Add SS prediction for multiple aligment into jpred.pl. Before this was a part of...
authorSasha Sherstnev <a.sherstnev@dundee.ac.uk>
Fri, 13 Sep 2013 14:47:42 +0000 (15:47 +0100)
committerSasha Sherstnev <a.sherstnev@dundee.ac.uk>
Fri, 13 Sep 2013 14:47:42 +0000 (15:47 +0100)
17 files changed:
binaries/src/jpred/jpred.pl
binaries/src/jpred/lib/Paths.pm
binaries/src/jpred/tests/alignment.clustal [new file with mode: 0644]
binaries/src/jpred/tests/alignment.fasta [new file with mode: 0644]
binaries/src/jpred/tests/alignment.msf [new file with mode: 0644]
binaries/src/jpred/tests/d1b3aa_.fas [new file with mode: 0644]
binaries/src/jpred/tests/res_d16vpa_.align [deleted file]
binaries/src/jpred/tests/res_d16vpa_.concise [deleted file]
binaries/src/jpred/tests/res_d16vpa_.hmm [deleted file]
binaries/src/jpred/tests/res_d16vpa_.jnet [deleted file]
binaries/src/jpred/tests/res_d16vpa_.profile [deleted file]
binaries/src/jpred/tests/res_d16vpa_.pssm [deleted file]
binaries/src/jpred/tests/res_d16vpa_.res [deleted file]
binaries/src/jpred/tests/res_d16vpa_.res.fasta [deleted file]
binaries/src/jpred/tests/todo.bash
binaries/src/jpred/x86_64/alscript [new file with mode: 0755]
binaries/src/jpred/x86_64/readseq [new file with mode: 0755]

index 74206dd..f5910fc 100755 (executable)
@@ -6,23 +6,26 @@ jpred - Secondary structure prediction program
 
 =head1 SYNOPSIS
 
-./jpred.pl -in/-sequence <FILE1> [-outfile <FILE2>] [-logfile <FILE3>] [-output <FILEPREFIX>] [-dbname <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>] [-pred-nohits] [-no-final] [-jabaws] [-verbose] [-debug] [-help] [-man]
+./jpred.pl -in <FILE1> [-outfile <FILE2>] [-logfile <FILE3>] [-output <FILEPREFIX>] [-dbname <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>] [-seq] [-pred-nohits] [-no-final] [-jabaws] [-verbose] [-debug] [-help] [-man]
 
 =head1 DESCRIPTION
 
-This is a program which predicts the secondary structure of a protein sequence given a path to a 
-FASTA sequence. It does all the PSI-BLAST searching and alignment 'meddling' as required by Jnet.
-
-The program is primarily design for use by the Jpred server, but it can be used directly by any user. 
-Some of the output may not be meaningful if used directly - it can be safely ignored.
+This is a program for predicting the secondary structure of a multiple sequence alignment (by default) or a protein sequence 
+(with the -seq option). The input file can be stored in 3 formats: FASTA, MSF, or BLC. 
+For the single sequence the program does all the PSI-BLAST searching, preparing PSSM and HMM profiles and predicting the 
+secondary structure with Jnet. For the multiple sequence alignment only the HMM profile, created from the alignment, is used in Jnet.
 
 =head1 OPTIONS
 
 =over 5
 
-=item -in/-sequence <FILE1>
+=item -in <FILE1>
+
+The path to the sequence file (in FASTA, MSF, or BLC format)
 
-The path to the sequence file (in FASTA format) you want to predict.
+=item -seq
+
+The input file is a FASTA file with one sequence only.
 
 =item -output <FILEPREFIX>
 
@@ -112,15 +115,13 @@ use Carp;
 use Data::Dumper;
 use File::Temp;
 
-#use UNIVERSAL;
-
 # path to Jpred modules
 use FindBin qw($Bin);
 use lib "$Bin/lib";
 
 # internal jpred modules
 use Jpred;
-use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin check_OS setup_env);
+use Paths qw($pairwise $oc $jnet $hmmbuild $hmmconvert $psiblastbin $alscript $readseq check_OS setup_env);
 use HMMER::Profile;
 use HMMER::Profile::Jnet;
 use PSIBLAST;
@@ -182,13 +183,17 @@ our $GAP = '-';
 
 #####################################################################################################
 my $infile;
+my $infastafile;
+my $format;
+my $goal = "align";
+my $seqgoal;
 my $outfile;
 my $prefix;
 my $psiblast;
 my $jabaws;
 my $logfile;
-my $ncpu       = 1;           # number of CPUs for psiblast calculations
-my $predNoHits = 0;           # define whether to make predictions when no PSI-BLAST hits are found
+my $ncpu       = 1;                              # number of CPUs for psiblast calculations
+my $predNoHits = 0;                              # define whether to make predictions when no PSI-BLAST hits are found
 my $db_path    = "/homes/www-jpred/databases";
 my $db_entry   = "cluster";
 my $nofinal;
@@ -196,30 +201,34 @@ my $nofinal;
 my ( $help, $man, $DEBUG, $VERBOSE );
 
 GetOptions(
-  "in|sequence=s" => \$infile,
-  "output=s"      => \$prefix,
-  "outfile=s"     => \$outfile,
-  "logfile=s"     => \$logfile,
-  "psi=s"         => \$psiblast,
-  "dbname=s"      => \$db_entry,
-  "dbpath=s"      => \$db_path,
-  "ncpu=s"        => \$ncpu,
-  "pred-nohits"   => \$predNoHits,
-  "no-final"      => \$nofinal,
-  "jabaws"        => \$jabaws,
-  "help"          => \$help,
-  "man"           => \$man,
-  "debug"         => \$DEBUG,
-  "verbose"       => \$VERBOSE
+  "in=s"        => \$infile,
+  "output=s"    => \$prefix,
+  "outfile=s"   => \$outfile,
+  "logfile=s"   => \$logfile,
+  "psi=s"       => \$psiblast,
+  "dbname=s"    => \$db_entry,
+  "dbpath=s"    => \$db_path,
+  "ncpu=s"      => \$ncpu,
+  "pred-nohits" => \$predNoHits,
+  "no-final"    => \$nofinal,
+  "seq"         => \$seqgoal,
+  "jabaws"      => \$jabaws,
+
+  "help"    => \$help,
+  "man"     => \$man,
+  "debug"   => \$DEBUG,
+  "verbose" => \$VERBOSE
 ) or pod2usage(2);
 pod2usage(1) if $help;
 pod2usage( verbose => 2 ) if $man;
 
+$goal = "seq" if ( defined $seqgoal );
+
 #####################################################################################################
 # Key to database information and information for accessing them
-if (defined $jabaws) {
-  $db_path    = "/data/UNIREFdb";
-  $db_entry   = "cluster";
+if ( defined $jabaws ) {
+  $db_path  = "/data/UNIREFdb";
+  $db_entry = "cluster";
 }
 
 my $database = {
@@ -270,22 +279,24 @@ my $database = {
 };
 
 my $dp = $database->{$db_entry}{database};
-pod2usage("ERROR! Input file with a sequence should be provided with -sequence/-in")                              unless $infile;
-pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database" )           unless exists $database->{$db_entry};
+pod2usage("ERROR! Input file should be provided with -sequence/-in")                                              unless $infile;
+pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database")            unless exists $database->{$db_entry};
 pod2usage("ERROR! UNIREF database is not available at $dp. Use -dbpath and -dbname for configuring the database") unless -f $dp;
 
+#####################################################################################################
+# lots of preparation steps
 if ( defined $prefix ) {
-  unless (defined $outfile) {
-    $outfile = $prefix. ".res.fasta";
+  unless ( defined $outfile ) {
+    $outfile = $prefix . ".res.fasta";
   }
 } else {
-  if (defined $outfile) {
+  if ( defined $outfile ) {
     print "WARNING! file prefix is not defined. Jpred will use $outfile.tmp as the prefix\n";
     $prefix = $outfile . ".tmp";
   } else {
     print "WARNING! file prefix is not defined. Jpred will use $infile.res as the prefix\n";
-    $prefix = $infile . ".res";
-    $outfile = $prefix. ".jnet";
+    $prefix  = $infile . ".res";
+    $outfile = $prefix . ".jnet";
   }
 }
 
@@ -297,7 +308,7 @@ if ( 1 > $ncpu or 8 < $ncpu ) {
 $VERBOSE = 1 if $DEBUG;
 
 my $LOG;
-if (defined $logfile) {
+if ( defined $logfile ) {
   open( $LOG, ">", $logfile ) or die "ERROR! unable to open '$logfile': ${!}\nDied";
 }
 
@@ -309,8 +320,7 @@ for ( [ "input file", $infile ], [ "out file", $outfile ], [ "outprefix", $prefi
   print $LOG "$par\n" if $LOG;
 }
 
-#####################################################################################################
-if (defined $jabaws) {
+if ( defined $jabaws ) {
   setup_jpred_env($Bin);
   setup_env($Bin);
 }
@@ -319,215 +329,269 @@ print "JPRED: checking platiform... $platform\n" if $DEBUG;
 print $LOG "JPRED: checking platiform... $platform\n" if $LOG;
 
 #####################################################################################################
-my $query = FASTA::File->new( read_file => $infile );
-
-my @seqs;
-my $psi = PSIBLAST->new;
-unless ( defined $psiblast && -e $psiblast ) {
-  ## potentially a better set of parameters (esp. -b & -v) which avoid PSI-BLAST dying with large number of hits
-  # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -F "m S"'  # 'soft' filtering of the query sequence
-  # args => '-e0.001 -h0.0001 -m6 -b10000 -v10000 -j3'        # stricter searching criteria
-  # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3'
-  my $psi_run = PSIBLAST::Run->new(
-    debug    => $DEBUG,
-    args     => "-a" . $ncpu . " -e0.05 -h0.01 -m6 -b10000 -v10000 -j3",
-    path     => $psiblastbin,
-    input    => $infile,
-    output   => "$prefix.blast",
-    matrix   => "$prefix.profile",
-    database => $database->{$db_entry}{database},
-  );
-
-  # For reduced databases, get the size of the orginal and use this as
-  # the equivilent DB size
-  if ( $db_entry =~ /^sp_red_/ ) {
-    ( my $entry = $db_entry ) =~ s/^sp_red_/sp_/;
-    $psi_run->args(
-      $psi_run->args . " -z " . fasta_seq_length( $database->{$entry}{database} )    # CC sub is below
-    );
+# check input file format
+if ( 'seq' eq $goal ) {
+  $format = "seq";
+  if ( 1 != check_FASTA_format($infile) ) {
+    die "\nERROR! jpred requires 1 sequence in the FASTA file if the option -seq used. exit\n";
   }
-  print "BLAST matrix: $ENV{BLASTMAT}\n" if $DEBUG;
-  print "BLASTDB path: $ENV{BLASTDB}\n"  if $DEBUG;
-  print $LOG "BLAST matrix: $ENV{BLASTMAT}\n" if $LOG;
-  print $LOG "BLASTDB path: $ENV{BLASTDB}\n"  if $LOG;
-
-  print "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $VERBOSE;
-  print $LOG "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $LOG;
-  $psi_run->run or die;                                                              # CC sub is from PSIBLAST::Run
-
-  $psi->read_file("$prefix.blast");                                                  # CC PSIBLAST.pm doesn't have a read_file(), but Read.pm does?
-  system("gzip -9f $prefix.blast");
 } else {
-  if   ( $psiblast =~ /.gz$/ ) { $psi->read_gzip_file($psiblast) }                   # CC PSIBALST.pm doesn't have a read_gzip_file() object, but Read.pm does?
-  else                         { $psi->read_file($psiblast) }                        # CC ditto above
+  my $nseq = check_FASTA_format($infile);
+  if ( 0 < $nseq ) {
+    $format = "fasta";
+    if ( 1 == $nseq ) {
+      die "\nERROR! jpred requires alignment with more than 1 sequence\n       if you provide only one sequence use the -seq option.\n";
+    }
+  } elsif ( 0 < check_MSF_format($infile) ) {
+    $format = "msf";
+  } elsif ( 0 < check_BLC_format($infile) ) {
+    $format = "blc";
+  } else {
+    die "ERROR! unknown input file format for multiple sequence alignment (can be FASTA, MSF, or BLC). exit...\n";
+  }
 }
+$infastafile = $infile . ".fasta" if ( 'msf' eq $format or 'blc' eq $format );
 
 #####################################################################################################
-# Convert the last itteration into a collection of PSISEQ objects
-for ( $psi->get_all ) {                                                              # CC sub is from PSIBLAST.pm
-  my ( $id, $start, $align ) = @{$_};
-  push @seqs,
-    PSISEQ->new(
-    id    => $id,
-    start => $start,
-    align => [ split( //, $align ) ]
+if ( 'seq' eq $goal ) {
+  my $query = FASTA::File->new( read_file => $infile );
+  my @seqs;
+  my $psi = PSIBLAST->new;
+  unless ( defined $psiblast && -e $psiblast ) {
+    ## potentially a better set of parameters (esp. -b & -v) which avoid PSI-BLAST dying with large number of hits
+    # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3 -F "m S"'  # 'soft' filtering of the query sequence
+    # args => '-e0.001 -h0.0001 -m6 -b10000 -v10000 -j3'        # stricter searching criteria
+    # args => '-e0.05 -h0.01 -m6 -b10000 -v10000 -j3'
+    my $psi_run = PSIBLAST::Run->new(
+      debug    => $DEBUG,
+      args     => "-a" . $ncpu . " -e0.05 -h0.01 -m6 -b10000 -v10000 -j3",
+      path     => $psiblastbin,
+      input    => $infile,
+      output   => "$prefix.blast",
+      matrix   => "$prefix.profile",
+      database => $database->{$db_entry}{database},
     );
-}
+
+    # For reduced databases, get the size of the orginal and use this as
+    # the equivilent DB size
+    if ( $db_entry =~ /^sp_red_/ ) {
+      ( my $entry = $db_entry ) =~ s/^sp_red_/sp_/;
+      $psi_run->args(
+        $psi_run->args . " -z " . fasta_seq_length( $database->{$entry}{database} )    # CC sub is below
+      );
+    }
+    print "BLAST matrix: $ENV{BLASTMAT}\n"      if $DEBUG;
+    print "BLASTDB path: $ENV{BLASTDB}\n"       if $DEBUG;
+    print $LOG "BLAST matrix: $ENV{BLASTMAT}\n" if $LOG;
+    print $LOG "BLASTDB path: $ENV{BLASTDB}\n"  if $LOG;
+
+    print "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $VERBOSE;
+    print $LOG "Running PSI-BLAST on query against \'$database->{$db_entry}{database}\'...\n" if $LOG;
+    $psi_run->run or die;                                                              # CC sub is from PSIBLAST::Run
+
+    $psi->read_file("$prefix.blast");                                                  # CC PSIBLAST.pm doesn't have a read_file(), but Read.pm does?
+    system("gzip -9f $prefix.blast");
+  } else {
+    if   ( $psiblast =~ /.gz$/ ) { $psi->read_gzip_file($psiblast) }                   # CC PSIBALST.pm doesn't have a read_gzip_file() object, but Read.pm does?
+    else                         { $psi->read_file($psiblast) }                        # CC ditto above
+  }
+
+#####################################################################################################
+  # Convert the last itteration into a collection of PSISEQ objects
+  for ( $psi->get_all ) {                                                              # CC sub is from PSIBLAST.pm
+    my ( $id, $start, $align ) = @{$_};
+    push @seqs,
+      PSISEQ->new(
+      id    => $id,
+      start => $start,
+      align => [ split( //, $align ) ]
+      );
+  }
 
 #####################################################################################################
-## When there are no PSI-BLAST hits generate an HMM from the query
-## and run Jnet against that only.
-## Accuracy won't be as good, but at least it's a prediction
-if ( @seqs == 0 ) {
-  if ( $predNoHits == 0 ) {
-    warn "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n";
-    print ">>100% complete\n";
-    print $LOG "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n" if $LOG;
-    print $LOG ">>100% complete\n" if $LOG;
-    close ($LOG) if $LOG;
-    exit;
+  # When there are no PSI-BLAST hits generate an HMM from the query and run Jnet against that only.
+  # Accuracy won't be as good, but at least it's a prediction
+  if ( @seqs == 0 ) {
+    if ( $predNoHits == 0 ) {
+      warn "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n";
+      print ">>100% complete\n";
+      print $LOG "\nJPRED: Warning! no PSI-BLAST hits found and '-pred-nohits' option not set. Exiting...\n" if $LOG;
+      print $LOG ">>100% complete\n"                                                                         if $LOG;
+      close($LOG)                                                                                            if $LOG;
+      exit;
+    } else {
+      print ">>50% complete\n";
+      warn "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n";
+      print "Running HMMer on query...\n"                                                            if $VERBOSE;
+      print $LOG ">>50% complete\n"                                                                  if $LOG;
+      print $LOG "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n" if $LOG;
+      print $LOG "Running HMMer on query...\n"                                                       if $LOG;
+
+      # copy input query to alignment
+      #system("cp $path $prefix.align") == 0 or croak "Error: unable to copy '$path'\n";
+      open( my $ifh, "<", $infile )            or die "JPRED: cannot open file $infile: $!";
+      open( my $ofh, ">", $prefix . ".align" ) or die "JPRED: cannot open file $prefix\.align: $!";
+      while (<$ifh>) { print $ofh, $_ }
+      close $ifh;
+      close $ofh;
+
+      # Temp files required for HMMer
+      my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2;
+      system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $infile");
+      system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out");
+      unlink $hmmbuild_out;
+
+      # Read in the HMMER file
+      my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out );
+
+      # Convert from HMMER::Profile to HMMER::Profile::Jnet
+      my $hmmer_jnet = HMMER::Profile::Jnet->new;
+      $hmmer_jnet->add_line( @{$_} ) for $hmmer->get_line;
+      $hmmer_jnet->write_file("$prefix.hmm");
+      print ">>70% complete\n";
+      print $LOG ">>70% complete\n" if $LOG;
+
+      # Run Jnet for the prediction
+      print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE;
+      print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG;
+      my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) );
+      print ">>90% complete\n";
+      print $LOG ">>90% complete\n" if $LOG;
+      print $jnetlog                if $VERBOSE;
+      print $LOG $jnetlog           if $LOG;
+    }
   } else {
+    psiseq2fasta( "0.fasta.gz", @seqs ) if $DEBUG;
+    print ">>40% complete\n";
+    print $LOG ">>40% complete\n" if $LOG;
+
+    #####################################################################################################
+    # Make PSIBLAST truncated alignments the right length
+    print "Untruncating the PSIBLAST alignments...\n" if $VERBOSE;
+    print $LOG "Untruncating the PSIBLAST alignments...\n" if $LOG;
+    @seqs = extend( $query, @seqs );
+    psiseq2fasta( "1.fasta.gz", @seqs ) if $DEBUG;
+
+    #####################################################################################################
+    # Remove masking from PSIBLAST alignment
+    print "Unmasking the alignments...\n" if $VERBOSE;
+    print $LOG "Unmasking the alignments...\n" if $LOG;
+    my $idx = Index->new( type => "Index::FastaCMD" ) or die "Index type cannot be found.";
+    remove_seq_masks( $idx, $_ ) for @seqs[ 1 .. $#seqs ];
+    psiseq2fasta( "2.fasta.gz", @seqs ) if $DEBUG;
+
+    #####################################################################################################
+    # Convert the sequences to upper case
+    print "Converting sequences to the same case...\n" if $VERBOSE;
+    print $LOG "Converting sequences to the same case...\n" if $LOG;
+    toupper($_) for @seqs;    # CC sub is below
+    psiseq2fasta( "${prefix}_backup.fasta.gz", @seqs );
+
+    #####################################################################################################
+    # Remove excessive sequences
+    print "Remove excessive sequences...\n" if $VERBOSE;
+    print $LOG "Remove excessive sequences...\n" if $LOG;
+    @seqs = reduce( $MAX_ALIGN, @seqs );
+    psiseq2fasta( "3.fasta.gz", @seqs ) if $DEBUG;
+
+    #####################################################################################################
+    # Remove sequences that are too long or too short
+    print "Remove sequences which too long or short...\n" if $VERBOSE;
+    print $LOG "Remove sequences which too long or short...\n" if $LOG;
+    @seqs = del_long_seqs( 50, @seqs );
+    psiseq2fasta( "4.fasta.gz", @seqs ) if $DEBUG;
+
+    #####################################################################################################
+    # Remove redundant sequences based upon pairwise identity and OC clustering
+    print "Remove redundant sequences...\n" if $VERBOSE;
+    print $LOG "Remove redundant sequences...\n" if $LOG;
+    @seqs = nonred( $NR_CUT, @seqs );
+    psiseq2fasta( "5.fasta.gz", @seqs ) if $DEBUG;
+
+    #####################################################################################################
+    # Check that we haven't got rid of all of the sequences
+    if ( @seqs < 2 ) {
+      warn "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n";
+      print $LOG "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n" if $LOG;
+      @seqs = fasta2psiseq("${prefix}_backup.fasta.gz");
+    }
+    unlink("${prefix}_backup.fasta.gz") unless $DEBUG;
+
+    # Remove gaps in the query sequence and same positions in the alignment
+    print "Removing gaps in the query sequence...\n" if $VERBOSE;
+    print $LOG "Removing gaps in the query sequence...\n" if $LOG;
+    degap(@seqs);
+    psiseq2fasta( "6.fasta.gz", @seqs ) if $DEBUG;
+
+    # Output the alignment for the prediction
+    print "Outputting cleaned-up PSI_BLAST alignment...\n" if $VERBOSE;
+    print $LOG "Outputting cleaned-up PSI_BLAST alignment...\n" if $LOG;
+    psiseq2fasta( "$prefix.align", @seqs );
+
+    #####################################################################################################
+    # Equivilent to getpssm script
+    print "Output the PSSM matrix from the PSI-BLAST profile...\n";
+    print $LOG "Output the PSSM matrix from the PSI-BLAST profile...\n" if $LOG;
+    my $pssm = PSIBLAST::PSSM->new( read_file => "$prefix.profile" );
+    $pssm->write_file("$prefix.pssm");    # CC write_file() sub is in Write.pm loaded via PSIBLAST::PSSM
     print ">>50% complete\n";
-    warn "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n";
-    print "Running HMMer on query...\n" if $VERBOSE;
     print $LOG ">>50% complete\n" if $LOG;
-    print $LOG "\nJPRED: no PSI-BLAST hits found. Continuing with single query sequence only.\n\n" if $LOG;
-    print $LOG "Running HMMer on query...\n" if $LOG;
-
-    # copy input query to alignment
-    #system("cp $path $prefix.align") == 0 or croak "Error: unable to copy '$path'\n";
-    open( my $ifh, "<", $infile )            or die "JPRED: cannot open file $infile: $!";
-    open( my $ofh, ">", $prefix . ".align" ) or die "JPRED: cannot open file $prefix\.align: $!";
-    while (<$ifh>) { print $ofh, $_ }
-    close $ifh;
-    close $ofh;
-
-    # Temp files required for HMMer
-    my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2;
-
-    system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $infile");
-    system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out");
-
-    # Read in the HMMER file
-    my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out );
-
-    # Convert from HMMER::Profile to HMMER::Profile::Jnet
-    my $hmmer_jnet = HMMER::Profile::Jnet->new;
-    $hmmer_jnet->add_line( @{$_} ) for $hmmer->get_line;
-    $hmmer_jnet->write_file("$prefix.hmm");    # write_file is in the Read.pm called from the HMMER::Profile module
+
+    #####################################################################################################
+    # Run HMMER on the sequences
+    print "Running HMMer on sequences found by PSI-BLAST...\n" if $VERBOSE;
+    print $LOG "Running HMMer on sequences found by PSI-BLAST...\n" if $LOG;
+    my $hmmer = hmmer(@seqs);             # CC sub is below
+    $hmmer->write_file("$prefix.hmm");    # write_file is in the Read.pm called from the HMMER::Profile module
     print ">>70% complete\n";
     print $LOG ">>70% complete\n" if $LOG;
-
+#####################################################################################################
     # Run Jnet for the prediction
-    print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE;
-    print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG;
-    my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) );
+    print "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $VERBOSE;
+    print $LOG "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $LOG;
+    my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet pssm) );    # CC sub is below
     print ">>90% complete\n";
     print $LOG ">>90% complete\n" if $LOG;
-    print $jnetlog if $VERBOSE;
-    print $LOG $jnetlog if $LOG;
+    print $jnetlog                if $VERBOSE;
+    print $LOG $jnetlog           if $LOG;
   }
 } else {
-  psiseq2fasta( "0.fasta.gz", @seqs ) if $DEBUG;
-  print ">>40% complete\n";
-  print $LOG ">>40% complete\n" if $LOG;
-
-  #####################################################################################################
-  # Make PSIBLAST truncated alignments the right length
-  print "Untruncating the PSIBLAST alignments...\n" if $VERBOSE;
-  print $LOG "Untruncating the PSIBLAST alignments...\n" if $LOG;
-  @seqs = extend( $query, @seqs );
-  psiseq2fasta( "1.fasta.gz", @seqs ) if $DEBUG;
-
-  #####################################################################################################
-  # Remove masking from PSIBLAST alignment
-  print "Unmasking the alignments...\n" if $VERBOSE;
-  print $LOG "Unmasking the alignments...\n" if $LOG;
-  my $idx = Index->new( type => "Index::FastaCMD" ) or die "Index type cannot be found.";
-  remove_seq_masks( $idx, $_ ) for @seqs[ 1 .. $#seqs ];
-  psiseq2fasta( "2.fasta.gz", @seqs ) if $DEBUG;
-
-  #####################################################################################################
-  # Convert the sequences to upper case
-  print "Converting sequences to the same case...\n" if $VERBOSE;
-  print $LOG "Converting sequences to the same case...\n" if $LOG;
-  toupper($_) for @seqs;    # CC sub is below
-  psiseq2fasta( "${prefix}_backup.fasta.gz", @seqs );
-
-  #####################################################################################################
-  # Remove excessive sequences
-  print "Remove excessive sequences...\n" if $VERBOSE;
-  print $LOG "Remove excessive sequences...\n" if $LOG;
-  @seqs = reduce( $MAX_ALIGN, @seqs );
-  psiseq2fasta( "3.fasta.gz", @seqs ) if $DEBUG;
-
-  #####################################################################################################
-  # Remove sequences that are too long or too short
-  print "Remove sequences which too long or short...\n" if $VERBOSE;
-  print $LOG "Remove sequences which too long or short...\n" if $LOG;
-  @seqs = del_long_seqs( 50, @seqs );
-  psiseq2fasta( "4.fasta.gz", @seqs ) if $DEBUG;
-
-  #####################################################################################################
-  # Remove redundant sequences based upon pairwise identity and OC clustering
-  print "Remove redundant sequences...\n" if $VERBOSE;
-  print $LOG "Remove redundant sequences...\n" if $LOG;
-  @seqs = nonred( $NR_CUT, @seqs );
-  psiseq2fasta( "5.fasta.gz", @seqs ) if $DEBUG;
-
-  #####################################################################################################
-  # Check that we haven't got rid of all of the sequences
-  if ( @seqs < 2 ) {
-    warn "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n";
-    print $LOG "JPRED: All the sequences found by PSIBLAST were removed during filtering, reverting to prefiltered sequences\n" if $LOG;
-    @seqs = fasta2psiseq("${prefix}_backup.fasta.gz");
+  if ( 'fasta' eq $format ) {
+    print "Read FASTA file\n";
+    my $hmmer1 = hmm_for_align($infile);
+    $hmmer1->write_file("$prefix.hmm");                              # write_file is in the Read.pm called from the HMMER::Profile module
+  } elsif ( 'msf' eq $format ) {
+    msf2fasta( $infile, $infastafile );
+    my $hmmer2 = hmm_for_align($infastafile);
+    $hmmer2->write_file("$prefix.hmm");                              # write_file is in the Read.pm called from the HMMER::Profile module
+  } elsif ( 'blc' eq $format ) {
+    my $tmpfile = File::Temp->new->filename;
+    blc2msf( $infile, $tmpfile );
+    msf2fasta( $infile, $infastafile );
+    my $hmmer3 = hmm_for_align($infastafile);
+    $hmmer3->write_file("$prefix.hmm");                              # write_file is in the Read.pm called from the HMMER::Profile module
+  } else {
+    die "ERROR! unknown input format '$format'. exit...\n";
   }
-  unlink("${prefix}_backup.fasta.gz") unless $DEBUG;
-
-  # Remove gaps in the query sequence and same positions in the alignment
-  print "Removing gaps in the query sequence...\n" if $VERBOSE;
-  print $LOG "Removing gaps in the query sequence...\n" if $LOG;
-  degap(@seqs);
-  psiseq2fasta( "6.fasta.gz", @seqs ) if $DEBUG;
-
-  # Output the alignment for the prediction
-  print "Outputting cleaned-up PSI_BLAST alignment...\n" if $VERBOSE;
-  print $LOG "Outputting cleaned-up PSI_BLAST alignment...\n" if $LOG;
-  psiseq2fasta( "$prefix.align", @seqs );
-
-  #####################################################################################################
-  # Equivilent to getpssm script
-  print "Output the PSSM matrix from the PSI-BLAST profile...\n";
-  print $LOG "Output the PSSM matrix from the PSI-BLAST profile...\n" if $LOG;
-  my $pssm = PSIBLAST::PSSM->new( read_file => "$prefix.profile" );
-  $pssm->write_file("$prefix.pssm");    # CC write_file() sub is in Write.pm loaded via PSIBLAST::PSSM
-  print ">>50% complete\n";
-  print $LOG ">>50% complete\n" if $LOG;
-
-  #####################################################################################################
-  # Run HMMER on the sequences
-  print "Running HMMer on sequences found by PSI-BLAST...\n" if $VERBOSE;
-  print $LOG "Running HMMer on sequences found by PSI-BLAST...\n" if $LOG;
-  my $hmmer = hmmer(@seqs);             # CC sub is below
-  $hmmer->write_file("$prefix.hmm");    # write_file is in the Read.pm called from the HMMER::Profile module
   print ">>70% complete\n";
   print $LOG ">>70% complete\n" if $LOG;
-
-  #####################################################################################################
+#####################################################################################################
   # Run Jnet for the prediction
-  print "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $VERBOSE;
-  print $LOG "Running JNet using the generated inputs from HMM and PSI-BLAST...\n" if $LOG;
-  my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet pssm) );    # CC sub is below
+  print "Running JNet using the generated inputs from HMM only...\n" if $VERBOSE;
+  print $LOG "Running JNet using the generated inputs from HMM only...\n" if $LOG;
+  my $jnetlog = jnet( map { "$prefix.$_" } qw(hmm jnet) );           # CC sub is below
   print ">>90% complete\n";
   print $LOG ">>90% complete\n" if $LOG;
-  print $jnetlog if $VERBOSE;
-  print $LOG $jnetlog if $LOG;
+  print $jnetlog                if $VERBOSE;
+  print $LOG $jnetlog           if $LOG;
 }
 
 unless ( defined $nofinal ) {
   my $aligfile      = $prefix . ".align";
   my $jnetfile      = $prefix . ".jnet";
   my $jnetfastafile = $prefix . ".jnet.fasta";
+  $aligfile = $infile if ( 'fasta' eq $format );
+  $aligfile = $infastafile if ( 'msf' eq $format or 'blc' eq $format );
   concise2fasta( $jnetfile, $jnetfastafile );
   open( my $IN1, "<", $aligfile )      or die "ERROR! unable to open '$aligfile': ${!}\nDied";
   open( my $IN2, "<", $jnetfastafile ) or die "ERROR! unable to open '$jnetfastafile': ${!}\nDied";
@@ -538,22 +602,146 @@ unless ( defined $nofinal ) {
   close($IN2);
   close($OUT);
   unlink $jnetfastafile;
+  my $seqs = FASTA::File->new( read_file => $outfile );
+  open( my $OUT2, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\n";
+  $seqs->write($OUT2);
+  close($OUT2);
 } else {
-  if (defined $outfile and $prefix.".jnet" ne $outfile) {
-    rename $prefix.".jnet", $outfile;
+  if ( defined $outfile and $prefix . ".jnet" ne $outfile ) {
+    rename $prefix . ".jnet", $outfile;
   }
 }
 
 print ">>100% complete\n";
 print "Jpred Finished\n";
 print $LOG ">>100% complete\n" if $LOG;
-print $LOG "Jpred Finished\n" if $LOG;
-close ($LOG) if $LOG;
+print $LOG "Jpred Finished\n"  if $LOG;
+close($LOG)                    if $LOG;
 exit;
 
 #####################################################################################################
 # Functions
 #####################################################################################################
+sub check_FASTA_format {
+  my $infile = shift;
+
+  open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n";
+  my $check_first_line = 1;
+  my $nseq             = 0;
+  local $/ = "\n>";
+  while (<$IN>) {
+    if ($check_first_line) {
+      return 0 unless (/^>/);
+      $check_first_line = 0;
+    }
+    s/^>//g;
+    s/>$//g;
+
+    my ( $id, @seqs ) = split /\n/, $_;
+    return 0 unless ( defined $id or @seqs );
+    my $seq = join( "", @seqs );
+    return 0 unless ( $seq =~ /[a-zA-Z\.-]/ );
+    ++$nseq;
+  }
+  close($IN);
+
+  return $nseq;
+}
+#####################################################################################################
+sub check_MSF_format {
+  my $infile = shift;
+  $? = 0;
+  system("$readseq -fMSF -a -p < $infile > /dev/null");
+  return 0 if ($?);
+
+  return 1;
+}
+#####################################################################################################
+sub check_BLC_format {
+  my $infile = shift;
+
+  my ( $tmpfile1, $tmpfile2 ) = map { File::Temp->new->filename } 1 .. 2;
+  open my $fh, ">$tmpfile1" or die "$tmpfile1: $!\n";
+  print $fh "silent_mode\nblock_file $infile\n";
+  print $fh "output_file /dev/null\nmax_nseq 2000\n";
+  print $fh "pir_save $tmpfile2\nsetup\n";
+  close $fh;
+
+  $? = 0;
+  system("$alscript -s -f $tmpfile1");
+  $? = 0;
+  system("$readseq -f8 -a -p < $tmpfile2 > /dev/null");
+  unlink $tmpfile1;
+  unlink $tmpfile2;
+  return 0 if ($?);
+
+  return 1;
+}
+############################################################################################################################################
+# convertor BLC -> MSF
+sub msf2fasta {
+  my $infile  = shift;
+  my $outfile = shift;
+
+  my $sequence = "";
+  open( my $IN, "<", $infile ) or die "ERROR! unable to open '$infile': ${!}\n";
+  while (<$IN>) {
+    $sequence .= $_;
+  }
+  close($IN);
+
+  $sequence =~ s/~/\./g;
+
+  ## check for non-unique sequence names - readseq has problems with these
+  my @lines = split /\n/, $sequence;
+  my %names;
+  foreach my $line (@lines) {
+    if ( $line =~ /Name:\s+(\S+)/ ) {
+      die "ERROR! Alignment has non-unique sequence ids. exit...\n" if ( defined( $names{$1} ) && $names{$1} >= 1 );
+      $names{$1}++;
+    }
+  }
+
+  my $tmpfile1 = File::Temp->new->filename;
+  my $tmpfile2 = File::Temp->new->filename;
+  open my $FILE, ">$tmpfile1" or die "open $tmpfile1 failed: $!";
+  print $FILE $sequence;
+  close $FILE;
+
+  $? = 0;
+  system("$readseq -fMSF -a -p < $tmpfile1 > $tmpfile2");
+  die "Reformatting of $infile failed. exit...\n" if ($?);
+  unlink $tmpfile1;
+
+  $? = 0;
+  system("$readseq -f8 -a -p < $tmpfile2 > $outfile");
+  die "Reformatting of $infile failed. exit...\n" if ($?);
+  unlink $tmpfile2;
+
+  die "Reformatting the input alignment has failed. exit...\n" unless ( -e $outfile );
+}
+
+############################################################################################################################################
+# convertor BLC -> MSF
+sub blc2msf {
+  my ( $in, $out ) = @_;
+
+  my ( $tmp, $tmp_pir ) = map { File::Temp->new->filename } 1 .. 2;
+
+  open my $fh, ">$tmp" or die "$tmp: $!\n";
+  print $fh "silent_mode\nblock_file $infile\n";
+  print $fh "output_file /dev/null\nmax_nseq 2000\n";
+  print $fh "pir_save $tmp_pir\nsetup\n";
+  close $fh;
+
+  $? = 0;
+  system("$alscript -s -f $tmp");
+  die "Reformatting of $infile failed. exit...\n" if ($?);
+  system("$readseq -f=MSF -o=$out -a $tmp_pir");
+
+  unlink $tmp;
+  unlink $tmp_pir;
+}
 
 #####################################################################################################
 
@@ -959,6 +1147,41 @@ Runs Jnet. Pass the paths of the filenames to do the prediction on
 
 =cut
 
+#################################################################################################################################################
+
+=head2 get_hmm($alignFile, $name)
+
+Adapted from the hmmer() function in Jpred as written by JDB.
+
+Generates an HMMer profile output compatible with Jnet.
+
+Equivilent to gethmm script.
+
+=cut
+
+sub hmm_for_align {
+  my $fastafile = shift;
+
+  # Temp files required
+  print "hmm_for_align: fastafile = $fastafile\n";
+  my ( $hmmbuild_out, $hmmconvert_out ) = map { File::Temp->new->filename } 1 .. 2;
+
+  system("$hmmbuild -F --fast --amino --gapmax 1 --wblosum $hmmbuild_out $fastafile");
+  system("$hmmconvert -F -p $hmmbuild_out $hmmconvert_out");
+
+  # Read in the HMMER file
+  my $hmmer = HMMER::Profile->new( read_file => $hmmconvert_out );
+
+  # Read in the HMMER file
+  my $hmmer_tmp = HMMER::Profile->new( read_file => $hmmconvert_out );
+
+  # Convert from HMMER::Profile to HMMER::Profile::Jnet
+  my $hmmer_jnet = HMMER::Profile::Jnet->new;
+  $hmmer_jnet->add_line( @{$_} ) for $hmmer_tmp->get_line;
+
+  return $hmmer_jnet;
+}
+
 #####################################################################################################
 sub jnet {
   my ( $hmmer, $outfile, $pssm ) = @_;
@@ -972,7 +1195,7 @@ sub jnet {
     system("$jnet --concise --hmmer $hmmer > $outfile");
   }
   check( "jnet", $? ) or exit 1;
-  my $res = "";
+  my $res     = "";
   my $logging = "";
   open( my $IN, "<", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
   while (<$IN>) {
@@ -984,7 +1207,7 @@ sub jnet {
   }
   close $IN;
   open( my $OUT, ">", $outfile ) or die "ERROR! unable to open '$outfile': ${!}\nDied";
-  print $OUT "\n".$res;
+  print $OUT "\n" . $res;
   close $OUT;
   return $logging;
 }
@@ -1097,6 +1320,8 @@ sub fasta2psiseq_lowmemory {
   return @seqs;
 }
 
+#####################################################################################################
+
 =head1 extend($FASTA::File, @PSISEQ)
 
 Sometimes PSIBLAST truncates the outputed alignment where it can't matched residues 
@@ -1105,7 +1330,6 @@ present in the alignment. The other sequences are extended with gap characters.
 
 =cut
 
-#####################################################################################################
 sub extend {
   my ( $query, @seqs ) = @_;
 
@@ -1156,13 +1380,14 @@ sub extend {
   return @seqs;
 }
 
+#####################################################################################################
+
 =head1 $int = fasta_seq_length($path)
 
 Given the path to a FASTA database, find the number of residues/bases in it. Counts whitespace as a residue.
 
 =cut
 
-#####################################################################################################
 sub fasta_seq_length {
   my ($fn) = @_;
   open my $fh, $fn or croak "Can't open file $fn: $!\n";
@@ -1177,9 +1402,3 @@ sub fasta_seq_length {
 
   return $length;
 }
-
-=head1 log(@messages)
-
-Report messages to STDERR
-
-=cut
index 9fa5ca3..9a51953 100644 (file)
@@ -33,6 +33,8 @@ our @EXPORT_OK = qw(
   $hmmbuild
   $hmmconvert
   $psiblastbin
+  $alscript
+  $readseq
   check_OS
   setup_env
 );
@@ -58,6 +60,8 @@ our $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
 our $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
 our $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
 our $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
+our $alscript    = "$SOFTDIR/$platform_name/alscript";
+our $readseq     = "$SOFTDIR/$platform_name/readseq";
 
 # required for training with SNNS, but unused currently
 our $ff_bignet = "$HOME/projects/Jnet/bin/snns/ff_bignet";    # CC modified for new path (SNNS app)
@@ -87,6 +91,8 @@ sub setup_env {
   $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
   $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
   $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+  $alscript    = "$SOFTDIR/$platform_name/alscript";
+  $readseq     = "$SOFTDIR/$platform_name/readseq";
 }
 
 sub check_OS {
@@ -103,8 +109,6 @@ sub check_OS {
     warn "check_OS: unknown platform, I'll try to use x86_64 binaries....";
   }
 
-#  print "\n\ncheck_OS: SOFTDIR -> $SOFTDIR\n\n";
-
   $oc          = "$SOFTDIR/$platform_name/oc";
   $jnet        = "$SOFTDIR/$platform_name/jnet";
   $fastacmd    = "$SOFTDIR/$platform_name/fastacmd";
@@ -112,6 +116,8 @@ sub check_OS {
   $hmmbuild    = "$SOFTDIR/$platform_name/hmmbuild";
   $psiblastbin = "$SOFTDIR/$platform_name/blastpgp";
   $hmmconvert  = "$SOFTDIR/$platform_name/hmmconvert";
+  $alscript    = "$SOFTDIR/$platform_name/alscript";
+  $readseq     = "$SOFTDIR/$platform_name/readseq";
 
   return $platform_name;
 }
diff --git a/binaries/src/jpred/tests/alignment.clustal b/binaries/src/jpred/tests/alignment.clustal
new file mode 100644 (file)
index 0000000..509e0d8
--- /dev/null
@@ -0,0 +1,186 @@
+CLUSTAL W(1.60) multiple sequence alignment
+
+QUERY                MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLK
+UniRef90_C0EK60      MKKIEAIIKPFKLDDVREILTEIGITGMTVSEVKGFGRQKGHTEIYRGAEYAVDFLPKVK
+UniRef90_Q21P81      MKLITAVIKPFKLDDVRNALSEIGVQGMTVTEVKGFGRQKGHTELYRGAEYVIDFLPKVK
+UniRef90_Q47GI8      MKKIEAIIKPFKLDEVREALSEIGISGLTVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK
+UniRef90_B9ZJ79      MKKIEAIIKPFKLEDVREALTEMGIAGMTATEVQGFGRQKGHTELYRGAEYVVDFLPKVK
+UniRef90_B5FAN6      MKIINAIIKPFKLDDVREALADAGVDGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKVK
+UniRef90_B5ZIL8      MKKIEAIIKPFKLDEVKDALHEIGLMGISVTEAKGFGRQKGHTELYRGAEYIVDFLPKVK
+UniRef90_B4RVM6      MKKIEAIIKPFKMDDVREALAEVGIAGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKIK
+UniRef90_B2FHB8      MKLISAIIRPFKLDEVREALSDAGVSGITVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK
+UniRef90_P21193      MKKIEAIIKPFKLDEVKEALHEVGIKGITVTEAKGFGRQKGHTELYRGAEYVVDFLPKVK
+UniRef90_B5JS45      MKKIEAVIKPFKLDDVRDALADIGVSGMTVTEVKGFGRQKGHTETYRGAEYVVDFLPKLK
+UniRef90_Q07UM0      MKLVVAIIKPFKLDEVRQALTDVGVHGMTVTEVKGYGRQRGHTEIYRGAEYLVNFLPKLR
+UniRef90_Q2RVB4      MKFVIAITKPFKLDEVREALGALGIQGMTVTEVKGFGRQKGQTEVYRGAEYVVNFLPKVK
+UniRef90_A9IPV3      MKLIIAIIKPFKLDEVRVALSGIGVQGLTVTEVKGFGRQKGHTELYRGAEYAVDFLPKLR
+UniRef90_A4TZT2      MKLIIAIIKPFKLDEVREALTQLGIQGLTATEVKGFGRQKGQTEIYRAAEYVVSFVPKIK
+UniRef90_B3DVA4      --KIEAIIKPFKLEEVKEALTEIGIAGLTVTEVKGFGRQKGHTEIYRGSEYTVDFLPKVK
+UniRef90_C1STD4      MRKIEIITRPFKLDEVKQRLTKLGIQGMTVTEVKGFGRQRGHKEIYRGAEYQVDFVAKVK
+UniRef90_A7HGG9      MKRIEAIIRPSKLEDVRRLLSHPWISAMTVSEVRGAGRQKGHAELYRGAEYVIDLIPKLK
+UniRef90_A9BCF1      MKKIEAIIRPFKLEDVKVALVNSGIVGMTVSEVRGFGRQKGQVERYRGSEFTVEFLQKLK
+UniRef90_B4U911      MKKVEAIIKPFKLDEVKDALVEIGIGGMTITEVKGFGQQKGKTEIYRATEYVIDFLPKIK
+UniRef90_B1ZSX2      MKLVTAIIKPFKLEEIKAALAEIQVEGMTVTEVKGFGRQKGHTEIYRGTEYTVDFLPKVR
+UniRef90_Q7X1L4      MKKVEAIIKPFKLDAVKEAVTALGVYGMTVTEVKGYGQQKGHTEQYRGAEYVVEFITKIK
+UniRef90_Q1NW36      MKKVEAIIKPFKLDAVKEAVTALGIHGMTVSEVKGFGRQKGHTEVYRGAEYVVDFVAKIK
+UniRef90_C0GRX0      MKKLEIITRPFKVEAVKEALAGMGIKGMTLTDVKGFGRQMGHKEIYRGAEYDVDFLPKVK
+UniRef90_B8DJ84      MKKIEAIIKPFKLDAVKDALIGIGVFGLTVTEVRGYGRQRGHVETYRGLEYEVQFNSKLK
+UniRef90_Q6ARG9      MKKIEAIIKPFKLEEIKEALTELAITGMTISEVKGYGRQKGHKEMYRGAEYSIDFNPKLK
+UniRef90_C1W154      MKLVTAIIQPHRLDAVKSALEAAGIRGMTVSEASGYGRQKGHTEVYRGAEYTIDLVPKIR
+UniRef90_C1UII8      MKLVTAIVKPFKLDDVKNALELIGIAGLTVSEVQGFGRQRGHTEVYRGAEYQVDFVPKVR
+UniRef90_UPI000      --KVTVITNQAKFYQLKTSLEAIGITGMTVIQVLGFGIQKGQPEYYRGNPIEATLLPKVK
+UniRef90_C1T022      MKLVIAYIRPECLNAVKQELYAKKIYNMSVTNVLGSGRQKGFTETYRGVVMEVNLLKKLR
+UniRef90_Q46G48      MKYIIAMIRPERLDAVKRELQKLEVNRLTVSSVAGYGAQKGHLEIYRATEHEANLLEKVK
+UniRef90_A2RJQ2      MKKIEAIIRTDKLEDLKKALSDNGVHGMTVSQVLGYGEQKGFAEYVRGQRIETTLLSKIK
+UniRef90_Q8KF33      MKKIEAIIRTSQYEAVKKALHEIDIDFFTWWDVTGQGNDKKHTEIYRGTVRDTSYISRRY
+UniRef90_B1HTS9      MKKIEVIIRPEVFGAVRDGLAQQGIAGLSVSEIAGCGRQLGRTGLFRGNTYEIEFLPKLK
+UniRef90_A2SPS9      MKMITAIIRPEKVDEVLNALEQNNIPGVTITEVLGRGEQGGVCLQYRAGKMQVKTLPKTK
+UniRef90_C0EAH3      --KLVIVTRQSKFEELKAAMNAIEVTGMTVTQVIGCGTQKGATEFYRGVPVEMNLLPKIK
+UniRef90_A7I8Z1      --MISAIIKPERFEFVKKALEDKGYVSMTITEVKGRGEQKGISLEYRGGKMTVDLLPKVK
+UniRef90_Q3AFZ0      MKKIEALIRPQKLGEVKEALNKLGISGMTVTEVVGCGRQKGQKEIYRGIEYEINLLPKVK
+UniRef90_A7I508      MKLVIALIRPERFGAVKKALEDKGYIGMTTAEAKGRGAQKGIALVYRGGRLTIDILVKVR
+UniRef90_P51604      MKEIIAIIRPNKINRTKEVLDALGFSSMTANAVFGRGRQKAIVGELREEEGSMRYIPKRM
+UniRef90_B0NXT3      --KINAIVREEKFEDVKEALNKIGVNGITVSQVMGCGAQKGFTEVIRGTKVDMMMRPKIK
+UniRef90_A8YG01      ----------------KIALVNAGIVGMTVSEVRGFGRQKGQSERYRGSEYTVEFLQKLK
+UniRef90_C0BMJ9      MKKVEAIIRKSKFDDVKKALHAIEVNFFSYWDVTGVGNEKQ-GHVYRGISYSTSDIQRRI
+UniRef90_Q466Y2      MCKIEAIIKPMKLHEVKDALEEAGYPSLTVTDVKGRGQQKGIVQQWRGKKYCVDLLPKTK
+UniRef90_O26760      MKEIVAIIRPEKLEEVKNALEAAGCHGMTVTEVRGRGRQLGITESYRGRDYRIDLLPKTK
+UniRef90_A0LYN2      MKKIEAIIRKSEFDETKEALHSIGVTFFSYWDVTGVGNEKV-GHVYRGVSYSTADIQRRY
+UniRef90_C1YA75      MKVVTAVIKPFKLDEVRAALLAFGVQGMTVSESSGYGRQRGHTEVYRGAEYTVELLPKVR
+UniRef90_A8KX44      MKLVTAIVRPHRVDDVRAALTTYGVHGITVSQVTGFGLEMWRTQTYRGNAFHDESTSNIR
+UniRef90_C0EZB6      --KLTIMCKEDRFAILKDAMSQIGVTGMTVSHVMGCGTQKGKTGQYRGVKIDMNLLPQLQ
+UniRef90_Q11P32      MKKIEAIVKPSKLKAIQAGLIKIGIPCMTVVPVKGVGLQQGFPEIYRGTEKSIVLLSKVM
+UniRef90_A7B6Y7      --KIEAIVREEKFEQVKSALQDIQVNGVTISQVMGYGTQRGYTEIVRGSEVDILLHPKIK
+UniRef90_A7VSI5      --KVVILFNQDKFIELKDAMNAIGVTGMTVIHVMGCGVQKGNTRYYRGVKLDIVLLPKIK
+UniRef90_A6G036      --KVEAMIRPFKLDDVKERLTELEVGGMTVTEVKGFGRTGGKTEFYRGSAYVIDFVPKIK
+UniRef90_C0ES36      MIKVEAYVREDKFEDVKAALNAIGVNGLTVSQVMGCGIQRGYKEIVRGMQVDMQMQPKIK
+UniRef90_B5IHX8      MKQIQAIVRPEKLDAVKDALVEIGINGITVTAVQGFGKQMGHTEVYRGVKVEAKLLTKMQ
+UniRef90_B0MIE7      ---------PEKLTDVKHILEAHKVSGLMISNIMGYGNQKGFTQKYRGNELNSNLLPKIK
+UniRef90_B4S395      MKLITAIIQEDKLDQVREALIQANISRISVSRISGHGRQE-DIDIYRGRKIAPNLRPKIK
+UniRef90_P51254      MKKIEAIIRPFKLNEVKLALVKGGIGGMTVVKVSGFGRQKGQTERYKGSEYSIDIIDKIK
+UniRef90_P71524      MKMIRAVVRPSKAEEVVDALAESGCVALTKMDVIGRGKQKG----IKIDQIYYDELPKTM
+UniRef90_A8JI83      ---IEAIFRPWRLPFVIDTLSKYGIRGLTNTPVKGVGVQGGSRERYAGTEFGPNLVDKEK
+UniRef90_B0CD03      MRTITAFIRPQQCDQVKLVLVQLGIIDITLSDVKGFGRQQGSLQQYRGSDAEIRLHRKLK
+UniRef90_B1QY06      MKRIEAIIRPSKLEEIKEALKNNNINGVTISQVMGCGKQLGWKEYHRGTELITNVLPKIE
+UniRef90_Q30VL0      MKLLIAYIRPEKLSTVKKALYARGIYAMSVTNALGSGQQKGFTETYRGIVTEVNLLKKVR
+UniRef90_A0T2Q5      MKEVLAIIRPNMVSKTGKALEAVGFPAMTVIRCFGRGKEKGYIDAGEKLGMRMKYIPKRM
+UniRef90_B3QXW9      MKEITAIIRINKMNETKKALIKAGISSFTASRVLGRGKGQVHYDLLKGAAEGYELVSKRY
+UniRef90_B6YRQ4      MKKIEAIIRKTRFDEVKEALLEADIEWFSYSDVRGVGKARQ-ERIYRGVVYDTSSIERIQ
+UniRef90_B0MJN0      MTKVDIIANQEKFEVLKHALSSIGITGMTVSHVMGCGMQKGSTEFYRGVPVDARLLPKMK
+UniRef90_C2C1T3      --KIEIITRPNRFDVFQKALKEIGVSGLTVTKAVGTGLEKGMIELYRGTIKENNVHERMK
+UniRef90_C1VTA2      --LVMAIVRPEKLSDVKAALAEAGAPSLTVTQVSGRGSQPAKTGQWRGEEYVIDLHQKIK
+UniRef90_A3XNG5      MKKIEAIIRKSKFTAVKKALHDKGVNFFSYWDVTGLGNEKE-GHVYRGVSYSTSDIQRRY
+UniRef90_P71525      MKEIIAIIRPSKMAQTKTVLEGLGFPAMTANRVLGRGKQKAIVGELGFEV-DMRYIPKTM
+UniRef90_Q46C91      MKEIIAIIRPKKVVPTKEALEKLGVPSLTAIPVFGRGKQKGIATELDIAGRRMEYIPKRL
+UniRef90_B7BWA8      MKEVMIILRPKMYFPTKDALDQAGFHSMTIREIIGRGKCPVHYDYDEGAPVKHRLVAKRM
+UniRef90_Q7UGU6      MKLIIAIVQPSKLDAIKEALTRVEVHRLTVVDCQGFGRQRGQTGSMRGRDYGVSLLRKVQ
+UniRef90_A3HVG6      MKKIEAIIRTSRFEQIHSCVAGLGVKFLTFYEVKGMGLEHAKQQTYRGVAYEPTYIPRTK
+UniRef90_A0YMH7      MKRIEALIRPVQFDSVVTALVEAGIVGMSVTNVRGYGRQKGQTESYRGVKHVIEFHPKMK
+UniRef90_Q46A23      MKYIIAMIRPEKLDSVKKEIQKIGAHGLTVSSISGYGAQGGHLNVDRTKKYEANLLDKVK
+UniRef90_B4VJP7      ----------------MKALLDAGYPAVTKVDVFGRGKQRG----LKIGNVLYDELPKAL
+UniRef90_B1QUW3      MYLVRAIIRTEKVNGVLSELVDAGFPQVTKMDVFGRGKQKG----IQVGEVHYDELPKEM
+UniRef90_A5N1U1      MKEIMAVIRMNMVGKTKKALAENGFPSITCKDVLGRGKKMVEEELHRIEDESYRLISKRL
+UniRef90_A9D1T1      -----------------------------------------------GAEYMVDFLPKVK
+UniRef90_A6LUZ0      MYMIRAIIRPERVSTVLSELLDAGFPEVTKMAVYGRGKQKG----IKVGEVYYDELPKEM
+UniRef90_A6LUZ1      MKEVMCIIRLNKVNKTKEALAEAGFPSITCRKVLGRGKKSALVEAYMETGEVPRLIPKRF
+UniRef90_B8GEW5      MKEIMAIVRMKKTGVTKRALVETGVAGFTALKVLGRGKLVEDTAVIEPAEQEVRFFPRRL
+UniRef90_C1FI34      --QVRAMVRPWRLSGVIDALNKYGIRGLTTYTVHGAGVQIGTVERYAGSTFDANLVEKVV
+UniRef90_C1TA34      MKEIIAIIRMNKVNITKKALADVGVCGLHAIKVMGRGKQLGVREEIDGLSGGTRLIPKRL
+UniRef90_C1T440      MKEVIAVIRMNMMNKTKKALQDAGVVAFFAHEAFGRGKGLVDVKPLEGARKGIELYPKRM
+UniRef90_A9A2H4      MKKVEAIVNESAQNAVIDAMRKVGISGVTVSKVQGQGAQD--------PPLVGDFFSRVL
+UniRef90_Q97ME3      MKEIMAIIRMNMVEKTKEALLKGGNPAITCLKVLGRGRQKVDIEDYKMAEELSELISKRL
+
+QUERY                LEIVVEDAQVDTVIDKIVAAARTGENGDGKIFVSPVDQTIRIRTGEKNADAISAWS
+UniRef90_C0EK60      IELVLADDKVDQAVDAILETAHSGKIGDGKIFIYPVEEAIRIRTGERSEAAL----
+UniRef90_Q21P81      LELVLGDELIDQAVEAISKAAQTGKIGDGKIFITPCEEVIRIRTGETGPEAV----
+UniRef90_Q47GI8      IEIVVNSNNVEPAIDAIIKAARTGKIGDGKIFVMPVEQVVRIRTGETDEAAV----
+UniRef90_B9ZJ79      LELVVDDDRVDACIDAIVKASRTGKIGDGKIFVSDMARVVRIRTGEEGSEAL----
+UniRef90_B5FAN6      LEIAVQAEGVDRIVEAISKAAHTGKIGDGKIFVYDLQQAVRIRTGETDTEAL----
+UniRef90_B5ZIL8      LEIVCADNLVDRAVETIMAAARTGRIGDGKIFILPVEDVIRIRTGEHGEEAI----
+UniRef90_B4RVM6      IELVLDDDRVEQAVEAIQSSAKTGKIGDGKIFVYSVESAVRIRTGEQNEDAI----
+UniRef90_B2FHB8      IETVVTDERADAVIEAIQSSAGTGKIGDGKIFVTAVEQVIRIRTGEIGADAL----
+UniRef90_P21193      IEVVMEDSLVERAIEAIQQAAHTGRIGDGKIFVTPVEEVVRIRTGEKGGDAI----
+UniRef90_B5JS45      LEIVVAEKDADACVESITNAAKTGQIGDGKIFVSDVERTIRIRTGEEDESAI----
+UniRef90_Q07UM0      IEVGVADTLVDKAVEAITRSARTGQIGDGKIFVTPLDHALRIRTGETNADAL----
+UniRef90_Q2RVB4      IELAVPDNLLDQVVETIQSTAQTGKIGDGKIFVFDLGEAVRIRTGERGEEAL----
+UniRef90_A9IPV3      VEAAVPDHLVDQVIDVIEQAARTGKIGDGKIFTAPLEQVIRIRTGESGEAAL----
+UniRef90_A4TZT2      IELVVNDDVVDRAVEAIQAAARTDKIGDGKIFVMDVAHALRIRTGEADTEAL----
+UniRef90_B3DVA4      VEIVLTEDILPKAVEAIIKSAKTGKIGDGKIFVLPVSEAIRIRTEEKGENAI----
+UniRef90_C1STD4      IEIVVDDGLVEEIVSTVQEGARTGKVGDGKIFISPVDNAVRIRTGESGAEAL----
+UniRef90_A7HGG9      LEIVLPDPLVDRVVADLESWLRTGRIGDGKIFVEPLDDAVRVRTGERGEDAL----
+UniRef90_A9BCF1      IEIVVADESVPTVLTAIAEAAKTGEIGDGKIFISPVESVVRIRTGELDGSAL----
+UniRef90_B4U911      IETVVKDSEVEKVVQTILKSAQTGKVGDGKIFIYNVEETVRIRTGERGESAI----
+UniRef90_B1ZSX2      IEILAADESVPKILETIISTAKTGKIGDGKIFISAAEDVVRIRTDERGEAAL----
+UniRef90_Q7X1L4      VEIVVADAKVSPVLEAIRRTAMSNSIGDGKVFVSPVETALRIRTGETGDAAL----
+UniRef90_Q1NW36      VEIVVESEKASLLVETITQAARNGNIGDGKIFVTPVESVCRIRTGELDQDAI----
+UniRef90_C0GRX0      IEVILDDANVDQAVEAAIKAARTDKVGDGKIFVYSVENAIRIRTGESGDEAI----
+UniRef90_B8DJ84      IETVVPDGMSDQVVKAITTAARTGSIGDGKIFISSLEEVIRIRTGEEGTDAI----
+UniRef90_Q6ARG9      IELVVRAEIADKVVEKIRLAARTGKIGDGKIFVLPIEEVVRVRTGEQGREAI----
+UniRef90_C1W154      LEILVDDPDAHRVGEVITQAAHTGRIGDGKVWTIPVDSVTRVRTGEEGPSAL----
+UniRef90_C1UII8      IEVVVGEIEAARVVDAIVEAASTGQIGDGKVWVTTIDEIVRVRTGERGADAL----
+UniRef90_UPI000      MKKIEAIIRPEAFQTLKDGLSAVGISGLTVTEAAGCGKQQGKKGVFRGTSFEIQLVPRVK
+UniRef90_C1T022      LEIGVNDDFAEQAVEAINAGARTGKEGDGVIFVLECAAAVRIRTQETGPAAMG---
+UniRef90_Q46G48      IEIAVEDHFLKSVIEAIKTGAKDGYIGSGKIFVLPLENVIRIRTNETGPEAL----
+UniRef90_A2RJQ2      IEIVSIDEKVDQIVNVITKAVRTGEVGDGKIFIQPVERVIRIRTSEEDAQAL----
+UniRef90_Q8KF33      LSIVVRDVNLQKTVDCLIKNARTGEVGDGKIFVSDIEQSYRIRTGESGDESL----
+UniRef90_B1HTS9      LEMIVDDSKVDGIVEILLREAATGKVGDGKIFIYPVEQAIRIRTKEVGSIAV----
+UniRef90_A2SPS9      LEIVVPDKDVDTLIKVIREHARTGKKGDGRIFVLPVEAAAWVRTDE----------
+UniRef90_C0EAH3      VEIVVCRVPVRTVIETAKKVLYTGHYGDGKIFVYDIENVVKVRTGEEGCAALQ---
+UniRef90_A7I8Z1      IEIVIRDKDLEDVIATLTGAARTGKIGDGKIFVIPVEKSIRIRTGD----------
+UniRef90_Q3AFZ0      IEIVTVDEKVEEIIKIISESARTGAIGDGKIFISEVLDAVRIRTGERGTAAITS--
+UniRef90_A7I508      IEIVSHDRDVEDLVSTIRESAWTGANGDGRIFVLPVEQAIRIRTGE----------
+UniRef90_P51604      ISLVVPDEDASLVVESIMKVNKTGQIGDGKIFVCPIEDAVRVRTKESGEDAI----
+UniRef90_B0NXT3      FEIVVSSEEWERTIEAIQKSAFTGEVGDGKIFSYEVRNVVKIRTGERDVDALQD--
+UniRef90_A8YG01      IEIVVEDKQVDMVVDKLISAARTGEIGDGKIFISPVEQIVRIRTGEKDLQAI----
+UniRef90_C0BMJ9      LSIVISDEFLEPTINAILEAACTGNVGDGKIFVSDVQDAYRIRTRENGKAGIN---
+UniRef90_Q466Y2      IEIAAPEDKIEEIIKIIQSSAYTGEIGDGKIFVTPIETVVRIRTGERNGDAL----
+UniRef90_O26760      IEIVVNDEDVDTVVETIVKSAQTGDIGDGKIFISGVDEVVRIRTGESGKKAV----
+UniRef90_A0LYN2      LSIVVTDSFVEKTVETLLKAAHTGKVGDGKIFILPVEEAYRIRTKEKGGESL----
+UniRef90_C1YA75      VEILVDDEDAEDVVDVIVRAARTGKIGDGKVWTQPVETVIRVRTGERGPEAL----
+UniRef90_A8KX44      LELVVADSDAPDVVNVIRRTAASTSSGAGKIWVLPVEGLARIRTGERGADAL----
+UniRef90_C0EZB6      VDIVVSTVPPELVVEAAKKALYTGEYGDGKIFLYDVENVVRIRTNETGIAAL----
+UniRef90_Q11P32      IICVVSDENLEKCIDVIIETGSEGKVGDGKIFVYDVLDAIRMRTRTRGDDAI----
+UniRef90_A7B6Y7      FEVVVSSEEWEQTISAIQKAAFTGEVGDGKIFSYEIRSAVKIRTKETGYNAVQS--
+UniRef90_A7VSI5      LEIVVSKVPVQTV-DTARKVLYTGNIGDGKIFIYDVENVIKVRTGAEGYYALQD--
+UniRef90_A6G036      IEVVVPAARSEEVIAAIREVAASDRIGDGKIFVTPVLEAVRIRTDERGESAL----
+UniRef90_C0ES36      FEIVVSSEEWEKTIEAIEKAAYTGEPGDGKIFTYEIRHAQKIRTKETGYDAIQAT-
+UniRef90_B5IHX8      ITSVVTDQAVDQVVQAILTAARTGEIGDGKIVITPVENAIRIRTGESGDSTLA---
+UniRef90_B0MIE7      VESVMPEEVVEKVTKDIVNTVRTGEFGDGKIFISPVEEAIRIRTGETGKDAL----
+UniRef90_B4S395      LEIAVNEEFVDVAIDTIVDSARSGEIGDGKIFVTPLEQCVRIRTNERGGSAI----
+UniRef90_P51254      IEIIVSDDKVNSITEIIIKTAKTGEIGDGKIFISDVEQVIRIRTNDLNSAAL----
+UniRef90_P71524      LMLVVEDDAAENVIELITKTAYTGSFGDGKIFVSPVDEAYTVRTRSCG--------
+UniRef90_A8JI83      LDIVVSRAQVDAVVRLVAASAYTGEIGDGKIFVHPVAEVVRIRTAETG--------
+UniRef90_B0CD03      VEVKVDEEMVAPVVEKITFAARTGQVGDGKIFVSPLQKVVQVRTGEE---------
+UniRef90_B1QY06      VKMVIEDSKVEEVIEIISSIAKTGEVGDGKIFVIDICDCVRIRTGERGNEAL----
+UniRef90_Q30VL0      IEVGVPADKAEDALAALQTGAHTGREGDGIIFVQDVARTVRVRTGE----------
+UniRef90_A0T2Q5      ISIVVDDADVPFVVGIIMKVNRTGKPGDGKIFVLPVEEAIRIRTGEFGVEAIG---
+UniRef90_B3QXW9      LVVVVNDNMLQPTIDAIISANQTGKPGDGKIFVSTIEDAVRVRTGETGSAIL----
+UniRef90_B6YRQ4      INLVVRDINVEKAIKAIEKSAHTGEVGDGRIFVSTIDNAYSIRTGEQGDETL----
+UniRef90_B0MJN0      VEIVVCKVPVEKVVEVAKNALYTGKIGDGKIFVYDVENVIKVRTGEEAYEALQD--
+UniRef90_C2C1T3      VEIVVSTVPVEAVLEVVKNTLRTGEPGDGKVFVYPLSDVIKISTGEHGVAALQD--
+UniRef90_C1VTA2      VECVVEPEDADDVVEAIREGANTGEKGDGKIFVLPVFDAVQVRTGDRGTDAI----
+UniRef90_A3XNG5      LSIVVNDDFEQAAVAAILDAAATGEVGDGKIFVSDVQDAYRIRTGKKGPDTLN---
+UniRef90_P71525      LTLIVPDEDASLVVEAIMKVNKSGQYGDGKIFVCPIEDIITVRTSERGEAAI----
+UniRef90_Q46C91      FSIVTRNEDVDTIIETIMKVNQTGDIGDGRIFICPVDDAIRVRTDEHGDNAL----
+UniRef90_B7BWA8      IDMFVRDEDLQKLIDTVVEVNKTNHAGDGKIFVLPVNDAIRVRTGEKGIEAI----
+UniRef90_Q7UGU6      LQIGVNEEFVQPTIDAIGRSGESGEIGDGKIFVLPMDDCVRIRTGERGGEAI----
+UniRef90_A3HVG6      LEIVTVDELVEPVINCILTEGKTGEVGDGKIFVYDVLEAHRIRNNDQGEQAL----
+UniRef90_A0YMH7      LEIVVEDEVCEFVVEKLVEAAQTGQIGDGKIFIQSMEHIIRTRTGESDLEAL----
+UniRef90_Q46A23      IEIAVKDEFLQTTVEAIERGSKDGYIGSGKIFVLPLENVMRIRTKETGNDAL----
+UniRef90_B4VJP7      LMVVVPDTEKEFVIRAILSSARTGAEGDGKIFVSPVEEVYTISSGKTDSS------
+UniRef90_B1QUW3      LLIVVKDEDKDDVVRVIMKNSRTGEYGDGKIFISKVDTAYTISTGKE---------
+UniRef90_A5N1U1      IWILAKDEDVKKIADIIIDINQTGHPGDGKIFVTKVTDVVRIRTGETQDEAV----
+UniRef90_A9D1T1      IELVIQDELLDRAIEVIVDTARTGKIGDGKIFVTEIERVIRIRTGEENEEAV----
+UniRef90_A6LUZ0      LLIAVKDEDKDDVIKVIIRNSRTGEFGDGKIFVAPIEEVYTVSSGKSG--------
+UniRef90_A6LUZ1      ITLVVKDDEVKTVVDTVISVNSTGTPGDGKIFVLPVEEVYRVRDGQIGEEAI----
+UniRef90_B8GEW5      FTILAHDEDVPRIVEAITKVNITEKVGDGIILVLPVDDAVRVRTGESGDAAI----
+UniRef90_C1FI34      VEIVVVREQCQEVVDVIVDAAQTGEIGDGKIFLSPVHDIVRIRTGEVGAAA-----
+UniRef90_C1TA34      LTILARDEDVKKIVDTVIKVNQEGNKGDGRIFIAPVIDAYRVRTAEKGEAAV----
+UniRef90_C1T440      LTVVVTDDLVPEVVKVITDTNKTGQPGDGKIFVLPMIDAVRVRTGEKGAKSI----
+UniRef90_A9A2H4      IVCVVDDPKLDEILDAIAGAACTGTKGDGKVYVSDICDALDICTKKRG--------
+UniRef90_Q97ME3      IIILAKDEDVKEIVDEIIEVNRTGNPGDGKIFVINIADAMRIRTEETGDMAI----
+
+QUERY                UniRef90_C0EK60      UniRef90_Q21P81      UniRef90_Q47GI8      UniRef90_B9ZJ79      UniRef90_B5FAN6      UniRef90_B5ZIL8      UniRef90_B4RVM6      UniRef90_B2FHB8      UniRef90_P21193      UniRef90_B5JS45      UniRef90_Q07UM0      UniRef90_Q2RVB4      UniRef90_A9IPV3      UniRef90_A4TZT2      UniRef90_B3DVA4      UniRef90_C1STD4      UniRef90_A7HGG9      UniRef90_A9BCF1      UniRef90_B4U911      UniRef90_B1ZSX2      UniRef90_Q7X1L4      UniRef90_Q1NW36      UniRef90_C0GRX0      UniRef90_B8DJ84      UniRef90_Q6ARG9      UniRef90_C1W154      UniRef90_C1UII8      UniRef90_UPI000      IEIVVCKIPTETVVATIKTALYTGHIGDGKIFVHAVENVHRISTGEEGYDALQD--VEMV
+UniRef90_C1T022      UniRef90_Q46G48      UniRef90_A2RJQ2      UniRef90_Q8KF33      UniRef90_B1HTS9      UniRef90_A2SPS9      UniRef90_C0EAH3      UniRef90_A7I8Z1      UniRef90_Q3AFZ0      UniRef90_A7I508      UniRef90_P51604      UniRef90_B0NXT3      UniRef90_A8YG01      UniRef90_C0BMJ9      UniRef90_Q466Y2      UniRef90_O26760      UniRef90_A0LYN2      UniRef90_C1YA75      UniRef90_A8KX44      UniRef90_C0EZB6      UniRef90_Q11P32      UniRef90_A7B6Y7      UniRef90_A7VSI5      UniRef90_A6G036      UniRef90_C0ES36      UniRef90_B5IHX8      UniRef90_B0MIE7      UniRef90_B4S395      UniRef90_P51254      UniRef90_P71524      UniRef90_A8JI83      UniRef90_B0CD03      UniRef90_B1QY06      UniRef90_Q30VL0      UniRef90_A0T2Q5      UniRef90_B3QXW9      UniRef90_B6YRQ4      UniRef90_B0MJN0      UniRef90_C2C1T3      UniRef90_C1VTA2      UniRef90_A3XNG5      UniRef90_P71525      UniRef90_Q46C91      UniRef90_B7BWA8      UniRef90_Q7UGU6      UniRef90_A3HVG6      UniRef90_A0YMH7      UniRef90_Q46A23      UniRef90_B4VJP7      UniRef90_B1QUW3      UniRef90_A5N1U1      UniRef90_A9D1T1      UniRef90_A6LUZ0      UniRef90_A6LUZ1      UniRef90_B8GEW5      UniRef90_C1FI34      UniRef90_C1TA34      UniRef90_C1T440      UniRef90_A9A2H4      UniRef90_Q97ME3      
+QUERY                UniRef90_C0EK60      UniRef90_Q21P81      UniRef90_Q47GI8      UniRef90_B9ZJ79      UniRef90_B5FAN6      UniRef90_B5ZIL8      UniRef90_B4RVM6      UniRef90_B2FHB8      UniRef90_P21193      UniRef90_B5JS45      UniRef90_Q07UM0      UniRef90_Q2RVB4      UniRef90_A9IPV3      UniRef90_A4TZT2      UniRef90_B3DVA4      UniRef90_C1STD4      UniRef90_A7HGG9      UniRef90_A9BCF1      UniRef90_B4U911      UniRef90_B1ZSX2      UniRef90_Q7X1L4      UniRef90_Q1NW36      UniRef90_C0GRX0      UniRef90_B8DJ84      UniRef90_Q6ARG9      UniRef90_C1W154      UniRef90_C1UII8      UniRef90_UPI000      IEESRLDEIVDVIIDSCSTDTIGDGK--------------------------
+UniRef90_C1T022      UniRef90_Q46G48      UniRef90_A2RJQ2      UniRef90_Q8KF33      UniRef90_B1HTS9      UniRef90_A2SPS9      UniRef90_C0EAH3      UniRef90_A7I8Z1      UniRef90_Q3AFZ0      UniRef90_A7I508      UniRef90_P51604      UniRef90_B0NXT3      UniRef90_A8YG01      UniRef90_C0BMJ9      UniRef90_Q466Y2      UniRef90_O26760      UniRef90_A0LYN2      UniRef90_C1YA75      UniRef90_A8KX44      UniRef90_C0EZB6      UniRef90_Q11P32      UniRef90_A7B6Y7      UniRef90_A7VSI5      UniRef90_A6G036      UniRef90_C0ES36      UniRef90_B5IHX8      UniRef90_B0MIE7      UniRef90_B4S395      UniRef90_P51254      UniRef90_P71524      UniRef90_A8JI83      UniRef90_B0CD03      UniRef90_B1QY06      UniRef90_Q30VL0      UniRef90_A0T2Q5      UniRef90_B3QXW9      UniRef90_B6YRQ4      UniRef90_B0MJN0      UniRef90_C2C1T3      UniRef90_C1VTA2      UniRef90_A3XNG5      UniRef90_P71525      UniRef90_Q46C91      UniRef90_B7BWA8      UniRef90_Q7UGU6      UniRef90_A3HVG6      UniRef90_A0YMH7      UniRef90_Q46A23      UniRef90_B4VJP7      UniRef90_B1QUW3      UniRef90_A5N1U1      UniRef90_A9D1T1      UniRef90_A6LUZ0      UniRef90_A6LUZ1      UniRef90_B8GEW5      UniRef90_C1FI34      UniRef90_C1TA34      UniRef90_C1T440      UniRef90_A9A2H4      UniRef90_Q97ME3      
diff --git a/binaries/src/jpred/tests/alignment.fasta b/binaries/src/jpred/tests/alignment.fasta
new file mode 100644 (file)
index 0000000..aa2b047
--- /dev/null
@@ -0,0 +1,267 @@
+>QUERY/1-116
+MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLK
+LEIVVEDAQVDTVIDKIVAAARTGENGDGKIFVSPVDQTIRIRTGEKNADAISAWS
+>UniRef90_C0EK60/1-112
+MKKIEAIIKPFKLDDVREILTEIGITGMTVSEVKGFGRQKGHTEIYRGAEYAVDFLPKVK
+IELVLADDKVDQAVDAILETAHSGKIGDGKIFIYPVEEAIRIRTGERSEAAL----
+>UniRef90_Q21P81/1-112
+MKLITAVIKPFKLDDVRNALSEIGVQGMTVTEVKGFGRQKGHTELYRGAEYVIDFLPKVK
+LELVLGDELIDQAVEAISKAAQTGKIGDGKIFITPCEEVIRIRTGETGPEAV----
+>UniRef90_Q47GI8/1-112
+MKKIEAIIKPFKLDEVREALSEIGISGLTVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK
+IEIVVNSNNVEPAIDAIIKAARTGKIGDGKIFVMPVEQVVRIRTGETDEAAV----
+>UniRef90_B9ZJ79/1-112
+MKKIEAIIKPFKLEDVREALTEMGIAGMTATEVQGFGRQKGHTELYRGAEYVVDFLPKVK
+LELVVDDDRVDACIDAIVKASRTGKIGDGKIFVSDMARVVRIRTGEEGSEAL----
+>UniRef90_B5FAN6/1-112
+MKIINAIIKPFKLDDVREALADAGVDGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKVK
+LEIAVQAEGVDRIVEAISKAAHTGKIGDGKIFVYDLQQAVRIRTGETDTEAL----
+>UniRef90_B5ZIL8/1-112
+MKKIEAIIKPFKLDEVKDALHEIGLMGISVTEAKGFGRQKGHTELYRGAEYIVDFLPKVK
+LEIVCADNLVDRAVETIMAAARTGRIGDGKIFILPVEDVIRIRTGEHGEEAI----
+>UniRef90_B4RVM6/1-112
+MKKIEAIIKPFKMDDVREALAEVGIAGMTVSEVKGFGRQKGHTELYRGAEYQVDFLPKIK
+IELVLDDDRVEQAVEAIQSSAKTGKIGDGKIFVYSVESAVRIRTGEQNEDAI----
+>UniRef90_B2FHB8/1-112
+MKLISAIIRPFKLDEVREALSDAGVSGITVTEVKGFGRQKGHTELYRGAEYVVDFLPKIK
+IETVVTDERADAVIEAIQSSAGTGKIGDGKIFVTAVEQVIRIRTGEIGADAL----
+>UniRef90_P21193/1-112
+MKKIEAIIKPFKLDEVKEALHEVGIKGITVTEAKGFGRQKGHTELYRGAEYVVDFLPKVK
+IEVVMEDSLVERAIEAIQQAAHTGRIGDGKIFVTPVEEVVRIRTGEKGGDAI----
+>UniRef90_B5JS45/1-112
+MKKIEAVIKPFKLDDVRDALADIGVSGMTVTEVKGFGRQKGHTETYRGAEYVVDFLPKLK
+LEIVVAEKDADACVESITNAAKTGQIGDGKIFVSDVERTIRIRTGEEDESAI----
+>UniRef90_Q07UM0/1-112
+MKLVVAIIKPFKLDEVRQALTDVGVHGMTVTEVKGYGRQRGHTEIYRGAEYLVNFLPKLR
+IEVGVADTLVDKAVEAITRSARTGQIGDGKIFVTPLDHALRIRTGETNADAL----
+>UniRef90_Q2RVB4/1-112
+MKFVIAITKPFKLDEVREALGALGIQGMTVTEVKGFGRQKGQTEVYRGAEYVVNFLPKVK
+IELAVPDNLLDQVVETIQSTAQTGKIGDGKIFVFDLGEAVRIRTGERGEEAL----
+>UniRef90_A9IPV3/1-112
+MKLIIAIIKPFKLDEVRVALSGIGVQGLTVTEVKGFGRQKGHTELYRGAEYAVDFLPKLR
+VEAAVPDHLVDQVIDVIEQAARTGKIGDGKIFTAPLEQVIRIRTGESGEAAL----
+>UniRef90_A4TZT2/1-112
+MKLIIAIIKPFKLDEVREALTQLGIQGLTATEVKGFGRQKGQTEIYRAAEYVVSFVPKIK
+IELVVNDDVVDRAVEAIQAAARTDKIGDGKIFVMDVAHALRIRTGEADTEAL----
+>UniRef90_B3DVA4/1-110
+--KIEAIIKPFKLEEVKEALTEIGIAGLTVTEVKGFGRQKGHTEIYRGSEYTVDFLPKVK
+VEIVLTEDILPKAVEAIIKSAKTGKIGDGKIFVLPVSEAIRIRTEEKGENAI----
+>UniRef90_C1STD4/1-112
+MRKIEIITRPFKLDEVKQRLTKLGIQGMTVTEVKGFGRQRGHKEIYRGAEYQVDFVAKVK
+IEIVVDDGLVEEIVSTVQEGARTGKVGDGKIFISPVDNAVRIRTGESGAEAL----
+>UniRef90_A7HGG9/1-112
+MKRIEAIIRPSKLEDVRRLLSHPWISAMTVSEVRGAGRQKGHAELYRGAEYVIDLIPKLK
+LEIVLPDPLVDRVVADLESWLRTGRIGDGKIFVEPLDDAVRVRTGERGEDAL----
+>UniRef90_A9BCF1/1-112
+MKKIEAIIRPFKLEDVKVALVNSGIVGMTVSEVRGFGRQKGQVERYRGSEFTVEFLQKLK
+IEIVVADESVPTVLTAIAEAAKTGEIGDGKIFISPVESVVRIRTGELDGSAL----
+>UniRef90_B4U911/1-112
+MKKVEAIIKPFKLDEVKDALVEIGIGGMTITEVKGFGQQKGKTEIYRATEYVIDFLPKIK
+IETVVKDSEVEKVVQTILKSAQTGKVGDGKIFIYNVEETVRIRTGERGESAI----
+>UniRef90_B1ZSX2/1-112
+MKLVTAIIKPFKLEEIKAALAEIQVEGMTVTEVKGFGRQKGHTEIYRGTEYTVDFLPKVR
+IEILAADESVPKILETIISTAKTGKIGDGKIFISAAEDVVRIRTDERGEAAL----
+>UniRef90_Q7X1L4/1-112
+MKKVEAIIKPFKLDAVKEAVTALGVYGMTVTEVKGYGQQKGHTEQYRGAEYVVEFITKIK
+VEIVVADAKVSPVLEAIRRTAMSNSIGDGKVFVSPVETALRIRTGETGDAAL----
+>UniRef90_Q1NW36/1-112
+MKKVEAIIKPFKLDAVKEAVTALGIHGMTVSEVKGFGRQKGHTEVYRGAEYVVDFVAKIK
+VEIVVESEKASLLVETITQAARNGNIGDGKIFVTPVESVCRIRTGELDQDAI----
+>UniRef90_C0GRX0/1-112
+MKKLEIITRPFKVEAVKEALAGMGIKGMTLTDVKGFGRQMGHKEIYRGAEYDVDFLPKVK
+IEVILDDANVDQAVEAAIKAARTDKVGDGKIFVYSVENAIRIRTGESGDEAI----
+>UniRef90_B8DJ84/1-112
+MKKIEAIIKPFKLDAVKDALIGIGVFGLTVTEVRGYGRQRGHVETYRGLEYEVQFNSKLK
+IETVVPDGMSDQVVKAITTAARTGSIGDGKIFISSLEEVIRIRTGEEGTDAI----
+>UniRef90_Q6ARG9/1-112
+MKKIEAIIKPFKLEEIKEALTELAITGMTISEVKGYGRQKGHKEMYRGAEYSIDFNPKLK
+IELVVRAEIADKVVEKIRLAARTGKIGDGKIFVLPIEEVVRVRTGEQGREAI----
+>UniRef90_C1W154/1-112
+MKLVTAIIQPHRLDAVKSALEAAGIRGMTVSEASGYGRQKGHTEVYRGAEYTIDLVPKIR
+LEILVDDPDAHRVGEVITQAAHTGRIGDGKVWTIPVDSVTRVRTGEEGPSAL----
+>UniRef90_C1UII8/1-112
+MKLVTAIVKPFKLDDVKNALELIGIAGLTVSEVQGFGRQRGHTEVYRGAEYQVDFVPKVR
+IEVVVGEIEAARVVDAIVEAASTGQIGDGKVWVTTIDEIVRVRTGERGADAL----
+>UniRef90_UPI000/1-118
+--KVTVITNQAKFYQLKTSLEAIGITGMTVIQVLGFGIQKGQPEYYRGNPIEATLLPKVK
+MKKIEAIIRPEAFQTLKDGLSAVGISGLTVTEAAGCGKQQGKKGVFRGTSFEIQLV
+>UniRef90_C1T022/1-113
+MKLVIAYIRPECLNAVKQELYAKKIYNMSVTNVLGSGRQKGFTETYRGVVMEVNLLKKLR
+LEIGVNDDFAEQAVEAINAGARTGKEGDGVIFVLECAAAVRIRTQETGPAAMG---
+>UniRef90_Q46G48/1-112
+MKYIIAMIRPERLDAVKRELQKLEVNRLTVSSVAGYGAQKGHLEIYRATEHEANLLEKVK
+IEIAVEDHFLKSVIEAIKTGAKDGYIGSGKIFVLPLENVIRIRTNETGPEAL----
+>UniRef90_A2RJQ2/1-112
+MKKIEAIIRTDKLEDLKKALSDNGVHGMTVSQVLGYGEQKGFAEYVRGQRIETTLLSKIK
+IEIVSIDEKVDQIVNVITKAVRTGEVGDGKIFIQPVERVIRIRTSEEDAQAL----
+>UniRef90_Q8KF33/1-112
+MKKIEAIIRTSQYEAVKKALHEIDIDFFTWWDVTGQGNDKKHTEIYRGTVRDTSYISRRY
+LSIVVRDVNLQKTVDCLIKNARTGEVGDGKIFVSDIEQSYRIRTGESGDESL----
+>UniRef90_B1HTS9/1-112
+MKKIEVIIRPEVFGAVRDGLAQQGIAGLSVSEIAGCGRQLGRTGLFRGNTYEIEFLPKLK
+LEMIVDDSKVDGIVEILLREAATGKVGDGKIFIYPVEQAIRIRTKEVGSIAV----
+>UniRef90_A2SPS9/1-106
+MKMITAIIRPEKVDEVLNALEQNNIPGVTITEVLGRGEQGGVCLQYRAGKMQVKTLPKTK
+LEIVVPDKDVDTLIKVIREHARTGKKGDGRIFVLPVEAAAWVRTDE----------
+>UniRef90_C0EAH3/1-111
+--KLVIVTRQSKFEELKAAMNAIEVTGMTVTQVIGCGTQKGATEFYRGVPVEMNLLPKIK
+VEIVVCRVPVRTVIETAKKVLYTGHYGDGKIFVYDIENVVKVRTGEEGCAALQ---
+>UniRef90_A7I8Z1/1-104
+--MISAIIKPERFEFVKKALEDKGYVSMTITEVKGRGEQKGISLEYRGGKMTVDLLPKVK
+IEIVIRDKDLEDVIATLTGAARTGKIGDGKIFVIPVEKSIRIRTGD----------
+>UniRef90_Q3AFZ0/1-114
+MKKIEALIRPQKLGEVKEALNKLGISGMTVTEVVGCGRQKGQKEIYRGIEYEINLLPKVK
+IEIVTVDEKVEEIIKIISESARTGAIGDGKIFISEVLDAVRIRTGERGTAAITS--
+>UniRef90_A7I508/1-106
+MKLVIALIRPERFGAVKKALEDKGYIGMTTAEAKGRGAQKGIALVYRGGRLTIDILVKVR
+IEIVSHDRDVEDLVSTIRESAWTGANGDGRIFVLPVEQAIRIRTGE----------
+>UniRef90_P51604/1-112
+MKEIIAIIRPNKINRTKEVLDALGFSSMTANAVFGRGRQKAIVGELREEEGSMRYIPKRM
+ISLVVPDEDASLVVESIMKVNKTGQIGDGKIFVCPIEDAVRVRTKESGEDAI----
+>UniRef90_B0NXT3/1-112
+--KINAIVREEKFEDVKEALNKIGVNGITVSQVMGCGAQKGFTEVIRGTKVDMMMRPKIK
+FEIVVSSEEWERTIEAIQKSAFTGEVGDGKIFSYEVRNVVKIRTGERDVDALQD--
+>UniRef90_A8YG01/1-96
+----------------KIALVNAGIVGMTVSEVRGFGRQKGQSERYRGSEYTVEFLQKLK
+IEIVVEDKQVDMVVDKLISAARTGEIGDGKIFISPVEQIVRIRTGEKDLQAI----
+>UniRef90_C0BMJ9/1-112
+MKKVEAIIRKSKFDDVKKALHAIEVNFFSYWDVTGVGNEKQ-GHVYRGISYSTSDIQRRI
+LSIVISDEFLEPTINAILEAACTGNVGDGKIFVSDVQDAYRIRTRENGKAGIN---
+>UniRef90_Q466Y2/1-112
+MCKIEAIIKPMKLHEVKDALEEAGYPSLTVTDVKGRGQQKGIVQQWRGKKYCVDLLPKTK
+IEIAAPEDKIEEIIKIIQSSAYTGEIGDGKIFVTPIETVVRIRTGERNGDAL----
+>UniRef90_O26760/1-112
+MKEIVAIIRPEKLEEVKNALEAAGCHGMTVTEVRGRGRQLGITESYRGRDYRIDLLPKTK
+IEIVVNDEDVDTVVETIVKSAQTGDIGDGKIFISGVDEVVRIRTGESGKKAV----
+>UniRef90_A0LYN2/1-111
+MKKIEAIIRKSEFDETKEALHSIGVTFFSYWDVTGVGNEKV-GHVYRGVSYSTADIQRRY
+LSIVVTDSFVEKTVETLLKAAHTGKVGDGKIFILPVEEAYRIRTKEKGGESL----
+>UniRef90_C1YA75/1-112
+MKVVTAVIKPFKLDEVRAALLAFGVQGMTVSESSGYGRQRGHTEVYRGAEYTVELLPKVR
+VEILVDDEDAEDVVDVIVRAARTGKIGDGKVWTQPVETVIRVRTGERGPEAL----
+>UniRef90_A8KX44/1-112
+MKLVTAIVRPHRVDDVRAALTTYGVHGITVSQVTGFGLEMWRTQTYRGNAFHDESTSNIR
+LELVVADSDAPDVVNVIRRTAASTSSGAGKIWVLPVEGLARIRTGERGADAL----
+>UniRef90_C0EZB6/1-110
+--KLTIMCKEDRFAILKDAMSQIGVTGMTVSHVMGCGTQKGKTGQYRGVKIDMNLLPQLQ
+VDIVVSTVPPELVVEAAKKALYTGEYGDGKIFLYDVENVVRIRTNETGIAAL----
+>UniRef90_Q11P32/1-112
+MKKIEAIVKPSKLKAIQAGLIKIGIPCMTVVPVKGVGLQQGFPEIYRGTEKSIVLLSKVM
+IICVVSDENLEKCIDVIIETGSEGKVGDGKIFVYDVLDAIRMRTRTRGDDAI----
+>UniRef90_A7B6Y7/1-112
+--KIEAIVREEKFEQVKSALQDIQVNGVTISQVMGYGTQRGYTEIVRGSEVDILLHPKIK
+FEVVVSSEEWEQTISAIQKAAFTGEVGDGKIFSYEIRSAVKIRTKETGYNAVQS--
+>UniRef90_A7VSI5/1-111
+--KVVILFNQDKFIELKDAMNAIGVTGMTVIHVMGCGVQKGNTRYYRGVKLDIVLLPKIK
+LEIVVSKVPVQTV-DTARKVLYTGNIGDGKIFIYDVENVIKVRTGAEGYYALQD--
+>UniRef90_A6G036/1-110
+--KVEAMIRPFKLDDVKERLTELEVGGMTVTEVKGFGRTGGKTEFYRGSAYVIDFVPKIK
+IEVVVPAARSEEVIAAIREVAASDRIGDGKIFVTPVLEAVRIRTDERGESAL----
+>UniRef90_C0ES36/1-115
+MIKVEAYVREDKFEDVKAALNAIGVNGLTVSQVMGCGIQRGYKEIVRGMQVDMQMQPKIK
+FEIVVSSEEWEKTIEAIEKAAYTGEPGDGKIFTYEIRHAQKIRTKETGYDAIQAT-
+>UniRef90_B5IHX8/1-113
+MKQIQAIVRPEKLDAVKDALVEIGINGITVTAVQGFGKQMGHTEVYRGVKVEAKLLTKMQ
+ITSVVTDQAVDQVVQAILTAARTGEIGDGKIVITPVENAIRIRTGESGDSTLA---
+>UniRef90_B0MIE7/1-103
+---------PEKLTDVKHILEAHKVSGLMISNIMGYGNQKGFTQKYRGNELNSNLLPKIK
+VESVMPEEVVEKVTKDIVNTVRTGEFGDGKIFISPVEEAIRIRTGETGKDAL----
+>UniRef90_B4S395/1-111
+MKLITAIIQEDKLDQVREALIQANISRISVSRISGHGRQE-DIDIYRGRKIAPNLRPKIK
+LEIAVNEEFVDVAIDTIVDSARSGEIGDGKIFVTPLEQCVRIRTNERGGSAI----
+>UniRef90_P51254/1-112
+MKKIEAIIRPFKLNEVKLALVKGGIGGMTVVKVSGFGRQKGQTERYKGSEYSIDIIDKIK
+IEIIVSDDKVNSITEIIIKTAKTGEIGDGKIFISDVEQVIRIRTNDLNSAAL----
+>UniRef90_P71524/1-104
+MKMIRAVVRPSKAEEVVDALAESGCVALTKMDVIGRGKQKG----IKIDQIYYDELPKTM
+LMLVVEDDAAENVIELITKTAYTGSFGDGKIFVSPVDEAYTVRTRSCG--------
+>UniRef90_A8JI83/1-105
+---IEAIFRPWRLPFVIDTLSKYGIRGLTNTPVKGVGVQGGSRERYAGTEFGPNLVDKEK
+LDIVVSRAQVDAVVRLVAASAYTGEIGDGKIFVHPVAEVVRIRTAETG--------
+>UniRef90_B0CD03/1-107
+MRTITAFIRPQQCDQVKLVLVQLGIIDITLSDVKGFGRQQGSLQQYRGSDAEIRLHRKLK
+VEVKVDEEMVAPVVEKITFAARTGQVGDGKIFVSPLQKVVQVRTGEE---------
+>UniRef90_B1QY06/1-112
+MKRIEAIIRPSKLEEIKEALKNNNINGVTISQVMGCGKQLGWKEYHRGTELITNVLPKIE
+VKMVIEDSKVEEVIEIISSIAKTGEVGDGKIFVIDICDCVRIRTGERGNEAL----
+>UniRef90_Q30VL0/1-106
+MKLLIAYIRPEKLSTVKKALYARGIYAMSVTNALGSGQQKGFTETYRGIVTEVNLLKKVR
+IEVGVPADKAEDALAALQTGAHTGREGDGIIFVQDVARTVRVRTGE----------
+>UniRef90_A0T2Q5/1-113
+MKEVLAIIRPNMVSKTGKALEAVGFPAMTVIRCFGRGKEKGYIDAGEKLGMRMKYIPKRM
+ISIVVDDADVPFVVGIIMKVNRTGKPGDGKIFVLPVEEAIRIRTGEFGVEAIG---
+>UniRef90_B3QXW9/1-112
+MKEITAIIRINKMNETKKALIKAGISSFTASRVLGRGKGQVHYDLLKGAAEGYELVSKRY
+LVVVVNDNMLQPTIDAIISANQTGKPGDGKIFVSTIEDAVRVRTGETGSAIL----
+>UniRef90_B6YRQ4/1-111
+MKKIEAIIRKTRFDEVKEALLEADIEWFSYSDVRGVGKARQ-ERIYRGVVYDTSSIERIQ
+INLVVRDINVEKAIKAIEKSAHTGEVGDGRIFVSTIDNAYSIRTGEQGDETL----
+>UniRef90_B0MJN0/1-114
+MTKVDIIANQEKFEVLKHALSSIGITGMTVSHVMGCGMQKGSTEFYRGVPVDARLLPKMK
+VEIVVCKVPVEKVVEVAKNALYTGKIGDGKIFVYDVENVIKVRTGEEAYEALQD--
+>UniRef90_C2C1T3/1-112
+--KIEIITRPNRFDVFQKALKEIGVSGLTVTKAVGTGLEKGMIELYRGTIKENNVHERMK
+VEIVVSTVPVEAVLEVVKNTLRTGEPGDGKVFVYPLSDVIKISTGEHGVAALQD--
+>UniRef90_C1VTA2/1-110
+--LVMAIVRPEKLSDVKAALAEAGAPSLTVTQVSGRGSQPAKTGQWRGEEYVIDLHQKIK
+VECVVEPEDADDVVEAIREGANTGEKGDGKIFVLPVFDAVQVRTGDRGTDAI----
+>UniRef90_A3XNG5/1-112
+MKKIEAIIRKSKFTAVKKALHDKGVNFFSYWDVTGLGNEKE-GHVYRGVSYSTSDIQRRY
+LSIVVNDDFEQAAVAAILDAAATGEVGDGKIFVSDVQDAYRIRTGKKGPDTLN---
+>UniRef90_P71525/1-111
+MKEIIAIIRPSKMAQTKTVLEGLGFPAMTANRVLGRGKQKAIVGELGFEV-DMRYIPKTM
+LTLIVPDEDASLVVEAIMKVNKSGQYGDGKIFVCPIEDIITVRTSERGEAAI----
+>UniRef90_Q46C91/1-112
+MKEIIAIIRPKKVVPTKEALEKLGVPSLTAIPVFGRGKQKGIATELDIAGRRMEYIPKRL
+FSIVTRNEDVDTIIETIMKVNQTGDIGDGRIFICPVDDAIRVRTDEHGDNAL----
+>UniRef90_B7BWA8/1-112
+MKEVMIILRPKMYFPTKDALDQAGFHSMTIREIIGRGKCPVHYDYDEGAPVKHRLVAKRM
+IDMFVRDEDLQKLIDTVVEVNKTNHAGDGKIFVLPVNDAIRVRTGEKGIEAI----
+>UniRef90_Q7UGU6/1-112
+MKLIIAIVQPSKLDAIKEALTRVEVHRLTVVDCQGFGRQRGQTGSMRGRDYGVSLLRKVQ
+LQIGVNEEFVQPTIDAIGRSGESGEIGDGKIFVLPMDDCVRIRTGERGGEAI----
+>UniRef90_A3HVG6/1-112
+MKKIEAIIRTSRFEQIHSCVAGLGVKFLTFYEVKGMGLEHAKQQTYRGVAYEPTYIPRTK
+LEIVTVDELVEPVINCILTEGKTGEVGDGKIFVYDVLEAHRIRNNDQGEQAL----
+>UniRef90_A0YMH7/1-112
+MKRIEALIRPVQFDSVVTALVEAGIVGMSVTNVRGYGRQKGQTESYRGVKHVIEFHPKMK
+LEIVVEDEVCEFVVEKLVEAAQTGQIGDGKIFIQSMEHIIRTRTGESDLEAL----
+>UniRef90_Q46A23/1-112
+MKYIIAMIRPEKLDSVKKEIQKIGAHGLTVSSISGYGAQGGHLNVDRTKKYEANLLDKVK
+IEIAVKDEFLQTTVEAIERGSKDGYIGSGKIFVLPLENVMRIRTKETGNDAL----
+>UniRef90_B4VJP7/1-90
+----------------MKALLDAGYPAVTKVDVFGRGKQRG----LKIGNVLYDELPKAL
+LMVVVPDTEKEFVIRAILSSARTGAEGDGKIFVSPVEEVYTISSGKTDSS------
+>UniRef90_B1QUW3/1-103
+MYLVRAIIRTEKVNGVLSELVDAGFPQVTKMDVFGRGKQKG----IQVGEVHYDELPKEM
+LLIVVKDEDKDDVVRVIMKNSRTGEYGDGKIFISKVDTAYTISTGKE---------
+>UniRef90_A5N1U1/1-112
+MKEIMAVIRMNMVGKTKKALAENGFPSITCKDVLGRGKKMVEEELHRIEDESYRLISKRL
+IWILAKDEDVKKIADIIIDINQTGHPGDGKIFVTKVTDVVRIRTGETQDEAV----
+>UniRef90_A9D1T1/1-65
+-----------------------------------------------GAEYMVDFLPKVK
+IELVIQDELLDRAIEVIVDTARTGKIGDGKIFVTEIERVIRIRTGEENEEAV----
+>UniRef90_A6LUZ0/1-104
+MYMIRAIIRPERVSTVLSELLDAGFPEVTKMAVYGRGKQKG----IKVGEVYYDELPKEM
+LLIAVKDEDKDDVIKVIIRNSRTGEFGDGKIFVAPIEEVYTVSSGKSG--------
+>UniRef90_A6LUZ1/1-112
+MKEVMCIIRLNKVNKTKEALAEAGFPSITCRKVLGRGKKSALVEAYMETGEVPRLIPKRF
+ITLVVKDDEVKTVVDTVISVNSTGTPGDGKIFVLPVEEVYRVRDGQIGEEAI----
+>UniRef90_B8GEW5/1-112
+MKEIMAIVRMKKTGVTKRALVETGVAGFTALKVLGRGKLVEDTAVIEPAEQEVRFFPRRL
+FTILAHDEDVPRIVEAITKVNITEKVGDGIILVLPVDDAVRVRTGESGDAAI----
+>UniRef90_C1FI34/1-109
+--QVRAMVRPWRLSGVIDALNKYGIRGLTTYTVHGAGVQIGTVERYAGSTFDANLVEKVV
+VEIVVVREQCQEVVDVIVDAAQTGEIGDGKIFLSPVHDIVRIRTGEVGAAA-----
+>UniRef90_C1TA34/1-112
+MKEIIAIIRMNKVNITKKALADVGVCGLHAIKVMGRGKQLGVREEIDGLSGGTRLIPKRL
+LTILARDEDVKKIVDTVIKVNQEGNKGDGRIFIAPVIDAYRVRTAEKGEAAV----
+>UniRef90_C1T440/1-112
+MKEVIAVIRMNMMNKTKKALQDAGVVAFFAHEAFGRGKGLVDVKPLEGARKGIELYPKRM
+LTVVVTDDLVPEVVKVITDTNKTGQPGDGKIFVLPMIDAVRVRTGEKGAKSI----
+>UniRef90_A9A2H4/1-100
+MKKVEAIVNESAQNAVIDAMRKVGISGVTVSKVQGQGAQD--------PPLVGDFFSRVL
+IVCVVDDPKLDEILDAIAGAACTGTKGDGKVYVSDICDALDICTKKRG--------
+>UniRef90_Q97ME3/1-112
+MKEIMAIIRMNMVEKTKEALLKGGNPAITCLKVLGRGRQKVDIEDYKMAEELSELISKRL
+IIILAKDEDVKEIVDEIIEVNRTGNPGDGKIFVINIADAMRIRTEETGDMAI----
diff --git a/binaries/src/jpred/tests/alignment.msf b/binaries/src/jpred/tests/alignment.msf
new file mode 100644 (file)
index 0000000..8fc3fec
--- /dev/null
@@ -0,0 +1,372 @@
+
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+ Name: UniRef90_C0EZB6/1-110  Len:    116  Check:  179  Weight:  1.00
+ Name: UniRef90_Q11P32/1-112  Len:    116  Check:  3377  Weight:  1.00
+ Name: UniRef90_A7B6Y7/1-112  Len:    116  Check:  676  Weight:  1.00
+ Name: UniRef90_A7VSI5/1-111  Len:    116  Check:  5848  Weight:  1.00
+ Name: UniRef90_A6G036/1-110  Len:    116  Check:  8450  Weight:  1.00
+ Name: UniRef90_C0ES36/1-115  Len:    116  Check:  1154  Weight:  1.00
+ Name: UniRef90_B5IHX8/1-113  Len:    116  Check:  7450  Weight:  1.00
+ Name: UniRef90_B0MIE7/1-103  Len:    116  Check:  2131  Weight:  1.00
+ Name: UniRef90_B4S395/1-111  Len:    116  Check:  8256  Weight:  1.00
+ Name: UniRef90_P51254/1-112  Len:    116  Check:  2366  Weight:  1.00
+ Name: UniRef90_P71524/1-104  Len:    116  Check:  2281  Weight:  1.00
+ Name: UniRef90_A8JI83/1-105  Len:    116  Check:  84  Weight:  1.00
+ Name: UniRef90_B0CD03/1-107  Len:    116  Check:  5133  Weight:  1.00
+ Name: UniRef90_B1QY06/1-112  Len:    116  Check:  1778  Weight:  1.00
+ Name: UniRef90_Q30VL0/1-106  Len:    116  Check:  975  Weight:  1.00
+ Name: UniRef90_A0T2Q5/1-113  Len:    116  Check:  3875  Weight:  1.00
+ Name: UniRef90_B3QXW9/1-112  Len:    116  Check:  2335  Weight:  1.00
+ Name: UniRef90_B6YRQ4/1-111  Len:    116  Check:  320  Weight:  1.00
+ Name: UniRef90_B0MJN0/1-114  Len:    116  Check:  2340  Weight:  1.00
+ Name: UniRef90_C2C1T3/1-112  Len:    116  Check:  7783  Weight:  1.00
+ Name: UniRef90_C1VTA2/1-110  Len:    116  Check:  8079  Weight:  1.00
+ Name: UniRef90_A3XNG5/1-112  Len:    116  Check:  4563  Weight:  1.00
+ Name: UniRef90_P71525/1-111  Len:    116  Check:  6955  Weight:  1.00
+ Name: UniRef90_Q46C91/1-112  Len:    116  Check:  9645  Weight:  1.00
+ Name: UniRef90_B7BWA8/1-112  Len:    116  Check:  484  Weight:  1.00
+ Name: UniRef90_Q7UGU6/1-112  Len:    116  Check:  2772  Weight:  1.00
+ Name: UniRef90_A3HVG6/1-112  Len:    116  Check:  3382  Weight:  1.00
+ Name: UniRef90_A0YMH7/1-112  Len:    116  Check:  3597  Weight:  1.00
+ Name: UniRef90_Q46A23/1-112  Len:    116  Check:  2151  Weight:  1.00
+ Name: UniRef90_B4VJP7/1-90   Len:    116  Check:  2329  Weight:  1.00
+ Name: UniRef90_B1QUW3/1-103  Len:    116  Check:  8604  Weight:  1.00
+ Name: UniRef90_A5N1U1/1-112  Len:    116  Check:  2241  Weight:  1.00
+ Name: UniRef90_A9D1T1/1-65   Len:    116  Check:  8348  Weight:  1.00
+ Name: UniRef90_A6LUZ0/1-104  Len:    116  Check:  2978  Weight:  1.00
+ Name: UniRef90_A6LUZ1/1-112  Len:    116  Check:  3539  Weight:  1.00
+ Name: UniRef90_B8GEW5/1-112  Len:    116  Check:  751  Weight:  1.00
+ Name: UniRef90_C1FI34/1-109  Len:    116  Check:  3899  Weight:  1.00
+ Name: UniRef90_C1TA34/1-112  Len:    116  Check:  116  Weight:  1.00
+ Name: UniRef90_C1T440/1-112  Len:    116  Check:  857  Weight:  1.00
+ Name: UniRef90_A9A2H4/1-100  Len:    116  Check:  7883  Weight:  1.00
+ Name: UniRef90_Q97ME3/1-112  Len:    116  Check:  8399  Weight:  1.00
+
+//
+
+
+                       1                                                   50
+QUERY/1-116            MKKIEAIIRP FKLDEVKIAL VNAGIVGMTV SEVRGFGRQK GQTERYRGSE 
+UniRef90_C0EK60/1-112  MKKIEAIIKP FKLDDVREIL TEIGITGMTV SEVKGFGRQK GHTEIYRGAE 
+UniRef90_Q21P81/1-112  MKLITAVIKP FKLDDVRNAL SEIGVQGMTV TEVKGFGRQK GHTELYRGAE 
+UniRef90_Q47GI8/1-112  MKKIEAIIKP FKLDEVREAL SEIGISGLTV TEVKGFGRQK GHTELYRGAE 
+UniRef90_B9ZJ79/1-112  MKKIEAIIKP FKLEDVREAL TEMGIAGMTA TEVQGFGRQK GHTELYRGAE 
+UniRef90_B5FAN6/1-112  MKIINAIIKP FKLDDVREAL ADAGVDGMTV SEVKGFGRQK GHTELYRGAE 
+UniRef90_B5ZIL8/1-112  MKKIEAIIKP FKLDEVKDAL HEIGLMGISV TEAKGFGRQK GHTELYRGAE 
+UniRef90_B4RVM6/1-112  MKKIEAIIKP FKMDDVREAL AEVGIAGMTV SEVKGFGRQK GHTELYRGAE 
+UniRef90_B2FHB8/1-112  MKLISAIIRP FKLDEVREAL SDAGVSGITV TEVKGFGRQK GHTELYRGAE 
+UniRef90_P21193/1-112  MKKIEAIIKP FKLDEVKEAL HEVGIKGITV TEAKGFGRQK GHTELYRGAE 
+UniRef90_B5JS45/1-112  MKKIEAVIKP FKLDDVRDAL ADIGVSGMTV TEVKGFGRQK GHTETYRGAE 
+UniRef90_Q07UM0/1-112  MKLVVAIIKP FKLDEVRQAL TDVGVHGMTV TEVKGYGRQR GHTEIYRGAE 
+UniRef90_Q2RVB4/1-112  MKFVIAITKP FKLDEVREAL GALGIQGMTV TEVKGFGRQK GQTEVYRGAE 
+UniRef90_A9IPV3/1-112  MKLIIAIIKP FKLDEVRVAL SGIGVQGLTV TEVKGFGRQK GHTELYRGAE 
+UniRef90_A4TZT2/1-112  MKLIIAIIKP FKLDEVREAL TQLGIQGLTA TEVKGFGRQK GQTEIYRAAE 
+UniRef90_B3DVA4/1-110  --KIEAIIKP FKLEEVKEAL TEIGIAGLTV TEVKGFGRQK GHTEIYRGSE 
+UniRef90_C1STD4/1-112  MRKIEIITRP FKLDEVKQRL TKLGIQGMTV TEVKGFGRQR GHKEIYRGAE 
+UniRef90_A7HGG9/1-112  MKRIEAIIRP SKLEDVRRLL SHPWISAMTV SEVRGAGRQK GHAELYRGAE 
+UniRef90_A9BCF1/1-112  MKKIEAIIRP FKLEDVKVAL VNSGIVGMTV SEVRGFGRQK GQVERYRGSE 
+UniRef90_B4U911/1-112  MKKVEAIIKP FKLDEVKDAL VEIGIGGMTI TEVKGFGQQK GKTEIYRATE 
+UniRef90_B1ZSX2/1-112  MKLVTAIIKP FKLEEIKAAL AEIQVEGMTV TEVKGFGRQK GHTEIYRGTE 
+UniRef90_Q7X1L4/1-112  MKKVEAIIKP FKLDAVKEAV TALGVYGMTV TEVKGYGQQK GHTEQYRGAE 
+UniRef90_Q1NW36/1-112  MKKVEAIIKP FKLDAVKEAV TALGIHGMTV SEVKGFGRQK GHTEVYRGAE 
+UniRef90_C0GRX0/1-112  MKKLEIITRP FKVEAVKEAL AGMGIKGMTL TDVKGFGRQM GHKEIYRGAE 
+UniRef90_B8DJ84/1-112  MKKIEAIIKP FKLDAVKDAL IGIGVFGLTV TEVRGYGRQR GHVETYRGLE 
+UniRef90_Q6ARG9/1-112  MKKIEAIIKP FKLEEIKEAL TELAITGMTI SEVKGYGRQK GHKEMYRGAE 
+UniRef90_C1W154/1-112  MKLVTAIIQP HRLDAVKSAL EAAGIRGMTV SEASGYGRQK GHTEVYRGAE 
+UniRef90_C1UII8/1-112  MKLVTAIVKP FKLDDVKNAL ELIGIAGLTV SEVQGFGRQR GHTEVYRGAE 
+UniRef90_UPI000/1-118  --KVTVITNQ AKFYQLKTSL EAIGITGMTV IQVLGFGIQK GQPEYYRGNP 
+UniRef90_C1T022/1-113  MKLVIAYIRP ECLNAVKQEL YAKKIYNMSV TNVLGSGRQK GFTETYRGVV 
+UniRef90_Q46G48/1-112  MKYIIAMIRP ERLDAVKREL QKLEVNRLTV SSVAGYGAQK GHLEIYRATE 
+UniRef90_A2RJQ2/1-112  MKKIEAIIRT DKLEDLKKAL SDNGVHGMTV SQVLGYGEQK GFAEYVRGQR 
+UniRef90_Q8KF33/1-112  MKKIEAIIRT SQYEAVKKAL HEIDIDFFTW WDVTGQGNDK KHTEIYRGTV 
+UniRef90_B1HTS9/1-112  MKKIEVIIRP EVFGAVRDGL AQQGIAGLSV SEIAGCGRQL GRTGLFRGNT 
+UniRef90_A2SPS9/1-106  MKMITAIIRP EKVDEVLNAL EQNNIPGVTI TEVLGRGEQG GVCLQYRAGK 
+UniRef90_C0EAH3/1-111  --KLVIVTRQ SKFEELKAAM NAIEVTGMTV TQVIGCGTQK GATEFYRGVP 
+UniRef90_A7I8Z1/1-104  --MISAIIKP ERFEFVKKAL EDKGYVSMTI TEVKGRGEQK GISLEYRGGK 
+UniRef90_Q3AFZ0/1-114  MKKIEALIRP QKLGEVKEAL NKLGISGMTV TEVVGCGRQK GQKEIYRGIE 
+UniRef90_A7I508/1-106  MKLVIALIRP ERFGAVKKAL EDKGYIGMTT AEAKGRGAQK GIALVYRGGR 
+UniRef90_P51604/1-112  MKEIIAIIRP NKINRTKEVL DALGFSSMTA NAVFGRGRQK AIVGELREEE 
+UniRef90_B0NXT3/1-112  --KINAIVRE EKFEDVKEAL NKIGVNGITV SQVMGCGAQK GFTEVIRGTK 
+UniRef90_A8YG01/1-96   ---------- ------KIAL VNAGIVGMTV SEVRGFGRQK GQSERYRGSE 
+UniRef90_C0BMJ9/1-112  MKKVEAIIRK SKFDDVKKAL HAIEVNFFSY WDVTGVGNEK Q-GHVYRGIS 
+UniRef90_Q466Y2/1-112  MCKIEAIIKP MKLHEVKDAL EEAGYPSLTV TDVKGRGQQK GIVQQWRGKK 
+UniRef90_O26760/1-112  MKEIVAIIRP EKLEEVKNAL EAAGCHGMTV TEVRGRGRQL GITESYRGRD 
+UniRef90_A0LYN2/1-111  MKKIEAIIRK SEFDETKEAL HSIGVTFFSY WDVTGVGNEK V-GHVYRGVS 
+UniRef90_C1YA75/1-112  MKVVTAVIKP FKLDEVRAAL LAFGVQGMTV SESSGYGRQR GHTEVYRGAE 
+UniRef90_A8KX44/1-112  MKLVTAIVRP HRVDDVRAAL TTYGVHGITV SQVTGFGLEM WRTQTYRGNA 
+UniRef90_C0EZB6/1-110  --KLTIMCKE DRFAILKDAM SQIGVTGMTV SHVMGCGTQK GKTGQYRGVK 
+UniRef90_Q11P32/1-112  MKKIEAIVKP SKLKAIQAGL IKIGIPCMTV VPVKGVGLQQ GFPEIYRGTE 
+UniRef90_A7B6Y7/1-112  --KIEAIVRE EKFEQVKSAL QDIQVNGVTI SQVMGYGTQR GYTEIVRGSE 
+UniRef90_A7VSI5/1-111  --KVVILFNQ DKFIELKDAM NAIGVTGMTV IHVMGCGVQK GNTRYYRGVK 
+UniRef90_A6G036/1-110  --KVEAMIRP FKLDDVKERL TELEVGGMTV TEVKGFGRTG GKTEFYRGSA 
+UniRef90_C0ES36/1-115  MIKVEAYVRE DKFEDVKAAL NAIGVNGLTV SQVMGCGIQR GYKEIVRGMQ 
+UniRef90_B5IHX8/1-113  MKQIQAIVRP EKLDAVKDAL VEIGINGITV TAVQGFGKQM GHTEVYRGVK 
+UniRef90_B0MIE7/1-103  ---------P EKLTDVKHIL EAHKVSGLMI SNIMGYGNQK GFTQKYRGNE 
+UniRef90_B4S395/1-111  MKLITAIIQE DKLDQVREAL IQANISRISV SRISGHGRQE -DIDIYRGRK 
+UniRef90_P51254/1-112  MKKIEAIIRP FKLNEVKLAL VKGGIGGMTV VKVSGFGRQK GQTERYKGSE 
+UniRef90_P71524/1-104  MKMIRAVVRP SKAEEVVDAL AESGCVALTK MDVIGRGKQK G----IKIDQ 
+UniRef90_A8JI83/1-105  ---IEAIFRP WRLPFVIDTL SKYGIRGLTN TPVKGVGVQG GSRERYAGTE 
+UniRef90_B0CD03/1-107  MRTITAFIRP QQCDQVKLVL VQLGIIDITL SDVKGFGRQQ GSLQQYRGSD 
+UniRef90_B1QY06/1-112  MKRIEAIIRP SKLEEIKEAL KNNNINGVTI SQVMGCGKQL GWKEYHRGTE 
+UniRef90_Q30VL0/1-106  MKLLIAYIRP EKLSTVKKAL YARGIYAMSV TNALGSGQQK GFTETYRGIV 
+UniRef90_A0T2Q5/1-113  MKEVLAIIRP NMVSKTGKAL EAVGFPAMTV IRCFGRGKEK GYIDAGEKLG 
+UniRef90_B3QXW9/1-112  MKEITAIIRI NKMNETKKAL IKAGISSFTA SRVLGRGKGQ VHYDLLKGAA 
+UniRef90_B6YRQ4/1-111  MKKIEAIIRK TRFDEVKEAL LEADIEWFSY SDVRGVGKAR Q-ERIYRGVV 
+UniRef90_B0MJN0/1-114  MTKVDIIANQ EKFEVLKHAL SSIGITGMTV SHVMGCGMQK GSTEFYRGVP 
+UniRef90_C2C1T3/1-112  --KIEIITRP NRFDVFQKAL KEIGVSGLTV TKAVGTGLEK GMIELYRGTI 
+UniRef90_C1VTA2/1-110  --LVMAIVRP EKLSDVKAAL AEAGAPSLTV TQVSGRGSQP AKTGQWRGEE 
+UniRef90_A3XNG5/1-112  MKKIEAIIRK SKFTAVKKAL HDKGVNFFSY WDVTGLGNEK E-GHVYRGVS 
+UniRef90_P71525/1-111  MKEIIAIIRP SKMAQTKTVL EGLGFPAMTA NRVLGRGKQK AIVGELGFEV 
+UniRef90_Q46C91/1-112  MKEIIAIIRP KKVVPTKEAL EKLGVPSLTA IPVFGRGKQK GIATELDIAG 
+UniRef90_B7BWA8/1-112  MKEVMIILRP KMYFPTKDAL DQAGFHSMTI REIIGRGKCP VHYDYDEGAP 
+UniRef90_Q7UGU6/1-112  MKLIIAIVQP SKLDAIKEAL TRVEVHRLTV VDCQGFGRQR GQTGSMRGRD 
+UniRef90_A3HVG6/1-112  MKKIEAIIRT SRFEQIHSCV AGLGVKFLTF YEVKGMGLEH AKQQTYRGVA 
+UniRef90_A0YMH7/1-112  MKRIEALIRP VQFDSVVTAL VEAGIVGMSV TNVRGYGRQK GQTESYRGVK 
+UniRef90_Q46A23/1-112  MKYIIAMIRP EKLDSVKKEI QKIGAHGLTV SSISGYGAQG GHLNVDRTKK 
+UniRef90_B4VJP7/1-90   ---------- ------MKAL LDAGYPAVTK VDVFGRGKQR G----LKIGN 
+UniRef90_B1QUW3/1-103  MYLVRAIIRT EKVNGVLSEL VDAGFPQVTK MDVFGRGKQK G----IQVGE 
+UniRef90_A5N1U1/1-112  MKEIMAVIRM NMVGKTKKAL AENGFPSITC KDVLGRGKKM VEEELHRIED 
+UniRef90_A9D1T1/1-65   ---------- ---------- ---------- ---------- -------GAE 
+UniRef90_A6LUZ0/1-104  MYMIRAIIRP ERVSTVLSEL LDAGFPEVTK MAVYGRGKQK G----IKVGE 
+UniRef90_A6LUZ1/1-112  MKEVMCIIRL NKVNKTKEAL AEAGFPSITC RKVLGRGKKS ALVEAYMETG 
+UniRef90_B8GEW5/1-112  MKEIMAIVRM KKTGVTKRAL VETGVAGFTA LKVLGRGKLV EDTAVIEPAE 
+UniRef90_C1FI34/1-109  --QVRAMVRP WRLSGVIDAL NKYGIRGLTT YTVHGAGVQI GTVERYAGST 
+UniRef90_C1TA34/1-112  MKEIIAIIRM NKVNITKKAL ADVGVCGLHA IKVMGRGKQL GVREEIDGLS 
+UniRef90_C1T440/1-112  MKEVIAVIRM NMMNKTKKAL QDAGVVAFFA HEAFGRGKGL VDVKPLEGAR 
+UniRef90_A9A2H4/1-100  MKKVEAIVNE SAQNAVIDAM RKVGISGVTV SKVQGQGAQD --------PP 
+UniRef90_Q97ME3/1-112  MKEIMAIIRM NMVEKTKEAL LKGGNPAITC LKVLGRGRQK VDIEDYKMAE 
+
+
+                       51                                                 100
+QUERY/1-116            YTVEFLQKLK LEIVVEDAQV DTVIDKIVAA ARTGENGDGK IFVSPVDQTI 
+UniRef90_C0EK60/1-112  YAVDFLPKVK IELVLADDKV DQAVDAILET AHSGKIGDGK IFIYPVEEAI 
+UniRef90_Q21P81/1-112  YVIDFLPKVK LELVLGDELI DQAVEAISKA AQTGKIGDGK IFITPCEEVI 
+UniRef90_Q47GI8/1-112  YVVDFLPKIK IEIVVNSNNV EPAIDAIIKA ARTGKIGDGK IFVMPVEQVV 
+UniRef90_B9ZJ79/1-112  YVVDFLPKVK LELVVDDDRV DACIDAIVKA SRTGKIGDGK IFVSDMARVV 
+UniRef90_B5FAN6/1-112  YQVDFLPKVK LEIAVQAEGV DRIVEAISKA AHTGKIGDGK IFVYDLQQAV 
+UniRef90_B5ZIL8/1-112  YIVDFLPKVK LEIVCADNLV DRAVETIMAA ARTGRIGDGK IFILPVEDVI 
+UniRef90_B4RVM6/1-112  YQVDFLPKIK IELVLDDDRV EQAVEAIQSS AKTGKIGDGK IFVYSVESAV 
+UniRef90_B2FHB8/1-112  YVVDFLPKIK IETVVTDERA DAVIEAIQSS AGTGKIGDGK IFVTAVEQVI 
+UniRef90_P21193/1-112  YVVDFLPKVK IEVVMEDSLV ERAIEAIQQA AHTGRIGDGK IFVTPVEEVV 
+UniRef90_B5JS45/1-112  YVVDFLPKLK LEIVVAEKDA DACVESITNA AKTGQIGDGK IFVSDVERTI 
+UniRef90_Q07UM0/1-112  YLVNFLPKLR IEVGVADTLV DKAVEAITRS ARTGQIGDGK IFVTPLDHAL 
+UniRef90_Q2RVB4/1-112  YVVNFLPKVK IELAVPDNLL DQVVETIQST AQTGKIGDGK IFVFDLGEAV 
+UniRef90_A9IPV3/1-112  YAVDFLPKLR VEAAVPDHLV DQVIDVIEQA ARTGKIGDGK IFTAPLEQVI 
+UniRef90_A4TZT2/1-112  YVVSFVPKIK IELVVNDDVV DRAVEAIQAA ARTDKIGDGK IFVMDVAHAL 
+UniRef90_B3DVA4/1-110  YTVDFLPKVK VEIVLTEDIL PKAVEAIIKS AKTGKIGDGK IFVLPVSEAI 
+UniRef90_C1STD4/1-112  YQVDFVAKVK IEIVVDDGLV EEIVSTVQEG ARTGKVGDGK IFISPVDNAV 
+UniRef90_A7HGG9/1-112  YVIDLIPKLK LEIVLPDPLV DRVVADLESW LRTGRIGDGK IFVEPLDDAV 
+UniRef90_A9BCF1/1-112  FTVEFLQKLK IEIVVADESV PTVLTAIAEA AKTGEIGDGK IFISPVESVV 
+UniRef90_B4U911/1-112  YVIDFLPKIK IETVVKDSEV EKVVQTILKS AQTGKVGDGK IFIYNVEETV 
+UniRef90_B1ZSX2/1-112  YTVDFLPKVR IEILAADESV PKILETIIST AKTGKIGDGK IFISAAEDVV 
+UniRef90_Q7X1L4/1-112  YVVEFITKIK VEIVVADAKV SPVLEAIRRT AMSNSIGDGK VFVSPVETAL 
+UniRef90_Q1NW36/1-112  YVVDFVAKIK VEIVVESEKA SLLVETITQA ARNGNIGDGK IFVTPVESVC 
+UniRef90_C0GRX0/1-112  YDVDFLPKVK IEVILDDANV DQAVEAAIKA ARTDKVGDGK IFVYSVENAI 
+UniRef90_B8DJ84/1-112  YEVQFNSKLK IETVVPDGMS DQVVKAITTA ARTGSIGDGK IFISSLEEVI 
+UniRef90_Q6ARG9/1-112  YSIDFNPKLK IELVVRAEIA DKVVEKIRLA ARTGKIGDGK IFVLPIEEVV 
+UniRef90_C1W154/1-112  YTIDLVPKIR LEILVDDPDA HRVGEVITQA AHTGRIGDGK VWTIPVDSVT 
+UniRef90_C1UII8/1-112  YQVDFVPKVR IEVVVGEIEA ARVVDAIVEA ASTGQIGDGK VWVTTIDEIV 
+UniRef90_UPI000/1-118  IEATLLPKVK MKKIEAIIRP EAFQTLKDGL SAVGISGLTV TEAAGCGKQQ 
+UniRef90_C1T022/1-113  MEVNLLKKLR LEIGVNDDFA EQAVEAINAG ARTGKEGDGV IFVLECAAAV 
+UniRef90_Q46G48/1-112  HEANLLEKVK IEIAVEDHFL KSVIEAIKTG AKDGYIGSGK IFVLPLENVI 
+UniRef90_A2RJQ2/1-112  IETTLLSKIK IEIVSIDEKV DQIVNVITKA VRTGEVGDGK IFIQPVERVI 
+UniRef90_Q8KF33/1-112  RDTSYISRRY LSIVVRDVNL QKTVDCLIKN ARTGEVGDGK IFVSDIEQSY 
+UniRef90_B1HTS9/1-112  YEIEFLPKLK LEMIVDDSKV DGIVEILLRE AATGKVGDGK IFIYPVEQAI 
+UniRef90_A2SPS9/1-106  MQVKTLPKTK LEIVVPDKDV DTLIKVIREH ARTGKKGDGR IFVLPVEAAA 
+UniRef90_C0EAH3/1-111  VEMNLLPKIK VEIVVCRVPV RTVIETAKKV LYTGHYGDGK IFVYDIENVV 
+UniRef90_A7I8Z1/1-104  MTVDLLPKVK IEIVIRDKDL EDVIATLTGA ARTGKIGDGK IFVIPVEKSI 
+UniRef90_Q3AFZ0/1-114  YEINLLPKVK IEIVTVDEKV EEIIKIISES ARTGAIGDGK IFISEVLDAV 
+UniRef90_A7I508/1-106  LTIDILVKVR IEIVSHDRDV EDLVSTIRES AWTGANGDGR IFVLPVEQAI 
+UniRef90_P51604/1-112  GSMRYIPKRM ISLVVPDEDA SLVVESIMKV NKTGQIGDGK IFVCPIEDAV 
+UniRef90_B0NXT3/1-112  VDMMMRPKIK FEIVVSSEEW ERTIEAIQKS AFTGEVGDGK IFSYEVRNVV 
+UniRef90_A8YG01/1-96   YTVEFLQKLK IEIVVEDKQV DMVVDKLISA ARTGEIGDGK IFISPVEQIV 
+UniRef90_C0BMJ9/1-112  YSTSDIQRRI LSIVISDEFL EPTINAILEA ACTGNVGDGK IFVSDVQDAY 
+UniRef90_Q466Y2/1-112  YCVDLLPKTK IEIAAPEDKI EEIIKIIQSS AYTGEIGDGK IFVTPIETVV 
+UniRef90_O26760/1-112  YRIDLLPKTK IEIVVNDEDV DTVVETIVKS AQTGDIGDGK IFISGVDEVV 
+UniRef90_A0LYN2/1-111  YSTADIQRRY LSIVVTDSFV EKTVETLLKA AHTGKVGDGK IFILPVEEAY 
+UniRef90_C1YA75/1-112  YTVELLPKVR VEILVDDEDA EDVVDVIVRA ARTGKIGDGK VWTQPVETVI 
+UniRef90_A8KX44/1-112  FHDESTSNIR LELVVADSDA PDVVNVIRRT AASTSSGAGK IWVLPVEGLA 
+UniRef90_C0EZB6/1-110  IDMNLLPQLQ VDIVVSTVPP ELVVEAAKKA LYTGEYGDGK IFLYDVENVV 
+UniRef90_Q11P32/1-112  KSIVLLSKVM IICVVSDENL EKCIDVIIET GSEGKVGDGK IFVYDVLDAI 
+UniRef90_A7B6Y7/1-112  VDILLHPKIK FEVVVSSEEW EQTISAIQKA AFTGEVGDGK IFSYEIRSAV 
+UniRef90_A7VSI5/1-111  LDIVLLPKIK LEIVVSKVPV QTV-DTARKV LYTGNIGDGK IFIYDVENVI 
+UniRef90_A6G036/1-110  YVIDFVPKIK IEVVVPAARS EEVIAAIREV AASDRIGDGK IFVTPVLEAV 
+UniRef90_C0ES36/1-115  VDMQMQPKIK FEIVVSSEEW EKTIEAIEKA AYTGEPGDGK IFTYEIRHAQ 
+UniRef90_B5IHX8/1-113  VEAKLLTKMQ ITSVVTDQAV DQVVQAILTA ARTGEIGDGK IVITPVENAI 
+UniRef90_B0MIE7/1-103  LNSNLLPKIK VESVMPEEVV EKVTKDIVNT VRTGEFGDGK IFISPVEEAI 
+UniRef90_B4S395/1-111  IAPNLRPKIK LEIAVNEEFV DVAIDTIVDS ARSGEIGDGK IFVTPLEQCV 
+UniRef90_P51254/1-112  YSIDIIDKIK IEIIVSDDKV NSITEIIIKT AKTGEIGDGK IFISDVEQVI 
+UniRef90_P71524/1-104  IYYDELPKTM LMLVVEDDAA ENVIELITKT AYTGSFGDGK IFVSPVDEAY 
+UniRef90_A8JI83/1-105  FGPNLVDKEK LDIVVSRAQV DAVVRLVAAS AYTGEIGDGK IFVHPVAEVV 
+UniRef90_B0CD03/1-107  AEIRLHRKLK VEVKVDEEMV APVVEKITFA ARTGQVGDGK IFVSPLQKVV 
+UniRef90_B1QY06/1-112  LITNVLPKIE VKMVIEDSKV EEVIEIISSI AKTGEVGDGK IFVIDICDCV 
+UniRef90_Q30VL0/1-106  TEVNLLKKVR IEVGVPADKA EDALAALQTG AHTGREGDGI IFVQDVARTV 
+UniRef90_A0T2Q5/1-113  MRMKYIPKRM ISIVVDDADV PFVVGIIMKV NRTGKPGDGK IFVLPVEEAI 
+UniRef90_B3QXW9/1-112  EGYELVSKRY LVVVVNDNML QPTIDAIISA NQTGKPGDGK IFVSTIEDAV 
+UniRef90_B6YRQ4/1-111  YDTSSIERIQ INLVVRDINV EKAIKAIEKS AHTGEVGDGR IFVSTIDNAY 
+UniRef90_B0MJN0/1-114  VDARLLPKMK VEIVVCKVPV EKVVEVAKNA LYTGKIGDGK IFVYDVENVI 
+UniRef90_C2C1T3/1-112  KENNVHERMK VEIVVSTVPV EAVLEVVKNT LRTGEPGDGK VFVYPLSDVI 
+UniRef90_C1VTA2/1-110  YVIDLHQKIK VECVVEPEDA DDVVEAIREG ANTGEKGDGK IFVLPVFDAV 
+UniRef90_A3XNG5/1-112  YSTSDIQRRY LSIVVNDDFE QAAVAAILDA AATGEVGDGK IFVSDVQDAY 
+UniRef90_P71525/1-111  -DMRYIPKTM LTLIVPDEDA SLVVEAIMKV NKSGQYGDGK IFVCPIEDII 
+UniRef90_Q46C91/1-112  RRMEYIPKRL FSIVTRNEDV DTIIETIMKV NQTGDIGDGR IFICPVDDAI 
+UniRef90_B7BWA8/1-112  VKHRLVAKRM IDMFVRDEDL QKLIDTVVEV NKTNHAGDGK IFVLPVNDAI 
+UniRef90_Q7UGU6/1-112  YGVSLLRKVQ LQIGVNEEFV QPTIDAIGRS GESGEIGDGK IFVLPMDDCV 
+UniRef90_A3HVG6/1-112  YEPTYIPRTK LEIVTVDELV EPVINCILTE GKTGEVGDGK IFVYDVLEAH 
+UniRef90_A0YMH7/1-112  HVIEFHPKMK LEIVVEDEVC EFVVEKLVEA AQTGQIGDGK IFIQSMEHII 
+UniRef90_Q46A23/1-112  YEANLLDKVK IEIAVKDEFL QTTVEAIERG SKDGYIGSGK IFVLPLENVM 
+UniRef90_B4VJP7/1-90   VLYDELPKAL LMVVVPDTEK EFVIRAILSS ARTGAEGDGK IFVSPVEEVY 
+UniRef90_B1QUW3/1-103  VHYDELPKEM LLIVVKDEDK DDVVRVIMKN SRTGEYGDGK IFISKVDTAY 
+UniRef90_A5N1U1/1-112  ESYRLISKRL IWILAKDEDV KKIADIIIDI NQTGHPGDGK IFVTKVTDVV 
+UniRef90_A9D1T1/1-65   YMVDFLPKVK IELVIQDELL DRAIEVIVDT ARTGKIGDGK IFVTEIERVI 
+UniRef90_A6LUZ0/1-104  VYYDELPKEM LLIAVKDEDK DDVIKVIIRN SRTGEFGDGK IFVAPIEEVY 
+UniRef90_A6LUZ1/1-112  EVPRLIPKRF ITLVVKDDEV KTVVDTVISV NSTGTPGDGK IFVLPVEEVY 
+UniRef90_B8GEW5/1-112  QEVRFFPRRL FTILAHDEDV PRIVEAITKV NITEKVGDGI ILVLPVDDAV 
+UniRef90_C1FI34/1-109  FDANLVEKVV VEIVVVREQC QEVVDVIVDA AQTGEIGDGK IFLSPVHDIV 
+UniRef90_C1TA34/1-112  GGTRLIPKRL LTILARDEDV KKIVDTVIKV NQEGNKGDGR IFIAPVIDAY 
+UniRef90_C1T440/1-112  KGIELYPKRM LTVVVTDDLV PEVVKVITDT NKTGQPGDGK IFVLPMIDAV 
+UniRef90_A9A2H4/1-100  LVGDFFSRVL IVCVVDDPKL DEILDAIAGA ACTGTKGDGK VYVSDICDAL 
+UniRef90_Q97ME3/1-112  ELSELISKRL IIILAKDEDV KEIVDEIIEV NRTGNPGDGK IFVINIADAM 
+
+
+                       101                                                150
+QUERY/1-116            RIRTGEKNAD AISAWS 
+UniRef90_C0EK60/1-112  RIRTGERSEA AL---- 
+UniRef90_Q21P81/1-112  RIRTGETGPE AV---- 
+UniRef90_Q47GI8/1-112  RIRTGETDEA AV---- 
+UniRef90_B9ZJ79/1-112  RIRTGEEGSE AL---- 
+UniRef90_B5FAN6/1-112  RIRTGETDTE AL---- 
+UniRef90_B5ZIL8/1-112  RIRTGEHGEE AI---- 
+UniRef90_B4RVM6/1-112  RIRTGEQNED AI---- 
+UniRef90_B2FHB8/1-112  RIRTGEIGAD AL---- 
+UniRef90_P21193/1-112  RIRTGEKGGD AI---- 
+UniRef90_B5JS45/1-112  RIRTGEEDES AI---- 
+UniRef90_Q07UM0/1-112  RIRTGETNAD AL---- 
+UniRef90_Q2RVB4/1-112  RIRTGERGEE AL---- 
+UniRef90_A9IPV3/1-112  RIRTGESGEA AL---- 
+UniRef90_A4TZT2/1-112  RIRTGEADTE AL---- 
+UniRef90_B3DVA4/1-110  RIRTEEKGEN AI---- 
+UniRef90_C1STD4/1-112  RIRTGESGAE AL---- 
+UniRef90_A7HGG9/1-112  RVRTGERGED AL---- 
+UniRef90_A9BCF1/1-112  RIRTGELDGS AL---- 
+UniRef90_B4U911/1-112  RIRTGERGES AI---- 
+UniRef90_B1ZSX2/1-112  RIRTDERGEA AL---- 
+UniRef90_Q7X1L4/1-112  RIRTGETGDA AL---- 
+UniRef90_Q1NW36/1-112  RIRTGELDQD AI---- 
+UniRef90_C0GRX0/1-112  RIRTGESGDE AI---- 
+UniRef90_B8DJ84/1-112  RIRTGEEGTD AI---- 
+UniRef90_Q6ARG9/1-112  RVRTGEQGRE AI---- 
+UniRef90_C1W154/1-112  RVRTGEEGPS AL---- 
+UniRef90_C1UII8/1-112  RVRTGERGAD AL---- 
+UniRef90_UPI000/1-118  GKKGVFRGTS FEIQLV 
+UniRef90_C1T022/1-113  RIRTQETGPA AMG--- 
+UniRef90_Q46G48/1-112  RIRTNETGPE AL---- 
+UniRef90_A2RJQ2/1-112  RIRTSEEDAQ AL---- 
+UniRef90_Q8KF33/1-112  RIRTGESGDE SL---- 
+UniRef90_B1HTS9/1-112  RIRTKEVGSI AV---- 
+UniRef90_A2SPS9/1-106  WVRTDE---- ------ 
+UniRef90_C0EAH3/1-111  KVRTGEEGCA ALQ--- 
+UniRef90_A7I8Z1/1-104  RIRTGD---- ------ 
+UniRef90_Q3AFZ0/1-114  RIRTGERGTA AITS-- 
+UniRef90_A7I508/1-106  RIRTGE---- ------ 
+UniRef90_P51604/1-112  RVRTKESGED AI---- 
+UniRef90_B0NXT3/1-112  KIRTGERDVD ALQD-- 
+UniRef90_A8YG01/1-96   RIRTGEKDLQ AI---- 
+UniRef90_C0BMJ9/1-112  RIRTRENGKA GIN--- 
+UniRef90_Q466Y2/1-112  RIRTGERNGD AL---- 
+UniRef90_O26760/1-112  RIRTGESGKK AV---- 
+UniRef90_A0LYN2/1-111  RIRTKEKGGE SL---- 
+UniRef90_C1YA75/1-112  RVRTGERGPE AL---- 
+UniRef90_A8KX44/1-112  RIRTGERGAD AL---- 
+UniRef90_C0EZB6/1-110  RIRTNETGIA AL---- 
+UniRef90_Q11P32/1-112  RMRTRTRGDD AI---- 
+UniRef90_A7B6Y7/1-112  KIRTKETGYN AVQS-- 
+UniRef90_A7VSI5/1-111  KVRTGAEGYY ALQD-- 
+UniRef90_A6G036/1-110  RIRTDERGES AL---- 
+UniRef90_C0ES36/1-115  KIRTKETGYD AIQAT- 
+UniRef90_B5IHX8/1-113  RIRTGESGDS TLA--- 
+UniRef90_B0MIE7/1-103  RIRTGETGKD AL---- 
+UniRef90_B4S395/1-111  RIRTNERGGS AI---- 
+UniRef90_P51254/1-112  RIRTNDLNSA AL---- 
+UniRef90_P71524/1-104  TVRTRSCG-- ------ 
+UniRef90_A8JI83/1-105  RIRTAETG-- ------ 
+UniRef90_B0CD03/1-107  QVRTGEE--- ------ 
+UniRef90_B1QY06/1-112  RIRTGERGNE AL---- 
+UniRef90_Q30VL0/1-106  RVRTGE---- ------ 
+UniRef90_A0T2Q5/1-113  RIRTGEFGVE AIG--- 
+UniRef90_B3QXW9/1-112  RVRTGETGSA IL---- 
+UniRef90_B6YRQ4/1-111  SIRTGEQGDE TL---- 
+UniRef90_B0MJN0/1-114  KVRTGEEAYE ALQD-- 
+UniRef90_C2C1T3/1-112  KISTGEHGVA ALQD-- 
+UniRef90_C1VTA2/1-110  QVRTGDRGTD AI---- 
+UniRef90_A3XNG5/1-112  RIRTGKKGPD TLN--- 
+UniRef90_P71525/1-111  TVRTSERGEA AI---- 
+UniRef90_Q46C91/1-112  RVRTDEHGDN AL---- 
+UniRef90_B7BWA8/1-112  RVRTGEKGIE AI---- 
+UniRef90_Q7UGU6/1-112  RIRTGERGGE AI---- 
+UniRef90_A3HVG6/1-112  RIRNNDQGEQ AL---- 
+UniRef90_A0YMH7/1-112  RTRTGESDLE AL---- 
+UniRef90_Q46A23/1-112  RIRTKETGND AL---- 
+UniRef90_B4VJP7/1-90   TISSGKTDSS ------ 
+UniRef90_B1QUW3/1-103  TISTGKE--- ------ 
+UniRef90_A5N1U1/1-112  RIRTGETQDE AV---- 
+UniRef90_A9D1T1/1-65   RIRTGEENEE AV---- 
+UniRef90_A6LUZ0/1-104  TVSSGKSG-- ------ 
+UniRef90_A6LUZ1/1-112  RVRDGQIGEE AI---- 
+UniRef90_B8GEW5/1-112  RVRTGESGDA AI---- 
+UniRef90_C1FI34/1-109  RIRTGEVGAA A----- 
+UniRef90_C1TA34/1-112  RVRTAEKGEA AV---- 
+UniRef90_C1T440/1-112  RVRTGEKGAK SI---- 
+UniRef90_A9A2H4/1-100  DICTKKRG-- ------ 
+UniRef90_Q97ME3/1-112  RIRTEETGDM AI---- 
+
+
diff --git a/binaries/src/jpred/tests/d1b3aa_.fas b/binaries/src/jpred/tests/d1b3aa_.fas
new file mode 100644 (file)
index 0000000..6e761aa
--- /dev/null
@@ -0,0 +1,2 @@
+>d1b3aa_ d.9.1.1 (A:) RANTES (regulated upon activation, normal T-cell expressed and secreted) {Human (Homo sapiens) [TaxId: 9606]}
+PYSSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS
diff --git a/binaries/src/jpred/tests/res_d16vpa_.align b/binaries/src/jpred/tests/res_d16vpa_.align
deleted file mode 100644 (file)
index e846252..0000000
+++ /dev/null
@@ -1,78 +0,0 @@
->QUERY
-SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA
-YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL
-HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES
-WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG
-YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL
->UniRef90_Q00028
------PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD
-SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ
-LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ
-RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG
-FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA--------------
->UniRef90_Q8B635
------PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN
-SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS
-IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH
-RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG
-FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA--------------
->UniRef90_Q9E205
------PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS
-ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS
-SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE
-NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG
-FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS--------------
->UniRef90_Q88530
---LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE
-NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L
-NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ
-GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG
-YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS--------------
->UniRef90_B4XS08
-------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S
-EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG
-VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ
-YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG
-FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP-------------
->UniRef90_P09265
----PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S
-TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT
-TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE
-RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG
-FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE-----------
->UniRef90_Q2QBC8
-------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA
-HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL
-HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ
-ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG
-YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL-------------------
->UniRef90_Q90603
----------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK
-NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD
-LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ
-ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV
-YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD----------------
->UniRef90_O89246
---------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE
-EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP
-SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ
-LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA
-YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR----
->UniRef90_Q5PP87
-----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA
-PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD
--------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ
-ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG
-YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG----------------------------
->UniRef90_Q65819
-----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL
-AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T
-AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ
-RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG
-FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS---------------
->UniRef90_O56869
--RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS
-GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV
-GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES
--QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA
-YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP-------------
diff --git a/binaries/src/jpred/tests/res_d16vpa_.concise b/binaries/src/jpred/tests/res_d16vpa_.concise
deleted file mode 100644 (file)
index 38a9914..0000000
+++ /dev/null
@@ -1,25 +0,0 @@
-align1;QUERY:S,R,M,P,S,P,P,M,P,V,P,P,A,A,L,F,N,R,L,L,D,D,L,G,F,S,A,G,P,A,L,C,T,M,L,D,T,W,N,E,D,L,F,S,A,L,P,T,N,A,D,L,Y,R,E,C,K,F,L,S,T,L,P,S,D,V,V,E,W,G,D,A,Y,V,P,E,R,T,Q,I,D,I,R,A,H,G,D,V,A,F,P,T,L,P,A,T,R,D,G,L,G,L,Y,Y,E,A,L,S,R,F,F,H,A,E,L,R,A,R,E,E,S,Y,R,T,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,V,R,Q,L,H,R,Q,A,H,M,R,G,R,D,R,D,L,G,E,M,L,R,A,T,I,A,D,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,T,R,E,I,L,W,A,A,Y,A,E,Q,M,M,R,P,D,L,F,D,C,L,C,C,D,L,E,S,W,R,Q,L,A,G,L,F,Q,P,F,M,F,V,N,G,A,L,T,V,R,G,V,P,I,E,A,R,R,L,R,E,L,N,H,I,R,E,H,L,N,L,P,L,V,R,S,A,A,T,E,E,P,G,A,P,L,T,T,P,P,T,L,H,G,N,Q,A,R,A,S,G,Y,F,M,V,L,I,R,A,K,L,D,S,Y,S,S,F,T,T,S,P,S,E,A,V,M,R,E,H,A,Y,S,R,A,P,T,K,N,N,Y,G,S,T,I,E,G,L,L,D,L,P,D,D,D,A,P,E,E,A,G,L,A,A,P,R,L,S,F,L,
-align2;UniRef90_Q00028:-,-,-,-,-,P,P,K,A,T,S,P,T,A,L,Y,Q,R,L,Q,A,E,L,G,F,P,E,G,Q,A,M,L,F,A,M,E,K,W,N,E,D,M,F,S,A,I,P,V,H,V,D,L,Y,T,E,I,A,L,L,S,T,S,V,N,E,V,V,K,A,G,L,D,S,L,P,I,P,T,E,V,D,L,N,A,H,G,S,E,P,F,P,E,V,P,A,L,E,D,E,L,E,T,Y,V,I,S,A,Q,R,F,Y,L,S,E,L,R,A,R,E,E,H,Y,S,R,L,L,R,G,Y,C,V,A,L,L,H,Y,L,Y,G,S,A,K,R,Q,L,R,G,A,-,-,-,G,S,D,S,A,L,M,H,K,F,K,Q,V,V,R,D,R,Y,Y,R,E,T,A,N,L,A,R,L,L,Y,L,H,L,Y,I,S,V,T,R,E,V,S,W,R,L,H,A,S,Q,V,V,N,Q,G,I,F,V,S,L,H,Y,T,W,P,Q,R,R,K,F,E,C,L,F,H,P,V,L,F,N,H,G,V,V,I,L,E,N,D,P,L,E,F,N,D,L,Q,R,I,N,Y,R,R,R,E,L,G,L,P,L,I,R,A,G,L,I,E,E,E,N,L,P,L,E,S,E,P,T,F,S,G,K,L,P,R,T,I,G,F,L,T,H,Q,I,R,T,K,M,E,A,Y,S,N,A,H,P,S,T,P,L,F,P,L,A,E,H,S,Y,S,R,I,D,G,R,L,S,Y,G,T,T,A,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align3;UniRef90_Q8B635:-,-,-,-,-,P,I,K,A,S,S,P,S,S,L,I,K,N,L,L,D,E,L,N,F,P,E,G,P,S,L,L,S,S,M,E,K,W,N,E,D,L,F,S,C,I,P,R,F,L,E,I,Y,I,E,N,S,I,L,S,T,S,V,D,E,V,I,K,N,L,D,N,S,L,N,Y,D,D,V,I,D,F,Q,V,H,G,P,E,T,F,P,K,T,P,L,L,E,E,E,L,E,N,Y,V,T,S,V,Q,K,Y,F,L,S,E,L,K,A,R,E,V,T,Y,S,F,L,L,T,K,Y,C,K,A,L,L,L,Y,L,R,Y,N,T,K,S,S,I,K,G,-,-,-,-,-,-,N,K,D,I,N,Q,K,F,K,Q,N,V,R,E,R,Y,Y,R,E,V,A,N,I,A,R,L,L,Y,L,H,L,Y,L,S,V,T,R,E,V,S,W,K,L,H,A,D,Q,V,L,L,Q,S,V,F,V,S,L,S,Y,S,W,S,H,R,R,Q,F,E,C,I,F,H,P,I,L,F,N,H,G,I,V,N,L,E,N,N,P,L,T,F,K,E,L,Q,K,I,N,Y,R,R,H,I,L,G,L,P,L,I,R,A,G,L,V,E,E,D,N,Q,P,L,M,I,P,P,E,F,S,S,K,L,P,R,T,I,G,F,L,T,Q,Q,I,R,A,K,M,E,A,Y,S,D,N,H,P,V,T,P,K,F,P,R,I,E,H,S,Y,A,K,P,I,D,P,I,N,Y,G,T,T,I,E,A,M,M,D,P,P,S,P,S,A,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align4;UniRef90_Q9E205:-,-,-,-,-,P,P,R,V,A,S,P,A,V,L,Y,Q,Q,L,I,N,D,L,H,F,S,E,G,P,R,I,I,A,L,L,E,T,C,N,E,D,I,F,S,C,F,P,L,N,E,D,L,Y,T,D,T,I,V,F,S,T,N,P,S,D,I,I,E,L,E,T,S,E,T,P,E,-,-,P,I,N,L,I,T,K,G,-,C,D,L,P,S,L,P,S,T,Y,T,E,L,P,M,Y,V,E,N,V,Q,N,T,F,F,T,E,L,R,V,R,E,K,A,Y,L,R,L,L,I,L,Y,C,K,S,L,L,R,H,L,Q,G,I,S,R,R,S,S,V,G,A,R,S,Q,D,C,E,H,K,Y,I,T,Q,F,K,Q,S,I,R,L,R,Y,Y,R,E,V,A,K,L,A,R,L,L,Y,L,H,L,Y,I,T,V,T,R,Q,F,S,W,R,L,F,A,Q,Q,S,K,Y,P,D,V,F,A,A,M,K,F,M,W,L,E,N,R,Q,F,T,C,A,F,H,P,I,L,C,N,H,G,I,V,L,L,E,G,K,P,L,S,S,Q,R,L,R,E,V,N,Y,R,R,R,Q,L,G,L,P,L,V,R,C,A,L,I,E,E,K,G,V,P,L,V,Q,R,P,E,F,S,A,H,M,P,R,S,L,G,F,L,T,H,H,I,K,A,K,L,D,V,Y,S,S,K,H,S,Q,E,P,G,N,V,R,V,D,H,P,Y,A,R,N,V,N,N,I,N,Y,G,S,S,V,E,A,M,I,V,S,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align5;UniRef90_Q88530:-,-,L,P,S,P,E,-,A,A,S,P,N,L,L,Y,D,R,L,I,L,E,L,D,F,A,E,G,P,S,L,L,A,K,L,E,R,V,N,V,D,L,F,S,C,L,P,L,N,S,H,L,Y,K,H,A,K,I,L,S,T,C,P,R,E,V,L,D,A,V,Y,E,N,T,W,Q,Y,T,A,L,N,L,N,E,H,G,K,S,S,I,P,P,V,P,A,S,K,D,D,L,P,A,Y,V,T,A,V,Q,E,F,Y,L,E,E,L,E,A,R,E,Q,I,Y,A,K,L,F,F,G,Y,C,R,A,L,I,M,H,I,I,K,S,V,-,-,L,N,E,S,R,G,V,R,V,S,D,D,Y,V,Q,N,K,A,R,W,Y,I,S,N,N,Y,Y,R,D,A,V,R,I,A,K,L,L,Y,L,H,L,Y,L,S,T,T,E,I,V,S,Q,R,L,E,A,M,Q,T,S,L,Q,D,L,F,V,Y,L,R,C,E,W,G,Q,G,R,Q,F,W,C,I,F,Q,P,M,I,Y,N,H,G,V,P,M,I,E,G,R,A,L,T,S,L,E,L,G,S,S,N,Y,I,R,S,E,L,G,L,P,L,I,R,C,E,L,L,E,E,L,E,S,P,V,V,F,P,P,T,F,T,A,T,A,P,R,S,S,G,Y,L,F,H,N,I,R,A,K,M,E,L,Y,S,N,I,H,P,S,P,Q,L,S,G,L,S,D,H,T,Y,V,R,T,H,V,P,V,N,Y,G,T,T,V,E,V,L,L,D,A,S,D,P,D,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align6;UniRef90_B4XS08:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,F,P,E,A,S,T,I,L,S,T,F,E,L,M,N,M,D,L,F,S,C,L,P,R,N,E,D,L,Y,R,N,A,A,L,L,S,G,S,V,T,E,V,I,E,A,-,-,S,E,I,P,I,D,G,E,I,D,L,N,A,H,G,S,K,Q,L,P,I,P,P,S,N,E,W,E,I,P,N,Y,V,E,A,V,Q,Q,F,F,L,S,E,L,R,A,R,E,E,S,Y,L,K,L,F,L,G,Y,C,R,A,I,V,N,Y,I,K,S,A,A,T,R,G,V,R,G,C,R,I,M,D,R,K,S,E,A,N,K,R,M,R,R,M,I,A,D,R,Y,Y,R,E,A,A,R,L,A,K,V,L,Y,L,H,L,Y,L,S,V,A,R,E,I,S,S,R,L,C,A,T,Q,M,Q,V,Q,N,V,F,V,Y,M,R,Y,E,W,Q,Q,Y,R,Q,F,T,C,L,F,H,P,I,M,F,N,H,G,V,V,L,L,N,G,E,P,L,Q,A,Q,K,L,R,E,V,N,Y,I,R,F,K,L,G,L,P,V,I,R,C,G,L,V,E,E,H,D,K,P,L,V,E,E,P,R,F,Y,G,N,L,P,R,S,S,G,F,L,T,E,L,I,R,S,K,M,E,A,Y,S,E,L,R,P,T,S,P,S,S,I,S,N,D,H,T,Y,A,K,Q,L,D,K,V,N,F,G,S,T,R,E,A,I,L,D,T,I,D,T,E,G,P,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align7;UniRef90_P09265:-,-,-,P,S,P,P,W,V,A,S,P,K,I,L,Y,Q,Q,L,I,R,D,L,D,F,S,E,G,P,R,L,L,S,C,L,E,T,W,N,E,D,L,F,S,C,F,P,I,N,E,D,L,Y,S,D,M,M,V,L,S,P,D,P,D,D,V,I,-,-,-,-,S,T,V,S,T,K,D,H,V,N,L,T,T,R,G,S,V,R,L,P,S,P,P,K,Q,P,T,G,L,P,A,Y,V,Q,E,V,Q,D,S,F,T,V,E,L,R,A,R,E,E,A,Y,T,K,L,L,V,T,Y,C,K,S,I,I,R,Y,L,Q,G,T,A,K,R,T,T,I,G,L,N,I,Q,N,P,D,Q,K,A,Y,T,Q,L,R,Q,S,I,L,L,R,Y,Y,R,E,V,A,S,L,A,R,L,L,Y,L,H,L,Y,L,T,V,T,R,E,F,S,W,R,L,Y,A,S,Q,S,A,H,P,D,V,F,A,A,L,K,F,T,W,T,E,R,R,Q,F,T,C,A,F,H,P,V,L,C,N,H,G,I,V,L,L,E,G,K,P,L,T,A,S,A,L,R,E,I,N,Y,R,R,R,E,L,G,L,P,L,V,R,C,G,L,V,E,E,N,K,S,P,L,V,Q,Q,P,S,F,S,V,H,L,P,R,S,V,G,F,L,T,H,H,I,K,R,K,L,D,A,Y,A,V,K,H,P,Q,E,P,R,H,V,R,A,D,H,P,Y,A,K,V,V,E,N,R,N,Y,G,S,S,I,E,A,M,I,L,A,P,-,-,P,S,P,S,E,-,-,-,-,-,-,-,-,-,-,-,
-align8;UniRef90_Q2QBC8:-,-,-,-,-,-,-,-,-,-,-,-,A,A,L,Y,N,R,L,L,E,D,L,G,F,G,D,G,P,A,L,C,T,I,L,D,S,W,N,E,D,L,F,S,G,L,P,A,N,P,D,L,Y,R,E,C,R,F,L,S,T,L,P,G,D,V,V,V,W,G,D,A,H,A,P,D,R,G,P,I,D,I,R,A,H,G,S,A,P,F,P,S,L,P,A,R,R,E,G,L,P,A,Y,C,E,A,L,T,R,F,F,H,S,E,L,R,A,R,E,E,S,Y,R,R,V,L,A,N,F,C,S,A,L,Y,R,Y,L,R,A,S,T,R,Q,L,H,R,Q,A,A,L,K,G,R,P,R,D,L,Q,E,M,L,R,A,A,V,A,E,R,Y,Y,R,E,T,A,R,L,A,R,V,L,F,L,H,L,Y,L,F,L,V,R,E,I,L,W,A,V,Y,A,E,Q,V,M,R,Q,D,L,F,E,G,L,R,C,D,L,E,Q,A,R,Q,L,S,C,L,F,Q,P,L,L,F,V,H,G,A,L,S,V,G,G,E,P,V,S,P,A,R,L,R,E,L,N,H,V,R,E,R,L,N,L,P,L,I,R,S,A,A,T,E,E,P,G,A,A,L,T,A,A,P,A,L,Q,T,Q,R,A,R,S,S,G,Y,F,M,T,L,I,R,V,K,L,D,A,Y,S,E,W,S,A,G,S,E,G,A,V,L,R,E,H,A,Y,S,R,R,R,E,R,T,N,Y,G,S,S,I,E,G,L,L,E,L,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align9;UniRef90_Q90603:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,Y,T,R,L,L,H,E,L,D,F,V,E,G,P,S,I,L,A,R,L,E,K,I,N,V,D,L,F,S,C,F,P,H,N,K,H,L,Y,E,H,A,K,I,L,S,V,S,P,S,E,V,L,E,E,L,S,K,N,T,W,T,Y,T,A,L,N,L,N,E,H,G,E,V,A,L,P,M,P,P,T,T,K,A,D,L,P,S,Y,V,D,D,I,Q,N,F,Y,L,G,E,L,E,A,R,E,K,S,Y,A,T,M,F,Y,G,Y,C,R,A,L,A,E,Y,I,R,Q,S,A,I,K,D,L,R,D,A,-,-,R,V,E,D,K,N,I,G,A,C,S,K,A,R,Q,Y,I,A,E,R,Y,Y,R,E,A,F,A,N,V,L,Y,V,H,L,Y,L,S,T,T,R,D,V,S,Q,R,L,E,A,S,Q,M,G,R,Q,N,I,F,V,Y,L,K,C,E,W,L,Q,E,R,H,F,H,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,V,L,T,A,P,E,L,R,A,Q,N,Y,I,R,S,E,F,G,L,P,L,I,R,C,K,L,V,E,E,P,D,M,P,L,I,S,P,P,P,F,S,G,D,A,P,R,A,S,V,Y,L,L,Q,C,I,R,S,K,L,E,V,Y,S,S,H,P,P,N,P,Q,L,H,V,H,K,E,H,V,H,Q,K,L,E,S,P,P,N,Y,G,T,T,V,E,A,L,L,M,D,S,S,D,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align10;UniRef90_O89246:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,E,L,D,F,T,E,G,P,S,L,L,S,R,L,E,K,L,N,V,D,L,F,S,C,F,P,I,N,G,H,L,Y,E,H,A,T,L,L,S,V,S,P,S,E,V,L,D,A,A,S,E,E,K,W,A,Y,T,A,I,N,L,N,E,H,C,G,M,E,V,P,R,P,P,L,T,K,D,G,L,P,V,Y,V,T,E,I,Q,K,F,F,S,M,E,L,E,A,R,E,K,S,Y,V,T,L,L,C,G,Y,C,R,A,L,A,C,Y,L,R,Q,G,A,N,E,P,S,R,C,D,M,C,V,G,G,S,-,-,-,-,E,T,P,R,R,S,I,A,G,A,Y,Y,R,E,A,A,R,F,A,R,L,L,Y,M,H,L,Y,L,S,V,T,R,D,V,S,R,R,L,E,A,S,Q,R,K,R,Q,N,L,F,A,H,L,R,C,D,W,H,Q,L,R,H,F,Q,C,L,F,Q,P,V,I,F,N,H,G,V,V,I,V,E,G,R,A,L,T,A,A,E,L,R,T,Q,N,Y,V,R,S,E,L,G,L,P,V,M,R,C,E,L,V,E,E,R,G,M,P,L,T,A,P,P,A,F,L,A,N,A,P,R,A,S,A,Y,L,F,Q,C,I,K,S,K,L,E,V,Y,S,L,M,H,P,P,R,P,R,S,S,A,R,G,E,S,G,R,A,G,K,A,G,P,S,H,G,T,I,V,K,A,M,L,R,D,S,T,H,P,G,P,A,I,A,D,I,A,A,A,R,-,-,-,-,
-align11;UniRef90_Q5PP87:-,-,-,-,-,-,-,-,-,-,S,P,D,A,L,Y,Q,R,L,I,S,D,L,A,F,D,E,G,P,A,L,L,G,A,M,E,R,W,N,E,D,L,F,S,C,L,P,G,N,E,D,L,Y,A,R,L,V,M,L,S,A,S,A,D,E,V,A,A,Q,V,R,A,P,T,A,D,A,S,-,V,D,L,G,V,P,G,A,E,P,M,P,R,V,P,A,V,E,E,E,L,P,A,Y,V,A,A,V,E,R,F,F,V,S,T,L,R,A,R,E,E,R,Y,A,R,L,L,D,A,Y,C,R,A,V,L,R,Y,L,H,A,Q,A,R,R,D,-,-,-,-,-,-,-,-,-,-,-,-,-,E,G,K,L,R,Q,L,V,R,G,R,Y,Y,R,D,V,A,R,L,A,P,W,L,F,L,H,L,Y,V,A,T,A,R,E,L,S,W,R,L,H,A,D,Q,V,V,A,Q,D,V,F,M,S,L,R,Y,E,W,D,Q,A,R,Q,L,T,C,L,F,H,P,V,L,F,N,H,G,V,V,L,L,S,G,A,P,V,P,A,A,Q,L,R,A,V,N,H,R,R,R,E,L,G,L,P,L,V,R,A,G,L,I,E,E,D,G,A,D,L,V,E,E,P,P,F,S,A,A,L,P,R,A,A,G,Y,L,S,H,Q,V,R,I,K,M,E,A,Y,S,-,-,-,-,-,-,-,-,R,E,Y,R,D,H,T,Y,C,R,P,P,S,P,V,S,Y,G,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align12;UniRef90_Q65819:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,E,R,M,Q,A,E,L,G,F,P,D,G,P,A,L,L,R,A,M,E,R,W,N,E,D,L,F,S,C,L,P,T,N,A,D,L,Y,A,D,A,A,L,L,S,A,D,A,D,A,V,V,G,A,M,Y,L,A,V,P,D,A,E,R,L,D,L,N,A,H,A,N,Q,P,L,P,A,P,P,A,S,E,E,G,L,P,E,Y,V,A,G,V,Q,A,H,F,L,A,E,L,R,A,R,E,E,R,Y,A,G,L,F,L,G,Y,C,R,A,L,L,Q,H,L,R,A,-,-,-,-,T,A,A,R,G,R,G,A,A,G,A,G,A,Q,A,D,R,L,R,Q,L,V,A,A,R,Y,Y,R,E,A,S,R,L,A,R,L,A,F,A,H,M,Y,V,A,T,A,R,E,V,S,W,R,L,H,S,Q,Q,S,Q,A,Q,G,V,F,V,S,L,Y,Y,A,W,P,Q,R,R,Q,F,T,C,L,F,H,P,V,L,F,N,H,G,V,V,A,L,E,D,G,F,L,D,A,A,E,L,R,R,L,N,Y,R,R,R,E,L,G,L,P,L,V,R,A,G,L,V,E,V,E,V,G,P,L,V,E,E,P,P,F,S,G,S,L,P,R,A,L,G,F,L,N,Y,Q,V,R,A,K,M,G,A,P,A,E,-,-,A,G,G,R,L,A,P,E,R,E,H,S,Y,A,R,P,R,G,A,I,N,Y,G,T,T,P,E,A,M,L,R,P,P,S,P,S,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-align13;UniRef90_O56869:-,R,N,P,G,P,P,A,L,V,S,A,S,F,L,A,K,N,A,L,T,E,L,Q,F,A,D,W,D,K,I,Q,H,V,L,K,T,I,N,I,D,I,F,S,C,V,P,V,G,E,N,G,L,C,N,M,D,W,F,S,L,D,T,E,K,I,W,T,L,M,D,S,G,T,P,N,V,S,P,N,L,L,I,T,P,G,P,P,-,-,P,E,C,I,K,T,P,E,E,A,P,A,Y,F,E,A,I,S,N,Y,F,E,S,V,L,A,A,R,E,A,E,Y,A,K,L,L,A,E,Y,A,K,S,L,A,K,Y,I,R,H,K,S,Q,K,V,G,R,-,-,G,L,R,A,L,E,L,D,T,E,E,A,K,K,R,L,M,K,S,E,Y,Y,K,G,I,E,K,L,L,I,I,F,L,V,H,L,V,L,N,A,C,R,D,V,A,R,I,I,W,V,Q,Q,R,D,S,S,S,V,L,Q,K,V,T,Y,R,W,E,S,-,Q,Q,L,H,C,I,F,Q,P,L,L,V,S,P,G,P,V,F,L,D,N,D,P,L,P,L,Q,T,L,Q,H,V,N,Y,V,R,Y,L,L,G,V,P,V,L,R,F,S,M,I,E,E,S,P,S,A,Q,Y,I,P,-,-,-,-,Y,D,K,T,A,P,S,A,Y,D,V,L,A,T,I,A,R,-,-,-,-,T,C,L,T,S,S,G,C,S,R,A,S,H,D,H,T,Y,A,R,D,N,E,K,P,N,Y,S,S,S,R,I,V,L,L,A,D,S,A,L,D,T,P,-,-,-,-,-,-,-,-,-,-,-,-,-,
-
-jnetpred:-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,E,E,-,-,-,-,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,E,E,E,E,E,E,E,-,-,-,H,-,H,H,E,E,-,-,-,-,E,E,-,-,-,-,E,E,E,E,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,H,H,H,-,-,-,-,-,E,E,E,E,E,-,-,-,-,-,-,-,-,-,E,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-JNETCONF:9,9,8,8,8,8,8,7,7,6,3,6,8,8,9,9,9,9,8,7,4,4,7,8,8,8,7,4,6,8,8,9,9,9,9,9,8,5,4,2,3,2,2,2,3,2,3,5,6,6,5,1,0,1,2,2,2,4,0,5,7,6,1,6,8,8,8,7,6,3,2,3,6,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,4,1,0,2,3,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,7,3,2,1,4,1,1,1,5,7,7,7,7,5,1,7,8,9,9,9,9,9,9,9,9,9,8,5,4,6,8,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,9,8,6,1,1,1,4,4,5,5,2,1,3,5,4,5,6,4,4,6,3,0,1,1,1,1,1,1,3,4,5,1,1,2,5,6,4,5,7,7,5,3,6,8,7,7,6,5,4,1,0,0,1,1,1,0,4,3,2,1,0,5,7,5,1,1,1,1,1,0,0,1,7,8,7,7,5,2,1,0,3,6,7,6,5,6,7,7,6,2,1,2,6,6,8,9,9,9,9,8,8,7,5,1,0,2,4,6,7,7,7,7,7,6,7,7,7,7,7,7,6,4,1,4,6,7,7,7,7,7,7,7,6,5,1,0,3,3,3,2,1,6,7,7,7,7,6,5,4,4,5,7,7,7,7,6,3,3,4,2,6,
-JNETSOL25:-,-,-,-,-,-,-,-,B,-,B,B,-,B,B,B,-,-,B,B,-,-,B,-,B,-,-,B,-,-,B,B,-,B,B,-,-,B,-,B,B,B,B,B,B,B,B,B,B,-,-,B,B,B,B,B,-,B,B,B,B,B,B,-,-,B,B,-,B,B,-,-,-,B,B,-,-,-,B,B,B,B,-,B,-,B,-,-,-,B,-,-,B,B,-,-,-,-,-,B,-,-,B,B,-,-,B,-,-,B,B,-,-,-,B,-,B,B,B,-,-,B,B,-,B,B,B,-,B,B,B,B,B,B,-,B,B,-,-,-,B,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,B,-,-,B,B,-,B,B,B,-,-,-,B,B,-,B,B,B,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,B,-,-,-,-,-,B,B,B,B,B,-,B,-,B,-,-,-,-,-,B,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,-,-,B,B,-,B,-,-,B,-,-,B,-,B,B,B,-,-,B,-,B,B,B,B,B,B,-,B,B,-,-,-,-,-,-,B,B,-,-,B,-,B,-,B,-,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,B,-,B,B,B,-,B,-,-,-,-,-,-,-,-,B,-,-,B,B,B,B,B,-,-,-,-,B,B,B,B,B,B,B,B,B,B,B,-,B,B,-,-,-,B,B,-,-,B,-,B,B,B,-,-,B,-,-,-,
-JNETSOL5:-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,B,-,-,B,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,B,-,-,-,-,-,-,B,B,-,B,B,-,-,-,-,-,-,B,-,-,B,-,B,B,-,-,-,-,-,-,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,B,-,-,-,-,-,-,-,B,-,-,-,-,-,-,B,-,-,B,B,-,-,B,B,-,B,B,B,-,-,B,-,-,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,-,-,-,-,-,-,B,-,-,B,B,-,B,B,-,B,-,-,-,B,-,B,B,-,-,B,B,-,-,B,-,-,-,-,-,-,-,-,-,B,B,-,-,B,-,B,-,-,-,-,-,-,-,B,-,B,B,B,-,B,-,B,B,-,-,B,B,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,B,B,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,B,-,B,-,-,-,B,-,-,-,B,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-JNETSOL0:-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,B,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,-,B,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
-JNETHMM:-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,H,H,H,-,-,-,E,-,-,-,-,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,E,E,E,E,E,E,E,-,-,-,-,-,-,E,E,E,-,-,-,-,E,E,-,-,-,-,E,E,E,E,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,H,H,-,-,-,-,-,-,E,E,E,E,E,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.hmm b/binaries/src/jpred/tests/res_d16vpa_.hmm
deleted file mode 100644 (file)
index c07a517..0000000
+++ /dev/null
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.jnet b/binaries/src/jpred/tests/res_d16vpa_.jnet
deleted file mode 100644 (file)
index a55c497..0000000
+++ /dev/null
@@ -1,12 +0,0 @@
-
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.profile b/binaries/src/jpred/tests/res_d16vpa_.profile
deleted file mode 100644 (file)
index 8e097f6..0000000
+++ /dev/null
@@ -1,365 +0,0 @@
-
-Last position-specific scoring matrix computed, weighted observed percentages rounded down, information per position, and relative weight of gapless real matches to pseudocounts
-           A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V   A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V
-    1 S    1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -2 -2 -1  4  1 -3 -2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.00    0.00
-    2 R   -1  6  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.00    0.00
-    3 M   -2 -2 -3 -4 -2 -2 -3 -4 -3  1  4 -2  5  0 -3 -2 -1 -2 -1  1    0   0   0   0   0   0   0   0   0   0  50   0  50   0   0   0   0   0   0   0  0.46 0.07
-    4 P   -1 -3 -3 -2 -3 -2 -2 -3 -3 -3 -4 -2 -3 -4  8 -1 -2 -4 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.20 0.13
-    5 S    1 -1  0 -1 -1  0 -1 -1 -1 -3 -3 -1 -2 -3 -1  5  1 -3 -2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0  0.63 0.13
-    6 P   -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -3 -5  8 -2 -2 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.29 0.21
-    7 P   -2 -2 -2 -1 -4 -1  2 -3 -2 -4 -4 -1 -3 -5  8 -1 -2 -4 -4 -3    0   0   0   0   0   0  19   0   0   0   0   0   0   0  81   0   0   0   0   0  1.76 0.21
-    8 M    1  3 -2 -3 -3  0 -1 -2 -2 -2 -1  3  4 -2 -3 -1 -2  7 -1 -2   19  17   0   0   0   0   0   0   0   0   0  27  20   0   0   0   0  17   0   0  0.46 0.21
-    9 P    2 -2 -2 -2 -1 -2 -2 -2 -2  0 -1 -2 -1 -2  4 -1 -1 -3 -2  3   28   1   1   1   0   1   1   1   0   1   2   1   0   1  21   1   1   0   1  35  0.36 0.17
-   10 V    4 -2 -2 -3 -1 -2 -2 -1 -3 -1 -2 -2 -1 -3 -2  0  2 -3 -2  2   66   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  13   0   0  20  0.44 0.21
-   11 P    0 -2  0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3  4  5  1 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0  20  80   0   0   0   0  0.73 0.21
-   12 P   -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  9 -2 -2 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.35 0.27
-   13 A    3 -2  2  2 -2 -1 -1  1 -2 -3 -3  1 -2 -4 -2  1  1 -4 -3 -2   40   0  12  11   0   0   0   7   0   0   0  11   0   0   0  10   7   0   0   0  0.36 0.30
-   14 A    4 -3 -3 -3 -2 -2 -2 -2 -3  1  1 -2 -1 -2 -2  1 -1 -4 -3  1   56   0   0   0   0   0   0   0   0  11  12   0   0   0   0  10   0   0   0  11  0.40 0.30
-   15 L   -3 -3 -5 -5 -2 -3 -4 -5 -4  1  6 -4  1 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  0.95 0.36
-   16 F    1 -3 -3 -4 -3 -3 -3 -4  0  0 -2 -3 -2  4 -4 -2 -2  0  7 -2   15   0   0   0   0   0   0   0   0   7   0   0   0  15   0   0   0   0  62   0  0.98 0.39
-   17 N   -2  0  3  1 -4  5  2 -3 -1 -4 -4  3 -2 -4 -3 -1  1 -4 -3 -4    0   0  20   8   0  32  12   0   0   0   0  21   0   0   0   0   8   0   0   0  0.61 0.41
-   18 R   -3  6  3 -2 -5  3 -1 -3 -1 -4 -4  1 -3 -4 -3 -1 -2 -4 -3 -4    0  64  21   0   0  15   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.97 0.41
-   19 L    1 -3 -4 -5 -2 -3 -4 -4 -4  0  5 -3  4 -1 -4 -3 -2 -3 -2  0   14   0   0   0   0   0   0   0   0   0  74   0  12   0   0   0   0   0   0   0  0.72 0.41
-   20 L   -3 -3 -4 -4 -3  3 -2 -5 -3  4  4 -2  0 -1 -4 -3 -2 -3 -2  0    0   0   0   0   0  21   0   0   0  30  49   0   0   0   0   0   0   0   0   0  0.59 0.41
-   21 D    1  1  1  3 -3 -1  0  0  3 -3 -1 -1 -2 -4 -3  1  2 -4 -3 -3   17   8   7  20   0   0   6   5   8   0   8   0   0   0   0   7  14   0   0   0  0.26 0.41
-   22 D   -2 -2 -1  5 -5  0  6 -3 -2 -5 -5 -1 -4 -5 -3 -1 -2 -5 -4 -4    0   0   0  39   0   0  61   0   0   0   0   0   0   0   0   0   0   0   0   0  1.12 0.43
-   23 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  1  6 -4  1 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  1.04 0.43
-   24 G    0 -2  1  4 -4  2 -1  4  2 -5 -5 -2 -3 -4 -3 -1 -2 -4 -3 -4    6   0   6  28   0  14   0  39   7   0   0   0   0   0   0   0   0   0   0   0  0.68 0.43
-   25 F   -4 -4 -4 -5 -4 -5 -5 -5 -3 -1 -1 -5 -1  8 -5 -4 -3  0  2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0  1.58 0.43
-   26 S    2 -3 -2  0 -3 -2 -2  0 -3 -3 -3 -2 -3 -4  5  3  1 -4 -3  0   21   0   0   6   0   0   0   6   0   0   0   0   0   0  26  27   6   0   0   7  0.57 0.43
-   27 A    1 -2 -1  4 -4  0  5 -3 -2 -4 -4 -1 -3 -5 -2 -1 -2 -5 -4 -4   13   0   0  30   0   0  57   0   0   0   0   0   0   0   0   0   0   0   0   0  0.91 0.43
-   28 G   -1 -4 -2 -3 -4 -3 -4  7 -3 -5 -5 -3 -4 -3 -4 -2 -3  6 -3 -5    0   0   0   0   0   0   0  86   0   0   0   0   0   0   0   0   0  14   0   0  1.48 0.43
-   29 P   -2 -3 -2  2 -4  1 -1 -3 -3 -4 -4 -2 -4 -5  8 -2 -2 -5 -4 -4    0   0   0  13   0   9   0   0   0   0   0   0   0   0  78   0   0   0   0   0  1.85 0.46
-   30 A    4  2 -2 -2 -3 -1  0 -2 -2 -3 -3  2 -3 -4 -2  3  0 -4 -3 -2   38  13   0   0   0   0   6   0   0   0   0  13   0   0   0  25   4   0   0   0  0.48 0.46
-   31 L   -1 -4 -5 -5 -3 -4 -4 -5 -4  4  5 -4  2 -1 -4 -3 -2 -3 -2  0    6   0   0   0   0   0   0   0   0  26  64   0   4   0   0   0   0   0   0   0  0.75 0.46
-   32 C   -2 -3 -4 -4  5  2 -3 -4 -3  1  4 -3  0 -2 -4 -1 -2 -3 -3 -1    0   0   0   0  17  13   0   0   0   6  57   0   0   0   0   6   0   0   0   0  0.62 0.46
-   33 T    2  1 -1 -2 -3 -2 -2  0  4 -3 -3 -1 -2  0 -3  3  3 -4 -2 -2   20  11   0   0   0   0   0   6  13   0   0   0   0   4   0  23  23   0   0   0  0.40 0.46
-   34 M    2  2 -3 -4  3 -2 -3 -3 -3  2  0  0  3 -3 -3  0 -2 -4 -3  2   25  12   0   0   7   0   0   0   0  11   6   7  12   0   0   6   0   0   0  13  0.28 0.46
-   35 L   -3 -3 -4 -5 -3 -3 -4 -5 -4  0  5 -3  6 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0  69   0  31   0   0   0   0   0   0   0  0.94 0.46
-   36 D   -2 -1 -1  3 -5  0  6 -3 -2 -5 -4  2 -3 -5 -2  0 -2 -5 -4 -4    0   0   0  17   0   0  64   0   0   0   0  13   0   0   0   6   0   0   0   0  0.93 0.46
-   37 T   -2  4 -1 -2 -3 -1 -1 -3 -2 -3 -3  3 -2 -4 -3  0  5 -4 -3 -2    0  23   0   0   0   0   0   0   0   0   0  27   0   0   0   5  44   0   0   0  0.68 0.46
-   38 W   -3 -4 -5 -5  3 -4 -4 -4 -4  2  0 -4 -1  1 -5 -4 -3 11  0  0    0   0   0   0   6   0   0   0   0  20   6   0   0   6   0   0   0  56   0   7  1.64 0.46
-   39 N   -3 -2  8  0 -4 -1 -2 -2 -1 -5 -5 -1 -4 -5 -3 -1 -1 -5 -4 -4    0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.50 0.46
-   40 E   -2 -2 -2 -1 -4  0  5 -4 -2  2 -2 -1  1 -3 -3 -2 -2 -4 -3  2    0   0   0   0   0   0  62   0   0  13   0   0   6   0   0   0   0   0   0  19  0.69 0.46
-   41 D   -3 -3  0  8 -5 -2  0 -3 -2 -5 -5 -2 -5 -5 -3 -1 -2 -6 -5 -5    0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.63 0.46
-   42 L   -3 -4 -5 -5 -3 -3 -4 -5 -4  3  5 -4  3 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0  20  72   0   9   0   0   0   0   0   0   0  0.85 0.46
-   43 F   -4 -4 -5 -5 -4 -5 -5 -5 -3 -1 -1 -5 -1  8 -5 -4 -4  0  2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0  1.62 0.46
-   44 S    0 -2 -1 -1 -2 -1 -1 -2 -2 -4 -4 -1 -3 -4 -2  6  0 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0  1.06 0.46
-   45 A    2 -4 -4 -4 10 -4 -4  1 -4 -3 -3 -4 -3 -4 -4 -2 -2 -4 -4 -2   16   0   0   0  74   0   0  10   0   0   0   0   0   0   0   0   0   0   0   0  1.59 0.46
-   46 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  2  4 -4  0  5 -5 -4 -3 -2  0  2    0   0   0   0   0   0   0   0   0  10  46   0   0  30   0   0   0   0   0  13  0.72 0.46
-   47 P   -2 -4 -3 -3 -4 -3 -2 -4 -4 -4 -4 -2 -4 -5  9 -2 -2 -5 -4 -4    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.52 0.46
-   48 T    0  1 -2 -3 -3 -2 -3  1  2  2  1 -2 -1 -3 -3 -2  3 -4 -3  2    5  12   0   0   0   0   0  10   7  13  13   0   0   0   0   0  23   0   0  18  0.25 0.46
-   49 N   -3 -2  7  0 -4 -1 -2  2  3 -5 -4 -2 -3  0 -4 -1 -2 -4 -2 -4    0   0  72   0   0   0   0  13   9   0   0   0   0   6   0   0   0   0   0   0  1.03 0.46
-   50 A    1 -2 -2 -1 -3 -1  4  0 -2 -2 -1  1 -2 -4  1  0 -2 -4 -3  0   12   0   0   0   0   0  38   6   0   0   6   7   0   0   5   7   0   0   0   9  0.27 0.46
-   51 D   -3 -2  3  6 -4 -1  1 -3  5 -4 -4 -2 -4 -4 -3 -2 -2 -5 -2 -4    0   0  13  51   0   0   6   0  19   0   0   0   0   0   0   0   0   0   0   0  0.84 0.46
-   52 L   -2 -3 -4 -4 -3 -3 -4  1 -4  1  5 -3  2 -1 -4 -3 -2 -3 -3 -1    0   0   0   0   0   0   0  13   0   6  66   0   4   0   0   0   0   0   0   0  0.54 0.46
-   53 Y   -3 -3 -3 -4 -3 -3 -3 -4  0 -2  1 -3 -2  2 -4 -3 -3  1  8 -2    0   0   0   0   0   0   0   0   0   0  13   0   0   0   0   0   0   0  76   0  1.16 0.46
-   54 R    0  3 -2 -2  5 -1  1 -3 -2 -1 -3  1 -2 -4 -3  0  2 -4 -3 -2    6  23   0   0  13   0  12   0   0   6   0   7   0   0   0   7  15   0   0   0  0.29 0.46
-   55 E   -3  1  3  3 -4  0  4 -3  5 -4 -4 -1 -3 -4 -3 -1 -2 -4 -2 -4    0   6  19  13   0   0  32   0  19   0   0   0   0   0   0   0   0   0   0   0  0.59 0.46
-   56 C    2 -3  0 -3  6 -2 -3 -3 -3  1  0 -3  5 -2 -3 -1  0 -3 -3 -1   25   0   6   0  17   0   0   0   0   9   6   0  20   0   0   0   6   0   0   0  0.36 0.46
-   57 K    1  1 -2  2 -3 -1 -1 -3 -3  0 -2  3  2 -3 -3  0  0 -4 -3  0   14   5   0  13   0   0   0   0   0   6   0  26   7   0   0   6   6   0   0   6  0.17 0.46
-   58 F   -3 -4 -4 -5 -3 -3 -4 -4 -4  3  2 -4  2  3 -4 -3 -2  6 -1  2    0   0   0   0   0   0   0   0   0  19  20   0   6  17   0   0   0  13   0  13  0.52 0.46
-   59 L   -3 -3 -4 -4 -3 -3 -4 -4 -3  0  5 -4  0  4 -4 -4 -3 -2 -1 -1    0   0   0   0   0   0   0   0   0   0  63   0   0  20   0   0   0   0   0   0  0.57 0.46
-   60 S    0 -2 -1 -2 -2 -1 -1 -2 -2 -3 -4 -2 -3 -3 -2  6  0 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  83   0   0   0   0  0.70 0.46
-   61 T    0 -3 -2 -3 -2 -2 -3  0 -3 -1  1 -2 -1 -3  1 -1  5 -3 -3  0    6   0   0   0   0   0   0   6   0   0  13   0   0   0   7   0  45   0   0   6  0.28 0.46
-   62 L   -2 -3  1  3  3 -2 -1 -2 -2 -2  1 -2 -2 -3 -3  3 -1 -4 -3 -2    0   0   6  20   7   0   0   0   0   0  17   0   0   0   0  32   0   0   0   0  0.24 0.46
-   63 P    0 -3 -3 -3 -3 -3 -3 -3 -3 -1 -2 -2 -2 -3  6 -2  2 -4 -3  2    6   0   0   0   0   0   0   0   0   0   0   0   0   0  43   0  13   0   0  20  0.73 0.46
-   64 S   -2  1  1  4 -3 -1  2  0 -2 -4 -4 -1 -3 -4 -3  3  0 -4 -3 -3    0   7   4  23   0   0  13   5   0   0   0   0   0   0   0  24   6   0   0   0  0.29 0.46
-   65 D   -2 -1 -1  4 -4  0  4 -3 -2 -4 -4  2 -3 -4 -2 -2 -2 -4 -3 -4    0   0   0  31   0   0  39   0   0   0   0  13   0   0   0   0   0   0   0   0  0.61 0.46
-   66 V   -2 -4 -4 -4 -2 -4 -4 -5 -4  4  0 -4  0 -2 -4 -3 -1 -4 -3  6    0   0   0   0   0   0   0   0   0  20   0   0   0   0   0   0   0   0   0  74  0.79 0.46
-   67 V    0 -4 -4 -4 -2 -4 -4 -4 -4  4  1 -4  0 -1 -4 -3 -2  6 -2  4    6   0   0   0   0   0   0   0   0  29  12   0   0   0   0   0   0  13   0  32  0.60 0.46
-   68 E    0  0 -1  3 -3 -1  3  1 -2 -3 -3  1 -3 -4 -2 -1  2 -4 -3 -1    7   5   0  17   0   0  20  11   0   0   1  10   0   0   0   1  14   0   0   6  0.24 0.42
-   69 W    3 -2  0 -3 -2  1 -2 -2 -3 -2  1 -2 -1 -2 -3 -1 -2  7 -1 -2   38   0   6   0   0   6   0   1   0   0  20   0   0   0   0   1   0  18   0   0  0.46 0.42
-   70 G    0 -3 -2 -3 -3 -2  0  3 -3 -1  0 -2  5 -2 -3  0 -2 -3 -3  1    6   0   0   0   0   0   7  27   0   0   6   0  24   0   0   6   0   0   0  13  0.29 0.42
-   71 D   -2  0 -1  5 -3 -1  1 -3 -1 -3 -2 -2 -2 -2 -3  0  1 -2  4 -3    1   6   0  37   0   0   6   1   0   0   5   0   0   0   0   6  11   0  17   0  0.42 0.42
-   72 A    2 -2  2  0 -3 -1  2 -2 -2 -3  0  1 -2 -3 -2  3 -1 -4 -3 -2   24   0  10   5   0   0  13   0   0   0  11   7   0   0   0  27   0   0   0   0  0.30 0.43
-   73 Y    1 -2  2 -1 -3 -1  1  2  3 -3 -3 -2 -3 -2  1  1  1 -3  3 -3   11   0  14   0   0   0  12  14  10   0   1   0   0   0   6  10   7   0  12   0  0.31 0.43
-   74 V    0 -3 -3 -3 -2 -3 -3 -4 -4  2  1  0 -1 -3 -3 -1  4 -4 -3  3    5   0   0   0   0   0   0   0   0  10  10   6   0   0   0   0  39   0   0  30  0.47 0.46
-   75 P    0 -3  0 -3 -4 -2 -3 -3 -3 -4 -4 -2 -3 -3  7  0 -2  7 -2 -4    6   0   6   0   0   0   0   0   0   0   0   0   0   0  62   7   0  19   0   0  1.58 0.46
-   76 E   -1 -2  2  4 -4  1  3 -3 -2 -1 -3 -1 -3 -3 -3 -1  2 -4  1 -3    6   0  13  22   0   7  23   0   0   6   0   0   0   0   0   0  18   0   6   0  0.44 0.46
-   77 R    1  3 -2  2 -3 -1 -1 -3 -1 -2 -2  1 -2 -1  2 -2 -2 -2  4  1   11  18   0  12   0   0   1   1   0   1   1   8   0   0  11   1   1   0  19  14  0.31 0.41
-   78 T    0 -2 -1  2 -3 -1  1  1 -2  0 -3 -2 -2 -4 -2  2  3 -4 -3 -2    6   0   0  13   0   0  11  11   0   7   0   0   0   0   0  22  27   0   0   0  0.36 0.44
-   79 Q    2  1  1 -2 -3  1  1 -2  2 -3 -3 -1 -3 -4  4  0 -2 -4 -3 -1   19  11   7   0   0   8  10   0   7   0   0   0   0   0  23   6   0   0   0   6  0.44 0.44
-   80 I   -2 -4  2 -4 -3 -3 -4 -4 -4  4  3 -3  0 -2 -4 -3 -2 -4 -3  3    0   0  13   0   0   0   0   0   0  35  30   0   0   0   0   0   0   0   0  22  0.57 0.46
-   81 D   -3 -3  4  6 -4 -2 -1 -3 -2  0  0 -2 -2 -4 -3 -2 -2 -5 -4 -3    0   0  26  54   0   0   0   0   0   6  13   0   0   0   0   0   0   0   0   0  0.84 0.46
-   82 I   -3 -4 -4 -5 -3 -4 -4 -5 -4  3  5 -4  1  1 -4 -3  0 -3 -2  0    0   0   0   0   0   0   0   0   0  17  70   0   0   6   0   0   6   0   0   0  0.76 0.46
-   83 R   -2  3  5 -1 -4  1 -2  0 -1  1 -3  1 -2 -4 -3 -1  0 -5 -3 -2    0  17  44   0   0   6   0   6   0  13   0   6   0   0   0   0   7   0   0   0  0.55 0.46
-   84 A    4 -3 -2 -2 -2 -1  2  0 -3 -2 -3 -2 -2 -4 -2  0  3 -4 -3  1   42   0   0   0   0   0  19   6   0   0   0   0   0   0   0   0  20   0   0  12  0.44 0.46
-   85 H   -3  1 -1 -2 -4 -1 -1 -3  9 -4 -4 -2 -3 -3  4 -2 -3 -4  0 -4    0   7   0   0   0   0   0   0  67   0   1   0   0   0  20   0   0   0   0   0  1.30 0.43
-   86 G    1 -3 -2 -3  2 -3 -3  6 -3 -4 -4 -3 -3 -4 -3 -1 -2 -3 -4 -3   11   0   0   0   6   0   0  78   0   0   1   0   0   0   0   0   0   0   0   0  1.15 0.43
-   87 D    0 -2  2  3 -3 -1  1  0 -2 -4 -4  0 -3 -4  4  2 -1 -4 -3 -3    7   0  11  17   0   0   7   6   0   0   1   7   0   0  19  23   0   0   0   0  0.48 0.43
-   88 V    0 -2 -2 -2  3  2  3 -3 -3 -1 -2  0  1 -3  3  0 -2 -4 -3  3    5   0   0   0   6  11  20   0   0   0   0   6   6   0  13   7   0   0   0  26  0.34 0.46
-   89 A    2  1 -2  1 -3  1  0 -2 -2 -3 -3 -1 -2 -3  5  1  0 -3 -3 -2   20   8   1   7   0   6   7   1   0   1   1   1   0   1  31   8   7   0   0   1  0.55 0.40
-   90 F   -2 -3 -3 -4 -2 -3 -3 -4 -3  1  3 -3  2  5 -3 -3 -2 -1  0  1    1   1   1   1   0   1   1   1   0   7  38   1   6  32   1   1   1   0   0   7  0.56 0.40
-   91 P   -2 -4 -3 -3 -4 -3 -2 -4 -4 -4 -4 -2 -4 -5  9 -2 -2 -5 -4 -4    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.52 0.46
-   92 T    1  2 -2 -2 -3 -1  3 -3 -2 -1 -3  1  2 -4  1  2  2 -4 -3 -2   11  12   0   0   0   0  22   0   0   6   0   6   7   0   7  19  12   0   0   0  0.31 0.46
-   93 L   -2 -4 -4 -4  5 -3 -3 -4 -4 -1  2 -3 -1 -3  5 -2  0 -4 -3  2    0   0   0   0  13   0   0   0   0   0  24   0   0   0  36   0   6   0   0  21  0.79 0.46
-   94 P   -2 -4 -4 -3 -4 -3 -3 -4 -4  1 -3 -3 -3 -4  8 -2 -2 -5 -4 -2    0   0   0   0   0   0   0   0   0  13   0   0   0   0  87   0   0   0   0   0  2.05 0.46
-   95 A    4 -1 -2 -3 -2 -1 -2 -2 -3 -2  0  2 -2 -3 -2  1  1 -4 -3 -2   49   0   0   0   0   0   0   0   0   0  11  20   0   0   0  12   7   0   0   0  0.46 0.46
-   96 T   -1  0  1 -2 -3  1 -2 -3 -3 -2  1 -2 -1 -3 -3  2  5 -4 -3  0    0   5   6   0   0   7   0   0   0   0  14   0   0   0   0  17  44   0   0   6  0.44 0.46
-   97 R   -2  3 -2 -1 -5  0  4 -4 -2 -4 -4  3 -3 -3  4 -2 -2 -4  1 -4    0  17   0   0   0   0  37   0   0   0   0  19   0   0  20   0   0   0   6   0  0.73 0.46
-   98 D    0 -2 -1  5 -4  0  4 -3 -2 -4 -4 -1 -3 -4 -3 -1  2  4 -3 -3    7   0   0  33   0   0  41   0   0   0   0   0   0   0   0   0  13   6   0   0  0.76 0.46
-   99 G   -2 -2 -1  3 -5 -1  5  4 -2 -5 -5 -1 -4 -5 -3 -1 -2 -4 -4 -4    0   0   0  18   0   0  46  36   0   0   0   0   0   0   0   0   0   0   0   0  0.86 0.46
-  100 L    1 -4 -5 -5 -2 -3 -4 -4 -4  1  5 -4  1 -1 -4 -3 -2 -3 -2  0   13   0   0   0   0   0   0   0   0   6  81   0   0   0   0   0   0   0   0   0  0.79 0.46
-  101 G   -2 -3 -3 -2 -4 -2  2  0 -3 -4 -4 -2 -4 -5  8 -2 -2 -5 -4 -4    0   0   0   0   0   0  14   8   0   0   0   0   0   0  78   0   0   0   0   0  1.81 0.46
-  102 L    3 -3  2 -2 -2 -2  1 -2 -3  0  0 -2  2 -3 -3  1  0 -4 -3  0   38   0  12   0   0   0  11   0   0   4   8   0   6   0   0  11   4   0   0   6  0.30 0.46
-  103 Y   -3 -3 -4 -5 -4 -3 -3 -5  1 -3 -2 -3 -2  2 -4 -3 -3  1  9 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0  1.77 0.46
-  104 Y   -2 -4 -4 -5  2 -4 -4 -5 -3  1 -1 -4 -1  3 -4 -3 -2 -2  3  5    0   0   0   0   5   0   0   0   0   0   0   0   0  13   0   0   0   0  12  69  0.74 0.46
-  105 E    1 -2 -2  1 -3  2  5 -3 -2  0 -3 -1 -2 -4 -3 -1  2 -4 -3 -2   17   0   0   7   0   7  43   0   0   9   0   0   0   0   0   0  18   0   0   0  0.51 0.46
-  106 A    4 -2  1  1 -3 -1  2  1 -2 -3 -4 -2 -3 -4 -2  2 -1 -4 -3 -2   49   0   6   7   0   0  13  11   0   0   0   0   0   0   0  14   0   0   0   0  0.50 0.46
-  107 L    0 -4 -4 -5 -2 -4 -4 -4 -4  4  1 -4  2 -2 -4 -3 -2 -4 -3  5    8   0   0   0   0   0   0   0   0  28  12   0   4   0   0   0   0   0   0  47  0.65 0.45
-  108 S    0 -1 -1 -1 -4  7  1 -3 -1 -4 -4  0 -2 -4 -2  2  0 -4 -3 -3    4   0   0   0   0  64   6   0   0   0   0   0   0   0   0  21   4   0   0   0  0.86 0.45
-  109 R    0  4  4  1 -4  2  1 -3 -1 -4 -4  2 -3 -4 -3 -1 -2 -5 -3 -4    9  26  29   8   0  10   7   0   0   0   0  11   0   0   0   0   0   0   0   0  0.58 0.45
-  110 F   -3 -3 -3 -4 -4 -3 -3 -4  3 -2 -1 -3 -2  7 -4  0  0  0  5 -2    0   0   0   0   0   0   0   0   9   0   0   0   0  58   0   8   6   0  19   0  0.97 0.45
-  111 F   -4 -4 -4 -5 -4 -4 -4 -5 -1 -2 -1 -4 -1  8 -5 -4 -3  0  5 -2    0   0   0   0   0   0   0   0   0   0   0   0   0  76   0   0   0   0  24   0  1.41 0.45
-  112 H   -2  0 -3 -3 -3 -2  1 -4  4 -1  3 -2  0  1 -4 -1  1 -3 -2  0    0   4   0   0   0   0  13   0  12   0  44   0   0   6   0   5   8   0   0   6  0.34 0.45
-  113 A    2 -2 -1 -2 -2 -2  0  2 -3 -2 -3 -2  1 -4 -3  4  1 -4 -3  0   16   0   0   0   0   0   7  14   0   0   0   0   5   0   0  42   6   0   0   8  0.42 0.45
-  114 E   -2 -2 -2  0 -4  0  6 -4 -2 -3 -3 -1 -3 -4 -3 -1  0 -4 -3  1    0   0   0   0   0   0  80   0   0   0   0   0   0   0   0   0   6   0   0  13  0.96 0.45
-  115 L   -3 -3 -4 -4 -3 -3 -4 -4 -4  0  5 -3  1 -1 -4 -3 -2 -3 -2 -1    0   0   0   0   0   0   0   0   0   0  80   0   0   0   0   0   0   0   0   0  0.64 0.45
-  116 R   -2  6 -2 -2 -4  0  3 -3 -2 -4 -3  1 -3 -4 -3 -2 -2 -4 -3 -3    0  53   0   0   0   0  22   0   0   0   0   5   0   0   0   0   0   0   0   0  0.64 0.45
-  117 A    5 -3 -3 -3 -2 -2 -2 -1 -3 -2 -2 -2 -2 -3 -2  0  0 -4 -3  0   70   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   4   0   0   6  0.49 0.45
-  118 R   -3  7 -2 -3 -4  0 -1 -3 -2 -4 -3  1 -3 -4 -3 -2 -2 -4 -3 -4    0  80   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.97 0.45
-  119 E   -2 -1 -2  0 -4  0  6 -3 -1 -4 -4 -1 -3 -4 -2 -1 -2 -4 -3 -3    0   0   0   0   0   0  80   0   0   0   0   0   0   0   0   0   0   0   0   0  0.88 0.45
-  120 E   -2 -1 -2 -1 -4  2  5 -3 -2 -3 -3  3 -3 -4 -2 -2 -2 -4 -3 -1    0   0   0   0   0   7  47   0   0   0   0  21   0   0   0   0   0   0   0   5  0.47 0.45
-  121 S    1  1 -1 -2 -2 -2 -2 -2  3  0 -3 -1 -2 -3 -2  4  1 -4 -2 -2   14   9   0   0   0   0   0   0   8   7   0   0   0   0   0  37   5   0   0   0  0.20 0.45
-  122 Y   -3 -3 -3 -4 -3 -3 -3 -4  0 -3 -2 -3 -2  2 -4 -3 -3  1  8 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  80   0  1.19 0.45
-  123 R    3  2 -2 -3 -2 -2 -2 -2 -3 -2  0 -1 -2 -3 -3  1  1 -3 -3  0   29  17   0   0   0   0   0   0   0   0  11   0   0   0   0   9   8   0   0   5  0.13 0.45
-  124 T   -2  3 -2 -2 -3 -1 -2  0 -2 -3 -3  3 -2  0 -3 -1  3 -3 -2 -3    0  18   0   0   0   0   0   9   0   0   0  21   0   5   0   0  27   0   0   0  0.24 0.45
-  125 V   -2 -3 -4 -4 -2 -3 -4 -4 -4  0  4 -3  3 -1 -4 -3 -2 -3 -2  2    0   0   0   0   0   0   0   0   0   0  54   0   9   0   0   0   0   0   0  17  0.44 0.45
-  126 L   -3 -3 -4 -4 -3 -3 -4 -4 -3  0  4 -4  0  5 -4 -3 -3 -2  0 -1    0   0   0   0   0   0   0   0   0   0  50   0   0  31   0   0   0   0   0   0  0.53 0.45
-  127 A    1  0 -3  0  2 -2 -3 -3 -2  0  1 -2 -1  1 -3 -2  0 -2  2  1   17   8   0   6   5   0   0   0   0   6  14   0   0   7   0   0   5   0   9   8  0.07 0.45
-  128 N    0 -2  3 -2 -3 -2 -2  5 -2 -3 -1  0 -3 -4 -3 -1  1 -4 -3 -3    6   0  17   0   0   0   0  44   0   0   6   5   0   0   0   0   8   0   0   0  0.46 0.45
-  129 F   -3 -3 -3 -4 -4 -3 -3 -4  0 -2 -2 -3 -2  4 -4 -3 -3  1  8 -2    0   0   0   0   0   0   0   0   0   0   0   0   0  17   0   0   0   0  70   0  1.18 0.45
-  130 C   -2 -4 -4 -4 10 -4 -5 -4 -4 -2 -3 -4 -3 -4 -4 -2 -2 -3 -4 -2    0   0   0   0  87   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.83 0.45
-  131 S   -2  5 -2 -2 -4 -1 -1 -3 -2 -3 -3  3 -2 -4 -3  2 -2 -4 -3  0    0  42   0   0   0   0   0   0   0   0   0  20   0   0   0  17   0   0   0   8  0.50 0.45
-  132 A    5 -3 -2 -3 -2 -2 -2 -1 -3 -3 -3 -2 -2 -4 -2  3 -1 -4 -3 -2   72   0   0   0   0   0   0   0   0   0   0   0   0   0   0  28   0   0   0   0  0.81 0.45
-  133 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  3  5 -4  1 -1 -4 -4 -2 -3 -2  1    0   0   0   0   0   0   0   0   0  14  80   0   0   0   0   0   0   0   0   6  0.88 0.45
-  134 Y    2 -3 -4 -4 -2 -3 -3 -3 -3  2  3 -3  0 -1 -4 -2 -2 -2  4  1   28   0   0   0   0   0   0   0   0  16  34   0   0   0   0   0   0   0  17   5  0.45 0.45
-  135 R   -2  5  0 -2  2  2  1 -3  3 -3 -1  2  2 -4 -3 -2 -2 -4 -3 -3    0  37   5   0   5   9   9   0   8   0   5  13   7   0   0   0   0   0   0   0  0.53 0.45
-  136 Y   -3 -3 -3 -4 -4 -2 -3 -4  6 -3 -3 -3 -2  1 -4 -3 -3  1  8 -3    0   0   0   0   0   0   0   0  22   0   0   0   0   0   0   0   0   0  78   0  1.49 0.45
-  137 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  4  5 -4  1 -1 -4 -4 -2 -3 -2  1    0   0   0   0   0   0   0   0   0  35  65   0   0   0   0   0   0   0   0   0  0.86 0.45
-  138 R   -3  6 -2 -3 -4  3 -1 -4  2  0 -3  1 -2 -3 -3 -2 -2 -3  2 -3    0  50   0   0   0  14   0   0   6   7   0   5   0   0   0   0   0   0   8   0  0.62 0.45
-  139 A    2 -2 -2 -2 -3  3 -1  3  4 -4 -4  1 -3 -3 -3  0 -2 -3  1 -3   23   0   0   0   0  15   0  22  13   0   0   7   0   0   0   5   0   0   5   0  0.35 0.45
-  140 S    0 -1  1 -2 -3  1 -1  0 -2 -1 -3  2 -2 -4 -2  4  1 -4 -3 -2    5   0   5   0   0   6   0   5   0   6   0  13   0   0   0  41   8   0   0   0  0.31 0.45
-  141 V    4 -3 -2 -3 -2 -2 -2 -2 -3 -1 -2 -2 -2 -3 -2  2  1 -4 -3  2   42   0   0   0   0   0   0   0   0   0   0   0   0   0   0  19  10   0   0  20  0.39 0.45
-  142 R   -2  4  1 -2 -3  3 -1 -3 -2  0 -2  3 -2 -3 -3 -1  0 -3 -3 -2    1  29   6   0   0  14   0   1   0  10   1  22   0   0   0   1   6   0   0   0  0.38 0.42
-  143 Q   -1  3 -1 -1 -3  3  1 -2 -1 -2 -2  3 -2 -3 -2 -1 -1 -2 -2 -2    2  21   1   1   1  18   7   2   1   1   2  24   1   1   1   2   2   0   1   2  0.34 0.33
-  144 L   -1 -2 -2  1 -2 -2 -2  0 -2 -1  2 -2 -1 -2  1  0  1 -3 -2  1    2   1   1  10   0   1   1   7   0   1  26   1   0   1   6   7   9   0   1  15  0.09 0.36
-  145 H   -1 -2  1 -2 -2 -1 -2  2  5 -2  0 -2 -1 -2 -2  1  1 -3 -1  0    2   1   8   1   0   1   1  15  17   1  11   1   0   1   1  13   9   0   1   7  0.16 0.36
-  146 R   -2  6 -2 -2 -3  0  1 -3 -2  0 -2  0 -2 -3 -3 -2 -2 -3 -2  0    1  58   1   1   0   0   8   1   0   9   1   1   0   0   1   1   1   0   0   7  0.58 0.40
-  147 Q   -1 -1 -1  2  2  4  0  3 -1 -3 -2 -1 -2 -3 -2  1 -1 -2 -2 -2    2   1   1  11   6  25   2  22   1   1   2   1   1   1   1   9   1   0   1   2  0.26 0.34
-  148 A    3  1 -2  0  2 -2 -2 -2 -2 -1  1 -1 -1 -2 -2  0 -1 -3 -2 -1   34   8   1   6   6   1   1   1   0   1  18   1   0   1   1   7   1   0   1   1  0.15 0.36
-  149 H    0  3  2 -2 -3 -1 -2  3  4 -3 -3 -1  1 -3 -2  0 -2 -3 -2 -3    6  20   9   1   0   1   1  22  13   1   1   1   6   1   1   7   1   0   1   1  0.26 0.38
-  150 M   -2 -3 -3 -3  2 -2 -3  0 -3  3  2 -2  4 -1 -3  0 -1 -3 -2  1    1   1   1   1   6   1   1   9   0  20  19   1  13   1   1   7   1   0   1   8  0.18 0.38
-  151 R   -1  5 -2 -2 -3  3 -1 -3 -2 -3 -2  2  1 -3 -3 -1 -2 -3 -3 -1    4  43   0   0   0  15   0   0   0   0   1  10   5   0   0   4   0   0   0   6  0.47 0.42
-  152 G    1 -2  1  2 -3 -2 -2  4 -2 -2 -2 -2 -2 -3 -2 -1 -2 -3 -3  1   14   1   9  12   0   1   1  36   0   1   1   1   0   1   1   1   1   0   0  18  0.40 0.38
-  153 R   -1  3 -1 -2  3 -1  1  0 -2 -2  1 -1 -1 -2  2  1 -1 -3 -2 -2    2  23   1   1   7   1  11   7   0   1  15   1   0   1   9  16   1   0   1   1  0.23 0.36
-  154 D   -2 -2  2  5 -3 -1  3 -2 -2 -3 -3  0 -3 -4  1  0 -2 -4 -3 -3    1   1  11  41   0   1  20   1   0   1   1   6   0   1   5   6   1   0   0   1  0.63 0.38
-  155 R   -1  4 -1  1 -3  2 -1 -2  2 -2  0  2 -1 -3 -2  1 -1 -3 -2 -2    5  24   1   8   0   9   1   1   6   1  15  16   0   1   1  10   1   0   0   1  0.28 0.39
-  156 D   -1 -1  2  5 -4 -1  1 -2 -2 -4 -4  2 -3 -3 -2  0 -2 -3  1 -3    4   0  10  42   0   0   6   0   0   0   0  15   0   0   0   4   0   0   7   0  0.50 0.42
-  157 L    1 -3 -3 -3 -2 -2  0 -3 -3  2  2 -2 -1 -1 -3 -2  2 -3  1  1   14   0   0   0   0   0   7   0   0  15  25   0   0   0   0   0  14   0   6   8  0.17 0.42
-  158 G   -2  0  2 -2 -3  2  2  3 -1  0 -2 -1  2 -2 -3 -2 -2 -3  2 -2    0   5  11   0   0  12  14  24   0   6   0   0   8   0   0   0   0   0   8   0  0.23 0.42
-  159 E    0 -1  1 -1 -4  1  4 -3  3 -4 -4  2 -3 -4 -2 -1  2 -4 -3 -3    9   0   7   0   0   5  35   0   8   0   0  12   0   0   0   0  14   0   0   0  0.40 0.45
-  160 M    1  1 -2 -2  4  3 -1 -3 -2 -2 -2  3  4 -3 -2 -1  0 -3 -3 -2   14   6   0   0  10  15   0   0   0   0   1  21  17   0   0   0   6   0   0   0  0.28 0.42
-  161 L    0 -2 -3 -4 -3 -2 -3 -4 -3 -1  3  1  2  4  0  0 -2 -3 -1 -1    7   0   0   0   0   0   0   0   0   0  40  13   5  19   5   9   0   0   0   0  0.36 0.45
-  162 R   -2  6 -2 -3 -5  0 -1 -3 -2 -4 -4  5 -3 -4 -3 -2 -2 -4 -3 -4    0  58   0   0   0   0   0   0   0   0   0  42   0   0   0   0   0   0   0   0  1.10 0.45
-  163 A    1  2 -2 -2 -3  5 -1 -3 -2 -2 -3 -1 -2 -3 -3 -1  0  4 -2  1   12  11   0   0   0  43   0   0   0   0   0   0   0   0   0   0   4   7   0  13  0.45 0.45
-  164 T    0 -3  0 -3 -2 -2 -3 -3 -2 -1  2 -2  2 -2 -3  2  2 -3  2  0    4   0   5   0   0   0   0   0   0   0  28   0   5   0   0  20  12   0   7   8  0.19 0.45
-  165 I   -2 -4 -4 -4 -2 -3 -4 -4 -4  5  0 -4  4 -2 -4 -3 -2 -4 -3  4    0   0   0   0   0   0   0   0   0  45   0   0  13   0   0   0   0   0   0  33  0.64 0.45
-  166 A    3  4 -2 -3 -3 -1 -2 -2 -2 -3 -1  2 -2 -3 -3  1 -2 -4 -3 -2   36  26   0   0   0   0   0   0   0   0   8  13   0   0   0   7   0   0   0   0  0.36 0.45
-  167 D    0 -3  1  4 -3 -2  1  1 -2 -3  0 -2 -2 -3 -3  1 -2 -4 -3 -3    9   0   7  25   0   0  10  12   0   0  14   0   0   0   0  13   0   0   0   0  0.25 0.45
-  168 R   -1  6  1 -2 -4  0  2 -3 -1 -4 -4  1 -3 -4 -3 -2 -2 -4 -3 -4    5  65   7   0   0   0  13   0   0   0   0   0   0   0   0   0   0   0   0   0  0.79 0.45
-  169 Y   -3 -3 -3 -4 -4 -3 -3 -4  1 -3 -2 -3 -2  2 -4 -3 -3  1  9 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  91   0  1.48 0.45
-  170 Y   -3 -3 -3 -4 -4 -3 -3 -4  1 -3 -2 -3 -2  2 -4 -3 -3  1  9 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  91   0  1.48 0.45
-  171 R   -3  7 -2 -3 -4  0 -1 -3 -2 -4 -3  3 -3 -4 -3 -2 -2 -4 -3 -4    0  77   0   0   0   0   0   0   0   0   0  13   0   0   0   0   0   0   0   0  1.07 0.45
-  172 E   -2 -2 -1  3 -5  0  6  1 -2 -4 -4 -1 -3 -4 -3 -1 -2 -4 -4 -4    0   0   0  14   0   0  64  13   0   0   0   0   0   0   0   0   0   0   0   0  0.78 0.45
-  173 T    3 -3 -3 -3 -2 -3 -3 -2 -3  2 -1 -2 -1 -3 -3 -1  3 -4 -3  2   31   0   0   0   0   0   0   0   0  13   0   0   0   0   0   0  20   0   0  18  0.24 0.45
-  174 A    4 -2 -2 -2 -2 -2  1 -2 -3 -2 -3 -2 -2 -3 -2  1 -1 -4 -3  0   53   0   0   0   0   0  13   0   0   0   0   0   0   0   0   9   0   0   0   7  0.34 0.45
-  175 R   -2  6  2 -2 -4  0 -1 -3 -2 -4 -3  3 -3 -4 -3 -2 -2 -4 -3 -4    0  50  13   0   0   0   0   0   0   0   0  19   0   0   0   0   0   0   0   0  0.63 0.45
-  176 L   -3 -4 -5 -5 -3 -4 -4 -5 -4  2  5 -4  0  3 -4 -4 -3 -2 -1  0    0   0   0   0   0   0   0   0   0  13  64   0   0  15   0   0   0   0   0   0  0.66 0.45
-  177 A    5 -3 -3 -3 -2 -2 -2 -1 -3 -2  1 -2 -2 -3 -2  0 -1 -4 -3 -1   78   0   0   0   0   0   0   0   0   0  13   0   0   0   0   0   0   0   0   0  0.65 0.45
-  178 R   -3  6  0 -3 -4 -1 -2 -3 -2  1 -3  3 -2 -4  1 -2 -2 -4 -3 -2    0  50   5   0   0   0   0   0   0  13   0  17   0   0   6   0   0   0   0   0  0.60 0.45
-  179 V   -2 -4 -4 -5 -2 -3 -4 -5 -4  3  4 -4  0 -1 -4 -3 -2  4 -2  3    0   0   0   0   0   0   0   0   0  13  45   0   0   0   0   0   0   6   0  27  0.56 0.45
-  180 L    0 -3 -4 -5 -3 -3 -4 -4 -4  0  5 -4  0  3 -4 -3 -2 -2 -1 -1    9   0   0   0   0   0   0   0   0   0  70   0   0  13   0   0   0   0   0   0  0.62 0.45
-  181 F   -3 -3 -4 -4 -3 -3 -4 -4 -1 -2  1 -4 -1  5 -4 -3 -3  0  7 -2    0   0   0   0   0   0   0   0   0   0  13   0   0  32   0   0   0   0  47   0  0.96 0.45
-  182 L    0 -3 -4 -4 -2 -3 -4 -4 -4  0  4 -3  2 -1 -4 -3 -2 -3 -2  3    9   0   0   0   0   0   0   0   0   0  55   0   5   0   0   0   0   0   0  23  0.51 0.45
-  183 H   -3 -2 -1 -2 -4 -1 -1 -3 10 -4 -4 -2 -3 -3 -3 -2 -3 -4  1 -4    0   0   0   0   0   0   0   0  92   0   0   0   0   0   0   0   0   0   0   0  1.65 0.45
-  184 L   -3 -3 -4 -5 -3 -3 -4 -5 -4  0  5 -4  3 -1 -4 -4 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0  83   0   9   0   0   0   0   0   0   0  0.81 0.45
-  185 Y   -3 -3 -3 -4 -3 -3 -3 -4  0 -2 -2 -3 -2  2 -4 -3 -3  1  8  1    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  78  13  1.21 0.45
-  186 L   -2 -4 -4 -5 -2 -3 -4 -5 -4  2  5 -4  1 -1 -4 -4 -2 -3 -2  2    0   0   0   0   0   0   0   0   0  10  63   0   0   0   0   0   0   0   0  19  0.64 0.45
-  187 F    2 -2  2 -2 -3 -2 -2 -2 -2 -3 -3 -2 -2  3 -3  4  1 -3 -1 -2   15   0  13   0   0   0   0   0   0   0   0   0   0  17   0  41   6   0   0   0  0.39 0.45
-  188 L    1 -3 -3 -3 -2 -3 -3 -3 -4  0  1 -3 -1 -2 -3 -1  4 -4 -3  3   13   0   0   0   0   0   0   0   0   0  17   0   0   0   0   0  32   0   0  30  0.36 0.45
-  189 T    2 -3 -2 -3  5 -2 -2 -2 -3 -2 -2 -2 -2 -3 -3  1  5 -4 -3  0   20   0   0   0  13   0   0   0   0   0   0   0   0   0   0   4  49   0   0   4  0.55 0.45
-  190 R   -3  7 -2 -2 -5  0  1 -4 -2 -4 -3  1 -3 -4 -3 -2 -2 -4 -3 -4    0  84   0   0   0   0   7   0   0   0   0   0   0   0   0   0   0   0   0   0  1.13 0.45
-  191 E   -2 -2 -1  4 -5  2  5 -3 -2  0 -4 -1 -3 -4 -3 -2 -2 -5 -4 -3    0   0   0  28   0   6  58   0   0   7   0   0   0   0   0   0   0   0   0   0  0.91 0.45
-  192 I   -2 -4 -5 -5 -2 -4 -4 -5 -4  4  1 -4  0  3 -4 -3 -2 -3 -1  5    0   0   0   0   0   0   0   0   0  22   6   0   0  14   0   0   0   0   0  57  0.73 0.45
-  193 L    2 -2 -1 -2 -2 -2 -2 -2 -3 -2  1 -2 -2 -3 -2  5  0 -4 -3 -2   13   0   0   0   0   0   0   0   0   0  17   0   0   0   0  70   0   0   0   0  0.64 0.45
-  194 W   -3  3 -3 -4 -4  3 -2 -4 -2 -4 -3 -1 -3 -1 -4 -1 -3 11  0 -4    0  19   0   0   0  17   0   0   0   0   0   0   0   0   0   5   0  59   0   0  1.77 0.45
-  195 A    1  6 -2 -3 -4 -1 -2 -3 -2  1 -3  1 -2 -4 -3 -2 -2 -4 -3 -2   17  65   0   0   0   0   0   0   0  13   0   5   0   0   0   0   0   0   0   0  0.80 0.45
-  196 A    1 -4 -5 -5 -2 -3 -4 -4 -4  2  5 -4  1 -1 -4 -3 -2 -3 -2  1   12   0   0   0   0   0   0   0   0  13  70   0   0   0   0   0   0   0   0   4  0.70 0.45
-  197 Y   -3 -2 -2 -2  2 -1  3 -4  6 -4 -3 -2 -3  2 -4 -2 -3  6  5 -3    0   0   0   0   5   0  22   0  28   0   0   0   0   6   0   0   0  13  25   0  0.90 0.45
-  198 A    5 -3 -3 -3 -2 -2 -2 -1 -3 -2 -2 -2 -2 -3 -2  1 -1 -4 -3  1   78   0   0   0   0   0   0   0   0   0   0   0   0   0   0   9   0   0   0  13  0.75 0.45
-  199 E   -1 -1 -1  2 -3  4  3 -3 -2 -3 -3 -1  2 -4 -2  3  0 -4 -3 -3    0   0   0  12   0  28  17   0   0   0   0   0   7   0   0  31   5   0   0   0  0.55 0.45
-  200 Q   -2  0 -1 -2 -4  8  1 -3 -1 -4 -4  0 -2 -5 -3 -1 -2 -3 -3 -4    0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.40 0.45
-  201 M   -1  3 -2 -3 -3 -2 -2 -3 -3 -1 -1 -1  5 -3 -3  2  1 -4 -3  3    0  19   0   0   0   0   0   0   0   0   0   0  27   0   0  23   7   0   0  24  0.44 0.45
-  202 M    0 -2 -2  2 -3  2 -1  1 -3  0  0  1  4 -3 -3  0 -2 -4 -3  1    8   0   0  13   0  14   0   9   0   4   5  12  17   0   0   7   0   0   0  10  0.22 0.45
-  203 R    1  4  1 -3 -3 -1 -2 -3  3 -2  0 -1 -2 -2 -3  1 -2 -3  1 -1   15  32   8   0   0   0   0   0   8   0  13   0   0   0   0  13   0   0   6   5  0.33 0.45
-  204 P   -2 -1 -2 -2 -4  6  0 -3 -1 -4 -4  0 -2 -5  5  1 -2 -4 -3 -4    0   0   0   0   0  60   0   0   0   0   0   0   0   0  27  13   0   0   0   0  1.04 0.45
-  205 D   -2 -3  4  5 -4 -2 -1  2 -2 -5 -5 -2 -4 -5 -3  2 -2 -5 -4 -4    0   0  20  45   0   0   0  16   0   0   0   0   0   0   0  19   0   0   0   0  0.81 0.45
-  206 L   -2 -4 -5 -5 -2 -4 -4 -5 -5  3  3 -4  0 -2 -4 -3 -2 -4 -2  5    0   0   0   0   0   0   0   0   0  13  29   0   0   0   0   0   0   0   0  57  0.75 0.45
-  207 F   -4 -4 -5 -5 -4 -5 -5 -5 -3 -1  1 -5 -1  8 -5 -4 -3  0  2 -2    0   0   0   0   0   0   0   0   0   0  13   0   0  87   0   0   0   0   0   0  1.37 0.45
-  208 D    2 -3 -2  2 -3  2  0 -3 -3  0 -1 -2  2 -3 -3 -2 -2 -4 -3  4   20   0   0  12   0  13   4   0   0   0   0   0   6   0   0   0   0   0   0  44  0.39 0.45
-  209 C    1 -2 -2 -3  3 -2 -2  1  2 -3 -3  1 -3 -1 -3  3 -1 -2  4 -3   14   0   0   0   8   0   0   9   5   0   0  13   0   0   0  28   0   0  22   0  0.42 0.45
-  210 L   -3 -4 -5 -5 -3 -3 -4 -5 -4  1  5 -4  4 -1 -4 -4 -2 -3 -2  2    0   0   0   0   0   0   0   0   0   0  75   0  11   0   0   0   0   0   0  13  0.84 0.45
-  211 C   -2  4 -2 -3  4 -1 -2 -3  3 -4 -3  3 -3 -3 -3  0  2 -3  2 -3    0  29   0   0  12   0   0   0   8   0   0  24   0   0   0   5  13   0   9   0  0.54 0.45
-  212 C   -3 -4 -4 -5  8 -4 -4 -4 -1 -2 -2 -4 -2  3 -4 -3 -3  0  7 -2    0   0   0   0  39   0   0   0   0   0   0   0   0  14   0   0   0   0  47   0  1.30 0.45
-  213 D    0  2 -1  3 -4 -1  3 -3 -2 -3 -3 -1  1 -1 -3  0  1 -4 -3 -3    9  13   0  22   0   0  28   0   0   0   0   0   6   4   0   5  12   0   0   0  0.43 0.45
-  214 L   -4 -4 -5 -6 -4 -3 -4 -4 -4 -3  1 -4 -2  0 -5 -4 -4 12  1 -3    0   0   0   0   0   0   0   0   0   0  17   0   0   0   0   0   0  83   0   0  2.60 0.45
-  215 E   -1 -2 -2  1 -4  1  4  0  2 -3  1 -1 -2 -3  3  0  1 -4 -3 -3    4   0   0   6   0   5  30   7   5   0  16   0   0   0  12   5   8   0   0   0  0.33 0.45
-  216 S   -1 -1 -1 -1 -4  6  2 -3  2 -4 -4  0 -2 -4 -2  3 -1 -4 -3 -4    0   0   0   0   0  55  14   0   5   0   0   0   0   0   0  25   0   0   0   0  0.83 0.45
-  217 W    1  4  1 -2 -3 -1  1  0 -2 -3 -1 -1 -2 -2 -3 -1 -2  6  1 -3   12  31   7   1   0   1  10   8   0   1   7   1   0   1   1   1   1  12   6   1  0.40 0.39
-  218 R   -2  7 -1 -2 -4  2 -1 -3 -1 -4 -3  1 -2 -4 -3 -2 -2 -4 -3 -3    0  88   0   0   0  12   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.08 0.26
-  219 Q   -2  0 -1 -1 -4  7  1 -3  4 -4 -3  2 -1 -4 -2 -1 -2 -3 -2 -3    0   0   0   0   0  80   0   0  12   0   0   8   0   0   0   0   0   0   0   0  0.93 0.26
-  220 L   -3 -4 -4 -5 -3 -4 -4 -4 -3  0  3 -4  0  6 -4 -3 -3 -1  1 -1    0   0   0   0   0   0   0   0   0   0  42   0   0  58   0   0   0   0   0   0  0.82 0.26
-  221 A    2 -2 -1 -1 -3  1  2 -2  5 -3 -3 -1 -2 -3 -2  1  3  5 -1 -2   20   0   0   0   0   4  16   0  20   0   0   0   0   0   0   6  25   9   0   0  0.42 0.26
-  222 G   -1 -4 -3 -4 10 -4 -4  1 -4 -2 -2 -4 -2 -3 -4 -2 -2 -3 -4 -2    0   0   0   0  87   0   0  13   0   0   0   0   0   0   0   0   0   0   0   0  1.60 0.26
-  223 L    0 -3 -4 -4 -2 -3 -4 -4 -4  4  4 -3  1 -1 -4 -3 -2 -3 -2  1    9   0   0   0   0   0   0   0   0  29  62   0   0   0   0   0   0   0   0   0  0.57 0.26
-  224 F   -3 -4 -4 -5 -3 -4 -4 -4 -2 -1  0 -4 -1  8 -5 -3 -3  0  3 -2    0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0  1.30 0.26
-  225 Q   -2  0  0 -1 -4  6  1 -3  7 -4 -3  0 -2 -3 -3 -1 -2 -3  0 -4    0   0   0   0   0  60   0   0  40   0   0   0   0   0   0   0   0   0   0   0  0.97 0.26
-  226 P   -2 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  8 -2 -2 -5 -4 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.35 0.26
-  227 F   -2 -3 -4 -4 -2 -3 -4 -4 -4  3  3 -3  3  3 -4 -3 -2 -2 -1  3    0   0   0   0   0   0   0   0   0  17  25   0   9  13   0   0   0   0   0  36  0.48 0.26
-  228 M   -2 -3 -4 -4 -2 -3 -4 -5 -4  3  4 -3  5 -1 -4 -3 -2 -3 -2  1    0   0   0   0   0   0   0   0   0  22  54   0  24   0   0   0   0   0   0   0  0.64 0.26
-  229 F   -3 -4 -4 -5  3 -4 -4 -4 -2 -1  0 -4 -1  7 -4 -3 -3  0  3  1    0   0   0   0   9   0   0   0   0   0   0   0   0  70   0   0   0   0   9  12  0.89 0.26
-  230 V   -2 -2  6  0 -3 -1 -2 -2 -1  0 -2 -1 -2 -3 -3  1 -1 -4 -3  1    0   0  62   0   0   0   0   0   0   7   0   0   0   0   0  12   0   0   0  19  0.59 0.26
-  231 N   -2 -1  3 -1 -4 -1 -1 -3  8 -4 -4 -1 -3 -3  2 -1 -2 -4  0 -4    0   0  20   0   0   0   0   0  68   0   0   0   0   0  12   0   0   0   0   0  1.08 0.26
-  232 G   -1 -3 -1 -2 -4 -3 -3  7 -3 -5 -5 -2 -4 -4 -3 -1 -3 -4 -4 -4    0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0   0  1.43 0.26
-  233 A    2 -3 -3 -3 -2 -3 -3 -3 -3  3 -1 -3 -1 -2  2  0 -1 -4 -2  4   19   0   0   0   0   0   0   0   0  17   0   0   0   0  12   7   0   0   0  45  0.40 0.26
-  234 L   -1 -3 -4 -4 -2 -3 -3 -4 -4  2  2 -3  0 -1  2 -3 -1 -4 -2  5    0   0   0   0   0   0   0   0   0   0  26   0   0   0   9   0   0   0   0  64  0.55 0.26
-  235 T    0 -3  1 -3 -2 -2 -3 -3 -3  2  2 -2  3  2 -3  0  2 -3 -1  0    8   0   8   0   0   0   0   0   0  20  17   0   9  12   0   6  20   0   0   0  0.22 0.26
-  236 V   -2 -3 -4 -4 -2 -3 -4 -5 -4  2  4 -3  1 -1 -4 -3 -1 -3 -2  4    0   0   0   0   0   0   0   0   0   9  52   0   0   0   0   0   0   0   0  38  0.59 0.26
-  237 R   -2  3  1  2 -4  1  5  0 -1 -4 -4  0 -3 -4 -2  0 -2 -4 -3 -4    0  20   4  12   0   0  54   6   0   0   0   0   0   0   0   4   0   0   0   0  0.64 0.26
-  238 G   -1 -3  4  1 -4 -2 -2  6 -2 -5 -5 -2 -4 -4 -3 -1 -2 -4 -4 -4    0   0  28   8   0   0   0  65   0   0   0   0   0   0   0   0   0   0   0   0  0.94 0.26
-  239 V   -1  3  1  3 -4 -1  2  1 -2 -2 -3  1 -3 -4 -3 -1 -2 -4 -3  1    5  18   7  21   0   0  12  13   0   0   0   9   0   0   0   0   0   0   0  15  0.33 0.38
-  240 P    1 -3 -3 -3 -3 -3 -3 -3 -3 -3 -3 -2 -3  2  7 -2 -2 -4 -2 -1   12   0   0   0   0   0   0   0   0   0   0   0   0  13  69   0   0   0   0   5  1.47 0.38
-  241 I   -2 -4 -5 -5 -2 -3 -4 -5 -4  2  5 -4  1 -1 -4 -4 -2 -3 -2  2    0   0   0   0   0   0   0   0   0  10  73   0   0   0   0   0   0   0   0  17  0.76 0.38
-  242 E   -2 -2 -1  2 -3  1  3 -3 -2 -1 -3 -1 -3 -4  4  1  3 -4 -3 -2    0   0   0  13   0   5  22   0   0   4   0   0   0   0  18  12  26   0   0   0  0.53 0.38
-  243 A    4 -3 -3 -3 -2 -2 -2 -2 -3 -2  1 -2 -1  3  1  1 -1 -3 -1 -1   53   0   0   0   0   0   0   0   0   0  14   0   0  15   7  12   0   0   0   0  0.44 0.38
-  244 R    3  2  0 -2 -3  4 -1 -2  1 -3 -1  1 -2 -4  1  0 -2 -4 -3 -2   30  15   4   0   0  23   0   0   4   0   7   7   0   0   5   5   0   0   0   0  0.35 0.38
-  245 R   -1  4 -1  1 -4  1  4 -3 -2 -4 -4  1 -3 -4 -3 -1  1 -4 -3 -3    5  26   0   8   0   5  38   0   0   0   0   5   0   0   0   0  14   0   0   0  0.58 0.38
-  246 L   -3 -3 -4 -4 -2 -3 -4 -4 -4  0  5 -3  1 -1 -4 -3 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   0  87   0   0   0   0   0   0   0   0   0  0.72 0.38
-  247 R   -2  6 -1 -2 -4  4 -1  0 -1 -4 -3  1 -2 -4 -3 -2 -2 -3 -3 -3    0  51   0   0   0  29   0   7   0   0   0   0   0   0   0   0   0   0   0   0  0.67 0.38
-  248 E    0  1 -1 -1 -3  0  4 -3  4 -4 -3  1 -3 -4 -2  0  0 -4 -2 -3   10   8   0   0   0   0  36   0  14   0   0   7   0   0   0   7   5   0   0   0  0.35 0.38
-  249 L   -2 -3 -3 -3 -2  1 -3 -4 -3  3  2 -3  0 -2 -3  0 -2 -3 -2  3    0   0   0   0   0  11   0   0   0  20  22   0   0   0   0   7   0   0   0  28  0.26 0.38
-  250 N   -3 -2  7  0 -4 -1 -1 -2 -1 -4 -4 -1 -3 -4 -3 -1 -1 -5 -3 -4    0   0  87   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.07 0.38
-  251 H   -3 -2 -2 -3 -4 -2 -2 -4  6 -3 -3 -3 -2  1 -4 -3 -3  0  7 -3    0   0   0   0   0   0   0   0  27   0   0   0   0   0   0   0   0   0  60   0  1.03 0.38
-  252 I   -2  4 -3 -4 -3 -2 -3 -4 -3  4 -1 -1 -1 -2 -3 -3 -2 -4 -3  3    0  29   0   0   0   0   0   0   0  32   0   0   0   0   0   0   0   0   0  26  0.39 0.38
-  253 R   -3  7 -2 -3 -4  0 -1 -3 -1 -4 -3  1 -2 -4 -3 -2 -2 -4 -3 -4    0  87   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.06 0.38
-  254 E   -2  3 -1 -2 -4 -1  3 -3  3 -3 -3 -1 -2  0 -3  2 -2 -2  3 -3    0  22   0   0   0   0  22   0   7   0   0   0   0   5   0  18   0   0  14   0  0.31 0.38
-  255 H   -2  1 -2 -1 -4  1  4 -3  4  0  0  0 -2 -3 -3 -2 -2 -3 -2 -2    0   7   0   0   0   5  35   0  15   7  14   5   0   0   0   0   0   0   0   0  0.30 0.38
-  256 L   -3 -3 -4 -4 -2 -3 -4 -4 -4  0  5 -3  1  1 -4 -3 -2 -2 -2  0    0   0   0   0   0   0   0   0   0   0  82   0   0   5   0   0   0   0   0   0  0.66 0.38
-  257 N   -1 -3  3 -2 -4 -2 -3  6 -2 -4 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4    0   0  22   0   0   0   0  65   0   0   0   0   0   0   0   0   0   0   0   0  0.89 0.38
-  258 L   -2 -3 -4 -4 -2 -3 -4 -4 -4  1  5 -3  1 -1 -4 -3 -2 -3 -2  2    0   0   0   0   0   0   0   0   0   0  73   0   0   0   0   0   0   0   0  14  0.59 0.38
-  259 P   -2 -3 -3 -3 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5  9 -2 -2 -5 -4 -4    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.46 0.38
-  260 L   -2 -4 -5 -5 -2 -3 -4 -5 -4  1  5 -4  1 -1 -4 -4 -2 -3 -2  3    0   0   0   0   0   0   0   0   0   0  77   0   0   0   0   0   0   0   0  23  0.79 0.38
-  261 V   -2 -4 -4 -5 -2 -4 -4 -5 -4  5  2 -4  2 -1 -4 -3 -2 -4 -2  4    0   0   0   0   0   0   0   0   0  39  14   0   5   0   0   0   0   0   0  42  0.70 0.38
-  262 R   -3  7 -2 -3 -5  0 -1 -4 -1 -4 -3  1 -3 -4 -3 -2 -2 -4 -3 -4    0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  1.39 0.38
-  263 S    3 -3 -2 -3  7 -3 -3 -2 -3 -2 -2 -3 -2  2 -3  2 -1 -3 -2 -2   33   0   0   0  32   0   0   0   0   0   0   0   0  14   0  22   0   0   0   0  0.69 0.38
-  264 A    2 -2 -2 -2 -3 -1  1  3 -2 -3 -3  0 -3 -4 -2  1 -2 -3 -3 -3   19   0   0   0   0   0  12  29   0   0   0   5   0   0   0  14   0   0   0   0  0.26 0.38
-  265 A    1 -3 -4 -4 -2 -3 -3 -3 -3  0  4 -3  4 -1 -3 -2 -2 -3 -2 -1   15   0   0   0   0   0   0   0   0   0  51   0  14   0   0   0   0   0   0   0  0.33 0.38
-  266 T   -1 -3 -3 -4 -2 -3 -3 -4 -4  4  1 -3  0 -2 -3 -2  1 -3 -2  3    5   0   0   0   0   0   0   0   0  34   7   0   0   0   0   0  10   0   0  24  0.26 0.38
-  267 E   -2 -1 -1  0 -4  1  6 -3 -1 -4 -4  0 -3 -4 -2 -1 -2 -4 -3 -3    0   0   0   0   0   0  80   0   0   0   0   0   0   0   0   0   0   0   0   0  0.81 0.38
-  268 E   -2 -1 -1  0 -4  1  6 -3 -1 -4 -4  0 -3 -4 -2 -1 -2 -4 -3 -3    0   0   0   0   0   0  80   0   0   0   0   0   0   0   0   0   0   0   0   0  0.81 0.38
-  269 P   -2  0  0  2 -3 -1  1 -3  1 -3 -1  0 -2 -3  4  1 -2 -4 -3 -3    0   5   5  12   0   0   8   0   5   0   7   5   0   0  20  14   0   0   0   0  0.21 0.38
-  270 G   -2 -2  3  2 -4 -2  0  3 -2 -4 -4  0 -3 -4  3 -1 -2 -4 -3 -4    0   0  15  10   0   0   7  29   0   0   0   5   0   0  14   0   0   0   0   0  0.34 0.38
-  271 A    2 -2 -2 -2 -2  1 -2 -2 -2 -2 -1  0  3 -3 -2  3 -1 -3 -3 -1   19   0   0   0   0   7   0   0   0   0   4   5  11   0   0  29   0   0   0   5  0.13 0.38
-  272 P    1 -3 -3  0 -3 -2 -2 -3 -3 -3 -3 -2 -3 -4  7 -2 -2 -4 -3 -3   14   0   0   5   0   0   0   0   0   0   0   0   0   0  61   0   0   0   0   0  1.15 0.38
-  273 L   -2 -2 -3 -3 -2  2 -2 -4 -3  0  4 -2  0 -1 -3 -3 -2 -3 -2  1    0   0   0   0   0  14   0   0   0   0  59   0   0   0   0   0   0   0   0   7  0.34 0.38
-  274 T   -2 -3 -3 -3 -2 -2  0 -3 -2  1 -1 -2  2 -1 -3 -2  2 -2  3  3    0   0   0   0   0   0   8   0   0   5   0   0   7   0   0   0  20   0  14  26  0.15 0.38
-  275 T    0 -2 -2 -2 -2  1  1 -3 -2  2 -2 -2 -1  1 -3  1  2 -3 -2 -1    9   0   0   0   0   9   9   0   0  21   0   0   0   7   0   9  15   0   0   0  0.05 0.38
-  276 P   -2  0 -2 -2 -4  1  2 -3 -2 -4 -4 -1 -3 -4  7 -2 -2 -4 -3 -3    0   5   0   0   0   5  17   0   0   0   0   0   0   0  53   0   0   0   0   0  0.98 0.38
-  277 P   -2 -2 -2 -2 -3 -2 -2 -2 -2 -3 -3 -2 -3 -3  7 -2 -2 -3 -3 -3    1   1   1   1   0   1   1   1   0   1   1   1   0   1  67   1   1   0   0   1  1.24 0.33
-  278 T    0  0 -2 -1 -2 -1  1 -2 -2 -2 -1 -1 -2 -2  2  0  3 -3 -2  0    6   5   1   1   0   1  13   1   0   1   5   1   0   1  11   6  21   0   0   6  0.07 0.33
-  279 L   -2 -3 -3 -3 -3 -3 -3 -3 -2 -1  1 -3 -1  7 -3 -3 -2  0  1 -1    1   1   1   1   0   1   1   1   0   1  16   1   0  65   1   1   1   0   0   1  0.76 0.33
-  280 H   -1 -1 -1 -1 -2  1 -1 -2  3 -2 -1 -1 -2 -2 -2  4  1 -2  1 -2    1   1   1   1   0   6   1   1  10   1   6   1   0   1   1  49   8   0   5   1  0.32 0.33
-  281 G    2 -3 -2 -3 -3 -2 -3  5 -2 -3 -3 -2 -3 -2 -3  0 -2 -2  3 -1   22   0   0   0   0   0   0  45   0   0   0   0   0   0   0   7   0   0  14   5  0.54 0.38
-  282 N   -1 -1  4  3 -3 -1 -1 -2  3 -4 -4  2 -3 -4 -3  1  1 -4 -3 -3    5   0  25  19   0   0   0   0   9   0   0  15   0   0   0  13   7   0   0   0  0.41 0.38
-  283 Q    1 -1 -3 -3 -3  2 -2 -3 -3 -1  3  1  2 -2 -3 -2 -2 -3 -2 -1   18   0   0   0   0  15   0   0   0   0  42  14   5   0   0   0   0   0   0   0  0.28 0.38
-  284 A    1 -3 -3 -3 -3 -2 -2 -3 -3 -3 -3 -2 -3 -4  7 -1  1 -4 -4 -3   15   0   0   0   0   0   0   0   0   0   0   0   0   0  64   0  14   0   0   0  1.34 0.38
-  285 R    1  7 -2 -3 -4  0 -1 -3 -2 -4 -3  1 -2 -4 -3 -2 -2 -4 -3 -3   14  79   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.95 0.38
-  286 A    3 -2 -2 -2 -2 -2 -2 -2 -3 -3 -3 -2 -2 -4  3  3  2 -4 -3 -2   38   0   0   0   0   0   0   0   0   0   0   0   0   0  14  33  15   0   0   0  0.59 0.38
-  287 S    0 -3 -2 -2 -2 -2 -2 -2 -3  2  1 -2 -1 -2 -3  4  0 -4 -3  0    5   0   0   0   0   0   0   0   0  15  18   0   0   0   0  58   0   0   0   5  0.44 0.38
-  288 G    2 -3 -2 -3 -3 -3 -3  6 -3 -4 -4 -3 -3 -4 -3 -1 -2 -4 -4 -1   19   0   0   0   0   0   0  76   0   0   0   0   0   0   0   0   0   0   0   5  1.08 0.38
-  289 Y   -3 -3 -4 -5 -4 -3 -4 -4  0 -2 -1 -4 -2  6 -5 -3 -3  1  7 -2    0   0   0   0   0   0   0   0   0   0   0   0   0  42   0   0   0   0  58   0  1.32 0.38
-  290 F   -3 -3 -3  2 -3 -3 -3 -4 -3  0  4 -4  0  4 -4 -3 -3 -2 -1 -1    0   0   0  14   0   0   0   0   0   0  64   0   0  22   0   0   0   0   0   0  0.64 0.38
-  291 M   -2 -3  2 -3 -3 -2 -3 -3 -3 -1  0 -2  5  2 -3  0  3 -3 -1  1    0   0  13   0   0   0   0   0   0   0   5   0  22  12   0   5  29   0   0  14  0.37 0.38
-  292 V   -2 -2 -2 -3 -3  3  0 -4  6 -2  1 -2 -1 -1 -3 -2  0 -2  3  0    0   0   0   0   0  18   5   0  29   0  19   0   0   0   0   0   7   0  13  10  0.47 0.38
-  293 L    1 -2  1 -2  4  4 -1 -3  3 -2  2 -1 -1 -3 -3 -2 -2 -3 -2 -2   14   0   7   0  11  33   0   0   9   0  27   0   0   0   0   0   0   0   0   0  0.40 0.38
-  294 I   -2 -4 -4 -4 -2 -4 -4 -5 -4  6  0 -4  0 -2 -4 -3  2 -4 -3  3    0   0   0   0   0   0   0   0   0  69   0   0   0   0   0   0  14   0   0  18  0.74 0.38
-  295 R   -2  6 -2 -3 -4  0 -1 -4 -2  1 -2  3 -2 -4 -3 -2 -2 -4 -3 -2    0  72   0   0   0   0   0   0   0  14   0  15   0   0   0   0   0   0   0   0  0.93 0.38
-  296 A    5  0 -2 -3 -2 -2 -2 -1 -3  0 -2 -2 -2 -3 -2  2  1 -4 -3  0   60   5   0   0   0   0   0   0   0   5   0   0   0   0   0  15   8   0   0   7  0.51 0.38
-  297 K   -2  3 -1 -2 -4  0  0 -3 -2 -4 -4  6 -3 -4 -2 -1 -2 -4 -3 -4    0  14   0   0   0   0   0   0   0   0   0  86   0   0   0   0   0   0   0   0  1.03 0.38
-  298 L   -2 -2 -3 -3 -2 -2 -3 -3 -3  0  4 -2  7 -1 -3 -2 -2 -2 -2  0    1   1   1   1   0   1   1   1   0   1  43   1  45   1   1   1   1   0   0   1  0.68 0.33
-  299 D   -2 -2 -1  4 -4  0  5  1 -2 -4 -4 -1 -3 -4 -2 -1 -2 -3 -3 -3    1   1   1  32   0   1  43  14   0   1   1   1   0   1   1   1   1   0   0   1  0.68 0.33
-  300 S    4 -2 -2 -2 -1 -2 -2 -1 -2 -1  0 -2 -1 -2 -2  2 -1 -3 -2  2   44   1   1   1   0   1   1   1   0   1   9   1   0   1   1  16   1   0   1  16  0.31 0.31
-  301 Y   -2 -2 -2 -3 -2 -2 -2 -3  1 -2 -2 -2 -1  2 -2 -2 -2  1  8 -2    2   1   1   1   0   1   2   2   1   1   2   1   1   1   1   2   1   0  76   2  1.03 0.28
-  302 S    1 -2  0 -1 -2 -1 -1 -1 -2 -3 -3 -1 -2 -3 -2  5  2 -3 -2 -2    6   1   1   1   0   0   1   1   0   1   1   1   0   0   1  71  15   0   0   1  0.65 0.34
-  303 S   -1  0  2  2  5 -1  2 -2 -2 -3 -3 -1 -2 -3 -2  3 -1 -4 -3 -1    1   7  12  13  14   0  14   1   0   1   1   1   0   0   1  28   1   0   0   6  0.37 0.37
-  304 F    0 -2  1 -2 -2 -2 -2 -2  2  1  2  1 -1  2 -3 -2 -2  5 -1  0   10   1   9   1   0   1   1   1   7   8  21  12   0  10   1   1   1   8   1   6  0.19 0.34
-  305 T    0  1 -1 -2 -2 -1 -1 -2  7 -3 -3 -1 -2 -2  1  1  3 -3 -1 -2    7   7   1   1   0   1   1   1  35   1   1   1   0   1   8   9  24   0   1   1  0.54 0.34
-  306 T    1 -2 -2 -2 -2 -2 -2 -2 -2 -3 -3 -1 -2 -3  6  2  2 -3 -3 -2    9   1   1   1   0   1   1   1   0   1   1   1   0   1  44  20  16   0   1   1  0.85 0.34
-  307 S    2 -2  1 -2 -2  2 -1  1 -2 -2 -3 -1 -2 -3 -2  4  1 -4 -3  0   15   0   7   0   0  11   0   8   0   0   1   0   0   0   0  40   6   0   0   8  0.37 0.38
-  308 P   -1 -2 -2 -1 -3 -1  2  1 -2 -3 -3 -2 -3 -4  5  1  2 -4 -3 -3    0   0   0   0   0   0  16  14   0   0   1   0   0   0  35  14  17   0   0   0  0.71 0.38
-  309 S    1 -2 -2 -2  5  2  1  0 -2 -3 -3 -1 -3 -4  5  1 -2 -4 -3 -3   11   0   0   0  13  15   8   6   0   0   1   0   0   0  34  10   0   0   0   0  0.69 0.38
-  310 E   -1  0 -2 -1 -3 -1  3  1 -2 -2  2  1 -1 -3 -3  2 -1 -3 -3 -2    0   6   0   0   0   0  25  13   0   0  24   8   0   0   0  20   0   0   0   0  0.26 0.38
-  311 A    3  2  1 -2 -3 -1 -2 -2  4 -3 -3 -1 -2  3 -3  2 -1 -3 -1 -2   28  14   6   0   0   0   0   0  13   0   1   0   0  17   0  19   0   0   0   0  0.35 0.38
-  312 V    1 -3 -3 -3 -3 -3  0  2 -4  1 -2 -3 -2 -3  3 -2 -2 -4 -3  4   13   0   0   0   0   0   6  18   0   6   0   0   0   0  17   0   0   0   0  41  0.44 0.41
-  313 M   -2  3 -2 -3 -3 -2 -2  1  2 -2  2 -1  4 -2 -3  2 -2 -3  1 -2    0  19   0   0   0   0   0  10   7   0  24   0  15   0   0  19   0   0   6   0  0.29 0.41
-  314 R    1  5  1 -2 -3 -1 -2 -3  4  0 -3  1 -2 -3 -3  0 -2 -4 -2 -1   14  39   6   0   0   0   0   0  13   8   0   7   0   0   0   7   0   0   0   5  0.45 0.41
-  315 E   -2 -2 -1  5 -5  0  5 -3 -2 -5 -5 -1 -4 -5 -3 -1 -2 -5 -4 -4    0   0   0  44   0   0  56   0   0   0   0   0   0   0   0   0   0   0   0   0  1.11 0.41
-  316 H   -3 -1  0 -2 -4 -1 -1 -3 10 -5 -4 -2 -3 -2 -4 -2 -3 -4  1 -5    0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0   0   0  1.83 0.41
-  317 A    2 -2 -2 -2 -2 -2 -2 -2 -3 -2 -3 -2 -2 -4  2  3  4 -4 -3  0   23   0   0   0   0   0   0   0   0   0   0   0   0   0  11  27  33   0   0   7  0.52 0.41
-  318 Y   -3 -3 -3 -4 -4 -2 -3 -4  3 -3 -2 -3 -2  2 -4 -3 -3  1  9 -3    0   0   0   0   0   0   0   0   7   0   0   0   0   0   0   0   0   0  93   0  1.58 0.41
-  319 S    4 -2 -2 -2  3  1 -2 -2 -3 -2 -3 -2 -2 -4 -2  3 -1 -4 -3  0   48   0   0   0   6   7   0   0   0   0   0   0   0   0   0  31   0   0   0   7  0.53 0.41
-  320 R   -2  7 -2 -3 -5  0 -1 -3 -2 -4 -4  4 -3 -4 -3 -2 -2 -4 -3 -4    0  73   0   0   0   0   0   0   0   0   0  27   0   0   0   0   0   0   0   0  1.15 0.41
-  321 A    0  1  0  2 -3  0 -2 -1 -3  0 -1 -2 -2 -3  4 -1  0 -4 -3  0   10   8   5  13   0   6   0   5   0   8   7   0   0   0  24   0   7   0   0   6  0.33 0.41
-  322 P   -2  4  2  0 -4 -1  0 -1  2  0 -1 -1 -2 -3  2 -2 -2 -4 -3  1    0  28  13   4   0   0   7   4   7   8   6   0   0   0  11   0   0   0   0  11  0.30 0.41
-  323 T   -1 -2  1  2 -3 -1  3  2 -2 -3 -4 -1 -3 -4 -3  1  2 -4 -3  0    0   0   5  14   0   0  27  19   0   0   0   0   0   0   0  13  15   0   0   7  0.41 0.41
-  324 K    0  3  2 -2 -4 -1 -1 -3 -2 -4 -4  4 -3 -4  5 -1 -2 -5 -3 -3   10  21  11   0   0   0   0   0   0   0   0  29   0   0  29   0   0   0   0   0  0.75 0.41
-  325 N    0  0  2 -3 -3 -2 -3 -3 -3  3  0 -2 -1 -3  4 -2  1 -4 -3  2    6   6  15   0   0   0   0   0   0  23   8   0   0   0  20   0   8   0   0  13  0.38 0.41
-  326 N   -2 -2  7  0 -4 -1 -1 -2 -1 -5 -5 -1 -3 -4 -3  2 -1 -5 -3 -4    0   0  85   0   0   0   0   0   0   0   0   0   0   0   0  15   0   0   0   0  1.21 0.41
-  327 Y   -3 -3 -3 -5 -4 -3 -3 -4  1 -2 -2 -3 -2  3 -4 -3 -3  1  9 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   6   0   0   0   0  94   0  1.61 0.41
-  328 G   -1 -3 -1 -2 -4 -3 -3  7 -3 -5 -5 -3 -4 -4 -3  1 -2 -4 -4 -4    0   0   0   0   0   0   0  87   0   0   0   0   0   0   0  13   0   0   0   0  1.33 0.41
-  329 S    0 -2 -1 -2 -2 -1 -2 -2 -2 -3 -3 -1 -2 -4 -2  5  5 -4 -3 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  56  44   0   0   0  0.78 0.39
-  330 T   -1 -2 -1 -2 -2 -2 -2 -2 -3 -2 -3 -2 -2 -3 -2  4  6 -4 -3 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  34  66   0   0   0  0.82 0.39
-  331 I    0  0 -3 -4 -2 -3 -3 -4 -4  5  0 -2  0 -2  2 -2  0 -4 -3  3    5   8   0   0   0   0   0   0   0  45   0   0   0   0  12   0   5   0   0  24  0.47 0.34
-  332 E   -2 -1 -1  1 -5  1  6 -3 -1 -4 -4  0 -3 -4 -2 -1 -2 -4 -3 -3    0   0   0   0   0   0  92   0   0   0   0   0   0   0   0   0   0   0   0   0  1.03 0.33
-  333 G    5 -3 -2 -3 -2 -2 -2  2 -3 -2 -2 -2 -2 -3 -2  0 -1 -4 -3  0   65   0   0   0   0   0   0  18   0   0   0   0   0   0   0   0   0   0   0   9  0.51 0.33
-  334 L   -2 -3 -4 -4 -2 -2 -3 -4 -3  2  3 -3  7 -1 -4 -3 -2 -3 -2  0    0   0   0   0   0   0   0   0   0   8  36   0  48   0   0   0   0   0   0   0  0.64 0.33
-  335 L   -2 -3 -4 -4 -2 -3 -4 -4 -3  2  4 -3  5 -1 -4 -3 -2 -3 -2  0    0   0   0   0   0   0   0   0   0  14  56   0  22   0   0   0   0   0   0   0  0.58 0.33
-  336 D   -2  2  0  5 -4 -1  2 -3 -2 -2 -1 -1 -2 -3 -3 -1 -2 -4 -3 -1    0  13   0  51   0   0  11   0   0   0   8   0   0   0   0   0   0   0   0   8  0.52 0.31
-  337 L    1 -3 -3 -3 -2 -2 -2 -3 -3 -1  3 -2  0 -2  3  0  1 -3 -3 -1   19   0   0   0   0   0   0   0   0   0  38   0   0   0  18   8   9   0   0   0  0.31 0.31
-  338 P   -1 -3 -2 -2 -3 -2 -2 -3 -3  0 -3 -2 -3 -4  7  1 -1 -4 -3 -2    0   0   0   0   0   0   0   0   0  10   0   0   0   0  68  11   0   0   0   0  1.31 0.28
-  339 D   -1 -2  0  4  5 -2 -1  0 -2 -3 -3 -2 -3 -4 -2  2 -1 -4 -3 -3    0   0   0  38  17   0   0   8   0   0   0   0   0   0   0  24   0   0   0   0  0.45 0.25
-  340 D   -2 -2 -1  4 -3 -2 -1 -2 -2 -3 -3 -2 -3 -4  6 -1  1 -4 -3 -3    0   0   0  37   0   0   0   0   0   0   0   0   0   0  38   0  13   0   0   0  0.81 0.25
-  341 D   -1 -2 -1  3 -3 -1  2 -2 -2 -3 -4 -1 -3 -4  4  2 -1 -4 -3 -3    0   0   0  25   0   0  13   0   0   0   0   0   0   0  25  24   0   0   0   0  0.54 0.25
-  342 A    4 -2  1 -2 -2 -2 -2  2 -2 -3 -3 -1 -2 -3 -2  2 -1 -3 -3 -2   53   0   8   0   0   0   0  13   0   0   0   0   0   0   0  14   0   0   0   0  0.34 0.25
-  343 P   -1 -3 -2 -2 -3 -2 -2 -3 -3 -3 -3 -2 -3 -4  8 -1 -2 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0  84   0   0   0   0   0  1.68 0.17
-  344 E   -1 -1 -1  1 -3  1  5 -2 -1 -3 -3  0 -2 -3 -1 -1 -1 -3 -2 -2    0   0   0   0   0   0  72   0   0   0   0   0   0   0   0   0   0   0   0   0  0.40 0.08
-  345 E   -1 -1 -1  1 -2  1  4 -2 -1 -2 -2  0 -2 -2 -1 -1 -1 -2 -2 -2    0   0   0   0   0   0  50   0   0   0   0   0   0   0   0   0   0   0   0   0  0.08 0.01
-  346 A    3 -1 -1 -1 -1 -1 -1  0 -1 -1 -1 -1 -1 -2 -1  0  0 -2 -1 -1   50   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 -0.03 0.01
-  347 G    0 -2 -1 -1 -2 -1 -2  4 -2 -2 -2 -1 -2 -2 -2 -1 -1 -2 -2 -2    0   0   0   0   0   0   0  50   0   0   0   0   0   0   0   0   0   0   0   0  0.18 0.01
-  348 L   -2 -2 -4 -4 -1 -2 -3 -4 -3  2  4 -3  2  0 -3 -3 -1 -2 -1  1    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  0.46 0.01
-  349 A    4 -2 -2 -2  0 -1 -1  0 -2 -1 -2 -1 -1 -2 -1  1  0 -3 -2  0  100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.41 0.01
-  350 A    4 -2 -2 -2  0 -1 -1  0 -2 -1 -2 -1 -1 -2 -1  1  0 -3 -2  0  100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.41 0.01
-  351 P   -1 -2 -2 -2 -3 -1 -1 -2 -2 -3 -3 -1 -3 -4  8 -1 -1 -4 -3 -3    0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0  2.04 0.01
-  352 R   -2  6 -1 -2 -4  1  0 -3  0 -3 -2  2 -2 -3 -2 -1 -1 -3 -2 -3    0 100   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  0.75 0.01
-  353 L   -2 -2 -4 -4 -1 -2 -3 -4 -3  2  4 -3  2  0 -3 -3 -1 -2 -1  1    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  0.46 0.01
-  354 S    1 -1  1  0 -1  0  0  0 -1 -3 -3  0 -2 -3 -1  4  2 -3 -2 -2    0   0   0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0  0.46 0.01
-  355 F   -2 -3 -3 -4 -3 -4 -4 -3 -1  0  0 -3  0  7 -4 -3 -2  1  3 -1    0   0   0   0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0  0.74 0.01
-  356 L   -2 -2 -4 -4 -1 -2 -3 -4 -3  2  4 -3  2  0 -3 -3 -1 -2 -1  1    0   0   0   0   0   0   0   0   0   0 100   0   0   0   0   0   0   0   0   0  0.46 0.01
-
-                      K         Lambda
-Standard Ungapped    0.1374     0.3234
-Standard Gapped      0.0410     0.2670
-PSI Ungapped         0.1702     0.3177
-PSI Gapped           0.0521     0.2670
diff --git a/binaries/src/jpred/tests/res_d16vpa_.pssm b/binaries/src/jpred/tests/res_d16vpa_.pssm
deleted file mode 100644 (file)
index 8b8db6a..0000000
+++ /dev/null
@@ -1,356 +0,0 @@
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diff --git a/binaries/src/jpred/tests/res_d16vpa_.res b/binaries/src/jpred/tests/res_d16vpa_.res
deleted file mode 100644 (file)
index 55507ce..0000000
+++ /dev/null
@@ -1,114 +0,0 @@
->jnetpred
------------HHHHHHHHHH-------HHHHHHHHHHHHHHH-------------EE----HHHHHHHHH-
-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
-H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------EEEEEEE---
-H-HHEE----EE----EEEE--------HHHHH--HHH-----EEEEE---------E----------HHHH
-HHHHHHHHHHHH------------------------------HHHHH---------------------
->JNETSOL25
---------B-BB-BBB--BB--B-B--B--BB-BB--B-BBBBBBBBBB--BBBBB-BBBBBB--BB-BB--
--BB---BBBB-B-B---B--BB-----B--BB--B--BB---B-BBB--BB-BBB-BBBBBB-BB---B---
-B--B-B------B--BB-BBB---BB-BBB-BBBBBBBBBBBBBBBBBBBBBBB-B-----BBBBB-B-B--
----B-BBBBBBBBBBBBBBB---BB-B--B--B-BBB--B-BBBBBB-BB------BB--B-B-B-BBBBBB
-BBBBBBBBBB-BBB-B--------B--BBBBB----BBBBBBBBBBB-BB---BB--B-BBB--B---
->JNETSOL5
---------------BB--B--------B--BB--B------BB-BB------B--B-BB------B---B--
----------B-----------------B--BB--B-------B------B--BB--BB-BBB--B---B---
------B----------B---B-------B--BB-BB-B---B-BB--BB--B---------BB--B-B----
----B-BBB-B-BB--BBB-B-------------------B-B-BB-B-B------------------B-B-B
--B---B---B-B-----------------------------B--BBB---------------------
->JNETSOL0
-------------------B-------------------------B--------------------B------
----------------------------------------------------------B-B----B-------
--------------------------------------B---B--B--B------------------------
------B-----------------------------------------------------------------B
---------------------------------------------------------------------
->JNETHMM
------------HHHHHHHHHH-------HHHHHHHHHHHHHHH--------HHH---E----HHHHHHHHH-
-----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
-H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------EEEEEEE---
----EEE----EE----EEEE--------HHHHH--HH------EEEEEEEE-----------------HHHH
-HHHHHHHHHHHH-----------------------------HHHHHH---------------------
->JNETPSSM
------------HHHHHHHHHH-------HHHHHHHHHH-----------------EEE----HHHHHHHHH-
-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
----------HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEEEE--H
-HHHHHHHE---EE---EEEE---------H----HHHHH----HHHHHH-------EEE----------HHH
-HHHHHHHHHHH-H-----------------------------HEEEE-----------------EE--
->QUERY
-SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA
-YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL
-HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES
-WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG
-YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL
->UniRef90_Q00028
------PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD
-SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ
-LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ
-RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG
-FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA--------------
->UniRef90_Q8B635
------PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN
-SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS
-IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH
-RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG
-FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA--------------
->UniRef90_Q9E205
------PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS
-ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS
-SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE
-NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG
-FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS--------------
->UniRef90_Q88530
---LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE
-NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L
-NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ
-GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG
-YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS--------------
->UniRef90_B4XS08
-------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S
-EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG
-VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ
-YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG
-FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP-------------
->UniRef90_P09265
----PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S
-TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT
-TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE
-RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG
-FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE-----------
->UniRef90_Q2QBC8
-------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA
-HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL
-HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ
-ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG
-YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL-------------------
->UniRef90_Q90603
----------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK
-NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD
-LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ
-ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV
-YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD----------------
->UniRef90_O89246
---------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE
-EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP
-SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ
-LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA
-YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR----
->UniRef90_Q5PP87
-----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA
-PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD
--------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ
-ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG
-YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG----------------------------
->UniRef90_Q65819
-----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL
-AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T
-AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ
-RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG
-FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS---------------
->UniRef90_O56869
--RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS
-GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV
-GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES
--QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA
-YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP-------------
diff --git a/binaries/src/jpred/tests/res_d16vpa_.res.fasta b/binaries/src/jpred/tests/res_d16vpa_.res.fasta
deleted file mode 100644 (file)
index 55507ce..0000000
+++ /dev/null
@@ -1,114 +0,0 @@
->jnetpred
------------HHHHHHHHHH-------HHHHHHHHHHHHHHH-------------EE----HHHHHHHHH-
-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
-H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------EEEEEEE---
-H-HHEE----EE----EEEE--------HHHHH--HHH-----EEEEE---------E----------HHHH
-HHHHHHHHHHHH------------------------------HHHHH---------------------
->JNETSOL25
---------B-BB-BBB--BB--B-B--B--BB-BB--B-BBBBBBBBBB--BBBBB-BBBBBB--BB-BB--
--BB---BBBB-B-B---B--BB-----B--BB--B--BB---B-BBB--BB-BBB-BBBBBB-BB---B---
-B--B-B------B--BB-BBB---BB-BBB-BBBBBBBBBBBBBBBBBBBBBBB-B-----BBBBB-B-B--
----B-BBBBBBBBBBBBBBB---BB-B--B--B-BBB--B-BBBBBB-BB------BB--B-B-B-BBBBBB
-BBBBBBBBBB-BBB-B--------B--BBBBB----BBBBBBBBBBB-BB---BB--B-BBB--B---
->JNETSOL5
---------------BB--B--------B--BB--B------BB-BB------B--B-BB------B---B--
----------B-----------------B--BB--B-------B------B--BB--BB-BBB--B---B---
------B----------B---B-------B--BB-BB-B---B-BB--BB--B---------BB--B-B----
----B-BBB-B-BB--BBB-B-------------------B-B-BB-B-B------------------B-B-B
--B---B---B-B-----------------------------B--BBB---------------------
->JNETSOL0
-------------------B-------------------------B--------------------B------
----------------------------------------------------------B-B----B-------
--------------------------------------B---B--B--B------------------------
------B-----------------------------------------------------------------B
---------------------------------------------------------------------
->JNETHMM
------------HHHHHHHHHH-------HHHHHHHHHHHHHHH--------HHH---E----HHHHHHHHH-
-----------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
-H--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------EEEEEEE---
----EEE----EE----EEEE--------HHHHH--HH------EEEEEEEE-----------------HHHH
-HHHHHHHHHHHH-----------------------------HHHHHH---------------------
->JNETPSSM
------------HHHHHHHHHH-------HHHHHHHHHH-----------------EEE----HHHHHHHHH-
-------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
----------HHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----EEEEEEE--H
-HHHHHHHE---EE---EEEE---------H----HHHHH----HHHHHH-------EEE----------HHH
-HHHHHHHHHHH-H-----------------------------HEEEE-----------------EE--
->QUERY
-SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDA
-YVPERTQIDIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQL
-HRQAHMRGRDRDLGEMLRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLES
-WRQLAGLFQPFMFVNGALTVRGVPIEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASG
-YFMVLIRAKLDSYSSFTTSPSEAVMREHAYSRAPTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFL
->UniRef90_Q00028
------PPKATSPTALYQRLQAELGFPEGQAMLFAMEKWNEDMFSAIPVHVDLYTEIALLSTSVNEVVKAGLD
-SLPIPTEVDLNAHGSEPFPEVPALEDELETYVISAQRFYLSELRAREEHYSRLLRGYCVALLHYLYGSAKRQ
-LRGA---GSDSALMHKFKQVVRDRYYRETANLARLLYLHLYISVTREVSWRLHASQVVNQGIFVSLHYTWPQ
-RRKFECLFHPVLFNHGVVILENDPLEFNDLQRINYRRRELGLPLIRAGLIEEENLPLESEPTFSGKLPRTIG
-FLTHQIRTKMEAYSNAHPSTPLFPLAEHSYSRIDGRLSYGTTAEAMMDPPSPSA--------------
->UniRef90_Q8B635
------PIKASSPSSLIKNLLDELNFPEGPSLLSSMEKWNEDLFSCIPRFLEIYIENSILSTSVDEVIKNLDN
-SLNYDDVIDFQVHGPETFPKTPLLEEELENYVTSVQKYFLSELKAREVTYSFLLTKYCKALLLYLRYNTKSS
-IKG------NKDINQKFKQNVRERYYREVANIARLLYLHLYLSVTREVSWKLHADQVLLQSVFVSLSYSWSH
-RRQFECIFHPILFNHGIVNLENNPLTFKELQKINYRRHILGLPLIRAGLVEEDNQPLMIPPEFSSKLPRTIG
-FLTQQIRAKMEAYSDNHPVTPKFPRIEHSYAKPIDPINYGTTIEAMMDPPSPSA--------------
->UniRef90_Q9E205
------PPRVASPAVLYQQLINDLHFSEGPRIIALLETCNEDIFSCFPLNEDLYTDTIVFSTNPSDIIELETS
-ETPE--PINLITKG-CDLPSLPSTYTELPMYVENVQNTFFTELRVREKAYLRLLILYCKSLLRHLQGISRRS
-SVGARSQDCEHKYITQFKQSIRLRYYREVAKLARLLYLHLYITVTRQFSWRLFAQQSKYPDVFAAMKFMWLE
-NRQFTCAFHPILCNHGIVLLEGKPLSSQRLREVNYRRRQLGLPLVRCALIEEKGVPLVQRPEFSAHMPRSLG
-FLTHHIKAKLDVYSSKHSQEPGNVRVDHPYARNVNNINYGSSVEAMIVSPPSPS--------------
->UniRef90_Q88530
---LPSPE-AASPNLLYDRLILELDFAEGPSLLAKLERVNVDLFSCLPLNSHLYKHAKILSTCPREVLDAVYE
-NTWQYTALNLNEHGKSSIPPVPASKDDLPAYVTAVQEFYLEELEAREQIYAKLFFGYCRALIMHIIKSV--L
-NESRGVRVSDDYVQNKARWYISNNYYRDAVRIAKLLYLHLYLSTTEIVSQRLEAMQTSLQDLFVYLRCEWGQ
-GRQFWCIFQPMIYNHGVPMIEGRALTSLELGSSNYIRSELGLPLIRCELLEELESPVVFPPTFTATAPRSSG
-YLFHNIRAKMELYSNIHPSPQLSGLSDHTYVRTHVPVNYGTTVEVLLDASDPDS--------------
->UniRef90_B4XS08
-------------------------FPEASTILSTFELMNMDLFSCLPRNEDLYRNAALLSGSVTEVIEA--S
-EIPIDGEIDLNAHGSKQLPIPPSNEWEIPNYVEAVQQFFLSELRAREESYLKLFLGYCRAIVNYIKSAATRG
-VRGCRIMDRKSEANKRMRRMIADRYYREAARLAKVLYLHLYLSVAREISSRLCATQMQVQNVFVYMRYEWQQ
-YRQFTCLFHPIMFNHGVVLLNGEPLQAQKLREVNYIRFKLGLPVIRCGLVEEHDKPLVEEPRFYGNLPRSSG
-FLTELIRSKMEAYSELRPTSPSSISNDHTYAKQLDKVNFGSTREAILDTIDTEGP-------------
->UniRef90_P09265
----PSPPWVASPKILYQQLIRDLDFSEGPRLLSCLETWNEDLFSCFPINEDLYSDMMVLSPDPDDVI----S
-TVSTKDHVNLTTRGSVRLPSPPKQPTGLPAYVQEVQDSFTVELRAREEAYTKLLVTYCKSIIRYLQGTAKRT
-TIGLNIQNPDQKAYTQLRQSILLRYYREVASLARLLYLHLYLTVTREFSWRLYASQSAHPDVFAALKFTWTE
-RRQFTCAFHPVLCNHGIVLLEGKPLTASALREINYRRRELGLPLVRCGLVEENKSPLVQQPSFSVHLPRSVG
-FLTHHIKRKLDAYAVKHPQEPRHVRADHPYAKVVENRNYGSSIEAMILAP--PSPSE-----------
->UniRef90_Q2QBC8
-------------AALYNRLLEDLGFGDGPALCTILDSWNEDLFSGLPANPDLYRECRFLSTLPGDVVVWGDA
-HAPDRGPIDIRAHGSAPFPSLPARREGLPAYCEALTRFFHSELRAREESYRRVLANFCSALYRYLRASTRQL
-HRQAALKGRPRDLQEMLRAAVAERYYRETARLARVLFLHLYLFLVREILWAVYAEQVMRQDLFEGLRCDLEQ
-ARQLSCLFQPLLFVHGALSVGGEPVSPARLRELNHVRERLNLPLIRSAATEEPGAALTAAPALQTQRARSSG
-YFMTLIRVKLDAYSEWSAGSEGAVLREHAYSRRRERTNYGSSIEGLLEL-------------------
->UniRef90_Q90603
----------------YTRLLHELDFVEGPSILARLEKINVDLFSCFPHNKHLYEHAKILSVSPSEVLEELSK
-NTWTYTALNLNEHGEVALPMPPTTKADLPSYVDDIQNFYLGELEAREKSYATMFYGYCRALAEYIRQSAIKD
-LRDA--RVEDKNIGACSKARQYIAERYYREAFANVLYVHLYLSTTRDVSQRLEASQMGRQNIFVYLKCEWLQ
-ERHFHCLFQPVIFNHGVVIVEGRVLTAPELRAQNYIRSEFGLPLIRCKLVEEPDMPLISPPPFSGDAPRASV
-YLLQCIRSKLEVYSSHPPNPQLHVHKEHVHQKLESPPNYGTTVEALLMDSSD----------------
->UniRef90_O89246
---------------------HELDFTEGPSLLSRLEKLNVDLFSCFPINGHLYEHATLLSVSPSEVLDAASE
-EKWAYTAINLNEHCGMEVPRPPLTKDGLPVYVTEIQKFFSMELEAREKSYVTLLCGYCRALACYLRQGANEP
-SRCDMCVGGS----ETPRRSIAGAYYREAARFARLLYMHLYLSVTRDVSRRLEASQRKRQNLFAHLRCDWHQ
-LRHFQCLFQPVIFNHGVVIVEGRALTAAELRTQNYVRSELGLPVMRCELVEERGMPLTAPPAFLANAPRASA
-YLFQCIKSKLEVYSLMHPPRPRSSARGESGRAGKAGPSHGTIVKAMLRDSTHPGPAIADIAAAR----
->UniRef90_Q5PP87
-----------SPDALYQRLISDLAFDEGPALLGAMERWNEDLFSCLPGNEDLYARLVMLSASADEVAAQVRA
-PTADAS-VDLGVPGAEPMPRVPAVEEELPAYVAAVERFFVSTLRAREERYARLLDAYCRAVLRYLHAQARRD
--------------EGKLRQLVRGRYYRDVARLAPWLFLHLYVATARELSWRLHADQVVAQDVFMSLRYEWDQ
-ARQLTCLFHPVLFNHGVVLLSGAPVPAAQLRAVNHRRRELGLPLVRAGLIEEDGADLVEEPPFSAALPRAAG
-YLSHQVRIKMEAYS--------REYRDHTYCRPPSPVSYG----------------------------
->UniRef90_Q65819
-----------------ERMQAELGFPDGPALLRAMERWNEDLFSCLPTNADLYADAALLSADADAVVGAMYL
-AVPDAERLDLNAHANQPLPAPPASEEGLPEYVAGVQAHFLAELRAREERYAGLFLGYCRALLQHLRA----T
-AARGRGAAGAGAQADRLRQLVAARYYREASRLARLAFAHMYVATAREVSWRLHSQQSQAQGVFVSLYYAWPQ
-RRQFTCLFHPVLFNHGVVALEDGFLDAAELRRLNYRRRELGLPLVRAGLVEVEVGPLVEEPPFSGSLPRALG
-FLNYQVRAKMGAPAE--AGGRLAPEREHSYARPRGAINYGTTPEAMLRPPSPS---------------
->UniRef90_O56869
--RNPGPPALVSASFLAKNALTELQFADWDKIQHVLKTINIDIFSCVPVGENGLCNMDWFSLDTEKIWTLMDS
-GTPNVSPNLLITPGPP--PECIKTPEEAPAYFEAISNYFESVLAAREAEYAKLLAEYAKSLAKYIRHKSQKV
-GR--GLRALELDTEEAKKRLMKSEYYKGIEKLLIIFLVHLVLNACRDVARIIWVQQRDSSSVLQKVTYRWES
--QQLHCIFQPLLVSPGPVFLDNDPLPLQTLQHVNYVRYLLGVPVLRFSMIEESPSAQYIP----YDKTAPSA
-YDVLATIAR----TCLTSSGCSRASHDHTYARDNEKPNYSSSRIVLLADSALDTP-------------
index 030ea8a..47417f2 100755 (executable)
@@ -21,9 +21,11 @@ ln -s /data/UNIREFdb databases
 
 
 ####################################################################################################
-../jpred.pl -seq d16vpa_.fas -o res_d16vpa_ -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
-../jpred.pl -seq SCOP175B_nr.seq -o res_SCOP175B_nr -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
-../jpred.pl -seq T-state1.fas    -o res_T-state1.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
-../jpred.pl -seq T-state2.fas    -o res_T-state2.res -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq -in d16vpa_.fas  -outfile d16vpa_.res.fasta      -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq -in d1b3aa_.fas  -outfile d1b3aa_.res.fasta      -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq -in T-state1.fas -outfile res_T-state1.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -seq -in T-state2.fas -outfile res_T-state2.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
 
-./webscripts/fasta2concise < d16vpa_.res.align > d16vpa_.res.align.csv
+../jpred.pl -in alignment.msf   -outfile alignment_from_msf.res.fasta   -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -in alignment.blc   -outfile alignment_from_blc.res.fasta   -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
+../jpred.pl -in alignment.fasta -outfile alignment_from_fasta.res.fasta -dbname ported_db -dbpath /data/UNIREFdb/ -ncpu 4 -debug
diff --git a/binaries/src/jpred/x86_64/alscript b/binaries/src/jpred/x86_64/alscript
new file mode 100755 (executable)
index 0000000..e9e895d
Binary files /dev/null and b/binaries/src/jpred/x86_64/alscript differ
diff --git a/binaries/src/jpred/x86_64/readseq b/binaries/src/jpred/x86_64/readseq
new file mode 100755 (executable)
index 0000000..ee9663f
Binary files /dev/null and b/binaries/src/jpred/x86_64/readseq differ