Corrected issue 35 (output file not found)

.kdev4/fastcodeml.git.kdev4

+[Buildset]
+BuildItems=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x00\x00\x01\x00\x00\x00\x1c\x00f\x00a\x00s\x00t\x00c\x00o\x00d\x00e\x00m\x00l\x00.\x00g\x00i\x00t)
+
+[CMake]
+Build Directory Count=1
+Current Build Directory Index=0
+ProjectRootRelative=./
+
+[CMake][CMake Build Directory 0]
+Build Directory Path=file:///home/omid/Projects/fastcodeml.git/build
+Build Type=Debug
+CMake Binary=file:///usr/bin/cmake
+Environment Profile=
+Extra Arguments=
+Install Directory=file:///usr/local
+
+[Defines And Includes][Compiler]
+Name=GCC
+Path=gcc
+Type=GCC
+
+[Launch]
+Launch Configurations=Launch Configuration 0
+
+[Launch][Launch Configuration 0]
+Configured Launch Modes=execute
+Configured Launchers=nativeAppLauncher
+Name=fast
+Type=Native Application
+
+[Launch][Launch Configuration 0][Data]
+Arguments=-m 22 -bl -s 0 -nt 1  ../bad_cases/HBG010916-1.M0.009.nwk  ../bad_cases/HBG010916-1.phy
+Dependencies=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x00\x00\x02\x00\x00\x00\x1c\x00f\x00a\x00s\x00t\x00c\x00o\x00d\x00e\x00m\x00l\x00.\x00g\x00i\x00t\x00\x00\x00\x08\x00f\x00a\x00s\x00t)
+Dependency Action=Build
+EnvironmentGroup=
+Executable=file:///home/omid/Projects/fastcodeml.git/
+External Terminal=konsole --noclose --workdir %workdir -e %exe
+Project Target=fastcodeml.git,fast
+Use External Terminal=false
+Working Directory=
+isExecutable=false
+
+[Project]
+VersionControlSupport=kdevgit

BayesTest.cpp

@@ -547,14 +547,14 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
     }
 
 // Fill the matrices and compute their eigendecomposition.
-#ifdef _MSC_VER
-#pragma omp parallel sections default(none) shared(                            \
+//#ifdef _MSC_VER
+//#pragma omp parallel sections default(none) shared(                            \
     omega_fg, omega_bg, kappa, q_fg, q_bg, omega_fg_is_one, omega_bg_is_one)
-#else
-#pragma omp parallel sections default(shared)
-#endif
+//#else
+//#pragma omp parallel sections default(shared)
+//#endif
     {
-#pragma omp section
+//#pragma omp section
       {
         if (omega_fg_is_one)
           q_fg.fillMatrix(kappa);
@@ -563,7 +563,7 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
 
         q_fg.eigenQREV();
       }
-#pragma omp section
+//#pragma omp section
       {
         if (omega_bg_is_one)
           q_bg.fillMatrix(kappa);
@@ -580,6 +580,7 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
 
     // Compute likelihoods
     CacheAlignedDoubleVector likelihoods(mNumSites);
+    //probably main issue for beb non-determinism
     mForest.computeLikelihoods(mBEBset, likelihoods,
                                mDependencies.getDependencies());
     for (size_t site = 0; site < mNumSites; ++site) {
@@ -587,6 +588,15 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
       mPriors[iw * mNumSites + site] =
           (p > 0) ? log(p) : -184.2068074395237; // If p < 0 then the value in
                                                  // codeml.c is: log(1e-80);
+                                                 
+    // debug
+    if (site==982)
+      std::cout<<"before normalization mPriors[site] for cat " << iw << " is "<<  mPriors[iw * mNumSites + site] << std::endl;
+    // debug
+    if (site==982)
+      std::cout<<"likeliohoods[site] for cat " << iw << " is " <<  likelihoods[site] << std::endl;
+      
+    
     }
   }
 
@@ -604,9 +614,16 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
     // remove the previous log.
     for (size_t k = 0; k < BEB_NUM_CAT; ++k) {
       mPriors[k * mNumSites + site] = exp(mPriors[k * mNumSites + site] - fh);
+      
+       // debug
+    if (site==982)
+      std::cout<<"mPriors[site] for cat " << k << " is "<<  mPriors[k * mNumSites + site] << std::endl;
+    
     }
     scale += fh * aSiteMultiplicity[site];
   }
+  
+  
 
   return scale;
 }
@@ -821,7 +838,9 @@ void MfgBayesTest::computeBEB(const std::vector<double> &aVars,
     std::cout << std::endl
               << "Calculating f(w|X), posterior probs of site classes."
               << std::endl;
-
+  //debug
+  std::cout << "mNumSites: " << mNumSites << std::endl;   		
+	      
   for (unsigned int site = 0; site < mNumSites; ++site) {
     scale1 = -1e300;
 
@@ -857,6 +876,14 @@ void MfgBayesTest::computeBEB(const std::vector<double> &aVars,
     }
     for (unsigned int j = 0; j < BEB_DIMS; ++j)
       mSiteClassProb[j * mNumSites + site] *= exp(scale1 - fX);
+    
+    //debug
+    if (site==982) 
+    {
+      std::cout << "scale (t=log(fhk[codon_class]) + lnfXs[igrid]): " << scale1 << "  fX: " << fX << " site multiplicity " << site_multiplicity[site] <<" prob: " << mSiteClassProb[2 * mNumSites + site] + mSiteClassProb[3 * mNumSites + site] << std::endl;       
+    }
+  
+    
   }
 }
 
@@ -903,6 +930,8 @@ void MfgBayesTest::printPositiveSelSites(std::set<int> aFgBranchSet) const {
         ordered_map.insert(std::pair<size_t, size_t>(it->second, current_idx));
         probs.push_back(prob);
         ++current_idx;
+	//debug
+	std::cout<< "idx: " << current_idx-1 << " prob: " << prob << " site: " << site << std::endl;
       }
     }
   }
@@ -925,6 +954,11 @@ void MfgBayesTest::printPositiveSelSites(std::set<int> aFgBranchSet) const {
 
     std::cout << std::setw(6) << im->first + 1 << ' ' << std::fixed
               << std::setprecision(6) << prob << sig << std::endl;
+    //debug       
+    if (im->first+1 == 1030)
+      std::cout<<"reduced site num for 1030: "<<im->second<<std::endl;
+	      
+	      
   }
 }
 

CMakeLists.txt

@@ -194,3 +194,5 @@ endif(MPI_LIBRARY)
 
 
 
+
+add_subdirectory(bad_cases)
\ No newline at end of file

Forest.cpp

@@ -906,16 +906,16 @@ void Forest::computeLikelihoods(const mfgProbabilityMatrixSet &aSet,
     const int len = static_cast<int>(ivs->size());
     const unsigned int *tmp_ivs = &(*ivs)[0];
 
-#ifdef _MSC_VER
-#pragma omp parallel for default(none) shared(aSet, len, tmp_ivs, tmp_roots,   \
+//#ifdef _MSC_VER
+//#pragma omp parallel for default(none) shared(aSet, len, tmp_ivs, tmp_roots,   \
                                               likelihoods) schedule(static)
-#else
-#pragma omp parallel for default(shared)
-#endif
+//#else
+//#pragma omp parallel for default(shared)
+//#endif
     for (int i = 0; i < len; ++i) {
-#ifndef _MSC_VER
-#pragma omp task untied
-#endif
+//#ifndef _MSC_VER
+//#pragma omp task untied
+//#endif
       {
         // Compute likelihood array at the root of one tree (the access order is
         // the fastest)

HighLevelCoordinator.cpp

@@ -25,6 +25,8 @@
 #include "BayesTest.h"
 #include "VerbosityLevels.h"
 
+
+
 static const int INVALID_RANK = -1;
 
 enum JobStatus {

WriteResults.cpp

@@ -6,7 +6,7 @@
 #include "WriteResults.h"
 #include <string>
 
-void WriteResults::outputResults(void) {
+void WriteResults::outputResults(std::set<int> aIbSet, bool aBranchAll) {
   // If no file set, then do nothing
   if (!mFilename)
     return;
@@ -47,6 +47,9 @@ void WriteResults::outputResults(void) {
   // Write the log-likelihood values (if a value is not present, write NA)
 
   for (size_t branch = min_branch; branch <= max_branch; ++branch) {
+    
+    if (aBranchAll || (aIbSet.find(branch) != aIbSet.end())) {
+    
     out << "Branch: " << std::setw(4) << branch << std::endl
         << std::endl
         << "  LnL0: ";
@@ -78,6 +81,7 @@ void WriteResults::outputResults(void) {
           << std::fixed << "Branch lengths:" << ims->second << std::endl;
     }
     out << std::endl;
+    }
   }
 
   // Write the positive selection sites (adding one to the site number because
@@ -95,7 +99,7 @@ void WriteResults::outputResults(void) {
       size_t ns = site.size();
       for (size_t s = 0; s < ns; ++s) {
         size_t i = idx[s];
-        out << "PositiveSelectionSite for branch: " << std::setw(4) << branch;
+        out << "Positive Selection Sites for branch: " << std::setw(4) << branch;
         out << "  Site: " << std::setw(6) << site[i] + 1
             << "  Prob: " << std::setw(9) << std::setprecision(6) << std::fixed
             << prob[i] << std::endl;
@@ -164,3 +168,179 @@ void WriteResults::saveParameters(size_t aFgBranch, std::string &aParamStr,
   // Save the likelihood for later printing
   mParamStr[aHypothesis][aFgBranch] = aParamStr;
 }
+
+
+
+
+// reporting methods where fg branches are marked in the nwk file
+
+
+
+
+void WriteResultsMfg::outputResults(std::set<int> aFgSet) {
+  // If no file set, then do nothing
+  if (!mFilename)
+    return;
+
+  // Range of branches to be output (for H0 and H1)
+  std::map<size_t, double>::const_iterator im;
+  std::map<size_t, std::string>::const_iterator ims;
+
+  //size_t min_branch = std::numeric_limits<size_t>::max();
+  //size_t max_branch = 0;
+  //for (im = mLnL[0].begin(); im != mLnL[0].end(); ++im) {
+    //size_t v = im->first;
+    //if (v < min_branch)
+     // min_branch = v;
+    //if (v > max_branch)
+     // max_branch = v;
+ // }
+  //for (im = mLnL[1].begin(); im != mLnL[1].end(); ++im) {
+   // size_t v = im->first;
+   // if (v < min_branch)
+    //  min_branch = v;
+   // if (v > max_branch)
+   //   max_branch = v;
+ // }
+
+  // No entries, so do nothing
+//  if (min_branch == std::numeric_limits<size_t>::max())
+//    return;
+
+  // Open the output file
+  std::ofstream out(mFilename, std::ios_base::trunc | std::ios_base::out);
+  if (!out.good()) {
+    std::cout << "Cannot create results file <" << mFilename << ">"
+              << std::endl;
+    return;
+  }
+
+  // Write the log-likelihood values (if a value is not present, write NA)
+
+ // for (size_t branch = min_branch; branch <= max_branch; ++branch) {
+    
+ //   if (aBranchAll || (aIbSet.find(branch) != aIbSet.end())) {
+    
+    out << "Branch(es): " << std::setw(4) ;
+    for (std::set<int>::iterator it = aFgSet.begin();it != aFgSet.end(); ++it)
+    {out << " " << *it << " ";}
+    out << std::endl
+        << std::endl
+        << "  LnL0: ";
+
+    // Prints LnL for H0 if present
+    im = mLnL[0].find(0);
+    if (im == mLnL[0].end()) {
+      out << std::setw(22) << "NA" << std::endl
+          << std::endl;
+    } else {
+      out << std::setw(22) << std::setprecision(15) << std::fixed << im->second;
+
+      ims = mParamStr[0].find(0);
+      // This output does not work on BG/Q.
+      out << std::endl
+          << std::fixed << "Branch lengths:" << ims->second << std::endl;
+    }
+    out << "  LnL1: ";
+
+    // Prints LnL for H1 if present
+    im = mLnL[1].find(0);
+    if (im == mLnL[1].end()) {
+      out << std::setw(22) << "NA";
+    } else {
+      out << std::setw(22) << std::setprecision(15) << std::fixed << im->second;
+
+      ims = mParamStr[1].find(0);
+      out << std::endl
+          << std::fixed << "Branch lengths:" << ims->second << std::endl;
+    }
+    out << std::endl;
+    //}
+ // }
+
+  // Write the positive selection sites (adding one to the site number because
+  // they start from 1 and not zero)
+//  for (size_t branch = min_branch; branch <= max_branch; ++branch) {
+    std::map<size_t, std::pair<std::vector<unsigned int>,
+                               std::vector<double> > >::const_iterator ipss;
+    ipss = mPositiveSelSites.find(0);
+    if (ipss != mPositiveSelSites.end()) {
+      const std::vector<unsigned int> &site = ipss->second.first;
+      const std::vector<double> &prob = ipss->second.second;
+
+      const std::vector<size_t> &idx = orderSites(site);
+
+      size_t ns = site.size();
+      for (size_t s = 0; s < ns; ++s) {
+        size_t i = idx[s];
+        out << "Positive Selection Sites for branch(es): " << std::setw(4) ;
+	for (std::set<int>::iterator it = aFgSet.begin();it != aFgSet.end(); ++it)
+	{out << " " << *it << " ";}
+        out << "  Site: " << std::setw(6) << site[i] + 1
+            << "  Prob: " << std::setw(9) << std::setprecision(6) << std::fixed
+            << prob[i] << std::endl;
+      }
+    }
+ // }
+
+  out.close();
+}
+
+const std::vector<size_t> &
+WriteResultsMfg::orderSites(const std::vector<unsigned int> &aSites) const {
+  // Fill the map with pairs(site, its index)
+  std::multimap<unsigned int, size_t> ordered_map;
+  size_t end(aSites.size());
+  for (size_t i = 0; i < end; ++i)
+    ordered_map.insert(std::pair<unsigned int, size_t>(aSites[i], i));
+
+  // Take the list of indices after ordering the list of sites
+  mSiteOrder.clear();
+  std::multimap<unsigned int, size_t>::const_iterator im(ordered_map.begin());
+  std::multimap<unsigned int, size_t>::const_iterator endm(ordered_map.end());
+  for (; im != endm; ++im)
+    mSiteOrder.push_back(im->second);
+
+  return mSiteOrder;
+}
+
+void WriteResultsMfg::saveLnL(std::set<int> aFgBranchSet, double aLnL,
+                           unsigned int aHypothesis) {
+  // If no file set, then do nothing
+  if (!mFilename)
+    return;
+
+  // Sanity check
+  if (aHypothesis > 1)
+    return;
+
+  // Save the likelihood for later printing
+  mLnL[aHypothesis][0] = aLnL;
+}
+
+void WriteResultsMfg::savePositiveSelSites(
+    std::set<int> aFgBranchSet, const std::vector<unsigned int> &aPositiveSelSites,
+    const std::vector<double> &aPositiveSelSitesProb) {
+  // If no file set, then do nothing
+  if (!mFilename)
+    return;
+
+  // Save the positive selection sites and corresponding probabilities for later
+  // printing
+  mPositiveSelSites[0] =
+      std::make_pair(aPositiveSelSites, aPositiveSelSitesProb);
+}
+
+void WriteResultsMfg::saveParameters(std::set<int> aFgBranchSet, std::string &aParamStr,
+                                  unsigned int aHypothesis) {
+  // If no file set, then do nothing
+  if (!mFilename)
+    return;
+
+  // Sanity check
+  if (aHypothesis > 1)
+    return;
+
+  // Save the likelihood for later printing
+  mParamStr[aHypothesis][0] = aParamStr;
+}

WriteResults.h

@@ -3,6 +3,7 @@
 #define WRITERESULTS_H
 
 #include <map>
+#include <set>
 #include <vector>
 #include <utility>
 
@@ -31,8 +32,10 @@ public:
   }
 
   /// Output the results to the file given
+  /// @param[in] aIbSet Set of internal branches
+  /// @param[in] aBranchAll Whether fg branches are just internal or internals+leaves
   ///
-  void outputResults(void);
+  void outputResults(std::set<int> aIbSet, bool aBranchAll);
 
   /// Save the likelihood for later printing.
   ///
@@ -44,22 +47,9 @@ public:
   ///
   void saveLnL(size_t aFgBranch, double aLnL, unsigned int aHypothesis);
 
-  /// Save the likelihood for later printing (multiple fg).
-  ///
-  /// @param[in] aFgBranchSet The foreground branches to which the
-  /// log-likelihood refers
-  /// @param[in] aLnL The log-likelihood
-  /// @param[in] aHypothesis The hypothesis (0 for H0 and 1 for H1) for which
-  /// the log-likelihood has been computed
-  ///
-
-  ///
-  void savePositiveSelSites(size_t aFgBranch,
-                            const std::vector<unsigned int> &aPositiveSelSites,
-                            const std::vector<double> &aPositiveSelSitesProb);
 
   /// Save the positive selection sites and corresponding probabilities for
-  /// later printing. (multiple fg)
+  /// later printing. 
   ///
   /// @param[in] aFgBranch The foreground branch to which the sites refers
   /// @param[in] aPositiveSelSites The site in which the positive selection
@@ -67,8 +57,16 @@ public:
   /// @param[in] aPositiveSelSitesProb The corresponding probability as computed
   /// by the BEB test
   ///
+  
+  void savePositiveSelSites(size_t aFgBranch,
+                            const std::vector<unsigned int> &aPositiveSelSites,
+                            const std::vector<double> &aPositiveSelSitesProb);
 
+  /// Check if anything will be output at the end.
+  ///
+  /// @return True if the output to file is enabled.
   ///
+  
   bool isWriteResultsEnabled(void) const { return mFilename != NULL; }
 
   /// Returns the correct index order to have the sites printed in the correct
@@ -108,4 +106,100 @@ private:
   /// hypothesis
 };
 
+
+
+/// Write all results to a given file for the case of fg branches marked in nwk file.
+
+class WriteResultsMfg {
+public:
+  /// Constructor
+  ///
+  /// @param[in] aFilename The filename to which the output should go. If null
+  /// no printing will happen
+  ///
+  explicit WriteResultsMfg(const char *aFilename) : mFilename(aFilename) {}
+
+  /// Destructor.
+  ///
+  ~WriteResultsMfg() {
+    mLnL[0].clear();
+    mLnL[1].clear();
+    mPositiveSelSites.clear();
+  }
+
+  /// Output the results to the file given
+  /// @param[in] aFgSet The set of marked fg branches
+  ///
+  void outputResults(std::set<int> aFgSet);
+
+  /// Save the likelihood for later printing.
+  ///
+  /// @param[in] aFgBranchSet The marked foreground branches to which the log-likelihood
+  /// refers
+  /// @param[in] aLnL The log-likelihood
+  /// @param[in] aHypothesis The hypothesis (0 for H0 and 1 for H1) for which
+  /// the log-likelihood has been computed
+  ///
+  void saveLnL(std::set<int> aFgBranchSet, double aLnL, unsigned int aHypothesis);
+
+
+  /// Save the positive selection sites and corresponding probabilities for
+  /// later printing. 
+  ///
+  /// @param[in] aFgBranchSet The marked foreground branches to which the sites refers
+  /// @param[in] aPositiveSelSites The site in which the positive selection
+  /// appears as computed by the BEB test
+  /// @param[in] aPositiveSelSitesProb The corresponding probability as computed
+  /// by the BEB test
+  ///
+  
+  void savePositiveSelSites(std::set<int> aFgBranchSet,
+                            const std::vector<unsigned int> &aPositiveSelSites,
+                            const std::vector<double> &aPositiveSelSitesProb);
+
+  /// Check if anything will be output at the end.
+  ///
+  /// @return True if the output to file is enabled.
+  ///
+  
+  bool isWriteResultsEnabled(void) const { return mFilename != NULL; }
+
+  /// Returns the correct index order to have the sites printed in the correct
+  /// order.
+  ///
+  /// @param[in] aSites The vector of site numbers
+  ///
+  /// @return The list of indices that gives the sites in the correct order.
+  ///
+  const std::vector<size_t> &
+  orderSites(const std::vector<unsigned int> &aSites) const;
+
+  /// Save the parameters string for later printing.
+  ///
+  /// @param[in] aFgBranchSet The marked foreground branches to which the log-likelihood
+  /// refers
+  /// @param[in] aParamStr The parameters string
+  /// @param[in] aHypothesis The hypothesis (0 for H0 and 1 for H1) for which
+  /// the log-likelihood has been computed
+  ///
+  void saveParameters(std::set<int> aFgBranchSet, std::string &aParamStr,
+                      unsigned int aHypothesis);
+
+private:
+  const char *mFilename; ///< The file to which the results should be written.
+  /// If null, no printing appear
+  std::map<size_t, double> mLnL[2]; ///< The log-likelihood for the given marekd fg
+  /// branches and for the two hypothesis
+  std::map<size_t, std::pair<std::vector<unsigned int>, std::vector<double> > >
+      mPositiveSelSites; ///< The sites under positive selection and the
+  /// corresponding probabilities for a given marked fg branches
+  mutable std::vector<size_t>
+      mSiteOrder; ///< The new site+prob order computed by orderSites routine
+
+  std::map<size_t, std::string> mParamStr[2]; ///< The parameters string for the
+  /// given marked fg branches and for the two
+  /// hypothesis
+};
+
+
 #endif

bad_cases/HBG000784-1.M0.009.nwk

+(((((((((a0009:0.005122,a0005:0.005553):0.021588,(a0000:0.09922,a0003:0.056644):0.214725):0.010754,a0010:0.015175):0.074881,a0001:0.06595):0.010737,a0014:0.314409):0.007601,a0013:0.083805):0.264158,a0007:0.430493):0.340044,a0002:1.259416):0.66615,(((a0008:0.090909,a0011:0.107215):0.183011,(a0012:0.283332,a0004:0.851209):0.052773):0.459232,a0006:0.540195)#1:0.694423);

bad_cases/HBG005459-1.M0.000.nwk

+(((((((a0000:0.150779,a0011:0.366606):0.020186,(a0008:0.189257,a0012:0.064304):0.491414):0.003135,(a0005:0.027918,(a0014:0.008119,a0002:0.002763):0.019253):0.07771):0.185033,a0009:0.275464):0.185673,a0003:0.29294):0.394691,a0013:1.474877)#1:0.414072,(((a0006:0.64944,a0001:0.369005):0.077098,(a0004:0.342883,a0010:0.114781):0.128282):0.442747,a0007:3.987982):0.466218);

bad_cases/HBG005877-1.M0.002.nwk

+(((a0003:0.940287,(a0006:0.225433,((a0008:0.070547,(a0013:0.069575,((a0014:0.003074,a0001:0.01845):4e-06,a0005:0.005609):0.079689):0.000897):0.011044,(a0007:0.048967,a0009:0.066015):0.166874):0.139738)#1:0.1328):0.2447,a0012:0.90415):0.965229,((((a0010:0.146055,a0004:0.095622):0.272589,a0011:0.127978):0.109596,a0002:0.382271):0.498846,a0000:0.498494):1.032012);

bad_cases/HBG010916-1.M0.009.nwk

+(((((((a0001:0.075468,a0005:0.085411):0.207804,(a0010:0.720769,a0006:0.020905):0.105001):0.012384,(a0000:0.142497,a0012:0.282057)#1:0.018899):0.178792,a0009:0.443433)#1:0.714179,a0008:0.474661):0.143467,a0011:1.098262):0.162709,((a0007:0.348344,(a0003:0.324275,(a0013:0.17518,a0002:0.376901):0.198321):0.112915):0.242393,a0004:0.617143):0.19161);

bad_cases/output.out

+CODONML (in paml version 4.8a, July 2014)  ./bad_cases/HBG010916-1.phy
+Model: several dN/dS ratios for branches for branches,  omega = 1.000 fixed
+
+Codon frequency model: F3x4
+Site-class models:  PositiveSelection
+ns =  14  ls = 1038
+
+Codon usage in sequences
+--------------------------------------------------------------------------------------------------------------------------------------
+Phe TTT  34  22  18  11  16  21 | Ser TCT  13  19  16   5  19  16 | Tyr TAT  20  20  22   4  11  21 | Cys TGT  12  11   9   2  10   8
+    TTC  16  15  20  29  19  18 |     TCC  17  15  15  29  22  20 |     TAC  13  14  17  30  22  19 |     TGC   9   8   8  15   9  13
+Leu TTA  10   1   1   0   2   2 |     TCA  10   6  11   6  10   7 | *** TAA   0   0   0   0   0   0 | *** TGA   0   0   0   0   0   0
+    TTG  13  13  17   5  15  15 |     TCG   3   2   4   7   1   7 |     TAG   0   0   0   0   0   0 | Trp TGG  13   9   8   7   9   8
+--------------------------------------------------------------------------------------------------------------------------------------
+Leu CTT  12   7  13   4   8   7 | Pro CCT  12  14  13   6  12   6 | His CAT  12  11   8   1   9  10 | Arg CGT   9  11   6   4  10   7
+    CTC  22  21  15  20  22  17 |     CCC  13  13   8  25  16  20 |     CAC   8   6   9  16   9   9 |     CGC  14  15  11  32  20  16
+    CTA  13  15   2   1  11   7 |     CCA  19  16  15   1  15   7 | Gln CAA   5   6  10   0   5   3 |     CGA   7   9   6   2   5   7
+    CTG  42  49  38  67  47  53 |     CCG   1   2   5  11   3   8 |     CAG  39  38  28  38  39  39 |     CGG  13  13   4  13  13   6
+--------------------------------------------------------------------------------------------------------------------------------------
+Ile ATT  21  22  25   8  20  24 | Thr ACT  12  10  19   5  10  14 | Asn AAT  15  11  15   4   7  15 | Ser AGT   8   4  13   2   9  13
+    ATC  32  31  31  54  33  30 |     ACC  21  22  14  29  23  20 |     AAC  16  20  29  35  23  26 |     AGC  19  23  13  22  15  12
+    ATA  12   3   9   0   3   8 |     ACA  22  21  18   6  18  11 | Lys AAA  19  10  28   3   7  16 | Arg AGA   4   2  12   1   3   2
+Met ATG  26  20  34  24  21  29 |     ACG   3   6   5  18   7  11 |     AAG  33  36  35  51  38  34 |     AGG   4   6   7   2   7   5
+--------------------------------------------------------------------------------------------------------------------------------------
+Val GTT  13   9  29   4   7  18 | Ala GCT  22  26  27  12  28  20 | Asp GAT  18  16  22   8  16  19 | Gly GGT  18  20  18  12  15  10
+    GTC  18  19  18  23  24  22 |     GCC  32  46  30  47  41  42 |     GAC  26  28  26  37  28  25 |     GGC  28  30  14  42  30  26