Mercurial > repos > fubar > cmsearch_tblout_deoverlap_tool

Binary file cmsearch_tblout_deoverlap_tool/Galaxy-History-cmsearch.tar.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/LICENSE	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,47 @@
+MIT License
+
+Copyright (c) 2023 Ross
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+The wrapped perl script has the following license
+
+==============================================================
+                     PUBLIC DOMAIN NOTICE
+         National Center for Biotechnology Information
+
+This software is a "United States Government Work" under the terms of
+the United States Copyright Act.  It was written as part of the
+authors' official duties as United States Government employees and
+thus cannot be copyrighted.  This software is freely available to the
+public for use. The National Library of Medicine and the
+U.S. Government have not placed any restriction on its use or
+reproduction.
+
+Although all reasonable efforts have been taken to ensure the accuracy
+and reliability of the software and data, the NLM and the U.S.
+Government do not and cannot warrant the performance or results that
+may be obtained by using this software or data. The NLM and the U.S.
+Government disclaim all warranties, express or implied, including
+warranties of performance, merchantability or fitness for any
+particular purpose.
+
+Please cite the authors in any work or product based on this material.
+
+==============================================================
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/README.md	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,20 @@
+# cmsearch_tblout_deoverlap_tool
+Galaxy tool wrapper for https://github.com/nawrockie/cmsearch_tblout_deoverlap
+
+Tool form currently looks like:
+
+![Sample out](cmsearch_toolform.png)
+
+Output looks like:
+
+![Sample out](cmsearch_sampleout.png)
+
+Suggestions appreciated.
+
+
+## Tool made with the Galaxy ToolFactory: https://github.com/fubar2/galaxy_tf_overlay
+
+Importing the Galaxy history in this repository into a ToolFactory instance will allow you to "redo"
+the generating job and update anything you want. If you want a new tool, change the tool_id.
+Otherwise a new version will be created and ready to distribute.
+Keep that updated history because it's the easiest way to adapt the tool starting with the original ToolFactory form.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/cmsearch-deoverlap_ross.pl	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,923 @@
+#!/usr/bin/env perl
+#
+# cmsearch-deoverlap.pl: remove lower scoring overlaps from cmsearch
+#                        --tblout files.
+#
+# EPN, Mon May  8 08:41:36 2017
+#
+#
+# Without --maxkeep this script will exactly reproduce how cmscan removes overlapping hits.
+# With --maxkeep, it won't. Here's an example to explain the difference:
+#
+##target name         accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target
+##------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
+#1. contig--151565       -         LSU_rRNA_eukarya     RF02543   hmm      632     2329      410     1883      +     -    6 0.48   1.1  726.0  1.1e-216 !   -
+#2. contig--151565       -         LSU_rRNA_archaea     RF02540   hmm      170     2084       12     1882      +     -    6 0.47   3.0  490.0  2.3e-145 !   -
+#3. contig--151565       -         LSU_rRNA_bacteria    RF02541   hmm      187     2005       10     1883      +     -    6 0.47   5.7  331.4   1.8e-97 !   -
+#4. contig--151565       -         LSU_rRNA_eukarya     RF02543   hmm       29      431       12      366      +     -    6 0.41   7.8  100.0   6.3e-28 !   -
+#
+# hit 1: 410..1883 euk
+# hit 2: 12..1182 arc
+# hit 3: 10..1883 bac
+# hit 4: 12..366 euk
+#
+# Without --maxkeep (default behavior) hits 2, 3, and 4 will be removed because for all 3, there is a better scoring hit
+# that overlaps.
+#
+# With --maxkeep only hits 2 and 3 will be removed because only those 2 have
+# higher scoring hits that overlap with them AND are not removed. If we remove only hits 2 and 3
+# hits 1 and 4 no longer overlap.
+#
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $in_tblout  = "";   # name of input tblout file
+
+my $usage;
+$usage  = "cmsearch-deoverlap v0.09 [Aug 2023]\n\n";
+$usage .= "Usage:\n\n";
+$usage .= "cmsearch-deoverlap.pl    [OPTIONS] <tblout file>\n\tOR\n";
+$usage .= "cmsearch-deoverlap.pl -l [OPTIONS] <list of tblout files>\n\n";
+$usage .= "\tOPTIONS:\n";
+$usage .= "\t\t-l               : single command line argument is a list of tblout files, not a single tblout file\n";
+$usage .= "\t\t-s               : sort hits by bit score [default: sort by E-value]\n";
+$usage .= "\t\t-d               : run in debugging mode (prints extra info)\n";
+$usage .= "\t\t-v               : run in verbose mode (prints all removed and kept hits)\n";
+$usage .= "\t\t--noverlap <n>   : define an overlap as >= <n> or more overlapping residues [1]\n";
+$usage .= "\t\t--nhmmer         : tblout files are from nhmmer v3.x\n";
+$usage .= "\t\t--hmmsearch      : tblout files are from hmmsearch v3.x\n";
+$usage .= "\t\t--cmscan         : tblout files are from cmscan v1.1x, not cmsearch\n";
+$usage .= "\t\t--fcmsearch      : assert tblout files are cmsearch not cmscan\n";
+$usage .= "\t\t--besthmm        : with --hmmsearch, sort by evalue/score of *best* single hit not evalue/score of full seq\n";
+$usage .= "\t\t--clanin <s>     : only remove overlaps within clans, read clan info from file <s> [default: remove all overlaps]\n";
+$usage .= "\t\t--invclan        : w/--clanin, invert clan behavior: do not remove overlaps within clans, remove all other overlaps\n";
+$usage .= "\t\t--maxkeep        : keep hits that only overlap with other hits that are not kept [default: remove all hits with higher scoring overlap]\n";
+$usage .= "\t\t--overlapout <s> : create new tabular file with overlap information in <s>\n";
+$usage .= "\t\t--mdllenin <s>   : w/--overlapout, read model lengths from two-token-per-line-file <s>\n";
+$usage .= "\t\t--dirty          : keep intermediate files (sorted tblout files)\n\n";
+
+my $do_listfile      = 0;     # set to '1' if -l used
+my $rank_by_score    = 0;     # set to '1' if -s used, rank by score, not evalues
+my $do_debug         = 0;     # set to '1' if -d used
+my $be_verbose       = 0;     # set to '1' if -v used
+my $do_cmscan        = 0;     # set to '1' if --cmscan used
+my $do_fcmsearch     = 0;     # set to '1' if --fcmsearch used
+my $noverlap         = 1;     # set to <n> if --noverlap <n> used
+my $in_clanin        = undef; # defined if --clanin option used
+my $do_invclan       = 0;     # set to '1' if --invclan used
+my $do_nhmmer        = 0;     # set to '1' if --nhmmer used, input tblout file(s) are from hmmer3's nhmmer
+my $do_hmmsearch     = 0;     # set to '1' if --hmmsearch used, input tblout file(s) are from hmmer3's hmmsearch
+my $do_besthmm       = 0;     # set to '1' if --besthmm used, sorting by evalue/score of best hit with --hmmsearch
+my $do_maxkeep       = 0;     # set to '1' if --maxkeep, only remove hits that have
+                              # higher scoring overlap that is not removed
+my $do_dirty         = 0;     # set to '1' if --dirty used, keep intermediate files
+my $out_overlap      = undef; # defined if --overlapout <s> used
+my $in_mdllen        = undef; # defined if --mdllenin <s> used
+
+&GetOptions( "l"            => \$do_listfile,
+             "s"            => \$rank_by_score,
+             "d"            => \$do_debug,
+             "v"            => \$be_verbose,
+             "cmscan"       => \$do_cmscan,
+             "fcmsearch"    => \$do_fcmsearch,
+             "noverlap=s"   => \$noverlap,
+             "nhmmer"       => \$do_nhmmer,
+             "hmmsearch"    => \$do_hmmsearch,
+             "besthmm"      => \$do_besthmm,
+             "clanin=s"     => \$in_clanin,
+             "invclan"      => \$do_invclan,
+             "maxkeep"      => \$do_maxkeep,
+             "overlapout=s" => \$out_overlap,
+             "mdllenin=s"   => \$in_mdllen,
+             "dirty"        => \$do_dirty,
+             "in_tblout=s"    => \$in_tblout);
+
+#if(scalar(@ARGV) != 1) { die $usage; }
+# ($in_tblout) = @ARGV;
+
+if($do_hmmsearch && $do_nhmmer) {
+  die "ERROR, --hmmsearch and --nhmmer cannot be used in combination. Pick one.";
+}
+if($do_besthmm && (! $do_hmmsearch)) {
+  die "ERROR, --besthmm requires --hmmsearch.";
+}
+if($do_invclan && (! defined $in_clanin)) {
+  die "ERROR, --invclan requires --clanin";
+}
+my @tblout_file_A = ();
+
+if($do_listfile) {
+  # read the list file
+  my $list_file = $in_tblout;
+  open(IN, $list_file) || die "ERROR unable to open $list_file for reading";
+  while(my $line = <IN>) {
+    if($line =~ m/\w/ && $line !~ m/^\#/) {
+      chomp $line;
+      if(! -e $line) { die "ERROR file $line read from $list_file does not exist"; }
+      if(! -s $line) { die "ERROR file $line read from $list_file is empty"; }
+      push(@tblout_file_A, $line);
+    }
+  }
+  close(IN);
+}
+else {
+  $tblout_file_A[0] = ($in_tblout);
+}
+
+my %mdllen_H = ();
+if(defined $in_mdllen) { # read this file too
+  open(IN, $in_mdllen) || die "ERROR unable to open $in_mdllen for reading";
+  while(my $line = <IN>) {
+    chomp $line;
+    if($line =~ /^(\S+)\s+(\d+)$/) {
+      $mdllen_H{$1} = $2;
+    }
+    else {
+      die "ERROR unable to parse <model> <modellen> line in $in_mdllen\n$line\n";
+    }
+  }
+  close(IN);
+}
+
+my %clan_H = (); # key: model name, value: clan name
+if(defined $in_clanin) {
+  %clan_H = ();
+  parse_claninfo($in_clanin, \%clan_H)
+}
+
+my $sort_cmd           = undef; # command used to sort the tblout file
+my $sorted_tblout_file = undef; # sorted tblout file to create, temporarily
+my $output_file        = undef; # name of output file we create
+my $out_FH             = undef; # output file handle
+my $nkept              = undef; # number of sequences kept from a file
+my $nremoved           = undef; # number of sequences removed from a file
+
+my $overlap_FH = undef;
+if(defined $out_overlap) {
+  open($overlap_FH, ">", $out_overlap) || die "ERROR unable to open $out_overlap for writing";
+  my @fields_A = ();
+  my %fields_H = ();
+  push(@fields_A, "target");
+  $fields_H{"target"} = "sequence name";
+  push(@fields_A, "strand");
+  $fields_H{"strand"} = "strand (+ or -)";
+  push(@fields_A, "mdl1");
+  $fields_H{"mdl1"} = "name of model 1";
+  push(@fields_A, "mdl2");
+  $fields_H{"mdl2"} = "name of model 2";
+  push(@fields_A, "hitlen1");
+  $fields_H{"hitlen1"} = "length in sequence positions of hit to model 1";
+  push(@fields_A, "hitlen2");
+  $fields_H{"hitlen2"} = "length in sequence positions of hit to model 2";
+  push(@fields_A, "nres_olap");
+  $fields_H{"nres_olap"} = "number of residues that overlap between hit to model 1 and hit to model 2 in 'target' on strand 'strand'";
+  push(@fields_A, "score1");
+  $fields_H{"score1"} = "score of hit to model 1";
+  push(@fields_A, "score2");
+  $fields_H{"score2"} = "score of hit to model 2";
+  push(@fields_A, "evalue1");
+  $fields_H{"evalue1"} = "E-value of hit to model 1";
+  push(@fields_A, "evalue2");
+  $fields_H{"evalue2"} = "E-value of hit to model 2";
+  push(@fields_A, "seqfrom1");
+  $fields_H{"seqfrom1"} = "start position in 'target' of hit to model 1";
+  push(@fields_A, "seqto1");
+  $fields_H{"seqto1"} = "end position in 'target' of hit to model 1";
+  push(@fields_A, "seqfrom2");
+  $fields_H{"seqfrom2"} = "start position in 'target' of hit to model 2";
+  push(@fields_A, "seqto2");
+  $fields_H{"seqto2"} = "end position in 'target' of hit to model 2";
+  push(@fields_A, "olap-frac-of-hit1");
+  $fields_H{"olap-frac-of-hit1"} = "'nres_olap'/'hitlen1'";
+  push(@fields_A, "olap-frac-of-hit2");
+  $fields_H{"olap-frac-of-hit2"} = "'nres_olap'/'hitlen2'";
+  push(@fields_A, "mdllen1");
+  $fields_H{"mdllen1"} = "length of model 1 (\"-\" if not available)";
+  push(@fields_A, "mdllen2");
+  $fields_H{"mdllen2"} = "length of model 2 (\"-\" if not available)";
+  push(@fields_A, "olap-frac-of-mdl1");
+  $fields_H{"olap-frac-of-mdl1"} = "'nres_olap'/'mdllen1'";
+  push(@fields_A, "olap-frac-of-mdl2");
+  $fields_H{"olap-frac-of-mdl2"} = "'nres_olap'/'mdllen2'";
+  push(@fields_A, "mhitlen1");
+  $fields_H{"mhitlen1"} = "length in model positions of hit to model 1";
+  push(@fields_A, "mhitlen2");
+  $fields_H{"mhitlen2"} = "length in model positions of hit to model 2";
+  push(@fields_A, "mhit-frac-of-mdl1");
+  $fields_H{"mhit-frac-of-mdl1"} = "'mhitlen1'/'mdllen1'";
+  push(@fields_A, "mhit-frac-of-mdl2");
+  $fields_H{"mhit-frac-of-mdl2"} = "'mhitlen2'/'mdllen2'";
+  push(@fields_A, "desc1");
+  $fields_H{"desc1"} = "description for hit to model 1";
+  push(@fields_A, "desc2");
+  $fields_H{"desc2"} = "description for hit to model 2";
+  my $fidx = 1;
+  my $all_header_line = "#";
+  print $overlap_FH ("# cmsearch-deoverlap.pl --overlapout output file\n# Explanation of fields:\n");
+  foreach my $field (@fields_A) {
+    printf $overlap_FH ("# %d. %-20s: %s\n", $fidx, "'" . $field . "'", $fields_H{$field});
+    $all_header_line .= sprintf("%s%d:%s", ($fidx == 1) ? "" : " ", $fidx, $field);
+    $fidx++;
+  }
+  print $overlap_FH $all_header_line . "\n";
+}
+
+foreach my $tblout_file (@tblout_file_A) {
+  if(! -e $tblout_file) { die "ERROR tblout file $tblout_file does not exist"; }
+  if(! -s $tblout_file) { die "ERROR tblout file $tblout_file is empty"; }
+
+  # if($rank_by_score):
+  #   sort tblout file by target sequence name, then score, then E-value
+  # else:
+  #   sort tblout file by target sequence name, then E-value, then score
+  #
+  # keys to sort by depend on input tblout file type, which
+  # is controlled by
+  # $do_hmmsearch
+  # $do_nhmmer
+  # or default if both of those are false
+  #
+  $sorted_tblout_file = $tblout_file . ".sort";
+  # the 'sed' calls replace multiple spaces with a single one, because sort is weird about multiple spaces sometimes
+  if($do_hmmsearch) {
+    if($do_besthmm) {
+      $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 9,9rn -k 8,8g > $sorted_tblout_file" :
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 8,8g -k 9,9rn > $sorted_tblout_file";
+    }
+    else { # sort by full sequence evalue/score
+      $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 6,6rn -k 5,5g > $sorted_tblout_file" :
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 5,5g -k 6,6rn > $sorted_tblout_file";
+    }
+  }
+  elsif($do_nhmmer) {
+    $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+        "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 14,14rn -k 13,13g > $sorted_tblout_file" :
+        "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 13,13g -k 14,14rn > $sorted_tblout_file";
+  }
+  elsif($do_cmscan) {
+    $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 3,3 -k 15,15rn -k 16,16g > $sorted_tblout_file" :
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 3,3 -k 16,16g -k 15,15rn > $sorted_tblout_file";
+  }
+  else {
+    # cmsearch, default
+    $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 15,15rn -k 16,16g > $sorted_tblout_file" :
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 16,16g -k 15,15rn > $sorted_tblout_file";
+  }
+  run_command($sort_cmd, $do_debug);
+  $output_file = $tblout_file . ".deoverlapped";
+  $out_FH = undef;
+  open($out_FH, ">", $output_file) || die "ERROR unable to open $output_file for writing";
+
+  ($nkept, $nremoved) = parse_sorted_tblout_file($sorted_tblout_file,
+                                                 (defined $in_clanin) ? \%clan_H : undef,
+                                                 (defined $in_mdllen) ? \%mdllen_H : undef,
+                                                 $do_cmscan, $do_nhmmer, $do_hmmsearch, $do_besthmm, $rank_by_score, $do_maxkeep, $do_debug, $be_verbose,
+                                                 $out_FH,
+                                                 (defined $out_overlap) ? $overlap_FH : undef);
+  close $out_FH;
+  if(defined $out_overlap) { close $overlap_FH; }
+  if(! $do_dirty) {
+    unlink $sorted_tblout_file;
+  }
+  printf("Saved %5d hits (%5d removed) to $output_file\n", $nkept, $nremoved);
+  if(defined $out_overlap) {
+    printf("Saved tabular information on overlaps to $out_overlap\n");
+  }
+}
+
+#################################################################
+# Subroutine : parse_sorted_tblout_file()
+# Incept:      EPN, Mon May  8 08:57:54 2017
+#
+# Purpose:     Parse a sorted tabular output file, and output
+#              all hits that do not have a higher scoring overlap.
+#
+# Arguments:
+#   $sorted_tbl_file:  file with sorted tabular search results
+#   $clan_HR:          ref to hash of clan info, key is model, value is clan, undef unless --clanin
+#   $mdllen_HR:        ref to hash of mdllen info, key is model, value is mdllen, undef unless --mdllenin
+#   $do_cmscan:        '1' if we're parsing cmscan tblout output
+#   $do_nhmmer:        '1' if we're parsing nhmmer tblout output
+#   $do_hmmsearch:     '1' if we're parsing hmmsearch tblout output
+#   $do_besthmm:       '1' if we sorted hmmsearch tblout by best hit
+#                      not by full sequence
+#   $rank_by_score:    '1' if rank is determined by score, '0' if
+#                      determined by E-value
+#   $do_maxkeep:       '1' if --maxkeep option used
+#                      only remove hits with higher scoring overlaps
+#                      *THAT ARE NOT THEMSELVES REMOVED*
+#   $do_debug;         '1' if we should print debugging output
+#   $be_verbose;       '1' if we should be verbose
+#   $out_FH:           file handle to output to
+#   $overlap_FH:       file handle to output overlap info to (if --overlapout)
+#
+# Returns:     Two values:
+#              $nkept:    number of hits saved and output
+#              $nremoved: number of hits removed and not output
+#
+# Dies:        If we see a line of input that is an an unexpected
+#              format
+#
+#################################################################
+sub parse_sorted_tblout_file {
+  my $nargs_expected = 13;
+  my $sub_name = "parse_sorted_tblout_file";
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($sorted_tbl_file, $clan_HR, $mdllen_HR,
+      $do_cmscan, $do_nhmmer, $do_hmmsearch, $do_besthmm, $rank_by_score, $do_maxkeep, $do_debug, $be_verbose,
+      $out_FH, $overlap_FH) = @_;
+
+  my $prv_target = undef; # target name of previous line
+  my $prv_score  = undef; # bit score of previous line
+  my $prv_evalue = undef; # E-value of previous line
+  my $clan       = undef; # clan of current model
+  my $nkept      = 0;     # number of hits kept and output
+  my $nremoved   = 0;     # number of hits removed and not output
+  my $do_clans   = (defined $clan_HR) ? 1 : 0;
+
+  open(IN, $sorted_tbl_file) || die "ERROR unable to open sorted tabular file $sorted_tbl_file for reading";
+
+  my ($target, $tacc, $model, $macc, $domain, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) =
+      (undef, undef, undef, undef, undef, undef, undef, undef, undef, undef, undef, undef, undef);
+
+  my @line_A      = (); # array of output lines for kept hits for current sequence
+  my @seqfrom_A   = (); # array of seqfroms for kept hits for current sequence
+  my @seqto_A     = (); # array of seqtos for kept hits for current sequence
+  my @strand_A    = (); # array of strands for kept hits for current sequence
+  my @clan_A      = (); # array of clans for kept hits for current sequence
+  my @keepme_A    = (); # array of '1' and '0', '1' if we should keep this hit, '0' if it had a higher scoring overlap
+  my @noverlaps_A = (); # array of number of hits (lower scoring) that overlap with this sequence, **only valid for kept hits, -1 for removed hits**
+  my $nhits       = 0;  # number of hits for current sequence (size of all arrays)
+  # arrays only filled if $overlap_FH is defined (if --overlapout was used)
+  my @mdlfrom_A   = (); # array of mdlfroms for kept hits for current sequence
+  my @mdlto_A     = (); # array of mdltos for kept hits for current sequence
+  my @model_A     = (); # array of model names for kept hits for current sequence
+  my @desc_A      = (); # array of descriptions for kept hits for current sequence
+  my @score_A     = (); # array of scores for kept hits for current sequence
+  my @evalue_A    = (); # array of e-values for kept hits for current sequence
+  my $do_desc = (defined $overlap_FH) ? 1 : 0;
+
+  my %already_seen_H = (); # hash, key is sequence name, value is '1' if we have output info for this sequence
+
+  $prv_evalue = 0.;
+  while(my $line = <IN>) {
+    ######################################################
+    # Parse the data on this line, this differs depending
+    # on our annotation method
+    chomp $line;
+    $line =~ s/^\s+//; # remove leading whitespace
+
+    if($line =~ m/^\#/) {
+      die "ERROR, found line that begins with #, input should have these lines removed and be sorted by the first column:$line.";
+    }
+
+    if($do_hmmsearch) {
+      ($target, $model, $score, $evalue, $desc) = parse_hmmsearch_tblout_line($line, $do_besthmm, $do_desc);
+      # hmmsearch --tblout output lacks sequence ranges and strand information
+      # we want to allow only a single hit to the each target, so we set span as 1..1
+      # so that all hits to the same target will 'overlap'. Strand is set as "+"
+      # so all hits are considered on the same 'strand' for de-overlapping purposes.
+      $seqfrom = 1;
+      $seqto   = 1;
+      $strand  = "+"; # no strand for hmmsearch output, so we assert + for de-overlapping purposes
+      $mdlfrom = "-";
+      $mdlto   = "-";
+    }
+    elsif($do_nhmmer) {
+      ($target, $tacc, $model, $macc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) = parse_nhmmer_tblout_line($line, $do_desc);
+    }
+    elsif($do_cmscan) {
+      # call parse_cmsearch_tblout_line, just reverse $model and $target
+      ($model, $macc, $target, $tacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) = parse_cmsearch_tblout_line($line, $do_desc);
+    }
+    else { # default: cmsearch
+      ($target, $tacc, $model, $macc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) = parse_cmsearch_tblout_line($line, $do_desc);
+      if((! $do_fcmsearch) && ($tacc =~ /^RF\d+/)) {
+        die "ERROR, target accession $tacc looks like an Rfam accession suggesting this is cmscan tblout output,\ndid you mean to use --cmscan? Use --fcmsearch to assert this is cmsearch output and avoid this error.\n";
+      }
+    }
+
+    $clan = undef;
+    if(defined $clan_HR) {
+      if(exists $clan_HR->{$model}) {
+        $clan = $clan_HR->{$model};
+      }
+    }
+
+    # make sure we didn't output information for this sequence already
+    if(exists $already_seen_H{$target}) {
+      die "ERROR found line with target $target previously output, did you sort by sequence name?";
+    }
+
+    ##############################################################
+    # Are we now finished with the previous sequence?
+    # Yes, if target sequence we just read is different from it
+    # If yes, output info for it, and re-initialize data structures
+    # for new sequence just read
+    if((defined $prv_target) && ($prv_target ne $target)) {
+      output_one_target($out_FH, $be_verbose, \@line_A, \@keepme_A, \@noverlaps_A);
+      $already_seen_H{$prv_target} = 1;
+      @line_A      = ();
+      @seqfrom_A   = ();
+      @seqto_A     = ();
+      @strand_A    = ();
+      @clan_A      = ();
+      @keepme_A    = ();
+      @noverlaps_A = ();
+      @mdlfrom_A   = ();
+      @mdlto_A     = ();
+      @model_A     = ();
+      @desc_A      = ();
+      @score_A     = ();
+      @evalue_A    = ();
+      $nhits       = 0;
+    }
+    else { # this is not a new sequence
+      if(defined $prv_target) {
+        # make sure that our current score or E-value is less than previous
+        if($rank_by_score && ($score > $prv_score)) {
+          die "ERROR found lines with same target [$target] incorrectly sorted by score, did you sort by sequence name and score?";
+        }
+        elsif((! $rank_by_score) && ($evalue < $prv_evalue)) {
+          die "ERROR found lines with same target [$target] incorrectly sorted by E-value, did you sort by sequence name and E-value?";
+        }
+      }
+    }
+    ##############################################################
+
+    # look through all other hits $i on the same strand and see if any of them overlap with this one
+    # if (! $do_maxkeep) we look at all hits
+    # if (  $do_maxkeep) we only look at hits that haven't been removed yet
+    my $keep_me = 1; # set to '0' below if we find a better scoring hit
+    my $overlap_idx = -1;
+    my $cur_noverlap = 0;
+    my $clan_criteria_passed = 1; # set to '1' if --clanin not used OR
+                                  # --clanin used and --invclan NOT used and two hits are to families in the same clan
+                                  # --clanin used and --invclan IS  used and two hits are NOT to families in the same clan
+                                  # else set to '0'
+    for(my $i = 0; $i < $nhits; $i++) {
+      if($strand_A[$i] eq $strand) {  # same strand
+        if($do_clans) {
+          if($do_invclan) {
+            $clan_criteria_passed = (! determine_if_clans_match($clan, $clan_A[$i]));
+          }
+          else {
+            $clan_criteria_passed = determine_if_clans_match($clan, $clan_A[$i]);
+          }
+        }
+        if(($clan_criteria_passed) &&                   # clans match (or don't if --invclan), or --clanin not used
+           ((! $do_maxkeep) || ($keepme_A[$i] == 1))) { # either --maxkeep not enabled, or this hit is a keepter
+          if($strand eq "+") {
+            $cur_noverlap = get_overlap($seqfrom, $seqto, $seqfrom_A[$i], $seqto_A[$i]);
+          }
+          elsif($strand eq "-") {
+            $cur_noverlap = get_overlap($seqto, $seqfrom, $seqto_A[$i], $seqfrom_A[$i]);
+          }
+          else {
+            die "ERROR strand not + or - but $strand for hit $i line:\n$line\n";
+          }
+          if($cur_noverlap >= $noverlap) {
+            $keep_me = 0;
+            $overlap_idx = $i;
+            $i = $nhits; # breaks for loop
+          }
+        }
+      }
+    }
+    # add hit to list of hits we have for this sequence
+    $line_A[$nhits]    = $line . "\n";
+    $seqfrom_A[$nhits] = $seqfrom;
+    $seqto_A[$nhits]   = $seqto;
+    $strand_A[$nhits]  = $strand;
+    $clan_A[$nhits]    = $clan;
+    if(defined $overlap_FH) { # only need these if we're outputting to an overlap file
+      $mdlfrom_A[$nhits] = $mdlfrom;
+      $mdlto_A[$nhits]   = $mdlto;
+      $model_A[$nhits]   = $model;
+      $desc_A[$nhits]    = $desc;
+      $score_A[$nhits]   = $score;
+      $evalue_A[$nhits]  = $evalue;
+    }
+    if($keep_me) {
+      $nkept++;
+      $keepme_A[$nhits] = 1;
+      $noverlaps_A[$nhits] = 0;
+    }
+    else {
+      $nremoved++;
+      $keepme_A[$nhits] = 0;
+      $noverlaps_A[$nhits] = -1;
+      $noverlaps_A[$overlap_idx]++;
+      if($do_debug) {
+        printf("target: $target model: $model: removing $seqfrom..$seqto, it overlapped with $seqfrom_A[$overlap_idx]..$seqto_A[$overlap_idx]\n");
+      }
+      if($be_verbose) {
+        printf("REMOVED                      %-*s  $line\n", length($cur_noverlap), "");
+        printf("BECAUSE-IT-OVERLAPPED-BY-" . $cur_noverlap . "-WITH $line_A[$overlap_idx]\n");
+      }
+      if(defined $overlap_FH) {
+        my $hitlen1  = abs($seqfrom_A[$overlap_idx]-$seqto_A[$overlap_idx])+1;
+        my $hitlen2  = abs($seqfrom-$seqto)+1;
+        my $mhitlen1 = (($mdlfrom_A[$overlap_idx] ne "-") && ($mdlto_A[$overlap_idx] ne "-")) ? abs($mdlfrom_A[$overlap_idx]-$mdlto_A[$overlap_idx])+1 : "-";
+        my $mhitlen2 = (($mdlfrom ne "-") && ($mdlto ne "-")) ? abs($mdlfrom-$mdlto)+1 : "-";
+        my $mdllen1  = ((defined $mdllen_HR) && (defined $mdllen_HR->{$model_A[$overlap_idx]})) ? $mdllen_HR->{$model_A[$overlap_idx]} : "-";
+        my $mdllen2  = ((defined $mdllen_HR) && (defined $mdllen_HR->{$model})) ? $mdllen_HR->{$model} : "-";
+
+        printf $overlap_FH ("%-s\t%s\t%s\t%s\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%.3f\t%.3f\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
+                            $target, $strand, $model_A[$overlap_idx], $model,
+                            $hitlen1, $hitlen2, $cur_noverlap,
+                            $score_A[$overlap_idx], $score,
+                            $evalue_A[$overlap_idx], $evalue,
+                            $seqfrom_A[$overlap_idx], $seqto_A[$overlap_idx],
+                            $seqfrom, $seqto,
+                            $cur_noverlap/$hitlen1, $cur_noverlap/$hitlen2,
+                            $mdllen1, $mdllen2,
+                            ($mdllen1 ne "-") ? (sprintf("%.3f", $cur_noverlap/$mdllen1)) : "-",
+                            ($mdllen2 ne "-") ? (sprintf("%.3f", $cur_noverlap/$mdllen2)) : "-",
+                            $mhitlen1, $mhitlen2,
+                            (($mhitlen1 ne "-") && ($mdllen1 ne "-")) ? (sprintf("%.3f", $mhitlen1/$mdllen1)) : "-",
+                            (($mhitlen2 ne "-") && ($mdllen2 ne "-")) ? (sprintf("%.3f", $mhitlen2/$mdllen2)) : "-",
+                            $desc_A[$overlap_idx], $desc);
+      }
+    }
+    $nhits++;
+    $prv_target = $target;
+    $prv_score  = $score;
+    $prv_evalue = $evalue;
+  }
+
+  # output data for final sequence
+  output_one_target($out_FH, $be_verbose, \@line_A, \@keepme_A, \@noverlaps_A);
+
+  # close file handle
+  close(IN);
+
+  return ($nkept, $nremoved);
+}
+
+#################################################################
+# Subroutine : output_one_target()
+# Incept:      EPN, Mon May  8 10:20:40 2017
+#
+# Purpose:     Output all hits for a target. Overlapping hits
+#              are not included, they've been skipped.
+#
+# Arguments:
+#   $out_FH:        file handle to output short output to (can be undef to not output short output)
+#   $be_verbose:    '1' to output number of overlaps for each kept hit to stdout
+#   $line_AR:       array of lines to output
+#   $keepme_AR:     array of '1', '0', $keepme_AR->[$i]==1 indicates we should output $line_AR->[$i]
+#   $noverlaps_AR:  array of '1', '0', $keepme_AR->[$i]==1 indicates we should output $line_AR->[$i]
+#
+# Returns:     Nothing.
+#
+# Dies:        Never.
+#
+#################################################################
+sub output_one_target {
+  my $nargs_expected = 5;
+  my $sub_name = "output_one_target";
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($out_FH, $be_verbose, $line_AR, $keepme_AR, $noverlaps_AR) = @_;
+
+  for(my $i = 0; $i < scalar(@{$line_AR}); $i++) {
+    if($keepme_AR->[$i]) {
+      print $out_FH $line_AR->[$i];
+      if($be_verbose) { printf("NUM-OVERLAPS:%d $line_AR->[$i]", $noverlaps_AR->[$i]) };
+    }
+  }
+
+  return;
+}
+
+#################################################################
+# Subroutine : determine_if_clans_match()
+# Incept:      EPN, Mon May  8 10:28:41 2017
+#
+# Purpose:     Given two clan values return 1 if they
+#              match else 0.
+#
+# Arguments:
+#   $clan1:    clan 1, can be undef
+#   $clan2:    clan 2, can be undef
+#
+# Returns:     '1' if the clans match or if $do_clans is FALSE
+#
+# Dies:        Never.
+#
+#################################################################
+sub determine_if_clans_match {
+  my $nargs_expected = 2;
+  my $sub_name = "determine_if_clans_match";
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($clan1, $clan2) = @_;
+
+  if((! defined $clan1) || (! defined $clan2)) {
+    # 1 or both of $clan1 and $clan2 are undefined, can't be a match
+    return 0;
+  }
+  elsif($clan1 eq $clan2) {
+    # equal clans
+    return 1;
+  }
+  else {
+    return 0;
+  }
+
+}
+
+#################################################################
+# Subroutine: get_overlap()
+# Incept:     EPN, Mon Mar 14 13:47:57 2016 [dnaorg_scripts:dnaorg.pm:getOverlap()]
+#
+# Purpose:    Calculate number of nucleotides of overlap between
+#             two regions.
+#
+# Args:
+#  $start1: start position of hit 1 (must be <= $end1)
+#  $end1:   end   position of hit 1 (must be >= $end1)
+#  $start2: start position of hit 2 (must be <= $end2)
+#  $end2:   end   position of hit 2 (must be >= $end2)
+#
+# Returns:  $noverlap:    Number of nucleotides of overlap between hit1 and hit2,
+#                         0 if none
+#
+# Dies:     if $end1 < $start1 or $end2 < $start2.
+sub get_overlap {
+  my $sub_name = "get_overlap";
+  my $nargs_exp = 4;
+  if(scalar(@_) != 4) { die "ERROR $sub_name entered with wrong number of input args"; }
+
+  my ($start1, $end1, $start2, $end2) = @_;
+
+  # printf("in $sub_name $start1..$end1 $start2..$end2\n");
+
+  if($start1 > $end1) { die "ERROR in $sub_name start1 > end1 ($start1 > $end1)"; }
+  if($start2 > $end2) { die "ERROR in $sub_name start2 > end2 ($start2 > $end2)"; }
+
+  # Given: $start1 <= $end1 and $start2 <= $end2.
+
+  # Swap if nec so that $start1 <= $start2.
+  if($start1 > $start2) {
+    my $tmp;
+    $tmp   = $start1; $start1 = $start2; $start2 = $tmp;
+    $tmp   =   $end1;   $end1 =   $end2;   $end2 = $tmp;
+  }
+
+  # 3 possible cases:
+  # Case 1. $start1 <=   $end1 <  $start2 <=   $end2  Overlap is 0
+  # Case 2. $start1 <= $start2 <=   $end1 <    $end2
+  # Case 3. $start1 <= $start2 <=   $end2 <=   $end1
+  if($end1 < $start2) { return (0); }                    # case 1
+  if($end1 <   $end2) { return ($end1 - $start2 + 1); }  # case 2
+  if($end2 <=  $end1) { return ($end2 - $start2 + 1); }  # case 3
+  die "ERROR in $sub_name, unforeseen case in $start1..$end1 and $start2..$end2";
+
+  return; # NOT REACHED
+}
+
+#################################################################
+# Subroutine:  run_command()
+# Incept:      EPN, Mon Dec 19 10:43:45 2016
+#
+# Purpose:     Runs a command using system() and exits in error
+#              if the command fails. If $be_verbose, outputs
+#              the command to stdout.
+#
+# Arguments:
+#   $cmd:         command to run, with a "system" command;
+#   $be_verbose:  '1' to output command to stdout before we run it, '0' not to
+#
+# Returns:    nothing
+#
+# Dies:       if $cmd fails
+#################################################################
+sub run_command {
+  my $sub_name = "run_command()";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($cmd, $be_verbose) = @_;
+
+  if($be_verbose) {
+    print ("Running cmd: $cmd\n");
+  }
+
+  system($cmd);
+
+  if($? != 0) {
+    die "ERROR in $sub_name, the following command failed:\n$cmd\n";
+  }
+
+  return;
+}
+
+#################################################################
+# Subroutine:  parse_claninfo()
+# Incept:      EPN, Wed May 10 15:01:07 2017
+#
+# Purpose:     Parse a claninfo file and fill %{$clan_HR}.
+#
+# Arguments:
+#   $claninfo_file: clan info file
+#   $clan_HR:       ref to hash of clan info, key: model name, value: clan name
+#
+# Returns:    nothing
+#
+# Dies:       if $cmd fails
+#################################################################
+sub parse_claninfo {
+  my $sub_name = "parse_claninfo()";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($claninfo_file, $clan_HR) = @_;
+
+  open(IN, $claninfo_file) || die "ERROR unable to open clan info file";
+
+  %{$clan_HR} = ();
+
+  while(my $line = <IN>) {
+    if($line !~ m/^#/) {
+      chomp $line;
+      my @el_A = split(/\s+/, $line);
+      # first element is clan name, all other elements are model names in that clan
+      #CL00111  SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia SSU_trypano_mito
+      for(my $i = 1; $i < scalar(@el_A); $i++) {
+        if(exists $clan_H{$el_A[$i]}) {
+          die "ERROR in $sub_name, parsing clan info file $claninfo_file, read model $el_A[$i] more than once";
+        }
+        $clan_HR->{$el_A[$i]} = $el_A[0];
+      }
+    }
+  }
+  return;
+}
+
+#################################################################
+# Subroutine:  parse_cmsearch_tblout_line()
+# Incept:      EPN, Fri Dec  8 09:33:23 2017
+#
+# Purpose:     Given an infernal cmsearch --tblout line,
+#              return $target, $query, $seqfrom, $seqto, $strand, $score, $evalue.
+#
+#     # Example line
+#     #target name         accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target
+#     #------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
+#     5S_rRNA-sample10     -         5S_rRNA              RF00001    cm        1      119        1      121      +    no    1 0.61   0.0  108.2   1.5e-27 !   -
+#
+# Arguments:
+#   $line:  line to parse
+#
+# Returns:    $target:  name of target      (5S_rRNA-sample10)
+#             $tacc:    target accession    (-)
+#             $query:   query name          (5S_rRNA)
+#             $qacc:    query accession     (RF00005)
+#             $mdlfrom: hmmfrom coord       (1)
+#             $mdlto:   hmm to coord        (119)
+#             $seqfrom: sequence from coord (1)
+#             $seqto:   sequence to coord   (121)
+#             $strand:  strand of hit       (+)
+#             $score:   bit score of hit    (108.2)
+#             $evalue:  E-value of hit      (1.5e-27)
+#             $desc:    description, undef unless $do_desc is 1
+#
+# Dies:       if line has fewer than 18 space delimited characters
+#################################################################
+sub parse_cmsearch_tblout_line {
+  my $sub_name = "parse_cmsearch_tblout_line";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($line, $do_desc) = @_;
+
+  my @el_A = split(/\s+/, $line);
+
+  if(scalar(@el_A) < 18) { die "ERROR found less than 18 columns in cmsearch tabular output at line: $line"; }
+  my ($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue) =
+      ($el_A[0], $el_A[1], $el_A[2], $el_A[3], $el_A[5], $el_A[6], $el_A[7], $el_A[8], $el_A[9],  $el_A[14], $el_A[15]);
+
+  my $desc = undef;
+  if($do_desc) {
+    $desc = $el_A[17];
+    my $nel = scalar(@el_A);
+    for(my $i = 18; $i < $nel; $i++) { $desc .= "_" . $el_A[$i]; } # replace spaces with "_";
+  }
+
+  return($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc);
+}
+
+#################################################################
+# Subroutine:  parse_nhmmer_tblout_line()
+# Incept:      EPN, Fri Dec  8 09:42:28 2017
+#
+# Purpose:     Given an nhmmer --tblout line,
+#              return $target, $query, $seqfrom, $seqto, $strand, $score, $evalue.
+#
+#     # Example line
+#     # target name        accession  query name           accession  hmmfrom hmm to alifrom  ali to envfrom  env to  sq len strand   E-value  score  bias  description of target
+#     #------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- ---------------------
+#     5S_rRNA-sample10     -          5S_rRNA              RF00001          4     115       4     117       1     121     121    +     1.6e-17   53.3   4.8  -
+#
+# Arguments:
+#   $line:    line to parse
+#   $do_desc: '1' to parse and return description, else '0'
+#
+# Returns:    $target: name of target       (5S_rRNA-sample10)
+#             $tacc:    target accession    (-)
+#             $query:   query name          (5S_rRNA)
+#             $qacc:    query accession     (RF00005)
+#             $mdlfrom: hmmfrom coord       (4)
+#             $mdlto:   hmm to coord        (115)
+#             $seqfrom: ali from coord      (4)
+#             $seqto:   ali to coord        (117)
+#             $strand:  strand of hit       (+)
+#             $score:   bit score of hit    (53.3)
+#             $evalue:  E-value of hit      (1.6e-17)
+#             $desc:    description, undef unless $do_desc is 1
+#
+# Dies:       if line has fewer than 16 space delimited characters
+#################################################################
+sub parse_nhmmer_tblout_line {
+  my $sub_name = "parse_nhmmer_tblout_line";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($line, $do_desc) = @_;
+
+  my @el_A = split(/\s+/, $line);
+
+  if(scalar(@el_A) < 16) { die "ERROR found less than 16 columns in nhmmer tabular output at line: $line"; }
+  my ($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $evalue, $score) =
+      ($el_A[0], $el_A[1], $el_A[2], $el_A[3], $el_A[4], $el_A[5], $el_A[6], $el_A[7], $el_A[11], $el_A[12], $el_A[13]);
+  my $desc = undef;
+  if($do_desc) {
+    $desc = $el_A[15];
+    my $nel = scalar(@el_A);
+    for(my $i = 16; $i < $nel; $i++) { $desc .= "_" . $el_A[$i]; } # replace spaces with "_";
+  }
+
+  return($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc);
+}
+
+#################################################################
+# Subroutine:  parse_hmmsearch_tblout_line()
+# Incept:      EPN, Fri Dec  8 09:47:19 2017
+#
+# Purpose:     Given an hmmsearch --tblout line,
+#              return $target, $query, $score, $evalue.
+#
+#     # Example line
+#     #                                                               --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
+#     # target name        accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
+#     #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
+#     5S_rRNA-sample10     -          5S_rRNA              RF00001      1.1e-19   59.8   0.0   1.2e-19   59.7   0.0   1.0   1   0   0   1   1   1   1 -
+#
+# Arguments:
+#   $line:             line to parse
+#   $do_best:          '1' to return score and E-value of best hit, not full sequence
+#                      '0' to return score and E-value of sequence, not best hit
+#   $do_desc:          '1' to parse and return description, else '0'
+#
+# Returns:    $target: name of target       (5S_rRNA-sample10)
+#             $query:  query name           (5S_rRNA)
+#             $score:  bit score of sequence  (53.3)
+#             $evalue: E-value of hit      (1.6e-17)
+#             $desc:   description, undef unless $do_desc is 1
+#
+# Dies:       if line has fewer than 19 space delimited characters
+#################################################################
+sub parse_hmmsearch_tblout_line {
+  my $sub_name = "parse_hmmsearch_tblout_line";
+  my $nargs_expected = 3;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($line, $do_best, $do_desc) = @_;
+
+  my @el_A = split(/\s+/, $line);
+
+  if(scalar(@el_A) < 19) { die "ERROR found less than 16 columns in nhmmer tabular output at line: $line"; }
+  my ($target, $query, $full_evalue, $full_score, $best_evalue, $best_score) =
+      ($el_A[0], $el_A[2], $el_A[4], $el_A[5], $el_A[7], $el_A[8]);
+
+  my $desc = undef;
+  if($do_desc) {
+    $desc = $el_A[18];
+    my $nel = scalar(@el_A);
+    for(my $i = 19; $i < $nel; $i++) { $desc .= "_" . $el_A[$i]; } # replace spaces with "_";
+  }
+
+  if($do_best) {
+    return ($target, $query, $best_score, $best_evalue, $desc);
+  }
+  # else
+  return ($target, $query, $full_score, $full_evalue, $desc);
+}
Binary file cmsearch_tblout_deoverlap_tool/cmsearch_sampleout.png has changed
Binary file cmsearch_tblout_deoverlap_tool/cmsearch_toolform.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/cmsearchtbloutdeoverlap.xml	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,1007 @@
+<tool name="cmsearchtbloutdeoverlap" id="cmsearchtbloutdeoverlap" version="0.001">
+  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
+  <!--Created by toolfactory@galaxy.org at 16/08/2023 12:33:38 using the Galaxy Tool Factory.-->
+  <description>Wraps https://github.com/nawrockie/cmsearch_tblout_deoverlap</description>
+  <requirements>
+    <requirement version="5.34.0" type="package">perl</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
+  <version_command><![CDATA[echo "0.001"]]></version_command>
+  <command><![CDATA[perl
+$runme
+--in_tblout
+$in_tblout
+#if $clanin
+ --clanin $clanin
+#end if
+--overlapout
+$overlapout
+#if $sortbit == "set"
+ --s
+#end if
+#if $maxkeep == "set"
+ --maxkeep
+#end if
+
+'$input_kind']]></command>
+  <configfiles>
+    <configfile name="runme"><![CDATA[#raw
+
+#!/usr/bin/env perl
+#
+# cmsearch-deoverlap.pl: remove lower scoring overlaps from cmsearch
+#                        --tblout files.
+#
+# EPN, Mon May  8 08:41:36 2017
+#
+#
+# Without --maxkeep this script will exactly reproduce how cmscan removes overlapping hits.
+# With --maxkeep, it won't. Here's an example to explain the difference:
+#
+##target name         accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target
+##------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
+#1. contig--151565       -         LSU_rRNA_eukarya     RF02543   hmm      632     2329      410     1883      +     -    6 0.48   1.1  726.0  1.1e-216 !   -
+#2. contig--151565       -         LSU_rRNA_archaea     RF02540   hmm      170     2084       12     1882      +     -    6 0.47   3.0  490.0  2.3e-145 !   -
+#3. contig--151565       -         LSU_rRNA_bacteria    RF02541   hmm      187     2005       10     1883      +     -    6 0.47   5.7  331.4   1.8e-97 !   -
+#4. contig--151565       -         LSU_rRNA_eukarya     RF02543   hmm       29      431       12      366      +     -    6 0.41   7.8  100.0   6.3e-28 !   -
+#
+# hit 1: 410..1883 euk
+# hit 2: 12..1182 arc
+# hit 3: 10..1883 bac
+# hit 4: 12..366 euk
+#
+# Without --maxkeep (default behavior) hits 2, 3, and 4 will be removed because for all 3, there is a better scoring hit
+# that overlaps.
+#
+# With --maxkeep only hits 2 and 3 will be removed because only those 2 have
+# higher scoring hits that overlap with them AND are not removed. If we remove only hits 2 and 3
+# hits 1 and 4 no longer overlap.
+#
+use strict;
+use warnings;
+use Getopt::Long;
+
+my $in_tblout  = "";   # name of input tblout file
+
+my $usage;
+$usage  = "cmsearch-deoverlap v0.09 [Aug 2023]\n\n";
+$usage .= "Usage:\n\n";
+$usage .= "cmsearch-deoverlap.pl    [OPTIONS] <tblout file>\n\tOR\n";
+$usage .= "cmsearch-deoverlap.pl -l [OPTIONS] <list of tblout files>\n\n";
+$usage .= "\tOPTIONS:\n";
+$usage .= "\t\t-l               : single command line argument is a list of tblout files, not a single tblout file\n";
+$usage .= "\t\t-s               : sort hits by bit score [default: sort by E-value]\n";
+$usage .= "\t\t-d               : run in debugging mode (prints extra info)\n";
+$usage .= "\t\t-v               : run in verbose mode (prints all removed and kept hits)\n";
+$usage .= "\t\t--noverlap <n>   : define an overlap as >= <n> or more overlapping residues [1]\n";
+$usage .= "\t\t--nhmmer         : tblout files are from nhmmer v3.x\n";
+$usage .= "\t\t--hmmsearch      : tblout files are from hmmsearch v3.x\n";
+$usage .= "\t\t--cmscan         : tblout files are from cmscan v1.1x, not cmsearch\n";
+$usage .= "\t\t--fcmsearch      : assert tblout files are cmsearch not cmscan\n";
+$usage .= "\t\t--besthmm        : with --hmmsearch, sort by evalue/score of *best* single hit not evalue/score of full seq\n";
+$usage .= "\t\t--clanin <s>     : only remove overlaps within clans, read clan info from file <s> [default: remove all overlaps]\n";
+$usage .= "\t\t--invclan        : w/--clanin, invert clan behavior: do not remove overlaps within clans, remove all other overlaps\n";
+$usage .= "\t\t--maxkeep        : keep hits that only overlap with other hits that are not kept [default: remove all hits with higher scoring overlap]\n";
+$usage .= "\t\t--overlapout <s> : create new tabular file with overlap information in <s>\n";
+$usage .= "\t\t--mdllenin <s>   : w/--overlapout, read model lengths from two-token-per-line-file <s>\n";
+$usage .= "\t\t--dirty          : keep intermediate files (sorted tblout files)\n\n";
+
+my $do_listfile      = 0;     # set to '1' if -l used
+my $rank_by_score    = 0;     # set to '1' if -s used, rank by score, not evalues
+my $do_debug         = 0;     # set to '1' if -d used
+my $be_verbose       = 0;     # set to '1' if -v used
+my $do_cmscan        = 0;     # set to '1' if --cmscan used
+my $do_fcmsearch     = 0;     # set to '1' if --fcmsearch used
+my $noverlap         = 1;     # set to <n> if --noverlap <n> used
+my $in_clanin        = undef; # defined if --clanin option used
+my $do_invclan       = 0;     # set to '1' if --invclan used
+my $do_nhmmer        = 0;     # set to '1' if --nhmmer used, input tblout file(s) are from hmmer3's nhmmer
+my $do_hmmsearch     = 0;     # set to '1' if --hmmsearch used, input tblout file(s) are from hmmer3's hmmsearch
+my $do_besthmm       = 0;     # set to '1' if --besthmm used, sorting by evalue/score of best hit with --hmmsearch
+my $do_maxkeep       = 0;     # set to '1' if --maxkeep, only remove hits that have
+                              # higher scoring overlap that is not removed
+my $do_dirty         = 0;     # set to '1' if --dirty used, keep intermediate files
+my $out_overlap      = undef; # defined if --overlapout <s> used
+my $in_mdllen        = undef; # defined if --mdllenin <s> used
+
+&GetOptions( "l"            => \$do_listfile,
+             "s"            => \$rank_by_score,
+             "d"            => \$do_debug,
+             "v"            => \$be_verbose,
+             "cmscan"       => \$do_cmscan,
+             "fcmsearch"    => \$do_fcmsearch,
+             "noverlap=s"   => \$noverlap,
+             "nhmmer"       => \$do_nhmmer,
+             "hmmsearch"    => \$do_hmmsearch,
+             "besthmm"      => \$do_besthmm,
+             "clanin=s"     => \$in_clanin,
+             "invclan"      => \$do_invclan,
+             "maxkeep"      => \$do_maxkeep,
+             "overlapout=s" => \$out_overlap,
+             "mdllenin=s"   => \$in_mdllen,
+             "dirty"        => \$do_dirty,
+             "in_tblout=s"    => \$in_tblout);
+
+#if(scalar(@ARGV) != 1) { die $usage; }
+# ($in_tblout) = @ARGV;
+
+if($do_hmmsearch && $do_nhmmer) {
+  die "ERROR, --hmmsearch and --nhmmer cannot be used in combination. Pick one.";
+}
+if($do_besthmm && (! $do_hmmsearch)) {
+  die "ERROR, --besthmm requires --hmmsearch.";
+}
+if($do_invclan && (! defined $in_clanin)) {
+  die "ERROR, --invclan requires --clanin";
+}
+my @tblout_file_A = ();
+
+if($do_listfile) {
+  # read the list file
+  my $list_file = $in_tblout;
+  open(IN, $list_file) || die "ERROR unable to open $list_file for reading";
+  while(my $line = <IN>) {
+    if($line =~ m/\w/ && $line !~ m/^\#/) {
+      chomp $line;
+      if(! -e $line) { die "ERROR file $line read from $list_file does not exist"; }
+      if(! -s $line) { die "ERROR file $line read from $list_file is empty"; }
+      push(@tblout_file_A, $line);
+    }
+  }
+  close(IN);
+}
+else {
+  $tblout_file_A[0] = ($in_tblout);
+}
+
+my %mdllen_H = ();
+if(defined $in_mdllen) { # read this file too
+  open(IN, $in_mdllen) || die "ERROR unable to open $in_mdllen for reading";
+  while(my $line = <IN>) {
+    chomp $line;
+    if($line =~ /^(\S+)\s+(\d+)$/) {
+      $mdllen_H{$1} = $2;
+    }
+    else {
+      die "ERROR unable to parse <model> <modellen> line in $in_mdllen\n$line\n";
+    }
+  }
+  close(IN);
+}
+
+my %clan_H = (); # key: model name, value: clan name
+if(defined $in_clanin) {
+  %clan_H = ();
+  parse_claninfo($in_clanin, \%clan_H)
+}
+
+my $sort_cmd           = undef; # command used to sort the tblout file
+my $sorted_tblout_file = undef; # sorted tblout file to create, temporarily
+my $output_file        = undef; # name of output file we create
+my $out_FH             = undef; # output file handle
+my $nkept              = undef; # number of sequences kept from a file
+my $nremoved           = undef; # number of sequences removed from a file
+
+my $overlap_FH = undef;
+if(defined $out_overlap) {
+  open($overlap_FH, ">", $out_overlap) || die "ERROR unable to open $out_overlap for writing";
+  my @fields_A = ();
+  my %fields_H = ();
+  push(@fields_A, "target");
+  $fields_H{"target"} = "sequence name";
+  push(@fields_A, "strand");
+  $fields_H{"strand"} = "strand (+ or -)";
+  push(@fields_A, "mdl1");
+  $fields_H{"mdl1"} = "name of model 1";
+  push(@fields_A, "mdl2");
+  $fields_H{"mdl2"} = "name of model 2";
+  push(@fields_A, "hitlen1");
+  $fields_H{"hitlen1"} = "length in sequence positions of hit to model 1";
+  push(@fields_A, "hitlen2");
+  $fields_H{"hitlen2"} = "length in sequence positions of hit to model 2";
+  push(@fields_A, "nres_olap");
+  $fields_H{"nres_olap"} = "number of residues that overlap between hit to model 1 and hit to model 2 in 'target' on strand 'strand'";
+  push(@fields_A, "score1");
+  $fields_H{"score1"} = "score of hit to model 1";
+  push(@fields_A, "score2");
+  $fields_H{"score2"} = "score of hit to model 2";
+  push(@fields_A, "evalue1");
+  $fields_H{"evalue1"} = "E-value of hit to model 1";
+  push(@fields_A, "evalue2");
+  $fields_H{"evalue2"} = "E-value of hit to model 2";
+  push(@fields_A, "seqfrom1");
+  $fields_H{"seqfrom1"} = "start position in 'target' of hit to model 1";
+  push(@fields_A, "seqto1");
+  $fields_H{"seqto1"} = "end position in 'target' of hit to model 1";
+  push(@fields_A, "seqfrom2");
+  $fields_H{"seqfrom2"} = "start position in 'target' of hit to model 2";
+  push(@fields_A, "seqto2");
+  $fields_H{"seqto2"} = "end position in 'target' of hit to model 2";
+  push(@fields_A, "olap-frac-of-hit1");
+  $fields_H{"olap-frac-of-hit1"} = "'nres_olap'/'hitlen1'";
+  push(@fields_A, "olap-frac-of-hit2");
+  $fields_H{"olap-frac-of-hit2"} = "'nres_olap'/'hitlen2'";
+  push(@fields_A, "mdllen1");
+  $fields_H{"mdllen1"} = "length of model 1 (\"-\" if not available)";
+  push(@fields_A, "mdllen2");
+  $fields_H{"mdllen2"} = "length of model 2 (\"-\" if not available)";
+  push(@fields_A, "olap-frac-of-mdl1");
+  $fields_H{"olap-frac-of-mdl1"} = "'nres_olap'/'mdllen1'";
+  push(@fields_A, "olap-frac-of-mdl2");
+  $fields_H{"olap-frac-of-mdl2"} = "'nres_olap'/'mdllen2'";
+  push(@fields_A, "mhitlen1");
+  $fields_H{"mhitlen1"} = "length in model positions of hit to model 1";
+  push(@fields_A, "mhitlen2");
+  $fields_H{"mhitlen2"} = "length in model positions of hit to model 2";
+  push(@fields_A, "mhit-frac-of-mdl1");
+  $fields_H{"mhit-frac-of-mdl1"} = "'mhitlen1'/'mdllen1'";
+  push(@fields_A, "mhit-frac-of-mdl2");
+  $fields_H{"mhit-frac-of-mdl2"} = "'mhitlen2'/'mdllen2'";
+  push(@fields_A, "desc1");
+  $fields_H{"desc1"} = "description for hit to model 1";
+  push(@fields_A, "desc2");
+  $fields_H{"desc2"} = "description for hit to model 2";
+  my $fidx = 1;
+  my $all_header_line = "#";
+  print $overlap_FH ("# cmsearch-deoverlap.pl --overlapout output file\n# Explanation of fields:\n");
+  foreach my $field (@fields_A) {
+    printf $overlap_FH ("# %d. %-20s: %s\n", $fidx, "'" . $field . "'", $fields_H{$field});
+    $all_header_line .= sprintf("%s%d:%s", ($fidx == 1) ? "" : " ", $fidx, $field);
+    $fidx++;
+  }
+  print $overlap_FH $all_header_line . "\n";
+}
+
+foreach my $tblout_file (@tblout_file_A) {
+  if(! -e $tblout_file) { die "ERROR tblout file $tblout_file does not exist"; }
+  if(! -s $tblout_file) { die "ERROR tblout file $tblout_file is empty"; }
+
+  # if($rank_by_score):
+  #   sort tblout file by target sequence name, then score, then E-value
+  # else:
+  #   sort tblout file by target sequence name, then E-value, then score
+  #
+  # keys to sort by depend on input tblout file type, which
+  # is controlled by
+  # $do_hmmsearch
+  # $do_nhmmer
+  # or default if both of those are false
+  #
+  $sorted_tblout_file = $tblout_file . ".sort";
+  # the 'sed' calls replace multiple spaces with a single one, because sort is weird about multiple spaces sometimes
+  if($do_hmmsearch) {
+    if($do_besthmm) {
+      $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 9,9rn -k 8,8g > $sorted_tblout_file" :
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 8,8g -k 9,9rn > $sorted_tblout_file";
+    }
+    else { # sort by full sequence evalue/score
+      $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 6,6rn -k 5,5g > $sorted_tblout_file" :
+          "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 5,5g -k 6,6rn > $sorted_tblout_file";
+    }
+  }
+  elsif($do_nhmmer) {
+    $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+        "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 14,14rn -k 13,13g > $sorted_tblout_file" :
+        "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 13,13g -k 14,14rn > $sorted_tblout_file";
+  }
+  elsif($do_cmscan) {
+    $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 3,3 -k 15,15rn -k 16,16g > $sorted_tblout_file" :
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 3,3 -k 16,16g -k 15,15rn > $sorted_tblout_file";
+  }
+  else {
+    # cmsearch, default
+    $sort_cmd = ((defined $rank_by_score) && ($rank_by_score == 1)) ?
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 15,15rn -k 16,16g > $sorted_tblout_file" :
+      "grep -v ^\# $tblout_file | sed 's/  */ /g' | sort -k 1,1 -k 16,16g -k 15,15rn > $sorted_tblout_file";
+  }
+  run_command($sort_cmd, $do_debug);
+  $output_file = $tblout_file . ".deoverlapped";
+  $out_FH = undef;
+  open($out_FH, ">", $output_file) || die "ERROR unable to open $output_file for writing";
+
+  ($nkept, $nremoved) = parse_sorted_tblout_file($sorted_tblout_file,
+                                                 (defined $in_clanin) ? \%clan_H : undef,
+                                                 (defined $in_mdllen) ? \%mdllen_H : undef,
+                                                 $do_cmscan, $do_nhmmer, $do_hmmsearch, $do_besthmm, $rank_by_score, $do_maxkeep, $do_debug, $be_verbose,
+                                                 $out_FH,
+                                                 (defined $out_overlap) ? $overlap_FH : undef);
+  close $out_FH;
+  if(defined $out_overlap) { close $overlap_FH; }
+  if(! $do_dirty) {
+    unlink $sorted_tblout_file;
+  }
+  printf("Saved %5d hits (%5d removed) to $output_file\n", $nkept, $nremoved);
+  if(defined $out_overlap) {
+    printf("Saved tabular information on overlaps to $out_overlap\n");
+  }
+}
+
+#################################################################
+# Subroutine : parse_sorted_tblout_file()
+# Incept:      EPN, Mon May  8 08:57:54 2017
+#
+# Purpose:     Parse a sorted tabular output file, and output
+#              all hits that do not have a higher scoring overlap.
+#
+# Arguments:
+#   $sorted_tbl_file:  file with sorted tabular search results
+#   $clan_HR:          ref to hash of clan info, key is model, value is clan, undef unless --clanin
+#   $mdllen_HR:        ref to hash of mdllen info, key is model, value is mdllen, undef unless --mdllenin
+#   $do_cmscan:        '1' if we're parsing cmscan tblout output
+#   $do_nhmmer:        '1' if we're parsing nhmmer tblout output
+#   $do_hmmsearch:     '1' if we're parsing hmmsearch tblout output
+#   $do_besthmm:       '1' if we sorted hmmsearch tblout by best hit
+#                      not by full sequence
+#   $rank_by_score:    '1' if rank is determined by score, '0' if
+#                      determined by E-value
+#   $do_maxkeep:       '1' if --maxkeep option used
+#                      only remove hits with higher scoring overlaps
+#                      *THAT ARE NOT THEMSELVES REMOVED*
+#   $do_debug;         '1' if we should print debugging output
+#   $be_verbose;       '1' if we should be verbose
+#   $out_FH:           file handle to output to
+#   $overlap_FH:       file handle to output overlap info to (if --overlapout)
+#
+# Returns:     Two values:
+#              $nkept:    number of hits saved and output
+#              $nremoved: number of hits removed and not output
+#
+# Dies:        If we see a line of input that is an an unexpected
+#              format
+#
+#################################################################
+sub parse_sorted_tblout_file {
+  my $nargs_expected = 13;
+  my $sub_name = "parse_sorted_tblout_file";
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($sorted_tbl_file, $clan_HR, $mdllen_HR,
+      $do_cmscan, $do_nhmmer, $do_hmmsearch, $do_besthmm, $rank_by_score, $do_maxkeep, $do_debug, $be_verbose,
+      $out_FH, $overlap_FH) = @_;
+
+  my $prv_target = undef; # target name of previous line
+  my $prv_score  = undef; # bit score of previous line
+  my $prv_evalue = undef; # E-value of previous line
+  my $clan       = undef; # clan of current model
+  my $nkept      = 0;     # number of hits kept and output
+  my $nremoved   = 0;     # number of hits removed and not output
+  my $do_clans   = (defined $clan_HR) ? 1 : 0;
+
+  open(IN, $sorted_tbl_file) || die "ERROR unable to open sorted tabular file $sorted_tbl_file for reading";
+
+  my ($target, $tacc, $model, $macc, $domain, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) =
+      (undef, undef, undef, undef, undef, undef, undef, undef, undef, undef, undef, undef, undef);
+
+  my @line_A      = (); # array of output lines for kept hits for current sequence
+  my @seqfrom_A   = (); # array of seqfroms for kept hits for current sequence
+  my @seqto_A     = (); # array of seqtos for kept hits for current sequence
+  my @strand_A    = (); # array of strands for kept hits for current sequence
+  my @clan_A      = (); # array of clans for kept hits for current sequence
+  my @keepme_A    = (); # array of '1' and '0', '1' if we should keep this hit, '0' if it had a higher scoring overlap
+  my @noverlaps_A = (); # array of number of hits (lower scoring) that overlap with this sequence, **only valid for kept hits, -1 for removed hits**
+  my $nhits       = 0;  # number of hits for current sequence (size of all arrays)
+  # arrays only filled if $overlap_FH is defined (if --overlapout was used)
+  my @mdlfrom_A   = (); # array of mdlfroms for kept hits for current sequence
+  my @mdlto_A     = (); # array of mdltos for kept hits for current sequence
+  my @model_A     = (); # array of model names for kept hits for current sequence
+  my @desc_A      = (); # array of descriptions for kept hits for current sequence
+  my @score_A     = (); # array of scores for kept hits for current sequence
+  my @evalue_A    = (); # array of e-values for kept hits for current sequence
+  my $do_desc = (defined $overlap_FH) ? 1 : 0;
+
+  my %already_seen_H = (); # hash, key is sequence name, value is '1' if we have output info for this sequence
+
+  $prv_evalue = 0.;
+  while(my $line = <IN>) {
+    ######################################################
+    # Parse the data on this line, this differs depending
+    # on our annotation method
+    chomp $line;
+    $line =~ s/^\s+//; # remove leading whitespace
+
+    if($line =~ m/^\#/) {
+      die "ERROR, found line that begins with #, input should have these lines removed and be sorted by the first column:$line.";
+    }
+
+    if($do_hmmsearch) {
+      ($target, $model, $score, $evalue, $desc) = parse_hmmsearch_tblout_line($line, $do_besthmm, $do_desc);
+      # hmmsearch --tblout output lacks sequence ranges and strand information
+      # we want to allow only a single hit to the each target, so we set span as 1..1
+      # so that all hits to the same target will 'overlap'. Strand is set as "+"
+      # so all hits are considered on the same 'strand' for de-overlapping purposes.
+      $seqfrom = 1;
+      $seqto   = 1;
+      $strand  = "+"; # no strand for hmmsearch output, so we assert + for de-overlapping purposes
+      $mdlfrom = "-";
+      $mdlto   = "-";
+    }
+    elsif($do_nhmmer) {
+      ($target, $tacc, $model, $macc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) = parse_nhmmer_tblout_line($line, $do_desc);
+    }
+    elsif($do_cmscan) {
+      # call parse_cmsearch_tblout_line, just reverse $model and $target
+      ($model, $macc, $target, $tacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) = parse_cmsearch_tblout_line($line, $do_desc);
+    }
+    else { # default: cmsearch
+      ($target, $tacc, $model, $macc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc) = parse_cmsearch_tblout_line($line, $do_desc);
+      if((! $do_fcmsearch) && ($tacc =~ /^RF\d+/)) {
+        die "ERROR, target accession $tacc looks like an Rfam accession suggesting this is cmscan tblout output,\ndid you mean to use --cmscan? Use --fcmsearch to assert this is cmsearch output and avoid this error.\n";
+      }
+    }
+
+    $clan = undef;
+    if(defined $clan_HR) {
+      if(exists $clan_HR->{$model}) {
+        $clan = $clan_HR->{$model};
+      }
+    }
+
+    # make sure we didn't output information for this sequence already
+    if(exists $already_seen_H{$target}) {
+      die "ERROR found line with target $target previously output, did you sort by sequence name?";
+    }
+
+    ##############################################################
+    # Are we now finished with the previous sequence?
+    # Yes, if target sequence we just read is different from it
+    # If yes, output info for it, and re-initialize data structures
+    # for new sequence just read
+    if((defined $prv_target) && ($prv_target ne $target)) {
+      output_one_target($out_FH, $be_verbose, \@line_A, \@keepme_A, \@noverlaps_A);
+      $already_seen_H{$prv_target} = 1;
+      @line_A      = ();
+      @seqfrom_A   = ();
+      @seqto_A     = ();
+      @strand_A    = ();
+      @clan_A      = ();
+      @keepme_A    = ();
+      @noverlaps_A = ();
+      @mdlfrom_A   = ();
+      @mdlto_A     = ();
+      @model_A     = ();
+      @desc_A      = ();
+      @score_A     = ();
+      @evalue_A    = ();
+      $nhits       = 0;
+    }
+    else { # this is not a new sequence
+      if(defined $prv_target) {
+        # make sure that our current score or E-value is less than previous
+        if($rank_by_score && ($score > $prv_score)) {
+          die "ERROR found lines with same target [$target] incorrectly sorted by score, did you sort by sequence name and score?";
+        }
+        elsif((! $rank_by_score) && ($evalue < $prv_evalue)) {
+          die "ERROR found lines with same target [$target] incorrectly sorted by E-value, did you sort by sequence name and E-value?";
+        }
+      }
+    }
+    ##############################################################
+
+    # look through all other hits $i on the same strand and see if any of them overlap with this one
+    # if (! $do_maxkeep) we look at all hits
+    # if (  $do_maxkeep) we only look at hits that haven't been removed yet
+    my $keep_me = 1; # set to '0' below if we find a better scoring hit
+    my $overlap_idx = -1;
+    my $cur_noverlap = 0;
+    my $clan_criteria_passed = 1; # set to '1' if --clanin not used OR
+                                  # --clanin used and --invclan NOT used and two hits are to families in the same clan
+                                  # --clanin used and --invclan IS  used and two hits are NOT to families in the same clan
+                                  # else set to '0'
+    for(my $i = 0; $i < $nhits; $i++) {
+      if($strand_A[$i] eq $strand) {  # same strand
+        if($do_clans) {
+          if($do_invclan) {
+            $clan_criteria_passed = (! determine_if_clans_match($clan, $clan_A[$i]));
+          }
+          else {
+            $clan_criteria_passed = determine_if_clans_match($clan, $clan_A[$i]);
+          }
+        }
+        if(($clan_criteria_passed) &&                   # clans match (or don't if --invclan), or --clanin not used
+           ((! $do_maxkeep) || ($keepme_A[$i] == 1))) { # either --maxkeep not enabled, or this hit is a keepter
+          if($strand eq "+") {
+            $cur_noverlap = get_overlap($seqfrom, $seqto, $seqfrom_A[$i], $seqto_A[$i]);
+          }
+          elsif($strand eq "-") {
+            $cur_noverlap = get_overlap($seqto, $seqfrom, $seqto_A[$i], $seqfrom_A[$i]);
+          }
+          else {
+            die "ERROR strand not + or - but $strand for hit $i line:\n$line\n";
+          }
+          if($cur_noverlap >= $noverlap) {
+            $keep_me = 0;
+            $overlap_idx = $i;
+            $i = $nhits; # breaks for loop
+          }
+        }
+      }
+    }
+    # add hit to list of hits we have for this sequence
+    $line_A[$nhits]    = $line . "\n";
+    $seqfrom_A[$nhits] = $seqfrom;
+    $seqto_A[$nhits]   = $seqto;
+    $strand_A[$nhits]  = $strand;
+    $clan_A[$nhits]    = $clan;
+    if(defined $overlap_FH) { # only need these if we're outputting to an overlap file
+      $mdlfrom_A[$nhits] = $mdlfrom;
+      $mdlto_A[$nhits]   = $mdlto;
+      $model_A[$nhits]   = $model;
+      $desc_A[$nhits]    = $desc;
+      $score_A[$nhits]   = $score;
+      $evalue_A[$nhits]  = $evalue;
+    }
+    if($keep_me) {
+      $nkept++;
+      $keepme_A[$nhits] = 1;
+      $noverlaps_A[$nhits] = 0;
+    }
+    else {
+      $nremoved++;
+      $keepme_A[$nhits] = 0;
+      $noverlaps_A[$nhits] = -1;
+      $noverlaps_A[$overlap_idx]++;
+      if($do_debug) {
+        printf("target: $target model: $model: removing $seqfrom..$seqto, it overlapped with $seqfrom_A[$overlap_idx]..$seqto_A[$overlap_idx]\n");
+      }
+      if($be_verbose) {
+        printf("REMOVED                      %-*s  $line\n", length($cur_noverlap), "");
+        printf("BECAUSE-IT-OVERLAPPED-BY-" . $cur_noverlap . "-WITH $line_A[$overlap_idx]\n");
+      }
+      if(defined $overlap_FH) {
+        my $hitlen1  = abs($seqfrom_A[$overlap_idx]-$seqto_A[$overlap_idx])+1;
+        my $hitlen2  = abs($seqfrom-$seqto)+1;
+        my $mhitlen1 = (($mdlfrom_A[$overlap_idx] ne "-") && ($mdlto_A[$overlap_idx] ne "-")) ? abs($mdlfrom_A[$overlap_idx]-$mdlto_A[$overlap_idx])+1 : "-";
+        my $mhitlen2 = (($mdlfrom ne "-") && ($mdlto ne "-")) ? abs($mdlfrom-$mdlto)+1 : "-";
+        my $mdllen1  = ((defined $mdllen_HR) && (defined $mdllen_HR->{$model_A[$overlap_idx]})) ? $mdllen_HR->{$model_A[$overlap_idx]} : "-";
+        my $mdllen2  = ((defined $mdllen_HR) && (defined $mdllen_HR->{$model})) ? $mdllen_HR->{$model} : "-";
+
+        printf $overlap_FH ("%-s\t%s\t%s\t%s\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%.3f\t%.3f\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
+                            $target, $strand, $model_A[$overlap_idx], $model,
+                            $hitlen1, $hitlen2, $cur_noverlap,
+                            $score_A[$overlap_idx], $score,
+                            $evalue_A[$overlap_idx], $evalue,
+                            $seqfrom_A[$overlap_idx], $seqto_A[$overlap_idx],
+                            $seqfrom, $seqto,
+                            $cur_noverlap/$hitlen1, $cur_noverlap/$hitlen2,
+                            $mdllen1, $mdllen2,
+                            ($mdllen1 ne "-") ? (sprintf("%.3f", $cur_noverlap/$mdllen1)) : "-",
+                            ($mdllen2 ne "-") ? (sprintf("%.3f", $cur_noverlap/$mdllen2)) : "-",
+                            $mhitlen1, $mhitlen2,
+                            (($mhitlen1 ne "-") && ($mdllen1 ne "-")) ? (sprintf("%.3f", $mhitlen1/$mdllen1)) : "-",
+                            (($mhitlen2 ne "-") && ($mdllen2 ne "-")) ? (sprintf("%.3f", $mhitlen2/$mdllen2)) : "-",
+                            $desc_A[$overlap_idx], $desc);
+      }
+    }
+    $nhits++;
+    $prv_target = $target;
+    $prv_score  = $score;
+    $prv_evalue = $evalue;
+  }
+
+  # output data for final sequence
+  output_one_target($out_FH, $be_verbose, \@line_A, \@keepme_A, \@noverlaps_A);
+
+  # close file handle
+  close(IN);
+
+  return ($nkept, $nremoved);
+}
+
+#################################################################
+# Subroutine : output_one_target()
+# Incept:      EPN, Mon May  8 10:20:40 2017
+#
+# Purpose:     Output all hits for a target. Overlapping hits
+#              are not included, they've been skipped.
+#
+# Arguments:
+#   $out_FH:        file handle to output short output to (can be undef to not output short output)
+#   $be_verbose:    '1' to output number of overlaps for each kept hit to stdout
+#   $line_AR:       array of lines to output
+#   $keepme_AR:     array of '1', '0', $keepme_AR->[$i]==1 indicates we should output $line_AR->[$i]
+#   $noverlaps_AR:  array of '1', '0', $keepme_AR->[$i]==1 indicates we should output $line_AR->[$i]
+#
+# Returns:     Nothing.
+#
+# Dies:        Never.
+#
+#################################################################
+sub output_one_target {
+  my $nargs_expected = 5;
+  my $sub_name = "output_one_target";
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($out_FH, $be_verbose, $line_AR, $keepme_AR, $noverlaps_AR) = @_;
+
+  for(my $i = 0; $i < scalar(@{$line_AR}); $i++) {
+    if($keepme_AR->[$i]) {
+      print $out_FH $line_AR->[$i];
+      if($be_verbose) { printf("NUM-OVERLAPS:%d $line_AR->[$i]", $noverlaps_AR->[$i]) };
+    }
+  }
+
+  return;
+}
+
+#################################################################
+# Subroutine : determine_if_clans_match()
+# Incept:      EPN, Mon May  8 10:28:41 2017
+#
+# Purpose:     Given two clan values return 1 if they
+#              match else 0.
+#
+# Arguments:
+#   $clan1:    clan 1, can be undef
+#   $clan2:    clan 2, can be undef
+#
+# Returns:     '1' if the clans match or if $do_clans is FALSE
+#
+# Dies:        Never.
+#
+#################################################################
+sub determine_if_clans_match {
+  my $nargs_expected = 2;
+  my $sub_name = "determine_if_clans_match";
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($clan1, $clan2) = @_;
+
+  if((! defined $clan1) || (! defined $clan2)) {
+    # 1 or both of $clan1 and $clan2 are undefined, can't be a match
+    return 0;
+  }
+  elsif($clan1 eq $clan2) {
+    # equal clans
+    return 1;
+  }
+  else {
+    return 0;
+  }
+
+}
+
+#################################################################
+# Subroutine: get_overlap()
+# Incept:     EPN, Mon Mar 14 13:47:57 2016 [dnaorg_scripts:dnaorg.pm:getOverlap()]
+#
+# Purpose:    Calculate number of nucleotides of overlap between
+#             two regions.
+#
+# Args:
+#  $start1: start position of hit 1 (must be <= $end1)
+#  $end1:   end   position of hit 1 (must be >= $end1)
+#  $start2: start position of hit 2 (must be <= $end2)
+#  $end2:   end   position of hit 2 (must be >= $end2)
+#
+# Returns:  $noverlap:    Number of nucleotides of overlap between hit1 and hit2,
+#                         0 if none
+#
+# Dies:     if $end1 < $start1 or $end2 < $start2.
+sub get_overlap {
+  my $sub_name = "get_overlap";
+  my $nargs_exp = 4;
+  if(scalar(@_) != 4) { die "ERROR $sub_name entered with wrong number of input args"; }
+
+  my ($start1, $end1, $start2, $end2) = @_;
+
+  # printf("in $sub_name $start1..$end1 $start2..$end2\n");
+
+  if($start1 > $end1) { die "ERROR in $sub_name start1 > end1 ($start1 > $end1)"; }
+  if($start2 > $end2) { die "ERROR in $sub_name start2 > end2 ($start2 > $end2)"; }
+
+  # Given: $start1 <= $end1 and $start2 <= $end2.
+
+  # Swap if nec so that $start1 <= $start2.
+  if($start1 > $start2) {
+    my $tmp;
+    $tmp   = $start1; $start1 = $start2; $start2 = $tmp;
+    $tmp   =   $end1;   $end1 =   $end2;   $end2 = $tmp;
+  }
+
+  # 3 possible cases:
+  # Case 1. $start1 <=   $end1 <  $start2 <=   $end2  Overlap is 0
+  # Case 2. $start1 <= $start2 <=   $end1 <    $end2
+  # Case 3. $start1 <= $start2 <=   $end2 <=   $end1
+  if($end1 < $start2) { return (0); }                    # case 1
+  if($end1 <   $end2) { return ($end1 - $start2 + 1); }  # case 2
+  if($end2 <=  $end1) { return ($end2 - $start2 + 1); }  # case 3
+  die "ERROR in $sub_name, unforeseen case in $start1..$end1 and $start2..$end2";
+
+  return; # NOT REACHED
+}
+
+#################################################################
+# Subroutine:  run_command()
+# Incept:      EPN, Mon Dec 19 10:43:45 2016
+#
+# Purpose:     Runs a command using system() and exits in error
+#              if the command fails. If $be_verbose, outputs
+#              the command to stdout.
+#
+# Arguments:
+#   $cmd:         command to run, with a "system" command;
+#   $be_verbose:  '1' to output command to stdout before we run it, '0' not to
+#
+# Returns:    nothing
+#
+# Dies:       if $cmd fails
+#################################################################
+sub run_command {
+  my $sub_name = "run_command()";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($cmd, $be_verbose) = @_;
+
+  if($be_verbose) {
+    print ("Running cmd: $cmd\n");
+  }
+
+  system($cmd);
+
+  if($? != 0) {
+    die "ERROR in $sub_name, the following command failed:\n$cmd\n";
+  }
+
+  return;
+}
+
+#################################################################
+# Subroutine:  parse_claninfo()
+# Incept:      EPN, Wed May 10 15:01:07 2017
+#
+# Purpose:     Parse a claninfo file and fill %{$clan_HR}.
+#
+# Arguments:
+#   $claninfo_file: clan info file
+#   $clan_HR:       ref to hash of clan info, key: model name, value: clan name
+#
+# Returns:    nothing
+#
+# Dies:       if $cmd fails
+#################################################################
+sub parse_claninfo {
+  my $sub_name = "parse_claninfo()";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($claninfo_file, $clan_HR) = @_;
+
+  open(IN, $claninfo_file) || die "ERROR unable to open clan info file";
+
+  %{$clan_HR} = ();
+
+  while(my $line = <IN>) {
+    if($line !~ m/^#/) {
+      chomp $line;
+      my @el_A = split(/\s+/, $line);
+      # first element is clan name, all other elements are model names in that clan
+      #CL00111  SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia SSU_trypano_mito
+      for(my $i = 1; $i < scalar(@el_A); $i++) {
+        if(exists $clan_H{$el_A[$i]}) {
+          die "ERROR in $sub_name, parsing clan info file $claninfo_file, read model $el_A[$i] more than once";
+        }
+        $clan_HR->{$el_A[$i]} = $el_A[0];
+      }
+    }
+  }
+  return;
+}
+
+#################################################################
+# Subroutine:  parse_cmsearch_tblout_line()
+# Incept:      EPN, Fri Dec  8 09:33:23 2017
+#
+# Purpose:     Given an infernal cmsearch --tblout line,
+#              return $target, $query, $seqfrom, $seqto, $strand, $score, $evalue.
+#
+#     # Example line
+#     #target name         accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target
+#     #------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
+#     5S_rRNA-sample10     -         5S_rRNA              RF00001    cm        1      119        1      121      +    no    1 0.61   0.0  108.2   1.5e-27 !   -
+#
+# Arguments:
+#   $line:  line to parse
+#
+# Returns:    $target:  name of target      (5S_rRNA-sample10)
+#             $tacc:    target accession    (-)
+#             $query:   query name          (5S_rRNA)
+#             $qacc:    query accession     (RF00005)
+#             $mdlfrom: hmmfrom coord       (1)
+#             $mdlto:   hmm to coord        (119)
+#             $seqfrom: sequence from coord (1)
+#             $seqto:   sequence to coord   (121)
+#             $strand:  strand of hit       (+)
+#             $score:   bit score of hit    (108.2)
+#             $evalue:  E-value of hit      (1.5e-27)
+#             $desc:    description, undef unless $do_desc is 1
+#
+# Dies:       if line has fewer than 18 space delimited characters
+#################################################################
+sub parse_cmsearch_tblout_line {
+  my $sub_name = "parse_cmsearch_tblout_line";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($line, $do_desc) = @_;
+
+  my @el_A = split(/\s+/, $line);
+
+  if(scalar(@el_A) < 18) { die "ERROR found less than 18 columns in cmsearch tabular output at line: $line"; }
+  my ($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue) =
+      ($el_A[0], $el_A[1], $el_A[2], $el_A[3], $el_A[5], $el_A[6], $el_A[7], $el_A[8], $el_A[9],  $el_A[14], $el_A[15]);
+
+  my $desc = undef;
+  if($do_desc) {
+    $desc = $el_A[17];
+    my $nel = scalar(@el_A);
+    for(my $i = 18; $i < $nel; $i++) { $desc .= "_" . $el_A[$i]; } # replace spaces with "_";
+  }
+
+  return($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc);
+}
+
+#################################################################
+# Subroutine:  parse_nhmmer_tblout_line()
+# Incept:      EPN, Fri Dec  8 09:42:28 2017
+#
+# Purpose:     Given an nhmmer --tblout line,
+#              return $target, $query, $seqfrom, $seqto, $strand, $score, $evalue.
+#
+#     # Example line
+#     # target name        accession  query name           accession  hmmfrom hmm to alifrom  ali to envfrom  env to  sq len strand   E-value  score  bias  description of target
+#     #------------------- ---------- -------------------- ---------- ------- ------- ------- ------- ------- ------- ------- ------ --------- ------ ----- ---------------------
+#     5S_rRNA-sample10     -          5S_rRNA              RF00001          4     115       4     117       1     121     121    +     1.6e-17   53.3   4.8  -
+#
+# Arguments:
+#   $line:    line to parse
+#   $do_desc: '1' to parse and return description, else '0'
+#
+# Returns:    $target: name of target       (5S_rRNA-sample10)
+#             $tacc:    target accession    (-)
+#             $query:   query name          (5S_rRNA)
+#             $qacc:    query accession     (RF00005)
+#             $mdlfrom: hmmfrom coord       (4)
+#             $mdlto:   hmm to coord        (115)
+#             $seqfrom: ali from coord      (4)
+#             $seqto:   ali to coord        (117)
+#             $strand:  strand of hit       (+)
+#             $score:   bit score of hit    (53.3)
+#             $evalue:  E-value of hit      (1.6e-17)
+#             $desc:    description, undef unless $do_desc is 1
+#
+# Dies:       if line has fewer than 16 space delimited characters
+#################################################################
+sub parse_nhmmer_tblout_line {
+  my $sub_name = "parse_nhmmer_tblout_line";
+  my $nargs_expected = 2;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($line, $do_desc) = @_;
+
+  my @el_A = split(/\s+/, $line);
+
+  if(scalar(@el_A) < 16) { die "ERROR found less than 16 columns in nhmmer tabular output at line: $line"; }
+  my ($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $evalue, $score) =
+      ($el_A[0], $el_A[1], $el_A[2], $el_A[3], $el_A[4], $el_A[5], $el_A[6], $el_A[7], $el_A[11], $el_A[12], $el_A[13]);
+  my $desc = undef;
+  if($do_desc) {
+    $desc = $el_A[15];
+    my $nel = scalar(@el_A);
+    for(my $i = 16; $i < $nel; $i++) { $desc .= "_" . $el_A[$i]; } # replace spaces with "_";
+  }
+
+  return($target, $tacc, $query, $qacc, $mdlfrom, $mdlto, $seqfrom, $seqto, $strand, $score, $evalue, $desc);
+}
+
+#################################################################
+# Subroutine:  parse_hmmsearch_tblout_line()
+# Incept:      EPN, Fri Dec  8 09:47:19 2017
+#
+# Purpose:     Given an hmmsearch --tblout line,
+#              return $target, $query, $score, $evalue.
+#
+#     # Example line
+#     #                                                               --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
+#     # target name        accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg clu  ov env dom rep inc description of target
+#     #------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ -----   --- --- --- --- --- --- --- --- ---------------------
+#     5S_rRNA-sample10     -          5S_rRNA              RF00001      1.1e-19   59.8   0.0   1.2e-19   59.7   0.0   1.0   1   0   0   1   1   1   1 -
+#
+# Arguments:
+#   $line:             line to parse
+#   $do_best:          '1' to return score and E-value of best hit, not full sequence
+#                      '0' to return score and E-value of sequence, not best hit
+#   $do_desc:          '1' to parse and return description, else '0'
+#
+# Returns:    $target: name of target       (5S_rRNA-sample10)
+#             $query:  query name           (5S_rRNA)
+#             $score:  bit score of sequence  (53.3)
+#             $evalue: E-value of hit      (1.6e-17)
+#             $desc:   description, undef unless $do_desc is 1
+#
+# Dies:       if line has fewer than 19 space delimited characters
+#################################################################
+sub parse_hmmsearch_tblout_line {
+  my $sub_name = "parse_hmmsearch_tblout_line";
+  my $nargs_expected = 3;
+  if(scalar(@_) != $nargs_expected) { printf STDERR ("ERROR, $sub_name entered with %d != %d input arguments.\n", scalar(@_), $nargs_expected); exit(1); }
+
+  my ($line, $do_best, $do_desc) = @_;
+
+  my @el_A = split(/\s+/, $line);
+
+  if(scalar(@el_A) < 19) { die "ERROR found less than 16 columns in nhmmer tabular output at line: $line"; }
+  my ($target, $query, $full_evalue, $full_score, $best_evalue, $best_score) =
+      ($el_A[0], $el_A[2], $el_A[4], $el_A[5], $el_A[7], $el_A[8]);
+
+  my $desc = undef;
+  if($do_desc) {
+    $desc = $el_A[18];
+    my $nel = scalar(@el_A);
+    for(my $i = 19; $i < $nel; $i++) { $desc .= "_" . $el_A[$i]; } # replace spaces with "_";
+  }
+
+  if($do_best) {
+    return ($target, $query, $best_score, $best_evalue, $desc);
+  }
+  # else
+  return ($target, $query, $full_score, $full_evalue, $desc);
+}
+
+
+#end raw]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="in_tblout" type="data" optional="false" label="Tableout input file to de-overlap" help="" format="txt" multiple="false"/>
+    <param name="clanin" type="data" optional="true" label="Optional claninfo file" help="If claninfo provided, only remove overlaps within clans from file. Default is remove all overlaps" format="txt" multiple="false"/>
+    <param name="sortbit" type="select" label="Sort hits by bit score" help="default is to sort by E-value" display="radio">
+      <option value="notset">Do not set this flag</option>
+      <option value="set">Set this flag</option>
+    </param>
+    <param name="maxkeep" type="select" label="Set this flag to keep hits that only overlap with other hits that are not kept " help="Default is to remove all hits with higher scoring overlap" display="radio">
+      <option value="notset">Do not set this flag</option>
+      <option value="set">Set this flag</option>
+    </param>
+    <param name="input_kind" type="select" label="Package used to generate the input tablescan data" help="cmsearch is the default">
+      <option value="">cmsearch (default)</option>
+      <option value="--nhhmer">nhhmer v3.x</option>
+      <option value="--hmmsearch">hmmsearch v3.x</option>
+      <option value="--cmscan">cmscan v1.1</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="overlapout" format="txt" label="CMsearchtblout output on $in_tblout.element_identifier" hidden="false"/>
+  </outputs>
+  <tests>
+    <test>
+      <output name="overlapout" value="overlapout_sample" compare="diff" lines_diff="10"/>
+      <param name="in_tblout" value="in_tblout_sample"/>
+      <param name="clanin" value="clanin_sample"/>
+      <param name="sortbit" value="notset"/>
+      <param name="maxkeep" value="notset"/>
+      <param name="input_kind" value=""/>
+    </test>
+  </tests>
+  <help><![CDATA[
+
+**What it Does**
+
+
+
+Wrapper for https://github.com/nawrockie/cmsearch_tblout_deoverlap
+
+
+
+
+
+ ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+  </citations>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/test-data/clanin_sample	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,3 @@
+CL00111	SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia SSU_trypano_mito
+CL00112	LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya LSU_trypano_mito 5_8S_rRNA
+CL99999 5S_rRNA mtPerm-5S
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/test-data/in_tblout_sample	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,983 @@
+#target name         accession query name           accession mdl mdl from   mdl to seq from   seq to strand trunc pass   gc  bias  score   E-value inc description of target
+#------------------- --------- -------------------- --------- --- -------- -------- -------- -------- ------ ----- ---- ---- ----- ------ --------- --- ---------------------
+contig--95399        -         5S_rRNA              RF00001   hmm        3      116      465      575      +     -    6 0.55   0.0   53.3     5e-12 !   -
+contig--3320537      -         5S_rRNA              RF00001   hmm        4      115      219      329      +     -    6 0.55   0.0   50.4   4.2e-11 !   -
+contig--2298625      -         5S_rRNA              RF00001   hmm        6      113      132       24      -     -    6 0.57   0.0   47.0   4.6e-10 !   -
+contig--397992       -         5S_rRNA              RF00001   hmm        4      116     3051     3160      +     -    6 0.63   0.0   43.6   5.4e-09 !   -
+contig--3348019      -         5_8S_rRNA            RF00002   hmm        1      153      559      711      +     -    6 0.48   0.0  116.0     2e-31 !   -
+contig--3980131      -         5_8S_rRNA            RF00002   hmm        1      153      257      408      +     -    6 0.49   0.0  101.2   8.4e-27 !   -
+contig--2250940      -         5_8S_rRNA            RF00002   hmm        1      153      239      390      +     -    6 0.50   0.0   98.9   4.2e-26 !   -
+contig--364625       -         SSU_rRNA_bacteria    RF00177   hmm       18      957      954        2      -     -    6 0.52   5.2  654.3  1.7e-194 !   -
+contig--2249925      -         SSU_rRNA_bacteria    RF00177   hmm       19      914        2      898      +     -    6 0.50   5.7  638.4  1.1e-189 !   -
+contig--2255364      -         SSU_rRNA_bacteria    RF00177   hmm      325     1084      765        1      -     -    6 0.52   3.9  624.0  2.5e-185 !   -
+contig--2369838      -         SSU_rRNA_bacteria    RF00177   hmm       90      938       20      855      +     -    6 0.52   7.0  609.3  6.6e-181 !   -
+contig--2271497      -         SSU_rRNA_bacteria    RF00177   hmm        4      812      835        2      -     -    6 0.51   5.0  597.5  2.5e-177 !   -
+contig--3568828      -         SSU_rRNA_bacteria    RF00177   hmm      311      991      670        5      -     -    6 0.55   4.2  575.6    1e-170 !   -
+contig--1568447      -         SSU_rRNA_bacteria    RF00177   hmm      291      968        2      684      +     -    6 0.52   5.6  574.2  2.6e-170 !   -
+contig--2506583      -         SSU_rRNA_bacteria    RF00177   hmm      483     1531        4     1047      +     -    6 0.54   3.6  551.4  2.1e-163 !   -
+contig--2914153      -         SSU_rRNA_bacteria    RF00177   hmm      139      936      799        1      -     -    6 0.50   4.5  551.2  2.4e-163 !   -
+contig--3474644      -         SSU_rRNA_bacteria    RF00177   hmm        5      760       51      832      +     -    6 0.51   4.6  526.5  6.8e-156 !   -
+contig--2972876      -         SSU_rRNA_bacteria    RF00177   hmm      320      925      614        1      -     -    6 0.52   4.1  481.4  2.9e-142 !   -
+contig--365127       -         SSU_rRNA_bacteria    RF00177   hmm      343      925      567        1      -     -    6 0.56   4.3  478.1    3e-141 !   -
+contig--363722       -         SSU_rRNA_bacteria    RF00177   hmm      347      918      579        1      -     -    6 0.51   2.5  462.7  1.4e-136 !   -
+contig--498568       -         SSU_rRNA_bacteria    RF00177   hmm      895     1410      516        2      -     -    6 0.53   0.0  453.1    1e-133 !   -
+contig--401056       -         SSU_rRNA_bacteria    RF00177   hmm     1024     1532       17      525      +     -    6 0.53   0.1  435.4  2.3e-128 !   -
+contig--2491978      -         SSU_rRNA_bacteria    RF00177   hmm       11     1084     1024        1      -     -    6 0.54   4.9  434.2  5.3e-128 !   -
+contig--1720439      -         SSU_rRNA_bacteria    RF00177   hmm      298      906        2      611      +     -    6 0.48   1.4  433.7  7.5e-128 !   -
+contig--3076204      -         SSU_rRNA_bacteria    RF00177   hmm       91      697       13      601      +     -    6 0.52   2.2  427.5  5.7e-126 !   -
+contig--3787593      -         SSU_rRNA_bacteria    RF00177   hmm      357      932        2      584      +     -    6 0.51   2.2  420.1  9.5e-124 !   -
+contig--298893       -         SSU_rRNA_bacteria    RF00177   hmm        4      580       27      606      +     -    6 0.51   1.5  412.7  1.6e-121 !   -
+contig--2969992      -         SSU_rRNA_bacteria    RF00177   hmm      470      954        4      488      +     -    6 0.51   1.4  406.9  9.2e-120 !   -
+contig--828224       -         SSU_rRNA_bacteria    RF00177   hmm      202      735        7      519      +     -    6 0.58   6.6  405.3    3e-119 !   -
+contig--2252644      -         SSU_rRNA_bacteria    RF00177   hmm        7      805       42      784      +     -    6 0.48   1.6  404.9  3.7e-119 !   -
+contig--152048       -         SSU_rRNA_bacteria    RF00177   hmm        4      580      584        3      -     -    6 0.52   1.7  403.0  1.4e-118 !   -
+contig--1776240      -         SSU_rRNA_bacteria    RF00177   hmm      908     1370      463        1      -     -    6 0.53   0.1  396.4  1.4e-116 !   -
+contig--3286658      -         SSU_rRNA_bacteria    RF00177   hmm        4      579      583        3      -     -    6 0.50   0.1  391.7  3.8e-115 !   -
+contig--696001       -         SSU_rRNA_bacteria    RF00177   hmm        5      571       69      625      +     -    6 0.49   0.1  384.7    5e-113 !   -
+contig--2251500      -         SSU_rRNA_bacteria    RF00177   hmm      925     1398        1      473      +     -    6 0.52   0.0  382.1  2.9e-112 !   -
+contig--912998       -         SSU_rRNA_bacteria    RF00177   hmm      752     1411        3      666      +     -    6 0.55   0.5  377.0    1e-110 !   -
+contig--1029476      -         SSU_rRNA_bacteria    RF00177   hmm      832     1348      174      700      +     -    6 0.44   0.0  368.0  5.4e-108 !   -
+contig--2253054      -         SSU_rRNA_bacteria    RF00177   hmm      335      797        1      446      +     -    6 0.56   3.5  363.0  1.7e-106 !   -
+contig--862423       -         SSU_rRNA_bacteria    RF00177   hmm      929     1352        1      423      +     -    6 0.52   0.0  341.6  4.9e-100 !   -
+contig--258486       -         SSU_rRNA_bacteria    RF00177   hmm     1132     1514        4      386      +     -    6 0.57   0.1  315.0   5.5e-92 !   -
+contig--363016       -         SSU_rRNA_bacteria    RF00177   hmm     1132     1532     1141      741      -     -    6 0.53   0.1  314.7   6.6e-92 !   -
+contig--1346273      -         SSU_rRNA_bacteria    RF00177   hmm      741     1108      374        3      -     -    6 0.54   0.0  313.1     2e-91 !   -
+contig--3889059      -         SSU_rRNA_bacteria    RF00177   hmm      394      800        1      413      +     -    6 0.55   1.9  302.1   4.3e-88 !   -
+contig--1210200      -         SSU_rRNA_bacteria    RF00177   hmm      504      908      406        1      -     -    6 0.44   0.1  289.8   2.3e-84 !   -
+contig--2766474      -         SSU_rRNA_bacteria    RF00177   hmm     1164     1532      410       40      -     -    6 0.52   0.0  286.2   2.7e-83 !   -
+contig--1192886      -         SSU_rRNA_bacteria    RF00177   hmm     1035     1369      332        1      -     -    6 0.49   0.0  280.4   1.6e-81 !   -
+contig--2889438      -         SSU_rRNA_bacteria    RF00177   hmm     1045     1378      334        1      -     -    6 0.50   0.0  278.6   5.4e-81 !   -
+contig--1634977      -         SSU_rRNA_bacteria    RF00177   hmm     1041     1356        2      315      +     -    6 0.55   0.0  276.6   2.2e-80 !   -
+contig--2248804      -         SSU_rRNA_bacteria    RF00177   hmm     1042     1427      165      539      +     -    6 0.47   0.0  274.5   9.7e-80 !   -
+contig--151199       -         SSU_rRNA_bacteria    RF00177   hmm        9      569      538        3      -     -    6 0.41   0.0  270.9   1.1e-78 !   -
+contig--1085416      -         SSU_rRNA_bacteria    RF00177   hmm      124      547      392        1      -     -    6 0.49   0.1  263.5   2.1e-76 !   -
+contig--1001177      -         SSU_rRNA_bacteria    RF00177   hmm      640      954        4      319      +     -    6 0.52   0.8  257.9     1e-74 !   -
+contig--813107       -         SSU_rRNA_bacteria    RF00177   hmm      499      967       13      486      +     -    6 0.55   2.4  249.9   2.6e-72 !   -
+contig--3837490      -         SSU_rRNA_bacteria    RF00177   hmm       44      438      392        4      -     -    6 0.49   0.1  249.1   4.4e-72 !   -
+contig--3153031      -         SSU_rRNA_bacteria    RF00177   hmm        5      374       44      384      +     -    6 0.54   0.2  244.4   1.2e-70 !   -
+contig--1531838      -         SSU_rRNA_bacteria    RF00177   hmm      908     1226      313        1      -     -    6 0.50   0.0  235.1   7.5e-68 !   -
+contig--1238415      -         SSU_rRNA_bacteria    RF00177   hmm        5      363      216      571      +     -    6 0.55   0.8  229.4     4e-66 !   -
+contig--214407       -         SSU_rRNA_bacteria    RF00177   hmm       91      429       15      336      +     -    6 0.50   0.2  227.3   1.8e-65 !   -
+contig--3503719      -         SSU_rRNA_bacteria    RF00177   hmm     1066     1412      350        3      -     -    6 0.51   0.0  226.7   2.6e-65 !   -
+contig--24391        -         SSU_rRNA_bacteria    RF00177   hmm      510      819      311        2      -     -    6 0.49   1.1  224.6   1.1e-64 !   -
+contig--2618713      -         SSU_rRNA_bacteria    RF00177   hmm        4      347     1048     1400      +     -    6 0.53   0.2  223.9   1.8e-64 !   -
+contig--1209771      -         SSU_rRNA_bacteria    RF00177   hmm     1058     1336      278        1      -     -    6 0.50   0.0  220.9   1.5e-63 !   -
+contig--1149779      -         SSU_rRNA_bacteria    RF00177   hmm     1224     1526      303        2      -     -    6 0.51   0.0  219.3   4.4e-63 !   -
+contig--664472       -         SSU_rRNA_bacteria    RF00177   hmm       30      388        2      331      +     -    6 0.56   0.4  213.3   2.9e-61 !   -
+contig--1368084      -         SSU_rRNA_bacteria    RF00177   hmm       19      363      361        2      -     -    6 0.51   0.1  212.0   7.1e-61 !   -
+contig--3276943      -         SSU_rRNA_bacteria    RF00177   hmm      645     1527     2352     1448      -     -    6 0.45   0.0  211.9   7.6e-61 !   -
+contig--2693087      -         SSU_rRNA_bacteria    RF00177   hmm        4      341      132      439      +     -    6 0.53   0.0  209.9   3.1e-60 !   -
+contig--2706433      -         SSU_rRNA_bacteria    RF00177   hmm        4      345       22      364      +     -    6 0.55   0.4  209.8   3.4e-60 !   -
+contig--2251690      -         SSU_rRNA_bacteria    RF00177   hmm       18      350      334        1      -     -    6 0.58   0.6  206.9   2.6e-59 !   -
+contig--145250       -         SSU_rRNA_bacteria    RF00177   hmm        3      517        6      546      +     -    6 0.38   0.0  200.5   2.1e-57 !   -
+contig--3492742      -         SSU_rRNA_bacteria    RF00177   hmm        5      332      300        2      -     -    6 0.54   0.1  197.8   1.5e-56 !   -
+contig--1584065      -         SSU_rRNA_bacteria    RF00177   hmm       18      351      332        1      -     -    6 0.54   0.1  196.9   2.6e-56 !   -
+contig--1003442      -         SSU_rRNA_bacteria    RF00177   hmm       27      355      328        1      -     -    6 0.55   0.7  194.1   1.8e-55 !   -
+contig--362436       -         SSU_rRNA_bacteria    RF00177   hmm       18      333      311        2      -     -    6 0.56   0.5  185.7   6.6e-53 !   -
+contig--1214669      -         SSU_rRNA_bacteria    RF00177   hmm        5      321      299        1      -     -    6 0.53   0.1  184.4   1.6e-52 !   -
+contig--540576       -         SSU_rRNA_bacteria    RF00177   hmm       48      383      341        2      -     -    6 0.46   0.0  179.2   6.1e-51 !   -
+contig--866163       -         SSU_rRNA_bacteria    RF00177   hmm       21      324      310        1      -     -    6 0.45   0.0  170.6   2.4e-48 !   -
+contig--3171405      -         SSU_rRNA_bacteria    RF00177   hmm        4      318       33      332      +     -    6 0.43   0.0  163.0   4.8e-46 !   -
+contig--2755789      -         SSU_rRNA_bacteria    RF00177   hmm       18      324        1      309      +     -    6 0.51   0.0  152.4   7.5e-43 !   -
+contig--984009       -         SSU_rRNA_bacteria    RF00177   hmm        3      285      284        1      -     -    6 0.45   0.0  152.1   9.3e-43 !   -
+contig--3093712      -         SSU_rRNA_bacteria    RF00177   hmm      703      909        2      210      +     -    6 0.56   0.0  151.1   1.8e-42 !   -
+contig--159495       -         SSU_rRNA_bacteria    RF00177   hmm        5      274    11920    12194      +     -    6 0.52   0.1  148.0   1.6e-41 !   -
+contig--193617       -         SSU_rRNA_bacteria    RF00177   hmm      956     1291      306        1      -     -    6 0.55   0.0  136.8   3.9e-38 !   -
+contig--3575278      -         SSU_rRNA_bacteria    RF00177   hmm     1334     1532        3      191      +     -    6 0.54   0.0  132.9   5.6e-37 !   -
+contig--3128112      -         SSU_rRNA_bacteria    RF00177   hmm      539      943      410        5      -     -    6 0.46   0.0  130.8   2.5e-36 !   -
+contig--1211922      -         SSU_rRNA_bacteria    RF00177   hmm     1212     1431      300       81      -     -    6 0.40   0.0  125.2   1.2e-34 !   -
+contig--2254313      -         SSU_rRNA_bacteria    RF00177   hmm      642      974      346        3      -     -    6 0.52   0.1  123.2   4.9e-34 !   -
+contig--1604373      -         SSU_rRNA_bacteria    RF00177   hmm     1022     1396       26      423      +     -    6 0.47   0.0  117.1   3.4e-32 !   -
+contig--594041       -         SSU_rRNA_bacteria    RF00177   hmm       43      372        7      318      +     -    6 0.54   0.1  103.0     6e-28 !   -
+contig--186013       -         SSU_rRNA_bacteria    RF00177   hmm      644      917      290        5      -     -    6 0.43   0.0   96.7   5.1e-26 !   -
+contig--978828       -         SSU_rRNA_bacteria    RF00177   hmm      897     1229      341        2      -     -    6 0.45   0.0   96.6   5.4e-26 !   -
+contig--1209771      -         SSU_rRNA_bacteria    RF00177   hmm      934     1107      598      420      -     -    6 0.45   0.0   95.2   1.4e-25 !   -
+contig--293050       -         SSU_rRNA_bacteria    RF00177   hmm        4      177      171      341      +     -    6 0.55   0.0   94.0   3.2e-25 !   -
+contig--2248828      -         SSU_rRNA_bacteria    RF00177   hmm      645      919      292       10      -     -    6 0.44   0.1   92.5   9.1e-25 !   -
+contig--3348019      -         SSU_rRNA_bacteria    RF00177   hmm     1186     1529        3      378      +     -    6 0.47   0.0   91.6   1.7e-24 !   -
+contig--2252003      -         SSU_rRNA_bacteria    RF00177   hmm      642      919      304      593      +     -    6 0.42   0.0   90.4   3.9e-24 !   -
+contig--232952       -         SSU_rRNA_bacteria    RF00177   hmm      598      916      223      568      +     -    6 0.49   0.1   89.6   6.8e-24 !   -
+contig--2249727      -         SSU_rRNA_bacteria    RF00177   hmm     1167     1499        5      352      +     -    6 0.48   0.0   85.1   1.6e-22 !   -
+contig--314729       -         SSU_rRNA_bacteria    RF00177   hmm      924     1235      324        2      -     -    6 0.56   0.0   83.1   6.2e-22 !   -
+contig--3767142      -         SSU_rRNA_bacteria    RF00177   hmm      534      885        7      351      +     -    6 0.33   0.0   75.5   1.3e-19 !   -
+contig--2552028      -         SSU_rRNA_bacteria    RF00177   hmm      636      910      304      590      +     -    6 0.44   0.1   74.6   2.4e-19 !   -
+contig--2255117      -         SSU_rRNA_bacteria    RF00177   hmm      270      524      249        1      -     -    6 0.36   0.0   67.2   3.9e-17 !   -
+contig--2250377      -         SSU_rRNA_bacteria    RF00177   hmm      268      529       60      315      +     -    6 0.39   0.0   67.1   4.5e-17 !   -
+contig--2565011      -         SSU_rRNA_bacteria    RF00177   hmm       46      528      571       34      -     -    6 0.47   0.0   66.3   7.4e-17 !   -
+contig--3013908      -         SSU_rRNA_bacteria    RF00177   hmm     1045     1353      326        2      -     -    6 0.44   0.0   63.4   5.6e-16 !   -
+contig--486161       -         SSU_rRNA_bacteria    RF00177   hmm      930     1120       10      197      +     -    6 0.32   0.0   62.8   8.9e-16 !   -
+contig--151527       -         SSU_rRNA_bacteria    RF00177   hmm       46      577      928      346      -     -    6 0.42   0.0   60.6     4e-15 !   -
+contig--185316       -         SSU_rRNA_bacteria    RF00177   hmm     1073     1367        2      311      +     -    6 0.50   0.0   60.5   4.4e-15 !   -
+contig--363170       -         SSU_rRNA_bacteria    RF00177   hmm      229      583      687      354      -     -    6 0.49   0.0   58.4   1.9e-14 !   -
+contig--2514811      -         SSU_rRNA_bacteria    RF00177   hmm      644      892      490      746      +     -    6 0.46   0.0   56.9   5.1e-14 !   -
+contig--2726048      -         SSU_rRNA_bacteria    RF00177   hmm      228      667      235      652      +     -    6 0.50   0.0   54.9   2.1e-13 !   -
+contig--2506583      -         SSU_rRNA_archaea     RF01959   hmm      432     1476        4     1046      +     -    6 0.54   4.9  791.7  3.4e-236 !   -
+contig--2491978      -         SSU_rRNA_archaea     RF01959   hmm        2     1033     1028        1      -     -    6 0.54   5.5  777.7  6.1e-232 !   -
+contig--912998       -         SSU_rRNA_archaea     RF01959   hmm      701     1366        1      666      +     -    6 0.55   1.3  526.9  3.5e-156 !   -
+contig--813107       -         SSU_rRNA_archaea     RF01959   hmm      437      924        1      487      +     -    6 0.55   3.2  375.6  1.9e-110 !   -
+contig--364625       -         SSU_rRNA_archaea     RF01959   hmm       35      912      931        3      -     -    6 0.52   3.9  347.9  4.4e-102 !   -
+contig--2369838      -         SSU_rRNA_archaea     RF01959   hmm       70      894       17      855      +     -    6 0.52   5.4  346.7  9.9e-102 !   -
+contig--3568828      -         SSU_rRNA_archaea     RF01959   hmm      299      936      666       16      -     -    6 0.55   4.7  338.4   3.2e-99 !   -
+contig--2249925      -         SSU_rRNA_archaea     RF01959   hmm       36      868       23      897      +     -    6 0.50   3.9  334.0   7.1e-98 !   -
+contig--2255364      -         SSU_rRNA_archaea     RF01959   hmm      315     1033      759        1      -     -    6 0.52   3.2  324.5     5e-95 !   -
+contig--2914153      -         SSU_rRNA_archaea     RF01959   hmm      122      891      799        2      -     -    6 0.50   2.3  314.2   6.5e-92 !   -
+contig--1568447      -         SSU_rRNA_archaea     RF01959   hmm      276      921        3      681      +     -    6 0.52   4.7  297.1   9.6e-87 !   -
+contig--2271497      -         SSU_rRNA_archaea     RF01959   hmm        7      762      827        3      -     -    6 0.51   3.2  296.8   1.2e-86 !   -
+contig--401056       -         SSU_rRNA_archaea     RF01959   hmm      966     1476        7      523      +     -    6 0.54   0.1  289.2   2.3e-84 !   -
+contig--498568       -         SSU_rRNA_archaea     RF01959   hmm      851     1365      515        2      -     -    6 0.54   0.0  278.9   3.2e-81 !   -
+contig--3474644      -         SSU_rRNA_archaea     RF01959   hmm        8      711       59      832      +     -    6 0.51   1.9  267.5   8.7e-78 !   -
+contig--365127       -         SSU_rRNA_archaea     RF01959   hmm      328      875      566        6      -     -    6 0.55   4.8  260.0   1.6e-75 !   -
+contig--2969992      -         SSU_rRNA_archaea     RF01959   hmm      427      910       12      488      +     -    6 0.51   0.9  250.8   9.4e-73 !   -
+contig--3276943      -         SSU_rRNA_archaea     RF01959   hmm      590     1472     2354     1449      -     -    6 0.45   0.0  250.1   1.6e-72 !   -
+contig--1029476      -         SSU_rRNA_archaea     RF01959   hmm      790     1300      177      697      +     -    6 0.44   0.0  249.5   2.3e-72 !   -
+contig--2972876      -         SSU_rRNA_archaea     RF01959   hmm      304      873      614        8      -     -    6 0.52   3.2  247.8     8e-72 !   -
+contig--363722       -         SSU_rRNA_archaea     RF01959   hmm      332      873      578        1      -     -    6 0.51   1.3  245.2   4.7e-71 !   -
+contig--2251500      -         SSU_rRNA_archaea     RF01959   hmm      882     1353        2      473      +     -    6 0.52   0.0  240.0   1.7e-69 !   -
+contig--3787593      -         SSU_rRNA_archaea     RF01959   hmm      342      887        3      583      +     -    6 0.51   1.4  239.0   3.5e-69 !   -
+contig--1776240      -         SSU_rRNA_archaea     RF01959   hmm      863     1325      463        1      -     -    6 0.53   0.2  235.5     4e-68 !   -
+contig--1720439      -         SSU_rRNA_archaea     RF01959   hmm      281      861        1      611      +     -    6 0.48   0.2  233.2     2e-67 !   -
+contig--3076204      -         SSU_rRNA_archaea     RF01959   hmm       75      645       14      598      +     -    6 0.52   1.1  220.2   1.7e-63 !   -
+contig--1634977      -         SSU_rRNA_archaea     RF01959   hmm      989     1310        1      314      +     -    6 0.55   0.0  209.4   3.1e-60 !   -
+contig--594041       -         SSU_rRNA_archaea     RF01959   hmm       34      358        2      320      +     -    6 0.54   0.1  209.1   3.9e-60 !   -
+contig--1210200      -         SSU_rRNA_archaea     RF01959   hmm      455      863      405        1      -     -    6 0.44   0.0  208.3   6.6e-60 !   -
+contig--363016       -         SSU_rRNA_archaea     RF01959   hmm     1087     1476     1141      743      -     -    6 0.54   0.1  204.6   8.6e-59 !   -
+contig--862423       -         SSU_rRNA_archaea     RF01959   hmm      887     1306        3      422      +     -    6 0.52   0.0  203.9   1.4e-58 !   -
+contig--1346273      -         SSU_rRNA_archaea     RF01959   hmm      693     1058      373        2      -     -    6 0.54   0.0  198.1   7.9e-57 !   -
+contig--828224       -         SSU_rRNA_archaea     RF01959   hmm      187      685        6      518      +     -    6 0.58   7.3  197.8   9.8e-57 !   -
+contig--2889438      -         SSU_rRNA_archaea     RF01959   hmm      994     1330      334        4      -     -    6 0.50   0.0  195.6   4.7e-56 !   -
+contig--258486       -         SSU_rRNA_archaea     RF01959   hmm     1087     1459        4      385      +     -    6 0.57   0.4  193.8   1.6e-55 !   -
+contig--2252644      -         SSU_rRNA_archaea     RF01959   hmm        6      756       46      784      +     -    6 0.48   0.1  192.0   5.7e-55 !   -
+contig--2253054      -         SSU_rRNA_archaea     RF01959   hmm      322      747        4      445      +     -    6 0.56   3.3  191.6   7.5e-55 !   -
+contig--2766474      -         SSU_rRNA_archaea     RF01959   hmm     1119     1476      410       42      -     -    6 0.52   0.0  186.7   2.3e-53 !   -
+contig--3286658      -         SSU_rRNA_archaea     RF01959   hmm        7      528      575        4      -     -    6 0.50   0.0  186.0   3.7e-53 !   -
+contig--2248804      -         SSU_rRNA_archaea     RF01959   hmm      991     1368      165      525      +     -    6 0.47   0.0  182.5     4e-52 !   -
+contig--1192886      -         SSU_rRNA_archaea     RF01959   hmm      985     1324      331        1      -     -    6 0.49   0.0  178.1   8.6e-51 !   -
+contig--1001177      -         SSU_rRNA_archaea     RF01959   hmm      591      909        4      318      +     -    6 0.52   0.8  177.2   1.7e-50 !   -
+contig--298893       -         SSU_rRNA_archaea     RF01959   hmm        8      530       36      606      +     -    6 0.51   0.8  170.7   1.6e-48 !   -
+contig--152048       -         SSU_rRNA_archaea     RF01959   hmm        8      530      575        3      -     -    6 0.52   0.8  163.1     3e-46 !   -
+contig--3889059      -         SSU_rRNA_archaea     RF01959   hmm      427      748       91      410      +     -    6 0.55   1.2  155.3   7.1e-44 !   -
+contig--3503719      -         SSU_rRNA_archaea     RF01959   hmm     1015     1365      350        5      -     -    6 0.51   0.0  154.8   9.7e-44 !   -
+contig--24391        -         SSU_rRNA_archaea     RF01959   hmm      460      769      311        3      -     -    6 0.49   0.2  154.2   1.5e-43 !   -
+contig--696001       -         SSU_rRNA_archaea     RF01959   hmm       37      521      105      625      +     -    6 0.50   0.1  153.8   1.9e-43 !   -
+contig--2254313      -         SSU_rRNA_archaea     RF01959   hmm      593      930      346        3      -     -    6 0.52   0.1  150.9   1.5e-42 !   -
+contig--1604373      -         SSU_rRNA_archaea     RF01959   hmm      953     1351        7      423      +     -    6 0.47   0.0  150.7   1.7e-42 !   -
+contig--1209771      -         SSU_rRNA_archaea     RF01959   hmm     1003     1290      282        2      -     -    6 0.51   0.0  137.8   1.3e-38 !   -
+contig--1149779      -         SSU_rRNA_archaea     RF01959   hmm     1179     1473      303        1      -     -    6 0.51   0.0  133.6   2.4e-37 !   -
+contig--1531838      -         SSU_rRNA_archaea     RF01959   hmm      863     1180      313        2      -     -    6 0.50   0.0  130.8   1.7e-36 !   -
+contig--978828       -         SSU_rRNA_archaea     RF01959   hmm      852     1184      341        2      -     -    6 0.45   0.0  128.7   7.6e-36 !   -
+contig--3837490      -         SSU_rRNA_archaea     RF01959   hmm       43      392      389       34      -     -    6 0.49   0.0  124.5   1.4e-34 !   -
+contig--3093712      -         SSU_rRNA_archaea     RF01959   hmm      655      864        3      210      +     -    6 0.57   0.1  123.3   3.1e-34 !   -
+contig--314729       -         SSU_rRNA_archaea     RF01959   hmm      869     1190      335        2      -     -    6 0.56   0.1  120.0   3.2e-33 !   -
+contig--2618713      -         SSU_rRNA_archaea     RF01959   hmm        7      329     1056     1398      +     -    6 0.53   0.1  117.5   1.9e-32 !   -
+contig--3348019      -         SSU_rRNA_archaea     RF01959   hmm     1141     1473        3      376      +     -    6 0.47   0.0  115.9   5.4e-32 !   -
+contig--214407       -         SSU_rRNA_archaea     RF01959   hmm       77      391       18      314      +     -    6 0.50   0.1  112.7     5e-31 !   -
+contig--3153031      -         SSU_rRNA_archaea     RF01959   hmm        7      357       51      383      +     -    6 0.54   0.2  110.7   2.1e-30 !   -
+contig--2249727      -         SSU_rRNA_archaea     RF01959   hmm     1122     1445        5      352      +     -    6 0.48   0.0  110.6   2.3e-30 !   -
+contig--2693087      -         SSU_rRNA_archaea     RF01959   hmm        7      318      140      432      +     -    6 0.53   0.0  105.0   1.1e-28 !   -
+contig--664472       -         SSU_rRNA_archaea     RF01959   hmm       38      372       14      331      +     -    6 0.56   0.7  104.6   1.4e-28 !   -
+contig--151199       -         SSU_rRNA_archaea     RF01959   hmm        7      519      535        3      -     -    6 0.41   0.0  104.0   2.1e-28 !   -
+contig--540576       -         SSU_rRNA_archaea     RF01959   hmm       46      365      339        4      -     -    6 0.47   0.0  102.7   5.4e-28 !   -
+contig--3128112      -         SSU_rRNA_archaea     RF01959   hmm      495      898      404        6      -     -    6 0.47   0.0  102.3   6.9e-28 !   -
+contig--1085416      -         SSU_rRNA_archaea     RF01959   hmm      106      492      393        6      -     -    6 0.49   0.0  101.8     1e-27 !   -
+contig--1368084      -         SSU_rRNA_archaea     RF01959   hmm       35      345      341        4      -     -    6 0.51   0.1   99.5   4.8e-27 !   -
+contig--2248828      -         SSU_rRNA_archaea     RF01959   hmm      594      882      294        2      -     -    6 0.45   0.0   98.5   9.9e-27 !   -
+contig--2251690      -         SSU_rRNA_archaea     RF01959   hmm       31      333      315        2      -     -    6 0.58   0.9   98.0   1.5e-26 !   -
+contig--984009       -         SSU_rRNA_archaea     RF01959   hmm        7      269      275        1      -     -    6 0.46   0.0   97.6   1.9e-26 !   -
+contig--1238415      -         SSU_rRNA_archaea     RF01959   hmm        7      345      223      569      +     -    6 0.56   0.7   95.2   9.8e-26 !   -
+contig--3492742      -         SSU_rRNA_archaea     RF01959   hmm        7      315      293        3      -     -    6 0.54   0.1   94.3   1.8e-25 !   -
+contig--2252003      -         SSU_rRNA_archaea     RF01959   hmm      607      889      317      608      +     -    6 0.43   0.0   93.9   2.5e-25 !   -
+contig--2755789      -         SSU_rRNA_archaea     RF01959   hmm       26      308       15      309      +     -    6 0.50   0.0   93.2   3.9e-25 !   -
+contig--232952       -         SSU_rRNA_archaea     RF01959   hmm      596      871      284      568      +     -    6 0.50   0.1   93.0   4.5e-25 !   -
+contig--1584065      -         SSU_rRNA_archaea     RF01959   hmm       31      334      313        2      -     -    6 0.53   0.1   91.9   9.6e-25 !   -
+contig--362436       -         SSU_rRNA_archaea     RF01959   hmm       35      315      290        4      -     -    6 0.56   0.6   90.5   2.6e-24 !   -
+contig--186013       -         SSU_rRNA_archaea     RF01959   hmm      605      875      280        2      -     -    6 0.44   0.0   90.2   3.2e-24 !   -
+contig--159495       -         SSU_rRNA_archaea     RF01959   hmm        7      256    11927    12192      +     -    6 0.52   0.0   89.9   3.9e-24 !   -
+contig--151527       -         SSU_rRNA_archaea     RF01959   hmm       42      531      928      342      -     -    6 0.42   0.0   89.2   6.4e-24 !   -
+contig--3575278      -         SSU_rRNA_archaea     RF01959   hmm     1290     1476        4      189      +     -    6 0.55   0.0   88.8   8.6e-24 !   -
+contig--363170       -         SSU_rRNA_archaea     RF01959   hmm      217      532      683      355      -     -    6 0.49   0.0   87.9   1.6e-23 !   -
+contig--193617       -         SSU_rRNA_archaea     RF01959   hmm      913     1245      305        2      -     -    6 0.55   0.0   87.9   1.6e-23 !   -
+contig--2706433      -         SSU_rRNA_archaea     RF01959   hmm        8      329       31      364      +     -    6 0.55   0.4   87.7   1.8e-23 !   -
+contig--1003442      -         SSU_rRNA_archaea     RF01959   hmm       37      338      314        2      -     -    6 0.56   0.6   83.8   2.9e-22 !   -
+contig--2726048      -         SSU_rRNA_archaea     RF01959   hmm      217      594      240      628      +     -    6 0.51   0.0   80.9   2.1e-21 !   -
+contig--1214669      -         SSU_rRNA_archaea     RF01959   hmm        7      301      292        5      -     -    6 0.54   0.1   80.4   2.9e-21 !   -
+contig--2565011      -         SSU_rRNA_archaea     RF01959   hmm       42      490      571       22      -     -    6 0.47   0.0   79.4   5.8e-21 !   -
+contig--3013908      -         SSU_rRNA_archaea     RF01959   hmm      994     1308      326        2      -     -    6 0.44   0.0   79.3   6.5e-21 !   -
+contig--866163       -         SSU_rRNA_archaea     RF01959   hmm       30      308      295        1      -     -    6 0.44   0.0   79.1   7.5e-21 !   -
+contig--1211922      -         SSU_rRNA_archaea     RF01959   hmm     1167     1372      300       95      -     -    6 0.42   0.0   78.2   1.3e-20 !   -
+contig--185316       -         SSU_rRNA_archaea     RF01959   hmm     1023     1322        3      311      +     -    6 0.50   0.0   76.1   5.9e-20 !   -
+contig--2552028      -         SSU_rRNA_archaea     RF01959   hmm      587      865      304      590      +     -    6 0.44   0.0   70.4     3e-18 !   -
+contig--2514811      -         SSU_rRNA_archaea     RF01959   hmm      284      533       12      270      +     -    6 0.49   0.0   65.3     1e-16 !   -
+contig--2514811      -         SSU_rRNA_archaea     RF01959   hmm      593      847      488      746      +     -    6 0.45   0.0   57.8     2e-14 !   -
+contig--3171405      -         SSU_rRNA_archaea     RF01959   hmm        7      289       41      319      +     -    6 0.42   0.0   55.8     8e-14 !   -
+contig--3420575      -         SSU_rRNA_archaea     RF01959   hmm       73      460      472        1      -     -    6 0.45   0.0   52.6   7.2e-13 !   -
+contig--186013       -         SSU_rRNA_archaea     RF01959   hmm      323      532      741      518      -     -    6 0.44   0.0   51.6   1.5e-12 !   -
+contig--151527       -         SSU_rRNA_eukarya     RF01960   hmm       20     1010      950        2      -     -    6 0.41  10.8  596.2  4.3e-177 !   -
+contig--3276943      -         SSU_rRNA_eukarya     RF01960   hmm      812     1850     2407     1448      -     -    6 0.45   2.4  551.7  1.1e-163 !   -
+contig--363170       -         SSU_rRNA_eukarya     RF01960   hmm      102     1017      866        1      -     -    6 0.45   4.4  517.9  1.8e-153 !   -
+contig--2514811      -         SSU_rRNA_eukarya     RF01960   hmm      369     1146        2      746      +     -    6 0.46   2.2  506.7  4.3e-150 !   -
+contig--2726048      -         SSU_rRNA_eukarya     RF01960   hmm       50      951        1      869      +     -    6 0.47   0.3  501.9  1.3e-148 !   -
+contig--186013       -         SSU_rRNA_eukarya     RF01960   hmm      414     1175      745        1      -     -    6 0.44   4.8  487.0  3.8e-144 !   -
+contig--2565011      -         SSU_rRNA_eukarya     RF01960   hmm       24      622      589        1      -     -    6 0.46   0.1  421.6  2.2e-124 !   -
+contig--2252003      -         SSU_rRNA_eukarya     RF01960   hmm      567     1189        1      609      +     -    6 0.43   3.4  404.2  3.8e-119 !   -
+contig--2248828      -         SSU_rRNA_eukarya     RF01960   hmm      581     1182      581        1      -     -    6 0.44   3.5  385.6  1.6e-113 !   -
+contig--2506583      -         SSU_rRNA_eukarya     RF01960   hmm      886     1848      167     1041      +     -    6 0.55   0.0  382.5  1.4e-112 !   -
+contig--3420575      -         SSU_rRNA_eukarya     RF01960   hmm       50      571      503        1      -     -    6 0.44   0.5  336.8   8.5e-99 !   -
+contig--232952       -         SSU_rRNA_eukarya     RF01960   hmm      589     1172        1      570      +     -    6 0.51   0.0  325.9   1.7e-95 !   -
+contig--978828       -         SSU_rRNA_eukarya     RF01960   hmm     1151     1521      341        2      -     -    6 0.45   0.0  301.7   3.4e-88 !   -
+contig--1604373      -         SSU_rRNA_eukarya     RF01960   hmm     1247     1695        1      423      +     -    6 0.47   0.1  296.1   1.7e-86 !   -
+contig--2552028      -         SSU_rRNA_eukarya     RF01960   hmm      552     1164        1      590      +     -    6 0.45   1.6  292.0   2.9e-85 !   -
+contig--912998       -         SSU_rRNA_eukarya     RF01960   hmm      992     1701        2      657      +     -    6 0.55   0.0  288.0   4.6e-84 !   -
+contig--3348019      -         SSU_rRNA_eukarya     RF01960   hmm     1474     1850        1      376      +     -    6 0.47   0.0  279.3     2e-81 !   -
+contig--2249727      -         SSU_rRNA_eukarya     RF01960   hmm     1456     1823        4      353      +     -    6 0.48   0.0  250.6   9.5e-73 !   -
+contig--2253688      -         SSU_rRNA_eukarya     RF01960   hmm        3      444      443        1      -     -    6 0.40   0.9  249.9   1.5e-72 !   -
+contig--30742        -         SSU_rRNA_eukarya     RF01960   hmm       37      429        2      393      +     -    6 0.41   0.4  233.1   1.8e-67 !   -
+contig--256048       -         SSU_rRNA_eukarya     RF01960   hmm      420      829        1      469      +     -    6 0.49   0.0  231.1   7.1e-67 !   -
+contig--1379481      -         SSU_rRNA_eukarya     RF01960   hmm       30      443        1      406      +     -    6 0.35   2.5  214.3   8.4e-62 !   -
+contig--1171145      -         SSU_rRNA_eukarya     RF01960   hmm       23      410        2      365      +     -    6 0.41   0.8  211.7   5.2e-61 !   -
+contig--3013908      -         SSU_rRNA_eukarya     RF01960   hmm     1295     1653      326        1      -     -    6 0.44   0.0  202.8   2.5e-58 !   -
+contig--498568       -         SSU_rRNA_eukarya     RF01960   hmm     1151     1703      514        8      -     -    6 0.53   0.0  201.4   6.5e-58 !   -
+contig--2491978      -         SSU_rRNA_eukarya     RF01960   hmm      892     1333      432        2      -     -    6 0.56   0.1  199.1   3.3e-57 !   -
+contig--2254313      -         SSU_rRNA_eukarya     RF01960   hmm      879     1229      350        3      -     -    6 0.51   0.0  195.6   3.7e-56 !   -
+contig--2251634      -         SSU_rRNA_eukarya     RF01960   hmm       22      400      377        1      -     -    6 0.43   0.3  194.8   6.4e-56 !   -
+contig--3096224      -         SSU_rRNA_eukarya     RF01960   hmm      748     1033       21      305      +     -    6 0.45   0.5  190.7   1.1e-54 !   -
+contig--185316       -         SSU_rRNA_eukarya     RF01960   hmm     1323     1667        2      312      +     -    6 0.50   0.0  185.2   5.1e-53 !   -
+contig--2251500      -         SSU_rRNA_eukarya     RF01960   hmm     1180     1697        1      473      +     -    6 0.52   0.0  183.7   1.5e-52 !   -
+contig--1029476      -         SSU_rRNA_eukarya     RF01960   hmm     1129     1645      217      698      +     -    6 0.44   0.4  178.8   4.4e-51 !   -
+contig--314729       -         SSU_rRNA_eukarya     RF01960   hmm     1166     1526      337        3      -     -    6 0.56   0.0  178.5   5.4e-51 !   -
+contig--364755       -         SSU_rRNA_eukarya     RF01960   hmm      589      998        1      396      +     -    6 0.47   0.0  178.0   7.6e-51 !   -
+contig--401056       -         SSU_rRNA_eukarya     RF01960   hmm     1280     1848       23      518      +     -    6 0.54   0.0  174.0   1.3e-49 !   -
+contig--2252860      -         SSU_rRNA_eukarya     RF01960   hmm        3      355        1      348      +     -    6 0.43   0.1  167.8     9e-48 !   -
+contig--2255364      -         SSU_rRNA_eukarya     RF01960   hmm      885     1333      440        2      -     -    6 0.52   0.1  166.7     2e-47 !   -
+contig--285317       -         SSU_rRNA_eukarya     RF01960   hmm      580      938        1      339      +     -    6 0.40   3.5  160.8   1.2e-45 !   -
+contig--3568828      -         SSU_rRNA_eukarya     RF01960   hmm      888     1242      350        9      -     -    6 0.55   0.1  160.4   1.6e-45 !   -
+contig--3461222      -         SSU_rRNA_eukarya     RF01960   hmm       38      582       19      522      +     -    6 0.43   0.9  157.3   1.3e-44 !   -
+contig--1776240      -         SSU_rRNA_eukarya     RF01960   hmm     1162     1669      463        1      -     -    6 0.53   0.0  150.5   1.6e-42 !   -
+contig--1346273      -         SSU_rRNA_eukarya     RF01960   hmm      990     1358      366        3      -     -    6 0.54   0.0  148.3   7.3e-42 !   -
+contig--664339       -         SSU_rRNA_eukarya     RF01960   hmm      597      990      380        1      -     -    6 0.45   0.4  148.1   8.4e-42 !   -
+contig--813107       -         SSU_rRNA_eukarya     RF01960   hmm      886     1224      159      488      +     -    6 0.56   0.2  142.6   3.8e-40 !   -
+contig--2253412      -         SSU_rRNA_eukarya     RF01960   hmm       23      337        2      311      +     -    6 0.42   0.1  134.0   1.5e-37 !   -
+contig--363016       -         SSU_rRNA_eukarya     RF01960   hmm     1431     1848     1132      748      -     -    6 0.53   0.0  132.2   5.3e-37 !   -
+contig--862423       -         SSU_rRNA_eukarya     RF01960   hmm     1186     1650        3      422      +     -    6 0.52   0.0  131.4   9.1e-37 !   -
+contig--1568447      -         SSU_rRNA_eukarya     RF01960   hmm      890     1222      367      683      +     -    6 0.53   0.3  128.7   6.1e-36 !   -
+contig--2571986      -         SSU_rRNA_eukarya     RF01960   hmm      591      933      332        2      -     -    6 0.45   0.5  127.1   1.8e-35 !   -
+contig--364625       -         SSU_rRNA_eukarya     RF01960   hmm      887     1210      314        4      -     -    6 0.50   0.1  125.2   6.5e-35 !   -
+contig--2248804      -         SSU_rRNA_eukarya     RF01960   hmm     1292     1702      165      515      +     -    6 0.47   0.0  121.6   8.5e-34 !   -
+contig--258486       -         SSU_rRNA_eukarya     RF01960   hmm     1429     1827       11      376      +     -    6 0.56   0.0  121.1   1.1e-33 !   -
+contig--2835211      -         SSU_rRNA_eukarya     RF01960   hmm      588      901        1      301      +     -    6 0.43   0.9  120.6   1.6e-33 !   -
+contig--1656709      -         SSU_rRNA_eukarya     RF01960   hmm      586      940        1      331      +     -    6 0.39   5.2  119.5   3.6e-33 !   -
+contig--2491978      -         SSU_rRNA_eukarya     RF01960   hmm        5      661     1025      483      -     -    6 0.53   0.0  118.3   8.2e-33 !   -
+contig--2969992      -         SSU_rRNA_eukarya     RF01960   hmm      891     1209      184      488      +     -    6 0.51   0.3  118.2   8.8e-33 !   -
+contig--2766474      -         SSU_rRNA_eukarya     RF01960   hmm     1456     1845      408       50      -     -    6 0.52   0.0  117.4   1.5e-32 !   -
+contig--1098909      -         SSU_rRNA_eukarya     RF01960   hmm      596      928      314        1      -     -    6 0.45   0.2  115.9   4.3e-32 !   -
+contig--2914153      -         SSU_rRNA_eukarya     RF01960   hmm      890     1191      288        1      -     -    6 0.47   0.8  115.5   5.8e-32 !   -
+contig--1001177      -         SSU_rRNA_eukarya     RF01960   hmm      892     1209       15      319      +     -    6 0.52   0.4  113.2   2.9e-31 !   -
+contig--3787593      -         SSU_rRNA_eukarya     RF01960   hmm      890     1187      300      584      +     -    6 0.52   0.2  111.0   1.3e-30 !   -
+contig--2889438      -         SSU_rRNA_eukarya     RF01960   hmm     1295     1673      334        5      -     -    6 0.50   0.0  109.1   4.8e-30 !   -
+contig--2972876      -         SSU_rRNA_eukarya     RF01960   hmm      888     1171      280        9      -     -    6 0.52   0.3  108.6     7e-30 !   -
+contig--2369838      -         SSU_rRNA_eukarya     RF01960   hmm      885     1193      560      855      +     -    6 0.54   0.3  106.4   3.2e-29 !   -
+contig--365127       -         SSU_rRNA_eukarya     RF01960   hmm      890     1172      277        8      -     -    6 0.54   0.0  105.6   5.6e-29 !   -
+contig--1149779      -         SSU_rRNA_eukarya     RF01960   hmm     1517     1848      302        3      -     -    6 0.51   0.0  104.4   1.3e-28 !   -
+contig--1634977      -         SSU_rRNA_eukarya     RF01960   hmm     1290     1654        1      314      +     -    6 0.55   0.0  103.9   1.8e-28 !   -
+contig--1192886      -         SSU_rRNA_eukarya     RF01960   hmm     1287     1668      330        1      -     -    6 0.49   0.0   97.5   1.5e-26 !   -
+contig--363722       -         SSU_rRNA_eukarya     RF01960   hmm      879     1170      280        3      -     -    6 0.51   0.1   97.0   2.1e-26 !   -
+contig--3503719      -         SSU_rRNA_eukarya     RF01960   hmm     1317     1703      349       11      -     -    6 0.51   0.0   95.6   5.9e-26 !   -
+contig--1720439      -         SSU_rRNA_eukarya     RF01960   hmm      890     1160      355      611      +     -    6 0.46   0.7   95.3   7.3e-26 !   -
+contig--1210200      -         SSU_rRNA_eukarya     RF01960   hmm      872     1162      281        1      -     -    6 0.43   1.5   89.9     3e-24 !   -
+contig--2249925      -         SSU_rRNA_eukarya     RF01960   hmm      890     1168      633      898      +     -    6 0.50   0.2   89.6   3.9e-24 !   -
+contig--1531838      -         SSU_rRNA_eukarya     RF01960   hmm     1162     1518      313        1      -     -    6 0.50   0.0   84.3   1.5e-22 !   -
+contig--1211922      -         SSU_rRNA_eukarya     RF01960   hmm     1504     1750      300       61      -     -    6 0.39   0.0   79.6     4e-21 !   -
+contig--3474644      -         SSU_rRNA_eukarya     RF01960   hmm        9      654       60      665      +     -    6 0.50   0.2   76.6   3.1e-20 !   -
+contig--3093712      -         SSU_rRNA_eukarya     RF01960   hmm      945     1164        3      212      +     -    6 0.56   0.0   71.4   1.1e-18 !   -
+contig--2914153      -         SSU_rRNA_eukarya     RF01960   hmm      287      665      726      332      -     -    6 0.54   0.2   68.3     1e-17 !   -
+contig--3575278      -         SSU_rRNA_eukarya     RF01960   hmm     1633     1848        3      184      +     -    6 0.54   0.0   64.4   1.5e-16 !   -
+contig--1209771      -         SSU_rRNA_eukarya     RF01960   hmm     1310     1634      276        2      -     -    6 0.51   0.0   61.7     1e-15 !   -
+contig--2271497      -         SSU_rRNA_eukarya     RF01960   hmm       85      653      740      222      -     -    6 0.51   0.3   61.1   1.5e-15 !   -
+contig--3076204      -         SSU_rRNA_eukarya     RF01960   hmm      138      651       59      493      +     -    6 0.53   0.0   60.9   1.8e-15 !   -
+contig--2271497      -         SSU_rRNA_eukarya     RF01960   hmm      890     1052      165        3      -     -    6 0.50   0.1   58.6   8.9e-15 !   -
+contig--3128112      -         SSU_rRNA_eukarya     RF01960   hmm      865     1174      315       28      -     -    6 0.47   0.4   58.1   1.2e-14 !   -
+contig--3093712      -         SSU_rRNA_eukarya     RF01960   hmm      910     1058      214      361      +     -    6 0.57   0.0   58.0   1.4e-14 !   -
+contig--24391        -         SSU_rRNA_eukarya     RF01960   hmm      887     1059      175        3      -     -    6 0.48   0.3   57.8   1.5e-14 !   -
+contig--364625       -         SSU_rRNA_eukarya     RF01960   hmm       39      660      928      361      -     -    6 0.52   0.1   57.6   1.7e-14 !   -
+contig--193617       -         SSU_rRNA_eukarya     RF01960   hmm     1212     1581      305       10      -     -    6 0.54   0.0   57.2   2.2e-14 !   -
+contig--2250940      -         SSU_rRNA_eukarya     RF01960   hmm     1771     1850        3       82      +     -    6 0.43   0.0   56.5   3.7e-14 !   -
+contig--2252644      -         SSU_rRNA_eukarya     RF01960   hmm      880     1044      624      782      +     -    6 0.50   0.1   55.1     1e-13 !   -
+contig--828224       -         SSU_rRNA_eukarya     RF01960   hmm      301      642       27      365      +     -    6 0.57   0.0   53.7   2.6e-13 !   -
+contig--3980131      -         SSU_rRNA_eukarya     RF01960   hmm     1783     1850        2       69      +     -    6 0.44   0.0   51.2   1.4e-12 !   -
+contig--156996       -         LSU_rRNA_archaea     RF02540   hmm        9     2944     3613      744      -     -    6 0.52  16.4 1930.8         0 !   -
+contig--397992       -         LSU_rRNA_archaea     RF02540   hmm       12     2980       61     2969      +     -    6 0.57  34.6 1332.6         0 !   -
+contig--371157       -         LSU_rRNA_archaea     RF02540   hmm       14     2090     3350     5333      +     -    6 0.52  21.5 1265.3         0 !   -
+contig--2256050      -         LSU_rRNA_archaea     RF02540   hmm      891     2529        4     1660      +     -    6 0.53  11.4  673.0  1.5e-200 !   -
+contig--401056       -         LSU_rRNA_archaea     RF02540   hmm       13     1491      891     2326      +     -    6 0.50  10.7  576.4    2e-171 !   -
+contig--151601       -         LSU_rRNA_archaea     RF02540   hmm      480     1955        1     1375      +     -    6 0.46   8.4  536.2  2.6e-159 !   -
+contig--166397       -         LSU_rRNA_archaea     RF02540   hmm     1848     2980       22     1182      +     -    6 0.54   3.8  535.2  5.4e-159 !   -
+contig--395713       -         LSU_rRNA_archaea     RF02540   hmm      163     1558        5     1242      +     -    6 0.52  15.7  517.0  1.6e-153 !   -
+contig--423976       -         LSU_rRNA_archaea     RF02540   hmm       97     1787      412     1996      +     -    6 0.46  16.0  511.2  9.2e-152 !   -
+contig--151080       -         LSU_rRNA_archaea     RF02540   hmm     1708     2907     1279       77      -     -    6 0.37   0.0  446.8  2.5e-132 !   -
+contig--151876       -         LSU_rRNA_archaea     RF02540   hmm       24     1239        2     1084      +     -    6 0.47   9.5  439.7  3.3e-130 !   -
+contig--1202655      -         LSU_rRNA_archaea     RF02540   hmm     1708     2699       75     1031      +     -    6 0.45   0.0  422.8  4.2e-125 !   -
+contig--2330557      -         LSU_rRNA_archaea     RF02540   hmm     1570     2514      993       18      -     -    6 0.56   7.3  407.4  1.9e-120 !   -
+contig--185309       -         LSU_rRNA_archaea     RF02540   hmm     1994     2883      127     1035      +     -    6 0.48   0.0  405.2  8.2e-120 !   -
+contig--395713       -         LSU_rRNA_archaea     RF02540   hmm     1728     2554     1302     2144      +     -    6 0.53   3.3  387.8  1.5e-114 !   -
+contig--2634789      -         LSU_rRNA_archaea     RF02540   hmm     1339     2391     1087        2      -     -    6 0.50   3.2  387.0  2.5e-114 !   -
+contig--23096        -         LSU_rRNA_archaea     RF02540   hmm     2009     2706        2      708      +     -    6 0.51   0.1  386.9  2.8e-114 !   -
+contig--137819       -         LSU_rRNA_archaea     RF02540   hmm     1992     2710        6      734      +     -    6 0.50   0.0  378.6  9.1e-112 !   -
+contig--362861       -         LSU_rRNA_archaea     RF02540   hmm       22     1132        6     1097      +     -    6 0.47   5.5  350.3  3.1e-103 !   -
+contig--3743149      -         LSU_rRNA_archaea     RF02540   hmm     1679     2418      784        2      -     -    6 0.55   1.5  341.1  1.8e-100 !   -
+contig--2252929      -         LSU_rRNA_archaea     RF02540   hmm     1218     2072      859        1      -     -    6 0.52   2.6  335.7   7.6e-99 !   -
+contig--2254117      -         LSU_rRNA_archaea     RF02540   hmm      431     1332        3      802      +     -    6 0.50   6.2  305.9   7.5e-90 !   -
+contig--2250515      -         LSU_rRNA_archaea     RF02540   hmm       30      912        2      775      +     -    6 0.52  10.1  302.9   6.2e-89 !   -
+contig--4068604      -         LSU_rRNA_archaea     RF02540   hmm     1162     1771        2      562      +     -    6 0.53   2.7  300.4   3.5e-88 !   -
+contig--2298625      -         LSU_rRNA_archaea     RF02540   hmm     2314     2874      996      437      -     -    6 0.46   0.0  287.2   3.3e-84 !   -
+contig--3054101      -         LSU_rRNA_archaea     RF02540   hmm     2319     2867       31      576      +     -    6 0.47   0.0  269.5   7.3e-79 !   -
+contig--1210133      -         LSU_rRNA_archaea     RF02540   hmm       17      836      733        4      -     -    6 0.50   3.5  264.6   2.2e-77 !   -
+contig--3398090      -         LSU_rRNA_archaea     RF02540   hmm     2004     2572        2      568      +     -    6 0.50   0.1  256.5   6.1e-75 !   -
+contig--3715154      -         LSU_rRNA_archaea     RF02540   hmm     2035     2558      539        6      -     -    6 0.54   0.1  251.0   2.7e-73 !   -
+contig--364277       -         LSU_rRNA_archaea     RF02540   hmm       15      547      583        2      -     -    6 0.43   6.0  247.1     4e-72 !   -
+contig--151080       -         LSU_rRNA_archaea     RF02540   hmm      160     1515     2513     1352      -     -    6 0.31   0.9  243.5   4.9e-71 !   -
+contig--1040384      -         LSU_rRNA_archaea     RF02540   hmm      909     1596      774      115      -     -    6 0.45   0.3  240.5     4e-70 !   -
+contig--364074       -         LSU_rRNA_archaea     RF02540   hmm      868     1467      581        4      -     -    6 0.53   2.4  234.9   1.9e-68 !   -
+contig--10143        -         LSU_rRNA_archaea     RF02540   hmm      937     1546      798      202      -     -    6 0.49   0.9  234.0   3.5e-68 !   -
+contig--3784467      -         LSU_rRNA_archaea     RF02540   hmm     2572     2981      417       16      -     -    6 0.53   0.1  233.6   4.8e-68 !   -
+contig--35359        -         LSU_rRNA_archaea     RF02540   hmm     1697     2182       60      543      +     -    6 0.48   0.0  232.7   8.8e-68 !   -
+contig--3860305      -         LSU_rRNA_archaea     RF02540   hmm       19      727        7      621      +     -    6 0.45   3.1  232.5     1e-67 !   -
+contig--365125       -         LSU_rRNA_archaea     RF02540   hmm     2362     2872      622      114      -     -    6 0.45   0.0  229.7   7.2e-67 !   -
+contig--2699652      -         LSU_rRNA_archaea     RF02540   hmm     2541     2970        2      424      +     -    6 0.53   0.1  229.5   8.2e-67 !   -
+contig--3638238      -         LSU_rRNA_archaea     RF02540   hmm     1229     1933      719        5      -     -    6 0.48   0.8  221.6     2e-64 !   -
+contig--2531154      -         LSU_rRNA_archaea     RF02540   hmm       11      573       80      642      +     -    6 0.47   3.4  217.5   3.5e-63 !   -
+contig--2715420      -         LSU_rRNA_archaea     RF02540   hmm     2458     2862       11      422      +     -    6 0.55   0.3  211.8   1.8e-61 !   -
+contig--2575573      -         LSU_rRNA_archaea     RF02540   hmm     1069     1856        5      830      +     -    6 0.47   0.1  200.7   4.1e-58 !   -
+contig--3317407      -         LSU_rRNA_archaea     RF02540   hmm       12      527      284      752      +     -    6 0.45   2.9  199.5   9.3e-58 !   -
+contig--1082627      -         LSU_rRNA_archaea     RF02540   hmm     2570     2898        2      332      +     -    6 0.54   0.1  198.5   1.9e-57 !   -
+contig--363016       -         LSU_rRNA_archaea     RF02540   hmm       20      521      463        3      -     -    6 0.47   4.3  198.0   2.6e-57 !   -
+contig--2254060      -         LSU_rRNA_archaea     RF02540   hmm     2038     2580      627        3      -     -    6 0.47   0.0  197.1     5e-57 !   -
+contig--1213982      -         LSU_rRNA_archaea     RF02540   hmm     1942     2427      561        3      -     -    6 0.51   0.0  190.3   5.5e-55 !   -
+contig--1407263      -         LSU_rRNA_archaea     RF02540   hmm      978     1481      490        3      -     -    6 0.45   0.0  188.9   1.5e-54 !   -
+contig--2252346      -         LSU_rRNA_archaea     RF02540   hmm     2041     2599        2      634      +     -    6 0.54   0.1  188.4   2.1e-54 !   -
+contig--2250883      -         LSU_rRNA_archaea     RF02540   hmm     2595     2978      396        4      -     -    6 0.54   0.1  186.2   9.8e-54 !   -
+contig--1768180      -         LSU_rRNA_archaea     RF02540   hmm     2635     2979        2      340      +     -    6 0.53   0.1  183.3   7.2e-53 !   -
+contig--3176110      -         LSU_rRNA_archaea     RF02540   hmm     2302     2666       47      404      +     -    6 0.44   0.0  181.6   2.4e-52 !   -
+contig--1662509      -         LSU_rRNA_archaea     RF02540   hmm     1174     1781        1      645      +     -    6 0.53   0.1  178.2   2.5e-51 !   -
+contig--2220335      -         LSU_rRNA_archaea     RF02540   hmm     1700     2072      407        1      -     -    6 0.50   0.1  178.0   2.8e-51 !   -
+contig--185562       -         LSU_rRNA_archaea     RF02540   hmm      927     1575      789       68      -     -    6 0.52   0.8  174.9   2.4e-50 !   -
+contig--36603        -         LSU_rRNA_archaea     RF02540   hmm      160      534        2      411      +     -    6 0.54   1.0  174.1   4.3e-50 !   -
+contig--362412       -         LSU_rRNA_archaea     RF02540   hmm      154      539      419        4      -     -    6 0.44   4.5  174.0   4.5e-50 !   -
+contig--2254400      -         LSU_rRNA_archaea     RF02540   hmm     2640     2980      341        7      -     -    6 0.54   0.2  172.9     1e-49 !   -
+contig--2519402      -         LSU_rRNA_archaea     RF02540   hmm       33      442      420       16      -     -    6 0.45   1.2  172.4   1.3e-49 !   -
+contig--1596054      -         LSU_rRNA_archaea     RF02540   hmm      890     1444      603        5      -     -    6 0.49   0.1  172.4   1.4e-49 !   -
+contig--2304422      -         LSU_rRNA_archaea     RF02540   hmm       18      501      449        1      -     -    6 0.53   1.1  172.0   1.8e-49 !   -
+contig--363861       -         LSU_rRNA_archaea     RF02540   hmm      647     1232      651        2      -     -    6 0.48   0.0  170.7   4.4e-49 !   -
+contig--364116       -         LSU_rRNA_archaea     RF02540   hmm     2078     2503        2      426      +     -    6 0.54   0.2  164.8   2.8e-47 !   -
+contig--32925        -         LSU_rRNA_archaea     RF02540   hmm     1509     2020        4      551      +     -    6 0.52   0.9  164.4   3.6e-47 !   -
+contig--2701305      -         LSU_rRNA_archaea     RF02540   hmm     1467     1976        2      487      +     -    6 0.53   1.2  163.4   7.4e-47 !   -
+contig--942031       -         LSU_rRNA_archaea     RF02540   hmm     2637     2934      307        8      -     -    6 0.55   0.1  160.7   4.7e-46 !   -
+contig--2152327      -         LSU_rRNA_archaea     RF02540   hmm     1408     1959        7      581      +     -    6 0.50   0.2  159.3   1.2e-45 !   -
+contig--2940126      -         LSU_rRNA_archaea     RF02540   hmm      477      953      402       10      -     -    6 0.52   3.0  155.9   1.3e-44 !   -
+contig--2646754      -         LSU_rRNA_archaea     RF02540   hmm     1210     1828        1      592      +     -    6 0.51   2.0  155.9   1.3e-44 !   -
+contig--332136       -         LSU_rRNA_archaea     RF02540   hmm     2578     2877      322       19      -     -    6 0.57   0.2  155.2   2.1e-44 !   -
+contig--2680413      -         LSU_rRNA_archaea     RF02540   hmm       21      490      438        1      -     -    6 0.44   1.3  154.8   2.8e-44 !   -
+contig--2254163      -         LSU_rRNA_archaea     RF02540   hmm       21      470      446       10      -     -    6 0.40   2.5  152.6   1.3e-43 !   -
+contig--2713352      -         LSU_rRNA_archaea     RF02540   hmm     1352     1850      508       13      -     -    6 0.51   1.3  152.1   1.8e-43 !   -
+contig--759897       -         LSU_rRNA_archaea     RF02540   hmm     2652     2975        1      317      +     -    6 0.53   0.1  150.8   4.6e-43 !   -
+contig--2652964      -         LSU_rRNA_archaea     RF02540   hmm     1507     1977      494       15      -     -    6 0.49   0.2  150.2   6.8e-43 !   -
+contig--2918607      -         LSU_rRNA_archaea     RF02540   hmm      435      951      428        9      -     -    6 0.47   2.2  149.8     9e-43 !   -
+contig--3694746      -         LSU_rRNA_archaea     RF02540   hmm      480      944      382        8      -     -    6 0.50   2.1  149.2   1.3e-42 !   -
+contig--2805328      -         LSU_rRNA_archaea     RF02540   hmm     2635     2983        3      359      +     -    6 0.57   0.2  148.8   1.7e-42 !   -
+contig--147097       -         LSU_rRNA_archaea     RF02540   hmm     2659     2976        2      332      +     -    6 0.50   0.0  148.8   1.8e-42 !   -
+contig--3354354      -         LSU_rRNA_archaea     RF02540   hmm      750     1227      514        2      -     -    6 0.53   2.1  147.8   3.7e-42 !   -
+contig--151751       -         LSU_rRNA_archaea     RF02540   hmm      156      550      592      200      -     -    6 0.47   1.6  145.6   1.6e-41 !   -
+contig--365284       -         LSU_rRNA_archaea     RF02540   hmm      186      553      547      182      -     -    6 0.48   0.9  145.2   2.2e-41 !   -
+contig--747483       -         LSU_rRNA_archaea     RF02540   hmm     2630     2932      332       28      -     -    6 0.53   0.0  144.6   3.3e-41 !   -
+contig--1176662      -         LSU_rRNA_archaea     RF02540   hmm     2527     2796       22      290      +     -    6 0.49   0.0  142.9   1.1e-40 !   -
+contig--95399        -         LSU_rRNA_archaea     RF02540   hmm     2663     2982        2      329      +     -    6 0.53   0.3  141.3   3.3e-40 !   -
+contig--2251064      -         LSU_rRNA_archaea     RF02540   hmm      191      551        3      357      +     -    6 0.46   0.8  140.7     5e-40 !   -
+contig--1458589      -         LSU_rRNA_archaea     RF02540   hmm      888     1212        2      315      +     -    6 0.56   0.8  140.5   5.9e-40 !   -
+contig--2564558      -         LSU_rRNA_archaea     RF02540   hmm      460      947        1      398      +     -    6 0.44   0.5  140.3   6.6e-40 !   -
+contig--2722470      -         LSU_rRNA_archaea     RF02540   hmm      163      525        7      371      +     -    6 0.51   0.4  139.3   1.3e-39 !   -
+contig--236053       -         LSU_rRNA_archaea     RF02540   hmm       23      450      397        5      -     -    6 0.47   1.7  138.6   2.2e-39 !   -
+contig--473422       -         LSU_rRNA_archaea     RF02540   hmm       41      371      316        1      -     -    6 0.55   2.4  137.2   5.8e-39 !   -
+contig--3433834      -         LSU_rRNA_archaea     RF02540   hmm     1441     1915        1      488      +     -    6 0.47   0.0  137.1     6e-39 !   -
+contig--2835645      -         LSU_rRNA_archaea     RF02540   hmm     2659     2934      306       10      -     -    6 0.52   0.1  136.2   1.1e-38 !   -
+contig--1796896      -         LSU_rRNA_archaea     RF02540   hmm     2668     2971        3      299      +     -    6 0.49   0.1  136.0   1.3e-38 !   -
+contig--2254317      -         LSU_rRNA_archaea     RF02540   hmm      171      535      362        1      -     -    6 0.45   0.6  135.8   1.5e-38 !   -
+contig--2874819      -         LSU_rRNA_archaea     RF02540   hmm     2037     2385      359        1      -     -    6 0.57   0.0  134.5   3.6e-38 !   -
+contig--724357       -         LSU_rRNA_archaea     RF02540   hmm     1081     1426       14      347      +     -    6 0.47   0.3  134.4   3.9e-38 !   -
+contig--185811       -         LSU_rRNA_archaea     RF02540   hmm     1246     1784      524        2      -     -    6 0.49   0.5  134.0   5.4e-38 !   -
+contig--3890060      -         LSU_rRNA_archaea     RF02540   hmm       39      462      360        1      -     -    6 0.47   1.2  133.8   6.1e-38 !   -
+contig--2252661      -         LSU_rRNA_archaea     RF02540   hmm      188      549      776      405      -     -    6 0.49   2.0  133.1   9.8e-38 !   -
+contig--3659280      -         LSU_rRNA_archaea     RF02540   hmm     2119     2524        2      414      +     -    6 0.48   0.0  132.9   1.2e-37 !   -
+contig--3655473      -         LSU_rRNA_archaea     RF02540   hmm      927     1392      509        2      -     -    6 0.51   0.1  132.6   1.3e-37 !   -
+contig--185298       -         LSU_rRNA_archaea     RF02540   hmm      189      652        2      451      +     -    6 0.42   4.9  130.1   8.1e-37 !   -
+contig--2250797      -         LSU_rRNA_archaea     RF02540   hmm      155      516      363        3      -     -    6 0.49   0.5  129.5   1.2e-36 !   -
+contig--1042219      -         LSU_rRNA_archaea     RF02540   hmm     2180     2498      339       13      -     -    6 0.55   0.2  126.7   8.2e-36 !   -
+contig--97491        -         LSU_rRNA_archaea     RF02540   hmm     2194     2580        5      422      +     -    6 0.46   0.0  126.2   1.1e-35 !   -
+contig--2250093      -         LSU_rRNA_archaea     RF02540   hmm     2079     2505      486       15      -     -    6 0.47   0.0  123.9   5.8e-35 !   -
+contig--365471       -         LSU_rRNA_archaea     RF02540   hmm     2009     2342        2      348      +     -    6 0.46   0.0  123.5   7.7e-35 !   -
+contig--2249544      -         LSU_rRNA_archaea     RF02540   hmm     2154     2551      429        2      -     -    6 0.44   0.0  123.4     8e-35 !   -
+contig--2673585      -         LSU_rRNA_archaea     RF02540   hmm      170      510      373        1      -     -    6 0.42   1.6  122.7   1.4e-34 !   -
+contig--261342       -         LSU_rRNA_archaea     RF02540   hmm     2527     2789       25      285      +     -    6 0.39   0.0  122.6   1.4e-34 !   -
+contig--2412452      -         LSU_rRNA_archaea     RF02540   hmm     1879     2129       73      322      +     -    6 0.46   0.0  122.2   1.9e-34 !   -
+contig--2543224      -         LSU_rRNA_archaea     RF02540   hmm       15      255      311       55      -     -    6 0.51   0.4  122.0   2.2e-34 !   -
+contig--1214513      -         LSU_rRNA_archaea     RF02540   hmm      188      535        2      347      +     -    6 0.53   1.3  121.3   3.6e-34 !   -
+contig--2254733      -         LSU_rRNA_archaea     RF02540   hmm      918     1286      396       30      -     -    6 0.34   0.0  121.1   4.2e-34 !   -
+contig--1111206      -         LSU_rRNA_archaea     RF02540   hmm       85      465      359        2      -     -    6 0.42   1.9  119.6   1.1e-33 !   -
+contig--3748912      -         LSU_rRNA_archaea     RF02540   hmm      645     1043      374       10      -     -    6 0.47   0.0  118.0   3.5e-33 !   -
+contig--3652281      -         LSU_rRNA_archaea     RF02540   hmm     2082     2388      309        4      -     -    6 0.56   0.0  117.9   3.7e-33 !   -
+contig--1688622      -         LSU_rRNA_archaea     RF02540   hmm     2147     2496      365        9      -     -    6 0.52   0.0  117.7   4.4e-33 !   -
+contig--2251392      -         LSU_rRNA_archaea     RF02540   hmm     1395     1975        3      731      +     -    6 0.52   0.4  117.0   6.8e-33 !   -
+contig--1214168      -         LSU_rRNA_archaea     RF02540   hmm      170      505        2      331      +     -    6 0.46   0.4  117.0     7e-33 !   -
+contig--362625       -         LSU_rRNA_archaea     RF02540   hmm     2556     2876        2      321      +     -    6 0.43   0.0  116.2   1.2e-32 !   -
+contig--1215349      -         LSU_rRNA_archaea     RF02540   hmm      918     1251      331        2      -     -    6 0.52   0.1  115.4   2.2e-32 !   -
+contig--257393       -         LSU_rRNA_archaea     RF02540   hmm     1227     1764      590        6      -     -    6 0.60   1.6  114.3   4.6e-32 !   -
+contig--2906201      -         LSU_rRNA_archaea     RF02540   hmm      928     1235      304        2      -     -    6 0.43   0.0  112.9   1.2e-31 !   -
+contig--547077       -         LSU_rRNA_archaea     RF02540   hmm      913     1226      306        1      -     -    6 0.50   0.1  112.6   1.4e-31 !   -
+contig--1214754      -         LSU_rRNA_archaea     RF02540   hmm      198      553      512      168      -     -    6 0.38   3.2  111.1   4.3e-31 !   -
+contig--2255353      -         LSU_rRNA_archaea     RF02540   hmm     1410     1855       10      501      +     -    6 0.54   0.2  108.3     3e-30 !   -
+contig--130023       -         LSU_rRNA_archaea     RF02540   hmm      213      560      682      334      -     -    6 0.51   0.0  106.9   7.9e-30 !   -
+contig--3019708      -         LSU_rRNA_archaea     RF02540   hmm     1217     1781      608        4      -     -    6 0.44   0.0  106.0   1.4e-29 !   -
+contig--2983248      -         LSU_rRNA_archaea     RF02540   hmm      196      528      316        2      -     -    6 0.42   1.1  104.8   3.2e-29 !   -
+contig--2255132      -         LSU_rRNA_archaea     RF02540   hmm       52      416        1      362      +     -    6 0.37   0.6  103.7   7.1e-29 !   -
+contig--2251329      -         LSU_rRNA_archaea     RF02540   hmm     2669     2958        3      299      +     -    6 0.47   0.0  103.1   1.1e-28 !   -
+contig--2250342      -         LSU_rRNA_archaea     RF02540   hmm      640     1208       65      588      +     -    6 0.40   0.0  102.7   1.4e-28 !   -
+contig--3652175      -         LSU_rRNA_archaea     RF02540   hmm      636      946      286        8      -     -    6 0.49   0.0  102.0   2.4e-28 !   -
+contig--110110       -         LSU_rRNA_archaea     RF02540   hmm      164      484       12      322      +     -    6 0.42   1.3  101.6     3e-28 !   -
+contig--101864       -         LSU_rRNA_archaea     RF02540   hmm      177      500      307        2      -     -    6 0.48   0.1  100.9   4.9e-28 !   -
+contig--1214394      -         LSU_rRNA_archaea     RF02540   hmm     2615     2870      422      167      -     -    6 0.50   0.0  100.1   8.5e-28 !   -
+contig--1326571      -         LSU_rRNA_archaea     RF02540   hmm      709     1009        7      270      +     -    6 0.50   0.0   99.1   1.8e-27 !   -
+contig--2767514      -         LSU_rRNA_archaea     RF02540   hmm     2070     2369      310        1      -     -    6 0.45   0.0   99.0     2e-27 !   -
+contig--332136       -         LSU_rRNA_archaea     RF02540   hmm     2546     2702      487      331      -     -    6 0.58   0.1   97.4   5.8e-27 !   -
+contig--2937145      -         LSU_rRNA_archaea     RF02540   hmm     2615     2870        3      259      +     -    6 0.50   0.0   96.2   1.4e-26 !   -
+contig--2501086      -         LSU_rRNA_archaea     RF02540   hmm      432      907        4      390      +     -    6 0.40   0.3   95.7   1.8e-26 !   -
+contig--1210202      -         LSU_rRNA_archaea     RF02540   hmm      420      903      387        1      -     -    6 0.42   1.4   95.6   2.1e-26 !   -
+contig--2528721      -         LSU_rRNA_archaea     RF02540   hmm     2642     2885        1      305      +     -    6 0.56   0.0   95.2   2.6e-26 !   -
+contig--3925448      -         LSU_rRNA_archaea     RF02540   hmm      319      727       21      362      +     -    6 0.38   2.9   94.4   4.5e-26 !   -
+contig--1212351      -         LSU_rRNA_archaea     RF02540   hmm      164      486      317        1      -     -    6 0.53   0.1   92.8   1.4e-25 !   -
+contig--185227       -         LSU_rRNA_archaea     RF02540   hmm     1207     1490      302       15      -     -    6 0.53   0.3   92.2   2.2e-25 !   -
+contig--1437319      -         LSU_rRNA_archaea     RF02540   hmm      655      966      328        6      -     -    6 0.50   0.0   91.5   3.4e-25 !   -
+contig--669436       -         LSU_rRNA_archaea     RF02540   hmm     1478     1850      367        1      -     -    6 0.47   0.1   89.4   1.5e-24 !   -
+contig--1031478      -         LSU_rRNA_archaea     RF02540   hmm     1435     1814      372        2      -     -    6 0.54   0.3   88.8   2.3e-24 !   -
+contig--3276943      -         LSU_rRNA_archaea     RF02540   hmm      165     1064      968       47      -     -    6 0.44   0.0   87.9   4.1e-24 !   -
+contig--3290892      -         LSU_rRNA_archaea     RF02540   hmm     1411     1848        5      487      +     -    6 0.47   0.0   87.4   5.9e-24 !   -
+contig--3889622      -         LSU_rRNA_archaea     RF02540   hmm      864     1182       13      329      +     -    6 0.44   0.0   87.0   7.6e-24 !   -
+contig--2741341      -         LSU_rRNA_archaea     RF02540   hmm     1466     1851        1      418      +     -    6 0.51   0.0   85.0   3.2e-23 !   -
+contig--3414648      -         LSU_rRNA_archaea     RF02540   hmm     2031     2289      164      423      +     -    6 0.47   0.0   84.8   3.7e-23 !   -
+contig--1692849      -         LSU_rRNA_archaea     RF02540   hmm     2145     2444       12      333      +     -    6 0.44   0.0   84.3   5.2e-23 !   -
+contig--924893       -         LSU_rRNA_archaea     RF02540   hmm      647      917      296       10      -     -    6 0.52   0.1   83.8   7.5e-23 !   -
+contig--1644897      -         LSU_rRNA_archaea     RF02540   hmm     1065     1491       91      523      +     -    6 0.49   0.0   81.3   4.2e-22 !   -
+contig--185430       -         LSU_rRNA_archaea     RF02540   hmm     1502     1843       38      392      +     -    6 0.47   0.0   79.9   1.1e-21 !   -
+contig--1159799      -         LSU_rRNA_archaea     RF02540   hmm     2660     2873      374      162      -     -    6 0.47   0.0   79.9   1.1e-21 !   -
+contig--2252145      -         LSU_rRNA_archaea     RF02540   hmm     2655     2933        1      269      +     -    6 0.46   0.0   79.5   1.4e-21 !   -
+contig--1133023      -         LSU_rRNA_archaea     RF02540   hmm     1501     1855        9      379      +     -    6 0.52   0.0   77.3   6.8e-21 !   -
+contig--496748       -         LSU_rRNA_archaea     RF02540   hmm      177      466        1      294      +     -    6 0.55   0.0   76.8   9.1e-21 !   -
+contig--1834142      -         LSU_rRNA_archaea     RF02540   hmm      179      466        2      298      +     -    6 0.57   0.0   76.4   1.2e-20 !   -
+contig--3494982      -         LSU_rRNA_archaea     RF02540   hmm      914     1267       27      377      +     -    6 0.40   0.0   75.9   1.8e-20 !   -
+contig--2251231      -         LSU_rRNA_archaea     RF02540   hmm     2662     2884      464      243      -     -    6 0.46   0.0   75.7   1.9e-20 !   -
+contig--68307        -         LSU_rRNA_archaea     RF02540   hmm      214      520        2      307      +     -    6 0.42   0.1   75.3   2.7e-20 !   -
+contig--518767       -         LSU_rRNA_archaea     RF02540   hmm      396      619       31      243      +     -    6 0.44   0.0   72.7   1.6e-19 !   -
+contig--515926       -         LSU_rRNA_archaea     RF02540   hmm     1254     1658      494       49      -     -    6 0.47   0.2   72.2   2.3e-19 !   -
+contig--2251849      -         LSU_rRNA_archaea     RF02540   hmm     2662     2879        5      221      +     -    6 0.48   0.0   72.2   2.4e-19 !   -
+contig--1212661      -         LSU_rRNA_archaea     RF02540   hmm     2670     2880        1      212      +     -    6 0.51   0.0   70.5   7.2e-19 !   -
+contig--1583871      -         LSU_rRNA_archaea     RF02540   hmm     1433     1856        9      458      +     -    6 0.44   0.0   69.5   1.5e-18 !   -
+contig--3897242      -         LSU_rRNA_archaea     RF02540   hmm     1312     1576       18      289      +     -    6 0.48   0.0   68.4   3.2e-18 !   -
+contig--2255543      -         LSU_rRNA_archaea     RF02540   hmm     2667     2876        2      210      +     -    6 0.46   0.0   68.1     4e-18 !   -
+contig--1007451      -         LSU_rRNA_archaea     RF02540   hmm     2152     2407       15      307      +     -    6 0.51   0.0   67.8     5e-18 !   -
+contig--3875044      -         LSU_rRNA_archaea     RF02540   hmm      141      373      128      354      +     -    6 0.43   0.0   67.7     5e-18 !   -
+contig--3299936      -         LSU_rRNA_archaea     RF02540   hmm     1090     1446        8      379      +     -    6 0.38   0.0   65.1   3.1e-17 !   -
+contig--2253227      -         LSU_rRNA_archaea     RF02540   hmm     2680     2872        2      210      +     -    6 0.54   0.0   63.9   7.4e-17 !   -
+contig--2893879      -         LSU_rRNA_archaea     RF02540   hmm     1427     1789        2      363      +     -    6 0.49   0.0   61.9   2.9e-16 !   -
+contig--364298       -         LSU_rRNA_archaea     RF02540   hmm      907     1403        1      505      +     -    6 0.29   0.0   61.6   3.5e-16 !   -
+contig--2251533      -         LSU_rRNA_archaea     RF02540   hmm     2664     2866      425      223      -     -    6 0.48   0.0   61.1   4.9e-16 !   -
+contig--3050118      -         LSU_rRNA_archaea     RF02540   hmm     2668     2884        2      216      +     -    6 0.45   0.0   60.8   6.5e-16 !   -
+contig--2945976      -         LSU_rRNA_archaea     RF02540   hmm     1458     1789        1      329      +     -    6 0.50   0.1   58.0   4.4e-15 !   -
+contig--3756271      -         LSU_rRNA_archaea     RF02540   hmm     1274     1605        5      365      +     -    6 0.52   0.1   56.3   1.4e-14 !   -
+contig--362779       -         LSU_rRNA_archaea     RF02540   hmm     2682     2933      372       45      -     -    6 0.60   0.0   54.7   4.3e-14 !   -
+contig--1123361      -         LSU_rRNA_archaea     RF02540   hmm      819      941        1      121      +     -    6 0.52   0.0   54.3   5.8e-14 !   -
+contig--1572437      -         LSU_rRNA_archaea     RF02540   hmm     2675     2871        1      196      +     -    6 0.47   0.0   53.0   1.5e-13 !   -
+contig--64232        -         LSU_rRNA_archaea     RF02540   hmm     2661     2877        6      221      +     -    6 0.41   0.0   52.6   1.9e-13 !   -
+contig--1797769      -         LSU_rRNA_archaea     RF02540   hmm     1635     1855      438      213      -     -    6 0.53   0.0   50.8   6.5e-13 !   -
+contig--397992       -         LSU_rRNA_bacteria    RF02541   hmm        9     2922       59     2977      +     -    6 0.57  30.5 2226.7         0 !   -
+contig--395713       -         LSU_rRNA_bacteria    RF02541   hmm      179     2486        2     2147      +     -    6 0.52  22.4 1672.9         0 !   -
+contig--2256050      -         LSU_rRNA_bacteria    RF02541   hmm      811     2466        1     1670      +     -    6 0.52  12.2 1243.1         0 !   -
+contig--156996       -         LSU_rRNA_bacteria    RF02541   hmm       15     2891     3606      739      -     -    6 0.52  17.1 1219.6         0 !   -
+contig--151080       -         LSU_rRNA_bacteria    RF02541   hmm       49     2907     2627       17      -     -    6 0.33   6.6 1212.6         0 !   -
+contig--166397       -         LSU_rRNA_bacteria    RF02541   hmm     1762     2922       31     1190      +     -    6 0.53   3.7  998.5  1.2e-298 !   -
+contig--401056       -         LSU_rRNA_bacteria    RF02541   hmm        3     1408      882     2330      +     -    6 0.49  12.7  974.7  1.9e-291 !   -
+contig--151601       -         LSU_rRNA_bacteria    RF02541   hmm      488     1860        1     1375      +     -    6 0.46  11.5  921.8  1.6e-275 !   -
+contig--423976       -         LSU_rRNA_bacteria    RF02541   hmm       85     1697      400     2002      +     -    6 0.46  18.0  884.8  2.3e-264 !   -
+contig--371157       -         LSU_rRNA_bacteria    RF02541   hmm       18     2008     3355     5331      +     -    6 0.52  21.1  802.2  1.9e-239 !   -
+contig--151876       -         LSU_rRNA_bacteria    RF02541   hmm       23     1155        2     1085      +     -    6 0.47  10.0  788.1  3.5e-235 !   -
+contig--2330557      -         LSU_rRNA_bacteria    RF02541   hmm     1465     2458      998        1      -     -    6 0.56   7.7  752.9  1.4e-224 !   -
+contig--1202655      -         LSU_rRNA_bacteria    RF02541   hmm     1585     2628       48     1031      +     -    6 0.44   0.0  735.1  3.3e-219 !   -
+contig--2634789      -         LSU_rRNA_bacteria    RF02541   hmm     1247     2321     1092        2      -     -    6 0.50   5.1  719.6  1.5e-214 !   -
+contig--185309       -         LSU_rRNA_bacteria    RF02541   hmm     1915     2818      128     1039      +     -    6 0.47   0.0  711.7  3.9e-212 !   -
+contig--137819       -         LSU_rRNA_bacteria    RF02541   hmm     1910     2640        4      735      +     -    6 0.49   0.0  690.7  8.2e-206 !   -
+contig--23096        -         LSU_rRNA_bacteria    RF02541   hmm     1928     2636        1      709      +     -    6 0.51   0.2  669.2  2.5e-199 !   -
+contig--362861       -         LSU_rRNA_bacteria    RF02541   hmm       18     1052        3     1097      +     -    6 0.47   6.5  610.5  1.3e-181 !   -
+contig--3743149      -         LSU_rRNA_bacteria    RF02541   hmm     1568     2348      797        2      -     -    6 0.55   0.8  592.4  3.5e-176 !   -
+contig--2252929      -         LSU_rRNA_bacteria    RF02541   hmm     1132     1992      860        1      -     -    6 0.52   3.3  547.7  1.1e-162 !   -
+contig--2254117      -         LSU_rRNA_bacteria    RF02541   hmm      438     1247        2      805      +     -    6 0.50   6.0  530.1  2.2e-157 !   -
+contig--2250515      -         LSU_rRNA_bacteria    RF02541   hmm       28      836        1      776      +     -    6 0.52   9.4  502.0  6.4e-149 !   -
+contig--3398090      -         LSU_rRNA_bacteria    RF02541   hmm     1923     2502        1      569      +     -    6 0.50   0.1  488.0  1.1e-144 !   -
+contig--3715154      -         LSU_rRNA_bacteria    RF02541   hmm     1955     2491      539        2      -     -    6 0.54   0.1  470.4  2.3e-139 !   -
+contig--10143        -         LSU_rRNA_bacteria    RF02541   hmm      858     1739      800        1      -     -    6 0.49   3.4  446.1  4.8e-132 !   -
+contig--3860305      -         LSU_rRNA_bacteria    RF02541   hmm       13      696        2      634      +     -    6 0.45   2.9  433.3  3.5e-128 !   -
+contig--1040384      -         LSU_rRNA_bacteria    RF02541   hmm      832     1566      774       40      -     -    6 0.44   3.4  425.7  6.7e-126 !   -
+contig--1210133      -         LSU_rRNA_bacteria    RF02541   hmm       13      761      736        4      -     -    6 0.50   3.4  419.3  5.8e-124 !   -
+contig--2715420      -         LSU_rRNA_bacteria    RF02541   hmm     2376     2794        2      423      +     -    6 0.55   0.4  392.8  5.6e-116 !   -
+contig--2699652      -         LSU_rRNA_bacteria    RF02541   hmm     2469     2905        1      425      +     -    6 0.53   0.1  391.2  1.8e-115 !   -
+contig--364074       -         LSU_rRNA_bacteria    RF02541   hmm      789     1379      583        4      -     -    6 0.53   2.4  371.4  1.7e-109 !   -
+contig--3638238      -         LSU_rRNA_bacteria    RF02541   hmm     1144     1841      719        2      -     -    6 0.48   2.0  366.6  4.6e-108 !   -
+contig--3784467      -         LSU_rRNA_bacteria    RF02541   hmm     2501     2922      417        9      -     -    6 0.53   0.1  365.8  7.7e-108 !   -
+contig--2531154      -         LSU_rRNA_bacteria    RF02541   hmm       11      583       80      642      +     -    6 0.47   4.0  358.6  1.2e-105 !   -
+contig--35359        -         LSU_rRNA_bacteria    RF02541   hmm     1594     2103       53      544      +     -    6 0.48   0.0  355.4  1.1e-104 !   -
+contig--364277       -         LSU_rRNA_bacteria    RF02541   hmm       10      557      587        2      -     -    6 0.43   6.6  334.2   2.7e-98 !   -
+contig--3659280      -         LSU_rRNA_bacteria    RF02541   hmm     2038     2462        1      425      +     -    6 0.48   0.1  326.2   6.9e-96 !   -
+contig--2940126      -         LSU_rRNA_bacteria    RF02541   hmm      485      884      402        2      -     -    6 0.53   1.7  320.5   3.6e-94 !   -
+contig--364116       -         LSU_rRNA_bacteria    RF02541   hmm     1997     2443        1      439      +     -    6 0.54   0.3  319.5   7.3e-94 !   -
+contig--2250883      -         LSU_rRNA_bacteria    RF02541   hmm     2524     2912      396        4      -     -    6 0.54   0.1  317.4   3.2e-93 !   -
+contig--2220335      -         LSU_rRNA_bacteria    RF02541   hmm     1588     1992      423        1      -     -    6 0.49   0.1  316.5   5.7e-93 !   -
+contig--1082627      -         LSU_rRNA_bacteria    RF02541   hmm     2498     2842        1      334      +     -    6 0.54   0.1  314.4   2.6e-92 !   -
+contig--363016       -         LSU_rRNA_bacteria    RF02541   hmm        2      529      480        3      -     -    6 0.46   5.5  313.8   3.8e-92 !   -
+contig--2564558      -         LSU_rRNA_bacteria    RF02541   hmm      467      889        1      417      +     -    6 0.44   0.9  308.9   1.2e-90 !   -
+contig--3317407      -         LSU_rRNA_bacteria    RF02541   hmm       10      537      283      754      +     -    6 0.46   4.0  307.9   2.4e-90 !   -
+contig--2918607      -         LSU_rRNA_bacteria    RF02541   hmm      440      876      431        7      -     -    6 0.47   2.0  304.5   2.4e-89 !   -
+contig--1407263      -         LSU_rRNA_bacteria    RF02541   hmm      900     1395      490        2      -     -    6 0.45   0.3  298.9   1.2e-87 !   -
+contig--2152327      -         LSU_rRNA_bacteria    RF02541   hmm     1316     1865        3      582      +     -    6 0.50   0.6  294.4   2.7e-86 !   -
+contig--2874819      -         LSU_rRNA_bacteria    RF02541   hmm     1957     2315      359        1      -     -    6 0.57   0.0  294.0   3.6e-86 !   -
+contig--3694746      -         LSU_rRNA_bacteria    RF02541   hmm      488      874      382        1      -     -    6 0.49   1.2  293.6   4.9e-86 !   -
+contig--2254400      -         LSU_rRNA_bacteria    RF02541   hmm     2569     2912      341        9      -     -    6 0.54   0.2  288.8   1.4e-84 !   -
+contig--2304422      -         LSU_rRNA_bacteria    RF02541   hmm        2      509      464        1      -     -    6 0.53   1.7  285.0   1.8e-83 !   -
+contig--32925        -         LSU_rRNA_bacteria    RF02541   hmm     1417     1940        2      551      +     -    6 0.52   1.4  280.8   3.5e-82 !   -
+contig--2646754      -         LSU_rRNA_bacteria    RF02541   hmm     1125     1730        1      592      +     -    6 0.51   2.9  275.6   1.2e-80 !   -
+contig--2652964      -         LSU_rRNA_bacteria    RF02541   hmm     1399     1893      513        4      -     -    6 0.49   0.3  269.2   1.1e-78 !   -
+contig--1768180      -         LSU_rRNA_bacteria    RF02541   hmm     2563     2922        1      349      +     -    6 0.52   0.1  268.8   1.4e-78 !   -
+contig--1688622      -         LSU_rRNA_bacteria    RF02541   hmm     2054     2429      378        3      -     -    6 0.51   0.0  268.7   1.5e-78 !   -
+contig--185811       -         LSU_rRNA_bacteria    RF02541   hmm     1159     1688      526        2      -     -    6 0.49   1.3  268.3     2e-78 !   -
+contig--2805328      -         LSU_rRNA_bacteria    RF02541   hmm     2562     2920        1      361      +     -    6 0.57   0.1  268.2   2.2e-78 !   -
+contig--2701305      -         LSU_rRNA_bacteria    RF02541   hmm     1378     1893        1      499      +     -    6 0.53   1.9  266.7   6.3e-78 !   -
+contig--332136       -         LSU_rRNA_bacteria    RF02541   hmm     2507     2818      322        9      -     -    6 0.56   0.2  263.7   4.9e-77 !   -
+contig--759897       -         LSU_rRNA_bacteria    RF02541   hmm     2581     2910        1      318      +     -    6 0.53   0.1  263.6   5.3e-77 !   -
+contig--2713352      -         LSU_rRNA_bacteria    RF02541   hmm     1266     1758      507        7      -     -    6 0.51   2.3  262.0   1.6e-76 !   -
+contig--747483       -         LSU_rRNA_bacteria    RF02541   hmm     2559     2899      332        2      -     -    6 0.51   0.0  258.7   1.6e-75 !   -
+contig--147097       -         LSU_rRNA_bacteria    RF02541   hmm     2588     2911        2      333      +     -    6 0.51   0.0  256.0     1e-74 !   -
+contig--95399        -         LSU_rRNA_bacteria    RF02541   hmm     2591     2923        1      336      +     -    6 0.53   0.3  253.9   4.4e-74 !   -
+contig--2680413      -         LSU_rRNA_bacteria    RF02541   hmm       15      498      443        1      -     -    6 0.44   0.8  252.2   1.4e-73 !   -
+contig--3748912      -         LSU_rRNA_bacteria    RF02541   hmm      601      969      376        5      -     -    6 0.47   0.2  250.2   5.8e-73 !   -
+contig--362412       -         LSU_rRNA_bacteria    RF02541   hmm      149      551      444        2      -     -    6 0.43   4.3  246.6   7.2e-72 !   -
+contig--2254163      -         LSU_rRNA_bacteria    RF02541   hmm        4      486      462        1      -     -    6 0.40   2.6  243.0   8.9e-71 !   -
+contig--2835645      -         LSU_rRNA_bacteria    RF02541   hmm     2588     2883      306        3      -     -    6 0.52   0.1  242.7   1.1e-70 !   -
+contig--1796896      -         LSU_rRNA_bacteria    RF02541   hmm     2595     2906        1      300      +     -    6 0.49   0.1  242.6   1.1e-70 !   -
+contig--942031       -         LSU_rRNA_bacteria    RF02541   hmm     2566     2881      307        3      -     -    6 0.54   0.1  240.5   4.8e-70 !   -
+contig--36603        -         LSU_rRNA_bacteria    RF02541   hmm      179      543        2      411      +     -    6 0.54   1.8  238.2   2.3e-69 !   -
+contig--724357       -         LSU_rRNA_bacteria    RF02541   hmm      989     1339        3      348      +     -    6 0.49   0.8  236.5     8e-69 !   -
+contig--2298625      -         LSU_rRNA_bacteria    RF02541   hmm     2215     2811     1029      431      -     -    6 0.46   0.0  226.8   6.5e-66 !   -
+contig--2519402      -         LSU_rRNA_bacteria    RF02541   hmm       28      464      424        2      -     -    6 0.45   1.2  226.6   7.5e-66 !   -
+contig--2254733      -         LSU_rRNA_bacteria    RF02541   hmm      841     1231      396        2      -     -    6 0.34   0.0  226.4   8.5e-66 !   -
+contig--1458589      -         LSU_rRNA_bacteria    RF02541   hmm      811     1128        2      316      +     -    6 0.56   0.3  226.4     9e-66 !   -
+contig--2250342      -         LSU_rRNA_bacteria    RF02541   hmm      532     1122        1      587      +     -    6 0.40   1.3  224.8   2.6e-65 !   -
+contig--236053       -         LSU_rRNA_bacteria    RF02541   hmm       18      460      401        2      -     -    6 0.47   1.3  224.4   3.5e-65 !   -
+contig--1176662      -         LSU_rRNA_bacteria    RF02541   hmm     2436     2727        2      293      +     -    6 0.49   0.0  222.3   1.5e-64 !   -
+contig--3433834      -         LSU_rRNA_bacteria    RF02541   hmm     1353     1822        1      490      +     -    6 0.47   0.1  221.6   2.5e-64 !   -
+contig--547077       -         LSU_rRNA_bacteria    RF02541   hmm      835     1141      307        1      -     -    6 0.50   0.1  218.3   2.4e-63 !   -
+contig--3652281      -         LSU_rRNA_bacteria    RF02541   hmm     2000     2320      311        2      -     -    6 0.56   0.0  217.0   5.9e-63 !   -
+contig--1042219      -         LSU_rRNA_bacteria    RF02541   hmm     2100     2435      339        2      -     -    6 0.55   0.5  215.9   1.3e-62 !   -
+contig--365471       -         LSU_rRNA_bacteria    RF02541   hmm     1928     2274        1      349      +     -    6 0.47   0.0  214.1   4.5e-62 !   -
+contig--3054101      -         LSU_rRNA_bacteria    RF02541   hmm     2236     2798       17      576      +     -    6 0.47   0.0  211.4   2.9e-61 !   -
+contig--2251329      -         LSU_rRNA_bacteria    RF02541   hmm     2596     2906        1      313      +     -    6 0.46   0.0  210.9     4e-61 !   -
+contig--3890060      -         LSU_rRNA_bacteria    RF02541   hmm       35      469      364        1      -     -    6 0.48   0.9  208.6   2.1e-60 !   -
+contig--1326571      -         LSU_rRNA_bacteria    RF02541   hmm      661      957        3      300      +     -    6 0.51   0.0  208.3   2.6e-60 !   -
+contig--3652175      -         LSU_rRNA_bacteria    RF02541   hmm      576      875      302        2      -     -    6 0.48   0.1  206.5   8.9e-60 !   -
+contig--261342       -         LSU_rRNA_bacteria    RF02541   hmm     2434     2718        3      286      +     -    6 0.39   0.0  205.2   2.1e-59 !   -
+contig--2906201      -         LSU_rRNA_bacteria    RF02541   hmm      851     1151      304        1      -     -    6 0.43   0.0  201.2   3.4e-58 !   -
+contig--2501086      -         LSU_rRNA_bacteria    RF02541   hmm      439      830        3      390      +     -    6 0.39   0.5  199.8   8.9e-58 !   -
+contig--1215349      -         LSU_rRNA_bacteria    RF02541   hmm      840     1167      332        1      -     -    6 0.52   0.1  196.5   8.9e-57 !   -
+contig--1210202      -         LSU_rRNA_bacteria    RF02541   hmm      425      826      390        1      -     -    6 0.42   0.7  195.9   1.4e-56 !   -
+contig--2767514      -         LSU_rRNA_bacteria    RF02541   hmm     1990     2299      310        1      -     -    6 0.45   0.0  194.1     5e-56 !   -
+contig--2543224      -         LSU_rRNA_bacteria    RF02541   hmm        3      370      322        1      -     -    6 0.49   0.8  191.1   3.9e-55 !   -
+contig--1111206      -         LSU_rRNA_bacteria    RF02541   hmm       84      472      360        2      -     -    6 0.42   1.9  190.5   5.9e-55 !   -
+contig--4068604      -         LSU_rRNA_bacteria    RF02541   hmm     1081     1675        6      562      +     -    6 0.53   2.7  188.7   2.1e-54 !   -
+contig--365125       -         LSU_rRNA_bacteria    RF02541   hmm     2292     2801      622      116      -     -    6 0.45   0.0  180.6   5.6e-52 !   -
+contig--2673585      -         LSU_rRNA_bacteria    RF02541   hmm      188      518      374        1      -     -    6 0.42   0.9  178.7   2.2e-51 !   -
+contig--1031478      -         LSU_rRNA_bacteria    RF02541   hmm     1347     1717      372        1      -     -    6 0.54   0.5  177.9   3.7e-51 !   -
+contig--3925448      -         LSU_rRNA_bacteria    RF02541   hmm      331      688       27      367      +     -    6 0.38   2.2  176.2   1.2e-50 !   -
+contig--473422       -         LSU_rRNA_bacteria    RF02541   hmm       31      377      326        1      -     -    6 0.56   2.1  173.0   1.1e-49 !   -
+contig--3889622      -         LSU_rRNA_bacteria    RF02541   hmm      775     1097        1      329      +     -    6 0.45   0.3  171.2     4e-49 !   -
+contig--2983248      -         LSU_rRNA_bacteria    RF02541   hmm      215      538      316        1      -     -    6 0.42   0.5  161.3   3.7e-46 !   -
+contig--2893879      -         LSU_rRNA_bacteria    RF02541   hmm     1338     1700        1      370      +     -    6 0.49   0.1  160.6     6e-46 !   -
+contig--332136       -         LSU_rRNA_bacteria    RF02541   hmm     2475     2631      487      331      -     -    6 0.58   0.0  159.7   1.1e-45 !   -
+contig--669436       -         LSU_rRNA_bacteria    RF02541   hmm     1390     1751      368        2      -     -    6 0.47   0.2  158.7   2.3e-45 !   -
+contig--364298       -         LSU_rRNA_bacteria    RF02541   hmm      830     1415        1      615      +     -    6 0.29   0.0  154.7   3.7e-44 !   -
+contig--3494982      -         LSU_rRNA_bacteria    RF02541   hmm      817     1183        9      377      +     -    6 0.39   0.2  149.3   1.6e-42 !   -
+contig--2255132      -         LSU_rRNA_bacteria    RF02541   hmm       52      455        1      396      +     -    6 0.39   0.5  147.4   5.9e-42 !   -
+contig--363340       -         LSU_rRNA_bacteria    RF02541   hmm      459      898        7      412      +     -    6 0.32   0.1  145.5   2.1e-41 !   -
+contig--3414648      -         LSU_rRNA_bacteria    RF02541   hmm     1952     2209      165      423      +     -    6 0.47   0.0  145.4   2.3e-41 !   -
+contig--2575573      -         LSU_rRNA_bacteria    RF02541   hmm     1006     1759       23      831      +     -    6 0.47   0.1  142.5   1.7e-40 !   -
+contig--3176110      -         LSU_rRNA_bacteria    RF02541   hmm     2231     2591       39      400      +     -    6 0.45   0.0  133.1   1.2e-37 !   -
+contig--2968284      -         LSU_rRNA_bacteria    RF02541   hmm     1346     1681      333        2      -     -    6 0.51   0.1  133.0   1.3e-37 !   -
+contig--579351       -         LSU_rRNA_bacteria    RF02541   hmm     1147     1689        1      450      +     -    6 0.38   0.1  131.8   2.9e-37 !   -
+contig--1213982      -         LSU_rRNA_bacteria    RF02541   hmm     1847     2358      561        2      -     -    6 0.51   0.0  131.0   5.2e-37 !   -
+contig--2252346      -         LSU_rRNA_bacteria    RF02541   hmm     1962     2522        3      628      +     -    6 0.54   0.1  129.3   1.7e-36 !   -
+contig--2945976      -         LSU_rRNA_bacteria    RF02541   hmm     1371     1702        2      337      +     -    6 0.49   0.1  129.3   1.7e-36 !   -
+contig--2252661      -         LSU_rRNA_bacteria    RF02541   hmm      208      559      775      405      -     -    6 0.49   0.0  126.8   9.8e-36 !   -
+contig--151751       -         LSU_rRNA_bacteria    RF02541   hmm      173      561      594      199      -     -    6 0.47   0.4  126.3   1.4e-35 !   -
+contig--2722470      -         LSU_rRNA_bacteria    RF02541   hmm      178      535        3      372      +     -    6 0.51   0.5  124.1   6.4e-35 !   -
+contig--2254060      -         LSU_rRNA_bacteria    RF02541   hmm     1958     2510      627        2      -     -    6 0.47   0.0  123.7   8.3e-35 !   -
+contig--3158861      -         LSU_rRNA_bacteria    RF02541   hmm     1361     1684      329        1      -     -    6 0.48   0.2  119.7   1.3e-33 !   -
+contig--3299936      -         LSU_rRNA_bacteria    RF02541   hmm     1009     1373        8      394      +     -    6 0.38   0.0  119.2   1.8e-33 !   -
+contig--1276363      -         LSU_rRNA_bacteria    RF02541   hmm     1114     1445        3      334      +     -    6 0.27   0.0  117.5     6e-33 !   -
+contig--585322       -         LSU_rRNA_bacteria    RF02541   hmm     1365     1677        1      310      +     -    6 0.52   0.1  116.2   1.5e-32 !   -
+contig--185298       -         LSU_rRNA_bacteria    RF02541   hmm      208      572        2      371      +     -    6 0.42   1.0  113.8   8.2e-32 !   -
+contig--1662509      -         LSU_rRNA_bacteria    RF02541   hmm     1090     1683        2      643      +     -    6 0.52   0.1  113.6   9.2e-32 !   -
+contig--365284       -         LSU_rRNA_bacteria    RF02541   hmm      205      591      547      154      -     -    6 0.47   1.1  111.0   5.6e-31 !   -
+contig--2251064      -         LSU_rRNA_bacteria    RF02541   hmm      211      581        4      377      +     -    6 0.46   0.6  109.6   1.5e-30 !   -
+contig--2254317      -         LSU_rRNA_bacteria    RF02541   hmm      190      543      362        2      -     -    6 0.45   0.4  109.5   1.6e-30 !   -
+contig--1596054      -         LSU_rRNA_bacteria    RF02541   hmm      814     1342      602       20      -     -    6 0.49   0.3  105.8     2e-29 !   -
+contig--185562       -         LSU_rRNA_bacteria    RF02541   hmm      850     1478      789       83      -     -    6 0.52   0.8  105.1   3.3e-29 !   -
+contig--2250797      -         LSU_rRNA_bacteria    RF02541   hmm      177      524      360        3      -     -    6 0.48   0.4  104.6   4.6e-29 !   -
+contig--363861       -         LSU_rRNA_bacteria    RF02541   hmm      704     1146      488        3      -     -    6 0.47   0.3  103.2   1.3e-28 !   -
+contig--1214754      -         LSU_rRNA_bacteria    RF02541   hmm      217      561      512      170      -     -    6 0.38   0.4  102.2   2.5e-28 !   -
+contig--362625       -         LSU_rRNA_bacteria    RF02541   hmm     2489     2806        6      321      +     -    6 0.42   0.0  101.4   4.3e-28 !   -
+contig--1214513      -         LSU_rRNA_bacteria    RF02541   hmm      208      543        3      346      +     -    6 0.54   2.0   97.2   8.3e-27 !   -
+contig--3354354      -         LSU_rRNA_bacteria    RF02541   hmm      703     1142      491        2      -     -    6 0.53   0.2   96.4   1.4e-26 !   -
+contig--130023       -         LSU_rRNA_bacteria    RF02541   hmm      232      591      682      313      -     -    6 0.51   0.0   92.4   2.3e-25 !   -
+contig--2249544      -         LSU_rRNA_bacteria    RF02541   hmm     2079     2480      424        2      -     -    6 0.44   0.0   92.3   2.4e-25 !   -
+contig--97491        -         LSU_rRNA_bacteria    RF02541   hmm     2116     2510        7      423      +     -    6 0.46   0.0   92.2   2.6e-25 !   -
+contig--1214168      -         LSU_rRNA_bacteria    RF02541   hmm      190      515        3      333      +     -    6 0.47   0.3   91.6   3.9e-25 !   -
+contig--2412452      -         LSU_rRNA_bacteria    RF02541   hmm     1782     2046       71      319      +     -    6 0.45   0.0   87.3     8e-24 !   -
+contig--94612        -         LSU_rRNA_bacteria    RF02541   hmm       24      518       79      500      +     -    6 0.28   0.3   87.3   8.1e-24 !   -
+contig--110110       -         LSU_rRNA_bacteria    RF02541   hmm      178      492        7      322      +     -    6 0.42   0.8   83.2   1.3e-22 !   -
+contig--3535542      -         LSU_rRNA_bacteria    RF02541   hmm     2763     2922        1      148      +     -    6 0.48   0.0   83.2   1.3e-22 !   -
+contig--101864       -         LSU_rRNA_bacteria    RF02541   hmm      196      509      307        1      -     -    6 0.48   0.1   82.5   2.2e-22 !   -
+contig--2251392      -         LSU_rRNA_bacteria    RF02541   hmm     1306     1885        1      736      +     -    6 0.52   0.6   81.7   3.8e-22 !   -
+contig--1692849      -         LSU_rRNA_bacteria    RF02541   hmm     2078     2374       25      333      +     -    6 0.44   0.0   79.9   1.4e-21 !   -
+contig--3655473      -         LSU_rRNA_bacteria    RF02541   hmm      850     1302      509        5      -     -    6 0.51   0.1   78.4   3.7e-21 !   -
+contig--3320537      -         LSU_rRNA_bacteria    RF02541   hmm     2766     2921        1      157      +     -    6 0.40   0.0   78.2   4.4e-21 !   -
+contig--2250093      -         LSU_rRNA_bacteria    RF02541   hmm     2002     2426      483       20      -     -    6 0.47   0.0   76.7   1.2e-20 !   -
+contig--1214182      -         LSU_rRNA_bacteria    RF02541   hmm     1461     1719      258        1      -     -    6 0.55   0.1   76.3   1.6e-20 !   -
+contig--1212351      -         LSU_rRNA_bacteria    RF02541   hmm      177      494      323        1      -     -    6 0.54   0.2   75.1   3.8e-20 !   -
+contig--1214394      -         LSU_rRNA_bacteria    RF02541   hmm     2556     2805      410      163      -     -    6 0.49   0.0   74.2     7e-20 !   -
+contig--518767       -         LSU_rRNA_bacteria    RF02541   hmm      427      583       55      210      +     -    6 0.42   0.0   72.9   1.8e-19 !   -
+contig--2255353      -         LSU_rRNA_bacteria    RF02541   hmm     1321     1762        9      506      +     -    6 0.54   0.1   72.3   2.7e-19 !   -
+contig--2528721      -         LSU_rRNA_bacteria    RF02541   hmm     2572     2823        2      281      +     -    6 0.56   0.0   72.1     3e-19 !   -
+contig--2937145      -         LSU_rRNA_bacteria    RF02541   hmm     2556     2822       15      283      +     -    6 0.49   0.0   70.7   7.9e-19 !   -
+contig--1793538      -         LSU_rRNA_bacteria    RF02541   hmm      438      750      284        2      -     -    6 0.29   0.1   67.3   8.6e-18 !   -
+contig--2251231      -         LSU_rRNA_bacteria    RF02541   hmm     2594     2808      461      249      -     -    6 0.47   0.0   63.5   1.2e-16 !   -
+contig--2251849      -         LSU_rRNA_bacteria    RF02541   hmm     2593     2814        7      225      +     -    6 0.48   0.0   62.8     2e-16 !   -
+contig--257393       -         LSU_rRNA_bacteria    RF02541   hmm     1142     1671      590        4      -     -    6 0.60   0.5   62.6   2.2e-16 !   -
+contig--1159799      -         LSU_rRNA_bacteria    RF02541   hmm     2590     2819      373      147      -     -    6 0.48   0.0   61.3   5.4e-16 !   -
+contig--3019708      -         LSU_rRNA_bacteria    RF02541   hmm     1132     1682      608        7      -     -    6 0.44   0.0   61.3   5.5e-16 !   -
+contig--2252145      -         LSU_rRNA_bacteria    RF02541   hmm     2585     2823        2      296      +     -    6 0.48   0.0   59.9   1.4e-15 !   -
+contig--1212661      -         LSU_rRNA_bacteria    RF02541   hmm     2599     2803        1      204      +     -    6 0.51   0.0   59.0   2.7e-15 !   -
+contig--68307        -         LSU_rRNA_bacteria    RF02541   hmm      233      529        2      308      +     -    6 0.42   0.0   58.6   3.6e-15 !   -
+contig--1133023      -         LSU_rRNA_bacteria    RF02541   hmm     1416     1756       14      389      +     -    6 0.53   0.0   56.3   1.7e-14 !   -
+contig--3875044      -         LSU_rRNA_bacteria    RF02541   hmm       80      379       59      354      +     -    6 0.44   0.0   56.2   1.8e-14 !   -
+contig--2255543      -         LSU_rRNA_bacteria    RF02541   hmm     2596     2820        2      223      +     -    6 0.48   0.0   56.2   1.8e-14 !   -
+contig--1007451      -         LSU_rRNA_bacteria    RF02541   hmm     2078     2337       21      307      +     -    6 0.50   0.0   55.5   3.1e-14 !   -
+contig--1437319      -         LSU_rRNA_bacteria    RF02541   hmm      699      882      197       13      -     -    6 0.51   0.1   55.2   3.8e-14 !   -
+contig--185227       -         LSU_rRNA_bacteria    RF02541   hmm     1124     1407      300       11      -     -    6 0.52   0.4   54.8   4.9e-14 !   -
+contig--2741341      -         LSU_rRNA_bacteria    RF02541   hmm     1378     1755        1      420      +     -    6 0.51   0.0   53.9   9.2e-14 !   -
+contig--3290892      -         LSU_rRNA_bacteria    RF02541   hmm     1346     1749       29      486      +     -    6 0.47   0.1   53.5   1.2e-13 !   -
+contig--496748       -         LSU_rRNA_bacteria    RF02541   hmm      197      475        2      296      +     -    6 0.55   0.1   51.7   4.3e-13 !   -
+contig--2250940      -         LSU_rRNA_bacteria    RF02541   hmm       25      272      251      748      +     -    6 0.53   0.0   50.7   8.8e-13 !   -
+contig--2506583      -         SSU_rRNA_microsporidia RF02542   hmm      373     1309       10     1041      +     -    6 0.54   0.9  392.9  1.7e-115 !   -
+contig--3276943      -         SSU_rRNA_microsporidia RF02542   hmm      520     1311     2360     1448      -     -    6 0.45   0.5  355.4  3.9e-104 !   -
+contig--2491978      -         SSU_rRNA_microsporidia RF02542   hmm        6      942     1024        3      -     -    6 0.54   1.3  354.2  8.4e-104 !   -
+contig--151527       -         SSU_rRNA_microsporidia RF02542   hmm       26      652      943        2      -     -    6 0.41   3.9  296.3   2.7e-86 !   -
+contig--2514811      -         SSU_rRNA_microsporidia RF02542   hmm      226      769        2      746      +     -    6 0.46   2.3  275.6   5.1e-80 !   -
+contig--363170       -         SSU_rRNA_microsporidia RF02542   hmm      107      658      844        2      -     -    6 0.46   2.7  257.6   1.3e-74 !   -
+contig--186013       -         SSU_rRNA_microsporidia RF02542   hmm      272      797      744        2      -     -    6 0.44   4.0  252.4   5.3e-73 !   -
+contig--912998       -         SSU_rRNA_microsporidia RF02542   hmm      634     1210        2      664      +     -    6 0.55   0.0  240.1   2.7e-69 !   -
+contig--2726048      -         SSU_rRNA_microsporidia RF02542   hmm       50      593        2      869      +     -    6 0.47   0.4  239.5   4.2e-69 !   -
+contig--2565011      -         SSU_rRNA_microsporidia RF02542   hmm       26      446      586        1      -     -    6 0.46   0.0  232.8   4.5e-67 !   -
+contig--364625       -         SSU_rRNA_microsporidia RF02542   hmm       27      833      939        4      -     -    6 0.51   4.6  215.3   8.5e-62 !   -
+contig--3568828      -         SSU_rRNA_microsporidia RF02542   hmm      253      861      664       13      -     -    6 0.55   1.3  206.7   3.4e-59 !   -
+contig--2252003      -         SSU_rRNA_microsporidia RF02542   hmm      391      812        1      609      +     -    6 0.43   1.9  202.8   5.1e-58 !   -
+contig--813107       -         SSU_rRNA_microsporidia RF02542   hmm      379      846        8      487      +     -    6 0.55   0.6  198.7   8.9e-57 !   -
+contig--2914153      -         SSU_rRNA_microsporidia RF02542   hmm      123      814      796        1      -     -    6 0.49   4.9  198.1   1.3e-56 !   -
+contig--2255364      -         SSU_rRNA_microsporidia RF02542   hmm      271      943      755        2      -     -    6 0.52   3.0  192.1   8.6e-55 !   -
+contig--2369838      -         SSU_rRNA_microsporidia RF02542   hmm       65      815       14      854      +     -    6 0.51   6.0  188.6   9.6e-54 !   -
+contig--2552028      -         SSU_rRNA_microsporidia RF02542   hmm      376      786        1      589      +     -    6 0.45   2.0  175.6   8.5e-50 !   -
+contig--2248828      -         SSU_rRNA_microsporidia RF02542   hmm      405      804      581        2      -     -    6 0.43   3.9  173.8     3e-49 !   -
+contig--1568447      -         SSU_rRNA_microsporidia RF02542   hmm      252      843       27      681      +     -    6 0.52   4.1  172.0     1e-48 !   -
+contig--2249925      -         SSU_rRNA_microsporidia RF02542   hmm       28      791       17      898      +     -    6 0.51   5.8  169.7   5.2e-48 !   -
+contig--2254313      -         SSU_rRNA_microsporidia RF02542   hmm      524      852      347        3      -     -    6 0.52   0.1  166.5   4.8e-47 !   -
+contig--1604373      -         SSU_rRNA_microsporidia RF02542   hmm      869     1199       14      423      +     -    6 0.47   0.0  164.0   2.8e-46 !   -
+contig--2271497      -         SSU_rRNA_microsporidia RF02542   hmm        8      694      826        3      -     -    6 0.51   3.6  159.2   7.8e-45 !   -
+contig--978828       -         SSU_rRNA_microsporidia RF02542   hmm      774     1059      341        2      -     -    6 0.45   0.0  157.5   2.5e-44 !   -
+contig--3420575      -         SSU_rRNA_microsporidia RF02542   hmm       49      395      503        1      -     -    6 0.44   0.0  157.1   3.2e-44 !   -
+contig--498568       -         SSU_rRNA_microsporidia RF02542   hmm      773     1203      515       12      -     -    6 0.53   0.0  153.4   4.2e-43 !   -
+contig--232952       -         SSU_rRNA_microsporidia RF02542   hmm      414      795        2      570      +     -    6 0.51   0.3  150.8   2.7e-42 !   -
+contig--2969992      -         SSU_rRNA_microsporidia RF02542   hmm      381      832       30      488      +     -    6 0.51   0.9  148.4   1.5e-41 !   -
+contig--2251500      -         SSU_rRNA_microsporidia RF02542   hmm      803     1201        1      473      +     -    6 0.52   0.0  143.2   5.2e-40 !   -
+contig--3474644      -         SSU_rRNA_microsporidia RF02542   hmm        6      643       57      832      +     -    6 0.51   3.4  140.3   3.9e-39 !   -
+contig--1720439      -         SSU_rRNA_microsporidia RF02542   hmm      240      783        8      611      +     -    6 0.48   2.4  139.9   5.3e-39 !   -
+contig--365127       -         SSU_rRNA_microsporidia RF02542   hmm      280      796      566        7      -     -    6 0.55   0.8  139.6   6.6e-39 !   -
+contig--2253688      -         SSU_rRNA_microsporidia RF02542   hmm        4      301      442        1      -     -    6 0.40   0.0  139.4   7.5e-39 !   -
+contig--3787593      -         SSU_rRNA_microsporidia RF02542   hmm      364      810      125      584      +     -    6 0.52   1.4  137.7   2.4e-38 !   -
+contig--3348019      -         SSU_rRNA_microsporidia RF02542   hmm     1012     1311        1      376      +     -    6 0.47   0.0  135.0   1.6e-37 !   -
+contig--2249727      -         SSU_rRNA_microsporidia RF02542   hmm      995     1283        5      352      +     -    6 0.48   0.0  134.9   1.6e-37 !   -
+contig--401056       -         SSU_rRNA_microsporidia RF02542   hmm      884     1309       16      518      +     -    6 0.53   0.0  133.0   6.5e-37 !   -
+contig--2972876      -         SSU_rRNA_microsporidia RF02542   hmm      257      795      613        8      -     -    6 0.52   2.1  132.9   6.7e-37 !   -
+contig--1379481      -         SSU_rRNA_microsporidia RF02542   hmm       29      299        1      405      +     -    6 0.36   0.0  132.4   9.9e-37 !   -
+contig--1029476      -         SSU_rRNA_microsporidia RF02542   hmm      752     1149      217      698      +     -    6 0.44   0.1  130.8     3e-36 !   -
+contig--363722       -         SSU_rRNA_microsporidia RF02542   hmm      323      794      487        2      -     -    6 0.50   1.3  129.9   5.7e-36 !   -
+contig--314729       -         SSU_rRNA_microsporidia RF02542   hmm      789     1064      337        3      -     -    6 0.56   0.0  129.7   6.2e-36 !   -
+contig--1346273      -         SSU_rRNA_microsporidia RF02542   hmm      627      965      371        6      -     -    6 0.54   0.0  129.1   9.4e-36 !   -
+contig--2252644      -         SSU_rRNA_microsporidia RF02542   hmm        5      689       45      785      +     -    6 0.48   3.4  122.0   1.4e-33 !   -
+contig--1001177      -         SSU_rRNA_microsporidia RF02542   hmm      531      832       12      319      +     -    6 0.52   0.8  121.6   1.8e-33 !   -
+contig--1776240      -         SSU_rRNA_microsporidia RF02542   hmm      785     1172      463        2      -     -    6 0.53   0.0  119.1     1e-32 !   -
+contig--30742        -         SSU_rRNA_microsporidia RF02542   hmm       36      286        2      393      +     -    6 0.41   0.0  115.7   1.1e-31 !   -
+contig--3461222      -         SSU_rRNA_microsporidia RF02542   hmm       38      406       20      522      +     -    6 0.43   0.0  115.3   1.4e-31 !   -
+contig--256048       -         SSU_rRNA_microsporidia RF02542   hmm      277      469        1      224      +     -    6 0.44   0.0  114.7   2.1e-31 !   -
+contig--1210200      -         SSU_rRNA_microsporidia RF02542   hmm      390      783      405        3      -     -    6 0.44   1.5  113.2   6.2e-31 !   -
+contig--363016       -         SSU_rRNA_microsporidia RF02542   hmm      973     1309     1129      748      -     -    6 0.53   0.0  109.4   8.9e-30 !   -
+contig--1171145      -         SSU_rRNA_microsporidia RF02542   hmm       26      267        6      365      +     -    6 0.41   0.0  106.8   5.3e-29 !   -
+contig--3076204      -         SSU_rRNA_microsporidia RF02542   hmm       71      577       12      598      +     -    6 0.52   1.1  104.8   2.1e-28 !   -
+contig--828224       -         SSU_rRNA_microsporidia RF02542   hmm      153      618       20      519      +     -    6 0.59   2.1  101.9   1.6e-27 !   -
+contig--2248804      -         SSU_rRNA_microsporidia RF02542   hmm      903     1209      165      517      +     -    6 0.47   0.0   99.4   9.2e-27 !   -
+contig--2253054      -         SSU_rRNA_microsporidia RF02542   hmm      275      679        5      445      +     -    6 0.56   0.6   97.4   3.7e-26 !   -
+contig--2251634      -         SSU_rRNA_microsporidia RF02542   hmm       26      257      372        1      -     -    6 0.43   0.0   94.7   2.4e-25 !   -
+contig--2766474      -         SSU_rRNA_microsporidia RF02542   hmm      994     1308      408       48      -     -    6 0.52   0.0   94.4   3.1e-25 !   -
+contig--3013908      -         SSU_rRNA_microsporidia RF02542   hmm      906     1156      326        2      -     -    6 0.44   0.0   92.4   1.2e-24 !   -
+contig--185316       -         SSU_rRNA_microsporidia RF02542   hmm      935     1169        4      310      +     -    6 0.50   0.0   92.1   1.5e-24 !   -
+contig--862423       -         SSU_rRNA_microsporidia RF02542   hmm      809     1154        3      422      +     -    6 0.52   0.0   91.9   1.7e-24 !   -
+contig--258486       -         SSU_rRNA_microsporidia RF02542   hmm      973     1288       16      376      +     -    6 0.56   0.0   88.8   1.4e-23 !   -
+contig--3889059      -         SSU_rRNA_microsporidia RF02542   hmm      372      681       92      411      +     -    6 0.55   0.3   88.3   2.1e-23 !   -
+contig--24391        -         SSU_rRNA_microsporidia RF02542   hmm      395      695      311        9      -     -    6 0.50   0.7   86.2   8.9e-23 !   -
+contig--3286658      -         SSU_rRNA_microsporidia RF02542   hmm        6      463      576        4      -     -    6 0.50   0.1   85.9   1.1e-22 !   -
+contig--298893       -         SSU_rRNA_microsporidia RF02542   hmm        7      463       35      604      +     -    6 0.51   1.0   84.4   3.2e-22 !   -
+contig--594041       -         SSU_rRNA_microsporidia RF02542   hmm       41      305       10      315      +     -    6 0.54   0.0   83.8   4.7e-22 !   -
+contig--1149779      -         SSU_rRNA_microsporidia RF02542   hmm     1084     1309      257        3      -     -    6 0.51   0.0   82.9   8.8e-22 !   -
+contig--3096224      -         SSU_rRNA_microsporidia RF02542   hmm      473      675      104      305      +     -    6 0.47   0.2   81.5   2.4e-21 !   -
+contig--152048       -         SSU_rRNA_microsporidia RF02542   hmm       27      464      555        4      -     -    6 0.53   0.8   75.1     2e-19 !   -
+contig--1192886      -         SSU_rRNA_microsporidia RF02542   hmm      898     1171      330        2      -     -    6 0.49   0.0   75.1     2e-19 !   -
+contig--1531838      -         SSU_rRNA_microsporidia RF02542   hmm      785     1054      313        3      -     -    6 0.50   0.0   74.6   2.9e-19 !   -
+contig--696001       -         SSU_rRNA_microsporidia RF02542   hmm        5      457       74      626      +     -    6 0.49   0.2   74.4   3.2e-19 !   -
+contig--3093712      -         SSU_rRNA_microsporidia RF02542   hmm      587      788        3      213      +     -    6 0.56   0.0   74.3   3.7e-19 !   -
+contig--2889438      -         SSU_rRNA_microsporidia RF02542   hmm      906     1178      334        4      -     -    6 0.50   0.0   73.0   8.5e-19 !   -
+contig--3503719      -         SSU_rRNA_microsporidia RF02542   hmm      967     1203      308       15      -     -    6 0.51   0.0   69.6   9.2e-18 !   -
+contig--1634977      -         SSU_rRNA_microsporidia RF02542   hmm      901     1157        1      313      +     -    6 0.55   0.0   69.4   1.1e-17 !   -
+contig--3837490      -         SSU_rRNA_microsporidia RF02542   hmm       43      362      388       10      -     -    6 0.48   0.2   66.8   6.6e-17 !   -
+contig--3575278      -         SSU_rRNA_microsporidia RF02542   hmm     1136     1309        2      184      +     -    6 0.54   0.0   62.1   1.7e-15 !   -
+contig--2693087      -         SSU_rRNA_microsporidia RF02542   hmm        6      266      139      428      +     -    6 0.53   0.0   61.8   2.1e-15 !   -
+contig--193617       -         SSU_rRNA_microsporidia RF02542   hmm      835     1070      305       53      -     -    6 0.54   0.0   61.4   2.8e-15 !   -
+contig--3128112      -         SSU_rRNA_microsporidia RF02542   hmm      519      820      312        6      -     -    6 0.48   0.3   61.2   3.3e-15 !   -
+contig--3093712      -         SSU_rRNA_microsporidia RF02542   hmm      556      694      218      355      +     -    6 0.57   0.0   61.0   3.6e-15 !   -
+contig--3153031      -         SSU_rRNA_microsporidia RF02542   hmm        5      306       49      380      +     -    6 0.54   0.1   60.4   5.7e-15 !   -
+contig--2618713      -         SSU_rRNA_microsporidia RF02542   hmm        6      266     1055     1383      +     -    6 0.53   0.0   59.2   1.3e-14 !   -
+contig--364755       -         SSU_rRNA_microsporidia RF02542   hmm      414      639        2      395      +     -    6 0.48   0.4   58.7   1.8e-14 !   -
+contig--2252860      -         SSU_rRNA_microsporidia RF02542   hmm        4      212        2      348      +     -    6 0.43   0.0   57.7   3.8e-14 !   -
+contig--984009       -         SSU_rRNA_microsporidia RF02542   hmm        5      219      277        2      -     -    6 0.46   0.0   53.2   8.5e-13 !   -
+contig--1211922      -         SSU_rRNA_microsporidia RF02542   hmm     1042     1229      300       86      -     -    6 0.40   0.0   52.4   1.5e-12 !   -
+contig--2298625      -         LSU_rRNA_eukarya     RF02543   hmm     2510     3391     1079      248      -     -    6 0.44   3.1  636.8  8.8e-190 !   -
+contig--2575573      -         LSU_rRNA_eukarya     RF02543   hmm     1125     1991        1      862      +     -    6 0.47   2.3  604.4  5.3e-180 !   -
+contig--1596054      -         LSU_rRNA_eukarya     RF02543   hmm      914     1513      603        2      -     -    6 0.49   0.4  537.8  6.4e-160 !   -
+contig--185562       -         LSU_rRNA_eukarya     RF02543   hmm      951     1732      789        3      -     -    6 0.52   0.0  528.0  5.7e-157 !   -
+contig--397992       -         LSU_rRNA_eukarya     RF02543   hmm      809     3160      754     2865      +     -    6 0.56   0.0  520.8  8.5e-155 !   -
+contig--2255353      -         LSU_rRNA_eukarya     RF02543   hmm     1466     2259        1      810      +     -    6 0.55   0.0  510.6    1e-151 !   -
+contig--365125       -         LSU_rRNA_eukarya     RF02543   hmm     2643     3208      623       59      -     -    6 0.45   0.3  510.5  1.1e-151 !   -
+contig--363861       -         LSU_rRNA_eukarya     RF02543   hmm      635     1294      665        2      -     -    6 0.48   0.3  503.9  1.1e-149 !   -
+contig--3054101      -         LSU_rRNA_eukarya     RF02543   hmm     2581     3154       11      583      +     -    6 0.47   0.1  489.9  1.7e-145 !   -
+contig--2251392      -         LSU_rRNA_eukarya     RF02543   hmm     1459     2243        1      753      +     -    6 0.52   0.0  472.3  3.5e-140 !   -
+contig--1662509      -         LSU_rRNA_eukarya     RF02543   hmm     1236     1889        1      648      +     -    6 0.53   0.0  468.7  4.2e-139 !   -
+contig--2254060      -         LSU_rRNA_eukarya     RF02543   hmm     2282     2863      627        1      -     -    6 0.47   0.1  450.7  1.1e-133 !   -
+contig--2252346      -         LSU_rRNA_eukarya     RF02543   hmm     2284     2880        1      634      +     -    6 0.54   0.0  444.0  1.3e-131 !   -
+contig--1213982      -         LSU_rRNA_eukarya     RF02543   hmm     2187     2711      561        1      -     -    6 0.51   0.0  435.9  3.4e-129 !   -
+contig--3354354      -         LSU_rRNA_eukarya     RF02543   hmm      682     1290      620        1      -     -    6 0.57   0.0  427.9  8.7e-127 !   -
+contig--156996       -         LSU_rRNA_eukarya     RF02543   hmm     2113     3190     1819      776      -     -    6 0.53   0.0  426.2  2.8e-126 !   -
+contig--3655473      -         LSU_rRNA_eukarya     RF02543   hmm      951     1458      509        2      -     -    6 0.51   0.0  395.7  4.4e-117 !   -
+contig--1583871      -         LSU_rRNA_eukarya     RF02543   hmm     1491     2234        1      727      +     -    6 0.44   2.5  385.1  7.2e-114 !   -
+contig--3176110      -         LSU_rRNA_eukarya     RF02543   hmm     2554     2950       12      407      +     -    6 0.45   0.1  378.9    5e-112 !   -
+contig--2250093      -         LSU_rRNA_eukarya     RF02543   hmm     2322     2796      487        3      -     -    6 0.46   0.0  378.5  7.1e-112 !   -
+contig--257393       -         LSU_rRNA_eukarya     RF02543   hmm     1289     1874      590        2      -     -    6 0.60   0.0  373.7  1.9e-110 !   -
+contig--2249544      -         LSU_rRNA_eukarya     RF02543   hmm     2391     2833      435        1      -     -    6 0.44   0.9  362.4  4.9e-107 !   -
+contig--3019708      -         LSU_rRNA_eukarya     RF02543   hmm     1278     1889      609        1      -     -    6 0.44   1.7  348.9  5.6e-103 !   -
+contig--2412452      -         LSU_rRNA_eukarya     RF02543   hmm     2080     2389       30      338      +     -    6 0.48   0.0  339.6  3.7e-100 !   -
+contig--166397       -         LSU_rRNA_eukarya     RF02543   hmm     2131     3161       61     1074      +     -    6 0.53   0.0  320.4   2.3e-94 !   -
+contig--97491        -         LSU_rRNA_eukarya     RF02543   hmm     2434     2863        2      424      +     -    6 0.46   0.2  317.7   1.5e-93 !   -
+contig--3290892      -         LSU_rRNA_eukarya     RF02543   hmm     1473     1954        2      490      +     -    6 0.47   0.2  310.5   2.2e-91 !   -
+contig--156996       -         LSU_rRNA_eukarya     RF02543   hmm      653     1961     3005     1821      -     -    6 0.51   2.8  305.9   5.1e-90 !   -
+contig--2252661      -         LSU_rRNA_eukarya     RF02543   hmm       47      728      776        4      -     -    6 0.47   0.1  300.6   2.2e-88 !   -
+contig--371157       -         LSU_rRNA_eukarya     RF02543   hmm      648     1951     3943     5094      +     -    6 0.53   3.1  287.6   1.8e-84 !   -
+contig--362625       -         LSU_rRNA_eukarya     RF02543   hmm     2836     3383        1      505      +     -    6 0.39   3.3  286.0   5.4e-84 !   -
+contig--185309       -         LSU_rRNA_eukarya     RF02543   hmm     2241     3159      130     1031      +     -    6 0.48   1.1  280.8   1.9e-82 !   -
+contig--515926       -         LSU_rRNA_eukarya     RF02543   hmm     1316     1799      494        3      -     -    6 0.47   1.0  277.9   1.5e-81 !   -
+contig--2741341      -         LSU_rRNA_eukarya     RF02543   hmm     1532     1968        1      432      +     -    6 0.52   0.0  275.9   5.8e-81 !   -
+contig--1644897      -         LSU_rRNA_eukarya     RF02543   hmm     1047     1618       15      583      +     -    6 0.47   0.5  272.6   5.7e-80 !   -
+contig--137819       -         LSU_rRNA_eukarya     RF02543   hmm     2236     2983        6      726      +     -    6 0.49   0.1  272.3   7.2e-80 !   -
+contig--23096        -         LSU_rRNA_eukarya     RF02543   hmm     2252     2986        1      707      +     -    6 0.51   0.0  265.0   1.2e-77 !   -
+contig--1133023      -         LSU_rRNA_eukarya     RF02543   hmm     1590     2115        9      557      +     -    6 0.56   0.0  261.0   1.9e-76 !   -
+contig--1692849      -         LSU_rRNA_eukarya     RF02543   hmm     2377     2729        1      336      +     -    6 0.45   0.5  260.0   3.7e-76 !   -
+contig--1797769      -         LSU_rRNA_eukarya     RF02543   hmm     1669     2174      501        2      -     -    6 0.54   0.0  258.1   1.3e-75 !   -
+contig--2722470      -         LSU_rRNA_eukarya     RF02543   hmm       17      387        2      375      +     -    6 0.51   0.0  254.7   1.4e-74 !   -
+contig--151751       -         LSU_rRNA_eukarya     RF02543   hmm        4      454      603      155      -     -    6 0.47   0.4  249.9   4.2e-73 !   -
+contig--151080       -         LSU_rRNA_eukarya     RF02543   hmm     2105     3236     1140       34      -     -    6 0.37  21.0  249.4   5.8e-73 !   -
+contig--1437319      -         LSU_rRNA_eukarya     RF02543   hmm      658      989      327        7      -     -    6 0.50   0.0  241.2   1.7e-70 !   -
+contig--185227       -         LSU_rRNA_eukarya     RF02543   hmm     1268     1567      303        4      -     -    6 0.52   0.2  234.4   1.9e-68 !   -
+contig--185430       -         LSU_rRNA_eukarya     RF02543   hmm     1557     1946        8      392      +     -    6 0.47   0.0  230.5   2.8e-67 !   -
+contig--185298       -         LSU_rRNA_eukarya     RF02543   hmm       47      689        1      646      +     -    6 0.43   6.5  228.1   1.5e-66 !   -
+contig--1003814      -         LSU_rRNA_eukarya     RF02543   hmm     1502     1896        1      399      +     -    6 0.51   0.0  227.9   1.7e-66 !   -
+contig--2536708      -         LSU_rRNA_eukarya     RF02543   hmm     1512     1908      397        1      -     -    6 0.52   0.0  227.6   2.1e-66 !   -
+contig--1187407      -         LSU_rRNA_eukarya     RF02543   hmm      930     1237      305        1      -     -    6 0.47   0.0  225.3   1.1e-65 !   -
+contig--2251231      -         LSU_rRNA_eukarya     RF02543   hmm     2940     3398      467       11      -     -    6 0.44   0.3  223.7   3.2e-65 !   -
+contig--2250797      -         LSU_rRNA_eukarya     RF02543   hmm       11      375      366        2      -     -    6 0.48   0.2  222.6   6.7e-65 !   -
+contig--2252145      -         LSU_rRNA_eukarya     RF02543   hmm     2936     3376        1      422      +     -    6 0.47   0.0  220.6   2.9e-64 !   -
+contig--2251064      -         LSU_rRNA_eukarya     RF02543   hmm       48      477        1      424      +     -    6 0.46   1.7  218.0   1.6e-63 !   -
+contig--2254317      -         LSU_rRNA_eukarya     RF02543   hmm       30      392      362        2      -     -    6 0.45   0.9  216.6   4.3e-63 !   -
+contig--108732       -         LSU_rRNA_eukarya     RF02543   hmm     1486     1885        1      403      +     -    6 0.57   0.0  216.5   4.7e-63 !   -
+contig--365284       -         LSU_rRNA_eukarya     RF02543   hmm       46      459      546      135      -     -    6 0.48   0.4  215.9   7.2e-63 !   -
+contig--1007451      -         LSU_rRNA_eukarya     RF02543   hmm     2381     2690        1      308      +     -    6 0.50   0.0  214.7   1.7e-62 !   -
+contig--2937145      -         LSU_rRNA_eukarya     RF02543   hmm     2895     3339        2      425      +     -    6 0.47   0.0  209.8   4.9e-61 !   -
+contig--1214394      -         LSU_rRNA_eukarya     RF02543   hmm     2895     3341      423        2      -     -    6 0.48   0.0  205.5     1e-59 !   -
+contig--395713       -         LSU_rRNA_eukarya     RF02543   hmm     2108     2835     1438     2144      +     -    6 0.54   0.0  205.0   1.5e-59 !   -
+contig--3276943      -         LSU_rRNA_eukarya     RF02543   hmm       25     1147      967        1      -     -    6 0.44   1.8  203.4   4.4e-59 !   -
+contig--808802       -         LSU_rRNA_eukarya     RF02543   hmm     1647     2125        2      466      +     -    6 0.49   0.0  201.0   2.3e-58 !   -
+contig--2528721      -         LSU_rRNA_eukarya     RF02543   hmm     2923     3385        1      405      +     -    6 0.57   0.0  200.4   3.4e-58 !   -
+contig--2256050      -         LSU_rRNA_eukarya     RF02543   hmm     2135     2785     1000     1636      +     -    6 0.53   0.0  199.3   7.6e-58 !   -
+contig--3166946      -         LSU_rRNA_eukarya     RF02543   hmm     1844     2170        1      320      +     -    6 0.54   0.0  198.6   1.2e-57 !   -
+contig--924893       -         LSU_rRNA_eukarya     RF02543   hmm      642      950      303        1      -     -    6 0.51   0.1  197.5   2.6e-57 !   -
+contig--1214754      -         LSU_rRNA_eukarya     RF02543   hmm       57      490      512       93      -     -    6 0.36   8.5  194.9   1.5e-56 !   -
+contig--2251849      -         LSU_rRNA_eukarya     RF02543   hmm     2940     3386        2      425      +     -    6 0.50   0.0  194.1   2.7e-56 !   -
+contig--1159799      -         LSU_rRNA_eukarya     RF02543   hmm     2940     3340      375        2      -     -    6 0.47   0.0  192.7   7.1e-56 !   -
+contig--1214513      -         LSU_rRNA_eukarya     RF02543   hmm       47      392        2      346      +     -    6 0.54   0.0  190.5   3.3e-55 !   -
+contig--2251533      -         LSU_rRNA_eukarya     RF02543   hmm     2943     3386      427        5      -     -    6 0.51   0.0  186.2   6.4e-54 !   -
+contig--2255543      -         LSU_rRNA_eukarya     RF02543   hmm     2947     3341        1      367      +     -    6 0.44   0.0  185.5   1.1e-53 !   -
+contig--101864       -         LSU_rRNA_eukarya     RF02543   hmm       33      358      310        2      -     -    6 0.48   0.1  184.9   1.6e-53 !   -
+contig--2422438      -         LSU_rRNA_eukarya     RF02543   hmm     1526     1884      365        1      -     -    6 0.53   0.0  184.8   1.7e-53 !   -
+contig--362373       -         LSU_rRNA_eukarya     RF02543   hmm     1534     1895        1      357      +     -    6 0.48   0.0  183.9   3.2e-53 !   -
+contig--1214168      -         LSU_rRNA_eukarya     RF02543   hmm       28      364        1      332      +     -    6 0.47   0.4  182.3   9.6e-53 !   -
+contig--110110       -         LSU_rRNA_eukarya     RF02543   hmm       13      341        2      321      +     -    6 0.42   2.9  181.4   1.9e-52 !   -
+contig--151601       -         LSU_rRNA_eukarya     RF02543   hmm      799     1979      207     1278      +     -    6 0.46   9.7  180.0   4.9e-52 !   -
+contig--3756271      -         LSU_rRNA_eukarya     RF02543   hmm     1332     1713        1      380      +     -    6 0.51   0.1  179.7   5.9e-52 !   -
+contig--3809266      -         LSU_rRNA_eukarya     RF02543   hmm     1283     1564        1      290      +     -    6 0.37   0.6  175.9   8.2e-51 !   -
+contig--130023       -         LSU_rRNA_eukarya     RF02543   hmm       71      460      683      294      -     -    6 0.50   0.0  175.0   1.5e-50 !   -
+contig--2330557      -         LSU_rRNA_eukarya     RF02543   hmm     2136     2784      662       28      -     -    6 0.56   0.0  173.5   4.3e-50 !   -
+contig--64232        -         LSU_rRNA_eukarya     RF02543   hmm     2937     3375        1      398      +     -    6 0.42   1.0  172.8     7e-50 !   -
+contig--3050118      -         LSU_rRNA_eukarya     RF02543   hmm     2948     3351        1      367      +     -    6 0.45   0.0  170.5   3.4e-49 !   -
+contig--1212351      -         LSU_rRNA_eukarya     RF02543   hmm       10      344      330        1      -     -    6 0.53   0.0  162.9   6.8e-47 !   -
+contig--2967094      -         LSU_rRNA_eukarya     RF02543   hmm     1508     1882      370        1      -     -    6 0.56   0.0  162.6   8.4e-47 !   -
+contig--496748       -         LSU_rRNA_eukarya     RF02543   hmm       36      332        1      303      +     -    6 0.55   0.0  162.3     1e-46 !   -
+contig--371157       -         LSU_rRNA_eukarya     RF02543   hmm       12      429     3497     3910      +     -    6 0.50   1.0  161.7   1.7e-46 !   -
+contig--3897242      -         LSU_rRNA_eukarya     RF02543   hmm     1372     1709       13      347      +     -    6 0.46   0.5  159.7   6.5e-46 !   -
+contig--3743149      -         LSU_rRNA_eukarya     RF02543   hmm     2119     2700      573        2      -     -    6 0.53   0.0  158.0   2.1e-45 !   -
+contig--364277       -         LSU_rRNA_eukarya     RF02543   hmm       12      406      426        2      -     -    6 0.41  10.5  156.6   5.3e-45 !   -
+contig--397992       -         LSU_rRNA_eukarya     RF02543   hmm       18      420      229      623      +     -    6 0.56   0.0  155.4   1.2e-44 !   -
+contig--1572437      -         LSU_rRNA_eukarya     RF02543   hmm     2956     3211        1      257      +     -    6 0.47   0.0  153.9   3.6e-44 !   -
+contig--518767       -         LSU_rRNA_eukarya     RF02543   hmm      246      552       24      320      +     -    6 0.45   3.3  153.5   4.9e-44 !   -
+contig--3398090      -         LSU_rRNA_eukarya     RF02543   hmm     2247     2853        1      568      +     -    6 0.50   0.1  152.7   8.3e-44 !   -
+contig--1089773      -         LSU_rRNA_eukarya     RF02543   hmm     2963     3385      403        6      -     -    6 0.49   0.0  152.2   1.2e-43 !   -
+contig--1212661      -         LSU_rRNA_eukarya     RF02543   hmm     2951     3321        1      351      +     -    6 0.47   0.0  149.9   5.8e-43 !   -
+contig--3715154      -         LSU_rRNA_eukarya     RF02543   hmm     2279     2835      539       10      -     -    6 0.54   0.0  148.3   1.8e-42 !   -
+contig--362412       -         LSU_rRNA_eukarya     RF02543   hmm       13      401      419        1      -     -    6 0.44   6.6  148.2   1.9e-42 !   -
+contig--2256050      -         LSU_rRNA_eukarya     RF02543   hmm      915     1971        4      960      +     -    6 0.52   1.6  147.3   3.5e-42 !   -
+contig--362779       -         LSU_rRNA_eukarya     RF02543   hmm     2963     3385      372        3      -     -    6 0.60   0.0  147.0   4.2e-42 !   -
+contig--1202655      -         LSU_rRNA_eukarya     RF02543   hmm     2598     2980      655     1031      +     -    6 0.49   0.1  145.3   1.4e-41 !   -
+contig--1834142      -         LSU_rRNA_eukarya     RF02543   hmm       37      324        1      299      +     -    6 0.57   0.0  144.4   2.6e-41 !   -
+contig--401056       -         LSU_rRNA_eukarya     RF02543   hmm       18      437     1058     1511      +     -    6 0.46   1.2  138.6   1.4e-39 !   -
+contig--68307        -         LSU_rRNA_eukarya     RF02543   hmm       73      381        2      310      +     -    6 0.41   1.2  138.5   1.6e-39 !   -
+contig--2250515      -         LSU_rRNA_eukarya     RF02543   hmm       17      413      131      514      +     -    6 0.51   0.2  136.3   7.4e-39 !   -
+contig--2634789      -         LSU_rRNA_eukarya     RF02543   hmm     2135     2674      527        1      -     -    6 0.51   0.0  135.6   1.2e-38 !   -
+contig--423976       -         LSU_rRNA_eukarya     RF02543   hmm       15      439      476      883      +     -    6 0.41  10.3  134.9   1.9e-38 !   -
+contig--2699652      -         LSU_rRNA_eukarya     RF02543   hmm     2822     3163        2      345      +     -    6 0.55   0.0  134.6   2.4e-38 !   -
+contig--395713       -         LSU_rRNA_eukarya     RF02543   hmm      793     1634      463     1229      +     -    6 0.53   1.9  134.5   2.6e-38 !   -
+contig--151876       -         LSU_rRNA_eukarya     RF02543   hmm        7      442      141      528      +     -    6 0.46   4.0  134.4   2.7e-38 !   -
+contig--2715420      -         LSU_rRNA_eukarya     RF02543   hmm     2748     3141       21      421      +     -    6 0.55   0.0  133.5   5.1e-38 !   -
+contig--423976       -         LSU_rRNA_eukarya     RF02543   hmm      811     1884     1006     1988      +     -    6 0.49   6.7  133.0   7.1e-38 !   -
+contig--401056       -         LSU_rRNA_eukarya     RF02543   hmm      807     1555     1632     2324      +     -    6 0.51   0.9  131.6   1.9e-37 !   -
+contig--3860305      -         LSU_rRNA_eukarya     RF02543   hmm        8      462      153      550      +     -    6 0.44   4.2  131.0   2.8e-37 !   -
+contig--1210133      -         LSU_rRNA_eukarya     RF02543   hmm       16      445      603      186      -     -    6 0.49   0.0  130.9   3.1e-37 !   -
+contig--395713       -         LSU_rRNA_eukarya     RF02543   hmm       21      437        4      361      +     -    6 0.49   0.5  125.7   1.1e-35 !   -
+contig--3775208      -         LSU_rRNA_eukarya     RF02543   hmm     2963     3321        3      341      +     -    6 0.47   0.0  124.6   2.5e-35 !   -
+contig--2531154      -         LSU_rRNA_eukarya     RF02543   hmm       15      422      284      632      +     -    6 0.48   1.7  123.1     7e-35 !   -
+contig--156996       -         LSU_rRNA_eukarya     RF02543   hmm       13      424     3469     3064      -     -    6 0.45   4.1  122.9   8.1e-35 !   -
+contig--577902       -         LSU_rRNA_eukarya     RF02543   hmm     2963     3198        1      235      +     -    6 0.44   0.1  121.1   2.8e-34 !   -
+contig--3784467      -         LSU_rRNA_eukarya     RF02543   hmm     2854     3174      416       93      -     -    6 0.56   0.0  116.5   6.9e-33 !   -
+contig--2253227      -         LSU_rRNA_eukarya     RF02543   hmm     2961     3162        2      220      +     -    6 0.54   0.0  116.0   9.3e-33 !   -
+contig--36603        -         LSU_rRNA_eukarya     RF02543   hmm       23      392        6      411      +     -    6 0.54   0.0  113.7   4.7e-32 !   -
+contig--35359        -         LSU_rRNA_eukarya     RF02543   hmm     2113     2423      225      541      +     -    6 0.51   0.0  113.5   5.4e-32 !   -
+contig--4068604      -         LSU_rRNA_eukarya     RF02543   hmm     1229     1876        7      562      +     -    6 0.53   0.3  113.2   6.6e-32 !   -
+contig--371157       -         LSU_rRNA_eukarya     RF02543   hmm     2119     2335     5118     5334      +     -    6 0.47   0.0  113.0   7.6e-32 !   -
+contig--1082627      -         LSU_rRNA_eukarya     RF02543   hmm     2851     3157        2      311      +     -    6 0.54   0.0  110.7   3.7e-31 !   -
+contig--1123361      -         LSU_rRNA_eukarya     RF02543   hmm      844      966        1      122      +     -    6 0.52   0.0  110.0   6.1e-31 !   -
+contig--2253718      -         LSU_rRNA_eukarya     RF02543   hmm      329      678        2      400      +     -    6 0.44   0.1  108.2   2.1e-30 !   -
+contig--1213113      -         LSU_rRNA_eukarya     RF02543   hmm     3014     3353      323        4      -     -    6 0.42   0.2  108.0   2.6e-30 !   -
+contig--3875044      -         LSU_rRNA_eukarya     RF02543   hmm        6      228      134      355      +     -    6 0.43   0.2  105.9   1.1e-29 !   -
+contig--1123361      -         LSU_rRNA_eukarya     RF02543   hmm      914     1051      183      321      +     -    6 0.47   0.0  105.8   1.1e-29 !   -
+contig--363016       -         LSU_rRNA_eukarya     RF02543   hmm       12      380      312        2      -     -    6 0.45   4.4  102.1   1.5e-28 !   -
+contig--2254117      -         LSU_rRNA_eukarya     RF02543   hmm      809     1350      271      768      +     -    6 0.49   1.7  102.1   1.5e-28 !   -
+contig--362861       -         LSU_rRNA_eukarya     RF02543   hmm       29      447      179      626      +     -    6 0.42   5.2  100.7   3.8e-28 !   -
+contig--1251316      -         LSU_rRNA_eukarya     RF02543   hmm      621      857      104      323      +     -    6 0.50   0.0   99.2   1.2e-27 !   -
+contig--2853165      -         LSU_rRNA_eukarya     RF02543   hmm     3010     3321      298        3      -     -    6 0.40   0.6   98.8   1.5e-27 !   -
+contig--261342       -         LSU_rRNA_eukarya     RF02543   hmm     2809     3066       26      283      +     -    6 0.39   1.0   96.4   7.6e-27 !   -
+contig--151080       -         LSU_rRNA_eukarya     RF02543   hmm      797     1584     2084     1347      -     -    6 0.32  21.8   95.9   1.1e-26 !   -
+contig--3317407      -         LSU_rRNA_eukarya     RF02543   hmm        8      384      435      751      +     -    6 0.45   2.3   95.0   2.1e-26 !   -
+contig--1123361      -         LSU_rRNA_eukarya     RF02543   hmm      922     1052      342      469      +     -    6 0.50   0.0   92.7     1e-25 !   -
+contig--10143        -         LSU_rRNA_eukarya     RF02543   hmm     1139     1634      655      203      -     -    6 0.49   1.2   92.5   1.2e-25 !   -
+contig--2250883      -         LSU_rRNA_eukarya     RF02543   hmm     2878     3151      394      118      -     -    6 0.53   0.0   91.8   1.9e-25 !   -
+contig--2304422      -         LSU_rRNA_eukarya     RF02543   hmm       14      359      299        1      -     -    6 0.52   0.0   91.5   2.3e-25 !   -
+contig--151876       -         LSU_rRNA_eukarya     RF02543   hmm      798     1301      628     1084      +     -    6 0.49   0.2   89.1   1.2e-24 !   -
+contig--362861       -         LSU_rRNA_eukarya     RF02543   hmm      800     1075      741     1012      +     -    6 0.53   0.0   89.0   1.4e-24 !   -
+contig--2673585      -         LSU_rRNA_eukarya     RF02543   hmm       30      368      372        1      -     -    6 0.42   3.2   87.8     3e-24 !   -
+contig--3150945      -         LSU_rRNA_eukarya     RF02543   hmm     3041     3375        1      312      +     -    6 0.41   0.2   87.7   3.3e-24 !   -
+contig--364116       -         LSU_rRNA_eukarya     RF02543   hmm     2322     2776        2      419      +     -    6 0.54   0.0   86.6   6.8e-24 !   -
+contig--2250940      -         LSU_rRNA_eukarya     RF02543   hmm        2      113      638      749      +     -    6 0.48   0.0   85.6   1.4e-23 !   -
+contig--1042219      -         LSU_rRNA_eukarya     RF02543   hmm     2423     2781      339       10      -     -    6 0.55   0.1   84.9   2.3e-23 !   -
+contig--364074       -         LSU_rRNA_eukarya     RF02543   hmm      894     1495      578       41      -     -    6 0.52   0.1   83.2   7.3e-23 !   -
+contig--1440933      -         LSU_rRNA_eukarya     RF02543   hmm     3046     3361      299        3      -     -    6 0.46   0.0   83.2   7.3e-23 !   -
+contig--332136       -         LSU_rRNA_eukarya     RF02543   hmm     2864     3155      317       21      -     -    6 0.57   0.0   82.8     1e-22 !   -
+contig--1768180      -         LSU_rRNA_eukarya     RF02543   hmm     2917     3157        3      246      +     -    6 0.52   0.0   82.0   1.7e-22 !   -
+contig--3659280      -         LSU_rRNA_eukarya     RF02543   hmm     2391     2785       31      395      +     -    6 0.48   0.2   81.7   2.1e-22 !   -
+contig--2252929      -         LSU_rRNA_eukarya     RF02543   hmm     1280     1968      859      232      -     -    6 0.52   0.2   80.6   4.7e-22 !   -
+contig--2983248      -         LSU_rRNA_eukarya     RF02543   hmm       55      387      316        1      -     -    6 0.42   3.0   80.5   4.7e-22 !   -
+contig--2680413      -         LSU_rRNA_eukarya     RF02543   hmm        6      347      296        2      -     -    6 0.41   2.7   80.0   6.8e-22 !   -
+contig--3638238      -         LSU_rRNA_eukarya     RF02543   hmm     1292     1981      718       78      -     -    6 0.49   1.7   79.0   1.4e-21 !   -
+contig--1040384      -         LSU_rRNA_eukarya     RF02543   hmm      935     1648      772      140      -     -    6 0.44   6.7   78.7   1.7e-21 !   -
+contig--1407263      -         LSU_rRNA_eukarya     RF02543   hmm     1006     1547      489        3      -     -    6 0.45   1.7   78.5     2e-21 !   -
+contig--2519402      -         LSU_rRNA_eukarya     RF02543   hmm        7      269      300       49      -     -    6 0.40   1.1   75.3   1.8e-20 !   -
+contig--2805328      -         LSU_rRNA_eukarya     RF02543   hmm     2917     3159        4      249      +     -    6 0.57   0.0   74.3   3.6e-20 !   -
+contig--2254400      -         LSU_rRNA_eukarya     RF02543   hmm     2922     3161      340       98      -     -    6 0.55   0.0   72.2   1.5e-19 !   -
+contig--1688622      -         LSU_rRNA_eukarya     RF02543   hmm     2407     2780      348        5      -     -    6 0.51   0.0   71.0   3.6e-19 !   -
+contig--759897       -         LSU_rRNA_eukarya     RF02543   hmm     2934     3159        2      230      +     -    6 0.54   0.0   70.5   4.9e-19 !   -
+contig--1176662      -         LSU_rRNA_eukarya     RF02543   hmm     2810     3067       24      282      +     -    6 0.50   0.0   69.1   1.3e-18 !   -
+contig--3146147      -         LSU_rRNA_eukarya     RF02543   hmm      345      663      421        1      -     -    6 0.49   0.0   67.7   3.5e-18 !   -
+contig--1502032      -         LSU_rRNA_eukarya     RF02543   hmm     3093     3399      308       30      -     -    6 0.45   0.0   67.4   4.3e-18 !   -
+contig--1111206      -         LSU_rRNA_eukarya     RF02543   hmm       11      323      289        1      -     -    6 0.42   3.2   66.7     7e-18 !   -
+contig--365471       -         LSU_rRNA_eukarya     RF02543   hmm     2252     2503        1      279      +     -    6 0.47   0.1   66.6   7.5e-18 !   -
+contig--2879574      -         LSU_rRNA_eukarya     RF02543   hmm      340      458        1      117      +     -    6 0.43   0.0   66.0   1.1e-17 !   -
+contig--332136       -         LSU_rRNA_eukarya     RF02543   hmm     2827     2983      487      331      -     -    6 0.58   0.0   66.0   1.2e-17 !   -
+contig--3748912      -         LSU_rRNA_eukarya     RF02543   hmm      799     1072      275       10      -     -    6 0.47   0.3   65.8   1.3e-17 !   -
+contig--147097       -         LSU_rRNA_eukarya     RF02543   hmm     2942     3187        4      244      +     -    6 0.52   0.0   65.2   1.9e-17 !   -
+contig--2874819      -         LSU_rRNA_eukarya     RF02543   hmm     2281     2665      359        3      -     -    6 0.57   0.0   65.1   2.2e-17 !   -
+contig--95399        -         LSU_rRNA_eukarya     RF02543   hmm     2947     3198        5      259      +     -    6 0.55   0.1   64.1   4.3e-17 !   -
+contig--2918607      -         LSU_rRNA_eukarya     RF02543   hmm      306      439      415      283      -     -    6 0.44   0.6   63.3   7.2e-17 !   -
+contig--1796896      -         LSU_rRNA_eukarya     RF02543   hmm     2948     3185        2      241      +     -    6 0.51   0.0   63.2     8e-17 !   -
+contig--942031       -         LSU_rRNA_eukarya     RF02543   hmm     2919     3151      306       69      -     -    6 0.55   0.0   62.6   1.2e-16 !   -
+contig--2254163      -         LSU_rRNA_eukarya     RF02543   hmm       16      335      304        2      -     -    6 0.38   5.7   62.5   1.3e-16 !   -
+contig--2835645      -         LSU_rRNA_eukarya     RF02543   hmm     2943     3167      303       77      -     -    6 0.55   0.0   62.3   1.5e-16 !   -
+contig--2252929      -         LSU_rRNA_eukarya     RF02543   hmm     2129     2312      194        5      -     -    6 0.49   0.0   60.4   5.7e-16 !   -
+contig--747483       -         LSU_rRNA_eukarya     RF02543   hmm     2911     3160      332       79      -     -    6 0.54   0.0   58.6     2e-15 !   -
+contig--2255132      -         LSU_rRNA_eukarya     RF02543   hmm       16      236      118      325      +     -    6 0.37   2.9   58.4   2.2e-15 !   -
+contig--2254117      -         LSU_rRNA_eukarya     RF02543   hmm      305      437       19      152      +     -    6 0.48   0.1   58.3   2.4e-15 !   -
+contig--2634789      -         LSU_rRNA_eukarya     RF02543   hmm     1405     1960     1086      580      -     -    6 0.49   1.3   58.2   2.6e-15 !   -
+contig--3925448      -         LSU_rRNA_eukarya     RF02543   hmm      175      460       23      294      +     -    6 0.38   7.7   56.8   6.8e-15 !   -
+contig--236053       -         LSU_rRNA_eukarya     RF02543   hmm       17      269      248       45      -     -    6 0.44   1.0   56.0   1.2e-14 !   -
+contig--2918607      -         LSU_rRNA_eukarya     RF02543   hmm      806      969      177       15      -     -    6 0.47   0.1   55.5   1.7e-14 !   -
+contig--2251329      -         LSU_rRNA_eukarya     RF02543   hmm     2950     3195        3      252      +     -    6 0.49   0.1   53.8   5.5e-14 !   -
+contig--2713352      -         LSU_rRNA_eukarya     RF02543   hmm     1419     1947      507       19      -     -    6 0.51   0.3   53.4   7.2e-14 !   -
+contig--2220335      -         LSU_rRNA_eukarya     RF02543   hmm     2133     2312      200        5      -     -    6 0.48   0.0   53.3   7.9e-14 !   -
+contig--3433834      -         LSU_rRNA_eukarya     RF02543   hmm     1508     1962        2      414      +     -    6 0.47   0.1   53.1     9e-14 !   -
+contig--1326571      -         LSU_rRNA_eukarya     RF02543   hmm      792     1036       35      270      +     -    6 0.50   0.0   52.9     1e-13 !   -
+contig--2646754      -         LSU_rRNA_eukarya     RF02543   hmm     1272     1930        1      591      +     -    6 0.51   0.8   52.6   1.3e-13 !   -
+contig--473422       -         LSU_rRNA_eukarya     RF02543   hmm       18      224      198        2      -     -    6 0.54   0.0   52.0   1.9e-13 !   -
+contig--2564558      -         LSU_rRNA_eukarya     RF02543   hmm      317      455        1      140      +     -    6 0.44   0.1   52.0   1.9e-13 !   -
+contig--3694746      -         LSU_rRNA_eukarya     RF02543   hmm      791      966      184       10      -     -    6 0.50   0.1   51.0   3.9e-13 !   -
+contig--3652175      -         LSU_rRNA_eukarya     RF02543   hmm      792      967      185       11      -     -    6 0.49   0.1   50.8   4.5e-13 !   -
+#
+# Program:         cmsearch
+# Version:         1.1.2 (July 2016)
+# Pipeline mode:   SEARCH
+# Query file:      ribo.cm
+# Target file:     50000.1.fa
+# Option settings: cmsearch -Z 1000 --tblout 1.cmsearch.tblout --noali --cut_ga --hmmonly --cpu 4 ribo.cm 50000.1.fa
+# Current dir:     /nfs/production/xfam/users/nawrocki/notebook/17_0508_inf_ebi_cmsearch_deoverlap
+# Date:            Wed May 10 21:28:09 2017
+# [ok]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch_tblout_deoverlap_tool/test-data/overlapout_sample	Wed Aug 16 05:49:12 2023 +0000
@@ -0,0 +1,644 @@
+# cmsearch-deoverlap.pl --overlapout output file
+# Explanation of fields:
+# 1. 'target'            : sequence name
+# 2. 'strand'            : strand (+ or -)
+# 3. 'mdl1'              : name of model 1
+# 4. 'mdl2'              : name of model 2
+# 5. 'hitlen1'           : length in sequence positions of hit to model 1
+# 6. 'hitlen2'           : length in sequence positions of hit to model 2
+# 7. 'nres_olap'         : number of residues that overlap between hit to model 1 and hit to model 2 in 'target' on strand 'strand'
+# 8. 'score1'            : score of hit to model 1
+# 9. 'score2'            : score of hit to model 2
+# 10. 'evalue1'           : E-value of hit to model 1
+# 11. 'evalue2'           : E-value of hit to model 2
+# 12. 'seqfrom1'          : start position in 'target' of hit to model 1
+# 13. 'seqto1'            : end position in 'target' of hit to model 1
+# 14. 'seqfrom2'          : start position in 'target' of hit to model 2
+# 15. 'seqto2'            : end position in 'target' of hit to model 2
+# 16. 'olap-frac-of-hit1' : 'nres_olap'/'hitlen1'
+# 17. 'olap-frac-of-hit2' : 'nres_olap'/'hitlen2'
+# 18. 'mdllen1'           : length of model 1 ("-" if not available)
+# 19. 'mdllen2'           : length of model 2 ("-" if not available)
+# 20. 'olap-frac-of-mdl1' : 'nres_olap'/'mdllen1'
+# 21. 'olap-frac-of-mdl2' : 'nres_olap'/'mdllen2'
+# 22. 'mhitlen1'          : length in model positions of hit to model 1
+# 23. 'mhitlen2'          : length in model positions of hit to model 2
+# 24. 'mhit-frac-of-mdl1' : 'mhitlen1'/'mdllen1'
+# 25. 'mhit-frac-of-mdl2' : 'mhitlen2'/'mdllen2'
+# 26. 'desc1'             : description for hit to model 1
+# 27. 'desc2'             : description for hit to model 2
+#1:target 2:strand 3:mdl1 4:mdl2 5:hitlen1 6:hitlen2 7:nres_olap 8:score1 9:score2 10:evalue1 11:evalue2 12:seqfrom1 13:seqto1 14:seqfrom2 15:seqto2 16:olap-frac-of-hit1 17:olap-frac-of-hit2 18:mdllen1 19:mdllen2 20:olap-frac-of-mdl1 21:olap-frac-of-mdl2 22:mhitlen1 23:mhitlen2 24:mhit-frac-of-mdl1 25:mhit-frac-of-mdl2 26:desc1 27:desc2
+contig--1001177	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	316	315	315	257.9	177.2	1e-74	1.7e-50	4	319	4	318	0.997	1.000	-	-	-	-	315	319	-	-	-	-
+contig--1001177	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	316	308	308	257.9	121.6	1e-74	1.8e-33	4	319	12	319	0.975	1.000	-	-	-	-	315	302	-	-	-	-
+contig--1001177	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	316	305	305	257.9	113.2	1e-74	2.9e-31	4	319	15	319	0.965	1.000	-	-	-	-	315	318	-	-	-	-
+contig--1003442	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	328	313	313	194.1	83.8	1.8e-55	2.9e-22	328	1	314	2	0.954	1.000	-	-	-	-	329	302	-	-	-	-
+contig--1007451	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	308	293	293	214.7	67.8	1.7e-62	5e-18	1	308	15	307	0.951	1.000	-	-	-	-	310	256	-	-	-	-
+contig--1007451	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	308	287	287	214.7	55.5	1.7e-62	3.1e-14	1	308	21	307	0.932	1.000	-	-	-	-	310	260	-	-	-	-
+contig--10143	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	800	597	597	446.1	234.0	4.8e-132	3.5e-68	800	1	798	202	0.746	1.000	-	-	-	-	882	610	-	-	-	-
+contig--10143	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	800	453	453	446.1	92.5	4.8e-132	1.2e-25	800	1	655	203	0.566	1.000	-	-	-	-	882	496	-	-	-	-
+contig--101864	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	309	306	306	184.9	100.9	1.6e-53	4.9e-28	310	2	307	2	0.990	1.000	-	-	-	-	326	324	-	-	-	-
+contig--101864	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	309	307	306	184.9	82.5	1.6e-53	2.2e-22	310	2	307	1	0.990	0.997	-	-	-	-	326	314	-	-	-	-
+contig--1029476	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	527	521	521	368.0	249.5	5.4e-108	2.3e-72	174	700	177	697	0.989	1.000	-	-	-	-	517	511	-	-	-	-
+contig--1029476	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	527	482	482	368.0	178.8	5.4e-108	4.4e-51	174	700	217	698	0.915	1.000	-	-	-	-	517	517	-	-	-	-
+contig--1029476	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	527	482	482	368.0	130.8	5.4e-108	3e-36	174	700	217	698	0.915	1.000	-	-	-	-	517	398	-	-	-	-
+contig--1031478	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	372	371	371	177.9	88.8	3.7e-51	2.3e-24	372	1	372	2	0.997	1.000	-	-	-	-	371	380	-	-	-	-
+contig--1040384	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	735	660	660	425.7	240.5	6.7e-126	4e-70	774	40	774	115	0.898	1.000	-	-	-	-	735	688	-	-	-	-
+contig--1040384	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	735	633	633	425.7	78.7	6.7e-126	1.7e-21	774	40	772	140	0.861	1.000	-	-	-	-	735	714	-	-	-	-
+contig--1042219	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	338	327	327	215.9	126.7	1.3e-62	8.2e-36	339	2	339	13	0.967	1.000	-	-	-	-	336	319	-	-	-	-
+contig--1042219	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	338	330	330	215.9	84.9	1.3e-62	2.3e-23	339	2	339	10	0.976	1.000	-	-	-	-	336	359	-	-	-	-
+contig--1082627	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	334	331	331	314.4	198.5	2.6e-92	1.9e-57	1	334	2	332	0.991	1.000	-	-	-	-	345	329	-	-	-	-
+contig--1082627	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	334	310	310	314.4	110.7	2.6e-92	3.7e-31	1	334	2	311	0.928	1.000	-	-	-	-	345	307	-	-	-	-
+contig--1085416	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	392	388	387	263.5	101.8	2.1e-76	1e-27	392	1	393	6	0.987	0.997	-	-	-	-	424	387	-	-	-	-
+contig--110110	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	320	311	310	181.4	101.6	1.9e-52	3e-28	2	321	12	322	0.969	0.997	-	-	-	-	329	321	-	-	-	-
+contig--110110	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	320	316	315	181.4	83.2	1.9e-52	1.3e-22	2	321	7	322	0.984	0.997	-	-	-	-	329	315	-	-	-	-
+contig--1111206	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	359	358	358	190.5	119.6	5.9e-55	1.1e-33	360	2	359	2	0.997	1.000	-	-	-	-	389	381	-	-	-	-
+contig--1111206	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	359	289	288	190.5	66.7	5.9e-55	7e-18	360	2	289	1	0.802	0.997	-	-	-	-	389	313	-	-	-	-
+contig--1123361	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	122	121	121	110.0	54.3	6.1e-31	5.8e-14	1	122	1	121	0.992	1.000	-	-	-	-	123	123	-	-	-	-
+contig--1133023	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	549	371	371	261.0	77.3	1.9e-76	6.8e-21	9	557	9	379	0.676	1.000	-	-	-	-	526	355	-	-	-	-
+contig--1133023	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	549	376	376	261.0	56.3	1.9e-76	1.7e-14	9	557	14	389	0.685	1.000	-	-	-	-	526	341	-	-	-	-
+contig--1149779	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	302	303	302	219.3	133.6	4.4e-63	2.4e-37	303	2	303	1	1.000	0.997	-	-	-	-	303	295	-	-	-	-
+contig--1149779	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	302	300	300	219.3	104.4	4.4e-63	1.3e-28	303	2	302	3	0.993	1.000	-	-	-	-	303	332	-	-	-	-
+contig--1149779	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	302	255	255	219.3	82.9	4.4e-63	8.8e-22	303	2	257	3	0.844	1.000	-	-	-	-	303	226	-	-	-	-
+contig--1159799	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	374	213	213	192.7	79.9	7.1e-56	1.1e-21	375	2	374	162	0.570	1.000	-	-	-	-	401	214	-	-	-	-
+contig--1159799	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	374	227	227	192.7	61.3	7.1e-56	5.4e-16	375	2	373	147	0.607	1.000	-	-	-	-	401	230	-	-	-	-
+contig--1171145	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	364	360	360	211.7	106.8	5.2e-61	5.3e-29	2	365	6	365	0.989	1.000	-	-	-	-	388	242	-	-	-	-
+contig--1176662	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	292	269	269	222.3	142.9	1.5e-64	1.1e-40	2	293	22	290	0.921	1.000	-	-	-	-	292	270	-	-	-	-
+contig--1176662	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	292	259	259	222.3	69.1	1.5e-64	1.3e-18	2	293	24	282	0.887	1.000	-	-	-	-	292	258	-	-	-	-
+contig--1192886	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	332	331	331	280.4	178.1	1.6e-81	8.6e-51	332	1	331	1	0.997	1.000	-	-	-	-	335	340	-	-	-	-
+contig--1192886	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	332	330	330	280.4	97.5	1.6e-81	1.5e-26	332	1	330	1	0.994	1.000	-	-	-	-	335	382	-	-	-	-
+contig--1192886	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	332	329	329	280.4	75.1	1.6e-81	2e-19	332	1	330	2	0.991	1.000	-	-	-	-	335	274	-	-	-	-
+contig--1202655	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	984	957	957	735.1	422.8	3.3e-219	4.2e-125	48	1031	75	1031	0.973	1.000	-	-	-	-	1044	992	-	-	-	-
+contig--1202655	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	984	377	377	735.1	145.3	3.3e-219	1.4e-41	48	1031	655	1031	0.383	1.000	-	-	-	-	1044	383	-	-	-	-
+contig--1209771	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	278	281	277	220.9	137.8	1.5e-63	1.3e-38	278	1	282	2	0.996	0.986	-	-	-	-	279	288	-	-	-	-
+contig--1209771	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	278	275	275	220.9	61.7	1.5e-63	1e-15	278	1	276	2	0.989	1.000	-	-	-	-	279	325	-	-	-	-
+contig--1210133	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	733	730	730	419.3	264.6	5.8e-124	2.2e-77	736	4	733	4	0.996	1.000	-	-	-	-	749	820	-	-	-	-
+contig--1210133	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	733	418	418	419.3	130.9	5.8e-124	3.1e-37	736	4	603	186	0.570	1.000	-	-	-	-	749	430	-	-	-	-
+contig--1210200	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	406	405	405	289.8	208.3	2.3e-84	6.6e-60	406	1	405	1	0.998	1.000	-	-	-	-	405	409	-	-	-	-
+contig--1210200	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	406	403	403	289.8	113.2	2.3e-84	6.2e-31	406	1	405	3	0.993	1.000	-	-	-	-	405	394	-	-	-	-
+contig--1210200	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	406	281	281	289.8	89.9	2.3e-84	3e-24	406	1	281	1	0.692	1.000	-	-	-	-	405	291	-	-	-	-
+contig--1210202	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	390	387	387	195.9	95.6	1.4e-56	2.1e-26	390	1	387	1	0.992	1.000	-	-	-	-	402	484	-	-	-	-
+contig--1211922	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	220	240	220	125.2	79.6	1.2e-34	4e-21	300	81	300	61	1.000	0.917	-	-	-	-	220	247	-	-	-	-
+contig--1211922	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	220	206	206	125.2	78.2	1.2e-34	1.3e-20	300	81	300	95	0.936	1.000	-	-	-	-	220	206	-	-	-	-
+contig--1211922	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	220	215	215	125.2	52.4	1.2e-34	1.5e-12	300	81	300	86	0.977	1.000	-	-	-	-	220	188	-	-	-	-
+contig--1212351	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	330	317	317	162.9	92.8	6.8e-47	1.4e-25	330	1	317	1	0.961	1.000	-	-	-	-	335	323	-	-	-	-
+contig--1212351	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	330	323	323	162.9	75.1	6.8e-47	3.8e-20	330	1	323	1	0.979	1.000	-	-	-	-	335	318	-	-	-	-
+contig--1212661	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	351	212	212	149.9	70.5	5.8e-43	7.2e-19	1	351	1	212	0.604	1.000	-	-	-	-	371	211	-	-	-	-
+contig--1212661	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	351	204	204	149.9	59.0	5.8e-43	2.7e-15	1	351	1	204	0.581	1.000	-	-	-	-	371	205	-	-	-	-
+contig--1213982	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	561	559	559	435.9	190.3	3.4e-129	5.5e-55	561	1	561	3	0.996	1.000	-	-	-	-	525	486	-	-	-	-
+contig--1213982	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	561	560	560	435.9	131.0	3.4e-129	5.2e-37	561	1	561	2	0.998	1.000	-	-	-	-	525	512	-	-	-	-
+contig--1214168	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	332	330	330	182.3	117.0	9.6e-53	7e-33	1	332	2	331	0.994	1.000	-	-	-	-	337	336	-	-	-	-
+contig--1214168	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	332	331	330	182.3	91.6	9.6e-53	3.9e-25	1	332	3	333	0.994	0.997	-	-	-	-	337	326	-	-	-	-
+contig--1214394	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	422	256	256	205.5	100.1	1e-59	8.5e-28	423	2	422	167	0.607	1.000	-	-	-	-	447	256	-	-	-	-
+contig--1214394	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	422	248	248	205.5	74.2	1e-59	7e-20	423	2	410	163	0.588	1.000	-	-	-	-	447	250	-	-	-	-
+contig--1214513	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	345	346	345	190.5	121.3	3.3e-55	3.6e-34	2	346	2	347	1.000	0.997	-	-	-	-	346	348	-	-	-	-
+contig--1214513	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	345	344	344	190.5	97.2	3.3e-55	8.3e-27	2	346	3	346	0.997	1.000	-	-	-	-	346	336	-	-	-	-
+contig--1214669	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	299	288	288	184.4	80.4	1.6e-52	2.9e-21	299	1	292	5	0.963	1.000	-	-	-	-	317	295	-	-	-	-
+contig--1214754	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	420	345	345	194.9	111.1	1.5e-56	4.3e-31	512	93	512	168	0.821	1.000	-	-	-	-	434	356	-	-	-	-
+contig--1214754	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	420	343	343	194.9	102.2	1.5e-56	2.5e-28	512	93	512	170	0.817	1.000	-	-	-	-	434	345	-	-	-	-
+contig--1215349	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	332	330	330	196.5	115.4	8.9e-57	2.2e-32	332	1	331	2	0.994	1.000	-	-	-	-	328	334	-	-	-	-
+contig--1238415	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	356	347	347	229.4	95.2	4e-66	9.8e-26	216	571	223	569	0.975	1.000	-	-	-	-	359	339	-	-	-	-
+contig--130023	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	390	349	349	175.0	106.9	1.5e-50	7.9e-30	683	294	682	334	0.895	1.000	-	-	-	-	390	348	-	-	-	-
+contig--130023	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	390	370	370	175.0	92.4	1.5e-50	2.3e-25	683	294	682	313	0.949	1.000	-	-	-	-	390	360	-	-	-	-
+contig--1326571	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	298	264	264	208.3	99.1	2.6e-60	1.8e-27	3	300	7	270	0.886	1.000	-	-	-	-	297	301	-	-	-	-
+contig--1326571	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	298	236	236	208.3	52.9	2.6e-60	1e-13	3	300	35	270	0.792	1.000	-	-	-	-	297	245	-	-	-	-
+contig--1346273	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	372	372	371	313.1	198.1	2e-91	7.9e-57	374	3	373	2	0.997	0.997	-	-	-	-	368	366	-	-	-	-
+contig--1346273	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	372	364	364	313.1	148.3	2e-91	7.3e-42	374	3	366	3	0.978	1.000	-	-	-	-	368	369	-	-	-	-
+contig--1346273	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	372	366	366	313.1	129.1	2e-91	9.4e-36	374	3	371	6	0.984	1.000	-	-	-	-	368	339	-	-	-	-
+contig--1368084	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	360	338	338	212.0	99.5	7.1e-61	4.8e-27	361	2	341	4	0.939	1.000	-	-	-	-	345	311	-	-	-	-
+contig--137819	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	732	729	729	690.7	378.6	8.2e-206	9.1e-112	4	735	6	734	0.996	1.000	-	-	-	-	731	719	-	-	-	-
+contig--137819	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	732	721	721	690.7	272.3	8.2e-206	7.2e-80	4	735	6	726	0.985	1.000	-	-	-	-	731	748	-	-	-	-
+contig--1379481	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	406	405	405	214.3	132.4	8.4e-62	9.9e-37	1	406	1	405	0.998	1.000	-	-	-	-	414	271	-	-	-	-
+contig--1407263	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	489	488	488	298.9	188.9	1.2e-87	1.5e-54	490	2	490	3	0.998	1.000	-	-	-	-	496	504	-	-	-	-
+contig--1407263	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	489	487	487	298.9	78.5	1.2e-87	2e-21	490	2	489	3	0.996	1.000	-	-	-	-	496	542	-	-	-	-
+contig--1437319	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	321	323	321	241.2	91.5	1.7e-70	3.4e-25	327	7	328	6	1.000	0.994	-	-	-	-	332	312	-	-	-	-
+contig--1437319	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	321	185	185	241.2	55.2	1.7e-70	3.8e-14	327	7	197	13	0.576	1.000	-	-	-	-	332	184	-	-	-	-
+contig--1458589	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	315	314	314	226.4	140.5	9e-66	5.9e-40	2	316	2	315	0.997	1.000	-	-	-	-	318	325	-	-	-	-
+contig--147097	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	332	331	331	256.0	148.8	1e-74	1.8e-42	2	333	2	332	0.997	1.000	-	-	-	-	324	318	-	-	-	-
+contig--147097	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	332	241	241	256.0	65.2	1e-74	1.9e-17	2	333	4	244	0.726	1.000	-	-	-	-	324	246	-	-	-	-
+contig--151080	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	2611	1203	1203	1212.6	446.8	0	2.5e-132	2627	17	1279	77	0.461	1.000	-	-	-	-	2859	1200	-	-	-	-
+contig--151080	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2611	1107	1107	1212.6	249.4	0	5.8e-73	2627	17	1140	34	0.424	1.000	-	-	-	-	2859	1132	-	-	-	-
+contig--151080	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	2611	1162	1162	1212.6	243.5	0	4.9e-71	2627	17	2513	1352	0.445	1.000	-	-	-	-	2859	1356	-	-	-	-
+contig--151080	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2611	738	738	1212.6	95.9	0	1.1e-26	2627	17	2084	1347	0.283	1.000	-	-	-	-	2859	788	-	-	-	-
+contig--151199	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	536	533	533	270.9	104.0	1.1e-78	2.1e-28	538	3	535	3	0.994	1.000	-	-	-	-	561	513	-	-	-	-
+contig--151527	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	949	942	942	596.2	296.3	4.3e-177	2.7e-86	950	2	943	2	0.993	1.000	-	-	-	-	991	627	-	-	-	-
+contig--151527	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	949	587	587	596.2	89.2	4.3e-177	6.4e-24	950	2	928	342	0.619	1.000	-	-	-	-	991	490	-	-	-	-
+contig--151527	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	949	583	583	596.2	60.6	4.3e-177	4e-15	950	2	928	346	0.614	1.000	-	-	-	-	991	532	-	-	-	-
+contig--151601	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1375	1375	1375	921.8	536.2	1.6e-275	2.6e-159	1	1375	1	1375	1.000	1.000	-	-	-	-	1373	1476	-	-	-	-
+contig--151601	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1375	1072	1072	921.8	180.0	1.6e-275	4.9e-52	1	1375	207	1278	0.780	1.000	-	-	-	-	1373	1181	-	-	-	-
+contig--151751	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	449	393	393	249.9	145.6	4.2e-73	1.6e-41	603	155	592	200	0.875	1.000	-	-	-	-	451	395	-	-	-	-
+contig--151751	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	449	396	396	249.9	126.3	4.2e-73	1.4e-35	603	155	594	199	0.882	1.000	-	-	-	-	451	389	-	-	-	-
+contig--151876	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1084	1083	1083	788.1	439.7	3.5e-235	3.3e-130	2	1085	2	1084	0.999	1.000	-	-	-	-	1133	1216	-	-	-	-
+contig--151876	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1084	388	388	788.1	134.4	3.5e-235	2.7e-38	2	1085	141	528	0.358	1.000	-	-	-	-	1133	436	-	-	-	-
+contig--151876	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1084	457	457	788.1	89.1	3.5e-235	1.2e-24	2	1085	628	1084	0.422	1.000	-	-	-	-	1133	504	-	-	-	-
+contig--152048	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	582	573	573	403.0	163.1	1.4e-118	3e-46	584	3	575	3	0.985	1.000	-	-	-	-	577	523	-	-	-	-
+contig--152048	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	582	552	552	403.0	75.1	1.4e-118	2e-19	584	3	555	4	0.948	1.000	-	-	-	-	577	438	-	-	-	-
+contig--1531838	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	313	312	312	235.1	130.8	7.5e-68	1.7e-36	313	1	313	2	0.997	1.000	-	-	-	-	319	318	-	-	-	-
+contig--1531838	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	313	313	313	235.1	84.3	7.5e-68	1.5e-22	313	1	313	1	1.000	1.000	-	-	-	-	319	357	-	-	-	-
+contig--1531838	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	313	311	311	235.1	74.6	7.5e-68	2.9e-19	313	1	313	3	0.994	1.000	-	-	-	-	319	270	-	-	-	-
+contig--1568447	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	683	679	679	574.2	297.1	2.6e-170	9.6e-87	2	684	3	681	0.994	1.000	-	-	-	-	678	646	-	-	-	-
+contig--1568447	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	683	655	655	574.2	172.0	2.6e-170	1e-48	2	684	27	681	0.959	1.000	-	-	-	-	678	592	-	-	-	-
+contig--1568447	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	683	317	317	574.2	128.7	2.6e-170	6.1e-36	2	684	367	683	0.464	1.000	-	-	-	-	678	333	-	-	-	-
+contig--156996	-	LSU_rRNA_archaea	LSU_rRNA_bacteria	2870	2868	2863	1930.8	1219.6	0	0	3613	744	3606	739	0.998	0.998	-	-	-	-	2936	2877	-	-	-	-
+contig--156996	-	LSU_rRNA_archaea	LSU_rRNA_eukarya	2870	1044	1044	1930.8	426.2	0	2.8e-126	3613	744	1819	776	0.364	1.000	-	-	-	-	2936	1078	-	-	-	-
+contig--156996	-	LSU_rRNA_archaea	LSU_rRNA_eukarya	2870	1185	1185	1930.8	305.9	0	5.1e-90	3613	744	3005	1821	0.413	1.000	-	-	-	-	2936	1309	-	-	-	-
+contig--156996	-	LSU_rRNA_archaea	LSU_rRNA_eukarya	2870	406	406	1930.8	122.9	0	8.1e-35	3613	744	3469	3064	0.141	1.000	-	-	-	-	2936	412	-	-	-	-
+contig--1572437	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	257	196	196	153.9	53.0	3.6e-44	1.5e-13	1	257	1	196	0.763	1.000	-	-	-	-	256	197	-	-	-	-
+contig--1583871	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	727	450	450	385.1	69.5	7.2e-114	1.5e-18	1	727	9	458	0.619	1.000	-	-	-	-	744	424	-	-	-	-
+contig--1584065	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	332	312	312	196.9	91.9	2.6e-56	9.6e-25	332	1	313	2	0.940	1.000	-	-	-	-	334	304	-	-	-	-
+contig--159495	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	275	266	266	148.0	89.9	1.6e-41	3.9e-24	11920	12194	11927	12192	0.967	1.000	-	-	-	-	270	250	-	-	-	-
+contig--1596054	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	602	599	599	537.8	172.4	6.4e-160	1.4e-49	603	2	603	5	0.995	1.000	-	-	-	-	600	555	-	-	-	-
+contig--1596054	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	602	583	583	537.8	105.8	6.4e-160	2e-29	603	2	602	20	0.968	1.000	-	-	-	-	600	529	-	-	-	-
+contig--1604373	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	423	410	410	296.1	164.0	1.7e-86	2.8e-46	1	423	14	423	0.969	1.000	-	-	-	-	449	331	-	-	-	-
+contig--1604373	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	423	417	417	296.1	150.7	1.7e-86	1.7e-42	1	423	7	423	0.986	1.000	-	-	-	-	449	399	-	-	-	-
+contig--1604373	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	423	398	398	296.1	117.1	1.7e-86	3.4e-32	1	423	26	423	0.941	1.000	-	-	-	-	449	375	-	-	-	-
+contig--1634977	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	314	314	313	276.6	209.4	2.2e-80	3.1e-60	2	315	1	314	0.997	0.997	-	-	-	-	316	322	-	-	-	-
+contig--1634977	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	314	314	313	276.6	103.9	2.2e-80	1.8e-28	2	315	1	314	0.997	0.997	-	-	-	-	316	365	-	-	-	-
+contig--1634977	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	314	313	312	276.6	69.4	2.2e-80	1.1e-17	2	315	1	313	0.994	0.997	-	-	-	-	316	257	-	-	-	-
+contig--1644897	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	569	433	433	272.6	81.3	5.7e-80	4.2e-22	15	583	91	523	0.761	1.000	-	-	-	-	572	427	-	-	-	-
+contig--1662509	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	648	645	645	468.7	178.2	4.2e-139	2.5e-51	1	648	1	645	0.995	1.000	-	-	-	-	654	608	-	-	-	-
+contig--1662509	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	648	642	642	468.7	113.6	4.2e-139	9.2e-32	1	648	2	643	0.991	1.000	-	-	-	-	654	594	-	-	-	-
+contig--166397	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1160	1161	1152	998.5	535.2	1.2e-298	5.4e-159	31	1190	22	1182	0.993	0.992	-	-	-	-	1161	1133	-	-	-	-
+contig--166397	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1160	1014	1014	998.5	320.4	1.2e-298	2.3e-94	31	1190	61	1074	0.874	1.000	-	-	-	-	1161	1031	-	-	-	-
+contig--1688622	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	376	357	357	268.7	117.7	1.5e-78	4.4e-33	378	3	365	9	0.949	1.000	-	-	-	-	376	350	-	-	-	-
+contig--1688622	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	376	344	344	268.7	71.0	1.5e-78	3.6e-19	378	3	348	5	0.915	1.000	-	-	-	-	376	374	-	-	-	-
+contig--1692849	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	336	322	322	260.0	84.3	3.7e-76	5.2e-23	1	336	12	333	0.958	1.000	-	-	-	-	353	300	-	-	-	-
+contig--1692849	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	336	309	309	260.0	79.9	3.7e-76	1.4e-21	1	336	25	333	0.920	1.000	-	-	-	-	353	297	-	-	-	-
+contig--1720439	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	610	611	610	433.7	233.2	7.5e-128	2e-67	2	611	1	611	1.000	0.998	-	-	-	-	609	581	-	-	-	-
+contig--1720439	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	610	604	604	433.7	139.9	7.5e-128	5.3e-39	2	611	8	611	0.990	1.000	-	-	-	-	609	544	-	-	-	-
+contig--1720439	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	610	257	257	433.7	95.3	7.5e-128	7.3e-26	2	611	355	611	0.421	1.000	-	-	-	-	609	271	-	-	-	-
+contig--1768180	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	349	339	339	268.8	183.3	1.4e-78	7.2e-53	1	349	2	340	0.971	1.000	-	-	-	-	360	345	-	-	-	-
+contig--1768180	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	349	244	244	268.8	82.0	1.4e-78	1.7e-22	1	349	3	246	0.699	1.000	-	-	-	-	360	241	-	-	-	-
+contig--1776240	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	463	463	463	396.4	235.5	1.4e-116	4e-68	463	1	463	1	1.000	1.000	-	-	-	-	463	463	-	-	-	-
+contig--1776240	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	463	463	463	396.4	150.5	1.4e-116	1.6e-42	463	1	463	1	1.000	1.000	-	-	-	-	463	508	-	-	-	-
+contig--1776240	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	463	462	462	396.4	119.1	1.4e-116	1e-32	463	1	463	2	0.998	1.000	-	-	-	-	463	388	-	-	-	-
+contig--1796896	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	300	297	297	242.6	136.0	1.1e-70	1.3e-38	1	300	3	299	0.990	1.000	-	-	-	-	312	304	-	-	-	-
+contig--1796896	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	300	240	240	242.6	63.2	1.1e-70	8e-17	1	300	2	241	0.800	1.000	-	-	-	-	312	238	-	-	-	-
+contig--1797769	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	500	226	226	258.1	50.8	1.3e-75	6.5e-13	501	2	438	213	0.452	1.000	-	-	-	-	506	221	-	-	-	-
+contig--1834142	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	299	297	297	144.4	76.4	2.6e-41	1.2e-20	1	299	2	298	0.993	1.000	-	-	-	-	288	288	-	-	-	-
+contig--185227	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	300	288	288	234.4	92.2	1.9e-68	2.2e-25	303	4	302	15	0.960	1.000	-	-	-	-	300	284	-	-	-	-
+contig--185227	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	300	290	290	234.4	54.8	1.9e-68	4.9e-14	303	4	300	11	0.967	1.000	-	-	-	-	300	284	-	-	-	-
+contig--185298	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	646	450	450	228.1	130.1	1.5e-66	8.1e-37	1	646	2	451	0.697	1.000	-	-	-	-	643	464	-	-	-	-
+contig--185298	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	646	370	370	228.1	113.8	1.5e-66	8.2e-32	1	646	2	371	0.573	1.000	-	-	-	-	643	365	-	-	-	-
+contig--185309	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	912	909	908	711.7	405.2	3.9e-212	8.2e-120	128	1039	127	1035	0.996	0.999	-	-	-	-	904	890	-	-	-	-
+contig--185309	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	912	902	902	711.7	280.8	3.9e-212	1.9e-82	128	1039	130	1031	0.989	1.000	-	-	-	-	904	919	-	-	-	-
+contig--185316	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	311	307	307	185.2	92.1	5.1e-53	1.5e-24	2	312	4	310	0.987	1.000	-	-	-	-	345	235	-	-	-	-
+contig--185316	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	311	309	309	185.2	76.1	5.1e-53	5.9e-20	2	312	3	311	0.994	1.000	-	-	-	-	345	300	-	-	-	-
+contig--185316	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	311	310	310	185.2	60.5	5.1e-53	4.4e-15	2	312	2	311	0.997	1.000	-	-	-	-	345	295	-	-	-	-
+contig--185430	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	385	355	355	230.5	79.9	2.8e-67	1.1e-21	8	392	38	392	0.922	1.000	-	-	-	-	390	342	-	-	-	-
+contig--185562	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	787	722	722	528.0	174.9	5.7e-157	2.4e-50	789	3	789	68	0.917	1.000	-	-	-	-	782	649	-	-	-	-
+contig--185562	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	787	707	707	528.0	105.1	5.7e-157	3.3e-29	789	3	789	83	0.898	1.000	-	-	-	-	782	629	-	-	-	-
+contig--185811	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	525	523	523	268.3	134.0	2e-78	5.4e-38	526	2	524	2	0.996	1.000	-	-	-	-	530	539	-	-	-	-
+contig--186013	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	745	743	743	487.0	252.4	3.8e-144	5.3e-73	745	1	744	2	0.997	1.000	-	-	-	-	762	526	-	-	-	-
+contig--186013	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	745	286	286	487.0	96.7	3.8e-144	5.1e-26	745	1	290	5	0.384	1.000	-	-	-	-	762	274	-	-	-	-
+contig--186013	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	745	279	279	487.0	90.2	3.8e-144	3.2e-24	745	1	280	2	0.374	1.000	-	-	-	-	762	271	-	-	-	-
+contig--186013	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	745	224	224	487.0	51.6	3.8e-144	1.5e-12	745	1	741	518	0.301	1.000	-	-	-	-	762	210	-	-	-	-
+contig--193617	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	306	304	304	136.8	87.9	3.9e-38	1.6e-23	306	1	305	2	0.993	1.000	-	-	-	-	336	333	-	-	-	-
+contig--193617	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	306	253	253	136.8	61.4	3.9e-38	2.8e-15	306	1	305	53	0.827	1.000	-	-	-	-	336	236	-	-	-	-
+contig--193617	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	306	296	296	136.8	57.2	3.9e-38	2.2e-14	306	1	305	10	0.967	1.000	-	-	-	-	336	370	-	-	-	-
+contig--214407	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	322	297	297	227.3	112.7	1.8e-65	5e-31	15	336	18	314	0.922	1.000	-	-	-	-	339	315	-	-	-	-
+contig--2152327	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	580	575	575	294.4	159.3	2.7e-86	1.2e-45	3	582	7	581	0.991	1.000	-	-	-	-	550	552	-	-	-	-
+contig--2220335	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	423	407	407	316.5	178.0	5.7e-93	2.8e-51	423	1	407	1	0.962	1.000	-	-	-	-	405	373	-	-	-	-
+contig--2220335	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	423	196	196	316.5	53.3	5.7e-93	7.9e-14	423	1	200	5	0.463	1.000	-	-	-	-	405	180	-	-	-	-
+contig--2248804	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	375	361	361	274.5	182.5	9.7e-80	4e-52	165	539	165	525	0.963	1.000	-	-	-	-	386	378	-	-	-	-
+contig--2248804	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	375	351	351	274.5	121.6	9.7e-80	8.5e-34	165	539	165	515	0.936	1.000	-	-	-	-	386	411	-	-	-	-
+contig--2248804	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	375	353	353	274.5	99.4	9.7e-80	9.2e-27	165	539	165	517	0.941	1.000	-	-	-	-	386	307	-	-	-	-
+contig--2248828	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	581	580	580	385.6	173.8	1.6e-113	3e-49	581	1	581	2	0.998	1.000	-	-	-	-	602	400	-	-	-	-
+contig--2248828	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	581	293	293	385.6	98.5	1.6e-113	9.9e-27	581	1	294	2	0.504	1.000	-	-	-	-	602	289	-	-	-	-
+contig--2248828	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	581	283	283	385.6	92.5	1.6e-113	9.1e-25	581	1	292	10	0.487	1.000	-	-	-	-	602	275	-	-	-	-
+contig--2249544	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	435	428	428	362.4	123.4	4.9e-107	8e-35	435	1	429	2	0.984	1.000	-	-	-	-	443	398	-	-	-	-
+contig--2249544	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	435	423	423	362.4	92.3	4.9e-107	2.4e-25	435	1	424	2	0.972	1.000	-	-	-	-	443	402	-	-	-	-
+contig--2249727	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	350	348	348	250.6	134.9	9.5e-73	1.6e-37	4	353	5	352	0.994	1.000	-	-	-	-	368	289	-	-	-	-
+contig--2249727	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	350	348	348	250.6	110.6	9.5e-73	2.3e-30	4	353	5	352	0.994	1.000	-	-	-	-	368	324	-	-	-	-
+contig--2249727	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	350	348	348	250.6	85.1	9.5e-73	1.6e-22	4	353	5	352	0.994	1.000	-	-	-	-	368	333	-	-	-	-
+contig--2249925	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	897	875	875	638.4	334.0	1.1e-189	7.1e-98	2	898	23	897	0.975	1.000	-	-	-	-	896	833	-	-	-	-
+contig--2249925	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	897	882	882	638.4	169.7	1.1e-189	5.2e-48	2	898	17	898	0.983	1.000	-	-	-	-	896	764	-	-	-	-
+contig--2249925	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	897	266	266	638.4	89.6	1.1e-189	3.9e-24	2	898	633	898	0.297	1.000	-	-	-	-	896	279	-	-	-	-
+contig--2250093	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	485	472	472	378.5	123.9	7.1e-112	5.8e-35	487	3	486	15	0.973	1.000	-	-	-	-	475	427	-	-	-	-
+contig--2250093	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	485	464	464	378.5	76.7	7.1e-112	1.2e-20	487	3	483	20	0.957	1.000	-	-	-	-	475	425	-	-	-	-
+contig--2250342	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	587	524	523	224.8	102.7	2.6e-65	1.4e-28	1	587	65	588	0.891	0.998	-	-	-	-	591	569	-	-	-	-
+contig--2250515	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	776	774	774	502.0	302.9	6.4e-149	6.2e-89	1	776	2	775	0.997	1.000	-	-	-	-	809	883	-	-	-	-
+contig--2250515	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	776	384	384	502.0	136.3	6.4e-149	7.4e-39	1	776	131	514	0.495	1.000	-	-	-	-	809	397	-	-	-	-
+contig--2250797	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	365	361	361	222.6	129.5	6.7e-65	1.2e-36	366	2	363	3	0.989	1.000	-	-	-	-	365	362	-	-	-	-
+contig--2250797	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	365	358	358	222.6	104.6	6.7e-65	4.6e-29	366	2	360	3	0.981	1.000	-	-	-	-	365	348	-	-	-	-
+contig--2250883	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	393	393	393	317.4	186.2	3.2e-93	9.8e-54	396	4	396	4	1.000	1.000	-	-	-	-	389	384	-	-	-	-
+contig--2250883	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	393	277	277	317.4	91.8	3.2e-93	1.9e-25	396	4	394	118	0.705	1.000	-	-	-	-	389	274	-	-	-	-
+contig--2250940	+	5_8S_rRNA	LSU_rRNA_bacteria	152	498	140	98.9	50.7	4.2e-26	8.8e-13	239	390	251	748	0.921	0.281	-	-	-	-	153	248	-	-	-	-
+contig--2251064	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	424	355	355	218.0	140.7	1.6e-63	5e-40	1	424	3	357	0.837	1.000	-	-	-	-	430	361	-	-	-	-
+contig--2251064	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	424	374	374	218.0	109.6	1.6e-63	1.5e-30	1	424	4	377	0.882	1.000	-	-	-	-	430	371	-	-	-	-
+contig--2251231	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	457	222	222	223.7	75.7	3.2e-65	1.9e-20	467	11	464	243	0.486	1.000	-	-	-	-	459	223	-	-	-	-
+contig--2251231	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	457	213	213	223.7	63.5	3.2e-65	1.2e-16	467	11	461	249	0.466	1.000	-	-	-	-	459	215	-	-	-	-
+contig--2251329	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	313	297	297	210.9	103.1	4e-61	1.1e-28	1	313	3	299	0.949	1.000	-	-	-	-	311	290	-	-	-	-
+contig--2251329	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	313	250	250	210.9	53.8	4e-61	5.5e-14	1	313	3	252	0.799	1.000	-	-	-	-	311	246	-	-	-	-
+contig--2251392	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	753	729	729	472.3	117.0	3.5e-140	6.8e-33	1	753	3	731	0.968	1.000	-	-	-	-	785	581	-	-	-	-
+contig--2251392	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	753	736	736	472.3	81.7	3.5e-140	3.8e-22	1	753	1	736	0.977	1.000	-	-	-	-	785	580	-	-	-	-
+contig--2251500	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	473	472	472	382.1	240.0	2.9e-112	1.7e-69	1	473	2	473	0.998	1.000	-	-	-	-	474	472	-	-	-	-
+contig--2251500	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	473	473	473	382.1	183.7	2.9e-112	1.5e-52	1	473	1	473	1.000	1.000	-	-	-	-	474	518	-	-	-	-
+contig--2251500	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	473	473	473	382.1	143.2	2.9e-112	5.2e-40	1	473	1	473	1.000	1.000	-	-	-	-	474	399	-	-	-	-
+contig--2251533	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	423	203	203	186.2	61.1	6.4e-54	4.9e-16	427	5	425	223	0.480	1.000	-	-	-	-	444	203	-	-	-	-
+contig--2251634	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	377	372	372	194.8	94.7	6.4e-56	2.4e-25	377	1	372	1	0.987	1.000	-	-	-	-	379	232	-	-	-	-
+contig--2251690	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	334	314	314	206.9	98.0	2.6e-59	1.5e-26	334	1	315	2	0.940	1.000	-	-	-	-	333	303	-	-	-	-
+contig--2251849	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	424	217	217	194.1	72.2	2.7e-56	2.4e-19	2	425	5	221	0.512	1.000	-	-	-	-	447	218	-	-	-	-
+contig--2251849	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	424	219	219	194.1	62.8	2.7e-56	2e-16	2	425	7	225	0.517	1.000	-	-	-	-	447	222	-	-	-	-
+contig--2252003	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	609	609	609	404.2	202.8	3.8e-119	5.1e-58	1	609	1	609	1.000	1.000	-	-	-	-	623	422	-	-	-	-
+contig--2252003	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	609	292	292	404.2	93.9	3.8e-119	2.5e-25	1	609	317	608	0.479	1.000	-	-	-	-	623	283	-	-	-	-
+contig--2252003	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	609	290	290	404.2	90.4	3.8e-119	3.9e-24	1	609	304	593	0.476	1.000	-	-	-	-	623	278	-	-	-	-
+contig--2252145	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	422	269	269	220.6	79.5	2.9e-64	1.4e-21	1	422	1	269	0.637	1.000	-	-	-	-	441	279	-	-	-	-
+contig--2252145	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	422	295	295	220.6	59.9	2.9e-64	1.4e-15	1	422	2	296	0.699	1.000	-	-	-	-	441	239	-	-	-	-
+contig--2252346	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	634	633	633	444.0	188.4	1.3e-131	2.1e-54	1	634	2	634	0.998	1.000	-	-	-	-	597	559	-	-	-	-
+contig--2252346	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	634	626	626	444.0	129.3	1.3e-131	1.7e-36	1	634	3	628	0.987	1.000	-	-	-	-	597	561	-	-	-	-
+contig--2252644	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	743	739	739	404.9	192.0	3.7e-119	5.7e-55	42	784	46	784	0.995	1.000	-	-	-	-	799	751	-	-	-	-
+contig--2252644	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	743	741	740	404.9	122.0	3.7e-119	1.4e-33	42	784	45	785	0.996	0.999	-	-	-	-	799	685	-	-	-	-
+contig--2252644	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	743	159	159	404.9	55.1	3.7e-119	1e-13	42	784	624	782	0.214	1.000	-	-	-	-	799	165	-	-	-	-
+contig--2252661	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	773	372	372	300.6	133.1	2.2e-88	9.8e-38	776	4	776	405	0.481	1.000	-	-	-	-	682	362	-	-	-	-
+contig--2252661	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	773	371	371	300.6	126.8	2.2e-88	9.8e-36	776	4	775	405	0.480	1.000	-	-	-	-	682	352	-	-	-	-
+contig--2252860	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	348	347	347	167.8	57.7	9e-48	3.8e-14	1	348	2	348	0.997	1.000	-	-	-	-	353	209	-	-	-	-
+contig--2252929	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	860	859	859	547.7	335.7	1.1e-162	7.6e-99	860	1	859	1	0.999	1.000	-	-	-	-	861	855	-	-	-	-
+contig--2252929	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	860	628	628	547.7	80.6	1.1e-162	4.7e-22	860	1	859	232	0.730	1.000	-	-	-	-	861	689	-	-	-	-
+contig--2252929	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	860	190	190	547.7	60.4	1.1e-162	5.7e-16	860	1	194	5	0.221	1.000	-	-	-	-	861	184	-	-	-	-
+contig--2253054	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	446	442	442	363.0	191.6	1.7e-106	7.5e-55	1	446	4	445	0.991	1.000	-	-	-	-	463	426	-	-	-	-
+contig--2253054	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	446	441	441	363.0	97.4	1.7e-106	3.7e-26	1	446	5	445	0.989	1.000	-	-	-	-	463	405	-	-	-	-
+contig--2253227	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	219	209	209	116.0	63.9	9.3e-33	7.4e-17	2	220	2	210	0.954	1.000	-	-	-	-	202	193	-	-	-	-
+contig--2253688	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	443	442	442	249.9	139.4	1.5e-72	7.5e-39	443	1	442	1	0.998	1.000	-	-	-	-	442	298	-	-	-	-
+contig--2254060	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	627	625	625	450.7	197.1	1.1e-133	5e-57	627	1	627	3	0.997	1.000	-	-	-	-	582	543	-	-	-	-
+contig--2254060	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	627	626	626	450.7	123.7	1.1e-133	8.3e-35	627	1	627	2	0.998	1.000	-	-	-	-	582	553	-	-	-	-
+contig--2254117	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	804	800	800	530.1	305.9	2.2e-157	7.5e-90	2	805	3	802	0.995	1.000	-	-	-	-	810	902	-	-	-	-
+contig--2254117	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	804	498	498	530.1	102.1	2.2e-157	1.5e-28	2	805	271	768	0.619	1.000	-	-	-	-	810	542	-	-	-	-
+contig--2254117	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	804	134	134	530.1	58.3	2.2e-157	2.4e-15	2	805	19	152	0.167	1.000	-	-	-	-	810	133	-	-	-	-
+contig--2254163	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	462	437	437	243.0	152.6	8.9e-71	1.3e-43	462	1	446	10	0.946	1.000	-	-	-	-	483	450	-	-	-	-
+contig--2254163	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	462	303	303	243.0	62.5	8.9e-71	1.3e-16	462	1	304	2	0.656	1.000	-	-	-	-	483	320	-	-	-	-
+contig--2254313	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	348	345	345	195.6	166.5	3.7e-56	4.8e-47	350	3	347	3	0.991	1.000	-	-	-	-	351	329	-	-	-	-
+contig--2254313	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	348	344	344	195.6	150.9	3.7e-56	1.5e-42	350	3	346	3	0.989	1.000	-	-	-	-	351	338	-	-	-	-
+contig--2254313	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	348	344	344	195.6	123.2	3.7e-56	4.9e-34	350	3	346	3	0.989	1.000	-	-	-	-	351	333	-	-	-	-
+contig--2254317	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	361	362	361	216.6	135.8	4.3e-63	1.5e-38	362	2	362	1	1.000	0.997	-	-	-	-	363	365	-	-	-	-
+contig--2254317	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	361	361	361	216.6	109.5	4.3e-63	1.6e-30	362	2	362	2	1.000	1.000	-	-	-	-	363	354	-	-	-	-
+contig--2254400	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	333	335	333	288.8	172.9	1.4e-84	1e-49	341	9	341	7	1.000	0.994	-	-	-	-	344	341	-	-	-	-
+contig--2254400	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	333	243	243	288.8	72.2	1.4e-84	1.5e-19	341	9	340	98	0.730	1.000	-	-	-	-	344	240	-	-	-	-
+contig--2254733	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	395	367	367	226.4	121.1	8.5e-66	4.2e-34	396	2	396	30	0.929	1.000	-	-	-	-	391	369	-	-	-	-
+contig--2255132	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	396	362	362	147.4	103.7	5.9e-42	7.1e-29	1	396	1	362	0.914	1.000	-	-	-	-	404	365	-	-	-	-
+contig--2255132	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	396	208	208	147.4	58.4	5.9e-42	2.2e-15	1	396	118	325	0.525	1.000	-	-	-	-	404	221	-	-	-	-
+contig--2255353	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	810	492	492	510.6	108.3	1e-151	3e-30	1	810	10	501	0.607	1.000	-	-	-	-	794	446	-	-	-	-
+contig--2255353	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	810	498	498	510.6	72.3	1e-151	2.7e-19	1	810	9	506	0.615	1.000	-	-	-	-	794	442	-	-	-	-
+contig--2255364	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	765	759	759	624.0	324.5	2.5e-185	5e-95	765	1	759	1	0.992	1.000	-	-	-	-	760	719	-	-	-	-
+contig--2255364	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	765	754	754	624.0	192.1	2.5e-185	8.6e-55	765	1	755	2	0.986	1.000	-	-	-	-	760	673	-	-	-	-
+contig--2255364	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	765	439	439	624.0	166.7	2.5e-185	2e-47	765	1	440	2	0.574	1.000	-	-	-	-	760	449	-	-	-	-
+contig--2255543	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	367	209	209	185.5	68.1	1.1e-53	4e-18	1	367	2	210	0.569	1.000	-	-	-	-	395	210	-	-	-	-
+contig--2255543	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	367	222	222	185.5	56.2	1.1e-53	1.8e-14	1	367	2	223	0.605	1.000	-	-	-	-	395	225	-	-	-	-
+contig--2256050	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1670	1657	1657	1243.1	673.0	0	1.5e-200	1	1670	4	1660	0.992	1.000	-	-	-	-	1656	1639	-	-	-	-
+contig--2256050	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1670	637	637	1243.1	199.3	0	7.6e-58	1	1670	1000	1636	0.381	1.000	-	-	-	-	1656	651	-	-	-	-
+contig--2256050	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1670	957	957	1243.1	147.3	0	3.5e-42	1	1670	4	960	0.573	1.000	-	-	-	-	1656	1057	-	-	-	-
+contig--2271497	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	834	825	825	597.5	296.8	2.5e-177	1.2e-86	835	2	827	3	0.989	1.000	-	-	-	-	809	756	-	-	-	-
+contig--2271497	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	834	824	824	597.5	159.2	2.5e-177	7.8e-45	835	2	826	3	0.988	1.000	-	-	-	-	809	687	-	-	-	-
+contig--2271497	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	834	519	519	597.5	61.1	2.5e-177	1.5e-15	835	2	740	222	0.622	1.000	-	-	-	-	809	569	-	-	-	-
+contig--2271497	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	834	163	163	597.5	58.6	2.5e-177	8.9e-15	835	2	165	3	0.195	1.000	-	-	-	-	809	163	-	-	-	-
+contig--2298625	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	832	560	560	636.8	287.2	8.8e-190	3.3e-84	1079	248	996	437	0.673	1.000	-	-	-	-	882	561	-	-	-	-
+contig--2298625	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	832	599	599	636.8	226.8	8.8e-190	6.5e-66	1079	248	1029	431	0.720	1.000	-	-	-	-	882	597	-	-	-	-
+contig--2304422	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	464	449	449	285.0	172.0	1.8e-83	1.8e-49	464	1	449	1	0.968	1.000	-	-	-	-	508	484	-	-	-	-
+contig--2304422	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	464	299	299	285.0	91.5	1.8e-83	2.3e-25	464	1	299	1	0.644	1.000	-	-	-	-	508	346	-	-	-	-
+contig--23096	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	709	707	707	669.2	386.9	2.5e-199	2.8e-114	1	709	2	708	0.997	1.000	-	-	-	-	709	698	-	-	-	-
+contig--23096	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	709	707	707	669.2	265.0	2.5e-199	1.2e-77	1	709	1	707	0.997	1.000	-	-	-	-	709	735	-	-	-	-
+contig--232952	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	570	569	569	325.9	150.8	1.7e-95	2.7e-42	1	570	2	570	0.998	1.000	-	-	-	-	584	382	-	-	-	-
+contig--232952	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	570	285	285	325.9	93.0	1.7e-95	4.5e-25	1	570	284	568	0.500	1.000	-	-	-	-	584	276	-	-	-	-
+contig--232952	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	570	346	346	325.9	89.6	1.7e-95	6.8e-24	1	570	223	568	0.607	1.000	-	-	-	-	584	319	-	-	-	-
+contig--2330557	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	998	976	976	752.9	407.4	1.4e-224	1.9e-120	998	1	993	18	0.978	1.000	-	-	-	-	994	945	-	-	-	-
+contig--2330557	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	998	635	635	752.9	173.5	1.4e-224	4.3e-50	998	1	662	28	0.636	1.000	-	-	-	-	994	649	-	-	-	-
+contig--236053	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	400	393	393	224.4	138.6	3.5e-65	2.2e-39	401	2	397	5	0.983	1.000	-	-	-	-	443	428	-	-	-	-
+contig--236053	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	400	204	204	224.4	56.0	3.5e-65	1.2e-14	401	2	248	45	0.510	1.000	-	-	-	-	443	253	-	-	-	-
+contig--2369838	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	836	839	836	609.3	346.7	6.6e-181	9.9e-102	20	855	17	855	1.000	0.996	-	-	-	-	849	825	-	-	-	-
+contig--2369838	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	836	841	835	609.3	188.6	6.6e-181	9.6e-54	20	855	14	854	0.999	0.993	-	-	-	-	849	751	-	-	-	-
+contig--2369838	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	836	296	296	609.3	106.4	6.6e-181	3.2e-29	20	855	560	855	0.354	1.000	-	-	-	-	849	309	-	-	-	-
+contig--2412452	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	309	250	250	339.6	122.2	3.7e-100	1.9e-34	30	338	73	322	0.809	1.000	-	-	-	-	310	251	-	-	-	-
+contig--2412452	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	309	249	249	339.6	87.3	3.7e-100	8e-24	30	338	71	319	0.806	1.000	-	-	-	-	310	265	-	-	-	-
+contig--24391	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	310	309	309	224.6	154.2	1.1e-64	1.5e-43	311	2	311	3	0.997	1.000	-	-	-	-	310	310	-	-	-	-
+contig--24391	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	310	303	303	224.6	86.2	1.1e-64	8.9e-23	311	2	311	9	0.977	1.000	-	-	-	-	310	301	-	-	-	-
+contig--24391	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	310	173	173	224.6	57.8	1.1e-64	1.5e-14	311	2	175	3	0.558	1.000	-	-	-	-	310	173	-	-	-	-
+contig--2491978	-	SSU_rRNA_archaea	SSU_rRNA_bacteria	1028	1024	1024	777.7	434.2	6.1e-232	5.3e-128	1028	1	1024	1	0.996	1.000	-	-	-	-	1032	1074	-	-	-	-
+contig--2491978	-	SSU_rRNA_archaea	SSU_rRNA_microsporidia	1028	1022	1022	777.7	354.2	6.1e-232	8.4e-104	1028	1	1024	3	0.994	1.000	-	-	-	-	1032	937	-	-	-	-
+contig--2491978	-	SSU_rRNA_archaea	SSU_rRNA_eukarya	1028	431	431	777.7	199.1	6.1e-232	3.3e-57	1028	1	432	2	0.419	1.000	-	-	-	-	1032	442	-	-	-	-
+contig--2491978	-	SSU_rRNA_archaea	SSU_rRNA_eukarya	1028	543	543	777.7	118.3	6.1e-232	8.2e-33	1028	1	1025	483	0.528	1.000	-	-	-	-	1032	657	-	-	-	-
+contig--2501086	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	388	387	387	199.8	95.7	8.9e-58	1.8e-26	3	390	4	390	0.997	1.000	-	-	-	-	392	476	-	-	-	-
+contig--2506583	+	SSU_rRNA_archaea	SSU_rRNA_bacteria	1043	1044	1043	791.7	551.4	3.4e-236	2.1e-163	4	1046	4	1047	1.000	0.999	-	-	-	-	1045	1049	-	-	-	-
+contig--2506583	+	SSU_rRNA_archaea	SSU_rRNA_microsporidia	1043	1032	1032	791.7	392.9	3.4e-236	1.7e-115	4	1046	10	1041	0.989	1.000	-	-	-	-	1045	937	-	-	-	-
+contig--2506583	+	SSU_rRNA_archaea	SSU_rRNA_eukarya	1043	875	875	791.7	382.5	3.4e-236	1.4e-112	4	1046	167	1041	0.839	1.000	-	-	-	-	1045	963	-	-	-	-
+contig--2514811	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	745	745	745	506.7	275.6	4.3e-150	5.1e-80	2	746	2	746	1.000	1.000	-	-	-	-	778	544	-	-	-	-
+contig--2514811	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	745	259	259	506.7	65.3	4.3e-150	1e-16	2	746	12	270	0.348	1.000	-	-	-	-	778	250	-	-	-	-
+contig--2514811	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	745	259	259	506.7	57.8	4.3e-150	2e-14	2	746	488	746	0.348	1.000	-	-	-	-	778	255	-	-	-	-
+contig--2514811	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	745	257	257	506.7	56.9	4.3e-150	5.1e-14	2	746	490	746	0.345	1.000	-	-	-	-	778	249	-	-	-	-
+contig--2519402	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	423	405	405	226.6	172.4	7.5e-66	1.3e-49	424	2	420	16	0.957	1.000	-	-	-	-	437	410	-	-	-	-
+contig--2519402	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	423	252	252	226.6	75.3	7.5e-66	1.8e-20	424	2	300	49	0.596	1.000	-	-	-	-	437	263	-	-	-	-
+contig--2528721	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	405	305	305	200.4	95.2	3.4e-58	2.6e-26	1	405	1	305	0.753	1.000	-	-	-	-	463	244	-	-	-	-
+contig--2528721	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	405	280	280	200.4	72.1	3.4e-58	3e-19	1	405	2	281	0.691	1.000	-	-	-	-	463	252	-	-	-	-
+contig--2531154	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	563	563	563	358.6	217.5	1.2e-105	3.5e-63	80	642	80	642	1.000	1.000	-	-	-	-	573	563	-	-	-	-
+contig--2531154	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	563	349	349	358.6	123.1	1.2e-105	7e-35	80	642	284	632	0.620	1.000	-	-	-	-	573	408	-	-	-	-
+contig--2543224	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	322	257	257	191.1	122.0	3.9e-55	2.2e-34	322	1	311	55	0.798	1.000	-	-	-	-	368	241	-	-	-	-
+contig--2552028	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	590	589	589	292.0	175.6	2.9e-85	8.5e-50	1	590	1	589	0.998	1.000	-	-	-	-	613	411	-	-	-	-
+contig--2552028	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	590	287	287	292.0	74.6	2.9e-85	2.4e-19	1	590	304	590	0.486	1.000	-	-	-	-	613	275	-	-	-	-
+contig--2552028	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	590	287	287	292.0	70.4	2.9e-85	3e-18	1	590	304	590	0.486	1.000	-	-	-	-	613	279	-	-	-	-
+contig--256048	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	469	224	224	231.1	114.7	7.1e-67	2.1e-31	1	469	1	224	0.478	1.000	-	-	-	-	410	193	-	-	-	-
+contig--2564558	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	417	398	398	308.9	140.3	1.2e-90	6.6e-40	1	417	1	398	0.954	1.000	-	-	-	-	423	488	-	-	-	-
+contig--2564558	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	417	140	140	308.9	52.0	1.2e-90	1.9e-13	1	417	1	140	0.336	1.000	-	-	-	-	423	139	-	-	-	-
+contig--2565011	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	589	586	586	421.6	232.8	2.2e-124	4.5e-67	589	1	586	1	0.995	1.000	-	-	-	-	599	421	-	-	-	-
+contig--2565011	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	589	550	550	421.6	79.4	2.2e-124	5.8e-21	589	1	571	22	0.934	1.000	-	-	-	-	599	449	-	-	-	-
+contig--2565011	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	589	538	538	421.6	66.3	2.2e-124	7.4e-17	589	1	571	34	0.913	1.000	-	-	-	-	599	483	-	-	-	-
+contig--257393	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	589	585	585	373.7	114.3	1.9e-110	4.6e-32	590	2	590	6	0.993	1.000	-	-	-	-	586	538	-	-	-	-
+contig--257393	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	589	587	587	373.7	62.6	1.9e-110	2.2e-16	590	2	590	4	0.997	1.000	-	-	-	-	586	530	-	-	-	-
+contig--2575573	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	862	826	826	604.4	200.7	5.3e-180	4.1e-58	1	862	5	830	0.958	1.000	-	-	-	-	867	788	-	-	-	-
+contig--2575573	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	862	809	809	604.4	142.5	5.3e-180	1.7e-40	1	862	23	831	0.939	1.000	-	-	-	-	867	754	-	-	-	-
+contig--258486	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	383	382	382	315.0	193.8	5.5e-92	1.6e-55	4	386	4	385	0.997	1.000	-	-	-	-	383	373	-	-	-	-
+contig--258486	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	383	366	366	315.0	121.1	5.5e-92	1.1e-33	4	386	11	376	0.956	1.000	-	-	-	-	383	399	-	-	-	-
+contig--258486	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	383	361	361	315.0	88.8	5.5e-92	1.4e-23	4	386	16	376	0.943	1.000	-	-	-	-	383	316	-	-	-	-
+contig--261342	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	284	261	261	205.2	122.6	2.1e-59	1.4e-34	3	286	25	285	0.919	1.000	-	-	-	-	285	263	-	-	-	-
+contig--261342	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	284	258	258	205.2	96.4	2.1e-59	7.6e-27	3	286	26	283	0.908	1.000	-	-	-	-	285	258	-	-	-	-
+contig--2618713	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	353	343	343	223.9	117.5	1.8e-64	1.9e-32	1048	1400	1056	1398	0.972	1.000	-	-	-	-	344	323	-	-	-	-
+contig--2618713	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	353	329	329	223.9	59.2	1.8e-64	1.3e-14	1048	1400	1055	1383	0.932	1.000	-	-	-	-	344	261	-	-	-	-
+contig--2634789	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	1091	1086	1086	719.6	387.0	1.5e-214	2.5e-114	1092	2	1087	2	0.995	1.000	-	-	-	-	1075	1053	-	-	-	-
+contig--2634789	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1091	527	526	719.6	135.6	1.5e-214	1.2e-38	1092	2	527	1	0.482	0.998	-	-	-	-	1075	540	-	-	-	-
+contig--2634789	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1091	507	507	719.6	58.2	1.5e-214	2.6e-15	1092	2	1086	580	0.465	1.000	-	-	-	-	1075	556	-	-	-	-
+contig--2646754	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	592	592	592	275.6	155.9	1.2e-80	1.3e-44	1	592	1	592	1.000	1.000	-	-	-	-	606	619	-	-	-	-
+contig--2646754	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	592	591	591	275.6	52.6	1.2e-80	1.3e-13	1	592	1	591	0.998	1.000	-	-	-	-	606	659	-	-	-	-
+contig--2652964	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	510	480	480	269.2	150.2	1.1e-78	6.8e-43	513	4	494	15	0.941	1.000	-	-	-	-	495	471	-	-	-	-
+contig--2673585	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	374	373	373	178.7	122.7	2.2e-51	1.4e-34	374	1	373	1	0.997	1.000	-	-	-	-	331	341	-	-	-	-
+contig--2673585	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	374	372	372	178.7	87.8	2.2e-51	3e-24	374	1	372	1	0.995	1.000	-	-	-	-	331	339	-	-	-	-
+contig--2680413	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	443	438	438	252.2	154.8	1.4e-73	2.8e-44	443	1	438	1	0.989	1.000	-	-	-	-	484	470	-	-	-	-
+contig--2680413	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	443	295	295	252.2	80.0	1.4e-73	6.8e-22	443	1	296	2	0.666	1.000	-	-	-	-	484	342	-	-	-	-
+contig--2693087	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	308	293	293	209.9	105.0	3.1e-60	1.1e-28	132	439	140	432	0.951	1.000	-	-	-	-	338	312	-	-	-	-
+contig--2693087	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	308	290	290	209.9	61.8	3.1e-60	2.1e-15	132	439	139	428	0.942	1.000	-	-	-	-	338	261	-	-	-	-
+contig--2699652	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	425	423	423	391.2	229.5	1.8e-115	8.2e-67	1	425	2	424	0.995	1.000	-	-	-	-	437	430	-	-	-	-
+contig--2699652	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	425	344	344	391.2	134.6	1.8e-115	2.4e-38	1	425	2	345	0.809	1.000	-	-	-	-	437	342	-	-	-	-
+contig--2701305	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	499	486	486	266.7	163.4	6.3e-78	7.4e-47	1	499	2	487	0.974	1.000	-	-	-	-	516	510	-	-	-	-
+contig--2706433	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	343	334	334	209.8	87.7	3.4e-60	1.8e-23	22	364	31	364	0.974	1.000	-	-	-	-	342	322	-	-	-	-
+contig--2713352	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	501	496	495	262.0	152.1	1.6e-76	1.8e-43	507	7	508	13	0.988	0.998	-	-	-	-	493	499	-	-	-	-
+contig--2713352	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	501	489	489	262.0	53.4	1.6e-76	7.2e-14	507	7	507	19	0.976	1.000	-	-	-	-	493	529	-	-	-	-
+contig--2715420	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	422	412	412	392.8	211.8	5.6e-116	1.8e-61	2	423	11	422	0.976	1.000	-	-	-	-	419	405	-	-	-	-
+contig--2715420	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	422	401	401	392.8	133.5	5.6e-116	5.1e-38	2	423	21	421	0.950	1.000	-	-	-	-	419	394	-	-	-	-
+contig--2722470	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	374	365	365	254.7	139.3	1.4e-74	1.3e-39	2	375	7	371	0.976	1.000	-	-	-	-	371	363	-	-	-	-
+contig--2722470	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	374	370	370	254.7	124.1	1.4e-74	6.4e-35	2	375	3	372	0.989	1.000	-	-	-	-	371	358	-	-	-	-
+contig--2726048	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	869	868	868	501.9	239.5	1.3e-148	4.2e-69	1	869	2	869	0.999	1.000	-	-	-	-	902	544	-	-	-	-
+contig--2726048	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	869	389	389	501.9	80.9	1.3e-148	2.1e-21	1	869	240	628	0.448	1.000	-	-	-	-	902	378	-	-	-	-
+contig--2726048	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	869	418	418	501.9	54.9	1.3e-148	2.1e-13	1	869	235	652	0.481	1.000	-	-	-	-	902	440	-	-	-	-
+contig--2741341	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	432	418	418	275.9	85.0	5.8e-81	3.2e-23	1	432	1	418	0.968	1.000	-	-	-	-	437	386	-	-	-	-
+contig--2741341	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	432	420	420	275.9	53.9	5.8e-81	9.2e-14	1	432	1	420	0.972	1.000	-	-	-	-	437	378	-	-	-	-
+contig--2755789	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	309	295	295	152.4	93.2	7.5e-43	3.9e-25	1	309	15	309	0.955	1.000	-	-	-	-	307	283	-	-	-	-
+contig--2766474	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	371	369	369	286.2	186.7	2.7e-83	2.3e-53	410	40	410	42	0.995	1.000	-	-	-	-	369	358	-	-	-	-
+contig--2766474	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	371	359	359	286.2	117.4	2.7e-83	1.5e-32	410	40	408	50	0.968	1.000	-	-	-	-	369	390	-	-	-	-
+contig--2766474	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	371	361	361	286.2	94.4	2.7e-83	3.1e-25	410	40	408	48	0.973	1.000	-	-	-	-	369	315	-	-	-	-
+contig--2767514	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	310	310	310	194.1	99.0	5e-56	2e-27	310	1	310	1	1.000	1.000	-	-	-	-	310	300	-	-	-	-
+contig--2805328	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	361	357	357	268.2	148.8	2.2e-78	1.7e-42	1	361	3	359	0.989	1.000	-	-	-	-	359	349	-	-	-	-
+contig--2805328	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	361	246	246	268.2	74.3	2.2e-78	3.6e-20	1	361	4	249	0.681	1.000	-	-	-	-	359	243	-	-	-	-
+contig--2835645	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	304	297	297	242.7	136.2	1.1e-70	1.1e-38	306	3	306	10	0.977	1.000	-	-	-	-	296	276	-	-	-	-
+contig--2835645	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	304	227	227	242.7	62.3	1.1e-70	1.5e-16	306	3	303	77	0.747	1.000	-	-	-	-	296	225	-	-	-	-
+contig--2874819	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	359	359	359	294.0	134.5	3.6e-86	3.6e-38	359	1	359	1	1.000	1.000	-	-	-	-	359	349	-	-	-	-
+contig--2874819	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	359	357	357	294.0	65.1	3.6e-86	2.2e-17	359	1	359	3	0.994	1.000	-	-	-	-	359	385	-	-	-	-
+contig--2889438	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	334	331	331	278.6	195.6	5.4e-81	4.7e-56	334	1	334	4	0.991	1.000	-	-	-	-	334	337	-	-	-	-
+contig--2889438	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	334	330	330	278.6	109.1	5.4e-81	4.8e-30	334	1	334	5	0.988	1.000	-	-	-	-	334	379	-	-	-	-
+contig--2889438	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	334	331	331	278.6	73.0	5.4e-81	8.5e-19	334	1	334	4	0.991	1.000	-	-	-	-	334	273	-	-	-	-
+contig--2893879	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	370	362	362	160.6	61.9	6e-46	2.9e-16	1	370	2	363	0.978	1.000	-	-	-	-	363	363	-	-	-	-
+contig--2906201	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	304	303	303	201.2	112.9	3.4e-58	1.2e-31	304	1	304	2	0.997	1.000	-	-	-	-	301	308	-	-	-	-
+contig--2914153	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	799	798	798	551.2	314.2	2.4e-163	6.5e-92	799	1	799	2	0.999	1.000	-	-	-	-	798	770	-	-	-	-
+contig--2914153	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	799	796	796	551.2	198.1	2.4e-163	1.3e-56	799	1	796	1	0.996	1.000	-	-	-	-	798	692	-	-	-	-
+contig--2914153	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	799	288	288	551.2	115.5	2.4e-163	5.8e-32	799	1	288	1	0.360	1.000	-	-	-	-	798	302	-	-	-	-
+contig--2914153	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	799	395	395	551.2	68.3	2.4e-163	1e-17	799	1	726	332	0.494	1.000	-	-	-	-	798	379	-	-	-	-
+contig--2918607	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	425	420	420	304.5	149.8	2.4e-89	9e-43	431	7	428	9	0.988	1.000	-	-	-	-	437	517	-	-	-	-
+contig--2918607	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	425	133	133	304.5	63.3	2.4e-89	7.2e-17	431	7	415	283	0.313	1.000	-	-	-	-	437	134	-	-	-	-
+contig--2918607	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	425	163	163	304.5	55.5	2.4e-89	1.7e-14	431	7	177	15	0.384	1.000	-	-	-	-	437	164	-	-	-	-
+contig--2937145	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	424	257	257	209.8	96.2	4.9e-61	1.4e-26	2	425	3	259	0.606	1.000	-	-	-	-	445	256	-	-	-	-
+contig--2937145	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	424	269	269	209.8	70.7	4.9e-61	7.9e-19	2	425	15	283	0.634	1.000	-	-	-	-	445	267	-	-	-	-
+contig--2940126	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	401	393	393	320.5	155.9	3.6e-94	1.3e-44	402	2	402	10	0.980	1.000	-	-	-	-	400	477	-	-	-	-
+contig--2945976	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	336	329	328	129.3	58.0	1.7e-36	4.4e-15	2	337	1	329	0.976	0.997	-	-	-	-	332	332	-	-	-	-
+contig--2969992	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	485	477	477	406.9	250.8	9.2e-120	9.4e-73	4	488	12	488	0.984	1.000	-	-	-	-	485	484	-	-	-	-
+contig--2969992	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	485	459	459	406.9	148.4	9.2e-120	1.5e-41	4	488	30	488	0.946	1.000	-	-	-	-	485	452	-	-	-	-
+contig--2969992	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	485	305	305	406.9	118.2	9.2e-120	8.8e-33	4	488	184	488	0.629	1.000	-	-	-	-	485	319	-	-	-	-
+contig--2972876	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	614	607	607	481.4	247.8	2.9e-142	8e-72	614	1	614	8	0.989	1.000	-	-	-	-	606	570	-	-	-	-
+contig--2972876	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	614	606	606	481.4	132.9	2.9e-142	6.7e-37	614	1	613	8	0.987	1.000	-	-	-	-	606	539	-	-	-	-
+contig--2972876	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	614	272	272	481.4	108.6	2.9e-142	7e-30	614	1	280	9	0.443	1.000	-	-	-	-	606	284	-	-	-	-
+contig--2983248	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	316	315	315	161.3	104.8	3.7e-46	3.2e-29	316	1	316	2	0.997	1.000	-	-	-	-	324	333	-	-	-	-
+contig--2983248	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	316	316	316	161.3	80.5	3.7e-46	4.7e-22	316	1	316	1	1.000	1.000	-	-	-	-	324	333	-	-	-	-
+contig--298893	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	580	571	571	412.7	170.7	1.6e-121	1.6e-48	27	606	36	606	0.984	1.000	-	-	-	-	577	523	-	-	-	-
+contig--298893	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	580	570	570	412.7	84.4	1.6e-121	3.2e-22	27	606	35	604	0.983	1.000	-	-	-	-	577	457	-	-	-	-
+contig--3013908	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	326	325	325	202.8	92.4	2.5e-58	1.2e-24	326	1	326	2	0.997	1.000	-	-	-	-	359	251	-	-	-	-
+contig--3013908	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	326	325	325	202.8	79.3	2.5e-58	6.5e-21	326	1	326	2	0.997	1.000	-	-	-	-	359	315	-	-	-	-
+contig--3013908	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	326	325	325	202.8	63.4	2.5e-58	5.6e-16	326	1	326	2	0.997	1.000	-	-	-	-	359	309	-	-	-	-
+contig--3019708	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	609	605	605	348.9	106.0	5.6e-103	1.4e-29	609	1	608	4	0.993	1.000	-	-	-	-	612	565	-	-	-	-
+contig--3019708	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	609	602	602	348.9	61.3	5.6e-103	5.5e-16	609	1	608	7	0.989	1.000	-	-	-	-	612	551	-	-	-	-
+contig--3050118	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	367	215	215	170.5	60.8	3.4e-49	6.5e-16	1	367	2	216	0.586	1.000	-	-	-	-	404	217	-	-	-	-
+contig--3054101	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	573	546	546	489.9	269.5	1.7e-145	7.3e-79	11	583	31	576	0.953	1.000	-	-	-	-	574	549	-	-	-	-
+contig--3054101	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	573	560	560	489.9	211.4	1.7e-145	2.9e-61	11	583	17	576	0.977	1.000	-	-	-	-	574	563	-	-	-	-
+contig--30742	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	392	392	392	233.1	115.7	1.8e-67	1.1e-31	2	393	2	393	1.000	1.000	-	-	-	-	393	251	-	-	-	-
+contig--3076204	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	589	585	585	427.5	220.2	5.7e-126	1.7e-63	13	601	14	598	0.993	1.000	-	-	-	-	607	571	-	-	-	-
+contig--3076204	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	589	587	586	427.5	104.8	5.7e-126	2.1e-28	13	601	12	598	0.995	0.998	-	-	-	-	607	507	-	-	-	-
+contig--3076204	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	589	435	435	427.5	60.9	5.7e-126	1.8e-15	13	601	59	493	0.739	1.000	-	-	-	-	607	514	-	-	-	-
+contig--3093712	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	209	208	208	151.1	123.3	1.8e-42	3.1e-34	2	210	3	210	0.995	1.000	-	-	-	-	207	210	-	-	-	-
+contig--3093712	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	209	211	208	151.1	74.3	1.8e-42	3.7e-19	2	210	3	213	0.995	0.986	-	-	-	-	207	202	-	-	-	-
+contig--3093712	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	209	210	208	151.1	71.4	1.8e-42	1.1e-18	2	210	3	212	0.995	0.990	-	-	-	-	207	220	-	-	-	-
+contig--3093712	+	SSU_rRNA_microsporidia	SSU_rRNA_eukarya	138	148	138	61.0	58.0	3.6e-15	1.4e-14	218	355	214	361	1.000	0.932	-	-	-	-	139	149	-	-	-	-
+contig--3096224	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	285	202	202	190.7	81.5	1.1e-54	2.4e-21	21	305	104	305	0.709	1.000	-	-	-	-	286	203	-	-	-	-
+contig--3128112	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	406	399	399	130.8	102.3	2.5e-36	6.9e-28	410	5	404	6	0.983	1.000	-	-	-	-	405	404	-	-	-	-
+contig--3128112	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	406	307	307	130.8	61.2	2.5e-36	3.3e-15	410	5	312	6	0.756	1.000	-	-	-	-	405	302	-	-	-	-
+contig--3128112	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	406	288	288	130.8	58.1	2.5e-36	1.2e-14	410	5	315	28	0.709	1.000	-	-	-	-	405	310	-	-	-	-
+contig--314729	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	335	335	335	178.5	129.7	5.4e-51	6.2e-36	337	3	337	3	1.000	1.000	-	-	-	-	361	276	-	-	-	-
+contig--314729	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	335	334	333	178.5	120.0	5.4e-51	3.2e-33	337	3	335	2	0.994	0.997	-	-	-	-	361	322	-	-	-	-
+contig--314729	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	335	323	322	178.5	83.1	5.4e-51	6.2e-22	337	3	324	2	0.961	0.997	-	-	-	-	361	312	-	-	-	-
+contig--3153031	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	341	333	333	244.4	110.7	1.2e-70	2.1e-30	44	384	51	383	0.977	1.000	-	-	-	-	370	351	-	-	-	-
+contig--3153031	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	341	332	332	244.4	60.4	1.2e-70	5.7e-15	44	384	49	380	0.974	1.000	-	-	-	-	370	302	-	-	-	-
+contig--3171405	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	300	279	279	163.0	55.8	4.8e-46	8e-14	33	332	41	319	0.930	1.000	-	-	-	-	315	283	-	-	-	-
+contig--3176110	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	396	358	358	378.9	181.6	5e-112	2.4e-52	12	407	47	404	0.904	1.000	-	-	-	-	397	365	-	-	-	-
+contig--3176110	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	396	362	362	378.9	133.1	5e-112	1.2e-37	12	407	39	400	0.914	1.000	-	-	-	-	397	361	-	-	-	-
+contig--3276943	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	960	913	913	551.7	355.4	1.1e-163	3.9e-104	2407	1448	2360	1448	0.951	1.000	-	-	-	-	1039	792	-	-	-	-
+contig--3276943	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	960	906	906	551.7	250.1	1.1e-163	1.6e-72	2407	1448	2354	1449	0.944	1.000	-	-	-	-	1039	883	-	-	-	-
+contig--3276943	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	960	905	905	551.7	211.9	1.1e-163	7.6e-61	2407	1448	2352	1448	0.943	1.000	-	-	-	-	1039	883	-	-	-	-
+contig--3276943	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	967	922	921	203.4	87.9	4.4e-59	4.1e-24	967	1	968	47	0.952	0.999	-	-	-	-	1123	900	-	-	-	-
+contig--3286658	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	581	572	572	391.7	186.0	3.8e-115	3.7e-53	583	3	575	4	0.985	1.000	-	-	-	-	576	522	-	-	-	-
+contig--3286658	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	581	573	573	391.7	85.9	3.8e-115	1.1e-22	583	3	576	4	0.986	1.000	-	-	-	-	576	458	-	-	-	-
+contig--3290892	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	489	483	483	310.5	87.4	2.2e-91	5.9e-24	2	490	5	487	0.988	1.000	-	-	-	-	482	438	-	-	-	-
+contig--3290892	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	489	458	458	310.5	53.5	2.2e-91	1.2e-13	2	490	29	486	0.937	1.000	-	-	-	-	482	404	-	-	-	-
+contig--32925	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	550	548	548	280.8	164.4	3.5e-82	3.6e-47	2	551	4	551	0.996	1.000	-	-	-	-	524	512	-	-	-	-
+contig--3299936	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	387	372	372	119.2	65.1	1.8e-33	3.1e-17	8	394	8	379	0.961	1.000	-	-	-	-	365	357	-	-	-	-
+contig--3317407	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	472	469	469	307.9	199.5	2.4e-90	9.3e-58	283	754	284	752	0.994	1.000	-	-	-	-	528	516	-	-	-	-
+contig--3317407	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	472	317	317	307.9	95.0	2.4e-90	2.1e-26	283	754	435	751	0.672	1.000	-	-	-	-	528	377	-	-	-	-
+contig--332136	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	314	304	304	263.7	155.2	4.9e-77	2.1e-44	322	9	322	19	0.968	1.000	-	-	-	-	312	300	-	-	-	-
+contig--332136	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	157	157	157	159.7	97.4	1.1e-45	5.8e-27	487	331	487	331	1.000	1.000	-	-	-	-	157	157	-	-	-	-
+contig--332136	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	314	297	297	263.7	82.8	4.9e-77	1e-22	322	9	317	21	0.946	1.000	-	-	-	-	312	292	-	-	-	-
+contig--332136	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	157	157	157	159.7	66.0	1.1e-45	1.2e-17	487	331	487	331	1.000	1.000	-	-	-	-	157	157	-	-	-	-
+contig--3348019	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	376	376	376	279.3	135.0	2e-81	1.6e-37	1	376	1	376	1.000	1.000	-	-	-	-	377	300	-	-	-	-
+contig--3348019	+	SSU_rRNA_eukarya	SSU_rRNA_archaea	376	374	374	279.3	115.9	2e-81	5.4e-32	1	376	3	376	0.995	1.000	-	-	-	-	377	333	-	-	-	-
+contig--3348019	+	SSU_rRNA_eukarya	SSU_rRNA_bacteria	376	376	374	279.3	91.6	2e-81	1.7e-24	1	376	3	378	0.995	0.995	-	-	-	-	377	344	-	-	-	-
+contig--3354354	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	620	513	513	427.9	147.8	8.7e-127	3.7e-42	620	1	514	2	0.827	1.000	-	-	-	-	609	478	-	-	-	-
+contig--3354354	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	620	490	490	427.9	96.4	8.7e-127	1.4e-26	620	1	491	2	0.790	1.000	-	-	-	-	609	440	-	-	-	-
+contig--3398090	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	569	567	567	488.0	256.5	1.1e-144	6.1e-75	1	569	2	568	0.996	1.000	-	-	-	-	580	569	-	-	-	-
+contig--3398090	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	569	568	568	488.0	152.7	1.1e-144	8.3e-44	1	569	1	568	0.998	1.000	-	-	-	-	580	607	-	-	-	-
+contig--3414648	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	259	260	259	145.4	84.8	2.3e-41	3.7e-23	165	423	164	423	1.000	0.996	-	-	-	-	258	259	-	-	-	-
+contig--3420575	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	503	503	503	336.8	157.1	8.5e-99	3.2e-44	503	1	503	1	1.000	1.000	-	-	-	-	522	347	-	-	-	-
+contig--3420575	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	503	472	472	336.8	52.6	8.5e-99	7.2e-13	503	1	472	1	0.938	1.000	-	-	-	-	522	388	-	-	-	-
+contig--3433834	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	490	488	488	221.6	137.1	2.5e-64	6e-39	1	490	1	488	0.996	1.000	-	-	-	-	470	475	-	-	-	-
+contig--3433834	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	490	413	413	221.6	53.1	2.5e-64	9e-14	1	490	2	414	0.843	1.000	-	-	-	-	470	455	-	-	-	-
+contig--3461222	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	504	503	503	157.3	115.3	1.3e-44	1.4e-31	19	522	20	522	0.998	1.000	-	-	-	-	545	369	-	-	-	-
+contig--3474644	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	782	774	774	526.5	267.5	6.8e-156	8.7e-78	51	832	59	832	0.990	1.000	-	-	-	-	756	704	-	-	-	-
+contig--3474644	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	782	776	776	526.5	140.3	6.8e-156	3.9e-39	51	832	57	832	0.992	1.000	-	-	-	-	756	638	-	-	-	-
+contig--3474644	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	782	606	606	526.5	76.6	6.8e-156	3.1e-20	51	832	60	665	0.775	1.000	-	-	-	-	756	646	-	-	-	-
+contig--3492742	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	299	291	291	197.8	94.3	1.5e-56	1.8e-25	300	2	293	3	0.973	1.000	-	-	-	-	328	309	-	-	-	-
+contig--3494982	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	369	351	351	149.3	75.9	1.6e-42	1.8e-20	9	377	27	377	0.951	1.000	-	-	-	-	367	354	-	-	-	-
+contig--3503719	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	348	346	346	226.7	154.8	2.6e-65	9.7e-44	350	3	350	5	0.994	1.000	-	-	-	-	347	351	-	-	-	-
+contig--3503719	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	348	339	339	226.7	95.6	2.6e-65	5.9e-26	350	3	349	11	0.974	1.000	-	-	-	-	347	387	-	-	-	-
+contig--3503719	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	348	294	294	226.7	69.6	2.6e-65	9.2e-18	350	3	308	15	0.845	1.000	-	-	-	-	347	237	-	-	-	-
+contig--35359	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	492	484	484	355.4	232.7	1.1e-104	8.8e-68	53	544	60	543	0.984	1.000	-	-	-	-	510	486	-	-	-	-
+contig--35359	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	492	317	317	355.4	113.5	1.1e-104	5.4e-32	53	544	225	541	0.644	1.000	-	-	-	-	510	311	-	-	-	-
+contig--3568828	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	666	651	651	575.6	338.4	1e-170	3.2e-99	670	5	666	16	0.977	1.000	-	-	-	-	681	638	-	-	-	-
+contig--3568828	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	666	652	652	575.6	206.7	1e-170	3.4e-59	670	5	664	13	0.979	1.000	-	-	-	-	681	609	-	-	-	-
+contig--3568828	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	666	342	342	575.6	160.4	1e-170	1.6e-45	670	5	350	9	0.514	1.000	-	-	-	-	681	355	-	-	-	-
+contig--3575278	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	189	186	186	132.9	88.8	5.6e-37	8.6e-24	3	191	4	189	0.984	1.000	-	-	-	-	199	187	-	-	-	-
+contig--3575278	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	189	182	182	132.9	64.4	5.6e-37	1.5e-16	3	191	3	184	0.963	1.000	-	-	-	-	199	216	-	-	-	-
+contig--3575278	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	189	183	182	132.9	62.1	5.6e-37	1.7e-15	3	191	2	184	0.963	0.995	-	-	-	-	199	174	-	-	-	-
+contig--362412	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	443	416	416	246.6	174.0	7.2e-72	4.5e-50	444	2	419	4	0.939	1.000	-	-	-	-	403	386	-	-	-	-
+contig--362412	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	443	419	418	246.6	148.2	7.2e-72	1.9e-42	444	2	419	1	0.944	0.998	-	-	-	-	403	389	-	-	-	-
+contig--362436	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	310	287	287	185.7	90.5	6.6e-53	2.6e-24	311	2	290	4	0.926	1.000	-	-	-	-	316	281	-	-	-	-
+contig--362625	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	505	320	320	286.0	116.2	5.4e-84	1.2e-32	1	505	2	321	0.634	1.000	-	-	-	-	548	321	-	-	-	-
+contig--362625	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	505	316	316	286.0	101.4	5.4e-84	4.3e-28	1	505	6	321	0.626	1.000	-	-	-	-	548	318	-	-	-	-
+contig--362779	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	370	328	328	147.0	54.7	4.2e-42	4.3e-14	372	3	372	45	0.886	1.000	-	-	-	-	423	252	-	-	-	-
+contig--362861	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1095	1092	1092	610.5	350.3	1.3e-181	3.1e-103	3	1097	6	1097	0.997	1.000	-	-	-	-	1035	1111	-	-	-	-
+contig--362861	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1095	448	448	610.5	100.7	1.3e-181	3.8e-28	3	1097	179	626	0.409	1.000	-	-	-	-	1035	419	-	-	-	-
+contig--362861	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1095	272	272	610.5	89.0	1.3e-181	1.4e-24	3	1097	741	1012	0.248	1.000	-	-	-	-	1035	276	-	-	-	-
+contig--363016	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	401	399	399	314.7	204.6	6.6e-92	8.6e-59	1141	741	1141	743	0.995	1.000	-	-	-	-	401	390	-	-	-	-
+contig--363016	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	478	461	461	313.8	198.0	3.8e-92	2.6e-57	480	3	463	3	0.964	1.000	-	-	-	-	528	502	-	-	-	-
+contig--363016	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	401	385	385	314.7	132.2	6.6e-92	5.3e-37	1141	741	1132	748	0.960	1.000	-	-	-	-	401	418	-	-	-	-
+contig--363016	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	401	382	382	314.7	109.4	6.6e-92	8.9e-30	1141	741	1129	748	0.953	1.000	-	-	-	-	401	337	-	-	-	-
+contig--363016	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	478	311	310	313.8	102.1	3.8e-92	1.5e-28	480	3	312	2	0.649	0.997	-	-	-	-	528	369	-	-	-	-
+contig--363170	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	866	843	843	517.9	257.6	1.8e-153	1.3e-74	866	1	844	2	0.973	1.000	-	-	-	-	916	552	-	-	-	-
+contig--363170	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	866	329	329	517.9	87.9	1.8e-153	1.6e-23	866	1	683	355	0.380	1.000	-	-	-	-	916	316	-	-	-	-
+contig--363170	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	866	334	334	517.9	58.4	1.8e-153	1.9e-14	866	1	687	354	0.386	1.000	-	-	-	-	916	355	-	-	-	-
+contig--363722	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	579	578	578	462.7	245.2	1.4e-136	4.7e-71	579	1	578	1	0.998	1.000	-	-	-	-	572	542	-	-	-	-
+contig--363722	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	579	486	486	462.7	129.9	1.4e-136	5.7e-36	579	1	487	2	0.839	1.000	-	-	-	-	572	472	-	-	-	-
+contig--363722	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	579	278	278	462.7	97.0	1.4e-136	2.1e-26	579	1	280	3	0.480	1.000	-	-	-	-	572	292	-	-	-	-
+contig--3638238	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	718	715	715	366.6	221.6	4.6e-108	2e-64	719	2	719	5	0.996	1.000	-	-	-	-	698	705	-	-	-	-
+contig--3638238	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	718	641	641	366.6	79.0	4.6e-108	1.4e-21	719	2	718	78	0.893	1.000	-	-	-	-	698	690	-	-	-	-
+contig--363861	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	664	650	650	503.9	170.7	1.1e-149	4.4e-49	665	2	651	2	0.979	1.000	-	-	-	-	660	586	-	-	-	-
+contig--363861	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	664	486	486	503.9	103.2	1.1e-149	1.3e-28	665	2	488	3	0.732	1.000	-	-	-	-	660	443	-	-	-	-
+contig--364074	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	580	578	578	371.4	234.9	1.7e-109	1.9e-68	583	4	581	4	0.997	1.000	-	-	-	-	591	600	-	-	-	-
+contig--364074	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	580	538	538	371.4	83.2	1.7e-109	7.3e-23	583	4	578	41	0.928	1.000	-	-	-	-	591	602	-	-	-	-
+contig--364116	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	439	425	425	319.5	164.8	7.3e-94	2.8e-47	1	439	2	426	0.968	1.000	-	-	-	-	447	426	-	-	-	-
+contig--364116	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	439	418	418	319.5	86.6	7.3e-94	6.8e-24	1	439	2	419	0.952	1.000	-	-	-	-	447	455	-	-	-	-
+contig--364277	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	586	582	582	334.2	247.1	2.7e-98	4e-72	587	2	583	2	0.993	1.000	-	-	-	-	548	533	-	-	-	-
+contig--364277	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	586	425	425	334.2	156.6	2.7e-98	5.3e-45	587	2	426	2	0.725	1.000	-	-	-	-	548	395	-	-	-	-
+contig--364298	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	615	505	505	154.7	61.6	3.7e-44	3.5e-16	1	615	1	505	0.821	1.000	-	-	-	-	586	497	-	-	-	-
+contig--364625	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	953	929	929	654.3	347.9	1.7e-194	4.4e-102	954	2	931	3	0.975	1.000	-	-	-	-	940	878	-	-	-	-
+contig--364625	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	953	936	936	654.3	215.3	1.7e-194	8.5e-62	954	2	939	4	0.982	1.000	-	-	-	-	940	807	-	-	-	-
+contig--364625	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	953	311	311	654.3	125.2	1.7e-194	6.5e-35	954	2	314	4	0.326	1.000	-	-	-	-	940	324	-	-	-	-
+contig--364625	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	953	568	568	654.3	57.6	1.7e-194	1.7e-14	954	2	928	361	0.596	1.000	-	-	-	-	940	622	-	-	-	-
+contig--364755	+	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	396	394	394	178.0	58.7	7.6e-51	1.8e-14	1	396	2	395	0.995	1.000	-	-	-	-	410	226	-	-	-	-
+contig--365125	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	565	509	509	510.5	229.7	1.1e-151	7.2e-67	623	59	622	114	0.901	1.000	-	-	-	-	566	511	-	-	-	-
+contig--365125	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	565	507	507	510.5	180.6	1.1e-151	5.6e-52	623	59	622	116	0.897	1.000	-	-	-	-	566	510	-	-	-	-
+contig--365127	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	567	561	561	478.1	260.0	3e-141	1.6e-75	567	1	566	6	0.989	1.000	-	-	-	-	583	548	-	-	-	-
+contig--365127	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	567	560	560	478.1	139.6	3e-141	6.6e-39	567	1	566	7	0.988	1.000	-	-	-	-	583	517	-	-	-	-
+contig--365127	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	567	270	270	478.1	105.6	3e-141	5.6e-29	567	1	277	8	0.476	1.000	-	-	-	-	583	283	-	-	-	-
+contig--3652175	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	301	279	279	206.5	102.0	8.9e-60	2.4e-28	302	2	286	8	0.927	1.000	-	-	-	-	300	311	-	-	-	-
+contig--3652175	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	301	175	175	206.5	50.8	8.9e-60	4.5e-13	302	2	185	11	0.581	1.000	-	-	-	-	300	176	-	-	-	-
+contig--3652281	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	310	306	306	217.0	117.9	5.9e-63	3.7e-33	311	2	309	4	0.987	1.000	-	-	-	-	321	307	-	-	-	-
+contig--365284	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	412	366	365	215.9	145.2	7.2e-63	2.2e-41	546	135	547	182	0.886	0.997	-	-	-	-	414	368	-	-	-	-
+contig--365284	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	412	394	393	215.9	111.0	7.2e-63	5.6e-31	546	135	547	154	0.954	0.997	-	-	-	-	414	387	-	-	-	-
+contig--365471	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	349	347	347	214.1	123.5	4.5e-62	7.7e-35	1	349	2	348	0.994	1.000	-	-	-	-	347	334	-	-	-	-
+contig--365471	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	349	279	279	214.1	66.6	4.5e-62	7.5e-18	1	349	1	279	0.799	1.000	-	-	-	-	347	252	-	-	-	-
+contig--3655473	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	508	508	508	395.7	132.6	4.4e-117	1.3e-37	509	2	509	2	1.000	1.000	-	-	-	-	508	466	-	-	-	-
+contig--3655473	-	LSU_rRNA_eukarya	LSU_rRNA_bacteria	508	505	505	395.7	78.4	4.4e-117	3.7e-21	509	2	509	5	0.994	1.000	-	-	-	-	508	453	-	-	-	-
+contig--3659280	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	425	413	413	326.2	132.9	6.9e-96	1.2e-37	1	425	2	414	0.972	1.000	-	-	-	-	425	406	-	-	-	-
+contig--3659280	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	425	365	365	326.2	81.7	6.9e-96	2.1e-22	1	425	31	395	0.859	1.000	-	-	-	-	425	395	-	-	-	-
+contig--36603	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	410	410	410	238.2	174.1	2.3e-69	4.3e-50	2	411	2	411	1.000	1.000	-	-	-	-	365	375	-	-	-	-
+contig--36603	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	410	406	406	238.2	113.7	2.3e-69	4.7e-32	2	411	6	411	0.990	1.000	-	-	-	-	365	370	-	-	-	-
+contig--3694746	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	382	375	375	293.6	149.2	4.9e-86	1.3e-42	382	1	382	8	0.982	1.000	-	-	-	-	387	465	-	-	-	-
+contig--3694746	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	382	175	175	293.6	51.0	4.9e-86	3.9e-13	382	1	184	10	0.458	1.000	-	-	-	-	387	176	-	-	-	-
+contig--371157	+	LSU_rRNA_archaea	LSU_rRNA_bacteria	1984	1977	1977	1265.3	802.2	0	1.9e-239	3350	5333	3355	5331	0.996	1.000	-	-	-	-	2077	1991	-	-	-	-
+contig--371157	+	LSU_rRNA_archaea	LSU_rRNA_eukarya	1984	1152	1152	1265.3	287.6	0	1.8e-84	3350	5333	3943	5094	0.581	1.000	-	-	-	-	2077	1304	-	-	-	-
+contig--371157	+	LSU_rRNA_archaea	LSU_rRNA_eukarya	1984	414	414	1265.3	161.7	0	1.7e-46	3350	5333	3497	3910	0.209	1.000	-	-	-	-	2077	418	-	-	-	-
+contig--371157	+	LSU_rRNA_archaea	LSU_rRNA_eukarya	1984	217	216	1265.3	113.0	0	7.6e-32	3350	5333	5118	5334	0.109	0.995	-	-	-	-	2077	217	-	-	-	-
+contig--3715154	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	538	534	534	470.4	251.0	2.3e-139	2.7e-73	539	2	539	6	0.993	1.000	-	-	-	-	537	524	-	-	-	-
+contig--3715154	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	538	530	530	470.4	148.3	2.3e-139	1.8e-42	539	2	539	10	0.985	1.000	-	-	-	-	537	557	-	-	-	-
+contig--3743149	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	796	783	783	592.4	341.1	3.5e-176	1.8e-100	797	2	784	2	0.984	1.000	-	-	-	-	781	740	-	-	-	-
+contig--3743149	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	796	572	572	592.4	158.0	3.5e-176	2.1e-45	797	2	573	2	0.719	1.000	-	-	-	-	781	582	-	-	-	-
+contig--3748912	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	372	365	365	250.2	118.0	5.8e-73	3.5e-33	376	5	374	10	0.981	1.000	-	-	-	-	369	399	-	-	-	-
+contig--3748912	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	372	266	266	250.2	65.8	5.8e-73	1.3e-17	376	5	275	10	0.715	1.000	-	-	-	-	369	274	-	-	-	-
+contig--3756271	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	380	361	361	179.7	56.3	5.9e-52	1.4e-14	1	380	5	365	0.950	1.000	-	-	-	-	382	332	-	-	-	-
+contig--3784467	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	409	402	402	365.8	233.6	7.7e-108	4.8e-68	417	9	417	16	0.983	1.000	-	-	-	-	422	410	-	-	-	-
+contig--3784467	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	409	324	324	365.8	116.5	7.7e-108	6.9e-33	417	9	416	93	0.792	1.000	-	-	-	-	422	321	-	-	-	-
+contig--3787593	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	583	581	581	420.1	239.0	9.5e-124	3.5e-69	2	584	3	583	0.997	1.000	-	-	-	-	576	546	-	-	-	-
+contig--3787593	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	583	460	460	420.1	137.7	9.5e-124	2.4e-38	2	584	125	584	0.789	1.000	-	-	-	-	576	447	-	-	-	-
+contig--3787593	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	583	285	285	420.1	111.0	9.5e-124	1.3e-30	2	584	300	584	0.489	1.000	-	-	-	-	576	298	-	-	-	-
+contig--3837490	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	389	356	356	249.1	124.5	4.4e-72	1.4e-34	392	4	389	34	0.915	1.000	-	-	-	-	395	350	-	-	-	-
+contig--3837490	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	389	379	379	249.1	66.8	4.4e-72	6.6e-17	392	4	388	10	0.974	1.000	-	-	-	-	395	320	-	-	-	-
+contig--3860305	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	633	615	615	433.3	232.5	3.5e-128	1e-67	2	634	7	621	0.972	1.000	-	-	-	-	684	709	-	-	-	-
+contig--3860305	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	633	398	398	433.3	131.0	3.5e-128	2.8e-37	2	634	153	550	0.629	1.000	-	-	-	-	684	455	-	-	-	-
+contig--3875044	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	222	227	221	105.9	67.7	1.1e-29	5e-18	134	355	128	354	0.995	0.974	-	-	-	-	223	233	-	-	-	-
+contig--3875044	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	222	296	221	105.9	56.2	1.1e-29	1.8e-14	134	355	59	354	0.995	0.747	-	-	-	-	223	300	-	-	-	-
+contig--3889059	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	413	320	320	302.1	155.3	4.3e-88	7.1e-44	1	413	91	410	0.775	1.000	-	-	-	-	407	322	-	-	-	-
+contig--3889059	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	413	320	320	302.1	88.3	4.3e-88	2.1e-23	1	413	92	411	0.775	1.000	-	-	-	-	407	310	-	-	-	-
+contig--3889622	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	329	317	317	171.2	87.0	4e-49	7.6e-24	1	329	13	329	0.964	1.000	-	-	-	-	323	319	-	-	-	-
+contig--3890060	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	364	360	360	208.6	133.8	2.1e-60	6.1e-38	364	1	360	1	0.989	1.000	-	-	-	-	435	424	-	-	-	-
+contig--3897242	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	335	272	272	159.7	68.4	6.5e-46	3.2e-18	13	347	18	289	0.812	1.000	-	-	-	-	338	265	-	-	-	-
+contig--3925448	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	341	342	336	176.2	94.4	1.2e-50	4.5e-26	27	367	21	362	0.985	0.982	-	-	-	-	358	409	-	-	-	-
+contig--3925448	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	341	272	268	176.2	56.8	1.2e-50	6.8e-15	27	367	23	294	0.786	0.985	-	-	-	-	358	286	-	-	-	-
+contig--395713	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	2146	1238	1238	1672.9	517.0	0	1.6e-153	2	2147	5	1242	0.577	1.000	-	-	-	-	2308	1396	-	-	-	-
+contig--395713	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	2146	843	843	1672.9	387.8	0	1.5e-114	2	2147	1302	2144	0.393	1.000	-	-	-	-	2308	827	-	-	-	-
+contig--395713	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2146	707	707	1672.9	205.0	0	1.5e-59	2	2147	1438	2144	0.329	1.000	-	-	-	-	2308	728	-	-	-	-
+contig--395713	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2146	767	767	1672.9	134.5	0	2.6e-38	2	2147	463	1229	0.357	1.000	-	-	-	-	2308	842	-	-	-	-
+contig--395713	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2146	358	358	1672.9	125.7	0	1.1e-35	2	2147	4	361	0.167	1.000	-	-	-	-	2308	417	-	-	-	-
+contig--397992	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	2919	2909	2909	2226.7	1332.6	0	0	59	2977	61	2969	0.997	1.000	-	-	-	-	2914	2969	-	-	-	-
+contig--397992	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2919	2112	2112	2226.7	520.8	0	8.5e-155	59	2977	754	2865	0.724	1.000	-	-	-	-	2914	2352	-	-	-	-
+contig--397992	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	2919	395	395	2226.7	155.4	0	1.2e-44	59	2977	229	623	0.135	1.000	-	-	-	-	2914	403	-	-	-	-
+contig--401056	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1449	1436	1436	974.7	576.4	1.9e-291	2e-171	882	2330	891	2326	0.991	1.000	-	-	-	-	1406	1479	-	-	-	-
+contig--401056	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	509	517	507	435.4	289.2	2.3e-128	2.3e-84	17	525	7	523	0.996	0.981	-	-	-	-	509	511	-	-	-	-
+contig--401056	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	509	496	496	435.4	174.0	2.3e-128	1.3e-49	17	525	23	518	0.974	1.000	-	-	-	-	509	569	-	-	-	-
+contig--401056	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1449	454	454	974.7	138.6	1.9e-291	1.4e-39	882	2330	1058	1511	0.313	1.000	-	-	-	-	1406	420	-	-	-	-
+contig--401056	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1449	693	693	974.7	131.6	1.9e-291	1.9e-37	882	2330	1632	2324	0.478	1.000	-	-	-	-	1406	749	-	-	-	-
+contig--401056	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	509	503	502	435.4	133.0	2.3e-128	6.5e-37	17	525	16	518	0.986	0.998	-	-	-	-	509	426	-	-	-	-
+contig--4068604	+	LSU_rRNA_archaea	LSU_rRNA_bacteria	561	557	557	300.4	188.7	3.5e-88	2.1e-54	2	562	6	562	0.993	1.000	-	-	-	-	610	595	-	-	-	-
+contig--4068604	+	LSU_rRNA_archaea	LSU_rRNA_eukarya	561	556	556	300.4	113.2	3.5e-88	6.6e-32	2	562	7	562	0.991	1.000	-	-	-	-	610	648	-	-	-	-
+contig--423976	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	1603	1585	1585	884.8	511.2	2.3e-264	9.2e-152	400	2002	412	1996	0.989	1.000	-	-	-	-	1613	1691	-	-	-	-
+contig--423976	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1603	408	408	884.8	134.9	2.3e-264	1.9e-38	400	2002	476	883	0.255	1.000	-	-	-	-	1613	425	-	-	-	-
+contig--423976	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	1603	983	983	884.8	133.0	2.3e-264	7.1e-38	400	2002	1006	1988	0.613	1.000	-	-	-	-	1613	1074	-	-	-	-
+contig--473422	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	326	316	316	173.0	137.2	1.1e-49	5.8e-39	326	1	316	1	0.969	1.000	-	-	-	-	347	331	-	-	-	-
+contig--473422	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	326	197	197	173.0	52.0	1.1e-49	1.9e-13	326	1	198	2	0.604	1.000	-	-	-	-	347	207	-	-	-	-
+contig--496748	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	303	294	294	162.3	76.8	1e-46	9.1e-21	1	303	1	294	0.970	1.000	-	-	-	-	297	290	-	-	-	-
+contig--496748	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	303	295	295	162.3	51.7	1e-46	4.3e-13	1	303	2	296	0.974	1.000	-	-	-	-	297	279	-	-	-	-
+contig--498568	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	515	514	514	453.1	278.9	1e-133	3.2e-81	516	2	515	2	0.998	1.000	-	-	-	-	516	515	-	-	-	-
+contig--498568	-	SSU_rRNA_bacteria	SSU_rRNA_eukarya	515	507	507	453.1	201.4	1e-133	6.5e-58	516	2	514	8	0.984	1.000	-	-	-	-	516	553	-	-	-	-
+contig--498568	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	515	504	504	453.1	153.4	1e-133	4.2e-43	516	2	515	12	0.979	1.000	-	-	-	-	516	431	-	-	-	-
+contig--515926	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	492	446	446	277.9	72.2	1.5e-81	2.3e-19	494	3	494	49	0.907	1.000	-	-	-	-	484	405	-	-	-	-
+contig--518767	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	297	213	213	153.5	72.7	4.9e-44	1.6e-19	24	320	31	243	0.717	1.000	-	-	-	-	307	224	-	-	-	-
+contig--518767	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	297	156	156	153.5	72.9	4.9e-44	1.8e-19	24	320	55	210	0.525	1.000	-	-	-	-	307	157	-	-	-	-
+contig--540576	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	340	336	336	179.2	102.7	6.1e-51	5.4e-28	341	2	339	4	0.988	1.000	-	-	-	-	336	320	-	-	-	-
+contig--547077	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	307	306	306	218.3	112.6	2.4e-63	1.4e-31	307	1	306	1	0.997	1.000	-	-	-	-	307	314	-	-	-	-
+contig--594041	+	SSU_rRNA_archaea	SSU_rRNA_bacteria	319	312	312	209.1	103.0	3.9e-60	6e-28	2	320	7	318	0.978	1.000	-	-	-	-	325	330	-	-	-	-
+contig--594041	+	SSU_rRNA_archaea	SSU_rRNA_microsporidia	319	306	306	209.1	83.8	3.9e-60	4.7e-22	2	320	10	315	0.959	1.000	-	-	-	-	325	265	-	-	-	-
+contig--64232	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	398	216	216	172.8	52.6	7e-50	1.9e-13	1	398	6	221	0.543	1.000	-	-	-	-	439	217	-	-	-	-
+contig--664472	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	330	318	318	213.3	104.6	2.9e-61	1.4e-28	2	331	14	331	0.964	1.000	-	-	-	-	359	335	-	-	-	-
+contig--669436	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	367	367	366	158.7	89.4	2.3e-45	1.5e-24	368	2	367	1	0.997	0.997	-	-	-	-	362	373	-	-	-	-
+contig--68307	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	309	306	306	138.5	75.3	1.6e-39	2.7e-20	2	310	2	307	0.990	1.000	-	-	-	-	309	307	-	-	-	-
+contig--68307	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	309	307	307	138.5	58.6	1.6e-39	3.6e-15	2	310	2	308	0.994	1.000	-	-	-	-	309	297	-	-	-	-
+contig--696001	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	557	521	521	384.7	153.8	5e-113	1.9e-43	69	625	105	625	0.935	1.000	-	-	-	-	567	485	-	-	-	-
+contig--696001	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	557	553	552	384.7	74.4	5e-113	3.2e-19	69	625	74	626	0.991	0.998	-	-	-	-	567	453	-	-	-	-
+contig--724357	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	346	334	334	236.5	134.4	8e-69	3.9e-38	3	348	14	347	0.965	1.000	-	-	-	-	351	346	-	-	-	-
+contig--747483	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	331	305	305	258.7	144.6	1.6e-75	3.3e-41	332	2	332	28	0.921	1.000	-	-	-	-	341	303	-	-	-	-
+contig--747483	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	331	254	254	258.7	58.6	1.6e-75	2e-15	332	2	332	79	0.767	1.000	-	-	-	-	341	250	-	-	-	-
+contig--759897	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	318	317	317	263.6	150.8	5.3e-77	4.6e-43	1	318	1	317	0.997	1.000	-	-	-	-	330	324	-	-	-	-
+contig--759897	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	318	229	229	263.6	70.5	5.3e-77	4.9e-19	1	318	2	230	0.720	1.000	-	-	-	-	330	226	-	-	-	-
+contig--813107	+	SSU_rRNA_archaea	SSU_rRNA_bacteria	487	474	474	375.6	249.9	1.9e-110	2.6e-72	1	487	13	486	0.973	1.000	-	-	-	-	488	469	-	-	-	-
+contig--813107	+	SSU_rRNA_archaea	SSU_rRNA_microsporidia	487	480	480	375.6	198.7	1.9e-110	8.9e-57	1	487	8	487	0.986	1.000	-	-	-	-	488	468	-	-	-	-
+contig--813107	+	SSU_rRNA_archaea	SSU_rRNA_eukarya	487	330	329	375.6	142.6	1.9e-110	3.8e-40	1	487	159	488	0.676	0.997	-	-	-	-	488	339	-	-	-	-
+contig--828224	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	513	513	512	405.3	197.8	3e-119	9.8e-57	7	519	6	518	0.998	0.998	-	-	-	-	534	499	-	-	-	-
+contig--828224	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	513	500	500	405.3	101.9	3e-119	1.6e-27	7	519	20	519	0.975	1.000	-	-	-	-	534	466	-	-	-	-
+contig--828224	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	513	339	339	405.3	53.7	3e-119	2.6e-13	7	519	27	365	0.661	1.000	-	-	-	-	534	342	-	-	-	-
+contig--862423	+	SSU_rRNA_bacteria	SSU_rRNA_archaea	423	420	420	341.6	203.9	4.9e-100	1.4e-58	1	423	3	422	0.993	1.000	-	-	-	-	424	420	-	-	-	-
+contig--862423	+	SSU_rRNA_bacteria	SSU_rRNA_eukarya	423	420	420	341.6	131.4	4.9e-100	9.1e-37	1	423	3	422	0.993	1.000	-	-	-	-	424	465	-	-	-	-
+contig--862423	+	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	423	420	420	341.6	91.9	4.9e-100	1.7e-24	1	423	3	422	0.993	1.000	-	-	-	-	424	346	-	-	-	-
+contig--866163	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	310	295	295	170.6	79.1	2.4e-48	7.5e-21	310	1	295	1	0.952	1.000	-	-	-	-	304	279	-	-	-	-
+contig--912998	+	SSU_rRNA_archaea	SSU_rRNA_bacteria	666	664	664	526.9	377.0	3.5e-156	1e-110	1	666	3	666	0.997	1.000	-	-	-	-	666	660	-	-	-	-
+contig--912998	+	SSU_rRNA_archaea	SSU_rRNA_eukarya	666	656	656	526.9	288.0	3.5e-156	4.6e-84	1	666	2	657	0.985	1.000	-	-	-	-	666	710	-	-	-	-
+contig--912998	+	SSU_rRNA_archaea	SSU_rRNA_microsporidia	666	663	663	526.9	240.1	3.5e-156	2.7e-69	1	666	2	664	0.995	1.000	-	-	-	-	666	577	-	-	-	-
+contig--924893	-	LSU_rRNA_eukarya	LSU_rRNA_archaea	303	287	287	197.5	83.8	2.6e-57	7.5e-23	303	1	296	10	0.947	1.000	-	-	-	-	309	271	-	-	-	-
+contig--942031	-	LSU_rRNA_bacteria	LSU_rRNA_archaea	305	300	300	240.5	160.7	4.8e-70	4.7e-46	307	3	307	8	0.984	1.000	-	-	-	-	316	298	-	-	-	-
+contig--942031	-	LSU_rRNA_bacteria	LSU_rRNA_eukarya	305	238	238	240.5	62.6	4.8e-70	1.2e-16	307	3	306	69	0.780	1.000	-	-	-	-	316	233	-	-	-	-
+contig--95399	+	LSU_rRNA_bacteria	LSU_rRNA_archaea	336	328	328	253.9	141.3	4.4e-74	3.3e-40	1	336	2	329	0.976	1.000	-	-	-	-	333	320	-	-	-	-
+contig--95399	+	LSU_rRNA_bacteria	LSU_rRNA_eukarya	336	255	255	253.9	64.1	4.4e-74	4.3e-17	1	336	5	259	0.759	1.000	-	-	-	-	333	252	-	-	-	-
+contig--97491	+	LSU_rRNA_eukarya	LSU_rRNA_archaea	423	418	418	317.7	126.2	1.5e-93	1.1e-35	2	424	5	422	0.988	1.000	-	-	-	-	430	387	-	-	-	-
+contig--97491	+	LSU_rRNA_eukarya	LSU_rRNA_bacteria	423	417	417	317.7	92.2	1.5e-93	2.6e-25	2	424	7	423	0.986	1.000	-	-	-	-	430	395	-	-	-	-
+contig--978828	-	SSU_rRNA_eukarya	SSU_rRNA_microsporidia	340	340	340	301.7	157.5	3.4e-88	2.5e-44	341	2	341	2	1.000	1.000	-	-	-	-	371	286	-	-	-	-
+contig--978828	-	SSU_rRNA_eukarya	SSU_rRNA_archaea	340	340	340	301.7	128.7	3.4e-88	7.6e-36	341	2	341	2	1.000	1.000	-	-	-	-	371	333	-	-	-	-
+contig--978828	-	SSU_rRNA_eukarya	SSU_rRNA_bacteria	340	340	340	301.7	96.6	3.4e-88	5.4e-26	341	2	341	2	1.000	1.000	-	-	-	-	371	333	-	-	-	-
+contig--984009	-	SSU_rRNA_bacteria	SSU_rRNA_archaea	284	275	275	152.1	97.6	9.3e-43	1.9e-26	284	1	275	1	0.968	1.000	-	-	-	-	283	263	-	-	-	-
+contig--984009	-	SSU_rRNA_bacteria	SSU_rRNA_microsporidia	284	276	276	152.1	53.2	9.3e-43	8.5e-13	284	1	277	2	0.972	1.000	-	-	-	-	283	215	-	-	-	-