 0 55 0 40 0 45 0 56 0 20 0 19 -0 17 -0 04 0 62 0 20 0 39 0 45

62 TTC 0 60 -0 18 0 56 0 07 0 67 0 13 0 51 -0 06 0 50 0 06 0 51 0 09

63 TTG 0 44 0 78 0 55 0 46 0 01 0 53 -0 06 0 47 0 43 0 46 0 38 0 30

64 TTT 0 44 -0 53 0 31 -0 41 0 65 -0 23 0 62 -0 34 0 32 -0 49 0 11 -0 29

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.5 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 03 0 00 -0 03 -0 11 0 01 -0 21 0 13 0 00 -0 01 0 05 0 05

2 AAC 0 00 -0 24 0 00 0 06 0 15 -0 17 0 13 0 26 0 00 -0 24 -0 42 -0 17

3 AAG 0 00 0 09 0 00 0 12 -0 08 0 34 -0 26 0 03 0 00 0 08 -0 14 -0 18

4 AAT 0 00 0 03 0 00 0 20 0 15 0 44 0 50 0 37 0 00 0 29 0 90 0 37

5 ACA 0 00 0 38 0 00 0 41 -0 54 0 01 -0 34 0 02 0 00 0 51 0 06 0 15

6 ACC 0 00 -0 17 0 00 -0 07 0 17 0 02 -0 02 -0 08 0 00 -0 36 -0 43 -0 47

7 ACG 0 00 0 75 0 00 0 45 -0 04 0 54 0 05 0 35 0 00 0 88 0 66 0 84

8 ACT 0 00 -0 54 0 00 -0 41 -0 35 -0 46 -0 24 -0 41 0 00 0 19 0 90 0 19

9 AGA 0 00 0 47 0 00 0 16 0 42 0 68 0 24 0 67 0 00 0 44 0 53 0 07

10 AGC 0 00 -0 28 0 00 -0 19 0 58 0 31 0 43 0 55 0 00 0 13 -0 30 0 30

11 AGG 0 00 0 76 0 00 0 40 0 11 0 73 0 39 0 06 0 00 0 57 0 65 0 20

12 AGT 0 00 -0 30 0 00 -0 40 -0 34 -0 05 -0 23 0 00 0 00 -0 22 0 28 0 01

13 ATA 0 00 0 38 0 00 -0 09 -0 36 0 06 -0 09 -0 24 0 00 0 21 0 05 -0 30

14 ATC 0 00 -0 18 0 00 0 22 0 50 -0 36 0 39 -0 13 0 00 0 00 -0 44 0 15

15 ATG 0 00 -0 02 0 00 0 02 0 13 0 25 -0 27 0 16 0 00 0 03 0 00 -0 03

16 ATT 0 00 0 08 0 00 -0 12 0 13 -0 16 0 20 -0 12 0 00 -0 05 0 65 -0 04

17 CAA 0 00 0 01 0 00 -0 24 -0 22 -0 06 -0 01 -0 01 0 00 0 05 0 04 -0 14

18 CAC 0 00 -0 12 0 00 -0 03 -0 01 -0 27 0 12 -0 18 0 00 -0 36 -0 51 -0 11

19 CAG 0 00 0 01 0 00 0 15 -0 06 0 38 -0 20 0 23 0 00 -0 01 -0 02 0 07

20 CAT 0 00 -0 07 0 00 0 16 0 04 0 22 0 25 0 16 0 00 0 24 0 78 0 31

21 CCA 0 00 0 38 0 00 0 49 -0 44 0 05 -0 31 0 15 0 00 0 18 0 51 0 38

22 CCC 0 00 -0 17 0 00 -0 21 -0 22 -0 38 0 04 -0 27 0 00 -0 56 -0 42 -0 51

23 CCG 0 00 0 33 0 00 0 20 -0 20 0 37 0 00 0 16 0 00 0 26 -0 21 0 50

24 CCT 0 00 -0 51 0 00 -0 57 -0 65 -0 65 -0 49 -0 65 0 00 -0 39 0 87 -0 39 CGA 000 048 000 025 042 020 014 036 000 055 038 043

CGC 000 -005 000 -007 021 021 011 025 000 -029 -043 -0 14

CGG 000 081 000 054 039 085 056 076 000 067 074 0 61

CGT 000 -005 000 -025 -022 -018 -008 -032 000 001 046 0 03

CTA 000 034 000 014 012 031 -025 031 000 002 -043 -0 14

CTC 000 -056 000 -053 -030 -067 -019 -068 000 -042 -032 -0 36

CTG 000 033 000 025 043 082 021 053 000 030 017 0 37

CTT 000 -043 000 -055 -057 -076 -052 -074 000 -039 041 -0 45

GAA 000 008 000 005 011 003 032 020 000 029 021 0 14

GAC 000 -009 000 025 016 -021 034 014 000 -036 -060 -0 09

GAG 000 -018 000 -007 -016 007 -024 -006 000 -030 -032 -0 37

GAT 000 -020 000 009 025 012 037 032 000 010 090 0 34

GCA 000 053 000 048 -005 031 -021 023 000 072 -002 0 41

GCC 000 -004 000 -025 014 -006 -013 -020 000 -049 -048 -0 60

GCG 000 058 000 034 033 069 029 041 000 066 029 0 55

GCT 000 -056 000 -056 -036 -042 -027 -048 000 008 094 -0 22

GGA 000 031 000 -015 013 072 -049 047 000 -007 021 -0 12

GGC 0.00 0.02 0.00 0.04 0.41 0.33 0.38 0.45 0.00 -0.20 -0.44 -0 .22

GGG 000 070 000 031 052 084 042 068 000 079 078 0 46

GGT 000 -012 000 -026 -034 -030 -035 -042 000 015 052 -0 04

GTA 000 044 000 044 006 017 -014 018 000 038 -002 -0 04

GTC 000 -008 000 -022 031 -013 023 -016 000 -035 -061 -0 29

GTG 000 067 000 040 059 079 027 061 000 039 037 0 47

GTT 000 -039 000 -049 -028 -054 -023 -058 000 -026 079 -0 22

TAA 000 000 000 000 000 000 000 000 000 000 000 0 00

TAC 000 -030 000 032 029 -027 023 004 000 -033 -051 0 17

TAG 000 000 000 000 000 000 000 000 000 000 000 0 00

TAT 000 -030 000 033 -010 -028 034 031 000 003 078 0 31

TCA 000 059 000 054 -055 007 -040 -017 000 003 000 0 40

TCC 000 011 000 046 004 -015 027 -010 000 -053 -045 -0 50

TCG 000 074 000 058 -005 049 002 038 000 048 040 0 62

TCT 000 -027 000 -022 -051 -054 -026 -053 000 020 096 0 03

TGA 000 000 000 000 000 000 000 000 000 000 000 0 00

TGC 000 -014 000 009 -003 013 019 -004 000 -015 -033 -0 18

TGG 000 010 000 -007 -038 049 -035 040 000 010 000 -0 11

TGT 000 011 000 -004 -050 -031 -030 -026 000 037 061 0 09

TTA 000 062 000 031 -006 004 -026 013 000 -008 -011 -0 13

TTC 000 -013 000 012 002 -040 -018 -024 000 -025 -052 -0 08

TTG 000 038 000 001 -017 055 -035 034 000 003 -021 -0 17 64 TTT 0 00 0 10 0 00 -0 07 0 08 -0 03 0 35 0 08 0 00 0 10 0 80 0 25

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.5 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 15 -0 03 0 40 0 23

2 AAC 0 46 -0 30 0 58 0 19

3 AAG -0 02 -0 22 -0 02 -0 31

4 AAT -0 23 -0 04 0 06 0 20

5 ACA -0 50 0 16 -0 40 -0 13

6 ACC 0 43 -0 19 0 53 0 01

7 ACG -0 24 0 41 -0 34 0 27

8 ACT 0 24 -0 34 0 32 -0 09

9 AGA -0 34 0 66 -0 01 0 30

10 AGC 0 65 0 04 0 67 0 27

11 AGG -0 24 0 61 -0 44 0 37

12 AGT 0 06 -0 13 -0 27 -0 32

13 ATA -0 57 -0 25 -0 57 -0 49

14 ATC 0 66 -0 16 0 69 0 37

15 ATG 0 36 -0 15 -0 21 0 13

16 ATT -0 03 -0 16 -0 35 0 12

17 CAA -0 11 0 39 0 05 0 05

18 CAC 0 53 -0 16 0 68 0 08

19 CAG -0 07 -0 16 -0 25 -0 04

20 CAT -0 24 0 03 -0 21 0 03

21 CCA -0 32 0 19 -0 26 0 12

22 CCC 0 32 0 02 0 40 0 04

23 CCG -0 03 -0 09 -0 12 0 00

24 CCT -0 07 -0 07 0 31 -0 05

25 CGA -0 47 0 12 -0 44 -0 09

26 CGC 0 38 0 10 0 48 -0 08

27 CGG -0 36 0 78 -0 44 0 38

28 CGT 0 02 -0 05 -0 13 -0 24

29 CTA -0 46 0 18 -0 47 -0 33

30 CTC 0 77 0 26 0 85 0 15

31 CTG 0 22 0 09 0 07 -0 08 CTT 0 12 0 15 0 30 0 03

GAA 0 24 0 51 0 39 0 16

GAC 0 39 -0 05 0 59 0 33

GAG -0 25 -0 38 -0 35 -0 42

GAT -0 39 -0 18 -0 18 -0 01

GCA -0 41 0 06 -0 35 -0 19

GCC 0 47 0 16 0 57 -0 03

GCG -0 27 0 29 -0 29 -0 07

GCT 0 21 -0 04 0 27 -0 17

GGA -0 66 -0 18 -0 45 -0 37

GGC 0 32 0 08 0 41 0 03

GGG -0 49 0 57 -0 40 0 34

GGT -0 19 0 12 -0 18 -0 23

GTA -0 48 -0 19 -0 53 -0 27

GTC 0 62 -0 10 0 71 -0 15

GTG 0 12 0 16 -0 28 0 14

GTT 0 16 0 08 0 25 0 11

TAA 0.00 0.00 0.00 0.00

TAC 0 66 -0 28 0 72 0 28

TAG 0 00 0 00 0 00 0 00

TAT -0 10 -0 15 -0 10 0 14

TCA -0 53 0 09 -0 33 -0 18

TCC 0 48 0 00 0 58 0 23

TCG -0 23 0 12 -0 39 -0 09

TCT 0 14 -0 09 0 01 0 02

TGA 0 00 0 00 0 00 0 00

TGC 0 41 -0 03 0 55 0 10

TGG 0 09 0 22 0 01 -0 14

TGT -0 15 0 13 0 07 -0 16

TTA -0 42 0 19 -0 43 0 00

TTC 0 52 -0 39 0 50 -0 15

TTG -0 31 -0 18 -0 54 -0 15

TTT -0 34 0 14 -0 23 0 39

TTA TTC TTG TTT

61 62 63 64 Table C.6: CPW matrix Escherichi coli Kl 2 highly expressed sequences (left codon indicated in column 2, right codon indicated in row 2). Host cell: E. coli; Sequence data: full E. coli genome; Highly expressed group: 100 seqs.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 025 -047 055 083 088 -033 061 -059 100 049 100 088

2 AAC -040 -058 -048 029 078 -061 068 -035 100 -055 100 080

3 AAG -059 -002 025 086 061 043 100 040 100 -041 100 100

4 AAT 086 060 100 100 100 052 100 -005 100 100 100 100

5 ACA 079 075 100 100 100 100 070 052 100 064 100 100

6 ACC -033 -065 -057 055 064 -043 074 -069 031 -041 100 100

7 ACG 090 088 067 100 100 074 057 031 100 100 100 100

8 ACT -022 -036 -006 052 100 -056 031 -062 100 100 100 048

9 AGA 100 100 100 100 100 100 100 100 100 100 100 100

10 AGC 008 -035 010 071 100 014 082 100 100 022 100 100

11 AGG 100 100 100 100 100 100 100 100 100 100 100 100

12 AGT 100 056 100 100 100 080 100 100 100 100 100 100

13 ATA 100 100 100 100 100 100 100 100 100 100 100 100

14 ATC -053 -072 -038 055 100 -058 085 -077 100 -020 100 067

15 ATG 012 -038 -029 074 064 -025 048 -029 100 -011 100 079

16 ATT 064 073 093 095 087 046 087 -012 100 093 100 100

17 CAA 071 047 100 068 100 065 081 007 100 100 100 054

18 CAC -051 -065 -060 100 100 -065 100 -072 100 -063 100 -010

19 CAG -033 -046 -011 040 079 -032 100 -075 100 -041 100 100

20 CAT 092 000 073 100 100 057 077 024 100 055 100 100

21 CCA 043 030 100 071 100 -007 100 -013 100 -028 100 100

22 CCC 100 100 100 100 100 100 100 100 100 100 100 100

23 CCG -043 -064 -008 079 047 -052 100 -071 100 001 100 054

24 CCT 045 100 100 031 100 048 100 031 100 100 100 100

25 CGA 100 100 100 100 100 100 100 -019 100 100 100 100

26 CGC 043 -039 017 091 100 042 100 -014 100 052 100 100

27 CGG 100 100 100 100 100 100 100 100 100 100 100 100

28 CGT -045 -059 -059 041 021 -054 062 -083 100 023 100 053

29 CTA 100 100 100 100 100 100 100 100 100 100 100 100

30 CTC 076 038 074 100 100 066 100 055 100 046 100 100

31 CTG -053 -069 002 073 064 -060 066 -076 100 -035 100 090

32 CTT 084 079 100 100 100 100 100 100 100 073 100 100

33 GAA -011 -045 076 069 089 -043 063 -064 100 -026 100 076 34 GAC -051 -063 -051 091 076 -058 066 -051 100 -063 100 100

35 GAG -015 -021 -014 100 100 079 100 024 100 086 100 100

36 GAT 061 -020 064 100 100 -022 100 012 100 092 100 100

37 GCA 037 -045 091 100 024 -055 088 -080 100 -007 100 075

38 GCC 071 049 093 094 080 065 091 039 100 017 100 081

39 GCG -018 -022 -003 090 085 012 086 -043 100 076 100 085

40 GCT -064 -079 -042 068 100 -055 036 -061 100 065 100 100

41 GGA 094 068 100 100 100 084 100 100 100 076 100 100

42 GGC 029 -027 051 064 085 -004 086 -021 100 032 100 077

43 GGG 082 100 100 100 100 100 100 069 100 100 100 100

44 GGT -057 -064 -024 044 064 -029 032 -086 100 -004 100 086

45 GTA -015 -064 100 067 031 -050 -013 -083 100 -021 100 061

46 GTC 073 025 075 100 100 029 100 025 100 026 100 100

47 GTG 004 023 063 093 100 004 086 -050 100 083 100 068

48 GTT -047 -070 -053 090 100 -038 090 -047 100 037 100 100

49 TAA 000 000 000 000 000 000 000 000 000 000 000 000

50 TAC -047 -071 -029 084 100 -068 100 -073 100 -064 100 100

51 TAG 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

52 TAT 052 050 082 100 100 047 100 080 100 072 100 100

53 TCA 100 046 100 100 100 100 100 -024 100 100 100 100

54 TCC -063 -073 -057 073 031 -078 100 -069 100 -077 100 100

55 TCG 051 100 068 100 100 100 100 049 100 100 100 100

56 TCT -056 -076 031 100 029 -077 100 -083 100 100 100 100

57 TGA 000 000 000 000 000 000 000 000 000 000 000 000

58 TGC -022 -028 100 100 100 -048 100 027 100 -023 100 020

59 TGG -023 -037 100 071 100 -020 032 -039 100 028 100 100

60 TGT -025 -057 100 100 -015 066 100 -078 100 100 100 100

61 TTA 094 100 100 100 100 100 100 064 100 078 100 100

62 TTC -049 -069 014 065 051 -061 100 -077 100 -030 100 100

63 TTG 081 083 100 100 053 100 100 063 100 056 100 100

64 TTT 054 047 049 094 082 073 100 000 100 076 100 100

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.6 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA 100 -036 -004 044 020 -051 016 100 -017 100 005 038 AAC 100 -072 -041 069 054 -070 -056 047 024 100 -062 082

AAG 100 -049 015 032 024 -064 -050 054 071 100 -061 -003

AAT 100 062 087 094 100 071 070 100 081 100 046 100

ACA 100 083 100 100 100 100 076 100 100 100 081 100

ACC 100 -067 -047 030 019 -047 001 061 037 100 005 081

ACG 100 100 073 080 056 044 088 100 049 100 036 069

ACT 100 -064 035 035 -044 -085 -073 100 058 100 -082 -060

AGA 100 100 100 100 100 100 100 -033 100 100 100 100

AGC 100 -037 038 063 100 -051 -017 078 100 100 -029 100

AGG 100 100 100 100 100 100 100 100 100 100 100 100

AGT 100 084 100 086 053 100 100 100 100 100 048 100

ATA 100 100 100 100 100 100 100 100 100 100 100 100

ATC 100 -070 -053 004 045 -068 -042 050 -018 073 -057 -031

ATG 100 -048 000 064 033 -043 -015 056 -024 100 -017 030

ATT 100 023 082 088 100 -009 -024 072 086 100 002 100

CAA 100 032 066 091 082 -011 081 058 100 100 -004 000

CAC 100 -073 -038 027 100 -072 -052 055 -033 100 -064 100

CAG 1.00 -0.58 -0.26 0.31 0.52 -0.58 -0.48 0.78 0.78 1.00 -0.49 0.48

CAT 100 053 046 076 100 009 -010 100 100 100 040 033

CCA 100 -061 057 084 037 059 034 069 100 100 -023 100

CCC 100 070 100 100 100 100 100 100 100 100 100 100

CCG 100 -058 -037 024 033 -070 -053 056 -042 100 -050 -036

CCT 100 053 049 100 100 100 080 063 100 100 100 100

CGA 100 058 100 100 100 100 100 100 100 100 100 100

CGC 100 054 010 035 100 030 044 087 078 100 036 020

CGG 100 100 100 100 100 100 100 100 100 100 100 100

CGT 100 -074 -040 014 055 -073 -069 002 029 100 -066 -061

CTA 100 100 100 100 100 100 100 100 100 100 100 100

CTC 100 014 081 064 063 047 061 100 100 100 082 100

CTG 100 -071 -043 025 -028 -075 -054 067 -048 084 -060 -002

CTT 100 078 100 100 100 100 100 100 100 100 063 100

GAA 100 -056 -011 066 049 -028 012 067 -022 100 -006 -002

GAC 100 -066 -035 038 087 -066 -057 034 051 100 -040 100

GAG 100 -030 027 078 048 -064 -052 051 100 100 -048 062

GAT 100 -030 033 085 068 -028 016 094 042 100 -038 065

GCA 100 -056 -041 047 076 -047 -036 069 041 055 -062 -006

GCC 100 050 060 070 100 100 041 076 100 100 092 045

GCG 100 007 -001 017 072 -052 -004 063 065 073 -027 100

GCT 100 -078 -007 049 037 -076 -070 018 022 100 -070 100 41 GGA 100 100 088 100 100 100 100 100 100 100 023 100

42 GGC 100 025 007 058 092 -039 026 087 043 071 -013 077

43 GGG 100 071 100 084 100 007 088 100 049 100 027 100

44 GGT 100 -075 -045 -004 080 -067 -071 -001 032 100 -064 046

45 GTA 100 -052 -056 051 031 -068 -065 033 -047 100 -063 -055

46 GTC 100 044 077 083 100 100 049 076 021 100 053 037

47 GTG 100 -010 006 076 071 082 093 100 054 100 056 063

48 GTT 100 -078 003 061 039 -080 -065 020 033 100 -055 -053

49 TAA 000 000 000 000 000 000 000 000 000 000 000 000

50 TAC 100 -074 -055 033 100 -066 -055 -002 023 100 -048 100

51 TAG 000 000 000 000 000 000 000 000 000 000 000 000

52 TAT 100 057 091 078 100 018 001 100 071 100 -026 030

53 TCA 100 100 072 100 100 100 069 100 100 100 068 100

54 TCC 100 -081 -061 004 100 -069 -050 060 100 100 -062 100

55 TCG 100 084 011 074 100 100 100 100 029 100 075 100

56 TCT 100 -078 -047 072 100 -086 -082 058 100 100 -083 009

57 TGA 000 000 000 000 000 000 000 000 000 000 000 000

58 TGC 1.00 -0.24 -0.07 1.00 1.00 -0.58 -0.45 0.55 0.05 1.00 -0.58 1.00

59 TGG 100 -028 000 018 100 -057 -034 100 100 100 -047 100

60 TGT 100 -073 010 100 -054 025 100 044 -016 100 057 100

61 TTA 100 100 100 085 100 100 100 100 100 100 100 100

62 TTC 100 -074 -030 073 100 -079 -071 041 023 100 -073 -028

63 TTG 100 082 023 100 100 100 084 067 058 100 070 100

64 TTT 100 019 032 086 100 100 090 100 100 100 100 100

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.6 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA 100 043 100 -036 100 076 -046 084 -017 -053 -032 026

2 AAC 100 -026 100 -070 042 -038 -066 080 -047 -062 -015 001

3 AAG 033 -032 100 -061 100 019 -041 073 095 082 100 084

4 AAT 100 100 100 100 100 100 074 100 082 059 079 085

5 ACA 100 100 100 034 100 100 086 100 041 041 074 100

6 ACC 100 033 100 -056 100 062 -045 061 -036 -040 022 031

7 ACG 100 090 100 079 100 100 -031 100 089 100 100 100

8 ACT 100 -059 100 -077 -032 100 -075 100 -061 -083 018 -027 AGA 100 100 100 100 100 100 100 100 100 100 100 100

AGC 1 00 007 100 -0 69 100 100 -043 045 -020 -0 19 075 0 33

AGG 1 00 100 100 1 00 100 100 100 100 100 1 00 100 1 00

AGT 1 00 100 100 1 00 100 100 090 100 079 0 79 100 0 88

ATA 1 00 100 100 1 00 100 100 100 100 100 1 00 100 1 00

ATC 1 00 -034 100 -0 63 100 -067 -059 013 -057 -0 72 -008 -0 07

ATG 1 00 035 100 -0 49 100 027 -041 085 -010 -0 45 024 0 49

ATT 1 00 055 100 -0 12 100 064 -013 100 053 0 57 086 0 80

CAA 1 00 086 100 -0 07 100 071 026 070 065 0 03 -014 0 83

CAC -0 27 -048 100 -0 66 100 -062 -069 046 -055 -0 70 006 0 33

CAG 1 00 001 100 -0 57 056 -007 -053 022 -036 -0 40 060 -0 04

CAT 1 00 068 100 0 66 100 100 058 100 045 -0 25 100 1 00

CCA 1 00 068 100 0 32 100 033 072 100 -035 -0 53 046 0 64

CCC 1 00 100 100 1 00 100 100 100 100 088 1 00 100 0 73

CCG 1 00 -058 100 -0 45 100 076 -069 076 -038 -0 51 081 0 17

CCT 1 00 023 100 1 00 100 100 066 018 013 -0 31 014 0 78

CGA 1 00 100 100 1 00 100 100 072 100 100 0 47 100 1 00

CGC 1 .00 0.28 1.00 -0 .34 1.00 0.79 -0.02 0.79 -0.05 -0 .13 0.63 0 .22

CGG 1 00 100 100 1 00 100 100 100 100 100 1 00 100 1 00

CGT 1 00 -034 100 -0 65 100 033 -073 009 -049 -0 68 -019 0 28

CTA 1 00 100 100 1 00 100 100 100 100 100 0 47 100 0 68

CTC 1 00 100 100 0 79 100 037 087 037 008 -0 66 031 0 45

CTG 1 00 -040 100 -0 70 100 -005 -069 047 -052 -0 47 032 -0 07

CTT 1 00 100 100 1 00 100 100 073 100 061 -0 41 -028 0 67

GAA 0 83 051 100 -0 38 100 093 -047 066 -025 -0 57 -040 0 08

GAC 1 00 -037 100 -0 72 100 -015 -065 032 -054 -0 66 -020 0 30

GAG 1 00 -025 100 -0 56 100 085 -047 070 097 1 00 093 1 00

GAT 1 00 048 100 0 50 100 090 -007 090 044 -0 28 071 0 73

GCA 1 00 013 100 -0 62 100 040 -058 100 -037 -0 42 010 0 70

GCC 1 00 063 100 0 67 100 100 041 100 054 -0 05 095 0 77

GCG 1 00 034 100 -0 37 100 052 -048 052 052 0 62 092 0 77

GCT 0 33 -050 100 -0 69 100 100 -069 020 -074 -0 86 -027 -0 38

GGA 1 00 100 100 0 65 100 100 100 100 100 1 00 100 0 90

GGC 1 00 029 100 -0 39 100 013 -029 049 -038 -0 62 045 0 29

GGG 1 00 100 100 1 00 100 100 093 100 094 1 00 088 0 86

GGT 1 00 010 100 -0 74 100 085 -072 024 -044 -0 54 051 0 43

GTA 1 00 -025 100 -0 76 100 066 -075 032 -061 -0 52 -006 0 44

GTC 1 00 100 100 0 60 100 100 075 100 076 0 33 092 0 92

GTG 1 00 083 100 0 12 100 072 -010 100 080 0 73 100 0 84 48 GTT 049 -037 100 -069 100 000 -066 080 -065 -077 -001 -041

49 TAA 000 000 000 000 000 000 000 000 000 000 000 000

50 TAC 026 -038 100 -070 100 -031 -065 026 -045 -061 -001 000

51 TAG 000 000 000 000 000 000 000 000 000 000 000 000

52 TAT 100 091 100 035 100 017 019 072 041 010 045 064

53 TCA 100 100 100 100 100 100 087 100 061 074 100 100

54 TCC 100 026 100 -076 100 050 -064 100 005 -060 -039 050

55 TCG 100 100 100 100 100 100 009 100 100 100 100 100

56 TCT 100 -022 100 -072 100 100 -081 047 -076 -086 -048 -040

57 TGA 000 000 000 000 000 000 000 000 000 000 000 000

58 TGC 100 026 100 -075 100 -019 -061 100 -036 -041 042 100

59 TGG 100 017 100 -043 100 040 -043 100 -026 -035 077 032

60 TGT 100 100 100 100 100 100 036 -036 035 -065 027 037

61 TTA 100 084 100 083 100 100 100 100 100 070 100 082

62 TTC 100 -045 100 -075 100 -062 -073 -035 -040 -064 -009 002

63 TTG 100 084 100 100 100 100 078 048 094 055 086 091

64 TTT 100 100 100 080 100 100 094 100 023 -005 067 082

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.6 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -028 055 -019 -059 100 -035 079 -041 -036 058 -003 -051

2 AAC -049 -044 030 -056 100 -043 100 -061 -069 033 -007 -059

3 AAG 082 100 084 040 100 068 100 062 064 075 093 079

4 AAT 061 092 066 011 100 062 100 059 085 100 094 048

5 ACA 075 061 100 034 100 100 100 047 059 100 100 075

6 ACC -024 066 048 -059 075 035 091 -065 -070 091 050 -073

7 ACG 076 091 086 084 100 095 100 094 080 100 092 088

8 ACT -080 -045 -033 -084 100 -068 100 -072 -061 077 060 -067

9 AGA 100 100 100 100 100 100 100 100 100 100 100 100

10 AGC 059 047 051 064 100 045 100 -006 079 054 038 -022

11 AGG 100 100 100 100 100 100 100 100 100 100 100 100

12 AGT 075 080 055 100 100 087 100 085 100 100 100 100

13 ATA 100 100 100 100 100 100 100 100 100 100 100 100

14 ATC -018 001 -020 -079 082 -028 087 -074 -034 -013 019 -078

15 ATG 008 070 005 -059 100 -008 090 -038 -028 051 052 -048 ATT 040 050 084 -025 100 044 100 052 082 062 100 009

CAA 085 065 074 0 22 100 039 100 051 073 1 00 078 0 52

CAC 025 -036 -044 -0 75 100 -041 100 -072 -075 -0 11 083 -0 80

CAG -028 076 -005 -0 74 100 -036 100 -050 -050 0 30 030 -0 62

CAT 062 071 078 0 26 100 065 100 049 100 1 00 088 0 82

CCA 029 082 044 -0 36 044 041 100 -019 -044 1 00 100 -0 05

CCC 064 100 100 0 53 100 100 100 100 100 1 00 100 0 68

CCG -058 080 045 -0 68 080 -047 043 -036 -073 0 55 058 -0 68

CCT -041 078 -034 -0 46 100 -037 100 058 057 1 00 100 0 75

CGA 100 100 100 0 30 100 100 100 100 025 1 00 100 1 00

CGC -020 068 085 -0 57 100 010 087 -017 -066 0 83 042 -0 63

CGG 100 100 100 1 00 100 100 100 100 100 1 00 100 1 00

CGT -037 045 -034 -0 79 100 -041 086 -069 -058 0 82 054 -0 53

CTA 100 100 100 1 00 100 100 100 100 100 1 00 100 0 37

CTC 064 072 057 1 00 100 -010 100 -053 027 1 00 100 0 35

CTG -054 071 -023 -0 79 100 -037 087 -062 -070 0 19 002 -0 68

CTT 100 057 078 -0 17 100 -026 070 060 100 1 00 100 0 78

GAA -0.34 0.40 -0.27 -0 .65 0.93 -0.39 0.79 -0.52 -0.20 0 .37 -0.06 -0 .63

GAC -054 043 -008 -0 73 100 -052 079 -066 -075 0 64 -002 -0 73

GAG 093 100 100 0 91 100 096 100 074 100 0 83 095 0 93

GAT 006 075 063 -0 35 091 054 100 017 051 0 78 067 0 46

GCA -031 073 023 -0 68 100 -029 074 -051 -070 0 61 038 -0 32

GCC 025 096 097 -0 41 100 096 090 -005 036 0 92 087 -0 21

GCG 019 094 073 0 09 100 036 092 -004 -049 0 71 070 -0 17

GCT -075 015 -043 -0 87 100 -073 065 -064 -065 0 49 025 -0 79

GGA 100 100 100 1 00 100 100 100 100 100 1 00 100 1 00

GGC -039 088 -001 -0 58 100 -032 100 -053 -061 0 67 003 -0 65

GGG 086 100 091 0 81 100 100 100 091 100 1 00 100 0 87

GGT -044 055 -029 -0 72 100 018 100 -068 -037 0 87 046 -0 57

GTA -041 023 -025 -0 46 100 053 100 -065 -054 1 00 055 -0 49

GTC 080 092 076 -0 24 075 040 100 -034 038 1 00 074 0 27

GTG 065 091 083 0 39 100 084 100 -011 019 0 74 066 -0 51

GTT -046 009 -012 -0 88 100 -047 100 -070 -036 0 27 025 -0 76

TAA 000 000 000 0 00 000 000 000 000 000 0 00 000 0 00

TAC -056 053 028 -0 67 100 -056 100 -064 -035 -0 08 047 -0 53

TAG 000 000 000 0 00 000 000 000 000 000 0 00 000 0 00

TAT 019 073 038 -0 40 100 074 100 031 061 0 32 068 -0 49

TCA 069 100 081 0 17 100 100 058 081 100 1 00 080 1 00

TCC -077 080 -017 -0 79 052 -044 100 -079 -083 -0 11 -014 -0 75 55 TCG 100 100 100 035 100 100 100 085 100 073 100 077

56 TCT -078 -019 -062 -083 100 -052 100 -084 -087 -014 032 -074

57 TGA 000 000 000 000 000 000 000 000 000 000 000 000

58 TGC -067 047 040 055 100 041 100 -060 -044 036 025 -007

59 TGG -046 080 007 -028 100 -026 100 -026 -028 067 042 -048

60 TGT 057 067 -021 -041 030 007 100 -025 -070 100 006 033

61 TTA 071 077 100 042 100 091 076 068 041 100 100 082

62 TTC -037 011 019 -063 018 -019 071 -072 -070 072 043 -071

63 TTG 100 088 091 080 100 100 100 089 070 100 100 082

64 TTT 057 054 044 -055 100 080 089 023 026 079 069 012

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.6 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 000 -031 000 021 100 -035 066 -065 000 -006 002 020

2 AAC 000 -071 000 040 100 -074 081 -071 000 -062 -045 018

3 AAG 000 014 000 035 100 021 024 -081 000 -029 -007 011

4 AAT 000 100 000 100 100 051 100 100 000 100 100 100

5 ACA 000 100 000 100 100 100 100 031 000 100 040 100

6 ACC 000 -060 000 038 100 -015 081 -069 000 -027 -053 -061

7 ACG 000 100 000 085 100 100 100 067 000 100 100 100

8 ACT 000 -077 000 053 036 -088 000 -088 000 -045 100 100

9 AGA 000 100 000 100 100 100 100 100 000 100 100 100

10 AGC 000 -040 000 049 100 -054 100 -047 000 -028 070 042

11 AGG 000 100 000 100 100 100 100 100 000 100 100 100

12 AGT 000 069 000 100 100 032 100 030 000 100 100 100

13 ATA 000 100 000 100 100 100 100 100 000 100 100 100

14 ATC 000 -069 000 028 100 -084 084 -064 000 -041 -058 -053

15 ATG 000 -043 000 056 100 -060 080 -042 000 040 000 -033

16 ATT 000 030 000 070 100 003 087 -053 000 053 100 070

17 CAA 000 040 000 089 100 054 100 100 000 100 064 100

18 CAC 000 -077 000 061 -027 -040 100 -083 000 -060 -057 -005

19 CAG 000 -053 000 023 100 -031 077 -080 000 -051 -025 014

20 CAT 000 100 000 071 100 100 100 100 000 037 100 100

21 CCA 000 034 000 075 100 -022 100 034 000 -074 047 100

22 CCC 000 100 000 100 100 100 100 100 000 100 100 100 CCG 000 -044 000 037 044 -052 100 -078 000 032 -041 -041

CCT 000 -077 000 070 005 -068 100 -058 000 100 100 100

CGA 000 100 000 100 100 100 100 100 000 100 100 100

CGC 000 001 000 050 100 -011 100 -014 000 036 -052 100

CGG 000 100 000 100 100 100 100 100 000 100 100 100

CGT 000 -064 000 -016 013 -075 077 -087 000 -070 056 015

CTA 000 100 000 100 100 100 100 100 000 100 100 100

CTC 000 -031 000 100 100 -050 100 -036 000 100 100 100

CTG 000 -067 000 024 074 -060 070 -080 000 -048 -044 -042

CTT 000 002 000 100 037 -035 100 -052 000 -025 100 100

GAA 000 -054 000 064 100 -056 077 -057 000 040 028 -034

GAC 000 -066 000 037 071 -080 054 -049 000 -062 -061 040

GAG 000 -007 000 065 100 -053 100 -060 000 -025 -038 044

GAT 000 -018 000 083 083 -041 100 -015 000 043 094 046

GCA 000 -042 000 068 069 -043 076 -070 000 050 -062 -047

GCC 000 044 000 008 100 042 100 -038 000 022 -002 002

GCG 000 041 000 100 100 011 072 -061 000 041 069 -010

GCT 0.00 -0.83 0.00 0.00 1.00 -0.81 0.37 -0.89 0.00 -0.62 0.65 1.00

GGA 000 073 000 100 046 100 100 100 000 100 100 100

GGC 000 -036 000 057 100 -033 100 040 000 032 -050 -007

GGG 000 100 000 100 100 100 100 036 000 100 100 100

GGT 000 -068 000 016 015 -079 087 -087 000 -062 044 -003

GTA 000 -040 000 064 100 -082 100 -084 000 -046 -071 -068

GTC 000 -002 000 087 100 072 100 071 000 100 065 100

GTG 000 011 000 077 100 035 100 033 000 -002 017 100

GTT 000 -071 000 -016 100 -081 100 -085 000 -061 070 054

TAA 000 000 000 000 000 000 000 000 000 000 000 000

TAC 000 -078 000 061 100 -076 067 -077 000 -071 -057 100

TAG 000 000 000 000 000 000 000 000 000 000 000 000

TAT 000 081 000 100 100 022 100 100 000 100 100 034

TCA 000 024 000 100 100 100 100 014 000 100 032 100

TCC 000 -068 000 053 100 -063 035 -052 000 -071 -080 -054

TCG 000 100 000 100 100 100 100 -026 000 100 100 100

TCT 000 -082 000 003 014 -084 -063 -088 000 -044 043 -055

TGA 000 000 000 000 000 000 000 000 000 000 000 000

TGC 000 -076 000 100 100 -058 023 -076 000 -054 -044 -026

TGG 000 -041 000 052 100 -050 100 -071 000 100 000 -056

TGT 000 100 000 100 100 -001 100 -004 000 100 100 100

TTA 000 061 000 100 100 100 100 100 000 100 100 100 62 TTC 000 -074 000 011 100 -079 072 -086 000 -069 -057 -015

63 TTG 000 100 000 100 100 100 100 015 000 100 017 100

64 TTT 000 082 000 087 100 056 100 100 000 100 100 100

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.6 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 087 -043 087 069

2 AAC 100 -072 083 057

3 AAG 078 -053 078 042

4 AAT 080 100 100 093

5 ACA 100 100 100 100

6 ACC 084 -059 100 028

7 ACG 075 043 074 079

8 ACT 100 -064 058 031

9 AGA 100 100 100 100

10 AGC 100 -048 056 088

11 AGG 100 100 100 100

12 AGT 100 040 059 100

13 ATA 100 100 100 100

14 ATC 100 -069 100 029

15 ATG 076 -052 076 081

16 ATT 100 005 085 088

17 CAA 100 100 100 088

18 CAC 100 -077 056 049

19 CAG 100 -066 075 058

20 CAT 100 074 067 100

21 CCA 100 100 100 100

22 CCC 100 100 100 100

23 CCG 080 -070 041 040

24 CCT 100 066 100 050

25 CGA 100 100 100 100

26 CGC 100 -048 100 036

27 CGG 100 100 100 100

28 CGT 100 -061 100 051

29 CTA 100 100 100 100 CTC 100 100 100 073

CTG 057 -072 046 044

CTT 100 027 100 100

GAA 095 -035 095 076

GAC 086 -074 058 040

GAG 088 -063 100 046

GAT 084 022 084 087

GCA 100 -070 083 029

GCC 100 -006 100 084

GCG 100 -044 100 076

GCT 078 -044 100 073

GGA 100 100 100 100

GGC 100 -060 090 033

GGG 100 084 100 100

GGT 076 -048 088 036

GTA 100 -063 045 000

GTC 100 -043 100 076

GTG 1.00 -0.55 0.77 0.72

GTT 100 -006 084 090

TAA 000 000 000 000

TAC 100 -075 100 042

TAG 000 000 000 000

TAT 100 065 100 091

TCA 100 100 100 100

TCC 059 -079 059 033

TCG 100 042 100 078

TCT 058 -073 057 030

TGA 000 000 000 000

TGC 100 016 100 -047

TGG 051 -045 100 061

TGT 100 -005 100 100

TTA 100 100 100 100

TTC 100 -076 100 016

TTG 100 070 058 100

TTT 100 100 100 092

TTA TTC TTG TTT

61 62 63 64 Table C.7: CPW matrix Bacillus amyloliquefaciens full genome (left codon indicated in column 2, right codon indicated in row 2). Host cell: B. amyloliqueaciens; Sequence data: full B. amyloliqueaciens genome.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA -0 05 -0 25 -0 09 0 00 -0 34 -0 02 -0 08 0 42 -0 33 -0 40 -0 31 -0 19

2 AAC 0 05 -0 11 0 11 -0 07 0 21 0 18 0 08 0 18 -0 48 -0 61 -0 54 -0 58

3 AAG 0 12 0 35 0 23 0 38 0 32 0 34 0 20 0 37 0 18 0 20 0 04 0 21

4 AAT -0 12 0 07 0 10 0 12 -0 23 0 05 -0 15 0 00 0 53 0 79 0 64 0 32

5 ACA -0 43 -0 44 -0 32 -0 32 -0 20 -0 29 0 02 -0 27 -0 63 -0 38 -0 68 -0 44

6 ACC 0 60 0 33 0 56 -0 01 0 50 0 32 0 64 -0 08 -0 05 0 34 0 45 0 31

7 ACG 0 05 0 24 -0 10 0 11 -0 16 -0 09 -0 28 -0 16 -0 46 0 00 -0 37 0 27

8 ACT 0 48 0 67 0 64 0 51 0 44 0 50 0 71 0 08 0 46 0 90 0 22 0 53

9 AGA -0 60 -0 52 -0 64 -0 44 -0 42 -0 32 -0 41 -0 29 -0 32 -0 48 -0 38 -0 35

10 AGC -0 01 0 19 0 08 0 01 0 01 -0 14 -0 10 -0 08 -0 38 -0 30 -0 60 -0 25

11 AGG -0 06 0 17 -0 24 -0 08 -0 09 0 29 -0 11 0 09 0 23 0 19 0 13 -0 28

12 AGT -0 08 0 61 0 16 0 12 0 26 0 48 0 32 0 24 0 60 0 89 0 56 0 62

13 ATA -0 54 -0 26 -0 35 -0 19 -0 27 0 05 0 19 -0 15 -0 45 0 23 -0 40 -0 16

14 ATC 0 24 -0 06 0 16 -0 15 0 16 -0 20 0 25 -0 04 -0 60 -0 45 -0 59 -0 44

15 ATG 0 04 0 06 -0 07 -0 05 0 08 0 05 -0 08 0 04 -0 46 -0 19 -0 37 -0 17

16 ATT -0 02 0 25 0 18 0 16 -0 20 0 01 -0 05 0 01 0 63 0 91 0 74 0 70

17 CAA -0 39 -0 46 -0 41 -0 29 0 15 -0 28 -0 02 0 19 -0 22 -0 43 -0 26 -0 23

18 CAC 0 34 0 06 0 17 -0 05 0 29 -0 02 0 27 0 31 0 02 -0 46 -0 21 -0 33

19 CAG 0 48 0 39 0 33 0 43 0 11 0 07 -0 08 0 05 0 67 0 53 0 54 0 54

20 CAT -0 20 0 02 -0 13 -0 01 -0 22 -0 06 -0 15 -0 02 0 79 0 82 0 76 0 61

21 CCA -0 26 -0 45 -0 25 -0 20 -0 29 -0 42 0 14 -0 66 -0 47 -0 44 -0 53 -0 47

22 CCC 0 72 0 58 0 53 0 35 0 65 0 27 0 53 0 36 0 61 0 67 0 75 0 50

23 CCG -0 14 -0 13 -0 29 -0 20 -0 14 -0 18 -0 13 -0 43 0 02 0 05 0 37 0 18

24 CCT 0 30 0 42 0 46 0 56 0 39 0 60 0 74 -0 04 0 75 0 77 0 71 0 58

25 CGA -0 18 -0 22 -0 11 -0 15 0 04 -0 14 0 01 -0 32 0 48 -0 55 -0 33 -0 56

26 CGC 0 56 0 00 0 00 0 26 0 48 -0 06 -0 18 0 45 0 72 -0 07 0 43 0 22

27 CGG 0 08 0 17 0 19 -0 09 0 24 0 38 -0 19 0 01 0 70 0 48 0 66 0 60

28 CGT 0 42 0 71 0 48 0 48 0 37 0 53 0 29 -0 03 0 97 0 82 0 84 0 74

29 CTA -0 19 0 20 -0 21 -0 03 0 04 0 07 0 48 -0 36 -0 48 0 14 -0 52 -0 41

30 CTC 0 63 0 54 0 39 0 29 0 51 0 13 0 40 0 23 -0 37 -0 14 -0 34 -0 30

31 CTG -0 15 -0 18 -0 30 -0 15 -0 24 -0 26 -0 24 -0 29 0 01 0 28 0 02 0 33

32 CTT 0 64 0 59 0 75 0 59 0 49 0 42 0 70 0 16 0 70 0 87 0 56 0 64

33 GAA -0 16 -0 24 -0 03 0 00 -0 27 -0 18 -0 07 0 34 -0 05 -0 35 0 17 -0 22 34 GAC 0 13 -0 07 -0 17 -0 09 0 32 0 00 0 04 0 18 -0 36 -0 58 -0 49 -0 51

35 GAG 0 29 0 29 0 21 0 30 0 39 0 44 0 04 0 45 0 39 0 21 0 46 0 12

36 GAT -0 09 0 09 0 16 0 06 -0 13 0 10 -0 17 0 01 0 73 0 83 0 72 0 66

37 GCA -0 48 -0 50 -0 48 -0 37 -0 34 -0 43 -0 06 -0 53 -0 25 -0 51 -0 41 -0 50

38 GCC 0 25 0 27 0 27 -0 15 0 32 0 14 0 50 0 06 0 11 0 38 0 49 0 17

39 GCG 0 14 -0 08 -0 21 0 21 -0 13 -0 02 -0 31 -0 08 0 30 0 06 0 33 0 45

40 GCT 0 40 0 55 0 61 0 55 0 32 0 45 0 63 0 33 0 89 0 91 0 88 0 84

41 GGA -0 46 -0 41 -0 25 -0 38 -0 33 -0 21 -0 37 -0 15 -0 35 -0 48 -0 26 -0 30

42 GGC 0 43 0 07 -0 05 0 15 0 19 -0 02 -0 09 0 09 -0 13 -0 31 -0 23 -0 18

43 GGG -0 04 0 37 0 20 0 00 0 22 0 65 0 24 0 27 0 23 0 37 0 44 0 34

44 GGT 0 23 0 64 0 50 0 40 0 22 0 60 0 13 0 19 0 85 0 92 0 75 0 44

45 GTA -0 45 -0 39 -0 35 -0 25 -0 19 -0 18 -0 22 -0 22 -0 34 0 04 -0 37 -0 18

46 GTC 0 21 0 06 0 38 -0 16 0 13 -0 18 0 11 -0 07 -0 44 -0 39 -0 31 -0 45

47 GTG -0 17 0 00 -0 28 -0 10 -0 10 -0 01 -0 32 0 19 0 20 0 31 0 22 0 49

48 GTT 0 40 0 64 0 52 0 40 0 34 0 40 0 48 0 23 0 67 0 94 0 71 0 65

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 12 -0 16 -0 06 -0 17 0 13 0 05 -0 14 0 14 -0 59 -0 55 -0 61 -0 57

51 TAG 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

52 TAT -0 14 0 14 0 23 0 14 -0 15 0 28 -0 03 0 08 0 50 0 82 0 59 0 70

53 TCA -0 38 -0 39 -0 19 -0 39 -0 28 -0 36 0 06 -0 58 -0 50 -0 30 -0 42 -0 26

54 TCC 0 29 0 35 0 46 -0 18 0 25 0 11 0 54 -0 33 -0 44 0 35 0 37 -0 08

55 TCG 0 35 -0 06 -0 14 0 22 0 18 -0 26 -0 31 -0 24 0 09 0 00 0 16 0 41

56 TCT -0 04 0 40 0 33 0 24 0 20 0 49 0 63 -0 01 0 76 0 91 0 75 0 74

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 21 -0 16 -0 17 0 09 0 27 -0 15 -0 10 0 38 0 10 -0 27 -0 39 -0 22

59 TGG 0 05 0 18 -0 10 -0 15 0 16 0 21 -0 21 0 15 -0 32 -0 09 0 01 -0 27

60 TGT -0 18 0 46 0 00 -0 22 -0 11 0 46 -0 23 0 00 0 77 0 91 0 74 0 59

61 TTA -0 47 -0 45 -0 45 -0 43 -0 25 -0 32 -0 19 -0 34 -0 52 -0 18 -0 30 -0 33

62 TTC 0 19 -0 01 0 06 0 04 0 25 -0 20 0 20 -0 25 -0 62 -0 45 -0 63 -0 41

63 TTG -0 25 -0 09 -0 16 -0 28 -0 22 -0 19 -0 13 -0 35 -0 27 0 35 -0 20 0 13

64 TTT -0 18 0 06 0 13 -0 08 -0 15 -0 06 0 06 -0 04 0 58 0 93 0 67 0 66

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.7 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 41 -0 20 -0 08 0 26 -0 09 0 32 0 26 0 20 0 18 0 45 0 26 0 34 AAC 024 009 009 015 017 025 032 010 019 040 024 013

AAG 014 018 0 20 020 000 -028 -030 -040 -030 -028 -043 -037

AAT -031 -008 -0 08 -008 -034 -006 -007 -018 -011 -012 -022 -018

ACA -012 034 0 06 035 -015 014 005 017 023 011 008 007

ACC -009 -004 0 43 -039 015 024 030 -010 022 038 058 029

ACG -001 -013 -0 30 -021 025 -013 -012 017 003 -023 -027 -016

ACT 003 074 0 57 046 -053 -029 002 -041 -003 005 014 -042

AGA -040 -021 -0 37 -015 -010 047 -027 035 038 049 040 029

AGC 012 -001 -0 12 -011 -003 010 -012 -016 050 016 011 044

AGG -035 037 0 01 -011 000 -024 -037 -025 -013 -031 -024 021

AGT -021 023 -0 14 -006 -025 038 -006 -026 -029 -001 -003 -007

ATA -024 059 0 42 061 -037 -004 -013 -012 -020 012 003 -020

ATC 015 -011 -0 03 -016 049 049 050 036 038 041 039 039

ATG 013 007 0 00 -010 043 -015 -022 014 049 013 -009 -004

ATT -009 002 -0 08 -001 -036 -023 -025 -033 -019 -035 -030 -023

CAA -031 -010 -0 21 000 055 069 070 072 053 060 082 054

CAC 020 015 0 24 019 042 034 043 015 018 039 028 024

CAG 0.22 0.00 0 .17 0.10 0.07 -0.37 -0.42 -0.27 -0.18 -0.30 -0.32 -0.37

CAT -017 -005 -0 15 -016 -020 -019 -027 -011 -024 -017 -017 -016

CCA 000 027 0 04 039 019 004 036 038 -039 020 054 -004

CCC 030 050 0 53 030 047 040 062 023 -028 053 069 027

CCG 017 -025 -0 26 -032 -018 -023 -012 007 -025 -039 -013 -007

CCT 024 065 0 60 043 -022 -001 002 -012 021 -006 033 -015

CGA -050 -020 -0 04 031 012 -038 009 001 -045 031 041 002

CGC 031 001 0 30 047 056 033 039 040 007 022 033 055

CGG -033 -031 -0 30 -027 -023 -043 -039 -027 -048 -048 -037 -040

CGT 012 031 0 42 038 -002 -023 -009 005 -040 -024 -007 -015

CTA -038 032 0 38 047 -029 -001 066 -021 -057 -009 037 -044

CTC 028 020 0 39 011 060 067 068 038 049 053 056 031

CTG 027 -029 -0 30 -017 -025 -027 -014 -001 028 -034 -038 -012

CTT 045 055 0 51 042 -027 -036 -024 -034 -003 -023 -015 -040

GAA -012 -018 -0 09 016 012 034 023 034 026 044 033 038

GAC 017 -004 0 04 008 031 035 038 023 027 045 028 029

GAG 013 005 0 19 012 010 -040 -039 -039 -042 -040 -040 -039

GAT -010 014 -0 03 -016 -023 -025 -022 -013 -010 000 -028 -012

GCA -003 011 -0 06 021 010 029 019 045 -003 015 037 034

GCC 013 -002 0 11 -025 027 042 052 017 043 039 070 060

GCG 019 -026 -0 24 -010 -015 -039 -028 001 -030 -049 -038 -008

GCT 040 063 0 60 040 -033 -021 011 -013 -028 002 018 -025 41 GGA -0 05 -0 08 -0 22 0 00 -0 30 O 16 -0 23 -0 01 O 17 0 51 O 18 O 10

42 GGC 0 21 -O 12 0 07 -O 11 0 44 O 19 0 27 0 07 0 08 0 26 0 23 0 40

43 GGG -0 05 0 34 0 04 0 05 -0 09 -O 12 -0 35 -0 35 -0 27 -0 27 -0 43 -0 44

44 GGT 0 07 0 26 O 19 -0 04 0 08 0 09 0 09 -0 01 -0 60 -O 18 -0 07 O 12

45 GTA 0 26 0 43 0 26 0 67 0 23 O 14 -O 11 O 17 -O 14 0 56 0 38 0 08

46 GTC O i l -0 26 -0 12 -0 37 0 54 0 57 0 66 0 34 0 56 0 61 0 68 0 54

47 GTG 0 24 -O 12 -0 20 O 12 O 18 -0 03 -0 34 -0 04 0 23 -0 25 -0 47 -0 29

48 GTT 0 26 0 29 0 35 0 21 -0 46 -0 35 -0 36 -0 47 -0 21 -0 46 -O 19 -0 43

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 25 O 17 O 11 O 14 0 29 0 29 0 49 0 25 0 48 0 58 0 28 0 37

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 36 0 00 -0 07 0 00 -0 31 -0 06 -O 17 -0 22 -0 02 -O 14 -0 29 -0 05

53 TCA 0 03 0 27 -0 05 O 11 -O 10 0 35 0 23 0 33 -0 04 O 15 0 24 -O 19

54 TCC 0 17 -0 15 -0 02 -0 41 0 28 0 27 0 58 -0 06 0 47 0 43 0 63 0 38

55 TCG O 15 -O 12 -0 03 0 02 -0 04 -0 21 -O 16 0 05 -0 34 -0 46 -0 41 -0 37

56 TCT 0 08 0 38 0 44 O 12 -0 45 -O 14 O 15 -0 30 -0 38 -0 35 0 03 -0 38

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0.07 0.05 0.11 0.38 0.00 -0.09 0.12 0.11 -0.03 0.24 0.02 0.32

59 TGG -O 15 O 16 0 00 -O 10 0 40 -0 03 -0 21 0 02 0 53 O 15 -O 16 O 18

60 TGT -0 52 -0 23 -O 17 -O 18 -O 18 O 10 -0 06 -O 13 -0 02 -O 13 -O 14 -0 29

61 TTA -0 31 -O 18 -0 32 -0 22 O 14 0 50 0 32 O 17 0 28 0 63 0 81 0 46

62 TTC 0 34 O 19 0 23 0 21 O 19 0 24 0 34 0 27 O 16 0 38 0 04 -O 15

63 TTG O 13 -O 10 0 04 -0 33 0 00 O 13 -0 25 0 24 0 08 0 01 -0 06 0 04

64 TTT -O 15 -O 16 -O 15 -O 11 -0 31 0 01 -0 05 -0 26 -O 10 -O 17 -0 03 0 07

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.7 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA 0 32 0 37 -0 15 0 38 -0 15 0 56 0 31 0 57 -0 16 -0 17 0 08 0 11

2 AAC 0 16 -0 23 -0 23 -0 38 -0 21 0 25 -0 05 0 07 0 32 0 21 0 35 0 24

3 AAG 0 21 -0 16 -0 47 -0 07 -0 08 -0 47 -0 61 -0 59 0 14 0 17 0 36 0 00

4 AAT 0 10 0 54 0 34 0 23 -0 25 -0 01 -0 10 0 12 -0 32 -0 11 -0 02 -0 23

5 ACA 0 45 0 48 0 42 0 10 -0 19 0 40 0 37 0 27 -0 12 -0 03 0 07 0 08

6 ACC 0 27 0 16 0 07 -0 26 0 58 0 44 0 56 0 16 0 17 -0 20 -0 18 -0 11

7 ACG 0 32 -0 16 0 07 0 25 0 19 -0 42 -0 33 -0 28 0 14 0 38 0 28 0 11

8 ACT 0 22 0 46 0 57 -0 19 -0 46 0 38 0 58 -0 23 -0 40 -0 29 -0 32 -0 43 AGA 062 078 039 064 004 044 027 044 -027 012 -019 013

AGC -002 -013 -035 -0 24 038 029 -009 011 035 024 011 024

AGG 039 043 -011 0 42 003 -040 -064 -052 -022 028 -009 005

AGT -020 072 056 0 64 -024 -013 -028 -025 -056 -031 -036 -053

ATA -013 030 008 -0 02 -041 022 028 011 -023 -002 -002 -004

ATC 034 -034 -014 -0 33 035 039 041 044 037 006 015 038

ATG 061 010 004 0 18 028 -013 -030 -017 002 003 -004 -002

ATT 046 061 051 0 40 000 -014 007 000 -029 -005 004 -028

CAA 024 057 056 0 56 -018 075 064 076 016 009 010 018

CAC -020 -032 -014 -0 19 039 020 023 018 024 -011 -023 000

CAG 001 -034 -031 -0 35 002 -038 -034 -046 -014 005 005 -017

CAT -014 022 011 -0 07 -019 001 -008 014 -007 011 003 -001

CCA -014 -012 -007 -0 21 -049 044 069 054 030 026 023 035

CCC -026 004 008 -0 16 027 048 066 038 005 -036 -036 -017

CCG -005 -022 014 0 01 -020 -043 -018 -038 020 027 032 027

CCT -027 020 034 -0 05 -034 038 051 010 -044 -031 -038 -045

CGA -061 -033 -022 -0 24 -053 067 059 055 051 038 055 025

CGC -0.20 -0.11 0.25 0 .24 0.41 0.09 0.16 0.42 0.31 -0.35 -0.46 -0.03

CGG -036 -034 -022 -0 28 -062 -054 -045 -039 023 046 028 023

CGT -055 -014 008 -0 28 -042 -029 -019 -019 -012 -027 -025 -014

CTA -064 -016 -016 -0 37 -070 074 068 032 037 059 049 026

CTC 050 035 026 -0 10 032 056 071 049 028 -046 -030 -016

CTG 045 -039 -010 -0 04 018 -040 -036 -028 031 049 035 042

CTT -011 -003 016 -0 25 -008 -008 020 -002 -042 -017 -036 -045

GAA 029 048 002 0 37 033 060 027 051 -013 -006 -006 -002

GAC -001 -007 -020 -0 27 036 038 032 023 030 -007 -013 003

GAG -011 -043 -052 -0 36 -023 -032 -054 -058 022 020 027 -003

GAT -026 015 028 0 09 -025 -007 -012 004 -019 004 008 -001

GCA 032 047 045 0 52 -006 041 046 047 011 009 015 017

GCC 007 007 026 0 01 044 056 061 044 011 -026 -041 -020

GCG -024 -034 -005 0 04 -021 -057 -037 -036 022 037 035 032

GCT -056 -014 -005 -0 28 -032 022 045 -018 -039 -019 -011 -039

GGA 019 044 008 0 27 009 041 012 004 -024 -004 002 007

GGC 006 -010 -012 -0 05 062 031 024 034 032 -015 -023 003

GGG -028 -020 -032 -0 23 -004 -039 -045 -053 027 052 042 041

GGT -012 039 031 0 15 002 004 -007 -039 -032 -029 -021 -034

GTA -006 035 015 0 17 017 046 038 055 013 015 013 032

GTC 045 019 010 0 16 062 066 058 057 029 -030 -035 -011

GTG 044 -036 -015 0 13 039 -052 -057 -043 018 052 033 035 48 GTT -0 37 0 05 0 07 -0 20 -0 13 -0 11 0 18 -0 14 -0 35 -0 17 -0 12 -0 27

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 20 -0 20 -0 43 -0 44 0 32 0 46 0 24 0 47 0 32 0 05 0 14 0 16

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 39 0 54 0 24 0 41 -0 23 0 05 0 07 0 29 -0 24 -0 06 0 06 -0 09

53 TCA 0 45 0 43 0 43 0 42 -0 09 0 33 0 37 0 20 -0 10 -0 01 0 00 0 15

54 TCC 0 17 0 02 0 07 -0 19 0 50 0 51 0 58 0 32 0 34 0 06 0 14 0 04

55 TCG -0 24 -0 45 -0 13 0 11 -0 28 -0 50 -0 29 -0 26 0 40 0 36 0 36 0 41

56 TCT 0 12 0 50 0 47 0 22 -0 17 -0 04 0 38 -0 23 -0 38 -0 32 -0 15 -0 34

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 24 -0 27 -0 19 -0 02 0 67 0 09 0 10 0 21 0 47 -0 07 -0 04 0 27

59 TGG 0 41 0 06 -0 04 -0 02 0 01 -0 23 -0 28 0 02 0 06 0 04 -0 11 -0 03

60 TGT -0 10 0 49 0 53 0 34 -0 04 -0 21 -0 33 -0 14 -0 42 -0 24 -0 15 -0 12

61 TTA 0 63 0 77 0 44 0 60 0 29 0 66 0 63 0 61 -0 02 0 31 0 17 0 12

62 TTC 0 09 -0 30 -0 24 -0 44 0 37 0 37 0 36 0 44 0 46 0 11 -0 05 0 37

63 TTG 0 26 -0 14 -0 13 -0 15 -0 19 -0 05 -0 18 -0 26 0 10 0 43 0 25 0 09

64 TTT 0 38 0 47 0 42 0 34 -0 27 -0 04 0 24 0 16 -0 28 -0 12 0 14 -0 18

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.7 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -0 23 0 06 -0 16 0 28 -0 29 -0 04 -0 22 0 28 -0 26 0 18 -0 19 0 44

2 AAC -0 06 -0 08 -0 12 0 17 -0 45 -0 44 -0 12 -0 35 0 03 0 05 0 09 0 32

3 AAG 0 10 0 45 -0 09 0 19 0 21 0 28 0 27 0 47 -0 08 0 14 -0 32 0 07

4 AAT -0 07 -0 06 0 13 0 20 0 52 0 71 0 60 0 46 -0 34 -0 02 -0 12 0 07

5 ACA 0 05 0 23 0 50 0 15 -0 06 0 20 0 28 -0 09 0 37 0 49 0 52 0 43

6 ACC -0 24 -0 12 -0 17 -0 28 -0 52 -0 30 -0 12 -0 43 -0 30 -0 41 -0 18 -0 55

7 ACG -0 25 0 08 -0 01 -0 22 -0 10 0 21 0 26 0 07 0 14 0 20 -0 02 -0 08

8 ACT -0 12 0 03 0 27 -0 24 -0 10 0 65 0 63 -0 05 -0 41 0 04 0 19 -0 40

9 AGA 0 39 0 47 0 35 0 53 -0 21 0 24 -0 05 0 24 0 32 0 36 0 03 0 47

10 AGC 0 05 -0 16 0 00 0 16 -0 39 -0 34 -0 06 -0 26 0 18 0 13 0 16 0 36

11 AGG 0 33 0 59 0 34 0 29 -0 08 0 51 -0 28 0 44 0 24 0 40 -0 20 0 08

12 AGT 0 04 0 49 0 34 0 11 0 73 0 88 0 77 0 45 -0 41 -0 01 -0 14 -0 18

13 ATA 0 27 0 26 0 45 0 35 0 32 0 57 0 42 0 43 0 49 0 77 0 66 0 52

14 ATC -0 18 -0 38 -0 10 -0 10 -0 41 -0 54 -0 30 -0 49 -0 18 -0 37 -0 16 -0 17

15 ATG 0 16 0 23 -0 13 -0 15 -0 13 0 10 -0 09 0 08 0 24 0 06 -0 21 0 09 ATT 023 -010 035 020 077 089 079 058 009 006 029 024

CAA 0 04 022 0 29 004 -020 -016 -032 -036 -023 -002 -0 23 0 22

CAC 0 06 -028 -0 25 -023 -025 -054 -040 -046 -019 -016 -0 08 -0 07

CAG 0 01 011 -0 26 -007 003 023 010 052 015 018 -0 18 0 15

CAT 0 30 014 0 22 021 053 070 066 050 017 002 0 10 0 20

CCA 0 17 -008 0 48 -006 051 030 013 -035 -027 032 0 55 0 15

CCC -0 31 -054 -0 38 -048 -045 -066 -035 -058 -023 -052 -0 31 -0 57

CCG 0 09 019 0 29 -006 004 008 022 020 039 036 0 32 0 06

CCT -0 01 003 0 30 -032 063 072 060 038 -033 -024 0 18 -0 42

CGA -0 20 015 0 12 -006 014 014 051 003 037 075 0 60 0 40

CGC -0 14 -033 -0 36 -029 004 -055 -032 -042 -003 -033 -0 35 -0 12

CGG 0 36 045 0 27 018 050 059 023 053 039 038 0 10 0 26

CGT 0 24 006 0 13 -020 067 071 070 041 -024 -031 0 01 -0 30

CTA 0 41 052 0 84 037 054 052 044 003 027 072 0 30 0 36

CTC 0 00 -053 -0 52 -012 -050 -073 -047 -067 -027 -062 -0 44 -0 38

CTG 0 31 038 0 34 019 060 060 053 066 065 054 0 56 0 50

CTT -0 11 -039 -0 01 -011 042 047 061 027 -022 -041 -0 25 -0 28

GAA -0 .16 0.02 -0 .19 0.12 -0.28 -0.18 -0.10 0.07 -0.14 0.05 -0 .31 0 .24

GAC -0 01 -014 -0 22 004 -043 -052 -034 -039 009 008 -0 13 0 12

GAG 0 29 035 -0 01 025 043 038 027 047 029 037 -0 12 0 10

GAT 0 16 007 0 09 024 064 081 065 045 -015 000 -0 07 0 13

GCA 0 08 015 0 43 016 -001 004 011 -015 034 035 0 51 0 30

GCC -0 19 -028 -0 18 -025 -041 -041 -025 -046 -025 -037 -0 13 -0 49

GCG 0 10 018 0 01 005 008 010 021 024 034 036 0 06 0 17

GCT -0 08 -002 0 23 -018 070 079 069 044 -018 -003 0 29 -0 41

GGA 0 01 021 0 14 028 037 056 065 066 -006 053 0 39 0 49

GGC 0 01 003 -0 31 -019 -018 -025 005 -013 -007 -021 -0 23 -0 12

GGG -0 09 063 0 29 014 054 051 -087 081 033 062 0 42 0 16

GGT -0 14 010 0 03 -030 073 083 079 064 -045 -030 -0 26 -0 48

GTA 0 35 013 0 35 025 030 045 034 -001 023 052 0 54 0 61

GTC 0 07 -032 -0 34 -009 -039 -059 -035 -062 -032 -044 -0 28 -0 30

GTG 0 22 037 0 19 016 061 067 051 062 070 057 0 43 0 51

GTT 0 02 -015 0 14 003 075 080 073 048 -018 -024 0 03 -0 16

TAA 0 00 000 0 00 000 000 000 000 000 000 000 0 00 0 00

TAC -0 14 -004 -0 16 011 -058 -050 -036 -042 023 007 -0 07 0 40

TAG 0 00 000 0 00 000 000 000 000 000 000 000 0 00 0 00

TAT -0 08 006 0 06 023 060 080 072 057 -022 -003 -0 19 0 13

TCA -0 21 001 0 36 -005 -017 -004 016 -008 035 041 0 50 0 16

TCC -0 28 -027 0 12 -044 -046 -041 001 -049 -040 -037 0 12 -0 55 55 TCG -0 28 0 10 -0 12 -0 03 0 27 0 12 0 22 0 40 0 47 0 07 0 05 0 08

56 TCT -0 14 0 05 0 50 -0 25 0 66 0 83 0 75 0 53 -0 37 -0 23 0 33 -0 42

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 21 -0 20 -0 27 0 03 -0 28 -0 34 -0 22 -0 33 0 23 -0 07 -0 01 0 37

59 TGG 0 05 0 29 -0 20 0 07 -0 18 0 04 -0 08 0 36 0 27 0 26 -0 37 0 16

60 TGT 0 12 0 42 0 31 0 40 0 78 0 87 0 84 0 67 -0 13 -0 10 -0 17 -0 17

61 TTA 0 37 0 41 0 56 0 29 -0 07 0 26 0 05 0 14 0 28 0 49 0 55 0 41

62 TTC 0 17 -0 26 -0 14 -0 05 -0 45 -0 55 -0 32 -0 54 0 31 -0 23 0 20 0 10

63 TTG -0 15 0 22 0 09 -0 05 0 16 0 49 0 27 0 27 0 28 0 43 0 25 0 13

64 TTT -0 04 -0 01 0 23 0 14 0 67 0 77 0 77 0 57 -0 04 -0 16 0 16 0 05

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.7 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 10 0 00 -0 03 -0 26 0 15 0 23 0 38 0 00 0 00 -0 07 -0 13

2 AAC 0 00 0 10 0 00 0 03 0 38 0 41 0 39 0 27 0 00 -0 21 -0 17 -0 05

3 AAG 0 00 0 12 0 00 0 17 0 26 0 44 0 17 0 32 0 00 0 16 0 16 0 02

4 AAT 0 00 0 03 0 00 -0 11 -0 11 -0 05 0 21 0 05 0 00 0 33 0 19 -0 06

5 ACA 0 00 -0 20 0 00 -0 13 -0 17 -0 18 -0 06 -0 19 0 00 -0 15 -0 38 -0 12

6 ACC 0 00 0 25 0 00 0 05 0 37 0 26 0 19 0 08 0 00 -0 15 0 36 -0 29

7 ACG 0 00 0 22 0 00 0 13 0 26 0 30 0 02 0 32 0 00 0 36 0 33 0 48

8 ACT 0 00 -0 28 0 00 -0 26 -0 50 -0 40 -0 26 -0 58 0 00 -0 13 -0 27 -0 58

9 AGA 0 00 -0 13 0 00 -0 19 -0 03 0 11 -0 06 0 49 0 00 0 34 -0 40 0 08

10 AGC 0 00 0 02 0 00 -0 10 0 35 0 35 0 23 0 40 0 00 -0 03 -0 36 -0 09

11 AGG 0 00 0 49 0 00 0 39 0 01 0 64 0 10 0 19 0 00 0 48 -0 30 0 15

12 AGT 0 00 0 25 0 00 -0 12 -0 35 0 10 -0 10 -0 18 0 00 0 22 0 71 0 38

13 ATA 0 00 -0 29 0 00 -0 06 -0 21 -0 34 -0 17 -0 13 0 00 -0 16 -0 47 -0 47

14 ATC 0 00 0 39 0 00 0 36 0 46 0 34 0 36 0 56 0 00 -0 07 0 08 0 15

15 ATG 0 00 -0 03 0 00 0 03 0 16 0 09 -0 01 0 18 0 00 0 00 0 00 0 00

16 ATT 0 00 -0 18 0 00 -0 30 -0 29 -0 35 0 14 -0 44 0 00 0 35 0 17 -0 24

17 CAA 0 00 -0 37 0 00 -0 35 -0 39 -0 41 -0 35 -0 28 0 00 -0 31 -0 42 -0 26

18 CAC 0 00 0 27 0 00 0 33 0 41 0 21 0 28 0 35 0 00 0 06 0 08 0 06

19 CAG 0 00 0 25 0 00 0 45 0 31 0 40 0 19 0 37 0 00 0 20 0 48 0 41

20 CAT 0 00 -0 21 0 00 -0 17 -0 30 -0 32 -0 23 -0 07 0 00 0 05 -0 06 -0 18

21 CCA 0 00 -0 32 0 00 -0 28 -0 27 -0 54 0 01 -0 54 0 00 -0 57 -0 41 -0 45

22 CCC 0 00 0 56 0 00 0 41 0 49 0 42 0 49 0 46 0 00 0 18 0 49 0 19 CCG 000 017 000 015 008 006 -011 005 000 019 006 049

CCT 000 -032 000 -044 -041 -040 002 -054 000 -022 -018 -0 41

CGA 000 -016 000 022 -018 -058 -049 -050 000 -068 038 -0 37

CGC 000 -017 000 011 047 033 -019 052 000 -008 -031 0 26

CGG 000 035 000 011 040 062 022 044 000 036 064 0 51

CGT 000 -015 000 -026 -040 -030 -046 -044 000 008 054 0 53

CTA 000 -041 000 -044 -041 -054 -048 -062 000 -072 -056 -0 68

CTC 000 049 000 045 058 048 055 060 000 024 040 0 35

CTG 000 -010 000 014 -007 -001 -029 000 000 004 007 0 52

CTT 000 -009 000 -021 -016 -035 007 -053 000 002 022 -0 37

GAA 000 -020 000 000 -009 -009 -017 027 000 001 -011 -0 23

GAC 000 035 000 029 052 053 054 045 000 -010 -013 0 04

GAG 000 021 000 021 043 050 031 039 000 018 023 0 21

GAT 000 -021 000 -020 -022 -028 -022 -015 000 006 013 0 03

GCA 000 -035 000 -007 -035 -041 -040 -038 000 -032 -048 -0 14

GCC 000 038 000 015 043 036 033 046 000 -024 028 -0 13

GCG 000 021 000 040 048 037 -019 035 000 027 022 0 55

GCT 0.00 -0.45 0.00 -0.47 -0.50 -0.54 -0.33 -0.53 0.00 -0.05 -0.06 -0 .11

GGA 000 004 000 -009 -026 079 004 006 000 -006 016 0 16

GGC 000 -011 000 000 024 035 -010 036 000 -028 -035 -0 33

GGG 000 038 000 029 041 066 059 053 000 056 055 0 42

GGT 000 001 000 -026 -060 -028 -043 -050 000 049 055 0 63

GTA 000 -040 000 -028 -042 -047 -040 -042 000 -035 -043 -0 35

GTC 000 044 000 023 055 045 049 048 000 -008 017 0 03

GTG 000 003 000 012 027 018 -023 034 000 021 010 0 51

GTT 000 -014 000 -024 -024 -047 -002 -047 000 026 012 -0 27

TAA 000 000 000 000 000 000 000 000 000 000 000 0 00

TAC 000 023 000 034 035 038 035 028 000 -014 -008 -0 06

TAG 000 000 000 000 000 000 000 000 000 000 000 0 00

TAT 000 -019 000 -017 -025 -024 -001 -008 000 015 006 -0 02

TCA 000 018 000 025 -015 -022 021 -021 000 011 -013 0 09

TCC 000 036 000 -010 031 -010 045 -001 000 -029 025 -0 21

TCG 000 014 000 045 032 024 -039 035 000 -008 011 0 58

TCT 000 -028 000 -047 -041 -050 -002 -055 000 014 027 -0 19

TGA 000 000 000 000 000 000 000 000 000 000 000 0 00

TGC 000 -005 000 030 046 029 -025 026 000 -008 -030 -0 31

TGG 000 001 000 -001 016 033 -021 010 000 -003 000 0 06

TGT 000 002 000 -034 -032 -017 -029 -035 000 050 082 0 26

TTA 000 -026 000 -027 -038 -023 000 -021 000 -004 -044 -0 38 62 TTC 0 00 0 31 0 00 0 42 0 20 0 07 0 06 0 29 0 00 -0 18 -0 05 -0 13

63 TTG 0 00 0 26 0 00 0 06 0 10 -0 14 0 11 0 02 0 00 0 17 0 08 0 41

64 TTT 0 00 -0 18 0 00 -0 24 -0 26 -0 23 0 18 -0 34 0 00 0 27 0 04 -0 08

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.7 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 10 -0 15 0 17 0 24

2 AAC 0 19 -0 08 0 38 0 11

3 AAG 0 63 -0 11 0 69 -0 14

4 AAT -0 37 -0 07 -0 02 0 01

5 ACA -0 23 -0 16 -0 52 -0 12

6 ACC 0 46 0 17 0 16 0 07

7 ACG 0 44 0 03 0 66 0 26

8 ACT -0 45 -0 10 -0 45 -0 38

9 AGA 0 17 0 30 -0 20 0 34

10 AGC 0 36 0 15 0 25 0 19

11 AGG 0 18 0 19 0 52 0 01

12 AGT -0 40 0 06 -0 23 -0 28

13 ATA -0 48 -0 32 -0 61 -0 22

14 ATC 0 37 0 30 0 55 0 40

15 ATG 0 66 0 10 0 81 -0 07

16 ATT -0 62 -0 26 -0 52 -0 18

17 CAA -0 14 -0 27 -0 25 -0 32

18 CAC 0 36 0 12 0 20 0 40

19 CAG 0 76 0 19 0 49 0 34

20 CAT -0 36 -0 14 -0 43 -0 19

21 CCA -0 29 -0 19 -0 42 -0 19

22 CCC 0 65 0 56 0 43 0 48

23 CCG 0 43 0 07 0 62 -0 13

24 CCT -0 39 0 12 -0 29 -0 23

25 CGA 0 12 -0 28 -0 18 0 04

26 CGC 0 68 -0 14 0 46 0 39

27 CGG 0 64 0 17 0 64 0 01

28 CGT -0 10 -0 42 -0 23 -0 38

29 CTA -0 63 -0 25 -0 66 -0 33 CTC 0 58 0 53 0 30 0 46

CTG 0 16 -0 16 0 45 -0 20

CTT -0 41 0 24 -0 55 0 27

GAA 0 11 -0 02 -O 19 -0 04

GAC 0 27 0 29 O 11 0 39

GAG 0 65 O i l 0 61 0 03

GAT -0 42 -0 24 -0 34 -0 21

GCA -0 26 -0 31 -0 38 -0 24

GCC 0 50 0 35 0 44 0 28

GCG 0 59 0 02 0 57 0 23

GCT -0 39 -O 14 -0 47 -0 40

GGA -0 02 O 17 -0 34 -0 22

GGC 0 45 0 01 0 33 0 22

GGG 0 45 0 53 0 54 O 13

GGT -0 49 -0 27 -0 48 -0 45

GTA -0 40 -0 37 -0 50 -0 38

GTC 0 62 0 54 0 70 0 39

GTG 0.39 -0.13 0.55 -0.02

GTT -0 41 -O 12 -0 49 -O 18

TAA 0 00 0 00 0 00 0 00

TAC -0 05 O 14 O 15 0 31

TAG 0 00 0 00 0 00 0 00

TAT -0 52 -0 22 -0 50 -0 08

TCA -0 36 -0 01 -0 37 -O 13

TCC 0 16 0 22 0 27 -0 06

TCG 0 35 0 09 0 44 O 16

TCT -0 54 -0 08 -0 33 -0 26

TGA 0 00 0 00 0 00 0 00

TGC 0 37 O 12 0 43 0 37

TGG 0 54 O 11 0 76 -0 07

TGT -0 43 -O 19 -0 31 -0 41

TTA -0 36 -O 12 -0 40 -0 34

TTC 0 04 0 02 0 43 O 11

TTG 0 14 0 22 0 51 -0 27

TTT -0 61 -0 21 -0 47 O 10

TTA TTC TTG TTT

61 62 63 64 Table C.8: CPW matrix Bacillus amyloliqueaciens Kl 2 highly expressed sequences (left codon indicated in column 2, right codon indicated in row 2). Host cell: B. amyloliqueaciens; Sequence data: full B. amyloliqueaciens genome; Highly expressed group: 236 seqs.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 001 -027 -003 008 -025 -011 -016 063 -032 -014 009 042

2 AAC 020 -038 036 017 035 -026 001 050 -036 -055 059 -073

3 AAG 001 040 -001 062 031 037 003 065 050 -001 057 035

4 AAT -029 042 -002 026 -026 024 -026 016 100 100 048 048

5 ACA -041 -051 -036 -040 -015 -008 018 -017 -060 -054 -076 -021

6 ACC 052 006 023 032 100 -017 081 -025 -049 000 -010 100

7 ACG 001 037 019 019 -019 -047 -041 -020 -019 -003 -062 018

8 ACT 070 085 079 100 076 100 037 100 100 100 100 100

9 AGA -047 -020 -039 -018 -020 -003 -017 -041 -021 -034 -065 100

10 AGC -012 039 -024 -004 -011 022 -009 043 -051 -040 -053 -011

11 AGG 010 067 049 017 100 100 059 100 -030 100 100 100

12 AGT -002 041 036 062 059 -034 -044 017 100 100 100 100

13 ATA -051 031 -027 071 023 053 -010 -036 -022 016 -077 100

14 ATC 009 -010 044 -013 019 -036 022 -014 -030 -031 -008 -059

15 ATG 017 021 -032 -021 -015 -004 020 -005 -039 017 -035 -017

16 ATT 001 008 -009 000 018 -018 -016 017 083 094 100 084

17 CAA -034 -046 -046 -023 011 -027 036 024 045 017 -047 -038

18 CAC -004 045 027 -039 028 073 012 012 061 -053 -075 -061

19 CAG 042 040 051 047 -002 -016 -024 034 080 070 066 042

20 CAT -013 -023 031 045 -012 079 -037 -039 069 086 100 100

21 CCA 044 -039 -068 -005 100 -006 050 -057 000 -074 100 -076

22 CCC 085 010 100 071 100 100 059 100 100 061 100 -012

23 CCG -002 -011 -040 -031 -037 -023 -012 -057 024 005 048 015

24 CCT 014 089 020 033 034 059 100 100 100 045 -062 -006

25 CGA -018 -062 032 -011 -022 100 044 100 -066 -029 -070 100

26 CGC 041 -022 -005 -004 021 -021 -035 040 041 -051 100 -036

27 CGG 035 021 018 -041 -035 065 -050 061 042 037 -066 100

28 CGT 003 090 054 050 029 048 051 -014 100 100 100 055

29 CTA -044 -021 100 020 -020 -013 100 100 -033 017 100 -058

30 CTC 060 075 053 006 084 -016 058 001 -026 -022 -024 -047

31 CTG -019 -021 -018 -020 -040 -009 -036 -033 012 026 -033 011

32 CTT 059 054 065 080 050 035 074 -003 040 066 100 100

33 GAA -004 -022 003 -005 -033 -021 005 046 -004 -043 060 -010 34 GAC -0 12 -0 07 -O 19 O 14 0 54 -O 12 0 07 -0 20 -0 43 -0 64 -0 67 -0 63

35 GAG 0 13 0 41 -O 10 0 48 0 47 0 39 0 26 -O 17 0 71 0 76 0 35 0 66

36 GAT 0 21 -0 02 -0 08 -0 01 -0 03 0 53 -0 34 -0 05 0 92 1 OO 1 OO 0 62

37 GCA -0 48 -0 16 -0 42 -0 49 0 02 -0 22 0 27 -0 41 -O 16 -0 49 -0 67 -0 63

38 GCC 0 66 0 17 0 56 -O 17 0 06 O 13 0 49 0 28 -0 39 0 56 -0 54 -0 57

39 GCG -0 15 0 18 -0 12 -O 13 -0 49 -0 05 0 01 -0 25 -0 05 0 39 -O 16 0 82

40 GCT 0 32 0 24 0 63 0 74 0 04 0 49 0 52 0 44 0 85 1 OO 1 OO 1 OO

41 GGA -0 35 -0 39 -O 13 -0 23 -0 33 -0 38 -O 15 -O 19 -0 31 -0 44 -O 12 0 55

42 GGC 0 45 0 13 -0 25 0 26 O 14 0 03 -0 20 0 41 0 05 -0 48 -0 07 -O 11

43 GGG 0 08 0 19 0 07 -O 17 0 46 1 00 O 19 1 00 0 34 0 54 1 00 1 OO

44 GGT -0 13 0 10 0 74 0 71 0 33 0 59 -O 14 -0 26 0 82 1 OO 1 00 1 OO

45 GTA -0 43 -0 45 -0 33 -0 33 -0 23 -O 16 -0 35 0 01 -0 62 O 14 1 00 0 06

46 GTC 0 25 0 10 O 15 -O 18 0 07 0 01 -0 02 -0 09 -0 54 -0 45 -0 26 -0 24

47 GTG -0 26 O i l -0 19 0 01 -0 27 0 16 -0 30 0 19 0 19 -0 06 0 22 0 56

48 GTT 0 49 0 60 0 75 0 28 0 42 0 36 0 65 O 17 0 77 1 OO 0 60 0 78

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 06 0 51 0 23 -0 25 -O 10 -O 12 -O 15 -0 01 -O 19 -0 34 -O 17 -0 67

51 TAG 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

52 TAT -0 22 0 07 0 42 -0 27 -O 17 0 00 0 24 0 55 0 84 0 90 1 00 0 70

53 TCA -0 10 -0 49 -0 25 -0 05 O 15 0 21 -0 33 -0 31 -0 43 -0 45 -0 08 -0 74

54 TCC 0 33 0 65 0 25 -0 55 0 76 O 12 -0 04 0 02 -0 47 -0 09 1 OO -0 22

55 TCG 0 10 0 41 0 58 0 00 O 19 0 50 -O 15 -0 39 0 09 0 75 -0 51 1 OO

56 TCT -0 02 O 11 O 18 0 35 -0 37 0 03 0 70 -0 07 1 00 1 OO 1 00 1 OO

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 75 -0 40 0 28 -0 22 1 00 -0 56 -0 44 1 00 0 22 -0 41 -0 63 -O 19

59 TGG 0 11 -0 22 -0 24 0 35 -0 01 0 73 -O 12 -0 32 -0 35 O 11 -0 05 -0 61

60 TGT -0 55 1 00 -0 04 0 38 0 40 1 00 -0 36 -O 18 1 00 1 OO 1 OO 1 OO

61 TTA -0 38 -0 24 -0 46 -0 47 O 15 -O 12 -0 35 -0 65 0 08 -0 25 0 37 -O 16

62 TTC -0 06 -0 08 O 13 0 42 0 22 -0 21 0 55 -0 53 -0 58 -0 44 -0 59 -0 42

63 TTG -0 27 -0 35 -0 47 -0 36 0 59 -0 33 0 30 -0 39 -O 17 0 46 1 OO 0 61

64 TTT -0 01 -0 02 0 05 -O 18 -0 23 0 04 O 10 0 07 0 64 0 77 1 00 1 OO

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.8 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 14 -0 34 -0 02 0 51 -0 07 0 15 0 45 0 25 -0 28 0 09 0 43 0 31 AAC 043 018 -004 -003 -010 -005 039 005 002 019 035 050

AAG 011 0 06 006 0 11 020 -052 -056 -015 022 -038 -046 -0 56

AAT -059 0 05 005 -0 07 -020 043 -018 -026 -040 -042 -042 0 52

ACA 051 0 27 -022 0 61 -042 006 -011 050 012 028 -017 0 50

ACC -045 -0 09 056 -0 45 068 042 008 032 020 100 075 0 38

ACG -033 -0 24 -028 -0 35 040 -008 024 -022 -012 -020 -040 0 27

ACT 050 0 81 084 0 50 030 -022 -044 -043 011 027 032 -0 41

AGA -019 -0 13 001 -0 13 046 073 -007 -022 100 100 -024 0 63

AGC -001 0 00 010 -0 13 023 021 -028 -049 046 -044 042 1 00

AGG -064 0 48 033 0 16 008 -064 067 028 100 -063 -033 1 00

AGT 002 -0 09 076 0 02 063 062 -007 070 -084 -023 -031 -0 17

ATA 032 0 50 100 0 86 -067 010 -017 -007 005 -057 -047 0 64

ATC 024 -0 28 -003 -0 03 064 024 033 047 030 057 057 0 19

ATG 014 -0 06 000 0 03 047 -023 -025 023 014 029 005 -0 24

ATT -018 -0 06 -014 0 24 -043 -031 004 -026 -059 -041 -021 -0 14

CAA 015 -0 10 -025 -0 03 067 100 060 073 037 100 100 0 76

CAC -042 0 28 -007 -0 11 005 029 054 -011 055 100 010 -0 18

CAG 0.59 0 .12 0.25 -0 .14 0.11 -0.52 -0.46 -0.20 0.09 1.00 -0.45 -0 .56

CAT 032 -0 07 006 -0 02 -011 021 -027 -020 -030 -015 -017 0 18

CCA 100 0 36 -021 -0 52 046 002 100 100 100 100 100 1 00

CCC 100 1 00 100 0 72 011 020 068 005 100 100 100 -0 12

CCG 047 -0 32 -033 -0 24 -019 -036 016 006 -009 -045 -020 -0 21

CCT 100 0 38 088 0 47 -052 044 -005 012 100 -071 037 -0 06

CGA 100 -0 43 -063 -0 56 038 100 055 002 100 100 100 1 00

CGC 071 0 03 003 0 01 015 005 -003 -017 100 100 018 0 48

CGG -056 -0 14 -018 -0 20 026 -010 -032 012 -024 -077 020 -0 34

CGT 058 0 61 039 0 16 -039 017 -009 -008 100 019 -049 -0 47

CTA 100 -0 62 -027 1 00 100 100 100 100 100 100 041 1 00

CTC -061 0 10 002 -0 04 074 043 054 040 100 100 046 0 42

CTG -048 -0 25 -024 -0 19 -002 -017 010 022 -042 -029 -031 -0 09

CTT 054 0 48 028 0 77 -030 -030 -033 -038 -021 -061 -023 -0 41

GAA -001 -0 12 -013 0 04 011 035 019 027 021 022 023 0 64

GAC 038 0 12 021 0 13 035 066 029 012 011 051 014 0 43

GAG -020 0 30 038 0 00 -025 -038 -030 -047 -058 -048 -044 -0 34

GAT -032 0 12 -015 -0 24 -039 -018 001 -026 000 039 -031 0 04

GCA 020 -0 08 -003 0 36 008 082 004 058 -050 017 054 0 42

GCC -045 -0 01 -027 -0 35 -028 040 025 006 100 030 074 0 35

GCG 053 -0 16 -017 -0 20 022 -012 -023 002 -015 003 -015 -0 48

GCT 021 0 56 081 0 47 -010 -048 027 -044 001 -051 -022 -0 52 41 GGA 0 15 0 08 -0 12 -0 06 -0 44 -0 21 0 02 -0 09 1 00 0 59 0 02 -0 41

42 GGC 0 27 -0 10 0 02 -0 19 0 46 0 18 0 13 0 22 0 30 0 13 0 36 0 60

43 GGG -0 02 0 68 -0 24 -0 13 0 66 0 08 -0 41 -0 45 1 00 -0 38 -0 49 -0 34

44 GGT 0 16 0 27 0 45 -0 15 -0 49 0 05 0 70 0 25 0 19 0 33 -0 19 -0 54

45 GTA 0 74 0 51 0 30 0 69 0 52 0 57 -0 17 -0 17 0 53 0 62 0 64 -0 07

46 GTC 0 21 -0 38 -0 32 -0 17 0 35 0 60 0 74 0 38 0 72 0 53 0 70 0 78

47 GTG -0 09 0 01 0 01 -0 09 0 08 0 69 -0 43 -0 17 0 01 -0 47 -0 53 -0 43

48 GTT 0 06 -0 08 0 33 0 17 -0 39 -0 51 -0 10 -0 42 0 66 0 17 -0 25 -0 35

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 62 0 22 0 38 -0 12 0 06 0 52 0 23 -0 13 -0 40 0 66 0 23 0 36

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 40 0 19 -0 25 0 13 -0 13 0 15 -0 12 -0 26 1 00 0 39 -0 41 0 29

53 TCA -0 27 0 49 -0 13 0 32 -0 30 -0 06 -0 03 0 79 0 45 1 00 0 41 -0 05

54 TCC -0 13 -0 33 -0 10 -0 54 0 78 0 32 0 68 1 00 0 07 0 24 0 29 0 64

55 TCG 0 35 -0 08 0 06 0 09 0 51 -0 60 -0 20 0 00 -0 04 -0 42 -0 21 -0 58

56 TCT 0 16 0 14 -0 18 0 33 -0 37 -0 45 -0 04 0 09 -0 70 0 44 -0 12 -0 57

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 1.00 -0.44 0.44 0.57 -0.09 -0.37 -0.25 -0.21 -0.01 1.00 0.23 1.00

59 TGG 0 48 0 33 0 00 -0 31 0 63 -0 23 -0 31 0 23 1 00 -0 71 0 13 0 45

60 TGT -0 35 0 14 -0 39 0 07 -0 05 0 54 0 62 0 64 -0 66 -0 58 0 55 -0 75

61 TTA -0 43 -0 10 -0 16 -0 06 0 51 0 64 0 03 0 43 0 04 0 61 0 56 0 63

62 TTC 1 00 -0 16 0 15 0 13 0 75 -0 08 -0 20 -0 18 1 00 1 00 0 03 -0 09

63 TTG 0 53 0 05 0 44 -0 28 -0 22 -0 17 -0 34 -0 34 1 00 -0 36 0 61 0 03

64 TTT 0 34 0 06 -0 10 -0 19 0 16 -0 22 -0 26 0 45 -0 23 -0 65 0 01 0 33

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.8 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA -0 56 0 18 -0 22 0 32 -0 17 0 49 0 31 0 39 -0 17 -0 29 0 14 0 27

2 AAC -0 40 -0 26 -0 39 -0 09 1 00 0 00 -0 17 0 13 0 20 0 50 -0 07 0 33

3 AAG 1 00 -0 13 -0 03 0 36 0 15 -0 52 -0 63 -0 64 0 24 0 01 0 48 0 17

4 AAT -0 64 0 57 0 58 0 06 1 00 -0 35 -0 47 0 04 -0 18 -0 37 -0 01 -0 31

5 ACA 0 18 0 50 0 76 -0 09 0 21 0 59 0 18 0 10 0 24 0 10 -0 11 0 20

6 ACC 1 00 0 77 1 00 -0 25 1 00 0 24 0 14 -0 06 0 39 -0 31 0 03 0 22

7 ACG 0 29 0 67 -0 21 1 00 1 00 -0 14 -0 21 -0 42 0 00 0 61 0 15 -0 06

8 ACT 1 00 -0 22 0 50 -0 70 -0 79 0 37 0 64 -0 24 -0 38 -0 21 -0 50 -0 55 AGA 003 -016 042 014 -058 085 056 071 -020 002 -022 018

AGC -031 -036 -0 34 019 100 062 -007 -015 061 026 047 057

AGG 100 -001 -0 75 100 100 -036 -082 -056 -043 063 -054 038

AGT 100 068 1 00 100 100 -045 -020 009 -044 -053 -065 -060

ATA -049 040 -0 43 056 100 063 -021 100 -029 057 042 -008

ATC -032 -059 0 67 -012 -037 017 057 022 023 016 031 037

ATG 016 036 0 13 016 046 -004 -037 -023 000 005 -001 -004

ATT -016 058 0 41 039 043 -021 -006 017 -028 -002 015 -038

CAA 037 061 0 43 015 013 100 087 086 021 -019 -005 018

CAC -072 -027 0 47 -050 -040 078 001 046 011 045 019 038

CAG -046 -045 -0 39 -025 037 -036 -054 -047 -010 004 -006 -002

CAT -029 -023 0 58 069 -024 014 031 025 -013 -037 -001 -009

CCA 100 -029 -0 27 100 100 100 100 024 026 021 -046 100

CCC 100 -065 -0 70 100 100 000 043 037 039 -042 -034 010

CCG -064 -022 -0 04 038 028 -046 010 019 013 036 036 019

CCT 100 -007 0 48 -015 100 053 047 -032 -033 -024 -038 -054

CGA 100 032 -0 25 100 100 029 019 056 080 -034 100 016

CGC 0.32 -0.44 -0 .18 -0.53 0.17 0.24 0.14 0.26 0.48 0.23 0.25 0.35

CGG 100 059 -0 37 100 100 -066 -031 -016 017 040 -015 025

CGT 100 070 0 70 -035 100 084 001 -049 -013 -063 -043 -018

CTA 100 100 1 00 100 100 100 100 035 100 100 -021 -020

CTC -044 005 0 73 -028 100 032 069 041 041 -019 027 -008

CTG -001 -041 -0 27 010 040 -052 -046 -029 027 041 011 044

CTT 100 015 0 67 -042 035 049 023 -010 -039 -031 -046 -046

GAA 029 045 -0 22 041 057 050 038 056 -006 002 -016 008

GAC -063 -034 -0 59 -047 -002 014 036 001 025 014 003 021

GAG -025 -059 -0 46 -040 -038 -042 -055 -064 025 013 024 -026

GAT 025 088 0 78 058 015 -014 -010 038 -024 009 026 -026

GCA 100 047 0 79 -007 024 012 061 057 028 001 006 -004

GCC 042 -020 -0 28 -030 100 050 048 053 034 005 001 006

GCG 019 -023 -0 36 046 056 -058 -029 -040 -007 042 012 028

GCT 100 100 1 00 -053 -066 071 050 -017 -040 -028 001 -045

GGA 049 022 0 24 -020 100 042 020 028 -025 -004 -019 025

GGC 100 -033 -0 16 -023 -044 001 030 034 027 -017 016 026

GGG -001 022 -0 63 032 100 -049 -049 -065 039 060 030 001

GGT 016 049 0 50 007 -052 019 030 -041 -022 -051 -036 -009

GTA 100 054 0 55 033 -067 061 033 035 003 014 -010 028

GTC 054 -004 0 18 -024 -017 076 051 071 048 005 -019 -014

GTG 047 -046 -0 37 053 -029 -056 -055 -047 016 040 054 041 48 GTT -038 050 052 028 -030 -040 031 -009 -039 -033 -034 -033

49 TAA 000 000 000 000 000 000 000 000 000 000 000 000

50 TAC -038 001 -041 -072 100 028 010 046 027 036 031 002

51 TAG 000 000 000 000 000 000 000 000 000 000 000 000

52 TAT -054 056 079 084 -049 011 -008 045 -026 -026 001 000

53 TCA 100 -031 100 051 002 049 042 037 006 -004 -026 -006

54 TCC 100 -012 026 -009 -039 -007 051 020 014 037 009 -014

55 TCG 100 -006 -060 -019 -073 -058 -027 -017 038 057 -016 017

56 TCT 100 017 100 000 -058 -009 064 -032 -025 -016 -036 -014

57 TGA 000 000 000 000 000 000 000 000 000 000 000 000

58 TGC -045 -060 -007 -038 100 -013 -008 028 065 035 035 059

59 TGG 100 056 -021 -021 -049 024 -051 005 -001 010 003 -008

60 TGT 100 100 100 100 100 045 005 -052 -039 -046 -055 -036

61 TTA 015 048 024 081 100 061 071 076 003 038 030 012

62 TTC -070 -026 034 -059 100 032 054 043 048 022 004 055

63 TTG 100 -027 -062 -019 -024 -016 -043 -028 034 059 -011 -002

64 TTT 100 075 050 045 -050 -039 -007 057 -030 -035 015 -009

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.8 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -013 001 -016 014 -021 -021 -013 028 -022 040 -034 039

2 AAC 030 041 -038 -015 -035 -039 -026 -036 014 -022 034 021

3 AAG 030 052 -014 024 042 040 010 079 -028 003 -035 043

4 AAT -014 -026 021 074 083 079 065 043 -017 -028 001 021

5 ACA 017 -023 035 -009 062 -014 013 028 031 048 057 050

6 ACC -013 003 -011 -039 -028 -028 008 -052 -061 -060 -011 -037

7 ACG 004 049 005 -030 -012 004 003 -014 003 041 000 -007

8 ACT 001 -007 017 -028 011 073 049 -047 -056 004 013 -012

9 AGA 033 015 -027 084 022 -016 -022 -022 020 -017 016 071

10 AGC 035 -016 -018 014 -051 -021 -030 -049 -038 051 019 034

11 AGG 043 052 100 -040 -024 100 100 100 100 018 -065 -059

12 AGT 037 020 026 038 081 100 024 100 -050 019 -039 004

13 ATA 100 -028 -008 039 062 033 063 007 100 046 079 079

14 ATC -016 -025 -009 -022 -032 -054 -050 -040 -030 -029 -011 -013

15 ATG 023 009 001 -026 020 -009 015 -019 -012 019 -024 019 ATT 026 -015 030 039 085 095 063 075 023 -007 021 028

CAA 0 18 023 046 -O 14 -024 -033 -005 -043 008 -O 17 -038 045

CAC 0 02 -010 033 020 -023 -053 -032 -035 -O 13 003 -O 12 -033

CAG 0 14 011 -022 -036 O 17 027 037 058 022 026 -036 036

CAT -0 22 -046 017 049 034 074 042 052 028 034 -O 13 009

CCA -0 01 014 070 -033 005 032 100 -068 053 071 067 -002

CCC -0 70 030 -042 -O 19 -023 -073 -068 O 14 -035 -057 O 18 -078

CCG 0 38 -027 059 -O 12 -O 14 021 O 13 -022 043 043 029 -003

CCT -0 36 -024 043 -035 051 083 100 040 -038 -030 049 -036

CGA 1 00 100 100 024 -O 16 -021 100 002 -046 044 035 -049

CGC -0 06 -033 -028 O 19 -027 -036 -031 -026 030 -O 10 -022 -024

CGG 0 54 061 -047 -026 -020 024 -053 O 12 073 000 042 002

CGT -0 27 013 -009 O 16 047 091 100 O 13 -046 O 14 042 O 12

CTA 0 24 -048 Oil 026 038 -043 100 -051 -056 030 019 O 18

CTC 0 12 -057 -031 032 -041 -074 -063 -067 -033 -060 -021 -028

CTG 0 38 015 024 028 072 048 036 077 091 023 058 076

CTT -0 35 -026 -021 -008 045 025 090 -O 14 007 -034 -O 10 -040

GAA -0 .12 -0.09 -0.22 0.07 -0.04 -0.16 -0.18 0.06 -0.08 -0.08 -0.38 0.22

GAC -0 14 019 -003 006 -053 -049 -020 -045 O 12 029 O 12 031

GAG 0 16 039 O 19 071 055 O 16 -001 035 060 052 O 16 020

GAT 0 02 025 -020 004 067 088 061 062 -035 -008 -028 O 16

GCA -0 05 001 035 -022 O 10 028 O 17 001 059 050 037 047

GCC -0 32 -010 008 -041 -054 -037 -029 -043 O 17 -039 002 -053

GCG 0 13 032 O 10 -004 -O 16 020 002 007 -001 007 -005 -007

GCT 0 09 007 021 -033 082 062 088 022 036 007 038 -031

GGA 0 07 001 -O 17 039 047 048 028 035 O 18 051 042 031

GGC 0 21 -013 005 -023 -046 -025 002 -024 005 -025 -O 16 -O 15

GGG -0 26 079 -001 003 O 15 035 -088 068 056 029 O 17 037

GGT -0 11 031 -027 O 10 084 092 100 091 -042 -032 -O 11 -037

GTA 0 42 012 032 054 -O 12 -O 10 059 -035 050 054 047 064

GTC 0 09 -027 -022 -034 -050 -059 -O 11 -049 -027 -020 -044 -055

GTG -0 36 052 038 028 071 064 027 100 082 078 037 049

GTT -0 20 008 -024 O 10 055 073 070 051 037 -021 -O 17 -038

TAA 0 00 000 000 000 000 000 000 000 000 000 000 000

TAC 0 17 003 -022 007 -049 -042 -042 -057 084 021 054 O 18

TAG 0 00 000 000 000 000 000 000 000 000 000 000 000

TAT 0 26 -015 -008 027 079 085 086 066 -031 -037 -039 027

TCA 0 23 -037 022 035 -O 16 -024 034 045 -004 030 051 -O 14

TCC -0 23 006 024 -050 -051 -O 10 -O 10 -040 -027 -044 031 -049 55 TCG -0 40 -0 43 -0 09 -0 03 0 37 -0 07 1 00 0 58 0 78 -0 25 0 69 -0 30

56 TCT -0 26 0 31 0 52 0 07 0 67 0 65 0 84 0 33 -0 22 0 22 0 50 -0 43

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 50 0 16 0 03 0 02 -0 46 -0 54 0 47 -0 08 0 20 0 27 0 72 1 00

59 TGG -0 48 0 10 0 25 0 37 -0 19 0 26 -0 51 0 66 -0 19 0 25 -0 18 0 11

60 TGT 1 00 0 59 -0 41 0 53 0 81 1 00 1 00 1 00 -0 66 -0 43 -0 51 0 17

61 TTA 0 16 0 60 0 56 0 36 -0 07 0 02 -0 06 -0 21 -0 36 0 31 0 50 -0 11

62 TTC 0 58 -0 06 0 39 -0 03 -0 59 -0 53 0 06 -0 50 -0 18 0 20 0 22 0 37

63 TTG -0 19 0 17 0 06 -0 25 0 80 0 71 0 00 0 50 0 81 0 21 0 21 -0 17

64 TTT 0 21 -0 32 -0 20 -0 08 0 85 0 71 1 00 0 58 0 00 -0 45 0 18 0 28

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.8 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 26 0 00 0 06 -0 31 -0 02 0 08 0 35 0 00 0 02 0 17 0 05

2 AAC 0 00 -0 14 0 00 0 18 0 72 0 76 -0 26 0 30 0 00 0 07 -0 13 -0 40

3 AAG 0 00 0 40 0 00 0 36 0 09 0 62 -0 34 0 16 0 00 0 08 -0 32 -0 25

4 AAT 0 00 -0 08 0 00 0 04 0 10 -0 59 0 31 0 78 0 00 0 41 0 20 0 14

5 ACA 0 00 -0 16 0 00 -0 05 0 02 -0 10 -0 31 0 06 0 00 -0 26 0 15 0 03

6 ACC 0 00 -0 09 0 00 0 17 0 60 1 00 0 24 0 26 0 00 -0 19 0 61 1 00

7 ACG 0 00 0 26 0 00 0 41 0 34 0 36 0 28 -0 14 0 00 -0 14 -0 22 0 16

8 ACT 0 00 -0 42 0 00 -0 35 -0 10 0 25 -0 21 -0 67 0 00 -0 27 -0 23 1 00

9 AGA 0 00 1 00 0 00 0 22 -0 19 -0 23 -0 15 -0 12 0 00 0 22 0 01 -0 41

10 AGC 0 00 -0 15 0 00 0 07 0 35 0 78 -0 19 0 20 0 00 0 43 0 02 0 59

11 AGG 0 00 1 00 0 00 0 34 0 48 1 00 1 00 0 35 0 00 1 00 -0 56 1 00

12 AGT 0 00 0 32 0 00 0 09 -0 34 -0 22 -0 65 -0 28 0 00 1 00 0 05 1 00

13 ATA 0 00 -0 60 0 00 -0 37 -0 11 -0 30 1 00 -0 04 0 00 -0 38 -0 52 1 00

14 ATC 0 00 0 46 0 00 0 40 0 37 0 11 0 50 0 55 0 00 -0 04 -0 13 0 35

15 ATG 0 00 0 18 0 00 -0 14 -0 43 0 72 0 52 -0 04 0 00 0 58 0 00 -0 45

16 ATT 0 00 -0 19 0 00 -0 22 -0 23 -0 54 0 04 -0 42 0 00 0 20 0 38 -0 38

17 CAA 0 00 -0 32 0 00 -0 47 -0 21 -0 47 -0 58 0 14 0 00 -0 17 -0 42 -0 43

18 CAC 0 00 0 46 0 00 -0 30 0 46 0 70 -0 02 0 11 0 00 -0 11 0 18 -0 23

19 CAG 0 00 0 59 0 00 0 42 -0 18 0 32 0 42 0 00 0 00 -0 14 0 53 1 00

20 CAT 0 00 0 47 0 00 -0 29 -0 50 -0 31 0 46 0 47 0 00 0 11 -0 12 0 23

21 CCA 0 00 -0 33 0 00 -0 43 0 03 1 00 -0 46 -0 58 0 00 -0 17 0 05 -0 43

22 CCC 0 00 0 19 0 00 0 64 0 21 0 33 1 00 0 51 0 00 0 01 1 00 1 00 CCG 0 00 0 09 0 00 0 07 -0 03 0 50 0 44 0 36 0 00 0 45 -0 31 -0 25

CCT 0 00 -0 25 0 00 -0 01 -0 46 -0 36 -0 05 -0 37 0 00 1 OO 0 64 -0 70

CGA 0 00 -0 51 0 00 -0 44 0 29 -O 17 1 00 O 13 0 00 -0 45 1 OO 1 OO

CGC 0 00 -0 35 0 00 0 04 0 78 0 82 O 18 -0 32 0 00 -0 40 -0 46 -0 64

CGG 0 00 0 40 0 00 0 20 0 58 1 00 0 60 0 48 0 00 0 46 0 55 1 OO

CGT 0 00 -0 44 0 00 -0 16 -0 42 0 20 -0 58 -0 68 0 00 1 00 1 00 1 00

CTA 0 00 1 00 0 00 -0 78 -0 60 -0 29 -0 69 -0 03 0 00 1 OO -0 79 -0 82

CTC 0 00 0 17 0 00 0 56 0 24 0 63 -O 19 0 73 0 00 0 49 0 37 -0 32

CTG 0 00 -0 12 0 00 -0 21 -0 05 O 16 -0 35 0 01 0 00 0 42 -0 08 0 58

CTT 0 00 -0 13 0 00 0 45 -0 26 0 31 -0 03 -0 50 0 00 0 04 0 60 -0 57

GAA 0 00 -0 08 0 00 -0 06 -0 01 -O 18 0 09 0 29 0 00 -O 11 0 08 O 10

GAC 0 00 0 32 0 00 0 51 0 76 0 60 0 40 0 32 0 00 -0 34 -0 09 -O 18

GAG 0 00 0 04 0 00 0 32 0 76 -0 29 -O 12 0 26 0 00 -O 19 -O 17 0 55

GAT 0 00 -0 35 0 00 -0 16 -O i l -0 47 0 12 0 10 0 00 0 58 0 08 -0 02

GCA 0 00 -0 22 0 00 -0 02 -O 13 -0 06 -O 16 -0 23 0 00 0 28 -0 39 0 48

GCC 0 00 0 71 0 00 0 05 0 64 0 55 0 49 O 12 0 00 -0 53 -0 07 -0 55

GCG 0 00 0 52 0 00 0 34 0 07 0 58 0 06 0 39 0 00 0 36 0 47 0 69

GCT 0.00 -0.49 0.00 -0.51 -0.19 -0.75 -0.15 -0.61 0.00 0.29 -0.07 -0.03

GGA 0 00 -0 06 0 00 -0 29 0 45 1 00 O 11 O 13 0 00 0 40 0 41 0 71

GGC 0 00 -0 02 0 00 0 29 0 05 -0 04 -0 21 0 52 0 00 -0 45 -0 50 -0 39

GGG 0 00 0 70 0 00 -0 16 0 06 1 00 O 11 0 42 0 00 -0 37 1 00 1 OO

GGT 0 00 -0 11 0 00 -0 09 -0 36 0 34 -0 49 -0 65 0 00 0 67 0 81 1 OO

GTA 0 00 -0 47 0 00 -0 30 -0 39 -0 58 -0 03 -0 42 0 00 -O 13 -0 45 -0 20

GTC 0 00 0 59 0 00 0 27 0 41 0 67 0 50 0 68 0 00 -0 37 0 31 0 49

GTG 0 00 -0 25 0 00 0 16 0 39 -0 03 -O 14 0 62 0 00 0 80 0 04 0 71

GTT 0 00 0 22 0 00 -0 11 -O 14 -0 52 -O 15 -0 48 0 00 O 17 O 18 -0 58

TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

TAC 0 00 0 12 0 00 0 22 0 64 0 20 1 00 O 12 0 00 0 02 0 20 -0 47

TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

TAT 0 00 -0 10 0 00 -0 16 -0 32 -O 19 -0 37 -0 30 0 00 0 71 -O 15 -0 20

TCA 0 00 0 17 0 00 0 27 0 21 0 33 -0 33 0 84 0 00 0 42 -0 49 0 58

TCC 0 00 0 20 0 00 -0 29 0 78 -0 33 O 16 0 73 0 00 -0 59 1 00 -0 29

TCG 0 00 0 10 0 00 0 20 0 00 1 00 -0 30 -O 19 0 00 -0 77 -0 20 1 OO

TCT 0 00 0 12 0 00 -0 41 -0 31 -0 59 0 08 -0 28 0 00 -0 07 0 59 0 48

TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

TGC 0 00 -0 51 0 00 0 09 1 00 -0 54 -0 59 1 00 0 00 -0 30 1 00 -0 52

TGG 0 00 0 36 0 00 -0 24 0 32 1 00 -0 53 O 17 0 00 -0 32 0 00 0 69

TGT 0 00 0 26 0 00 1 00 -0 46 1 00 -0 57 0 24 0 00 1 00 -0 59 1 OO

TTA 0 00 0 37 0 00 -0 29 -0 46 0 48 0 02 -0 02 0 00 -0 49 -0 29 0 30 62 TTC 0 00 0 10 0 00 0 20 -0 17 -0 16 0 24 0 01 0 00 -0 30 -0 39 0 48

63 TTG 0 00 -0 20 0 00 0 08 0 18 -0 38 0 74 0 16 0 00 1 00 -0 24 0 08

64 TTT 0 00 -0 22 0 00 0 02 -0 27 -0 29 0 42 0 25 0 00 -0 07 0 47 0 22

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.8 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 29 -0 39 0 07 0 62

2 AAC 0 24 -0 36 0 75 0 37

3 AAG 0 68 -0 10 0 72 -0 24

4 AAT 0 39 -0 29 0 52 0 38

5 ACA -0 15 -0 31 -0 52 0 20

6 ACC 0 82 0 47 0 52 -0 38

7 ACG 0 41 0 17 0 89 0 06

8 ACT 0 00 -0 15 -0 62 0 26

9 AGA 0 27 0 69 0 61 0 65

10 AGC 0 28 0 25 -0 09 0 03

11 AGG 1 00 0 48 1 00 0 21

12 AGT -0 28 -0 20 0 08 0 53

13 ATA -0 72 -0 46 -0 69 -0 29

14 ATC 0 47 0 36 0 48 0 48

15 ATG 0 80 -0 14 0 83 0 12

16 ATT -0 60 -0 27 -0 33 -0 24

17 CAA -0 16 -0 33 0 29 -0 23

18 CAC -0 20 -0 10 -0 39 0 27

19 CAG 0 77 0 33 0 38 0 24

20 CAT -0 49 -0 09 -0 42 -0 07

21 CCA -0 43 -0 32 -0 35 0 17

22 CCC 1 00 0 40 -0 21 0 09

23 CCG -0 25 0 16 0 77 -0 21

24 CCT -0 63 0 72 -0 43 -0 22

25 CGA 0 33 -0 65 -0 72 -0 07

26 CGC 0 28 0 13 0 05 0 35

27 CGG 1 00 0 37 -0 06 -0 48

28 CGT -0 26 -0 42 -0 37 -0 40

29 CTA -0 50 1 00 -0 24 -0 75 CTC 0 48 0 73 -0 02 0 59

CTG 0 78 0 07 0 32 -0 29

CTT -0 27 0 06 -0 48 0 68

GAA 0 18 0 01 -0 32 0 03

GAC 0 43 0 33 0 17 0 37

GAG 0 41 -0 26 0 74 0 17

GAT -0 35 -0 41 -0 52 0 01

GCA -0 46 -0 33 -0 10 -0 26

GCC 0 21 0 66 0 17 0 24

GCG 0 29 0 30 0 78 0 17

GCT -0 32 -0 32 -0 59 -0 32

GGA -0 09 0 30 -0 39 -0 18

GGC 0 44 0 39 0 49 0 31

GGG 0 53 0 68 0 18 -0 05

GGT -0 14 -0 46 -0 51 -0 53

GTA -0 10 -0 23 0 03 -0 40

GTC 0 48 0 69 0 80 0 53

GTG 0.04 0.36 0.43 -0.24

GTT -0 29 -0 37 -0 22 -0 11

TAA 0 00 0 00 0 00 0 00

TAC -0 39 0 31 0 28 0 27

TAG 0 00 0 00 0 00 0 00

TAT -0 36 -0 09 -0 48 -0 27

TCA -0 17 -0 08 -0 30 -0 28

TCC 0 39 0 82 0 19 0 45

TCG 0 54 0 59 1 00 -0 36

TCT -0 66 -0 42 0 02 -0 01

TGA 0 00 0 00 0 00 0 00

TGC -0 31 -0 05 1 00 0 80

TGG 0 76 0 37 1 00 -0 22

TGT -0 05 -0 12 0 31 -0 50

TTA -0 42 -0 04 -0 23 -0 40

TTC -0 08 -0 01 0 43 -0 10

TTG 0 68 -0 03 -0 06 -0 45

TTT -0 59 -0 15 -0 23 0 22

TTA TTC TTG TTT

61 62 63 64 Table C.9: CPW matrix Saccharomyces cerevisiae full genome (left codon indicated in column 2, right codon indicated in row 2). Host cell: S. cerevisiae; Sequence data: full S. cerevisiae genome.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 0 18 0 05 0 13 -0 05 -0 12 0 12 0 00 0 05 -0 09 -0 24 -0 17 -0 23

2 AAC -0 12 -0 14 -0 19 -0 03 -0 06 -0 12 0 03 -0 11 -0 16 -0 28 -0 14 -0 17

3 AAG -0 17 -0 05 -0 20 0 05 -0 06 0 02 -0 08 0 09 -0 04 -0 05 -0 03 0 02

4 AAT 0 06 0 09 0 21 0 04 0 01 0 07 0 04 0 10 0 14 -0 04 0 02 -0 07

5 ACA 0 00 -0 06 -0 10 -0 13 -0 11 0 16 0 06 0 20 -0 33 -0 01 -0 30 -0 11

6 ACC -0 23 -0 27 -0 33 -0 11 -0 11 -0 31 -0 16 -0 28 -0 09 -0 05 0 05 0 02

7 ACG -0 10 0 06 0 00 0 01 0 15 0 33 0 19 0 38 -0 09 0 01 -0 19 0 13

8 ACT 0 30 0 31 0 29 0 17 0 12 -0 10 0 12 -0 07 0 26 0 30 0 36 0 12

9 AGA 0 04 -0 16 -0 10 -0 10 -0 11 0 00 0 01 -0 06 -0 25 -0 13 -0 17 -0 13

10 AGC -0 13 -0 21 0 04 -0 19 -0 08 -0 25 -0 21 -0 14 0 01 -0 31 -0 16 -0 22

11 AGG -0 24 0 09 -0 06 0 16 -0 07 0 12 -0 03 0 05 0 11 0 02 0 11 0 14

12 AGT -0 02 0 05 0 28 -0 03 0 02 -0 01 0 00 0 18 0 27 0 00 0 15 0 00

13 ATA -0 05 -0 08 0 04 -0 12 -0 14 0 19 -0 16 0 06 -0 12 -0 01 -0 17 0 07

14 ATC -0 35 -0 34 -0 35 -0 24 -0 11 -0 27 -0 05 -0 25 -0 22 -0 04 -0 12 -0 19

15 ATG -0 05 0 00 0 08 0 00 -0 13 -0 01 -0 09 0 18 -0 09 -0 17 -0 03 -0 14

16 ATT 0 30 0 31 0 34 0 29 0 22 0 12 0 23 0 06 0 25 0 39 0 28 0 31

17 CAA 0 05 0 01 -0 08 -0 06 -0 11 0 06 -0 15 -0 09 -0 07 -0 14 -0 10 -0 28

18 CAC -0 17 -0 22 -0 27 -0 16 -0 22 -0 09 -0 10 -0 16 -0 09 -0 06 0 16 0 08

19 CAG -0 05 0 16 0 11 0 01 -0 02 0 31 0 04 0 33 0 28 -0 01 0 10 0 09

20 CAT 0 11 0 17 0 22 0 10 0 05 0 16 0 19 0 09 0 24 0 29 0 27 0 28

21 CCA 0 01 -0 04 -0 18 -0 08 -0 04 0 01 0 07 -0 13 -0 28 0 09 -0 17 0 01

22 CCC -0 25 -0 12 -0 28 -0 18 -0 24 -0 25 -0 22 -0 15 0 05 -0 15 0 09 -0 11

23 CCG 0 09 0 02 0 05 0 08 0 00 0 53 0 17 0 37 0 20 0 31 0 11 0 28

24 CCT 0 21 0 22 0 34 0 12 0 13 -0 06 0 05 0 19 0 44 0 45 0 41 0 32

25 CGA 0 12 -0 08 0 30 -0 14 0 02 -0 07 -0 24 0 19 0 06 -0 08 -0 03 -0 26

26 CGC 0 05 0 07 0 05 0 07 -0 22 -0 14 -0 08 0 17 0 31 -0 49 0 16 -0 30

27 CGG -0 10 0 21 0 04 -0 15 -0 07 0 40 0 11 0 52 0 44 0 27 -0 05 -0 06

28 CGT 0 27 0 40 0 29 0 26 0 24 -0 08 0 18 0 12 0 47 0 38 0 45 0 15

29 CTA 0 12 0 05 0 11 -0 02 -0 08 O i l 0 05 0 14 -0 06 -0 05 -0 06 -0 01

30 CTC -0 02 -0 09 -0 01 -0 15 -0 07 -0 35 -0 21 -0 19 0 32 -0 22 0 19 -0 27

31 CTG -0 11 -0 08 0 00 -0 01 0 15 0 20 -0 10 0 21 0 22 0 02 0 06 0 16

32 CTT 0 53 0 39 0 59 0 46 0 33 0 24 0 19 0 18 0 54 0 48 0 61 0 53

33 GAA 0 05 0 00 -0 05 -0 05 -0 07 0 05 -0 11 -0 08 -0 10 -0 24 -0 06 -0 31 34 GAC -0 11 -0 18 -0 24 -0 05 -0 03 -0 17 0 06 -0 19 -0 11 -0 15 -0 11 -0 10

35 GAG -0 04 0 06 0 02 0 10 0 08 0 19 0 05 0 21 0 18 -0 14 0 09 -0 10

36 GAT 0 04 0 14 0 22 0 02 0 06 0 07 0 06 0 08 0 15 0 12 0 18 0 12

37 GCA 0 05 -0 05 0 03 -0 11 0 05 0 31 0 15 0 21 -0 34 -0 10 -0 29 -0 06

38 GCC -0 18 -0 18 -0 41 -0 19 -0 10 -0 34 -0 19 -0 32 0 06 -0 08 -0 07 -0 08

39 GCG 0 07 0 01 -0 06 0 17 0 18 0 45 0 08 0 25 0 21 0 25 0 20 0 28

40 GCT 0 22 0 14 0 20 0 21 0 15 -0 04 0 20 -0 19 0 21 0 30 0 33 0 27

41 GGA -0 12 -0 15 -0 02 -0 26 -0 16 0 14 -0 29 0 05 -0 26 -0 22 -0 24 -0 30

42 GGC 0 10 0 04 0 05 -0 03 0 01 0 03 0 11 -0 03 0 04 -0 24 -0 04 -0 27

43 GGG -0 19 0 02 -0 13 0 13 -0 01 0 24 -0 06 0 23 0 06 -0 01 0 01 0 21

44 GGT 0 10 0 02 0 02 0 18 0 12 -0 13 0 16 -0 09 0 00 0 12 0 40 0 27

45 GTA -0 05 -0 02 0 09 -0 10 -0 05 0 14 -0 18 0 11 -0 09 -0 01 -0 16 0 12

46 GTC -0 19 -0 25 -0 36 -0 16 -0 14 -0 40 0 06 -0 29 -0 11 -0 10 -0 07 -0 16

47 GTG -0 13 -0 07 -0 13 0 07 0 02 0 07 0 03 0 21 -0 01 0 01 -0 02 0 14

48 GTT 0 26 0 16 0 29 0 17 0 27 0 01 0 29 -0 04 0 26 0 26 0 40 0 28

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 13 -0 18 -0 23 -0 10 -0 14 -0 04 -0 09 -0 10 -0 02 0 11 -0 15 0 04

51 TAG 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

52 TAT 0 12 0 15 0 22 0 10 0 06 0 13 -0 14 0 17 0 21 0 30 0 07 0 26

53 TCA 0 03 0 04 0 07 -0 05 0 16 0 30 0 06 0 12 -0 27 0 03 -0 27 0 10

54 TCC -0 28 -0 17 -0 31 -0 13 -0 16 -0 22 -0 12 -0 34 -0 05 -0 14 -0 02 -0 14

55 TCG -0 15 0 03 -0 14 -0 04 0 12 0 33 0 02 0 30 -0 15 0 07 -0 21 0 21

56 TCT 0 21 0 28 0 27 0 19 0 05 0 03 0 11 -0 07 0 35 0 33 0 24 0 30

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 12 -0 03 -0 14 -0 10 -0 04 -0 11 0 04 -0 02 0 09 -0 15 -0 17 0 00

59 TGG -0 04 0 02 0 06 -0 01 -0 03 -0 02 -0 11 0 09 -0 17 0 15 -0 15 0 18

60 TGT 0 00 0 00 0 21 0 08 0 13 -0 06 -0 05 0 02 0 30 0 27 0 16 0 36

61 TTA 0 14 0 05 0 06 0 10 -0 12 -0 07 -0 10 -0 06 -0 08 -0 03 -0 09 -0 07

62 TTC -0 35 -0 32 -0 34 -0 28 0 03 -0 28 -0 07 -0 19 -0 18 -0 17 -0 17 -0 16

63 TTG -0 28 -0 25 -0 29 -0 15 0 07 -0 18 -0 06 -0 05 -0 13 -0 10 -0 09 -0 07

64 TTT 0 30 0 28 0 44 0 29 0 26 -0 06 0 07 0 11 0 14 0 13 0 15 0 18

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.9 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 16 0 00 -0 10 -0 06 0 10 0 18 0 05 0 13 0 00 0 10 -0 08 -0 01 AAC 006 -005 000 001 -015 -007 -012 -007 001 006 018 -002

AAG 011 0 10 015 0 13 -012 -021 -010 -015 -007 003 011 0 04

AAT 005 0 01 000 -0 05 006 011 023 001 003 015 -015 -0 10

ACA -010 0 27 -013 0 07 009 -002 -005 -013 -005 004 004 -0 17

ACC -019 -0 33 -015 -0 24 004 007 020 021 014 021 035 0 36

ACG -016 0 25 -005 0 30 -012 -019 -026 -023 002 -028 -035 -0 24

ACT 013 0 04 026 0 09 -007 013 011 009 -011 013 005 0 09

AGA -014 0 03 -006 -0 01 010 005 010 012 004 023 008 0 04

AGC -021 -0 02 009 -0 02 010 005 021 004 036 014 039 0 23

AGG -021 0 27 010 0 14 -009 014 -018 -002 -018 -029 -032 -0 19

AGT -015 0 14 024 0 04 025 021 047 018 042 028 033 0 30

ATA -019 0 17 -008 0 18 020 -008 006 009 005 -003 -039 0 09

ATC -006 -0 30 -022 -0 14 007 018 002 004 010 024 029 0 30

ATG 001 0 08 000 -0 05 -007 007 016 -004 007 -021 007 0 02

ATT 018 0 01 021 0 06 -014 -008 -004 -006 -007 001 -019 -0 10

CAA -013 0 04 -009 -0 01 019 016 -006 008 000 031 -021 -0 01

CAC 003 -0 05 -007 -0 06 -007 -009 -009 010 005 019 023 0 33

CAG -0.05 0 .10 0.22 0 .16 -0.05 -0.15 -0.40 -0.22 0.06 -0.03 -0.27 0 .01

CAT 008 -0 09 004 0 04 002 -001 011 -002 -004 017 -029 -0 16

CCA -006 0 14 -003 0 03 018 009 -011 012 -018 036 -017 0 00

CCC -028 -0 29 -025 -0 21 034 026 031 002 033 049 055 0 38

CCG -018 0 13 003 0 07 -010 -011 -045 -015 -008 -007 005 0 00

CCT 017 0 09 021 0 13 -018 -010 002 -013 -018 000 -009 -0 04

CGA -032 0 13 -024 0 07 011 025 -020 -023 016 012 053 0 01

CGC -021 0 03 005 0 18 -009 -033 -013 -030 002 -025 -013 0 04

CGG 002 0 27 -002 0 26 010 -009 -041 012 009 -047 -029 -0 11

CGT 016 0 01 020 -0 08 -002 -008 -001 -014 024 005 011 0 19

CTA -010 0 10 -001 0 19 -002 000 -010 -003 -007 -008 -025 -0 06

CTC -026 -0 24 003 -0 16 042 008 025 009 019 -006 036 0 19

CTG -022 0 03 003 0 08 001 -011 -015 -005 022 -028 -006 0 19

CTT 030 0 21 042 0 13 011 -005 025 -013 -009 -015 -018 -0 08

GAA -009 0 03 -007 -0 08 010 010 007 014 014 017 004 0 03

GAC 005 -0 05 -002 0 03 -017 -017 -022 -016 -001 -005 010 -0 10

GAG 015 0 16 018 0 12 -016 -019 -021 -025 -017 -027 010 -0 25

GAT 009 -0 07 001 -0 03 011 011 016 010 010 015 -011 -0 09

GCA 014 0 15 -009 0 16 003 012 001 -008 -006 001 031 -0 16

GCC -005 -0 38 -022 -0 38 010 023 027 013 010 018 054 0 34

GCG 019 0 33 013 0 26 -015 -012 -029 -026 -015 -028 000 -0 13

GCT 032 0 02 021 -0 04 -011 -011 018 007 -013 -013 027 -0 01 41 GGA -0 10 0 25 -0 07 0 11 -0 03 -0 17 -0 07 0 14 0 20 -0 13 0 14 -0 07

42 GGC -0 06 0 14 0 17 0 13 -0 27 -0 31 -0 33 -0 27 -0 10 -0 30 0 38 -0 11

43 GGG 0 10 0 29 0 10 0 33 -0 03 -0 11 -0 10 -0 02 -0 26 -0 52 -0 48 -0 36

44 GGT 0 07 -0 18 -0 06 -0 19 0 09 0 12 0 49 0 22 0 13 0 21 0 45 0 15

45 GTA -0 11 0 28 -0 04 0 24 0 03 0 22 -0 17 -0 03 -0 10 -0 09 -0 26 -0 04

46 GTC 0 04 -0 35 -0 18 -0 32 0 08 -0 13 0 21 -0 05 0 13 0 15 0 53 0 27

47 GTG -0 01 0 23 -0 03 0 21 -0 04 0 16 -0 15 0 13 0 14 -0 13 -0 03 0 15

48 GTT 0 19 -0 03 0 15 -0 05 -0 06 -0 05 0 15 -0 06 -0 11 -0 02 0 13 -0 15

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 13 -0 24 -0 09 0 05 -0 11 -0 17 -0 06 -0 01 -0 01 0 27 0 36 0 29

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 15 -0 06 0 07 -0 02 0 02 0 10 0 21 0 03 -0 14 0 09 -0 21 -0 13

53 TCA -0 05 0 25 -0 08 0 20 -0 01 0 15 -0 18 -0 03 -0 17 -0 15 -0 09 -0 27

54 TCC -0 19 -0 34 -0 24 -0 26 0 10 0 01 0 17 0 18 0 32 0 21 0 46 0 30

55 TCG -0 15 0 15 -0 15 0 20 -0 17 -0 36 -0 27 -0 26 -0 16 -0 32 -0 30 -0 17

56 TCT 0 19 0 05 0 14 0 08 -0 20 -0 01 0 03 -0 10 -0 24 -0 23 -0 11 -0 11

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0.17 0.02 -0.16 -0.02 -0.20 -0.13 -0.13 -0.07 0.21 -0.17 0.16 0.15

59 TGG -0 12 0 11 0 00 0 02 -0 04 -0 13 0 09 0 09 -0 02 -0 19 0 14 0 10

60 TGT 0 11 -0 04 0 12 0 04 0 08 -0 03 0 25 0 11 0 14 -0 33 0 14 -0 18

61 TTA 0 00 0 06 -0 07 0 06 -0 15 0 00 -0 14 0 07 -0 09 0 08 -0 25 -0 02

62 TTC 0 09 -0 26 -0 18 -0 16 -0 15 -0 20 -0 16 -0 15 -0 06 -0 37 0 21 -0 04

63 TTG -0 07 -0 07 -0 12 -0 14 0 05 0 02 0 09 0 04 0 12 -0 10 0 21 0 20

64 TTT 0 27 0 07 0 15 0 02 0 10 0 14 0 19 0 14 0 18 -0 16 0 06 0 06

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table C.9 continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA 0 08 0 33 0 01 0 25 -0 27 0 09 -0 20 -0 05 0 08 0 08 0 00 0 04

2 AAC 0 26 -0 17 0 09 -0 13 0 08 -0 11 0 06 -0 06 0 15 0 12 0 20 0 11

3 AAG 0 28 0 22 0 12 0 20 -0 11 0 06 -0 11 0 04 -0 07 -0 14 -0 08 -0 03

4 AAT -0 02 0 06 0 15 0 09 0 08 -0 04 0 12 0 10 -0 10 -0 11 -0 11 -0 05

5 ACA 0 00 0 04 -0 06 0 12 0 08 0 16 0 13 0 14 -0 05 0 05 -0 06 -0 05

6 ACC 0 46 0 31 0 36 0 14 0 34 0 31 0 23 0 05 0 24 0 19 0 20 0 13

7 ACG -0 22 0 12 -0 11 0 34 -0 22 -0 11 -0 31 -0 17 0 02 -0 07 -0 13 -0 06

8 ACT 0 32 0 23 0 16 0 21 0 10 0 14 0 23 0 15 -O i l 0 03 0 02 -0 08 AGA 035 034 023 029 001 032 006 029 -004 003 O OO -004

AGC -007 -024 -012 0 23 038 025 035 022 -003 -O 13 -O 11 -O 15

AGG -014 -002 -030 0 08 -027 -020 -O 17 -O 17 003 001 -O 03 O 11

AGT 010 006 013 0 28 044 022 031 O 15 -029 -028 -O 25 -031

ATA -046 002 -053 0 15 -012 019 -O 18 -004 O 15 009 O Ol O 12

ATC 022 -008 023 0 16 009 -015 015 008 015 006 O 02 009

ATG 026 026 003 0 11 -018 -008 -029 -030 -002 -007 O 06 004

ATT 008 005 017 -0 05 008 000 O 12 -020 -O 15 -O 10 -O Ol -O 10

CAA -003 022 -001 0 12 -003 026 -O 14 022 -004 O 11 -O 05 -003

CAC 012 -020 -015 -0 32 041 -006 O 18 002 006 -004 O 08 001

CAG -013 -026 -035 -0 19 -013 -011 -O 19 -004 O 14 -O 10 O 02 000

CAT -048 -019 -004 -0 20 008 -001 O 16 001 -005 000 O OO 001

CCA 016 006 001 0 09 010 020 O 12 O 18 -002 O 16 -O 09 004

CCC 024 -001 032 0 09 019 -Oil 029 017 027 O 19 O 30 020

CCG -014 -022 -034 0 18 -045 -003 -041 -O 17 001 -008 -O 13 -004

CCT -038 -021 006 -0 29 020 009 001 001 -006 -009 -O 08 -O 19

CGA 030 008 004 0 36 -038 007 003 -007 007 -O 16 -O 09 000

CGC -0.03 -0.47 -0.49 -0 .38 0.15 -0.23 -0.10 -0.01 0.33 0.21 -O .16 0.01

CGG 016 -022 -054 0 29 -031 -042 -043 -036 O 13 O 14 -O Ol 022

CGT 001 -032 005 -0 48 004 -O 11 022 001 -005 -O 11 O 07 -009

CTA -029 010 -010 -0 10 -020 -O 13 -027 006 -003 O 10 -O 02 008

CTC -025 -022 018 0 21 019 -O 11 O 15 005 029 009 O 08 -008

CTG -042 -019 -039 0 16 -016 -O 11 -022 -001 -008 -O 18 -O 14 -004

CTT -049 005 -029 -0 04 -011 -036 -003 -027 O 15 000 O 28 -003

GAA 001 021 -014 0 08 -013 O 11 -006 O 11 000 002 O Ol -002

GAC 005 -030 -002 -0 42 018 001 006 -003 O 11 O 11 O 17 O 13

GAG 020 -016 -003 0 07 -020 -024 -030 -O 13 004 -003 -O 11 003

GAT 007 001 035 -0 11 023 001 022 002 -006 -005 -O 07 -007

GCA 018 -007 027 0 03 001 002 005 O 19 -O 15 -O 10 -O 09 -O 13

GCC 057 016 043 -0 16 013 -005 021 -009 033 033 O 43 030

GCG 041 -019 -008 0 18 -037 -030 -036 -024 -001 -O 15 -O 11 -005

GCT 024 002 -010 -0 13 014 O 12 031 -009 -O 12 000 O 05 -007

GGA 011 -017 -005 0 16 -003 001 -O 10 002 005 O 15 -O 03 O 13

GGC 029 -033 003 -0 38 005 -020 -002 -005 008 004 O 11 008

GGG -016 -010 -010 -0 17 -039 -043 -042 -039 O 18 023 O 03 033

GGT 051 026 063 -0 08 004 007 041 008 -O 13 -021 O 05 -O 11

GTA -051 -018 -029 -0 27 001 -O 12 -O 14 -009 002 002 -O 17 -007

GTC 049 -007 037 -0 07 026 -004 O 17 -020 023 004 O 32 023

GTG 013 -009 -036 0 16 -010 -O 13 -O 16 -O 11 -026 -O 14 -O 32 -O 10 48 GTT 0 23 -0 11 0 20 -0 31 0 19 -O 17 O 18 -0 25 0 06 0 02 O 15 0 00

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 23 -0 19 -0 05 -0 27 0 06 0 00 -0 05 O 18 0 06 0 02 0 07 0 08

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 04 -0 02 -0 03 -0 18 0 14 -0 02 0 06 0 01 -0 05 -O 10 -0 04 -0 01

53 TCA -0 37 0 02 -0 01 0 27 -O i l O 14 -O i l -0 04 0 02 O 15 0 05 0 05

54 TCC -0 11 0 02 0 32 -0 05 O 14 O 18 O 17 O 13 0 33 0 36 0 21 0 30

55 TCG -0 02 -0 22 0 06 0 23 -0 32 -O 10 -0 34 -O 11 O 19 0 27 0 01 O 15

56 TCT -0 17 -0 30 0 20 -0 18 0 06 0 04 O 13 0 01 -0 01 0 09 0 07 -0 05

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 26 -0 19 -0 46 -0 41 O 16 -0 27 0 01 -O 11 0 23 O 14 O 15 O 17

59 TGG 0 17 0 51 0 36 0 52 -0 09 -0 09 -O 18 0 05 0 04 -O 10 -0 08 0 06

60 TGT -0 17 -0 15 0 05 -0 23 0 08 -O 19 0 03 -0 03 -0 07 -0 09 -0 20 -0 09

61 TTA -0 22 -0 19 -0 15 0 01 -0 19 -0 08 -0 19 -0 05 -0 02 0 03 -0 02 0 04

62 TTC -0 08 -0 22 -0 01 -0 25 0 09 -O 14 O 15 0 06 0 27 0 23 0 28 0 23

63 TTG 0 12 0 08 0 13 0 11 O 14 0 27 O 15 0 27 -0 06 -0 03 -0 04 -0 02

64 TTT -0 05 0 13 -0 20 0 38 0 21 -0 03 O 19 0 04 -O 19 -O 14 -0 07 -O 13

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.9 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA 0 09 0 22 0 20 O 10 0 01 O 10 0 01 0 11 -0 04 -0 01 -0 10 -0 08

2 AAC 0 24 O 19 0 35 O 15 O 19 O 14 0 17 0 18 0 14 -0 14 0 22 0 01

3 AAG -O 10 -O 13 -O 17 -0 21 -0 07 -0 26 0 10 -0 06 0 14 0 01 0 21 0 05

4 AAT -O 12 -O 15 -0 21 -0 08 -O 15 -0 21 -0 27 0 05 0 02 -0 08 0 10 -0 09

5 ACA -0 06 0 25 -0 06 0 30 -O 12 0 06 -0 04 0 13 -0 18 0 24 -0 03 0 24

6 ACC O 16 0 08 0 21 0 08 0 28 0 27 0 30 -0 08 0 06 -0 09 0 08 0 04

7 ACG -O 12 0 26 -0 27 0 23 -O 12 -0 09 -0 21 0 24 -0 25 0 12 -0 22 0 22

8 ACT -0 20 -0 21 -O 10 -O 18 0 03 0 08 -0 12 -0 21 -0 07 -0 03 -0 08 -0 11

9 AGA 0 00 -0 01 O 11 -0 02 -0 03 -0 04 0 23 -0 13 -0 08 0 08 0 13 0 02

10 AGC O 12 -O 16 0 28 0 05 -O 13 -0 21 -0 16 0 03 -0 10 0 14 0 02 0 14

11 AGG -O 13 -0 02 -O 18 -O 10 O 19 O 15 0 42 0 39 -0 11 0 12 -0 13 0 22

12 AGT -0 23 -0 22 -0 29 -O 19 -0 32 -0 22 -0 33 -0 20 -0 16 -0 14 -0 04 -0 08

13 ATA O 11 0 25 -0 09 0 31 O 14 O 17 0 11 0 40 0 06 0 30 0 00 0 33

14 ATC 0 35 0 26 0 29 0 31 0 21 0 06 0 03 0 07 0 30 0 07 0 24 0 21

15 ATG -0 05 -0 01 -0 09 0 08 -0 04 -0 03 -0 12 0 07 0 02 -0 01 0 02 -0 02 ATT -017 -030 -022 -022 -011 -009 -020 -023 -009 -026 -019 -021

CAA 0 05 0 04 -005 -004 006 -004 -002 -005 -010 005 -017 004

CAC 0 21 0 15 029 022 023 010 009 006 010 -001 015 -009

CAG -0 03 0 00 -026 012 -018 -018 010 029 -005 017 -009 021

CAT -0 03 -0 19 -020 -007 -010 002 -017 -003 006 000 002 -005

CCA -0 02 0 27 016 013 012 000 020 -006 001 026 015 018

CCC 0 21 0 25 041 009 022 014 042 020 -029 007 -011 004

CCG -0 11 0 29 005 016 -024 -026 -017 047 -028 017 -003 015

CCT -0 22 -0 10 -024 -030 -012 -011 -030 -010 -025 001 -015 -011

CGA -0 15 0 28 025 030 -023 -002 017 047 -016 028 -004 017

CGC 0 00 0 40 052 032 -003 -012 -011 031 026 040 015 000

CGG 0 33 0 12 000 035 004 030 039 062 -007 028 010 036

CGT -0 04 -0 18 -005 -008 -016 -036 -027 -040 -025 -027 -018 -029

CTA -0 03 0 20 001 006 -004 009 012 018 000 011 -002 022

CTC 0 34 0 21 029 030 020 010 006 -013 002 005 009 014

CTG -0 18 -0 17 -032 017 -021 -017 -005 009 -028 -008 -022 013

CTT 0 00 -0 08 -017 -004 -026 -016 -015 -009 002 -004 -016 -006

GAA 0 .08 0 .11 0.06 -0.02 0.01 0.03 -0.01 -0.07 -0.01 0.02 -0.04 -0.06

GAC 0 24 0 13 038 013 025 008 017 008 011 018 015 002

GAG -0 25 -0 03 -016 005 -013 -012 004 026 003 014 -003 011

GAT -0 02 -0 06 -008 -016 -004 -006 -013 -006 008 -012 -002 -009

GCA 0 00 0 30 026 022 -008 -003 016 004 -011 027 011 026

GCC 0 29 0 04 049 -006 043 031 048 -006 025 003 019 -004

GCG -0 05 0 14 -003 013 -014 -019 016 031 -028 025 -008 021

GCT -0 01 -0 22 005 -033 010 -004 023 -030 001 -019 -013 -021

GGA 0 11 0 36 022 033 -008 018 008 038 022 042 028 037

GGC 0 14 -0 05 039 -006 009 -005 020 012 018 018 020 012

GGG 0 11 0 17 016 034 032 021 033 056 015 046 020 038

GGT 0 05 -0 29 003 -027 011 -002 -006 -037 -004 -037 -009 -031

GTA -0 11 0 26 -016 027 -003 009 -008 032 004 026 -010 021

GTC 0 13 0 18 043 016 013 019 013 -003 028 009 032 007

GTG -0 21 -0 18 -013 008 -011 -001 -030 023 -031 000 -028 007

GTT 0 02 -0 16 004 -015 -020 006 002 -017 018 -021 011 -019

TAA 0 00 0 00 000 000 000 000 000 000 000 000 000 000

TAC 0 30 0 10 027 012 021 020 015 003 019 -011 006 002

TAG 0 00 0 00 000 000 000 000 000 000 000 000 000 000

TAT -0 12 -0 11 -018 -012 -009 002 -014 -010 026 -014 -013 -006

TCA -0 01 0 42 001 020 -015 007 003 022 -011 040 005 027

TCC 0 26 0 24 035 022 025 029 033 013 007 007 012 003 55 TCG 0 09 0 43 -0 04 0 44 0 24 0 23 0 26 0 48 -0 14 0 39 -0 01 0 20

56 TCT -0 17 -0 17 -0 20 -0 21 -0 03 0 02 -0 04 -0 13 -0 08 -0 14 -0 24 -0 14

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 26 0 20 0 20 0 33 0 30 0 24 0 00 0 23 -0 03 0 23 0 25 0 17

59 TGG 0 01 0 04 -0 12 0 01 0 18 -0 02 -0 24 0 01 -0 08 0 03 0 21 -0 07

60 TGT -0 03 -0 13 -0 19 -0 20 0 07 -0 14 -0 18 -0 16 0 08 -0 21 0 05 -0 15

61 TTA 0 06 0 12 -0 04 0 22 -0 02 0 14 0 03 0 08 0 09 0 11 -0 03 0 17

62 TTC 0 45 0 36 0 52 0 46 0 44 0 36 0 47 0 17 0 43 0 16 0 40 0 26

63 TTG -0 10 -0 17 -0 12 -0 12 0 08 0 05 0 07 -0 08 -0 05 -0 11 -0 13 -0 08

64 TTT -0 17 -0 36 -0 21 -0 19 -0 16 -0 19 -0 09 -0 19 -0 06 -0 21 0 01 -0 27

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.9 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 03 0 00 -0 09 -0 17 0 08 -0 13 0 01 0 00 -0 08 -0 15 -0 14

2 AAC 0 00 -0 14 0 00 -0 06 0 15 -0 03 0 10 0 00 0 00 0 00 -0 14 -0 12

3 AAG 0 00 0 01 0 00 0 16 0 22 0 28 0 16 0 30 0 00 0 12 0 26 0 23

4 AAT 0 00 0 09 0 00 0 06 -0 01 0 12 0 03 0 09 0 00 0 07 0 11 0 05

5 ACA 0 00 0 07 0 00 -0 11 -0 05 0 07 0 07 0 04 0 00 -0 17 -0 07 -0 08

6 ACC 0 00 -0 01 0 00 0 12 0 06 0 12 0 20 0 01 0 00 0 13 0 04 0 00

7 ACG 0 00 -0 05 0 00 -0 16 -0 05 0 21 0 07 0 28 0 00 -0 21 0 04 0 05

8 ACT 0 00 0 04 0 00 0 06 -0 16 -0 14 0 01 -0 20 0 00 0 21 0 03 0 07

9 AGA 0 00 0 18 0 00 0 13 -0 04 0 27 -0 01 0 17 0 00 0 27 0 08 0 12

10 AGC 0 00 0 09 0 00 -0 08 0 16 0 19 0 12 0 05 0 00 -0 08 0 03 0 00

11 AGG 0 00 0 06 0 00 0 14 -0 09 0 20 -0 18 0 11 0 00 0 09 0 13 0 35

12 AGT 0 00 0 10 0 00 0 01 0 02 0 23 0 18 0 18 0 00 -0 17 0 01 -0 16

13 ATA 0 00 -0 20 0 00 -0 24 -0 28 -0 12 -0 29 -0 14 0 00 -0 13 -0 18 -0 09

14 ATC 0 00 0 11 0 00 0 27 0 27 0 02 0 29 0 22 0 00 0 06 0 19 0 13

15 ATG 0 00 -0 04 0 00 0 03 0 05 0 05 -0 03 0 13 0 00 -0 07 0 00 0 05

16 ATT 0 00 0 08 0 00 0 04 0 00 -0 13 0 10 -0 11 0 00 -0 07 0 03 0 07

17 CAA 0 00 0 10 0 00 0 08 0 04 0 16 -0 02 0 01 0 00 0 21 -0 06 -0 08

18 CAC 0 00 0 02 0 00 -0 08 -0 03 -0 04 0 15 0 02 0 00 -0 04 -0 01 0 04

19 CAG 0 00 -0 23 0 00 -0 11 -0 01 0 25 -0 09 0 24 0 00 -0 23 0 13 0 09

20 CAT 0 00 0 17 0 00 -0 08 -0 08 -0 05 -0 13 -0 14 0 00 0 14 0 01 -0 08

21 CCA 0 00 0 07 0 00 -0 07 -0 08 0 14 0 04 -0 07 0 00 -0 19 -0 17 0 08

22 CCC 0 00 0 13 0 00 0 20 -0 03 -0 12 -0 02 -0 26 0 00 -0 03 0 17 -0 05 CCG 000 -025 000 -014 007 023 020 028 000 015 020 030

CCT 000 011 000 -004 -015 -013 -013 -011 000 0 00 010 -003

CGA 000 -028 000 -012 003 032 -006 006 000 -0 45 004 -009

CGC 000 -045 000 -017 -006 003 -010 -016 000 -0 41 -034 -018

CGG 000 -022 000 -027 -020 -011 -051 -012 000 -0 37 024 004

CGT 000 -023 000 -016 -006 -022 000 -008 000 -0 30 -025 -038

CTA 000 -005 000 -006 -009 -022 -023 -001 000 0 03 -022 -010

CTC 000 -005 000 -015 001 -019 -019 -013 000 -0 35 000 -030

CTG 000 -004 000 010 013 025 -001 034 000 0 01 019 020

CTT 000 -029 000 -036 -029 -043 -030 -033 000 -0 31 -025 -034

GAA 000 006 000 002 010 014 011 006 000 0 11 -005 -009

GAC 000 -013 000 -006 023 -001 001 -010 000 -0 07 -005 -019

GAG 000 -014 000 -004 013 030 -006 021 000 -0 11 013 014

GAT 000 016 000 -003 002 -003 -001 -007 000 0 20 003 003

GCA 000 -004 000 -010 004 003 -004 001 000 -0 31 -005 -005

GCC 000 018 000 011 028 -001 023 -007 000 0 17 017 -014

GCG 000 -019 000 -023 -001 010 001 012 000 -0 09 -010 018

GCT 0.00 0.04 0.00 0.09 -0.03 -0.30 -0.02 -0.16 0.00 0 .35 -0.02 0.05

GGA 000 011 000 -015 011 008 -008 002 000 0 01 -008 -003

GGC 000 -017 000 -012 -009 -020 011 -012 000 -0 07 -019 -027

GGG 000 -002 000 015 017 -011 007 -002 000 0 08 022 023

GGT 000 000 000 014 011 001 023 -002 000 0 08 008 007

GTA 000 000 000 -009 -011 -018 -014 003 000 -0 11 -006 014

GTC 000 -004 000 030 028 -006 028 007 000 0 12 010 003

GTG 000 015 000 017 023 018 006 031 000 0 01 016 023

GTT 000 -012 000 -010 -013 -024 000 -025 000 -0 12 -009 -011

TAA 000 000 000 000 000 000 000 000 000 0 00 000 000

TAC 000 -014 000 000 010 -001 015 -003 000 0 12 -010 -012

TAG 000 000 000 000 000 000 000 000 000 0 00 000 000

TAT 000 016 000 -002 -005 -015 -013 -018 000 0 07 009 001

TCA 000 -004 000 -019 -018 002 -017 006 000 -0 19 -013 -007

TCC 000 015 000 021 007 -002 -003 -002 000 0 14 015 017

TCG 000 -026 000 -018 005 001 -017 026 000 0 00 -020 008

TCT 000 011 000 008 -014 -015 -010 -020 000 0 14 011 013

TGA 000 000 000 000 000 000 000 000 000 0 00 000 000

TGC 000 -012 000 -016 000 -020 005 -010 000 -0 13 -006 -014

TGG 000 -011 000 009 -015 005 -008 -002 000 0 01 000 -001

TGT 000 017 000 005 -005 -004 -004 -005 000 0 09 004 011

TTA 000 009 000 008 -011 -005 -015 -002 000 0 04 -016 -003 62 TTC 0 00 0 01 0 00 0 22 0 27 0 07 0 23 0 21 0 00 0 02 0 09 0 10

63 TTG 0 00 0 17 0 00 0 22 0 30 0 23 0 37 0 35 0 00 0 27 0 42 0 35

64 TTT 0 00 -0 15 0 00 -0 02 -0 10 -0 15 -0 09 -0 15 0 00 -0 10 -0 06 0 00

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table C.9 continued

61 62 63 64

TTA TTC TTG TTT

1 AAA -0 03 0 00 0 10 -0 08

2 AAC 0 10 -0 01 -0 07 0 03

3 AAG 0 24 0 12 0 16 0 04

4 AAT -0 07 -0 02 -0 07 0 00

5 ACA 0 00 0 22 0 22 -0 09

6 ACC 0 08 0 05 0 20 0 23

7 ACG 0 05 0 11 0 03 -0 02

8 ACT -0 30 -0 17 -0 31 -0 09

9 AGA -0 03 0 14 0 09 -0 09

10 AGC 0 28 0 15 0 31 0 11

11 AGG 0 00 0 01 0 13 -0 21

12 AGT -0 05 -0 08 -0 02 0 02

13 ATA -0 05 -0 04 0 10 -0 17

14 ATC 0 21 0 07 0 16 0 24

15 ATG 0 22 0 11 0 29 -0 07

16 ATT -0 13 -0 12 -0 03 0 07

17 CAA 0 02 0 10 -0 01 0 09

18 CAC 0 25 -0 06 0 04 0 22

19 CAG 0 02 -0 07 0 00 -0 23

20 CAT -0 20 -0 09 -0 15 -0 03

21 CCA -0 06 0 08 -0 01 -0 12

22 CCC -0 07 -0 10 0 11 -0 12

23 CCG -0 27 0 08 0 05 0 02

24 CCT -0 06 0 01 0 02 0 19

25 CGA -0 12 0 14 0 12 -0 12

26 CGC 0 05 0 17 0 30 0 25

27 CGG -0 12 -0 14 -0 17 -0 34

28 CGT -0 08 0 17 -0 13 0 34

29 CTA -0 10 0 09 0 04 0 03 CTC 0 15 -0 29 0 08 -0 18

CTG 0 21 0 01 0 13 0 11

CTT -0 34 -0 49 -0 32 -0 17

GAA 0 10 0 20 0 05 -0 02

GAC 0 12 0 05 -0 06 0 13

GAG 0 06 0 02 0 08 -0 23

GAT -0 11 -0 05 -0 16 -0 05

GCA -0 01 0 01 0 04 -0 20

GCC 0 21 0 00 0 13 0 01

GCG -0 08 -0 11 -0 07 -0 21

GCT -0 04 0 12 -0 18 0 22

GGA -0 06 -0 03 0 11 -0 33

GGC 0 16 0 24 0 22 0 18

GGG -0 19 -0 45 -0 27 -0 50

GGT 0 05 0 15 0 03 0 44

GTA 0 19 0 09 0 08 -0 14

GTC 0 20 0 00 -0 01 0 10

GTG 0.31 0.21 0.17 0.05

GTT -0 11 -0 22 -0 16 0 10

TAA 0 00 0 00 0 00 0 00

TAC 0 19 0 01 -0 06 0 15

TAG 0 00 0 00 0 00 0 00

TAT -0 06 -0 12 -0 16 -0 02

TCA -0 18 -0 01 -0 03 -0 15

TCC 0 05 0 02 0 09 -0 03

TCG -0 14 -0 06 -0 09 -0 14

TCT -0 17 0 07 -0 19 0 13

TGA 0 00 0 00 0 00 0 00

TGC 0 07 0 04 0 18 -0 18

TGG 0 02 0 00 0 11 0 00

TGT 0 00 0 04 -0 09 0 08

TTA -0 01 0 06 0 06 0 00

TTC 0 09 -0 09 -0 02 0 16

TTG 0 34 0 27 0 26 0 21

TTT -0 13 -0 20 -0 15 0 11

TTA TTC TTG TTT

61 62 63 64 Table ClO: CPW matrix Saccaromyces.cerevisiae highly expressed sequences (left codon indicated in column 2, right codon indicated in row 2). Host cell: S.cerevisiae; Sequence data: full S.cerevisiae genome; Highly expressed group: 300 seqs.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 0 67 0 35 0 49 0 42 0 66 0 30 0 47 0 24 0 43 0 44 0 51 0 55

2 AAC -0 05 -0 62 -0 63 0 07 0 12 -0 62 -0 11 -0 52 -0 53 -0 26 -0 04 -0 25

3 AAG -0 10 -0 61 -0 65 0 12 0 21 -0 59 0 26 -0 53 -0 59 -0 16 0 20 0 11

4 AAT 0 61 0 16 0 35 0 58 0 63 0 28 0 62 0 40 0 42 0 44 0 38 0 44

5 ACA 0 49 0 22 0 13 0 28 0 52 0 49 0 78 0 49 -0 19 0 62 -0 07 0 38

6 ACC -0 13 -0 71 -0 71 -0 18 -0 15 -0 67 0 00 -0 56 -0 54 -0 15 0 12 0 14

7 ACG 0 50 0 37 0 29 0 53 0 57 0 56 0 62 0 61 0 07 0 89 0 17 0 49

8 ACT 0 31 -0 16 0 07 0 61 0 19 -0 34 0 49 -0 34 -0 27 0 48 0 83 0 53

9 AGA 0 25 -0 53 -0 59 0 10 0 03 -0 59 0 27 -0 38 -0 53 0 19 0 24 -0 01

10 AGC 0 54 -0 04 0 21 0 55 0 59 0 17 1 00 0 19 0 38 -0 02 0 31 0 46

11 AGG 0 42 0 44 0 45 0 47 0 68 0 33 0 69 0 71 0 29 0 66 0 56 0 84

12 AGT 0 49 0 04 0 48 0 46 0 72 0 47 0 69 0 31 0 70 0 57 0 39 0 52

13 ATA 0 56 0 50 0 64 0 67 0 53 0 32 0 63 0 47 0 58 0 75 0 58 0 59

14 ATC -0 31 -0 66 -0 68 -0 28 -0 11 -0 55 0 04 -0 63 -0 67 0 30 0 14 -0 10

15 ATG 0 23 -0 30 -0 25 0 29 0 39 -0 12 0 56 -0 33 -0 30 0 47 0 16 0 20

16 ATT 0 49 -0 20 0 02 0 50 0 55 -0 15 0 49 0 01 -0 07 0 67 0 48 0 64

17 CAA 0 22 -0 40 -0 43 0 25 0 26 -0 48 0 50 -0 29 -0 36 0 00 0 23 -0 16

18 CAC 0 10 -0 55 -0 67 0 07 0 12 -0 62 0 44 -0 53 -0 59 0 31 0 61 -0 02

19 CAG 0 54 0 40 0 20 0 16 0 43 0 35 -0 08 0 60 0 19 0 11 0 62 0 39

20 CAT 0 54 -0 09 0 31 0 50 0 51 0 07 0 45 0 36 0 46 0 74 0 62 0 87

21 CCA 0 20 -0 52 -0 64 -0 15 0 12 -0 54 0 45 -0 53 -0 61 0 13 -0 09 -0 11

22 CCC 0 41 -0 03 -0 07 0 27 0 58 0 09 0 18 -0 08 0 21 0 63 0 65 0 49

23 CCG 0 84 0 75 0 63 0 75 0 80 1 00 0 85 0 94 0 73 0 53 1 00 0 89

24 CCT 0 45 0 10 0 28 0 51 0 71 -0 20 0 22 0 10 0 54 0 81 0 64 0 61

25 CGA 0 83 0 56 0 92 0 70 0 87 0 80 0 40 0 88 0 83 0 67 1 00 0 09

26 CGC 0 46 0 34 0 33 0 65 0 52 -0 14 0 29 0 42 0 80 1 00 1 00 0 19

27 CGG 0 71 0 44 0 73 0 62 0 54 1 00 0 49 1 00 0 86 0 43 0 68 1 00

28 CGT 0 19 -0 25 -0 18 0 13 0 32 -0 44 0 39 -0 23 0 07 0 66 0 53 -0 04

29 CTA 0 39 0 19 0 24 0 47 0 47 0 61 0 41 0 22 -0 39 0 74 0 34 0 41

30 CTC 0 67 0 17 0 03 0 40 0 68 -0 21 -0 29 0 57 0 65 0 69 0 74 0 68

31 CTG 0 42 0 38 0 29 0 35 0 62 0 33 0 72 0 54 0 78 0 50 0 79 0 66

32 CTT 0 78 0 60 0 61 0 71 0 89 0 54 0 61 0 55 0 76 0 72 1 00 0 81

33 GAA 0 22 -0 35 -0 37 0 24 0 28 -0 40 0 28 -0 31 -0 39 -0 03 0 50 0 13 34 GAC -0 04 -0 57 -0 62 -0 07 0 20 -0 62 0 44 -0 50 -0 44 0 17 0 22 0 02

35 GAG 0 49 -0 03 -0 03 0 30 0 46 0 38 0 47 0 30 0 32 0 19 0 53 0 41

36 GAT 0 44 0 19 0 27 0 40 0 68 -0 05 0 42 0 12 0 34 0 55 0 53 0 78

37 GCA 0 58 0 37 0 27 0 62 0 51 0 40 0 60 0 61 -0 07 0 56 0 22 0 45

38 GCC -0 02 -0 58 -0 62 -0 07 0 10 -0 57 0 41 -0 53 -0 51 0 51 0 48 0 70

39 GCG 0 83 0 45 0 26 0 56 0 79 0 50 0 71 0 65 0 67 0 81 0 82 0 67

40 GCT 0 26 -0 46 -0 40 0 21 0 35 -0 55 0 38 -0 37 -0 28 0 56 0 52 0 43

41 GGA 0 64 0 46 0 46 0 58 0 69 0 39 0 63 0 50 0 43 0 72 0 89 0 74

42 GGC 0 55 0 00 0 27 0 49 0 68 0 49 0 79 0 02 0 37 0 24 0 27 0 44

43 GGG 0 62 0 55 0 40 0 73 0 49 0 48 0 43 0 30 0 39 0 39 0 61 0 86

44 GGT 0 03 -0 61 -0 60 0 08 0 32 -0 56 0 41 -0 58 -0 55 0 53 0 52 0 55

45 GTA 0 66 0 37 0 47 0 42 0 59 0 53 0 58 0 26 0 54 0 72 0 34 0 69

46 GTC -0 17 -0 63 -0 70 -0 17 0 27 -0 65 0 67 -0 60 -0 56 -0 36 0 74 0 21

47 GTG 0 51 0 10 0 07 0 64 0 54 0 25 0 52 0 48 -0 20 0 50 0 66 0 57

48 GTT 0 31 -0 27 -0 21 0 21 0 59 -0 45 0 66 -0 37 -0 17 0 56 0 52 0 67

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC -0 09 -0 58 -0 61 0 08 0 04 -0 56 0 42 -0 57 -0 57 0 30 0 52 -0 09

51 TAG 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

52 TAT 0 60 0 06 0 43 0 61 0 67 0 42 0 66 0 30 0 59 0 52 0 64 0 64

53 TCA 0 69 0 22 0 07 0 48 0 37 0 20 0 29 0 52 -0 29 0 19 0 03 0 39

54 TCC 0 04 -0 68 -0 74 -0 25 -0 17 -0 66 -0 13 -0 59 -0 60 -0 09 0 10 -0 02

55 TCG -0 01 0 17 -0 05 0 38 0 68 0 80 0 59 0 12 -0 23 0 65 0 22 0 21

56 TCT 0 21 -0 45 -0 36 0 38 0 29 -0 54 0 11 -0 44 0 06 0 67 0 50 0 41

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 26 0 62 0 12 0 42 0 11 0 02 0 50 0 70 0 34 0 29 0 76 0 51

59 TGG 0 15 -0 17 -0 17 0 14 0 59 -0 25 0 16 -0 28 -0 33 0 35 0 17 0 33

60 TGT 0 09 -0 43 -0 30 0 00 0 45 -0 52 0 23 -0 30 -0 26 0 13 0 40 0 70

61 TTA 0 57 -0 21 0 06 0 61 0 25 -0 38 0 58 -0 14 -0 19 0 16 0 18 0 35

62 TTC -0 20 -0 61 -0 64 -0 13 0 26 -0 60 0 42 -0 51 -0 58 -0 10 0 44 -0 07

63 TTG -0 27 -0 64 -0 68 -0 28 0 17 -0 65 0 43 -0 59 -0 62 -0 04 0 21 -0 06

64 TTT 0 68 0 33 0 47 0 61 0 54 0 07 0 47 0 34 0 32 0 39 0 43 0 53

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table ClO continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA 0 52 0 14 0 16 0 15 0 22 0 25 0 34 0 54 0 04 0 54 0 59 0 32 AAC 053 -061 -024 -041 -045 -053 005 -033 -050 040 O 18 -O 19

AAG 062 -056 -018 -031 -041 -055 035 -021 -051 O 16 057 -O 16

AAT 071 003 022 039 026 044 063 052 020 009 044 036

ACA 068 051 029 041 060 033 041 022 001 050 094 052

ACC 044 -061 -054 -059 -026 -049 033 008 -040 O 13 045 030

ACG 054 012 018 063 014 043 034 042 009 000 044 055

ACT 038 -030 041 -012 -048 -044 043 008 -054 046 060 -O 12

AGA 047 -048 -021 -032 -026 -041 021 006 -054 044 044 -O 11

AGC 036 002 059 054 009 013 039 051 054 056 1 OO O 10

AGG 050 046 028 027 051 025 039 039 O 19 058 047 050

AGT 063 052 054 019 052 063 079 042 061 090 062 048

ATA 066 051 037 068 079 078 068 049 053 059 077 065

ATC 041 -064 -047 -046 -044 -039 038 009 -039 035 043 -002

ATG 071 -025 000 -019 -005 -019 Oil 013 -033 027 059 026

ATT 062 -024 028 -013 -030 -051 021 O 17 -048 030 039 -002

CAA 054 -050 -022 -016 -019 -017 026 -008 -037 036 042 -005

CAC 069 -052 -045 -046 -027 -061 -O 17 028 -021 078 032 O 12

CAG 0.85 0.27 0.60 0.29 0.22 0.37 0.07 0.23 0.45 0.60 0.37 -0.02

CAT 048 009 046 023 007 013 041 026 -027 058 062 -O 19

CCA 053 -052 -038 -042 -012 -021 002 036 -047 053 074 -022

CCC 058 -036 036 019 035 012 009 067 006 065 100 029

CCG 069 042 043 062 059 026 049 079 040 -009 072 078

CCT 078 013 045 013 -033 -054 028 -028 -022 021 O 10 O 14

CGA 033 076 070 079 090 051 078 100 068 1 OO 1 OO 1 OO

CGC 047 -001 010 075 -010 -043 -038 035 043 051 1 OO 001

CGG 100 079 100 053 082 100 062 100 100 030 1 OO 1 OO

CGT 043 -035 -018 -032 -056 -060 054 003 -038 -003 047 005

CTA 061 058 045 031 012 -023 004 -O 10 -028 -O 12 090 O 14

CTC 058 046 047 033 074 059 066 089 065 082 077 072

CTG 060 -010 035 012 016 -017 027 -004 025 -020 088 046

CTT 085 063 053 054 030 026 069 059 046 027 059 034

GAA 060 -032 -019 -029 -019 -031 033 034 -026 053 056 -O 11

GAC 061 -040 -031 -024 -047 -041 -O 19 -021 -041 043 061 -023

GAG 064 012 054 023 003 015 037 -022 O 14 042 026 -024

GAT 069 -029 024 -002 027 024 060 022 -O 12 036 058 O 16

GCA 082 045 044 058 039 029 069 049 027 076 082 051

GCC 040 -058 -041 -058 -022 011 051 O 12 -044 036 076 031

GCG 081 059 078 057 046 034 O 12 041 027 050 084 074

GCT 075 -042 -015 -030 -048 -059 046 -003 -061 046 066 -O 10 41 GGA 0 74 0 69 0 63 0 52 0 41 0 48 0 65 0 60 0 52 0 39 0 89 0 33

42 GGC 0 82 0 42 0 52 0 47 -0 32 -0 32 0 14 -0 03 -0 18 0 30 0 87 -0 07

43 GGG 0 81 0 33 0 64 0 79 0 66 0 53 0 51 0 73 0 31 -0 11 0 59 0 01

44 GGT 0 49 -0 62 -0 42 -0 50 -0 41 -0 52 0 60 0 03 -0 53 0 34 0 78 0 01

45 GTA 0 72 0 63 0 67 0 68 0 43 0 48 0 65 0 34 0 27 0 74 0 75 0 54

46 GTC 0 60 -0 70 -0 32 -0 54 -0 46 -0 64 0 57 -0 28 -0 43 0 16 0 91 0 32

47 GTG 0 72 0 40 0 20 0 49 0 16 0 09 0 22 0 54 0 26 -0 19 0 72 0 41

48 GTT 0 76 -0 42 -0 19 -0 26 -0 32 -0 18 0 50 0 20 -0 54 0 34 0 44 -0 06

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 30 -0 57 -0 26 -0 19 -0 27 -0 27 -0 12 -0 32 -0 53 0 48 0 72 -0 09

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 59 0 26 0 26 0 10 0 10 0 18 0 49 0 42 0 01 0 66 0 50 0 25

53 TCA 0 61 0 55 0 04 0 56 0 38 0 38 0 25 0 31 -0 16 0 09 0 61 0 22

54 TCC 0 29 -0 71 -0 59 -0 56 -0 14 -0 52 0 25 0 14 -0 27 0 48 0 61 0 31

55 TCG 0 52 -0 19 0 01 0 41 -0 16 -0 19 -0 17 0 04 -0 19 0 01 1 00 0 15

56 TCT 0 55 -0 49 0 24 -0 29 -0 50 -0 50 0 16 -0 22 -0 62 -0 15 -0 02 -0 10

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0.32 0.26 0.19 0.32 -0.27 -0.49 0.84 0.11 -0.25 0.21 1.00 0.60

59 TGG 0 70 -0 33 0 00 -0 13 -0 16 -0 36 0 42 0 31 -0 28 0 40 0 34 0 16

60 TGT 0 43 -0 48 -0 11 -0 13 -0 02 -0 25 0 03 0 46 -0 37 0 35 0 39 0 01

61 TTA 0 62 -0 27 0 07 0 16 -0 20 -0 25 0 14 0 26 -0 14 0 41 0 50 0 00

62 TTC 0 54 -0 55 -0 23 -0 32 -0 55 -0 62 0 04 -0 19 -0 62 -0 37 0 83 -0 35

63 TTG 0 39 -0 58 -0 44 -0 58 -0 34 -0 55 0 00 0 19 -0 56 -0 24 0 65 -0 10

64 TTT 0 79 -0 01 0 21 0 09 0 52 0 32 0 67 0 60 0 54 0 28 0 83 0 59

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table ClO continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA 0 64 0 63 0 82 0 24 0 21 0 83 0 06 0 62 0 33 0 42 0 39 0 33

2 AAC 0 87 -0 17 -0 08 -0 53 0 28 -0 23 -0 17 0 20 -0 30 -0 27 0 03 -0 04

3 AAG 0 85 0 30 0 75 -0 49 -0 12 0 52 -0 02 0 31 -0 40 -0 54 -0 05 -0 14

4 AAT 0 66 0 49 0 85 0 35 0 22 0 56 0 44 0 56 0 15 -0 10 0 30 0 22

5 ACA 0 73 0 35 0 30 0 38 0 69 0 42 0 57 0 64 0 34 0 27 0 29 0 45

6 ACC 0 80 1 00 0 32 -0 01 0 28 0 36 0 77 0 43 -0 23 -0 20 0 25 -0 18

7 ACG 1 00 0 27 1 00 0 38 0 59 0 51 -0 11 0 05 0 47 0 38 0 35 0 56

8 ACT 1 00 0 70 0 79 -0 12 -0 06 0 80 0 44 0 08 -0 36 -0 42 -0 02 -0 20 AGA 075 051 029 -024 006 063 021 031 -031 -038 011 -014

AGC 071 -027 051 041 059 036 091 064 014 033 028 0 17

AGG 045 078 005 053 042 045 020 063 038 033 043 0 55

AGT 100 029 066 030 072 056 076 090 005 -009 000 -0 04

ATA 086 100 030 086 046 082 046 071 069 071 055 0 65

ATC 100 029 024 -049 049 050 -001 024 -015 -026 007 -0 08

ATG 100 058 080 017 015 050 -014 -005 -017 -031 049 0 24

ATT 083 060 071 -027 002 026 024 -023 -034 -044 007 -0 05

CAA 091 049 085 -016 018 051 011 056 -021 -010 010 -0 09

CAC 100 100 051 -054 057 066 046 024 -027 -042 -003 0 01

CAG 044 -011 004 -005 024 047 037 071 026 -007 048 0 39

CAT 068 -042 072 -032 032 053 019 032 013 -017 020 0 32

CCA 073 036 054 -013 -008 052 031 031 -043 -024 007 -0 10

CCC 100 -039 042 065 022 059 056 072 067 029 068 0 52

CCG 057 100 026 100 056 -004 -010 018 041 026 043 0 04

CCT 082 -004 070 -041 -010 047 044 081 003 004 045 -0 07

CGA 100 100 100 100 083 019 100 064 073 088 074 0 80

CGC 1.00 0.23 -0.09 -0.49 -0.01 0.52 0.49 1.00 0.67 0.71 0.85 0 .22

CGG -046 100 100 100 042 -027 -009 069 081 058 100 0 89

CGT 100 100 100 -075 -011 080 -039 008 -048 -040 015 -0 25

CTA 084 100 072 -053 -005 076 -007 036 013 003 029 0 11

CTC 062 008 100 080 076 100 085 075 069 004 085 0 72

CTG 038 051 030 027 005 -017 -027 039 013 -026 030 0 17

CTT 083 079 -032 039 009 024 012 049 042 010 070 0 50

GAA 076 071 042 -031 -018 061 016 050 -020 -018 018 -0 05

GAC 057 -002 051 -070 042 063 027 055 -012 -021 011 0 15

GAG 077 -008 061 002 -007 015 021 030 030 016 027 0 32

GAT 092 063 087 -039 027 053 043 040 -009 -021 033 0 14

GCA 079 051 012 000 064 082 067 048 044 018 041 0 50

GCC 100 050 076 -038 017 034 056 -003 014 -012 047 0 18

GCG 100 036 100 018 033 -010 023 043 057 014 010 0 45

GCT 083 050 086 -049 002 046 018 020 -048 -046 008 -0 20

GGA 069 082 100 045 057 063 055 071 058 063 060 0 57

GGC 082 -021 100 -050 046 036 037 042 036 045 041 0 27

GGG 043 066 051 028 -008 -003 008 023 078 074 058 0 78

GGT 084 081 087 -057 -027 049 030 014 -048 -054 -005 -0 27

GTA 082 058 070 002 061 054 056 034 029 036 019 0 46

GTC 081 009 100 -059 033 060 015 -003 -022 -044 036 0 04

GTG 080 006 100 030 026 059 017 016 -002 -009 004 0 28 48 GTT 1 00 0 05 0 83 -0 56 0 25 0 27 0 50 0 04 -0 24 -0 41 0 41 0 09

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 29 0 16 0 70 -0 66 0 25 0 25 0 05 0 37 -0 21 -0 33 -0 03 -0 08

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 87 0 84 0 54 -0 02 0 40 0 50 0 24 0 55 0 10 -0 11 0 26 0 34

53 TCA 1 00 0 64 0 23 0 24 0 23 0 50 0 33 0 59 0 32 0 52 0 48 0 36

54 TCC 0 80 0 03 1 00 -0 60 0 19 0 43 0 52 0 29 -0 20 -0 29 -0 06 -0 01

55 TCG 1 00 0 22 1 00 0 34 0 08 0 64 -0 31 0 43 0 54 0 07 0 31 0 28

56 TCT 0 63 -0 02 1 00 -0 63 -0 29 0 32 0 31 0 29 -0 45 -0 48 0 34 -0 09

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 1 00 -0 41 1 00 0 28 0 58 0 34 0 47 -0 04 0 05 0 06 0 70 0 94

59 TGG 1 00 0 42 0 58 0 51 0 23 0 54 -0 18 0 79 -0 15 -0 29 0 41 0 21

60 TGT 1 00 -0 36 1 00 -0 65 0 14 -0 02 -0 29 0 36 -0 20 -0 19 0 09 -0 32

61 TTA 0 75 0 70 0 86 0 07 0 02 0 82 0 28 0 26 0 15 0 25 0 38 0 28

62 TTC 0 67 0 03 1 00 -0 57 0 08 -0 01 0 28 0 21 -0 10 -0 22 0 20 0 03

63 TTG 0 83 0 70 0 72 -0 39 -0 29 0 64 0 19 0 59 -0 52 -0 49 -0 08 -0 28

64 TTT 0 89 0 20 0 81 0 60 0 59 0 83 0 60 0 72 -0 10 -0 17 0 29 0 19

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table ClO continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA 0 64 0 29 0 72 0 30 0 68 0 54 0 46 0 09 0 57 0 10 0 31 0 24

2 AAC 0 43 -0 37 0 73 -0 33 0 52 0 27 0 16 -0 46 0 50 -0 49 0 32 -0 43

3 AAG 0 24 -0 51 0 33 -0 58 0 39 -0 28 0 41 -0 56 0 65 -0 58 0 38 -0 48

4 AAT 0 45 -0 09 0 14 -0 14 0 48 0 26 0 20 -0 11 0 69 0 00 0 27 0 03

5 ACA 0 60 0 51 0 70 0 41 0 44 0 61 0 60 0 32 0 64 0 50 0 40 0 57

6 ACC 0 40 -0 38 0 62 -0 44 0 72 0 27 0 61 -0 57 0 50 -0 60 0 12 -0 39

7 ACG 0 63 0 55 0 42 0 31 0 62 0 26 0 50 0 54 0 19 0 36 0 15 0 63

8 ACT 0 25 -0 45 -0 12 -0 52 0 67 0 47 0 47 -0 61 0 27 -0 49 0 16 -0 42

9 AGA 0 51 -0 33 0 34 -0 48 0 62 0 11 0 63 -0 57 0 55 -0 43 0 25 -0 35

10 AGC 0 54 -0 15 0 89 0 29 0 33 0 23 0 66 0 33 0 26 0 35 0 77 0 43

11 AGG 0 51 0 24 0 72 -0 05 0 72 0 17 0 80 0 44 0 58 0 30 0 33 0 63

12 AGT 0 40 0 19 0 62 0 28 0 46 0 38 0 54 -0 16 0 58 0 10 0 17 0 27

13 ATA 0 70 0 90 0 86 0 75 0 69 0 62 0 64 0 75 0 78 0 58 0 68 0 68

14 ATC 0 58 -0 09 0 42 0 09 0 70 0 27 0 22 -0 49 0 60 -0 10 0 08 -0 18

15 ATG 0 40 -0 23 0 60 -0 25 0 38 0 35 0 36 -0 31 0 55 -0 17 0 30 -0 26 ATT 018 -055 032 -054 037 004 021 -049 028 -059 017 -038

CAA 044 -007 063 -0 51 058 009 043 -052 039 -0 41 -0 03 -0 28

CAC 039 -029 056 -0 36 080 014 075 -058 059 -0 48 0 23 -0 32

CAG 045 059 036 0 31 081 045 082 052 043 0 57 0 50 0 40

CAT 053 -011 -012 -0 11 066 043 037 -018 047 -0 13 0 23 -0 02

CCA 022 -030 059 -0 52 052 005 030 -059 043 -0 31 0 36 -0 30

CCC 040 040 074 0 32 067 026 100 039 043 -0 22 0 58 0 50

CCG 068 075 067 0 69 079 017 081 085 052 0 23 0 46 0 55

CCT 031 -011 020 -0 22 067 -009 069 -023 004 -0 42 0 20 -0 26

CGA 100 086 100 0 92 100 081 100 100 083 0 81 1 00 0 70

CGC 063 034 068 0 50 042 055 -007 022 079 0 55 0 53 0 41

CGG 100 076 100 0 71 016 100 -035 072 040 0 68 0 66 0 66

CGT 037 -051 059 -0 54 067 -019 008 -050 012 -0 75 -0 28 -0 41

CTA 057 032 065 0 16 047 014 065 -013 060 0 30 0 23 0 22

CTC 081 032 083 0 64 073 080 018 028 071 0 79 0 46 0 51

CTG 039 -008 047 0 26 009 029 056 000 018 -0 10 0 25 0 24

CTT 072 005 055 0 40 064 045 063 007 087 0 30 0 32 0 22

GAA 0.49 -0.25 0.50 -0 .38 0.57 0.31 0.52 -0.49 0.54 -0 .36 0 .13 -0 .38

GAC 072 -019 035 -0 19 067 051 030 -030 051 -0 11 0 32 0 02

GAG 026 014 022 0 25 058 034 083 024 074 0 40 0 62 0 30

GAT 052 -022 043 -0 36 046 050 005 -036 058 -0 38 0 24 -0 26

GCA 053 063 079 0 53 058 045 067 019 063 0 53 0 60 0 56

GCC 042 -031 079 -0 37 068 045 090 -055 041 -0 53 0 17 -0 20

GCG 071 050 045 0 51 064 029 052 048 060 0 01 0 55 0 51

GCT 031 -047 068 -0 60 074 019 059 -058 040 -0 60 0 08 -0 42

GGA 077 053 095 0 67 077 061 064 065 078 0 76 0 75 0 84

GGC 062 014 075 0 10 084 067 064 027 078 0 31 0 57 0 47

GGG 085 059 080 0 63 084 082 090 066 085 0 89 0 88 0 71

GGT 039 -054 040 -0 62 053 012 017 -067 037 -0 67 0 35 -0 60

GTA 066 055 074 0 58 070 058 069 060 071 0 63 0 68 0 69

GTC 049 -027 044 -0 30 042 -004 053 -064 060 -0 41 0 41 -0 39

GTG 040 -012 077 0 28 051 065 065 030 029 -0 01 0 20 0 41

GTT 028 -048 047 -0 52 045 028 061 -051 056 -0 60 0 52 -0 47

TAA 000 000 000 0 00 000 000 000 000 000 0 00 0 00 0 00

TAC 058 -034 065 -0 45 062 014 041 -050 028 -0 44 0 37 -0 39

TAG 000 000 000 0 00 000 000 000 000 000 0 00 0 00 0 00

TAT 045 -001 047 -0 13 072 037 044 -019 068 -0 17 0 36 0 07

TCA 070 051 060 0 32 024 053 053 035 041 0 25 0 33 0 52

TCC 050 -041 054 -0 48 036 016 053 -059 005 -0 63 -0 19 -0 40 55 TCG 0 67 0 43 0 14 0 66 0 72 0 53 0 37 0 41 0 62 0 34 0 74 0 66

56 TCT 0 15 -0 61 0 21 -0 59 0 59 0 35 0 43 -0 61 0 34 -0 56 -0 29 -0 41

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 75 0 20 0 56 0 59 0 90 0 33 -0 07 0 22 1 00 0 87 1 00 0 39

59 TGG 0 46 -0 20 0 44 -0 26 0 62 0 48 -0 21 -0 31 0 58 -0 06 0 53 -0 36

60 TGT 0 63 -0 47 -0 48 -0 38 0 76 -0 03 0 23 -0 48 0 19 -0 45 0 01 -0 46

61 TTA 0 49 0 16 0 36 -0 05 0 48 0 29 0 54 -0 25 0 52 -0 22 0 04 0 03

62 TTC 0 47 0 03 0 50 0 20 0 70 0 18 0 63 -0 51 0 73 -0 44 0 17 -0 01

63 TTG 0 18 -0 58 0 08 -0 62 0 48 0 05 0 50 -0 59 0 32 -0 58 -0 16 -0 50

64 TTT 0 20 -0 40 0 25 -0 26 0 73 0 24 0 47 -0 23 0 53 -0 29 0 34 -0 23

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table ClO continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 -0 14 0 00 0 31 0 10 0 12 0 26 -0 18 0 00 0 34 -0 03 0 01

2 AAC 0 00 -0 53 0 00 -0 15 -0 03 -0 48 -0 17 -0 40 0 00 0 25 -0 43 -0 57

3 AAG 0 00 -0 43 0 00 0 32 0 35 -0 37 0 07 -0 42 0 00 0 24 0 05 -0 31

4 AAT 0 00 0 34 0 00 0 44 0 46 0 08 0 34 0 11 0 00 0 60 0 51 0 41

5 ACA 0 00 0 31 0 00 0 63 0 41 0 16 0 46 0 19 0 00 0 66 0 27 -0 16

6 ACC 0 00 -0 54 0 00 0 24 0 25 -0 45 -0 15 -0 44 0 00 -0 33 -0 39 -0 42

7 ACG 0 00 -0 02 0 00 0 66 0 56 0 70 0 52 0 46 0 00 0 75 0 57 0 53

8 ACT 0 00 -0 50 0 00 0 11 -0 11 -0 49 -0 11 -0 54 0 00 0 90 -0 08 -0 34

9 AGA 0 00 -0 31 0 00 0 43 0 05 -0 44 0 37 -0 41 0 00 0 46 -0 17 -0 34

10 AGC 0 00 0 23 0 00 0 60 0 39 0 01 0 56 0 17 0 00 0 20 0 10 0 51

11 AGG 0 00 0 23 0 00 0 54 0 00 0 12 0 49 0 19 0 00 1 00 0 61 0 71

12 AGT 0 00 0 14 0 00 0 63 0 41 0 51 0 57 0 47 0 00 0 45 0 44 0 49

13 ATA 0 00 0 25 0 00 0 56 0 43 0 37 0 44 0 50 0 00 0 71 0 76 0 53

14 ATC 0 00 -0 49 0 00 -0 06 -0 06 -0 57 0 03 -0 53 0 00 0 37 -0 44 -0 46

15 ATG 0 00 -0 24 0 00 0 23 0 31 -0 33 0 28 -0 27 0 00 0 29 0 00 -0 15

16 ATT 0 00 -0 21 0 00 0 18 0 34 -0 45 0 14 -0 39 0 00 -0 06 -0 02 -0 17

17 CAA 0 00 -0 27 0 00 0 20 0 36 -0 27 0 59 -0 33 0 00 0 44 -0 20 -0 30

18 CAC 0 00 -0 31 0 00 -0 09 0 52 -0 60 -0 14 -0 60 0 00 0 45 -0 31 -0 32

19 CAG 0 00 -0 21 0 00 0 35 0 13 0 16 0 33 0 08 0 00 0 19 0 55 0 25

20 CAT 0 00 -0 06 0 00 0 29 0 30 0 05 0 42 -0 16 0 00 0 08 0 25 0 06

21 CCA 0 00 -0 45 0 00 0 26 0 15 -0 39 0 24 -0 58 0 00 0 16 -0 48 -0 45

22 CCC 0 00 0 47 0 00 0 14 0 36 0 04 0 30 -0 09 0 00 0 28 0 90 0 12 CCG 000 052 000 056 076 078 082 080 000 054 O 88 O 44

CCT 000 -036 000 024 034 -039 -018 -009 000 -009 O 40 O 55

CGA 000 084 000 063 100 100 063 072 000 1 OO O 81 1 OO

CGC 000 003 000 041 100 -028 -025 O 16 000 O 17 O 54 1 OO

CGG 000 044 000 058 -015 060 100 076 000 1 OO O 67 O 26

CGT 000 -068 000 -047 030 -053 -025 -050 000 -044 -O 51 -O 69

CTA 000 -018 000 008 032 003 004 -005 000 031 -O 38 -O 30

CTC 000 001 000 055 060 -035 082 021 000 067 O 59 O OO

CTG 000 010 000 052 048 041 034 026 000 031 O 42 -O 22

CTT 000 -025 000 015 017 -039 -010 -025 000 056 O 39 -O 07

GAA 000 -026 000 023 055 -044 053 -038 000 030 -O 12 -O 26

GAC 000 -048 000 007 031 -057 000 -058 000 -001 -O 25 -O 56

GAG 000 -017 000 022 058 -006 003 O 13 000 037 O 32 O 15

GAT 000 009 000 028 039 002 -Oil 000 000 070 O 18 O 24

GCA 000 024 000 059 032 -012 021 007 000 061 O 35 O 33

GCC 000 -024 000 045 006 -056 -O 10 -040 000 068 O 08 -O 26

GCG 000 000 000 034 060 039 057 051 000 039 -O 02 O 75

GCT 0.00 -0.55 0.00 0.07 0.29 -0.56 0.30 -0.50 0.00 0.43 -O .24 -O .54

GGA 000 055 000 053 054 053 088 032 000 072 O 17 O 20

GGC 000 -034 000 040 031 -046 036 -033 000 O 14 -O 24 O Ol

GGG 000 061 000 058 068 000 054 -007 000 031 O 47 O 47

GGT 000 -055 000 014 024 -059 022 -057 000 025 -O 07 -O 41

GTA 000 037 000 055 062 025 043 O 10 000 -O 18 O 54 O 48

GTC 000 -044 000 010 047 -060 046 -049 000 021 -O 42 -O 44

GTG 000 015 000 046 071 011 072 031 000 059 O 43 O 24

GTT 000 -041 000 002 006 -061 039 -050 000 -003 -O 12 -O 13

TAA 000 000 000 000 000 000 000 000 000 000 O OO O OO

TAC 000 -054 000 015 011 -049 O 14 -040 000 O 14 -O 39 -O 47

TAG 000 000 000 000 000 000 000 000 000 000 O OO O OO

TAT 000 029 000 035 048 -005 024 -021 000 071 O 48 O 16

TCA 000 -007 000 021 020 026 054 007 000 -020 O 03 -O 13

TCC 000 -032 000 011 031 -045 -006 -049 000 029 -O 38 -O 28

TCG 000 -029 000 014 050 031 -O 17 036 000 -037 -O Ol O 30

TCT 000 -051 000 010 -015 -064 021 -059 000 032 O 03 -O 34

TGA 000 000 000 000 000 000 000 000 000 000 O OO O OO

TGC 000 -027 000 026 072 -020 040 O 10 000 -025 -O 02 O 32

TGG 000 -033 000 037 046 -030 009 -034 000 047 O OO -O 23

TGT 000 -021 000 022 038 -057 051 -047 000 059 O Ol -O 30

TTA 000 -009 000 037 042 -020 024 -026 000 065 -O 36 -O 15 62 TTC 0 00 -0 48 0 00 0 08 0 22 -0 64 -0 20 -0 40 0 00 0 37 -0 22 -0 40

63 TTG 0 00 -0 50 0 00 0 19 0 20 -0 60 0 39 -0 51 0 00 0 23 0 38 -0 30

64 TTT 0 00 0 05 0 00 0 39 0 27 -0 02 0 36 0 34 0 00 -0 06 0 19 0 34

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table ClO continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 0 15 -0 20 -0 19 0 40

2 AAC -0 11 -0 53 -0 59 -0 02

3 AAG 0 20 -0 44 -0 53 0 20

4 AAT 0 28 0 16 0 04 0 42

5 ACA 0 42 0 47 0 26 0 34

6 ACC -0 11 -0 42 -0 42 0 07

7 ACG 0 54 0 52 0 30 0 67

8 ACT -0 29 -0 52 -0 65 -0 03

9 AGA -0 21 -0 44 -0 57 0 06

10 AGC 0 65 0 53 0 31 0 46

11 AGG 0 55 0 28 0 26 0 26

12 AGT 0 50 0 28 -0 12 0 48

13 ATA 0 42 0 34 0 38 0 47

14 ATC -0 13 -0 38 -0 60 -0 05

15 ATG 0 24 -0 17 -0 25 0 14

16 ATT 0 18 -0 35 -0 37 0 21

17 CAA -0 16 -0 21 -0 48 0 06

18 CAC 0 34 -0 52 -0 51 0 34

19 CAG 0 40 -0 24 0 17 0 47

20 CAT 0 10 -0 27 -0 39 0 48

21 CCA -0 31 -0 42 -0 60 -0 19

22 CCC 0 15 -0 31 0 29 0 63

23 CCG 0 38 0 62 0 61 0 63

24 CCT 0 34 -0 23 0 00 0 58

25 CGA 1 00 0 60 0 83 0 46

26 CGC 0 79 0 37 0 48 0 79

27 CGG 0 55 0 10 0 26 0 08

28 CGT -0 06 -0 38 -0 45 0 41

29 CTA -0 14 0 20 -0 19 0 19 CTC 0 57 -0 23 0 03 0 32

CTG 0 45 -0 09 0 03 0 39

CTT 0 18 -0 54 -0 36 0 41

GAA 0 11 -0 22 -0 37 O 17

GAC 0 11 -0 40 -0 52 0 27

GAG 0 40 -O i l -0 18 O 15

GAT 0 10 -0 23 -0 37 0 31

GCA 0 60 0 62 0 32 0 36

GCC -0 03 -0 47 -0 24 -O 19

GCG 0 59 -0 05 0 45 0 39

GCT -0 21 -0 48 -0 67 0 39

GGA 0 52 O 19 0 46 0 31

GGC 0 49 0 65 0 26 0 50

GGG -0 16 -0 58 -0 48 -0 25

GGT -0 08 -0 53 -0 57 0 48

GTA 0 56 0 54 0 54 0 43

GTC -0 18 -0 52 -0 65 -0 01

GTG 0.39 -0.06 -0.07 0.32

GTT 0 08 -0 43 -0 51 0 31

TAA 0 00 0 00 0 00 0 00

TAC 0 15 -0 32 -0 57 -O 14

TAG 0 00 0 00 0 00 0 00

TAT 0 22 -O 13 -0 21 0 48

TCA 0 13 -O 18 0 03 0 24

TCC -0 05 -0 44 -0 51 0 04

TCG 0 02 -O 11 O 14 0 39

TCT -0 29 -0 60 -0 67 0 35

TGA 0 00 0 00 0 00 0 00

TGC 0 21 0 60 0 57 0 24

TGG -0 24 -0 25 -O 17 0 23

TGT 0 08 -0 43 -0 49 O 11

TTA 0 27 -0 20 -O 16 0 23

TTC -0 11 -0 54 -0 65 0 03

TTG 0 05 -0 27 -0 58 0 06

TTT 0 28 O 11 -O 16 0 46

TTA TTC TTG TTT

61 62 63 64 Table CI l: CPW matrix Streytomyces coelicolor A3 (2) full genome (left codon indicated in column 2, right codon indicated in row 2). Host cell: S. coelicolor, Sequence data: full S. coelicilor genome.

1 2 3 4 5 6 7 8 9 10 11 12

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 AAA 0 00 0 79 0 70 -0 65 -0 60 0 28 0 48 -0 48 -0 86 0 24 -0 66 -0 69

2 AAC 0 44 -0 05 -0 06 0 30 0 52 -0 13 0 15 0 32 0 10 -0 27 0 09 0 36

3 AAG 0 58 -0 05 -0 06 0 45 -0 01 0 03 -0 10 0 15 0 08 -0 03 0 21 0 52

4 AAT -0 02 0 89 0 87 1 00 0 22 0 80 0 57 -0 63 1 00 0 77 0 62 0 60

5 ACA 1 00 0 83 0 74 -0 23 -0 60 0 71 0 50 -0 58 -0 75 0 30 -0 40 -0 15

6 ACC 0 08 -0 16 -0 11 -0 18 -0 05 -0 03 -0 02 -0 26 0 15 -0 17 -0 34 -0 29

7 ACG 0 19 0 31 0 12 -0 08 -0 39 0 22 -0 30 -0 22 -0 32 0 22 0 00 -0 14

8 ACT 1 00 0 85 0 87 0 40 -0 37 0 69 0 63 -0 61 -0 26 0 88 -0 06 -0 38

9 AGA -0 47 0 37 0 44 -0 82 -0 80 0 35 -0 03 -0 66 -0 88 -0 26 -0 72 -0 60

10 AGC -0 23 -0 11 -0 14 -0 47 -0 35 0 05 -0 03 -0 32 -0 62 -0 34 -0 60 -0 58

11 AGG -0 64 -0 13 -0 27 -0 58 -0 62 0 06 -0 27 -0 35 -0 60 -0 22 -0 22 -0 51

12 AGT -0 64 0 74 0 87 0 14 0 19 0 51 -0 40 -0 67 0 55 0 74 0 91 -0 47

13 ATA -0 12 0 91 0 74 0 32 1 00 0 84 0 41 0 02 -0 69 0 46 -0 20 0 14

14 ATC -0 02 -0 04 -0 03 0 07 0 32 -0 11 0 15 -0 07 -0 05 -0 22 -0 31 -0 19

15 ATG 0 07 -0 01 0 00 0 24 0 01 0 08 -0 14 0 01 0 54 -0 17 0 43 -0 02

16 ATT 0 39 0 85 0 78 -0 54 -0 48 0 77 0 67 -0 36 -0 12 0 95 0 55 -0 27

17 CAA 0 12 0 80 0 62 -0 22 -0 65 0 62 0 59 -0 06 -0 42 0 58 -0 01 0 31

18 CAC 0 05 -0 06 -0 07 0 01 0 08 -0 15 0 19 -0 10 0 51 -0 23 0 54 0 00

19 CAG -0 01 -0 05 -0 03 0 38 -0 15 -0 03 -0 01 0 13 0 49 -0 07 0 66 0 47

20 CAT 0 66 0 90 0 89 -0 37 0 31 0 90 0 61 -0 39 0 39 0 75 0 82 0 61

21 CCA -0 34 0 53 0 55 -0 66 -0 65 0 63 0 36 -0 54 -0 75 0 55 -0 41 -0 42

22 CCC -0 10 -0 11 -0 09 -0 13 -0 13 -0 18 0 05 -0 28 0 23 0 03 -0 38 -0 17

23 CCG 0 00 0 05 0 03 0 15 -0 20 0 20 -0 16 -0 23 -0 12 0 23 -0 22 0 10

24 CCT -0 40 0 81 0 81 -0 51 -0 27 0 71 0 32 -0 64 0 50 0 83 0 51 1 00

25 CGA 0 07 0 27 0 20 -0 63 -0 43 0 54 0 42 -0 12 -0 79 -0 06 -0 33 -0 41

26 CGC -0 46 -0 34 -0 34 -0 51 -0 08 -0 28 0 01 -0 23 -0 56 -0 35 -0 58 -0 42

27 CGG 0 21 0 56 0 57 -0 10 -0 11 0 45 0 22 0 29 0 36 0 51 0 54 0 41

28 CGT 0 18 0 79 0 75 -0 36 -0 28 0 01 -0 57 -0 57 0 45 0 75 0 75 0 62

29 CTA -0 22 0 52 0 67 1 00 0 27 0 81 0 49 -0 83 -0 70 0 81 0 34 -0 70

30 CTC -0 30 -0 30 -0 23 -0 13 0 29 -0 38 0 28 -0 14 0 04 -0 15 -0 31 -0 03

31 CTG 0 15 0 20 0 17 0 55 0 36 0 10 0 23 0 53 0 31 0 19 0 29 0 43

32 CTT 0 44 0 95 0 94 0 16 0 84 0 79 0 67 -0 62 0 63 0 92 0 78 0 27

33 GAA 0 57 0 82 0 78 0 19 -0 35 0 57 0 46 0 05 -0 06 0 47 0 28 0 52 34 GAC 0 12 -0 05 -0 05 0 18 0 28 -0 09 0 07 0 09 0 34 -O 17 0 40 0 03

35 GAG 0 29 -0 14 -0 14 0 31 -0 14 0 01 -0 24 0 21 0 57 -O 10 0 49 0 36

36 GAT 0 71 0 91 0 89 -0 23 0 19 0 76 0 54 -0 28 0 42 0 80 0 85 0 54

37 GCA -0 09 0 84 0 75 0 17 -0 50 0 68 0 49 -0 20 -0 20 0 48 -0 06 -O 10

38 GCC 0 14 -0 18 -0 10 -0 22 0 14 -O 12 0 07 -0 01 0 06 0 41 -0 24 -0 02

39 GCG -0 05 0 20 0 04 0 27 -0 18 0 15 -0 21 0 10 0 17 -0 08 0 20 -0 02

40 GCT 0 29 0 86 0 93 0 50 -0 24 0 72 0 53 -0 52 0 59 0 87 0 72 0 78

41 GGA -0 40 0 40 0 48 -0 16 -0 49 0 47 O 11 -0 08 -0 61 O 10 -0 28 -0 35

42 GGC -0 11 -0 20 -0 20 -0 31 -0 05 -O 14 -O 12 -0 03 -0 36 -0 26 -0 42 -0 34

43 GGG -0 27 0 28 0 24 -0 20 -0 21 0 45 -0 20 0 04 -0 33 0 28 O 15 -0 08

44 GGT 0 66 0 91 0 88 0 64 0 34 0 60 -O 17 0 35 0 44 0 90 0 83 0 58

45 GTA 0 18 0 91 0 90 0 20 0 33 0 92 0 88 0 21 -0 20 0 86 -0 02 0 24

46 GTC -0 16 -0 19 -0 03 -0 28 0 27 -0 25 O 19 0 06 O 17 -O 13 O 10 O 12

47 GTG -0 09 0 22 -0 04 0 35 O i l 0 23 -O 14 0 31 0 38 0 06 0 42 0 22

48 GTT 0 39 0 97 0 87 1 00 0 28 0 87 0 71 0 26 0 61 0 88 0 69 0 59

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 47 -0 08 -0 07 0 83 0 20 0 00 -O 16 0 92 0 75 -0 20 0 79 0 70

51 TAG 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

52 TAT 1 00 0 91 0 90 1 00 0 39 0 82 0 71 1 00 0 44 0 74 0 67 0 03

53 TCA 0 12 0 89 0 70 0 38 -0 57 0 73 0 29 -0 50 0 35 O 13 -O 14 -0 54

54 TCC 0 30 -0 17 -0 02 0 28 0 01 -0 07 -O 12 -0 28 0 05 -0 04 -0 04 -0 03

55 TCG 0 03 0 24 0 00 0 21 -0 24 0 32 -0 30 0 27 0 21 0 49 0 38 0 20

56 TCT 1 00 0 91 1 00 -0 05 -0 32 0 62 0 46 1 00 -0 55 0 58 0 78 1 OO

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 10 -0 07 -0 07 -0 26 -0 21 0 02 -O 12 0 40 0 04 0 29 0 42 -0 09

59 TGG -0 36 -0 01 0 03 0 34 -0 20 O 15 -0 23 -0 20 0 47 -0 02 0 51 0 00

60 TGT -0 46 0 97 0 81 -0 56 1 00 0 51 -O 10 -0 50 O 12 0 92 0 31 0 64

61 TTA 1 00 1 00 1 00 1 00 -0 76 0 84 0 67 1 00 -0 90 0 46 1 00 1 OO

62 TTC -0 20 -0 02 0 00 0 19 0 58 -O 13 0 22 0 28 0 21 -0 01 0 33 0 20

63 TTG -0 70 0 24 -0 23 -0 60 0 04 0 35 -0 20 -0 32 -0 71 -0 22 -0 49 -0 54

64 TTT -0 05 0 95 0 73 1 00 -0 07 0 72 0 62 -0 55 -0 41 0 61 0 00 1 OO

AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT

1 2 3 4 5 6 7 8 9 10 11 12

Table C.11 continued

13 14 15 16 17 18 19 20 21 22 23 24

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

1 AAA -0 50 0 74 0 22 -0 69 -0 42 -0 21 -0 24 -0 69 -0 67 -0 47 -0 58 -0 57 AAC 058 -005 -003 021 037 -002 000 047 055 023 -003 022

AAG 046 -005 -001 023 050 -001 -001 037 036 006 004 033

AAT 100 075 083 -039 -074 -010 -018 -074 -082 -062 -072 -070

ACA 100 085 068 -007 -067 -024 -044 -076 -089 -073 -075 -080

ACC 059 011 016 -010 015 009 004 -021 040 038 018 015

ACG 018 -026 -030 -035 -015 -005 002 -027 005 -015 -010 -029

ACT 031 082 086 -032 -070 013 -037 -078 -087 -075 -075 -090

AGA -030 039 037 -067 -074 -013 -013 -017 -086 -019 -028 -079

AGC 100 013 030 -017 012 -012 -007 -048 004 008 012 -037

AGG 072 000 006 -045 -064 020 -002 -030 -062 -023 -010 -018

AGT 051 070 085 -052 -033 -022 -020 -069 -065 -030 -037 -079

ATA 100 087 091 -057 043 012 006 -025 044 -067 -065 -066

ATC 082 -005 -004 -012 044 000 -001 018 050 018 008 043

ATG 097 -003 000 017 015 -001 -001 017 009 007 -006 007

ATT 100 073 080 -019 -083 -044 -024 -058 -091 -079 -081 -091

CAA 063 080 077 -017 -032 022 002 045 -019 -025 -019 -072

CAC -025 -006 -005 037 020 001 000 004 028 003 020 014

CAG -0.18 -0.04 -0.04 0.07 0.01 -0.02 0.00 0.12 -0.24 -0.05 0.09 -0.02

CAT 019 079 065 057 -068 -008 -006 -037 -059 -060 -065 -067

CCA -058 096 069 -083 -070 003 -037 -042 -093 -067 -073 -087

CCC -018 030 025 -028 032 056 044 021 029 082 048 007

CCG -029 -021 -020 -018 -018 -030 -023 007 -035 -028 -018 -016

CCT 030 084 075 -078 -070 -008 -023 -065 -084 -060 -055 -084

CGA -060 063 064 -059 -060 034 -018 -058 -078 -006 -034 -065

CGC -009 003 008 005 013 031 024 -005 028 005 034 039

CGG -037 -012 -021 -026 -027 -029 -018 -022 -001 -015 008 -006

CGT 035 047 061 011 -061 021 -004 -056 -067 -049 -046 -071

CTA -044 075 083 -048 -080 014 -034 -067 -088 -054 -047 -082

CTC 007 023 030 -001 -023 054 -038 052 056 041 057 054

CTG 016 -014 -017 028 -048 -027 056 032 025 -032 -007 019

CTT 060 089 085 -021 -069 008 -072 -039 -086 -075 -064 -082

GAA 050 080 071 040 -035 -015 -015 020 -064 -038 -048 -043

GAC -006 -005 -004 036 034 004 001 001 046 024 000 037

GAG -017 -013 -011 020 022 001 003 032 026 021 008 042

GAT 016 086 075 -044 -068 -036 -027 -068 -080 -066 -072 -074

GCA 026 083 081 -042 -069 -033 -047 -058 -084 -070 -072 -078

GCC -004 022 017 022 020 014 011 -009 044 033 030 025

GCG -049 -032 -029 -018 012 -011 -003 008 005 -013 001 008

GCT 047 086 085 -012 -075 -003 -042 -080 -085 -077 -070 -086 41 GGA -0 15 0 54 0 40 -0 49 -0 57 -0 37 -0 32 -0 41 -0 73 -0 33 -0 51 -0 57

42 GGC -0 13 -0 16 -0 12 O 15 0 41 0 26 0 26 0 25 0 36 0 24 0 29 0 36

43 GGG -0 22 0 13 -0 02 -0 28 -0 47 -0 36 -0 41 -0 51 -0 38 -O 16 -0 27 -0 42

44 GGT 0 72 0 62 0 68 O 16 -0 06 -0 04 0 01 -0 46 -0 38 -0 30 -0 38 -0 52

45 GTA 0 11 0 88 0 85 -0 40 -0 67 0 21 -0 34 -0 32 -0 47 -0 50 -0 68 -0 53

46 GTC 0 10 0 05 0 15 O 19 0 43 0 25 O 14 O i l 0 71 0 33 0 37 0 54

47 GTG 0 35 -0 16 -0 23 0 21 0 28 -0 27 -O 14 0 27 0 04 -O 18 -0 25 0 30

48 GTT 0 58 0 81 0 70 -0 44 -0 55 -O 17 -0 39 -0 77 -0 86 -0 75 -0 72 -0 85

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 27 -0 05 -0 04 0 40 0 24 -0 05 0 00 0 79 0 33 0 35 0 00 0 63

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT 0 13 0 75 0 80 -0 46 -0 60 -0 22 -O 18 1 00 -0 81 -0 69 -0 80 -0 65

53 TCA -0 29 0 82 0 87 -0 74 -0 53 O 13 -0 40 -0 56 -0 87 -0 65 -0 74 -0 83

54 TCC -0 12 0 09 O i l O 12 0 34 0 23 O 14 0 31 0 28 0 28 0 18 0 20

55 TCG -0 43 -0 28 -0 38 -0 31 O 19 -O 12 -0 07 O 13 0 04 -O 10 -0 05 0 09

56 TCT -0 72 0 80 0 87 -0 22 0 40 -0 25 -0 35 -0 79 -0 37 -0 70 -0 62 -0 90

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0.22 -0.07 -0.04 -0.45 0.02 0.02 0.00 -0.11 -0.06 0.10 0.04 0.18

59 TGG -0 18 0 01 0 00 -0 01 0 27 -0 02 -0 01 0 20 0 04 0 00 -0 01 O 19

60 TGT 1 00 0 91 0 41 -0 29 -0 42 0 02 0 01 -0 69 -0 67 -0 31 -0 44 -0 46

61 TTA 1 00 1 00 1 00 -0 91 -0 86 1 00 -0 31 -0 88 -0 91 -0 36 -0 61 1 OO

62 TTC 0 41 -0 02 -0 01 0 20 0 47 -0 01 -0 02 0 35 0 70 0 05 0 03 0 33

63 TTG 0 21 -0 05 -O 19 -0 68 -0 44 0 05 -0 60 -0 30 -0 68 -0 01 -O 16 -0 43

64 TTT 1 00 0 72 0 85 -0 84 -0 79 -0 34 -0 21 -0 84 -0 89 -0 83 -0 71 -0 94

ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT

13 14 15 16 17 18 19 20 21 22 23 24

Table CI l continued

25 26 27 28 29 30 31 32 33 34 35 36

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

1 AAA -0 82 -0 59 -0 56 -0 28 -0 85 -0 65 -0 45 -0 58 0 20 0 67 0 50 0 10

2 AAC 0 02 -0 01 -0 05 0 31 0 60 -0 17 0 15 0 08 0 14 -0 03 -0 04 0 27

3 AAG O 19 0 12 -0 05 0 34 0 37 -0 07 0 13 0 29 -0 10 -0 05 -0 01 0 38

4 AAT -0 68 0 03 0 24 -0 43 -0 74 -0 56 -0 38 -0 80 -0 44 0 48 0 46 -0 65

5 ACA -0 80 -0 08 -0 34 -0 69 -0 63 -0 35 -0 36 -0 68 -0 09 0 57 0 55 -0 07

6 ACC 0 07 -0 09 -0 12 -0 21 0 80 0 00 0 25 0 02 -0 07 -0 05 -0 12 -0 29

7 ACG 0 08 0 43 0 35 0 02 0 44 -0 16 -0 23 -0 27 0 22 0 10 0 20 -0 16

8 ACT -0 58 -0 18 -0 05 -0 40 -0 59 -0 44 -0 08 -0 86 -0 16 0 50 0 49 -0 49 AGA -076 -008 -012 -022 -037 -039 -017 -078 -040 056 047 -035

AGC -041 -016 -011 -0 42 089 012 023 -036 -020 -013 -025 -049

AGG -044 028 010 -0 11 -021 -013 001 -042 -048 019 023 -041

AGT -042 047 053 -0 51 -045 011 002 -062 -050 -003 -012 -071

ATA -075 -053 -060 -0 72 -059 -039 -015 -037 021 052 028 028

ATC 047 -006 019 0 08 066 -022 018 -018 022 -003 -006 018

ATG 010 -008 002 0 16 075 -013 005 028 015 -001 -003 023

ATT -077 -030 012 -0 66 100 -050 -038 -091 036 056 051 -073

CAA -073 -038 -040 -0 36 -091 -063 -067 -068 -026 061 049 -007

CAC 009 -007 -005 0 04 -053 -002 012 016 000 -003 -004 -001

CAG 004 -006 005 0 18 -019 -013 036 011 -009 -004 000 017

CAT -044 020 052 0 05 -076 -045 -051 -071 030 043 047 -054

CCA -085 -047 -048 -0 72 -078 -012 -044 -060 -007 073 060 -027

CCC -008 006 013 -0 05 017 044 048 032 -018 -015 -025 -022

CCG -001 -014 028 0 08 -026 -009 -029 -006 025 010 020 018

CCT -076 -022 -011 -0 67 -074 -010 032 -082 -033 027 040 -074

CGA -078 -031 -038 -0 50 -069 -020 -032 -074 002 057 045 -057

CGC -0.15 -0.07 0.06 -0 .26 0.38 0.29 0.42 0.26 -0.01 -0.04 -0.11 -0.05

CGG 010 009 013 0 10 -032 -025 -033 000 007 000 012 018

CGT -036 037 036 -0 39 -040 014 027 -065 -038 -002 -008 -061

CTA -094 -057 -067 -0 78 -092 -043 -037 -087 -018 059 031 -009

CTC 072 065 070 0 56 034 026 057 036 -043 -028 065 -022

CTG 015 -041 -006 -0 06 038 -028 -017 029 -008 018 -022 050

CTT -071 -001 015 -0 26 -077 -032 003 -077 -037 052 -004 -066

GAA -058 -045 -040 0 02 -075 -061 -056 -053 012 060 044 010

GAC 030 011 -021 0 05 022 005 002 017 011 -003 -005 007

GAG 025 022 -010 0 40 023 079 -004 030 -006 -010 -007 016

GAT -050 038 055 -0 24 -087 -050 -045 -077 009 050 055 -039

GCA -072 -038 -054 -0 50 -066 -038 -047 -059 024 064 068 -023

GCC 016 -015 -004 -0 16 009 024 021 017 -020 -015 -018 -027

GCG -005 041 016 0 26 011 -008 -024 025 023 021 026 022

GCT -058 017 010 -0 49 -080 -034 -022 -074 -005 053 057 -061

GGA -067 -031 -037 -0 39 -070 -040 -040 -058 020 049 053 -006

GGC 011 010 003 -0 09 025 031 023 022 014 -006 -007 012

GGG -005 005 -032 -0 21 -039 -024 -037 -027 012 014 010 011

GGT 025 067 066 0 06 -043 -020 -025 -059 -032 -018 -019 -058

GTA -080 -069 -083 -0 60 -051 -045 -056 -050 062 088 076 063

GTC 046 017 034 0 22 045 007 028 022 -001 -015 -013 -012

GTG 023 -013 -014 0 19 050 -013 -020 029 028 015 007 025 48 GTT -0 73 0 00 0 03 -0 49 -0 78 -0 49 -0 22 -0 83 0 04 0 56 0 48 -0 58

49 TAA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

50 TAC 0 15 0 00 -0 18 0 37 0 57 0 01 0 11 0 32 0 26 -0 06 -0 07 0 71

51 TAG 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

52 TAT -0 59 0 44 0 34 -0 07 -0 87 -0 59 -0 69 -0 67 0 46 0 64 0 63 0 55

53 TCA -0 75 -0 31 -0 49 -0 55 -0 90 -0 43 -0 55 -0 57 0 35 0 65 0 77 -0 20

54 TCC 0 09 -0 05 -0 01 -0 05 0 11 0 15 0 17 0 24 -0 07 -0 06 -0 03 0 03

55 TCG 0 39 0 31 0 32 0 25 -0 10 -0 11 -0 30 0 02 0 39 0 22 0 28 0 24

56 TCT -0 81 0 16 0 08 -0 67 -0 78 -0 19 0 08 -0 86 -0 22 0 42 0 59 -0 66

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC -0 27 0 03 -0 10 -0 31 0 46 0 24 -0 04 0 16 0 02 -0 03 -0 04 0 15

59 TGG 0 01 0 12 -0 19 0 13 -0 45 0 16 -0 09 0 34 0 18 -0 02 -0 03 0 39

60 TGT -0 03 0 53 0 66 -0 32 -0 45 -0 20 -0 53 -0 69 -0 11 0 37 0 40 -0 63

61 TTA -0 88 -0 58 -0 70 -0 87 1 00 -0 16 -0 48 1 00 0 00 0 68 0 64 1 00

62 TTC 0 37 -0 05 0 01 0 03 0 56 -0 11 0 06 0 30 0 15 -0 03 -0 03 0 39

63 TTG -0 34 -0 23 -0 36 -0 46 -0 47 -0 03 -0 21 -0 58 -0 20 0 50 -0 11 -0 19

64 TTT -0 83 -0 33 -0 08 -0 62 -0 84 -0 42 -0 31 -0 50 0 03 0 57 0 52 -0 72

CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT

25 26 27 28 29 30 31 32 33 34 35 36

Table C.11 continued

37 38 39 40 41 42 43 44 45 46 47 48

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

1 AAA -0 31 0 44 0 43 -0 27 -0 23 0 43 0 30 0 30 0 09 0 66 0 57 -0 12

2 AAC 0 40 -0 05 0 01 0 22 0 21 -0 15 0 25 0 31 0 33 -0 10 0 13 0 26

3 AAG -0 13 0 10 -0 17 0 12 0 29 -0 16 0 23 0 39 0 58 -0 10 0 02 0 23

4 AAT -0 23 0 13 0 26 -0 48 0 25 0 67 0 45 0 19 0 51 -0 05 0 02 -0 69

5 ACA -0 61 0 39 0 32 -0 62 -0 29 0 62 0 21 0 20 0 29 0 68 0 56 -0 50

6 ACC -0 14 0 08 0 07 -0 21 -0 20 -0 15 -0 12 -0 27 0 38 0 02 0 20 -0 12

7 ACG -0 46 0 05 -0 28 -0 33 0 18 0 40 0 21 0 35 0 43 -0 16 -0 32 0 01

8 ACT -0 05 0 38 0 16 -0 79 -0 07 0 68 0 52 0 18 0 39 0 49 0 45 -0 51

9 AGA -0 55 0 21 0 13 -0 47 -0 62 0 47 -0 26 -0 25 0 75 0 35 0 36 -0 58

10 AGC 0 13 0 14 0 03 -0 08 -0 14 -0 07 -0 14 -0 26 0 71 0 13 0 15 -0 31

11 AGG -0 42 0 09 -0 11 -0 38 -0 14 0 28 0 28 0 42 0 60 0 07 -0 12 -0 62

12 AGT 0 02 -0 09 -0 15 -0 72 -0 27 0 41 -0 05 -0 22 0 68 0 16 -0 15 -0 50

13 ATA 0 36 -0 16 -0 14 0 81 0 04 0 27 -0 10 0 66 1 00 0 54 0 58 -0 42

14 ATC 0 45 -0 12 0 14 0 30 0 37 -0 13 0 21 0 10 0 85 -0 14 0 09 0 03

15 ATG 0 12 0 03 -0 06 0 07 0 33 -0 12 0 21 0 24 0 93 -0 01 -0 06 0 04 ATT -002 050 049 -059 029 074 033 076 075 060 064 -082

CAA -049 035 040 -048 -062 040 -043 000 008 0 55 051 -023

CAC 024 -005 005 037 008 -009 000 009 -011 -0 04 018 000

CAG -029 002 -002 -006 010 -009 014 034 012 -0 02 -004 -012

CAT -036 -006 015 -063 026 074 061 022 -052 -0 25 -046 -074

CCA -049 050 042 -060 -059 047 000 -019 019 0 68 044 -049

CCC -036 -014 -002 -040 -029 -030 -014 -033 -037 0 09 024 -013

CCG -010 011 012 -009 018 030 017 034 009 0 00 -024 -012

CCT -017 -010 014 -082 -033 052 015 -040 -034 0 35 051 -076

CGA -059 016 014 -056 -061 015 -035 -036 -053 0 53 020 -060

CGC 020 003 022 024 -018 -022 -021 -028 018 0 10 041 009

CGG -013 -005 -014 004 027 024 030 042 -017 -0 10 -040 -009

CGT -001 -024 -015 -049 019 048 026 -023 015 0 16 038 -032

CTA 018 047 080 -032 -007 067 038 003 056 0 78 049 -076

CTC 024 -039 005 010 005 -048 -016 -037 001 -0 17 039 006

CTG 040 009 031 045 052 029 051 057 054 -0 07 -008 047

CTT -015 -012 036 -057 029 061 027 000 041 0 35 043 -073

GAA -0.24 0.37 0.23 -0.07 -0.36 0.32 -0.23 0.44 -0.13 0 .52 0.45 0.42

GAC 033 001 -007 036 001 -006 -006 015 -034 0 05 -003 033

GAG -019 011 -023 016 014 -012 006 039 028 -0 06 -013 011

GAT 004 -003 021 -065 031 076 060 057 -047 -0 06 -008 -070

GCA -051 041 042 -036 -035 049 005 016 036 0 71 053 -044

GCC -009 -004 008 -012 -041 033 -042 -045 -050 0 03 010 -004

GCG -023 007 -016 004 008 001 000 015 -005 0 08 -030 012

GCT -001 007 014 -076 005 071 035 -014 -019 0 37 048 -074

GGA -052 022 -005 017 001 052 028 039 -032 0 38 009 -010

GGC 026 005 001 027 -015 -021 -019 -030 -020 0 02 014 002

GGG -019 034 -027 -010 018 059 079 054 033 0 22 -034 -012

GGT 017 -029 -034 -062 009 039 030 -029 007 -0 27 -035 -055

GTA 045 073 074 006 038 073 050 054 064 0 85 080 013

GTC 035 -021 014 021 006 -030 001 -014 -027 -0 23 023 029

GTG 020 011 -005 023 037 031 027 045 053 0 11 -012 039

GTT -017 011 039 -068 060 057 057 015 003 0 40 047 -058

TAA 000 000 000 000 000 000 000 000 000 0 00 000 000

TAC 037 001 -010 059 016 -013 -002 055 011 -0 12 019 028

TAG 000 000 000 000 000 000 000 000 000 0 00 000 000

TAT 030 024 017 016 018 076 072 072 -058 0 03 -034 037

TCA -039 045 034 -029 -043 063 033 -005 038 0 78 057 -051

TCC -014 008 004 -015 -015 -011 -017 -022 -029 0 11 016 -005 55 TCG -0 31 0 07 -0 34 -0 23 0 22 0 31 0 15 0 39 -0 09 -0 09 -0 43 -0 18

56 TCT -0 37 0 12 0 02 -0 87 -0 48 0 66 0 20 -0 32 -0 05 0 24 0 56 -0 71

57 TGA 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00 0 00

58 TGC 0 19 0 12 -0 10 0 06 -0 13 0 05 -0 23 -0 19 -0 06 0 14 -0 04 -0 01

59 TGG -0 03 0 14 -0 19 0 30 0 05 -0 09 0 20 0 21 0 26 0 16 -0 20 0 24

60 TGT -0 10 -0 23 -0 32 -0 50 0 05 0 71 0 56 0 37 -0 08 -0 23 -0 49 -0 69

61 TTA 1 00 0 92 0 24 -0 84 -0 51 0 88 -0 16 1 00 -0 61 0 58 0 03 1 00

62 TTC 0 39 -0 09 0 09 0 41 0 31 -0 07 0 08 0 05 0 25 -0 09 0 09 0 16

63 TTG -0 34 0 43 0 21 -0 36 0 13 0 57 0 28 0 15 0 48 0 48 0 18 -0 18

64 TTT 0 28 0 24 0 48 -0 76 -0 07 0 63 0 68 0 36 -0 32 0 47 0 49 -0 71

GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT

37 38 39 40 41 42 43 44 45 46 47 48

Table C.11 continued

49 50 51 52 53 54 55 56 57 58 59 60

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

1 AAA 0 00 0 20 0 00 -0 13 -0 48 0 26 0 57 -0 48 0 00 0 33 -0 35 -0 40

2 AAC 0 00 -0 04 0 00 0 45 0 41 0 02 0 22 0 08 0 00 -0 06 -0 03 0 46

3 AAG 0 00 -0 04 0 00 0 62 0 27 0 01 -0 10 0 26 0 00 -0 05 0 03 0 39

4 AAT 0 00 0 46 0 00 1 00 -0 43 -0 07 -0 07 -0 75 0 00 0 58 0 75 -0 53

5 ACA 0 00 0 57 0 00 -0 37 -0 64 0 13 -0 02 -0 79 0 00 0 15 0 17 -0 59

6 ACC 0 00 0 12 0 00 -0 28 -0 20 0 13 -0 12 -0 17 0 00 -0 17 -0 22 -0 39

7 ACG 0 00 -0 20 0 00 -0 50 -0 16 0 18 0 05 -0 34 0 00 0 55 0 56 -0 07

8 ACT 0 00 0 68 0 00 -0 08 -0 76 -0 22 -0 45 -0 90 0 00 0 39 0 16 1 00

9 AGA 0 00 0 74 0 00 -0 42 -0 86 0 16 -0 31 -0 80 0 00 0 04 0 11 0 12

10 AGC 0 00 0 22 0 00 -0 54 0 35 0 43 0 42 -0 17 0 00 0 05 -0 07 -0 27

11 AGG 0 00 0 39 0 00 -0 37 -0 62 0 15 -0 29 -0 58 0 00 0 24 0 48 -0 18

12 AGT 0 00 0 12 0 00 -0 51 -0 59 -0 27 -0 56 -0 78 0 00 -0 27 0 08 -0 51

13 ATA 0 00 0 51 0 00 0 18 0 38 -0 38 -0 43 -0 76 0 00 0 37 0 22 0 21

14 ATC 0 00 -0 03 0 00 0 18 0 49 0 01 0 24 0 29 0 00 -0 05 -0 01 0 31

15 ATG 0 00 -0 02 0 00 0 39 0 34 0 11 -0 01 -0 03 0 00 -0 03 0 00 0 36

16 ATT 0 00 0 30 0 00 -0 43 -0 75 -0 24 0 02 -0 70 0 00 0 83 0 45 -0 41

17 CAA 0 00 0 80 0 00 -0 13 -0 39 0 47 0 49 1 00 0 00 0 58 0 11 1 00

18 CAC 0 00 -0 05 0 00 -0 05 0 07 -0 02 0 21 0 42 0 00 -0 08 -0 06 0 27

19 CAG 0 00 -0 07 0 00 0 63 0 09 -0 02 -0 06 0 39 0 00 -0 07 -0 01 0 40

20 CAT 0 00 0 64 0 00 0 26 0 15 -0 06 0 24 -0 48 0 00 0 66 0 79 0 69

21 CCA 0 00 0 72 0 00 0 41 -0 75 0 43 0 34 -0 81 0 00 0 11 0 15 -0 72

22 CCC 0 00 0 12 0 00 -0 15 -0 17 0 00 -O i l -0 51 0 00 -0 29 -0 25 -0 42 CCG 000 -011 000 -009 -008 -001 -001 017 000 033 023 040

CCT 000 058 000 -061 -083 -053 -050 -086 000 013 045 -0 76

CGA 000 041 000 -046 -072 024 014 -072 000 -017 -005 -0 65

CGC 000 -019 000 -043 -018 -011 006 005 000 -021 -031 -0 38

CGG 000 019 000 -002 002 032 017 032 000 033 041 0 11

CGT 000 034 000 -011 -066 -042 -042 -064 000 038 058 -0 42

CTA 000 059 000 -076 -072 071 049 -050 000 068 -010 -0 68

CTC 000 -016 000 004 052 -023 042 031 000 040 043 0 37

CTG 000 008 000 037 043 -011 005 052 000 -023 -020 0 27

CTT 000 058 000 -053 -062 -037 -018 -083 000 072 075 0 30

GAA 000 065 000 045 -035 044 042 001 000 021 016 0 75

GAC 000 -005 000 039 033 002 009 051 000 -006 -004 0 27

GAG 000 -013 000 056 015 -002 -017 057 000 -009 -003 0 45

GAT 000 060 000 037 -078 -008 -017 -068 000 064 088 0 59

GCA 000 056 000 028 -053 013 -010 -068 000 032 005 -0 32

GCC 000 000 000 -016 -004 -012 -011 -009 000 -018 -019 -0 41

GCG 000 -007 000 -010 005 006 003 005 000 038 033 0 24

GCT 0.00 0.59 0.00 0.00 -0.75 -0.53 -0.52 -0.87 0.00 0.44 0.52 -0 .52

GGA 000 -001 000 -029 -047 032 -009 020 000 022 023 -0 46

GGC 000 001 000 -032 013 012 004 024 000 -011 -021 -0 32

GGG 000 -007 000 -006 -007 033 000 015 000 025 038 -0 12

GGT 000 023 000 026 -056 -026 -049 -070 000 057 080 0 01

GTA 000 088 000 047 038 055 046 -046 000 075 035 -0 13

GTC 000 -010 000 -007 040 -022 016 017 000 -004 014 0 21

GTG 000 005 000 021 027 019 -003 047 000 -007 -020 0 24

GTT 000 064 000 -024 -083 -022 -033 -049 000 068 081 0 28

TAA 000 000 000 000 000 000 000 000 000 000 000 0 00

TAC 000 -008 000 094 026 010 -011 080 000 -009 -003 0 62

TAG 000 000 000 000 000 000 000 000 000 000 000 0 00

TAT 000 073 000 061 -046 057 004 100 000 062 064 0 45

TCA 000 078 000 100 -063 038 -012 -085 000 018 007 0 41

TCC 000 -001 000 028 010 -007 -024 -002 000 -025 -022 -0 05

TCG 000 -021 000 022 001 010 -007 007 000 045 045 0 42

TCT 000 076 000 -046 -062 -052 -055 -090 000 041 048 1 00

TGA 000 000 000 000 000 000 000 000 000 000 000 0 00

TGC 000 -002 000 -025 003 006 -020 -003 000 -003 -007 -0 08

TGG 000 -001 000 015 -014 015 -017 039 000 -003 000 0 27

TGT 000 043 000 -026 -072 -031 -045 -084 000 043 076 -0 42

TTA 000 100 000 -094 -085 067 052 -091 000 -045 -069 1 00 62 TTC 000 -002 000 038 040 -012 014 040 000 -003 -001 029

63 TTG 000 008 000 -055 -073 -010 -027 -057 000 001 -044 -052

64 TTT 000 047 000 -048 -048 -002 011 -069 000 057 062 -069

TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT

49 50 51 52 53 54 55 56 57 58 59 60

Table CIl continued

61 62 63 64

TTA TTC TTG TTT

1 AAA 100 043 -028 -073

2 AAC 008 -002 078 057

3 AAG 100 -002 027 -002

4 AAT 100 035 044 -065

5 ACA 100 065 -014 -051

6 ACC 062 -012 028 001

7 ACG -037 022 -025 -001

8 ACT -093 025 -057 -082

9 AGA 100 048 -014 -076

10 AGC 100 018 051 -041

11 AGG -044 013 -048 020

12 AGT 100 015 060 -080

13 ATA 100 041 -005 -043

14 ATC 100 -001 076 018

15 ATG 100 -001 063 038

16 ATT 100 025 -070 -091

17 CAA -090 077 -069 -085

18 CAC -019 -004 049 016

19 CAG -046 -004 -074 039

20 CAT 100 050 -031 100

21 CCA -084 071 -064 -059

22 CCC -037 -015 -007 -015

23 CCG 004 009 -058 -007

24 CCT 100 034 -041 -065

25 CGA -088 041 -039 -069

26 CGC 051 -009 064 -030

27 CGG -043 009 -051 021

28 CGT -072 -005 003 -056

29 CTA -095 056 -070 -067 CTC 0 32 -0 09 0 71 0 04

CTG 0 29 0 04 0 02 0 54

CTT -0 94 0 36 -0 56 -0 79

GAA -0 29 0 65 O 19 0 00

GAC 1 00 -0 03 0 62 0 38

GAG -0 12 -O i l -0 52 0 26

GAT -0 57 0 40 -0 39 0 37

GCA -0 59 0 68 -0 52 -0 55

GCC 0 26 -O 10 0 47 -O 12

GCG -0 52 0 09 -0 43 -0 20

GCT -0 85 0 36 -0 53 -0 70

GGA -0 50 O 19 0 08 -0 33

GGC 0 65 -0 04 0 63 -O 12

GGG -0 48 0 05 -0 43 -O 19

GGT -0 35 0 05 0 31 -0 58

GTA 1 00 0 82 -0 21 0 65

GTC 0 61 -O 18 0 84 0 57

GTG 0.64 0.20 0.32 0.41

GTT 1 00 0 26 -0 53 -0 24

TAA 0 00 0 00 0 00 0 00

TAC 0 65 -0 02 0 60 0 37

TAG 0 00 0 00 0 00 0 00

TAT -0 86 0 37 -0 31 -0 41

TCA -0 87 0 65 -0 42 -0 81

TCC 0 27 -0 24 O 12 -O 10

TCG -0 06 0 25 -0 52 0 25

TCT -0 92 0 33 -0 72 -0 67

TGA 0 00 0 00 0 00 0 00

TGC -0 52 -0 02 0 50 -0 21

TGG -0 17 0 00 -0 01 -O 11

TGT 1 00 0 31 -0 25 -0 22

TTA 1 00 0 72 -0 82 1 OO

TTC 0 16 -0 02 0 63 0 51

TTG 1 00 0 20 -0 74 -0 55

TTT 1 00 0 45 -0 86 -0 47

TTA TTC TTG TTT

61 62 63 64 I Applicant's or agent's file reference number 2505 IWO International application No

INDICATIONS RELATING TO A DEPOSITED MICROORGANISM

(PCT Rule Ubis)

A The indications made below relate to the microorganism referred to in the description first mentioned on page 26 line 24

B IDENTIFICATION OF DEPOSIT Further deposits are identified on an additional sheet

Name of depositary institution

CENTRAAL BUREAU VOOR SCHIMMELCULTURES

Address of depositary institution (including postal code and country) Uppsalalaan 8 P O Box 85167 NL-3508 AD Utrecht The Netherlands

Date of deposit 10-08-1988 Accession Number CBS 513 !

C ADDITIONAL INDICATIONS (leave blank if not applicable) This information is continued on an additional sheet

We inform you that the availability of the microorganism identified above, referred to Rule 13bis PCT, shall be effected only by issue of a sample to an expert nominated by the requester until the publication of the mention of grant of the national patent or, where applicable, for twenty years from the date of filing if the application has been refused, withdrawn or deemed to be withdrawn

D DESIGNATED STATES FOR WHICH INDICATIONS ARE MADE (if the indications are not for all designated States)

SEPARATE FURNISHING OF INDICATIONS (leave blank if not applicable)

The indications listed below will be submitted to the International Bureau later (specify the general nature of the indications e g , "Accession Number of Deposit")

For receiving Office use only

This sheet was received with the international application

Authorized officer

Wallentin, Marko

Form PCT/RO/134 (July 1992) I Applicant's or agent's file reference number 25Q51WO I International application NoT

INDICATIONS RELATING TO A DEPOSITED MICROORGANISM

(PCT Rule Ubis)

The indications made below relate to the microorganism referred to in the description first mentioned on page 26 line 26

B IDENTIFICATION OF DEPOSIT Further deposits are identified on an additional sheet

Name of depositary institution

CENTRAAL BUREAU VOOR SCHIMMELCULTURES

Address of depositary institution (including postal code and country) Uppsalalaan 8 P O Box 85167 NL-3508 AD Utrecht The Netherlands

Date of deposit 02-06- 1995 Accession Number CBS 455 95

C ADDITIONAL INDICATIONS (leave blank if not applicable) This information is continued on an additional sheet

We inform you that the availability of the microorganism identified above, referred to Rule 13bis PCT, shall be effected only by issue of a sample to an expert nominated by the requester until the publication of the mention of grant of the national patent or, where applicable, for twenty years from the date of filing if the application has been refused, withdrawn or deemed to be withdrawn

D DESIGNATED STATES FOR WHICH INDICATIONS ARE MADE (if the indications are not for all designated States)

SEPARATE FURNISHING OF INDICATIONS (leave blank if not applicable)

The indications listed below will be submitted to the International Bureau later (specify the general nature of the indications e g., "Accession Number of Deposit")

For receiving Office use only For International Bureau use only —

This sheet was received with the international This sheet was received by the International Bureau application on-

Authorized officer Authorized officer

Wallentin, Marko

Form PCT/RO/134 (July 1992)

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Reference
1 *BOYCHEVA S. ET AL.,: "codon pairs in the genome of escherichia coli" BIOINFORMATICS, vol. 19, no. 8, 2003, pages 987-998, XP002406004 cited in the application
2 *IRWIN B. ET AL.,: "codon pair utilization biases influence translational elongation step times" J. BIOL. CHEM., vol. 270, no. 39, 29 September 1995 (1995-09-29), pages 22801-22806, XP002406003 cited in the application
3 *MAKRIDES: "Strategies for Achieving High-Level Expression of Genes in Escherichia coli" MICROBIOLOGICAL REVIEWS, AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, DC, US, vol. 60, no. 3, September 1996 (1996-09), pages 512-538, XP002095235 ISSN: 0146-0749
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WO2009109633A1 *Mar 5, 2009Sep 11, 2009Dsm Ip Assets B.V.A pentose sugar fermenting cell
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Classifications
International ClassificationC12N15/67
Cooperative ClassificationC12N15/67, C12N9/92, C12N15/81, C12N2800/22, C12N9/242, C12N15/80
European ClassificationC12N15/80, C12N15/67, C12N15/81
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