Mercurial > repos > iuc > codeml
changeset 0:961a712f9743 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 5e46bc6be71912be9b1982b3c2f0d30a36d9b3a8
| author | iuc |
|---|---|
| date | Tue, 29 Aug 2017 19:12:01 -0400 |
| parents | |
| children | ba71e26d5bdc |
| files | codeml.xml macros.xml test-data/1_2ngdn test-data/1_2ngds test-data/1_2ngt test-data/1_codeml.ctl test-data/1_run_codeml test-data/2_2ngdn test-data/2_2ngds test-data/2_2ngt test-data/2_codeml.ctl test-data/2_run_codeml test-data/3_2ngdn test-data/3_2ngds test-data/3_2ngt test-data/3_codeml.ctl test-data/3_run_codeml test-data/RAxML_bestTree test-data/concat.fasta test-data/tree_model2 test-data/tree_model3 |
| diffstat | 21 files changed, 1188 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/codeml.xml Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,465 @@ +<tool name="codeML" id="codeml" version="1.0"> + <description> + Detects positive selection (paml package) + </description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + <requirement type="package" version="4.9">paml</requirement> + </requirements> + + <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command> + + <command><![CDATA[ + +codeml '$codeml_ctl' +&& +mv '$codeml_ctl' '$ctl' + + ]]></command> + + <configfiles> + <configfile name="codeml_ctl"><![CDATA[ + seqfile = $concat_nuc * sequence data file name + outfile = run_codeml * main result file name + treefile = $tree * tree structure file name + noisy = 9 * 0,1,2,3,9: how much rubbish on the screen + verbose = $adv.verbose * 1: detailed output, 0: concise output + runmode = $adv.runmode * 0: user tree; 1: semi-automatic; 2: automatic + * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise + seqtype = $adv.seqtype * 1:codons; 2:AAs; 3:codons-->AAs + CodonFreq = $adv.CodonFreq * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table + clock = $adv.clock * 0:no clock, 1:clock; 2:local clock + aaDist = $adv.aaDist * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a + * 7:AAClasses + aaRatefile = $adv.aaRateFile * only used for aa seqs with model=empirical(_F) + * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own + model = $compat_model.brmodel + * models for codons: + * 0:one, 1:b, 2:2 or more dN/dS ratios for branches + * models for AAs or codon-translated AAs: + * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F + * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189) + NSsites = $compat_model.NSsites * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; + * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ + * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; + * 13:3normal>0 + icode = $adv.icode * 0:universal code; 1:mammalian mt; 2-11:see below + Mgene = $adv.Mgene * 0:rates, 1:separate; + fix_kappa = $adv.fix_kappa * 1: kappa fixed, 0: kappa to be estimated + kappa = $adv.kappa * initial or fixed kappa + fix_omega = $adv.fix_omega * 1: omega or omega_1 fixed, 0: estimate + omega = $adv.omega * initial or fixed omega, for codons or codon-based AAs + fix_alpha = $adv.fix_alpha * 0: estimate gamma shape parameter; 1: fix it at alpha + alpha = $adv.alpha * initial or fixed alpha, 0:infinity (constant rate) + Malpha = $adv.Malpha * 1: different alphas for genes, 0 : one alpha + ncatG = $adv.ncatG * # of categories in dG of NSsites models + fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho + rho = $adv.rho * initial or fixed rho, 0:no correlation + getSE = $adv.getSE * 0: don't want them, 1: want S.E.s of estimates + RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) + Small_Diff = $adv.Small_Diff + cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)? + fix_blength = $adv.fix_blength * 0: ignore, -1: random, 1: initial, 2: fixed + method = $adv.method * 0: simultaneous; 1: one branch at a time + + ]]></configfile> + </configfiles> + + <inputs> + + <param name="concat_nuc" type="data" format="fasta" label="Sequences file" help="The fasta file with the sequences to be analyzed" /> + <param name="tree" type="data" format="nhx" label="tree file" help="Tree file in Newick format" /> + + <conditional name="compat_model" > + <param argument="brmodel" type="select" label="Branch model ; for tree file editing in model 2 and 3, see paml manual (chap.3)" > + <option value="0" selected="true">'0' : one dN/dS ratio for all branches (e.g. basic model if NSsites=0)</option> + <option value="1">'1' : one dN/dS ratio for each branch ("free-ratio model") ; its use is discouraged</option> + <option value="2">'2' : arbitrary number of ratios ; implies to manually edit your tree file</option> + <option value="3">'3' : clade-model ; implies to manually edit your tree file</option> + </param> + + <when value="0" > + <expand macro="FSsites_br0" /> + </when> + <when value="1"> + <expand macro="FSsites_br1" /> + </when> + <when value="2" > + <expand macro="FSsites_br2_and_3" /> + </when> + <when value="3" > + <expand macro="FSsites_br2_and_3" /> + </when> + </conditional> + + <!-- advanced parameters --> + <section name="adv" title="Advanced Options" expanded="False" > + <param argument="verbose" type="select" label="Set the level of details in the log file"> + <option value="0" selected="true">0 : concise output</option> + <option value="1">1 : detailed output</option> + </param> + + <param argument="runmode" type="select" label="Tree analysis mode" > + <option value="0" selected="true">0 : user tree</option> + <option value="1">1 : heuristic tree search starting from a multifurcating tree from the tree structure file</option> + <option value="2">2 : heuristic tree search starting from the tree file</option> + <option value="3">3 : StepwiseAddition</option> + <option value="4">4 : PerturbationNNI with the starting tree obtained by a parsimony algorithm</option> + <option value="5">5 : PerturbationNNI with the starting tree read from the tree structure file</option> + <option value="-2">-2 : ML estimation of dS and dN in pairwise comparisons of protein-coding sequences</option> + </param> + + <param argument="seqtype" type="select" label="Sequences format in the fasta file" > + <option value="1" selected="true">1 : codons</option> + <option value="2">2 : Amino acids (only compatible with FSsites=0) </option> + <option value="3">3 : codons-->amino acids (only compatible with FSsites=0)</option> + </param> + + <param argument="CodonFreq" type="select" label="Equilibrium codon frequencies in codon substitution model"> + <option value="0">0 : 1/61 each:</option> + <option value="1" selected="true">1 : FIX4</option> + <option value="2">2 : codon table</option> + </param> + + <param argument="clock" type="select" label="Specifies models concerning rate constancy or variation among lineages" > + <option value="0" selected="true">0 : no clock ; An unrooted tree should be used under this model</option> + <option value="1">1 : clock</option> + <option value="2">2 : local clock (needed : branch labels in the tree)</option> + </param> + + <param argument="aaDist" type="select" label="Amino acid distances" > + <option value="0" selected="true">0 : equal (warning : the only one compatible with NSsites and seqtype=codons</option> + <option value="+">+ : geometric</option> + <option value="-">- : linear</option> + <option value="1">1 : G1974</option> + <option value="2">2 : Miyata</option> + <option value="3">3 : c</option> + <option value="4">4 : p</option> + <option value="5">5 : v</option> + <option value="6">6 : a</option> + <option value="7">7 : AAClasses</option> + </param> + + <param argument="aaRateFile" type="select" label="Amino acide substitution rate matrix" > + <option value="wag.dat" selected="true">wag.dat</option> + <option value="dayhoff.dat">dayhoff.dat</option> + <option value="jones.dat">jones.dat</option> + <option value="mtmam.dat">mtmam.dat</option> + </param> + + <param argument="icode" type="select" label="Icode : specifies the genetic code" > + <option value="0" selected="true">0 : universal code</option> + <option value="1">1 : mammalian mt</option> + <option value="3">3 : mold mt</option> + <option value="4">4 : invertebrate mt</option> + <option value="5">5 : ciliate nuclear code mt</option> + <option value="6">6 : echinoderm mt</option> + <option value="7">7 : euplotid mt</option> + <option value="8">8 : alternative yeast nuclear</option> + <option value="9">9 : scidian mt</option> + <option value="10">10 : blepharisma nuclear</option> + <option value="11">11 : Yang's regularized code</option> + </param> + + <param argument="Mgene" type="select" value="0" label="Multiple genes" + help="Used in combination with option G in the sequence data file, for combined analysis of data from multiple genes or multiple site partitions" > + <option value="0">0 : complete homogeneity among genes </option> + <option value="1">1 : equivalent to a separate analysis</option> + <option value="2">2 : different frequency parameters for different genes but the same rate ratio parameters</option> + <option value="3">3 : different rate ratio parameters and the same frequency parameters</option> + <option value="4">4 : both different rate ratio parameters and different frequency parameters for different genes </option> + </param> + + <param argument="fix_kappa" type="select" label="Specifies wether kappa in K80, F84, or HKY85 is fixed or estimated"> + <option value="0" selected="true">0 : estimated</option> + <option value="1">1 : fixed (the next parameter below)</option> + </param> + + <param argument="kappa" type="float" value="2" label="Initial or fixed value of kappa" help="kappa refers to the transition/tranversion rate ratio"/> + + <param argument="fix_omega" type="select" label="Fixed or estimated omega" > + <option value="0" selected="true">0 : estimated</option> + <option value="1">1 : fixed</option> + </param> + + <param argument="omega" type="float" value="0.2" label="Initial or fixed omega (according to your choice for fix_omega), for codons or codon-based AAs"/> + + <param argument="fix_alpha" type="select" label="Estimated or fixed gamma shape parameter" > + <option value="0">0 : estimate gamma shape parameter. Not recommended</option> + <option value="1" selected="true">1 : fix it at alpha (the next parameter below)</option> + </param> + + <param argument="alpha" type="float" value="0" label="Initial or fixed value of alpha (gamma shape parameter)" + help="0: constant rate. fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0"/> + + <param argument="Malpha" type="select" label="Different alphas for genes" > + <option value="0">0 : one gamma distribution will be applied across all sites (one alpha)</option> + <option value="1">1 : different gamma distribution is used for each gene or codon position (different alphas for genes)</option> + </param> + + <param argument="ncatG" type="integer" value="3" label="# of categories in dG of NSsites models" /> + + <param argument="fix_rho" type="select" label="Independence or correlation of rates at adjacent sites" > + <option value="0">0 : estimate rho</option> + <option value="1" selected="true">1 : fix it at rho (the next parameter below)</option> + </param> + + <param argument="rho" type="float" value="0" label="Initial or fixed rho" help="fix_rho=1 and rho=0 : independent rates" /> + + <param argument="getSE" type="select" label="Estimates of the standard errors of estimated parameters." > + <option value="0" selected="true">0 : don't want them</option> + <option value="1">1 : want S.E.s of estimates</option> + </param> + + <param argument="RateAncestor" type="select" label="RateAncestor ; set 1 to force the program to do two additional analyses" > + <option value="0" selected="true">0 : usually use 0</option> + <option value="1">1 : model of variable rates across site + empirical Bayesian reconstruction of ancestral sequences</option> + </param> + + <param argument="Small_Diff" type="float" value=".5e-6" label="Value used in the difference approximation of derivatives"/> + + <param argument="cleandata" type="select" label="Remove sites with ambiguity data" help="Warning : choosing 'yes' may remove a lot (possibly all) of data."> + <option value="0" selected="true">0 : no (don't remove ambiguous data)</option> + <option value="1">1 : yes (remove ambiguous data)</option> + </param> + + <param argument="fix_blength" type="select" label="branch length dealing" > + <option value="0" selected="true">0 : ignore branch lengths</option> + <option value="-1">-1 : start from random starting points</option> + <option value="1">1 : initial values as written in the tree file</option> + <option value="2">2 : fixed at values in the tree file</option> + </param> + + <param argument="method" type="select" label="Controls the iteration algorithm for estimating branch lengths" > + <option value="0" selected="true">0 : simultaneous (old paml algorithm)</option> + <option value="1">1 : one branch at a time (newly implemented in paml ; does not work with clock=1,2,3)</option> + </param> + </section> + </inputs> + + <outputs> + <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" /> + <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" > + <filter>adv['seqtype']=="1"</filter> + </data> + <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" > + <filter>adv['seqtype']=="1"</filter> + </data> + <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" > + <filter>adv['seqtype']=="1"</filter> + </data> + <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/> + <data format="txt" name="rst" from_work_dir="rst" label="${tool.name} on ${on_string}: rst"/> + <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/> + <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/> + <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/> + <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc"> + <filter>adv['verbose']=="1"</filter> + </data> + </outputs> + + <tests> + <test> + <conditional name="compat_model" > + <param name="brmodel" value="0" /> + <param name="NSsites" value="0" /> + </conditional> + <param name="adv.fix_omega" value="0" /> + <param name="adv.omega" value="0.2" /> + <param name="RateAncestor" value="1" /> + <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> + <param name="tree" ftype="txt" value="RAxML_bestTree" /> + <output name="2ngdn" value="1_2ngdn" /> + <output name="2ngds" value="1_2ngds" /> + <output name="2ngt" value="1_2ngt" /> + <output name="run" value="1_run_codeml" lines_diff="20"/> + <output name="ctl" value="1_codeml.ctl" lines_diff="4" /> + </test> + <test> + <conditional name="compat_model" > + <param name="brmodel" value="2" /> + <param name="NSsites" value="0" /> + </conditional> + <param name="adv.fix_omega" value="0" /> + <param name="adv.omega" value="0.2" /> + <param name="RateAncestor" value="1" /> + <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> + <param name="tree" ftype="txt" value="tree_model2" /> + <output name="2ngdn" value="2_2ngdn" /> + <output name="2ngds" value="2_2ngds" /> + <output name="2ngt" value="2_2ngt" /> + <output name="run" value="2_run_codeml" lines_diff="20" /> + <output name="ctl" value="2_codeml.ctl" lines_diff="4" /> + </test> + <test> + <conditional name="compat_model" > + <param name="brmodel" value="3" /> + <param name="NSsites" value="2" /> + </conditional> + <param name="adv.fix_omega" value="0" /> + <param name="adv.omega" value="0.2" /> + <param name="RateAncestor" value="1" /> + <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> + <param name="tree" ftype="txt" value="tree_model3" /> + <output name="2ngdn" value="3_2ngdn" /> + <output name="2ngds" value="3_2ngds" /> + <output name="2ngt" value="3_2ngt" /> + <output name="run" value="3_run_codeml" lines_diff="20"/> + <output name="ctl" value="3_codeml.ctl" lines_diff="4" /> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**Galaxy integration** Victor Mataigne and ABIMS TEAM. + + Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + +---------- + +**CompCodeML (from paml package)** + +A few help is detailed below ; full and detailed codeml readme can be found on the paml website_ + +.. _website: http://abacus.gene.ucl.ac.uk/software/paml.html + +.. class:: warningmark + +Due to their high number, some parameters incompatibility can remain. + +This Galaxy implementation : +- handles incompatibilities between branch and sites models (the tool CANNOT be run with incompatible models). +- warns the user in a help section when an advanced parameter has known incompatibilities (the tool CAN be run, but the output files will be empty). + +We recommand to have a look at the full paml manual before looking at the advanced parameters, in order to spot parameters incompatibilities and to know what each model does. If you choose by mistake incompatible parameters, the output files will be empty, except the log file ("run_codeml" output) which will normally explicit the error. + +.. class:: infomark + +Known incompatibilities: + - 'seqtype' = 3 : only compatible with 'FSsites' = 0. + - 'clock' = 2 : needs branch labels in the tree. + - fix_alpha !=1 combined with alpha !=0 are not compatible with NSsites !=0 + - 'aaDist' = 0 is the only one compatible with 'NSsites' different than 0 and 'seqtype' = 1. + - 'method' = 1 : does not work with 'clock' different than 0. + +---------- + +**Description** + +.. class:: infomark + +codeML finds positive selection within branches or codons within a tree and a set of sequences. + +---------- + +**Input files** + +- a treefile in Newick format (with or without branch lengths). +- a fasta file with sequences from the species of the tree file (one header/sequence per species) and run codeml (from the paml suite). + +---------- + +**Parameters** + +Several models are available. +- branch models ("model" parameter). +- sites models ("NSsites" parameter, model is left at 0). +- branch-sites models (when model = 2 NSsites=2,3). +- Clade models (when model=3 NSsites=2,3). +Basically, this tool write a configfile called codeml.ctl with the specified parameters and then launches codeml. + +.. class:: infomark + +Branch models allow the omega ratio to vary among branches in the phylogeny and are useful for detecting positive selection acting on particular lineages. Sites models allow the omega ratio to vary among sites (codons or amino acids). + +Two pairs of models appear to be particularly useful, forming two likelihood ratio tests of positive selection. The first compares M1a ('NearlyNeutral', NSsites=1) and M2a ('PositiveSelection', NSsites=2), while the second compares M7 ('beta', NSsites=7) and M8 ('beta&ω', NSsites=8). + +**Other examples of model** + +How to run the branch-site models (A & B in Yang & Nielsen 2002 MBE) ? +The options are : + Model A: (model=2, NSsites=2). + Model B: (model=2, NSsites=3). + +How to run the M0 (one-ratio) model : + model = 0, NSsites= = 0. + +---------- + +**Advanced Parameters** + +.. class:: infomark + +See paml complete manual and FAQ on paml website_ + +.. _website: http://abacus.gene.ucl.ac.uk/software/paml.html + +**Details of some parameters :** + + - 'kappa' denotes the transition/transversion rate ratio. + - 'fix_kappa' specifies whether kappa in K80, F84, or HKY85 is given at a fixed value or is to be estimated by iteration from the data. + -> If fix_kappa = 1 (fixed), the value of kappa is the given value + -> If fix_kappa = 0 (estimated) the value of kappa is used as the initial estimate for iteration. + + - 'alpha' refers to the shape parameter alpha of the gamma distribution for variable substitution rates across sites (Yang 1994a). + - 'fix_alpha' works in a similar way that fix_kappa. + -> The model of a single rate for all sites is specified as fix_alpha = 1 and alpha = 0 (0 means infinity) + -> The (discrete-) gamma model is specified by a positive value for alpha, and 'ncatG' is then the number of categories for the discrete-gamma model. Values such as 5, 4, 8, or 10 are reasonable. + + - fix_rho and rho work in a similar way and concern independence or correlation of rates at adjacent sites, where rho is the correlation parameter of the auto-discrete-gamma model (Yang 1995). + -> The model of independent rates for sites is specified as fix_rho = 1 and rho = 0; choosing alpha = 0 further means a constant rate for all sites. + -> The auto-discrete-gamma model is specified by positive values for both alpha and rho. + -> The model of a constant rate for sites is a special case of the (discrete) gamma model with alpha = 0 (means infinity). + -> The model of independent rates for sites is a special case of the auto-discrete-gamma model with rho = 0. + +---------- + +**Output files** + +- codeml.ctl : a copy of the control file (list of all the parameters used for the codeml run). +- run_codeml : main result file name. +- The 2NG.dN and 2NG.dS files are the Nei an Gojobori (1986) dN and dS values; +- lnf, rst and rst1: Supplemental results. +- rub : records of the iteration progress (i.e. the minimization of the negative log-likelihood). + +---------- + +**How to edit manually the tree file : Branch or node labels** + +Some models implemented in codeml allow several groups of branches on the tree, which are assigned different parameters of interest. + + - For example, in the local clock models (clock = 2 or 3), you can have, say, 3 branch rate groups, with low, medium, and high rates respectively. + + - Also the branch-specific codon models (model = 2 or 3 or codonml) allow different branch groups to have different ωs, leading to so called “two-ratios” and “three-ratios” models. + + - All those models require branches or nodes in the tree to be labeled. Branch labels are specified in the same way as branch lengths except that the symbol “#” is used rather than “:”. The branch labels are consecutive integers starting from 0, which is the default and does not have to be specified. + +In ((Hsa_Human, Hla_gibbon) #1, ((Cgu/Can_colobus, Pne_langur), Mmu_rhesus), (Ssc_squirrelM, Cja_marmoset)); : + The internal branch ancestral to human and gibbon has the ratio ω1, while all other branches (with the default label #0) have the background ratio ω0. + +The following trees are equivalent : + ((rabbit, rat) $1, human), goat_cow, marsupial); + (((rabbit #1, rat #1) #1, human), goat_cow, marsupial); + +$ is the symbol for clade labels. + +Rules concerning nested clade labels : The symbol # takes precedence over the symbol $, and clade labels close to the tips take precedence over clade labels for ancestral nodes close to the root. + +In the tree ((((rabbit, rat) $2, human #3), goat_cow) $1, marsupial); : + $1 is first applied to the whole clade of placental mammals (except for the human lineage), and then $2 is applied to the rabbit-rat clade. + Equivalent tree with only '#' : + ((((rabbit #2, rat #2) #2, human #3) #1, goat_cow #1) #1, marsupial); + + + ]]></help> + + <citations> + <citation type="doi">10.1093/molbev/msm088</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,26 @@ +<macros> + <xml name="FSsites_br0" > + <param argument="NSsites" type="select" label="Site model ; fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0" > + <option value="0" selected="true">0 : e.g. basic model if model=0</option> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + <option value="7">7</option> + <option value="8">8</option> + </param> + </xml> + + <xml name="FSsites_br1" > + <param argument="NSsites" type="select" label="Site model ; fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0" > + <option value="0" selected="true">0 : e.g. basic model if model=0</option> + </param> + </xml> + + <xml name="FSsites_br2_and_3" > + <param argument="NSsites" type="select" label="Site model ; fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0" > + <option value="0" selected="true">0</option> + <option value="2">2 (Warning: only two branch type allowed for branch models)</option> + <option value="3">3 (Warning: only two branch type allowed for branch models)</option> + </param> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_2ngdn Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 0.0628 +Ap 0.0536 0.0422 +Pg 0.1215 0.0396 0.1403 +Th 0.0137 0.0000 0.0932 0.0625 +Ph 0.0858 0.0613 0.1166 0.1673 -1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_2ngds Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 1.4398 +Ap 0.1327 1.2410 +Pg 0.5783 3.0000 0.3631 +Th 2.0454 0.0066 1.0019 4.0052 +Ph 0.7837 1.5834 0.4563 0.2459 -1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_2ngt Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 1.1652 +Ap 0.2186 0.9823 +Pg 0.6879 2.1378 0.5820 +Th 1.4515 0.0048 0.9174 2.9292 +Ph 0.7412 1.2821 0.5897 0.5567 -nan
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_codeml.ctl Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,45 @@ + + seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_1.dat * sequence data file name + outfile = run_codeml * main result file name + treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_2.dat * tree structure file name + noisy = 9 * 0,1,2,3,9: how much rubbish on the screen + verbose = 0 * 1: detailed output, 0: concise output + runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic + * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise + seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs + CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table + clock = 0 * 0:no clock, 1:clock; 2:local clock + aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a + * 7:AAClasses + aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) + * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own + model = 0 + * models for codons: + * 0:one, 1:b, 2:2 or more dN/dS ratios for branches + * models for AAs or codon-translated AAs: + * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F + * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189) + NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; + * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ + * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; + * 13:3normal>0 + icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below + Mgene = 0 * 0:rates, 1:separate; + fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated + kappa = 2.0 * initial or fixed kappa + fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate + omega = 0.2 * initial or fixed omega, for codons or codon-based AAs + fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha + alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate) + Malpha = 0 * 1: different alphas for genes, 0 : one alpha + ncatG = 3 * # of categories in dG of NSsites models + fix_rho = 1 * 0: estimate rho; 1: fix it at rho + rho = 0.0 * initial or fixed rho, 0:no correlation + getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) + Small_Diff = 5e-07 + cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? + fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed + method = 0 * 0: simultaneous; 1: one branch at a time + + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1_run_codeml Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,152 @@ +CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_1.dat +Model: One dN/dS ratio for branches, +Codon frequency model: F1x4 +ns = 6 ls = 13754 + +Codon usage in sequences +-------------------------------------------------------------------------------------------------------------------------------------- +Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40 + TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34 +Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 + TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27 +-------------------------------------------------------------------------------------------------------------------------------------- +Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25 + CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39 + CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17 + CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11 +-------------------------------------------------------------------------------------------------------------------------------------- +Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39 + ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40 + ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30 +Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23 +-------------------------------------------------------------------------------------------------------------------------------------- +Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34 + GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41 + GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26 + GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24 +-------------------------------------------------------------------------------------------------------------------------------------- + +Codon position x base (3x4) table for each sequence. + +#1: Ac +position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210 +position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767 +position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232 +Average T:0.27704 C:0.24321 A:0.24905 G:0.23070 + +#2: Am +position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269 +position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611 +position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689 +Average T:0.19140 C:0.26973 A:0.26031 G:0.27856 + +#3: Ap +position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243 +position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521 +position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042 +Average T:0.28066 C:0.24824 A:0.24175 G:0.22935 + +#4: Pg +position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604 +position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839 +position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761 +Average T:0.27943 C:0.23894 A:0.27762 G:0.20401 + +#5: Th +position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642 +position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623 +position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572 +Average T:0.20850 C:0.27659 A:0.24546 G:0.26946 + +#6: Ph +position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682 +position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737 +position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074 +Average T:0.26575 C:0.25975 A:0.24286 G:0.23164 + +Sums of codon usage counts +------------------------------------------------------------------------------ +Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547 + TTC 765 | TCC 595 | TAC 364 | TGC 398 +Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0 + TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445 +------------------------------------------------------------------------------ +Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259 + CTC 418 | CCC 233 | CAC 400 | CGC 215 + CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217 + CTG 651 | CCG 181 | CAG 553 | CGG 153 +------------------------------------------------------------------------------ +Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378 + ATC 623 | ACC 405 | AAC 516 | AGC 441 + ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431 +Met M ATG 832 | ACG 230 | AAG 661 | AGG 374 +------------------------------------------------------------------------------ +Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397 + GTC 531 | GCC 585 | GAC 513 | GGC 435 + GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405 + GTG 592 | GCG 159 | GAG 424 | GGG 202 +------------------------------------------------------------------------------ + +(Ambiguity data are not used in the counts.) + + +Codon position x base (3x4) table, overall + +position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819 +position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582 +position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601 +Average T:0.27338 C:0.24787 A:0.24874 G:0.23001 + + +Nei & Gojobori 1986. dN/dS (dN, dS) +(Pairwise deletion) +(Note: This matrix is not used in later ML. analysis. +Use runmode = -2 for ML pairwise comparison.) + +Ac +Am 0.0436 (0.0628 1.4398) +Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410) +Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631) +Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052) +Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000) +NOTE: -1 means that NG86 is inapplicable. + + +TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1 +lnL(ntime: 9 np: 11): -71862.094834 +0.000000 + 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 + 0.246863 0.000004 0.279150 0.179426 0.225632 0.000004 0.478467 0.076909 0.146872 3.015798 0.345817 + +Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). + +tree length = 1.63333 + +(((4: 0.279150, 2: 0.179426): 0.000004, 5: 0.225632): 0.246863, (6: 0.478467, 3: 0.076909): 0.000004, 1: 0.146872); + +(((Pg: 0.279150, Am: 0.179426): 0.000004, Th: 0.225632): 0.246863, (Ph: 0.478467, Ap: 0.076909): 0.000004, Ac: 0.146872); + +Detailed output identifying parameters + +kappa (ts/tv) = 3.01580 + +omega (dN/dS) = 0.34582 + +dN & dS for each branch + + branch t N S dN/dS dN dS N*dN S*dS + + 7..8 0.247 29225.7 12036.3 0.3458 0.0530 0.1533 1549.7 1845.6 + 8..9 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0 + 9..4 0.279 29225.7 12036.3 0.3458 0.0600 0.1734 1752.4 2087.0 + 9..2 0.179 29225.7 12036.3 0.3458 0.0385 0.1114 1126.4 1341.4 + 8..5 0.226 29225.7 12036.3 0.3458 0.0485 0.1401 1416.5 1686.9 + 7..10 0.000 29225.7 12036.3 0.3458 0.0000 0.0000 0.0 0.0 + 10..6 0.478 29225.7 12036.3 0.3458 0.1028 0.2972 3003.7 3577.1 + 10..3 0.077 29225.7 12036.3 0.3458 0.0165 0.0478 482.8 575.0 + 7..1 0.147 29225.7 12036.3 0.3458 0.0315 0.0912 922.0 1098.1 + +tree length for dN: 0.3508 +tree length for dS: 1.0145 + + +Time used: 1:09
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_2ngdn Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 0.0628 +Ap 0.0536 0.0422 +Pg 0.1215 0.0396 0.1403 +Th 0.0137 0.0000 0.0932 0.0625 +Ph 0.0858 0.0613 0.1166 0.1673 -1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_2ngds Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 1.4398 +Ap 0.1327 1.2410 +Pg 0.5783 3.0000 0.3631 +Th 2.0454 0.0066 1.0019 4.0052 +Ph 0.7837 1.5834 0.4563 0.2459 -1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_2ngt Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 1.1652 +Ap 0.2186 0.9823 +Pg 0.6879 2.1378 0.5820 +Th 1.4515 0.0048 0.9174 2.9292 +Ph 0.7412 1.2821 0.5897 0.5567 -nan
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_codeml.ctl Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,45 @@ + + seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_12.dat * sequence data file name + outfile = run_codeml * main result file name + treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_13.dat * tree structure file name + noisy = 9 * 0,1,2,3,9: how much rubbish on the screen + verbose = 0 * 1: detailed output, 0: concise output + runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic + * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise + seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs + CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table + clock = 0 * 0:no clock, 1:clock; 2:local clock + aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a + * 7:AAClasses + aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) + * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own + model = 2 + * models for codons: + * 0:one, 1:b, 2:2 or more dN/dS ratios for branches + * models for AAs or codon-translated AAs: + * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F + * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189) + NSsites = 0 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; + * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ + * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; + * 13:3normal>0 + icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below + Mgene = 0 * 0:rates, 1:separate; + fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated + kappa = 2.0 * initial or fixed kappa + fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate + omega = 0.2 * initial or fixed omega, for codons or codon-based AAs + fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha + alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate) + Malpha = 0 * 1: different alphas for genes, 0 : one alpha + ncatG = 3 * # of categories in dG of NSsites models + fix_rho = 1 * 0: estimate rho; 1: fix it at rho + rho = 0.0 * initial or fixed rho, 0:no correlation + getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) + Small_Diff = 5e-07 + cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? + fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed + method = 0 * 0: simultaneous; 1: one branch at a time + + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2_run_codeml Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,160 @@ +CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_12.dat +Model: several dN/dS ratios for branches for branches, +Codon frequency model: F1x4 +ns = 6 ls = 13754 + +Codon usage in sequences +-------------------------------------------------------------------------------------------------------------------------------------- +Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40 + TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34 +Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 + TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27 +-------------------------------------------------------------------------------------------------------------------------------------- +Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25 + CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39 + CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17 + CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11 +-------------------------------------------------------------------------------------------------------------------------------------- +Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39 + ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40 + ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30 +Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23 +-------------------------------------------------------------------------------------------------------------------------------------- +Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34 + GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41 + GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26 + GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24 +-------------------------------------------------------------------------------------------------------------------------------------- + +Codon position x base (3x4) table for each sequence. + +#1: Ac +position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210 +position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767 +position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232 +Average T:0.27704 C:0.24321 A:0.24905 G:0.23070 + +#2: Am +position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269 +position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611 +position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689 +Average T:0.19140 C:0.26973 A:0.26031 G:0.27856 + +#3: Ap +position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243 +position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521 +position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042 +Average T:0.28066 C:0.24824 A:0.24175 G:0.22935 + +#4: Pg +position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604 +position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839 +position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761 +Average T:0.27943 C:0.23894 A:0.27762 G:0.20401 + +#5: Th +position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642 +position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623 +position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572 +Average T:0.20850 C:0.27659 A:0.24546 G:0.26946 + +#6: Ph +position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682 +position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737 +position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074 +Average T:0.26575 C:0.25975 A:0.24286 G:0.23164 + +Sums of codon usage counts +------------------------------------------------------------------------------ +Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547 + TTC 765 | TCC 595 | TAC 364 | TGC 398 +Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0 + TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445 +------------------------------------------------------------------------------ +Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259 + CTC 418 | CCC 233 | CAC 400 | CGC 215 + CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217 + CTG 651 | CCG 181 | CAG 553 | CGG 153 +------------------------------------------------------------------------------ +Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378 + ATC 623 | ACC 405 | AAC 516 | AGC 441 + ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431 +Met M ATG 832 | ACG 230 | AAG 661 | AGG 374 +------------------------------------------------------------------------------ +Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397 + GTC 531 | GCC 585 | GAC 513 | GGC 435 + GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405 + GTG 592 | GCG 159 | GAG 424 | GGG 202 +------------------------------------------------------------------------------ + +(Ambiguity data are not used in the counts.) + + +Codon position x base (3x4) table, overall + +position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819 +position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582 +position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601 +Average T:0.27338 C:0.24787 A:0.24874 G:0.23001 + + +Nei & Gojobori 1986. dN/dS (dN, dS) +(Pairwise deletion) +(Note: This matrix is not used in later ML. analysis. +Use runmode = -2 for ML pairwise comparison.) + +Ac +Am 0.0436 (0.0628 1.4398) +Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410) +Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631) +Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052) +Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000) +NOTE: -1 means that NG86 is inapplicable. + + +TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1 +lnL(ntime: 9 np: 14): -71787.227810 +0.000000 + 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 + 0.289241 0.000004 0.219684 0.262034 0.350843 0.000004 0.491088 0.068009 0.152428 3.034323 0.539520 0.332686 0.087098 0.034121 + +Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). + +tree length = 1.83334 + +(((4: 0.219684, 2: 0.262034): 0.000004, 5: 0.350843): 0.289241, (6: 0.491088, 3: 0.068009): 0.000004, 1: 0.152428); + +(((Pg: 0.219684, Am: 0.262034): 0.000004, Th: 0.350843): 0.289241, (Ph: 0.491088, Ap: 0.068009): 0.000004, Ac: 0.152428); + +Detailed output identifying parameters + +kappa (ts/tv) = 3.03432 + +w (dN/dS) for branches: 0.53952 0.33269 0.08710 0.03412 + +dN & dS for each branch + + branch t N S dN/dS dN dS N*dN S*dS + + 7..8 0.289 29216.6 12045.4 0.5395 0.0772 0.1431 2255.0 1723.2 + 8..9 0.000 29216.6 12045.4 0.0871 0.0000 0.0000 0.0 0.0 + 9..4 0.220 29216.6 12045.4 0.0871 0.0180 0.2071 527.0 2494.5 + 9..2 0.262 29216.6 12045.4 0.0871 0.0215 0.2470 628.6 2975.4 + 8..5 0.351 29216.6 12045.4 0.0341 0.0126 0.3700 368.8 4456.6 + 7..10 0.000 29216.6 12045.4 0.3327 0.0000 0.0000 0.0 0.0 + 10..6 0.491 29216.6 12045.4 0.3327 0.1032 0.3103 3016.4 3738.0 + 10..3 0.068 29216.6 12045.4 0.3327 0.0143 0.0430 417.7 517.7 + 7..1 0.152 29216.6 12045.4 0.5395 0.0407 0.0754 1188.4 908.1 + +tree length for dN: 0.2876 +tree length for dS: 1.3959 + +dS tree: +(((Pg: 0.207095, Am: 0.247017): 0.000004, Th: 0.369987): 0.143059, (Ph: 0.310329, Ap: 0.042976): 0.000003, Ac: 0.075391); +dN tree: +(((Pg: 0.018038, Am: 0.021515): 0.000000, Th: 0.012624): 0.077183, (Ph: 0.103242, Ap: 0.014298): 0.000001, Ac: 0.040675); + +w ratios as labels for TreeView: +(((Pg #0.0870978 , Am #0.0870978 ) #0.0870978 , Th #0.0341211 ) #0.53952 , (Ph #0.332686 , Ap #0.332686 ) #0.332686 , Ac #0.53952 ); + + +Time used: 2:11
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_2ngdn Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 0.0628 +Ap 0.0536 0.0422 +Pg 0.1215 0.0396 0.1403 +Th 0.0137 0.0000 0.0932 0.0625 +Ph 0.0858 0.0613 0.1166 0.1673 -1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_2ngds Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 1.4398 +Ap 0.1327 1.2410 +Pg 0.5783 3.0000 0.3631 +Th 2.0454 0.0066 1.0019 4.0052 +Ph 0.7837 1.5834 0.4563 0.2459 -1.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_2ngt Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,7 @@ + 6 +Ac +Am 1.1652 +Ap 0.2186 0.9823 +Pg 0.6879 2.1378 0.5820 +Th 1.4515 0.0048 0.9174 2.9292 +Ph 0.7412 1.2821 0.5897 0.5567 -nan
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_codeml.ctl Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,45 @@ + + seqfile = /tmp/saskia/tmphfQhiQ/files/000/dataset_23.dat * sequence data file name + outfile = run_codeml * main result file name + treefile = /tmp/saskia/tmphfQhiQ/files/000/dataset_24.dat * tree structure file name + noisy = 9 * 0,1,2,3,9: how much rubbish on the screen + verbose = 0 * 1: detailed output, 0: concise output + runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic + * 3: StepwiseAddition; (4,5):PerturbationNNI; -2: pairwise + seqtype = 1 * 1:codons; 2:AAs; 3:codons-->AAs + CodonFreq = 1 * 0:1/61 each, 1:F1X4, 2:F3X4, 3:codon table + clock = 0 * 0:no clock, 1:clock; 2:local clock + aaDist = 0 * 0:equal, +:geometric; -:linear, 1-6:G1974,Miyata,c,p,v,a + * 7:AAClasses + aaRatefile = wag.dat * only used for aa seqs with model=empirical(_F) + * dayhoff.dat, jones.dat, wag.dat, mtmam.dat, or your own + model = 3 + * models for codons: + * 0:one, 1:b, 2:2 or more dN/dS ratios for branches + * models for AAs or codon-translated AAs: + * 0:poisson, 1:proportional,2:Empirical,3:Empirical+F + * 6:FromCodon, 8:REVaa_0, 9:REVaa(nr=189) + NSsites = 2 * 0:one w;1:neutral;2:selection; 3:discrete;4:freqs; + * 5:gamma;6:2gamma;7:beta;8:beta&w;9:betaγ + * 10:beta&gamma+1; 11:beta&normal>1; 12:0&2normal>1; + * 13:3normal>0 + icode = 0 * 0:universal code; 1:mammalian mt; 2-11:see below + Mgene = 0 * 0:rates, 1:separate; + fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated + kappa = 2.0 * initial or fixed kappa + fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate + omega = 0.2 * initial or fixed omega, for codons or codon-based AAs + fix_alpha = 1 * 0: estimate gamma shape parameter; 1: fix it at alpha + alpha = 0.0 * initial or fixed alpha, 0:infinity (constant rate) + Malpha = 0 * 1: different alphas for genes, 0 : one alpha + ncatG = 3 * # of categories in dG of NSsites models + fix_rho = 1 * 0: estimate rho; 1: fix it at rho + rho = 0.0 * initial or fixed rho, 0:no correlation + getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) + Small_Diff = 5e-07 + cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)? + fix_blength = 0 * 0: ignore, -1: random, 1: initial, 2: fixed + method = 0 * 0: simultaneous; 1: one branch at a time + + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_run_codeml Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,172 @@ +CODONML (in paml version 4.9, March 2015) /tmp/tmpMdbfK7/files/000/dataset_23.dat +Model: NSbranch3 for branches, +Codon frequency model: F1x4 +Site-class models: PositiveSelection +ns = 6 ls = 13754 + +Codon usage in sequences +-------------------------------------------------------------------------------------------------------------------------------------- +Phe TTT 232 13 253 68 16 40 | Ser TCT 276 5 291 78 8 58 | Tyr TAT 98 3 95 29 3 27 | Cys TGT 218 5 219 52 13 40 + TTC 251 14 308 87 34 71 | TCC 227 8 241 55 15 49 | TAC 126 7 151 37 18 25 | TGC 150 3 155 45 11 34 +Leu TTA 131 1 125 33 5 32 | TCA 250 4 275 58 12 47 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0 + TTG 245 6 291 67 18 42 | TCG 104 6 106 19 7 16 | TAG 0 0 0 0 0 0 | Trp TGG 168 9 195 28 18 27 +-------------------------------------------------------------------------------------------------------------------------------------- +Leu CTT 171 0 186 54 9 28 | Pro CCT 164 3 170 42 14 40 | His CAT 157 2 143 47 15 41 | Arg CGT 88 5 98 33 10 25 + CTC 147 9 160 47 20 35 | CCC 81 6 95 16 17 18 | CAC 137 10 158 42 21 32 | CGC 57 16 58 16 29 39 + CTA 64 0 66 14 5 10 | CCA 232 10 229 63 14 48 | Gln CAA 140 3 126 32 12 28 | CGA 75 18 66 22 19 17 + CTG 249 18 261 55 25 43 | CCG 65 9 63 6 19 19 | CAG 192 19 213 53 25 51 | CGG 51 4 58 17 12 11 +-------------------------------------------------------------------------------------------------------------------------------------- +Ile ATT 173 9 175 60 9 32 | Thr ACT 145 5 140 39 9 40 | Asn AAT 159 5 159 53 12 39 | Ser AGT 146 1 143 44 5 39 + ATC 218 27 238 54 36 50 | ACC 123 18 154 62 12 36 | AAC 184 17 188 65 26 36 | AGC 160 6 185 36 14 40 + ATA 186 5 165 68 4 27 | ACA 255 4 262 76 13 40 | Lys AAA 197 11 186 82 22 40 | Arg AGA 165 4 167 59 6 30 +Met ATG 308 14 341 83 19 67 | ACG 81 6 100 22 8 13 | AAG 224 48 231 53 59 46 | AGG 140 10 150 36 15 23 +-------------------------------------------------------------------------------------------------------------------------------------- +Val GTT 176 8 185 40 17 30 | Ala GCT 184 5 184 51 15 40 | Asp GAT 182 5 189 64 15 54 | Gly GGT 160 7 140 40 16 34 + GTC 200 16 209 42 26 38 | GCC 209 20 224 48 35 49 | GAC 191 16 189 38 30 49 | GGC 164 10 183 21 16 41 + GTA 166 3 149 50 14 23 | GCA 183 4 176 58 17 34 | Glu GAA 148 6 152 58 16 40 | GGA 163 7 155 35 19 26 + GTG 224 17 242 40 22 47 | GCG 53 10 53 14 12 17 | GAG 149 20 142 44 36 33 | GGG 80 6 75 8 9 24 +-------------------------------------------------------------------------------------------------------------------------------------- + +Codon position x base (3x4) table for each sequence. + +#1: Ac +position 1: T:0.24656 C:0.20613 A:0.28520 G:0.26210 +position 2: T:0.31279 C:0.26210 A:0.22744 G:0.19767 +position 3: T:0.27176 C:0.26140 A:0.23452 G:0.23232 +Average T:0.27704 C:0.24321 A:0.24905 G:0.23070 + +#2: Am +position 1: T:0.14841 C:0.23322 A:0.33569 G:0.28269 +position 2: T:0.28269 C:0.21731 A:0.30389 G:0.19611 +position 3: T:0.14311 C:0.35866 A:0.14134 G:0.35689 +Average T:0.19140 C:0.26973 A:0.26031 G:0.27856 + +#3: Ap +position 1: T:0.25796 C:0.20504 A:0.28457 G:0.25243 +position 2: T:0.31986 C:0.26349 A:0.22144 G:0.19521 +position 3: T:0.26416 C:0.27618 A:0.21924 G:0.24042 +Average T:0.28066 C:0.24824 A:0.24175 G:0.22935 + +#4: Pg +position 1: T:0.23785 C:0.20268 A:0.32342 G:0.23604 +position 2: T:0.31255 C:0.25635 A:0.25272 G:0.17839 +position 3: T:0.28789 C:0.25780 A:0.25671 G:0.19761 +Average T:0.27943 C:0.23894 A:0.27762 G:0.20401 + +#5: Th +position 1: T:0.17315 C:0.25875 A:0.26167 G:0.30642 +position 2: T:0.27140 C:0.22082 A:0.30156 G:0.20623 +position 3: T:0.18093 C:0.35019 A:0.17315 G:0.29572 +Average T:0.20850 C:0.27659 A:0.24546 G:0.26946 + +#6: Ph +position 1: T:0.23410 C:0.22350 A:0.27558 G:0.26682 +position 2: T:0.28341 C:0.25991 A:0.24931 G:0.20737 +position 3: T:0.27972 C:0.29585 A:0.20369 G:0.22074 +Average T:0.26575 C:0.25975 A:0.24286 G:0.23164 + +Sums of codon usage counts +------------------------------------------------------------------------------ +Phe F TTT 622 | Ser S TCT 716 | Tyr Y TAT 255 | Cys C TGT 547 + TTC 765 | TCC 595 | TAC 364 | TGC 398 +Leu L TTA 327 | TCA 646 | *** * TAA 0 | *** * TGA 0 + TTG 669 | TCG 258 | TAG 0 | Trp W TGG 445 +------------------------------------------------------------------------------ +Leu L CTT 448 | Pro P CCT 433 | His H CAT 405 | Arg R CGT 259 + CTC 418 | CCC 233 | CAC 400 | CGC 215 + CTA 159 | CCA 596 | Gln Q CAA 341 | CGA 217 + CTG 651 | CCG 181 | CAG 553 | CGG 153 +------------------------------------------------------------------------------ +Ile I ATT 458 | Thr T ACT 378 | Asn N AAT 427 | Ser S AGT 378 + ATC 623 | ACC 405 | AAC 516 | AGC 441 + ATA 455 | ACA 650 | Lys K AAA 538 | Arg R AGA 431 +Met M ATG 832 | ACG 230 | AAG 661 | AGG 374 +------------------------------------------------------------------------------ +Val V GTT 456 | Ala A GCT 479 | Asp D GAT 509 | Gly G GGT 397 + GTC 531 | GCC 585 | GAC 513 | GGC 435 + GTA 405 | GCA 472 | Glu E GAA 420 | GGA 405 + GTG 592 | GCG 159 | GAG 424 | GGG 202 +------------------------------------------------------------------------------ + +(Ambiguity data are not used in the counts.) + + +Codon position x base (3x4) table, overall + +position 1: T:0.24425 C:0.20932 A:0.28824 G:0.25819 +position 2: T:0.31094 C:0.25937 A:0.23386 G:0.19582 +position 3: T:0.26495 C:0.27494 A:0.22410 G:0.23601 +Average T:0.27338 C:0.24787 A:0.24874 G:0.23001 + + +Nei & Gojobori 1986. dN/dS (dN, dS) +(Pairwise deletion) +(Note: This matrix is not used in later ML. analysis. +Use runmode = -2 for ML pairwise comparison.) + +Ac +Am 0.0436 (0.0628 1.4398) +Ap 0.4042 (0.0536 0.1327) 0.0340 (0.0422 1.2410) +Pg 0.2101 (0.1215 0.5783)-1.0000 (0.0396 -1.0000) 0.3864 (0.1403 0.3631) +Th 0.0067 (0.0137 2.0454)-1.0000 (0.0000 0.0066) 0.0930 (0.0932 1.0019) 0.0156 (0.0625 4.0052) +Ph 0.1095 (0.0858 0.7837) 0.0387 (0.0613 1.5834) 0.2555 (0.1166 0.4563) 0.6800 (0.1673 0.2459)-1.0000 (-1.0000 -1.0000) +NOTE: -1 means that NG86 is inapplicable. + + +TREE # 1: (((4, 2), 5), (6, 3), 1); MP score: -1 +lnL(ntime: 9 np: 15): -71845.285288 +0.000000 + 7..8 8..9 9..4 9..2 8..5 7..10 10..6 10..3 7..1 + 0.253789 0.000004 0.294642 0.199868 0.242499 0.000004 0.471201 0.102634 0.122472 3.060446 0.693669 0.106076 0.279090 0.015724 0.820701 + +Note: Branch length is defined as number of nucleotide substitutions per codon (not per neucleotide site). + +tree length = 1.68711 + +(((4: 0.294642, 2: 0.199868): 0.000004, 5: 0.242499): 0.253789, (6: 0.471201, 3: 0.102634): 0.000004, 1: 0.122472); + +(((Pg: 0.294642, Am: 0.199868): 0.000004, Th: 0.242499): 0.253789, (Ph: 0.471201, Ap: 0.102634): 0.000004, Ac: 0.122472); + +Detailed output identifying parameters + +kappa (ts/tv) = 3.06045 + + +MLEs of dN/dS (w) for site classes (K=3) + +site class 0 1 2 +proportion 0.69367 0.10608 0.20025 +branch type 0: 0.27909 1.00000 0.01572 +branch type 1: 0.27909 1.00000 0.82070 + + +Bayes Empirical Bayes (BEB) analysis (Yang, Wong & Nielsen 2005. Mol. Biol. Evol. 22:1107-1118) + +The grid (see ternary graph for p0-p1) + +w0: 0.050 0.150 0.250 0.350 0.450 0.550 0.650 0.750 0.850 0.950 +w2: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850 +w3: 0.150 0.450 0.750 1.050 1.350 1.650 1.950 2.250 2.550 2.850 + + +Posterior on the grid + +w0: 0.000 0.016 0.738 0.171 0.066 0.006 0.002 0.000 0.000 0.000 +w2: 0.988 0.012 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 +w3: 0.000 0.828 0.064 0.033 0.057 0.014 0.001 0.001 0.000 0.001 + +Posterior for p0-p1 (see the ternary graph) (YWN2015, fig. 1) + + 0.000 + 0.000 0.000 0.000 + 0.000 0.000 0.000 0.000 0.000 + 0.000 0.000 0.000 0.000 0.000 0.000 0.000 + 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 + 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 + 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 + 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 + 0.001 0.001 0.010 0.010 0.072 0.038 0.202 0.053 0.170 0.020 0.034 0.002 0.046 0.000 0.006 0.000 0.000 + 0.000 0.000 0.000 0.003 0.004 0.039 0.014 0.031 0.010 0.101 0.007 0.020 0.001 0.026 0.001 0.072 0.003 0.001 0.000 + +sum of density on p0-p1 = 1.000000 + +Time used: 4:22
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RAxML_bestTree Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,1 @@ +(((Pg:0.09616539105673740928,Am:0.18952716489066595562):0.03831049025178590028,Th:0.15207937554419623249):0.09631839546127254903,(Ph:0.14632947629352840990,Ap:0.01138142236754203541):0.01631824366568397633,Ac:0.01822503877829063923):0.0;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/concat.fasta Tue Aug 29 19:12:01 2017 -0400 @@ -0,0 +1,12 @@ +>Ac 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----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgttttgggattctgccatgcccactcaaaccgcaaagctgcaatctggtttggaaatccatggactatcaataccatgtcccatgggcctctgccacttgtttttttggcgccaccggcttgagtgcccctgttgtgttgtttgactcgtctgttgggatcaactgtgaaacctatgtacgtctgacctttatatttaggatttatacaata---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atcatgtctctgatcgtgccagagaagtttcagcacattctgcgtgttctcaacacgaacgaggaagaggtagagaaggtgatcacgatcatgtcgaaccctcgccagtacaagatcccggactggttcctgaacagacagaaggacgtcaaggacgggaagtacggccagattctgtctaacatcctcgacagcaagatccgagaggacctcgaacgactcaagaagatccgggctcaccgcgggctccgtcactactggggtctgcgcgtgcgaggccagcacaccaagacgaccgggcgacgtggacgaactgttggtgtctccaagaagaag---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ggggacgcctcgtcacggtcagccttcaccttcataccgccagtcacacgcacgatcgtctctttgccagacagatccgtgatgtggacgaatgtgtcattgaagctggcgaatatgtgtgctacaccaaaa---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aagaagtccgtgacccaggaggtcgtgacccgagaatacaccatcaacatccacaagcgtatacatggcattggcttcaagaggagggcgcctcgcgcggtgaaagccatccgagagtttgccttcaagcagatgggcacagaggatgtccgaatcgagacccgactcaacaagcacgtctggtccaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ +>Ap 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-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tgtgagctctccaaaatcttcatatatgcagcttcagtttctgcgatggttttgtcaaattcattccttgatgccattttcttgctcaaactttcattaattttggcaagtttttcagtcagaatccggatgtcattctggacttttctcttctcctcctcttcatctaggatttgtttctggagctcatccctctttgtacaaagatcttctatgcattttaccagttcattatta------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tccctctctatttcttcaacagtttttagtgtaatgccttcagaccgaagtgattccgctattttattgaatatagattcctcctccacaccagacttagccatatcactgtacatagttataaatctttcacttaaaggtacagattttgaatctttcatgtcaataatatctggactgccaaacatcttgacatcggaacaactattaatctcaccatcctcaaaaaggtcaaactttgtggcaccatctattgcccaggaacagaattttccaagaccaactgtgatgacaattgcactggacagtgtcataaacattattatcatgtttatgaacataaacagagggttgatgctcataaca------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtcagctttcagacagcggaatgccgactacattgctacgaatgtgccacgtcgaccttgccatctatgtcccgacaagactgcctcgacggcaaagcggagttcgtacagtgcgggaccactgataaatactgcgtgatgttacgatacaccgaacacgaatctcaaggacacgacgctaacgacataggaatgttaatgtcagctggaacctcagcacgagctatttctgtgaacgttttcgcatccaacacgagcagaaaagactgcaaatcatcctttgttctaatcataggtgataagataataccatcatcctcttctcaatcagctgatctgacatattcgcatcatcttcctcagcttcctcagcatcttcatcataatcctcaccttgctcagccctgtaacttgctagagcatcctggtactcctggttgtctggatcgtgaccagcacgatgccgcaataggttgcccttgtgagcaaatgccttgtcacagtctggacactcatggatcttatcctttggagctggtggcacatagtctggattgtggtagaggttcttgtgcctctggcacccacgtgatgaagagtagaaagttaacgaggacacagatggcggcgaacatgccaaagcaccggatggctgtgacgtcgttgacgaagttcgccaatagggccgtcgacgtcgtgaagctcgtcacaaacaccgacgtgccgcccttgcggagcgtgtgcgagataagctcctcgtgtccacttcagacatcttgtatcctgatgtgtaccgagacatctgacagtacagtaacgagctccacactgtacacaggtatagttagatggaaaaccacaaacactacagaagtgtctctccggaaagtgagatggtggcacacatgccgtctggtagccaggcaaatcaccagtcatcatttgctcttcttcaaggagtgctgcaaagttctttctgaatcgttccttgaaaatatcacttcttcgttttttcttctttctgccaacttgttaaatgtctttccattgtatacaccaacaatgctgccaatcatttcaggaacaataatcatatcacgtaaatgtgtcttgatacactctggcttttccattggaggtgcctccttcttggctttgcgaaggcgtttaatgagagccattggtttacgcttcaaaccacgggagaaacgtctgcgagcccgacaagtggacttgagctttcttttgttttctaatgtagtgatgacattctggtacttccagcccacttcatgtgacaggcggccaagaacacatgacttgcgtctagctttaagtcgaaggaccttcaaagccgagggaaccaccatacgtttctgcttgtcaaatggtggagggatgccctcaaagaccttgagacggtccagagcttgcttaccacgtgtcagcttatgtggcaacataccacgcacagttctccaaaatattttacttggggcacggaagtggtatgggccacggcttggattggtgttcattcgtttccttaggaaagcaaggtacttcagtttgttcctgatggagtacaacccacactccatcaccagctttgttaacttgttctacataatctgctctagatatttccattacactaccaaactgagcagatttatatgcttgctgcatctcggccattcttttccgtcgatattcttcaaatattctttcttcctcttcatcaatttcatcttctttttcattgccagcctgagtaaatctgaagatgttgtcaataaagagcagcacgtcctgtccttctacatcacggaaatattcggcaacagtcaaaccggtcagagctacgcgagcacgggcacctggaggctcattcatttgaccatacaccaacgacaccttagaagacttgtccttcagactgatcacaccaccctcaatcatctcatgatacaagtcattgccctcacgggtacgttctccaacaccagcaaacaccgagtagccaccatgtgccttggccacattgttaatcagttccatgatcaacacagtcttaccgacaccagcaccaccaaacagaccaatttttccacccttagcataaggggccaacatgtcgataactttaattccagtctccaggatttcttgttcaagactcatctcaacaaatgctggcgcctcagcatggattttcttaggtacagtaccttcacggaatccattcctaaatcttctgaagaccttcttcatatgcctcatacgtcctacaccttgggtcctcctcctcttcgccttctcactccagttgtattttctcattcttttagcaggatatccgcaactggcacaagtcttcttctgtatgtggtaacatctgccaccacaacgacgacacagtgtgtgtgtcttgttgtggcgttttccaa----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atgtctggagatgaaacaagacagcggcccgatttctgtaaagatgccaaccttgttaacctgtgtcacgacagcctccagtacttctcctttaaacggtcgaaacacgatggctttgtacttgatcggataaacaacaaaacctcggctcggctgaatgaggccagctccaatgtcatcaataattgtcacggcaacgacgaaaccatattttccagtacaggttccttccacttcagtaaa---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------acaacttctcctttaaagttcatcccttctacaaccatttcagctgccttttttatagacacttcatcttcttctccaactgaaagaatgattggatcaatctctggatattctctaagtacccagataaagagtctcgcaagatccagagaa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gaagccatggcacgccgggagaagggcaagaagaagtctgttaccaatgaggtggtaactagagaatacacagtgaatatccacaaaagaattcatggaataggtttcaagaagagggcacctcgtgcgatcaaggctatcaggcagtttgcctttaaacagatgggcactgaggatgtgcgtatagagacgagactcaacaaacacatttggtcaaagggaattagaaatgtcccattccgtgtgcgtgtaagattggctcgtaaaaggaatgaagatgaagactcgccacacaaactttacaccttggtctcctatgtacctgttacaacattcaaaggtacacagacagtaaatgtggagagtagtgac--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- +>Th +-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gttttacggggtagcttcttggggtgccaacgcgaggtcacacccttgaatccttttcctttggtcacaccaatgacatcaatgaattcatcttgtgcaaacacctcttccagtggtacggtcttttcaaagtgttcccgtgcccagtctaccttttgggcaatggtacctccattgagttggatctccatgatgtgggctttcttttggcgtttcttaagaagcttcatctgggtgtgtgcaatcactctgatcacagtgcagtacttcttgatcttgttaaggtccttttcgatctcctttttaccaaggtcatcctgccacttcttggtggctttggtgaatgccttcttcttggacttgtacatgccgaaagtccgccgcagccggaagcccccgcccgacggctgggagctgatcgagccgacactggacgaactcgaccagaagatgcgcgaggccgagacggagtcgcacgagggcaagcgcaaggtcgagggcctgtggccgatcttccgcatccaccaccagaagtcgcgctacctcttcgaactcttctacaagcgcaaggccatcagccgcgagctctacgagttctgtctgaaggagaacatcgccgacaagaacctgatcgccaagtggaagaaacctggctacgagaacctgtgctgcctgcgctgcatccagacgagggacacaaatttcggcgcgaactgtgtctgtcgcgtgcccaagcccaagctggaggaggggaagatcgtcgagtgcgtgaactgtggctgtaggggttgtgcggacatgtccgaggacatgcagcaagatgccgtggactgcgccatgcaagcgctcgaaaagtacaacatcgagaaagacatcgcagccttcatcaagaaggaattcgacaagaagtacaacccaacgtggcactgcatcgtcggccgaaattttggcagctacgtcacgcacgagacaaaacatttcatctatttttacctcggccaagttgctatcctactcttcaagtcggaagtaattcaagttcatcgagaagtcatagtccttataaaggagttcgtaaaccctatcatccgaaaacatccaagcccttattcctcatactctgctagctcatcatctcatcataaatctgcaaaaagaggtaagcatgatcgtcatgat---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aaaatggcgccaaaaaggaataatgttattccgaaccagcacttccgcaaggactggcagcgatgggtgaagggatggttcaaccagcccgcccgcaagaagaggaggagggacacccgccagaagaaggctcgcaccattgctccacggccggtcaaggccctcaggcccgcagtgcgctgtatgaccttcaaatacaactccaagatccgactgggacgaggcttctcgctggatgaactcaaacaagccggtctgaacaaggacttcgccaggaccatcggtatctcggtggaccaccgacgccggaaccgatccgtcgagtcgctgcagatgaacgtccagaggctgaaggagtacaagagcaagctgatcctgttccccagaaagaccagcaagcccaagaagggtgatgcaactgaggaggagatcaagatggcgacccagaccccgggcatcgtgatgccgctgccgaagcccgtcgctcgccgagagaaggcccgcgccgtcacggacgaggagaagggccacagcgttttcgtggcgctgcgacagggacgcgccgacactcgattggtcggagtgcgcgcgaagaaggccaaggaggcagccgaggccaacagc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gcccgtaagatgaaggaccatcgtcgagaccagaaatggcacgacaaagattacaagaaaagccacttgggtactcgctggaaggccaacgccttcggaggtgcatcccatgccaagggaatcgtgctcgagaaagtaggtgttgaggccaagcagcccaactctgccatccgcaagtgtgtgcgagttcagctgatcaagaacggcaaaaagatcacggccttcgtaccgcgggacggttgtctcaactacattgaggagaacgatgaggtgctgatcgctggattcggacgaaagggccacgctgtcggagatattcccggcgttcgcttcaag---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------accatacgcttctgcttgtcatatggaggggggatgccttcaaacactttcattctctccaaagctgccttgccacggggtaacttatgtggcaacattcctctgactgttctccagaaaatcttgctgggagcacggaagtggaatggaccacggcttggtttggtgttcatacgctttctaaggaaatccaagtacttgagt------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cctgcgggagcaccggctgttcacgtccaaccccaagctggactgttgtccgacggtgacggaactcgcccaccgaggcgtgggcatcaacccacagggcctgctcctcgagctgttccacacgcccaacttcacgcagactttctacgagaccgtgtgccacccgcacatcaaggaccggccgtgtcagttcatcgacagggagtacctgcagtactcgcgctgtacgcagcagtactcctacgtgtacgcgctcgggcggacctacggcacacatgctttgagtttcaaaatattagccgaatgttcgacatcaaaagcacgaatcagccagataactttgccacatggcttggtagatgccccagttttcatgccagttggaacacaagggacattgaaaggcttgattccagaacaactggagaatttgaactgtcaaataattcttggaaatacgtatcatttgggaaa------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cacagagaagccatgcggcttgggccggtagtcgcagtggaagatctcgatgatctccccccgccgcttgccgccctcccacacgttaccgagcgtctccatgtagtccttggagacgtccgggtagttgtccagcagcaccaggttgttggtgcgcaccatccgccgcaggtggaagtagtccgacagactctccctgaacgtgtgaccgccgtcgatcacgacgatgtcacagcggaaatccttgttcgcttcccggaacctggg +>Ph +------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atgggtgacgataataagagtaatgaacacattaatctcaaagtgacgggacaagatggaagtgttgtccattttaaaatcaagaaaaacactcctctgcggaagctgatgaatgcctattgtgacagaactggtgttaaaagtggtgccatgcggttccgttttgatggccagccaatcaatgagacggacactcctacacagttggatatggaagatggcgatgtgatcgacgtattccagcagcagactgggggc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttctctgataccgctttccttcagagtcactcggaatcctttgataatattgccatatttgtcagggtcaacctgcatgcggcacttgaccagatccaggggtacgacggctgtgtgagtgatcccacaactcaggatgccaccgaaaccacagagggcaaagaatttcgcactgccatattcacagctctccccctctgctattgcagcagctgcaatactccgcgttggattaatctgcagcccatcatcacattgagcctgaaaaggact------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------atgccgtgtagttggggtttcccatgccgctgtttccataaccaccccccatgctgttgctgccgaagttgttgctatttccactgccgtaaccacctccgtagccactgccacttccaaagctgtcgttcatccccatgcccgatcccattccactgcccattccgcctcccattcggtttacccatgaagtctttgtcttcaattatcctcaggccagccttctccgacatgccaagcttcttcactaacgcctccgcaatgccgttggccttctcgaaatctgatcccgcccctgtcgtgactttgtcactaccaaatattaattcctctgcaacacgtccgccgagagcaacgtccatttcagccaaaagctgtaccttcgttagattatactggtccttttctgggataaacgccgtatacgaaaacaattctcagagttattacggacttggcgacccaatgaaagaggcaacgatgtactgccagcaggggaagcacgaccgcgaggtgcgccagcagctcgaggagaagttccccgggcacacgctggaggtcggctacgaggacttcatcaacaacccgatagcgtacaccgagttcttcttccgcttcgtcgacttcccgatcgactccgacgtcagcgactacataaccgcctacgccccgctgctccagaaggaggtcaacgactggttcgccgacgccccgtacaacgtcgcccgggacatccgcgacaagtgcaacgtgctctggtacgggaaggcctacggattcatgattgactggccaaccagtttagcattacgcaccatgtgtaacacctcttcatattttctgttgacaagagccaatttgaacttaaattccgtggcatcgatgccaagtactcgaggacgacattccctgtccagacagtacacctggttacctttgatgcgagtgatgcgtacattagctgacttgttgttaagacgccacagaatggtaccacagatctgtggcaggtatggcttgactcgcttaccaagagcatttaccactgtaccaaatccattcagcatcaccacatcctctgtcgtttgttcctggaaggcatataatatcccatcaatgagctgttcctcaagacgtgagtcaatgtcagctgagcccagattagccatgactttctctatggtctccatgaccatcttacgatattgttcagattcatctttcagatcatctaccacacgactgatgatttcagctgctccaactttattagcaatctccactgtggtgtcaacgagctgtctgagaagtatctacaggacagaggtgaccagatacttgttatattacacgccaaagtggcgcagaagtcttatggaaatgagaaaaggtttttctgcccaccgccgtgtatttacctctttggcaatggatggaagagaaaaagggagcagctggagagggatggctgcagtgagcaggacacacaggtctgtgccttcatgggcatccctgtacatatctgccagcttctgtgcttgcttcagctgccacttcagcgtctgtatttcttcatcctgtcgtattcttcctgctcctgtagatgccgacacattaaggacattttcattggttgaattcatgtgctgtttgcacatgtccagttctcgcagtagacgatctttctcactcatccatttcttttcatgggcacggtgttcatatagtcaacattacagagtatgttacccactctggtatcctgataggctggcggtaactgaaccgatgtactctggtcaaagtttgcttccagtgcaatgctcggaagttggtttaaaacataaatcccaacagtcaattcacgtaaaaagtgtcaaattcggatgcgatgtctatttctacaaactcctgcctatctccgcctttccttccaatacctgcatcatcatccatgtcatcttggcgagcaaaacatgcaccaaaactccaggtaaatgcaaacacatacagcttaccaag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------actgcggagaagatggtgagtactgtggtgaggaaggactgtactctggcgaggatggactatacttggggctggttggtgtgtatgtgggtgatgtgggcgagtactttggtgatgctggggagtatgaggggctggtcggagaatactgaggtgatgatggggtgtactgtggcgagc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------agcagcgtgaggttctgtttttcaagctgcttcaccttcttctgtagttgcatgttgttcaaatcacaagctttcactcgccgctccagtccatcaatgtattcctgcttgcgcttgcgactttcttttgctgacaccttatttctgatctttcgtcggacagacttcagcgcgcgttcttcctcctttgtcagtggcaggttc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttagttacctcggcttttactgtctgtggcgtcgattctacaaacttctttgcctgtacaagattcatgccagccataacattctttatctgtttaataagagctactttcttggcttcatcaaaaccagcaagtttaacggtaaatgccaccttttctggcttcttctctgatggcgtttcctcgtcttcctttggagcaatagccggcatggctcccatggccatcataggagtgtctgtaatgttcagtgttttttttaataac------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cgctctccctctttggcttttcctgcttttcctggtttagattttgcaaagagagctgggtccaattcatcaagctttttgcccttggttgaaaatagtctctgtgccctttcttccagggtacctccacatttcaggccaagagcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aggaaccctgatattaatccactgatatatggaggccatgctttcctttcaaacatcggtgcatccggaagcttcatctggatttcacctgaccatgggaaaaggatttcaaatgcacagaccagtataccaaacatggccacaagtggtaaggcaagcacaaaatatggtgaacctatccatggattgctggactctttaatggatggtgccagtagtgaatcaaatacaggacaaagtatgcca---------atgacgcgcggcaaccagcgtgagttggctcgcctcaagaacttaaagaaacaacaacaagtggcaaagggaaagaaagcttcggaaaaaggggctaatgctggccagtccctacaggaaaggcgccatagggatgcagaacgaatgagagagaagcagcgtaaggcagaggagatgagacagaaacagtcg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctgtatggctgtgttggtgcaggctcatccttaggttcaactatgctgatgttgtcagggagtggacgctttgggcctatcttaccagagggatcccatggcagcataattttcactttgattcccagcacaccttgccttagcagcacatgtctaacagcagtgtccacatattcattgcacggctcaccactg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cacgtacagcttggccgccacgcacacgtgagctcccatggcgaacgccagggcggcgccgagaccctgcagcatccggaagttctggaacgccacgtcgtggtcgtctggacagctgaggttaaccaaaaagttacactgggtctgccagatggcgtcgcagaggccccacagcgcggaaacgacgaagaacaccggaaacagcgtcttgtcgggaatccagaccaacaggaagaccatgatgccgatgtgcaggatactgcctactccgattatcgcctctcggggaaggttccgcgccacgatcccgatcaggatcgagaagag------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aatgataccggaatattaatgtcggaaggaaccaaagcacgagcaatttctgtgaagctttttgcatccaataccagcagaaatgactgcagatcatcctttaatctgattacaggtgaaagtataacaccatcatcttcttctcaatcagctgattggacatatttggatcttcttcctcctcttcctcagcttcctcatcataatcctcacctcgttccgccctgtagtttgccaatgcctcctggtattcctgattatctggatcatgcccagctcggtgacgtagaaggttgcctttgtgagcaaatgccttatcacagtctggacactcatggatcttgtcctttggcgccggtggcacataatctggat------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gatggagttggtgatcgtgacatcggtatttcgacgtgtggcggtggtgatggtgatggcgagaaggtaaagtctggcacgatctccatgggagagttctgtttgatgactggcattacatcaagtgacatatctctcctcagtgatgcatctcgagaaggtcccaactcttccttcaactcatcaaagtctggctggttaagctcttcccaagccactgcttgctctttcagatctgtcacagcttctatgttatacatacattttctgatgacatcttctcggcctatcttcttcagtgctctctctaattcatttccagttgctctactcctgttcttcaacattgcctccttcatgatcagcgtgtatcatgaggtaaagcctcatcaactcgacgaacttcggatcctcgtatcccagcatcgagacgaaatttgctgcccagtccttttctggatcgatggcaccgacactggttccatccctgtacagatttctgtagatgatggcggctatcgtggggagttcagcgtgtatgggacggctattaaaccagcgattgttcagatcagccacagccttctccgcatcttcctcataacggaacttcacatagacatttccaacaagatgatcaccaagattgtcacagacgttcatctcctcaatctcaccatacttgtcctcgagttcttgatacatatggtggatggggtgcccatggtggtggcgctttctctggcaaagacttctccaaagttgatcgttctgctgcctatgctgctcgttgggtggctaagtctctggtcaaaggtggtctctgtcgacgtgtcttggtgcagctctcctatgccattggtg------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgttgcagctgggatttgggcatgtccagtctcctgatcgacctgatccactgtcacgtccaccaggccatatctttcttgtagctgtctcaactttcagaactttacccatgaattctttattgttaaaccagctgatggctgattctgctgcctgc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------aagaagatcgagtcggttaaaccagccaagtgtgtgctggaagacaaaaaatgggttgttgaatatcaacatggtaatcgtaacctggttatatctgacaccaacatcaggcagaccgtctacatctttaaatgtgacaactccacaatacaaatcaagggaaaagtcaactccatagccatggataattgtaagaagactgccttgctgtttgaagacgtcatctcgtcgtttgacgtcgttaattgtaacagcgtccaagcccaggtcacaggtaaaataaacactattaacattgacaagacagatggctgccaggtgtatttacaaag-ctccaa---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------catcctgacgtgcaccgcctcgatcctgaacctgtgcgcgatcgccatcgaccgctactacgccatacacgacccgatccggtacgcgcagaagcgcacgtgcaagcgcgtgctggtcagcatcgccctggtgtggctggtcagcgccctgatctcggtgccgccgctcgtcggctggaacaacagcggcggcaattcgctgtacaacgtcatctacagcgcgtcgggctcgttctacataccgctgctcatcatgacgttcgtctacttcaacatctttcgcgccacccggaagcggctgcgagcccgcgccaaggcggcggc------------cgccgtgagaagggaaagaagaagtccgttaccaatgaagtggtaacaagggaatacaccataaacatccataaacgaattcacggaattgggttcaagaagagggcgccacgtgccatcaaagccatcagacagtttgcc------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------