Binary file ._ITSx has changed

Binary file ._ITSx.xml has changed

Binary file ._ITSx_db has changed

Binary file ._tool_dependencies.xml has changed

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ITSx	Tue Mar 24 12:02:48 2015 -0400
@@ -0,0 +1,2695 @@
+#!/usr/bin/perl
+# ITSx ITS Extractor
+$app_title     = "ITSx -- Identifies ITS sequences and extracts the ITS region";
+$app_author    = "Johan Bengtsson-Palme et al., University of Gothenburg";
+$app_version   = "1.0.11";
+$app_message   = "";
+# ----------------------------------------------------------------- #
+
+# License information
+$license =
+"    ITSx - ITS Extractor -- Identifies ITS sequences and extracts the ITS region\
+    Copyright (C) 2012-2014 Johan Bengtsson-Palme et al.\
+\
+    This program is free software: you can redistribute it and/or modify\
+    it under the terms of the GNU General Public License as published by\
+    the Free Software Foundation, either version 3 of the License, or\
+    (at your option) any later version.\
+\
+    This program is distributed in the hope that it will be useful,\
+    but WITHOUT ANY WARRANTY; without even the implied warranty of\
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\
+    GNU General Public License for more details.\
+\
+    You should have received a copy of the GNU General Public License\
+    along with this program, in a file called 'license.txt'\
+    If not, see: http://www.gnu.org/licenses/.\
+";
+
+## BUGS:
+$bugs = "New features in this version ($app_version):\
+- None\
+\
+Fixed bugs in this version ($app_version):\
+- Fixed a bug causing newline characters to be occasionally skipped in the 'its1.full_and_partial.fasta' FASTA output file when the '--anchor' option was used\
+\
+Known bugs in this version ($app_version):\
+- None\
+";
+
+## OPTIONS:
+$options = "\
+-i {file} : DNA FASTA input file to investigate\
+-o {file} : Base for the names of output file(s)\
+-p {directory} : A path to a directory of HMM-profile collections representing ITS conserved regions, default is in the same directory as ITSx itself\
+--date {T or F} : Adds a date and time stamp to the output directory, off (F) by default\
+--reset {T or F} : Re-creates the HMM-database before ITSx is run, off (F) by default\
+
+Sequence selection options:\
+-t {character code} : Profile set to use for the search, see the User's Guide (comma-separated), default is all\
+-E {value} : Domain E-value cutoff for a sequence to be included in the output, default = 1e-5\
+-S {value} : Domain score cutoff for a sequence to be included in the output, default = 0\
+-N {value} : The minimal number of domains that must match a sequence before it is included, default = 2\
+--selection_priority {sum, domains, eval, score} : Selects what will be of highest priority when determining the origin of the sequence, default is sum\
+--search_eval {value} : The E-value cutoff used in the HMMER search, high numbers may slow down the process, cannot be used with the --search_score option, default is 0.01\
+--search_score {value} : The score cutoff used in the HMMER search, low numbers may slow down the process, cannot be used with the --search_eval option, default is to used E-value cutoff, not score\
+--allow_single_domain {e-value,score or F} : Allow inclusion of sequences that only find a single domain, given that they meet the given E-value and score thresholds, on with parameters 1e-9,0 by default\
+--allow_reorder {T or F} : Allows profiles to be in the wrong order on extracted sequences, off (F) by default\
+--complement {T or F} : Checks both DNA strands against the database, creating reverse complements, on (T) by default\
+--cpu {value} : the number of CPU threads to use, default is 1\
+--multi_thread {T or F} : Multi-thread the HMMER-search, on (T) if number of CPUs (--cpu option > 1), else off (F) by default\
+--heuristics {T or F} : Selects whether to use HMMER's heuristic filtering, off (F) by default\
+
+Output options:\
+--summary {T or F} : Summary of results output, on (T) by default\
+--graphical {T or F} : 'Graphical' output, on (T) by default\
+--fasta {T or F} : FASTA-format output of extracted ITS sequences, on (T) by default\
+--preserve {T or F} : Preserve sequence headers in input file instead of printing out ITSx headers, off (F) by default\
+--save_regions {SSU,ITS1,5.8S,ITS2,LSU,all,none} : A comma separated list of regions to output separate FASTA files for, 'ITS1,ITS2' by default\
+--anchor {integer or HMM} : Saves an additional number of bases before and after each extracted region. If set to 'HMM' all bases matching the corresponding HMM will be output, default = 0\
+--only_full {T or F} : If true, output is limited to full-length regions, off (F) by default\
+--partial {integer} : Saves additional FASTA-files for full and partial ITS sequences longer than the specified cutoff, default = 0 (off)\
+--concat {T or F} : Saves a FASTA-file with concatenated ITS sequences (with 5.8S removed), off (F) by default\
+--minlen {integer} : Minimum length the ITS regions must be to be outputted in the concatenated file (see above), default = 0\
+--positions {T or F} : Table format output containing the positions ITS sequences were found in, on (T) by default\
+--table {T or F} : Table format output of sequences containing probable ITS sequences, off (F) by default\
+--not_found {T or F} : Saves a list of non-found entries, on (T) by default\
+--detailed_results {T or F} : Saves a tab-separated list of all results, off (F) by default\
+--truncate {T or F} : Truncates the FASTA output to only contain the actual ITS sequences found, on (T) by default\
+--silent {T or F} : Supresses printing progress info to stderr, off (F) by default\
+--graph_scale {value} : Sets the scale of the graph output, if value is zero, a percentage view is shown, default = 0\
+--save_raw {T or F} : Saves all raw data for searches etc. instead of removing it on finish, off (F) by default\
+
+-h : displays this help message\
+--help : displays this help message\
+--bugs : displays the bug fixes and known bugs in this version of ITSx\
+--license : displays licensing information\
+";
+
+
+## Print title message
+print STDERR "$app_title\nby $app_author\nVersion: $app_version\n$app_message";
+print STDERR "-----------------------------------------------------------------\n";
+
+## Setup default variable values
+use List::Util qw(first max maxstr min minstr reduce shuffle sum);
+
+$bindir = $0;
+$bindir =~ s/_x//;
+$input = "";
+$output = "ITSx_out";
+$hmmscan = "";
+$profileDB = "$bindir\_db/HMMs";
+$type = "all";
+$E = 1e-5;
+$S = 0;
+$N = 2;
+$priority = "sum";
+$search_eval = 0.01;
+$search_score = "";
+$allow_single_E = 1e-9;
+$allow_single_score = 0;
+#$allow_single_E = -1;   # Turns off single-domain matching by E-value
+#$allow_single_score = 0;   # Turns off single-domain matching by score
+$allow_reorder = 0;
+$complement = 1;
+$cpu = 1;
+$multi_thread = "unset";
+$heuristics = 0;
+$out_sum = 1;
+$out_graph = 1;
+$out_fasta = 1;
+$out_preserve = 0;
+$out_ssu = 0;
+$out_its1 = 1;
+$out_its2 = 1;
+$out_58S = 0;
+$out_lsu = 0;
+$out_pos = 1;
+$out_table = 0;
+$out_not = 1;
+$out_date = 0;
+$out_joined = 0;
+$out_results = 0;
+$out_partial = 0;
+$out_concat = 0;
+$concat_minlen = 0;
+$truncate = 1;
+$anchor = 0;
+$only_full = 0;
+$graph_scale = 0;
+$debug = 0;
+$reset = 0;
+
+## Read command-line options
+for ($i = 0; $i <= scalar(@ARGV); $i++) {   # Goes through the list of arguments
+  $arg = @ARGV[$i];   # Stores the current argument in $arg
+
+  if ($arg eq "-i") {   # Read input files from -i flag
+    $i++;
+    $input = @ARGV[$i];
+  }
+  if ($arg eq "-o") {   # Read output files from -o flag
+    $i++;
+    $output = @ARGV[$i];
+  }
+  if ($arg eq "-p") {   # Read profile database from -p flag
+    $i++;
+    $profileDB = @ARGV[$i];
+  }
+  if ($arg eq "--hmmscan") {   # Read pre-computed hmmscan output file from --hmmscan flag ('undocumented' feature)
+    $i++;
+    $hmmscan = @ARGV[$i];
+  }
+  if ($arg eq "--date") {   # Determine whether or not to add a date stamp based on the --date flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Ff0]/) {   # Check if argument begins with "F", "f", or "0"
+      $out_date = 0;
+    } else {
+      $out_date = 1;
+    }
+  }
+  if ($arg eq "--reset") {   # Reset HMM database?
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Ff0]/) {   # Check if argument begins with "F", "f", or "0"
+      $reset = 0;
+    } else {
+      $reset = 1;
+    }
+  }
+
+  if ($arg eq "-t") {   # Select what types of ITSs to look for using the -t flag
+    $i++;
+    $type = @ARGV[$i];
+  }
+  if ($arg eq "-E") {   # Set the E-value cutoff using the -E flag
+    $i++;
+    $E = @ARGV[$i];
+  }
+  if ($arg eq "-S") {   # Set the score cutoff using the -S flag
+    $i++;
+    $S = @ARGV[$i];
+  }
+  if ($arg eq "-N") {   # Set the number of found domains cutoff using the -N flag
+    $i++;
+    $N = @ARGV[$i];
+  }
+  if ($arg eq "--selection_priority") {   # Set how to order the ITS types using the --selection_priority flag
+    $i++;
+    $priority = @ARGV[$i];
+  }
+  if ($arg eq "--search_eval") {   # Set the E-value cutoff for the HMMER search using the --search_eval flag
+    $i++;
+    $search_eval = @ARGV[$i];
+    $search_score = "";   #  Turns off score cutoff
+  }
+  if ($arg eq "--search_score") {   # Set the score cutoff for the HMMER search using the --search_score flag
+    $i++;
+    $search_score = @ARGV[$i];
+    $search_eval = "";   #  Turns off E-value cutoff
+  }
+  if ($arg eq "--allow_single_domain") {   # Determine whether or not to allow single domain matches based on the --allow_single_domain flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Ff0]/) {   # Check if argument begins with "F", "f", or "0"
+      $allow_single_E = -1;   # Turns off single-domain matching by E-value
+      $allow_single_score = 0;   # Turns off single-domain matching by score
+    } else {
+      ($allow_single_E,$allow_single_score) = split(',',@ARGV[$i]);   # Turns on single-domain matching, assigning the first given value as the E-value cutoff, and the second as score cutoff
+    }
+  }
+  if ($arg eq "--allow_reorder") {   # Determine whether or not to allow the domains to be in the wrong order based on the --allow_reorder flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $allow_reorder = 1;
+    } else {
+      $allow_reorder = 0;
+    }
+  }
+  if ($arg eq "--complement") {   # Determine whether or not to scan the complementary strand of the input file based on the --complement flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $complement = 1;
+    } else {
+      $complement = 0;
+    }
+  }
+  if ($arg eq "--cpu") {   # Set the number of CPUs to use based on the --cpu flag
+    $i++;
+    $cpu = @ARGV[$i];
+  }
+  if ($arg eq "--multi_thread") {   # Determine whether or not to multi-thread the HMMER step based on the --multi_thread flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $multi_thread = 1;
+    } else {
+      $multi_thread = 0;
+    }
+  }
+  if ($arg eq "--heuristics") {   # Determine whether or not to use HMMER's heuristic filtering based on the --heuristics flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $heuristics = 1;
+    } else {
+      $heuristics = 0;
+    }
+  }
+
+  if ($arg eq "--summary") {   # Determine whether or not to output a summary based on the --summary flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_sum = 1;
+    } else {
+      $out_sum = 0;
+    }
+  }
+  if ($arg eq "--graphical") {   # Determine whether or not to output a graphical representation of matches based on the --graphical flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_graph = 1;
+    } else {
+      $out_graph = 0;
+    }
+  }
+  if ($arg eq "--detailed_results") {   # Determine whether or not to output a detailed results list, based on the --detailed_results flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_results = 1;
+    } else {
+      $out_results = 0;
+    }
+  }
+  if ($arg eq "--partial") {   # Set the full-and-partial cutoff
+    $i++;
+    $out_partial = @ARGV[$i];
+  }
+  if ($arg eq "--anchor") {   # Set the length of the sequence "anchors"
+    $i++;
+    $anchor = @ARGV[$i];
+  }
+  if ($arg eq "--only_full") {   # Output only full-length regions
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $only_full = 1;
+    } else {
+      $only_full = 0;
+    }
+  }
+  if ($arg eq "--save_regions") {   # Determine which regions to output FASTA files for based on the --save_regions flag
+    $i++;
+    @save_regions = split(',',uc(@ARGV[$i]));
+    $out_ssu = 0;
+    $out_its1 = 0;
+    $out_its2 = 0;
+    $out_58S = 0;
+    $out_lsu = 0;
+    foreach $save_region (@save_regions) {
+      if ($save_region eq "SSU") {
+	$out_ssu = 1;
+      }
+      if ($save_region eq "ITS1") {
+	$out_its1 = 1;
+      }
+      if ($save_region eq "5.8S") {
+	$out_58S = 1;
+      }
+      if ($save_region eq "ITS2") {
+	$out_its2 = 1;
+      }
+      if ($save_region eq "LSU") {
+	$out_lsu = 1;
+      }
+      if ($save_region eq "ALL") {
+	$out_ssu = 1;
+	$out_its1 = 1;
+	$out_its2 = 1;
+	$out_58S = 1;
+	$out_lsu = 1;
+      }
+      if ($save_region eq "NONE") {
+	$out_ssu = 0;
+	$out_its1 = 0;
+	$out_its2 = 0;
+	$out_58S = 0;
+	$out_lsu = 0;
+      }
+    }
+  }
+  if ($arg eq "--positions") {   # Determine whether or not to output a positions file based on the --positions flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_pos = 1;
+    } else {
+      $out_pos = 0;
+    }
+  }
+  if ($arg eq "--concat") {   # Determine whether or not to output a concatednated ITS1 + ITS2 file
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_concat = 1;
+    } else {
+      $out_concat = 0;
+    }
+  }
+  if ($arg eq "--minlen") {   # Set the min length of the combined ITS1 and ITS2 sequences for concatenation
+    $i++;
+    $concat_minlen = @ARGV[$i];
+  }
+  if ($arg eq "--fasta") {   # Determine whether or not to output FASTA-files based on the --fasta flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_fasta = 1;
+    } else {
+      $out_fasta = 0;
+    }
+  }
+  if ($arg eq "--preserve") {   # Determine whether or not to preserve FASTA-headers based on the --preserve flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_preserve = 1;
+    } else {
+      $out_preserve = 0;
+    }
+  }
+  if ($arg eq "--joined") {   # Determine whether or not to output a FASTA-file containing ALL sorts of output sequences (for debugging)
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_joined = 1;
+    } else {
+      $out_joined = 0;
+    }
+  }
+  if ($arg eq "--table") {   # Determine whether or not to output tables of all potential matches based on the --table flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_table = 1;
+    } else {
+      $out_table = 0;
+    }
+  }
+  if ($arg eq "--not_found") {   # Determine whether or not to output a list of sequences that are not ITSs based on the --not_found flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $out_not = 1;
+    } else {
+      $out_not = 0;
+    }
+  }
+  if ($arg eq "--silent") {   # Determine whether or not to output anything to the screen based on the --silent flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $silent = 1;
+    } else {
+      $silent = 0;
+    }
+  }
+  if ($arg eq "--graph_scale") {   # Set the scale of the graphical output based on the --graph_scale flag
+    $i++;
+    $graph_scale = @ARGV[$i];
+  }
+  if ($arg eq "--save_raw") {   # Determine whether or not to save all the raw intermediate data based on the --save_raw flag
+    $i++;
+    if (substr(@ARGV[$i],0,1) =~ m/^[Tt1]/) {   # Check if argument begins with "T", "t", or "1"
+      $save_raw = 1;
+    } else {
+      $save_raw = 0;
+    }
+  }
+
+  ## If "-h" or "--help" are among the options, output usage data and options
+  if (($arg eq "-h") || ($arg eq "--help")) {
+    print "Usage: ITSx -i <input file> -o <output file>\nOptions:$options";
+    print "-----------------------------------------------------------------\n";
+    exit;   # Exit ITSx
+  }
+
+  ## If "--bugs" is among the options, output bugs and features information
+  if ($arg eq "--bugs") {
+    print "$bugs\n";
+    exit;   # Exit ITSx
+  }
+
+  ## If "--license" is among the options, output license information
+  if ($arg eq "--license") {
+    print "$license\n";
+    exit;   # Exit ITSx
+  }
+
+  if ($arg eq "--debug") {   # Run ITSx in debug mode
+    $debug = 1;
+  }
+  if ($arg eq "--pipeline") {   # Run ITSx in pipeline mode
+    $pipeline = 1;
+  }
+}
+
+## Setup some variables dependent on input
+
+if ($multi_thread eq "unset") {   # If the multi-thread option is not set
+  if ($cpu > 1) {   # Then if the number of CPUs used > 1, then multi-thread HMMER searches
+    $multi_thread = 1;
+  } else {   # Else, run HMMER searches sequentially on one CPU
+    $multi_thread = 0;
+  }
+}
+
+if ($hmmscan ne "") {   # If a pre-computed hmmscan output is supplied
+  $output = $hmmscan;   # Then set the base of the output directory name to be the same as that hmmscan output file
+}
+
+## Check for binaries
+
+chomp($path = `which hmmpress`);   # Get the path for hmmpress
+if ($path eq "") {   # If the path is empty, then show an error message and exit ITSx
+  print STDERR "FATAL ERROR :: Could not locate HMMER binaries! It seems that hmmpress is not installed properly.\
+Consult the manual for installation instructions. Note that HMMER3 is required. Previous HMMER-versions will not work.\
+This error is fatal, and ITSx will now abort.\n";
+  print STDERR "-----------------------------------------------------------------\n";
+  exit;
+}
+
+chomp($path = `which hmmscan`);   # Get the path for hmmscan
+if ($path eq "") {   # If the path is empty, then show an error message and exit ITSx
+  print STDERR "FATAL ERROR :: Could not locate HMMER binaries! It seems that hmmscan is not installed properly.\
+Consult the manual for installation instructions. Note that HMMER3 is required. Previous HMMER-versions will not work.\
+This error is fatal, and ITSx will now abort.\n";
+  print STDERR "-----------------------------------------------------------------\n";
+  exit;
+}
+
+
+## Check for database
+chomp($errormsg = `ls $profileDB* 2>&1 1>/dev/null`);   # Get the error msg when looking for the profile database
+if (substr($errormsg,0,4) eq "ls: ") {   # If the error message begins with "ls: ", then show an error message and exit ITSx
+  print STDERR "FATAL ERROR :: The specified profile database could not be found.\
+Consult the manual for installation instructions.\
+This error is fatal, and ITSx will now abort.\n";
+  print STDERR "-----------------------------------------------------------------\n";
+  exit;
+}
+
+if ($pipeline == 0) {   # If ITSx is not run in pipeline mode (i.e. from ITSx)
+  if ($out_date == 1) {   # If a date and time stamp should be supplied
+    ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);   # Get the date and time
+    $year = $year + 1900;   # Format the year
+    $mon = $mon + 1;   # Format the month
+    if ($mon < 10) {   # Add a zero to the month, if needed
+      $mon = "0" . $mon;
+    }
+    if ($mday < 10) {   # Add a zero to the day, if needed
+      $mday = "0" . $mday;
+    }
+    if ($hour < 10) {   # Add a zero to the hour, if needed
+      $hour = "0" . $hour;
+    }
+    if ($min < 10) {   # Add a zero to the minute, if needed
+      $min = "0" . $min;
+    }
+    $outputDate = ".$year\-$mon\-$mday\_$hour.$min";   # Create a date and time stamp
+    $outputDate =~ s./.-.g;   # Remove any potential slashes in the output name (as this will confuse ITSx's file naming)
+    $output = $output . $outputDate;   # Add the date and time stamp top the output base name
+  }
+}
+
+$tempDir = "ITSx_temp_directory__$output";   # Setup a temporary directory variable
+$tempDir =~ s./.-.g;   # Remove any potential slashes in the output name (as this will confuse ITSx's file naming)
+
+if ($pipeline == 0) {   # If not running in pipeline mode
+  ## Create a summary file
+  if ($out_sum == 1) {   # If summary output is on
+    $now = localtime;   # Get the current time
+    open (SUMMARY, ">$output.summary.txt");   # Create the summary file
+    print SUMMARY "ITSx run started at $now.\n";   # Output the starting time for the analysis
+    print SUMMARY "-----------------------------------------------------------------\n";
+    close (SUMMARY);   # Close summary file
+  }
+}
+
+## Create a temporary directory for ITSx
+if ($pipeline == 0) {   # If ITSx is not run in pipeline mode (i.e. from ITSx)
+  `mkdir $tempDir 2> /dev/null`;   # Create a temporary directory
+}
+
+
+## Prepare profile database
+## Get the current time and output info message
+$now = localtime;
+if ($silent == 0) {
+  print STDERR "$now : Preparing HMM database (should be quick)...\n";
+}
+
+## Setup profile index
+%profileIndex = {};
+
+# A = Alveolata
+# B = Bryophyta
+# C = Bacillariophyta
+# D = Amoebozoa
+# E = Euglenozoa
+# F = Fungi
+# G = Chlorophyta (green algae)
+# H = Rhodophyta (red algae)
+# I = Phaeophyceae (brown algae)
+# L = Marchantiophyta (liverworts)
+# M = Metazoa
+# N = Microsporidia
+# O = Oomycota
+# P = Haptophyceae (prymnesiophytes)
+# Q = Raphidophyceae
+# R = Rhizaria
+# S = Synurophyceae
+# T = Tracheophyta (higher plants)
+# U = Eustigmatophyceae
+# X = Apusozoa
+# Y = Parabasalia
+
+$profileIndex{"A"} = "alveolates";
+$profileIndex{"B"} = "bryophyta";
+$profileIndex{"C"} = "bacillariophyta";
+$profileIndex{"D"} = "amoebozoa";
+$profileIndex{"E"} = "euglenozoa";
+$profileIndex{"F"} = "fungi";
+$profileIndex{"G"} = "chlorophyta";
+$profileIndex{"H"} = "rhodophyta";
+$profileIndex{"I"} = "phaeophyceae";
+$profileIndex{"J"} = "undefined";
+$profileIndex{"K"} = "undefined";
+$profileIndex{"L"} = "marchantiophyta";
+$profileIndex{"M"} = "metazoa";
+$profileIndex{"N"} = "microsporidia";
+$profileIndex{"O"} = "oomycota";
+$profileIndex{"P"} = "haptophyceae";
+$profileIndex{"Q"} = "raphidophyceae";
+$profileIndex{"R"} = "rhizaria";
+$profileIndex{"S"} = "synurophyceae";
+$profileIndex{"T"} = "tracheophyta";
+$profileIndex{"U"} = "eustigmatophyceae";
+$profileIndex{"V"} = "undefined";
+$profileIndex{"W"} = "undefined";
+$profileIndex{"X"} = "apusozoa";
+$profileIndex{"Y"} = "parabasalia";
+$profileIndex{"Z"} = "undefined";
+
+
+@profileList = split(',',uc($type));   # Get the list of profile types
+foreach $entry (@profileList) {   # Go through the entered types
+  if (($entry eq "ALL") || ($entry eq ".")) {   # If "all" among the entries
+    push(@profileSet,"A");   # Add the alveolates profiles to the investigation set
+    push(@profileSet,"B");   # Add the bryophytes profiles to the investigation set
+    push(@profileSet,"C");   # Add the bacillariophyta profiles to the investigation set
+    push(@profileSet,"D");   # Add the amoebozoa profiles to the investigation set
+    push(@profileSet,"E");   # Add the euglenozoa profiles to the investigation set
+    push(@profileSet,"F");   # Add the fungi profiles to the investigation set
+    push(@profileSet,"G");   # Add the green algae profiles to the investigation set
+    push(@profileSet,"H");   # Add the red algae profiles to the investigation set
+    push(@profileSet,"I");   # Add the brown algae profiles to the investigation set
+    push(@profileSet,"L");   # Add the liverworts profiles to the investigation set
+    push(@profileSet,"M");   # Add the metazoa profiles to the investigation set
+    #push(@profileSet,"N");   # Add the microsporidia profiles to the investigation set
+    push(@profileSet,"O");   # Add the oomycetes profiles to the investigation set
+    push(@profileSet,"P");   # Add the prymnesiophytes profiles to the investigation set
+    push(@profileSet,"Q");   # Add the raphidophytes profiles to the investigation set
+    push(@profileSet,"R");   # Add the rhizaria profiles to the investigation set
+    push(@profileSet,"S");   # Add the synurophyceae profiles to the investigation set
+    push(@profileSet,"T");   # Add the tracheophyta (higher plants) profiles to the investigation set
+    push(@profileSet,"U");   # Add the eustigmatophytes profiles to the investigation set
+    #push(@profileSet,"X");   # Add the apusozoa profiles to the investigation set
+    #push(@profileSet,"Y");   # Add the parabasalia profiles to the investigation set
+  } else {
+    if (length($entry) == 1) {  # If the name has only one character
+      if ($entry =~ m/[ABCDERFHILMNOPQRSTUXY]/) {  # If the selected set exists
+	push(@profileSet,$entry);   # Add the selected profiles to the investigation set
+      }
+    } else {
+      if ($entry =~ m/ALVEOL/) {
+	push(@profileSet,"A");   # Add the alveolates profiles to the investigation set
+      }
+      if ($entry =~ m/BRYO/) {
+	push(@profileSet,"B");   # Add the bryophytes profiles to the investigation set
+      }
+      if ($entry =~ m/MOSS/) {
+	push(@profileSet,"B");   # Add the bryophytes profiles to the investigation set
+      }
+      if ($entry =~ m/BACILL/) {
+	push(@profileSet,"C");   # Add the bacillariophyta profiles to the investigation set
+      }
+      if ($entry =~ m/DIATOM/) {
+	push(@profileSet,"C");   # Add the bacillariophyta profiles to the investigation set
+      }
+      if ($entry =~ m/AMOEB/) {
+	push(@profileSet,"D");   # Add the amoebozoa profiles to the investigation set
+      }
+      if ($entry =~ m/EUGLE/) {
+	push(@profileSet,"E");   # Add the euglenozoa profiles to the investigation set
+      }
+      if ($entry =~ m/FUNG/) {
+	push(@profileSet,"F");   # Add the fungi profiles to the investigation set
+      }
+      if ($entry =~ m/GREEN/) {
+	push(@profileSet,"G");   # Add the green algae profiles to the investigation set
+      }
+      if ($entry =~ m/CHLORO/) {
+	push(@profileSet,"G");   # Add the green algae profiles to the investigation set
+      }
+      if ($entry =~ m/RED-AL/) {
+	push(@profileSet,"H");   # Add the red algae profiles to the investigation set
+      }
+      if ($entry =~ m/RHODO/) {
+	push(@profileSet,"H");   # Add the red algae profiles to the investigation set
+      }
+      if ($entry =~ m/BROWN/) {
+	push(@profileSet,"I");   # Add the brown algae profiles to the investigation set
+      }
+      if ($entry =~ m/PHAEOP/) {
+	push(@profileSet,"I");   # Add the brown algae profiles to the investigation set
+      }
+      if ($entry =~ m/LIVER/) {
+	push(@profileSet,"L");   # Add the liverworts profiles to the investigation set
+      }
+      if ($entry =~ m/MARCH/) {
+	push(@profileSet,"L");   # Add the liverworts profiles to the investigation set
+      }
+      if ($entry =~ m/METAZ/) {
+	push(@profileSet,"M");   # Add the metazoa profiles to the investigation set
+      }
+      if ($entry =~ m/ANIMAL/) {
+	push(@profileSet,"M");   # Add the metazoa profiles to the investigation set
+      }
+      if ($entry =~ m/MICROSPOR/) {
+	push(@profileSet,"N");   # Add the microsporidia profiles to the investigation set
+      }
+      if ($entry =~ m/OOMYC/) {
+	push(@profileSet,"O");   # Add the oomycetes profiles to the investigation set
+      }
+      if ($entry =~ m/PRYMN/) {
+	push(@profileSet,"P");   # Add the prymnesiophytes profiles to the investigation set
+      }
+      if ($entry =~ m/HAPTO/) {
+	push(@profileSet,"P");   # Add the prymnesiophytes profiles to the investigation set
+      }
+      if ($entry =~ m/RAPHID/) {
+	push(@profileSet,"Q");   # Add the raphidophytes profiles to the investigation set
+      }
+      if ($entry =~ m/RHIZA/) {
+	push(@profileSet,"R");   # Add the rhizaria profiles to the investigation set
+      }
+      if ($entry =~ m/SYNUR/) {
+	push(@profileSet,"S");   # Add the synurophyceae profiles to the investigation set
+      }
+      if ($entry =~ m/TRACHE/) {
+	push(@profileSet,"T");   # Add the tracheophyta profiles to the investigation set
+      }
+      if ($entry =~ m/PLANTS/) {
+	push(@profileSet,"T");   # Add the tracheophyta profiles to the investigation set
+      }
+      if ($entry =~ m/EUSTIG/) {
+	push(@profileSet,"U");   # Add the eustigmatophytes profiles to the investigation set
+      }
+      if ($entry =~ m/APUSO/) {
+	push(@profileSet,"X");   # Add the apusozoa profiles to the investigation set
+      }
+      if ($entry =~ m/PARAB/) {
+	push(@profileSet,"Y");   # Add the parabasalia profiles to the investigation set
+      }
+    }
+  }
+}
+
+foreach $set (@profileSet) {   # For each set of profiles in the the full profile set for investigation
+  $hmmPath = $profileDB . "/" . $set . ".hmm";   # Determine the path to the HMM-file
+  chomp($modelCount = `grep -c "//" $hmmPath`);   # Count the number of models in the HMM-file
+  push(@modelCount,$modelCount);   # Add the number of models in this HMM-file to the list of model counts
+  if ($reset == 1) {
+    `rm -f $hmmPath.h3* 2> /dev/null`;   # Delete old HMM-files
+    `hmmpress $hmmPath 2> /dev/null`;   # Prepare the HMM-file for searching
+    ## Redirecting stderr is a quick and dirty solution to get rid of the messages... Could be made more elegant
+  }
+}
+
+## Clean-up input files and create complementary strand if needed
+## Get the current time and output an info message
+$now = localtime;
+if ($silent == 0) {
+  print STDERR "$now : Checking and handling input sequence data (should not take long)...\n";
+}
+
+## Open the summary file for writing
+if ($out_sum == 1) {   # If summary output is on
+  open (SUMMARY, ">>$output.summary.txt");   # Append to the summary file
+}
+
+if ($input ne "") {   # If an input file is given
+  ## Read from file
+  open (SEQUENCES, $input);   # Open the input file for reading
+  open (MAIN, ">$tempDir/main.fasta");   # Create a temporary file for storing the cleaned sequences representing the main strand
+  open (COMPLEMENT, ">$tempDir/complement.fasta");   # Create a temporary file for storing the cleaned sequences representing the complementary strand
+  $inputSequenceCount = 0;   # Reset input sequence counter
+  while ($sequence = <SEQUENCES>) {   # Repeat for every line in the input file
+    chomp($sequence);   # Truncate any potential line feeds
+    $sequence =~ tr/\r\n//d;  # Remove all carriage return and new line characters
+    if (substr($sequence,0,1) eq ">") {   # If a new FASTA entry is found in the input file
+      $inputSequenceCount++;   # Add one to the input sequence counter
+      print MAIN $mainSeq . "\n";   # Write the previous main DNA sequence to the main sequence file
+      print MAIN $sequence . " main\n";   # Write the definition line of the new sequence to the main sequence file
+      $sequenceDB{"$sequenceID"} = $mainSeq;  # Add sequence to sequence database
+      $headers{"$sequenceID"} = $header;  # Add the header to the header database
+      push(@sequenceOrder,$sequenceID);  # Add this sequence ID to the ordered list of sequences
+      ($sequenceID) = split(" ",substr($sequence,1));
+      $header = $sequence;  # Save the sequence header
+      $mainSeq = "";   # Empty the main sequence entry
+      if ($complement == 1) {   # If the complementary file should be written
+	$complementSeq = reverse($complementSeq);   # Reverse the complementary DNA sequence
+	print COMPLEMENT $complementSeq . "\n";   # Write the previous complementary DNA sequence to the complementary sequence file
+	print COMPLEMENT $sequence . " complement\n";   # Write the definition line of the new sequence to the complement sequence file
+	$complementSeq = "";   # Empty the complementary sequence entry
+      }
+    } else {    # If this line is just a continuation of the current DNA sequence
+      $mseq = $sequence;   # Store this part of the DNA sequence in the intermediate varaible $mseq
+      $mseq =~ s/[ .-]//g;   # Remove any gap characters present in this sequence part (good if input was an alignment)
+      $mseq =~ tr/[a-z]/[A-Z]/;   # Make all letters uppercase
+      $mseq =~ s/[^A-Z]//g;  # Remove all non-alphabetic characters
+      $mseq =~ tr/U/T/;   # Exchanges U:s for T:s (Uracil to Thymine, good if input was RNA sequence)
+      $mainSeq = $mainSeq . $mseq;   # Add the intermediate DNA sequence to the end of the main DNA sequence entry
+      
+      if ($complement == 1) {   # If the complementary file should be written
+	$cseq = $sequence;   # Store this part of the DNA sequence in the intermediate varaible $cseq
+	$cseq =~ s/[ .-]//g;   # Remove any gap characters present in this sequence part (good if input was an alignment)
+	$cseq =~ tr/[a-z]/[A-Z]/;   # Make all letters uppercase
+	$cseq =~ s/[^A-Z]//g;  # Remove all non-alphabetic characters
+	$cseq =~ tr/ACGTURYSWKMBDHVN/TGCAAYRWSMKVHDBN/;   # Replace all characters with its complementary base
+	$complementSeq = $complementSeq . $cseq;   # Add the intermediate DNA sequence to the end of the complementary DNA sequence entry
+      }
+    }
+  }
+  ## When the input file's end is reached
+  print MAIN $mainSeq . "\n";   # Write the last main DNA sequence to the main sequence file
+  if ($complement == 1) {   # If the complementary file should be written
+    $complementSeq = reverse($complementSeq);   # Reverse the complementary DNA sequence
+    print COMPLEMENT $complementSeq . "\n";   # Write the last complementary DNA sequence to the complementary sequence file
+  }
+  $sequenceDB{"$sequenceID"} = $mainSeq;  # Add sequence to sequence database
+  $headers{"$sequenceID"} = $header;  # Add the header to the header database
+  push(@sequenceOrder,$sequenceID);  # Add this sequence ID to the ordered list of sequences
+  $mainSeq = "";   # Empty the main sequence entry
+  $complementSeq = "";   # Empty the complementary sequence entry
+  close (SEQUENCES);   # Close the sequence input file
+  close (COMPLEMENT);   # Close the complementary output file
+  close (MAIN);   # Close the main output file
+} else {   # If no input file is supplied, then read from stdin instead
+  $input = "$tempDir/main.fasta";   # Set up a temporary input file path
+  open (MAIN, ">$tempDir/main.fasta");   # Create a temporary file for storing the cleaned sequences representing the main strand
+  open (COMPLEMENT, ">$tempDir/complement.fasta");   # Create a temporary file for storing the cleaned sequences representing the complementary strand
+  $inputSequenceCount = 0;   # Reset input sequence counter
+  while ($sequence = <STDIN>) {   # Repeat for every line in the standard input
+    chomp($sequence);   # Truncate any potential line feeds
+    if (substr($sequence,0,1) eq ">") {   # If a new FASTA entry is found in the input
+      $inputSequenceCount++;   # Add one to the input sequence counter
+      print MAIN $mainSeq . "\n";   # Write the previous main DNA sequence to the main sequence file
+      print MAIN $sequence . " main\n";   # Write the definition line of the new sequence to the main sequence file
+      $sequenceDB{"$sequenceID"} = $mainSeq;  # Add sequence to sequence database
+      $headers{"$sequenceID"} = $header;  # Add the header to the header database
+      push(@sequenceOrder,$sequenceID);  # Add this sequence ID to the ordered list of sequences
+      $sequenceID = split(" ",substr($sequence,1));
+      $header = $sequence;  # Save the sequence header
+      $mainSeq = "";   # Empty the main sequence entry
+      if ($complement == 1) {   # If the complementary file should be written
+	$complementSeq = reverse($complementSeq);   # Reverse the complementary DNA sequence
+	print COMPLEMENT $complementSeq . "\n";   # Write the previous complementary DNA sequence to the complementary sequence file
+	print COMPLEMENT $sequence . " complement\n";   # Write the definition line of the new sequence to the complement sequence file
+	$complementSeq = "";   # Empty the complementary sequence entry
+      }
+    } else {    # If this line is just a continuation of the current DNA sequence
+      $mseq = $sequence;   # Store this part of the DNA sequence in the intermediate varaible $mseq
+      $mseq =~ s/[ .-]//g;   # Remove any gap characters present in this sequence part (good if input was an alignment)
+      $mseq =~ tr/[a-z]/[A-Z]/;   # Make all letters uppercase
+      $mseq =~ s/[^A-Z]//g;  # Remove all non-alphabetic characters
+      $mseq =~ tr/U/T/;   # Exchanges U:s for T:s (Uracil to Thymine, good if input was RNA sequence)
+      $mainSeq = $mainSeq . $mseq;   # Add the intermediate DNA sequence to the end of the main DNA sequence entry
+      
+      if ($complement == 1) {   # If the complementary file should be written
+	$cseq = $sequence;   # Store this part of the DNA sequence in the intermediate varaible $cseq
+	$cseq =~ s/[ .-]//g;   # Remove any gap characters present in this sequence part (good if input was an alignment)
+	$cseq =~ tr/[a-z]/[A-Z]/;   # Make all letters uppercase
+	$cseq =~ s/[^A-Z]//g;  # Remove all non-alphabetic characters
+	$cseq =~ tr/ACGTURYSWKMBDHVN/TGCAAYRWSMKVHDBN/;   # Replace all characters with its complementary base
+	$complementSeq = $complementSeq . $cseq;   # Add the intermediate DNA sequence to the end of the complementary DNA sequence entry
+      }
+    }
+  }
+  ## When the input file's end is reached
+  print MAIN $mainSeq . "\n";   # Write the last main DNA sequence to the main sequence file
+  if ($complement == 1) {   # If the complementary file should be written
+    $complementSeq = reverse($complementSeq);   # Reverse the complementary DNA sequence
+    print COMPLEMENT $complementSeq . "\n";   # Write the last complementary DNA sequence to the complementary sequence file
+  }
+  $sequenceDB{"$sequenceID"} = $mainSeq;  # Add sequence to sequence database
+  $headers{"$sequenceID"} = $header;  # Add the header to the header database
+  push(@sequenceOrder,$sequenceID);  # Add this sequence ID to the ordered list of sequences
+  $mainSeq = "";   # Empty the main sequence entry
+  $complementSeq = "";   # Empty the complementary sequence entry
+  close (COMPLEMENT);   # Close the complementary output file
+  close (MAIN);   # Close the main output file
+}
+
+if ($out_sum == 1) {   # If summary output should be written
+  print SUMMARY "Number of sequences in input file:       \t$inputSequenceCount\n";   # Write info on the number of input sequences to the summary file
+}
+
+
+## Perform HMM-scan
+if ($hmmscan eq "") {   # If a pre-computed hmmscan output file is not supplied
+  if ($heuristics == 0) {  # If HMMER's heuristic filtering should not be used
+    $heurMax = "--max";  # Set the heurMax to "--max" (indicating that HMMER should turn off filtering)
+  } else {
+    $heurMax = "";  # Set the heurMax to empty (indicating that HMMER should turn on filtering)
+  }
+  if ($multi_thread == 0) {   # If multi-threading is off
+    ## Get the current time and output info message
+    $now = localtime;
+    if ($silent == 0) {
+      print STDERR "$now : Comparing sequences to HMM database (this may take a long while)...\n";
+    }
+    foreach $set (@profileSet) {   # Go sequentially through all profile sets to search for
+      $hmmPath = $profileDB . "/" . $set . ".hmm";   # Set the path to the HMM-file of the current set
+      if ($search_eval ne "") {   # If E-value cutoff is use for the search
+	hmmerSearch("hmmscan --cpu $cpu $heurMax -E $search_eval $hmmPath $tempDir/main.fasta","$tempDir/main.$set.hmmscan","M",$set);   # Call HMMER with E-value cutoff
+      } else {   # If score cutoff is use for the search
+	hmmerSearch("hmmscan --cpu $cpu $heurMax -T $search_score $hmmPath $tempDir/main.fasta","$tempDir/main.$set.hmmscan","M",$set);   # Call HMMER with score cutoff
+      }
+      if ($complement == 1) {   # If the complementary file should be scanned
+	if ($search_eval ne "") {   # If E-value cutoff is use for the search
+	  hmmerSearch("hmmscan --cpu $cpu $heurMax -E $search_eval $hmmPath $tempDir/complement.fasta","$tempDir/complement.$set.hmmscan","C",$set);   # Call HMMER with E-value cutoff
+	} else {   # If score cutoff is use for the search
+	  hmmerSearch("hmmscan --cpu $cpu $heurMax -T $search_score $hmmPath $tempDir/complement.fasta","$tempDir/complement.$set.hmmscan","C",$set);   # Call HMMER with score cutoff
+	}
+      }
+    }
+  } else {   # If multi-threading is on
+    ## Get the current time and output info message
+    $now = localtime;
+    if ($silent == 0) {
+      print STDERR "$now : Doing paralellised comparison to HMM database (this may take a long while)...\n";
+    }
+
+    ## Determining number of cpus per thread
+    if ($complement == 1) {   # If the complementary file should be scanned
+      $hmmcpu = int(0.5 * $cpu / scalar(@profileSet));   # Assign X CPUs to each thread, X = 0.5 * (TOTAL_CPUs_USED) / (TOTAL_NUMBER_OF_PROFILE_SETS)
+    } else {   # If the complementary file should not be scanned
+      $hmmcpu = int($cpu / scalar(@profileSet));   # Assign X CPUs to each thread, X = (TOTAL_CPUs_USED) / (TOTAL_NUMBER_OF_PROFILE_SETS)
+    }
+    if ($hmmcpu < 1) {   # If the number of CPUs per thread is smaller than 1
+      $hmmcpu = 1;   # Give each thread at least one CPU to work on
+    }
+    ## Main strand searches...
+    $cpuCount = 0;
+    foreach $set (@profileSet) {   # Go through each profile set to investigate
+      if ($cpuCount < $cpu) {
+	$cpuCount++;
+	$pid = fork();   # Fork off a copy of this process for this set
+      } else {
+	$deceasedPID = wait();   # Wait until a PID is finished, and gather its number
+	$pid = fork();   # Fork off a copy of this process for this set
+      }
+      if ($pid != 0) {   # If this is the parent process
+	push(@pids,$pid);   # Add the new process ID to the list of active process IDs
+      } else {   # If this is the new child process
+	$hmmPath = $profileDB . "/" . $set . ".hmm";   # Set the path to the HMM-file of the current set
+	if ($search_eval ne "") {   # If E-value cutoff is use for the search
+	  hmmerSearch("hmmscan --cpu $hmmcpu $heurMax -E $search_eval $hmmPath $tempDir/main.fasta","$tempDir/main.$set.hmmscan","M",$set);   # Call HMMER with E-value cutoff
+	} else {   # If score cutoff is use for the search
+	  hmmerSearch("hmmscan --cpu $hmmcpu $heurMax -T $search_score $hmmPath $tempDir/main.fasta","$tempDir/main.$set.hmmscan","M",$set);   # Call HMMER with score cutoff
+	}
+	## Stop child process...
+	exit;   # Exits the child process
+      }
+    }
+    ## Revese strand searches...
+    if ($complement == 1) {   # If the complementary file should be scanned
+      foreach $set (@profileSet) {   # Go through each profile set to investigate
+	if ($cpuCount < $cpu) {
+	  $cpuCount++;
+	  $pid = fork();   # Fork off a copy of this process for this set
+	} else {
+	  $deceasedPID = wait();   # Wait until a PID is finished, and gather its number
+	  $pid = fork();   # Fork off a copy of this process for this set
+	}
+	if ($pid != 0) {   # If this is the parent process
+	  push(@pids,$pid);   # Add the new process ID to the list of active process IDs
+	} else {   # If this is the new child process
+	  $hmmPath = $profileDB . "/" . $set . ".hmm";   # Set the path to the HMM-file of the current set
+	  if ($search_eval ne "") {   # If E-value cutoff is use for the search
+	    hmmerSearch("hmmscan --cpu $hmmcpu $heurMax -E $search_eval $hmmPath $tempDir/complement.fasta","$tempDir/complement.$set.hmmscan","C",$set);   # Call HMMER with E-value cutoff
+	  } else {   # If score cutoff is use for the search
+	    hmmerSearch("hmmscan --cpu $hmmcpu $heurMax -T $search_score $hmmPath $tempDir/complement.fasta","$tempDir/complement.$set.hmmscan","C",$set);   # Call HMMER with score cutoff
+	  }
+	  ## Stop child process...
+	  exit;   # Exits the child process
+	}
+      }
+    }
+    ## Get the current time and output the active process IDs
+    $now = localtime;
+    #print STDERR "    $now : Active PIDs: ";
+    #foreach $p (@pids) {   # Go through the list of PIDs
+    #  print STDERR "$p ";   # Print the PID
+    #}
+    #print STDERR "\n";   # Print a new line
+    do {   # Loop until all child PIDs have finished.
+      $deceasedPID = wait();   # Wait until a PID is finished, and gather its number
+      $now = localtime;   # Get the current time
+      if ($deceasedPID > -1) {   # If the PID that finished wasn't the last active one
+#	print STDERR "    $now : PID $deceasedPID finished.\n";   # Print finished PID
+      } else {   # If PID that finished was the last
+	print STDERR "    $now : All processes finished.\n";   # Print that all PIDs have finished
+      }
+    } until (wait() == -1);   # Do this loop until all PIDs have finished
+    $now = localtime;   # Get current time
+    print STDERR "$now : Parallel HMM-scan finished.\n";   # Print informative finishing message
+  }
+} else {    # If a pre-computed hmmscan file is supplied then
+## Get the current time and output that the hmmscan step is skipped
+  $now = localtime;
+  if ($silent == 0) {
+    print STDERR "$now : Skipping hmmscan! Using $hmmscan as input for the analysis instead.\n";
+  }
+}
+
+## Analyse HMM-scan output
+## Get the current time and output info
+$now = localtime;
+if ($silent == 0) {
+  print STDERR "$now : Analysing results of HMM-scan (this might take quite some time)...\n";
+}
+
+## Set up output files
+if ($out_table == 1) {   # If table output is on
+  open (TABLE, ">$output.hmmer.table");   # Create a table output file
+}
+if ($out_graph == 1) {   # If graphical output is on
+  open (GRAPH, ">$output.graph");   # Create a graph output file
+}
+if ($out_not == 1) {   # If not-found output is on
+  open (NOTFOUND, ">$tempDir/$output\_hmmer_no_detections.txt");   # Create a HMMER not-found output file
+}
+
+$setI = 0;   # Set the profile set indicator to zero
+foreach $set (@profileSet) {   # Go through all the profile sets to be investigated
+  for ($co = 0; $co <= 1; $co++) {   # Do main (and complementary) strand analysis in order
+    if ($co > 0) {   # If main strand analysis is finished
+      if ($complement == 1) {   # If complementary strand should be analysed
+	open (HMMOUTPUT, "$tempDir/complement.$set.hmmscan");   # Open hmmscan output for reading
+	open (SEQUENCES, "$tempDir/complement.fasta");   # Open complementary sequence file for reading
+	if ($out_table == 1) {   # If table output is on, write a header for this set
+	  print TABLE "***********************************************************\n";
+	  print TABLE "$set matches on complementary strand:\n";
+	}
+	if ($out_graph == 1) {   # If graphical output is on, write a header for this set
+	  print GRAPH "***********************************************************\n";
+	  print GRAPH "$set matches on complementary strand:\n";
+	}
+      } else {   # If complementary strand should not be analysed
+	last;   # Exit this loop
+      }
+    }
+    if ($co == 0) {   # If main strand analysis is not finished
+      open (HMMOUTPUT, "$tempDir/main.$set.hmmscan");   # Open hmmscan output for reading
+      open (SEQUENCES, "$tempDir/main.fasta");   # Open main sequence file for reading
+      if ($out_table == 1) {   # If table output is on, write a header for this set
+	print TABLE "***********************************************************\n";
+	print TABLE "$set matches on main strand:\n";
+      }
+      if ($out_graph == 1) {   # If graphical output is on, write a header for this set
+	print GRAPH "***********************************************************\n";
+	print GRAPH "$set matches on main strand:\n";
+      }
+    }
+  ## Read and analyse hmmscan output file
+  while ($line = <HMMOUTPUT>) {   # Read in the hmmscan output file, line by line
+    chomp($line);   # Remove any potential line feeds
+    if (substr($line,0,13) eq "## New query:") {   # If this line begin with "## New query:", then this is a new entry
+      undef %hits;   # Empty the hits hash
+      undef %evals;   # Empty the e-value hash
+      undef %scores;   # Empty the score hash
+      $querytemp = substr($line,14);   # Extract everything from this line, except for the start ("## New query:")
+      ($query,$length) = split('\t',$querytemp);  # Split query name, length and DNA sequence
+      if ($co == 0) {   # If main strand analysis
+	$DNA = $sequenceDB{"$query"};
+      } else {  # If complementary strand
+	$cseq = $sequenceDB{"$query"};   # Store the DNA sequence in the intermediate varaible $cseq
+	$cseq =~ tr/[a-z]/[A-Z]/;   # Make all letters uppercase
+	$cseq =~ s/[^A-Z]//g;  # Remove all non-alphabetic characters
+	$cseq =~ tr/ACGTURYSWKMBDHVN/TGCAAYRWSMKVHDBN/;   # Replace all characters with its complementary base
+	$DNA = reverse($cseq);
+      }
+    } else {
+      
+      if ($line ne "//") {
+	## Find domain annotations...
+	($query,$matchProfile,$length,$domNo,$sign,$score,$bias,$cE,$iE,$hmmFrom,$hmmTo,$hmmends,$queryFrom,$queryTo,$queryends,$envFrom,$envTo,$envends,$acc) = split('\t',$line);   # Split the line into a collection of stat variables
+
+	$useQueryFrom = $queryFrom;
+	if ($hmmFrom > 1) {  # If the HMM-profile is not matched from the beginning
+	  $hmmDiff = $hmmFrom - 1;
+	  if ($useQueryFrom > $hmmDiff) {
+	    $useQueryFrom = $queryFrom - $hmmDiff;
+	  } else {
+	    $useQueryFrom = 1;
+	  }
+	}
+
+	if (uc($anchor) eq "HMM") {
+	  $anchorLen = $hmmTo - $hmmFrom + 1;
+	} else {
+	  $anchorLen = $anchor;
+	}
+	  
+
+	$query_profile_match = $query . ":" . $matchProfile;
+	$profileExists = 0;   # Assume that the newly found match profile ($matchProfile) is not already found for this sequence
+	if (exists($hits{$query_profile_match})) {   # If a profile from the list is the same as the match profile
+	  ($hitFrom,$hitTo,$hitProfile,$hitScore,$hitE) = split('\t',$hits{$query_profile_match});   # Split the entry in list into stat variables
+	  if ($iE < $hitE) {   # If the new match profile has a smaller E-value than the one from the list
+	    $hits{$query_profile_match} = "$useQueryFrom\t$envTo\t$matchProfile\t$score\t$iE\t$anchorLen";   # Replace the data in the hit list with the data for the newly found match profile
+	    $evals{$query_profile_match} = $iE;   # Replace the E-value in the hit list with the E-value for the newly found match profile
+	    $scores{$query_profile_match} = $score;   # Replace the score in the hit list with the score for the newly found match profile
+	  }
+	  $profileExists = 1;   # Indicate that this match profile was found in the hit list
+	}
+	if ($profileExists == 0) {   # If the match profile was not found in the hit list
+	  if (($iE <= $E) && ($score >= $S)) {  # If this hits lives up to the minimal score and E-value cutoffs
+	    $hits{$query_profile_match} = "$useQueryFrom\t$envTo\t$matchProfile\t$score\t$iE\t$anchorLen";   # Add the data for the newly found match profile
+	    $evals{$query_profile_match} = $iE;   # Add the E-value for the newly found match profile
+	    $scores{$query_profile_match} = $score;   # Add the score for the newly found match profile
+	  }
+	}
+      } else {   # If the line only contains "//", the end of this sequence's hmmscan entry is reached
+      ## Save analysis results
+	@sortedKeys = sort {$hits{$a} <=> $hits{$b}} keys(%hits);   # Sort the the list of hits numerically ascending (smallest first)
+	undef @sortedHits;
+	undef @scores;
+	undef @evals;
+	foreach $key (@sortedKeys) {
+	  push(@sortedHits, $hits{$key});   # Add the hit to the list of hits numerically ascending (smallest first)
+	  push(@scores, $scores{$key});  # Add the score to the scores array
+	  push(@evals, $evals{$key});  # Add the E-value to the evals array
+	}
+
+	## If the number of hits > N, the min eval < E and the max score > S then include query sequence
+	## OR if a single domain satisfies the thresholds and this is allowed, include it!
+	if ( ((scalar(@sortedHits) >= $N) && (min(@evals) <= $E) && (max(@scores) >= $S)) ||
+	     ((scalar(@sortedHits) > 0) && ($allow_single_E >= 0) && (min(@evals) <= $allow_single_E) && (max(@scores) >= $allow_single_score)) ) {
+	  if ($debug == 1) {   # If debugging mode is on
+	    print STDERR $query . " :\t" . scalar(@sortedHits) . "\t" . min(@evals) . "\t" . max(@scores) . "\n";   # Print some top hit statistics
+	  }
+	  
+	  ## Save some total stats to be able to determine origin of ITS sequence
+	  if (scalar(@evals) > 0) {   # If there are any E-values stored
+	    $averageE = sum(@evals) / scalar(@evals);   # Calculate the average E-value for this profile set
+	    $averageScore = sum(@scores) / scalar(@scores);   # Calculate the average score for this profile set
+	    $numberOfDomains = scalar(@sortedHits);   # Calculate the number of domains matched on this sequence
+	    
+	    #$scoreSum = sum(@scores) / @modelCount[$setI];   # Calculate score sum as: sum / (no. of profiles of this given type)
+	    $scoreSum = sum(@scores) / 4;   # Calculate score sum as: sum / (no. of profiles of this given type)
+	    
+	    $saveThis = "$query\t$set\t$co\t$numberOfDomains\t$averageE\t$averageScore\t$scoreSum\t$DNA\t";   # Collect the variables to save for this sequence and this profile set
+	    foreach $hit (@sortedHits) {   # Go through the list of hits and add specific information to save from each hit
+	      ($hitFrom,$hitTo,$hitProfile,$hitScore,$hitE,$hitanchorlen) = split('\t',$hit);   # Extract information from this hit
+	      $saveThis = $saveThis . "$hitFrom;$hitTo;$hitProfile;$hitScore;$hitE;$hitanchorlen\t";   # Add information to the list of variables to save
+	    }
+	    #push(@allHits, $saveThis);   # Add this information to the collection of all hits for this sequence, across all profile sets
+	    if (exists($allHits{$query})) {
+	      $allHits{$query} = $allHits{$query} . "\n" . $saveThis;
+	    } else {
+	      $allHits{$query} = $saveThis;
+	    }
+	  }
+	  
+	  if ($out_table == 1) {   # If table output is on
+	    print TABLE $query . "\t" . $length . "\t";   # Print query and length information to table
+	    foreach $hit (@sortedHits) {   # Go through each hit in the hit list
+	      ($hitFrom,$hitTo,$hitProfile,$hitScore,$hitE,$hitanchorlen) = split('\t',$hit);   # Extract data corresponding to this hit
+	      print TABLE "$hitFrom - $hitTo: $hitProfile ($hitScore, $hitE)\t";   # Print hit information to table
+	    }
+	    print TABLE "\n";   # Print new line
+	  }
+	  
+	  if ($out_graph == 1) {   # If graphical output is on
+	    print GRAPH ">> " . $query . "\t" . $length . " bp\n";   # Print a sequence header
+	    $insertPoint = 0;   # Set the domain insert point to beginning of line
+	    $hi = 0;   # Set hit number to zero
+	    foreach $hit (@sortedHits) {   # Go through the hit list
+	      ($hitFrom,$hitTo,$hitProfile,$hitScore,$hitE,$anchorLen) = split('\t',$hit);   # Split the hit into stat variables
+	      if ($graph_scale == 0) {   # If the graph scale is scaled individually to 100% for each sequence
+		$pFrom = $hitFrom / $length * 100;   # Set the profile start on graph relative to its position in the sequence
+		$pTo = $hitTo / $length * 100;   # Set the profile end on graph relative to its position in the sequence
+		$pEnd = 100;   # Set the end of the sequence graph to be at 100
+	      } else {   # If the scale is the same for all sequences
+		$pFrom = $hitFrom * $graph_scale;   # Set the profile start on graph scaled to the parameter given
+		$pTo = $hitTo * $graph_scale;   # Set the profile end on graph scaled to the parameter given
+		$pEnd = $length * $graph_scale;   # Set the end of the sequence graph to be at the end of the sequence scaled to the parameter given
+	      }
+	      for ($insertPoint = $insertPoint; $insertPoint <= $pFrom; $insertPoint++) {   # Go forward through the sequence, moving the insert point one step at a time until the beginning of the next profile is reached
+		print GRAPH "-";   # Print a "-"
+	      }
+	      print GRAPH substr($hitProfile,2,3);   # When the profile is reached, print its name
+	      $insertPoint = $insertPoint + 3;   # Move the insert point three steps forward, to account for the inserted name
+	      ($nextHitStart,$nextHitEnd,$nextProfile) = split('\t',@sortedHits[$hi + 1]);   # Check where the next hit in the list is located
+	      if (($nextHitStart <= $hitTo) && ($nextHitStart > 0)) {   # If the next hit in the list overlaps with this profile
+		if ($graph_scale == 0) {   # If the scale is relative
+		  $pTo = $nextHitStart / $length * 100 - 1;   # Change the profile end on the graph to be where this next profile starts
+		} else {   # If the scale is the same for all sequences
+		  $pTo = $nextHitStart * $graph_scale - 1;   # Change the profile end on the graph to be where this next profile starts
+		}
+	      }
+	      for ($insertPoint = $insertPoint; $insertPoint <= $pTo; $insertPoint++) {   # Go forward through the sequence, moving the insert point one step at a time until the end of the current profile is reached
+		print GRAPH "=";   # Print a "="
+	      }
+	      if (($nextHitStart <= $hitTo) && ($nextHitStart > 0)) {   # If the next hit in the list overlaps with this profile
+		print GRAPH ">";   # Print a ">" to indicate the profile overlap
+		$insertPoint++;   # Move the insert point one additional step forward to account for the ">" inserted
+	      }
+	      $hi++;   # Increase the hit number by one
+	    }
+	    for ($insertPoint = $insertPoint; $insertPoint <= $pEnd; $insertPoint++) {   # If there is no more profile matches to sequence, go forward through the sequence, moving the insert point one step at a time until the end of the sequence is reached
+	      print GRAPH "-";   # Print a "-"
+	    }
+	    print GRAPH "\n";   # Print a new line, indicating the end of this sequence entry
+	  }
+	} else {   # If this sequence didn't find any good-enough profile matches
+	  if ($out_not == 1) {   # If not-found output is on
+	    print NOTFOUND $query . "\n";   # Print the name of this query to the not-found list
+	  }
+	}
+      }
+    }
+  }
+  close (SEQUENCES);   # Close the input sequence file
+  close (HMMOUTPUT);   # Close the hmmscan output file
+  }
+  $setI++;   # Add one to the profile set indicator
+}
+
+## Close output files
+if ($out_table == 1) {   # If table output is on, close the table file
+  close (TABLE);
+}
+if ($out_graph == 1) {   # If graphical output is on, close the graph file
+  close (GRAPH);
+}
+if ($out_not == 1) {   # If not-found output is on, close the not-found file
+  close (NOTFOUND);
+  #$profileCount = scalar(@profileSet);   # Count the number of profile sets
+  #if ($complement == 1) {   # If complementary strand was scanned
+  #  $profileCount = $profileCount * 2;   # Double the number of profile sets that was investigated (and thus the number of not-founds that could at max be found)
+  #}
+  #`sort $tempDir/hmmer_no_detections.txt | uniq -c | grep "  *$profileCount " | sed "s/  *$profileCount //" > $output\_no_detections.txt`;   # Sort the not-found list, count the number of profile sets having no matches for each query. Save those that have only non-matches to the hmmer-not-found file
+}
+
+
+## Create total collected output and FASTA output
+
+if ($out_results == 1) {
+  open (RESULTS, ">$output.extraction.results");   # Create a results file
+}
+open (RAWOUT, ">$tempDir/ITSx_output.raw");   # Create a raw output file for ALL data
+open (PROBLEM, ">$output.problematic.txt");   # Create a file for problematic entries
+$foundProblem = 0;
+if ($out_pos == 1) {
+  open (POS, ">$output.positions.txt");   # Create a positions file
+}
+if ($out_fasta == 1) {   # If FASTA output should be written
+  open (FASTA, ">$output.full.fasta");   # Create a FASTA output file for found sequences
+  if ($allow_reorder == 0) {   # If reordering of domains is not allowed
+    open (CHIMERA, ">$output.chimeric.fasta");   # Create a FASTA file for potential chimera sequences with profile matches in the wrong order
+    $foundChimera = 0;
+  }
+  if ($out_partial > 0) {
+    open (FULLPARTIAL, ">$output.full_and_partial.fasta");
+  }
+}
+
+if ($out_joined == 1) {   # If SSU FASTA output should be written
+  open (JOINED, ">$output.joined.fasta");
+}
+if ($out_ssu == 1) {   # If SSU FASTA output should be written
+  open (SSU, ">$output.SSU.fasta");
+}
+if ($out_lsu == 1) {   # If LSU FASTA output should be written
+  open (LSU, ">$output.LSU.fasta");
+}
+if ($out_58S == 1) {   # If 5.8S FASTA output should be written
+  open (MID, ">$output.5_8S.fasta");
+}
+if ($out_its1 == 1) {   # If ITS1 FASTA output should be written
+  open (ITS1, ">$output.ITS1.fasta");
+  if ($out_partial > 0) {
+    open (ITS1PARTIAL, ">$output.ITS1.full_and_partial.fasta");
+  }
+}
+if ($out_its2 == 1) {   # If ITS2 FASTA output should be written
+  open (ITS2, ">$output.ITS2.fasta");
+  if ($out_partial > 0) {
+    open (ITS2PARTIAL, ">$output.ITS2.full_and_partial.fasta");
+  }
+}
+if ($out_concat == 1) {  # If concatenated output should be written
+  open (CONCAT, ">$output.concat.fasta");
+}
+
+undef @sortedHits;   # Empty the array of sorted hits
+
+# @sortedHits = sort @allHits;   # Sort the full list of hits in alphabetical order (to be able to analyse all sequences with same ID at once)
+if ($out_not == 1) {   # If not-found output is on
+  open (NOTFOUND, ">$output\_no_detections.txt");   # Create a not-found output file
+  $noDetect = 0;
+}
+foreach $sequenceID (@sequenceOrder) {   # Sort the full list of hits in their original order (to be able to analyse all sequences with same ID at once)
+  if ($sequenceID ne "") {
+    $countsInList = 0;
+    if (exists($allHits{$sequenceID})) {
+      @allHits = split('\n',$allHits{$sequenceID});
+    } else {
+      undef @allHits;
+    }
+    foreach $line (@allHits) {
+      @item = split('\t',$line);   # Split the line into an array
+      if (@item[0] eq $sequenceID) {  # If this item corresponds to the current sequence ID
+	push(@sortedHits,$line);  # Add it to the sorted list of hits
+	$countsInList++;
+      }
+    }
+    if ($countsInList == 0) {  # If no matches were found
+      if ($out_not == 1) {   # If not-found output is on
+	print NOTFOUND "$sequenceID\n";  # Output the sequence ID
+	$noDetect++;
+      }
+    }
+  }
+}
+if ($out_not == 1) {   # If not-found output is on
+  close (NOTFOUND);
+  if ($noDetect == 0) {
+    `rm $output\_no_detections.txt 2> /dev/null`;
+  }
+}
+
+## Set all counts for different ITS types to zero
+undef @itsCounts;
+$itsChimeric = 0;
+$itsMain = 0;
+$itsCompl = 0;
+
+push(@sortedHits,"--END--");   # Add a last item to the sorted list, so that all items are securely saved
+$lc = 1;   # Set the line count to one
+foreach $line (@sortedHits) {   # Go through the list of found hits
+  print RAWOUT "$line\n";   # Write the raw data associated with this hit to the raw data output file
+  @item = split('\t',$line);   # Split the line into an array
+  ## If this sequence ID is the same as the saved ones, then add it, else empty the array sequence ID and save
+  if ((@seqID[0] ne @item[0]) && (@item[0] ne "") || ($lc > scalar(@sortedHits))) {   # If this sequence ID is not the same as the last one and is non-empty, or if the end of the list has been reached
+    ## Save profile-type which is most likely...
+    if ($priority eq "sum") {   # If the sum-of-scores algorithm should be used to determine the most likely profile-type
+      ## Reset variables to unrealisticly high or low values
+      $best = 0;
+      $bestCount = 0;
+      $bestEval = 1000;
+      $bestScore = -1000;
+      $bestSum = -1000;
+      
+      for ($i = 0; $i < scalar(@seqScoreSum); $i++) {   # Go through all sum-of-scores entries
+	if (@seqScoreSum[$i] > $bestSum) {   # If the current value is larger than the previous top value
+	  $best = $i;   # Set the best value to be the current value
+	  ## Set all other best variables to those corresponding to the current value
+	  $bestCount = @seqDomCounts[$i];
+	  $bestEval = @seqAvgE[$i];
+	  $bestScore = @seqAvgScore[$i];
+	  $bestSum = @seqScoreSum[$i];
+	}
+	if (@seqScoreSum[$i] == $bestSum) {   # If the current value is equal to the previous top value
+	  if (@seqDomCounts[$i] > $bestCount) {   # If the current domain count is larger than the previous top domain count
+	    $best = $i;   # Set the best value to be the current value
+	    ## Set all other best variables to those corresponding to the current value
+	    $bestCount = @seqDomCounts[$i];
+	    $bestEval = @seqAvgE[$i];
+	    $bestScore = @seqAvgScore[$i];
+	    $bestSum = @seqScoreSum[$i];
+	  }
+	  if (@seqDomCounts[$i] == $bestCount) {   # If the current domain count is equal to the previous top domain count
+	    if (@seqAvgE[$i] < $bestEval) {   # If the current E-value is smaller than the previous top E-value
+	      $best = $i;   # Set the best value to be the current value
+	      ## Set all other best variables to those corresponding to the current value
+	      $bestCount = @seqDomCounts[$i];
+	      $bestEval = @seqAvgE[$i];
+	      $bestScore = @seqAvgScore[$i];
+	      $bestSum = @seqScoreSum[$i];
+	    }
+	  }
+	}
+      }
+    }
+    if ($priority eq "domains") {   # If the number of found domains should be used to determine the most likely profile-type
+      ## Reset variables to unrealisticly high or low values
+      $best = 0;
+      $bestCount = 0;
+      $bestEval = 1000;
+      $bestScore = -1000;
+
+      for ($i = 0; $i < scalar(@seqDomCounts); $i++) {   # Go through all domain count entries
+	if (@seqDomCounts[$i] > $bestCount) {   # If the current domain count is larger than the previous top domain count
+	  $best = $i;   # Set the best value to be the current value
+	  ## Set all other best variables to those corresponding to the current value
+	  $bestCount = @seqDomCounts[$i];
+	  $bestEval = @seqAvgE[$i];
+	  $bestScore = @seqAvgScore[$i];
+	}
+	if (@seqDomCounts[$i] == $bestCount) {   # If the current domain count is equal to the previous top domain count
+	  if (@seqAvgE[$i] < $bestEval) {   # If the current E-value is smaller than the previous top E-value
+	    $best = $i;   # Set the best value to be the current value
+	    ## Set all other best variables to those corresponding to the current value
+	    $bestCount = @seqDomCounts[$i];
+	    $bestEval = @seqAvgE[$i];
+	    $bestScore = @seqAvgScore[$i];
+	  }
+	  if (@seqAvgE[$i] == $bestEval) {   # If the current E-value is equal to the previous top E-value
+	    if (@seqAvgScore[$i] > $bestScore) {   # If the current average score is larger than the previous top average score
+	      $best = $i;   # Set the best value to be the current value
+	      ## Set all other best variables to those corresponding to the current value
+	      $bestCount = @seqDomCounts[$i];
+	      $bestEval = @seqAvgE[$i];
+	      $bestScore = @seqAvgScore[$i];
+	    }
+	  }
+	}
+      }
+    }
+    if ($priority eq "eval") {   # If the average E-value should be used to determine the most likely profile-type
+      ## Reset variables to unrealisticly high or low values
+      $best = 0;
+      $bestCount = 0;
+      $bestEval = 1000;
+      $bestScore = -1000;
+
+      for ($i = 0; $i < scalar(@seqDomCounts); $i++) {   # Go through all domain counts entries
+	if (@seqAvgE[$i] < $bestEval) {   # If the current E-value is smaller than the previous top E-value
+	  $best = $i;   # Set the best value to be the current value
+	  ## Set all other best variables to those corresponding to the current value
+	  $bestCount = @seqDomCounts[$i];
+	  $bestEval = @seqAvgE[$i];
+	  $bestScore = @seqAvgScore[$i];
+	}
+	if (@seqAvgE[$i] == $bestEval) {   # If the current E-value is equal to the previous top E-value
+	  if (@seqAvgScore[$i] > $bestScore) {   # If the current average score is larger than the previous top average score
+	    $best = $i;   # Set the best value to be the current value
+	    ## Set all other best variables to those corresponding to the current value
+	    $bestCount = @seqDomCounts[$i];
+	    $bestEval = @seqAvgE[$i];
+	    $bestScore = @seqAvgScore[$i];
+	  }
+	  if (@seqAvgScore[$i] == $bestScore) {   # If the current average score is equal to the previous top average score
+	    if (@seqDomCounts[$i] > $bestCount) {   # If the current number of domains is larger than the previous top number of domains
+	      $best = $i;   # Set the best value to be the current value
+	      ## Set all other best variables to those corresponding to the current value
+	      $bestCount = @seqDomCounts[$i];
+	      $bestEval = @seqAvgE[$i];
+	      $bestScore = @seqAvgScore[$i];
+	    }
+	  }
+	}
+      }
+    }
+    if ($priority eq "score") {   # If the average score should be used to determine the most likely profile-type
+      ## Reset variables to unrealisticly high or low values
+      $best = 0;
+      $bestCount = 0;
+      $bestEval = 1000;
+      $bestScore = -1000;
+
+      for ($i = 0; $i < scalar(@seqDomCounts); $i++) {   # Go through all domain counts entries
+	if (@seqAvgScore[$i] > $bestScore) {   # If the current average score is larger than the previous top average score
+	  $best = $i;   # Set the best value to be the current value
+	  ## Set all other best variables to those corresponding to the current value
+	  $bestCount = @seqDomCounts[$i];
+	  $bestEval = @seqAvgE[$i];
+	  $bestScore = @seqAvgScore[$i];
+	}
+	if (@seqAvgScore[$i] == $bestScore) {   # If the current average score is equal to the previous top average score
+	  if (@seqAvgE[$i] < $bestEval) {   # If the current E-value is smaller than the previous top E-value
+	    $best = $i;   # Set the best value to be the current value
+	    ## Set all other best variables to those corresponding to the current value
+	    $bestCount = @seqDomCounts[$i];
+	    $bestEval = @seqAvgE[$i];
+	    $bestScore = @seqAvgScore[$i];
+	  }
+	  if (@seqAvgE[$i] == $bestEval) {   # If the current E-value is equal to the previous top E-value
+	    if (@seqDomCounts[$i] > $bestCount) {   # If the current number of domains is larger than the previous top number of domains
+	      $best = $i;   # Set the best value to be the current value
+	      ## Set all other best variables to those corresponding to the current value
+	      $bestCount = @seqDomCounts[$i];
+	      $bestEval = @seqAvgE[$i];
+	      $bestScore = @seqAvgScore[$i];
+	    }
+	  }
+	}
+      }
+    }
+    
+    if (@seqID[$best] ne "") {   # If the sequence ID of the most likely profile is not empty
+
+      $allanchorLens = @anchorLens[$best];  # Get the best anchor lengths
+      @allanchorLens = split(',', $allanchorLens);  # Split the anchor lens into an array
+
+      $chimeric = 0;   # Assume the sequence is not chimeric
+      if ($allow_reorder == 0) {   # If re-order of domain is not allowed
+	$domain_order = @allSeqDomains[$best];   # Gather the order the domains are found in
+	@domain_order = split(' ',$domain_order);   # Split the list into an array
+	@sorted_domain_order = sort {$a cmp $b} @domain_order;   # Sort the array alphabetically
+	for ($di = 0; $di <= scalar(@domain_order); $di++) {   # Go through the sorted array
+	  if ((@domain_order[$di] ne @sorted_domain_order[$di]) || (@problemCode[$best] =~ m/C/)) {    # Check if the order of the arrays differ at any poiny
+	    $chimeric = 1;   # If they do differ, mark the sequence as chimeric
+	  }
+	}
+      }
+
+      $seqDNALength = length(@seqDNA[$best]);   # Get the length of the DNA sequence
+
+      ## Print sequence and match data...
+      ## Order of columns in the output file:
+      ## ID Length Type Main/Compl Domains Avg.Eval Avg.Score Start End Start_domain End_domain Chimeric
+      if ($out_results == 1) {
+	print RESULTS @seqID[$best] . "\t" . $seqDNALength . "\t" . @seqITSType[$best] . "\t" . @seqCompl[$best] . "\t" . @seqDomCounts[$best] . "\t" . @seqAvgE[$best] . "\t" . @seqAvgScore[$best] . "\t" . @seqScoreSum[$best] . "\t" . @dnaStart[$best] . "\t" . @dnaEnd[$best] . "\t" . @startDomain[$best] . "\t" . @endDomain[$best] . "\t";   # Print sequence and match data to the results file
+	if ($chimeric == 1) {   # If the sequence was regarded chimeric
+	  print RESULTS "Chimeric\t";   # Add a chimeric tag to the entry
+	} else {   # If not chimeric
+	  print RESULTS "\t";   # Add an empty column
+	}
+	$allDomains = @allSeqDomains[$best];   # Get the domain order of the entry
+	$allDomains =~ tr/ /,/;   # Replace spaces with commas in the domain order string
+	$allDomains = substr($allDomains,0,length($allDomains) - 1);   # Remove the last character (a comma)
+	print RESULTS $allDomains;   # Write the domain order to the results file
+	print RESULTS "\t";   # Write a tab to the results file
+      }
+
+      if ($out_pos == 1) {
+	$out_all_pos = 1;
+	if ($out_all_pos == 1) {  # Output positions of all domains
+	  $seqPartLen = @dnaEnd[$best] - @dnaStart[$best] + 1;
+	  if ($seqPartLen < 0) {
+	    $seqPartLen = $seqPartLen * -1;
+	  }
+	  ## Print the positions of all identified domains to the position file
+	  print POS @seqID[$best] . "\t" . $seqDNALength . " bp." . "\t";
+	  if (@problemCode[$best] !~ m/S/) {
+	    print POS "SSU: " . @ssuStart[$best] . "-" . @ssuEnd[$best] . "\t";
+	  } else {
+	    print POS "SSU: Not found\t";
+	  }
+	  if ((@problemCode[$best] =~ m/X/) || ((@problemCode[$best] =~ m/[15]/) && (@problemCode[$best] =~ m/S/))) {
+	    print POS "ITS1: Not found\t";
+	  } else {
+	    if (@problemCode[$best] =~ m/O/) {
+	      print POS "ITS1: " . (@ssuEnd[$best] + 1) . "-" . (@ssuEnd[$best] + 1) . "\t";
+	    } else {
+	      print POS "ITS1: " . @its1Start[$best] . "-" . @its1End[$best] . "\t";
+	    }
+	  }
+	  if (@problemCode[$best] !~ m/[125OP]/) {
+	    print POS "5.8S: " . @midStart[$best] . "-" . @midEnd[$best] . "\t";
+	  } else {
+	    if (@problemCode[$best] =~ m/5/) {
+	      print POS "5.8S: Not found\t";
+	    } else {
+	      if (@problemCode[$best] =~ m/1/) {
+		print POS "5.8S: No start\t";
+	      } else {
+		if (@problemCode[$best] =~ m/O/) {
+		  print POS "5.8S: Overlap SSU\t";
+		} else {
+		  if (@problemCode[$best] =~ m/P/) {
+		    print POS "5.8S: Overlap LSU\t";
+		  } else {
+		    print POS "5.8S: No end\t";
+		  }
+		}
+	      }
+	    }
+	  }
+	  if ((@problemCode[$best] =~ m/Y/) ||((@problemCode[$best] =~ m/[25]/) && (@problemCode[$best] =~ m/L/))) {
+	    print POS "ITS2: Not found\t";
+	  } else {
+	    if (@problemCode[$best] =~ m/O/) {
+	      print POS "ITS2: " . (@lsuStart[$best] - 1) . "-" . (@lsuStart[$best] - 1) . "\t";
+	    } else {
+	      print POS "ITS2: " . @its2Start[$best] . "-" . @its2End[$best] . "\t";
+	    }
+	  }
+	  if (@problemCode[$best] !~ m/L/) {
+	    print POS "LSU: " . @lsuStart[$best] . "-" . @lsuEnd[$best] . "\t";
+	  } else {
+	    print POS "LSU: Not found" . "\t";
+	  }
+
+	  if (@problemCode[$best] =~ m/5/) {
+	    print POS "Broken or partial sequence, no 5.8S! ";
+	  } else {
+	    if (@problemCode[$best] =~ m/[12]/) {
+	      print POS "Broken or partial sequence, only partial 5.8S! ";
+	    }
+	  }
+	  if (@problemCode[$best] =~ m/B/) {
+	    print POS "ITS region too long! ";
+	  }
+	  if (@problemCode[$best] =~ m/O/) {
+	    print POS "5.8S seem to overlap with SSU! ";
+	  }
+	  if (@problemCode[$best] =~ m/P/) {
+	    print POS "5.8S seem to overlap with LSU! ";
+	  }
+	  if (@problemCode[$best] =~ m/C/) {
+	    print POS "Chimeric! ";
+	  }
+	  print POS "\n";
+
+	} else {  # Output only ITS positions
+	  $seqPartLen = @dnaEnd[$best] - @dnaStart[$best] + 1;
+	  print POS @seqID[$best] . "\t" . $seqDNALength . " bp." . "\t" . "ITS1: " . @its1Start[$best] . "-" . @its1End[$best] . "\t" . "ITS2: " . @its2Start[$best] . "-" . @its2End[$best] . "\n";  # Print the positions of the ITS sequences to the position file
+	}
+      }
+
+      if (@problem[$best] ne "") {
+	$foundProblem++;
+	print PROBLEM @seqID[$best] . "\t" . @problem[$best] . "\n";
+      }
+      
+      ## Set extended type string (the string going into the definition line of the FASTA file)
+      $extendedType = $profileIndex{@seqITSType[$best]} . " ITS sequence";
+      @itsCounts[ord(@seqITSType[$best])]++;   # Add one ITS to the appropriate counter
+
+      if (@seqCompl[$best] == 1) {   # If domains were found on complementary strand
+	$extendedStrand = "complementary strand";   # Set the strand string to complementary
+	$itsCompl++;   # Add one to the complementary strand counter
+      } else {   # If domains were found on the main strand
+	$extendedStrand = "main strand";   # Set the strand string to main
+	$itsMain++;   # Add one to the main strand counter
+      }
+      
+      ## Print (extracted) ITS sequence...
+      if ($out_fasta == 1) {   # If FASTA-output is on
+	if ($truncate == 0) {   # If the whole sequence should be kept in output file
+	  if ($chimeric == 0) {   # If the sequence is not chimeric
+	    if (@problemCode[$best] !~ m/[SL]/) {
+	      if ($out_preserve == 1) {  # If sequence headers should be preserved
+		print FASTA $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	      } else {
+		print FASTA ">" . @seqID[$best] . "|" . @seqITSType[$best] ." " . $extendedType . " (" . $seqDNALength . " bp)  on " . $extendedStrand . "\n";   # Write FASTA definition line
+	      }
+	      print FASTA  @seqDNA[$best] . "\n";   # Write DNA sequence
+	    }
+	    if ($out_partial > 0) {
+	      if (@problemCode[$best] !~ m/[SL125]/) {
+	      if ($out_preserve == 1) {  # If sequence headers should be preserved
+		print FULLPARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	      } else {
+		print FULLPARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] ." " . $extendedType . " (" . $seqDNALength . " bp) Full ITS region on " . $extendedStrand . "\n";   # Write FASTA defline
+	      }
+		print FULLPARTIAL  @seqDNA[$best] . "\n";   # Write DNA sequence
+	      } else {
+		$its1PartLen = @its1End[$best] - @its1Start[$best] + 1;
+		$its2PartLen = @its2End[$best] - @its2Start[$best] + 1;
+		if (($out_partial < $its1PartLen) && ($out_partial < $its2PartLen)) {
+		  if ($out_preserve == 1) {  # If sequence headers should be preserved
+		    print FULLPARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+		  } else {
+		    print FULLPARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] ." " . $extendedType . " (" . $seqDNALength . " bp) Partial ITS region on " . $extendedStrand . "\n";   # Write FASTA defline
+		  }
+		  print FULLPARTIAL  @seqDNA[$best] . "\n";   # Write DNA sequence
+		}
+	      }
+	    }
+	  } else {   # If sequence is regarded chimeric
+	    $itsChimeric++;   # Add one to the chimeric counter
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print CHIMERA $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print CHIMERA ">" . @seqID[$best] . "|" . @seqITSType[$best] ." Chimeric " . $extendedType . " (" . length(@seqDNA[$best]) . " bp)  on " . $extendedStrand . "\n";   # Write FASTA definition line
+	    }
+	    print CHIMERA  @seqDNA[$best] . "\n";   # Write DNA sequence
+	    $foundChimera++;
+	  }
+	} else {    # If only the ITS part of the sequence should be saved to output file
+	  $fastaStartPoint = @dnaStart[$best] - 1;   # Start extraction at the start of the first domain
+	  $fastaEndPoint = @dnaEnd[$best]+10;   # End extraction 10 bp after the last domain
+
+	  if (@seqDomCounts[$best] > 1) {   # If more than one domain was found
+	    if (substr(@startDomain[$best],0,5) eq "1_SSU")  {   # If the first domain was SSU
+	      $fastaStartPoint = @ssuEnd[$best];   # Set the start point of the extraction to the end of the SSU domain
+	    }
+	    if (substr(@startDomain[$best],0,5) eq "4_LSU")  {   # If the first domain was LSU
+	      $fastaStartPoint = @lsuEnd[$best];   # Set the start point of the extraction to the end of the LSU domain
+	    }
+	    if (substr(@endDomain[$best],0,5) eq "1_SSU")  {   # If the last domain was SSU
+	      $fastaEndPoint = @ssuStart[$best] - 1;   # Set the end point of the extraction to the start of the SSU domain
+	    }
+	    if (substr(@endDomain[$best],0,5) eq "4_LSU")  {   # If the last domain was LSU
+	      $fastaEndPoint = @lsuStart[$best] - 1;   # Set the end point of the extraction to the start of the LSU domain
+	    }
+	  }
+	  
+	  if ($fastaStartPoint < 0) {   # If the start point is smaller than zero, set the start point to zero
+	    $fastaStartPoint = 0;
+	  }
+	  if ($fastaEndPoint > length(@seqDNA[$best])) {   # If the end point is larger than the length of the sequence, set the end point to the sequence end
+	    $fastaEndPoint = length(@seqDNA[$best]);
+	  }
+
+	  $fastaLength = $fastaEndPoint - $fastaStartPoint + 1;
+
+	  if ($chimeric == 0) {   # If the sequence is not chimeric
+	    if (@problemCode[$best] !~ m/[SL]/) {
+	      if ($out_preserve == 1) {  # If sequence headers should be preserved
+		print FASTA $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	      } else {
+		print FASTA ">" . @seqID[$best] . "|" . @seqITSType[$best] . " " . $extendedType . " (" . $fastaLength . " bp) on " . $extendedStrand . "\n";   # Write FASTA definition line
+	      }
+	      if ($anchorLen > 0) {
+		if ($fastaStartPoint - @allanchorLens[0] > 0) {
+		  print FASTA substr(@seqDNA[$best],$fastaStartPoint - @allanchorLens[0],$fastaLength + @allanchorLens[0] + @allanchorLens[3]) . "\n";   # Write DNA sequence
+		} else {
+		  print FASTA substr(@seqDNA[$best],0,$fastaLength + $fastaStartPoint + @allanchorLens[3]) . "\n";   # Write DNA sequence
+		}
+	      } else {
+		print FASTA substr(@seqDNA[$best],$fastaStartPoint,$fastaLength) . "\n";   # Write DNA sequence
+	      }
+	    }
+	    if ($out_partial > 0) {
+	      if (@problemCode[$best] !~ m/[SL125]/) {
+		if ($out_preserve == 1) {  # If sequence headers should be preserved
+		  print FULLPARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+		} else {
+		  print FULLPARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] ." " . $extendedType . " (" . $seqDNALength . " bp) Full ITS region on " . $extendedStrand . "\n";   # Write FASTA defline
+		}
+		print FULLPARTIAL substr(@seqDNA[$best],$fastaStartPoint,$fastaLength) . "\n";   # Write DNA sequence
+	      } else {
+		$its1PartLen = @its1End[$best] - @its1Start[$best] + 1;
+		$its2PartLen = @its2End[$best] - @its2Start[$best] + 1;
+		if (($out_partial < $its1PartLen) && ($out_partial < $its2PartLen)) {
+		  if ($out_preserve == 1) {  # If sequence headers should be preserved
+		    print FULLPARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+		  } else {
+		    print FULLPARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] ." " . $extendedType . " (" . $seqDNALength . " bp) Partial ITS region on " . $extendedStrand . "\n";   # Write FASTA defline
+		  }
+		  print FULLPARTIAL substr(@seqDNA[$best],$fastaStartPoint,$fastaLength) . "\n";   # Write DNA sequence
+		}
+	      }
+	    }
+	  } else {   # If sequence is regarded chimeric
+	    $itsChimeric++;   # Add one to the chimeric counter
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print CHIMERA $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print CHIMERA ">" . @seqID[$best] . "|" . @seqITSType[$best] . " Chimeric " . $extendedType . " (" . $fastaLength . " bp) on " . $extendedStrand . "\n";   # Write FASTA definition line
+	    }
+	    print CHIMERA @seqDNA[$best] . "\n";   # Write DNA sequence
+	    $foundChimera++;
+	  }
+	}
+      }
+
+      if ($out_joined == 1) {
+	if ($chimeric == 0) {   # If the sequence is not chimeric
+	  if ($out_preserve == 1) {  # If sequence headers should be preserved
+	    print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	  } else {
+	    print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . " " . $extendedType . " (" . $fastaLength . " bp) From domain " . @startDomain[$best] . " to " . @endDomain[$best] . " on " . $extendedStrand . " Found domains: ";   # Write FASTA definition line
+	    print JOINED substr(@allSeqDomains[$best],0,length(@allSeqDomains[$best]) - 1) . "\n";   # Write domain order
+	  }
+	  print JOINED substr(@seqDNA[$best],$fastaStartPoint,$fastaLength) . "\n";   # Write DNA sequence
+	} else {   # If sequence is regarded chimeric
+	  if ($out_preserve == 1) {  # If sequence headers should be preserved
+	    print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	  } else {
+	    print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . " Chimeric " . $extendedType . " (" . $fastaLength . " bp) From domain " . @startDomain[$best] . " to " . @endDomain[$best] . " on " . $extendedStrand . " Found domains: ";   # Write FASTA definition line
+	    print JOINED substr(@allSeqDomains[$best],0,length(@allSeqDomains[$best]) - 1) . "\n";   # Write domain order
+	  }
+	  print JOINED substr(@seqDNA[$best],$fastaStartPoint,$fastaLength) . "\n";   # Write DNA sequence
+	}
+      }
+
+      ## Write SSU sequence to file
+      if ($out_ssu == 1) {  # If SSU output is on
+	if (@problemCode[$best] !~ m/S/) {
+	  if ($only_full == 0) {
+	    $seqPartLen =  @ssuEnd[$best] - @ssuStart[$best] + 1;
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print SSU $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print SSU ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|SSU " . "Extracted SSU sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	    }
+	    if (uc($anchor) ne "HMM") {
+	      if (@ssuStart[$best] - 1 - $anchorLen > 0) {
+		print SSU substr(@seqDNA[$best], @ssuStart[$best] - 1 - $anchorLen, $anchorLen);
+	      } else {
+		print SSU substr(@seqDNA[$best], 0, @ssuStart[$best] - 1);
+	      }
+	      print SSU substr(@seqDNA[$best], @ssuStart[$best] - 1, @ssuEnd[$best] - @ssuStart[$best] + 1);
+	      if (@ssuEnd[$best] - @ssuStart[$best] + 1 - $anchorLen > 0) {
+		print SSU substr(@seqDNA[$best], @ssuEnd[$best], $anchorLen);
+	      } else {
+		print SSU substr(@seqDNA[$best], @ssuEnd[$best]);
+	      }
+	    } else {
+	      print SSU substr(@seqDNA[$best], @ssuStart[$best] - 1, @ssuEnd[$best] - @ssuStart[$best] + 1);
+	    }
+	    print SSU "\n";   # Write DNA sequence
+	  }
+	}
+      }
+
+      ## Write LSU sequence to file
+      if ($out_lsu == 1) {  # If LSU output is on
+	if ($only_full == 0) {
+	  if (@problemCode[$best] !~ m/L/) {
+	    $seqPartLen = @lsuEnd[$best] - @lsuStart[$best] + 1;
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print LSU $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print LSU ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|LSU " . "Extracted LSU sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	    }
+	    if (uc($anchor) ne "HMM") {
+	      if (@lsuStart[$best] - 1 - $anchorLen > 0) {
+		print LSU substr(@seqDNA[$best], @lsuStart[$best] - 1 - $anchorLen, $anchorLen);
+	      } else {
+		print LSU substr(@seqDNA[$best], 0, @lsuStart[$best] - 1);
+	      }
+	      print LSU substr(@seqDNA[$best], @lsuStart[$best] - 1, @lsuEnd[$best] - @lsuStart[$best] + 1);
+	      #if (@lsuEnd[$best] - @lsuStart[$best] + 1 - $anchorLen > 0) {
+	      #  print LSU substr(@seqDNA[$best], @lsuEnd[$best] - @lsuStart[$best] + 1, $anchorLen);
+	      #} else {
+	      #  print LSU substr(@seqDNA[$best], @lsuEnd[$best] - @lsuStart[$best] + 1);
+	      #}
+	    } else {
+	      print LSU substr(@seqDNA[$best], @lsuStart[$best] - 1, @lsuEnd[$best] - @lsuStart[$best] + 1);
+	    }
+	    print LSU "\n";   # Write DNA sequence
+	  }
+	}
+      }
+
+      ## Write 5.8S sequence to file
+      if ($out_58S == 1) {  # If 5.8S output is on
+	if (@problemCode[$best] !~ m/[125]/) {
+	  $seqPartLen = @midEnd[$best] - @midStart[$best] + 1;
+	  if ($out_preserve == 1) {  # If sequence headers should be preserved
+	    print MID $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	  } else {
+	    print MID ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|5.8S " . "Extracted 5.8S sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	  }
+	  if (uc($anchor) ne "HMM") {
+	    if (@midStart[$best] - 1 - $anchorLen > 0) {
+	      print MID substr(@seqDNA[$best], @midStart[$best] - 1 - $anchorLen, $anchorLen);
+	    } else {
+	      print MID substr(@seqDNA[$best], 0, @midStart[$best] - 1);
+	    }
+	    print MID substr(@seqDNA[$best], @midStart[$best] - 1, @midEnd[$best] - @midStart[$best] + 1);
+	    if (@midEnd[$best] - @midStart[$best] + 1 - $anchorLen > 0) {
+	      print MID substr(@seqDNA[$best], @midEnd[$best], $anchorLen);
+	    } else {
+	      print MID substr(@seqDNA[$best], @midEnd[$best]);
+	    }
+	  } else {
+	    print MID substr(@seqDNA[$best], @midStart[$best] - 1, @midEnd[$best] - @midStart[$best] + 1);
+	  }
+	  print MID "\n";   # Write DNA sequence
+	}
+      }
+
+      ## Write ITS1 sequence to file
+      if ($out_its1 == 1) {  # If ITS1 output is on
+	$seqPartLen = @its1End[$best] - @its1Start[$best] + 1;
+	if ($seqPartLen > 1) {
+	  if ( (($only_full == 0) && (@problemCode[$best] !~ m/[15]/)) || (($only_full == 1) && (@problemCode[$best] !~ m/[S15]/))) {
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print ITS1 $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print ITS1 ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS1 " . "Extracted ITS1 sequence " . @its1Start[$best] . "-" . @its1End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	    }
+	    if (uc($anchor) ne "HMM") {
+	      if (@its1Start[$best] - 1 - $anchorLen > 0) {
+		print ITS1 substr(@seqDNA[$best], @its1Start[$best] - 1 - $anchorLen, $anchorLen);
+	      } else {
+		print ITS1 substr(@seqDNA[$best], 0, @its1Start[$best] - 1);
+	      }
+	      print ITS1 substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);
+	      if (length(@seqDNA[$best]) - @its1End[$best] - $anchorLen > 0) {
+		print ITS1 substr(@seqDNA[$best], @its1End[$best], $anchorLen);
+	      } else {
+		print ITS1 substr(@seqDNA[$best], @its1End[$best]);
+	      }
+	    } else {
+	      if (@its1Start[$best] - 1 - @allanchorLens[0] > 0) {
+		print ITS1 substr(@seqDNA[$best], @its1Start[$best] - 1 - @allanchorLens[0], @allanchorLens[0]);
+	      } else {
+		print ITS1 substr(@seqDNA[$best], 0, @its1Start[$best] - 1);
+	      }
+	      print ITS1 substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);
+	      if (length(@seqDNA[$best]) - @its1End[$best] - @allanchorLens[1] > 0) {
+		print ITS1 substr(@seqDNA[$best], @its1End[$best], @allanchorLens[1]);
+	      } else {
+		print ITS1 substr(@seqDNA[$best], @its1End[$best]);
+	      }
+	      
+	    }
+	    print ITS1 "\n";   # Write DNA sequence
+	  }
+	}
+	if ($out_partial > 0) {
+	  if (@problemCode[$best] !~ m/[S15]/) {
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print ITS1PARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print ITS1PARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS1 " . "Extracted Full ITS1 sequence " . @its1Start[$best] . "-" . @its1End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	    }
+	    if (uc($anchor) ne "HMM") {
+	      if (@its1Start[$best] - 1 - $anchorLen > 0) {
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1 - $anchorLen, $anchorLen);
+	      } else {
+		print ITS1PARTIAL substr(@seqDNA[$best], 0, @its1Start[$best] - 1);
+	      }
+	      print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);
+	      if (length(@seqDNA[$best]) - @its1End[$best] - $anchorLen > 0) {
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best], $anchorLen);
+	      } else {
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best]);
+	      }
+	    } else {
+	      if (@its1Start[$best] - 1 - @allanchorLens[0] > 0) {
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1 - @allanchorLens[0], @allanchorLens[0]);
+	      } else {
+		print ITS1PARTIAL substr(@seqDNA[$best], 0, @its1Start[$best] - 1);
+	      }
+	      print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);
+	      if (length(@seqDNA[$best]) - @its1End[$best] - @allanchorLens[1] > 0) {
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best], @allanchorLens[1]);
+	      } else {
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best]);
+	      }
+	      
+	    }
+	    print ITS1PARTIAL "\n";   # Write DNA sequence
+	  } else {
+	    if ($out_partial < $seqPartLen) {
+	      if ($out_preserve == 1) {  # If sequence headers should be preserved
+		print ITS1PARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	      } else {
+		print ITS1PARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS1 " . "Extracted Partial ITS1 sequence " . @its1Start[$best] . "-" . @its1End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	      }
+	      if (uc($anchor) ne "HMM") {
+		if (@its1Start[$best] - 1 - $anchorLen > 0) {
+		  print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1 - $anchorLen, $anchorLen);
+		} else {
+		  print ITS1PARTIAL substr(@seqDNA[$best], 0, @its1Start[$best] - 1);
+		}
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);
+		if (length(@seqDNA[$best]) - @its1End[$best] - $anchorLen > 0) {
+		  print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best], $anchorLen);
+		} else {
+		  print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best]);
+		}
+	      } else {
+		if (@its1Start[$best] - 1 - @allanchorLens[0] > 0) {
+		  print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1 - @allanchorLens[0], @allanchorLens[0]);
+		} else {
+		  print ITS1PARTIAL substr(@seqDNA[$best], 0, @its1Start[$best] - 1);
+		}
+		print ITS1PARTIAL substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);
+		if (length(@seqDNA[$best]) - @its1End[$best] - @allanchorLens[1] > 0) {
+		  print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best], @allanchorLens[1]);
+		} else {
+		  print ITS1PARTIAL substr(@seqDNA[$best], @its1End[$best]);
+		}
+	      }
+	      print ITS1PARTIAL "\n";   # Write DNA sequence
+	    }
+	  }
+	}
+      }
+      
+      ## Write ITS2 sequence to file
+      if ($out_its2 == 1) {  # If ITS2 output is on
+	$seqPartLen = @its2End[$best] - @its2Start[$best] + 1;
+	if ($seqPartLen > 1) {
+	  if ( (($only_full == 0) && (@problemCode[$best] !~ m/[25]/)) || (($only_full == 1) && (@problemCode[$best] !~ m/[L25]/))) {
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print ITS2 $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print ITS2 ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS2 " . "Extracted ITS2 sequence " . @its2Start[$best] . "-" . @its2End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	    }
+	    if (uc($anchor) ne "HMM") {
+	      if (@its2Start[$best] - 1 - $anchorLen > 0) {
+		print ITS2 substr(@seqDNA[$best], @its2Start[$best] - 1 - $anchorLen, $anchorLen);
+	      } else {
+		print ITS2 substr(@seqDNA[$best], 0, @its2Start[$best] - 1);
+	      }
+	      print ITS2 substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);
+	      if (length(@seqDNA[$best]) - @its2End[$best] - $anchorLen > 0) {
+		print ITS2 substr(@seqDNA[$best], @its2End[$best], $anchorLen);
+	      } else {
+		print ITS2 substr(@seqDNA[$best], @its2End[$best]);
+	      }
+	    } else {
+	      if (@its2Start[$best] - 1 - @allanchorLens[2] > 0) {
+		print ITS2 substr(@seqDNA[$best], @its2Start[$best] - 1 - @allanchorLens[2], @allanchorLens[2]);
+	      } else {
+		print ITS2 substr(@seqDNA[$best], 0, @its2Start[$best] - 1);
+	      }
+	      print ITS2 substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);
+	      if (length(@seqDNA[$best]) - @its2End[$best] - @allanchorLens[3] > 0) {
+		print ITS2 substr(@seqDNA[$best], @its2End[$best], @allanchorLens[3]);
+	      } else {
+		print ITS2 substr(@seqDNA[$best], @its2End[$best]);
+	      }
+	    }
+	    print ITS2 "\n";   # Write DNA sequence
+	  }
+	  if ($out_partial > 0) {
+	    if (@problemCode[$best] !~ m/[L25]/) {
+	      if ($out_preserve == 1) {  # If sequence headers should be preserved
+		print ITS2PARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	      } else {
+		print ITS2PARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS2 " . "Extracted Full ITS2 sequence " . @its2Start[$best] . "-" . @its2End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	      }
+	      if (uc($anchor) ne "HMM") {
+		if (@its2Start[$best] - 1 - $anchorLen > 0) {
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1 - $anchorLen, $anchorLen);
+		} else {
+		  print ITS2PARTIAL substr(@seqDNA[$best], 0, @its2Start[$best] - 1);
+		}
+		print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);
+		if (length(@seqDNA[$best]) - @its2End[$best] - $anchorLen > 0) {
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best], $anchorLen);
+		} else {
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best]);
+		}
+	      } else {
+		if (@its2Start[$best] - 1 - @allanchorLens[2] > 0) {
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1 - @allanchorLens[2], @allanchorLens[2]);
+		} else {
+		  print ITS2PARTIAL substr(@seqDNA[$best], 0, @its2Start[$best] - 1);
+		}
+		print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);
+		if (length(@seqDNA[$best]) - @its2End[$best] - @allanchorLens[3] > 0) {
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best], @allanchorLens[3]);
+		} else {
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best]);
+		}
+	      }
+	      print ITS2PARTIAL "\n";   # Write DNA sequence
+	    } else {
+	      if ($out_partial < $seqPartLen) {
+		if ($out_preserve == 1) {  # If sequence headers should be preserved
+		  print ITS2PARTIAL $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+		} else {
+		  print ITS2PARTIAL ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS2 " . "Extracted Partial ITS2 sequence " . @its2Start[$best] . "-" . @its2End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+		}
+		if (uc($anchor) ne "HMM") {
+		  if (@its2Start[$best] - 1 - $anchorLen > 0) {
+		    print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1 - $anchorLen, $anchorLen);
+		  } else {
+		    print ITS2PARTIAL substr(@seqDNA[$best], 0, @its2Start[$best] - 1);
+		  }
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);
+		  if (length(@seqDNA[$best]) - @its2End[$best] - $anchorLen > 0) {
+		    print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best], $anchorLen);
+		  } else {
+		    print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best]);
+		  }
+		} else {
+		  if (@its2Start[$best] - 1 - @allanchorLens[2] > 0) {
+		    print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1 - @allanchorLens[2], @allanchorLens[2]);
+		  } else {
+		    print ITS2PARTIAL substr(@seqDNA[$best], 0, @its2Start[$best] - 1);
+		  }
+		  print ITS2PARTIAL substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);
+		  if (length(@seqDNA[$best]) - @its2End[$best] - @allanchorLens[3] > 0) {
+		    print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best], @allanchorLens[3]);
+		  } else {
+		    print ITS2PARTIAL substr(@seqDNA[$best], @its2End[$best]);
+		  }
+		}
+		print ITS2PARTIAL "\n";   # Write DNA sequence
+	      }
+	    }
+	  }
+	}
+      }
+
+      ## Output concatenated ITS1 + ITS2 sequences
+      if ($out_concat == 1) {
+	$seqPartLen1 = @its1End[$best] - @its1Start[$best] + 1;
+	$seqPartLen2 = @its2End[$best] - @its2Start[$best] + 1;
+	if (($seqPartLen1 >= $concat_minlen) && ($seqPartLen2 >= $concat_minlen)) {
+	  if ($out_preserve == 1) {  # If sequence headers should be preserved
+	    print CONCAT $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	  } else {
+	    print CONCAT ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS1+2 " . "Concatenated ITS1 and ITS2 sequences (" . ($seqPartLen1 + $seqPartLen2) . " bp)\n";   # Write FASTA definition line
+	  }
+	  print CONCAT substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);   # Write ITS1 DNA sequence
+	  print CONCAT "-----";  # Write spacer
+	  print CONCAT substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);   # Write ITS2 DNA sequence
+	  print CONCAT "\n";  # Write newline
+	} else {
+	  if ($seqPartLen1 >= $concat_minlen) {
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print CONCAT $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print CONCAT ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS1 " . "ITS1 sequence (ITS2 too short) (" . $seqPartLen1 . " bp)\n";   # Write FASTA definition line
+	    }
+	    print CONCAT substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1);   # Write ITS1 DNA sequence
+	    print CONCAT "-----";  # Write spacer
+	    print CONCAT "\n";  # Write newline
+	  }
+	  if ($seqPartLen2 >= $concat_minlen) {
+	    if ($out_preserve == 1) {  # If sequence headers should be preserved
+	      print CONCAT $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	    } else {
+	      print CONCAT ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS2 " . "ITS2 sequence (ITS1 too short) (" . $seqPartLen2 . " bp)\n";   # Write FASTA definition line
+	    }
+	    print CONCAT "-----";  # Write spacer
+	    print CONCAT substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1);   # Write ITS2 DNA sequence
+	    print CONCAT "\n";  # Write newline
+	  }
+	}
+      }
+
+      ## Print all sequences to the joined file for debugging
+      if ($out_joined == 1) {
+	$seqPartLen =  @ssuEnd[$best] - @ssuStart[$best] + 1;
+	if ($out_preserve == 1) {  # If sequence headers should be preserved
+	  print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	} else {
+	  print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|SSU " . "Extracted SSU sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	}
+	print JOINED substr(@seqDNA[$best], @ssuStart[$best] - 1, @ssuEnd[$best] - @ssuStart[$best] + 1) . "\n";   # Write DNA sequence
+	
+	$seqPartLen = @its1End[$best] - @its1Start[$best] + 1;
+	if ($out_preserve == 1) {  # If sequence headers should be preserved
+	  print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	} else {
+	  print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS1 " . "Extracted ITS1 sequence " . @its1Start[$best] . "-" . @its1End[$best] . " (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	}
+	print JOINED substr(@seqDNA[$best], @its1Start[$best] - 1, @its1End[$best] - @its1Start[$best] + 1) . "\n";   # Write DNA sequence
+	
+	$seqPartLen = @midEnd[$best] - @midStart[$best] + 1;
+	if ($out_preserve == 1) {  # If sequence headers should be preserved
+	  print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	} else {
+	  print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|5.8S " . "Extracted 5.8S sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	}
+	print JOINED substr(@seqDNA[$best], @midStart[$best] - 1, @midEnd[$best] - @midStart[$best] + 1) . "\n";   # Write DNA sequence
+	
+	$seqPartLen = @its2End[$best] - @its2Start[$best] + 1;
+	if ($out_preserve == 1) {  # If sequence headers should be preserved
+	  print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	} else {
+	  print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|ITS2 " . "Extracted ITS2 sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	}
+	print JOINED substr(@seqDNA[$best], @its2Start[$best] - 1, @its2End[$best] - @its2Start[$best] + 1) . "\n";   # Write DNA sequence
+	
+	$seqPartLen = @lsuEnd[$best] - @lsuStart[$best] + 1;
+	if ($out_preserve == 1) {  # If sequence headers should be preserved
+	  print JOINED $headers{@seqID[$best]} . "\n";   # Write FASTA definition line
+	} else {
+	  print JOINED ">" . @seqID[$best] . "|" . @seqITSType[$best] . "|LSU " . "Extracted LSU sequence (" . $seqPartLen . " bp)\n";   # Write FASTA definition line
+	}
+	print JOINED substr(@seqDNA[$best], @lsuStart[$best] - 1, @lsuEnd[$best] - @lsuStart[$best] + 1) . "\n";   # Write DNA sequence
+      }
+      
+      
+      if ($out_results == 1) {
+	## Print info on all matches, also not top ones to the results file...
+	for ($i = 0; $i < scalar(@seqITSType); $i++) {   # Go through all the possible ITS types...
+	  print RESULTS @seqITSType[$i] . ": " . @seqDomCounts[$i] . " " . @seqAvgE[$i] . " " . @seqAvgScore[$i];   # Write some info on this type (Type, Domain count, Average E-value, Average score)
+	  if ($i < scalar(@seqITSType) - 1) {   # If this is no the last domain type
+	    print RESULTS ", ";   # Write a comma
+	  }
+	}
+	print RESULTS "\n";   # Write end of line
+      }
+    }
+    
+    ## Undefine all used arrays for the next round...
+    undef @seqID;
+    undef @seqITSType;
+    undef @seqCompl;
+    undef @seqDomCounts;
+    undef @seqAvgE;
+    undef @seqAvgScore;
+    undef @seqScoreSum;
+    undef @seqDNA;
+    undef @allSeqDomains;
+    undef @dnaStart;
+    undef @dnaEnd;
+    undef @ssuStart;
+    undef @ssuEnd;
+    undef @lsuStart;
+    undef @lsuEnd;
+    undef @midStart;
+    undef @midEnd;
+    undef @its1Start;
+    undef @its1End;
+    undef @its2Start;
+    undef @its2End;
+    undef @startDomain;
+    undef @endDomain;
+    undef @domain_order;
+    undef @sorted_domain_order;
+    undef @problem;
+    undef @problemCode;
+    undef @anchorLens;
+  }
+  if (@item[0] ne "") {   # Add this entry to the set (regardless if the entry has the same ID as entries already in the set), as long as it is non-empty
+    push(@seqID, @item[0]);   # Add sequence ID
+    push(@seqITSType, @item[1]);   # Add ITS type
+    push(@seqCompl, @item[2]);   # Add main/complementary strand info
+    push(@seqDomCounts, @item[3]);   # Add domain count
+    push(@seqAvgE, @item[4]);   # Add average E-value
+    push(@seqAvgScore, @item[5]);   # Add average score
+    push(@seqScoreSum, @item[6]);   # Add sum-of-scores
+    push(@seqDNA, @item[7]);   # Add DNA sequence
+    
+    ## Determine first and last domains, and their positions
+    ## Set variables to unrealistic values
+    $dnaEnd = length(@item[7]);
+    $startDomain = "***";
+    $endDomain = "***";
+    $dnaStart = 1;
+    $allDomains = "";
+    $ssuStart = 1;
+    $ssuEnd = 0;
+    $midStart = 1;
+    $midEnd = 0;
+    $lsuStart = 1;
+    $lsuEnd = 0;
+    $its1Start = 1;
+    $its1End = length(@item[7]);
+    $its2Start = 1;
+    $its2End = length(@item[7]);
+    $problem = "";
+    $problemCode = "";
+
+    $ssuFound = 0;
+    $lsuFound = 0;
+    $midSFound = 0;
+    $midEFound = 0;
+    $order = "";
+    undef @hitanchorlens;
+    
+    for ($i = 8; $i < scalar(@item); $i++) {   # Go through the list of found domains in this sequence
+      ($hitStart,$hitEnd,$hitProfile,$hitScore,$hitEval,$hitanchorlen) = split(';',@item[$i]);   # Separate the hit stats into variables
+      $allDomains = $allDomains . $hitProfile . " ";   # Add found domain to the list of all domains
+
+#      if ($hitStart < $dnaStart) {   # If this domain is the first one so far
+#	$dnaStart = $hitStart;   # Set the start of the ITS sequence to this domain's start
+#	$startDomain = $hitProfile;   # Set this domain as the starting domain
+#      }
+#      if ($hitEnd > $dnaEnd) {   # If this domain is the last one so far
+#	$dnaEnd = $hitEnd;   # Set the end of the ITS sequence to this domain's end
+#	$endDomain = $hitProfile;   # Set this domain as the ending domain
+#      }
+
+      if (substr($hitProfile,0,5) eq "1_SSU" ) {   # If this domain is the SSU's end
+	$dnaStart = $hitStart;   # Set the start of the ITS sequence to this domain's start
+	$startDomain = $hitProfile;   # Set this domain as the starting domain
+	$ssuStart = 1;   # Set the start of the SSU sequence to the start of the sequence
+	$ssuEnd = $hitEnd;   # Set the end of the SSU sequence to this domain's end
+	$its1Start = $hitEnd + 1;   # Set the start of the ITS1 sequence to right after this domain's end
+	if ($midEFound == 0) {
+	  $its2Start = $hitEnd + 1;   # Set the end of the ITS2 sequence to right after this domain's end
+	}
+	$ssuFound = 1;
+	$order = $order . "1";
+	@hitanchorlens[1] = $hitanchorlen;
+      }
+
+      if (substr($hitProfile,0,5) eq "2_5.8" ) {   # If this domain is the 5.8S's start
+	if ($startDomain eq "***") {
+	  $dnaStart = 1;   # Set the start of the ITS sequence to the start of the sequence
+	  $startDomain = $hitProfile;   # Set this domain as the starting domain
+	}
+	$its1End = $hitStart - 1;   # Set the end of the ITS1 sequence to right before this domain's start
+	if ($midEFound == 0) {
+	  $its2Start = $hitEnd + 1;   # Set the start of the ITS2 sequence to right after this domain's end
+	}
+	$midStart = $hitStart;   # Set the start of the 5.8S sequence to this domain's start
+	$midSFound = 1;
+	$order = $order . "2";
+	@hitanchorlens[2] = $hitanchorlen;
+      }
+
+      if (substr($hitProfile,0,5) eq "3_End" ) {   # If this domain is the 5.8S's end
+	if ($startDomain eq "***") {
+	  $dnaStart = 1;   # Set the start of the ITS sequence to the start of the sequence
+	  $startDomain = $hitProfile;   # Set this domain as the starting domain
+	}
+	if ($midSFound == 0) {
+	  $its1End = $hitStart - 1;   # Set the end of the ITS1 sequence to right before this domain's start
+	}
+	$its2Start = $hitEnd + 1;   # Set the end of the ITS2 sequence to right after this domain's end
+	$midEnd = $hitEnd;   # Set the end of the 5.8S sequence to this domain's end
+	$midEFound = 1;
+	$order = $order . "3";
+	@hitanchorlens[3] = $hitanchorlen;
+      }
+
+      if (substr($hitProfile,0,5) eq "4_LSU" ) {   # If this domain is the LSU's start
+	if ($startDomain eq "***") {
+	  $dnaStart = 1;   # Set the start of the ITS sequence to the start of the sequence
+	  $startDomain = $hitProfile;   # Set this domain as the starting domain
+	}
+	$dnaEnd = $hitEnd;   # Set the end of the ITS sequence to this domain's end
+	$endDomain = $hitProfile;   # Set this domain as the ending domain
+	$lsuStart = $hitStart;   # Set the start of the LSU sequence to the start of the this domain
+	$lsuEnd = length(@item[7]);   # Set the end of the LSU sequence to the end of the sequence
+	$its2End = $hitStart - 1;   # Set the end of the ITS2 sequence to right before this domain's start
+	if ($midSFound == 0) {
+	  $its1End = $hitStart - 1;   # Set the end of the ITS1 sequence to right before this domain's start
+	}
+	$lsuFound = 1;
+	$order = $order . "4";
+	@hitanchorlens[4] = $hitanchorlen;
+      }
+    }
+
+    if ($ssuFound == 0) {
+      if ($problem ne "") {
+	$problem = $problem . "; ";
+      }
+      $problem = $problem . "End of SSU sequence not found";
+      $problemCode = $problemCode . "S";
+      $order = "1" .  $order;
+    }
+
+    if ($lsuFound == 0) {
+      if ($problem ne "") {
+	$problem = $problem . "; ";
+      }
+      $problem = $problem . "Start of LSU sequence not found";
+      $problemCode = $problemCode . "L";
+      $order = $order . "4";
+    }
+
+    if (($midSFound == 0) && ($midEFound == 0)) {
+      if ($problem ne "") {
+	$problem = $problem . "; ";
+      }
+      $problem = $problem . "The 5.8S sequence was not found at all";
+      $problemCode = $problemCode . "5";
+    } else {
+      if ($midSFound == 0) {
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "Start of 5.8S sequence not found";
+	$problemCode = $problemCode . "1";
+      }
+      if ($midEFound == 0) {
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "End of 5.8S sequence not found";
+	$problemCode = $problemCode . "2";
+      }
+    }
+
+    if ($dnaEnd - $dnaStart > 1500) {
+      if ($problem ne "") {
+	$problem = $problem . "; ";
+      }
+      $problem = $problem . "ITS region is suspiciously long (> 1500 bp)";
+      $problemCode = $problemCode . "B";
+    }
+
+    if (length($order) == 4) {
+      if ($order ne "1234") {
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "Domains found in wrong order, sequence may be chimeric";
+	$problemCode = $problemCode . "C";
+      }
+    } else {
+      if ((substr($order,0,1) ne "1") || (substr($order,-1) ne "4")) {
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "Domains found in wrong order, sequence may be chimeric";
+	$problemCode = $problemCode . "C";
+      } else {
+	if (($midSFound == 1) && ($midEFound == 1)) {
+	  if ($order !~ m/23/) {
+	    if ($problem ne "") {
+	      $problem = $problem . "; ";
+	    }
+	    $problem = $problem . "Domains found in wrong order, sequence may be chimeric";
+	    $problemCode = $problemCode . "C";
+	  }
+	}
+      }
+    }
+
+    if ($its1End - $its1Start < 0) {  # 5.8S overlaps SSU
+      if (($midSFound == 1) && ($ssuFound == 1)) {
+	$problemCode = $problemCode . "OC";
+	$its1Start = 0;
+	$its1End = 0;
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "SSU seems to overlap 5.8S, sequence may be chimeric";
+      } else {
+	$problemCode = $problemCode . "X";
+	$its1Start = 0;
+	$its1End = 0;
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "No ITS1 sequence";
+      }
+    }
+    if ($its2End - $its2Start < 0) {  # 5.8S overlaps LSU
+      if (($midEFound == 1) && ($lsuFound == 1)) {
+	$problemCode = $problemCode . "PC";
+	$its2Start = 0;
+	$its2End = 0;
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "LSU seems to overlap 5.8S, sequence may be chimeric";
+       } else {
+	$problemCode = $problemCode . "Y";
+	$its2Start = 0;
+	$its2End = 0;
+	if ($problem ne "") {
+	  $problem = $problem . "; ";
+	}
+	$problem = $problem . "No ITS2 sequence";
+      }
+    }
+
+
+    if (($problemCode =~ m/[15]/) && ($problemCode =~ m/[S]/)) {  # Sequence lack all indications of ITS1
+      $its1Start = 0;
+      $its1End = 0;
+    }
+    if (($problemCode =~ m/[25]/) && ($problemCode =~ m/[L]/)) {  # Sequence lack all indications of ITS2
+      $its2Start = 0;
+      $its2End = 0;
+    }
+
+
+    $allhitanchorlens = @hitanchorlens[1] . "," . @hitanchorlens[2] . "," . @hitanchorlens[3] . "," . @hitanchorlens[4];
+
+    push(@allSeqDomains,$allDomains);   # Add list of all domains
+    push(@dnaStart, $dnaStart);   # Add start of the ITS sequence
+    push(@startDomain, $startDomain);   # Add start domain
+    push(@dnaEnd, $dnaEnd);   # Add end of ITS sequence
+    push(@endDomain, $endDomain);   # Add end domain
+    push(@ssuStart, $ssuStart);   # Add start of the SSU sequence
+    push(@ssuEnd, $ssuEnd);   # Add end of the SSU sequence
+    push(@midStart, $midStart);   # Add start of the 5.8S sequence
+    push(@midEnd, $midEnd);   # Add end of the 5.8S sequence
+    push(@lsuStart, $lsuStart);   # Add start of the LSU sequence
+    push(@lsuEnd, $lsuEnd);   # Add end of the LSU sequence
+    push(@its1Start, $its1Start);   # Add start of the ITS1 sequence
+    push(@its1End, $its1End);   # Add end of the ITS1 sequence
+    push(@its2Start, $its2Start);   # Add start of the ITS2 sequence
+    push(@its2End, $its2End);   # Add end of the ITS2 sequence
+    push(@problem, $problem);  # Add potential problem info
+    push(@problemCode, $problemCode);  # Add potential problem info in code form
+    push(@anchorLens, $allhitanchorlens);  # Add the anchor lengths
+  }
+  $lc++;   # Increase the line count by one
+}
+
+## Save results to the summary file
+if ($out_sum == 1) {   # If summary file should be written
+  $itsTotal = 0;   # Reset the total ITS sum
+  foreach $typeCount (@itsCounts) {   # Add ITSs from all different origins
+    $itsTotal += $typeCount;   # Add the number of ITSs for this origin
+  }
+  ## Write info on the found ITS sequences to the summary file
+  print SUMMARY "Sequences detected as ITS by ITSx:\t$itsTotal\n";
+  print SUMMARY "  On main strand:         \t$itsMain\n";
+  print SUMMARY "  On complementary strand:\t$itsCompl\n";
+  if ($allow_reorder == 0) {   # If re-ordering of domains is not allowed
+    print SUMMARY "Sequences detected as chimeric by ITSx:\t$itsChimeric\n";   # Write the number of reported chimeric sequences to the summary file
+  }
+  ## Write info on the found ITS sequence types to the summary file
+  print SUMMARY "ITS sequences by preliminary origin:\n";
+  print SUMMARY "  Alveolates:      \t" . int(@itsCounts[ord("A")]) . "\n";
+  print SUMMARY "  Amoebozoa:       \t" . int(@itsCounts[ord("D")]) . "\n";
+  print SUMMARY "  Bacillariophyta: \t" . int(@itsCounts[ord("C")]) . "\n";
+  print SUMMARY "  Brown algae:     \t" . int(@itsCounts[ord("I")]) . "\n";
+  print SUMMARY "  Bryophytes:      \t" . int(@itsCounts[ord("B")]) . "\n";
+  print SUMMARY "  Euglenozoa:      \t" . int(@itsCounts[ord("E")]) . "\n";
+  print SUMMARY "  Eustigmatophytes:\t" . int(@itsCounts[ord("U")]) . "\n";
+  print SUMMARY "  Fungi:           \t" . int(@itsCounts[ord("F")]) . "\n";
+  print SUMMARY "  Green algae:     \t" . int(@itsCounts[ord("G")]) . "\n";
+  print SUMMARY "  Liverworts:      \t" . int(@itsCounts[ord("L")]) . "\n";
+  print SUMMARY "  Metazoa:         \t" . int(@itsCounts[ord("M")]) . "\n";
+  print SUMMARY "  Microsporidia:   \t" . int(@itsCounts[ord("N")]) . "\n";
+  print SUMMARY "  Oomycetes:       \t" . int(@itsCounts[ord("O")]) . "\n";
+  print SUMMARY "  Prymnesiophytes: \t" . int(@itsCounts[ord("P")]) . "\n";
+  print SUMMARY "  Raphidophytes:   \t" . int(@itsCounts[ord("Q")]) . "\n";
+  print SUMMARY "  Red algae:       \t" . int(@itsCounts[ord("H")]) . "\n";
+  print SUMMARY "  Rhizaria:        \t" . int(@itsCounts[ord("R")]) . "\n";
+  print SUMMARY "  Synurophyceae:   \t" . int(@itsCounts[ord("S")]) . "\n";
+  print SUMMARY "  Tracheophyta:    \t" . int(@itsCounts[ord("T")]) . "\n";
+  print SUMMARY "-----------------------------------------------------------------\n";
+  close (SUMMARY);   # Close the summary file
+}
+
+if ($out_results == 1) {
+  close (RESULTS);   # Close the results file
+}
+close (RAWOUT);   # Close the raw output file
+close (PROBLEM);   # Close the file for problematic entries
+if ($foundProblem == 0) {
+  `rm $output.problematic.txt 2> /dev/null`;
+}
+if ($out_pos == 1) {
+  close (POS);   # Close the positions file
+}
+if ($out_fasta == 1) {   # If FASTA output is on
+  close (FASTA);   # Close the FASTA output file
+  if ($allow_reorder == 0) {   # If re-ordering of domains is not allowed
+    close (CHIMERA);   # Close the chimera file
+    if ($foundChimera == 0) {
+      `rm $output.chimeric.fasta 2> /dev/null`;
+    }
+  }
+  if ($out_partial > 0) {
+    close FULLPARTIAL;
+  }
+}
+if ($out_ssu == 1) {
+  close (SSU);   # Close the SSU file
+}
+if ($out_lsu == 1) {
+  close (LSU);   # Close the LSU file
+}
+if ($out_58S == 1) {
+  close (MID);   # Close the 58S file
+}
+if ($out_its1 == 1) {
+  close (ITS1);   # Close the ITS1 file
+  if ($out_partial > 0) {
+    close ITS1PARTIAL;
+  }
+}
+if ($out_its2 == 1) {
+  close (ITS2);   # Close the ITS2 file
+  if ($out_partial > 0) {
+    close ITS2PARTIAL;
+  }
+}
+if ($out_concat == 1) {
+  close CONCAT;
+}
+
+if ($out_not == 1) {   # If not-found output is on
+  open (NOTFOUND, "$output\_no_detections.txt");   # Open the not-found output file
+  while ($line = <NOTFOUND>) {  # Read all entries from file
+    chomp($line);  # Remove newline char
+    push(@nodetectionlist,$line);  # Add to non-detection list
+  }
+  close NOTFOUND;
+
+  open (NOTFOUND, ">$output\_no_detections.fasta");   # Create a not-found FASTA output file
+  foreach $seqID (@nodetectionlist) {  # For all non-detections
+    $seq = $sequenceDB{"$seqID"};  # Get sequence from sequence database
+    print NOTFOUND ">$seqID\n";  # Print not found sequence ID
+    print NOTFOUND $seq . "\n";  # Print not found sequence
+  }
+  close NOTFOUND;
+}
+
+## Clean up and finish
+
+if ($pipeline == 0) {   # If ITSx is not called from the pipeline mode (i.e. from ITSx)
+  if ($save_raw == 1) {   # If raw data should be saved
+    `mv $tempDir $output\_ITSx_raw_output`;   # Change the name of the temporary directory to ..._ITSx_raw_output
+  } else {   # Else, discard the raw data
+    `rm -rf $tempDir`;   # Remove the temporary directory
+  }
+}
+
+## Get the current time and output a finished message
+$now = localtime;
+if ($silent == 0) {
+  print STDERR "$now : Extraction finished!\n";
+  print STDERR "-----------------------------------------------------------------\n";
+  print STDERR "Thank you for using ITSx!\n";
+  print STDERR "Please report bugs or unsupported lineages to itsx\@microbiology.se\n";
+  print STDERR "\n";
+}
+
+## Write end time a summary file
+if ($pipeline == 0) {    # If not running in pipeline mode
+  if ($out_sum == 1) {   # If summary output is on
+    open (SUMMARY, ">>$output.summary.txt");   # Append to the summary file
+    print SUMMARY "ITSx run finished at $now.\n";   # Write ending time for the analysis
+    close (SUMMARY);   # Close summary file
+  }
+}
+
+sub hmmerSearch {
+  $hmmerCommand = $_[0];
+  $outputFile = $_[1];
+  $strand = $_[2];
+  $profileSet = $_[3];
+  open (HMMEROUTPUT, ">$outputFile");
+  open (HMMER, "$hmmerCommand |");
+  $totalHitCount = 0;
+  $hitCount = 0;
+  $SSUCount = 0;
+  $LSUCount = 0;
+  $startCount = 0;
+  $endCount = 0;
+  $maxCount = 1;
+  while (chomp($line = <HMMER>)) {
+    if (substr($line,0,6) eq "Query:") {
+      $hitCount = 0;
+      $SSUCount = 0;
+      $LSUCount = 0;
+      $startCount = 0;
+      $endCount = 0;
+      undef @bestScore;
+      undef @bestEntry;
+      
+      $query = substr($line,7);
+      $queryLength = $query;
+      $queryLength =~ s/.*  *//;
+      $queryLength =~ s/[^0-9]//g;
+      $query =~ s/  *//;
+      $query =~ s/  *.*//;
+      
+      print HMMEROUTPUT "## New query:\t$query\t$queryLength\n";
+
+    }
+    if (substr($line,0,12) eq "Description:") {
+      $desc = $line;
+    }
+    if (substr($line,0,3) eq ">> ") {
+      ($tempshit,$hmmerSubjectName) = split(' ',$line);
+    }
+    if ($line =~ m/[0-9] ! /) {
+      $stats = $line;
+      $stats =~ s/  */\t/g;
+      ($empty,$no,$excl,$score) = split('\t',$stats);
+      $hitCount++;
+      $totalHitCount++;
+      if ($maxCount == 0) {
+	print HMMEROUTPUT "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+      } else {
+	if (substr($hmmerSubjectName,0,5) eq "1_SSU") {
+	  $SSUCount++;
+	  if ($SSUCount <= $maxCount) {
+	    @bestScore[1] = $score;
+	    @bestEntry[1] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	  } else {
+	    if ($score > @bestScore[1]) {
+	      @bestScore[1] = $score;
+	      @bestEntry[1] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	    }
+	  }
+	}
+	if (substr($hmmerSubjectName,0,5) eq "4_LSU") {
+	  $LSUCount++;
+	  if ($LSUCount <= $maxCount) {
+	    @bestScore[4] = $score;
+	    @bestEntry[4] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	  } else { 
+	    if ($score > @bestScore[4]) {
+	      @bestScore[4] = $score;
+	      @bestEntry[4] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	    }
+	  }
+	}
+	if (substr($hmmerSubjectName,0,5) eq "2_5.8") {
+	  $startCount++;
+	  if ($startCount <= $maxCount) {
+	    @bestScore[2] = $score;
+	    @bestEntry[2] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	  } else {
+	    if ($score > @bestScore[2]) {
+	      @bestScore[2] = $score;
+	      @bestEntry[2] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	    }
+	  }
+	}
+	if (substr($hmmerSubjectName,0,5) eq "3_End") {
+	  $endCount++;
+	  if ($endCount <= $maxCount) {
+	    @bestScore[3] = $score;
+	    @bestEntry[3] = "$query\t$hmmerSubjectName\t$queryLength$stats\n";
+	  } else {
+	    if ($score > @bestScore[3]) {
+	      @bestScore[3] = $score;
+	      @bestEntry[3] = "$query\t$hmmerSubjectName\t$queryLength$stats\n"
+	    }
+	  }
+	}
+      }
+    }
+    if (substr($line,0,2) eq "//") {
+      if ($maxCount > 0) {
+	if ($SSUCount > 0) {
+	  print HMMEROUTPUT @bestEntry[1];
+	}
+	if ($startCount > 0) {
+	  print HMMEROUTPUT @bestEntry[2];
+	}
+	if ($endCount > 0) {
+	  print HMMEROUTPUT @bestEntry[3];
+	}
+	if ($LSUCount > 0) {
+	  print HMMEROUTPUT @bestEntry[4];
+	}
+      }
+      print HMMEROUTPUT "//\n";
+    }
+  }
+  close(HMMEROUTPUT);
+  $now = localtime;
+  if ($silent == 0) {
+    if ($strand eq "M") {
+      print STDERR "    $now : " . ucfirst($profileIndex{$profileSet}) . " analysis of main strand finished.\n";   # Print finished type
+    } else {
+      print STDERR "    $now : " . ucfirst($profileIndex{$profileSet}) . " analysis of complementary strand finished.\n";   # Print finished type
+    }
+  }
+}
+
+
+## Please send beers, pizzas, cakes, fruit pies, job positions and other types of feedback to:
+## johan.bengtsson [at] microbiology.se
+## Looking forward to hearing from you.... visit my website: www.microbiology.se for info on my research
+## //Johan Bengtsson, 2012-2014

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ITSx.xml	Tue Mar 24 12:02:48 2015 -0400
@@ -0,0 +1,172 @@
+<tool id="ITSx" name="ITSx Extractor" version="1.0.6">
+
+  <description> 
+  ITSx -- Identifies ITS sequences and extracts the ITS region
+  </description>
+
+  <command interpreter="perl">
+  ITSx -i $input --detailed_results T --cpu $cpu $preserve $reset 
+  </command>
+  <requirements>
+	<requirement type="package" version="3.1b1">hmmer</requirement>
+  </requirements>
+  <inputs>
+	<param name="input" type="data" format="fasta" label="Input Fasta"/>
+	<param name="cpu" type="integer" value="1" label="cpu"/>
+	<param name="complement" type="boolean" checked="true" truevalue="--complement T" falsevalue="--complement F" label="Checks both DNA strands against the database"/>
+	<param name="heuristics" type="boolean" checked="false" truevalue="--heuristics T" falsevalue="--heuristics F" label="Use HMMER's heuristic filtering"/>
+	<param name="reset" type="boolean" checked="false" truevalue="--reset T" falsevalue="--reset F" label="Re-creates the HMM-database before ITSx is run"/>
+	<param name="preserve" type="boolean" checked="false" truevalue="--preserve T" falsevalue="--preserve F" label=" Preserve sequence headers instead of printing out ITSx headers"/>
+  </inputs>
+
+  <outputs>
+    <data name="ITS1" format="fasta" label="Extracted ITS1 Fasta File" from_work_dir="ITSx_out.ITS1.fasta"/>
+    <data name="ITS2" format="fasta" label="Extracted ITS2 Fasta File" from_work_dir="ITSx_out.ITS2.fasta"/>
+    <data name="fullfasta" format="fasta" label="Full Fasta of ITS extracted" from_work_dir="ITSx_out.full.fasta"/>
+    <data name="graph" format="txt" label="Graph of ITS regions" from_work_dir="ITSx_out.graph"/>
+    <data name="nodetect" format="fasta" label="No ITS region" from_work_dir="ITSx_out_no_detections.fasta"/>
+    <data name="positions" format="tabular" label="ITSx feature positions" from_work_dir="ITSx_out.positions.txt"/>
+    <data name="problematic" format="tabular" label="Problematic sequences" from_work_dir="ITSx_out.problematic.txt"/>
+    <data name="summary" format="txt" label="ITSx summary" from_work_dir="ITSx_out.summary.txt"/>
+    <data name="extractions" format="tabular" label="ITSx extraction results" from_work_dir="ITSx_out.extraction.results"/>
+  </outputs>
+
+  <stdio>
+        <regex match="ITSx" source="both" level="log"/>
+        <regex match="analysis" source="both" level="log"/>
+        <regex match="ERROR" source="both" level="fatal"/>
+        <regex match="error" source="both" level="fatal"/>
+  </stdio>
+
+  <test></test>
+  <help>
+ITSx -- Identifies ITS sequences and extracts the ITS region
+
+Source code available at:
+http://microbiology.se/software/itsx
+
+Version: 1.0.6
+ITSx -- Identifies ITS sequences and extracts the ITS region
+Copyright (C) 2012-2013 Johan Bengtsson-Palme et al.
+Contact: Johan Bengtsson-Palme, johan[at]microbiology.se
+Programmer: Johan Bengtsson-Palme
+
+Full installation instructions can be found in the User's Guide.
+A quick installation guide follows below.
+
+ITSx requires Perl and HMMER3.
+
+1) Perl is usually installed on Unix-like systems by default. If not, it can be retrieved from http://www.perl.org/
+
+2) HMMER3 can be found at http://hmmer.janelia.org/software
+Download it and follow the on site instructions for installation.
+
+3) Obtain the ITSx package from http://microbiology.se/software/itsx
+Unpack the tarball and move into the newly created "ITSx" directory.
+
+4) Copy the ITSx file and the ITSx_db directory to your preferred bin directory.
+
+5) To test if ITSx was successfully installed type "ITSx --help" on the command-line. You should now see the ITSx help message.
+
+To run ITSx, you need a FASTA-formatted output file. You can e.g. use the test.fasta file supplied with the package. To check for ITS sequences in the test file, type "ITSx -i test.fasta -o test" on the command line. If you are on a multicore machine, you might want to use the "--cpu 2" option to speed up the processes by using two (or more) cores.
+
+New features in this version:
+- Fixed a bug causing over-reporting of chimeras
+
+
+If you encounter a bug or some other strange behaviour, please report it to:
+johan[at]microbiology.se
+
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.You should have received a copy of the GNU General Public License along with this program, in a file called 'license.txt'. If not, see: http://www.gnu.org/licenses/.
+
+----
+
+Usage: ITSx -i [input file] -o [output file]
+
+Options:
+
+-i {file} : DNA FASTA input file to investigate
+
+-o {file} : Base for the names of output file(s)
+
+-p {directory} : A path to a directory of HMM-profile collections representing ITS conserved regions, default is in the same directory as ITSx itself
+
+--date {T or F} : Adds a date and time stamp to the output directory, off (F) by default
+
+--reset {T or F} : Re-creates the HMM-database before ITSx is run, off (F) by default
+
+Sequence selection options:
+
+-t {character code} : Profile set to use for the search, see the User's Guide (comma-separated), default is all
+
+-E {value} : Domain E-value cutoff for a sequence to be included in the output, default = 1e-5
+
+-S {value} : Domain score cutoff for a sequence to be included in the output, default = 0
+
+-N {value} : The minimal number of domains that must match a sequence before it is included, default = 2
+
+--selection_priority {sum, domains, eval, score} : Selects what will be of highest priority when determining the origin of the sequence, default is sum
+
+--search_eval {value} : The E-value cutoff used in the HMMER search, high numbers may slow down the process, cannot be used with the --search_score option, default is 0.01
+
+--search_score {value} : The score cutoff used in the HMMER search, low numbers may slow down the process, cannot be used with the --search_eval option, default is to used E-value cutoff, not score
+
+--allow_single_domain {e-value,score or F} : Allow inclusion of sequences that only find a single domain, given that they meet the given E-value and score thresholds, on with parameters 1e-9,0 by default
+
+--allow_reorder {T or F} : Allows profiles to be in the wrong order on extracted sequences, off (F) by default
+
+--complement {T or F} : Checks both DNA strands against the database, creating reverse complements, on (T) by default
+
+--cpu {value} : the number of CPU threads to use, default is 1
+
+--multi_thread {T or F} : Multi-thread the HMMER-search, on (T) if number of CPUs (--cpu option > 1), else off (F) by default
+
+--heuristics {T or F} : Selects whether to use HMMER's heuristic filtering, off (F) by default
+
+Output options:
+
+--summary {T or F} : Summary of results output, on (T) by default
+
+--graphical {T or F} : 'Graphical' output, on (T) by default
+
+--fasta {T or F} : FASTA-format output of extracted ITS sequences, on (T) by default
+
+--preserve {T or F} : Preserve sequence headers in input file instead of printing out ITSx headers, off (F) by default
+
+--save_regions {SSU,ITS1,5.8S,ITS2,LSU,all,none} : A comma separated list of regions to output separate FASTA files for, 'ITS1,ITS2' by default
+
+--anchor {integer or HMM} : Saves an additional number of bases before and after each extracted region. If set to 'HMM' all bases matching the corresponding HMM will be output, default = 0
+
+--partial {integer} : Saves additional FASTA-files for full and partial ITS sequences longer than the specified cutoff, default = 0 (off)
+
+--concat {T or F} : Saves a FASTA-file with concatenated ITS sequences (with 5.8S removed), off (F) by default
+
+--minlen {integer} : Minimum length the ITS regions must be to be outputted in the concatenated file (see above), default = 0
+
+--positions {T or F} : Table format output containing the positions ITS sequences were found in, on (T) by default
+
+--table {T or F} : Table format output of sequences containing probable ITS sequences, off (F) by default
+
+--not_found {T or F} : Saves a list of non-found entries, on (T) by default
+
+--detailed_results {T or F} : Saves a tab-separated list of all results, off (F) by default
+
+--truncate {T or F} : Truncates the FASTA output to only contain the actual ITS sequences found, on (T) by default
+
+--silent {T or F} : Supresses printing progress info to stderr, off (F) by default
+
+--graph_scale {value} : Sets the scale of the graph output, if value is zero, a percentage view is shown, default = 0
+
+--save_raw {T or F} : Saves all raw data for searches etc. instead of removing it on finish, off (F) by default
+
+-h : displays this help message
+
+--help : displays this help message
+
+--bugs : displays the bug fixes and known bugs in this version of ITSx
+
+--license : displays licensing information
+
+  </help>
+
+</tool>

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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ITSx_db/HMMs/A.hmm	Tue Mar 24 12:02:48 2015 -0400
@@ -0,0 +1,13640 @@
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_eighta_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:49 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 875354829
+STATS LOCAL MSV       -7.4772  0.72750
+STATS LOCAL VITERBI   -8.4131  0.72750
+STATS LOCAL FORWARD   -3.2493  0.72750
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.02810  1.19053  1.12475  1.42869
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.53331  3.02441  0.20344  2.88069      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.81865  0.23582  2.88868  2.35662      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.81865  0.23582  2.88868  2.35662      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.53331  3.02441  0.20344  2.88069      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.57915  2.25909  2.64442  0.28946      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   0.23862  2.84929  2.43386  2.70756      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.81865  0.23582  2.88868  2.35662     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.53331  3.02441  0.20344  2.88069     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.57915  2.25909  2.64442  0.28946     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.81865  0.23582  2.88868  2.35662     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.53331  3.02441  0.20344  2.88069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.81865  0.23582  2.88868  2.35662     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.57915  2.25909  2.64442  0.28946     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.81865  0.23582  2.88868  2.35662     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.81865  0.23582  2.88868  2.35662     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.53331  3.02441  0.20344  2.88069     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.81865  0.23582  2.88868  2.35662     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.57915  2.25909  2.64442  0.28946     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.53331  3.02441  0.20344  2.88069     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_eightb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:56 2012
+NSEQ  5
+EFFN  3.334961
+CKSUM 2194532692
+STATS LOCAL MSV       -8.0757  0.71931
+STATS LOCAL VITERBI   -7.9285  0.71931
+STATS LOCAL FORWARD   -3.6374  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.20861  1.12285  1.26075  1.26814
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01367  4.01367  1.46634  0.26236  0.00000        *
+      1   2.95026  3.59174  0.11672  3.49682      1 - -
+          1.38629  1.38629  1.38629  1.38629
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+     44   3.09257  2.59766  3.14057  0.17804     44 - -
+          1.38629  1.38629  1.38629  1.38629
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+     45   3.09257  2.59766  3.14057  0.17804     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01857  3.99544        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_eightc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:49:01 2012
+NSEQ  5
+EFFN  3.686523
+CKSUM 4049282212
+STATS LOCAL MSV       -7.6145  0.71933
+STATS LOCAL VITERBI   -7.6391  0.71933
+STATS LOCAL FORWARD   -3.8726  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.75248  1.41803  1.36097  1.11458
+          1.38629  1.38629  1.38629  1.38629
+          0.03457  4.07525  4.07525  1.46634  0.26236  0.00000        *
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+     43   3.02261  3.69787  0.10579  3.61425     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03457  4.07525  4.07525  1.46634  0.26236  1.09861  0.40547
+     44   0.12822  3.48998  2.87277  3.40223     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03457  4.07525  4.07525  1.46634  0.26236  1.09861  0.40547
+     45   3.20077  2.66632  3.24458  0.16161     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01743  4.05812        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_eightd_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:49:07 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 1872219876
+STATS LOCAL MSV       -7.3853  0.72989
+STATS LOCAL VITERBI   -8.4090  0.72989
+STATS LOCAL FORWARD   -3.4944  0.72989
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.71692  1.44276  1.18984  1.27355
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.81865  0.23582  2.88868  2.35662      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   0.23862  2.84929  2.43386  2.70756      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.53331  3.02441  0.20344  2.88069     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.57915  2.25909  2.64442  0.28946     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   0.23862  2.84929  2.43386  2.70756     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.57915  2.25909  2.64442  0.28946     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.81865  0.23582  2.88868  2.35662     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.57915  2.25909  2.64442  0.28946     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   1.88179  1.10717  1.04597  1.79675     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.57915  2.25909  2.64442  0.28946     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.15554  1.00938  2.23102  0.88601     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.15554  1.00938  2.23102  0.88601     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.53331  3.02441  0.20344  2.88069     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_elevena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:49:27 2012
+NSEQ  5
+EFFN  3.393555
+CKSUM 1575714051
+STATS LOCAL MSV       -7.4839  0.71934
+STATS LOCAL VITERBI   -7.6990  0.71934
+STATS LOCAL FORWARD   -4.2620  0.71934
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.55028  1.30282  1.33321  1.37666
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  0.00000        *
+      1   2.68973  1.71652  2.75247  0.37304      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      2   2.96311  3.61046  0.11471  3.51750      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      3   3.45893  0.12717  3.50729  2.84776      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      4   3.45893  0.12717  3.50729  2.84776      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      5   3.45893  0.12717  3.50729  2.84776      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      6   3.11130  2.60957  3.15859  0.17506      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      7   3.11130  2.60957  3.15859  0.17506      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      8   2.96311  3.61046  0.11471  3.51750      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+      9   2.96311  3.61046  0.11471  3.51750      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     10   2.96311  3.61046  0.11471  3.51750     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     11   3.45893  0.12717  3.50729  2.84776     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     12   3.45893  0.12717  3.50729  2.84776     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     13   0.13897  3.40269  2.81647  3.30648     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     14   3.45893  0.12717  3.50729  2.84776     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     15   3.11130  2.60957  3.15859  0.17506     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     16   3.45893  0.12717  3.50729  2.84776     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     17   3.45893  0.12717  3.50729  2.84776     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     18   3.45893  0.12717  3.50729  2.84776     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     19   0.13897  3.40269  2.81647  3.30648     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     20   0.13897  3.40269  2.81647  3.30648     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     21   3.11130  2.60957  3.15859  0.17506     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     22   2.96311  3.61046  0.11471  3.51750     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     23   2.96311  3.61046  0.11471  3.51750     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     24   3.11130  2.60957  3.15859  0.17506     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     25   2.37392  1.92307  0.39398  2.44920     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     26   3.11130  2.60957  3.15859  0.17506     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     27   2.96311  3.61046  0.11471  3.51750     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     28   3.45893  0.12717  3.50729  2.84776     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     29   3.11130  2.60957  3.15859  0.17506     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     30   2.96311  3.61046  0.11471  3.51750     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     31   3.45893  0.12717  3.50729  2.84776     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     32   0.13897  3.40269  2.81647  3.30648     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     33   3.11130  2.60957  3.15859  0.17506     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     34   3.11130  2.60957  3.15859  0.17506     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     35   3.11130  2.60957  3.15859  0.17506     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     36   2.96311  3.61046  0.11471  3.51750     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     37   0.13897  3.40269  2.81647  3.30648     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     38   0.13897  3.40269  2.81647  3.30648     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     39   0.13897  3.40269  2.81647  3.30648     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     40   3.45893  0.12717  3.50729  2.84776     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     41   0.13897  3.40269  2.81647  3.30648     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     42   2.96311  3.61046  0.11471  3.51750     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     43   0.13897  3.40269  2.81647  3.30648     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     44   3.11130  2.60957  3.15859  0.17506     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03641  4.02420  4.02420  1.46634  0.26236  1.09861  0.40547
+     45   2.96311  3.61046  0.11471  3.51750     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01837  4.00616        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_elevenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:49:36 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 1545265678
+STATS LOCAL MSV       -7.4771  0.72838
+STATS LOCAL VITERBI   -8.1550  0.72838
+STATS LOCAL FORWARD   -3.6556  0.72838
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.43027  1.45972  1.24052  1.43038
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.57915  2.25909  2.64442  0.28946      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.81865  0.23582  2.88868  2.35662      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.81865  0.23582  2.88868  2.35662     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.53331  3.02441  0.20344  2.88069     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.57915  2.25909  2.64442  0.28946     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   0.23862  2.84929  2.43386  2.70756     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.57915  2.25909  2.64442  0.28946     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.53331  3.02441  0.20344  2.88069     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.81865  0.23582  2.88868  2.35662     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   0.23862  2.84929  2.43386  2.70756     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   0.23862  2.84929  2.43386  2.70756     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.57915  2.25909  2.64442  0.28946     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.92825  2.28391  0.95698  2.13014     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   0.23862  2.84929  2.43386  2.70756     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.81865  0.23582  2.88868  2.35662     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   0.23862  2.84929  2.43386  2.70756     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.53331  3.02441  0.20344  2.88069     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.57915  2.25909  2.64442  0.28946     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.53331  3.02441  0.20344  2.88069     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.81865  0.23582  2.88868  2.35662     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fifteena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:25 2012
+NSEQ  25
+EFFN  3.335571
+CKSUM 500672324
+STATS LOCAL MSV       -7.9016  0.71932
+STATS LOCAL VITERBI   -7.7396  0.71932
+STATS LOCAL FORWARD   -4.0992  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.72722  1.31020  1.32957  1.24527
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  0.00000        *
+      1   3.09277  2.59779  3.14076  0.17801      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      2   2.95040  3.59193  0.11670  3.49704      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      3   2.95040  3.59193  0.11670  3.49704      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      4   3.43785  0.12964  3.48711  2.83245      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      5   2.95040  3.59193  0.11670  3.49704      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      6   3.43785  0.12964  3.48711  2.83245      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      7   3.09277  2.59779  3.14076  0.17801      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      8   2.54795  2.32143  0.27713  2.72309      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+      9   3.09277  2.59779  3.14076  0.17801      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     10   3.09277  2.59779  3.14076  0.17801     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     11   2.95040  3.59193  0.11670  3.49704     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     12   2.95040  3.59193  0.11670  3.49704     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     13   2.95040  3.59193  0.11670  3.49704     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     14   0.14135  3.38438  2.80460  3.28643     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     15   3.43785  0.12964  3.48711  2.83245     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     16   3.09277  2.59779  3.14076  0.17801     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     17   0.14135  3.38438  2.80460  3.28643     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     18   3.43785  0.12964  3.48711  2.83245     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     19   3.43785  0.12964  3.48711  2.83245     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     20   3.43785  0.12964  3.48711  2.83245     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     21   0.14135  3.38438  2.80460  3.28643     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     22   0.14135  3.38438  2.80460  3.28643     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     23   3.43785  0.12964  3.48711  2.83245     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     24   0.14135  3.38438  2.80460  3.28643     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     25   2.95040  3.59193  0.11670  3.49704     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     26   3.43785  0.12964  3.48711  2.83245     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     27   0.14135  3.38438  2.80460  3.28643     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     28   3.43785  0.12964  3.48711  2.83245     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     29   2.95040  3.59193  0.11670  3.49704     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     30   3.09277  2.59779  3.14076  0.17801     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     31   3.43785  0.12964  3.48711  2.83245     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     32   3.09277  2.59779  3.14076  0.17801     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     33   2.95040  3.59193  0.11670  3.49704     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     34   3.09277  2.59779  3.14076  0.17801     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     35   3.09277  2.59779  3.14076  0.17801     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     36   3.09277  2.59779  3.14076  0.17801     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     37   3.43785  0.12964  3.48711  2.83245     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     38   0.14135  3.38438  2.80460  3.28643     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     39   2.95040  3.59193  0.11670  3.49704     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     40   3.09277  2.59779  3.14076  0.17801     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     41   2.95040  3.59193  0.11670  3.49704     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     42   3.09277  2.59779  3.14076  0.17801     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     43   3.43785  0.12964  3.48711  2.83245     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     44   3.09277  2.59779  3.14076  0.17801     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01378  4.01378  1.46634  0.26236  1.09861  0.40547
+     45   3.09277  2.59779  3.14076  0.17801     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01857  3.99555        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fifteenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:32 2012
+NSEQ  16
+EFFN  3.605469
+CKSUM 2100785171
+STATS LOCAL MSV       -7.3453  0.71933
+STATS LOCAL VITERBI   -7.7419  0.71933
+STATS LOCAL FORWARD   -4.2360  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.83616  1.45443  1.24425  1.14294
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  0.00000        *
+      1   3.17670  2.65106  3.22145  0.16511      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      2   3.00689  3.67468  0.10808  3.58855      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      3   3.00689  3.67468  0.10808  3.58855      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      4   3.53238  0.11897  3.57752  2.90072      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      5   3.00689  3.67468  0.10808  3.58855      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      6   3.53238  0.11897  3.57752  2.90072      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      7   3.17670  2.65106  3.22145  0.16511      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      8   3.00689  3.67468  0.10808  3.58855      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+      9   3.17670  2.65106  3.22145  0.16511      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     10   3.17670  2.65106  3.22145  0.16511     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     11   3.00689  3.67468  0.10808  3.58855     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     12   3.00689  3.67468  0.10808  3.58855     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     13   3.00689  3.67468  0.10808  3.58855     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     14   0.13100  3.46667  2.85777  3.37664     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     15   3.17670  2.65106  3.22145  0.16511     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     16   3.17670  2.65106  3.22145  0.16511     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     17   0.13100  3.46667  2.85777  3.37664     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     18   2.46082  0.82174  2.53269  0.92754     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     19   3.53238  0.11897  3.57752  2.90072     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     20   2.46082  0.82174  2.53269  0.92754     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     21   3.00689  3.67468  0.10808  3.58855     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     22   0.24265  3.10343  2.11836  2.98922     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     23   3.53238  0.11897  3.57752  2.90072     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     24   0.13100  3.46667  2.85777  3.37664     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     25   3.00689  3.67468  0.10808  3.58855     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     26   3.53238  0.11897  3.57752  2.90072     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     27   0.13100  3.46667  2.85777  3.37664     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     28   3.53238  0.11897  3.57752  2.90072     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     29   3.00689  3.67468  0.10808  3.58855     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     30   3.17670  2.65106  3.22145  0.16511     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     31   3.53238  0.11897  3.57752  2.90072     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     32   3.17670  2.65106  3.22145  0.16511     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     33   3.00689  3.67468  0.10808  3.58855     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     34   3.17670  2.65106  3.22145  0.16511     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     35   3.17670  2.65106  3.22145  0.16511     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     36   3.17670  2.65106  3.22145  0.16511     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     37   3.53238  0.11897  3.57752  2.90072     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     38   0.13100  3.46667  2.85777  3.37664     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     39   3.00689  3.67468  0.10808  3.58855     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     40   3.17670  2.65106  3.22145  0.16511     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     41   3.00689  3.67468  0.10808  3.58855     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     42   3.17670  2.65106  3.22145  0.16511     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     43   3.53238  0.11897  3.57752  2.90072     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     44   3.17670  2.65106  3.22145  0.16511     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03506  4.06139  4.06139  1.46634  0.26236  1.09861  0.40547
+     45   3.17670  2.65106  3.22145  0.16511     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01768  4.04401        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fifteenc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:38 2012
+NSEQ  6
+EFFN  3.237305
+CKSUM 442242702
+STATS LOCAL MSV       -8.0313  0.71932
+STATS LOCAL VITERBI   -7.8597  0.71932
+STATS LOCAL FORWARD   -3.7770  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.05939  1.25473  1.20217  1.24906
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  0.00000        *
+      1   3.06071  2.57738  3.10992  0.18324      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      2   2.92809  3.55954  0.12029  3.46131      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      3   2.92809  3.55954  0.12029  3.46131      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      4   3.40113  0.13409  3.45193  2.80566      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      5   2.92809  3.55954  0.12029  3.46131      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      6   3.40113  0.13409  3.45193  2.80566      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      7   3.40113  0.13409  3.45193  2.80566      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      8   2.92809  3.55954  0.12029  3.46131      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+      9   3.40113  0.13409  3.45193  2.80566      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     10   3.06071  2.57738  3.10992  0.18324     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     11   2.92809  3.55954  0.12029  3.46131     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     12   2.92809  3.55954  0.12029  3.46131     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     13   2.92809  3.55954  0.12029  3.46131     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     14   0.14561  3.35254  2.78388  3.25159     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     15   3.06071  2.57738  3.10992  0.18324     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     16   3.06071  2.57738  3.10992  0.18324     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     17   3.06071  2.57738  3.10992  0.18324     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     18   3.40113  0.13409  3.45193  2.80566     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     19   3.40113  0.13409  3.45193  2.80566     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     20   3.40113  0.13409  3.45193  2.80566     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     21   2.92809  3.55954  0.12029  3.46131     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     22   2.92809  3.55954  0.12029  3.46131     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     23   3.40113  0.13409  3.45193  2.80566     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     24   0.14561  3.35254  2.78388  3.25159     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     25   2.92809  3.55954  0.12029  3.46131     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     26   3.40113  0.13409  3.45193  2.80566     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     27   0.14561  3.35254  2.78388  3.25159     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     28   3.40113  0.13409  3.45193  2.80566     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     29   2.92809  3.55954  0.12029  3.46131     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     30   3.06071  2.57738  3.10992  0.18324     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     31   3.40113  0.13409  3.45193  2.80566     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     32   3.06071  2.57738  3.10992  0.18324     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     33   2.92809  3.55954  0.12029  3.46131     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     34   3.06071  2.57738  3.10992  0.18324     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     35   3.06071  2.57738  3.10992  0.18324     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     36   3.06071  2.57738  3.10992  0.18324     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     37   3.40113  0.13409  3.45193  2.80566     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     38   0.14561  3.35254  2.78388  3.25159     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     39   2.92809  3.55954  0.12029  3.46131     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     40   3.06071  2.57738  3.10992  0.18324     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     41   2.92809  3.55954  0.12029  3.46131     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     42   3.06071  2.57738  3.10992  0.18324     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     43   3.40113  0.13409  3.45193  2.80566     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     44   3.06071  2.57738  3.10992  0.18324     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03748  3.99587  3.99587  1.46634  0.26236  1.09861  0.40547
+     45   3.06071  2.57738  3.10992  0.18324     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01891  3.97731        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fifteend_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:44 2012
+NSEQ  7
+EFFN  3.298340
+CKSUM 2869266091
+STATS LOCAL MSV       -8.1459  0.71931
+STATS LOCAL VITERBI   -7.9055  0.71931
+STATS LOCAL FORWARD   -3.8325  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.06625  1.24709  1.32281  1.14065
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  0.00000        *
+      1   2.94206  3.57981  0.11803  3.48366      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      2   2.94206  3.57981  0.11803  3.48366      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      3   3.42409  0.13129  3.47393  2.82243      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      4   2.94206  3.57981  0.11803  3.48366      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      5   3.42409  0.13129  3.47393  2.82243      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      6   3.08072  2.59012  3.12917  0.17995      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      7   3.08072  2.59012  3.12917  0.17995      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      8   3.42409  0.13129  3.47393  2.82243      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+      9   3.08072  2.59012  3.12917  0.17995      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     10   2.94206  3.57981  0.11803  3.48366     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     11   2.94206  3.57981  0.11803  3.48366     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     12   2.94206  3.57981  0.11803  3.48366     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     13   0.14293  3.37244  2.79684  3.27336     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     14   3.08072  2.59012  3.12917  0.17995     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     15   3.08072  2.59012  3.12917  0.17995     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     16   3.08072  2.59012  3.12917  0.17995     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     17   3.08072  2.59012  3.12917  0.17995     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     18   3.42409  0.13129  3.47393  2.82243     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     19   3.42409  0.13129  3.47393  2.82243     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     20   3.42409  0.13129  3.47393  2.82243     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     21   3.42409  0.13129  3.47393  2.82243     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     22   2.94206  3.57981  0.11803  3.48366     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     23   3.08072  2.59012  3.12917  0.17995     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     24   0.14293  3.37244  2.79684  3.27336     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     25   2.94206  3.57981  0.11803  3.48366     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     26   3.42409  0.13129  3.47393  2.82243     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     27   0.14293  3.37244  2.79684  3.27336     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     28   3.42409  0.13129  3.47393  2.82243     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     29   2.94206  3.57981  0.11803  3.48366     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     30   3.08072  2.59012  3.12917  0.17995     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     31   3.42409  0.13129  3.47393  2.82243     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     32   3.08072  2.59012  3.12917  0.17995     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     33   2.94206  3.57981  0.11803  3.48366     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     34   3.08072  2.59012  3.12917  0.17995     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     35   3.08072  2.59012  3.12917  0.17995     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     36   3.08072  2.59012  3.12917  0.17995     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     37   3.42409  0.13129  3.47393  2.82243     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     38   0.14293  3.37244  2.79684  3.27336     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     39   2.94206  3.57981  0.11803  3.48366     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     40   3.08072  2.59012  3.12917  0.17995     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     41   2.94206  3.57981  0.11803  3.48366     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     42   3.08072  2.59012  3.12917  0.17995     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     43   3.42409  0.13129  3.47393  2.82243     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     44   3.08072  2.59012  3.12917  0.17995     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03705  4.00703  4.00703  1.46634  0.26236  1.09861  0.40547
+     45   3.42409  0.13129  3.47393  2.82243     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01870  3.98868        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fifteene_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:49 2012
+NSEQ  14
+EFFN  3.612793
+CKSUM 3599068610
+STATS LOCAL MSV       -7.2495  0.71932
+STATS LOCAL VITERBI   -7.7818  0.71932
+STATS LOCAL FORWARD   -3.9403  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   2.01810  1.29360  1.24959  1.18356
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  0.00000        *
+      1   3.17890  2.65245  3.22356  0.16478      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      2   3.00833  3.67681  0.10787  3.59090      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      3   3.00833  3.67681  0.10787  3.59090      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      4   3.53482  0.11871  3.57985  2.90247      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      5   3.00833  3.67681  0.10787  3.59090      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      6   3.53482  0.11871  3.57985  2.90247      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      7   3.17890  2.65245  3.22356  0.16478      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      8   3.00833  3.67681  0.10787  3.59090      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      9   3.53482  0.11871  3.57985  2.90247      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     10   0.90681  1.49378  2.06689  1.40614     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     11   3.00833  3.67681  0.10787  3.59090     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     12   3.00833  3.67681  0.10787  3.59090     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     13   3.00833  3.67681  0.10787  3.59090     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     14   0.13074  3.46880  2.85915  3.37898     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     15   2.82437  1.87604  2.88303  0.31267     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     16   3.17890  2.65245  3.22356  0.16478     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     17   3.17890  2.65245  3.22356  0.16478     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     18   3.53482  0.11871  3.57985  2.90247     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     19   2.99789  0.26576  3.06012  1.99066     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     20   3.53482  0.11871  3.57985  2.90247     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     21   3.17890  2.65245  3.22356  0.16478     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     22   3.00833  3.67681  0.10787  3.59090     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     23   3.53482  0.11871  3.57985  2.90247     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     24   0.13074  3.46880  2.85915  3.37898     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     25   3.00833  3.67681  0.10787  3.59090     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     26   3.53482  0.11871  3.57985  2.90247     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     27   0.13074  3.46880  2.85915  3.37898     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     28   3.53482  0.11871  3.57985  2.90247     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     29   3.00833  3.67681  0.10787  3.59090     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     30   3.17890  2.65245  3.22356  0.16478     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     31   3.53482  0.11871  3.57985  2.90247     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     32   3.17890  2.65245  3.22356  0.16478     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     33   3.00833  3.67681  0.10787  3.59090     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     34   3.17890  2.65245  3.22356  0.16478     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     35   3.17890  2.65245  3.22356  0.16478     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     36   3.17890  2.65245  3.22356  0.16478     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     37   3.53482  0.11871  3.57985  2.90247     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     38   0.13074  3.46880  2.85915  3.37898     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     39   3.00833  3.67681  0.10787  3.59090     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     40   3.17890  2.65245  3.22356  0.16478     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     41   3.00833  3.67681  0.10787  3.59090     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     42   3.17890  2.65245  3.22356  0.16478     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     43   3.53482  0.11871  3.57985  2.90247     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     44   3.17890  2.65245  3.22356  0.16478     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     45   2.82437  1.87604  2.88303  0.31267     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01766  4.04529        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fifteenf_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:55 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 4191745197
+STATS LOCAL MSV       -8.0134  0.72148
+STATS LOCAL VITERBI   -7.9970  0.72148
+STATS LOCAL FORWARD   -3.9305  0.72148
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.88034  1.41850  1.31106  1.09109
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   2.86982  3.47591  0.13017  3.36931      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   2.86982  3.47591  0.13017  3.36931      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   3.30705  0.14631  3.36166  2.73626      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   0.15719  3.27118  2.73043  3.16274      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   3.30705  0.14631  3.36166  2.73626      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   3.30705  0.14631  3.36166  2.73626      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   1.30792  2.11152  2.18422  0.70118      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   2.97980  2.52563  3.03204  0.19727      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   2.86982  3.47591  0.13017  3.36931     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   2.86982  3.47591  0.13017  3.36931     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   0.15719  3.27118  2.73043  3.16274     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.97980  2.52563  3.03204  0.19727     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   0.15719  3.27118  2.73043  3.16274     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   2.42752  1.34012  2.49742  0.56628     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   2.97980  2.52563  3.03204  0.19727     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   3.30705  0.14631  3.36166  2.73626     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.97980  2.52563  3.03204  0.19727     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   3.30705  0.14631  3.36166  2.73626     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   3.30705  0.14631  3.36166  2.73626     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   2.97980  2.52563  3.03204  0.19727     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.97980  2.52563  3.03204  0.19727     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   2.86982  3.47591  0.13017  3.36931     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   2.86982  3.47591  0.13017  3.36931     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   0.15719  3.27118  2.73043  3.16274     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   3.30705  0.14631  3.36166  2.73626     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   2.86982  3.47591  0.13017  3.36931     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.97980  2.52563  3.03204  0.19727     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   3.30705  0.14631  3.36166  2.73626     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   2.97980  2.52563  3.03204  0.19727     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.86982  3.47591  0.13017  3.36931     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   2.97980  2.52563  3.03204  0.19727     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   2.97980  2.52563  3.03204  0.19727     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   3.30705  0.14631  3.36166  2.73626     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   0.15719  3.27118  2.73043  3.16274     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.97980  2.52563  3.03204  0.19727     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   2.86982  3.47591  0.13017  3.36931     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.97980  2.52563  3.03204  0.19727     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   3.30705  0.14631  3.36166  2.73626     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.97980  2.52563  3.03204  0.19727     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.97980  2.52563  3.03204  0.19727     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fivea_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:57 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 630474797
+STATS LOCAL MSV       -7.1031  0.72876
+STATS LOCAL VITERBI   -8.2897  0.72876
+STATS LOCAL FORWARD   -3.3234  0.72876
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.65817  1.49734  1.37580  1.09916
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.81865  0.23582  2.88868  2.35662      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.57915  2.25909  2.64442  0.28946      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.53331  3.02441  0.20344  2.88069     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.81865  0.23582  2.88868  2.35662     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.57915  2.25909  2.64442  0.28946     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.53331  3.02441  0.20344  2.88069     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.57915  2.25909  2.64442  0.28946     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.57915  2.25909  2.64442  0.28946     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.81865  0.23582  2.88868  2.35662     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.57915  2.25909  2.64442  0.28946     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fiveb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:04 2012
+NSEQ  9
+EFFN  3.361816
+CKSUM 2438455031
+STATS LOCAL MSV       -8.0408  0.71932
+STATS LOCAL VITERBI   -7.6304  0.71932
+STATS LOCAL FORWARD   -4.1626  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.73808  1.37131  1.38409  1.14001
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  0.00000        *
+      1   3.44745  0.12851  3.49630  2.83942      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      2   0.24046  3.06994  2.16140  2.95373      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      3   3.44745  0.12851  3.49630  2.83942      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      4   3.10119  2.60314  3.14886  0.17666      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      5   3.44745  0.12851  3.49630  2.83942      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      6   3.10119  2.60314  3.14886  0.17666      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      7   3.10119  2.60314  3.14886  0.17666      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      8   2.95619  3.60037  0.11579  3.50635      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+      9   2.95619  3.60037  0.11579  3.50635      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     10   2.95619  3.60037  0.11579  3.50635     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     11   0.14026  3.39271  2.81000  3.29556     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     12   3.44745  0.12851  3.49630  2.83942     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     13   0.14026  3.39271  2.81000  3.29556     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     14   3.44745  0.12851  3.49630  2.83942     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     15   2.95619  3.60037  0.11579  3.50635     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     16   3.44745  0.12851  3.49630  2.83942     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     17   3.44745  0.12851  3.49630  2.83942     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     18   3.10119  2.60314  3.14886  0.17666     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     19   2.95619  3.60037  0.11579  3.50635     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     20   0.14026  3.39271  2.81000  3.29556     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     21   2.95619  3.60037  0.11579  3.50635     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     22   0.14026  3.39271  2.81000  3.29556     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     23   2.95619  3.60037  0.11579  3.50635     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     24   3.10119  2.60314  3.14886  0.17666     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     25   0.14026  3.39271  2.81000  3.29556     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     26   3.10119  2.60314  3.14886  0.17666     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     27   2.95619  3.60037  0.11579  3.50635     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     28   3.10119  2.60314  3.14886  0.17666     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     29   3.44745  0.12851  3.49630  2.83942     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     30   3.10119  2.60314  3.14886  0.17666     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     31   2.95619  3.60037  0.11579  3.50635     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     32   3.44745  0.12851  3.49630  2.83942     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     33   3.10119  2.60314  3.14886  0.17666     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     34   3.10119  2.60314  3.14886  0.17666     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     35   3.44745  0.12851  3.49630  2.83942     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     36   0.14026  3.39271  2.81000  3.29556     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     37   2.95619  3.60037  0.11579  3.50635     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     38   3.10119  2.60314  3.14886  0.17666     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     39   2.95619  3.60037  0.11579  3.50635     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     40   3.44745  0.12851  3.49630  2.83942     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     41   3.10119  2.60314  3.14886  0.17666     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     42   3.10119  2.60314  3.14886  0.17666     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     43   3.10119  2.60314  3.14886  0.17666     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     44   3.10119  2.60314  3.14886  0.17666     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03662  4.01851  4.01851  1.46634  0.26236  1.09861  0.40547
+     45   3.10119  2.60314  3.14886  0.17666     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01848  4.00037        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_foura_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:28 2012
+NSEQ  8
+EFFN  3.347656
+CKSUM 1565564952
+STATS LOCAL MSV       -8.1688  0.71931
+STATS LOCAL VITERBI   -7.7321  0.71931
+STATS LOCAL FORWARD   -4.0847  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.72680  1.38541  1.31835  1.18958
+          1.38629  1.38629  1.38629  1.38629
+          0.03672  4.01596  4.01596  1.46634  0.26236  0.00000        *
+      1   3.44228  0.12912  3.49135  2.83567      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03672  4.01596  4.01596  1.46634  0.26236  1.09861  0.40547
+      2   2.95307  3.59583  0.11628  3.50134      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03672  4.01596  4.01596  1.46634  0.26236  1.09861  0.40547
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+     44   3.09665  2.60026  3.14450  0.17739     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03672  4.01596  4.01596  1.46634  0.26236  1.09861  0.40547
+     45   0.14085  3.38823  2.80709  3.29064     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01853  3.99777        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fourb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:35 2012
+NSEQ  14
+EFFN  3.325684
+CKSUM 2052394201
+STATS LOCAL MSV       -8.1103  0.71933
+STATS LOCAL VITERBI   -7.7143  0.71933
+STATS LOCAL FORWARD   -3.9821  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.63564  1.44468  1.38366  1.14353
+          1.38629  1.38629  1.38629  1.38629
+          0.03687  4.01199  4.01199  1.46634  0.26236  0.00000        *
+      1   2.94820  3.58873  0.11705  3.49350      1 - -
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+      2   3.43422  0.13008  3.48363  2.82980      2 - -
+          1.38629  1.38629  1.38629  1.38629
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+      3   0.14177  3.38122  2.80255  3.28298      3 - -
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+      4   3.43422  0.13008  3.48363  2.82980      4 - -
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+     44   0.14177  3.38122  2.80255  3.28298     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03687  4.01199  4.01199  1.46634  0.26236  1.09861  0.40547
+     45   3.43422  0.13008  3.48363  2.82980     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01860  3.99373        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fourc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:41 2012
+NSEQ  7
+EFFN  3.612793
+CKSUM 277781406
+STATS LOCAL MSV       -7.4130  0.71933
+STATS LOCAL VITERBI   -7.7029  0.71933
+STATS LOCAL FORWARD   -3.9206  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.78948  1.40356  1.28233  1.17168
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  0.00000        *
+      1   3.00833  3.67681  0.10787  3.59090      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      2   3.53482  0.11871  3.57985  2.90247      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      3   0.13074  3.46880  2.85915  3.37898      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      4   3.53482  0.11871  3.57985  2.90247      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      5   2.83792  1.90216  2.89608  0.30521      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      6   3.53482  0.11871  3.57985  2.90247      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      7   3.17890  2.65245  3.22356  0.16478      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      8   2.46560  0.79961  2.53748  0.95069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+      9   3.00833  3.67681  0.10787  3.59090      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     10   3.00833  3.67681  0.10787  3.59090     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     11   3.00833  3.67681  0.10787  3.59090     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     12   1.03144  2.58673  0.73117  2.44303     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     13   3.17890  2.65245  3.22356  0.16478     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     14   3.17890  2.65245  3.22356  0.16478     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     15   3.17890  2.65245  3.22356  0.16478     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     16   3.53482  0.11871  3.57985  2.90247     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     17   3.53482  0.11871  3.57985  2.90247     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     18   3.17890  2.65245  3.22356  0.16478     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     19   3.00833  3.67681  0.10787  3.59090     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     20   0.13074  3.46880  2.85915  3.37898     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     21   3.00833  3.67681  0.10787  3.59090     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     22   0.13074  3.46880  2.85915  3.37898     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     23   3.00833  3.67681  0.10787  3.59090     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     24   3.17890  2.65245  3.22356  0.16478     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     25   0.13074  3.46880  2.85915  3.37898     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     26   3.17890  2.65245  3.22356  0.16478     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     27   3.00833  3.67681  0.10787  3.59090     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     28   3.17890  2.65245  3.22356  0.16478     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     29   3.53482  0.11871  3.57985  2.90247     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     30   3.17890  2.65245  3.22356  0.16478     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     31   3.00833  3.67681  0.10787  3.59090     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     32   3.53482  0.11871  3.57985  2.90247     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     33   3.17890  2.65245  3.22356  0.16478     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     34   3.17890  2.65245  3.22356  0.16478     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     35   3.53482  0.11871  3.57985  2.90247     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     36   0.13074  3.46880  2.85915  3.37898     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     37   3.00833  3.67681  0.10787  3.59090     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     38   3.17890  2.65245  3.22356  0.16478     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     39   3.00833  3.67681  0.10787  3.59090     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     40   3.53482  0.11871  3.57985  2.90247     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     41   3.17890  2.65245  3.22356  0.16478     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     42   3.17890  2.65245  3.22356  0.16478     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     43   0.13074  3.46880  2.85915  3.37898     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     44   3.00833  3.67681  0.10787  3.59090     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06265  4.06265  1.46634  0.26236  1.09861  0.40547
+     45   3.53482  0.11871  3.57985  2.90247     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01766  4.04529        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fourd_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:47 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 945311865
+STATS LOCAL MSV       -8.1412  0.72023
+STATS LOCAL VITERBI   -7.6990  0.72023
+STATS LOCAL FORWARD   -3.8381  0.72023
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.81287  1.32079  1.20046  1.31365
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   2.86982  3.47591  0.13017  3.36931      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   3.30705  0.14631  3.36166  2.73626      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   2.86982  3.47591  0.13017  3.36931      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   3.30705  0.14631  3.36166  2.73626      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   2.97980  2.52563  3.03204  0.19727      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   3.30705  0.14631  3.36166  2.73626      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.97980  2.52563  3.03204  0.19727      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   3.30705  0.14631  3.36166  2.73626      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   2.86982  3.47591  0.13017  3.36931     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   0.15719  3.27118  2.73043  3.16274     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   2.97980  2.52563  3.03204  0.19727     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.97980  2.52563  3.03204  0.19727     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   2.97980  2.52563  3.03204  0.19727     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   3.30705  0.14631  3.36166  2.73626     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   3.30705  0.14631  3.36166  2.73626     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.97980  2.52563  3.03204  0.19727     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   0.15719  3.27118  2.73043  3.16274     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   2.86982  3.47591  0.13017  3.36931     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   0.15719  3.27118  2.73043  3.16274     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.86982  3.47591  0.13017  3.36931     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   3.30705  0.14631  3.36166  2.73626     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.86982  3.47591  0.13017  3.36931     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   2.86982  3.47591  0.13017  3.36931     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   2.97980  2.52563  3.03204  0.19727     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   3.30705  0.14631  3.36166  2.73626     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.97980  2.52563  3.03204  0.19727     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   2.86982  3.47591  0.13017  3.36931     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   3.30705  0.14631  3.36166  2.73626     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.97980  2.52563  3.03204  0.19727     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   3.30705  0.14631  3.36166  2.73626     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   0.15719  3.27118  2.73043  3.16274     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.86982  3.47591  0.13017  3.36931     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.97980  2.52563  3.03204  0.19727     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   3.30705  0.14631  3.36166  2.73626     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   2.97980  2.52563  3.03204  0.19727     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.97980  2.52563  3.03204  0.19727     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   0.15719  3.27118  2.73043  3.16274     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.86982  3.47591  0.13017  3.36931     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   3.30705  0.14631  3.36166  2.73626     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_fourteen_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:14 2012
+NSEQ  19
+EFFN  3.975342
+CKSUM 4093622679
+STATS LOCAL MSV       -7.2188  0.71932
+STATS LOCAL VITERBI   -7.4754  0.71932
+STATS LOCAL FORWARD   -4.0594  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.44172  1.86242  1.47496  0.96917
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  0.00000        *
+      1   0.11939  3.56822  2.92300  3.48820      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      2   0.11939  3.56822  2.92300  3.48820      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      3   3.07459  3.77484  0.09858  3.69966      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      4   3.07459  3.77484  0.09858  3.69966      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      5   3.28256  2.71819  3.32315  0.15032      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      6   0.11939  3.56822  2.92300  3.48820      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      7   3.64801  0.10726  3.68789  2.98308      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      8   3.28256  2.71819  3.32315  0.15032      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+      9   3.28256  2.71819  3.32315  0.15032      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     10   3.64801  0.10726  3.68789  2.98308     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     11   3.28256  2.71819  3.32315  0.15032     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     12   0.11939  3.56822  2.92300  3.48820     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     13   0.11939  3.56822  2.92300  3.48820     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     14   0.11939  3.56822  2.92300  3.48820     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     15   3.28256  2.71819  3.32315  0.15032     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     16   3.28256  2.71819  3.32315  0.15032     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     17   1.36120  0.63933  2.33750  2.12501     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     18   3.28256  2.71819  3.32315  0.15032     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     19   3.07459  3.77484  0.09858  3.69966     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     20   3.07459  3.77484  0.09858  3.69966     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     21   3.07459  3.77484  0.09858  3.69966     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     22   0.11939  3.56822  2.92300  3.48820     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     23   3.07459  3.77484  0.09858  3.69966     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     24   3.28256  2.71819  3.32315  0.15032     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     25   0.11939  3.56822  2.92300  3.48820     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     26   3.28256  2.71819  3.32315  0.15032     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     27   3.07459  3.77484  0.09858  3.69966     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     28   3.28256  2.71819  3.32315  0.15032     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     29   3.28256  2.71819  3.32315  0.15032     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     30   3.28256  2.71819  3.32315  0.15032     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     31   0.11939  3.56822  2.92300  3.48820     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     32   2.20880  2.30847  0.72114  1.18890     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     33   3.28256  2.71819  3.32315  0.15032     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     34   3.28256  2.71819  3.32315  0.15032     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     35   3.64801  0.10726  3.68789  2.98308     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     36   0.11939  3.56822  2.92300  3.48820     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     37   3.07459  3.77484  0.09858  3.69966     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     38   3.28256  2.71819  3.32315  0.15032     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     39   3.07459  3.77484  0.09858  3.69966     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     40   3.64801  0.10726  3.68789  2.98308     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     41   3.28256  2.71819  3.32315  0.15032     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     42   3.28256  2.71819  3.32315  0.15032     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     43   2.57102  2.40862  1.92099  0.37522     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     44   3.28256  2.71819  3.32315  0.15032     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03292  4.12315  4.12315  1.46634  0.26236  1.09861  0.40547
+     45   2.86994  0.35159  2.93552  1.67865     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01660  4.10682        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_nine_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:49:16 2012
+NSEQ  4
+EFFN  3.660156
+CKSUM 2693919103
+STATS LOCAL MSV       -7.6646  0.71933
+STATS LOCAL VITERBI   -7.7506  0.71933
+STATS LOCAL FORWARD   -4.2563  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.41247  1.34559  1.34393  1.44710
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  0.00000        *
+      1   3.01755  3.69041  0.10652  3.60597      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      2   3.19300  2.66139  3.23711  0.16273      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      3   0.12911  3.48247  2.86794  3.39398      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      4   0.12911  3.48247  2.86794  3.39398      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      5   3.55045  0.11705  3.59478  2.91367      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      6   3.19300  2.66139  3.23711  0.16273      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      7   0.12911  3.48247  2.86794  3.39398      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      8   0.12911  3.48247  2.86794  3.39398      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+      9   3.55045  0.11705  3.59478  2.91367      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     10   3.01755  3.69041  0.10652  3.60597     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     11   3.55045  0.11705  3.59478  2.91367     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     12   2.46500  0.94717  2.53631  0.80297     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     13   3.01755  3.69041  0.10652  3.60597     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     14   3.01755  3.69041  0.10652  3.60597     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     15   3.55045  0.11705  3.59478  2.91367     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     16   0.12911  3.48247  2.86794  3.39398     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     17   3.55045  0.11705  3.59478  2.91367     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     18   0.12911  3.48247  2.86794  3.39398     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     19   0.12911  3.48247  2.86794  3.39398     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     20   3.55045  0.11705  3.59478  2.91367     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     21   3.55045  0.11705  3.59478  2.91367     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     22   0.84829  2.57052  0.89883  2.42686     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     23   3.01755  3.69041  0.10652  3.60597     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     24   3.55045  0.11705  3.59478  2.91367     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     25   0.12911  3.48247  2.86794  3.39398     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     26   3.19300  2.66139  3.23711  0.16273     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     27   3.01755  3.69041  0.10652  3.60597     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     28   3.19300  2.66139  3.23711  0.16273     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     29   3.19300  2.66139  3.23711  0.16273     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     30   3.19300  2.66139  3.23711  0.16273     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     31   3.01755  3.69041  0.10652  3.60597     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     32   3.01755  3.69041  0.10652  3.60597     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     33   3.19300  2.66139  3.23711  0.16273     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     34   3.19300  2.66139  3.23711  0.16273     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     35   3.55045  0.11705  3.59478  2.91367     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     36   0.12911  3.48247  2.86794  3.39398     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     37   3.01755  3.69041  0.10652  3.60597     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     38   3.19300  2.66139  3.23711  0.16273     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     39   3.01755  3.69041  0.10652  3.60597     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     40   3.19300  2.66139  3.23711  0.16273     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     41   3.01755  3.69041  0.10652  3.60597     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     42   3.55045  0.11705  3.59478  2.91367     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     43   1.00233  1.43748  2.06192  1.31588     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     44   3.55045  0.11705  3.59478  2.91367     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03472  4.07076  4.07076  1.46634  0.26236  1.09861  0.40547
+     45   0.12911  3.48247  2.86794  3.39398     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01751  4.05355        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_nineteena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:55:44 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 1579425985
+STATS LOCAL MSV       -8.0867  0.72116
+STATS LOCAL VITERBI   -7.9812  0.72116
+STATS LOCAL FORWARD   -3.7009  0.72116
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.79232  1.40617  1.18456  1.26419
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   3.30705  0.14631  3.36166  2.73626      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   0.15719  3.27118  2.73043  3.16274      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   0.15719  3.27118  2.73043  3.16274      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   2.86982  3.47591  0.13017  3.36931      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   2.97980  2.52563  3.03204  0.19727      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.86982  3.47591  0.13017  3.36931      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.86982  3.47591  0.13017  3.36931      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   3.30705  0.14631  3.36166  2.73626      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   3.30705  0.14631  3.36166  2.73626     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   0.15719  3.27118  2.73043  3.16274     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   2.86982  3.47591  0.13017  3.36931     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   3.30705  0.14631  3.36166  2.73626     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   2.43440  0.61908  2.50724  1.22957     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   2.97980  2.52563  3.03204  0.19727     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   3.30705  0.14631  3.36166  2.73626     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.86982  3.47591  0.13017  3.36931     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   3.30705  0.14631  3.36166  2.73626     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   2.97980  2.52563  3.03204  0.19727     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   2.86982  3.47591  0.13017  3.36931     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.97980  2.52563  3.03204  0.19727     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   3.30705  0.14631  3.36166  2.73626     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   2.86982  3.47591  0.13017  3.36931     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   2.12334  2.11792  1.37287  0.67982     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   2.97980  2.52563  3.03204  0.19727     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.97980  2.52563  3.03204  0.19727     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   2.86982  3.47591  0.13017  3.36931     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   2.97980  2.52563  3.03204  0.19727     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.97980  2.52563  3.03204  0.19727     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   3.30705  0.14631  3.36166  2.73626     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   0.15719  3.27118  2.73043  3.16274     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.86982  3.47591  0.13017  3.36931     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.97980  2.52563  3.03204  0.19727     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.97980  2.52563  3.03204  0.19727     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   0.15719  3.27118  2.73043  3.16274     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.97980  2.52563  3.03204  0.19727     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   3.30705  0.14631  3.36166  2.73626     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   3.30705  0.14631  3.36166  2.73626     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.86982  3.47591  0.13017  3.36931     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_nineteenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:55:50 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 2871410458
+STATS LOCAL MSV       -8.0750  0.72053
+STATS LOCAL VITERBI   -7.9443  0.72053
+STATS LOCAL FORWARD   -3.7952  0.72053
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.54304  1.52189  1.31521  1.20546
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   3.30705  0.14631  3.36166  2.73626      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   0.15719  3.27118  2.73043  3.16274      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   0.15719  3.27118  2.73043  3.16274      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   2.86982  3.47591  0.13017  3.36931      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   2.97980  2.52563  3.03204  0.19727      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.86982  3.47591  0.13017  3.36931      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.86982  3.47591  0.13017  3.36931      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   3.30705  0.14631  3.36166  2.73626      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   0.15719  3.27118  2.73043  3.16274     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   2.97980  2.52563  3.03204  0.19727     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   0.15719  3.27118  2.73043  3.16274     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   2.86982  3.47591  0.13017  3.36931     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   3.30705  0.14631  3.36166  2.73626     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   2.97980  2.52563  3.03204  0.19727     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   0.15719  3.27118  2.73043  3.16274     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   2.97980  2.52563  3.03204  0.19727     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.86982  3.47591  0.13017  3.36931     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   3.30705  0.14631  3.36166  2.73626     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   2.97980  2.52563  3.03204  0.19727     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   0.15719  3.27118  2.73043  3.16274     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.97980  2.52563  3.03204  0.19727     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   3.30705  0.14631  3.36166  2.73626     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   2.86982  3.47591  0.13017  3.36931     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   2.97980  2.52563  3.03204  0.19727     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   2.97980  2.52563  3.03204  0.19727     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.97980  2.52563  3.03204  0.19727     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   2.86982  3.47591  0.13017  3.36931     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   3.30705  0.14631  3.36166  2.73626     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.97980  2.52563  3.03204  0.19727     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   3.30705  0.14631  3.36166  2.73626     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   0.15719  3.27118  2.73043  3.16274     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.86982  3.47591  0.13017  3.36931     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.97980  2.52563  3.03204  0.19727     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.97980  2.52563  3.03204  0.19727     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   0.15719  3.27118  2.73043  3.16274     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.97980  2.52563  3.03204  0.19727     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   3.30705  0.14631  3.36166  2.73626     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   3.30705  0.14631  3.36166  2.73626     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.86982  3.47591  0.13017  3.36931     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_onea_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:42:30 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 634275971
+STATS LOCAL MSV       -7.4720  0.73173
+STATS LOCAL VITERBI   -8.2528  0.73173
+STATS LOCAL FORWARD   -3.4391  0.73173
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.40721  1.72349  1.41702  1.09573
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.57915  2.25909  2.64442  0.28946      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   0.23862  2.84929  2.43386  2.70756      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.57915  2.25909  2.64442  0.28946     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.57915  2.25909  2.64442  0.28946     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.57915  2.25909  2.64442  0.28946     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   1.89532  1.96405  1.06955  1.00436     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   0.92825  2.28391  0.95698  2.13014     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.15554  1.00938  2.23102  0.88601     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.81865  0.23582  2.88868  2.35662     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   0.23862  2.84929  2.43386  2.70756     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   0.23862  2.84929  2.43386  2.70756     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   1.88179  1.10717  1.04597  1.79675     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_oneb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:42:36 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 470675090
+STATS LOCAL MSV       -7.4696  0.73050
+STATS LOCAL VITERBI   -8.4860  0.73050
+STATS LOCAL FORWARD   -3.6496  0.73050
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.40317  1.51763  1.41931  1.22734
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   0.23862  2.84929  2.43386  2.70756      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.15554  1.00938  2.23102  0.88601      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.57915  2.25909  2.64442  0.28946     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.57915  2.25909  2.64442  0.28946     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.57915  2.25909  2.64442  0.28946     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   0.23862  2.84929  2.43386  2.70756     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.81865  0.23582  2.88868  2.35662     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   0.23862  2.84929  2.43386  2.70756     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   1.03732  1.95876  1.96551  1.00928     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   1.01448  1.11006  1.95471  1.79419     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_onec_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:42:41 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3218648575
+STATS LOCAL MSV       -7.4834  0.72855
+STATS LOCAL VITERBI   -8.3698  0.72855
+STATS LOCAL FORWARD   -3.5469  0.72855
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.45349  1.57174  1.37327  1.18652
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   0.23862  2.84929  2.43386  2.70756      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.57915  2.25909  2.64442  0.28946     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.57915  2.25909  2.64442  0.28946     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.53331  3.02441  0.20344  2.88069     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   0.23862  2.84929  2.43386  2.70756     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   0.23862  2.84929  2.43386  2.70756     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_sevena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:25 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 1500803962
+STATS LOCAL MSV       -7.4752  0.72898
+STATS LOCAL VITERBI   -8.3128  0.72898
+STATS LOCAL FORWARD   -3.5618  0.72898
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.51945  1.36263  1.43442  1.24854
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   0.23862  2.84929  2.43386  2.70756     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.57915  2.25909  2.64442  0.28946     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   0.23862  2.84929  2.43386  2.70756     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.15554  1.00938  2.23102  0.88601     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_sevenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:32 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3235530884
+STATS LOCAL MSV       -7.4473  0.72886
+STATS LOCAL VITERBI   -8.3269  0.72886
+STATS LOCAL FORWARD   -3.6806  0.72886
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.51904  1.26407  1.41546  1.36351
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.53331  3.02441  0.20344  2.88069      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.81865  0.23582  2.88868  2.35662     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.81865  0.23582  2.88868  2.35662     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   1.88179  1.10717  1.04597  1.79675     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.81865  0.23582  2.88868  2.35662     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   0.23862  2.84929  2.43386  2.70756     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_sevenc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:38 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 677190326
+STATS LOCAL MSV       -7.4805  0.73144
+STATS LOCAL VITERBI   -8.3647  0.73144
+STATS LOCAL FORWARD   -3.3920  0.73144
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.49596  1.51275  1.43591  1.14645
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.57915  2.25909  2.64442  0.28946      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+     44   0.92825  2.28391  0.95698  2.13014     44 - -
+          1.38629  1.38629  1.38629  1.38629
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+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_seventeen_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:55:31 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 252461474
+STATS LOCAL MSV       -7.9979  0.72109
+STATS LOCAL VITERBI   -7.8792  0.72109
+STATS LOCAL FORWARD   -3.7137  0.72109
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.11444  1.67387  1.87820  1.10408
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   3.30705  0.14631  3.36166  2.73626      1 - -
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+      2   2.86982  3.47591  0.13017  3.36931      2 - -
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+      3   3.30705  0.14631  3.36166  2.73626      3 - -
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+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.97980  2.52563  3.03204  0.19727     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   0.15719  3.27118  2.73043  3.16274     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_six_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:48:16 2012
+NSEQ  6
+EFFN  3.565430
+CKSUM 1641114563
+STATS LOCAL MSV       -7.2926  0.71932
+STATS LOCAL VITERBI   -7.7152  0.71932
+STATS LOCAL FORWARD   -3.9190  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.71905  1.32555  1.24979  1.31474
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  0.00000        *
+      1   2.44789  0.93687  2.51948  0.81833      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      2   0.13242  3.45492  2.85021  3.36375      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      3   3.51892  0.12042  3.56466  2.89106      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      4   3.16462  2.64340  3.20984  0.16690      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      5   3.16462  2.64340  3.20984  0.16690      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      6   3.16462  2.64340  3.20984  0.16690      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      7   3.51892  0.12042  3.56466  2.89106      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      8   2.99892  3.66295  0.10925  3.57556      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+      9   2.99892  3.66295  0.10925  3.57556      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     10   2.99892  3.66295  0.10925  3.57556     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     11   0.13242  3.45492  2.85021  3.36375     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     12   3.16462  2.64340  3.20984  0.16690     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     13   0.13242  3.45492  2.85021  3.36375     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     14   2.99892  3.66295  0.10925  3.57556     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     15   3.51892  0.12042  3.56466  2.89106     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     16   3.51892  0.12042  3.56466  2.89106     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     17   3.16462  2.64340  3.20984  0.16690     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     18   3.16462  2.64340  3.20984  0.16690     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     19   2.99892  3.66295  0.10925  3.57556     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     20   3.51892  0.12042  3.56466  2.89106     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     21   0.13242  3.45492  2.85021  3.36375     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     22   0.13242  3.45492  2.85021  3.36375     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     23   2.99892  3.66295  0.10925  3.57556     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     24   2.54831  1.34093  2.61616  0.53256     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     25   2.99892  3.66295  0.10925  3.57556     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     26   3.16462  2.64340  3.20984  0.16690     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     27   2.99892  3.66295  0.10925  3.57556     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     28   3.51892  0.12042  3.56466  2.89106     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     29   3.51892  0.12042  3.56466  2.89106     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     30   3.16462  2.64340  3.20984  0.16690     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     31   2.99892  3.66295  0.10925  3.57556     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     32   3.51892  0.12042  3.56466  2.89106     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     33   2.99892  3.66295  0.10925  3.57556     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     34   3.16462  2.64340  3.20984  0.16690     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     35   2.54831  1.34093  2.61616  0.53256     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     36   2.99892  3.66295  0.10925  3.57556     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     37   2.99892  3.66295  0.10925  3.57556     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     38   3.51892  0.12042  3.56466  2.89106     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     39   2.99892  3.66295  0.10925  3.57556     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     40   3.16462  2.64340  3.20984  0.16690     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     41   3.51892  0.12042  3.56466  2.89106     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     42   3.16462  2.64340  3.20984  0.16690     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     43   0.13242  3.45492  2.85021  3.36375     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     44   3.51892  0.12042  3.56466  2.89106     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03531  4.05446  4.05446  1.46634  0.26236  1.09861  0.40547
+     45   0.13242  3.45492  2.85021  3.36375     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01781  4.03697        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_sixteena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:55:08 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 3202956986
+STATS LOCAL MSV       -7.8599  0.72111
+STATS LOCAL VITERBI   -7.8497  0.72111
+STATS LOCAL FORWARD   -4.1451  0.72111
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.35816  1.44270  1.58441  1.19895
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   0.15719  3.27118  2.73043  3.16274      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   3.30705  0.14631  3.36166  2.73626      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   0.15719  3.27118  2.73043  3.16274      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   0.15719  3.27118  2.73043  3.16274      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   0.15719  3.27118  2.73043  3.16274      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.86982  3.47591  0.13017  3.36931      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.86982  3.47591  0.13017  3.36931      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   2.86982  3.47591  0.13017  3.36931      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   0.15719  3.27118  2.73043  3.16274     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   2.97980  2.52563  3.03204  0.19727     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   2.97980  2.52563  3.03204  0.19727     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   2.97980  2.52563  3.03204  0.19727     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   0.15719  3.27118  2.73043  3.16274     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   2.97980  2.52563  3.03204  0.19727     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   3.30705  0.14631  3.36166  2.73626     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   3.30705  0.14631  3.36166  2.73626     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.97980  2.52563  3.03204  0.19727     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   3.30705  0.14631  3.36166  2.73626     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   2.97980  2.52563  3.03204  0.19727     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   2.97980  2.52563  3.03204  0.19727     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   2.97980  2.52563  3.03204  0.19727     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.86982  3.47591  0.13017  3.36931     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   2.97980  2.52563  3.03204  0.19727     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   3.30705  0.14631  3.36166  2.73626     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   0.15719  3.27118  2.73043  3.16274     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   2.97980  2.52563  3.03204  0.19727     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   0.15719  3.27118  2.73043  3.16274     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   3.30705  0.14631  3.36166  2.73626     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   0.54133  2.56226  1.37841  2.42004     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   2.97980  2.52563  3.03204  0.19727     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   0.15719  3.27118  2.73043  3.16274     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   3.30705  0.14631  3.36166  2.73626     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   0.15719  3.27118  2.73043  3.16274     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.86982  3.47591  0.13017  3.36931     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.97980  2.52563  3.03204  0.19727     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.97980  2.52563  3.03204  0.19727     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   3.30705  0.14631  3.36166  2.73626     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.86982  3.47591  0.13017  3.36931     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   3.30705  0.14631  3.36166  2.73626     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.97980  2.52563  3.03204  0.19727     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   3.30705  0.14631  3.36166  2.73626     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_sixteenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:55:15 2012
+NSEQ  4
+EFFN  3.339844
+CKSUM 3480860732
+STATS LOCAL MSV       -8.0392  0.71933
+STATS LOCAL VITERBI   -7.6464  0.71933
+STATS LOCAL FORWARD   -4.2449  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.40398  1.37647  1.61533  1.19373
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  0.00000        *
+      1   0.14117  3.38574  2.80548  3.28793      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      2   3.43942  0.12946  3.48861  2.83359      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      3   0.14117  3.38574  2.80548  3.28793      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      4   0.14117  3.38574  2.80548  3.28793      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      5   0.14117  3.38574  2.80548  3.28793      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      6   2.95135  3.59331  0.11655  3.49856      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      7   2.95135  3.59331  0.11655  3.49856      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      8   2.95135  3.59331  0.11655  3.49856      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+      9   2.95135  3.59331  0.11655  3.49856      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     10   0.14117  3.38574  2.80548  3.28793     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     11   3.09414  2.59866  3.14209  0.17779     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     12   3.43942  0.12946  3.48861  2.83359     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     13   3.09414  2.59866  3.14209  0.17779     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     14   3.09414  2.59866  3.14209  0.17779     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     15   3.09414  2.59866  3.14209  0.17779     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     16   3.43942  0.12946  3.48861  2.83359     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     17   3.43942  0.12946  3.48861  2.83359     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     18   3.09414  2.59866  3.14209  0.17779     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     19   3.43942  0.12946  3.48861  2.83359     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     20   3.09414  2.59866  3.14209  0.17779     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     21   3.09414  2.59866  3.14209  0.17779     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     22   3.09414  2.59866  3.14209  0.17779     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     23   2.95135  3.59331  0.11655  3.49856     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     24   3.09414  2.59866  3.14209  0.17779     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     25   0.14117  3.38574  2.80548  3.28793     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     26   3.43942  0.12946  3.48861  2.83359     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     27   0.14117  3.38574  2.80548  3.28793     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     28   3.09414  2.59866  3.14209  0.17779     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     29   0.14117  3.38574  2.80548  3.28793     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     30   3.43942  0.12946  3.48861  2.83359     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     31   0.14117  3.38574  2.80548  3.28793     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     32   3.09414  2.59866  3.14209  0.17779     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     33   0.14117  3.38574  2.80548  3.28793     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     34   3.09414  2.59866  3.14209  0.17779     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     35   3.43942  0.12946  3.48861  2.83359     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     36   0.14117  3.38574  2.80548  3.28793     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     37   2.95135  3.59331  0.11655  3.49856     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     38   3.09414  2.59866  3.14209  0.17779     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     39   2.95135  3.59331  0.11655  3.49856     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     40   3.09414  2.59866  3.14209  0.17779     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     41   3.43942  0.12946  3.48861  2.83359     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     42   2.95135  3.59331  0.11655  3.49856     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     43   3.43942  0.12946  3.48861  2.83359     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     44   3.09414  2.59866  3.14209  0.17779     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03677  4.01455  4.01455  1.46634  0.26236  1.09861  0.40547
+     45   3.43942  0.12946  3.48861  2.83359     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01855  3.99634        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_thirteena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:53:44 2012
+NSEQ  9
+EFFN  3.335449
+CKSUM 139984797
+STATS LOCAL MSV       -8.1484  0.71932
+STATS LOCAL VITERBI   -7.6823  0.71932
+STATS LOCAL FORWARD   -3.7855  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.48084  1.04177  1.71496  1.42815
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  0.00000        *
+      1   0.14136  3.38434  2.80457  3.28639      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      2   3.43781  0.12965  3.48707  2.83242      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      3   0.14136  3.38434  2.80457  3.28639      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      4   3.43781  0.12965  3.48707  2.83242      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      5   0.14136  3.38434  2.80457  3.28639      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      6   3.43781  0.12965  3.48707  2.83242      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      7   3.43781  0.12965  3.48707  2.83242      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      8   0.14136  3.38434  2.80457  3.28639      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+      9   3.43781  0.12965  3.48707  2.83242      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     10   3.43781  0.12965  3.48707  2.83242     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     11   3.09273  2.59776  3.14073  0.17801     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     12   3.43781  0.12965  3.48707  2.83242     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     13   3.09273  2.59776  3.14073  0.17801     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     14   2.95037  3.59189  0.11671  3.49699     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     15   3.43781  0.12965  3.48707  2.83242     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     16   3.09273  2.59776  3.14073  0.17801     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     17   3.09273  2.59776  3.14073  0.17801     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     18   2.95037  3.59189  0.11671  3.49699     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     19   3.43781  0.12965  3.48707  2.83242     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     20   0.14136  3.38434  2.80457  3.28639     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     21   3.00628  0.24684  3.06821  2.09759     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     22   2.95037  3.59189  0.11671  3.49699     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     23   3.09273  2.59776  3.14073  0.17801     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     24   2.95037  3.59189  0.11671  3.49699     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     25   2.95037  3.59189  0.11671  3.49699     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     26   3.09273  2.59776  3.14073  0.17801     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     27   0.14136  3.38434  2.80457  3.28639     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     28   3.43781  0.12965  3.48707  2.83242     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     29   3.09273  2.59776  3.14073  0.17801     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     30   3.43781  0.12965  3.48707  2.83242     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     31   3.43781  0.12965  3.48707  2.83242     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     32   3.43781  0.12965  3.48707  2.83242     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     33   0.14136  3.38434  2.80457  3.28639     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     34   2.82574  2.00897  2.88356  0.28679     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     35   3.09273  2.59776  3.14073  0.17801     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     36   3.09273  2.59776  3.14073  0.17801     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     37   3.43781  0.12965  3.48707  2.83242     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     38   0.14136  3.38434  2.80457  3.28639     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     39   2.95037  3.59189  0.11671  3.49699     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     40   3.09273  2.59776  3.14073  0.17801     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     41   2.95037  3.59189  0.11671  3.49699     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     42   0.14136  3.38434  2.80457  3.28639     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     43   0.14136  3.38434  2.80457  3.28639     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     44   3.43781  0.12965  3.48707  2.83242     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03680  4.01376  4.01376  1.46634  0.26236  1.09861  0.40547
+     45   3.43781  0.12965  3.48707  2.83242     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01857  3.99553        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_thirteenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:53:51 2012
+NSEQ  20
+EFFN  3.344727
+CKSUM 3926777842
+STATS LOCAL MSV       -8.0192  0.71933
+STATS LOCAL VITERBI   -7.8856  0.71933
+STATS LOCAL FORWARD   -3.6871  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.72605  0.97133  1.46172  1.55306
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  0.00000        *
+      1   0.14097  3.38729  2.80649  3.28963      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      2   3.44121  0.12925  3.49032  2.83489      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      3   0.14097  3.38729  2.80649  3.28963      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      4   3.44121  0.12925  3.49032  2.83489      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      5   0.14097  3.38729  2.80649  3.28963      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      6   3.44121  0.12925  3.49032  2.83489      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      7   3.44121  0.12925  3.49032  2.83489      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      8   2.95243  3.59489  0.11638  3.50030      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+      9   3.44121  0.12925  3.49032  2.83489      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     10   3.44121  0.12925  3.49032  2.83489     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     11   3.09571  2.59966  3.14360  0.17754     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     12   3.44121  0.12925  3.49032  2.83489     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     13   3.09571  2.59966  3.14360  0.17754     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     14   2.95243  3.59489  0.11638  3.50030     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     15   3.44121  0.12925  3.49032  2.83489     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     16   3.09571  2.59966  3.14360  0.17754     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     17   3.44121  0.12925  3.49032  2.83489     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     18   2.95243  3.59489  0.11638  3.50030     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     19   3.44121  0.12925  3.49032  2.83489     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     20   0.14097  3.38729  2.80649  3.28963     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     21   2.88258  0.29778  2.94754  1.90330     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     22   2.95243  3.59489  0.11638  3.50030     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     23   3.44121  0.12925  3.49032  2.83489     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     24   2.95243  3.59489  0.11638  3.50030     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     25   2.95243  3.59489  0.11638  3.50030     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     26   3.09571  2.59966  3.14360  0.17754     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     27   0.14097  3.38729  2.80649  3.28963     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     28   3.44121  0.12925  3.49032  2.83489     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     29   3.09571  2.59966  3.14360  0.17754     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     30   3.44121  0.12925  3.49032  2.83489     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     31   3.44121  0.12925  3.49032  2.83489     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     32   3.44121  0.12925  3.49032  2.83489     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     33   2.95243  3.59489  0.11638  3.50030     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     34   3.09571  2.59966  3.14360  0.17754     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     35   3.09571  2.59966  3.14360  0.17754     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     36   3.09571  2.59966  3.14360  0.17754     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     37   3.44121  0.12925  3.49032  2.83489     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     38   0.14097  3.38729  2.80649  3.28963     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     39   2.95243  3.59489  0.11638  3.50030     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     40   3.09571  2.59966  3.14360  0.17754     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     41   2.95243  3.59489  0.11638  3.50030     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     42   0.14097  3.38729  2.80649  3.28963     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     43   2.95243  3.59489  0.11638  3.50030     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     44   3.03924  0.23563  3.10030  2.14542     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03674  4.01543  4.01543  1.46634  0.26236  1.09861  0.40547
+     45   2.38711  0.31887  2.45124  2.35442     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01854  3.99723        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_thirteenbb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:53:55 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 1469591864
+STATS LOCAL MSV       -8.0813  0.72030
+STATS LOCAL VITERBI   -7.7552  0.72030
+STATS LOCAL FORWARD   -3.4416  0.72030
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.55466  1.04845  1.61897  1.42646
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   0.15719  3.27118  2.73043  3.16274      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   3.30705  0.14631  3.36166  2.73626      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   0.15719  3.27118  2.73043  3.16274      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   3.30705  0.14631  3.36166  2.73626      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   0.15719  3.27118  2.73043  3.16274      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   3.30705  0.14631  3.36166  2.73626      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   3.30705  0.14631  3.36166  2.73626      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   0.15719  3.27118  2.73043  3.16274      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   3.30705  0.14631  3.36166  2.73626      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   3.30705  0.14631  3.36166  2.73626     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   2.97980  2.52563  3.03204  0.19727     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   3.30705  0.14631  3.36166  2.73626     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   2.97980  2.52563  3.03204  0.19727     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.86982  3.47591  0.13017  3.36931     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   3.30705  0.14631  3.36166  2.73626     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   2.97980  2.52563  3.03204  0.19727     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   3.30705  0.14631  3.36166  2.73626     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.86982  3.47591  0.13017  3.36931     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   3.30705  0.14631  3.36166  2.73626     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   0.15719  3.27118  2.73043  3.16274     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   3.30705  0.14631  3.36166  2.73626     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   2.86982  3.47591  0.13017  3.36931     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.97980  2.52563  3.03204  0.19727     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   2.86982  3.47591  0.13017  3.36931     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   2.86982  3.47591  0.13017  3.36931     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   0.15719  3.27118  2.73043  3.16274     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   3.30705  0.14631  3.36166  2.73626     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   2.97980  2.52563  3.03204  0.19727     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   3.30705  0.14631  3.36166  2.73626     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   3.30705  0.14631  3.36166  2.73626     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   3.30705  0.14631  3.36166  2.73626     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   0.15719  3.27118  2.73043  3.16274     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   3.30705  0.14631  3.36166  2.73626     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   2.97980  2.52563  3.03204  0.19727     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   3.30705  0.14631  3.36166  2.73626     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   0.15719  3.27118  2.73043  3.16274     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.97980  2.52563  3.03204  0.19727     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   2.86982  3.47591  0.13017  3.36931     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   0.15719  3.27118  2.73043  3.16274     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   2.86982  3.47591  0.13017  3.36931     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.97980  2.52563  3.03204  0.19727     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.97980  2.52563  3.03204  0.19727     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_thirteenc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:54:02 2012
+NSEQ  6
+EFFN  3.676758
+CKSUM 138006768
+STATS LOCAL MSV       -7.7146  0.71932
+STATS LOCAL VITERBI   -7.6336  0.71932
+STATS LOCAL FORWARD   -4.1384  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.56284  1.02897  1.71089  1.37681
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  0.00000        *
+      1   0.12855  3.48721  2.87098  3.39919      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      2   3.55586  0.11648  3.59995  2.91754      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      3   0.12855  3.48721  2.87098  3.39919      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      4   3.55586  0.11648  3.59995  2.91754      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      5   0.12855  3.48721  2.87098  3.39919      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      6   3.55586  0.11648  3.59995  2.91754      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      7   3.19790  2.66450  3.24182  0.16202      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      8   3.02074  3.69511  0.10606  3.61119      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+      9   3.55586  0.11648  3.59995  2.91754      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     10   3.55586  0.11648  3.59995  2.91754     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     11   3.19790  2.66450  3.24182  0.16202     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     12   3.55586  0.11648  3.59995  2.91754     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     13   3.19790  2.66450  3.24182  0.16202     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     14   3.02074  3.69511  0.10606  3.61119     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     15   3.19790  2.66450  3.24182  0.16202     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     16   3.19790  2.66450  3.24182  0.16202     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     17   3.19790  2.66450  3.24182  0.16202     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     18   0.94052  1.00771  2.17954  2.02929     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     19   3.55586  0.11648  3.59995  2.91754     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     20   0.12855  3.48721  2.87098  3.39919     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     21   0.66712  2.29396  2.24218  1.27396     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     22   3.02074  3.69511  0.10606  3.61119     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     23   3.55586  0.11648  3.59995  2.91754     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     24   0.12855  3.48721  2.87098  3.39919     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     25   3.02074  3.69511  0.10606  3.61119     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     26   3.19790  2.66450  3.24182  0.16202     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     27   3.02074  3.69511  0.10606  3.61119     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     28   3.55586  0.11648  3.59995  2.91754     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     29   0.12855  3.48721  2.87098  3.39919     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     30   3.55586  0.11648  3.59995  2.91754     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     31   3.55586  0.11648  3.59995  2.91754     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     32   3.55586  0.11648  3.59995  2.91754     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     33   0.12855  3.48721  2.87098  3.39919     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     34   3.19790  2.66450  3.24182  0.16202     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     35   3.19790  2.66450  3.24182  0.16202     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     36   3.19790  2.66450  3.24182  0.16202     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     37   3.55586  0.11648  3.59995  2.91754     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     38   0.12855  3.48721  2.87098  3.39919     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     39   3.02074  3.69511  0.10606  3.61119     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     40   3.55586  0.11648  3.59995  2.91754     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     41   3.02074  3.69511  0.10606  3.61119     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     42   3.55586  0.11648  3.59995  2.91754     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     43   3.55586  0.11648  3.59995  2.91754     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     44   3.19790  2.66450  3.24182  0.16202     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03462  4.07359  4.07359  1.46634  0.26236  1.09861  0.40547
+     45   2.56017  0.58808  2.63122  1.21967     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01746  4.05643        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_threea_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:46:58 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 1268247449
+STATS LOCAL MSV       -7.3625  0.72824
+STATS LOCAL VITERBI   -8.2348  0.72824
+STATS LOCAL FORWARD   -3.6133  0.72824
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.66059  1.44581  1.26603  1.22940
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.81865  0.23582  2.88868  2.35662     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   0.23862  2.84929  2.43386  2.70756     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.57915  2.25909  2.64442  0.28946     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.57915  2.25909  2.64442  0.28946     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.53331  3.02441  0.20344  2.88069     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.53331  3.02441  0.20344  2.88069     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_threeb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:05 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 3892526639
+STATS LOCAL MSV       -7.9454  0.72246
+STATS LOCAL VITERBI   -7.9639  0.72246
+STATS LOCAL FORWARD   -4.0448  0.72246
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.78275  1.43417  1.30656  1.13083
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   2.97980  2.52563  3.03204  0.19727      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   2.86982  3.47591  0.13017  3.36931      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   3.30705  0.14631  3.36166  2.73626      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   2.97980  2.52563  3.03204  0.19727      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   2.10551  2.22611  0.68843  1.31713      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.97980  2.52563  3.03204  0.19727      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.97980  2.52563  3.03204  0.19727      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   2.86982  3.47591  0.13017  3.36931      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   0.15719  3.27118  2.73043  3.16274     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   2.97980  2.52563  3.03204  0.19727     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   0.15719  3.27118  2.73043  3.16274     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.97980  2.52563  3.03204  0.19727     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   0.15719  3.27118  2.73043  3.16274     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   3.30705  0.14631  3.36166  2.73626     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   3.30705  0.14631  3.36166  2.73626     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.97980  2.52563  3.03204  0.19727     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   0.15719  3.27118  2.73043  3.16274     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   3.30705  0.14631  3.36166  2.73626     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   0.15719  3.27118  2.73043  3.16274     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.86982  3.47591  0.13017  3.36931     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   3.30705  0.14631  3.36166  2.73626     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   2.86982  3.47591  0.13017  3.36931     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   3.30705  0.14631  3.36166  2.73626     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   3.30705  0.14631  3.36166  2.73626     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.97980  2.52563  3.03204  0.19727     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   2.86982  3.47591  0.13017  3.36931     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   2.09516  1.42731  0.67263  2.06647     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.97980  2.52563  3.03204  0.19727     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   2.97980  2.52563  3.03204  0.19727     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   2.86982  3.47591  0.13017  3.36931     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.86982  3.47591  0.13017  3.36931     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.42587  0.63365  2.49879  1.20810     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.42586  1.33558  2.49582  0.56887     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   3.30705  0.14631  3.36166  2.73626     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.97980  2.52563  3.03204  0.19727     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   2.97980  2.52563  3.03204  0.19727     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   3.30705  0.14631  3.36166  2.73626     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.97980  2.52563  3.03204  0.19727     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_threec_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:11 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 4079785563
+STATS LOCAL MSV       -8.0314  0.72082
+STATS LOCAL VITERBI   -7.8511  0.72082
+STATS LOCAL FORWARD   -3.9522  0.72082
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.62542  1.59063  1.38012  1.05605
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   2.97980  2.52563  3.03204  0.19727      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   2.86982  3.47591  0.13017  3.36931      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   3.30705  0.14631  3.36166  2.73626      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   2.97980  2.52563  3.03204  0.19727      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   2.97980  2.52563  3.03204  0.19727      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.97980  2.52563  3.03204  0.19727      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.97980  2.52563  3.03204  0.19727      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   2.86982  3.47591  0.13017  3.36931      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.86982  3.47591  0.13017  3.36931      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   0.15719  3.27118  2.73043  3.16274     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   2.97980  2.52563  3.03204  0.19727     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   0.15719  3.27118  2.73043  3.16274     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.97980  2.52563  3.03204  0.19727     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   0.15719  3.27118  2.73043  3.16274     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   3.30705  0.14631  3.36166  2.73626     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   3.30705  0.14631  3.36166  2.73626     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.97980  2.52563  3.03204  0.19727     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   0.15719  3.27118  2.73043  3.16274     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   0.15719  3.27118  2.73043  3.16274     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   0.15719  3.27118  2.73043  3.16274     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.86982  3.47591  0.13017  3.36931     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   3.30705  0.14631  3.36166  2.73626     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   2.86982  3.47591  0.13017  3.36931     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   3.30705  0.14631  3.36166  2.73626     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   3.30705  0.14631  3.36166  2.73626     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.97980  2.52563  3.03204  0.19727     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   2.86982  3.47591  0.13017  3.36931     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   3.30705  0.14631  3.36166  2.73626     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.97980  2.52563  3.03204  0.19727     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   2.97980  2.52563  3.03204  0.19727     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   2.97980  2.52563  3.03204  0.19727     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   2.86982  3.47591  0.13017  3.36931     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.86982  3.47591  0.13017  3.36931     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.97980  2.52563  3.03204  0.19727     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.97980  2.52563  3.03204  0.19727     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   3.30705  0.14631  3.36166  2.73626     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.97980  2.52563  3.03204  0.19727     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   0.15719  3.27118  2.73043  3.16274     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.97980  2.52563  3.03204  0.19727     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.97980  2.52563  3.03204  0.19727     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_threed_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:47:17 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3952366831
+STATS LOCAL MSV       -7.3931  0.72871
+STATS LOCAL VITERBI   -8.1902  0.72871
+STATS LOCAL FORWARD   -3.4651  0.72871
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.70464  1.38559  1.24625  1.27151
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.81865  0.23582  2.88868  2.35662      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.81865  0.23582  2.88868  2.35662     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.57915  2.25909  2.64442  0.28946     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   0.23862  2.84929  2.43386  2.70756     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.57915  2.25909  2.64442  0.28946     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.53331  3.02441  0.20344  2.88069     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.81865  0.23582  2.88868  2.35662     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.53331  3.02441  0.20344  2.88069     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.92825  2.28391  0.95698  2.13014     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_twelvea_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:49:56 2012
+NSEQ  6
+EFFN  3.606445
+CKSUM 1425331606
+STATS LOCAL MSV       -7.6440  0.71933
+STATS LOCAL VITERBI   -7.7492  0.71933
+STATS LOCAL FORWARD   -4.2833  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.27087  1.33665  1.80281  1.23151
+          1.38629  1.38629  1.38629  1.38629
+          0.03505  4.06155  4.06155  1.46634  0.26236  0.00000        *
+      1   3.17699  2.65124  3.22173  0.16506      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03505  4.06155  4.06155  1.46634  0.26236  1.09861  0.40547
+      2   3.00708  3.67496  0.10805  3.58886      2 - -
+          1.38629  1.38629  1.38629  1.38629
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+     44   2.78284  1.79931  2.84298  0.33621     44 - -
+          1.38629  1.38629  1.38629  1.38629
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+     45   2.78284  1.79931  2.84298  0.33621     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01768  4.04418        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_twelveb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:50:00 2012
+NSEQ  4
+EFFN  3.613281
+CKSUM 327718252
+STATS LOCAL MSV       -7.7152  0.71933
+STATS LOCAL VITERBI   -7.8787  0.71933
+STATS LOCAL FORWARD   -4.2409  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.22953  1.30344  1.79734  1.30847
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06273  4.06273  1.46634  0.26236  0.00000        *
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+     44   3.17904  2.65254  3.22370  0.16476     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03501  4.06273  4.06273  1.46634  0.26236  1.09861  0.40547
+     45   3.17904  2.65254  3.22370  0.16476     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01766  4.04538        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_twelvec_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:50:07 2012
+NSEQ  12
+EFFN  3.870117
+CKSUM 3267954346
+STATS LOCAL MSV       -7.1098  0.71933
+STATS LOCAL VITERBI   -7.7778  0.71933
+STATS LOCAL FORWARD   -4.1940  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.25985  1.20243  1.78234  1.39595
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  0.00000        *
+      1   3.61664  0.11030  3.65797  2.96085      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      2   3.25346  2.69972  3.29520  0.15423      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      3   3.05634  3.74778  0.10105  3.66961      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      4   0.12243  3.54056  2.90525  3.45780      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      5   0.12243  3.54056  2.90525  3.45780      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      6   3.61664  0.11030  3.65797  2.96085      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      7   3.05634  3.74778  0.10105  3.66961      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      8   3.25346  2.69972  3.29520  0.15423      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+      9   0.12243  3.54056  2.90525  3.45780      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     10   0.12243  3.54056  2.90525  3.45780     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     11   3.61664  0.11030  3.65797  2.96085     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     12   3.61664  0.11030  3.65797  2.96085     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     13   0.12243  3.54056  2.90525  3.45780     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     14   0.12243  3.54056  2.90525  3.45780     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     15   3.61664  0.11030  3.65797  2.96085     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     16   0.12243  3.54056  2.90525  3.45780     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     17   3.61664  0.11030  3.65797  2.96085     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     18   0.12243  3.54056  2.90525  3.45780     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     19   3.61664  0.11030  3.65797  2.96085     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     20   2.26557  2.24150  1.36887  0.62448     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     21   3.61664  0.11030  3.65797  2.96085     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     22   3.25346  2.69972  3.29520  0.15423     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     23   3.25346  2.69972  3.29520  0.15423     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     24   3.05634  3.74778  0.10105  3.66961     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     25   3.25346  2.69972  3.29520  0.15423     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     26   0.12243  3.54056  2.90525  3.45780     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     27   3.61664  0.11030  3.65797  2.96085     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     28   3.05634  3.74778  0.10105  3.66961     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     29   2.26012  2.49659  2.82398  0.28246     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     30   3.61664  0.11030  3.65797  2.96085     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     31   3.61664  0.11030  3.65797  2.96085     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     32   0.12243  3.54056  2.90525  3.45780     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     33   3.25346  2.69972  3.29520  0.15423     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     34   2.77036  0.40521  2.83796  1.55128     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     35   3.25346  2.69972  3.29520  0.15423     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     36   3.61664  0.11030  3.65797  2.96085     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     37   0.12243  3.54056  2.90525  3.45780     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     38   3.05634  3.74778  0.10105  3.66961     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     39   3.25346  2.69972  3.29520  0.15423     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     40   3.05634  3.74778  0.10105  3.66961     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     41   0.12243  3.54056  2.90525  3.45780     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     42   0.12243  3.54056  2.90525  3.45780     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     43   3.25346  2.69972  3.29520  0.15423     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     44   2.52094  0.74045  2.59225  1.00004     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03350  4.10596  4.10596  1.46634  0.26236  1.09861  0.40547
+     45   2.52094  0.74045  2.59225  1.00004     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01689  4.08935        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_twentya_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:56:02 2012
+NSEQ  4
+EFFN  3.566406
+CKSUM 1107581771
+STATS LOCAL MSV       -7.4293  0.71932
+STATS LOCAL VITERBI   -7.8373  0.71932
+STATS LOCAL FORWARD   -3.8028  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.82161  1.57746  1.30423  1.02067
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  0.00000        *
+      1   3.51925  0.12039  3.56498  2.89129      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      2   2.99911  3.66324  0.10922  3.57588      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      3   3.51925  0.12039  3.56498  2.89129      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      4   0.13239  3.45521  2.85039  3.36407      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      5   3.51925  0.12039  3.56498  2.89129      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      6   2.65809  1.57623  2.72240  0.41939      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      7   3.16491  2.64359  3.21012  0.16685      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      8   2.99911  3.66324  0.10922  3.57588      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+      9   2.99911  3.66324  0.10922  3.57588      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     10   3.51925  0.12039  3.56498  2.89129     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     11   2.99911  3.66324  0.10922  3.57588     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     12   3.51925  0.12039  3.56498  2.89129     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     13   3.16491  2.64359  3.21012  0.16685     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     14   0.13239  3.45521  2.85039  3.36407     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     15   2.99911  3.66324  0.10922  3.57588     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     16   3.16491  2.64359  3.21012  0.16685     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     17   3.16491  2.64359  3.21012  0.16685     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     18   3.16491  2.64359  3.21012  0.16685     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     19   0.13239  3.45521  2.85039  3.36407     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     20   3.51925  0.12039  3.56498  2.89129     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     21   3.16491  2.64359  3.21012  0.16685     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     22   0.13239  3.45521  2.85039  3.36407     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     23   2.99911  3.66324  0.10922  3.57588     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     24   3.51925  0.12039  3.56498  2.89129     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     25   0.13239  3.45521  2.85039  3.36407     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     26   3.16491  2.64359  3.21012  0.16685     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     27   2.99911  3.66324  0.10922  3.57588     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     28   3.16491  2.64359  3.21012  0.16685     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     29   3.16491  2.64359  3.21012  0.16685     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     30   3.16491  2.64359  3.21012  0.16685     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     31   2.99911  3.66324  0.10922  3.57588     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     32   3.16491  2.64359  3.21012  0.16685     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     33   3.16491  2.64359  3.21012  0.16685     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     34   3.16491  2.64359  3.21012  0.16685     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     35   3.51925  0.12039  3.56498  2.89129     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     36   0.13239  3.45521  2.85039  3.36407     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     37   2.99911  3.66324  0.10922  3.57588     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     38   3.16491  2.64359  3.21012  0.16685     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     39   2.99911  3.66324  0.10922  3.57588     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     40   3.16491  2.64359  3.21012  0.16685     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     41   2.99911  3.66324  0.10922  3.57588     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     42   3.16491  2.64359  3.21012  0.16685     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     43   3.16491  2.64359  3.21012  0.16685     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     44   2.31607  2.25114  1.58918  0.52430     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03530  4.05463  4.05463  1.46634  0.26236  1.09861  0.40547
+     45   2.99911  3.66324  0.10922  3.57588     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01781  4.03714        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_twentyb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:56:09 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 708606259
+STATS LOCAL MSV       -7.4772  0.72918
+STATS LOCAL VITERBI   -8.3653  0.72918
+STATS LOCAL FORWARD   -3.3564  0.72918
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.62240  1.63643  1.25842  1.12764
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   0.23862  2.84929  2.43386  2.70756      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.53331  3.02441  0.20344  2.88069      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   0.23862  2.84929  2.43386  2.70756      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   0.23862  2.84929  2.43386  2.70756      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.57915  2.25909  2.64442  0.28946      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.53331  3.02441  0.20344  2.88069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.81865  0.23582  2.88868  2.35662     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.81865  0.23582  2.88868  2.35662     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   0.23862  2.84929  2.43386  2.70756     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.81865  0.23582  2.88868  2.35662     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   1.03732  1.95876  1.96551  1.00928     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.57915  2.25909  2.64442  0.28946     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.53331  3.02441  0.20344  2.88069     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.57915  2.25909  2.64442  0.28946     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.53331  3.02441  0.20344  2.88069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.57915  2.25909  2.64442  0.28946     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.57915  2.25909  2.64442  0.28946     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.57915  2.25909  2.64442  0.28946     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   2.57915  2.25909  2.64442  0.28946     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.53331  3.02441  0.20344  2.88069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   2.57915  2.25909  2.64442  0.28946     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.57915  2.25909  2.64442  0.28946     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.53331  3.02441  0.20344  2.88069     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.53331  3.02441  0.20344  2.88069     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  3_End_Alveolata_58S_end_two_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 22:42:51 2012
+NSEQ  10
+EFFN  3.500977
+CKSUM 3395317246
+STATS LOCAL MSV       -7.5727  0.71933
+STATS LOCAL VITERBI   -7.6197  0.71933
+STATS LOCAL FORWARD   -4.0622  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.62863  1.30265  1.45636  1.20762
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  0.00000        *
+      1   3.49685  0.12286  3.54356  2.87517      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      2   2.98580  3.64368  0.11122  3.55423      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      3   3.49685  0.12286  3.54356  2.87517      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      4   3.14491  2.63090  3.19089  0.16986      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      5   3.14491  2.63090  3.19089  0.16986      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      6   3.14491  2.63090  3.19089  0.16986      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      7   3.49685  0.12286  3.54356  2.87517      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      8   2.98580  3.64368  0.11122  3.55423      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+      9   2.98580  3.64368  0.11122  3.55423      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     10   2.98580  3.64368  0.11122  3.55423     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     11   0.13479  3.43568  2.83780  3.34265     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     12   3.14491  2.63090  3.19089  0.16986     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     13   0.13479  3.43568  2.83780  3.34265     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     14   3.14491  2.63090  3.19089  0.16986     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     15   3.49685  0.12286  3.54356  2.87517     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     16   3.49685  0.12286  3.54356  2.87517     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     17   3.49685  0.12286  3.54356  2.87517     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     18   3.14491  2.63090  3.19089  0.16986     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     19   2.98580  3.64368  0.11122  3.55423     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     20   0.13479  3.43568  2.83780  3.34265     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     21   0.13479  3.43568  2.83780  3.34265     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     22   0.13479  3.43568  2.83780  3.34265     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     23   2.98580  3.64368  0.11122  3.55423     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     24   3.49685  0.12286  3.54356  2.87517     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     25   0.13479  3.43568  2.83780  3.34265     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     26   3.14491  2.63090  3.19089  0.16986     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     27   2.98580  3.64368  0.11122  3.55423     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     28   3.49685  0.12286  3.54356  2.87517     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     29   3.49685  0.12286  3.54356  2.87517     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     30   3.14491  2.63090  3.19089  0.16986     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     31   2.62489  2.97458  0.24797  2.34233     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     32   3.49685  0.12286  3.54356  2.87517     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     33   3.14491  2.63090  3.19089  0.16986     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     34   3.14491  2.63090  3.19089  0.16986     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     35   3.49685  0.12286  3.54356  2.87517     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     36   0.13479  3.43568  2.83780  3.34265     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     37   2.98580  3.64368  0.11122  3.55423     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     38   3.14491  2.63090  3.19089  0.16986     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     39   2.98580  3.64368  0.11122  3.55423     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     40   3.14491  2.63090  3.19089  0.16986     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     41   3.49685  0.12286  3.54356  2.87517     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     42   3.14491  2.63090  3.19089  0.16986     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     43   0.13479  3.43568  2.83780  3.34265     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     44   1.77036  2.10336  1.59709  0.68280     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03571  4.04322  4.04322  1.46634  0.26236  1.09861  0.40547
+     45   3.14491  2.63090  3.19089  0.16986     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01802  4.02553        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_eighta_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:07 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 3325641686
+STATS LOCAL MSV       -7.9406  0.72105
+STATS LOCAL VITERBI   -7.8084  0.72105
+STATS LOCAL FORWARD   -4.1819  0.72105
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.44871  1.52892  1.22347  1.36984
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   2.86982  3.47591  0.13017  3.36931      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   2.97980  2.52563  3.03204  0.19727      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   2.97980  2.52563  3.03204  0.19727      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   3.30705  0.14631  3.36166  2.73626      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   0.15719  3.27118  2.73043  3.16274      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.86982  3.47591  0.13017  3.36931      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   2.97980  2.52563  3.03204  0.19727      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   3.30705  0.14631  3.36166  2.73626      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   0.15719  3.27118  2.73043  3.16274      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   3.30705  0.14631  3.36166  2.73626     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   0.15719  3.27118  2.73043  3.16274     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   3.30705  0.14631  3.36166  2.73626     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.97980  2.52563  3.03204  0.19727     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   2.86982  3.47591  0.13017  3.36931     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   2.86982  3.47591  0.13017  3.36931     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   0.15719  3.27118  2.73043  3.16274     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   2.97980  2.52563  3.03204  0.19727     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   2.97980  2.52563  3.03204  0.19727     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   2.97980  2.52563  3.03204  0.19727     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   2.97980  2.52563  3.03204  0.19727     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   2.97980  2.52563  3.03204  0.19727     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   2.86982  3.47591  0.13017  3.36931     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   2.86982  3.47591  0.13017  3.36931     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   3.30705  0.14631  3.36166  2.73626     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   3.30705  0.14631  3.36166  2.73626     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   3.30705  0.14631  3.36166  2.73626     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   0.15719  3.27118  2.73043  3.16274     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   2.86982  3.47591  0.13017  3.36931     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   3.30705  0.14631  3.36166  2.73626     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   2.97980  2.52563  3.03204  0.19727     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   2.86982  3.47591  0.13017  3.36931     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   0.15719  3.27118  2.73043  3.16274     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   3.30705  0.14631  3.36166  2.73626     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   0.54754  2.55777  1.36722  2.41535     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   0.15719  3.27118  2.73043  3.16274     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   2.97980  2.52563  3.03204  0.19727     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   2.86982  3.47591  0.13017  3.36931     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   0.15719  3.27118  2.73043  3.16274     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   0.15719  3.27118  2.73043  3.16274     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   2.86982  3.47591  0.13017  3.36931     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   0.54754  2.55777  1.36722  2.41535     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   2.86982  3.47591  0.13017  3.36931     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.97980  2.52563  3.03204  0.19727     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_eightb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:12 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3604720587
+STATS LOCAL MSV       -7.3490  0.72800
+STATS LOCAL VITERBI   -8.3720  0.72800
+STATS LOCAL FORWARD   -3.6028  0.72800
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.39767  1.46026  1.31436  1.37831
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.57915  2.25909  2.64442  0.28946      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.57915  2.25909  2.64442  0.28946      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   0.23862  2.84929  2.43386  2.70756      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.81865  0.23582  2.88868  2.35662      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   0.23862  2.84929  2.43386  2.70756      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.81865  0.23582  2.88868  2.35662     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.81865  0.23582  2.88868  2.35662     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.53331  3.02441  0.20344  2.88069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.81865  0.23582  2.88868  2.35662     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.81865  0.23582  2.88868  2.35662     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.57915  2.25909  2.64442  0.28946     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.57915  2.25909  2.64442  0.28946     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.57915  2.25909  2.64442  0.28946     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.53331  3.02441  0.20344  2.88069     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   0.23862  2.84929  2.43386  2.70756     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   0.23862  2.84929  2.43386  2.70756     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   0.23862  2.84929  2.43386  2.70756     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.53331  3.02441  0.20344  2.88069     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.57915  2.25909  2.64442  0.28946     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.53331  3.02441  0.20344  2.88069     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_elevena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:36 2012
+NSEQ  32
+EFFN  3.675781
+CKSUM 3417897911
+STATS LOCAL MSV       -7.3843  0.71933
+STATS LOCAL VITERBI   -7.6506  0.71933
+STATS LOCAL FORWARD   -4.0339  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.25458  1.46041  1.35155  1.49690
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  0.00000        *
+      1   0.30737  2.17041  2.53008  2.64736      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      2   0.40424  1.86056  2.41150  2.43900      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      3   0.12858  3.48693  2.87081  3.39888      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      4   3.55554  0.11651  3.59965  2.91731      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      5   3.19761  2.66431  3.24155  0.16206      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      6   2.80026  2.50234  2.42463  0.26292      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      7   3.19761  2.66431  3.24155  0.16206      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      8   2.86129  0.33229  2.92687  1.76049      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+      9   0.12858  3.48693  2.87081  3.39888      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     10   3.02055  3.69484  0.10609  3.61089     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     11   3.55554  0.11651  3.59965  2.91731     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     12   3.02055  3.69484  0.10609  3.61089     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     13   0.44013  2.76228  1.51098  2.62826     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     14   3.19761  2.66431  3.24155  0.16206     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     15   3.02055  3.69484  0.10609  3.61089     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     16   3.02055  3.69484  0.10609  3.61089     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     17   0.12858  3.48693  2.87081  3.39888     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     18   3.19761  2.66431  3.24155  0.16206     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     19   3.02055  3.69484  0.10609  3.61089     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     20   3.19761  2.66431  3.24155  0.16206     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     21   3.55554  0.11651  3.59965  2.91731     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     22   3.19761  2.66431  3.24155  0.16206     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     23   3.19761  2.66431  3.24155  0.16206     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     24   3.02055  3.69484  0.10609  3.61089     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     25   3.02055  3.69484  0.10609  3.61089     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     26   3.55554  0.11651  3.59965  2.91731     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     27   3.19761  2.66431  3.24155  0.16206     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     28   3.55554  0.11651  3.59965  2.91731     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     29   0.12858  3.48693  2.87081  3.39888     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     30   3.55554  0.11651  3.59965  2.91731     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     31   0.12858  3.48693  2.87081  3.39888     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     32   3.55554  0.11651  3.59965  2.91731     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     33   0.21326  3.19501  2.24953  3.08698     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     34   0.12858  3.48693  2.87081  3.39888     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     35   3.55554  0.11651  3.59965  2.91731     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     36   3.02055  3.69484  0.10609  3.61089     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     37   0.12858  3.48693  2.87081  3.39888     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     38   3.19761  2.66431  3.24155  0.16206     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     39   3.02055  3.69484  0.10609  3.61089     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     40   0.12858  3.48693  2.87081  3.39888     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     41   0.12858  3.48693  2.87081  3.39888     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     42   3.02055  3.69484  0.10609  3.61089     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     43   3.02055  3.69484  0.10609  3.61089     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     44   0.12858  3.48693  2.87081  3.39888     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03463  4.07342  4.07342  1.46634  0.26236  1.09861  0.40547
+     45   3.55554  0.11651  3.59965  2.91731     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01747  4.05626        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_elevenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:41 2012
+NSEQ  5
+EFFN  3.208008
+CKSUM 4067533443
+STATS LOCAL MSV       -8.1074  0.71934
+STATS LOCAL VITERBI   -7.6996  0.71934
+STATS LOCAL FORWARD   -3.9608  0.71934
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.27246  1.46892  1.31219  1.51207
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  0.00000        *
+      1   0.14694  3.34284  2.77755  3.24098      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      2   0.14694  3.34284  2.77755  3.24098      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      3   0.14694  3.34284  2.77755  3.24098      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      4   3.05099  2.57118  3.10057  0.18486      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      5   3.05099  2.57118  3.10057  0.18486      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      6   3.05099  2.57118  3.10057  0.18486      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      7   3.05099  2.57118  3.10057  0.18486      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      8   3.38993  0.13548  3.44120  2.79746      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+      9   0.14694  3.34284  2.77755  3.24098      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     10   2.92124  3.54964  0.12142  3.45039     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     11   3.38993  0.13548  3.44120  2.79746     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     12   2.92124  3.54964  0.12142  3.45039     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     13   2.92124  3.54964  0.12142  3.45039     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     14   3.05099  2.57118  3.10057  0.18486     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     15   2.92124  3.54964  0.12142  3.45039     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     16   2.92124  3.54964  0.12142  3.45039     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     17   0.14694  3.34284  2.77755  3.24098     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     18   3.05099  2.57118  3.10057  0.18486     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     19   2.92124  3.54964  0.12142  3.45039     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     20   3.05099  2.57118  3.10057  0.18486     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     21   3.38993  0.13548  3.44120  2.79746     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     22   3.05099  2.57118  3.10057  0.18486     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     23   3.38993  0.13548  3.44120  2.79746     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     24   2.92124  3.54964  0.12142  3.45039     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     25   2.92124  3.54964  0.12142  3.45039     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     26   3.38993  0.13548  3.44120  2.79746     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     27   3.05099  2.57118  3.10057  0.18486     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     28   3.38993  0.13548  3.44120  2.79746     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     29   0.14694  3.34284  2.77755  3.24098     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     30   3.38993  0.13548  3.44120  2.79746     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     31   0.14694  3.34284  2.77755  3.24098     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     32   3.38993  0.13548  3.44120  2.79746     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     33   0.14694  3.34284  2.77755  3.24098     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     34   0.14694  3.34284  2.77755  3.24098     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     35   3.38993  0.13548  3.44120  2.79746     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     36   2.92124  3.54964  0.12142  3.45039     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     37   0.14694  3.34284  2.77755  3.24098     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     38   3.05099  2.57118  3.10057  0.18486     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     39   2.92124  3.54964  0.12142  3.45039     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     40   0.14694  3.34284  2.77755  3.24098     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     41   0.14694  3.34284  2.77755  3.24098     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     42   2.92124  3.54964  0.12142  3.45039     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     43   2.92124  3.54964  0.12142  3.45039     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     44   0.14694  3.34284  2.77755  3.24098     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03768  3.99047  3.99047  1.46634  0.26236  1.09861  0.40547
+     45   3.38993  0.13548  3.44120  2.79746     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01902  3.97180        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_elevenc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:45 2012
+NSEQ  20
+EFFN  3.481445
+CKSUM 987744611
+STATS LOCAL MSV       -7.5848  0.71932
+STATS LOCAL VITERBI   -7.4852  0.71932
+STATS LOCAL FORWARD   -4.0632  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.25409  1.53980  1.40804  1.36407
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  0.00000        *
+      1   3.13887  2.62707  3.18509  0.17078      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      2   0.13553  3.42977  2.83398  3.33617      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      3   3.13887  2.62707  3.18509  0.17078      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      4   3.49007  0.12362  3.53707  2.87028      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      5   3.13887  2.62707  3.18509  0.17078      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      6   3.13887  2.62707  3.18509  0.17078      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      7   3.13887  2.62707  3.18509  0.17078      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      8   3.49007  0.12362  3.53707  2.87028      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+      9   0.13553  3.42977  2.83398  3.33617      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     10   2.98175  3.63775  0.11183  3.54767     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     11   3.49007  0.12362  3.53707  2.87028     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     12   2.98175  3.63775  0.11183  3.54767     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     13   0.13553  3.42977  2.83398  3.33617     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     14   3.13887  2.62707  3.18509  0.17078     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     15   2.98175  3.63775  0.11183  3.54767     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     16   2.98175  3.63775  0.11183  3.54767     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     17   0.13553  3.42977  2.83398  3.33617     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     18   3.13887  2.62707  3.18509  0.17078     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     19   2.98175  3.63775  0.11183  3.54767     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     20   0.98772  2.55500  0.77629  2.41045     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     21   3.49007  0.12362  3.53707  2.87028     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     22   3.13887  2.62707  3.18509  0.17078     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     23   3.49007  0.12362  3.53707  2.87028     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     24   2.98175  3.63775  0.11183  3.54767     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     25   2.98175  3.63775  0.11183  3.54767     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     26   0.13553  3.42977  2.83398  3.33617     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     27   3.13887  2.62707  3.18509  0.17078     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     28   3.49007  0.12362  3.53707  2.87028     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     29   3.13887  2.62707  3.18509  0.17078     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     30   3.49007  0.12362  3.53707  2.87028     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     31   0.13553  3.42977  2.83398  3.33617     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     32   3.13887  2.62707  3.18509  0.17078     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     33   0.13553  3.42977  2.83398  3.33617     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     34   0.13553  3.42977  2.83398  3.33617     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     35   3.49007  0.12362  3.53707  2.87028     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     36   2.98175  3.63775  0.11183  3.54767     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     37   0.13553  3.42977  2.83398  3.33617     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     38   3.13887  2.62707  3.18509  0.17078     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     39   2.98175  3.63775  0.11183  3.54767     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     40   0.13553  3.42977  2.83398  3.33617     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     41   0.13553  3.42977  2.83398  3.33617     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     42   2.98175  3.63775  0.11183  3.54767     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     43   0.13553  3.42977  2.83398  3.33617     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     44   0.22376  3.13411  2.22332  3.02203     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03584  4.03979  4.03979  1.46634  0.26236  1.09861  0.40547
+     45   3.06247  0.19963  2.76820  2.63920     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01808  4.02203        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_five_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:27 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3440808981
+STATS LOCAL MSV       -7.7336  0.72845
+STATS LOCAL VITERBI   -8.5172  0.72845
+STATS LOCAL FORWARD   -3.3604  0.72845
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.33246  1.71713  1.20095  1.36382
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.53331  3.02441  0.20344  2.88069      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.81865  0.23582  2.88868  2.35662      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.81865  0.23582  2.88868  2.35662      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   0.23862  2.84929  2.43386  2.70756      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.57915  2.25909  2.64442  0.28946     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.53331  3.02441  0.20344  2.88069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   0.23862  2.84929  2.43386  2.70756     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.53331  3.02441  0.20344  2.88069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.81865  0.23582  2.88868  2.35662     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.57915  2.25909  2.64442  0.28946     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.57915  2.25909  2.64442  0.28946     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.57915  2.25909  2.64442  0.28946     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.53331  3.02441  0.20344  2.88069     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.53331  3.02441  0.20344  2.88069     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.57915  2.25909  2.64442  0.28946     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.57915  2.25909  2.64442  0.28946     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   0.23862  2.84929  2.43386  2.70756     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   0.23862  2.84929  2.43386  2.70756     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   0.23862  2.84929  2.43386  2.70756     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   0.23862  2.84929  2.43386  2.70756     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.15554  1.00938  2.23102  0.88601     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.53331  3.02441  0.20344  2.88069     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   0.23862  2.84929  2.43386  2.70756     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.53331  3.02441  0.20344  2.88069     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.53331  3.02441  0.20344  2.88069     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.53331  3.02441  0.20344  2.88069     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.57915  2.25909  2.64442  0.28946     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_foura_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:14 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3441996736
+STATS LOCAL MSV       -7.3600  0.72755
+STATS LOCAL VITERBI   -8.3191  0.72755
+STATS LOCAL FORWARD   -3.0189  0.72755
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.28872  1.35377  1.31697  1.61865
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   0.23862  2.84929  2.43386  2.70756      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.57915  2.25909  2.64442  0.28946      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.81865  0.23582  2.88868  2.35662      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   0.23862  2.84929  2.43386  2.70756      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.81865  0.23582  2.88868  2.35662     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.81865  0.23582  2.88868  2.35662     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.53331  3.02441  0.20344  2.88069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   0.23862  2.84929  2.43386  2.70756     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.57915  2.25909  2.64442  0.28946     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   0.23862  2.84929  2.43386  2.70756     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.81865  0.23582  2.88868  2.35662     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.81865  0.23582  2.88868  2.35662     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.57915  2.25909  2.64442  0.28946     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.81865  0.23582  2.88868  2.35662     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.53331  3.02441  0.20344  2.88069     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.53331  3.02441  0.20344  2.88069     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   2.81865  0.23582  2.88868  2.35662     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.57915  2.25909  2.64442  0.28946     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   0.23862  2.84929  2.43386  2.70756     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   0.23862  2.84929  2.43386  2.70756     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.53331  3.02441  0.20344  2.88069     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.81865  0.23582  2.88868  2.35662     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   0.23862  2.84929  2.43386  2.70756     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   2.81865  0.23582  2.88868  2.35662     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.53331  3.02441  0.20344  2.88069     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   0.23862  2.84929  2.43386  2.70756     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   2.53331  3.02441  0.20344  2.88069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   0.23862  2.84929  2.43386  2.70756     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.53331  3.02441  0.20344  2.88069     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   2.53331  3.02441  0.20344  2.88069     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.53331  3.02441  0.20344  2.88069     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   2.81865  0.23582  2.88868  2.35662     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_fourb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:19 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 909930947
+STATS LOCAL MSV       -7.5897  0.72766
+STATS LOCAL VITERBI   -8.2123  0.72766
+STATS LOCAL FORWARD   -3.0207  0.72766
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.34189  1.34952  1.31824  1.55270
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   0.23862  2.84929  2.43386  2.70756      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+     44   2.53331  3.02441  0.20344  2.88069     44 - -
+          1.38629  1.38629  1.38629  1.38629
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+     45   2.81865  0.23582  2.88868  2.35662     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_fourteen_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:28:14 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 3318248282
+STATS LOCAL MSV       -7.9911  0.72105
+STATS LOCAL VITERBI   -7.7365  0.72105
+STATS LOCAL FORWARD   -4.0158  0.72105
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.21240  1.73126  1.43760  1.24493
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
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+      2   2.43223  0.62271  2.50508  1.22417      2 - -
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+      4   3.30705  0.14631  3.36166  2.73626      4 - -
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+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   3.30705  0.14631  3.36166  2.73626     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_one_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:25:26 2012
+NSEQ  4
+EFFN  3.691406
+CKSUM 2670710095
+STATS LOCAL MSV       -7.7237  0.71932
+STATS LOCAL VITERBI   -7.6214  0.71932
+STATS LOCAL FORWARD   -3.8013  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.05540  2.03553  1.56163  1.16622
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  0.00000        *
+      1   0.96133  2.18963  2.20654  0.92741      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      2   3.20221  2.66723  3.24596  0.16140      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      3   0.12806  3.49137  2.87366  3.40376      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      4   3.20221  2.66723  3.24596  0.16140      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      5   3.02354  3.69924  0.10566  3.61577      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      6   3.20221  2.66723  3.24596  0.16140      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      7   3.20221  2.66723  3.24596  0.16140      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      8   3.20221  2.66723  3.24596  0.16140      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+      9   3.20221  2.66723  3.24596  0.16140      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     10   3.02354  3.69924  0.10566  3.61577     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     11   3.56062  0.11598  3.60449  2.92094     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     12   0.12806  3.49137  2.87366  3.40376     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     13   0.12806  3.49137  2.87366  3.40376     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     14   0.12806  3.49137  2.87366  3.40376     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     15   3.02354  3.69924  0.10566  3.61577     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     16   0.12806  3.49137  2.87366  3.40376     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     17   0.12806  3.49137  2.87366  3.40376     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     18   3.20221  2.66723  3.24596  0.16140     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     19   3.02354  3.69924  0.10566  3.61577     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     20   3.20221  2.66723  3.24596  0.16140     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     21   3.56062  0.11598  3.60449  2.92094     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     22   3.20221  2.66723  3.24596  0.16140     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     23   3.20221  2.66723  3.24596  0.16140     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     24   0.12806  3.49137  2.87366  3.40376     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     25   3.02354  3.69924  0.10566  3.61577     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     26   3.56062  0.11598  3.60449  2.92094     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     27   3.20221  2.66723  3.24596  0.16140     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     28   3.56062  0.11598  3.60449  2.92094     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     29   0.12806  3.49137  2.87366  3.40376     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     30   0.12806  3.49137  2.87366  3.40376     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     31   3.20221  2.66723  3.24596  0.16140     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     32   0.12806  3.49137  2.87366  3.40376     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     33   0.84713  2.57557  0.89799  2.43206     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     34   0.12806  3.49137  2.87366  3.40376     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     35   3.20221  2.66723  3.24596  0.16140     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     36   3.02354  3.69924  0.10566  3.61577     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     37   0.12806  3.49137  2.87366  3.40376     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     38   3.20221  2.66723  3.24596  0.16140     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     39   3.02354  3.69924  0.10566  3.61577     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     40   0.12806  3.49137  2.87366  3.40376     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     41   0.12806  3.49137  2.87366  3.40376     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     42   3.02354  3.69924  0.10566  3.61577     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     43   0.12806  3.49137  2.87366  3.40376     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     44   0.12806  3.49137  2.87366  3.40376     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03454  4.07608  4.07608  1.46634  0.26236  1.09861  0.40547
+     45   3.20221  2.66723  3.24596  0.16140     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01742  4.05896        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_sixa_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:35 2012
+NSEQ  15
+EFFN  3.687744
+CKSUM 797667666
+STATS LOCAL MSV       -7.6502  0.71933
+STATS LOCAL VITERBI   -7.7243  0.71933
+STATS LOCAL FORWARD   -4.2597  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.16124  1.50955  1.53139  1.38767
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  0.00000        *
+      1   0.12818  3.49033  2.87299  3.40262      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      2   0.12818  3.49033  2.87299  3.40262      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      3   0.12818  3.49033  2.87299  3.40262      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      4   3.20113  2.66655  3.24493  0.16155      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      5   3.20113  2.66655  3.24493  0.16155      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      6   3.55943  0.11610  3.60336  2.92009      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      7   3.20113  2.66655  3.24493  0.16155      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      8   3.55943  0.11610  3.60336  2.92009      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+      9   0.12818  3.49033  2.87299  3.40262      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     10   0.12818  3.49033  2.87299  3.40262     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     11   3.55943  0.11610  3.60336  2.92009     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     12   3.02284  3.69821  0.10576  3.61463     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     13   0.94059  2.58194  0.80594  2.43831     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     14   3.20113  2.66655  3.24493  0.16155     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     15   3.02284  3.69821  0.10576  3.61463     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     16   3.02284  3.69821  0.10576  3.61463     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     17   0.12818  3.49033  2.87299  3.40262     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     18   3.20113  2.66655  3.24493  0.16155     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     19   0.94059  2.58194  0.80594  2.43831     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     20   3.20113  2.66655  3.24493  0.16155     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     21   3.55943  0.11610  3.60336  2.92009     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     22   3.20113  2.66655  3.24493  0.16155     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     23   3.20113  2.66655  3.24493  0.16155     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     24   3.02284  3.69821  0.10576  3.61463     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     25   3.02284  3.69821  0.10576  3.61463     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     26   3.20113  2.66655  3.24493  0.16155     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     27   3.20113  2.66655  3.24493  0.16155     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     28   3.55943  0.11610  3.60336  2.92009     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     29   3.55943  0.11610  3.60336  2.92009     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     30   3.55943  0.11610  3.60336  2.92009     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     31   0.12818  3.49033  2.87299  3.40262     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     32   2.51659  1.18738  2.58588  0.61820     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     33   0.12818  3.49033  2.87299  3.40262     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     34   0.12818  3.49033  2.87299  3.40262     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     35   3.55943  0.11610  3.60336  2.92009     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     36   3.02284  3.69821  0.10576  3.61463     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     37   0.12818  3.49033  2.87299  3.40262     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     38   3.20113  2.66655  3.24493  0.16155     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     39   3.02284  3.69821  0.10576  3.61463     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     40   0.12818  3.49033  2.87299  3.40262     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     41   0.12818  3.49033  2.87299  3.40262     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     42   3.02284  3.69821  0.10576  3.61463     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     43   0.12818  3.49033  2.87299  3.40262     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     44   0.12818  3.49033  2.87299  3.40262     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03456  4.07546  4.07546  1.46634  0.26236  1.09861  0.40547
+     45   3.55943  0.11610  3.60336  2.92009     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01743  4.05833        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_sixb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:43 2012
+NSEQ  8
+EFFN  3.558594
+CKSUM 2758897519
+STATS LOCAL MSV       -7.6565  0.71933
+STATS LOCAL VITERBI   -7.6277  0.71933
+STATS LOCAL FORWARD   -3.9158  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.10338  1.44505  1.58840  1.47724
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  0.00000        *
+      1   0.13267  3.45290  2.84891  3.36153      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      2   0.13267  3.45290  2.84891  3.36153      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      3   0.13267  3.45290  2.84891  3.36153      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      4   3.16254  2.64208  3.20785  0.16721      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      5   3.51660  0.12068  3.56245  2.88939      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      6   3.51660  0.12068  3.56245  2.88939      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      7   3.16254  2.64208  3.20785  0.16721      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      8   3.51660  0.12068  3.56245  2.88939      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+      9   0.13267  3.45290  2.84891  3.36153      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     10   0.13267  3.45290  2.84891  3.36153     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     11   3.51660  0.12068  3.56245  2.88939     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     12   2.99754  3.66093  0.10946  3.57332     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     13   0.13267  3.45290  2.84891  3.36153     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     14   3.16254  2.64208  3.20785  0.16721     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     15   2.99754  3.66093  0.10946  3.57332     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     16   2.99754  3.66093  0.10946  3.57332     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     17   0.13267  3.45290  2.84891  3.36153     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     18   3.16254  2.64208  3.20785  0.16721     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     19   0.39802  2.79742  1.62044  2.66543     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     20   3.16254  2.64208  3.20785  0.16721     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     21   3.51660  0.12068  3.56245  2.88939     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     22   3.16254  2.64208  3.20785  0.16721     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     23   0.13267  3.45290  2.84891  3.36153     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     24   2.99754  3.66093  0.10946  3.57332     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     25   2.99754  3.66093  0.10946  3.57332     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     26   3.16254  2.64208  3.20785  0.16721     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     27   3.16254  2.64208  3.20785  0.16721     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     28   3.51660  0.12068  3.56245  2.88939     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     29   3.51660  0.12068  3.56245  2.88939     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     30   2.63794  1.53936  2.70289  0.43547     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     31   0.13267  3.45290  2.84891  3.36153     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     32   3.51660  0.12068  3.56245  2.88939     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     33   1.49627  2.23192  2.35305  0.55576     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     34   0.13267  3.45290  2.84891  3.36153     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     35   3.51660  0.12068  3.56245  2.88939     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     36   2.99754  3.66093  0.10946  3.57332     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     37   0.13267  3.45290  2.84891  3.36153     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     38   3.16254  2.64208  3.20785  0.16721     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     39   2.99754  3.66093  0.10946  3.57332     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     40   0.13267  3.45290  2.84891  3.36153     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     41   0.13267  3.45290  2.84891  3.36153     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     42   2.99754  3.66093  0.10946  3.57332     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     43   0.13267  3.45290  2.84891  3.36153     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     44   0.13267  3.45290  2.84891  3.36153     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03535  4.05328  4.05328  1.46634  0.26236  1.09861  0.40547
+     45   3.51660  0.12068  3.56245  2.88939     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01783  4.03576        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_sixc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:50 2012
+NSEQ  13
+EFFN  3.443604
+CKSUM 4173496295
+STATS LOCAL MSV       -7.6779  0.71933
+STATS LOCAL VITERBI   -7.6270  0.71933
+STATS LOCAL FORWARD   -4.2468  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.09130  1.57353  1.59959  1.36677
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  0.00000        *
+      1   0.13699  3.41821  2.82651  3.32349      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      2   0.13699  3.41821  2.82651  3.32349      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      3   0.13699  3.41821  2.82651  3.32349      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      4   3.12708  2.61958  3.17375  0.17260      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      5   3.12708  2.61958  3.17375  0.17260      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      6   3.12708  2.61958  3.17375  0.17260      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      7   3.12708  2.61958  3.17375  0.17260      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      8   3.47678  0.12512  3.52437  2.86068      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+      9   0.13699  3.41821  2.82651  3.32349      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     10   0.13699  3.41821  2.82651  3.32349     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     11   3.47678  0.12512  3.52437  2.86068     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     12   2.97381  3.62611  0.11305  3.53480     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     13   0.13699  3.41821  2.82651  3.32349     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     14   3.12708  2.61958  3.17375  0.17260     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     15   2.97381  3.62611  0.11305  3.53480     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     16   2.97381  3.62611  0.11305  3.53480     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     17   0.13699  3.41821  2.82651  3.32349     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     18   3.12708  2.61958  3.17375  0.17260     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     19   0.13699  3.41821  2.82651  3.32349     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     20   3.12708  2.61958  3.17375  0.17260     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     21   3.47678  0.12512  3.52437  2.86068     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     22   3.12708  2.61958  3.17375  0.17260     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     23   0.13699  3.41821  2.82651  3.32349     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     24   2.97381  3.62611  0.11305  3.53480     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     25   2.97381  3.62611  0.11305  3.53480     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     26   3.47678  0.12512  3.52437  2.86068     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     27   3.12708  2.61958  3.17375  0.17260     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     28   3.47678  0.12512  3.52437  2.86068     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     29   3.47678  0.12512  3.52437  2.86068     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     30   3.12708  2.61958  3.17375  0.17260     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     31   0.13699  3.41821  2.82651  3.32349     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     32   3.12708  2.61958  3.17375  0.17260     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     33   0.13699  3.41821  2.82651  3.32349     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     34   1.39388  0.65071  2.27615  2.05938     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     35   3.47678  0.12512  3.52437  2.86068     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     36   2.97381  3.62611  0.11305  3.53480     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     37   0.13699  3.41821  2.82651  3.32349     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     38   3.12708  2.61958  3.17375  0.17260     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     39   2.97381  3.62611  0.11305  3.53480     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     40   0.13699  3.41821  2.82651  3.32349     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     41   0.13699  3.41821  2.82651  3.32349     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     42   2.97381  3.62611  0.11305  3.53480     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     43   0.13699  3.41821  2.82651  3.32349     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     44   0.13699  3.41821  2.82651  3.32349     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03608  4.03311  4.03311  1.46634  0.26236  1.09861  0.40547
+     45   3.47678  0.12512  3.52437  2.86068     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01820  4.01523        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_sixd_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:56 2012
+NSEQ  18
+EFFN  3.739746
+CKSUM 2077131438
+STATS LOCAL MSV       -7.3089  0.71933
+STATS LOCAL VITERBI   -7.8161  0.71933
+STATS LOCAL FORWARD   -4.1699  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.13317  1.60280  1.55991  1.32237
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  0.00000        *
+      1   0.12648  3.50496  2.88239  3.41868      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      2   0.12648  3.50496  2.88239  3.41868      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      3   0.12648  3.50496  2.88239  3.41868      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      4   3.21631  2.67616  3.25951  0.15939      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      5   3.21631  2.67616  3.25951  0.15939      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      6   3.21631  2.67616  3.25951  0.15939      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      7   3.21631  2.67616  3.25951  0.15939      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      8   3.57612  0.11437  3.61930  2.93201      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+      9   0.12648  3.50496  2.88239  3.41868      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     10   0.12648  3.50496  2.88239  3.41868     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     11   3.57612  0.11437  3.61930  2.93201     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     12   3.03265  3.71270  0.10436  3.63069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     13   0.28094  3.03315  1.94829  2.91416     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     14   3.21631  2.67616  3.25951  0.15939     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     15   3.03265  3.71270  0.10436  3.63069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     16   3.03265  3.71270  0.10436  3.63069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     17   0.12648  3.50496  2.88239  3.41868     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     18   3.21631  2.67616  3.25951  0.15939     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     19   0.12648  3.50496  2.88239  3.41868     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     20   3.21631  2.67616  3.25951  0.15939     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     21   3.57612  0.11437  3.61930  2.93201     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     22   3.21631  2.67616  3.25951  0.15939     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     23   2.14675  2.21275  0.89986  1.00208     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     24   3.03265  3.71270  0.10436  3.63069     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     25   3.03265  3.71270  0.10436  3.63069     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     26   2.92927  2.02237  2.98433  0.26965     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     27   3.21631  2.67616  3.25951  0.15939     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     28   3.57612  0.11437  3.61930  2.93201     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     29   3.57612  0.11437  3.61930  2.93201     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     30   3.57612  0.11437  3.61930  2.93201     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     31   0.12648  3.50496  2.88239  3.41868     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     32   3.21631  2.67616  3.25951  0.15939     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     33   0.12648  3.50496  2.88239  3.41868     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     34   0.94678  2.19731  2.21189  0.93798     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     35   3.57612  0.11437  3.61930  2.93201     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     36   3.03265  3.71270  0.10436  3.63069     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     37   0.12648  3.50496  2.88239  3.41868     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     38   3.21631  2.67616  3.25951  0.15939     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     39   3.03265  3.71270  0.10436  3.63069     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     40   0.12648  3.50496  2.88239  3.41868     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     41   0.12648  3.50496  2.88239  3.41868     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     42   3.03265  3.71270  0.10436  3.63069     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     43   0.12648  3.50496  2.88239  3.41868     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     44   0.12648  3.50496  2.88239  3.41868     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03425  4.08425  4.08425  1.46634  0.26236  1.09861  0.40547
+     45   3.57612  0.11437  3.61930  2.93201     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01727  4.06727        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_ten_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:21 2012
+NSEQ  22
+EFFN  3.236084
+CKSUM 2896313313
+STATS LOCAL MSV       -8.1273  0.71932
+STATS LOCAL VITERBI   -7.6160  0.71932
+STATS LOCAL FORWARD   -3.9033  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.53686  1.12476  1.25556  1.74127
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  0.00000        *
+      1   1.49846  0.59962  2.29674  2.06420      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      2   0.14567  3.35213  2.78361  3.25115      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      3   0.14567  3.35213  2.78361  3.25115      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      4   3.40067  0.13415  3.45149  2.80532      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      5   3.06030  2.57712  3.10954  0.18331      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      6   3.40067  0.13415  3.45149  2.80532      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      7   3.40067  0.13415  3.45149  2.80532      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      8   3.40067  0.13415  3.45149  2.80532      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+      9   0.14567  3.35213  2.78361  3.25115      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     10   2.92780  3.55913  0.12034  3.46085     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     11   3.40067  0.13415  3.45149  2.80532     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     12   2.92780  3.55913  0.12034  3.46085     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     13   0.14567  3.35213  2.78361  3.25115     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     14   3.06030  2.57712  3.10954  0.18331     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     15   2.92780  3.55913  0.12034  3.46085     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     16   2.92780  3.55913  0.12034  3.46085     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     17   0.14567  3.35213  2.78361  3.25115     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     18   3.06030  2.57712  3.10954  0.18331     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     19   2.92780  3.55913  0.12034  3.46085     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     20   3.40067  0.13415  3.45149  2.80532     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     21   3.40067  0.13415  3.45149  2.80532     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     22   3.06030  2.57712  3.10954  0.18331     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     23   3.40067  0.13415  3.45149  2.80532     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     24   2.92780  3.55913  0.12034  3.46085     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     25   2.92780  3.55913  0.12034  3.46085     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     26   3.40067  0.13415  3.45149  2.80532     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     27   3.06030  2.57712  3.10954  0.18331     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     28   3.40067  0.13415  3.45149  2.80532     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     29   2.92780  3.55913  0.12034  3.46085     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     30   3.40067  0.13415  3.45149  2.80532     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     31   2.92780  3.55913  0.12034  3.46085     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     32   3.40067  0.13415  3.45149  2.80532     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     33   3.40067  0.13415  3.45149  2.80532     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     34   3.06030  2.57712  3.10954  0.18331     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     35   3.40067  0.13415  3.45149  2.80532     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     36   2.92780  3.55913  0.12034  3.46085     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     37   0.14567  3.35213  2.78361  3.25115     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     38   3.06030  2.57712  3.10954  0.18331     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     39   2.92780  3.55913  0.12034  3.46085     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     40   0.14567  3.35213  2.78361  3.25115     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     41   0.14567  3.35213  2.78361  3.25115     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     42   2.92780  3.55913  0.12034  3.46085     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     43   2.92780  3.55913  0.12034  3.46085     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     44   0.14567  3.35213  2.78361  3.25115     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03749  3.99564  3.99564  1.46634  0.26236  1.09861  0.40547
+     45   3.40067  0.13415  3.45149  2.80532     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01892  3.97708        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_thirteen_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:28:05 2012
+NSEQ  8
+EFFN  3.175781
+CKSUM 2342198515
+STATS LOCAL MSV       -8.1781  0.71931
+STATS LOCAL VITERBI   -7.7853  0.71931
+STATS LOCAL FORWARD   -4.2608  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.21574  1.40301  1.31193  1.66943
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  0.00000        *
+      1   0.14843  3.33206  2.77050  3.22920      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      2   0.14843  3.33206  2.77050  3.22920      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      3   0.14843  3.33206  2.77050  3.22920      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      4   3.37748  0.13704  3.42926  2.78832      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      5   3.04021  2.56430  3.09020  0.18668      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      6   3.37748  0.13704  3.42926  2.78832      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      7   3.04021  2.56430  3.09020  0.18668      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      8   3.37748  0.13704  3.42926  2.78832      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+      9   0.14843  3.33206  2.77050  3.22920      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     10   0.14843  3.33206  2.77050  3.22920     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     11   3.37748  0.13704  3.42926  2.78832     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     12   2.91360  3.53861  0.12268  3.43825     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     13   0.14843  3.33206  2.77050  3.22920     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     14   3.04021  2.56430  3.09020  0.18668     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     15   2.91360  3.53861  0.12268  3.43825     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     16   2.91360  3.53861  0.12268  3.43825     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     17   0.14843  3.33206  2.77050  3.22920     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     18   3.04021  2.56430  3.09020  0.18668     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     19   2.91360  3.53861  0.12268  3.43825     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     20   3.37748  0.13704  3.42926  2.78832     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     21   3.37748  0.13704  3.42926  2.78832     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     22   3.04021  2.56430  3.09020  0.18668     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     23   3.37748  0.13704  3.42926  2.78832     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     24   2.91360  3.53861  0.12268  3.43825     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     25   2.91360  3.53861  0.12268  3.43825     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     26   3.37748  0.13704  3.42926  2.78832     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     27   3.04021  2.56430  3.09020  0.18668     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     28   3.37748  0.13704  3.42926  2.78832     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     29   2.91360  3.53861  0.12268  3.43825     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     30   0.14843  3.33206  2.77050  3.22920     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     31   2.91360  3.53861  0.12268  3.43825     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     32   0.14843  3.33206  2.77050  3.22920     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     33   0.14843  3.33206  2.77050  3.22920     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     34   3.04021  2.56430  3.09020  0.18668     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     35   3.37748  0.13704  3.42926  2.78832     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     36   2.91360  3.53861  0.12268  3.43825     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     37   0.14843  3.33206  2.77050  3.22920     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     38   3.04021  2.56430  3.09020  0.18668     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     39   2.91360  3.53861  0.12268  3.43825     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     40   0.14843  3.33206  2.77050  3.22920     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     41   0.14843  3.33206  2.77050  3.22920     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     42   2.91360  3.53861  0.12268  3.43825     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     43   2.91360  3.53861  0.12268  3.43825     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     44   0.14843  3.33206  2.77050  3.22920     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03791  3.98449  3.98449  1.46634  0.26236  1.09861  0.40547
+     45   3.37748  0.13704  3.42926  2.78832     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01914  3.96571        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_three_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:26:06 2012
+NSEQ  6
+EFFN  3.249023
+CKSUM 954103482
+STATS LOCAL MSV       -8.0739  0.71932
+STATS LOCAL VITERBI   -7.8238  0.71932
+STATS LOCAL FORWARD   -4.1109  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.47195  1.61868  1.19247  1.31344
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  0.00000        *
+      1   3.06457  2.57984  3.11364  0.18260      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      2   3.06457  2.57984  3.11364  0.18260      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      3   2.93080  3.56347  0.11985  3.46564      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      4   3.40558  0.13354  3.45619  2.80891      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      5   3.06457  2.57984  3.11364  0.18260      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      6   3.06457  2.57984  3.11364  0.18260      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      7   3.06457  2.57984  3.11364  0.18260      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      8   3.40558  0.13354  3.45619  2.80891      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+      9   0.14509  3.35639  2.78639  3.25580      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     10   2.93080  3.56347  0.11985  3.46564     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     11   3.40558  0.13354  3.45619  2.80891     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     12   2.93080  3.56347  0.11985  3.46564     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     13   0.14509  3.35639  2.78639  3.25580     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     14   3.06457  2.57984  3.11364  0.18260     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     15   2.93080  3.56347  0.11985  3.46564     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     16   2.93080  3.56347  0.11985  3.46564     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     17   0.14509  3.35639  2.78639  3.25580     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     18   3.06457  2.57984  3.11364  0.18260     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     19   2.93080  3.56347  0.11985  3.46564     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     20   3.06457  2.57984  3.11364  0.18260     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     21   3.40558  0.13354  3.45619  2.80891     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     22   3.06457  2.57984  3.11364  0.18260     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     23   3.06457  2.57984  3.11364  0.18260     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     24   2.93080  3.56347  0.11985  3.46564     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     25   2.93080  3.56347  0.11985  3.46564     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     26   3.40558  0.13354  3.45619  2.80891     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     27   3.06457  2.57984  3.11364  0.18260     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     28   3.40558  0.13354  3.45619  2.80891     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     29   2.93080  3.56347  0.11985  3.46564     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     30   0.14509  3.35639  2.78639  3.25580     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     31   0.14509  3.35639  2.78639  3.25580     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     32   3.40558  0.13354  3.45619  2.80891     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     33   0.14509  3.35639  2.78639  3.25580     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     34   0.14509  3.35639  2.78639  3.25580     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     35   3.06457  2.57984  3.11364  0.18260     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     36   2.93080  3.56347  0.11985  3.46564     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     37   0.14509  3.35639  2.78639  3.25580     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     38   3.06457  2.57984  3.11364  0.18260     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     39   2.93080  3.56347  0.11985  3.46564     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     40   0.14509  3.35639  2.78639  3.25580     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     41   0.14509  3.35639  2.78639  3.25580     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     42   2.93080  3.56347  0.11985  3.46564     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     43   2.93080  3.56347  0.11985  3.46564     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     44   2.93080  3.56347  0.11985  3.46564     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03739  3.99802  3.99802  1.46634  0.26236  1.09861  0.40547
+     45   3.40558  0.13354  3.45619  2.80891     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01887  3.97950        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_twelve_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:27:55 2012
+NSEQ  74
+EFFN  3.410034
+CKSUM 388750452
+STATS LOCAL MSV       -7.4871  0.71933
+STATS LOCAL VITERBI   -7.6504  0.71933
+STATS LOCAL FORWARD   -4.1874  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.28425  1.46318  1.36431  1.44356
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  0.00000        *
+      1   0.13831  3.40783  2.81980  3.31211      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      2   0.13831  3.40783  2.81980  3.31211      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      3   0.13831  3.40783  2.81980  3.31211      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      4   3.25133  0.17525  3.30615  2.46070      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      5   3.11652  2.61288  3.16360  0.17424      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      6   3.11652  2.61288  3.16360  0.17424      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      7   3.11652  2.61288  3.16360  0.17424      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      8   3.46484  0.12649  3.51294  2.85204      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+      9   0.13831  3.40783  2.81980  3.31211      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     10   2.96666  3.61565  0.11415  3.52323     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     11   3.46484  0.12649  3.51294  2.85204     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     12   0.13831  3.40783  2.81980  3.31211     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     13   0.13831  3.40783  2.81980  3.31211     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     14   3.11652  2.61288  3.16360  0.17424     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     15   2.96666  3.61565  0.11415  3.52323     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     16   2.96666  3.61565  0.11415  3.52323     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     17   0.13831  3.40783  2.81980  3.31211     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     18   3.11652  2.61288  3.16360  0.17424     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     19   2.96666  3.61565  0.11415  3.52323     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     20   3.11652  2.61288  3.16360  0.17424     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     21   3.46484  0.12649  3.51294  2.85204     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     22   3.11652  2.61288  3.16360  0.17424     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     23   3.11652  2.61288  3.16360  0.17424     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     24   2.96666  3.61565  0.11415  3.52323     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     25   2.96666  3.61565  0.11415  3.52323     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     26   3.46484  0.12649  3.51294  2.85204     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     27   3.11652  2.61288  3.16360  0.17424     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     28   3.46484  0.12649  3.51294  2.85204     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     29   0.41203  2.75544  1.60231  2.62160     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     30   3.46484  0.12649  3.51294  2.85204     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     31   2.96666  3.61565  0.11415  3.52323     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     32   3.46484  0.12649  3.51294  2.85204     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     33   0.13831  3.40783  2.81980  3.31211     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     34   2.31167  2.32835  2.73359  0.30319     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     35   3.46484  0.12649  3.51294  2.85204     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     36   2.96666  3.61565  0.11415  3.52323     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     37   0.16646  3.30237  2.57918  3.20130     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     38   3.11652  2.61288  3.16360  0.17424     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     39   2.96666  3.61565  0.11415  3.52323     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     40   0.13831  3.40783  2.81980  3.31211     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     41   0.13831  3.40783  2.81980  3.31211     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     42   2.96666  3.61565  0.11415  3.52323     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     43   2.96666  3.61565  0.11415  3.52323     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     44   0.13831  3.40783  2.81980  3.31211     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03630  4.02714  4.02714  1.46634  0.26236  1.09861  0.40547
+     45   3.46484  0.12649  3.51294  2.85204     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01832  4.00916        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_twoa_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:25:36 2012
+NSEQ  24
+EFFN  3.858398
+CKSUM 3088050842
+STATS LOCAL MSV       -7.0905  0.71932
+STATS LOCAL VITERBI   -7.7638  0.71932
+STATS LOCAL FORWARD   -3.7065  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.35209  1.39088  1.23234  1.60528
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  0.00000        *
+      1   3.61308  0.11065  3.65457  2.95832      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      2   0.12278  3.53742  2.90323  3.45435      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      3   0.12278  3.53742  2.90323  3.45435      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      4   2.85962  0.34778  2.92534  1.69931      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      5   3.02517  2.16151  3.07670  0.23548      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      6   3.25017  2.69764  3.29205  0.15468      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      7   3.25017  2.69764  3.29205  0.15468      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      8   3.61308  0.11065  3.65457  2.95832      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+      9   0.12278  3.53742  2.90323  3.45435      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     10   3.05426  3.74470  0.10134  3.66619     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     11   3.61308  0.11065  3.65457  2.95832     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     12   3.05426  3.74470  0.10134  3.66619     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     13   0.12278  3.53742  2.90323  3.45435     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     14   2.56518  1.23160  2.63342  0.58082     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     15   3.05426  3.74470  0.10134  3.66619     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     16   3.05426  3.74470  0.10134  3.66619     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     17   0.12278  3.53742  2.90323  3.45435     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     18   3.25017  2.69764  3.29205  0.15468     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     19   3.05426  3.74470  0.10134  3.66619     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     20   2.87164  1.85703  2.92932  0.30948     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     21   3.61308  0.11065  3.65457  2.95832     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     22   3.25017  2.69764  3.29205  0.15468     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     23   3.61308  0.11065  3.65457  2.95832     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     24   3.05426  3.74470  0.10134  3.66619     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     25   3.05426  3.74470  0.10134  3.66619     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     26   3.38961  0.15768  3.43962  2.52474     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     27   3.25017  2.69764  3.29205  0.15468     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     28   2.98238  0.28720  3.04518  1.88795     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     29   2.20598  2.99459  0.26627  2.60951     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     30   0.63005  2.64466  1.15619  2.50444     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     31   0.20489  3.24864  2.26976  3.14424     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     32   3.61308  0.11065  3.65457  2.95832     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     33   0.12278  3.53742  2.90323  3.45435     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     34   0.12278  3.53742  2.90323  3.45435     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     35   3.61308  0.11065  3.65457  2.95832     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     36   2.69512  3.58668  0.13413  3.49662     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     37   0.12278  3.53742  2.90323  3.45435     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     38   3.25017  2.69764  3.29205  0.15468     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     39   3.05426  3.74470  0.10134  3.66619     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     40   0.12278  3.53742  2.90323  3.45435     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     41   0.12278  3.53742  2.90323  3.45435     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     42   3.05426  3.74470  0.10134  3.66619     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     43   3.05426  3.74470  0.10134  3.66619     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     44   3.05426  3.74470  0.10134  3.66619     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03357  4.10403  4.10403  1.46634  0.26236  1.09861  0.40547
+     45   3.61308  0.11065  3.65457  2.95832     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01693  4.08739        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_twob_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:25:43 2012
+NSEQ  8
+EFFN  3.222656
+CKSUM 2547926137
+STATS LOCAL MSV       -7.7534  0.71932
+STATS LOCAL VITERBI   -7.7335  0.71932
+STATS LOCAL FORWARD   -4.0829  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.40323  1.39104  1.31591  1.43906
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  0.00000        *
+      1   3.39555  0.13478  3.44658  2.80157      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      2   0.14627  3.34770  2.78072  3.24630      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      3   0.14627  3.34770  2.78072  3.24630      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      4   3.05586  2.57429  3.10526  0.18405      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      5   3.05586  2.57429  3.10526  0.18405      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      6   3.05586  2.57429  3.10526  0.18405      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      7   3.05586  2.57429  3.10526  0.18405      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      8   3.39555  0.13478  3.44658  2.80157      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+      9   0.14627  3.34770  2.78072  3.24630      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     10   2.92468  3.55461  0.12085  3.45586     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     11   3.39555  0.13478  3.44658  2.80157     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     12   2.92468  3.55461  0.12085  3.45586     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     13   0.14627  3.34770  2.78072  3.24630     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     14   3.39555  0.13478  3.44658  2.80157     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     15   2.92468  3.55461  0.12085  3.45586     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     16   2.92468  3.55461  0.12085  3.45586     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     17   0.14627  3.34770  2.78072  3.24630     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     18   3.05586  2.57429  3.10526  0.18405     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     19   0.14627  3.34770  2.78072  3.24630     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     20   3.05586  2.57429  3.10526  0.18405     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     21   3.39555  0.13478  3.44658  2.80157     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     22   3.05586  2.57429  3.10526  0.18405     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     23   3.05586  2.57429  3.10526  0.18405     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     24   2.92468  3.55461  0.12085  3.45586     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     25   2.92468  3.55461  0.12085  3.45586     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     26   3.39555  0.13478  3.44658  2.80157     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     27   3.05586  2.57429  3.10526  0.18405     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     28   3.39555  0.13478  3.44658  2.80157     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     29   2.92468  3.55461  0.12085  3.45586     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     30   0.14627  3.34770  2.78072  3.24630     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     31   2.92468  3.55461  0.12085  3.45586     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     32   3.39555  0.13478  3.44658  2.80157     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     33   0.14627  3.34770  2.78072  3.24630     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     34   3.39555  0.13478  3.44658  2.80157     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     35   3.39555  0.13478  3.44658  2.80157     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     36   3.05586  2.57429  3.10526  0.18405     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     37   0.14627  3.34770  2.78072  3.24630     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     38   3.05586  2.57429  3.10526  0.18405     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     39   2.92468  3.55461  0.12085  3.45586     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     40   0.14627  3.34770  2.78072  3.24630     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     41   0.14627  3.34770  2.78072  3.24630     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     42   2.92468  3.55461  0.12085  3.45586     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     43   2.92468  3.55461  0.12085  3.45586     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     44   2.92468  3.55461  0.12085  3.45586     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03758  3.99317  3.99317  1.46634  0.26236  1.09861  0.40547
+     45   3.39555  0.13478  3.44658  2.80157     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01897  3.97456        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_twoc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:25:48 2012
+NSEQ  25
+EFFN  3.573608
+CKSUM 3334689644
+STATS LOCAL MSV       -7.4338  0.71933
+STATS LOCAL VITERBI   -7.6275  0.71933
+STATS LOCAL FORWARD   -3.9955  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.54120  1.41879  1.21665  1.39575
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  0.00000        *
+      1   3.52168  0.12012  3.56730  2.89304      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      2   0.13213  3.45734  2.85176  3.36640      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      3   0.13213  3.45734  2.85176  3.36640      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      4   3.52168  0.12012  3.56730  2.89304      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      5   3.16710  2.64497  3.21222  0.16653      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      6   3.16710  2.64497  3.21222  0.16653      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      7   3.16710  2.64497  3.21222  0.16653      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      8   3.52168  0.12012  3.56730  2.89304      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+      9   0.13213  3.45734  2.85176  3.36640      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     10   3.00056  3.66536  0.10901  3.57823     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     11   2.46586  0.76758  2.53784  0.98915     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     12   3.00056  3.66536  0.10901  3.57823     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     13   0.13213  3.45734  2.85176  3.36640     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     14   3.16710  2.64497  3.21222  0.16653     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     15   3.00056  3.66536  0.10901  3.57823     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     16   3.00056  3.66536  0.10901  3.57823     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     17   0.13213  3.45734  2.85176  3.36640     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     18   3.16710  2.64497  3.21222  0.16653     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     19   0.21940  3.16112  2.23213  3.05081     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     20   3.16710  2.64497  3.21222  0.16653     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     22   3.16710  2.64497  3.21222  0.16653     22 - -
+          1.38629  1.38629  1.38629  1.38629
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+     23   3.16710  2.64497  3.21222  0.16653     23 - -
+          1.38629  1.38629  1.38629  1.38629
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+     24   3.00056  3.66536  0.10901  3.57823     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     25   3.00056  3.66536  0.10901  3.57823     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     26   3.52168  0.12012  3.56730  2.89304     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     27   3.16710  2.64497  3.21222  0.16653     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     28   3.52168  0.12012  3.56730  2.89304     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     29   2.32922  3.31349  0.19164  3.20305     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     30   2.32922  3.31349  0.19164  3.20305     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     31   3.00056  3.66536  0.10901  3.57823     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     32   3.52168  0.12012  3.56730  2.89304     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     33   0.13213  3.45734  2.85176  3.36640     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     34   3.52168  0.12012  3.56730  2.89304     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     35   3.52168  0.12012  3.56730  2.89304     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     36   3.16710  2.64497  3.21222  0.16653     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     37   2.31883  2.50191  0.47001  1.63638     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     38   3.16710  2.64497  3.21222  0.16653     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     39   3.00056  3.66536  0.10901  3.57823     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     40   0.13213  3.45734  2.85176  3.36640     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     41   0.13213  3.45734  2.85176  3.36640     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     42   3.00056  3.66536  0.10901  3.57823     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     43   3.00056  3.66536  0.10901  3.57823     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     44   3.00056  3.66536  0.10901  3.57823     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03525  4.05588  4.05588  1.46634  0.26236  1.09861  0.40547
+     45   3.52168  0.12012  3.56730  2.89304     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01778  4.03841        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  2_5.8_Alveolata_58S_start_twod_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Wed Feb 29 13:25:53 2012
+NSEQ  12
+EFFN  3.430664
+CKSUM 3640048188
+STATS LOCAL MSV       -7.2425  0.71931
+STATS LOCAL VITERBI   -7.5607  0.71931
+STATS LOCAL FORWARD   -3.7783  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.41933  1.31164  1.25837  1.58655
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  0.00000        *
+      1   3.47220  0.12564  3.51998  2.85737      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      2   0.13749  3.41422  2.82393  3.31912      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      3   0.13749  3.41422  2.82393  3.31912      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      4   3.47220  0.12564  3.51998  2.85737      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      5   3.12302  2.61701  3.16985  0.17323      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      6   3.12302  2.61701  3.16985  0.17323      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      7   3.12302  2.61701  3.16985  0.17323      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      8   3.47220  0.12564  3.51998  2.85737      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+      9   0.13749  3.41422  2.82393  3.31912      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     10   2.97107  3.62210  0.11347  3.53036     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     11   3.47220  0.12564  3.51998  2.85737     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     12   2.97107  3.62210  0.11347  3.53036     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     13   0.13749  3.41422  2.82393  3.31912     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     14   3.47220  0.12564  3.51998  2.85737     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     15   2.97107  3.62210  0.11347  3.53036     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     16   2.97107  3.62210  0.11347  3.53036     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     17   0.13749  3.41422  2.82393  3.31912     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     18   3.12302  2.61701  3.16985  0.17323     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     19   0.13749  3.41422  2.82393  3.31912     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     21   3.47220  0.12564  3.51998  2.85737     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     22   3.12302  2.61701  3.16985  0.17323     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     23   2.60677  1.53439  2.67234  0.44387     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
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+     25   2.97107  3.62210  0.11347  3.53036     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     26   3.47220  0.12564  3.51998  2.85737     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     27   3.12302  2.61701  3.16985  0.17323     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     29   1.96943  3.04589  0.27579  2.91993     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     30   2.97107  3.62210  0.11347  3.53036     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     31   2.97107  3.62210  0.11347  3.53036     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     32   3.47220  0.12564  3.51998  2.85737     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     33   0.13749  3.41422  2.82393  3.31912     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     34   3.47220  0.12564  3.51998  2.85737     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     35   3.47220  0.12564  3.51998  2.85737     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     36   0.55266  2.36283  2.26915  1.48267     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     37   0.13749  3.41422  2.82393  3.31912     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     38   3.12302  2.61701  3.16985  0.17323     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     39   2.97107  3.62210  0.11347  3.53036     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     40   0.13749  3.41422  2.82393  3.31912     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     41   0.13749  3.41422  2.82393  3.31912     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     42   2.97107  3.62210  0.11347  3.53036     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     43   2.97107  3.62210  0.11347  3.53036     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     44   2.97107  3.62210  0.11347  3.53036     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03617  4.03081  4.03081  1.46634  0.26236  1.09861  0.40547
+     45   3.47220  0.12564  3.51998  2.85737     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01825  4.01289        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_elevena_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:31 2012
+NSEQ  12
+EFFN  3.272461
+CKSUM 1146151681
+STATS LOCAL MSV       -8.0339  0.71932
+STATS LOCAL VITERBI   -7.7952  0.71932
+STATS LOCAL FORWARD   -4.0279  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.47342  1.38843  1.32140  1.36794
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  0.00000        *
+      1   3.07227  2.58474  3.12105  0.18133      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      2   3.07227  2.58474  3.12105  0.18133      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      3   3.07227  2.58474  3.12105  0.18133      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      4   2.93618  3.57128  0.11898  3.47424      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      5   3.41441  0.13246  3.46466  2.81537      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      6   3.07227  2.58474  3.12105  0.18133      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      7   3.41441  0.13246  3.46466  2.81537      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      8   3.41441  0.13246  3.46466  2.81537      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+      9   3.07227  2.58474  3.12105  0.18133      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     10   2.93618  3.57128  0.11898  3.47424     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     11   0.14405  3.36405  2.79138  3.26418     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     12   2.93618  3.57128  0.11898  3.47424     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     13   0.14405  3.36405  2.79138  3.26418     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     14   3.07227  2.58474  3.12105  0.18133     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     15   3.41441  0.13246  3.46466  2.81537     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     16   2.93618  3.57128  0.11898  3.47424     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     17   2.37276  3.26979  0.19096  3.15593     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     18   2.93618  3.57128  0.11898  3.47424     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     19   3.07227  2.58474  3.12105  0.18133     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     20   2.93618  3.57128  0.11898  3.47424     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     21   0.14405  3.36405  2.79138  3.26418     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     22   2.93618  3.57128  0.11898  3.47424     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     23   2.93618  3.57128  0.11898  3.47424     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     24   3.41441  0.13246  3.46466  2.81537     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     25   3.41441  0.13246  3.46466  2.81537     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     26   0.14405  3.36405  2.79138  3.26418     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     27   3.07227  2.58474  3.12105  0.18133     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     28   3.41441  0.13246  3.46466  2.81537     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     29   3.41441  0.13246  3.46466  2.81537     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     30   2.93618  3.57128  0.11898  3.47424     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     31   3.41441  0.13246  3.46466  2.81537     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     32   3.41441  0.13246  3.46466  2.81537     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     33   2.93618  3.57128  0.11898  3.47424     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     34   0.14405  3.36405  2.79138  3.26418     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     35   0.14405  3.36405  2.79138  3.26418     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     36   3.07227  2.58474  3.12105  0.18133     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     37   3.07227  2.58474  3.12105  0.18133     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     38   3.07227  2.58474  3.12105  0.18133     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     39   0.14405  3.36405  2.79138  3.26418     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     40   0.14405  3.36405  2.79138  3.26418     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     41   2.93618  3.57128  0.11898  3.47424     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     42   3.41441  0.13246  3.46466  2.81537     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     43   0.14405  3.36405  2.79138  3.26418     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     44   3.07227  2.58474  3.12105  0.18133     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03723  4.00231  4.00231  1.46634  0.26236  1.09861  0.40547
+     45   0.14405  3.36405  2.79138  3.26418     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01879  3.98387        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_elevenb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:38 2012
+NSEQ  7
+EFFN  3.749512
+CKSUM 2366441104
+STATS LOCAL MSV       -7.0652  0.71931
+STATS LOCAL VITERBI   -7.5685  0.71931
+STATS LOCAL FORWARD   -4.4492  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.38524  1.47412  1.40056  1.29354
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  0.00000        *
+      1   1.79493  1.75931  2.34666  0.56914      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      2   2.88109  1.92354  2.93805  0.29455      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      3   2.49444  0.76834  2.56603  0.97594      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      4   2.27102  2.42071  0.55082  1.46337      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      5   3.57922  0.11406  3.62226  2.93422      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      6   3.21913  2.67796  3.26222  0.15899      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      7   3.57922  0.11406  3.62226  2.93422      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      8   3.57922  0.11406  3.62226  2.93422      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+      9   3.21913  2.67796  3.26222  0.15899      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     10   3.03446  3.71539  0.10410  3.63368     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     11   0.12616  3.50768  2.88414  3.42167     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     12   0.12616  3.50768  2.88414  3.42167     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     13   0.12616  3.50768  2.88414  3.42167     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     14   3.21913  2.67796  3.26222  0.15899     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     15   3.57922  0.11406  3.62226  2.93422     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     16   3.03446  3.71539  0.10410  3.63368     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     17   3.03446  3.71539  0.10410  3.63368     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     18   3.03446  3.71539  0.10410  3.63368     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     19   3.21913  2.67796  3.26222  0.15899     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     20   3.03446  3.71539  0.10410  3.63368     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     21   0.12616  3.50768  2.88414  3.42167     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     22   3.03446  3.71539  0.10410  3.63368     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     23   3.03446  3.71539  0.10410  3.63368     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     24   3.57922  0.11406  3.62226  2.93422     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     25   3.21913  2.67796  3.26222  0.15899     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     26   0.12616  3.50768  2.88414  3.42167     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     27   3.21913  2.67796  3.26222  0.15899     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     28   3.57922  0.11406  3.62226  2.93422     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     29   3.57922  0.11406  3.62226  2.93422     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     30   3.03446  3.71539  0.10410  3.63368     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     31   3.57922  0.11406  3.62226  2.93422     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     32   3.21913  2.67796  3.26222  0.15899     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     33   3.03446  3.71539  0.10410  3.63368     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     34   0.12616  3.50768  2.88414  3.42167     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     35   0.12616  3.50768  2.88414  3.42167     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     36   3.21913  2.67796  3.26222  0.15899     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     37   3.21913  2.67796  3.26222  0.15899     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     38   3.21913  2.67796  3.26222  0.15899     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     39   0.12616  3.50768  2.88414  3.42167     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     40   0.12616  3.50768  2.88414  3.42167     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     41   3.03446  3.71539  0.10410  3.63368     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     42   3.57922  0.11406  3.62226  2.93422     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     43   0.12616  3.50768  2.88414  3.42167     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     44   3.21913  2.67796  3.26222  0.15899     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03419  4.08589  4.08589  1.46634  0.26236  1.09861  0.40547
+     45   0.12616  3.50768  2.88414  3.42167     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01724  4.06894        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_elevenc_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:44 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 4069155507
+STATS LOCAL MSV       -7.5533  0.72843
+STATS LOCAL VITERBI   -8.3163  0.72843
+STATS LOCAL FORWARD   -3.8936  0.72843
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.45663  1.50989  1.37466  1.22718
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.57915  2.25909  2.64442  0.28946      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.57915  2.25909  2.64442  0.28946      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.81865  0.23582  2.88868  2.35662      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.57915  2.25909  2.64442  0.28946      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.81865  0.23582  2.88868  2.35662      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   0.23862  2.84929  2.43386  2.70756     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.57915  2.25909  2.64442  0.28946     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.53331  3.02441  0.20344  2.88069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.53331  3.02441  0.20344  2.88069     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.57915  2.25909  2.64442  0.28946     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.53331  3.02441  0.20344  2.88069     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.57915  2.25909  2.64442  0.28946     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.57915  2.25909  2.64442  0.28946     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_elevend_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:50 2012
+NSEQ  6
+EFFN  3.483398
+CKSUM 493634052
+STATS LOCAL MSV       -7.4999  0.71933
+STATS LOCAL VITERBI   -7.8190  0.71933
+STATS LOCAL FORWARD   -4.2484  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.28412  1.78988  1.37130  1.19617
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  0.00000        *
+      1   3.13947  2.62745  3.18567  0.17069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      2   3.13947  2.62745  3.18567  0.17069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      3   0.38809  2.59438  2.41106  1.84999      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      4   3.13947  2.62745  3.18567  0.17069      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      5   2.98216  3.63834  0.11177  3.54832      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      6   2.98216  3.63834  0.11177  3.54832      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      7   3.49075  0.12354  3.53772  2.87077      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      8   3.49075  0.12354  3.53772  2.87077      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+      9   3.13947  2.62745  3.18567  0.17069      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     10   2.98216  3.63834  0.11177  3.54832     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     11   0.13545  3.43036  2.83437  3.33682     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     12   0.13545  3.43036  2.83437  3.33682     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     13   0.13545  3.43036  2.83437  3.33682     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     14   3.13947  2.62745  3.18567  0.17069     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     15   3.13947  2.62745  3.18567  0.17069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     16   2.98216  3.63834  0.11177  3.54832     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     17   2.98216  3.63834  0.11177  3.54832     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     18   0.13545  3.43036  2.83437  3.33682     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     19   3.13947  2.62745  3.18567  0.17069     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     20   2.98216  3.63834  0.11177  3.54832     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     21   3.13947  2.62745  3.18567  0.17069     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     22   2.98216  3.63834  0.11177  3.54832     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     23   0.13545  3.43036  2.83437  3.33682     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     24   2.76674  1.82415  2.82709  0.33325     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     25   2.98216  3.63834  0.11177  3.54832     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     26   0.13545  3.43036  2.83437  3.33682     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     27   3.13947  2.62745  3.18567  0.17069     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     28   3.49075  0.12354  3.53772  2.87077     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     29   3.49075  0.12354  3.53772  2.87077     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     30   2.98216  3.63834  0.11177  3.54832     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     31   3.49075  0.12354  3.53772  2.87077     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     32   3.13947  2.62745  3.18567  0.17069     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     33   2.98216  3.63834  0.11177  3.54832     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     34   0.13545  3.43036  2.83437  3.33682     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     35   0.13545  3.43036  2.83437  3.33682     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     36   3.13947  2.62745  3.18567  0.17069     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     37   3.13947  2.62745  3.18567  0.17069     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     38   3.13947  2.62745  3.18567  0.17069     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     39   0.13545  3.43036  2.83437  3.33682     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     40   0.13545  3.43036  2.83437  3.33682     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     41   2.98216  3.63834  0.11177  3.54832     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     42   3.49075  0.12354  3.53772  2.87077     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     43   0.13545  3.43036  2.83437  3.33682     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     44   3.13947  2.62745  3.18567  0.17069     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03582  4.04013  4.04013  1.46634  0.26236  1.09861  0.40547
+     45   0.13545  3.43036  2.83437  3.33682     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01807  4.02238        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_five_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:40:33 2012
+NSEQ  4
+EFFN  3.371094
+CKSUM 2728876017
+STATS LOCAL MSV       -7.6702  0.71933
+STATS LOCAL VITERBI   -7.7190  0.71933
+STATS LOCAL FORWARD   -3.9488  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.14299  1.32265  1.60290  1.54461
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  0.00000        *
+      1   3.10416  2.60503  3.15172  0.17619      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      2   3.10416  2.60503  3.15172  0.17619      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      3   3.10416  2.60503  3.15172  0.17619      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      4   2.95822  3.60333  0.11547  3.50963      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      5   3.45082  0.12812  3.49952  2.84187      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      6   0.13988  3.39564  2.81190  3.29876      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      7   3.45082  0.12812  3.49952  2.84187      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      8   3.45082  0.12812  3.49952  2.84187      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+      9   3.10416  2.60503  3.15172  0.17619      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     10   2.95822  3.60333  0.11547  3.50963     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     11   0.13988  3.39564  2.81190  3.29876     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     12   0.13988  3.39564  2.81190  3.29876     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     13   3.45082  0.12812  3.49952  2.84187     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     14   0.97314  2.14888  2.16446  0.93987     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     15   3.45082  0.12812  3.49952  2.84187     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     16   0.13988  3.39564  2.81190  3.29876     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     17   0.13988  3.39564  2.81190  3.29876     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     18   2.95822  3.60333  0.11547  3.50963     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     19   3.45082  0.12812  3.49952  2.84187     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     20   0.13988  3.39564  2.81190  3.29876     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     21   0.13988  3.39564  2.81190  3.29876     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     22   2.95822  3.60333  0.11547  3.50963     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     23   0.13988  3.39564  2.81190  3.29876     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     24   3.10416  2.60503  3.15172  0.17619     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     25   2.95822  3.60333  0.11547  3.50963     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     26   0.13988  3.39564  2.81190  3.29876     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     27   3.45082  0.12812  3.49952  2.84187     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     28   3.45082  0.12812  3.49952  2.84187     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     29   3.45082  0.12812  3.49952  2.84187     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     30   2.95822  3.60333  0.11547  3.50963     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     31   3.45082  0.12812  3.49952  2.84187     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     32   3.10416  2.60503  3.15172  0.17619     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     33   2.95822  3.60333  0.11547  3.50963     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     34   0.13988  3.39564  2.81190  3.29876     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     35   0.13988  3.39564  2.81190  3.29876     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     36   3.45082  0.12812  3.49952  2.84187     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     37   3.10416  2.60503  3.15172  0.17619     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     38   3.10416  2.60503  3.15172  0.17619     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     39   0.13988  3.39564  2.81190  3.29876     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     40   0.13988  3.39564  2.81190  3.29876     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     41   2.95822  3.60333  0.11547  3.50963     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     42   3.45082  0.12812  3.49952  2.84187     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     43   0.13988  3.39564  2.81190  3.29876     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     44   3.10416  2.60503  3.15172  0.17619     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03656  4.02018  4.02018  1.46634  0.26236  1.09861  0.40547
+     45   0.13988  3.39564  2.81190  3.29876     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01845  4.00206        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_four_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:40:26 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 998262845
+STATS LOCAL MSV       -7.6891  0.73003
+STATS LOCAL VITERBI   -8.4068  0.73003
+STATS LOCAL FORWARD   -3.2433  0.73003
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.11611  1.39855  1.45506  1.64970
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.15554  1.00938  2.23102  0.88601      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   0.23862  2.84929  2.43386  2.70756      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.53331  3.02441  0.20344  2.88069      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   0.23862  2.84929  2.43386  2.70756      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   0.23862  2.84929  2.43386  2.70756      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.53331  3.02441  0.20344  2.88069     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.81865  0.23582  2.88868  2.35662     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.15554  1.00938  2.23102  0.88601     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   0.23862  2.84929  2.43386  2.70756     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.53331  3.02441  0.20344  2.88069     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.15554  1.00938  2.23102  0.88601     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.81865  0.23582  2.88868  2.35662     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.92825  2.28391  0.95698  2.13014     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.81865  0.23582  2.88868  2.35662     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_fourteen_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:42:14 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 551182428
+STATS LOCAL MSV       -7.6363  0.72784
+STATS LOCAL VITERBI   -8.3274  0.72784
+STATS LOCAL FORWARD   -3.4964  0.72784
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.19067  1.40884  1.42869  1.55148
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.57915  2.25909  2.64442  0.28946      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.53331  3.02441  0.20344  2.88069      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.81865  0.23582  2.88868  2.35662      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.53331  3.02441  0.20344  2.88069      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   0.23862  2.84929  2.43386  2.70756      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   0.23862  2.84929  2.43386  2.70756      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.57915  2.25909  2.64442  0.28946     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.81865  0.23582  2.88868  2.35662     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   0.23862  2.84929  2.43386  2.70756     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.53331  3.02441  0.20344  2.88069     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   2.81865  0.23582  2.88868  2.35662     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.81865  0.23582  2.88868  2.35662     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_ninea_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:00 2012
+NSEQ  7
+EFFN  3.790527
+CKSUM 4206231787
+STATS LOCAL MSV       -7.2724  0.71933
+STATS LOCAL VITERBI   -7.6144  0.71933
+STATS LOCAL FORWARD   -4.2349  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.36808  1.51781  1.52107  1.17852
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  0.00000        *
+      1   0.89002  1.69049  2.09997  1.26421      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      2   2.66645  0.48139  2.73592  1.39537      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      3   2.88838  1.91919  2.94521  0.29435      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      4   2.65817  1.47680  2.72315  0.45273      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      5   3.23093  2.68543  3.27356  0.15734      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      6   3.23093  2.68543  3.27356  0.15734      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      7   3.59213  0.11274  3.63458  2.94342      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      8   3.59213  0.11274  3.63458  2.94342      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+      9   3.23093  2.68543  3.27356  0.15734      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     10   3.04202  3.72657  0.10304  3.64608     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     11   0.12486  3.51901  2.89141  3.43411     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     12   3.04202  3.72657  0.10304  3.64608     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     13   0.12486  3.51901  2.89141  3.43411     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     14   3.23093  2.68543  3.27356  0.15734     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     15   3.04202  3.72657  0.10304  3.64608     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     16   3.23093  2.68543  3.27356  0.15734     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     17   0.12486  3.51901  2.89141  3.43411     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     18   3.59213  0.11274  3.63458  2.94342     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     19   3.04202  3.72657  0.10304  3.64608     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     20   0.12486  3.51901  2.89141  3.43411     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     21   3.04202  3.72657  0.10304  3.64608     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     22   3.04202  3.72657  0.10304  3.64608     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     23   3.59213  0.11274  3.63458  2.94342     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     24   3.23093  2.68543  3.27356  0.15734     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     25   0.12486  3.51901  2.89141  3.43411     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     26   3.23093  2.68543  3.27356  0.15734     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     27   3.59213  0.11274  3.63458  2.94342     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     28   3.59213  0.11274  3.63458  2.94342     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     29   3.04202  3.72657  0.10304  3.64608     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     30   3.59213  0.11274  3.63458  2.94342     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     31   3.23093  2.68543  3.27356  0.15734     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     32   3.04202  3.72657  0.10304  3.64608     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     33   0.12486  3.51901  2.89141  3.43411     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     34   0.12486  3.51901  2.89141  3.43411     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     35   3.23093  2.68543  3.27356  0.15734     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     36   3.23093  2.68543  3.27356  0.15734     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     37   3.23093  2.68543  3.27356  0.15734     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     38   0.12486  3.51901  2.89141  3.43411     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     39   0.12486  3.51901  2.89141  3.43411     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     40   3.04202  3.72657  0.10304  3.64608     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     41   3.59213  0.11274  3.63458  2.94342     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     42   0.12486  3.51901  2.89141  3.43411     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     43   3.23093  2.68543  3.27356  0.15734     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     44   0.12486  3.51901  2.89141  3.43411     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03396  4.09276  4.09276  1.46634  0.26236  1.09861  0.40547
+     45   3.23093  2.68543  3.27356  0.15734     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01712  4.07593        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_nineb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:05 2012
+NSEQ  3
+EFFN  3.000000
+CKSUM 3743554959
+STATS LOCAL MSV       -8.1311  0.72123
+STATS LOCAL VITERBI   -7.9839  0.72123
+STATS LOCAL FORWARD   -4.0562  0.72123
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.30454  1.51465  1.59551  1.18413
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  0.00000        *
+      1   0.70020  2.19823  2.14894  1.28770      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      2   2.97980  2.52563  3.03204  0.19727      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      3   2.97980  2.52563  3.03204  0.19727      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      4   2.97980  2.52563  3.03204  0.19727      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      5   2.97980  2.52563  3.03204  0.19727      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      6   2.97980  2.52563  3.03204  0.19727      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      7   3.30705  0.14631  3.36166  2.73626      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      8   3.30705  0.14631  3.36166  2.73626      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+      9   2.97980  2.52563  3.03204  0.19727      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     10   2.86982  3.47591  0.13017  3.36931     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     11   0.15719  3.27118  2.73043  3.16274     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     12   0.15719  3.27118  2.73043  3.16274     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     13   0.15719  3.27118  2.73043  3.16274     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     14   2.97980  2.52563  3.03204  0.19727     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     15   2.97980  2.52563  3.03204  0.19727     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     16   2.86982  3.47591  0.13017  3.36931     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     17   0.15719  3.27118  2.73043  3.16274     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     18   3.30705  0.14631  3.36166  2.73626     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     19   2.86982  3.47591  0.13017  3.36931     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     20   0.15719  3.27118  2.73043  3.16274     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     21   2.86982  3.47591  0.13017  3.36931     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     22   2.86982  3.47591  0.13017  3.36931     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     23   3.30705  0.14631  3.36166  2.73626     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     24   3.30705  0.14631  3.36166  2.73626     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     25   0.15719  3.27118  2.73043  3.16274     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     26   2.97980  2.52563  3.03204  0.19727     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     27   3.30705  0.14631  3.36166  2.73626     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     28   3.30705  0.14631  3.36166  2.73626     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     29   2.86982  3.47591  0.13017  3.36931     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     30   3.30705  0.14631  3.36166  2.73626     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     31   2.97980  2.52563  3.03204  0.19727     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     32   2.86982  3.47591  0.13017  3.36931     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     33   0.15719  3.27118  2.73043  3.16274     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     34   0.15719  3.27118  2.73043  3.16274     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     35   2.97980  2.52563  3.03204  0.19727     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     36   2.97980  2.52563  3.03204  0.19727     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     37   2.97980  2.52563  3.03204  0.19727     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     38   0.15719  3.27118  2.73043  3.16274     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     39   0.15719  3.27118  2.73043  3.16274     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     40   2.86982  3.47591  0.13017  3.36931     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     41   3.30705  0.14631  3.36166  2.73626     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     42   0.15719  3.27118  2.73043  3.16274     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     43   2.97980  2.52563  3.03204  0.19727     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     44   0.15719  3.27118  2.73043  3.16274     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03922  3.95124  3.95124  1.46634  0.26236  1.09861  0.40547
+     45   2.97980  2.52563  3.03204  0.19727     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01980  3.93183        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_onea_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:39:33 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 781382756
+STATS LOCAL MSV       -7.5283  0.72797
+STATS LOCAL VITERBI   -8.3724  0.72797
+STATS LOCAL FORWARD   -3.0815  0.72797
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.09830  1.60161  1.42113  1.49812
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.81865  0.23582  2.88868  2.35662      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.57915  2.25909  2.64442  0.28946      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   0.23862  2.84929  2.43386  2.70756      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   0.23862  2.84929  2.43386  2.70756      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.53331  3.02441  0.20344  2.88069      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.53331  3.02441  0.20344  2.88069     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   0.23862  2.84929  2.43386  2.70756     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   0.23862  2.84929  2.43386  2.70756     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.81865  0.23582  2.88868  2.35662     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.57915  2.25909  2.64442  0.28946     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_oneb_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:39:39 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 1194618091
+STATS LOCAL MSV       -7.4605  0.72829
+STATS LOCAL VITERBI   -8.3928  0.72829
+STATS LOCAL FORWARD   -3.2424  0.72829
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.09633  1.66831  1.48615  1.38192
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   0.23862  2.84929  2.43386  2.70756      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.57915  2.25909  2.64442  0.28946      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.57915  2.25909  2.64442  0.28946      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.53331  3.02441  0.20344  2.88069      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   0.23862  2.84929  2.43386  2.70756      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.53331  3.02441  0.20344  2.88069     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   0.23862  2.84929  2.43386  2.70756     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   0.23862  2.84929  2.43386  2.70756     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.81865  0.23582  2.88868  2.35662     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.57915  2.25909  2.64442  0.28946     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   0.23862  2.84929  2.43386  2.70756     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_onec_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:39:45 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 620831756
+STATS LOCAL MSV       -7.6900  0.72827
+STATS LOCAL VITERBI   -8.3711  0.72827
+STATS LOCAL FORWARD   -3.1028  0.72827
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.18992  1.52066  1.49124  1.37796
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.81865  0.23582  2.88868  2.35662      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.57915  2.25909  2.64442  0.28946      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.53331  3.02441  0.20344  2.88069      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.57915  2.25909  2.64442  0.28946      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   0.23862  2.84929  2.43386  2.70756      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.53331  3.02441  0.20344  2.88069     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   0.23862  2.84929  2.43386  2.70756     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   0.23862  2.84929  2.43386  2.70756     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
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+     21   2.81865  0.23582  2.88868  2.35662     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.57915  2.25909  2.64442  0.28946     23 - -
+          1.38629  1.38629  1.38629  1.38629
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+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.81865  0.23582  2.88868  2.35662     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_oned_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:39:50 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3374549336
+STATS LOCAL MSV       -7.6531  0.72839
+STATS LOCAL VITERBI   -8.1622  0.72839
+STATS LOCAL FORWARD   -3.1511  0.72839
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.18847  1.58865  1.48979  1.32542
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.57915  2.25909  2.64442  0.28946      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   2.57915  2.25909  2.64442  0.28946      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   2.53331  3.02441  0.20344  2.88069      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   2.57915  2.25909  2.64442  0.28946      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   0.23862  2.84929  2.43386  2.70756      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   0.23862  2.84929  2.43386  2.70756      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   2.81865  0.23582  2.88868  2.35662     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   0.23862  2.84929  2.43386  2.70756     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.53331  3.02441  0.20344  2.88069     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.53331  3.02441  0.20344  2.88069     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   0.23862  2.84929  2.43386  2.70756     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   0.23862  2.84929  2.43386  2.70756     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   2.53331  3.02441  0.20344  2.88069     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   2.81865  0.23582  2.88868  2.35662     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   0.23862  2.84929  2.43386  2.70756     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.57915  2.25909  2.64442  0.28946     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   0.23862  2.84929  2.43386  2.70756     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.57915  2.25909  2.64442  0.28946     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
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+     29   2.57915  2.25909  2.64442  0.28946     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   2.53331  3.02441  0.20344  2.88069     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_seven_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:40:49 2012
+NSEQ  2
+EFFN  2.000000
+CKSUM 3028493390
+STATS LOCAL MSV       -7.5398  0.72776
+STATS LOCAL VITERBI   -8.1250  0.72776
+STATS LOCAL FORWARD   -3.1186  0.72776
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.18774  1.47240  1.36573  1.55818
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  0.00000        *
+      1   2.53331  3.02441  0.20344  2.88069      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      2   0.23862  2.84929  2.43386  2.70756      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      3   0.23862  2.84929  2.43386  2.70756      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      4   0.23862  2.84929  2.43386  2.70756      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      5   2.53331  3.02441  0.20344  2.88069      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      6   2.53331  3.02441  0.20344  2.88069      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      7   2.81865  0.23582  2.88868  2.35662      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      8   2.81865  0.23582  2.88868  2.35662      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+      9   2.57915  2.25909  2.64442  0.28946      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     10   2.53331  3.02441  0.20344  2.88069     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     11   0.23862  2.84929  2.43386  2.70756     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     12   2.53331  3.02441  0.20344  2.88069     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     13   2.81865  0.23582  2.88868  2.35662     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     14   2.57915  2.25909  2.64442  0.28946     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     15   2.57915  2.25909  2.64442  0.28946     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     16   2.53331  3.02441  0.20344  2.88069     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     17   2.53331  3.02441  0.20344  2.88069     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     18   0.23862  2.84929  2.43386  2.70756     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     19   2.81865  0.23582  2.88868  2.35662     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     20   0.23862  2.84929  2.43386  2.70756     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     21   0.23862  2.84929  2.43386  2.70756     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     22   2.53331  3.02441  0.20344  2.88069     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     23   2.53331  3.02441  0.20344  2.88069     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     24   2.81865  0.23582  2.88868  2.35662     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     25   2.57915  2.25909  2.64442  0.28946     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     26   0.23862  2.84929  2.43386  2.70756     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     27   2.81865  0.23582  2.88868  2.35662     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     28   2.81865  0.23582  2.88868  2.35662     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     29   2.81865  0.23582  2.88868  2.35662     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     30   0.23862  2.84929  2.43386  2.70756     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     31   2.81865  0.23582  2.88868  2.35662     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     32   2.57915  2.25909  2.64442  0.28946     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     33   2.53331  3.02441  0.20344  2.88069     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     34   0.23862  2.84929  2.43386  2.70756     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     35   0.23862  2.84929  2.43386  2.70756     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     36   2.57915  2.25909  2.64442  0.28946     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     37   2.57915  2.25909  2.64442  0.28946     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     38   2.57915  2.25909  2.64442  0.28946     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     39   0.23862  2.84929  2.43386  2.70756     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     40   0.23862  2.84929  2.43386  2.70756     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     41   2.53331  3.02441  0.20344  2.88069     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     42   2.81865  0.23582  2.88868  2.35662     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     43   0.23862  2.84929  2.43386  2.70756     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     44   2.57915  2.25909  2.64442  0.28946     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.04879  3.73767  3.73767  1.46634  0.26236  1.09861  0.40547
+     45   0.23862  2.84929  2.43386  2.70756     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.02469  3.71357        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_six_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:40:41 2012
+NSEQ  10
+EFFN  3.530273
+CKSUM 1801102075
+STATS LOCAL MSV       -7.6787  0.71931
+STATS LOCAL VITERBI   -7.8111  0.71931
+STATS LOCAL FORWARD   -3.8984  0.71931
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.05070  1.31736  1.76014  1.55853
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  0.00000        *
+      1   3.15391  2.63661  3.19954  0.16850      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      2   3.15391  2.63661  3.19954  0.16850      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      3   1.71207  2.06815  1.14271  0.98314      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      4   0.23016  3.12439  2.18555  3.01164      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      5   3.50695  0.12174  3.55321  2.88245      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      6   0.13370  3.44448  2.84348  3.35230      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      7   3.50695  0.12174  3.55321  2.88245      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      8   3.50695  0.12174  3.55321  2.88245      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+      9   3.15391  2.63661  3.19954  0.16850      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     10   2.99181  3.65250  0.11032  3.56399     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     11   0.13370  3.44448  2.84348  3.35230     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     12   0.13370  3.44448  2.84348  3.35230     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     13   0.13370  3.44448  2.84348  3.35230     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     14   3.15391  2.63661  3.19954  0.16850     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     15   3.50695  0.12174  3.55321  2.88245     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     16   0.13370  3.44448  2.84348  3.35230     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     17   0.13370  3.44448  2.84348  3.35230     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     18   2.99181  3.65250  0.11032  3.56399     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     19   3.50695  0.12174  3.55321  2.88245     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     20   0.13370  3.44448  2.84348  3.35230     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     21   0.13370  3.44448  2.84348  3.35230     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     22   2.99181  3.65250  0.11032  3.56399     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     23   0.13370  3.44448  2.84348  3.35230     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     24   2.07180  2.39292  2.65785  0.33886     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     25   3.50695  0.12174  3.55321  2.88245     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     26   0.13370  3.44448  2.84348  3.35230     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     27   3.50695  0.12174  3.55321  2.88245     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     28   3.50695  0.12174  3.55321  2.88245     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     29   3.50695  0.12174  3.55321  2.88245     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     30   2.99181  3.65250  0.11032  3.56399     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     31   3.50695  0.12174  3.55321  2.88245     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     32   3.15391  2.63661  3.19954  0.16850     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     33   2.99181  3.65250  0.11032  3.56399     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     34   0.13370  3.44448  2.84348  3.35230     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     35   0.13370  3.44448  2.84348  3.35230     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     36   3.50695  0.12174  3.55321  2.88245     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     37   3.15391  2.63661  3.19954  0.16850     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     38   3.15391  2.63661  3.19954  0.16850     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     39   0.13370  3.44448  2.84348  3.35230     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     40   0.13370  3.44448  2.84348  3.35230     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     41   2.99181  3.65250  0.11032  3.56399     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     42   3.50695  0.12174  3.55321  2.88245     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     43   0.13370  3.44448  2.84348  3.35230     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     44   3.15391  2.63661  3.19954  0.16850     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03553  4.04835  4.04835  1.46634  0.26236  1.09861  0.40547
+     45   0.13370  3.44448  2.84348  3.35230     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01792  4.03074        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_ten_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:41:15 2012
+NSEQ  9
+EFFN  3.827637
+CKSUM 3971025725
+STATS LOCAL MSV       -7.3204  0.71932
+STATS LOCAL VITERBI   -7.7155  0.71932
+STATS LOCAL FORWARD   -4.1318  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.23642  1.73329  1.50126  1.17110
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  0.00000        *
+      1   3.24149  2.69213  3.28371  0.15587      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      2   3.24149  2.69213  3.28371  0.15587      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      3   0.67762  2.30348  2.25602  1.24654      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      4   3.04875  3.73654  0.10210  3.65714      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      5   3.24149  2.69213  3.28371  0.15587      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      6   3.24149  2.69213  3.28371  0.15587      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      7   3.60365  0.11159  3.64557  2.95161      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      8   3.16295  0.21850  3.22065  2.17116      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+      9   3.24149  2.69213  3.28371  0.15587      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     10   3.04875  3.73654  0.10210  3.65714     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     11   0.12371  3.52912  2.89791  3.44523     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     12   3.04875  3.73654  0.10210  3.65714     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     13   0.12371  3.52912  2.89791  3.44523     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     14   3.24149  2.69213  3.28371  0.15587     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     15   3.24149  2.69213  3.28371  0.15587     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     16   3.04875  3.73654  0.10210  3.65714     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     17   3.04875  3.73654  0.10210  3.65714     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     18   3.04875  3.73654  0.10210  3.65714     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     19   3.24149  2.69213  3.28371  0.15587     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     20   3.04875  3.73654  0.10210  3.65714     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     21   0.12371  3.52912  2.89791  3.44523     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     22   3.04875  3.73654  0.10210  3.65714     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     23   0.21841  3.20443  2.20335  3.09683     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     24   2.80375  0.37853  2.87066  1.62006     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     25   2.39794  2.30920  1.65829  0.47918     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     26   0.12371  3.52912  2.89791  3.44523     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     27   3.24149  2.69213  3.28371  0.15587     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     28   3.60365  0.11159  3.64557  2.95161     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     29   3.60365  0.11159  3.64557  2.95161     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     30   0.12371  3.52912  2.89791  3.44523     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     31   3.60365  0.11159  3.64557  2.95161     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     32   3.24149  2.69213  3.28371  0.15587     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     33   3.04875  3.73654  0.10210  3.65714     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     34   0.12371  3.52912  2.89791  3.44523     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     35   0.12371  3.52912  2.89791  3.44523     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     36   3.24149  2.69213  3.28371  0.15587     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     37   3.24149  2.69213  3.28371  0.15587     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     38   3.24149  2.69213  3.28371  0.15587     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     39   0.12371  3.52912  2.89791  3.44523     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     40   0.12371  3.52912  2.89791  3.44523     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     41   0.12371  3.52912  2.89791  3.44523     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     42   3.60365  0.11159  3.64557  2.95161     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     43   0.12371  3.52912  2.89791  3.44523     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     44   3.24149  2.69213  3.28371  0.15587     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03374  4.09894  4.09894  1.46634  0.26236  1.09861  0.40547
+     45   0.12371  3.52912  2.89791  3.44523     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01701  4.08221        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_thirteen_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:42:05 2012
+NSEQ  24
+EFFN  3.893555
+CKSUM 191642901
+STATS LOCAL MSV       -7.2444  0.71933
+STATS LOCAL VITERBI   -7.7058  0.71933
+STATS LOCAL FORWARD   -4.3034  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.16586  1.50746  1.51087  1.40179
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  0.00000        *
+      1   1.46824  2.04571  2.31358  0.61346      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      2   1.05286  2.20903  2.24595  0.83143      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      3   2.32070  1.97985  2.68818  0.36284      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      4   0.12173  3.54680  2.90925  3.46466      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      5   3.06047  3.75390  0.10049  3.67641      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      6   0.12173  3.54680  2.90925  3.46466      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      7   3.62373  0.10960  3.66473  2.96588      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      8   3.62373  0.10960  3.66473  2.96588      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+      9   3.26001  2.70388  3.30149  0.15334      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     10   3.06047  3.75390  0.10049  3.67641     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     11   0.12173  3.54680  2.90925  3.46466     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     12   0.12173  3.54680  2.90925  3.46466     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     13   0.12173  3.54680  2.90925  3.46466     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     14   3.26001  2.70388  3.30149  0.15334     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     15   3.62373  0.10960  3.66473  2.96588     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     16   0.12173  3.54680  2.90925  3.46466     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     17   3.06047  3.75390  0.10049  3.67641     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     18   2.54857  2.39251  1.90817  0.38264     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     19   3.62373  0.10960  3.66473  2.96588     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     20   3.06047  3.75390  0.10049  3.67641     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     21   0.12173  3.54680  2.90925  3.46466     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     22   3.06047  3.75390  0.10049  3.67641     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     23   2.39260  3.42516  0.17435  3.32257     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     24   3.10643  2.32027  3.15457  0.20538     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     25   3.26001  2.70388  3.30149  0.15334     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     26   0.12173  3.54680  2.90925  3.46466     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     27   3.62373  0.10960  3.66473  2.96588     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     28   3.62373  0.10960  3.66473  2.96588     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     29   3.62373  0.10960  3.66473  2.96588     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     30   3.06047  3.75390  0.10049  3.67641     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     31   3.62373  0.10960  3.66473  2.96588     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     32   3.26001  2.70388  3.30149  0.15334     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     33   3.06047  3.75390  0.10049  3.67641     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     34   0.12173  3.54680  2.90925  3.46466     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     35   0.12173  3.54680  2.90925  3.46466     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     36   2.88119  1.85984  2.93863  0.30748     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     37   3.26001  2.70388  3.30149  0.15334     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     38   3.26001  2.70388  3.30149  0.15334     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     39   0.12173  3.54680  2.90925  3.46466     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     40   0.12173  3.54680  2.90925  3.46466     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     41   3.06047  3.75390  0.10049  3.67641     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     42   3.62373  0.10960  3.66473  2.96588     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     43   0.12173  3.54680  2.90925  3.46466     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     44   3.26001  2.70388  3.30149  0.15334     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03337  4.10982  4.10982  1.46634  0.26236  1.09861  0.40547
+     45   0.12173  3.54680  2.90925  3.46466     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01683  4.09327        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  4_LSU_Alveolata_4_LSU_start_two_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Thu Mar  1 14:39:59 2012
+NSEQ  8
+EFFN  3.683594
+CKSUM 435453820
+STATS LOCAL MSV       -7.5820  0.71933
+STATS LOCAL VITERBI   -7.6593  0.71933
+STATS LOCAL FORWARD   -3.8838  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.11795  1.68208  1.35544  1.47302
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  0.00000        *
+      1   3.02205  3.69704  0.10587  3.61333      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      2   0.98857  1.72053  2.09224  1.12236      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      3   3.02205  3.69704  0.10587  3.61333      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      4   0.12832  3.48915  2.87223  3.40132      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      5   3.02205  3.69704  0.10587  3.61333      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      6   0.12832  3.48915  2.87223  3.40132      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      7   3.55808  0.11624  3.60208  2.91913      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      8   0.12832  3.48915  2.87223  3.40132      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+      9   3.19991  2.66577  3.24376  0.16173      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     10   3.02205  3.69704  0.10587  3.61333     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     11   0.12832  3.48915  2.87223  3.40132     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     12   0.12832  3.48915  2.87223  3.40132     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     13   3.02205  3.69704  0.10587  3.61333     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     14   3.19991  2.66577  3.24376  0.16173     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     15   3.19991  2.66577  3.24376  0.16173     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     16   0.12832  3.48915  2.87223  3.40132     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     17   3.02205  3.69704  0.10587  3.61333     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     18   3.02205  3.69704  0.10587  3.61333     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     19   3.55808  0.11624  3.60208  2.91913     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     20   3.19991  2.66577  3.24376  0.16173     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     21   0.49923  1.63631  2.32597  2.29642     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     22   3.02205  3.69704  0.10587  3.61333     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     23   3.55808  0.11624  3.60208  2.91913     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     24   0.12832  3.48915  2.87223  3.40132     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     25   0.60696  1.83062  2.18714  1.70132     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     26   0.12832  3.48915  2.87223  3.40132     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     27   3.55808  0.11624  3.60208  2.91913     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     28   3.55808  0.11624  3.60208  2.91913     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     29   3.19991  2.66577  3.24376  0.16173     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     30   3.02205  3.69704  0.10587  3.61333     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     31   3.55808  0.11624  3.60208  2.91913     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     32   3.19991  2.66577  3.24376  0.16173     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     33   3.02205  3.69704  0.10587  3.61333     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     34   0.12832  3.48915  2.87223  3.40132     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     35   0.12832  3.48915  2.87223  3.40132     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     36   3.19991  2.66577  3.24376  0.16173     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     37   3.19991  2.66577  3.24376  0.16173     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     38   3.19991  2.66577  3.24376  0.16173     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     39   0.12832  3.48915  2.87223  3.40132     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     40   0.12832  3.48915  2.87223  3.40132     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     41   3.02205  3.69704  0.10587  3.61333     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     42   3.55808  0.11624  3.60208  2.91913     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     43   0.12832  3.48915  2.87223  3.40132     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     44   3.19991  2.66577  3.24376  0.16173     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03458  4.07475  4.07475  1.46634  0.26236  1.09861  0.40547
+     45   0.12832  3.48915  2.87223  3.40132     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01744  4.05761        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  1_SSU_Alveolata_1_SSU_end_one_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Sat Jan 28 01:43:03 2012
+NSEQ  69
+EFFN  3.642883
+CKSUM 3148699463
+STATS LOCAL MSV       -7.4489  0.71932
+STATS LOCAL VITERBI   -7.6281  0.71932
+STATS LOCAL FORWARD   -4.1382  0.71932
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.33776  1.55982  1.24507  1.42932
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  0.00000        *
+      1   0.12970  3.47751  2.86475  3.38854      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      2   2.93148  3.51149  0.13230  3.20034      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      3   3.18787  2.65814  3.23219  0.16347      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      4   3.54478  0.11764  3.58937  2.90961      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      5   3.01421  3.68548  0.10701  3.60051      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      6   3.18787  2.65814  3.23219  0.16347      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      7   0.12970  3.47751  2.86475  3.38854      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      8   0.12970  3.47751  2.86475  3.38854      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+      9   3.54478  0.11764  3.58937  2.90961      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     10   0.12970  3.47751  2.86475  3.38854     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     11   0.36931  1.96424  2.44668  2.50172     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     12   2.93148  3.51149  0.13230  3.20034     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     13   3.01421  3.68548  0.10701  3.60051     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     14   3.18787  2.65814  3.23219  0.16347     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     15   2.33627  2.48307  2.82552  0.27372     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     16   3.18787  2.65814  3.23219  0.16347     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     17   3.54478  0.11764  3.58937  2.90961     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     18   3.19125  0.20146  3.24795  2.27802     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     19   3.01421  3.68548  0.10701  3.60051     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     20   3.18787  2.65814  3.23219  0.16347     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     21   0.12970  3.47751  2.86475  3.38854     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     22   3.01421  3.68548  0.10701  3.60051     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     23   3.01421  3.68548  0.10701  3.60051     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     24   3.18787  2.65814  3.23219  0.16347     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     25   3.01421  3.68548  0.10701  3.60051     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     26   0.12970  3.47751  2.86475  3.38854     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     27   0.12970  3.47751  2.86475  3.38854     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     28   3.54478  0.11764  3.58937  2.90961     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     29   3.54478  0.11764  3.58937  2.90961     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     30   3.18787  2.65814  3.23219  0.16347     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     31   3.01421  3.68548  0.10701  3.60051     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     32   3.54478  0.11764  3.58937  2.90961     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     33   2.50860  3.43763  0.16147  3.33578     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     34   3.01421  3.68548  0.10701  3.60051     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     35   0.12970  3.47751  2.86475  3.38854     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     36   0.23093  3.00620  2.64834  2.45388     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     37   3.01421  3.68548  0.10701  3.60051     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     38   3.01421  3.68548  0.10701  3.60051     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     39   0.12970  3.47751  2.86475  3.38854     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     40   3.18787  2.65814  3.23219  0.16347     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     41   3.54478  0.11764  3.58937  2.90961     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     42   0.12970  3.47751  2.86475  3.38854     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     43   2.81519  2.59339  3.07078  0.19973     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     44   3.18787  2.65814  3.23219  0.16347     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03483  4.06781  4.06781  1.46634  0.26236  1.09861  0.40547
+     45   2.10397  0.41821  2.56367  1.94643     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01757  4.05055        *  1.46634  0.26236  0.00000        *
+//
+HMMER3/b [3.0 | March 2010]
+NAME  1_SSU_Alveolata_1_SSU_end_two_long
+LENG  45
+ALPH  DNA
+RF    no
+CS    no
+MAP   yes
+DATE  Sat Jan 28 01:43:11 2012
+NSEQ  7
+EFFN  3.373535
+CKSUM 347251863
+STATS LOCAL MSV       -7.4282  0.71933
+STATS LOCAL VITERBI   -7.6473  0.71933
+STATS LOCAL FORWARD   -4.1966  0.71933
+HMM          A        C        G        T   
+            m->m     m->i     m->d     i->m     i->i     d->m     d->d
+  COMPO   1.33048  1.59392  1.30706  1.33977
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  0.00000        *
+      1   0.13978  3.39641  2.81240  3.29960      1 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      2   2.95876  3.60411  0.11539  3.51048      2 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      3   3.10493  2.60552  3.15246  0.17607      3 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      4   3.45170  0.12801  3.50037  2.84251      4 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      5   2.95876  3.60411  0.11539  3.51048      5 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      6   3.10493  2.60552  3.15246  0.17607      6 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      7   0.13978  3.39641  2.81240  3.29960      7 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      8   0.13978  3.39641  2.81240  3.29960      8 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+      9   3.45170  0.12801  3.50037  2.84251      9 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     10   0.13978  3.39641  2.81240  3.29960     10 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     11   2.43739  1.12083  2.50826  0.68281     11 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     12   2.95876  3.60411  0.11539  3.51048     12 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     13   2.95876  3.60411  0.11539  3.51048     13 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     14   3.10493  2.60552  3.15246  0.17607     14 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     15   0.13978  3.39641  2.81240  3.29960     15 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     16   3.10493  2.60552  3.15246  0.17607     16 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     17   3.45170  0.12801  3.50037  2.84251     17 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     18   3.10493  2.60552  3.15246  0.17607     18 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     19   2.95876  3.60411  0.11539  3.51048     19 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     20   3.10493  2.60552  3.15246  0.17607     20 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     21   0.13978  3.39641  2.81240  3.29960     21 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     22   2.95876  3.60411  0.11539  3.51048     22 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     23   2.95876  3.60411  0.11539  3.51048     23 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     24   3.10493  2.60552  3.15246  0.17607     24 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     25   2.95876  3.60411  0.11539  3.51048     25 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     26   0.13978  3.39641  2.81240  3.29960     26 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     27   0.13978  3.39641  2.81240  3.29960     27 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     28   3.45170  0.12801  3.50037  2.84251     28 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     29   3.45170  0.12801  3.50037  2.84251     29 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     30   3.10493  2.60552  3.15246  0.17607     30 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     31   2.95876  3.60411  0.11539  3.51048     31 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     32   3.45170  0.12801  3.50037  2.84251     32 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     33   0.13978  3.39641  2.81240  3.29960     33 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     34   2.95876  3.60411  0.11539  3.51048     34 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     35   0.13978  3.39641  2.81240  3.29960     35 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     36   3.10493  2.60552  3.15246  0.17607     36 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     37   2.95876  3.60411  0.11539  3.51048     37 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     38   2.95876  3.60411  0.11539  3.51048     38 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     39   0.13978  3.39641  2.81240  3.29960     39 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     40   3.10493  2.60552  3.15246  0.17607     40 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     41   3.45170  0.12801  3.50037  2.84251     41 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     42   0.13978  3.39641  2.81240  3.29960     42 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     43   3.10493  2.60552  3.15246  0.17607     43 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     44   3.10493  2.60552  3.15246  0.17607     44 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.03654  4.02061  4.02061  1.46634  0.26236  1.09861  0.40547
+     45   3.45170  0.12801  3.50037  2.84251     45 - -
+          1.38629  1.38629  1.38629  1.38629
+          0.01844  4.00251        *  1.46634  0.26236  0.00000        *
+//