bio-maf 0.3.2 → 1.0.0

data/lib/bio/maf/writer.rb

@@ -20,8 +20,8 @@ module Bio::MAF
     end
 
     def write_header(header)
-      f.puts "##maf #{flatten_vars(header.vars)}"
-      f.puts "##{header.alignment_params}" if header.alignment_params
+      f.write "##maf #{flatten_vars(header.vars)}\n"
+      f.write "##{header.alignment_params}\n" if header.alignment_params
     end
 
     def write_blocks(blocks)
@@ -36,8 +36,8 @@ module Bio::MAF
       block.sequences.each do |seq| 
         write_seq(seq, lines)
       end
-      lines << " "
-      f.puts lines.join("\n")
+      lines << "\n"
+      f.write(lines.join("\n"))
     end
 
     def write_seq(s, lines)

data/man/maf_bgzip.1

@@ -0,0 +1,101 @@
+.\" generated with Ronn/v0.7.3
+.\" http://github.com/rtomayko/ronn/tree/0.7.3
+.
+.TH "MAF_BGZIP" "1" "August 2012" "BioRuby" "BioRuby Manual"
+.
+.SH "NAME"
+\fBmaf_bgzip\fR \- optimally BGZF\-compresses and indexes MAF files
+.
+.SH "SYNOPSIS"
+\fBmaf_bgzip\fR [\-d dir] \fImaf\fR \.\.\.
+.
+.br
+\fBmaf_bgzip\fR [\-d dir] \-\-index [\-\-all] \fImaf\fR \.\.\.
+.
+.br
+.
+.SH "DESCRIPTION"
+\fBmaf_bgzip\fR is part of the bioruby\-maf library and compresses Multiple Alignment Format (MAF) files in the Blocked GZip Format (BGZF), enabling efficient random access\. It can optionally index these files as well\.
+.
+.P
+\fBmaf_bgzip\fR can be used as an import tool to prepare MAF files from an external source such as UCSC for use by the other bioruby\-maf tools\. Such MAF files are often gzipped; these can be handled transparently by \fBmaf_bgzip\fR, without a separate gunzip(1) step\.
+.
+.P
+This is a MAF\-specific replacement for the bgzip(1) tool shipped with samtools\. Unlike the output of bgzip(1), each BGZF block (which can be up to 64 KB of uncompressed data) will contain an integer number of MAF blocks, except in the case of MAF blocks larger than 64 KB\. This means that except in unusual cases, a MAF block will be able to be read without having to read more than one BGZF block\.
+.
+.SH "EXAMPLES"
+Compress \fBmm8\.chrM\.maf\fR, creating \fBmm8\.chrM\.maf\.bgz\fR in the current directory:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_bgzip mm8\.chrM\.maf
+.
+.fi
+.
+.IP "" 0
+.
+.P
+Re\-compress and index \fBmm8\.chrM\.maf\.gz\fR (on all sequences) into the \fB/data/maf/\fR directory, creating \fB/data/maf/mm8\.chrM\.maf\.bgz\fR and \fB/data/maf/mm8\.chrM\.kct\fR:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_bgzip \-\-dir /data/maf \-\-index \-\-all mm8\.chrM\.maf\.gz
+.
+.fi
+.
+.IP "" 0
+.
+.P
+As above, but with all \fB\.maf\.gz\fR files in the current directory:
+.
+.IP "" 4
+.
+.nf
+
+$ maf_bgzip \-\-dir /data/maf \-\-index \-\-all *\.maf\.gz
+.
+.fi
+.
+.IP "" 0
+.
+.SH "OPTIONS"
+.
+.TP
+\fB\-d\fR, \fB\-\-dir DIR\fR
+The directory to write the compressed MAF files and indexes to\.
+.
+.TP
+\fB\-i\fR, \fB\-\-index\fR
+Index the compressed MAF files as by maf_index(1)\.
+.
+.TP
+\fB\-a\fR, \fB\-\-all\fR
+When \fB\-\-index\fR is specified, index all sequences, not just the reference sequence\.
+.
+.SH "FILES"
+The MAF files must be valid and have names ending in \fB\.maf\fR\. They may be gzip\-compressed, in which case their names should end with \fB\.maf\.gz\fR\.
+.
+.P
+The BGZF\-compressed MAF files will be optimally compressed for random access and named with a \fB\.maf\.bgz\fR suffix\.
+.
+.P
+Indexes created will be Kyoto Cabinet databases as created by maf_index(1) and have the \fB\.maf[\.gz]\fR suffix replaced with \fB\.kct\fR\.
+.
+.SH "ENVIRONMENT"
+\fBmaf_bgzip\fR is a Ruby program and relies on ordinary Ruby environment variables\.
+.
+.SH "BUGS"
+None known\.
+.
+.SH "COPYRIGHT"
+\fBmaf_index\fR is copyright (C) 2012 Clayton Wheeler\.
+.
+.SH "SEE ALSO"
+ruby(1), maf_index(1), bgzip(1)
+.
+.P
+BGZF is specified in the SAM/BAM specification: \fIhttp://samtools\.sourceforge\.net/SAM1\.pdf\fR

data/man/maf_bgzip.1.ronn

@@ -0,0 +1,85 @@
+maf_bgzip(1) -- optimally BGZF-compresses and indexes MAF files
+===============================================================
+
+## SYNOPSIS
+
+`maf_bgzip` [-d dir] <maf> ...<br>
+`maf_bgzip` [-d dir] --index [--all] <maf> ...<br>
+
+## DESCRIPTION
+
+**maf_bgzip** is part of the bioruby-maf library and compresses
+Multiple Alignment Format (MAF) files in the Blocked GZip Format
+(BGZF), enabling efficient random access. It can optionally index
+these files as well.
+
+`maf_bgzip` can be used as an import tool to prepare MAF files from an
+external source such as UCSC for use by the other bioruby-maf
+tools. Such MAF files are often gzipped; these can be handled
+transparently by `maf_bgzip`, without a separate gunzip(1) step.
+
+This is a MAF-specific replacement for the bgzip(1) tool shipped with
+samtools. Unlike the output of bgzip(1), each BGZF block (which can be
+up to 64 KB of uncompressed data) will contain an integer number of
+MAF blocks, except in the case of MAF blocks larger than 64 KB. This
+means that except in unusual cases, a MAF block will be able to be
+read without having to read more than one BGZF block.
+
+## EXAMPLES
+
+Compress `mm8.chrM.maf`, creating `mm8.chrM.maf.bgz` in the current
+directory:
+
+    $ maf_bgzip mm8.chrM.maf
+
+Re-compress and index `mm8.chrM.maf.gz` (on all sequences) into the
+`/data/maf/` directory, creating `/data/maf/mm8.chrM.maf.bgz` and
+`/data/maf/mm8.chrM.kct`:
+
+    $ maf_bgzip --dir /data/maf --index --all mm8.chrM.maf.gz
+
+As above, but with all `.maf.gz` files in the current directory:
+
+    $ maf_bgzip --dir /data/maf --index --all *.maf.gz
+
+## OPTIONS
+
+ * `-d`, `--dir DIR`:
+   The directory to write the compressed MAF files and indexes to.
+
+ * `-i`, `--index`:
+   Index the compressed MAF files as by maf_index(1).
+   
+ * `-a`, `--all`:
+   When `--index` is specified, index all sequences, not just the
+   reference sequence.
+   
+## FILES
+
+The MAF files must be valid and have names ending in `.maf`. They may
+be gzip-compressed, in which case their names should end with `.maf.gz`.
+
+The BGZF-compressed MAF files will be optimally compressed for random
+access and named with a `.maf.bgz` suffix. 
+
+Indexes created will be Kyoto Cabinet databases as created by
+maf_index(1) and have the `.maf[.gz]` suffix replaced with `.kct`.
+
+## ENVIRONMENT
+
+`maf_bgzip` is a Ruby program and relies on ordinary Ruby environment
+variables.
+
+## BUGS
+
+None known.
+
+## COPYRIGHT
+
+`maf_index` is copyright (C) 2012 Clayton Wheeler.
+
+## SEE ALSO
+
+ruby(1), maf_index(1), bgzip(1)
+
+BGZF is specified in the SAM/BAM specification: <http://samtools.sourceforge.net/SAM1.pdf>

data/man/maf_extract.1

@@ -1,7 +1,7 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_EXTRACT" "1" "July 2012" "BioRuby" "BioRuby Manual"
+.TH "MAF_EXTRACT" "1" "August 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_extract\fR \- extract blocks from MAF files
@@ -40,6 +40,9 @@ This tool exposes almost all the random\-access functionality of the Bio::MAF::A
 A single MAF file can be processed by specifying it with \fB\-\-maf\fR\. Its accompanying index, created by maf_index(1), is specified with \fB\-\-index\fR\. If \fB\-\-maf\fR is given but no index is specified, the entire file will be parsed to build a temporary in\-memory index\. This facilitates processing small, transient MAF files\. However, on a large file this will incur a great deal of overhead; files expected to be used more than once should be indexed with maf_index(1)\.
 .
 .P
+MAF files can optionally be BGZF\-compressed, as produced by bgzip(1) from samtools\.
+.
+.P
 Alternatively, a directory of indexed MAF files can be specified with \fB\-\-maf\-dir\fR; in this case, they will all be used to satisfy queries\.
 .
 .SH "OPTIONS"
@@ -265,4 +268,4 @@ FASTA description lines are always in the format \fB>source:start\-end\fR\.
 \fBmaf_index\fR is copyright (C) 2012 Clayton Wheeler\.
 .
 .SH "SEE ALSO"
-ruby(1), maf_index(1), maf_tile(1)
+ruby(1), maf_index(1), maf_tile(1), bgzip(1)

data/man/maf_extract.1.ronn

@@ -49,6 +49,9 @@ facilitates processing small, transient MAF files. However, on a large
 file this will incur a great deal of overhead; files expected to be
 used more than once should be indexed with maf_index(1).
 
+MAF files can optionally be BGZF-compressed, as produced by bgzip(1)
+from samtools.
+
 Alternatively, a directory of indexed MAF files can be specified with
 `--maf-dir`; in this case, they will all be used to satisfy queries.
 
@@ -210,4 +213,4 @@ FASTA description lines are always in the format `>source:start-end`.
 
 ## SEE ALSO
 
-ruby(1), maf_index(1), maf_tile(1)
+ruby(1), maf_index(1), maf_tile(1), bgzip(1)

data/man/maf_index.1

@@ -1,7 +1,7 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_INDEX" "1" "July 2012" "BioRuby" "BioRuby Manual"
+.TH "MAF_INDEX" "1" "August 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_index\fR \- build and examine MAF indexes
@@ -22,7 +22,7 @@ In its default mode, \fBmaf_index\fR parses the \fImaf\fR file given as an argum
 The index data is stored in binary form, so with the \fB\-\-dump\fR argument, \fBmaf_index\fR can dump out the index data in human\-readable form for debugging\.
 .
 .SH "FILES"
-The \fImaf\fR input file must be a valid MAF file of any length\.
+The \fImaf\fR input file must be a valid MAF file of any length\. It can optionally be BGZF\-compressed, as produced by bgzip(1) from samtools\.
 .
 .P
 The index created is a Kyoto Cabinet TreeDB (B+ tree) database; \fIindex\fR must have a \fB\.kct\fR extension\.
@@ -104,7 +104,7 @@ $ maf_index \-d chr22\.kct > /tmp/chr22\.dump
 \fBmaf_index\fR is copyright (C) 2012 Clayton Wheeler\.
 .
 .SH "SEE ALSO"
-ruby(1), kctreemgr(1)
+ruby(1), kctreemgr(1), bgzip(1)
 .
 .IP "\(bu" 4
 \fIhttps://github\.com/csw/bioruby\-maf/\fR

data/man/maf_index.1.ronn

@@ -22,7 +22,8 @@ form for debugging.
 
 ## FILES
 
-The <maf> input file must be a valid MAF file of any length.
+The <maf> input file must be a valid MAF file of any length. It can
+optionally be BGZF-compressed, as produced by bgzip(1) from samtools.
 
 The index created is a Kyoto Cabinet TreeDB (B+ tree) database;
 <index> must have a `.kct` extension.
@@ -83,7 +84,7 @@ to be set.
 
 ## SEE ALSO
 
-ruby(1), kctreemgr(1)
+ruby(1), kctreemgr(1), bgzip(1)
 
  * <https://github.com/csw/bioruby-maf/>
  * <http://fallabs.com/kyotocabinet/>

data/man/maf_tile.1

@@ -1,7 +1,7 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_TILE" "1" "July 2012" "BioRuby" "BioRuby Manual"
+.TH "MAF_TILE" "1" "August 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_tile\fR \- synthesize an alignment for a given region
@@ -99,6 +99,9 @@ The output is generated in FASTA format, with one sequence per species\.
 The \fImaf\fR parameter must specify either a Multiple Alignment Format (MAF) file or a directory of such files, with indexes\.
 .
 .P
+MAF files can optionally be BGZF\-compressed, as produced by bgzip(1) from samtools\.
+.
+.P
 The \fIindex\fR must be a MAF index built with maf_index(1)\. This parameter is ignored if the \fImaf\fR parameter is a directory\. It can be omitted if a single MAF file is given, but in this case the entire file will be parsed to build a temporary index\. For large files which will be reused, this is not advisable\.
 .
 .P
@@ -111,7 +114,7 @@ If \fB\-\-bed\fR \fIbed\fR is specified, its argument must be a BED file\. Only
 \fBmaf_tile\fR is copyright (C) 2012 Clayton Wheeler\.
 .
 .SH "SEE ALSO"
-maf_index(1), ruby(1)
+maf_index(1), ruby(1), bgzip(1)
 .
 .IP "\(bu" 4
 \fIhttps://github\.com/csw/bioruby\-maf/\fR

data/man/maf_tile.1.ronn

@@ -95,6 +95,9 @@ species.
 The <maf> parameter must specify either a Multiple Alignment Format
 (MAF) file or a directory of such files, with indexes.
 
+MAF files can optionally be BGZF-compressed, as produced by bgzip(1)
+from samtools.
+
 The <index> must be a MAF index built with maf_index(1). This
 parameter is ignored if the <maf> parameter is a directory. It can be
 omitted if a single MAF file is given, but in this case the entire
@@ -116,6 +119,6 @@ variables.
 
 ## SEE ALSO
 
-maf_index(1), ruby(1)
+maf_index(1), ruby(1), bgzip(1)
 
  * <https://github.com/csw/bioruby-maf/>

data/man/maf_to_fasta.1

@@ -1,7 +1,7 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_TO_FASTA" "1" "July 2012" "BioRuby" "BioRuby Manual"
+.TH "MAF_TO_FASTA" "1" "August 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_to_fasta\fR \- convert MAF file to FASTA

data/spec/bio/maf/index_spec.rb

@@ -115,6 +115,13 @@ module Bio
             @idx.close
           }.not_to raise_error
         end
+        it "works from a pipe" do
+          IO.popen("cat #{TestData + 'mm8_chr7_tiny.maf'}") do |pipe|
+            @p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
+            @idx = KyotoIndex.build(@p, '%')
+            @idx.db.count.should > 10
+          end
+        end
         it "accepts .kct paths"
         it "rejects other paths"
         context "mm8_chr7" do

data/spec/bio/maf/parser_spec.rb

@@ -181,6 +181,12 @@ module Bio
           end
           it_behaves_like "any chunk size"
         end
+        it "handles a skipped block in a BGZF file" do
+          @p = described_class.new(TestData + 'mm8.chrM.maf.bgz')
+          blocks = @p.fetch_blocks([[5141084112, 2100],
+                                    [5141087379, 2006]])
+          blocks.collect { |b| b.offset }.should == [5141084112, 5141087379]
+        end
         after(:each) do
           @p.f.close
         end
@@ -191,6 +197,13 @@ module Bio
           p = described_class.new(TestData + 'mm8_chr7_tiny.maf')
           p.each_block.count.should == 8
         end
+        it "works when parsing from a pipe" do
+          IO.popen("cat #{TestData + 'mm8_chr7_tiny.maf'}") do |pipe|
+            p = described_class.new(pipe)
+            p.each_block.count.should == 8
+          end
+        end
+
       end
 
       describe "sequence_filter" do

data/spec/spec_helper.rb

@@ -1,3 +1,5 @@
+require 'bundler/setup'
+
 unless ENV.has_key?('TRAVIS') || RUBY_PLATFORM == 'java'
   begin
     require 'simplecov'

data/test/data/mm8.chrM.maf

@@ -0,0 +1,2421 @@
+##maf version=1 scoring=autoMZ.v1
+a score=360695.000000
+s mm8.chrM                        0 81 +     16299 GTTAATGTAGCTTAA--TAACAAAGCAAAGCACTGAAAATGCTTAGATG-GATAATTG--TA-TCCCATAAAC-ACAAAGGTTTGGTC
+s galGal2.chrM                 1234 75 +     16775 -------TAGCTTAAC-CCACAAAGCATGGCACTGAAGATGCCAAGATGGTACCTACT--AT-ACCTGTGGGC-A-AAAGACTTAGTC
+i galGal2.chrM            N 0 C 0
+s oryCun1.scaffold_140182       113 82 +     20791 GTTAATGTAGCTTAA--CAACAAAGCAAAGCACTGAAAATGCTTAGATGAGCCTTCCC--GG-CTCCATAAAC-ATAAAGGTTTGGTC
+i oryCun1.scaffold_140182 N 0 C 0
+s rn4.chrM                        2 78 +     16300 --TAATGTAGCTTA---TAATAAAGCAAAGCACTGAAAATGCTTAGATG-GATTCAAA--AA-TCCCATAAAC-ACAAAGGTTTGGTC
+i rn4.chrM                N 0 C 0
+s hg18.chrM                     578 84 +     16571 GTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACAT--CA-CCCCATAAAC-AAATAGGTTTGGTC
+i hg18.chrM               N 0 C 0
+s panTro2.chrM                    4 80 +     16554 ----ATGTAGCTTACCCCCTCAAAGCAATACACTGAAAATGTTTCGACGGGTTTACAT--CA-CCCCATAAAC-AAACAGGTTTGGTC
+i panTro2.chrM            N 0 C 0
+s rheMac2.chr14            30986862 84 - 133002572 GTTAATGTAGCTTAATTATTTACAGCAAGACATTGAAAATGTCTAGATGGGATTACAC--AA-CCCTATAAAC-AGATAAATTTGGTC
+i rheMac2.chr14           N 0 N 0
+s bosTau2.chrM                  363 80 +     16338 GTTGATGTAGCTTAAC-C--CAAAGCAAGGCACTGAAAATGCCTAGATG-AGTCTCCC--AA-CTCCATAAAC-ACATAGGTTTGGTC
+i bosTau2.chrM            N 0 C 0
+s canFam2.chrM                    2 80 +     16727 --TAATGTAGCTTAAT-TAATAAAGCAAGGCACTGAAAATGCCAAGATG-AGTCGCAC--GA-CTCCATAAAC-ATAAAGGTTTGGTC
+i canFam2.chrM            N 0 C 0
+s dasNov1.scaffold_23239       3802 82 -     16977 GTCAACGTAGCTTAA--GTCTAAAGCGAGGCACTGAAAATGCCTAAACGAATCCTAAT--GA-TTCCGCAGAC-ACACAGGTCTGGTC
+i dasNov1.scaffold_23239  N 0 C 0
+s loxAfr1.scaffold_36650       3007 83 +     16266 GTTAATGTAGCTTAA--AACAAAAGCAAGGTACTGAAAATACCTAGACGAGTATATCC--AA-CTCCATAAACAACAAAGGTTTGGTC
+i loxAfr1.scaffold_36650  N 0 C 0
+s echTel1.scaffold_49882        260 78 -      7170 GTTAATGTAGCTTAA--TA-AAAAGTGAGGCACTGAAAATGCCTAGATGAGTAT---T--AA-CTCCATAAAC-ATAAAGGTTTGGTT
+i echTel1.scaffold_49882  N 0 C 0
+s monDom4.chrUn           117151420 82 + 174229318 GTTGATGTAGCTTAA--CTTAAAAGCAAAGCACTGAAAATGCTTAGATG-GTTTATACTAAA-ACCCATAAAC-A-AAAGGTTTGGTC
+i monDom4.chrUn           N 0 C 0
+s tetNig1.chrUn_random    103509752 81 + 171761319 GCTAGTGTAGCTTAA--TA--AAAGCATAACACTGAAGATGTTAAGATGGGCCCTAGA--AAGCCCCACAGGC-ACAAAGGCTTGGTC
+i tetNig1.chrUn_random    N 0 C 0
+s fr1.chrUn               320907090 81 + 349519338 GCTAGCGTAGCTTAA--CC--AAAGCAGAGTACTGAAGATGCTAAGATGGGCCCTGAA--AAGTCCCGCAGGC-ACAAAAGCTTGGTC
+i fr1.chrUn               N 0 C 0
+s danRer4.chrM                  950 82 +     16596 GCTAGCGTAGCTTAA--AA-TAAAGCACGGCACTGAAGCTGCCAAGATGGGCCCTAAT--AAGCTCCGCATGC-ACAAAGGCATGGTC
+i danRer4.chrM            N 0 C 0
+
+a score=1709796.000000
+s mm8.chrM                       81 379 +     16299 CTGGCCTTATAATTAATTAGAGGTAAAATTACACATGCAAACCTCCATAGACCGGTGTAA-AATCCCTTAAACATTT-ACTTA--------AAATTTAAGGAGAGGGTATCAAGCACAT--------TAA--AATAGCTTAAGACACCTTGCCT-AGCCACACCCCCACGGG-ACTCAGCAGTGATAAATATTAAGCAATAAACG---AAAGTTTGACTAAGTTA-TACCT---C-TTAGGGTT-GGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAAT-TATCTT-CGGCGTAAAACGTGTCAACT----ATAAATAAATA-----AATAGAATTAAAATCCAACTTA-TATGT-GAAAATTCATTGTTAGGACCT-AAACTCAATAACGAAAGTAATTCT----AGTCA---------TT
+s oryCun1.scaffold_140182       195 382 +     20791 CTGGCCTTTTTATTGTTTTGTAGCAACCTTACACATGCAAGACTCCTCACGCCAGTG-AG-AATGCCCTTAACATCA-AACTA--------GATCAAGAGGAGCGGACATTAAGCACAC--------TAATCAGTAGCTCAAGATGCCTTGCTT-AACCACACCCCCAAGGG-ATACAGCAGTGATAAATATTTAGCAATGAACG---TAAGTTTGACTAAGTTA-TGCTA---CTTTAGGGTT-GGTAAATCTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAATAAATATC-CGGCGTAAAGCGTGATTAGA----ATAAACAACAA-----AATAAAATCAAATAACAACTAA-GCTGT-AAAAAGTAATAGTTGCAAACA-AAAATAAACAACGAAAGTGATTTT----ATACT---------CT
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                       80 379 +     16300 CTGGCCTTATAATTAATTGGAGGTAAGATTACACATGCAAACATCCATAAACCGGTGTAA-AATCCCTTAAAGATTT-GCCTA--------AAACTTAAGGAGAGGGCATCAAGCACAT---------AA--TATAGCTCAAGACGCCTTGCCT-AGCCACACCCCCACGGG-ACTCAGCAGTGATAAATATTAAGCAATGAACG---AAAGTTTGACTAAGCTAGTACCT---C-TCAGGGTT-GGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAAT-TATTTT-CGGCGTAAAACGTGCCAACT----ATAAATCTCAT-----AATAGAATTAAAATCCAACTTA-TATGT-GAAAATTCATTGTTAGGACCT-AAGCCCAATAACGAAAGTAATTCT----AATCA---------TT
+i rn4.chrM                C 0 C 0
+s hg18.chrM                     662 382 +     16571 CTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTG-AG-TTCACCCTCTAAATC--ACCAC--------GATCAAAAGGGACAAGCATCAAGCACGCAG------CAA--TGCAGCTCAAAACGCTTAGCCT-AGCCACACCCCCACGGG-AAACAGCAGTGATTAACCTTTAGCAATAAACG---AAAGTTTAACTAAGCTA-TACTAAC-C-CCAGGGTT-GGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAAT-AGAAGC-CGGCGTAAAGAGTGTTTTAG----ATCACCCCCTC--CCCAATAAAGCTAAAACTCACCTGA-GTTGT-AAAAAACTCCAGTT--GACAC-AAAATAGACTACGAAAGTGGCTTT----AACAT---------AT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                   84 376 +     16554 CTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGCCCC-GTG-AG--TCACCCTCTAAATC--GCCAT--------GATCAAAAGGAACAAGTATCAAGCACGCAG------CAA--TGCAGCTCAAAACGCTTAGCCT-AGCCACACCCCCACGGG-AGACAGCAGTGATAAACCTTTAGCAATAAACG---AAAGTTTAACTAAGCCA-TACTAAC-C-TCAGGGTT-GGTCAATTTCGTGCTAGCCACCGCGGTCATACGATTAACCCAAGTCAAT-AGAAAC-CGGCGTAAAGAGTGTTTTAG----ATCACCCCCCC------ATAAAGCTAAAATTCACCTGA-GTTGT-AAAAAACTCCAGCT--GATAC-AAAATAAACTACGAAAGTGGCTTT----AACAC---------AT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34435460 378 - 182086969 ctgGCCTTTTCCTTAGCTCTTAGTAGGATTACACATGCAAGCATCCCCACCCCAGTG-AAAAATGCCCTCTAGATC--ACCG---------GATCAAAAGGAGCAGGTATCAAGCATGCAT------GAA--TGCACCTCAAAACACTTTGCTC-AACCACACCCCCACGGG-AAACAGCAGTGATAAATCCTTAGTAATAAATG---GAAGTTTGACCAAGCCA-TACTAATAT-TTAGGGTT-GGTTAATTTCGTGCCAGTCA-CGTGGCCATAAGATTAACCCAAGCTAAT-AGAACT-TGGCGTAAAGAATGTTTAAG----GTCTACCCTCA------ATAAAGCTAAACTCCATTTAA-GCTGTAAAAAAACTCCAGCT--GAAAT-AAAATATACTACAAAAGTGGCTTT----AATAT----------C
+i rheMac2.chr5            N 0 C 0
+s bosTau2.chrM                  443 376 +     16338 CCAGCCTTCCTGTTAACTCTTAATAAACTTACACATGCAAGCATCTACACCCCAGTG-AG-AATGCCCTCTAGGTT--ATTAA--------AACTAAGAGGAGCTGGCATCAAGCACACAC------CC---TGTAGCTCACGACGCCTTGCTT-AACCACA-CCCCACGGG-AAACAGCAGTGACAAAAATTAAGCCATAAACG---AAAGTTTGACTAAGTTA-TATTA---A-TTAGGGTT-GGTAAATCTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAGCTAAC-AGGAGTACGGCGTAAAACGTGTTAAAG----CACCATACCAA------ATAGGGTTAAATTCTAACTAA-GCTGT-AAAAAGCCATGATT--AAAATAAAAATAAATGACGAAAGTGACCCT----ACAAT---------AG
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                   82 378 +     16727 CTAGCCTTCCTATTAGTTTTTAGTAGACTTACACATGCAAGCCTCCACGCCCCAGTG-AG-AATGCCCTTAAAATC--ACCAG-------TGATCTAAAGGAGCAGGTATCAAGCACACTC------TTA--AGTAGCTCATAACACCTTGCTA-AGCCACACCCCCACGGG-ATACAGCAGTGATAAAAATTAAGCCATAAACG---AAAGTTTGACTAAGCCA-TACTA---A-ATAGGGTT-GGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAACTAAT-AGGCCTACGGCGTAAAGCGTGTTCAAG----ATACTTTTACA------CTAAAGTTAAAACTTAACTAA-GCCGT-AAAAAGCTACAGTT--ATCAT-AAAATAAACCACGAAAGTGACTTT----ATAAT---------AA
+i canFam2.chrM            C 0 I 1
+s dasNov1.scaffold_23239       3884 386 -     16977 CTAGCCTTACTATTAATTCATAACAAAATTACACATGCAAGTATCAGCACACCAGTG-AG-AATGCCCTCTAACTC--TTATA--------GATCAAAAGGAGCAAGCATCAAGTACACACAGCCCTTAC--AGTAGCTCATAACGCTTTGCTC-AACCACACCCCCACGGG-ATACAGCAGTGATAAAAATTAAGCAATAAGCG---AAAGCTTGACTAAGTTA-TGTTATT-A-TAAGGGTT-GGTAAATTTCGTGCCAGCAACCGCGGTCATACGATTAACCCAAATTAAT-AGTTAT-CGGCGTAAAGCGTGTTTAAG----ACACCTAGACA------ATAGAGTTAAACCCTTACTAC-GCTGT-AAAAAGCCTTAGTAGGACCAT-AAACCCTTCAACGAAAGTGACTCT----AATTT---------AT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       3090 383 +     16266 CCGGCCTTCTTATTGGTTACTAGGAAACTTATACATGCAAGTATCCGCCCGCCAGTG-AA-TACGCCTTCTAAATC--ATCAC-------CGATCAAAGAGAGCTGGCATCAAGCACACAC---TCTAAG--TGTAGCTCATGACGTCTCGCCT-AGCCACACCCCCACGGG-AAACAGCAGTAGTAAATATTTAGCAATTAACA---AAAGTTAGACTAAGTTA-TCCTAA--T-AAAGGACT-GGTCAATTTCGTGCCAGCAACCGCGGCCATACGATTAGTCCAAATTAAT-AAGCATACGGCGTAAAGCGTATCAGAA----GAATTAAGAAA------ATAAAGTTAAATCTTATACTA-GCTGT-TTAAAGCTCAAGATAAGACAT-A-AATAACCTACGAAAGTGACTTT----AATAA---------TC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_49882        338 378 -      7170 CTAGCCTTTTTATTAGTTCTTAATAAAATTATACATGCAAGTATCCACCCCCCAGTG-AA-AATGCCCTTAAACTT--ACTTA-------TAATTAAGAGGAGCAGGTATCAAGCACA-------CTTAA--TGTAGCTCACAACACCTTGCTA-AGCCACACCCTCACGGG-ACACAGCAGTAATAAAAATTAAGCAATTAACG---GAAGTTTGACTTAGTTA-TATTAT--T-TAATTAGTCGGTCAACTTCGTGCCAGCCACCGCGGTCATACGAAGGACTTGAACTAAT-AAATAC-CGGCGTAAAGCGTGATTAAG----ATCTTTAAACA------ATAAAACAAAAAC-TATTCTATGCCGT-AAAAAGCC--AGAGAATACTT-ATAATAAATAACGAAGGTAATTTT----ATAAT---------TT
+i echTel1.scaffold_49882  C 0 C 0
+s monDom4.chrUn           117151502 391 + 174229318 CTAGCCTTCTTGTTAATTTTAATTAGACCTACACATGCAAGTTTCCGCTGCCCTGTG-AG-AATGCCCTCAAAACT--ACTCAATTCTCCAAGATAAGAGGAGCTGGTATCAGGCACACAC------TACT-AGTAGCCAACTACACCTTGCTC-AACCACACCCCCACGGG-AAACAGCAGTGATTAAAATTAAGCTATAAACG---AAAGTTTGACTAAATCA-TAGTTAT-C-TAAGGGTT-GGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTAAC-AAGCCTCCGGCGTAAAGCGTGTCCAAA----CAAAAGACTAA----TAATAAAGTTAATACTTAACTAA-GTTGT-AACACACTCCAGTTA-ATACT-AAGATAAACTATTAAAATAACTTT----AATAA---------AG
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 1309 395 +     16775 CTAACCTTTCTATTGGTTTTTGCTAGACATATACATGCAAGTATCCGCATCCCAGTG-AA-AATGCCCCCAAACCT--TTCTT-----CCCAAGCAAAAGGAGCAGGTATCAGGCACACTC------AGC--AGTAGCCCAAGACGCCTTGCTTAAGCCACACCCCCACGGGTACTCAGCAGTAATTAACCTTAAGCAATAAGTG---TAAACTTGACTTAGCCA-TAGCAA--C-CCAGGGTT-GGTAAATCTTGTGCCAGCCACCGCGGTCATACAAGAAACCCAAATCAAT-AGCTACCCGGCGTAAAGAGTGGCCACATGTTATCTGCACCAG------CTAAGATTAAAATGCAACCAA-GCTGT-CATAAGCCTAAGATC-CACCT-AAACCCAAC--CCAAATCCATCTT----AGCCTCAACGATTAAT
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18005        958 384 +      3405 CCAGCCTTGTCATCAACTTTATCTGAACTTACACATGCAAGCATCCGCATTCCCGTG-AA-AATGCCCTTAAGCCC--CTAAA-----ACAGAGGATAAGGAGCCGGTATCAGGCACGACC-----------ATCAGCCCACGACACCTTGCTA-TGCCACACCCACAAGGGAACTCAGCAGTGATAAACATTGAAC-ATGAGCGATTAAAGCTCGACTCAGTTA-CAGAT---A-ACAGAGTT-GGTCAATCTCGTGCCAGCCGCCGCGGTTATACGAGAAACTCAAGTTGAT-AATTCA-CGGCGTAAAGCGTGATTAAG----GTTCACCCTCA------CTAGAGTCAAACCCTAGCTAA-GCTGT-CGCACGCTTTCGCTA-GACTG-AAGAACACTAACGAAAGTAACTCTACCCAACAT---------AC
+i xenTro2.scaffold_18005  N 0 C 0
+s tetNig1.chrUn_random    103509833 382 + 171761319 CTGACTTTACTAACAGCTCTAGCCAAACTTACACATGCAAGTATCCGCACCCCCGTG-AG-AATGCCCTACACACCC-TGCCC--------GGGAATTAGGAGCCGGTATCAGGCACAC-C------CCT--CGTAGCCCATGACGCCTTGCTT-AGCCACACCCCCAAGGGAACTCAGCAGTGATAAACATTAAGCCATAAGTG---AAAACTTGACTTAGCTA-CGGCT---T-AGAGGGCC-GGTAAAACTCGTGCCAGCCACCGCGGTTATACGAGAGACCCAAGTTGTT-AGCCCC-CGGCGTAAAGAGTGGTTAAA----ACACCAAACAC--CAAACTGAGGCCGAACGCCCTCAAG-GCAGT-TATACGCTCCCGAGG-ACATG-AAGGACAATTACGAAGGTAGCCTC----ACCCC---------CT
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320907171 383 + 349519338 CTGACTTTACTAACAACTCTGATCAAACTTACACATGCAAGTATCCGCATCCCAGTG-AA-AATGCCCCCCGCCCCC-CGTCC--------GGAAATAGGGAGTTGGTATCAGGCACACAA------ATT--TGTAGCCCATGACACCTAGCTT-TGCCACGCCCCCAAGGGAATTCAGCAGTGATAAACATTAAGCCATAAGTG---AAAACTTGACTTAGTCA-TGATC---T-AAAGAGTC-GGTAAAACTCGTGCCAGCCACCGCGGTTATACGAGAGACCCAAGTTGTT-AGCCAA-CGGCGTAAAGGGTGGTTAGA----ACTAAAAACAA--CAAACTGAGACCGAACACCTTCAAG-GCTGT-TATACGCTTCCGAAG-CAACG-AAGAACAATAACGAAAGTAGCCTC----ACTAA---------CT
+i fr1.chrUn               C 0 N 0
+s danRer4.chrM                 1032 378 +     16596 CCGACCTTTTGATCAGCTTTTACCTAATTTACACATGCAAGTCTCCGCACCCCTGTG-AA-TACGCCCTCAATCCCCAAACCT--------GGGGACGAGGAGCAGGTATCAGGCACAA-A------ATT--TTTAGCCCAAGACGCCTAGCCA-AGCCACACCCCCAAGGGGATCCAGCAGTGACAAACATTAAGCTATAAGTG---AAAACTTGACTCAGTTA-AGGTA---A-AGAGAGCC-GGTAAAACTCGTGCCAGCAACCGCGGTTAAACGAGAGGCTCTAGTTGAT-ATACTA-CGGCGTAAAGGGTGGTTAAG---------GAACAATGTAAAATAAAGCCAAACGGCCCTTTA-ACTGT-TATACGCTTTTAGAT-GCTAG-AGGCCCAAACACGAAAGTAGCTTT----A--AA---------TT
+i danRer4.chrM            C 0 I 6
+
+a score=1731261.000000
+s mm8.chrM                      460 260 +     16299 TATA--ATACACGACAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACCTAAATAATTAAATTTAACA-AAAC-TATTTGCCAGAGAACTACTAG--CCATAGCTTAAAACTCAAAGGACT---TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGCTCTACCTCACCATCTCTTGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAA--AAAGGTATTAAAGT
+s oryCun1.scaffold_140182       577 256 +     20791 TCGA--ACTCACGATAGCTAAGGCCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACTTTGATAATTTCA--TAACA-AAAT-TATTCGCCAGAGAACTACAAG--CCAAAGCTTAAAACTCAAAGGACT---TGGCGGTGCTTTATACCCACCTAGAGGAGCCTGTTCCGTAATCGATAAACCCCGATAAACCTTACCACTCTTTGCCAACTCAGCCTATATACCGCCATCTTCAGCGA--CCTAA--AAAGGAGAAAAAGT
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                      459 261 +     16300 TATATAATGCACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTTAATAATTAAACCTA-CA-AAAT-TATTTGCCAGAGAACTACTAG--CTACAGCTTAAAACTCAAAGGACT---TGGCGGTACTTTATATCCATCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGTTCTACCTTACCCCTTCTCGCTAATTCAGCCTATATACCGCCATCTTCAGCAAACCCTAA--AAAGGCACTAAAGT
+i rn4.chrM                C 0 C 0
+s hg18.chrM                    1044 256 +     16571 CTGA--ACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAA-TCAACA-AAAC-TGCTCGCCAGAACACTACGAG--CCACAGCTTAAAACTCAAAGGACC---TGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC----TCAGCCTATATACCGCCATCTTCAGCAAACCCTGA-TGAAGGCTACAAAGT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                  460 256 +     16554 CTGA--ATACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACTTCAACAGTTAAA-TTAACA-AAAC-TGCTCGCCAGAACACTACGAG--CCACAGCTTAAAACTCAAAGGACC---TGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCGCCTCTTGC----TCAGCCTATATACCGCCATCTTCAGCAAACCCTGA-TGAAGGTTACAAAGT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34435838 239 - 182086969 CTGA--AGACACAATAGCTAAGATCGAAACTTGGATTAGATACCCCACTATGCTCAGCTCTAAACTCTAATAGTTAGA-TTAACA-AAAC-CACTCGCCAGAGTACTACAAG--AAACAGCTGAAAACTCAAAGGACT---TGGTGGTGCTTTATATCCCCCTAGAGGAGCCTGTTCTAT-ATTGATAAACCCTGATGCACCTCAGTACCTCTTGCCA--CCAGCCTATATACCGCCATCTTCAGCAAACCC-------------------
+i rheMac2.chr5            C 0 I 233
+s bosTau2.chrM                  819 258 +     16338 CCGA--C-GCACTATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACACAGATAATTACA-TAAACA-AAAT-TATTCGCCAGAGTACTACTAG--CAACAGCTTAAAACTCAAAGGACT---TGGCGGTGCTTTATATCCTTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTCACCAATTCTTGCTAATACAGTCTATATACCGCCATCTTCAGCAAACCCTAA--AAAGGAAAAAAAGT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                  461 258 +     16727 CTGA--CTACACGATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTA-C-AACA-AAAT-AATTCGCCAGAGGACTACTAG--CAATAGCTTAAAACTCAAAGGACT---TGGCGGTGCTTTATATCCCTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTCACCACCTTTCGCTAATTCAGTCTATATACCGCCATCTTCAGCAAACCCTCA--AAAGGTAGAACAGT
+i canFam2.chrM            I 1 C 0
+s dasNov1.scaffold_23239       4270 258 -     16977 CTGA--CTACACGATAGCTAGGACCCAAACTGGGATTAGATACCCCACTATGCCTAGCCCTAAACTAAAACAGTT-CA-CAAACA-AAAC-TGTTCGCCAGAGTACTACTAG--CAACAGCTTAAAACTCAAAGGACT---TGGCGGTGCTTTACATCCTTCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATATACCTCACCACCCCTTGCTAATACAGCCTATATACCGCCATCTTCAGCAGACCCTAG--TAAGGCACCACAGT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       3473 259 +     16266 CTAA--ACATACGATAGCTAGGGTACAAACTGAGATTAGATACCTCACTATGCCTAGCCCTAAACTTTGATAGCTACC-TTTACA-AAGC-TATCCGCCAGAGAACTACTAG--CCAGAGCTTAAAACTTAAAGGACT---TGGCGGTGCTTTATATCCACCTAGGGGAGCCTGTCTCGTAACCGATGAACCCCGATATACCTTACCGTCACTTGCTAATTCAGTCCATATACCACCATCTTCAGCAAACCCCTA--TAGGGCACAAAAGT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_49882        716 260 -      7170 CTGA--ACCCACGATAGCTAAGAAACAAACTGGGATTAGATACCCCACTATGCTTAGCCTTAAACCTAGATAGT--CT-ATAACA-AGACATATCCGCCAGAGAACTACTAG---CAAAGCTAAAAACTTAAAGAACTCTGTGGCGGTGCTTCACACCCACCTAGAGGAGCCTGTTATGTAATTGATACACCCCACTAAACCCTACCACCACTTGCTAAGTCAGTCTATATACCGCCATCCTCAGCAAAACCCCA--AAAGGCATATCAGT
+i echTel1.scaffold_49882  C 0 C 0
+s monDom4.chrUn           117151893 257 + 174229318 CTGA---TACACGAAAACTAAGGTACAAACTGGGATTAGATACCCCACTATGCTTAGTCATAAACCAAAGTAGTTAGA--TAACA-AAAC-TACTCGCCAGAGAACTACTAG--CTACTGCTTAAAACTCAAAGGACT---TGGCGGTGCCCTAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATATACCCAACCCCATCTTGCCAATACAGCCTATATACCGCCATCGTCAGCCCACCTTAA--AAAAGATACAAAGT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 1704 263 +     16775 TTTA--ACCCACGAAAGCTAGGACCCAAACTGGGATTAGATACCCCACTATGCCTAGCCCTAAATCTAGATACCTCCC-ATCACA-CATG-TATCCGCCTGAGAACTACGAGCACAAACGCTTAAAACTCTAAGGACT---TGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAATCCACGATTCACCCAACCACCCCTTGCCAGCACAGCCTACATACCGCCGTCGCCAGCCCACCTCTAATGAAAGAACAACAGT
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18005       1342 254 +      3405 CTGA--ACTCACGACCGCTAGGAAACAAACTGGGATTAGATACCCCACTATGCCTAGCCTTAAACCTTGAC-----CA-ATTACA-CTTC-AATCCGCCAGGGAACTACGAG--CCCAAGCTTAAAACCCAAAGGACT---TGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATACCCCCCGCTTAACCTCACCACTTCTTGCCAAACCCGCCTATATACCACCGTCGCCAGCCCACCCCGT--GAGGGGACACAAGT
+i xenTro2.scaffold_18005  C 0 C 0
+s tetNig1.chrUn_random    103510215 258 + 171761319 TTGA--ACCCACGAAAGCTAGGGTACAAACTGGGATTAGATACCCCACTATGCCTAGCCCTAAACAATGATATTCTAA---TACATTCCT-TATCCGCCCGGGTACTACGAG--CATTAGCTTAAAACCCAAAGGACT---TGGCGGTGCTTTAAACCCATCTAGAGGAGCCTGTTCTAGAACCGATAATCCCCGTTAAACCTCACCCCTTCTTGTCTAATCCGCCTATATACCACCGTCGTCAGCCTACCCTGT--GAAGGACTAACAGT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 1416 257 +     16596 CTGA--ACCCACGAAAGCTAAGAAACAAACTGGGATTAGATACCCCACTATGCTTAGCCATAAACAAAGACATTTAAT---CACA-ACAA-TGTTCGCCCGGACACTACAAG--CATAAGCTTAAAACCCAAAGGACC---TGACGGTGCCTTAGATCCCCCTAGAGGAGCCTGTTCTAGAACCGATTATCCCCGTTAAACCTCACCATTTCTAGCAAAATCAGCCTATATACCACCGTCGCCAGCTTACCCTGT--GAAGGAATAACAGT
+i danRer4.chrM            I 6 C 0
+
+a score=-15759.000000
+s mm8.chrM                      720  22 +     16299 AAGCAAAAGAAT---------------------------------CAAACAT-------------------------------------------------------------AAA
+s oryCun1.scaffold_140182       833  20 +     20791 AAGCTCAATTA----------------------------------CTACCGT--------------------------------------------------------------AA
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                      720  21 +     16300 AAGCACAAGAA----------------------------------CAAACAT-------------------------------------------------------------AAA
+i rn4.chrM                C 0 C 0
+s hg18.chrM                    1300  21 +     16571 AAGCGCAAGTA----------------------------------CCCACGT-------------------------------------------------------------AAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                  716  21 +     16554 AAGCACAAGTA----------------------------------CCCACGT-------------------------------------------------------------AAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34436310 116 - 182086969 aagcaggagaatggcgtgaacccgggaggtggagcttgcagtgagcccagatcaggccactgtagtccagcctgggcaacagagtgagactctgtctcaaaaaacaaaaaacaaaa
+i rheMac2.chr5            I 233 C 0
+s bosTau2.chrM                 1077  22 +     16338 AAGCGTAATTAT---------------------------------GATACAT-------------------------------------------------------------AAA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                  719  22 +     16727 AAGCACAATCAT---------------------------------TTTACAT-------------------------------------------------------------AAA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       4528  21 -     16977 GAGCACAATAA----------------------------------CATACAT-------------------------------------------------------------AAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       3732  22 +     16266 GAGCTTAATCAT---------------------------------AACCCAT-------------------------------------------------------------GAA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_49882        976  22 -      7170 AAGCATAATGAT---------------------------------AAGACAT-------------------------------------------------------------AAA
+i echTel1.scaffold_49882  C 0 I 1561
+s monDom4.chrUn           117152150  23 + 174229318 AAGCAAAATTATT--------------------------------TTTTCAT-------------------------------------------------------------AAA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 1967  22 +     16775 GAGCTCAATAGC---------------------------------CCCTCGC-------------------------------------------------------------TAA
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18005       1596  22 +      3405 AGGCTCAATGAT---------------------------------CAAACAT-------------------------------------------------------------CAA
+i xenTro2.scaffold_18005  C 0 C 0
+s tetNig1.chrUn_random    103510473  22 + 171761319 AGGCAAAGTTGG---------------------------------CACAGCC-------------------------------------------------------------CAA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 1673  22 +     16596 AAGCAAGATGGG---------------------------------CATAGCC-------------------------------------------------------------CAG
+i danRer4.chrM            C 0 C 0
+
+a score=558754.000000
+s mm8.chrM                      742 124 +     16299 AACGTTAGGTCAAGGTGTAGCCAATGAAATGGGAAGAAATGGGCTACATTTTCT---TA-TA--AAAGAACATT-----ACTATACCCTTT--ATGAAA----CTAAAG--GACTAAGGAGGATTTAGTAGTAAATTAAGAAT-
+s oryCun1.scaffold_140182       853 123 +     20791 AACGTTAGGTCAAGGTGTAGCTCATAGAGTGAGA--GCATGGGCTACATTTTCT---AC-TT---CAGAATATA-----CGAATTGCCCTT--ATGAAAC--TCTAAGG--GCCAAAGGAGGATTTAGTAGTAAATTAAGAAT-
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                      741 125 +     16300 AACGTTAGGTCAAGGTGTAGCCAATGAAGCGGAAAGAAATGGGCTACATTTTCT---TT-TCCCAGAGAACATT-----ACGA-AACCTTT--ATGAAA----CTAAAG--GACAAAGGAGGATTTAGTAGTAAATTAAGAAT-
+i rn4.chrM                C 0 C 0
+s hg18.chrM                    1321 124 +     16571 GACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCT---AC-CC---CAGAAAACT-----ACGATAGCCCTT--ATGAAAC---TTAAGG--GTCGAAGGTGGATTTAGCAGTAAACTGAGAGT-
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                  737 124 +     16554 GACGTTAGGTCAAGGTGTAGCCTATGAGGTGGCAAGAAATGGGCTACATTTTCT---AC-CC---CAGAAAATT-----ACGATAACCCTT--ATGAAAC---CTAAGG--GTCAAAGGTGGATTTAGCAGTAAACTAAGAGT-
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34436426 127 - 182086969 aaTGTTAGGTCAAGGTGTAGCCCATGAAGTGGCATGAAATGGGCTACATTTTCT---ATGTC---CAGAAAATT--T-CACAACAACCTTT--ATGAAAT---CTAAGA--GCTCAAGGAGGATTTAGCAGTAAACCAAGAGC-
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 1099 128 +     16338 AACGTTAGGTCAAGGTGTAACCTATGAAATGGGAAGAAATGGGCTACATTCTCT---ACACC---AAGAGAATCAAG-CACGAAAGTTATT--ATGAAA----CCAATA--ACCAAAGGAGGATTTAGCAGTAAACTAAGAAT-
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                  741 125 +     16727 AAAGTTAGGTCAAGGTGTAACTTATGAGGTGGGAAGAAATGGGCTACATTTTCT---AC-CC---AAGAACATT--T-CACGAATGTTTTT--ATGAAA----TTAAAA--ACTGAAGGAGGATTTAGTAGTAAATTAAGAAT-
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       4549 126 -     16977 GACGTTAGGTCAAGGTGTAGCTTATGGGGTGGGAAGAAATGGGCTACATTTTCT---AA-TA---AAGAGCAAA----TACAAAAAACTTA--ATGAAACAATTTAAGA----CTAAGGTGGATTTAGTAGTAAGCTAAAAAT-
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       3754 126 +     16266 AAAGTTAGGCCGAGGTGTCGCCTACGTGACGGTCAAAGATGGGCTACATTTTCT---AT-TA---TAGAACAGA--CAAACGGATATCACT--CTGAAA----TGGGTG--GTTGAAGGCGGATTTAGTAGTAAACTAAGAAT-
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343         2 129 +     18297 AACGTTAGGTCAAGGTGTAACCCATGTGGTGGAACCTAATGGGCTACATTTTCTAGCAT-TA---GAAAACCTT--C-AACGAAAGTACTA--ATGAAA----TTTCAGT-ACTAAAGGAGGATTTAGTAGTAAACTGAGAAT-
+i echTel1.scaffold_181343 n 1561 C 0
+s monDom4.chrUn           117152173 125 + 174229318 AACGTTAGGTCAAGGTGTAGCATATGATAGGGAAAGAAATGGGCTACATTATCT---AG-CT---TAGATTACA------CGAATCACATT--ATGAAAT---CTAATGTGCCTGAAGGAGGATTTAGTAGTAAATTAAGAAT-
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 1989 122 +     16775 TAAGACAGGTCAAGGTATAGCCTATGGGGTGGGA-GAAATGGGCTACATTTTCT---AA-CA---TAGAACAAA------CGAAAAAGGAT--GTGAAAC---CCGCCC--TTAGAAGGAGGATTTAGCAGTAAAGTGAGATC-
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18005       1618 123 +      3405 TACGTCAGGTCAAGGTGTAGCANATGAAGTGGGAAGAAATGGGCTACATTTTCT---AA-TA--CTAGAAAAAA-----CGAAAGATCTTT--ATGAAAC---C--AGA--TCAGAAGGCGGATTTAGCAGTAAAGAGAGACA-
+i xenTro2.scaffold_18005  C 0 N 0
+s tetNig1.chrUn_random    103510495 123 + 171761319 AACGTCAGGTCGAGGTGTAGCGTATGGAGGGGGAAGAAATGGGCTACATTCTCT---GC-CC---AGAGAACCA------CGAATGACATA--ATGAAA----CACATG--TCTGAAGGAGGATTTAGCAGTAAGTAAAGAAAC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 1695 122 +     16596 AAAGTCAGGTCGAGGTGTAGCACATGAAATGGGAAGAAATGGGCTACACTTTCT---AC-CC---CAGAATATA------CGAA-AATGTAACATGAAA----CA-ATA--CTTGAAGGAGGATTTAGCAGTAAA-AGAGAAGC
+i danRer4.chrM            C 0 C 0
+
+a score=2286094.000000
+s mm8.chrM                      866 631 +     16299 AGA------GAGCTTAATTGAATTGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCT--CAAAT----------TA-AATTAAACTTAACA-TA---AT-TAATTTCTAGACATCCGTTT-ATG-AGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAAT--A-ATCATAGTGTAGCT-TA-A-TATTAAAGCATCTGGCCTACACCCAGAAGAT---TTCATGACCAA--TGAACACTCTGA-AC--TAATC-----CTAGCCCTA--G-CCC-TA---------CACAAATAT--AA---------TTA-TACT--ATTAT------------ATAAATCAAAACATT-TATCC--TA-----CTAAAAGTATTGGAGAAAGAA-----AT-----TCGTACATCTAGGAGCTATAGAA----CTAGTACCGCAAGGGAAA-GATGAAA-G--ACTAATTAA------------AAGTAAGAACAAG-CAAAGATTAAACCTTGTACCTTTTGCATAATGAACTAACTAG-AAAACTTCTAACTAAAAGAATTACAGCTAGAAACCCCGAAA-CCAAACGAGCTACCTAAAAACAATTT-----T--AT---GAATCAACTCGTCTATGTGGCAAAATAGTGAGAAGATTTTTAGGTAGAGGTGAAAAGCCTAACGAGCTTGGTGATAGCTGGTTACCCA-AAAA-ATGAATTTAAGTTCAATTTTAAA------C-------TTGCTA------------------AAAA------AA-CAA
+s oryCun1.scaffold_140182       976 628 +     20791 AGA------GTGCTTAATTGAACAAGGCCATGAAGCACGCACACACCGCCCGTCACCCTCCT--CAAGT-------------GACAAATATTTACT-TATACCT-AATTACATAAATAGACAAGC-ATA-AGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGACA--C-TTCAGAGCGTAGCT-TA-A--CTTAAAGCACTTGGCTTACACCCAAGAGAT---TTCAT--TTAC--TGACCACTCTGA-GC--CAACA-----CTAGCCCTA--T-GA---A----------ACTAACACTGAA---------CCA-GAGTA-ATTAG------------CTAAACTAAACCATT-CACCC--CAT---ATTAAAAGTATAGGAGATAGAA-----AT-----TTA--TATCCAGGCGCTATAGAG----AAAGTACCGTAAGGGAAA-GATGAAA-G--ATTAGTTAA------------TAGCACAAAAAAG-CAGAGATTACTTCTCTTACCTTTTGCATAATGAATTAGCTAG-AAAATCCTTAGCAAAAAGAATTTTAGTTAAGAACCCCGAAA-CCAGACGAGCTATTTATGAGCAGTTG-----A--AA---GAACGAACCCGTCCATGTGGCAAAATGGTGGGAAGACTTGTAAATAGAGGTGAAAAGCCAACCGAGCCTGGTGATAGCTGGTTGTCCA-GAAT-A-GAATTTTAGTTCAACTTTAAA------T-------TTTCCT------------------AAAG------GA-CAT
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                      866 628 +     16300 AGA------GAGCTTAATTGAATAGAGCAATGAAGTACGCACACACCGCCCGTCACCCTCCT--CAAAT----------TA-GATTGACATTCACA-TATACAT-AATTTCACTAACA--AATTT-ATG-AGAGGAGATAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAAT--A-ATCACAGTGTAGCT-TA-A-TCACAAAGCATCTGGCCTACACCCAGAAGAA---TTCATAAAAAA--TGAACACTTTGA-AC--TAACC-----CTAGCCCTA--C-AAC-CA----------ACCAACAT--AA---------CTA-AACC--CCCAC------------ATAAACTAAAACATT-TAACT--CA-------AAAAGTATTGGAGAAAGAA-----AT-----TTACTTACC-AAGAGCTATAGAG----AAAGTACCGCAAGGGAAATGATGAAA-G--ACTAATTTA------------AAGTAAAAACAAGACAAAGATTAAACCT-GTACCTTTTGCATAATGAATTAACTAG-AAAATCCTTAACAAAAAGAATTTAAGCTAAGAACCCCGAAA-CCAAACGAGCTACCTAAAAACAATTT-----C--AT---GAATCAACCCGTCTATGTAGCAAAATAGTGGGAAGATTTTTAGGTAGAGGTGAAAAGCCTATCGAGCTTGGTGATAGCTGGTTGCCCA-AAAA-A-GAATTTCAGTTCAAACTTTAA------G-------CTTCCA------------------TCAG------AA-CAA
+i rn4.chrM                C 0 C 0
+s hg18.chrM                    1445 625 +     16571 AGA------GTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCT--CAAGTA---------TA-CTTCAAAGGACATT-TA---AC-TAAAACCCCTACG--CATTT-ATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG--A-ACCAGAGTGTAGCT-TA-A--CACAAAGCACCCAACTTACACTTAGGAGAT---TTCAACTTAAC-TTGACCGCTCTGA-GC--TAAAC-----CTAGCCCCA--A-ACC-CA----------CTCCACCT--TA---------CTA-CCAG--ACAAC------------CTTAGCCAAACCATT-TACCC--AA------ATAAAGTATAGGCGATAGAA-----AT-----TGA--AACC-TGGCGCAATAGAT----ATAGTACCGCAAGGGAAA-GATGAAA-A--ATTATAACC------------AAGCATAATATAG-CAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAG-AAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAA-CCAGACGAGCTACCTAAGAACAGCTA-----A--AA---GAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCA-AGAT-A-GAATCTTAGTTCAACTTTAAA------T-------TTGCCC------------------ACAG------AA-CCC
+i hg18.chrM               C 0 I 2
+s panTro2.chrM                  861 626 +     16554 AGA------GTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCT--CAAGTA---------TA-CTTCAAAGGATACT-TA---ACTTAAACCCCCTACG--TATTT-ATATAGAGGAGATAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG--A-ACCAGAGTGTAGCT-TA-A--CATAAAGCACCCAACTTACACTTAGGAGAT---TTCAACTCAAC-TTGACCACTCTGA-GC--CAAAC-----CTAGCCCCA--A-ACC-CC----------CTCCACCC--TA---------CTA-CCAA--ACAAC------------CTTAACCAAACCATT-TACCC--AA------ATAAAGTATAGGCGATAGAA-----AT-----TGT--AAAC-CGGCGCAATAGAC----ATAGTACCGCAAGGGAAA-GATGAAA-A--ATTATACCC------------AAGCATAATACAG-CAAGGACTAACCCCTGTACCTTTTGCATAATGAATTAACTAG-AAATAACTTTGCAAAGAGAACCAAAGCTAAGACCCCCGAAA-CCAGACGAGCTACCTAAGAACAGCTA-----A--AA---GAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCA-AGAT-A-GAATCTTAGTTCAACTTTAAA------T-------TTACCT------------------ACAG------AA-CCC
+i panTro2.chrM            C 0 I 2
+s rheMac2.chr5             34436553 630 - 182086969 AGA------GTGCTTGGTTGAATAAGACCATGAAGCATGCACACACCACCCGTCACCCTCCT--CAAATA--------TTA-CTGTAGAAATCACTATT---AC-TAATAGTTTTATA--TGCAC-ATATAGAAGAGATAAGTTGTAACATGTTAGGCATACTGGCAAGTGTGCTTGGACA--A-ACCAAAGTGTAGCT-TA-A--ACCAAAGCATCTGGCTTACACCTGGAAAAT---TTCACTGTGAA-CTGATCACTTTGA-GC--TAACT-----CTAGTACCA--A-ACCTCG----------CTAAAAAA--TA---------TTA-TTAA--ACTAT------------CTTAATCAGGTGATT-TACTTTAGA------AAAAAGTATAGGTGATAGAA-----AT-----TTT--TACCATGGCGCAATAGAC----ATAGTACCATAAGGGAAA-GATGAAAGA--ACTATA-TC------------AAGCACTAAAAAG-CAAAGACAAGCCCTCATACTTTCTGCATAATGTATTAACTAG-AAAT-ACTTTACACAGAGAACTATAGCCAAGTCCCCCAAAA-ACAGACGAGCTACCCAAGAATAACTG-----A--AA---GAGCACACTCATCTATGTGGCAAAGTAGTGGGAAGATTCAGCAGCAGCGGTGACAAGCCTACCAAGCCTGGTGATAGCTGGTTATCCA-AGAT-A-GAATCTTAATTCAACTTTAAA------C-------TTAGCC------------------ACAG------AA-TTA
+i rheMac2.chr5            C 0 I 1
+s bosTau2.chrM                 1227 638 +     16338 AGA------GTGCTTAGTTGAATTAGGCCATGAAGCACGCACACACCGCCCGTCACCCTCCT--CAAATAG--ATTCAGTG-CATCTAACCCTATT-TA---AA-CGCACTAGCTACA--TG--------AGAGGAGACAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGATA--A-ATCAAGATATAGCT-TA-A---ACAAAGCATCCAGTTTACACCTAGAAGAC---TTCATTCATTA--TGAATATCTTGA-AC--TAGAC-----CTAGCCCAAAGA-TAC-CC----------TCTCGACT--AA---------ACA-ACCAAGATAGA------------ATAAAACAAAACATT-TAATC--CCA---ATTTAAAGTATAGGAGATAGAA-----AT-----CTA--AGTA-CGGCGCTATAGAG----AAAGTACCGCAAGGGAAC-GATGAAA-GAAAAAAACTAA------------AAGTATAAAAAAG-CAAAGATTACCCCTTGTACCTTTTGCATAATGAATTAACTAGTATAAGACTTAACAAAATGAATTTTAGCTAAGCAGCCCGAAA-CCAGACGAGCTACTCACAAACAGTTT-----ACCAA---GAACTAACTCATCTATGTGGCAAAATAGTGAGAAGATTTGTAAGTAGAGGTGACATGCCTAACGAGCCTGGTGATAGCTGGTTGTCCAGAAAA-T-GAATCTAAGTTCAGCTTTAAA------G-------ATACCA------------------AAAAT----TCA-AAT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                  866 628 +     16727 AGA------GAGCTTAATTGAATAGGGCCATGAAGCACGCACACACCGCCCGTCACCCTCCT--CAAGTA---ATAAGACA-CAACCATAACCATA-TT---AA-CTTAACTAAAACA--CA--------AGAGGAGACAAGTCGTAACAAGGTAAGCATACCGGAAGGTGTGCTTGGATT--A-ATCAAAGTGTAGCT-TA-A---CTAAAGCGTCTGGCCTACACCCAGAAGAT---TTCATTACTTA--TGGCCACTTTGA-AC--AAAAG-----CTAGCCCAA--C-TAA-CC----------CCAAACTT--AA---------GTA-TTACAGACA-C------------ATAAAATAAAACATT-TAGTT--AAA--CAATAAAAGTATAGGAGATAGAA-----AT-----TTT--AAT--TGGAGCGATAGAG----ATAGTACCGTAAGGGAAT-GATGAAA-G--ACATCTTAA------------CAGTATTAAACAG-CAAAGATTACCCCTTCTACCTTTTGCATAATGAACTAGCCAG-AAACAACTTAACAAAGAGAACTTAAGCTAAGCTCCCCGAAA-CCAGACGAGCTACCCATAAACAATCT-----A-AAA---GGATCAACTCATCTATGTAGCAAAATAGTGAGAAGATTTGTGGGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTACCCACAGAC-A-GAATTTTAGTTCAACTTTAAA------T-------TTACCt------------------aaaa------aa-aat
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       4675 637 -     16977 AGA------GAGTTTAGCTGAACCAGGCCATAAAGCACGCACACACCGCCCGTCACCCTCTT--CAATTAT--AAGCGCCA-CATAAACTAAAACA-C----AT-TAATTCAGTAGCA--ACTAT-ATA-AGAAGAGACAAGTCGTAACAAGGTAAACATACTGGAAAGTGTGTTTGGAT---A-ACCAAAGTGTAGCT-TA-C-AACCAAAGCATCCGGCTTACACCCAGAAGAC---TTCAGATAGAC--TGACCACTTTGA-AC--TAGAC-----CTAGCCCTA--A-ACC-CA---------CAACAACAA--TA---------CTA-TCAC--ACAGC-----------AATAAATCAAAACATT-TACCA--AATACTAACTAAAGTATAGGAGATAGAA-----AT-----TTT--ACTA-AGGCGCTATAGAA----ATAGTACCGCAAGGGAAA-GATGAAA-G--ACCCCCTGA------------TAGTAAGAAACAG-CAAAGACTAATACTTTTACCTTTTGCATAATGAATTAACTAG-ACTAATTTTGGCAAAGAGAACTTTAGTCAAATATCCCGAAA-CCAGACGAGCTACTTATGGACAGTAA-----T--TA---GTACTAACTCATCTATGTCGCAAAATAGTGAGAAGATCTGTAAGTAGAGGTGAAAGACCAACCGAGCCTGGTGATAGCTGGTTGCCCA-GAAC-A-GAATTTTAGTTCAACTTAAAA------C-------TTATCT------------------CAAG------AA-CCA
+i dasNov1.scaffold_23239  C 0 I 4
+s loxAfr1.scaffold_36650       3880 627 +     16266 AGA------GAGCTTAATTGAACAAGGCTATGAAGCGCGTACACACCGCCCGTCACTCTCCT--CAAGTATCCCCACATCA-----AACAATCATA-TT---AC-AG--ATTTAAACA--AATAC-A---AGAGGAGACAAGTCGTAACAAGGTAAGCGTACTGGAAAGTGCGCTTGGATA--A-CTCAAAGTGTAGCT-TA-A--CAAAAAGCATCTGGCTTACACCTAGAAGAC---CTCATTTACAA--TGATCACTTTGA-AC--TAAAT-----CTAGCCCTA--C-CAA-CC----------CTACACTC--AA---------TTC-TCAT--ATTAT-----------ATTAAATCAAAACATT-CACTT--AC-----CAAAAAGTATAGGAGATAGAA-----AT-----TTC--ACTA-AGGCGCAATAGAG----ATAGTACCGCAAGGGAAT-GATGAAA-G--ATAGTTTAA------------TAGTAAAAAATAG-CAAGGATTAACCCCTTTACCTTTTGCATAATGAATTAACTAG-AAAA-ATCTGACAAAGAGAACTATAGCCAGAAACCCCGAAA-TCAGACGAGCTATCTGATAGTAATCC-----C--CA---GGATCAATTCATCTATGTGGCAAAATAGTGAAGAAACTTACAGATAGAGGTGAAATACCAATCGAGCCTGATGATAGCTGGTTGTCCA-GAAATA-GAATTTTAGTTCTACCTAAAA------C-------TTACCA------------------CAAA------AACAAA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343       131 630 +     18297 AGA------GTGCTCAGTTGAAACTGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCT--TA---ATTTATATATTATAAGTAACCTCCATA--A---AC-AGCTACTTATACA--CCCCA-T---AAAGGAGACAAGTCGTAACAAGGTAAGCATACTGGAAAGTGTGCTTGGAAA--ACCTCAAAACGTAGCT-TA-A--T-AAAAGCATCTGGCCTACACCCAGAAGAT---TTCA-TGACAC--TGACCGTTTTGA-AC--TAAAT-----CTAGCCCAA--CTCAA-AT----------AGAAACTT--AA----------CC-AAAT--AAAAC-----------TTTAATATAAAACATT-TG-TA--GA-----CATAAAGTATAGGAGATAGAA---ATAT-----TCC--ATAG-ATGCGCTATAGAG----ATAGTACCGTAAGGGAAA-AATGAAA-G--ATAACTTAA------------TAGTACCAAAAAG-CAAAGCTTAAACCTTATACCTTTTGCATAATGAGTAAACTAG-AAAATTTTTGACAAAGGGAACTTTAGCCAAAAACCCCGAAA-CCAGACGAGCTACCCTAGAGCAATCT-----T-GTT---GGATCAACTCATCTATGTGGCAAAATAGTGAGAAGACTTTAAGGTAGAGGTGAAAAGCCAACCGAGCCTGGTGATAGCTGGTTGCCCA-AGAA-A-GAATTTAAGTTCGACCTAAAA------A-------TTACTA------------------CCAA------TA-ACt
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117152298 631 + 174229318 AGA------GTGCTTAATTGAATTAGGCAATAGGGCGCGCACACACCGCCCGTCACCCTCCT--CAACTC---------AA-CCTACAAAAATACT-TA---AT-AA-------TATA--TCTAA-GTAAAGAGGAGAAAAGTCGTAACACGGTAAGTGTACTGGAAAGTGCACTTGGAAT--A--TCAAAATGTAGCT-TA-ACTACTAAAGCATTTAGCTTACACCTAAAAGAT---TTCAGTTAATT-CTGACCATTTTGA-GC--CAATT-----ATAGCTCTA--A-CAA-TC----------TTCAAATA--AA---------CTATTTAT--ACACT------------TATATTTAAAACATT-TTAAT--TC------CCCTAGTATAGGAGATAGAACAGAAAC-----ATA--A----TGAAGCAATAACA----ATAGTACCGTAAGGGAAAAAATGAAA-G--ATAGATTGA------------TAGCATAAAAAAG-CAAAGATTAAACCTTGTACCTTTTGCATAATGATTTAGCCAG-TCAA-CATAGGCAAAAAGAATTTAAGCCTAGAACCCCGAAA-TTAAGTGAGCTACTATAGAACAGTTA-----TTTAT---GAACTTACTCCTCTATGTGGCAAAATAGTGAGAAGATTTTATAGTAGAAGTGAAAAACCTATCGAACTTAATGATAGCTGGTTATCCA-AAAT-ACGAATTTTAGTTCAACCTTAAG------T-------TTAACA------------------CAAAGCATACGA-TAT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 2111 664 +     16775 ATACCCCCTAAGCTCACTTTAAGACGGCTCTGAGGCACGTACATACCGCCCGTCACCCTCTT--CACAAGCCATC----AA-CATCAATAAATATA-TA---CT-TCCCCTCCCGGCT--AA--------AGACGAGGCAAGTCGTAACAAGGTAAGTGTACCGGAAGGTGCACTTAGACT--A--CCAAGGCGTAGCTATA-A-CTTCAAAGCATTCAGCTTACACCTGAAAGATACCCTCAACAGACA--AGGTCGCCTTGA-CT--TGCCCCCCCTCTAGCCCGA--C-AAA-CT----------CGTACCCT--TA---------ACA-TAAA--AAACT-TACCTCCCCCTCTTAACCAAAACATTATAAAT--TG------TCCCAGTATAGGCGATAGAA-----AA-----GAC--TACCCCGGCGCAATAGAGGCTAACTGTACCGCAAGGGAAA-GATGAAA-T--AGCAATGAAAACCAT------AAGCAAAAAACAG-CAAAGACCAACCCTTGTACCTTTTGCATCATGATTTAGCAAG-AACA-ACCAAGCAAAGTGAGCTAAAGTTTGCCTTCCCGAAACCCAAGCGAGCTACTTGCGAGCAGCTA-----A--AATTTGAGCGAACCCGTCTCTGTTGCAAAAGAGCGGGATGACTTGCCAGTAGAGGTGAAAAGCCTACCGAGCTGGGTGATAGCTGGTTACCTG-TCAA-ACGAATCTAAGTTCCCCCTTAAC------C-------CACCCC------------------CTAA------AG-ACA
+i galGal2.chrM            C 0 I 23
+s xenTro2.scaffold_18215          7 644 +      3330 AGA------GAGCTCTCTTTAA-ATGGCCCTGGGGCGCGCACACACCGCCCGTCACCCTTCTTCCAAAAACCACC----TA-CCTTAAATAAAACA-TT---AC-AA------AAACA--A---------AGAAGAGGCAAGTCGTAACATGGTAAGCGCACCGGAAGGTGCGCTTGGA------ATCAAAGTATAGCT-TA-A--CCTAAAGCCCCTCGCTTACACCGAGACGAT---ATCCGTTAAACCCAGATTACTTTGA-GCCATAAAC-----CTAGCCTTA--T-TAT-TT----------ACCAACAA--AAGATTACCCCCTA-CACCA-ACCCC------------ACCAACTAAACCATT-T---T--AA----ACTTTTAGTATAGGCGATAGAA-----AC-----AAG--TCT--AAGAGCTACATAT----CCAGTACCGCAAGGGAAA-GGTGAAA-T--AGAAATGAAACAAAT--AATAAAGCAACAAACAG-CAGAGAAAAACCCTCGTACCTTTTGCATAATGGTCTAGCAAG-TCCTAGTCAAGCAAAAAGAATTTAAGTTTGACCCCCCGAAA-CTAAGCGAGCTACTCCGAGACAGCTT-----T-TTA---GAGCCAACCCGTCTCTGTGGCAAAAGAGTGGGAAGATCTCCGAGTAGGGGTGACAGACCAAACGAGCTTAGTGATAGCTGGTTGCTCA-GGAA-ACGAATATAAGATCAACTCTAAG------TCCCGTTATTAGCA------------------AACA------AA-GCA
+i xenTro2.scaffold_18215  N 0 C 0
+s tetNig1.chrUn_random    103510618 674 + 171761319 AGA------GTGTCTTACTGAAACCGGCCATGAAGCGCGCACACACCGCCCGTCACTCTCCC--CAAAT----------CA-AACCCAC----CAA-TA---AT-TAATACACTATCA--CACACAA---AGGGGAGGCAAGTCGTAACATGGTAAGTGTACCGGAAGGTGCACTTGGAAA--A-ATCAGAATATAGCT-TAGA-TAGAAAAGCACCTCCCTTACACCGAGGAGCC---ACCCGTGCAAATCGGATTATTCTGACAC--CTAAT---AGCTAGCCCCT--C-CCC-CAAAAACAAAAAATAACTAT--TA---------ATA-CCCC--CTAATACACTTAATTAACCAAAACAAACCATT-TTTCC--CC-------CTAAGTATGGGCGACAGAA-----AAGGACCTAA---------GAGCTACAGAC----AAAGTACCGCAAGGGAAC-GCTGAAA-G--AGAAGTGAAACAACCCAGTTTAAGTACAAAAAAG-CAGAGATTAAACCTCGTACCTTTTGCATCATGATTTAGCCAG-CAAACCTTAGGCAAAGAGCACTTTAGTCTAATTCCCCGAAA-CTGGACGAGCTACTCCAAGACAGCCT-----TCATA---GGGCACATCCGTCTCTGTGGCAAAAGAGTGGAAAGAGCTTTGAGTAGAGGTGACAAACCTACCGAGCCCAGTAATAGCTGGTTGCCCG-AAAA-TTGAGTTTAAGCTCAGCTTTTTAGCTTCTT-------GCCTCACCAACAGTAAAAACACAA----------------
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 1817 657 +     16596 AGA------GTGTCTCTTTGAACCCGGCTCTAAGGCGCGTACACACCGCCCGTCACTCCCTC--C-GGT----------CA-ATTGCACAAG-AAA-TA---AT-TAATACAGAAGCA--CAGAC-A---AGGGGGGAAAAGTCGTAACAAGGTAAGTGTACCGGAAGGTGCACTTGGACATTA-TCCAAGACGTGGCT-GA-A-CAGTTAAGCATCTCACTTACACCGAGAAAAC---ATCCGTGCAAATCGGATCGTCCTGA-GC--TAAAT---AGCTAGCTTAA--C-CAT-CAAGATCAACTTAAAAACAT--CA---------ATA-ACCT--ATAATCAACCTAAAACCACAAACTAAACCATT-ATATT--AT-------CCTAGTATGGGAGACAGAA-----AAGA---TAA--AATA-CTAAGCAATAGAG----AAAGTACCGCAAGGGAAC-GCTGAAA-G--AGAAATGAAATAACCC-GTAAAAGCAATAAAAAG-CAAAGATTAAACCTTGTACCTTTTGCATCATGATTTAGCCAA-C-ACCACTAGGCAAAGAGACCTTTAGTTTAAAGCCCCGAAT-CCAGGTGAGCTACCCCGAGACAGCCTATTTAACTTA---GGGCCAACCCGTCTCTGTGGCAATAGAGTGGGAAGAGCTCCGGGTAGAAGTGACAGACCTATCGAACCCGGCAATAGCTGGTTGTCTG-GGAG-ATGAATAAAAGTTCAGCTTCGTA------C-------ACCCCa----------------------------------
+i danRer4.chrM            C 0 I 27
+
+a score=160222.000000
+s mm8.chrM                     1497 81 +     16299 CAAAATCAAA------AAGTAAG----TTTAGATTATAGCCAAAAGAGGGACAGCTCTTCTGGAA--CGGAAAAAACCTT-TAATAGTGAATAA---------
+s oryCun1.scaffold_140182      1604 81 +     20791 AAAA-CCCTA------ATGAAAA----TTTAAATGTTACTCTAAAGAGGGACAGCTCTTTAGATA-TAGGACACAGCCTT-TTATAAAGAGTAA---------
+i oryCun1.scaffold_140182 C 0 M 1789
+s rn4.chrM                     1494 81 +     16300 CAAA-TCAAA------ATGTAAA----CTTAAAATATAGCCAAAAGAGGGACAGCTCTTTAGGAA-ACGGAAAAAACCTT-AAATAGTGAATAA---------
+i rn4.chrM                C 0 C 0
+s hg18.chrM                    2072 82 +     16571 TAAA-TCCCC------TTGTAAA----TTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTT-GTAGAGAGAGTAA---------
+i hg18.chrM               I 2 C 0
+s panTro2.chrM                 1489 82 +     16554 TAAA-TCCCC------TTGTAAA----CTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTAGACACTAGGAAAAAACCTT-GTAAAGAGAGTAA---------
+i panTro2.chrM            I 2 C 0
+s rheMac2.chr5             34437184 76 - 182086969 TTAA-TTTCC------CAGTAAG----TGTAACTA-------ACTAAGGGACAGCTCTTTAGACCCTAGGAAACAACCTTCCTACAGAGAGTAA---------
+i rheMac2.chr5            I 1 C 0
+s bosTau2.chrM                 1865 79 +     16338 -AAA-CCCCA------CTGTAGC----TTTAAAAGTTAGTCTAAAAAGGTACAGCCTTTTAGAAA-C-GGATACAACCTT-GACTAGAGAGTAA---------
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 1494 81 +     16727 aaaa-tttta------atgtaaa----tttaaaatataGTCTAAGAAGGTACAGCTTCTTAGAAT-CAGGATACAACCTT-TATTAGAGAGTAT---------
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       5316 82 -     16977 TTAA-TCTTA------ATATAAG----TTTTAAATATACTCAATAGAGGTACAGCTCCATTGAAACAGGTATTAAACCTG-CACAGGAGAGTAA---------
+i dasNov1.scaffold_23239  I 4 C 0
+s loxAfr1.scaffold_36650       4507 81 +     16266 ATAA-TTCCA------ATGTAAG----TTTTAGAGATATTCAAAAGGGGTACAGCTCTTTTGACC-AAGGATACAACCTT-GATTAGCGAGTAA---------
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343       761 81 +     18297 ataa-attta------atgtaat----ttttagttataattaaaaGAGGTACAGCTCTTTTAATT-GAGGAAACAACCTT-ATTTAGAGAGTAA---------
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117152929 81 + 174229318 CAAA-GCATA------TCTTAGA----CTTAATAGTTAATCAAATGAGGGACATCTCATTTGATA-AAGTGGACAAACTT-CATAAGAGGGTAA---------
+i monDom4.chrUn           C 0 C 0
+s xenTro2.scaffold_18215        651 75 +      3330 AAA-----------------AACACTTCTTAGAATTTATTCAACCAGGGTACAGCCTGGTTGAAA-CAGGATACAACCTA-CAACTATGGGTAA---------
+i xenTro2.scaffold_18215  C 0 I 10
+s tetNig1.chrUn_random    103511292 89 + 171761319 ------CCGATTTA--AAGAAAC----TAAAAAAGTTAGTCAAAGGGGGTACAGCCCCTCTGACC-CAAGAAACAACTTT-CCCAGGAGAATAAGGATCCTAA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 2501 91 +     16596 ------CAAAATTAAGAGAAAAA----TACGAAAGTTAGTTAAAGAGGGTACAGCCCCTTTAACA-AAGGATACAACCTT-TTCAGGAGAATAAAGATCATAA
+i danRer4.chrM            I 27 C 0
+s galGal2.chrM                 2798 72 +     16775 ----------------CGTTGGG----GTTAAGAGCAATTCGATGGGGGTACAGCTCCATCGAAA-AAGAACACAACCTC-CTCCAGCGGATAA---------
+i galGal2.chrM            I 23 C 0
+
+a score=164919.000000
+s mm8.chrM                     1578 166 +     16299 TTAACAAAAC---------AGCTTTT--------------AACCAT-------TGTAGGCCTAAAAGCA-GCCACCAAT-AAAGAAAGCGTTCAAGCTCAACATAAAATTTCA-----ATTAATTCCA--TAA-------TTTACACCAA----------CT-TCCTAA-----ACT-TA-AAATTGGGTTAA-TCTATAACTTTATAGATGCAACACTGTTAGTATGAGT
+s rn4.chrM                     1575 163 +     16300 ACAACTACA----------ATCACTT--------------AACCAT-------TGTAGGCTTAAAAGCAAGCCATCAAT-AAAGAAAGCGT-CAAGCC--ACATCATCTTACACACACACTAATTCCA--CAA-------ACCTCAAAAA-----------T-TCCAAA-----ATT-AC-AAATTGGGCTAAATCTATGATCCTAGTGA----ATACTGTTAATATGTG-
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_116167      3974 163 +     15695 -------------------GTTATTTTC-----------AATCCAT-------AGTTGGCTTAAAAGCA-GCCATCAAT-TAAGAAAGCGTTAAAGCT---CAACAACTAAAA-----ACCAACTTAA--TAAGAATATTTTAAAACGAA----------CT-CTTATA-----AAC-CC-TAACTGGACTAA-TCTATAAATCTATAGAAGAAATAATGCTAATATAAGT
+i oryCun1.scaffold_116167 n 0 C 0
+s hg18.chrM                    2154 159 +     16571 ------AAA----------ATTTAAC--------------ACCCAT-------AGTAGGCCTAAAAGCA-GCCACCAAT-TAAGAAAGCGTTCAAGCT---CAACACCC---------ACTACCTAAA--AAA-------TCCCAAACATATAAC---TGAA-CTCCTC-----ACA-CC-CAATTGGACCAA-TCTATCACCCTATAGAAGAACTAATGTTAGTATAAGT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 1571 159 +     16554 ------AAA----------ATTTAAC--------------ACCCAT-------AGTAGGCCTAAAAGCA-GCCACCAAT-TAAGAAAGCGTTCAAGCT---CAACACCC---------ACAACCTTAA--AGA-------TCCCAAACATACAAC---CGAA-CTCCTT-----ACA-CC-CAATTGGACCAA-TCTATTACCCCATAGAAGAACTAATGTTAGTATAAGT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34437260 158 - 182086969 ------AAA----------ATATTAC--------------CACCAT-------AGATGGCCCAAAAGCA-ACCACCAGT-TAAGAAAGCATTTAAATT---CAACTTCT---A-----ACTATCTTCA----A-------TTCTAATCACTCTAC---TGTT-CTCCTA-----ACA-CC-ACATTGGACTAA-TCTATTATGTAATAGAAGCAATAATGTTAATATAAGT
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 1944 161 +     16338 ------AAT----------TTAACAC--------------TACCAT-------AGTAGGCCTAAAAGCA-GCCATCAAT-TAAGAAAGCGTTAAAGCT---CAACAACA---------AAAATTAAAT--AGA-------TTCCAACAACAAATG--ATTAA-CTCCTA-----GCC-CCAATACTGGACTAA-TCTATTATAGAATAGAAGCAATAATGTTAATATGAGT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 1575 161 +     16727 ------ATA----------CTAATAT--------------CACCAT-------AGTTGGCTTAAAAGCA-GCCACCAAT-TGAGAAAGCGTTCCAGCT---CAACAAAC---------AATA-TAACT--TAA-------TCCCAACCATACTAC--ATCAA-CTCCTAATTATACC-CC----CTGGGTCAT-TCTATTTAAGTATAGAAGCAATAATGCTAGTATGAGT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       5398 161 -     16977 --GCCGTAT----------AAAACAC--------------TTACAT-------AGTTGGCCTAAAAGCA-GCCATCAAT-AAAGAAAGCGTTAAAGCT---CAACAACA---------AAACAATGAC--AGA-------TACCAAAAAC-CACT--GCCAC-CTCCCA-----ACC-TA-ATACTGGGCCAA-TCTATA--TAAATAGAAGAGATAATGTTAGTATAAGT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       4588 164 +     16266 ---------ATTCA-----CCATTAA--------------TTTCAT-------AGTTGGCTTAGAAGCA-GCCATCAAT-TAAGAAAGCGTTAAAGCT---CAACAACC---A-----ACCAAACTAAAAAGA-------TTCCAAA-ATTAATT-AATGAT-CTCCTA-----AACATA-ATACTGGACTAA-TCTAT--ATAAATAGAAGAAATAATGTTAGTATAAGT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343       842 159 +     18297 ---------ACAC------CAAATAA--------------TTTCAT-------AGTTGGCCTAAAAGCA-GCCACCAAT-TAAGACAGCGTTAAAGCT---CAACAATT---T-----ATTTCTCT----AGA-------TTCC----ATTAATTCAATTCTACTCCTA-----AAT-TT-ATATTGGGCAAA-TCTATTCTTATATAGAAGCTAATCTGTTAACATAAGT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117153010 162 + 174229318 -------------TGACTTATTTTAA--------------CCCCAT-------CGTAGGCCTAAGAGCA-GCCACCAAT-TAAGAAAGCGTTAAAGCT---CAAACATA--GA-----ATTTTATTCA--ATA-------CCCTAAAACTATCAA-----AA-CCCCTA-----TAA-CA-ATATTGGATGAT-TCTATTAAACTATAGAAGACATAATGCTAAAATCAGT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 2870 152 +     16775 -------------TAATCACCCCTCC--------------CCGCAC-------TGTGGGCCTTCAAGCA-GCCACCAACAAAAGAGTGCGTCAAAGCT---C----------------CCTCATTAAA--AAA-------TCTAAAACCCTATTT-----GA-CTCCCT-----CAA-CC-AAAGCAGGTTAA-CCTATGA--CAATAGAAGAATCAATGCTAAAATGAGT
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18215        736 160 +      3330 --------------------------TCGACAGGAAAATGAACCA---------GTGGGCCTAAAAGCA-GCCACCTGT-TAAGAAAGCGTCAAAGCT---CCCTCATA---------TACCTTCCGC--CAA-------TACCGACATCTCCTC----CGA-ACCCTT-----TTT-CC-GTACTGAGCTGT-TCAATTCTAATATTGAAGCACCTATGCTAGAACTAGT
+i xenTro2.scaffold_18215  I 10 M 106
+s tetNig1.chrUn_random    103511381 162 + 171761319 -------------------TAACAAA--------------GGCCATGTGTTTAGGTGGGCCTAAAAGCA-GCCACCC-T-ATTGAAAGCGTTAAAGCT---CAAACACA---------CCCCCGCCAC--TAA-------TACCGATAAATACAT---CCTA-ACCCCT-----GAC-CC-TTATCGGGCCTT-TCTATGCATACATAGAAGAGACTATGCTAATATGAGT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 2592 163 +     16596 ------------------TTTACAAA--------------ACACGT-TGTCGTAGTGGGCCTGGAAGCA-GCCACCTAA-AAAGAAAGCGTTAAAGCT---CAGGTAAG---------AAGAAATTCA--TAA-------TTCTGACAATAATAT---CTTA-CTTCCC-----TAA-AA-ATACCAGACTAA-TCCATACAAATATGGAAGAAATTATGCTAAAATGAGT
+i danRer4.chrM            C 0 C 0
+
+a score=-81423.000000
+s mm8.chrM                     1744 113 +     16299 AACAAGAA----TTCCAATTCTC---------------CA--GGCATACGCG-TATAACA----A---CTCGGATA-ACC--ATTGTTAGTTAATCAGACT------------ATAGGC-----A-------ATAATCACA-CTATA-AATAATCCACCTATAACTT-CT-CT---
+s galGal2.chrM                 3022 103 +     16775 AATCTGGA-----ACCTATCCTC---------------CTACGGCGTAAACT-TACATTA----A--------TAC-ATT--ATTAACAGAAC-TCAACTT------------ATACCC-----C--------CACACTAA-CAAGC-AAT-ACGTAT---TCCTCA-AT-CT---
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117153172 110 + 174229318 AATAAGAA------CTCATTCTC---------------CT--TGCATAAGCC-TAAGTTA----GCCAACGGATTA-CCC--ACTAACACCTA-ACAAATAC----------AATATCT-----T--------TAATT-AA-CAACC-AGTGAATTAC---CCCAAT-AA-TT---
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      1001 107 +     18297 AACAAGAGA---ATAAATCTCTC---------------CC--CGCACAAGTA-TATATCA----G---AACGAATA-CTC--GCTGATAATTA-ACAACCT-----------AGTAATT----------------ATACAA-ACTCT-AGACTATTAT---ATTTAC-AC-TT---
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650       4752 106 +     16266 AATAAGAA------GTATTTCTC---------------CC--TGCATAAGCT-TATATCA----G---GTCGGATG-CCC--GCTGATAGTTA-ACAACCG-----------AATAATT-----A---------GATACAA-AAATA-GAACCTTTAT---TATACC-AA-TT---
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239       5559 109 -     16977 AACAAGAA------TATTTTCTC---------------CG--TGCATAAGTG-TATATCA----G---ACCGGATAGACC--ACTGATAGTTA-ACA---------------AATAGGC-----ACCAAACTACCACCAAA-CAATA-ACAATGCCAT---ACACCT-----T---
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 1736 110 +     16727 AACAAGAA-----CCATTTTCTC---------------CC--CGCATAAGCT-TATATCA----G-GAACGGATAG-ACC--ACTGATAGTTA-ACAATCT-----------GATAATA-----T--------CAACCCAA-AAATG-AAATACTTAT---CCACCC-CA-TT---
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 2105 109 +     16338 AACAAGAA-----AAATTTTCTC---------------CT--TGCATAAGTC-TAAGTCA----G-TGCCTGATAA-TAC--TCTGACCACTA-ACAGTC------------AATAAAA-----A--------TAATCCAA-CAATA-AACAATTTAT---TGATTA-TA-CT---
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34437418 121 - 182086969 AACATGAA------GATATTCTCTATTACATAAGCTTACA-CTGCATAAGCC-TACATCA----G---AATAACCC------ACTAACAGTTA-ACAGCCT-----------AATATTA-----A--------TAAACGATATAATA-AGCACCCTAT---TATTTA-CA-CT---
+i rheMac2.chr5            C 0 C 0
+s panTro2.chrM                 1730 109 +     16554 AACATGAA------AACATTCTC---------------CT-CCGCATAAGCC-TACATCA----G---ACCAAAAT-ATTAAACTGACAATTA-ACAGCCT-----------AATATCT-----A--------CAATCAAC-CAACA-AGC-CATTAT---TACCCC-CG-CT---
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    2313 109 +     16571 AACATGAA------AACATTCTC---------------CT-CCGCATAAGCC-TGCGTCA----G---ATCAAAAC-ACTGAACTGACAATTA-ACAGCCC-----------AATATCT-----A--------CAATCAAC-CAACA-AGT-CATTAT---TACCCT-CA-CT---
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_116167      4137 110 +     15695 AACAAGAA-----TACTATTCTC---------------CT--TGCACAAGCT-TATATCA----G---ATCGGATG-CCC--ACTGATAGTTA-ACAGCCCT----------AATAGAA-----A--------TAATCCAC-AAATT-AATAATCTAT---TAACTTTCA-CT---
+i oryCun1.scaffold_116167 C 0 C 0
+s rn4.chrM                     1738 106 +     16300 AACAAGAA------CCAATCCAC---------------CA--AGCACAAGTGCTAAGACA----A---C-CGGATA-ACC--ATTGTTAATTA-TTGAATC------------ATAGGC-----A--------TAACCCAA-CAATAGAATTACCTATCCCTAACTC---------
+i rn4.chrM                C 0 C 0
+s tetNig1.chrUn_random    103511543 130 + 171761319 AATAAG--GGGCCAGACCCCCTC---------------CA--AGCACAAGTG-TACATCG----G---AACGAACT-CGC--ACCGAAGACTA-ACGAACCCAACCAAAGAGGGCAATGAATATC--------AAACCAAA-CAACA-AGAAAAACAT---TCACAA-CC-CCACC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 2755 127 +     16596 AACAAGAAGAACCTGTACTTCTC---------------CA--AGCACAAGTG-TAAGCCAAGTTG---GACAAAC----C--ATTGGCAATTA-ACGAGCCCAAACAAAGAGGGCAATG-----T--------GAGTTAAA-AACTG-AGAAAA--AT---CCACAA-CAGACATC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_18215        896 106 +      3330 M
+
+a score=2385506.000000
+s mm8.chrM                     1857 323 +     16299 GTTAACCCAACACCGGAATGC---C-T----AAAGGAAAGATCCAAAAAGATAAAAGGAACTCGGCAAA--CAAGAACCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTACAAGT--ATTAGAGGCACTGCCTGCCCAGTGAC-TA---A-A-GTTTaacggccgcggtatcctgaccgtgcaaaggtagcataatcacttgttccttaattagggactagcatgaacggctaaacgagggtccaactgtctcttatctttaatcagtgaaattgacctttcagtgaagaggctgaaatataataataagacgagaagaccctatggagcttaaATT
+s rn4.chrM                     1844 320 +     16300 GTTAGCCCAACACAGGCGTGC---T-T----TAAGGAAAGTTTAAAAAAGT--AAAGGAACTCGGCAAA--CACGAACCCCGC-CTGTTTACCAAAAACATCTCCTCTAGC---ATAACAAGT--ATTAGTGGCATCGCCTGCCCAGTGAC-TA---A-A-GTTCCACGGCCGCGGTATCCCGACCGTGCAaaggtaggataatcacttgttccttaattagggactagaatgaatggctaaacgagggtccaaccgtctcttacttgcaatcagtgaaattgaccttccagtgaaggggcggactcataataa-aagacgagaagaccctatggagcttTAATT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_116167      4247 324 +     15695 GTTAACCCAACACAGGAGTGC---TAT----ATAGGAAAGATTAAAAGAAGAAAAAGGAACTCGGCAAA--CCCTAACCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTACTAGT--ATTAGAGGCACTGCCTGCCCAGTGAC-GT---A-C-GTTCAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAATTGGGGACTAGCATGAATGGCAACACGAGGGTTAAACTGTCTCTTTCTTCCAATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGATAAAATAATAAGACGAGAAGACCCTATGGAGCTTTAATT
+i oryCun1.scaffold_116167 C 0 C 0
+s hg18.chrM                    2422 323 +     16571 GTCAACCCAACACAGGCATGC---T-CA---TAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAA--C-CTTACCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATCACCAGT--ATTAGAGGCACCGCCTGCCCAGTGAC-AC---A-T-GTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggctccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagaggcgggcatgacacagcaagacgagaagaccctatggagctttaatt
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 1839 323 +     16554 GTTAACCCAACACAGGCATGC---C-CA---CAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAA--T-CTTACCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTACCAGT--ATTAGAGGCACCGCCTGCCCGGTGAC-AT---A-T-GTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacttgtatgaatggctccacgagggtttagctgtctcttactttcaaccagtgaaattgacctacccgtgaagaggcgggcataacataacaagacgagaagaccctatggagcttTAATT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34437539 315 - 182086969 GTTAACCCAACAAAGGCATGC---T-C----TAAGGAAAGTTTACAAAAAGTGAAAGGAACTCAGCAAA--T-CTTACCCTGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTACCAGT--ATTAGAGGCACTGCCTGCCCAGTGAC-GT---A-T-GTTCAACAGCTGCCATATCCTGACCATGCAAAGGTAGCATAATCACTTGTTCCCTAAGTAGGCACTTGTATGAATTGCTACACGAGGGTTCATCAGTCTCTTACTTT-------TGAAATTGACCTATCCGTGAAGAGATGGATATAAACAAATAAGATGAGAAGACCCTATGGAGCTTTAATT
+i rheMac2.chr5            C 0 I 384
+s bosTau2.chrM                 2214 324 +     16338 GTTAACCCAACACAGGAGTGC---A-TC---TAAGGAAAGATTAAAAGAAGTAAAAGGAACTCGGCAAA--CACAAACCCCGC-CTGTTTACCAAAAACATCACCTCCAGC---ATTCCCAGT--ATTGGAGGCATTGCCTGCCCAGTGAC-AA---C-T-GTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATCATTTGTTCTCTAAATAAGGACTTGTATGAATGGCCGCACGAGGGTTTTACTGTCTCTTACTTCCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATGCACAAATAAGACGAGAAGACCCTATGGAGCTTTACCT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 1846 324 +     16727 GTTAACCCAACACAGGTATGC---A-TT---CAAGGAAAGATTAAAAGGAGTAAAAGGAACTCGGCAAA--CACAAACCCCGC-CTGTTTACCAAAAACATCACCTCCAGC---ATTTCTAGT--ATTGGAGGCACTGCCTGCCCGGTGAC-AC---T-T-GTTTAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAATCATTTGTTCTCTAAATAGGGACTTGTATGAATGGCCACACGAGGGTTTAACTGTCTCTTACTCCCAATCAGTGAAATTGACCTTCCCGTGAAGAGGCGGGAATACCACAATAAGACGAGAAGACCCTATGGAGCTTTAATT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       5668 327 -     16977 GTTAATCCAACACAGGCATGC---A-TAACTAACGGAAAGATTTAAAGGAATAGAAGGAACTCGGCAAA--CACGAATCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTACAATT--ATTAGAGGCACCGCCTGCCCAGTGAC-AC---A-C-GTTTAACGGCCGCGGTACCCTGACCGTGCAAAGGTAGCATAATCACTTGTTCTCTAATTAAGGACCCGTATGAATGGCTAAACGAGGTTTCTACTGTCTCCTATTCCCTATCAGTAAAATTGACCTTCCCGTGAAGAGGCGGGAATAATCATATAAGACGAGAAGACCCTGTGGAGCTTAAATT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       4858 324 +     16266 GTTAACCCAACACAGGCATGC---T-T----AAGGGAAAGATTAAAAGAAGGAAAAGGAACTCGGCAAA--CACAAACCCCGC-CTGTTTACCAAAAACATCACCTCGAGC---ATTACTAGT--ATTCGAGGCACTGCCTGCCCAGTGAC-CA---AGC-GTTAAACGGCCGCGGTACTCTGACCGTGCAAAGGTAGCATAATCATTTGTTCCTTAATTAGGGACTTGTATGAACGGCCACACGAGGGTTTAACTGTCTCTTTCCTCTAATCAATGAAATTGACCTTCTCGTGAAGAGGCGAGAATAAACATATAAGACGAGAAGACCCTATGGAGCTTAAATT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      1108 326 +     18297 GTTAACCCAACACAGGAGTGCACTC-T----AAAGGAAAGATAAAAAGAAGTAAAAGGAACTCGGCAAA--CTAAAATCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTACTAGT--ATTGGAGGCACTGCCTGCCCAGTGAC-CC---A-T-GTTTAACGGCCGCGGTACTCTGACCGTGCAAAGGTAGCATAATCATTTGTTCTCTAAATAAGGACTTGTATGAATGGCAACACGAGGATTTAACTGTCTCTTACTTCTTATCAGTGAAATTGACCTCCCCGTGAAGAGGCGGGGATTAGAACATAAGACGAGAAGACCCTATGGAGCTTAAATT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117153282 327 + 174229318 GTTAACCCAACACAGGCATGC---A-CTACTAAAGGACAGATTAAAAAGAATAAAAGGAACTCGGCAAA--CCAAAACCCCGC-CTGTTTACCAAAAACATCACCTCTAGC---ATTTCAAGT--ATTAGAGGCACTGCCTGCCCAGTGAA-TT---A-A-TTTTaacggccgcggtatcctgaccgtgcaaaggtagcataatcacttgtctcctaaatagagacttgtatgaatggcaaaacgagggtttaactgtctctttttctcaatcaatgaaattgacctacccgtgcagaggcgggtataactttataagacgagaagaccctgtggagcttaaAAT
+i monDom4.chrUn           C 0 I 9
+s galGal2.chrM                 3125 327 +     16775 GTTAAGCCAACCCAGGAGCGC---C------CACAGGATGATTAAAACCTACAGAAGGAACTCGGCAAA--CCAAAGACCCGA-CTGTTTCCCAAAAACATAGCCTTCAGCT-AACAACAAGT--ATTGAAGGTGATGCCTGCCCAGTGAC-CCCCAA-A-GTTCAACGGCCGCGGTATCCTAACCGTGCGAAGGTAGCGCAATCAATTGTCCCGTAAATTGAGACTTGTATGAATGGCTAAACGAGGTCTTAACTGTCTCCTGTAGGTAATCTATGAAATTAGTATTCCCGTGCAAAAACGAGAATGTGAACATAAGACGAGAAGACCCTGTGGAACTTTAAAA
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18215       1002 327 +      3330 GTTAACCTAACACAAGAGCAT---T------TAAAGAAAGATTAAAAGATGCAGAAGGAACTCGGCAAA--AGTGAACCCCGCNCTGTTTACCAAAAACATCGCCTCTTGCCAAACAACACGT--ATAAGAGGTCCAGCCTGCCCAGTGACTAT---A-T-GTTCAACGGCCGCGGTATTCTGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATAAAGACTGGTATGAATGGCACCACGAAGGTTCAACTGTCTCCTGCATCCAATCCATTAAACTGACCTCCCCGTGCAGAGGCGGGGATATTCCCATAAGACGAGAAGACCCTATGGAGCTTTAAAC
+i xenTro2.scaffold_18215  M 106 C 0
+s tetNig1.chrUn_random    103511673 329 + 171761319 GTTAACCCTACACTGGCGTGC---C-TA---ATTGGAAAGACTTAAAGAAAAAGAAGGAACTCGGCAAACCCATAAGCCTCGC-CTGTTTACCAAAAACATCGCCTCTTGC---AAAAACAATGAATAAGAGGTCCCGCCTGCCCTGTGAC-TA---T-ACGTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCCTTTAAATGGGGACCTGTATGAATGGCACGACGAGGGCTTAACTGTCTCCTTTTTCAAGTCAATGAAATTGATCTTTCCGTGCAGAAGCGGGAATAAAAACATAAGACGAGAAGACCCTATGGAGCTTTAGAC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 2882 324 +     16596 GTTACCCCCACACTGGAGTGC---A-TA---TAAGGAAAGACTAAAAGAAAGGGAAGGAACTCGGCAAA--CACAAGCCTCGC-CTGTTTACCAAAAACATCGCCTCCTGA---CATCCCAAT--ATAGGAGGTCCAGCCTGCCCAGTGAC-AA---T-A-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTCGTCCTTTAAATAGGGACCTGTATGAATGGCCAAACGAGGGCTTAACTGTCTCCCCCATCAAGTCAGTGAAATTGATCTATCCGTGCAGAAGCGGATATAATAATACAAGACGAGAAGACCCTTTGGAGCTTAAGGT
+i danRer4.chrM            C 0 C 0
+
+a score=-149774.000000
+s mm8.chrM                     2180 39 +     16299 ATATAACTT-A--TCTATTTAATTTATTAAACCT--AAT------GGCCC
+s rn4.chrM                     2164 37 +     16300 TACTAATTT-----CAATTTATATAAAAAAACCT--AAT------GGGCG
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_116167      4571 41 +     15695 ATTTAACCC-A--ACACTTCCTTTATTCTACTCTACAAT------GAGCC
+i oryCun1.scaffold_116167 C 0 C 0
+s panTro2.chrM                 2162 37 +     16554 CATTAATGCAA--ACAAT---ACTTAACAAACCT--ACA------GGTCC
+i panTro2.chrM            C 0 I 2
+s hg18.chrM                    2745 37 +     16571 taTTAATGCAA--ACAGT---ACCTAACAAACCC--ACA------GGTCC
+i hg18.chrM               C 0 I 2
+s bosTau2.chrM                 2538 17 +     16338 -------------------------AACCAACCC--AAA------GAGAA
+i bosTau2.chrM            C 0 I 21
+s canFam2.chrM                 2170 23 +     16727 -------------------------AACTAACCC--AAACTTATGGATAC
+i canFam2.chrM            C 0 I 18
+s dasNov1.scaffold_23239       5995 38 -     16977 AACTAGATC-A--GCAATATCAACATATCCATCA--ACA------GATA-
+i dasNov1.scaffold_23239  C 0 I 1
+s loxAfr1.scaffold_36650       5182 37 +     16266 AACTAATTTAA--TTGCT---AGCCTATAAATCT--ATA------AGATA
+i loxAfr1.scaffold_36650  C 0 I 1
+s echTel1.scaffold_181343      1434 35 +     18297 AA-TAACCCAA--TTGTT----TCTCACAAAACC--AAA------AGGCA
+i echTel1.scaffold_181343 C 0 I 1
+s monDom4.chrUn           117153618 28 + 174229318 AATTAATTTAT--ACTAT-----------ACCCT--AAG------GGAT-
+i monDom4.chrUn           I 9 C 0
+s galGal2.chrM                 3452 29 +     16775 -------------TCACGACCACCTTACAACCTT--ACA------CAGCC
+i galGal2.chrM            C 0 I 11
+s xenTro2.scaffold_18215       1329 36 +      3330 ---TTACGGCA--ACTGCTAAACAATCCAACCCC--ACA------CGGG-
+i xenTro2.scaffold_18215  C 0 I 4
+s tetNig1.chrUn_random    103512002 26 + 171761319 -----ATAAAA--CAGATCACGTCAAACACCCT-----------------
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3206 28 +     16596 -----ACAAGATTTAATTTACATCAAGCAAACC-----------------
+i danRer4.chrM            C 0 C 0
+e rheMac2.chr5             34437854 384 - 182086969 I
+
+a score=88545.000000
+s mm8.chrM                     2219  80 +     16299 ------------AAAA-------------ACTATAG---TATAAGT---T-TG-------AAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCC-----GAAT-----GA----------------TTATAACCTAGA
+s rn4.chrM                     2201  83 +     16300 ------------AAAACA-----------ACAAAAT---TATGAAC---TACC-------AAATTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCC-----GAAT-----GA----------------TTATAACCGAGT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_116167      4612  83 +     15695 ------------TAACCA-----------AGGAAAT--CCCTGGGT---T-AA-------AAATTTTGGTTGGGGTGACCTCGGAGTATAAATCAACCTCC-----GAAT-----GA----------------TTTTAGCCTAGA
+i oryCun1.scaffold_116167 C 0 C 0
+s hg18.chrM                    2784  79 +     16571 --------------AACT-----------ACCAAA----CCTGCAT---T-AA-------AAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCC-----GAGC-----AG----------------TACATGCTAAGA
+i hg18.chrM               I 2 C 0
+s panTro2.chrM                 2201  79 +     16554 --------------AACT-----------ATTAAA----CCTGCAT---T-AA-------AAATTTCGGTTGGGGCGACCTCGGAGCACAACCCAACCTCC-----GAGC-----AA----------------TACATGCTAAGA
+i panTro2.chrM            I 2 C 0
+s rheMac2.chr5             34438238  81 - 182086969 --------------aaaa-----------aatata----tatatatatat-at-------atatGTTGGTT-GGGTGACCCCGGAGCATAATTCAACCTCC-----GAAC-----GA----------------CCTAAACTAAGA
+i rheMac2.chr5            I 384 C 0
+s bosTau2.chrM                 2576  83 +     16338 --------------AACA-----------ACAATCT--CCATGAGT---T-GG-------TAGTTTCGGTTGGGGTGACCTCGGAGAATAAAAAATCCTCC-----GAGC-----GAT-----------T---TTAAAGACTAGA
+i bosTau2.chrM            I 21 C 0
+s canFam2.chrM                 2211  85 +     16727 --------------AACATAA-------CACCATTA--TTATGAGT---T-AG-------CAATTTAGGTTGGGGTGACCTCGGAATATAAAAAAACTCCC-----GAGT-----GA----------------TTAAAATTTAGA
+i canFam2.chrM            I 18 C 0
+s dasNov1.scaffold_23239       6034  80 -     16977 ------------AAAACA-----------GAATGA----TATGAAC---T-AT-------TAATTTTGGTTGGGGTGACCTCGGAGCACAGCAAAACCTCC-----GAAT-----GA-----------------CAGCGCCAAGA
+i dasNov1.scaffold_23239  I 1 C 0
+s loxAfr1.scaffold_36650       5220  84 +     16266 --------------AACT-----------A-AACAG---CATGATAAATT-AA-------CAATTTTGGTTGGGGTGACCTCGGAGAAGAAAAAATCCTCC-----GAAC-----GAT-----------A---TTATAATTTAGA
+i loxAfr1.scaffold_36650  I 1 I 1
+s echTel1.scaffold_181343      1470  81 +     18297 --------------AACT-----------ATAACTA---TATGGAG-----AA-------AGATTTCGGTTGGGGTGACCTCGGAGCATAATTAAACCTCC-----GAAT-----GAT-----------A---TATACATCTAGA
+i echTel1.scaffold_181343 I 1 M 388
+s monDom4.chrUn           117153646  83 + 174229318 ------------------TAATCT----TACAAAAC--TTTTTAAG---C-TG-------AATTTTTGGTTGGGGTGACCTCGGAGCACAAGCAACCCTCC-----GAAT-----GA-----------------CATAACTAAGA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 3492  96 +     16775 ---------------------ACCCACACATAAACC---CCTGGTC---G-AC-------ATTTTTCGGTTGGGGCGACCTTGGAGAAAAAAAAATCCTCC-----AAACCCACAGACCAC------AAC---TCTTCACTAAGA
+i galGal2.chrM            I 11 C 0
+s xenTro2.scaffold_18215       1369 100 +      3330 ------------CAGACA-----------ATTAAGCAACAATGACC---T-AA-------AGTTTTCGGTTGGGGCGACCACGGAGAAAAAAAAATCCTCCTTGATGTAC-----GGGGCCT---TACCC---TCTTAACCAAGA
+i xenTro2.scaffold_18215  I 4 C 0
+s tetNig1.chrUn_random    103512028 111 + 171761319 TAGATAAAAGAACAAACT-----------------A---AGTGAGC---C-CTGTTCAAATGTCTTTGGTTGGGGCGACCGCGGGGTAACAAAAAACCCCC-----ATGT-----GGAATAAAAACACCCTTTTTAAAACCAAGA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3234 107 +     16596 AATAAAAGTGATTAAACT-----------AGTAAAA---GATAAAC---C-TC-------TACCTTCGGTTGGGGCGACCACGGAGTAAAAAACAACCTCC-----AAGC-----GGAACGGGCACAGCC---CTAAAACCAAGA
+i danRer4.chrM            C 0 C 0
+
+a score=173589.000000
+s mm8.chrM                     2299 79 +     16299 CT---------TACAAGTCA---AAGTAAAATCAACATATCT------TATT------GACCCAGATA---TATTTTGATCAACGGACCAAGTTACCCTAGGGATA
+s rn4.chrM                     2284 84 +     16300 CGGTAACCGTGTCCGACCCAGTCAAGTAATACTAA--TATCT------TATT------GACCCAATTA---T----TGATCAACGGACCAAGTTACCCTAGGG-TA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_116167      4695 76 +     15695 CC--------CAACAAGTCA---AAGCAATTATAA--TCATA------AATT------GACCCAAATA---A--TTTGATCAACGGAACAAGTTACCCTAGGGATA
+i oryCun1.scaffold_116167 C 0 n 0
+s hg18.chrM                    2863 76 +     16571 CT--------TCACCAGTCA---AAGCGA-ACTACTATACTC------AATT------GATCCAA-TA---A--CTTGACCAACGGAACAAGTTACCCTAGGGATA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 2280 76 +     16554 CC--------TCACCAGTCA---AAGCGA-ATTACTACATCC------AATT------GATCCAA-TG---A--CTTGACCAACGGAACAAGTTACCCTAGGGATA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34438319 74 - 182086969 CC--------ACACCAGTCT---ACGCGA-GTTAACACAC---------ATT------GGCCCAATTA---A--TTTGATCAATGGAGTAAGTTATCCTATGGATA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 2659 72 +     16338 CC---------CACAAGTCA---AATCAC----TCTATCGCT------CATT------GATCCAA-AA---A--CTTGATCAACGGAACAAGTTACCCTAGGGATA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 2296 74 +     16727 CC---------CACAAGTCA---AAATAC----AACATCACT------TATT------GATCCAA-TA---ATTTTTGATCAACGGAACAAGTTACCCTAGGGATA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       6114 73 -     16977 CC---------AACCGGTCA---AAGCCC--ATAACGAAACC------AATT------GATCCAA--A---A--ATTGACCAACGGAACCAGTTACCCCAGGGATA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       5305 72 +     16266 ---------TCTACAAGTCA---AAATTT-ACTAA--TCGCT------TATT------GACCCAA--T---A--CTTGATCAACGGAACAAGTTACCCTAGGGATA
+i loxAfr1.scaffold_36650  I 1 C 0
+s echTel1.scaffold_49882       2559 71 -      7170 ---------CCTACAAGTCG---CAATTA-A--AA--TCACT------TATT------GACCCAA-TT---A--CTTGAGCAACGGACCAAGTTACCCTAGGGATA
+i echTel1.scaffold_49882  I 1561 C 0
+s monDom4.chrUn           117153729 75 + 174229318 ---------CTAACACATCT---AAGTGCAACCTAAGCCAGT------AATT------GACCCAA--A---A--CTTGATCAACGGAACAAGTTACCCCAGGGATA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 3588 72 +     16775 ---------CCAACTCCTCA---AAGTACCAACAG--TAACC------A---------GACCCAATAT---A--ATTGAGCAATGGACCAAGCTACCCCAGGGATA
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18215       1469 80 +      3330 ---------ACGACAGTTCT---AAGTAA---CAAAACATTTGACCACTATT------GATCCAGTCC---A--ACTGATCAACGAACCAAGTTACCCTAGGGATA
+i xenTro2.scaffold_18215  C 0 C 0
+s tetNig1.chrUn_random    103512139 79 + 171761319 ---------GCCACCGCTCT---AATGAA---CAGAACATCT------GACCAATCA-GATCCGGCCT---A--GCCGATCAACGAACCGAGTTACCCTAGGGATA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3341 83 +     16596 ---------GAAACATCTCT---AAGCCT---CAGAACACCT------GACCAAAGACGATCCGGCCTATAA--GCCGATCAACGAACCAAGTTACCCTAGGGATA
+i danRer4.chrM            C 0 C 0
+
+a score=1521193.000000
+s mm8.chrM                     2378 161 +     16299 ACAGCGCAATCCTATTTAA-GAGTTCATATCGACAATTAGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCCAATGGTGTAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTT
+s rn4.chrM                     2368 153 +     16300 ACAGCGCGA-CCTATTTAA-GAGTTCATATCGACAATTAGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCCAATGGTGCAGAAGCTATTAATGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTAAGTCCGG-------CAATCCAGGTCGGTT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_205008         2 161 -    118789 ACAGCGCAATCCTATTTTA-GAGTCCCTATCGACAATAGCGGTTTAC-GACCTCGATGTTGGATCAGGACATCCCAATGGTGTAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGAAATCCAGGTCGGTT
+i oryCun1.scaffold_205008 n 0 C 0
+s hg18.chrM                    2939 160 +     16571 ACAGCGCAATCCTATTCTA-GAGTCCATATCAACAAT-AGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 2356 160 +     16554 ACAGCGCAATCCTATTCCA-GAGTCCATATCAACAAT-AGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34438393 161 - 182086969 ACAACAAAATCCTATTCTAGGATTCCCTATTGGCAAT-AGGGTTTAC-AACCTCGATGTTGGATCAGGACATCCTAATGGTGTAGCTGCTATTAAGGGTTCATTTATTCAATGATTAA-AGTCCTACCTGATCTGAGTTCAGACCGGAGTAATCCAGGTTGGTT
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 2731 160 +     16338 ACAGCGCAATCCTATTCAA-GAGTCCATATCGACAAT-AGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCTGATGGTGCAACCGCTATCAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 2370 160 +     16727 ACAGCGCAATCCTATTCAA-GAGTCCATATCGACAAT-AGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCAGCTATTAAGGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       6187 160 -     16977 ACAGCGCAATCCTATTCCA-GAGCCCATATCAACAAT-AGGGTTTAC-GACCTCGATGTTGGATCAGGACACCCAAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       5377 160 +     16266 ACAGCGCAATCCTACTCTA-GAGTCCCTATCGACAGC-AGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAGGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_49882       2630 161 -      7170 ACAGCGCAATCCTATTTAA-GAGTTCATATCGACGAT-AGGGTTTACTGACCTCGATGTTGGATCAGGACACCCAGATGGTGCAACAGCTATCAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTT
+i echTel1.scaffold_49882  C 0 I 1469
+s monDom4.chrUn           117153804 161 + 174229318 ACAGCGCAATCCTATTTAA-GAGCCCATATCGACAATTAGGGTTTAC-GACCTCGATGTTGGATCAGGACACCCCAATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGAAATCCAGGTCGGTT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 3660 161 +     16775 ACAGCGCAATCTCCTCCAA-GAGCCCATATCGACAAG-GAGGTTTAC-GACCTCGATGTTGGATCAGGACAACCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTTCAACGATTAACAGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTT
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18215       1549 160 +      3330 ACAGCGCAATCCATTTCGA-AAGTTCCTATCGACAAA-TGGGTTTAC-GACCTCGATGTTGGATCAGGGCATCCCAGTGGTGCAGCCGCTACTAAAGGTTCGTTTGTTCAACGATTAA-AGCCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCAGTT
+i xenTro2.scaffold_18215  C 0 C 0
+s tetNig1.chrUn_random    103512218 160 + 171761319 ACAGCGCAATCCTCTTTTA-GAGCCCATATCGACAAG-AGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAGGGTTCGTTTGTTCAACGATTAA-AGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCAGTT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3424 161 +     16596 ACAGCGCAATCCTCTCTAA-GAGTCCATATCGACGAG-GGGGTTTAC-GACCTCGATGTTGGATCAGGACATCCTAATGGTGCAGCCGCTATTAAGGGTTCGTTTGTTCAACGATTAATAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCAGTT
+i danRer4.chrM            C 0 C 0
+
+a score=51271.000000
+s mm8.chrM                     2539 136 +     16299 TCTATCTATTTAC--G-ATTTCTCCC-AGT-ACGAAAGGACAAGAGAAATAGAGCC-ACCTTACAAATAAG-CG--CTCTCAACT----TAATTTATGAATAAAATCTAAAT--AAAA---TAT---ATACG---T-ACACCCTCT---AACCTAGAGA----AGGTT-
+s rn4.chrM                     2521 132 +     16300 TCTATCTATTTAC--A-ATTTCTCCC-AGTTACGAAAGGACAAGAGAAATGGAG---ACCAACCAATCCTA-GG--CTTCCAACC-----AATTTAG----AAAAACTTAAT--AAAG---TAT---ATATG---T-ACAATAAAT---AACCT-TAGACCC-AAGTT-
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_205008       163 136 -    118789 TCTATCTATTAAG--T-ATTTCTCCC-AGT-ACGAAAGGACAAGAGAAATAGAGCCTACTGCACCA--CAG-AG--CTCTAAGTC----CAAAAGATGAA-ATAATCTTAAT--CTAG---TAC---ACTTA---C-CCAACATAG---AGCCC-TAGACCA-GAGCT-
+i oryCun1.scaffold_205008 C 0 C 0
+s hg18.chrM                    3099 129 +     16571 TCTATCTACTTCA--A-ATTCCTCCC-TGT-ACGAAAGGACAAGAGAAATAAGGCCTACTTCACAA---AG-CG-CCTTCCCCCG----TAAATGAT----ATCATCTCAAC--TTAGTATTAT---ACCCA---C-ACCCAC---------CC-AAGAACA-GGGT--
+i hg18.chrM               C 0 I 89
+s panTro2.chrM                 2516 117 +     16554 TCTATCTGTTCTA--A-ATTTCTCCC-TGT-ACGAAAGGACAAGAGAAATGAGGCCTACTTCACAA---AG-CG-CCTTCCCCAA----TAAATGAT----ATTATCTCAAT--TTAGCGCCAT---GCCAA---C-ACCCACT-------------------------
+i panTro2.chrM            C 0 I 92
+s rheMac2.chr5             34438554 132 - 182086969 TCTATATATTTAA--T-ATTTCTCCT-AGT-ATGAAAGGACAAGAGAAATAGGGCCCACTTCATAA---AG-TGCCCTTGCCGCA----TAAATGAT----GCTATCTCTGT--CTAA---CAA---ACCAT---C-ACACACCCT---A-CCC-AGAAACA-GGGT--
+i rheMac2.chr5            C 0 I 2
+s bosTau2.chrM                 2891 130 +     16338 TCTATCTATTACG--T-ATTTCTCCC-AGT-ACGAAAGGACAAGAGAAATAAGGCCAACTTTAAAT-CAAG-CG--CCTTAAGAC-----AACCAATGAT-AACATCTCAA---CTGA---CAA---CACAA---A-ACCCT--------GCCC-TAGAACA-GGGCT-
+i bosTau2.chrM            C 0 I 2
+s canFam2.chrM                 2530 138 +     16727 TCTATCTATTATA--CAACCTCCCCC-AGT-ACGAAAGGACAAGGGATGTAAGGCCTACCTCACAG--AGG-CG--CCTTAAAAC----TAATAGATGAA-GTCAACTCAAT--CTAA---CCA---GTTTA---T-CTCCTCATA---AGCCC-GAGAAAAGGGGCT-
+i canFam2.chrM            C 0 I 2
+s dasNov1.scaffold_23239       6347 137 -     16977 TCTATCTATAACC--A-ATTTCTCCC-AGT-ACGAAAGGACAAGAGAAATAAGGCCAACTTTACAA-GAGG-CG-CCTTAAATCA----AAATAGATGAA-ATAATCTCAAC--CTAA---AAC---AT-TA---C-ATAAACATT---AGTCC-TAAGCCA-GGACC-
+i dasNov1.scaffold_23239  C 0 I 2
+s loxAfr1.scaffold_36650       5537 134 +     16266 TCTATCTATAGTT--T-ATTTATTCC-AGT-ACGAAAGGACAGAAAAAATGAGGCCAATCTTACCA---AGACG--CCTCCAGCT----AAATTTATGAA-TAAATCTCAAT--CTAG-----------ATAAGCT-AAACCACCC---AATCC-AAGAACA-GGATT-
+i loxAfr1.scaffold_36650  C 0 I 1
+s echTel1.scaffold_181343      1939 126 +     18297 TCTATCTATTTTA--T-ATCTCCTCCTAGT-ACGAAGGACCAGAGAGA---TAGCCACTTTCAACC---AG-CG--CCTTAA--C----AAACCAATGAT-ATAATCTTAAT--TTAC-----------CTA---T-ATCCATTTC---TGCTC-TAGATAA-GAGCT-
+i echTel1.scaffold_181343 M 388 I 1
+s monDom4.chrUn           117153965 135 + 174229318 TCTATCTATATAA--TAATTTCTCCT-AGT-ACGAAAGGACAAGAGAATTAAGGCCAACATTACAA--ACA-AG--CCTTACAAC----TAACTAATGAT-CTTATCTCAAT--TAGT---TAA---TGCAA---G-ATTTTATT-----ACTC-TAGAGAA-GAGTT-
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 3821 142 +     16775 TCTATCTATGGAC----ACTCCTCCT-AGT-ACGAAAGGACCGGAGAAGTGGGGTCAATACCACTG---AG-CA--CACCCCAACCTTCTAAGCAATGAA-TACAACTCAACTGCCAA---GAA---CCCCT---C-CCCCACACCCGAACTCC-TAGAAAA-GGAT--
+i galGal2.chrM            C 0 I 3
+s xenTro2.scaffold_18215       1709 136 +      3330 TCTATCTATGCAG--T-ATTTTCTCT-AGT-ACGAAAGGACCGAGAAAATGAGGTCTATGTCACAA--ACA-AG--CCTCCTCCC----TTATCAATGAA-AACAACTTAAT--TGAA---TAA---AGGAC---T-AACAACTTC---AGCCC-AAGATAA-GGGCT-
+i xenTro2.scaffold_18215  C 0 M 690
+s tetNig1.chrUn_random    103512378 139 + 171761319 TCTATCTATGAAG-TG-CCCTTTTCT-AGT-ACGAAAGGACCGAAAAGGAGAGACCCCTGCCAAAA--GCA-CG--TCCCCCTCT----CACCCGTTGTC-TCCAACTAAAA--CAGA---CAA---GAGAG---CACACAACAAC---AGCCA-AAGAACA-TGACAT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3585 141 +     16596 TCTATCTGTAAAGCTA-TTTTTTCCT-AGT-ACGAAAGGATCGGAAAAAGGGGGCCCATACTAAAA--GCA-CG--CCCCACCCT----AAATTTATGAA-TAAAGATAAAA--AAAA---TAAAAGGAGAG---C-TAAAACCTC---TTCCC-GA-AATA-AGGGTT
+i danRer4.chrM            C 0 C 0
+
+a score=312226.000000
+s mm8.chrM                     2675 76 +     16299 A-ttagggtggcagagccaggaaattgcgtaagacttaaaaccttgttcccagaggttcaaatcctctccctaa-ta--G
+s rn4.chrM                     2653 76 +     16300 A-ttagggtggcagagccaagtaattgcgtaagacttaaaaccttgttcccagaggttcaaatcctctccctaa-ta--G
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_205008       299 79 -    118789 Agttaaggtggcagagcccggtaattgcgtaaaacttaaaactttataaccagaggttcaactcctctccttaa-caATA
+i oryCun1.scaffold_205008 C 0 C 0
+s rheMac2.chr5             34438688 76 - 182086969 -gttaagatggaggagcttggtaattgcataaaacttaaaattttataataagaggttcaactcctcttcttaa-ca--A
+i rheMac2.chr5            I 2 I 2
+s bosTau2.chrM                 3023 76 +     16338 -gttaaggtggcagagcccggtaattgcataaaacttaaacttttatatccagagattcaaatcctctccttaa-ca--A
+i bosTau2.chrM            I 2 I 2
+s canFam2.chrM                 2670 75 +     16727 -gttagggt-gcagggcccggtaactgcgtaaaacttaaacctttactatcagaggttcaattcctctccctaa-ca--A
+i canFam2.chrM            I 2 I 2
+s dasNov1.scaffold_23239       6486 76 -     16977 -gttaagatggcagagacaggtaattgcataagacttaaacctttattaccagaggttcaaatcctcttcttaa-ca--t
+i dasNov1.scaffold_23239  I 2 I 3
+s loxAfr1.scaffold_36650       5672 76 +     16266 -gttaagatagcaaaaactggtcactgcataaaacttaagcttttactcacggaggttcaactcctcttcttaa-ca--A
+i loxAfr1.scaffold_36650  I 1 C 0
+s echTel1.scaffold_181343      2066 76 +     18297 -Attaagatggcagagcccggtaattgcacaagacttaaacccttgccgtcagaggttcaatccctcttcttaa-ta--A
+i echTel1.scaffold_181343 I 1 C 0
+s monDom4.chrUn           117154100 75 + 174229318 -Attaaggtggcagag-caggtaattgcataaaacttaagcctttactatcagaggttcaacccctctccttaa-ta--T
+i monDom4.chrUn           C 0 I 1
+s galGal2.chrM                 3966 75 +     16775 -GCTAGCGTGGCAGAGCTCGGCAAATGCAAAAGGCTTAAGCCCTT-TATCCAGAGGTTCAAATCCTCTCCCTAG-CT--A
+i galGal2.chrM            I 3 I 30
+s tetNig1.chrUn_random    103512517 75 + 171761319 -gttagggtggcagagcccggtaaatgcaaaagacctaagcccttt-atacagaggttcaactcctctccttaa-cT--A
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3726 77 +     16596 -GCTGGGATGGCAGAGCTCGGTAATTGCAAAAGGCCTAAGCCCTTTCACCCAAAGGTTCAAATCCTTTTCCCAGTTT--A
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_18215       1845 690 +      3330 M
+e panTro2.chrM                 2633 92 +     16554 I
+e hg18.chrM                    3228 89 +     16571 I
+
+a score=353365.000000
+s mm8.chrM                     2751  92 +     16299 ------------------TGTTCTTTATTAATATCCTAACACTCCTCGTCCCCATTCTAATC---GCCATAGCCTTCCTAACATTAGTAGAACGCAAAATCTTAGGGTACATA
+s galGal2.chrM                 4071  92 +     16775 ------------------ACCTTCTAATCATAACCTTATCCTATATTCTCCCCATCCTAATC---GCCGTGGCCTTCTTAACACTTGTAGAACGAAAAATCCTAAGCTACATG
+i galGal2.chrM            I 30 C 0
+s monDom4.chrUn           117154176  92 + 174229318 ------------------TGTTCCTAATCAATCTACTAATCTATATTATTCCTATTCTACTA---GCAGTAGCTTTTTTAACATTAATCGAACGAAAAGTCCTAGGTTATATA
+i monDom4.chrUn           I 1 C 0
+s echTel1.scaffold_181343      2142  92 +     18297 ------------------TGTTTATTATTAATCTCTTATCACTGATTGTTCCTATCCTCCTA---GCAGTAGCTTTCCTTACACTTCTTGAACGAAAAGTACTAGGATATATG
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650       5748  92 +     16266 ------------------TGTTCTTAATCAATGTCCTAACAGTAACCTTACCTATCCTCCTA---GCAGTAGCCTTCCTTACCTTAGTTGAACGAAAGGCCTTAGGCTATATA
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239       6565  92 -     16977 ------------------TGTACTTAATCAATGTTCTATCTCTAATTATCCCAATTCTCCTA---GCAGTAGCCTTCCTAACGTTACTAGAACGAAAAATTCTAGGCTATATA
+i dasNov1.scaffold_23239  I 3 C 0
+s canFam2.chrM                 2747  92 +     16727 ------------------TGTTCTTTATCAACATTATCTCTCTTATTATCCCAATCCTTCTT---GCCGTAGCCTTCCTCACCCTCGTTGAACGAAAAGTCTTAGGCTATATA
+i canFam2.chrM            I 2 C 0
+s bosTau2.chrM                 3101  92 +     16338 ------------------TGTTCATAATTAACATCTTAATACTAATTATTCCCATCCTATTG---GCCGTAGCATTCCTTACGTTAGTGGAACGAAAAGTTCTAGGCTATATA
+i bosTau2.chrM            I 2 C 0
+s rheMac2.chr5             34438766  92 - 182086969 ------------------TGCCTTTAATTAACCTTCTCCTACTCATTATCCCCACTCTTATC---GCTATAGCGTTCCTTACACTCATCAAACGAAAAATCTTAGGCTATACA
+i rheMac2.chr5            I 2 C 0
+s hg18.chrM                    3317  83 +     16571 ---------------------------CCAACCTCCTACTCCTCATTGTACCCATTCTAATC---GCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA
+i hg18.chrM               I 89 C 0
+s panTro2.chrM                 2725  92 +     16554 ------------------CACCCATGACCAACCTCCTACTCCTCATTGTACCCATCCTAATC---GCAATAGCATTCCTAATGCTAACCGAACGAAAAATTCTAGGCTACATA
+i panTro2.chrM            I 92 C 0
+s oryCun1.scaffold_205008       378  92 -    118789 ------------------TGTTCCTAATTAATACACT---CCTTTTAATCCTACCTGTACTTTTAGCCATAGCATTCCTCACCTTAGTCGAACGAAAAATCTTAGGGTACATA
+i oryCun1.scaffold_205008 C 0 C 0
+s rn4.chrM                     2729  92 +     16300 ------------------TGTACTTTATTAATATCCTAACACTCCTAATCCCAATCTTAATT---GCCATAGGCCTTCTCACCCTAGTAGAACGGAAAATCCTAGGCTACATA
+i rn4.chrM                C 0 C 0
+s tetNig1.chrUn_random    103512592 110 + 171761319 TGATTACAACCCTCATCACACACATCCTAAACCCTCTTGCCTTTATTGTCCCCGTCCTACTA---GCCGTCGCTTTTCTGACACTCCTAGAACGAAAAGTTCTAGGATACATA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3803 110 +     16596 TGCTAGACATCTTAACAAGCCACTTAATTAACCCCCTAGCCTACGCCGTACCAGTATTAATT---GCAGTAGCCTTCCTTACCTTAGTTGAACGAAAAGTGTTAGGCTATATA
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_18215       1845 690 +      3330 M
+
+a score=1741996.000000
+s mm8.chrM                     2843 346 +     16299 CAACTACGAAAAGGCCCTAACATTGTTGGTCCATACGGCATTTTACAACCATTTGCAGACGCCATAAAATTATTTATAAAAGAACCAATACGCCCTTTAACAAC-CTCTATATCCTTATTTATTATTGCACCTACCCTATCACTCACACTAGCATTAAGTCTATGAGTTCCCCTACCAAT---ACCACACCCA---TTAATTAATTTAAACCTAGGGATTTTATTTATTTTAGCAACATCTAGCCTATCAGTTTACTCCATTCTATGATCAGGATGAGCCTCAAACTCCAAATACTCACTATTCGGAGCTTTACGAGCCGTAGCCCAAACAATTTCATATGAAGTAACCATAG
+s rn4.chrM                     2821 346 +     16300 CAATTACGCAAAGGCCCCAACAACGAAGGCCCATATGGTAAACTACAACCATTTGCAGATGCCATAAAACTATTCATAAAAGAACCCATACGCCCTCTAACCAC-CTCAATATCACTATTTATTATCGCCCCAACCCTCTCCCTTACACTAGCTCTAAGCCTATGAATTCCCTTACCAAT---ACCCCACCCC---CTTATCAACCTCAACCTAGGCATACCATTTATTCTAGCCACATCCAGCCTTTCGGTCTACTCCATTCTATGATCGGGATGAGCCTCAAATTCAAAATACTCCCTATTCGGAGCCCTACGAGCCGTTGCCCAAACCATCTCTTACGAAGTCACAATAG
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_205008       470 347 -    118789 CAACTACGTAAAGGCCCAAACATTGTAGGACCCTATGGCCTCCTCCAACCAATCGCAGACGCTATTAAGCTATTCACTAAAGAACCCCTACGACCCCTAACATCGCTCTCCGCTACTCTTTATTATCGCCCCAACCCTAGCTCTAACTCTCGCACTATCAATGTGACTTCCTATCCCCAT---ACCTTACCCA---CTAGTCAACCTAAATATAGGCATTCTATTCATCCTAGCAACCTCCAGCTTAGCCGTTTACTCAATCCTATGATCAGGATGAGCATCCAACTCAAAATACGCCCTATTTGGTGCTCTCCGAGCAGTCGCACAAACCATTTCCTACGAAGTCACACTTG
+i oryCun1.scaffold_205008 C 0 C 0
+s panTro2.chrM                 2817 346 +     16554 CAACTACGCAAAGGTCCCAACATTGTAGGTCCTTACGGGCTATTACAGCCCTTCGCTGACGCCATAAAACTCTTCACTAAAGAACCCTTAAAACCCTCCACTTC-AACCATTACCCTCTACATCACCGCCCCAACCCTAGCCCTCACCATTGCCCTCTTACTATGAACCCCCCTCCCCAT---ACCCAACCCC---CTAGTCAATCTTAACTTAGGCCTCCTATTTATTCTAGCCACCTCCAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCGAACTACGCCTTAATCGGTGCACTACGAGCAGTAGCCCAAACAATCTCATACGAAGTCACTCTAG
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    3400 346 +     16571 CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATC-TACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCAT---ACCCAACCCC---CTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAG
+i hg18.chrM               C 0 C 0
+s rheMac2.chr5             34438858 346 - 182086969 CAACTATGCAGAAGACACAGAATTGTCGGTCTCGATGGGCTGCTTCAACCATTCGCTGATGCAATAAAACTTTTCACCAAAGAACCCTTACGGCCTTCAAAATC-TGCTATTACCCTTCACATTATTGCTTCAACACTAGCCTTTTCCATCACTCTCCTCTTATGAACTCCCCTCCCTAT---CCCAGACCCT---CTAATTAATTTTAACATAAGCCTCCTATTTATACTAGCCACATCAAGCCCAGCCGTCTCCTCTATTCTATGATCAGGATGAGCATCTAATTCAAATTATGCACTAATCAGCACATTACGAGCTGTGGCCCAAACAATTTCATATGAGGTCACCTTGG
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 3193 346 +     16338 CAACTCCGAAAAGGTCCAAATGTCGTAGGTCCATATGGCCTACTTCAACCCATCGCCGATGCAATCAAACTTTTCATTAAAGAACCACTACGACCCGCTACATC-TTCAGCCTCAATATTTATCCTAGCACCTATCATAGCTTTAGGCCTAGCCTTAACCATGTGAATTCCCCTACCAAT---ACCCTATCCT---CTTATCAACATAAACCTAGGAGTCCTATTTATACTAGCCATATCAAGCCTAGCCGTATACTCCATTCTCTGATCAGGCTGAGCTTCCAACTCAAAATACGCACTAATCGGAGCCCTACGAGCAGTAGCACAAACAATCTCATACGAAGTAACGCTAG
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 2839 346 +     16727 CAACTTCGAAAAGGACCTAATATTGTAGGCCCCTACGGCCTCCTTCAACCAATCGCAGACGCAGTAAAACTCTTCACAAAAGAACCTCTACGACCACTTACATC-CTCTATATCAATATTCATCCTAGCCCCCATTCTAGCTCTATCACTAGCCCTAACTATGTGAATTCCCCTCCCAAT---ACCCTACCCA---CTCATTAATATAAACTTGGGAGTCCTATTCATACTAGCAATATCAAGCCTCGCCGTGTACTCCATCCTCTGATCAGGATGAGCCTCAAACTCCAAATACGCCCTAATCGGAGCCCTTCGAGCAGTAGCTCAAACAATCTCATATGAAGTAACGCTAG
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       6657 346 -     16977 CAGTTACGTAAAGGCCCAAACATCGTAGGACCATACGGCCTACTACAACCAATCGCAGACGCCATTAAACTATTCATCAAAGAACCACTACGACCAGCCACATC-ATCAAAACTCATATTTACCTTAGCACCCACACTAGCACTAACTCTCGCACTTTCACTTTGAATCCCCATCCCAAT---ACCTTACCCA---TTGGTTAACTTAAATTTAGGGGTACTATTCATTTTAGCCATATCAAGCCTAGCTGTCTATTCAATCTTATGGTCAGGATGAGCATCAAACTCCAAATACGCCCTCATCGGAGCCCTTCGAGCAGTAGCACAAACAATTTCCTACGAAGTAACCCTGG
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       5840 346 +     16266 CAACTTCGTAAAGGTCCCAATGTAGTAGGACCTTACGGTCTTCTCCAACCTATTGCAGATGCAATCAAGCTATTTACTAAAGAACCCATCTACCCACAAACCTC-ATCAAAATTCCTATTTACCGTCGCCCCAATTCTAGCCCTAACCTTAGCCCTAACTGTATGAGCTCCTCTTCCAAT---ACCATATCCT---CTAATTAACTTAAATCTGAGCCTACTATTCATTCTCGCAATATCAAGTCTGATAGTTTATTCCATCCTATGATCAGGCTGAGCATCAAACTCAAAATATGCCCTCATAGGAGCCCTGCGAGCAGTAGCCCAAACCATCTCCTATGAAGTCTCTATAA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      2234 346 +     18297 CAACTTCGTAAAGGCCCTAACGTTGTTGGCCCATATGGGCTCTTTCAACCATTTGCTGACGCAATCAAACTATTTACTAAAGAACCGCTACGCCCAATGACTTC-ATCTATAACTATATTTTTACTTGCCCCAATCCTAGCGCTATCCCTAGCTCTTACACTGTGGGTTCCTCTGCCAAT---ACCTCATTCC---CTTGTTAATCTTAACCTAAGCCTCTTATTCATCTTAGCCATATCTAGCCTAGCTGTCTACTCTATTCTATGATCAGGATGAGCATCTAACTCCAACTATGCTCTAATTGGCGCACTCCGAGCAGTCGCCCAAACAATCTCTTATGAAGTCTCTCTAG
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117154268 346 + 174229318 CAACTCCGAAAAGGCCCAAACGTTATTGGACCATACGGCATCCTACAGCCATTCGCAGACGCTGTAAAATTATTCACAAAAGAACCCCTCCGACCTCTAACTTC-ATCAATCTCAATATTTATTATTGCACCTATTTTAGCCCTAACCTTAGCTCTAACAATCTGAACCCCTCTACCTAT---ACCCCACACC---CTAATTGACTTAAACCTAGGACTTTTATTTATTTTATCCTTATCAGGACTATCAGTTTACTCAATTCTATGATCAGGATGAGCATCAAATTCTAAATATGCACTCATTGGAGCCTTACGAGCCGTAGCTCAAACAATTTCATACGAAGTCACATTAG
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 4163 346 +     16775 CAGGCCCGAAAGGGCCCAAACATTGTGGGCCCTTTTGGTCTACTCCAACCCGTTGCAGACGGGGTAAAACTATTCATTAAAGAGCCAATCCGACCATCTACCTC-CTCCCCCTTCCTCTTCATTATTACTCCAATCCTAGCACTACTCCTAGCCCTGACTATTTGAGTCCCCCTCCCACT---ACCATTCCCC---CTTGCAGACCTCAACCTAGGACTACTATTTCTCCTAGCCATATCAAGCCTAACTGTCTACTCTCTACTCTGATCCGGATGAGCATCAAACTCCAAGTATGCCCTAATCGGAGCCCTTCGAGCCGTCGCACAAACAATCTCATACGAAGTCACCCTAG
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_8452       11274 352 +     23823 CAAGTGCGCGTGGGCCCGAACCGCGTCGGCCCGCTGGGCCTGCTGCAACCGCTTGCCGATGGCCTGAAGCTCCTGACCAAGGAAATCATCACACCAACGGCGGC-CAGCAAGGGCCTGTTCTTCCTGGGGCCGGTGATGGCCATCATGCCGGCCCTGGCCGCCTGGGCGGCCATCCCCTTCGGCCCCGACGTCGTGCTGGCGAACGTGAATGCCGGGCTGCTGCTCATCATTGCCATCGCCTCGATCGAGGTCTATGGCGTCATCATCGCGGGCTGGGCGTCCAACTCCAAGTACGCCTTCCTGGGCGCACTGCGTGCCTCGGCGCAGATGGTGAGCTATGAAATCGCCATGG
+i xenTro2.scaffold_8452   n 0 I 124
+s tetNig1.chrUn_random    103512702 346 + 171761319 CAACTACGAAAAGGTCCAAACATCGTAGGCCCTTATGGCCTTCTCCAACCAATTGCAGACGGGGTAAAACTATTTATTAAAGAGCCCGTACGACCCTCAACCTC-CTCCCCAATCCTATTCATCCTCACCCCCATACTAGCCCTCACATTAGCCATAACACTATGAGCCCCCCTACCCCT---TCCATACCCA---GTCCTAGACCTAAACCTAGCCATCCTTTTCATTCTCGCCCTCTCTAGTCTCGCAGTGTATTCAATCCTCGGTTCCGGTTGAGCCTCAAACTCAAAATATGCCTTAGTAGGAGCCCTACGAGCCGTCGCACAAACCATCTCCTATGAAGTAAGCCTAG
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 3913 346 +     16596 CAACTCCGAAAAGGACCAAATGTAATAGGCCCCCGAGGACTGTTACAATCAGTAGCTGATGGCGTGAAACTTTTTATTAAAGAACCCATTCGACCATCTATGGC-TTCTCCAATTTTATTTTTAACAGCTCCAGTTCTTGCACTAATCCTAGCAATAATGCTATGGGCACCCATACCCAT---GCCCTATCCA---GTACTCGACCTAAATCTTGGAATTTTATTTATTATAGCCATCTCAAGCCTAGCAGTATACTCAATCCTGGGATCAGGTTGAGCATCAAACTCAAAATACGCATTAATTGGGGCCTTACGAGCTGTAGCGCAAACAATTTCATATGAAGTTAGCCTAG
+i danRer4.chrM            C 0 C 0
+
+a score=274539.000000
+s mm8.chrM                     3189 85 +     16299 CTATTATCCTTTTATCAGTTCTATTAATAAATGGATCCTACTCTCTACAAACACTTATTACAACCCAAGAACACATATGATTACT
+s galGal2.chrM                 4509 85 +     16775 CCATCATCCTGTTATCCACAATCATACTGAGCGGCAATTACACCTTAAGCACCCTGGCCATCACCCAAGAGCCCATCTACCTCAT
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117154614 85 + 174229318 CAATTATTCTGCTTTCAATTATACTAATTAATGGCTCCTTTACCCTAAAAAATTTAATAATTACCCAAGAAAATATATGATTAAT
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      2580 85 +     18297 CTATTATTCTGCTATCAGTAATATTATTTAATGGTTCATTCTCTTTGTCCTCCCTCACTATTACTCAAGAACATTTATGACTGCT
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650       6186 85 +     16266 CAACTATCACCTTATCAATAGTACTAATAAATGGGTCCTTCACACTAACCGCCTTCGCTATAACACAAGAACATCTATGACTAAT
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239       7003 85 -     16977 CCATCATCTTACTATCAATCATAATAACAAATGGCTCATTCACCCTATCTACCCTAACAACAACACAAGAACACATATGACTAAT
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 3185 85 +     16727 CAATTATTCTTCTATCAGTCCTCCTAATAAACGGGTCATTTACACTATCCACGCTAATTATTACCCAAGAACATATATGATTAAT
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 3539 85 +     16338 CAATTATCCTGTTATCAGTACTCCTAATAAGTGGGTCCTTTACCCTCTCCACATTAATTACTACACAAGAACAAATATGGTTAAT
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34439204 85 - 182086969 CCATTATCCTGCTATCAGTTCTACTGATAAGCCGCTCGTTTAACTTATACAAACTCTTCACCATGCAAGAATTCCTCTGACTGCT
+i rheMac2.chr5            C 0 C 0
+s hg18.chrM                    3746 85 +     16571 CCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 3163 85 +     16554 CCATTATCCTACTGTCAACGCTACTAATAAGTGGCTCCTTCAATCTCTCTACCCTTGTCACAACACAAGAGCACCTCTGACTAAT
+i panTro2.chrM            C 0 C 0
+s oryCun1.scaffold_205008       817 85 -    118789 CAATTATCCTCCTATGCATCCTCCTAATAAATGGCTCATTTACATTATCATCCCTAATCACAACACAAGAATATATATGAATCCT
+i oryCun1.scaffold_205008 C 0 C 0
+s rn4.chrM                     3167 85 +     16300 CCTTATACCTCTTATCCGTCCTCCTAATAAGCGGCTCCTTCTCCCTACAAATACTTATCACTACACAAGAACATATCTGACTATT
+i rn4.chrM                C 0 C 0
+s tetNig1.chrUn_random    103513048 85 + 171761319 GCCTAATCCTACTCTCCCTAATTATCTTCACTGGGGGCTTCACACTACAAACCTTCAACACCGCCCAAGAAAGTATTTGACTTAT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 4259 85 +     16596 GACTTATTCTATTATCTGCCGTTATTTTTTCTGGGGGATACACCCTACAAACATTTAATACAACTCAGGAAGACACATGACTTCT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_8452       11626 124 +     23823 I
+
+a score=377866.000000
+s mm8.chrM                     3274 64 +     16299 TCTGCCAGCCTGACCCATAGCCATAATATGATTTATCTCAACCCTAGCAGAAACAAACCGGGCC
+s rn4.chrM                     3252 64 +     16300 AATCCCCGCCTGACCAATAGCCATAATATGATACATTTCAACCCTCGCAGAAACAAATCGAGCT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_205008       902 64 -    118789 ACTACCAGCATGACCACTTGCCATAATATGATTTATCTCAACCCTAGCAGAAACCAACCGGGCT
+i oryCun1.scaffold_205008 C 0 I 2359
+s panTro2.chrM                 3248 64 +     16554 CCTGCCAACATGACCCCTGGCCATAATATGATTTATCTCTACACTAGCAGAGACCAACCGAACT
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    3831 64 +     16571 CCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACC
+i hg18.chrM               C 0 C 0
+s rheMac2.chr5             34439289 63 - 182086969 CCTACCATCATGGCCC-TAGCCATAACATGATTCATCTCCACACTAGCAGAAACTAACCGAGCC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 3624 64 +     16338 CCTCCCAGCATGGCCTCTAGCAATAATATGATTTATCTCAACACTAGCAGAAACAAACCGAGCT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 3270 64 +     16727 CTTTCCGGCCTGACCCCTAGCCATGATATGATTCATCTCTACCCTAGCAGAAACTAATCGAGCC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       7088 64 -     16977 CTTTCCCCTCTGGCCACTAGCAATAATATGATTTATCTCCACACTAGCAGAAACCAATCGCGCC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       6271 64 +     16266 CCTTCCTATATGACCCCTGATAATAATATGATTCACATCAACCTTAGCAGAAACTAACCGAGCC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      2665 64 +     18297 AGTCCCCTCATGACCCCTAGCAATAATATGATTCATCTCAACACTAGCAGAAACTAACCGGGCC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117154699 64 + 174229318 TATAACCGCATGACCTCTAACTATAATATGGTATATTTCTACATTAGCCGAGACAAACCGAGCT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 4594 64 +     16775 TTTTTCCGCATGACCCCTCGCAATAATATGATACATCTCTACCCTTGCTGAAACCAACCGCGCC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_8452       11750 64 +     23823 GCTGCCGCTGCTGCCCATCTTCGTGGTCTACCTGATTTCCAGCGTGGCCGAAACCAACCGCCAC
+i xenTro2.scaffold_8452   I 124 C 0
+s tetNig1.chrUn_random    103513133 64 + 171761319 CATCCCAACCTGACCCCTTGCCGCAATATGATACATCTCCACCCTAGCAGAAACCAACCGAGCC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 4344 64 +     16596 ACTTCCACTATGACCATTAGCCATTATATGATTTATCTCAACGCTGGCAGAAACAAACCGAGCA
+i danRer4.chrM            C 0 C 0
+
+a score=1445299.000000
+s mm8.chrM                     3338 294 +     16299 CCCTTCGACCTGACAGAAGGAGAATCAGAATTAGTATCAGGGTTTAACGTAGAATACGCAGCCGGCCCATTCGCGTTATTCTTTATAGCAGAGTACACTAACATTATTCTAATAAACGCCCTAACAACTATTATCTTCCTAGGACCCCTATA--CTATATCAATTTACCAGAACTCTACTCA-------ACTAACTTCATAATAGAAGCTCTACTACTATCATCAACATTCCTATGGATCCGAGCATCTTATCCACGCTTCCGTTACGATCAACTTATACATCTTCTATGAAAAAACTTTCTA
+s rn4.chrM                     3316 294 +     16300 CCCTTCGACTTAACAGAAGGAGAATCAGAATTAGTCTCAGGCTTTAACGTCGAATACGCCGCAGGACCATTCGCCCTATTCTTCATAGCCGAGTACACCAACATTATTCTAATAAACGCCCTAACATCAATTGTATTCCTAGGCCCCTTATA--TCATATCAATTACCCTGAATTATACTCA-------ACCAGCTTCATAACAGAAACACTACTTCTATCCACAACTTTCCTATGGATTCGAGCATCCTACCCCCGTTTTCGATATGACCAACTAATGCACCTCCTATGAAAAAATTTCCTC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      3485 294 +     20791 CTCATTGACTTAACCGAAGGTGAATCAGAGCTCGTCTCCGGCTTCAATGTGGAGTACGCAGGAGGCCCCTTTGCTCTTTTCTTTTTAGCTGAATATACTAATATTATCCTTATAAATGCCCTTACAGCCATCCTATTCCTAGGCTCATTTCA--CAGCCACACTAACCCAGAAATATTTACA-------GTCAACTTTGCCACAAAGACTCTCCTACTCACAATAACATTTCTATGGATTCGAGCATCCTATCCCCGATTTCGCTATGACCAGCTAATACACCTCTTGTGAAAAAGTTTTCTA
+i oryCun1.scaffold_140182 M 1789 C 0
+s panTro2.chrM                 3312 294 +     16554 CCCTTCGACCTTACTGAAGGAGAATCTGAACTAGTCTCAGGCTTTAATATCGAGTATGCCGCAGGCCCCTTTGCCCTATTTTTCATAGCCGAATACATAAACATTATTATAATAAACACCCTCACTGCTACAATCTTCCTAGGAGCAACATA--CAATACTCACTCCCCTGAACTCTACACG-------ACATATTTTGTCACCAAAGCTCTACTTCTAACCTCCCTGTTCCTATGAATTCGAACAGCATATCCCCGATTTCGCTACGACCAGCTCATACACCTCCTATGAAAAAACTTCCTA
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    3895 294 +     16571 CCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATTATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATA--TGACGCACTCTCCCCTGAACTCTACACA-------ACATATTTTGTCACCAAGACCCTACTTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAACTTCCTA
+i hg18.chrM               C 0 C 0
+s rheMac2.chr5             34439352 294 - 182086969 CCTTTTGATCTATCAGAAGGAGAGTCAGAGTTAGTCTCAGGCTTCAACATCGAATACGCCACAGGCTCATTTGTCCTCTTCTTTATAGCAGAATATATGAATATTATCATAATAAATGCCCTAACTACTGCTATTTTCATAGGAGTACTACA--CACTATATACTCACCAGAATTCTATACT-------ACAAATTTCATTACCAAGACCCTTCTTTTAACCACTCTATTTTTATGAATTTGAATGGCATACCCTCAATTCCACTGTGACCAACTCATACATCTTTTATGAAAAAACTTCCTA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 3688 294 +     16338 CCATTTGATTTAACTGAAGGAGAATCAGAGCTAGTCTCGGGCTTCAACGTAGAATATGCAGCAGGACCATTTGCCCTCTTCTTCATAGCAGAGTACGCAAATATTATCATAATAAATATCTTTACAGCAATTTTATTCCTAGGAACATCCCA--CAATCCACACATACCAGAACTCTACACA-------ATCAATTTTACCATTAAATCCCTACTGCTCACAATATCCTTCCTATGAATCCGAGCATCCTACCCTCGATTTCGCTATGACCAACTAATACACTTACTATGAAAAAATTTTCTA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 3334 294 +     16727 CCCTTCGACTTAACTGAAGGAGAATCCGAACTAGTCTCTGGATTTAACGTAGAGTATGCAGCAGGTCCTTTCGCCCTATTCTTTCTAGCAGAGTACGCAAATATTATTATAATAAACATCCTCACAACAATTCTGTTCTTCGGCGCATTCCA--CAACCCATTCATACCAGAACTCTACTCT-------ATTAACTTCACTATAAAAACCCTCTTATTAACCATCTGCTTCCTATGAATTCGAGCATCATACCCTCGATTCCGCTACGATCAGTTAATACACTTATTATGAAAAAATTTTCTA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       7152 294 -     16977 CCATTCGACCTAACAGAAGGTGAATCAGAATTAGTGTCCGGATTCAACGTCGAATATGCAGCAGGGCCATTTGCCCTATTCTTTTTAGCTGAGTATGCCAACATCATTATAATAAATGCACTAACAGCCATTTTATTTTTTGGGGCCATACA--CAACCCAATATTCCCAGAACTACACACC-------CTAAACTTAATCACAAAAACCCTGATTCTTACTATAATATTTCTATGAGTACGCGCATCCTATCCACGATTCCGCTATGACCAACTAATACACCTCCTATGAAAAAGCTTTCTC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       6335 294 +     16266 CCATTTGATTTAACCGAAGGAGAATCAGAATTAGTTTCTGGCTTCAATGTCGAATACTCAGCTGGCCCTTTCGCCCTATTTTTTATAGCTGAATACGCTAACATCATCATAATAAACGCTCTTACTGTGATTCTATTTATAGGAACCTCTTA--TGACCCCCAAATACCAGAAATTAGTACC-------ATTAACTTTGTCATAAAAACTATTATCCTAACCATCTGCTTTCTATGAGTACGAGCATCTTACCCACGATTCCGATACGACCAACTAATACATCTCCTCTGAAAAAATTTTCTC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      2729 294 +     18297 CCATTTGACTTAACAGAAGGGGAATCAGAATTAGTTTCAGGCTTTAACGTTGAATATGCAGCAGGGCCCTTCGCTCTATTTTTCCTTGCAGAATACGCTAACATCATTATAATGAATGCTCTAACCACTATTCTATTTATAGGAGCATTTCA--TAATATATCTGTTACAGAAATTTACACG-------TTAAATTTTATTACAAAAACACTACTTCTCACTATACTATTTTTATGAGTTCGAGCATCATACCCTCGATTTCGATATGATCAACTAATACATTTATTATGAAAAAACTTCTTA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117154763 294 + 174229318 CCTTTTGACCTGACAGAAGGAGAGTCGGAATTAGTCTCAGGTTTTAATGTGGAATATGCCGCTGGACCCTTCGCTATATTCTTTTTAGCAGAGTACGCCAACATTATAGCAATAAATGCCATAACAACAATTCTCTTCCTGGGGCCCCCCCT--AAACCACAACCACACTTATACCTGCACC-------ATTAGCTTCATATTCAAAACAATATTACTAACATCAGCCTTCCTATGAGTACGAGCATCATACCCTCGCTTTCGATATGATCAATTAATGTACTTATTATGAAAAAGCTTCCTC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 4658 294 +     16775 CCATTTGACCTAACAGAAGGAGAGTCAGAGCTAGTCTCAGGATTTAATGTAGAATATGCCGCCGGACCATTCGCCATATTCTTCTTAGCCGAATACGCCAACATTATACTAATAAACACACTAACCACCGTCCTATTCCTGAACCCAAGCTT--CCTAAATCTCCCACCAGAATTATTTCCC-------ATTGCACTCGCTACAAAAACCCTCCTCCTTTCATCCTCATTTCTATGAATCCGGGCCTCATATCCACGGTTCCGCTATGACCAACTAATACATCTTCTATGAAAAAACTTCCTC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_8452       11814 303 +     23823 CCGTTCGACGTGGTCGAAGGCGAGGCCGAGATCGTGGCTGGTCATATGGTCGAGTATTCGGGCATGGGCTTCGCCATCTTCTTCCTGGCTGAATACGCCGCGATGTGGCTGGTTTCCATCCTGGCCGTGCTGATGTTCCTGGGCGGCTGGCTGCCACCGTTCGCGGCCCTGTCCTTCATCCCGGGCTGGATCTGGCTGGCGGCCAAGACCTTCCTGGTGGTCTCCATGTTCATCTGGATCCGTGCCACCTTCCCGCGCTACCGCTATGACCAGATCATGCGCCTGGGCTGGAAGATCTTCATC
+i xenTro2.scaffold_8452   C 0 I 1675
+s tetNig1.chrUn_random    103513197 294 + 171761319 CCATTTGATCTAACTGAAGGCGAGTCAGAACTAGTTTCTGGTTTTAACGTAGAATACGCAGGAGGCCCTTTCGCCCTATTCTTCCTCGCAGAATACGCCAACATCCTATTTATAAACACCCTTTCCGCCAGCCTCTTCCTAGGAGCCTCCCA--TATCCCAATACTTCCAGAACTGACCACA-------ATAAACCTAATAACCAAAGCAGCCGTCCTCTCACTCGTCTTCCTATGGGTACGAGCCTCCTACCCACGATTTCGCTATGACCAACTAATACACCTTATCTGAAAAAACTTCTTA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 4408 294 +     16596 CCGTTCGATCTTACAGAGGGGGAATCAGAACTAGTCTCAGGCTTCAATGTAGAGTATGCAGCAGGACCATTTGCCTTATTCTTTTTGGCTGAGTACTCAAATATTTTACTAATAAACACCCACTCAACAGTACTATTTTTAGGAGCATCGTT--TACCCCAGATGCACCTGAGCTAATAACA-------ATCAGTATTGCAACCAAAACTGCAATACTATCTATTTTGTTTCTCTGAATACGAGCATCATACCCACGATTCCGATACGACCAACTTATGCATCTTATCTGGAAAAACTTTCTT
+i danRer4.chrM            C 0 C 0
+
+a score=692934.000000
+s mm8.chrM                     3632 140 +     16299 CCCCTAACACTAGCATTATGTATGTGACATATTTCTTTACCAATTTTTACAGCGGGAGTACCACCATACATATA------GAAATATGTCTGA--T---AA--AAGAATTACTTTGATAGAGTAAATTATAGAGG-TTCA--AGCCCTCTTAT-TTc-
+s rn4.chrM                     3610 140 +     16300 CCACTAACACTAGCATTCTGCATATGATACATTTCCCTGCCAATTTTCCTAGCAGGAATTCCACCCTACACATA------GAAATATGTCTGA--C---AA--AAGAGTTACTTTGATAGAGTAAATAATAGAGG-TTTA--AATCCTCTTAT-TTc-
+i rn4.chrM                C 0 I 71
+s oryCun1.scaffold_140182      3779 141 +     20791 CCCCTCACATTAGCCCTGTGCATATGACATATCTCAATACCTATCATACTTTCAAGTATCCCTCCTCAGATATA------GAAATATGTCTGA--T---AA--AAGAGTTACTTTGATAGAGTAAATAATAGAGGATCTT--AGCCCTCTTAT-TTc-
+i oryCun1.scaffold_140182 C 0 I 77
+s panTro2.chrM                 3606 141 +     16554 CCACTCACCCTAGCATCACTCATGTGATATATCTCCATACCCACTACAATCTCCAGCATCCCCCCTCAAACCTAA-----GAAATATGTCTGA--T---AA--AAGAATTACTTTGATAGAGTAAATAATAGGAG-TTCA--AATCCCCTTAT-TTc-
+i panTro2.chrM            C 0 I 70
+s hg18.chrM                    4189 141 +     16571 CCACTCACCCTAGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTCCCCCTCAAACCTAA-----GAAATATGTCTGA--T---AA--AAGAGTTACTTTGATAGAGTAAATAATAGGAG-CTTA--AACCCCCTTAT-TTc-
+i hg18.chrM               C 0 I 70
+s rheMac2.chr5             34439646 136 - 182086969 CCACTTACACTAGCATTTTGC-----ATATATCTCAATGCTTGTCCTAATTTCCACCATCCCACCCTAAACATAG-----GCAATATGTCAGA--C---AA--AAGAATTACTTTGATAGAGTAAACAATAGAGA-TTAA--AATCCTCTGAT-TTc-
+i rheMac2.chr5            C 0 I 71
+s bosTau2.chrM                 3982 141 +     16338 CCTCTGACACTAGCCCTGTGCATGTGACACGTATCCCTACCCATCCTTACATCAGGCATCCCACCACAAACATAA-----GAAATATGTCTGA--C---AA--AAGAGTTACTTTGATAGAGTAAATAATAGAGG-TTCA--AACCCTCTTAT-TTc-
+i bosTau2.chrM            C 0 I 71
+s canFam2.chrM                 3628 141 +     16727 CCCTTAACTTTAGCCCTATGCATATGACATGTTGCCTTACCCATTATCACCGCAAGTATCCCACCCCAAACATAA-----GAAATATGTCTGA--T---AA--AAGAGTTACTTTGATAGAGTAAATAATAGAGG-TTTA--AATCCTCTTAT-TTc-
+i canFam2.chrM            C 0 I 72
+s dasNov1.scaffold_23239       7446 140 -     16977 CCACTTACATTAGCATTATGTATACTCCACGTATCAGCCCCAGCAACATTCGCAGGCGTACCCCCACACATATA------GGAATATGTCTGA--T---AA--AAGAATTACTTTGATAGAGTAAATAATAGAGG-TTTG--AACCCTCTTAT-TCc-
+i dasNov1.scaffold_23239  C 0 I 72
+s loxAfr1.scaffold_36650       6629 140 +     16266 CCACTAACTCTAGCTCTATGCATATGACACATCTCAGTCCTAATCTCACTAGCATGTATTCCACCACAAGCATA------GAAATATGTCTGA--C---AA--AAGAATTACTTTGATAGAGTAAATTATAGAGG-TCTG--AACCCTCTTAT-TTc-
+i loxAfr1.scaffold_36650  C 0 I 71
+s echTel1.scaffold_181343      3023 140 +     18297 CCAATAACCTTAGCCCTATGCATATGATACATCTCCATTCCTGTCATATTAGCTAGTATTCCCCCTCAAATATA------GAAACATGTCTGA--T---AA--AAGAGTTACTTTGATGGAGTAAATAATAGAGG-TTTA--AATCCCCTTGT-TTc-
+i echTel1.scaffold_181343 C 0 I 67
+s monDom4.chrUn           117155057 141 + 174229318 CCAATTACCCTAGCACTATGTCTAATATTTATCTCTATTCCAATTGCACTATCAAGTATCCCACCACAAATATAA-----GAAATATGTCTGA--C---AA--AAGAATTATCTTGATAGGATAAATAATAGGGG-TTCA--AACCCCCTTAT-TTc-
+i monDom4.chrUn           C 0 I 70
+s galGal2.chrM                 4952 142 +     16775 CCCCTAACCCTAGCCTTATGCCTCTGACATACCAGCATACCAATCAGCTACGCCGGCCTCCCCCC---AATCTAAG----GAAGCGTGCCTGAACA---AA--AAGGATCACTATGATAAAGTGAAC-ATAGAGG-TATAACAACCCTCTCAC-TTC-
+i galGal2.chrM            C 0 I 75
+s xenTro2.scaffold_18215       2547 143 +      3330 CCAATCACACTAGCAATAACACTATGACACATCTCCTTACCAATCTCTCTATCAGGCCTACCACCTCAGATATAG-----GAAACGTGCCCGA--A---AGTTAGGGATCACTNTGATAGAGTGAAACATAGGGG-TTCA--AACCCCCTCGT-CTC-
+i xenTro2.scaffold_18215  M 690 I 2
+s tetNig1.chrUn_random    103513491 148 + 171761319 CCCCTAACATTAGCACTTGTTATCTGACACCTGGCACTCCCAATCACATTTGCAGGCCTCCCGCCTCAAATATAGC-CAGGAGCTGTGCCTGA--AT--TA--AAGGGCCACTTTGATAGAGTGAACCATGGGGG-TTAA--ATTCCCCCCAGCTCCT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 4702 150 +     16596 CCAATCACATTAGTTCTAGTACTATGACATATCGCCCTACCAATCGCACTAGCTGGTCTACCCCCACAAACATAACTCAAGAACCGTGCCCGA--ATGCTA--AGGGGTCACTTTGATGGAGTGAACCATAGGGG-TTAA--AATCCCCTCGG-TTCT
+i danRer4.chrM            C 0 C 0
+
+a score=14911.000000
+s mm8.chrM                     3772 70 +     16299 taggacaataggaattgaacctacacttaag-----------aattcaaaattctccgtgctacctaaacaccttatccta
+s xenTro2.scaffold_18215       2692 70 +      3330 TAGAAAGACAGGAATTGAACCTGCACCTGAG-----------AGATCAAAACCCTCCGTACTCCCACTATACCACTCTCTA
+i xenTro2.scaffold_18215  I 2 C 0
+s tetNig1.chrUn_random    103513639 70 + 171761319 TAGAAAGAAGGGACTCGAACCCAACCCAGAGAGATCAAAACT-----------CTCAGTGCTTCCACTACACCACTTTCTA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 4852 70 +     16596 TAGAAAGAAGGGGGTCGAACCCATGCCCAAG-----------AGATCAAAACTCTTAGTGCTTCCACTACACCACTTTCTA
+i danRer4.chrM            C 0 C 0
+e monDom4.chrUn           117155198 70 + 174229318 I
+e echTel1.scaffold_181343      3163 67 +     18297 I
+e loxAfr1.scaffold_36650       6769 71 +     16266 I
+e dasNov1.scaffold_23239       7586 72 -     16977 I
+e canFam2.chrM                 3769 72 +     16727 I
+e bosTau2.chrM                 4123 71 +     16338 I
+e rheMac2.chr5             34439782 71 - 182086969 I
+e panTro2.chrM                 3747 70 +     16554 I
+e hg18.chrM                    4330 70 +     16571 I
+e rn4.chrM                     3750 71 +     16300 I
+e oryCun1.scaffold_140182      3920 77 +     20791 I
+e galGal2.chrM                 5094 75 +     16775 I
+
+a score=791168.000000
+s mm8.chrM                     3842 168 +     16299 ATAG--TAAGGTCAGCT-AA-T-TAAGCTATCGGGCCCATACCCCGAAAACGTTGGTTTAAATCCTTCCCGTACTAATAAATCCTATCACCCTTGCCATCATCTACTTCA--CAATCTTCTTAGGTCCTGTAATCACAATATCCAGCACCAACCTAATACTAATATGAGTAGGCC
+s rn4.chrM                     3821 167 +     16300 ATAG--TAAGGTCAGCT-AA-C-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTT-AAACCCTTCCCGTACTAATAAATCCAATTACCCTAACCATTATTTACTTAA--CCACCTTTAAAGGCCGCCTAATCACGACACTTAGCACCAACTTACCACCAATATGAGTAGGAT
+i rn4.chrM                I 71 C 0
+s oryCun1.scaffold_140182      3997 168 +     20791 TAAG--TAAGGTCAGCT-AA-A-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTATATCCTTCCCGTACTAATTAACCCCCTAACTCTTATTATTATTATATTTA--CTCTATTTATAGGCACGATAATCACAGTATTTAGCTCCCACTGACTAACTATATGAATCGGAT
+i oryCun1.scaffold_140182 I 77 C 0
+s hg18.chrM                    4400 167 +     16571 aAAG--TAAGGTCAGCT-AA-A-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTT-ATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTACTCTA--CCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATTTTTTACCTGAGTAGGCC
+i hg18.chrM               I 70 C 0
+s panTro2.chrM                 3817 167 +     16554 aAAG--TAAGGTCAGCT-AA-A-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTT-ACACCCTTCCCGTACTAATTAATCCCCTAGCCCAACCCATCATCTACTCTA--CCATCCTTACAGGCACGCTCATTACAGCGCTAAGCTCACACTGATTTTTCACCTGAGTAGGCC
+i panTro2.chrM            I 70 C 0
+s rheMac2.chr5             34439853 160 - 182086969 -GAT--TAAGGTCAGCT-AA-A-TAAGCTATTGGGCCCATACACCGAAAATGTTGGTT-ATACCCTTCCCGTAC--------CCCTTAGCTCAACTTATTATTTCCCTCAGCCCATTTTCACAGGAACTCATATCACAATGCTATGCTCACACTGATTTCTAATCTGAACAGGGC
+i rheMac2.chr5            I 71 C 0
+s bosTau2.chrM                 4194 168 +     16338 TTAG--TAAGGTCAGCT-AA-T-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTATATCCTTCCCGTACTAATAAACCCAATTATCTTTATTATTATTCTACTAA--CCATTATACTAGGAACTATTATTGTCATAATCAGTTCTCACTGACTACTTGTCTGAATCGGGT
+i bosTau2.chrM            I 71 C 0
+s canFam2.chrM                 3841 169 +     16727 aCAG--TAAGGTCAGCTAAA-T-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTATACCCTTCCCGTACTAATAAAACCCCCTATTCTCATTATCATCATAGCAA--CTATCATGACAGGAACCATAATCGTCATACTAAGCTCGCACTGATTACTGATCTGAATTGGAT
+i canFam2.chrM            I 72 C 0
+s dasNov1.scaffold_23239       7658 166 -     16977 --AG--TAAGGTCAGCT-AA-C-AAAGCTATCGGGCCCATACCCCGAAAATGTAGGCTCATACCCTTCCCGTACTAATAAATCCCttaatttttattattattatattta--CCTTAATCTTAGGAACAGTAATTACCATAATTAGCTCCCATTGATTATTAATCTGGATAGGCC
+i dasNov1.scaffold_23239  I 72 C 0
+s loxAfr1.scaffold_36650       6840 169 +     16266 CTAG--TAAGGTCAGCT-AA-ATTAAGCTATCGGGCCCATACCCCGAAAATGTCGGATCACACCCCTCCCATACTAATAAACCCACTAGCTCTTAGCCTAATCCTAACAA--CACTACTCGCAGGAACACTGATTACCATAATAAGCTCCCATTGATTGACAGCCTGAATGGGAC
+i loxAfr1.scaffold_36650  I 71 C 0
+s echTel1.scaffold_181343      3230 167 +     18297 ctaG--TAAGGTCAGCT-AA-A-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTAT-TCCTTCCCATACTAATTAACCCATTAGCTTCCATTATTATGTCTAGTA--CTCTAATTTCAGGCACTCTAATTACTTTAATCAGCTCTCACTGACTTATAGCATGAATAGGTC
+i echTel1.scaffold_181343 I 67 M 371
+s monDom4.chrUn           117155268 165 + 174229318 ---G--TAAGGTCAGCT-AA-A-TAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTTGCACCCTTCCCATACTAATGTCCCCCTATGTATTAACCATTGTTTCGCTCA--GCTTATTAACAGGAACTTCAGTAACTCTAATTAGCAACCATTGGTTAACTGCCTGAATAGGCC
+i monDom4.chrUn           I 70 C 0
+s galGal2.chrM                 5169 168 +     16775 CTAG--TAAGGTCAGCT-AA-C-TAAGCTATCGGGCCCATACCCCGAAAATGATGGTTTAACCCCTTCCCCTACTAATGAACCCCCATGCAAAACTAATCTGCACAGTAA--GCCTCATCATGGGAACCAGCATCACAATCTCCAGCAACCATTGAATCTTAGCCTGAACAGGCT
+i galGal2.chrM            I 75 C 0
+s xenTro2.scaffold_18215       2762 165 +      3330 ---G--TAAAGTCAGCT-AA-A-AAAGCTTTTGGGCCCATACCCCAAACATGTTGGTTAAACTCCTTCCTTTACTAATGAACCCTATCGCACTATCAATAATCCTCTCAA--GCCTAGCATTAGGCACTATCCTCACTGTATCAAGCAATCATTGATTCCTAGCCTGAATAGGCC
+i xenTro2.scaffold_18215  C 0 C 0
+s tetNig1.chrUn_random    103513709 166 + 171761319 ---G--TAAAGTCAGCT-AAGT-TAAGCTTTTAGGCCCATACCCTAAAGATGTAGGTTAAAATCCTTCCTTTACTAATGAGCCCTTACATTACAGCCTCCTTGCTATTTG--GCCTACTCCTAGGCACAACAATCACCGCAACCAGCTCCCACTGACTAATTGCCTGAATAGGCC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 4922 167 +     16596 ---GGATGAGGTCAGCT-AA-T-TAAGCTACCGGGCCCATACCCCGAACATGATGGTTAAAGTCCCTCCTTCATCAATGAACCCTTATGTCCTTATAATTTTAATATCCA--GCCTAGGTCTAGGAACCACATTAACTTTTTCTAGCTCACACTGAATTTTAGCCTGAATAGGAT
+i danRer4.chrM            C 0 C 0
+
+a score=1213783.000000
+s mm8.chrM                     4010 399 +     16299 TGGAATTCAGCCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGCAACAAAATACTTCGTCACACAAGCAACAGCCTCAATAATTATCCTCCTGGCCATCGTACTCAACTATAAACAACTAGGAACATGAAT--ATTTCAACAACAAAC-AAACGGTCTTATCCTTAAC----ATAACATTAATAGCCCTATC------CATAAAACTAGGCCTCGCCCCATTCCACTTCTGATTACCAGAAGTAACTCAAGGGATCCCACTGCACATAGGACTTATTCTTCTTACATGACAAAAAATTGCTCCCCTATCAATTTTAATTCAAATTTACCCGCTACTCAACTCTA--CTATCATTTT----------AATA-CTAGCAATTACTTCTATTTTCATAGGGG
+s rn4.chrM                     3988 399 +     16300 TGGAAATAAGCCTTTTAGCTATCATCCCACTTCTAGCCAACAAAAAAAGCCCACGATCAACTGAAGCAGCAACAAAATATTTTCTAACCCAAGCTACAGCCTCAATAATTATCCTACTAGTCATCATCCTCAACTACAAACAATCAGGAATATGAAC--CCTTCAACAACAAAC-CAATAACATACTACTCAAC----ATAATACTCATTTCACTGGC------CATAAAACTTGGACTAGCCCCATTCCACTACTGACTACCCGAAGTCACCCAAGGAATTCCCCTACACATTGGATTAATCTTACTAACATGACAAAAAATTGCTCCACTATCAATTCTATACCAATTTTATCAACTCCTAAACCCAA--CTATCACCAC----------CATT-CTCGCAATTTCATCAGTCTTTGTTGGCG
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      4165 399 +     20791 TAGAAATAAACATACTAGCAATTATCCCTATTCTAATCAACAAAGCCACCCCACGATCAACAGAAGCTGCAACCAAATATTTTCTAACACAAGCCACAGCATCTATAATCTTAATAATAGCTATTACACTTAATATCCTTGACTCCGGACAATGAAC--CCT-----AATTAAT-CCACAGAATCA-ACTTACT----CCAGTCCTAATTACACTGGCACTAATCATTAAACTAGGAATAGCCCCCTTCCACTTCTGAGTACCAGAGGTCACCCAAGGAGTTCCCCTAAAATCAGGATTAATCCTTCTCACGTGACAAAAATTAGCCCCCCTATCCATCCTTTACCAAATCTCCCCATCAATTAATCCAA--CTATAATAAT----------ATCA-GTAGCCATTCTATCAATTATAGTTGGCG
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    4567 399 +     16571 TAGAAATAAACATGCTAGCTTTTATTCCAGTTCTAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTCCTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAACAATATACTCTCCGGACAATGAAC--CAT-----AACCAATACTACCAATCAATACTCATCATTAATAATCATAATGGCTATAGC------AATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACCAAATCTCTCCCTCACTAAACGTAA--GCCTTCTCCT----------CACT-CTCTCAATCTTATCCATCATAGCAGGCA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 3984 399 +     16554 TAGAAATAAATATACTAGCTTTTATCCCAATCCTAACCAAAAAAATAAGCCCCCGCTCCACAGAAGCCGCCATCAAATACTTTCTCACACAAGCAACTGCGTCCATAATTCTCCTGATAGCTATCCTCTCCAACAGCATACTCTCCGGACAATGAAC--CAT-----AACCAATACTACCAATCAATACTCATCATTAATAATTATAATAGCAATGGC------AATAAAACTAGGAATAGCCCCCTTTCACTTTTGAGTTCCAGAAGTTACCCAAGGCACCCCCCTAATATCCGGCCTACTCCTCCTCACATGACAAAAATTAGCCCCTATTTCAATTATATACCAAATCTCCTCATCACTGAACGTAA--ACCTTCTCCT----------CACC-CTTTCAATCTTGTCCATTATAGCAGGCA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34440013 395 - 182086969 TAGAAATAAACATACTAGCACTTACCCTAATCTTAATTAAAAAAATAAATCCCCGCTCTACAGAAGCAGCCACCAAATATTTCCTTACACAAGCAACCATATCTATAATTCTCATGACAGGTATCCTTTCCAATAACCTGTTCTCCAGACAATGAAA--AAT-----AATAAACACTATCAATCAATTCTTATCCTTAATAATAATAGTGGCCCTAGT------AATAAAACTAGGAATATTCCCCTTTCACTTCTGAGTCTCAGTGATAACCCAAGGAATCTCTTTAATGTCTGGTATACTTCTCCTCACATGACAAAAAGTAGCTCTTATCTCTATTATGTTTCAAAGTTTTTCATCAACAAACAGGA--ACATCCTCCT----------AACA-----CAATCCTATCCATTATAGTGGGTG
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 4362 399 +     16338 TTGAAATAAATATACTCGCCATCATCCCCATCATAATAAAAAATCACAACCCACGAGCTACAGAAGCATCAACTAAATATTTTTTGACTCAATCAACAGCCTCAATACTACTAATAATAGCCGTCATCATTAACCTAATATTCTCAGGCCAATGAAC--CGT-----AATAAAACTATTTAACCCAATAGCCTCAATACTTATAACGATAGCCCTAGC------TATAAAACTAGGAATAGCCCCATTTCACTTCTGAGTCCCAGAAGTAACACAGGGCATCCCCCTATCCTCAGGCCTTATCCTACTGACATGACAAAAACTAGCACCTATATCTGTACTTTACCAAATCTTCCCATCAATTAACCTAA--ACTTAATTCT----------AACC-CTATCAGTTTTATCAATCCTAATTGGAG
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 4010 399 +     16727 TCGAAATAAACATGCTAGCCATCATCCCTATTCTCATAAAAAAGTACAATCCACGAGCCATAGAGGCCTCTACAAAATATTTTCTTACACAAGCTACAGCCTCAATATTACTAATAATAGGAGTCACTATCAACCTCCTTTACTCCGGCCAATGGGT--AAT-----CTCAAAAATCTCAAACCCCATCGCATCCATCATGATAACCACTGCCCTAAC------AATAAAACTAGGCCTATCTCCATTCCACTTCTGAGTTCCCGAAGTAACACAGGGAATTACGCTCATATCAGGAATAATCCTACTAACATGACAAAAAATCGCACCTATATCCATCCTATATCAAATCTCTCCATCAATTAACACTA--ACCTTCTTAT----------ACTA-ATAGCCCTTACATCCGTTCTAGTAGGAG
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       7824 399 -     16977 TAGAAATAAACATATTCTCAATAATCCCCATTATCATAATAAAATCACACCCTCGATCAACAGAAGCCGCCACCAAATATTTCATGACACAAGCAACAGCATCTATACTTCTAATAATAGGCGTAATCATTAACTTATACTACTCAGGACAATGAAC--AAT-----TATAAATTCACTCAACCCAGTTACATCATATATAATAACCATCGCACTTGC------CATAAAACTAGGACTAGCCCCATTCCACTTCTGAGTGCCAGAGGTAACGCAAGGTACCCAACTAACATCAGGAATAATTCTTCTCACATGACAAAAACTAGCCCCAATAACAATCCTCTATCAAATCCACTCATCCCTAAACCTAA--ATCTAATACT----------AACC-CTAGCTATCCTTTCAATCCTAATCGGGG
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       7009 399 +     16266 TAGAAATGAACATACTTACTATAATTCCCATTCTAATAAAGACAACCAATCCACGATCCACAGAAGCCGCCACAAAGTACTTTATAACCCAAGCCATAGCATCCATAATACTTATAATGGCTTTAACAATTAACCTAATATACTCAGGACAATGATC--AAT-----TACAAAAATAACCAACCCTGTAGCATCAAACATAGCATTAATAGCTTTAAT------AACCAAACTAGGCTCAGCCCCATTCCACTTCTGAGTTCCAGAAGTAACGCAAGGAGTCGAACTTACACCAGGGATGATCTTGTTAACCTGACAAAAATTAGCACCATTATCCCTACTATATCAAATGGCCACCTACACTAACACTA--ACCTAATCTA----------CCTT-TCTGGTCTACTTTCAATCCTAATTGGGG
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_49882       4260 392 -      7170 TTGAAATGAATATATTTGCTATTATTCCTATGATCATAAAAAATAACTCCCCCCGAGCAATTGAGGCTGCAATAAAATATTTCCTCATTCAAGCATCCGCCTCCATACTACTACTTATAGCAGCCTCCCTTAATTTTATATACTCAGGTCAATGAAC--GTT-----AACAGAAATAAATGTCTCAATAGCATCCCTAATTATATTAATTGCTATACT------GATAAAATTAGGTATGGCACCATTTCACTTCTGAGTCCCAGAAGTTACTCAAGGTACTGTTTTATTGACCAGCCTCATTATTTTAACTTGACAAAAGCTAGCCCCCCTAGCTATTCTTTTCCAAATCGCCCCCTCAATTAATGTAG--ATATTATTCT----------TACA-ACAGCTATCCTATCAATTCTA-------
+i echTel1.scaffold_49882  I 1469 n 67
+s monDom4.chrUn           117155433 399 + 174229318 TAGAAATTAATACACTGGCCATTATTCCACTAATAACTTACCCCCACCACACACGAAACACAGAATCAGCCATCAAATATTTCATAACTCAAGCTACAGCTTCAATACTCCTCATATTCTCTATTATTTATAATGCATCCTTCACTAACCAATGGAC--CAT-----TAACCACTCACCCAACCAATGAGCCTCCTTACTAATAACCCTAGCCCTAGC------AATAAAACTAGGACTAGCCCCCTTTCACTTTTGAGTGCCAGAAGTTACACAAGGAATCCCACTATTATCTGGTATAATACTCCTAACATGACAAAAAATTGCTCCCATCTCAATCATATACCAAATTTCACCCTCACTTAATATAC--AAGTACTAAT----------AACC-TTAAGCATTTTATCCACACTATTAGGAG
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 5337 399 +     16775 TAGAGATCAACACCTTAGCCATCATCCCCCTCATCTCCAAGTCACACCACCCCCGAGCGATTGAAGCCACTATCAAATATTTCCTCACCCAATCAACTGCATCAGCCCTAATCCTCTTCTCGAGCATAACCAACGCCTGATCCACCGGACAATGAGA--CAT-----TACACAACTAAACCACCCGACATCATGCCTAATATTAACAATAGCAATCGC------AATCAAATTAGGACTAGTCCCATTCCACTTCTGATTCCCAGAAGTACTCCAAGGCTCCTCCCTAATCACTGCCCTACTACTCTCCACCCTAATAAAACTCCCCCCAATCACACTCCTCCTCCTAACATCACAGTCTCTTAATACCA--CCTTACTCAC----------CCTC-CTAGCAATCTCCTCCACCCTAATCGGAG
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18215       2927 399 +      3330 TAGAAATCAATACCCTAGCTATCATCCCACTGATAGCCCAAAACCACCACCCACGAGCAGTTGAAGCCTCAACCAAATACTTTCTAACTCAAGCTGCAGCCTCAGCTCTTCTCTTATTCTCAGCTTTAAATAATGCTTGGTTCACTGGAGAATGGTC--AAT-----TATAAACTTGACCAACTCAATCTCATGCACCACCATAACCATCGCCATCTG------CATGAAACTCGGACTAGCACCATTCCACTTCTGACTCCCAGAGGTCCTCCAAGGACTTAATTTAACAACAGGTCTTATCCTATCTACCTGACAAAAACTTGCCCCAATGGCCATCCTCTACCAGATCTCTCCATCAATAAACACCT--CCCTTCTTCT----------TTTA-ATTGGACTAACCTCAACATTAATCGGGG
+i xenTro2.scaffold_18215  C 0 n 0
+s tetNig1.chrUn_random    103513875 396 + 171761319 TAGAAATCAACACCCTCGCCATTATTCCCCTGATAGCCCAACACCACCACCCACGAGCAGTAGAGGCCACAACCAAATATTTCCTCACACAAGCCACCGCAGCAGCCATACTCCTATTCGCAAGCACAACCAACGCATGACTGACCGGACAGTGAGAACTGC-----AACAA--ATAACACACCCCCTTCCCTCCACATTAATTATTCTTGCCCTGGC------CCTAAAAATTGGACTAGCCCCACTACACACTTGACTCCCAGAAGTCCTCCAAGGATTAGACCTAACAACCGGACTCGTCCTCTCCACATGACAAAAGCTCGCACCCTTTGCCCTCCTCCTCCAACT---TCAACCAAACAACCCAA--CACTGCTCGT----------CATC-CTAGGAGTGCTATCAACACTAATCGGAG
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 5089 399 +     16596 TAGAAATTAATACTTTAGCAATTGTCCCTCTAATAGCACAACAACACCACCCACGGGCAGTAGAAGCCACCACAAAATACTTCCTTATTCAAGCTGCTGCCGCAGCAATAATTCTATTCACAAGTACAACAAATGCCTGAATTTCAGGACAATGGGA--TGT-----TACAGGTATACCAGGCCCAGCCACCAGTACAGCAATAATGTTTGCATTGGC------TCTCAAAATCGGTCTAGCACCAATACATTTTTGATTACCAGAAGTTCTTCAAGGATTAGATCTGTTGACAGGACTAATTTTGTCAACCTGACAAAAACTTGCCCCAATAGCATT--------AA-----TTATCCAAACGACCCAAACCACTGACCCTCTTATTCTTACATCACTAGGAATTGCTTCCTCTCTCATTGGAG
+i danRer4.chrM            C 0 C 0
+
+a score=552799.000000
+s mm8.chrM                     4409 135 +     16299 CATGAGGAGGACTTAACCAAACACAAATACGAAAAATTATAGCCTATTCATCAATTGCCCACATAGGATGAATATTAGCAATTCTTCCTTACAACCCATCCCTCACTCTACTCAACCTCATAATCTATATTATTC
+s galGal2.chrM                 5736 135 +     16775 GCTGAATGGGCCTAAACCAAACACAAACACGAAAAATCCTAGCCTTCTCATCCATCTCCCATTTAGGATGAATAATTATAATTATCTCCTATAACCCACAACTCACTATTCTCACCTTCATCCTCTACACAATTA
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117155832 135 + 174229318 GATGAGGAGGACTAAACCAAACACACCTACGAAAAATACTAGCATACTCATCAATCGCTCACATAGGGTGAATAACAATTATTATCATTATTTACCCTACACTCACTATACTAAATTTACTAATTTATTTTACTA
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      3775 135 +     18297 GCTGGGGCGGCCTAAACCAAACCCAACTACGAAAAATTATAGCGTACTCGTCAATTGCTCACATGGGCTGAATAGCTGCCGTAATAATTTATAATCCCACCCTAATATTACTTAACCTATTATTATACTTAATCT
+i echTel1.scaffold_181343 M 371 C 0
+s loxAfr1.scaffold_36650       7408 135 +     16266 GATGAGGAGGCCTAAATCAAACACAACTACGAAAAATCTTAGCCTATTCATCAATCTCCCATATAGGCTGAATACTCATTATCTTGCCCTTCAATCCCACCCTTACCCTACTAAACTTAACCATTTACATTATAC
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239       8223 135 -     16977 GATGAGGAGGACTAAACCAAACACAACTACGAAAAATTATAGCGTATTCATCCATTGCACACATAGGATGAATAACAGCAATCATTATATACAATACATCATTAATGATACTAAACCTAGTGATCTACCTAATAA
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 4409 135 +     16727 GCTGAGGCGGACTAAATCAAACTCAACTACGAAAAATCATAGCATACTCCTCCATTGCCCACATAGGCTGAATAGCCGCTATCATTACTTATAACCCTACAATAATAGTTCTAAACTTAACTTTATATATTCTAA
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 4761 135 +     16338 GCTGAGGGGGACTAAACCAAACACAACTCCGAAAAATCATAGCCTACTCATCAATCGCTCATATAGGCTGAATAACAGCAGTACTACCATATAACCCCACCATAACATTGCTAAACTTAATTATCTATATCATTA
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34440408  87 - 182086969 GTTGAGGGGAACTTAACCAAA--CAACTGCGTCAAATCCTAGCCCACTCCTC----------------------------------------------AACATTACCACCCTAAACCTGATTATTTACCTTATCT
+i rheMac2.chr5            C 0 C 0
+s panTro2.chrM                 4383 135 +     16554 GCTGAGGCGGACTAAACCAAACCCAACTACGCAAAATCCTAGCATACTCCTCAATCACCCACATAGGCTGAATAATAGCAGTCCTACCATATAACCCTAACATAACCATTCTTAATTTAACCATTTACATCATCC
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    4966 135 +     16571 GTTGAGGTGGATTAAACCAAACCCAGCTACGCAAAATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATCC
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182      4564 135 +     20791 GTTGAGGTGGACTAAACCAAACCCAACTACGAAAAATCCTAGCATACTCTTCAATCGCCCACATAGGATGAATAGCAGCTATCATCACATTTAACCCAAATACTATAGTCCTAAACCTAATTATCTATATTCTCA
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                     4387 135 +     16300 CCTGAGGAGGACTTAACCAGACCCAAACACGAAAAATCATAGCATACTCATCAATTGCCCACATAGGATGAATAACAGCAATCCTTCCATACAACCCTAACTTAACCCTCCTAAACTTAACAATTTACATCCTAC
+i rn4.chrM                C 0 C 0
+s tetNig1.chrUn_random    103514271 135 + 171761319 GCTGAGGAGGCCTAAACCAAACCCAGCTACGAAAAATCCTGGCATACTCATCCATCGCCCACCTAGGTTGAATAATCTTAATTCTGCAATTTTCACCAACCCTCACCCTCCTCACACTTATATTATACCTAATCA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 5488 135 +     16596 GGTGAAGCGGACTTAACCAAACCCAACTCCGAAAAATTCTAGCTTATTCATCAATTGCCCACATAGGGTGAATAATTATTGTTATCCAGTACGCTCCGCAACTTACTCTGATTGCTTTAGGAACATATATCTTTA
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_18215       3326   0 +      3330 I
+
+a score=401805.000000
+s mm8.chrM                     4544 198 +     16299 TTACAGCCCCTATATTCATAGCACTTATACTAAAT-AA-----CT-CTATAACCATC---AACTCAATCTCACTTCTATGAAATAAAACTCCAGCAATACTAACTATAATCTCACTGATATTACTATCCCTAGGAGGCCTTCCACCACTAA----------CAGGATTCTTACCAAAATGAATTATCATCACAGAACTTATAAAAAACAACTGTCTAA
+s rn4.chrM                     4522 198 +     16300 TTACTGTTCCAATATTCAATTACATCATAACAAAC-TC-----AG-CAACAACAATC---AACACACTCTCACTCGCATGAAATAAAACTCCCATAATCCTAACCATAGCATCCATCATCCTCCTATCACTAGGAGGACTCCCCCCTCTCA----------CAGGATTTTTACCAAAATGAGCAATTATCTCCGAGCTTCTAAAAAACAACTGCTCAA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      4699 198 +     20791 TGACAATCCCTATATTCATAATATTCATACAGCAC-TC-----AA-GTACAACCACT---CTATCACTATCACAAATGTGAAACAAAAATCCACTAATAGTATCTACTATCCTAATCACCCTAATATCCCTAGGAGGCCTGCCCCCACTCA----------CAGGTTTTATCCCTAAATGAATTATCATCCAGGAATTAACAAAAAATGGCAATATCA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    5101 198 +     16571 TAACTACTACCGCATTCCTACTACTCAACTTAAAC-TC-----CA-GCACCACGACC---CTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAA----------CCGGCTTTTTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 4518 198 +     16554 TAACTACTACCGCATTTCTGCTACTCAACTTAAAC-TC-----CA-GCACCACAACC---CTACTACTATCTCGCACCTGAAACAAGCTAACATGATTAACTCCCCTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTACCCCCACTAA----------CTGGCTTCTTACCCAAATGAGTTATCATCGAAGAATTCACAAAAAATAATAGCCTCA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34440495 198 - 182086969 TAACAACAACTGCATTTCCAGCACTCAACCTGAGT-AT-----AA-GCACCACAAAG---CTATCATTATTTCACACCTGAAACAAATGAACATGGTTGACACCTGTAATTCCACTAATTCTACTATCCTTAGGAGGTTTATCCCCATTAA----------CAGGGTTCCTGCCTTAATGAATCACCATTCAAGAATTTACAGAAAACAATAGCCTTA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 4896 198 +     16338 TAACTTCCACCATATTTACCATATTTATAGCCAAT-TC-----CA-CCACCACTACC---CTGTCATTATCACACACATGAAATAAAACACCCATTATAACCGTCCTAATTCTTGCCACTCTCCTATCCATAGGAGGACTCCCTCCCCTAT----------CTGGGTTTATACCAAAATGAATAATCATCCAAGAGATAACAAAAAATAACAGCATCA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 4544 198 +     16727 TAACACTATCTACCTTCATACTATTTATATTAAAC-TC-----AT-CCACCACGACC---CTATCTTTATCCCACATATGAAACAAATTTCCCCTAATCACTTCCATAATCTTAATCTTAATACTATCCCTAGGAGGACTACCCCCATTAT----------CTGGCTTCATCCCCAAATGAATAATTATTCAAGAATTAACGAAAAATAACATAATTA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       8358 198 -     16977 TAACAATCACAATATTTGCCCTCTTTA---TTAAC-TC-----AA-CAACAACAACTACACTATCTCTATCTCTTACATGAAACAGTACACCAATCCTAACAACAATGCTCCTAACAACCCTACTATCACTAGGAGGCCTTCCCCCACTAT----------CAGGCTTCGCACCAAAATGAATAATCATCCAAGAGATGACAAAAAACAACATACTCC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       7543 198 +     16266 TAACACTGTCCATCTTTATAATTCTAA-CAAATAC-TT-----TCACAACTTCAATA---TCATCCCTAACTCTAATATGAAACAAAACACCTGCAATAACCATTATACTTATAACTACTTTACTATCTTTAGGAGGACTACCCCCACTAT----------CGGGATTCATACCCAAATGACTTATGATTCACGAACTAACCAAAAACAACAGTATTA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      3910 198 +     18297 TCACATTTTCAGCATTCACCATCTTAATTAAATGC-TC-----TT-CAACCTCAACT---TCTATACTAACAATAACCTGAAATTCCTACCCATTAATAGTCTCTATCCTATTAATTATTCTTTTATCAATGGGAGGATTACCTCCATTAA----------CAGGTTTTGTACCTAAATGACTAATTATCTATGAACTGATTAAAAATACTAACATTG
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117155967 198 + 174229318 CAACCATTACCATATTCCTTATATTCAACCACTCA-TC-----AA-TAACCAAAATC---AACTCACTATCAACCCTATGAAACAAGTCTACCCCCATTACCATCATTATTATATTAACACTTCTATCCTTAGGGGGACTACCCCCATTAA----------CAGGTTTTATACCCAAATGATTAATTCTCCAAGAACTAATTTCATATAAAAATATAC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 5871 198 +     16775 TGACCTCAACTGTATTCCTATCCCTAGCCCAAATC-AA-----AG-TCCTAAAACTG---TCAACACTACTCATCTCATGAACTAAAACCCCAATACTAAATGCAACTGTAATACTAACCCTCCTCTCCCTAGCTGGCCTCCCACCATTAA----------CCGGCTTCATGCCAAAATGACTCATTATCCAAGAACTAACCAAACAAGAAATAACCC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_96       2673143 176 -   2855184 TCACAGGCGAGACATCCCTGGCACATATACTAAATATT-----TC-TAACAATAATT------------------ACACAATATAA------------------TATGCACCTTCCAAACTTAGTGTCCCTGGGGTGCTGCCCTCTGCTAAAGCTTTATTTAAACATTCTCATTAAGAAAAATACTTTGTATAAAACTAACTGAGGGCATATTTTTAA
+i xenTro2.scaffold_96     n 0 I 6355
+s tetNig1.chrUn_random    103514406 198 + 171761319 TAACCTCCTCCGCCTTCCTCACATT-----CATCC-TCAACAAAA-CCACAACAATC---AATGCACTAGCCACATCCTGAGCCAAAACCCCCATTCTTACATCCCTCTTACCCCTTGTTCTCCTATCCCTCGGAGGCCTCCCTCCGCTAA----------CTGGCTTCATACCAAAATGACTAATCCTACAAGAACTAACTAAACACGATCTCGCCC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 5623 198 +     16596 TAACATCCGCGGCATTCCTTACTTTAAAAGTATTA-TC-----AG-CCACAAAAATT---AACACCCTAACAACGACCTGACCGAAAAGCCCAATCCTGGCAGCAATTGCTACTTTAGTTATATTATCACTGGGAGGACTTCCCCCACTGA----------CGGGATTCATACCAAAATGATTAATCCTACAAGAGTTAACGAAACAAGACCTACCAG
+i danRer4.chrM            C 0 C 0
+
+a score=271987.000000
+s mm8.chrM                     4742 205 +     16299 TTATAGCAACACTCATAGCAATAATAGCTCTACTAAACCTATTCTTTTATACTCGCCTAATTTATTCCACTTCACTAACAATATTTCCAA---CCAACAATAACTCAAAAATAATA-ACTCACCAAACAAAAACTAAACCCAACCTA---ATATTTTCCACC--CTAGCTATCATAAGCACAATA---------ACCCTACCCCTAGC-------CCCCC-------AACTAATTAC
+s rn4.chrM                     4720 205 +     16300 CCCTATCAACACTAATAGCTATCATAGCCCTATTAAGCCTATTCTTCTATACTCGACTAATTTACTCTATATCCCTCACCACATTCCCAA---CCAACAACAACTCCAAAATAATC-TCCCACCACCAAAACCCAAAACATAATTTT---ATCCTCCCAACC--CTCACAGTATTAAGTACCCTA---------ACCCTACCGCTTTC-------CTCCC-------AACTAATCAC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      4897 219 +     20791 TTTTACCCACCGCTATAGCCATGCTTGCCCTCCTAAATCTATATTTTTATATACGCCTTATCTATTCTTCCTCACTAACTATATTCCCTA---CCACCAACAATCTAAAAATAAAA-TGACAATTTGAATCAACAAAACGCATACCC---CTCATCACTCCA--CTAATTATTTTATCAACCATA---------CTCCTCCCCCTCACACCAGCACTCTCAGTATTAAATTAGCTTT
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    5299 211 +     16571 TCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTAATCTACTCCACCTCAATCACACTACTCCCCA---TATCTAACAACGTAAAAATAAAA-TGACAGTTTGAACATACAAAACCCACCCCA---TTCCTCCCCACA--CTCATCGCCCTTACCACGCTA---------CTCCTACCTATCTC-------CCCTT-TTATACTAATAATCTT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 4716 211 +     16554 TCATCCCCACCATCATAGCCATCATCACTCTCCTTAACCTCTATTTCTACCTACGCCTAATCTACTCCACCTCAATTACACTACTTCCCA---TATCTAATAACGTAAAAATAAAA-TGACAATTCGAACATACAAAACCCACCCCC---TTCCTCCCTACA--CTCATCACCCTTACCACACTG---------CTTCTACCCATCTC-------CCCCT-TCATACTAATAATCTT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34440693 211 - 182086969 TTACCCCAATCATTACAGCCATCATAACCCTACTCAACCTGTACTTTTACATACGCCTAGTCTATTCCTTCTCAGTAATACTATTCCCCT---CATCTAACAATATGAAAATAAAA-TGACAATTTGGAAACACAAAACCCATACTA---CTTTTCCCCCAG--CTTGTCATCTCTTCTACCCTC---------CTCTTATCCATCTC-------TCCAT-TAATATTAAATATAAC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 5094 211 +     16338 TTCTACCCACTTTCATAGCAATCACAGCTCTACTAAACTTATATTTTTATATACGACTCACGTATTCTACCACACTAACAATATTTCCCT---CCACAAACAACATAAAAATAAAA-TGACAATTTCCCCTTATGAAAAAAATAACT---TTTCTACCAACA--ATAGTCGTATTATCTACCATA---------ATACTACCACTCAC-------GCCAA-TACTATCAGTGTTAGA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 4742 211 +     16727 TTATTCCAACACTAATGGCTATCACCGCTCTACTTAACTTATATTTCTACCTGCGACTCACATATAGCACCGCACTTACCATATTTCCAT---CCACAAACAACATAAAAATAAAA-TGACAGTTCGAATACACAAAAAAGGCAACC---CTATTACCCCCC--TTAATTATTACCTCAACTATA---------CTACTCCCACTAAC-------ACCTA-TATTATCAGTCTTGGA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       8556 211 -     16977 TACTACCAACAACAATAGCCATTATGGCACTACTGAACCTCTATTTCTACATACGACTTATCTACTCAACATCACTCACAATATTCCCAA---CGACCAATAACAACAAAATAAAA-TGAAAATACAAAACACAAAATTTTATCCCC---CTATCACCAACA--TTAATTACACTATCCACAATA---------CTCATCCCCCTCAC-------TCCAA-TAATATTAATCTTAAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       7741 211 +     16266 TCATACCACTAACCATGGCCATTATAGCATTACTAAACATGTACTTCTACATACGACTAATCTACTACTCATCACTAACAATCCTACCAT---CTACAAATAATATGAAAATAACC-TGACGATTTACTAATACTAAACACACAATA---ACATTACCCACC--CTAATCACCCTATCTAACATA---------CTACTTCCCCTAAC-------CCCAA-TAATTTCAATGCTAGA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      4108 211 +     18297 CCATAACACTAACAATATCTATCCTAGCCCTCTTGAATCTCTTCTTTTATTTACGCTTAATTTATGCATCCTCACTCACCCTGTTCCCGA---CAAGTAGTAATCTAAAATTCAAA-TGGAAA---ATCAATACCCCAAACAAAATATATTTTTTACCAACA--ATAGTCTCAATTTCACTACTT---------TTCCTTCCTGTCTC-------CCCAA-TAATTCTTATATTAAA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117156165 211 + 174229318 CCCTAGCAACAGCACTAGCATTATCCGCACTACTAAACCTATTCTTTTATATACGAATTATTTATTTATCAACACTTACCATAGCACCGT---CCATTAATAACTCAAAAATACAA-TGAACTCTTCTACCCCCAAAAACACTCACA---CTCATTCCAACA--CTGACAATAATCTCATTACTA---------TTCTTACCTCTTAC-------CCCTA-TATTTATTGTACTCAC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 6069 208 +     16775 CAATAGCCACAATCATCACAATACTATCACTCCTAAGCCTATTCTTCTACCTCCGACTTGCATACCACTCAACAATCACACTCCCCCCCAACTCATCAAACCACATAAAACTCTGA-CGA--------ACTAACAAAACCCTAAACA---CCCCCACCGCCATTCTAACTGCGCTATCAACCACC---------CTATTGCCCCTTTC-------CCCCC-TAATTATTACCATACT
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random    103514604 205 + 171761319 CAACAGCCACCCTGGCAGCACTCAGCGCCCTACTAAGCCTCTACTTCTATCTTCGCCTCTCCTACGCCATAACCCTAACAATCGCCCCCA---ACAAC-TTAACAGGGACCCTCCCATGACGTACCCAAACAACCCAACCAAACATG---ATAACCGCCACC--ATAACAGCCTCTTCAATCCTT---------CTCCTCCCCATGAC-------CCCTG-GAATTCTTAC------
+i tetNig1.chrUn_random    C 0 N 0
+s danRer4.chrM                 5821 205 +     16596 CCACAGCTACTATCATGGCGCTTACCGCCCTCCTAAGCTTATTTTTTTACCTACGTCTATGTCATGCAATAACATTAACGACTTCACCAA---ACACTATCAATTCAGCCCCTCAC-TGACGGGTACAAACGACCCA---AAAC-------TCACTAC--CC--CTAACAATCTCTGTTACTGTTACTATAGGACTTTTACCACTGAC-------CCCAG-CCATCTTAAT------
+i danRer4.chrM            C 0 I 9
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=105153.000000
+s mm8.chrM                     4947 33 +     16299 CTAGAAG---------TTTAGGATATA-CT------AGTCCGCGAGC--CT
+s rn4.chrM                     4925 32 +     16300 ATAGAAG---------TTTAGGATATA-C-------AGTTCAAGAGC--CT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      5116 32 +     20791 AAAGGAG---------TTTAGGTTACA-C-------AGACCAAGAGC--CT
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    5510 34 +     16571 ATAGAAA---------TTTAGGTTAAA-TA-----CAGACCAAGAGC--CT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 4927 34 +     16554 ATAGAAA---------TTTAGGTTAAG-CA-----CAGACCAAGAGC--CT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34440904 33 - 182086969 TTAGAAA---------TTTAGGTTAAA-TA------AGACCGAGGAC--CT
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 5305 32 +     16338 ATAGGAA---------TTTAGGTTAAA-C-------AGACCAAGAGC--CT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 4953 33 +     16727 CTAGGAG---------TTTAGGTTAGACC-------AGACCAAGAGC--CT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       8767 33 -     16977 CTAGGGA---------TTTAGGTTAGA-CA------AGACCAAGAGC--CT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       7952 32 +     16266 ATAGGAA---------TTTAGGTTAAA-C-------AGACCAAGAGC--CT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      4319 33 +     18297 TTAGGGG---------GTTAGGTTAAATT-------AGACCAAGAGC--CT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117156376 43 + 174229318 ATAAGAATTACAAGCTTTTATCTTGCA-T-------ACTTCGAACGCAAAT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 6277 39 +     16775 ATAGAAA---------CTTAGGATTAA-CTGTCACCAAACCAAAGGC--CT
+i galGal2.chrM            C 0 C 0
+s danRer4.chrM                 6035 33 +     16596 ATAGAGA---------CTTAGGATAAC-CT------AGACCAAGAGC--CT
+i danRer4.chrM            I 9 C 0
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=2531764.000000
+s mm8.chrM                     4980 575 +     16299 TCAAAGCCCTAAGA--AAAC---ACA-CAAGTTTAACTTCTG--------A------------TAAGGACTGTAAGACTTCA-TC--CTACATCTATTGAA--TGCAAATCAAT---------TGCTTTA-------AT-TAAGCTAAGACCTC--------AA-CTAGATTGGCAGGAATTAAA--CCTACG-AAA---ATTTAGTTAACAGCTAAATAC-CCTA----T-TACTGGCTTCAATCTA-CTTCTACC--GCCG--A--A------AAAAAAA--AATGGCGGTA-----GAAGTCTTAGTA-GAGAT--TT-CTCTACACCTTCGAAT-----------------TTGCAATTCGACATGA-ATAT---CACCTT----AAGACCTCT-------------------GGTAAAAAGA--GGATTTAAACCTCTGTGTTTAGATTTACAGTCTAATGCT---T----ACTCAGCCATTTTA----------------------------------CC-----------TATG---TTCATTAATCGTTGATTATTCTCAACCAATCACAAAGATATCGGAACCCTCTATCTACTATTCGGAGCCTGAGCGGGAATAGTGGGTACTGCACTAAGTATTTTAATTCGAGCAGAATTAGGTCAACCAGGTGCACTTTTAGGAGATGACCAAATTTACAATGTTATCGTAACTGCCCATGCTTTTGTTATAATTTTCTTCATAGTAATACCAATAATAATTGGA
+s rn4.chrM                     4957 579 +     16300 TCAAAGCCCTTAGA--AAAC---AAA-CAAGTTTAACTTCTG--------A------------TAAGGACTGTAAGACTATA-TC--TTACATCTGTTAAA--TGCAAATCAAC---------TGCTTTA-------AT-TAAGCTAAATCCTC--------AA-CTAGATTGGAAGGAATCAAATTCCTACG-AAA---ATTTAGTTAACAGCTAAATAC-CCTA---CT-TACTGGCTTCAATCTA-CTTCTCCC--GCCT--A--T------CAGAAAA--GA-GGCGGGA-----GAAGCCTTAGTA-GAGGAGATT-CTCTACACCTTCGAAC-----------------TTGCAATTCGACATGA-TAAT---CACCTT----AAGGCTTTT------------------TGGTAAAAAGG--GGGCTCAA-CCCCTGTCTTTAGATTTACAGTCTAATGCT---T----ACTCAGCCATTTTA----------------------------------CC-----------TATG---TTCGTAAACCGTTGACTCTTTTCAACTAACCACAAAGATATCGGAACCCTCTACCTATTATTTGGAGCCTGAGCAGGAATAGTAGGGACAGCTTTGAGTATTCTAATTCGAGCTGAACTAGGACAGCCAGGCGCACTCCTAGGAGATGACCAAATCTATAATGTCATCGTCACAGCCCATGCATTCGTAATAATTTTCTTTATAGTAATACCTATAATAATTGGA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      5148 581 +     20791 TCAAAGCTCTAAGC--AAGT---AGATCATACTTAACCCCTG--------CT-----------TAAGGACTGCAAA--TTAA-CT--TTACATCTCCTGAA--TGCAAACCAGG---------TGCTTTA-------AT-TAAGCTAAATCCTC-----------CTAGATTGGTGGGCTCCAAC--CCCACG-AAG---CTTTAGTTAACAGCTAAATAC-CCTAG--TC-AACTGGCTTCAACCTA-CTTCTCCC--GCCGTAA--G------AAAAAAA--AA-GGCGGGA-----GAAGCCCCGGCA-GAGTT--GA-AGCTGCTTCTTTGAAT-----------------TTGCAATTCAATATGT-GAGTACCCACCTC----AGGGCTT---------------------GGTAAAAAGA--GGGCTTAA-CCTCTGTCTTTAGATTTACAGTCTAATACC---T----ACTCGGCCATTTTA----------------------------------CCCTT-----ACTTATG---TTCGTCAATCGTTGACTTTTCTCTACCAACCACAAAGACATCGGCACTCTTTATCTCCTATTTGGAGCTTGAGCTGGGATGGTGGGAACAGCCCTTAGCCTGCTAATTCGAGCAGAATTAGGTCAGCCAGGGACTCTACTCGGGGATGATCAAATCTATAATGTAATCGTCACCGCACATGCCTTTGTAATAATCTTCTTTATAGTCATACCTAT-ATAATTGGA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    5544 588 +     16571 TCAAAGCCCTCAGT--AAGT---TGC-AATACTTAATTTCTGCAACAG--C------------TAAGGACTGCAAAACCCCA-CT--CTGCATCAACTGAA--CGCAAATCAGC---------CACTTTA-------AT-TAAGCTAAGCCCTT---------A-CTAGACCAATGGGACTTAAA--CCCACA-AAC---ACTTAGTTAACAGCTAAGCAC-CCTAA--TC-AACTGGCTTCAATCTA-CTTCTCCC--GCCG--C--C------GGGAAAA--AA-GGCGGGA-----GAAGCCCCGGCA-GGTTT--GA-AGCTGCTTCTTCGAAT-----------------TTGCAATTCAATATGA-AAAT---CACCTC----GGAGCT----------------------GGTAAAAAG---AGGCCTAA-CCCCTGTCTTTAGATTTACAGTCCAATGCT---T---CACTCAGCCATTTTA----------------------------------CCTCACCCCCACTGATG---TTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTGGAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCTCTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 4961 587 +     16554 TCAAAGCCCTCAGC--AAGT---TAC-AATACTTAATTTCTGCAACAA--C------------TAAGGACTGCAAAACCCCA-CT--CTGCATCAACTGAA--CGCAAATCAGC---------CACTTTA-------AT-TAAGCTAAGCCCTT---------A-CTAGATTAATGGGACTTAAA--CCCACA-AAC---ATTTAGTTAACAGCTAAACAC-CCTAA--TC-AACTGGCTTCAATCTA-CTTCTCCC--GCCG--C--A------AGAAAAA--AA-GGCGGGA-----GAAGCCCCGGCA-GGTTT--GA-AGCTGCTTCTTCGAAT-----------------TTGCAATTCAATATGA-AAAT---CACCTC----AGAGCT----------------------GGTAAAAAG---AGGCTTAA-CCCCTGTCTTTAGATTTACAGTCCAATGCT---T---CACTCAGCCATTTTA----------------------------------CCCCA-CCCTACTGATG---TTCACCGACCGCTGACTATTCTCTACAAACCACAAAGATATTGGAACACTATACCTACTATTCGGTGCATGAGCTGGAGTCCTGGGCACAGCCCTAAGTCTCCTTATTCGGGCTGAACTAGGCCAACCAGGCAACCTCCTAGGTAATGACCACATCTACAATGTCATCGTCACAGCCCATGCATTCGTAATAATCTTCTTCATAGTAATGCCTATTATAATCGGA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34440937 590 - 182086969 TCAAAGTCCTTAGT--AAGTA--AGT-TACTCTTAATTTCTGTAACAGATC------------TAAAGATGGCAAGATGCTA-TT--CTGCATCAATTGAA--CGCAAATCAAC---------CACTTTG-------AT-TAAGCTAAGCCCTT---------A-CTAGATTTATGGAATTCAAA--CCCACG-AATAAAATTTAGTTAACGGCTAAGCAC-CCTAA--TC-AACTGGCTTCAATCTA-CCCCCGCC--GCCG--T--T------GGGGGAG--AA-AGGCAGA-----GAAGACCCAGCA-GGATT--GA-AGCTTCTCCTTTGACT-----------------TTGCAATTCAACATGAGAAAT---CACCTC----AGGGCT----------------------GCTAAAAAGC--AGCCTTGA-CCTCTGTCTTTAGATTTACAGTCTAATGCT---T----ACTCAGCCATTTTA----------------------------------CCTTTTCCCCACTTATG---TTCATCAATCATTGATTGTTTTCAGCTAACCACGAAGATATCGGAACACTATACCTGCTAT--GGCGC---AGTGGAGATAGTAGGCACCGCCTTAAGCCTTCTAATTCCAGCAGAACTAGGCCAACCAGGAACTCTGCTAGGAGATGATCAGATCTACAATGTTATTGTTACCGCTCACACATTCGTTATAATTTTATTTATGATAACACTAATCATGATTGGG
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 5337 577 +     16338 TCAAAGCCCTAAGC--AAGTA--CAA-TTTACTTAATTCCTG--------A------------TAAGGATTGCAAGACTACA-CC--TTACATCAATTGAA--TGCAAATCAAC---------CACTTTA-------AT-TAAGCTAAATCCTC---------A-CTAGACTGGTGGGCTCCACC--CCCACG-AAA---CTTTAGTTAACAGCTAAACAC-CCTAG--CT-AACTGGCTTCAATCTA-CTTCTCCC--GCCG--CA-A------GAAAAAA--AA-GGCGGGA-----GAAGCCCCGGCA-GAATT--GA-AGCTGCTTCTCTGAAT-----------------TTGCAATTCAACGTGT-AAAT--TCACCAC----AGGGCTT---------------------GGTAAAAAGA--GGAGTCAAACCTCTATCTTTAGATTTACAGTCTAATGCT---T---TGCTCAGCCATTTTA----------------------------------CC-----------CATG---TTCATTAACCGCTGACTATTCTCAACCAACCATAAAGATATTGGTACCCTTTATCTACTATTTGGTGCTTGGGCCGGTATAGTAGGAACAGCTCTAAGCCTTCTAATTCGCGCTGAATTAGGCCAACCCGGAACTCTGCTCGGAGACGACCAAATCTACAACGTAGTTGTAACCGCACACGCATTTGTAATAATCTTCTTCATAGTAATACCAATCATAATTGGA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 4986 590 +     16727 TCAAAGCTCTAAGC--AAGTG--CTA-CACACTTAACCCCTG--------ATCAAATCACCTCTAAGGGCTGCAAGAATCTA-TC--TTACATCAATTGAA--TGCAAATCAAA---------CACTTTA-------AT-TAAGCTAAGCCCTC---------C-CTAGATTGGTGAGCTTCTAC--CTCACG-AAA---TTTTAGTTAACAGCTAAATAC-CCTAG---T-AACTGGCTTCAATCTACCTTCTCCC--GCCG--CGTA------GAAAAAA--AA-GGCGGGA-----GAAGCCCCGGCG-GCGTC--TA-GGCTGCTTCTTTGAAT-----------------TTGCAATTCAATATGA-AAAT--TCACCAC----GGAGCTT---------------------GGCAAAAAGA--GGACTTAAACCCCTATCTTTAGATTTACAGTCTAATGCT---T---TTATCAGCCATTTTA----------------------------------CC-----------TATG---TTCATTAACCGATGACTGTTCTCCACTAATCACAAGGATATTGGTACTTTATACTTACTATTTGGAGCATGAGCCGGTATAGTAGGCACTGCTTTGAGCCTCCTCATCCGAGCCGAACTAGGTCAGCCCGGTACTTTACTAGGTGACGATCAAATTTATAATGTCATCGTAACCGCCCATGCTTTCGTAATAATCTTCTTCATAGTCATGCCCATCATAATTGGG
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       8800 579 -     16977 TCAAAGCCCTTAGC--AAGTA--AAA-ATTACTTAATCCCTG--------ACG----------TAAGGACTGCAAGATTTAG-CC--CCACATCTCCTGAA--CGCAAATCAGG---------CACTTTA-------AT-TAAGCTAAGTCCTC---------T-CTAGACTGGTGGGCTCCAAC--CCCACG-AAA---TTTTAGTTAACAGCTAAATAC-CATAA--TC-ACCTGGCTTCAATCTA----TTCCC--ACCT--C--A------AAAACAA--GC-CAAAGGAATCATAAAGCCCTGGCA-GAGTT--TACAGCTGCTTCTCTGAAC-----------------TTGCAATTCAA-ATAG-TATT--------C----AAGGCTTAT--------------TTAATGGTAAAAAAA--GGACTTCA-CCTTTGTCTTTAGATTTACAGTCTAATGCT---T----ACTCAGCCATTTTA----------------------------------CC-----------CATG---TTCATTACCCGTTGACTATTTTCAACAAACCACAAAGATATTGGAACTCTATATTTACTATTTGGCGCCTGGGCTGGAATAGTAGGCACCGCCCTAAGTCTACTAATTCGTGCCGAGCTTGGCCAACCAGGCACATTACTAGGAGACGATCAAATTTATAATGTAATTGTTACCGCCCATGCATTCATCATAATTTTCTTTATAGTAATACCAATCATGATCGGG
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       7984 579 +     16266 TCAAAGCCCTAAGT--AAGTA--CAT-TATACTTAACTCCTG----AA--A------------TAAGGACTGCAAGATACTA-TC--TTACATCAACTGAA--TGCAAATCAGA---------CGCTTTA-------AC-TAAACTAAGCCCT----------T-CTAGATTGGAGGGCTTCAAT--CCCACGAAAT---TCTTAGTTAACAACTAAACAC-CCTAG--CT-AACTGGCTTCAATCTA-CTTCTCCC--GCCT--T--GAGGGAGGGGGAAA--AA-GGCGGGA-----GAAGCCCCGGCA-GAATT--GA-AGCTGCTTCTTCGAAT-----------------TTGCAGTTCGACATGT-TTAC--AC-TTTC----AAGGCCT---------------------GGCAAAAA----GAGATTAC-TCTCTGTGGTTAGATTTACAGTCTAATGCC---T----ACTCAGCCATTTTA----------------------------------CC-----------TATG---TTTGCTAACCGCTGACTATATTCAACGAACCACAAAGATATCGGAACACTGTATCTATTATTTGGTGCTTGAGCTGGTATAGTAGGGACTGCTTTTAGTATCCTAATTCGGGCAGAACTAGGCCAACCAGGCTCTCTTCTTGGAGATGATCAAATCTACAATGTTATTGTCACAGCACACGCCTTCGTAATAATCTTCTTTATAGTCATGCCAATTATAATTGGA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      4352 619 +     18297 TCAAAGCTCTAAGC--AAGTA--AAC-AATACTTACCCTCTG-----A--A------------TAAGGACTGCAAGACTGTACTC--TTACATCAATTGGA--CGCAAACCAAA---------CACTTTA-------ACTTAAGCTAAATCC-----------T-CTAGATTGATGGGGTTTAAA--CCCATG-AAC---TATTAGTTAACAGCTAATTAC-CCTAC--CTCAACTGGCTTCAATCTA-C-TCTCCC--GCCT--T--T-GAATAGAAAAAA--AA-GGCGGGA-----GAAGCCCCGGCA-GATTT--GA-AGCTGCTTCTTCGAAT-----------------TTGCAATTCAATATGA-ATAC--TCACTTC----AGAGCCT---------------------AGTAAAAAGGAGGAGCCTCC-CTCCTGTCTTTAGATTTACAGTCTAATGCCTATT----ACTCAGCCATTTTACTTTCATATATTAGAACTTCCTTCTATACCCTTTCT-----------TATG---TTCATAAACCGTTGACTATACTCTACTAACCATAAAGACATTGGAACCCTCTACTTATTATTCGGAGCTTGAGCTGGCACAGTAGGAACTGCTCTTAGCCTCCTAATCCGTGCTGAACTCGGACAGCCAGGAGCCCTACTAGGTGATGATCAAATCTATAACGTAATCGTAACTGCACACGCCTTCGTTATAATTTTCTTTATAGTTATACCCATTATGATTGGG
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117156419 635 + 174229318 CGAACGCTTTAATT--AAGC---TAA-ACCCTTAAACTACTA--------T------------TTAAACCTCGGTAGCTTTA-CTAACTAC-TTTTTTGAATTTGCAATTCAACGTATTAATATACTTCAAGATTAGAT-TATCCTAAAGGCTTAGGATAAAAT-CTAGACCGAAGG----------CCTTCA-AAG---CCTTAAGCAGGTGATAAATCCACCTAGCCTT-TACTAATTAC-ATCAA-GCTCTCCC--GCCT--TG-G------AGAAAAA--AA-GGCGGGA-----GAGCCCCGGGCA-GCCCT--ATTAATTGTTTCATAAACTAAACTGGTGGGTATTTATCCCACTCTATCTTAA-TTAA---CAGTTA----AGCGCCTGTCTTTCGGCCTCAGTTTAGTGGTAAAAAGA--GATGTTAT-TCTCTGTCTTTGAATTTACAGTTCAATGCC---T---AGCTCAGCCATTTTA----------------------------------CC-----------TATG---TTCATTAATCGTTGACTCTTCTCAACTAACCATAAAGATATTGGTACTTTATATTTATTATTTGGTGCTTGAGCAGGAATAGTTGGAACCGCACTAAGCCTCCTAATTCGAGCAGAATTAGGCCAACCAGGGACTCTAATTGGTGATGATCAAATTTATAACGTAATCGTAACTGCCCACGCTTTCGTTATAATTTTCTTCATAGTAATACCTATCATGATTGGA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 6316 559 +     16775 TCAAAGCCTTAAAT--AAGAGTTAAA-CTCTCTTAGTTTCTG-CCCAA--C------------TAAGACCAACAGGACATTA-AC--CTGTATCTCCTGAA--TGCAAATCAGA---------CGCTTTA-------AT-TAAGCTAAGGCCTC-------TAC-CTAGACAGATGGGCTTCGAT--CCCATA-CAA---TTTTAGTTAACAGCTAAATGC-CAACA--CC-AATTGGCTTCTGCCTA-----------------C--A------------------------------GA--CCCCGGCA-CACTT--TA-GTGTACATCAACGAGT-----------------TTGCAACTCATTATGA-ACTT---CACTAC----AGAGTC----------------------GATAAGAAGA--GGAATTGAACCTCTGTAAAAAGGACTACAGCCTAACGCT---TCAACACTCAGCCATCTTA----------------------------------CC-----------TGTGACCTTCATCAACCGATGATTATTCTCAACCAACCACAAAGACATTGGCACTCTTTACCTAATTTTCGGCACATGGGCGGGCATAGCCGGCACAGCACTTAGCCTTCTAATTCGCGCAGAACTAGGACAGCCCGGAACTCTCTTAGGAGACGATCAAATTTACAATGTAATCGTCACAGCCCATGCTTTCGTCATAATCTTCTTTATAGTTATACCCATCATGATCGGT
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random    161619026 580 + 171761319 TCAAAGCCCTCAGCGGGAGTG--AAA-ATCTCCCAGTCCCTG--------A------------TAAGACTTGCGGGACACTA-CC--CCACATCTCCTGCA--TGCAAAACAGA---------CACTTTA-------AT-TAAGCTAAAGCCTT---------ACCTAGACAGGCAGGCCTCGAT--CCTACA-AAC---TCTTAGTTAACAGCTAAGCGC-TCAAA--CC-AGCGAGCATCTATCTA-CCTTTCCCCGCCTG--T--C------AAAACAA--AA-GGCGGGG-----AAAGCCCCGGCA-GACGT--CA-ATCTGCTTCTTTAGAT-----------------TTGCAATCTAACATGT---AA---CACCCC----AGGGCTT---------------------GGTAGAAAGA--GGAATTTAACCTCCGTACGTGGGGCTACAATCCACCGCT---T-AACACTCAGCCATCCTA----------------------------------CC-----------TGTG---GCAATCACACGCTGATTTTTCTCAACCAACCATAAAGACATCGGCACCCTCTACCTAGTATTTGGTGCCTGAGCCGGAATAGTGGGAACGGCCCTTAGCCTCCTCATCCGAGCTGAACTTAGCCAACCAGGCGCACTCTTGGGTGATGACCAGATTTATAATGTAATCGTCACAGCCCATGCATTTGTAATAATTTTCTTTATAGTAATGCCAATCATGATTGAA
+i tetNig1.chrUn_random    N 0 N 0
+s danRer4.chrM                 6068 584 +     16596 TCAAAGCTCTCAGTAGAAGTG--AAA-ATCTTCTAGTCTCTG--------A------------TAGGACTTAC-AGACGTTA-CT--CCGCATCTTCTAAA--TGCAAATCAGA---------TATTTTA-------AT-TAAACTAAAGCCCT---------A-CTAGATGGGAAGGCCTCGAT--CCTACA-AAA---TCTTAGTTAACAGCTAAGCGC-CCAAG--CC-AGCGAGCATCCATCTA-CTTTTCCC--GCCG--T--T------GAACCCGGTAA-GGCGGGA-----AAAGCCCCGGCAGGAGGT--TT-ACCTGCGTCTTCAGAT-----------------TTGCAATCTGATATGT---AT---CATCACCACGAGGCCAT---------------------GGTAGAAAAA--GGACTCAAACCTCTGTCCGCGGAGCTACAATCCGCCGCC---TAAACACTCGGCCACCCTA----------------------------------CC-----------TGTG---ACAATCACACGTTGATTTTTCTCAACTAATCATAAAGACATTGGCACCCTGTATCTAGTATTTGGTGCTTGAGCCGGAATAGTAGGGACCGCATTAAGCCTCTTAATCCGAGCTGAACTTAGCCAACCAGGAGCACTTCTTGGTGATGATCAAATCTATAATGTTATTGTTACTGCCCATGCTTTTGTAATAATTTTCTTTATAGTAATACCCATTCTTATTGGG
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=799335.000000
+s mm8.chrM                     5555 131 +     16299 GGCTTTGGAAACTGACTTGTCCCACTAATAATCGGAGCCCCAGATATAGCATTCCCACGAATAAATAATATAAGTTTTTGACTCCTACCACCATCATTTCTCCTTCTCCTAGCATCATCAATAGTAGAAGC
+s rn4.chrM                     5536 131 +     16300 GGCTTCGGAAACTGACTTGTACCACTAATAATTGGAGCCCCTGATATAGCATTCCCACGAATAAATAACATAAGCTTTTGACTGCTTCCTCCATCATTTCTACTCCTTTTAGCATCCTCCATAGTAGAAGC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      5729 131 +     20791 GGCTTCGGGAACTGGCTTGTCCCCCTGATAATTGGGGCTCCTGACATAGCCTTCCCCCGAATAAATAATATGAGCTTCTGACTTCTCCCCCCTTCATTCCTTCTTCTACTAGCCTCCTCAATAGTAGAAGC
+i oryCun1.scaffold_140182 C 0 M 264
+s hg18.chrM                    6132 131 +     16571 GGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAACATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTGCTATAGTGGAGGC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 5548 131 +     16554 GGCTTTGGCAACTGGCTAGTTCCCTTGATAATTGGTGCCCCCGACATGGCATTCCCCCGCATAAACAACATAAGCTTCTGGCTCCTGCCCCCTTCTCTCCTACTTCTACTTGCATCTGCCATAGTAGAAGC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34441527 131 - 182086969 GTTTTCGGCAACTGGCTAGTCCCTCTGACCATTGGTTGACTGGACATGGCATCCCCCTGAATAAATAATATGATTTTCTGACTTCTCCCCCTATCTTTTCTACTCCTACTTGCGTCTTCAATAGTAGAAGC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 5914 131 +     16338 GGATTCGGTAACTGACTTGTTCCCCTAATAATTGGTGCTCCCGATATAGCATTTCCCCGAATAAATAATATAAGCTTCTGACTCCTCCCTCCCTCATTCCTACTACTCCTCGCATCCTCTATAGTTGAAGC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 5576 131 +     16727 GGCTTTGGAAACTGACTAGTGCCGTTAATAATTGGTGCTCCGGACATGGCATTCCCCCGAATAAATAACATGAGCTTCTGACTCCTTCCTCCATCCTTTCTTCTACTATTAGCATCTTCTATGGTAGAAGC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       9379 131 -     16977 GGCTTCGGAAACTGATTAGTCCCATTAATAATTGGCGCGCCCGATATAGCCTTCCCACGAATAAACAACATAAGTTTCTGACTATTACCCCCTTCATTCCTACTCCTACTAGCCTCCTCTATAGTAGAAGC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       8563 131 +     16266 GGCTTTGGAAACTGGTTAATTCCACTTATAATTGGAGCACCTGATATAGCTTTTCCTCGAATAAACAATATGAGTTTTTGACTACTGCCTCCATCTTTCCTACTACTTTTAGCATCCTCTATAGTAGAAGC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      4971 131 +     18297 GGATTTGGTAACTGACTGATCCCATTAATGATTGGTGCCCCTGACATAGCTTTCCCCCGAATAAATAACATAAGTTTCTGGCTCCTTCCCCCCTCTTTTCTTCTTCTGTTAGCTTCATCTATAGTTGAAGC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117157054 131 + 174229318 GGTTTTGGTAACTGACTAGTACCACTAATAATTGGAGCACCAGATATAGCATTTCCCCGAATAAATAATATAAGTTTCTGACTACTACCACCCTCATTCCTTCTTTTACTAGCATCATCCACAGTTGAAGC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 6875 131 +     16775 GGCTTCGGAAACTGACTAGTCCCACTTATAATCGGTGCCCCAGACATAGCATTCCCCCGCATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCCTTCTCCTACTAGCCTCATCTACCGTAGAAGC
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random       417498 131 - 171761319 GGTTTTGGTAATTGGTTTGTTCCTTTGATGTTGGGAGCTCCAGATATAGCATTTCCAAGGTTGAACAACATTAGTTTTTGGCTTTTGCCACCTTCTTTGCTTCTATTGGTAAGTTCTTCTTTGGTAGAGGC
+i tetNig1.chrUn_random    N 0 C 0
+s danRer4.chrM                 6652 131 +     16596 GGATTTGGAAACTGACTTGTGCCACTAATGATTGGGGCCCCCGATATGGCATTTCCCCGAATAAATAATATAAGCTTCTGACTTCTTCCACCCTCATTTCTTCTTCTATTAGCTTCTTCTGGAGTTGAAGC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=1518153.000000
+s mm8.chrM                     5686 281 +     16299 AGGAGCAGGAACAGGATGAACAGTCTACCCACCTCTAGCCGGAAATCTAGCCCATGCAGGAGCATCAGTAGACCTAACAATTTTCTCCCTTCATTTAGCTGGAGTGTCATCTATTTTAGGTGCAATTAATTTTATTACCACTATTATCAACATGAAACCCCCAGCCATAACACAGTATCAAACTCCACTATTTGTCTGATCCGTACTTATTACAGCCGTACTGCTCCTATTATCACTACCAGTGCTAGCCGCAGGCATTACTATACTACTAACAGACCGCA
+s rn4.chrM                     5667 281 +     16300 TGGAGCTGGAACAGGATGAACAGTATATCCCCCCTTAGCCGGAAACCTAGCCCATGCTGGGGTATCCGTAGATTTAACTATTTTTTCCCTCCACCTAGCCGGGGTGTCTTCTATCTTAGGAGCTATCAACTTTATCACCACTATCATTAATATAAAACCCCCTGCTATAACCCAATATCAGACACCTCTCTTTGTATGATCCGTACTAATTACAGCCGTCCTACTACTTCTCTCACTGCCAGTATTAGCAGCAGGTATCACTATACTCCTTACAGACCGAA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_205008      3325 279 -    118789 TGGGGCGGGGACTGGCTGAACTGTTTATCCACCTCTAGCCGGTAATCTTGCACATGCTGGAGCCTCAGTGGATCTTACTATTTTCTCCCTTCACTTAGCTGGAGTATCATCTATTTTAGGGGCTATTAACTTTATTACAACTATTATTAATATGAAACCCCCTGCAATATCTCAATATCAAACCCCCTTATTCGTATGATCTGTTCTAATCACAGCCGTACTTCTTCTTCTCTCTTTACCGGTCCTAGCTGCTGGCATTACAATGCTTTTAACAGACCG--
+i oryCun1.scaffold_205008 I 2359 n 0
+s hg18.chrM                    6263 281 +     16571 CGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCACAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCTCCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 5679 281 +     16554 CGGCGCGGGAACAGGTTGAACAGTCTACCCTCCCTTAGCGGGAAACTACTCGCATCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTTACATCTGGCAGGCATCTCCTCTATCCTAGGAGCCATTAACTTCATCACAACAATTATTAATATAAAACCTCCTGCCATGACCCAATACCAAACACCCCTCTTCGTCTGATCCGTCCTAATCACAGCAGTCTTACTTCTCCTATCCCTCCCAGTCCTAGCTGCTGGCATCACCATACTATTGACAGATCGTA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34441658 280 - 182086969 TGGAGCTGGAACCAGCTGGACAGTTCGTCCCCCTTTAGCAGGAAACCTAGCACATGTAGGATCCTCTGTGGCTCTGACCATCTTCCCGCCCCACTTAGCAGGTGTTTTTTCTATTTTAGGGGCTATTAATTTTATTACCACAATTATTAACATAAAACCCCCAACCATATCCCAGTATCAAACACCCCTTTTCGTCTAATCAGTCCTCATTATGGCAGCCCTTCTGCTCCTTTCCCTCCTAGTCCTAGCCGCC-GCATTACTATACTGTTAACTGACCGTA
+i rheMac2.chr5            C 0 M 981
+s bosTau2.chrM                 6045 281 +     16338 TGGGGCAGGAACAGGCTGAACCGTGTACCCTCCCTTAGCAGGCAACCTAGCCCATGCAGGAGCTTCAGTAGATCTAACCATTTTCTCTTTACACTTAGCAGGAGTTTCCTCAATTTTAGGAGCCATCAACTTCATTACAACAATTATCAACATAAAGCCCCCCGCAATGTCACAATACCAAACCCCTCTGTTCGTATGATCCGTAATAATTACCGCCGTACTACTACTACTCTCGCTCCCTGTATTAGCAGCCGGCATCACAATGCTATTAACAGACCGGA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 5707 281 +     16727 AGGTGCAGGAACGGGATGAACCGTATACCCCCCACTGGCTGGCAATCTGGCCCATGCAGGAGCATCCGTTGACCTTACAATTTTCTCCTTACACTTAGCCGGAGTCTCTTCTATTTTAGGGGCAATTAATTTCATCACTACTATTATCAACATAAAACCCCCTGCAATATCCCAGTATCAAACTCCCCTGTTTGTATGATCAGTACTAATTACAGCAGTTCTACTCTTACTATCCCTGCCTGTACTGGCTGCTGGAATTACAATACTTTTAACAGACCGGA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       9510 281 -     16977 TGGAGCAGGAACAGGCTGAACAGTATACCCGCCACTAGCAGGAAACCTAGCCCACGCAGGAGCATCCGTAGACCTAACAATTTTCTCCCTCCACCTTGCAGGAATCTCATCCATTCTAGGAGCCATCAACTTTATTACTACTATCATCAACATAAAACCCCCCGCAATAACACAATACCAAACCCCATTATTTGTATGATCAGTACTAGTAACAGCAGTCCTACTGCTGCTTTCCCTCCCAGTTCTAGCCGCTGGCATTACCATACTCCTAACAGACCGAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       8694 281 +     16266 TGGGGCAGGCACTGGTTGGACCGTATACCCTCCCCTGGCAGGAAACCTGGCCCATGCAGGAGCTTCTGTGGATTTAACTATTTTTTCACTTCACCTTGCAGGAGTATCCTCTATTCTAAGTGCAATTAATTTTATCACTACCATCATCAACATAAAACCTCCAGCTATATCTCAATACCATATACCCTTATTTGTATGGTCCATTTTAATTACAGCCGTCCTTCTTCTTCTATCCCTCCCAGTTCTAGCAGCAGGTATTACAATATTACTAACGGATCGCA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      5102 281 +     18297 AGGAGCAGGAACAGGCTGAACTGTTTATCCCCCCTTAGCTGGTAATCTCGCACATGCCGGAGCCTCAGTTGACTTAACAATTTTTTCTCTTCACTTAGCAGGTGTTTCATCAATTTTAGGGGCTATTAATTTTATCACTACAGTAATTAATATAAAACCTCCAGCTATAACCCAATACCAAATACCCTTATTTGTCTGGTCAGTAGCTATTACTGCCGTACTTCTTCTACTTTCATTACCTGTACTTGCTGCAGGAATCACTATACTTCTGACAGACCGTA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117157185 281 + 174229318 AGGGGCAGGAACTGGTTGAACAGTATATCCCCCATTAGCAGGAAACCTAGCCCACGCAGGTGCCTCAGTAGACCTAGCAATCTTCTCACTTCACTTAGCTGGTATTTCCTCCATCTTAGGTGCTATTAATTTTATTACCACTATTATCAACATAAAACCCCCAGCAATATCTCAATACCAGACCCCGCTGTTTGTATGATCAGTTATAATTACAGCCGTGCTTCTACTACTGTCTCTTCCAGTTCTAGCTGCAGGCATTACTATACTATTAACTGATCGAA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 7006 278 +     16775 TGGGGCCGGCACAGGATGGACAGTTTACCCCCCTTTAGCCGGCAACCTAGCCCACGCTGGCGCATCAGTAGACCTAGCCATCTTT---CATTACTTAGCAGGTGTTTCCTCCATTCTAGGAGCCATCAACTTTATCACTACCATCATCAACATAAAACCCCCCGCACTGTCACAATACCAAACACCCCTATTCGTATGATCCGTCCTCATTACTGCCATCCTACTACTCCTCTCCTTACCCGTCCTAGCAGCTGGGATTACCATACTACTTACCGACCGCA
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random       417629 281 - 171761319 AGGGGCTGGGACTGGGTGGACAGTTTATCCTCCATTGTCTGGAGTAGAAGCCCATTCTGGTTCTTCTGTAGATTTGGCTATTTTTAGTTTGCATTTGGCAGGGGTGTCTTCTTTGTTGGGAGCTATTAATTTTATTACTACTATTTTTAATATACGGGCTCCAGGGATAACAATGCATAGATTGCCTTTGTTTTGTTGGGCAGTTTTGATTACCGCTTTTTTGTTGTTGTTGTCGTTGCCAGTTTTGGCGGGGGCTATTACAATGCTATTGACAGATAGAA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                 6783 281 +     16596 AGGAGCTGGAACAGGATGAACAGTTTATCCACCTCTTGCAGGCAACCTTGCCCATGCAGGAGCATCTGTTGATCTAACAATTTTTTCACTACACTTAGCAGGTGTTTCATCTATTCTTGGAGCAATTAATTTTATTACTACTACAATTAACATGAAGCCACCAACTATCTCTCAGTATCAAACTCCATTATTTGTATGAGCTGTCTTAGTTACAGCTGTACTACTTCTTTTATCTTTACCAGTGTTAGCTGCCGGAATTACAATACTTCTTACAGACCGAA
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=292962.000000
+s mm8.chrM                     5967 43 +     16299 ACCTAAACACAACTTTCTTTGATCCCGCTGGAGGAGGGGACCC
+s galGal2.chrM                 7284 43 +     16775 ACCTTAACACCACATTCTTCGACCCAGCTGGAGGAGGAGACCC
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117157466 43 + 174229318 ATCTTAATACTACCTTCTTTGATCCTGCAGGTGGAGGAGATCC
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      5383 43 +     18297 ATCTCAACACTACATTTTTTGACCCTGCAGGAGGAGGAGACCC
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650       8975 43 +     16266 ATCTCAATACTACTTTTTTTGATCCTGCAGGAGGAGGAGACCC
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239       9791 43 -     16977 ACCTTAATACCACATTCTTCGACCCAGCAGGAGGAGGGGACCC
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 5988 43 +     16727 ATCTTAATACAACATTTTTTGATCCCGCTGGAGGAGGAGACCC
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 6326 43 +     16338 ACCTAAATACAACCTTCTTCGACCCGGCAGGAGGAGGAGACCC
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr15            38001514 41 - 110119387 ACCTCAACACTAC--TTTTTGACCCTGCTGGTGGGGGTGATCC
+i rheMac2.chr15           n 0 C 0
+s panTro2.chrM                 5960 43 +     16554 ACCTCAACACTACCTTCTTCGACCCAGCCGGGGGAGGAGACCC
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    6544 43 +     16571 ACCTCAACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCC
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182      6129 43 +     20791 AACTTAATACAACCTTCTTTGATCCTGCAGGAGGAGGAGACCC
+i oryCun1.scaffold_140182 M 264 C 0
+s rn4.chrM                     5948 43 +     16300 ATCTAAATACTACTTTCTTCGACCCCGCTGGAGGTGGAGACCC
+i rn4.chrM                C 0 C 0
+s tetNig1.chrUn_random       417910 43 - 171761319 ACTTTAATACCACTTTTTTTGATCCTGCTGGAGGGGGAGATCC
+i tetNig1.chrUn_random    C 0 N 0
+s danRer4.chrM                 7064 43 +     16596 ATCTTAACACAACGTTCTTTGACCCGGCAGGAGGGGGAGATCC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=238157.000000
+s mm8.chrM                     6010 38 +     16299 AATTCTCTACCAGCATCTGTTCTGATTCTTTGGGCACC
+s galGal2.chrM                 7327 38 +     16775 AATCCTATACCAACACCTATTCTGATTCTTCGGTCACC
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117157509 38 + 174229318 CATCCTTTATCAGCACCTGTTTTGATTTTTTGGTCACC
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      5426 38 +     18297 TATTCTATATCAACACTTATTCTGATTCTTCGGCCATC
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650       9018 38 +     16266 AATTCTATATCAACACCTATTCTGGTTTTTTGGACACC
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239       9834 38 -     16977 AATTCTCTATCAACATCTATTCTGATTCTTTGGACACC
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 6031 38 +     16727 TATCCTATATCAACACCTATTCTGATTCTTCGGACATC
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 6369 38 +     16338 TATTCTATATCAACACTTATTCTGATTCTTTGGACACC
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr15            38001555 38 - 110119387 TATCGTGTATCAACATTTATTCTGATTCTTTAGTCACC
+i rheMac2.chr15           C 0 C 0
+s panTro2.chrM                 6003 38 +     16554 TATTCTATATCAACACTTATTCTGATTTTTTGGCCACC
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    6587 38 +     16571 CATTCTATACCAACACCTATTCTGATTTTTCGGTCACC
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182      6172 38 +     20791 TATCCTCTACCAACACCTATTCTGATTTTTCGGGCACC
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                     5991 38 +     16300 AATTCTTTATCAACACCTATTCTGATTCTTCGGCCACC
+i rn4.chrM                C 0 C 0
+s danRer4.chrM                 7107 38 +     16596 AATTCTTTATCAACACTTATTTTGATTCTTTGGCCACC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2673319 6355 -   2855184 I
+
+a score=2355067.000000
+s mm8.chrM                     6048 371 +     16299 CAGAAGTTTATATTCTTATCCTCCCAGGATTTGGAATTATTTCACATGTAGTTACTTACTACTCCGGAAAAAAAGAACCTTTCGGCTATATAGGAATAGTATGAGCAATAATGTCTATTGG-CTTTCTAGGCTTTATTGTATGAGCCCACCACATATTCACAGTAGGATTAGATGTAGACACACGAGCTTACTTTACATCAGCCACTATAATTATCGCAATTCCTACCGGTGTCAAAGTATTTAGCTGACTTGCAACCCTACACGGAGGTAATATTAAATGATCTCCAGCTATACTATGAGCCTTAGGCTTTATTTTCTTATTTACAGTTGGTGGTCTAACCGGAATTGTTTTATCCAACTCATCCCTTGAC
+s rn4.chrM                     6029 371 +     16300 CAGAAGTGTACATCTTAATTCTTCCAGGGTTTGGAATTATTTCACATGTAGTTACCTATTACTCTGGAAAAAAAGAACCCTTCGGATATATAGGTATGGTATGAACCATAATATCTATTGG-CTTCCTAGGATTTATTGTATGAGCACATCACATATTCACAGTAGGCCTAGATGTAGACACCCGAGCCTACTTTACATCTGCCACTATAATTATCGCAATTCCTACAGGCGTAAAAGTATTCAGCTGACTCGCTACACTACATGGAGGAAATATCAAATGATCCCCCGCCATATTATGAGCCTTAGGGTTTATCTTCTTATTCACAGTAGGGGGCCTAACAGGGATCGTACTATCTAACTCATCCCTTGAC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      6210 371 +     20791 CCGAAGTATATATTCTTATTCTTCCAGGATTTGGAATAATTTCGCACATTGTGACATACTATTCCGGGAAAAAAGAGCCATTTGGCTATATAGGAATAGTATGAGCTATAATATCAATTGG-TTTCCTTGGATTTATCGTATGGGCCCATCATATATTTACAGTAGGAATAGATGTAGACACACGAGCCTACTTTACATCAGCTACCATAATCATCGCTATCCCTACTGGAGTCAAAGTATTTAGCTGGCTAGCAACACTGCATGGCGGCAACATCAAATGATCCCCCGCTATGCTCTGAGCTCTAGGCTTTATTTTCCTATTTACAGTAGGCGGTCTTACAGGAATTGTGCTAGCCAACTCCTCTTTAGAC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    6625 371 +     16571 CTGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAGAACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGG-CTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGTAGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCACCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATGAAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCACCGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGAC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 6041 371 +     16554 CCGAAGTTTATATTCTTATCCTACCAGGCTTCGGAATAATTTCCCACATTGTAACTTATTACTCCGGAAAAAAAGAACCATTTGGATATATAGGCATGGTTTGAGCTATAATATCAATTGG-CTTCCTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGGATAGACGTAGACACCCGAGCCTATTTCACCTCCGCTACCATAATCATTGCTATTCCTACCGGCGTCAAAGTATTCAGCTGACTCGCTACACTTCACGGAAGCAATATGAAATGATCTGCCGCAGTACTCTGAGCCCTAGGGTTTATCTTTCTCTTCACCGTAGGTGGCCTAACCGGCATTGTACTAGCAAACTCATCATTAGAC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr15            38001593 371 - 110119387 CTGAAGTTTGTTTCCTTATTCTATCAGTATTTGGGATGATCTCCCATATCGTGATGTATTGCTCTGGATAAAAGGAGCCATTTGGGTATATGGGCATAGTATGAGCCATAATATCTATTGG-CTTCTTAGGGTTTATCGTATGAGCACACCATATATTTACAGTAGGATCAGACGTAGACACATGAGCATACTTCACCTCTGCTACCATAATTATTGCTATCCCTACTGGTGTCAAGGTCTTTAGCTGATTAGCTACACTGCACAGCAGTAGCATCAAATGATCTCCTGCAATGTTCTGAACCCTAGGATTCATCTTCCTTTTCACAGTAGGAGGTCTCACTGGCATTGTACTAGCTAATTCATCACTAGAT
+i rheMac2.chr15           C 0 C 0
+s bosTau2.chrM                 6407 371 +     16338 CCGAAGTCTATATTTTAATCTTACCTGGGTTTGGAATAATCTCTCATATCGTGACCTACTACTCAGGAAAAAAAGAACCATTCGGATATATGGGAATAGTTTGGGCTATAATGTCAATCGG-ATTTCTAGGTTTCATCGTATGAGCCCACCATATATTCACTGTCGGAATAGACGTCGACACACGAGCCTACTTCACATCAGCCACTATAATTATTGCTATTCCAACCGGGGTAAAAGTCTTCAGCTGATTGGCAACACTTCATGGAGGTAATATCAAATGGTCTCCTGCTATAATGTGAGCCCTAGGCTTTATTTTCTTATTTACAGTAGGGGGTTTAACTGGAATTGTCTTAGCCAACTCTTCCCTCGAT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 6069 371 +     16727 CTGAAGTTTACATTCTTATCCTGCCCGGATTCGGAATAATTTCTCACATTGTCACTTACTACTCAGGGAAAAAAGAGCCTTTCGGTTATATAGGAATAGTATGAGCAATAATATCTATTGG-GTTTTTAGGCTTTATCGTATGAGCTCACCATATGTTTACCGTAGGAATAGATGTAGACACACGAGCGTACTTTACGTCCGCCACTATAATTATCGCTATTCCAACGGGAGTAAAAGTATTTAGTTGACTGGCAACACTTCATGGAGGCAATATTAAATGATCTCCAGCTATGCTATGAGCTTTAGGGTTTATTTTCTTATTTACAGTAGGCGGGTTAACAGGTATTGTCCTAGCTAATTCGTCCTTAGAC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       9872 371 -     16977 CTGAAGTCTACATCCTCATCTTACCAGGGTTCGGTATAATTTCACACATCGTCACATATTATTCAGGAAAAAAAGAACCATTCGGCTATATGGGCATAGTTTGAGCCATGATATCCATTGG-CTTCTTAGGGTTCATTGTATGAGCTCATCACATATTCACAGTAGGAATGGACGTAGATACACGAGCCTATTTCACATCAGCCACAATAATTATCGCTATTCCAACAGGGGTCAAAGTGTTTAGCTGACTAGCTACCCTGCATGGCGGCAACATCAAATGATCCCCAGCAATACTCTGAGCCTTAGGATTTATTTTCTTGTTCACAGTAGGGGGCCTCACAGGAATCGTACTAGCCAACTCATCCCTAGAC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       9056 371 +     16266 CTGAAGTCTATATTCTAATTCTCCCAGGATTTGGAATAGTTTCTCATATCGTTACATACTACTCAGGAAAAAAAGAACCCTTCGGTTATATAGGGATAGTATGGGCTATAATATCAATTGG-CTTCCTAGGATTTATTGTATGAGCCCACCATATATTCACCGTAGGCATAGACGTTGACACTCGAGCTTACTTTACATCAGCTACTATAATTATTGCTATTCCAACTGGCGTAAAAGTCTTTAGTTGACTAGCTACCCTTCATGGCGGTAATATTAAATGATCCCCCGCTATAATATGAGCTCTAGGATTTATCTTCTTGTTTACAATTGGAGGATTAACTGGCATTGTTCTTGCTAATTCTTCACTAGAC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      5464 372 +     18297 CAGAGGTCTATATTCTGATTCTTCCAGGGTTTGGTATAATTTCTCATATCGTTACCTATTATTCAGGAAAAAAAGAACCATTCGGGTATATAGGAATAGTATGGGCCATAATATCAATCGGTTTTCTTAGGATTCATCGTCTGGGCTCATCATATATTTACTGTTGGTATAGACGTTGATACCCGAGCATACTTTACATCTGCAACTATAATTATTGCAATTCCTACAGGAGTAAAAGTGTTCAGCTGATTAGCTACACTTCACGGAGGTGACATTAAATGGAGCCCCGCTATAATATGGGCCCTAGGCTTCATCTTTCTGTTTACAGTTGGAGGCCTTACTGGTATTATTCTTGCTAACTCATCTCTAGAT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117157547 371 + 174229318 CAGAAGTTTATATTCTTATTCTCCCAGGATTTGGGATCATCTCGCACATTGTTACATATTATTCAGGTAAAAAAGAGCCTTTTGGCTATATAGGAATAGTGTGGGCTATAATATCTATTGG-GTTTTTAGGTTTTATTGTATGAGCCCATCATATATTTACTGTAGGACTAGACGTTGATACTCGAGCATATTTTACTTCCGCAACAATAATTATTGCTATCCCAACAGGAGTGAAAGTATTTAGCTGGTTAGCCACACTACACGGAGGTAACATTAAGTGATCCCCAGCAATACTATGAGCCTTAGGCTTTATTTTCTTATTTACAATTGGAGGTTTAACAGGTATTGTTTTAGCCAACTCCTCACTAGAC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 7365 371 +     16775 CCGAAGTTTACATCCTCATCCTCCCAGGTTTCGGAATAATTTCCCACGTAGTAGCATACTATGCAGGAAAAAAAGAACCATTCGGATACATAGGAATAGTCTGAGCCATACTGTCAATCGG-ATTCCTTGGCTTCATTGTATGAGCCCACCATATATTCACAGTCCGAATGGACGTAGACACCCGAGCCTACTTTACATCAGCCACAATAATCATCGCCATCCCAACTGGTATTAAAGTCTTCAGCTGACTAGCAACCCTGCACGGAGGAACAATTAAATGAGACCCCCCTATGCTATGAGCCCTAGGATTCATCTTCCTCTTCACTATCGGAGGCCTAACGGGAATCGTCCTTGCTAACTCATCACTAGAT
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_43       2619821 371 +   3852807 CAGAAGTCTACATTCTAATCCTTCCAGGATTTGGTATGATCTCGCACATTGTGACCTACTACTCAGGGAAAAAAGAGCCCTTCGGATACATAGGAATAGTCTGAGCAATGATATCCATTGG-ACTCTTAGGTTTTATTGTATGAGCCCACCACATATTTACAGTAGACTTAAATGTTGATACCCGAGCCTACTTCACCTCAGCAACAATAATTATCGCAATCCCAACAGGGGTTAAAGTATTTAGCTGACTAGCTACAATGCATGGAGGAACAATCAAATGAGACGCCCCAATGCTTTGAGCCCTTGGCTTTATTTTCCTATTTACTGTAGGCGGACTAACAGGGATCGTCCTTGCCAACTCTTCTTTAGAC
+i xenTro2.scaffold_43     n 6355 C 0
+s danRer4.chrM                 7145 371 +     16596 CAGAAGTCTACATTCTTATTTTACCAGGATTCGGCATTATCTCCCATGTTGTAGCATACTACGCAGGGAAAAAAGAACCATTCGGGTATATAGGAATAGTATGAGCTATAATGGCTATTGG-TCTCTTAGGTTTTATTGTATGAGCCCATCACATATTCACTGTAGGAATGGATGTAGACACCCGAGCATACTTCACATCCGCCACAATGATTATTGCTATTCCAACTGGTGTAAAAGTATTTAGCTGATTAGCCACTCTCCACGGAGGAGCTATTAAATGAGAAACCCCTATACTATGGGCACTAGGATTTATTTTCTTATTTACAGTAGGAGGGTTAACCGGAATCGTTTTAGCCAACTCATCATTAGAC
+i danRer4.chrM            C 0 C 0
+
+a score=2704170.000000
+s mm8.chrM                     6419 451 +     16299 ATCGTGCTTCACGATACATACTATGTAGTAGCCCATTTCCACTATGTTCTATCAATGGGAGCAGTGTTTGCTATCATAGCAGGATTTGTTCACTGATTCCCATTATTTTCAGGCTTCACCCTAGATGACACATGAGCAAAAGCCCACTTCGCCATCATATTCGTAGGAGTAAACATAACATTCTTCCCTCAACATTTCCTGGGCCTTTCAGGAATACCACGACGCTACTCAGACTACCCAGATGCTTACACCACATGAAACACTGTCTCTTCTATAGGATCATTTATTTCACTAACAGCTGTTCTCATCATGATCTTTATAATTTGAGAGGCCTTTGCTTCAAAACGAGAAGTAATATCAGTATCGTATGCTTCAACAAATTTAGAATGACTTCATGGCTGCCCTCCACCATATCACACATTCGAGGAACCAACCTATGTAAAAG--TAAAAt
+s rn4.chrM                     6400 451 +     16300 ATTGTACTTCATGATACATACTACGTAGTAGCTCACTTCCACTATGTCTTATCTATAGGAGCAGTATTCGCCATCATAGCTGGCTTCGTCCACTGATTCCCACTATTCTCAGGCTATACCCTAAATGACACATGAGCAAAAGCCCACTTTGCCATTATATTTGTAGGTGTAAACATAACATTTTTTCCTCAACACTTCCTAGGATTAGCAGGGATACCTCGTCGTTACTCTGATTATCCAGATGCTTATACCACATGAAATACAGTCTCCTCTATAGGCTCATTCATCTCACTTACGGCCGTCCTTGTAATGATCTTCATGATTTGAGAAGCCTTCGCATCAAAACGAGAAGTGCTCTCAATTTCCTACTCTTCAACTAACCTAGAATGACTGCATGGATGCCCCCCACCTTACCACACATTCGAAGAACCTTCCTATGTAAAAG--TTAAAt
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      6581 453 +     20791 ATCGTACTACATGACACCTACTATGTAGTAGCTCACTTCCACTATGTCCTATCTATGGGGGCTGTATTTGCTATTATAGGAGGATTTGCCCATTGATTCCCCCTATTCTCAGGCTATACCCTTGACCCAACCTGAGCTAAAATTCACTTCACTGTGATATTTGTAGGAGTCAACTTAACCTTCTTCCCTCAACATTTCCTTGGCCTCTCAGGTATACCCCGACGGTACTCAGACTACCCGGACGCCTATACAATATGAAATACTGTTTCATCAATAGGCTCATTCATTTCCCTAACTGCCGTAATAGTAATAATTTTTATAATCTGAGAAGCCTTCGCCTCAAAACGAGAAGTAGAGACTATTGAACTAACCACCACAAACCTAGAATGACTTCATGGATGCCCTCCCCCATACCATACATTTGAAGAACCCGCTTTCGTAAAAGCTTAGTAC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    6996 444 +     16571 ATCGTACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCAATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCTATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTATCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGCCTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTCCTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAA---------
+i hg18.chrM               C 0 I 75
+s panTro2.chrM                 6412 444 +     16554 ATCGTGCTACACGACACATACTACGTCGTAGCCCACTTCCACTACGTTCTATCAATAGGAGCTGTATTCGCCATCATAGGAGGCTTCATTCACTGATTCCCCCTATTCTCAGGCTATACCCTAGACCAAACCTATGCCAAAATCCAATTTGCCATCATGTTCATTGGCGTAAACCTAACCTTCTTCCCACAGCACTTCCTTGGCCTATCTGGGATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCACATGAAATGTCCTATCATCCGTAGGCTCATTTATCTCCCTGACAGCAGTAATATTAATAATTTTCATGATTTGAGAAGCCTTTGCTTCAAAACGAAAAGTCCTAATAGTAGAAGAGCCCTCCGCAAACCTGGAATGACTATATGGATGCCCCCCACCCTACCACACATTCGAAGAACCCGTATACATAAAA---------
+i panTro2.chrM            C 0 I 75
+s rheMac2.chr15            38001964 444 - 110119387 ATTATTTTACACGATACACACTATGTTGTAGCTCATTTCCACTACATCCTATCAACAGGAGCGGTGTTCGCCATCATAGGAGGCTTTAACCACTGGTTCCCCCTATTCTCAGGTTATACGCTTAATCGGACCTACACTAAAATTCAGTTCACCATTATATTCATAGGTGTTAATTTAACCTTTTTCCCACAGCACTTCCTTGGCCTATCCAGTATGCCTCAACGTTATTCCCATCATCCTGATGCGTATACTGCATGAAATATTATCTCATTCTTAGGCTCATTTATCTCATTAACAGCAGTTATGCTAACAATTTTTATAATCTGAGAAGCCTTTGTTTCTAAAAGAAAAACTATAACAACTGAACAACCATCTACTAATTTAGAGTGACTTTACGGCTGTCCACCATCTTACCACACATTTGAAGAGCCAACCTACATTAAA---------
+i rheMac2.chr15           C 0 I 9
+s bosTau2.chrM                 6778 451 +     16338 ATTGTTCTTCACGACACATACTACGTTGTCGCACATTTCCACTATGTTTTATCAATAGGAGCTGTATTTGCTATTATAGGGGGATTTGTTCATTGATTCCCACTATTCTCAGGTTATACTCTCAACGATACATGAGCCAAAATCCACTTCGCAATTATATTTGTAGGCGTCAATATAACCTTCTTCCCACAACACTTTCTAGGACTATCTGGCATGCCTCGACGATACTCCGACTACCCAGATGCATACACAATATGAAATACTATCTCATCAATAGGCTCATTCATTTCCCTAACAGCAGTTATACTAATAGTTTTCATCATCTGAGAAGCATTTGCATCTAAACGAGAAGTCTTGACTGTAGACTTAACCACGACAAATCTAGAATGATTAAACGGATGCCCTCCACCATATCACACATTTGAAGAACCCACCTATGTTAAC--CTAAAAt
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 6440 451 +     16727 ATCGTTCTTCATGATACATATTATGTTGTGGCTCATTTTCACTATGTGCTTTCAATAGGAGCAGTTTTTGCCATTATGGGAGGATTTGCCCACTGATTCCCTTTATTCTCAGGTTATACTCTTAACGATACTTGAGCAAAGATTCACTTTACAATTATGTTTGTGGGAGTAAATATAACTTTCTTCCCTCAACATTTCCTAGGTTTATCTGGAATACCTCGTCGATACTCTGACTACCCAGATGCATATACTACCTGAAATACCGTCTCCTCTATAGGATCGTTTATCTCGCTTACAGCGGTGATGCTTATAATTTTTATGATCTGGGAAGCCTTTGCATCCAAACGAGAAGTTGCTATAGTAGAACTTACTACAACTAACATTGAGTGACTACATGGATGTCCCCCTCCATACCACACGTTCGAAGAACCTACATATGTGATC--CAAAAAt
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      10243 452 -     16977 ATTGTATTACACGACACATACTATGTAGTAGCCCACTTCCACTATGTACTTTCCATAGGAGCCGTATTTGCCATTATAGGAGGCTTTGTCCACTGATTCCCACTATTTTCAGGTTACACCCTAAACTTAACATGAGCTAAAATTCACTTCATTATCATGTTTGTTGGTGTCAACCTAACATTCTTCCCCCAACACTTCCTAGGCCTCTCCGGAATACCACGACGATATTCAGACTACCCTGATGCATACACAATATGAAACACTGTATCATCAATAGGCTCATTTATCTCGCTAACAGCAGTAATACTAATAATTTTCATAATCTGAGAAGCATTTGCATCAAAACGAGAGGTTGATGTAGTAGAATTAACACCAACCAACCTTGAATGACTTCACGGGTGTCCACCACCATACCACACATTCGAAGAACCTGCGTTCGTAAAA-GTTTAACC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       9427 452 +     16266 ATTGTCCTACATGACACCTACTACGTTGTAGCTCACTTTCACTACGTCTTGTCTATAGGTGCAGTTTTCGCCATTATGGGTGGATTTATCCACTGATTTCCACTATTTTCAGGATACACATTAAATTATACATGAGCTAAAATTCAATTCCTAGTTATATTTATTGGTGTTAATTTGACATTTTTTCCCCAACACTTTCTTGGACTATCTGGTATGCCACGTCGATATTCTGACTATCCAGATGCCTATACTGCATGAAATACTGCCTCTTCTATAGGTTCATTTATCTCTTTAGTAGCCGTAATTCTAATAGTCTTTATAATTTGAGAGGCATTTGCTTCTAAGCGCGAAGTTTCTGTGATAGAACTCACAACAACAAACGTAGAATGACTCAACGGATGTCCACCTCCACATCATACATTCGAAGAACCAGCCTACGTAAAA-TCTAACTC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      5836 451 +     18297 ATTGTTCTTCATGATACCTATTATGTAGTAGCCCATTTTCACTATGTCCTCTCCATAGGAGCAGTATTTGCTATTATAGGGGGGTTCATCCATTGATTCCCCCTATTCACAGGCTATACATTAAGTGAAGCATGAGCTAAAGCCCACTTCATTATTATATTTATTGGGGTAAACTTAACATTTTTCCCTCAACATTTTTTAGGCCTTTCAGGTATGCCACGACGTTATTCGGACTACCCTGATGCCTACACTACCTGGAACTCCGTGTCATCAGTCGGATCTTTTATTTCGCTAACAGCTGTAATCCTCATAATCTTCATAGTATGGGAAGCATTTGCTTCAAAACGAGAAGTTACTTCAGTAAACCTAGTTCATACTAATCTTGAATGAATTCACGGATCTCCTCCCCCCTTTCATACATTTGAAGAACCAGTCTATATAAAA-TCCTAA-C
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117157918 453 + 174229318 ATTGTACTTCACGACACATACTATGTAGTAGCCCACTTTCACTATGTGTTATCAATAGGAGCCGTATTCGCTATCATAGGGGGTTTCGTCCATTGATTTCCACTATTCACAGGTTATATACTCAATGACCTATGAACAAAAATTCACTTCTTTATCATATTTGTTGGAGTAAACTTAACCTTCTTCCCCCAACACTTTTTAGGACTTGCTGGCATACCACGACGATACTCTGACTACCCAGATGCTTACACTATATGAAATGTTTTATCCTCAATTGGATCATTTATTTCACTAACAGCTGTAATCCTTATAGTTTTTATTATCTGAGAAGCATTTGCATCTAAACGAGAAGTTCTTAATGTAGAATTAACAACAACTAATATTGAATGACTTTACGGATGTCCACCCCCATATCACACATTCGAACAGCCTGTTTTCATTAAAGCCTAGTTt
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 7736 451 +     16775 ATTGCCCTTCATGACACCTACTATGTAGTCGCCCACTTCCACTATGTCCTCTCAATGGGGGCAGTTTTTGCCATTCTAGCAGGATTTACCCACTGATTTCCCCTCTTCACAGGCTTTACCCTACACCCATCATGAACCAAGGCACATTTCGGAGTAATATTTACCGGAGTTAACCTAACCTTTTTCCCCCAACATTTCCTGGGCCTAGCTGGAATACCCCGACGATACTCAGATTACCCAGACGCCTACACACTATGAAACACACTATCCTCAATCGGCTCCTTAATTTCAATAACAGCCGTAATCATACTCATATTCATCGTCTGAGAAGCCTTCTCAGCAAAACGAAAAGTACTCCAACCCGAATTAACTGCCACTAATATCGAATGAATTCATGGCTGCCCACCCCCATACCACACCTTCGAAGAACCAGCCTTTGTACAAGTGCAAG--
+i galGal2.chrM            C 0 I 71
+s xenTro2.scaffold_43       2620192 436 +   3852807 ATCGTCCTTCACGATACCTATTATGTCGTAGCACACTTCCATTATGTTCTCTCAATAGGAGCAGTATTCGCAATTATAGGAGGCTTTGTTCATTGATTACCGTTATTCACAGGGTACACCCTTCACGAAACATGAGCAAAAATCCACTTCGGCGTTATATTTGCAGGGGTTAACCTAACCTTCTTTCCCCAACACTTCCTAGGATTAGCGGGTATACCTCGACGTTATTCTGATTACCCAGATGCCTACACACTTTGAAACACCGTCTCATCTGTCGGCTCCTTAATTTCCCTAGTGGCGGTAATTATGATGATATTCATTATCTGAGAAGCATTCGCAGCANAACGGGAAGTCACTCTAACAGAACTAACTTCAACAAATATTGAATGACTTCACGGATGCCCTCCCCCTTACCACACATTCGAAGAACCAGCCT-----------------
+i xenTro2.scaffold_43     C 0 n 0
+s fr1.chrUn               326222607 451 + 349519338 ATCGTATTACACGACACCTACTACGTAGTTGCCCATTTCCACTACGTCCTCTCCATGGGTGCTGTATTTGCAATTATGGGTGCATTCGTACACTGATTCCCACTATTTTCAGGATACACACTCCACAGCACTTGAACTAAAATCCACTTCGGAGTAATGTTCATTGGTGTCAACCTAACCTTCTTCCCTCAACACTTCCTTGGTCTAGCTGGAATACCTCGACGATACTCCGACTACCCCGACGCCTACGCCCTATGAAACTCCGTCTCCTCAATTGGCTCAATAGTCTCTCTAGTGGCAGTAATTATGTTCCTCTTTATCCTCTGAGAGGCCTTCACCGCTAAGCGAGAAGTCCAATCAGTTGAACTAACAATGACAAATGTAGAATGACTACACGGGTGCCCTCCTCCTTACCACACATTCGAAGAGCCCGCCTTTGTCCAAACTCAAA--
+i fr1.chrUn               N 0 I 9
+s danRer4.chrM                 7516 451 +     16596 ATCGTACTACATGACACATACTACGTAGTAGCACACTTTCACTATGTTCTTTCAATAGGAGCTGTATTCGCTATTATAGCAGGCTTTGTTCACTGATTCCCACTATTTACAGGCTACACCCTAAACAGTGTATGAACAAAAATCCATTTCGGGGTTATATTTATCGGAGTAAATCTCACATTCTTCCCACAACATTTCCTAGGTTTAGCAGGAATACCACGACGGTACTCTGACTACCCAGACGCCTATGCACTCTGAAATACAGTATCTTCTATTGGGTCACTAATTTCTTTAGTAGCAGTAATCATGTTCTTATTTATCTTATGAGAAGCCTTTACCGCCAAACGAGAAGTTCTGTCAGTTGAATTGACCGCAACAAATGTAGAATGATTACACGGCTGCCCTCCCCCCTACCACACATTTGAGGAGCCAGCATTCGTTCAAATTCAAT--
+i danRer4.chrM            C 0 I 79
+
+a score=206045.000000
+s mm8.chrM                     6870 68 +     16299 aagaaaggaaggaatcgaaccccctaaaattggtttcaagc--------------caatctcatatcctatatgtctttctc--
+s rn4.chrM                     6851 67 +     16300 aagaaaggaaggaatcga-ccccctacaactggtttcaagc--------------caatttcataaccattatgtctttctc--
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      7034 68 +     20791 Aagaaaggaaggaatcgaacctcctaaaactggtttcaagc--------------cagccccatagccactatgactttctT--
+i oryCun1.scaffold_140182 C 0 C 0
+s rheMac2.chr15            38002417 67 - 110119387 gaaaaaggaaggaattgaaccttcagaaactggtttcaagc--------------caatc-aataacctctatgactttctc--
+i rheMac2.chr15           I 9 C 0
+s bosTau2.chrM                 7229 68 +     16338 aagaaaggaaggaatcgaacccccta--------------ctattggtttcaagccaacatcataacctctatgtctctctc--
+i bosTau2.chrM            C 0 I 4
+s canFam2.chrM                 6891 68 +     16727 aagaaaggaaggaatcgaaccccctaaaattggtttcaagc--------------caatgtcataaccattatgtctttctc--
+i canFam2.chrM            C 0 I 4
+s dasNov1.scaffold_23239      10695 68 -     16977 Aagaaaggaaggaatcgaacccccaaaaactagtttcaagc--------------cagctccataacctctatgactttctc--
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       9879 68 +     16266 gagaagggaaggaatcgaacctccaacagttagtttcaagc--------------caactctataacctttatgccttcccC--
+i loxAfr1.scaffold_36650  C 0 I 6
+s echTel1.scaffold_181343      6287 67 +     18297 Aagaaaggaaggaatcgaacccccaaaaattagtttcaagc--------------caactccgtaacctctacgactttct---
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117158371 68 + 174229318 aagaaagggaggaattgaaccccctcagattaatttcaagt--------------caaccccataacctttatgactttctc--
+i monDom4.chrUn           C 0 C 0
+s fr1.chrUn               326223067 70 + 349519338 GAGAAAGGGAGGAATCGAACCCCCGTAAACTGGTTTCAAGC--------------CAGCTACAAAACCACTCTGTCACTTTCTT
+i fr1.chrUn               I 9 C 0
+e xenTro2.scaffold_43       2620628  0 +   3852807 I
+e danRer4.chrM                 7967 79 +     16596 I
+e panTro2.chrM                 6856 75 +     16554 I
+e hg18.chrM                    7440 75 +     16571 I
+e galGal2.chrM                 8187 71 +     16775 I
+
+a score=1505774.000000
+s mm8.chrM                     6938 316 +     16299 -AATAAGATATTAGTAAAA---TCAATTACATAACTTTGTCAAAGTTAAATTATAGATCAATAATCTATATATCTT-----------ATATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGT-AATCCTTATCATAATTGCTCTCCCCTCTCT
+s echTel1.scaffold_181343      6354 314 +     18297 -TACAAGATATTAGTAAAA---T--ATTACCTAGCTTTGTCAGGGCTAAATTACAGGCTAAACCCCTGTATATCTT------------TATGGCATACCCATCCCAATTAGGTTTCCAAGATGCCTCCTCTCCCATCATAGAAGAACTGCTATACTTTCACGACCATGCCCTTATAATTGTTTTCCTAATTAGCTCCCTGGTTCTGTATATCATTCTAGCTATACTCAGTACTAAACTAATACATACTAACACAATAGACGCCCAAGTAATCGAAACTATCTGGACTATCTTACCAGCAGTAAATTCTTGTATTAATCGCCCTACCTTCCTT
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650       9953 314 +     16266 -CATGAAATTTTAGTAAAA---C-AATTACATAGCCTTGTCAAAGCTAAGCTACAGGTTTAAATCCCGTAAATTTC------------TATGGCCTATCCGTTACAATTGGGGTTCCAAGATGCCACATCTCCTGTTATAGAAGAACTCCTTCACTTCCATGACCACACCCTAATAATCATTTTCCTTATTAGCTCCTTAGTCTTGTATATTATTATGCTTATATTAACTTCTAAGCTAGTCCATACAAATATAATAAACGTCCAAGAGATAGAAATAATCTGAACCATTCTCCCAGCTAT-TATCCTTATCTTAATTGCCCTGCCCTCTTT
+i loxAfr1.scaffold_36650  I 6 C 0
+s dasNov1.scaffold_23239      10763 315 -     16977 -AATAAGGTATTAATAAAA---C-AATTATATAACTTTGTCAAAGTTAAATTATAGGTTAAAGCCCTTTATACCTT-----------TTATGCCTTACCCATTACAACTAGGATTCCAAGACGCAACATCACCAATCATAGAAGAACTCCTACATTTCCATGACCACACACTAATAATTGTGTTCCTAATTAGCTCTTTAGTCCTTTACATTATTACCCTGATATTAACAACAAAACTAACCCATACAAGCACAATAGACGCACAAGAAGTAGAAACCGTATGAACAATCTTGCCCGCAGT-TATCCTAATCCTAATTGCACTACCCTCACT
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 6963 312 +     16727 -AG-GAGGTATTAGTAAAA---C--ATTACATGACTTTGTCAAAGTTAAATTATAGGTGAAACCCCTATATATCTC------------TATGGCGTACCCATTTCAACTCGGATTACAGGACGCAACCTCCCCTATTATAGAGGAGCTACTTCATTTTCATGACCATACACTAATAATTGTATTCTTAATCAGTTCTTTAGTTCTCTATATCATTTCACTAATATTGACTACAAAATTAACCCATACAAGCACAATAGACGCACAAGAAGTGGAAACAGTATGAACCATTCTACCCGCCAT-TATCCTAATCCTAATCGCTCTACCTTCCCT
+i canFam2.chrM            I 4 C 0
+s bosTau2.chrM                 7301 314 +     16338 -AACGAGGTGTTAGTAAAA---C--ATTATATAATTTTGTCAAAGTTAAGTTACAAGTGAAAGTCCTGTACACCTC-----------ATATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCAT-CATCTTAATTCTAATTGCTCTTCCTTCTTT
+i bosTau2.chrM            I 4 C 0
+s rheMac2.chr15            38002484 307 - 110119387 -GATAAGATATTAGTAAAC---T-CATTACATAACTTTGTCAAAGTTAAGTTATAGGCTAA-ATCCTATATGTCTT------------AATGGCTCATCCAGTTCAATTAGGCCTTCAAGATGCTACATCCCCTATCATAAAAGAACCACTCACTTTCCATGACCACGTTCTTATAATTATTTTCCTAATTAGTTCCCTGGTTCTATACATTATTTCTCTAA----TACAACAAAATTAACTCATATTAGCACCACAGATGCCCAAGAAATCGAGACTGTCGGAACTATTTTACCTGCCAT-TGTCTTAATTTTAA--GCCCTTCCATCCCT
+i rheMac2.chr15           C 0 I 1750
+s panTro2.chrM                 6931 313 +     16554 -AAAAAGATATTAGAAAAA---C-TATTTCATAACTTTGTCAAAGTTAAATTACAGGTTAA-CCCCCGTATATCTT------------AATGGCACATGCAGCGCAAGTAGGTCTACAAGATGCTACTTCCCCTATCATAGAAGAACTTATTATCTTTCACGACCATGCCCTCATAATTATCTTTCTCATCTGCTTTCTAGTCCTATACGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAGTATTTCAGACGCCCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCAT-CATCCTAGTCCTTATTGCCCTACCATCCCT
+i panTro2.chrM            I 75 C 0
+s hg18.chrM                    7515 313 +     16571 -AAAAAGGTATTAGAAAAA---C-CATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAA-ATCCTATATATCTT------------AATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCAT-CATCCTAGTCCTCATCGCCCTCCCATCCCT
+i hg18.chrM               I 75 C 0
+s oryCun1.scaffold_140182      7102 314 +     20791 -GATAAGATATTAGTAAAA---C-CATTACATAACTTTGTCGAAGTTAATTTATAGGTTCAACTCCTATATATCTT------------TATGGCGTACCCCTTCCAACTGGGCTTTCAGGATGCCTCATCCCCTATTATAGAAGAATTACTTCACTTTCATGACCACACTCTCATAATCGTCTTTCTAATCAGCTCCCTAGTCCTTTATATTATTTCTCTTATATTAACTACAAAGCTCACTCACACAAGCACAATGGACGCTCAAGAGGTAGAGACAATCTGAACCATCCTCCCAGCCAT-TATTCTTATTTTAATTGCGCTGCCCTCCCT
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                     6918 314 +     16300 -AATGAGATATTAGTAAAA---T-AATTACATAACCTTGTCAAGGTTAAGTTATAGACCTA-ATCCTATATATCTT-----------ACATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGT-CATTCTTATTCTAATTGCCCTTCCCTCCCT
+i rn4.chrM                C 0 C 0
+s fr1.chrUn               326223137 310 + 349519338 C-ATAAGACTCTAGTAAAATGGC-AATTACACTACTTTGTCAAGGTAGAATTGTGGGTTAAACCCCCACGTGTCTTATTAT------TAATGGCACATCCTTCACAACTAGGGTTTCAAGATGCAGCTTCACCAGTAATAGAAGAACTCCTTCACTTCCACGACCATGCTCTAATAATCGTATTCCTTATTAGCACATTAGTACTTTACATTATTGTTGCTATAGTCTCCACCAAACTAACTAACAAGTACATTCTAGACTCTCAAGAGATTGAAATTATCTGAACTATCCTACCAGCTAT-TATTCTTATCCTCATTG-------------
+i fr1.chrUn               C 0 M 131
+s danRer4.chrM                 8046 325 +     16596 --ATAAGACATTAGCAAAA---A-CATTACACCACTTTGTCAAGGTGAAATTACAAGTTAAAACCTTGTATGTCTTAACCTAAATTCTAATGGCACACCCTGCACAACTAGGATTCCAAGACGCAGCATCACCTGTAATAGAAGAACTTTTATGTTTTCACGACCATGCTTTAATAATTGTATTTTTAATCAGCACCTTAGTTCTATACATTATCATCGCAATAGTGTCAACCAAACTAACGAATAAATTTATTCTAGATTCCCAAGAAATCGAAATCGTATGAACAGTCCTTCCGGCCAT-CATTCTTATTTTGATTGCTTTACCATCACT
+i danRer4.chrM            I 79 C 0
+s monDom4.chrUn           117158439 314 + 174229318 --ACAAGATATTAGTAAAA---T-AATTACATAACTTTGCCATAGTTAAATTACAAGCTCAATTCTTGTATATCTT-----------AAATGCCGTACCCTATACAGACAGGTTTCCAAGATGCCACATCCCCTATTATAGAAGAACTCATATATTTTCATGATCACACATTAATAATTGTGTTCCTAATTAGCTCCCTAGTTCTTTATATTATTATTCTAATGCTAACTACTAAACTAACTCACACAAGCACTATAGATGCTCAAGAAGTAGAAACAATTTGAACTATTATACCAGCAGT-TATTCTAGTTCTAATTGCTCTCCCATCACT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 8258 311 +     16775 --ATGAGACGTTAGTAAAC---C-AATTACATAGACCTGTCAAGACTAAATCACAGGTGCAAACCCTGTACATCTC-----------ATATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCAT---CAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTAT-TGTCCTAGTCCTGCTTGCCCTCCCCTCCCT
+i galGal2.chrM            I 71 C 0
+e xenTro2.scaffold_43       2620628   0 +   3852807 I
+
+a score=410417.000000
+s mm8.chrM                     7254 86 +     16299 ACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTA-ACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAAT
+s galGal2.chrM                 8569 86 +     16775 CCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTC-ACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAAT
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117158753 86 + 174229318 ACGAATTCTTTACATAATAGACGAAATTTATAACCCCTATCTT-ACAGTCAAAGCTATAGGACATCAATGATACTGAAGTTATGAAT
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      6668 86 +     18297 ACGAATTTTATACATAATAGATGAAATTAATGATCCCACTATT-ACAGGTAAAACTCTGGGTCACCAATGATATTGAAGTTACGAAT
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650      10267 86 +     16266 ACACACTCTGTATATAATAGATGAAATCAATAACCCC-CTATTAACAATCAAGACCATAGGACACCAATGATTCTGGAGTTATGAAT
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239      11078 86 -     16977 ACGAATTTTATATATAATAGACGAAATCAACAACCCACTCCTC-ACCATTAAAGCTATAGGTCACCAGTGATACTGAAGCTATGAAT
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 7275 86 +     16727 CCGAATCCTTTATATAATGGACGAAATTAATAACCCCTCTTTA-ACCGTGAAAACAATAGGCCACCAATGATACTGAAGCTATGAAT
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 7615 86 +     16338 ACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTT-ACAGTAAAAACCATAGGACATCAGTGATACTGAAGCTATGAGT
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34442919 77 - 182086969 ATGTATTCTGTAAATAAC---------TAACAACCCTTCTCTT-ACCGCCAAATCAATTGGCCACCAATAATATTGAAGCTATGAAT
+i rheMac2.chr5            M 981 C 0
+s panTro2.chrM                 7244 86 +     16554 GCGTATCCTTTACATAACAGACGAGGTCAACGACCCCTCCTTT-ACTATTAAATCAATCGGCCATCAATGATATTGAACCTACGAAT
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    7828 86 +     16571 ACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTT-ACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGT
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182      7416 86 +     20791 ACGAATCCTATATATAATAGATGAAATCAACAACCCCTCTTTA-ACAGTAAAAACGATAGGCCACCAATGATATTGAAGCTATGAGT
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                     7232 86 +     16300 ACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTA-ACAGTAAAAACTATAGGACACCAATGATACTGAAGCTATGAAT
+i rn4.chrM                C 0 C 0
+s danRer4.chrM                 8371 86 +     16596 TCGAATTTTATACCTTATAGATGAAATTAATGACCCCCACGTT-ACTATTAAAGCCGTAGGACATCAATGGTACTGAAGCTACGAAT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_43       2620628  0 +   3852807 I
+e fr1.chrUn               326223447 131 + 349519338 M
+
+a score=450960.000000
+s mm8.chrM                     7340 102 +     16299 ATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTC
+s galGal2.chrM                 8655 102 +     16775 ACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAA
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117158839 102 + 174229318 ACACCGACTATGAAAATTTGACATTTGATTCCTATATGGTTCCTACCCAAGACCTTATACCAGGACAACTTCGACTGTTAGAAGTAGATAATCGAGTTGTCC
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      6754 102 +     18297 ATACAGACTATGAAGACCTAGTATTTGACTCATACATAGTCCCCTCTGAGGAATTAAAGCCTGGGGACCTGCGACTTCTTGAAGTAGACAACCGAGTTGTTT
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650      10353 102 +     16266 ATACTGATTACGAAGATTTAGCTTTCGACTCATACATAATCACTACTGATAGCCTAAAATTTGGAGAACTTCGATTATTAGAGGTAGACAATCGGATGGTAT
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239      11164 102 -     16977 ACACAGATTATGAAGACCTAAATTTTGACTCCTATATAGTCCCAACATCAGACCTCAAACCAGGAGAACTACGACTATTAGAAGTCGATAATCGACTTGTTC
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 7361 102 +     16727 ATACTGACTATGAAGACTTAAACTTTGACTCCTACATAATCCCAACACAAGAATTAAAGCCAGGAGAACTCCGACTATTAGAAGTAGACAACCGAGTTGTCC
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                 7701 102 +     16338 ATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTAC
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34442996 102 - 182086969 GTACAGACTGTGAAGAATTAAGCTTCGATTCTTATATAATTCCAACAGCAGACTTAAAGCCAGGAGAACTTCAACTCCTCGAAGTTGATAACCAAACAATTC
+i rheMac2.chr5            C 0 C 0
+s panTro2.chrM                 7330 102 +     16554 ACACCGACTACGGCGGGCTAATCTTCAACTCCTACATACTCCCCCCATTATTTCTAGAACCAGGTGATCTACGACTCCTTGACGTTGATAACCGAGTGGTCC
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                    7914 102 +     16571 ACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTAC
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182      7502 102 +     20791 ACACAGACTATGAGGATTTAAATTTTGATTCTTATATGATCCCAACATCAGACCTGAATCCAGGTGACCTACGACTACTAGAAGTTGACAATCGAGTTGTAC
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                     7318 102 +     16300 ATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCT
+i rn4.chrM                C 0 C 0
+s fr1.chrUn               326223582 100 + 349519338 ATACAGACTATAGCGA-CTAGCCTTTGACTCATATATAGT-CCCACACAAGACCTGGCCCCCGGCCAATTCCGCCTTTTAGAAACTGACCATCGAATGGTCG
+i fr1.chrUn               M 131 C 0
+s danRer4.chrM                 8457 102 +     16596 ATACAGACTACGAAAACCTAGAATTTGACTCTTATATAGTACCAACCCAAGACCTCACACCAGGGGGCTTTCGGCTTCTTGAAACAGACCATCGAATAGTAG
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_43       2620628   0 +   3852807 I
+
+a score=1442452.000000
+s mm8.chrM                     7442 469 +     16299 TGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAAT---AATTTAA--------------TT-----------------------TCACTATGAAGCTAAG--------AGCGTTAACCTTT--TAAGTTAAAGTTAGAGACCTTAAAA----TCTCCAT-AGTGATATGCCACAACTAGATACATCAACATGATTTATCACAATTATCTCATCAATAATTACCCTATTTATCTTATTTCAACTAAAA-GTCTCA--TCACAAACATTC---CCA-CTG----GCACCTTCA-----------------CCAAAATCA-CTAA--CAACCATAAAA--------GTAAAAAC
+s rn4.chrM                     7420 468 +     16300 TACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGCGGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCTAT---AATTTAA--------------AC-----------------------TCATTGCGAAGCTTAG--------AGCGTTAACCTTT--TAAGTTAAAGTTAGAGACAACAAA-----TCTCCAC-AATGACATGCCACAACTAGACACATCCACATGATTTATTACAATCATCTCCTCAATAGCCACACTATTTATTTTATTTCAATTAAAA-ATTTCT--TCCCAAACCTTT---CCT-GCA----CCTCCCTCA-----------------CCCAAAACT-ATAG--CCACAGAAAAA--------ACGAATAA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      7604 473 +     20791 TTCCCATAGAACTCCCAATCCGCATGCTAATCTCCTCGGAAGACGTACTTCACTCATGAGCCGTACCATCACTAGGACTAAAAACAGATGCCATTCCCGGACGCTTAAATCAAGCCACACTTATCTCAACTCGACCAGGACTTTTCTATGGTCAGTGCTCAGAAATTTGTGGCTCAAACCATAGCTTTATACCTATTGTCCTCGAAATAGTTCCACTTAAACACTTCGAAAACTGATCCCTATCTAT---GATTTAG--------------AC-----------------------TCGCTATGAAGCTAAAC-------AGCGCTAGCCTTT--TAAGCTAGAGAGTGAGAGTTAAATG-GTCTCTCCAT-AGTGAAATGCCACAACTTGACACATCCACATGATTTACTACCATTGTCGCCATAATTCTTTCACTATTTATCCTAATACAACTCAAA-TTCCAC--AAATACACATAC---CCT-ATG----AACCCAGTA-----------------CTAAAATCA-CTTG--AGTTTACTTCA--------TTCCCTTG
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    8016 496 +     16571 TCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCCGTATTTAC---CCTATAG--------------CACCCCCTCTACCCC-CTCTAGAGCCCACTGTAAAGCTAACT------TAGCATTAACCTTT--TAAGTTAAAGATTAAGAGAACCAAC-ACCTCTTTAC-AGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAA-ATATTA--AACACAAACTAC---CAC-CTA----CCTCCCTCA-----------------CCAAAGCCC-ATAA--AAATAAAAAAT--------TATAACAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 7432 497 +     16554 TCCCAGTTGAAGCCCCCGTTCGTATAATAATTACATCACAAGATGTTCTACACTCATGAGCTGTTCCCACATTAGGCCTAAAAACAGACGCAATTCCCGGACGCCTAAACCAAACCACTTTCACCGCCACACGACCAGGAGTATACTACGGCCAATGCTCAGAAATCTGTGGAGCAAACCACAGTTTTATACCCATCGTCCTAGAATTAATCCCTCTAAAAATCTTTGAAATAGGACCCGTATTCAC---TCTATAG--------------CACCTTCTCTACCCCTCTCCAGAGCTCACTGTAAAGCTAACC------TAGCATTAACCTTT--TAAGTTAAAGATTAAGAGGACCGAC-ACCTCTTTAC-AGTGAAATGCCCCAACTAAATACCGCCGTATGACCCACCATAATTACCCCCATACTCCTGACACTATTTCTCGTCACCCAACTAAAA-ATATTA--AATTCAAATTAC---CAT-CTA----CCCCCCTCA-----------------CCAAAACCC-ATAA--AAATAAAAAAC--------TACAATAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34443098 468 - 182086969 TCCCAACAGATATCCCCATCCATATATTAATCTCATCCGAAGACGTCCTGCACTCATGAACTATCCCCTCATTGGGCCTGAAAACAGGTGCAATCCCTGGATGCCTAAATCAAACCACCCTAACTGCTATATGACCAGACCTTTACTATGGACAGTGCTCAGAAATCTTTGGGTCCCACCACAGTGTTATACCTATTGTCCTAGAATTAACACCCTTAAAATGCTTCAAAACCTGATCCACGTCCAC---ACTATAA--------------CA-----------------------TCACTGTAAAGCT-ATC------TAGCATTAATCTTT--TAAGTTAAAGACTGAGGGGATCTAC-ACTTCTCTGC-AGTG-AATGCCTCAACTAGATACTTCCACATGATCCATTGTCATCCTGTCAACAACCATAACTTTATTCTCCATTATTCAGTTAAAA-TTATTA--AATT----TCAT---TAT-ACA----TCTCGTACA-----------------CCAAAAAGA-ATCA--AAATGCAAAAA--------CATAAAGC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 7803 471 +     16338 TACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGCGGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCAAT---ATTATAA--------------AA-----------------------TCACTAAGAAGCTATAT-------AGCACTAACCTTT--TAAGTTAGAGATTGAGAGCCATATA---CTCTCCTT-GGTGACATGCCGCAACTAGACACGTCAACATGACTGACAATGATCTTATCAATATTCTTGACCCTTTTTATCATCTTTCAACTAAAA-GTTTCA--AAACACAACTTT---TAT-CAC----AATCCAGAA-----------------CTGACACCA-ACAA--AAATATTAAAA--------CAAAACAC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 7463 485 +     16727 TCCCAATAGAAATAACCATCCGAATACTTATCTCTTCAGAAGACGTTTTGCATTCATGAGCCGTTCCATCACTAGGTCTAAAAACTGACGCTATTCCAGGACGACTAAACCAAACCACCCTTATAGCCATACGACCAGGACTGTACTATGGCCAGTGCTCTGAAATCTGCGGATCTAACCACAGCTTTATACCCATTGTTCTTGAAATAGTCCCCCTATCTTACTTTGAGACCTGATCTGCCTTAAT---AGTATAACCTAGACTAGATCTAC-----------------------TCATTAAGAAGCTATAA-------AGCATTAACCTTT--TAAGTTAAAGACTGGGAGTTTTAAC---CTCTCCTT-AATGAAATGCCACAGCTAGATACATCCACCTGATTTATTATAATCTTTTCAATATTTCTCACCCTCTTCATCCTATTTCAACTAAAA-ATTTCA--AATCACTACT-----------------ACCCAGAAAA--------------CCCGATAAC---CAA--ATCTGCTAAAATTGCTGGTCAACATAA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      11266 474 -     16977 TACCAATAGAGCTATCAATTCGTATACTAATTTCATCCGAAGATGTACTACACTCATGAGCCGTACCATCCTTAGGACTAAAAACAGACGCAATCCCAGGTCGCCTAAACCAAGCCACATTAATAGCAACACGACCTGGCCTATATTACGGTCAATGCTCAGAAATCTGTGGGTCCAACCACAGCTTCATACCTATTGTACTTGAACTAGTCCCCCTAAAACACTTCGAAGACTGATCTGCCTCAAT---ACTTTAA--------------TC-----------------------TCCTTGAGATGCTATAA------TAGCATTAACCTTT--TAAGTTAAAGACTGAGAGTGCAACAAATCTCTCCTC-AATG-AATGCCTCAACTAGATACATCCACATGATTTATTACAATTGTATCAATGCTACTATCATTATTTATCCTAATACAACTAAAG-TTCATT--AAATTCAGCTCA---TTC-TCA----ACCCCATGT-----------------CCAACAACA-ATAG--AAAAAACAAAA--------CACCTAAC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      10455 469 +     16266 TACCTACAGACCTACCAGTTCGAGTACTAGTCTCATCAGAAGATGTTCTCCATTCATGGGCTGTTCCATCTCTAGGTCTAAAAACAGATGCAATTCCAGGACGACTTAATCAAGTAACTTTAACATCAATACGACCTGGCTTATTTTATGGTCAGTGTTCCGAAATCTGCGGAGCAAACCATAGCTTCATACCAATTGTCCTAGAACTAGTTCCACTTAAATACTTTGAAAACTGGTCAGCATCACT---AGCACAA---------------------------------------TCATTAAGAAGCTATAA------TAGCACTAACCTTT--TAAGTTAGAGTATGAGAACACAGAA---TTCTCCTT-AATGA-ATGGAACGAATAGATA------------TTATTATTTGATTACTAGCAGTCGTAATTGTA---CTTACGACACTAAT-------------AATCTTTCTTCA---TCT-TAA----AACTCTGAAGATCATTCGCCTTCTTTTCCCAATCT-CTAAAGAACTATCCAAGAAGTCA--TGTGTTTT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      6856 467 +     18297 TACCAATGGAATTGACTATCCGCATATTAATCTCTTCTGAGGATG-TATCCATTCATGAGCAATACCATCACTAGGTCTAAAAACTGACGCAATCCCAGGCCGACTTAATCAAGCTACCTTAACATCAACCCGCCCAGGATTATTTTATGAGCAATGCTCAGAAATCTGTGGCTCAAACCATAGTTTTATACCTATCGTTTTAGAAATAGTACCCTTAAAATTCTTCGAAAGTTGATCAACCTCAAT---AGTCTAG---------------------------------------GCATTAAGAAGCTATTC------AAGCATTAACCTTT--TAAGTTAAAGACAGGGAGCCC--TA---GTCCCCTT-AATGATATGCCACAATTAGATACATCACCCTGACTTATCTCTATCCTATCAATAATATTTACTCTATACCTTCTGATACCTATTAAA-ATCTCCAAAATTTTGGTTAA---TCA-TGATATTAACTCTGAA-------------CCCTCTAAAATTA-CTAA--GCCTACCAA------------------
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117158941 464 + 174229318 TACCTATAGAACTGCCGATCCGAATGCTAGTCTCTTCAGAAGATGTTCTACATGCATGGGCAGTTCCATCTCTAGGCCTAAAAGCAGATGCTATCCCCGGACGCCTAAACCAAGTCACTCTAACCTCCTCCCGCCCCGGAGTGTTTTACGGCCAATGTTCAGAAATTTGTGGGTCAAACCACAGCTTTATGCCCATTGTCCTAGAAATGACCTCCCTAAAATATTTCGAAAAATGATCC---TCCAT---AATGCAA---------------------------------------GCATATTTAAGCAATT--------AGTCTATACTTTTGGTATGCAAGAGAT-------ATAATA---ATCTCCTTAAATAAAATGCCTCAACTCGACACTTCAACATGAACCTTAACAATTATACTCATAATTATCTCACTATTTTGCATCTATCAGCTTAAA-ATAATG--AATC-AAGTAAT---TAT-CCAAATTACCCCTTCA-----------------AATGAAAAG-AAAA--AAGCTACAAAA--------AGCACCTT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 8757 467 +     16775 TCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTACTGTCATCTTAA---------------------------------------CCATTAAGAAGCTATGCA----CCAGCACTAGCCTTT--TAAGCTAGAGAGAGGGGACACCCTC-----CCCCTT-AATGACATGCCCCAATTAAACCCAAACCCATGATTCTCCATCATACTCCTAACTTGATTCACCTTCTCTCTGCTTATCCAACCCAAACTTCTTT--CATTCACTCTAA---CAA-ACA----ACCCTGCAA-----------------ACAAAATTA-CAAC--AACT---------------AAACCCAC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_96       2679674 480 -   2855184 TTCCCATGGAGTCTCCTATTCGGCTCTTAGTGACCGCTGAAGACGTTCTTCACTCCTGAGCTCTCCCATCCTTCGGAGTAAAAACAGATGCTATCCCAGGACGACTTAATCAAACATCATTCATCGCCACTCGACCAGGAGTATTCTACGGACAATGCTCAGAAATTTGCGGAGCTAATCACAGCTTCATACCGATCGTAGTCGAAGCAGTCCCACTAAACGACTTCGAGAACTGATCTTCATCAAT---ACTAGAA--------------GCC----------------------TCACTAAGAAGCTAAACAGGGCCAAGCGACAGCCTTT--TAAGCTGTAGACTGGTGACTCCCAA---CCACCCTT-AGTGATATGCCACAACTAAACCCAGGCCCATGATTCGCTATTCTAATTTTCTCGTGACTAGTTCTTCTTGTCATTATTCCCCCCAAA-ATTCTC--AAACACACATACAGTCAT-ACA----Gacacacac-----------------acacagtcatacag--acacacacata--------cacac---
+i xenTro2.scaffold_96     I 6355 n 0
+s fr1.chrUn               326223682 478 + 349519338 TT-CAGTGGACTCCCCCATTCGAATCCTAGTCTCAGCAGAAGATGTCCTCCACTCCTGAGCCGTCCCCTCTCTAGGTGTAAAAATGGATGCCGTACCCGGCCGTCTAAACCAAACAGCCTTTATCCTGTCCCGACCTGGTGTTTTCTACGGCCAATGCTCCGAAATCTGCGGAGCTAACCACAGCTTCATACCAATCGTTGTTGAAGCCGTCCCCCTAGAACACTTTGAAAACTGATCCTCACTAAT---GCTCGAA--------------GATGCC-------------------TCACTAAGAAGCTAAAACGGACACAGCGTTAGCCTTT--TAAGCTAAAAA-TGGTGCCTACCAA---ACACCCTT-AGTGAAATGCCTCAACTCAACCCCGCACCTTGATTCCTCATTATGGTCTTCTCTTGATGTGTATTCCTAATCTTCCTCCCTCCAAAA-ATCATA--GCTCACTTATTC---CCAAATG----AACCCTCCT-----------------CTCAAAACA-CTTG--CCCCAAAGAAA--------TCAAA---
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                 8559 475 +     16596 TTCCCAAAGAATCACCAATTCGAATTTTAGTTTCAGCTGAAGACGTACTGCACTCTTGAGCTGTTCCATCATTAGGCATTAAAATAGACGCGGTACCCGGACGATTAAACCAAACCGCTTTTATTGTTTCACGTCCAGGTGTATTCTACGGACAATGCTCTGAAATCTGCGGGGCTAACCACAGCTTTATGCCCATTGTAGTCGAAGCCGTCCCACTTGAATTCTTTGAAAACTGATCTTCAGCTAT---ACTAGAA--------------GACGCC-------------------TCACTAAGATGCTAAAATTGG-ATAGCGTTGACCTTT--TAAGTCAAAACTTGGTGCTTACCGA---CCACCCTT-AGTG-AATGCCTCAGCTTAATCCAAAACCCTGATTTATAATCCTTTTTTTCTCATGAGTCATTTTCCTTACTATTATTCCAACCAAA-ATCATT--AATCACATTCAA---CCTAATG----A---CCCAA-----------------CTCAA---G-TTGA--TGCTAAAGAGC--------ACAAAAAT
+i danRer4.chrM            C 0 C 0
+
+a score=2840419.000000
+s mm8.chrM                     7911 701 +     16299 --CCCTTGAGAATTAAAATGAACGAAAATCTATTTGCCTCATTCAT--TACCCCAACAA-TAATAGGATTCCCAATCGTTGTAGCCATCATTATATTTCCTTCAATCCTATTCCCATCCTC---AA---AACGCCTAATCAACAACCG---TCTCCATTCTTTCCAACACTGACTAGTTAAACTTATTATCAAACAAATAATGCTAATCCACACACCAAAAGGACGAACATGAACCCTAATAATTGTTTCCCTAATCATATTTATTGGATCAACAAATCTCCTAGGCCTTTTACCACATACATTTACACCTACTACCCAACTATCCATAAATCTAAGTATAGCCATTCCACTATGAGCTGGAGCCGTAATTACAGGCTTCCGACACAAACTAAAAAGCTCACTTGCCCACTTCCTTCCACAAGGAACTCCAATTTCACTAATTCCAATACTTATTATTATTGAAACAATTAGCCTATTTATTCAACCAATGGCATTAGCAGTCCGGCTTACAGCTAACATTACTGCAGGACACTTATTAATACACCTA-ATCGGAGGAGCTACTCTAGTATTAATAAATATTAGCCCACCAACAGCTACCATTACATTTATTATTTTACTTCTACTCACAATTCTAGAATTTGCAGTAGCATTAATTCAAGCCTACGTATTCACCCTCCTAGTAAGCCTATATCTACATGATAATACATAATGACC
+s rn4.chrM                     7888 701 +     16300 --CCCTTGAGAATCAAAATGAACGAAAATCTATTTGCCTCTTTCAT--TACCCCCACAA-TAATAGGTCTACCAATTGTTGTGACCATTATTATGTTCCCATCAATTCTATTCCCATCATC---AG---AACGCCTAATCAGCAACCG---ACTACACTCATTTCAACACTGACTAATCAAACTTATCATCAAACAAATAATGTTAATTCACACACCAAAAGGACGAACCTGAGCCCTAATAATTGTATCCCTAATTATATTTATTGGCTCAACCAACCTTCTAGGGCTTCTTCCCCATACATTTACCCCTACCACTCAGCTATCTATAGACCTAAGCATAGCCATCCCCCTATGAGCAGGAGCCGTAATTCTAGGTTTCCGACACAAACTAAAAAATTCTTTAGCCCACTTCTCACCGCAAGGAACCCCCATCTCACTAATTCCCATACTAATCATCATCGAAACTATCAGCCTATTTATTCAACCGATAGCACTAGCAGTACGACTAACAGCAAACATTACAGCAGGCCATCTATTAATGCATCTA-ATCGGAGGAGCTACCCTAGTACTTATAGACATCAGCCCACCAACCGCTACAATTACATTTATTATTCTACTTCTACTTACAGTACTTGAATTTGCCGTAGCCTTAATTCAAGCCTATGTATTCACCCTTCTAGTCAGCCTGTACCTACATGATAACACATAATGACC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      8077 701 +     20791 --CCCATGAGAAACAAAATGAACGAAAATTTATTCTCCTCTTTCGC--TACCCCAACAC-TAATAGGGCTCCCTATTGTAGCCTTAATTATCATATTCCCAACTTTACTATTTCCCTCCCC---TA---GCCGACTAATTAACAACCG---ACTAGTCTCAACCCAACAATGATTAGCCCAACTTATCTTAAAGCAAATAATATTAATACATTCCCCCAAAGGACGAACCTGATCTCTAATATTAATTTCCCTAATCATATTTATTGGCTCAACCAACCTCCTAGGCCTCCTGCCTCACTCATTCACACCAACAACTCAATTATCAATAAATTTAGGGATAGCAATCCCCCTATGAGCAGGAGCCGTAATCACCGGGTTTCGATACAAAACTAAGGCGTCACTAGCCCATTTCCTCCCACAAGGAACCCCTATTCCTCTTATTCCTATGCTAATTGTTATTGAAACTATTAGTCTCTTCATTCAACCTATAGCCCTAGCCGTACGGCTTACAGCCAATATCACAGCAGGCCACCTTCTCATACACCTT-ATTGGAGGCGCTGCACTAGCTTTAGTCTCAATTAGTCCAACAACAGCCCTAATTACCTTTATTATCCTTATTCTACTAACAATTCTAGAATTCGCCGTAGCCTTGATCCAAGCTTACGTCTTTACTCTCCTTGTAAGCCTATACCTACATGACAATACCTAATGACA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    8512 701 +     16571 --ACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTCATTCAT--TGCCCCCACAA-TCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCCCTCTATTGATCCCCACCTC---CA---AATATCTCATCAACAACCG---ACTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGATAGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTTATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTA-ATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTTAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAATGACC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 7929 701 +     16554 --ACCCTGAGAACCAAAATGAACGAAAATCTATTCGCTTCATTCGC--TGCCCCCACAA-TCCTAGGCTTACCCGCCGCAGTACTAATCATTCTATTCCCCCCTCTACTGGTCCCCACTTC---TA---AACATCTCATCAACAACCG---ACTAATTACCACCCAACAATGACTAATTCAACTGACCTCAAAACAAATAATAACTATACACAGCACTAAAGGACGAACCTGATCTCTCATACTAGTATCCTTAATCATTTTTATTACCACAACCAATCTTCTTGGGCTTCTACCCCACTCATTCACACCAACCACCCAACTATCTATAAACCTAGCCATGGCTATCCCCCTATGAGCAGGCGCAGTAGTCATAGGCTTTCGCTTTAAGACTAAAAATGCCCTAGCCCACTTCTTACCGCAAGGCACACCTACACCCCTTATCCCCATACTAGTTATCATCGAAACTATTAGCCTACTCATTCAACCAATAGCCTTAGCCGTACGTCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTA-ATTGGAAGCGCCACACTAGCATTATCAACTATCAATCTACCCTATGCACTCATTATCTTCACAATTCTAATCCTACTGACTATTCTAGAGATCGCCGTCGCCTTAATCCAAGCCTACGTTTTTACACTTCTAGTGAGCCTCTACCTGCACGACAACACATAATGACC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34443566 700 - 182086969 --CCCCTGAGAATTAAAATTGAAGAAAATCTATTTACCCCTTTTAC--TACCCCAACAA-TTCTAGGCCTACCCACAGTAGTATTAATCATTTTATTTCCCACCCTACTATTTCCAACCTC---CA---ATCATCTAATTAGTAACCA---ATTGGTTTCCATTCAACAGTGACTAATTCAACTTGTACTAAAACAAATAATAAGTACCCATAACATTAAACGAAAAACCTGATCCCTTATACTGATCTCCCTAATTCTCTTCATTGCCTCAACCAATCTCCTCAGGCTTCTACCCCATTCATTTACACCAACTACCCAATTATCAATAAATCTAGGTATAGCAATCCCCTTATGAGCAGGTGCAGTAATTATA-ACTTCCACTTTAAGACGAACACATCCTTAGCTCACTTTTTACCACAAGGCACACCTATACCACTTATCTCTATGCTAGTGATCATTGAAACTACTAGCCTATTCATTCAACTGATGGCATTAGCTATGCAGTTAACAGCCAACATTACAGCCGGACACCTACTAATGCATTTATATTGGAGGAGCTACACTAGTACTATAAACTATCAGTCTTCCCACAGCTCCAATT-TCTTCATTATTCTAATCCTACTGAACATCCTCGAATTCACCGTAGCTCTTATTCAGGCCTATGTCTTCACACTACTTGTAAGCCTTTACCTATATGACAACACATAATGACC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                 8274 701 +     16338 --CCCTTGAGAAACAAAATGAACGAAAATTTATTTACCTCTTTTAT--TACCCCTGTAA-TTTTAGGTCTCCCTCTCGTAACCCTTATCGTACTATTCCCAAGCCTACTATTCCCAACATC---AA---ACCGACTAGTAAGCAATCG---CTTTGTAACCCTCCAACAATGAATACTTCAACTTGTATCAAAACAAATAATGAGTATCCACAATTCTAAAGGACAAACATGAACATTAATATTAATATCTCTGATCCTATTTATTGGATCAACAAACCTACTAGGCCTATTACCCCATTCATTCACACCAACAACACAACTATCAATAAACCTAGGCATAGCCATCCCCCTGTGAGCAGGAGCCGTAATTACAGGATTCCGCAATAAAACTAAAGCATCACTTGCCCATTTCTTACCACAAGGAACACCCACTCCACTAATCCCAATACTAGTAATTATTGAAACTATCAGCCTTTTTATTCAACCTATAGCCCTCGCCGTGCGGTTAACAGCTAACATCACTGCAGGACACCTATTAATTCACCTA-ATCGGAGGAGCTACACTTGCACTAATAAGCATTAGCACTACAACAGCTCTAATTACATTCACCATTCTAATCCTACTAACAATTCTAGAGTTTGCAGTAGCTATAATCCAAGCCTATGTATTCACTCTCCTAGTCAGCCTATATCTGCATGACAACACATAATGACA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 7948 701 +     16727 --TCCTTGAGAAAACAAATGAACGAAAATCTATTCGCTTCTTTCGC--TGCCCCCTCAA-TAATAGGTCTCCCTATTGTGGTACTGATCGTCATATTCCCTTCCATTTTATTCCCAACACC---CA---GTCGCCTAATCAATAATCG---GTTAATCTCCATTCAGCAATGACTAATTCAACTAACATCAAAACAAATACTAGCAATTCATAACCAAAAGGGACGAACCTGAGCTCTCATACTTATATCACTAATTCTATTTATTGGCTCAACTAATCTACTTGGACTATTACCTCACTCATTTACGCCCACAACACAACTCTCTATAAACCTCGGAATAGCAATTCCCCTATGAGCAGGGACAGTAATTACCGGTTTCCGCTATAAAACCAAAGCATCCTTAGCACACTTTCTACCCCAAGGCACCCCTCTCCCCCTAATTCCAATACTAGTAGTCATCGAAACTATTAGTCTATTTATTCAACCCATGGCTCTAGCCGTTCGATTAACCGCCAATATTACTGCAGGACACCTCCTAATCCATTTG-ATTGGAGGGGCTACCTTAGCTCTTATCAATATTAGCGCGACCACAGCTTTTATCACTTTTATTATTCTAATCCTACTTACGATCCTAGAATTTGCTGTTGCCTTAATTCAAGCCTATGTTTTTACCTTACTAGTGAGTCTATACTTACATGACAACACCTAATGACC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      11740 701 -     16977 --TCCTTGAGAAATAAAATGAACGAAAACCTATTTGCCTCATTCGC--TACCCCTACCA-TAATAGGCCTGCCAATCATCATATTAATCATCATATTCCCAAGTATTCTTTTCCCTACCCC---TA---AACGGATAATTACCAACCG---AGTGGTATCAGTCCAACAATGATTAATCAACATGATCATAAAGCAAATAATGAATATTCACAACAACAAAGGACGAACATGAACTCTTATATTAATCTCTCTCATCACATTCATCGGCACTACCAACCTACTAGGCCTATTACCACACACTTTTACACCCACCACACAACTCTCTATAAACTTAGGCATAGCTATTCCATTATGAGCAGGCGCAGTAGTAACAGGCTTCCGACATAAAACCAAAGCCTCACTAGCACACTTCCTACCACAAGGCACACCAATTCCACTGATTCCCATACTAATTATCATTGAAACCATCAGCCTGTTTATTCAACCAATAGCCCTAGCTGTCCGACTCACAGCAAACATCACAGCAGGACACCTTCTAATCCATCTA-ATTGGAGGAGCCACATTAGCCTTAATATCAATTAGCCCAACAACAGCCTCAATCACATTTATCATCTTAATTCTACTAACAATTCTAGAATTCGCAGTAGCCCTAATTCAAGCATACGTCTTCACACTACTAGTAAGCCTGTACTTACATGATAATACTTAATGACC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      10924 689 +     16266 --CCCTTGAAAGAAGAAGTGAACGAAGAACTATCCACCTTCTTCTATGTACCCGTAGGTACAATAATACTAGCTA---------------TTGCATTTCCAGCAATCCTACTTCCAACCCC---AA---ATCGCCTAATTACCAACCG---TTGAATTACAATCCAACAATGACTAATCCAATTAATCATAAAACAACTTCTATCTATTCATAATACAAAAGGACTGTCATGATCTCTAATATTAATTACTCTAACTTTATTCATTGGTCTAACCAATCTACTAGGTCTATTACCCTATTCATTCGCTCCCACAACACAACTAACCGTAAACTTAAGCATAGCAATCCCCCTATGGACTGGTACAGTTGTCCTGGGTTTCCGATATAAAACTAAAATCTCACTAGCCCATCTTCTCCCACAAGGAACACCTATATTCCTTATCCCTATAATTATTATTATCGAAACCATTAGTCTCCTCATTCGACCAGTCACCCTAGCGGTTCGACTCACCGCCAATATCACGGCAGGTCACTTACTTATTCATTTA-ACCGGAACCGCCACACTAACTTTATCATCCATCCATTCAATAACAATTACAGTAACATTTGTTACAGTAATTCTACTTACGATCCTGGAACTTGCCGTAGCACTAATTCAGGCCTACGTCTTTGCTCTACTAATTAGCCTCTACCTACATGAGAATGCTTAATGACT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      7323 699 +     18297 --CCCATGAAACAATAAATGAACGAAAATCTATTTGCCTCATTCTC--TACCCCTACAT-TAATAGGACTACCTATTAGTATTATAATTGTTGCATTCCCTGCCTTACTATACCCTACATC---TA---ACCGTTTAATTAGCAACCGCATTCGA---ACCCTCCAACAATACCTAATTAACCTTATTCTAAAACAAATAATAGCTACCCATAGCCCTAAAGGTCGAACCTGATCACTAATACTTATATCACTTATTATTTTTATTGCATCAACAAATCTTTTAGGTCTTTTACCCCATACATTTACACCTACTACACAACTATCTATTAATTTGGGTTTAGCAATTCCACTGTGAGCAGGAGCAGTAATTTTAGGCTTTCGCTACAAATTTAAAACATCTGTGTCCCAT-TTTTACCTCAAGGTACCCCAATCCT-CTAATCCCCATACTTATTATTATCGAAACTATTAGCCTATTTATTCAACCCATAGCACTAGCCGTTCGATTGACAGCCAATATTACAGCTGGGCACCTTCTCATACACCTA-ATTGGGGCTGCTACCCTAGCATTATTCTCAATCAGTACCTCAACAGCCCTTATTACTTTTATCATTCTTCTACTTCTTACAATACTAGAATTTGCTGTGGCACTGATTCAAGCCTATGTCTTCACTCTTCTAGTAAGCCTCTATTTACACGATAACACTTAATGACT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117159405 701 + 174229318 --ACCCTGACAAACAAAATGAACGAAAATTTATTTGCCCCATTCGT--CACACCAACAA-TTATAGGTATTACAACCCTACCTATTATTATTATATTTCCCTGTGTTATACTATCATCCCC---AA---AACGATGACTACCAAACCG---AATTCAAACACTACAAATCTGACTAATTCGCTTAATTACTAAACAAATAATGACAATGCATAACAAACAAGGACGAACCTGGACCCTAATACTAATCTCTTTAATTCTCTTTATCGCTTCTACTAATCTCTTAGGGCTACTCCCATATTCATTCACACCTACAACTCAACTATCAATAAATATTGGAATAGCTATCCCACTATGAGCCGGAACAGTAATTATAGGATTCCGAAACAAACCTAAAATCTCTTTAGCTCACTTCCTACCACAAGGTACTCCAACACCCCTAATTCCTATATTAATTATTATTGAGACAATTAGCTTATTTATTCAACCCCTAGCCTTAGCTGTACGATTAACTGCCAATATCACTGCAGGACATCTCCTAATTCACCTA-ATTGGAGCAGCCACTTTAGCCCTATCATCAATTAATACAACCGTTTCAACCATTACATTTTCAATTCTATTCCTTCTAACCATCTTAGAGCTAGCAGTAGCTATAATTCAAGCCTACGTATTCACGCTCCTAGTTAGTCTATACTTACACGATAATTCATAATGACC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 9224 704 +     16775 --CCCCTGAACCTGACCATGAACCTAAGCTTCTTCGACCAATTCTC--AAGCCCCTGCC-TACTAGGAATCCCTCTAATCCTCCCATCACTCCTTCTTCCAGCCCTCCTACTTCCATCACCAGGAA---ACCGATGGATCAACAACCG---CCTCTCCACCATCCAACTCTGATTCACCCACCTAATCACAAAACAACTAATAACCCCCCTAAACAAGGCAGGTCACAAATGAGCCCTCCTACTCACCTCACTTATCCTAATACTCCTCTCCATTAACCTCCTAGGCCTCCTCCCCTACACCTTCACCCCAACTACCCAACTATCAATAAACATGGCCTTAGCCCTGCCACTATGACTAGCCACCTTACTAACAGGCCTGCGAAACCAACCCTCCGCCTCCTTAGGACACCTACTCCCTGAAGGCACCCCCACCCCACTGATTCCAGCCCTAATCATAATCGAAACAACCAGCCTACTTATTCGGCCATTAGCCCTAGGAGTACGCCTAACAGCAAACCTCACAGCTGGTCACCTACTTATCCAACTT-ATCTCTACAGCCACAATCGCCCTACTACCAATAATGCCATCAATCTCCGCCCTAACGGCACTCATCCTATTCCTACTAACCATCCTAGAAGTGGCAGTAGCAATAATCCAAGCCTACGTCTTCGTCCTCCTCCTAAGCCTCTACTTACAAGAAAATATTTAATGGCA
+i galGal2.chrM            C 0 C 0
+s fr1.chrUn               326224160 703 + 349519338 ---CCCTGACCCTGATCATGACACTAAGCTTCTTCGACCAATTTCT--TAGCCCCACCG-CCTTTGGTATTCCCCTGATTGCCCTCGCTCTCCTATTACCTTGGACCCTCTTCCCCACACC---AACCAACCGTTGAACCAACAATCG---TCTTTTAACACTTCAAAGCCAATTTATTAATCGATTTACTCAACAACTGCTCCTCCCACTAAACATAGGAGGGCACAAATGAGCCCTTATATTCGCCTCATTAATAGTGTTCCTAATTACCATTAATATGCTAGGACTCCTTCCATACACATTCACCCCCACCACACAGCTTTCCGTAAATATAGCCCTAGCTGTACCCCTATGACTCGCAACAGTAATCATCGGAATACGAAACAACCCAACAGCAGCCCTAGGCCACCTTCTTCCAGAAGGCACCCCCAACGCTCTAATCCCTATCCTAATTATTATCGAAACTGTCAGCCTCTTCATTCGACCTTTAGCACTAGGAGTTCGACTAACCGCTAACCTCACAGCAGGCCACCTGTTGATTCAACTA-ATCGCTACAGCAGCTTTCGTACTCCTCCCCCTTATACCAACTGTCGCCATTCTGACATCAACCCTATTATTCCTCCTGACACTTCTAGAAGTCGCCGTCGCAATAATCCAAGCCTATGTTTTCGTACTTCTTCTAAGCCTCTACCTACAAGAAAACGTTTAATGCCC
+i fr1.chrUn               C 0 N 0
+s danRer4.chrM                 9034 706 +     16596 GACACTTGAAACTGACCATGATAACAAGCTTCTTCGATCAATTCGC--GAGCCCCTACC-TTTTAGGTATCCCCCTTATCCTCGTTGCCATACTTCTACCTTGACTTCTTTTTCCTGCTCC---AACATCACGATGAATCAACAATCG---ACTTATCACCGTCCAAACATGATTGACTGGACGATTCACAAACCAACTTATGACCCCACTAAACTTTAGCGGCCACAAATGAGCACTTTTATTTGCCTCTCTAATAGTATTCTTAATCACAATTAATCTTTTAGGACTTCTTCCTTATACTTTTACACCAACAACCCAACTCTCTCTGAATATAGGATTTGCAGTACCCCTATGACTTGCCACAGTAATTATCGGAATAAAAAATCAACCGACTATTGCCCTAGGACATCTTTTACCAGAAGGAACCCCCATCCCATTAATTCCGGCCCTTATTATTATCGAAACAATTAGCTTATTTATTCGACCATTAGCTTTAGGGGTACGACTTACTGCAAACCTCACAGCAGGCCACCTACTAATTCAACTT-ATTGCCACAGCAGTATTTGTTCTACTACCAATAATACCAGCAGTAGCAATTTTAACTGCCTCCGTCCTTTTCTTACTTACCCTGCTAGAAGTTGCAGTAGCAATAATCCAAGCCTACGTCTTTATTCTTCTTTTAAGCCTATATCTGCAAGAAAACATTTAATGGCC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154   0 -   2855184 I
+
+a score=507751.000000
+s mm8.chrM                     8612 99 +     16299 CACCAAACTCATGCATATCACATAGTTAATCCAAGTCCATGACCATTAACTGGAGCCTTTTCAGCCCTCCTTCTAACATCAGGTCTAGTAATATGATTT
+s rn4.chrM                     8589 99 +     16300 CACCAAACCCATGCATACCATATAGTAAACCCAAGCCCATGACCACTAACAGGAGCCCTATCAGCTCTTCTACTCACATCCGGCTTAGTAATATGATTC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      8778 99 +     20791 CACCAAACTCACGCTTACCATATAGTCAACCCAAGCCCCTGACCACTCACCGGAGCCCTATCTGCCCTTCTTATGACATCAGGCCTAGCCATATGATTT
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    9213 99 +     16571 CACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 8630 99 +     16554 CACCAATCACATGCCTACCACATAGTAAAACCCAGCCCATGACCCCTAACAGGGGCCCTCTCGGCCCTCCTAATAACCTCCGGCCTGGCCATATGATTC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34444266 99 - 182086969 CACCAAACACATGCCTACCATATAGTCAAACCTAGCCCCTGACCACTAACAGGAGCTCTCTCATCTCTCCTAATAACATCTGGCCTGGCCATGTGATTT
+i rheMac2.chr5            C 0 M 987
+s bosTau2.chrM                 8975 99 +     16338 CACCAAACTCATGCTTATCATATAGTAAACCCAAGCCCTTGACCTCTTACAGGAGCTTTGTCTGCCCTCTTAATAACATCCGGCCTAACCATGTGATTT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 8649 99 +     16727 CACCAAACTCACGCTTACCACATAGTCAACCCAAGCCCATGACCGCTGACAGGGGCCCTTTCTGCCCTCCTTATAACATCGGGTCTTATCATATGATTT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      12441 99 -     16977 CACGAGACACATGCATACCATATAGTAAACCCAAGCCCTTGACCTCTGACAGGCGCTCTATCAGCTCTACTAATAACATCAGGCCTAATCATATGATTC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      11613 99 +     16266 CACCAAACACATGCCTATCACATAGTAGATCCAAGCCCTTGACCTCTTACCGGAGCATTATCTGCCCTACTTATAACATCCGGCCTAACTATATGGTTT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      8022 99 +     18297 CACCAAACCCATGCTTATCATATAGTTAATCCTAGCCCTTGACCACTTACAGGGGCTCTTTCAGCACTTCTACTCACTTCAGGCCTTGCGATTTGATTC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117160106 99 + 174229318 CACCAAACTCACGCGTATCATATAGTTAACCCCAGCCCATGGCCATTAACAGGAGCTCTTTCAGCTCTACTTTTAACCTCCGGTATAATTATATGGTTT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                 9928 99 +     16775 CACCAAGCACACTCCTACCACATAGTTGACCCAAGCCCATGACCAATCTTCGGCGCAGCCGCAGCACTACTAACCACCTCTGGCCTAATCATATGGTTC
+i galGal2.chrM            C 0 C 0
+s danRer4.chrM                 9740 99 +     16596 CACCAAGCACATGCATATCACATAGTTGACCCAAGCCCATGACCACTAACTGGAGCTGTAGCCGCCCTATTAATATCATCTGGCTTAGCAATTTGGTTT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154  0 -   2855184 I
+
+a score=95613.000000
+s mm8.chrM                     8711 42 +     16299 CACTATAATTCAATTACACTATTAACCCTTGGCCTACTCACC
+s rn4.chrM                     8688 42 +     16300 CATTACAACTCCACAATTCTCCTATCATTAGGCCTCCTGACA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      8877 42 +     20791 CATTTTAACTCCCCCTCACTTCTATTAATCGGCTTAGTGACC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    9312 42 +     16571 CACTTCCACTCCATAACGCTCCTCATACTAGGCCTACTAACC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 8729 42 +     16554 CACTTCTACTCCACAACACTACTCACACTAGGCTTACTAACT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr15            38004541 42 - 110119387 CATTTTAATTCTACTACTCTTTTAACCCTAGGCTTATTAATC
+i rheMac2.chr15           I 1750 C 0
+s bosTau2.chrM                 9074 42 +     16338 CACTTTAACTCAATGACCCTGCTAATAATTGGCCTAACAACA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 8748 42 +     16727 CACTATAACTCAATAGCCCTACTTACATTAGGATTCACAACC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      12540 42 -     16977 CACTTTAATTCTCCCCTATTACTAGTTCTAGGCTTAACCACT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      11712 42 +     16266 CATTATCACTCTGTAACCCTCCTGCTTTTAGGATTAACAACC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      8121 42 +     18297 CACTATAACTCTCCCCTCTTACTTCTTATTGGCTTGTCAACT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117160205 42 + 174229318 CATTATAACTCAATATTTCTTTTAATAGTTGGATTAATCTCT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                10027 42 +     16775 CACTACAGCTCGACCACCCTACTGACAATAGGCCTCCTCTCT
+i galGal2.chrM            C 0 C 0
+s danRer4.chrM                 9839 42 +     16596 CACCTTCACTCAATGACATTAATTGTTCTAGGAATAATTCTT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154  0 -   2855184 I
+
+a score=2914356.000000
+s mm8.chrM                     8753 529 +     16299 --AATATCCTCACAATATATCAATGATGACGAGACGTAATTCGTGAAGGAACCTACCAAGGCCACCACACTCCTATTGTACAAAAAGGACTACGATATGGTATAATTCTATTCATCGTCTCGGAAGTATTTTTCTTTGCAGGATTCTTCTGAGCGTTCTATCATTCTAGCCTCGTACCAACACATGATCTAGGAGGCTGCTGACCTCCAACAGGAATTTCACCACTTAACCCTCTAGAAGTCCCACTACTTAATACTTCAGTACTTCTAGCATCAGGTGTTTCAATTACATGAGCTCATCATAGCCTTATAGAAGGTAAACGAAACCACATAAATCAAGCCCTACTAATTACCATTATACTAGGACTTTACTTCACCATCCTCCAAGCTTCAGAATACTTTGAAACATCATTCTCCATTTCAGATGGTATCTATGGTTCTACATTCTTCATGGCTACTGGATTCCATGGACTCCATGTAATTATTGGATCAACATTCCTTATTGTTTGCCTACTACGACAACTAAAATTTC
+s rn4.chrM                     8730 529 +     16300 --AACATCCTAACTATATATCAATGATGACGAGATATCATCCGTGAAGGAACATACCAAGGCCACCACACCCCTATTGTACAAAAAGGCCTCCGATACGGAATAATCCTGTTTATTGTCTCCGAAGTATTCTTCTTTGCCGGATTTTTCTGAGCATTTTATCATTCCAGCCTAGTTCCTACCCACGACCTAGGCGGTTGCTGACCCCCAACAGGAATCACCCCTTTAAATCCCCTAGAAGTACCCCTTCTAAATACATCAGTCCTCTTAGCATCAGGAGTCTCAATTACATGAGCCCATCACAGCCTAATAGAAGGCAACCGAAACCATATAAACCAAGCCCTACTAATCACCATTCTCTTAGGATTATATTTCACTATCTTACAAGCCTCAGAGTATTTCGAAACATCATTTTCTATCTCAGACGGAATTTACGGCTCAACATTCTTCATAGCAACGGGATTTCATGGCCTCCACGTAATTATTGGCTCAACTTTCCTAATTGTCTGTCTACTACGACAACTAAAATTCC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      8919 529 +     20791 --AACACTCTCACCATATACCAATGATGACGAGACATCGTACGAGAAGGTACATTCCAAGGCCACCATACTCCTATTGTACAAAAAGGCCTACGATATGGCATAATTCTCTTTATCATCTCAGAAGTATTCTTTTTCGCGGGCTTCTTCTGAGCCTTCTACCACTCAAGCCTAGCTCCTACCCCAGAACTAGGAGGATGCTGACCTCCAACAGGCATCAACCCCCTTAATCCCCTTGAAGTGCCGCTACTAAACACTTCAGTCCTCCTGGCTTCAGGAGTCTCAATCACCTGGGCCCACCACAGTTTAATAGAAGGCAATCGCAAAAACATACAGCAAGCTCTAGCCATTACCATTCTCCTAGGTATCTATTTTACCCTACTTCAAGCATCGGAGTATTACGAAACATCTTTTACTATTTCAGATGGAGTCTACGGATCAACATTCTTCATAGCCACAGGATTTCACGGTCTTCACGTCATCATTGGGTCCACTTTTCTTACGGTCTGCCTTCTACGACAATTTAACTTTC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    9354 529 +     16571 --AACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGCACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTACTTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTTTGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCCTCACTATCTGCTTCATCCGCCAACTAATATTTC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 8771 529 +     16554 --AACACATTGACCATATATCAATGATGACGCGATGTTATACGAGAAGGCACATACCAAGGCCACCACACACCACCCGTCCAAAAAGGTCTCCGATATGGGATAATTCTTTTTATTACCTCAGAAGTTTTTTTCTTTGCAGGATTTTTTTGAGCTTTCTACCACTCCAGCCTAGCCCCTACCCCCCAGCTAGGAGGACACTGGCCCCCAACAGGTATTACCCCACTAAATCCCCTAGAAGTCCCACTCCTAAACACATCTGTATTACTCGCATCAGGAGTATCAATTACTTGAGCCCATCACAGCTTAATAGAAAATAACCGAAACCAAATAATTCAAGCACTGCTTATTACGATTCTACTAGGTCTTTATTTTACCCTCCTACAAGCCTCAGAATATTTCGAATCCCCTTTTACCATTTCCGATGGCATCTACGGCTCAACATTCTTTGTAGCCACAGGCTTCCACGGACTCCACGTCATTATTGGATCAACTTTCCTCACTATCTGCCTCATCCGCCAACTAATATTTC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr15            38004583 528 - 110119387 --AACACACTAACTGTATACCAATGATGATGTAATATTATCCGAGAAAGTAAATTTCAAGGCCACCATATAACAGTTGTCCAAAAAGGCCTCCAATATGGAATAATTCTATTTATTATCTCAGAAG-TTTCTTCTTTGCTGGTTTCTTCTGGGCATTCTATCACTCTGGTCTAGCCCTAATGCCAGAATTAGGAGGACAGTGACCCCCAACAGGCATTTTTCCCCTCAACCCCTTAGCAGTACCCCTCTTGAATACATCTGTATTACTTGCATCAGGAGTTTCAGTTACTTGGGCTCATCACAGCCTGATAGAAGGTAATCGAAAGCAAATAATTCTAGCACTATCCATCAGAATTACCTTAGGTATTTACTTCACCCTCCTACAAATCTCAGAATACTTTGAGGCCGCTTTTACTATCTCTGATGGGATCTACGGCTCAACAATCTTTTTAGCCACAGGCTTTCATGGATTTCATGTTATTACTGGATCAACATTTCTCACTATCTGCTTCCTCCACCAATTAAAATATC
+i rheMac2.chr15           C 0 I 6148
+s bosTau2.chrM                 9116 529 +     16338 --AATATACTAACAATATACCAATGATGACGAGATGTTATCCGAGAAAGCACCTTCCAAGGGCACCATACCCCAGCTGTCCAAAAAGGCCTCCGTTATGGAATAATTCTTTTTATTATCTCCGAAGTACTATTCTTTACCGGATTTTTCTGAGCTTTCTACCACTCAAGCCTCGCCCCCACCCCTGAACTAGGCGGCTGCTGACCCCCAACAGGCATTCACCCACTAAACCCCCTAGAAGTCCCACTGCTCAACACCTCTGTCCTATTGGCTTCCGGAGTTTCTATTACCTGAGCCCATCATAGTTTAATAGAAGGGGACCGAAAGCATATATTACAAGCCCTATTTATCACCATCACATTAGGAGTCTACTTCACACTACTACAAGCCTCAGAATACTATGAAGCACCTTTTACTATCTCCGACGGAGTTTACGGCTCAACTTTTTTTGTAGCCACAGGCTTCCACGGCCTCCACGTCATCATTGGGTCCACCTTCTTAATTGTCTGCTTCTTCCGCCAATTAAAATTTC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 8790 529 +     16727 --AACCTGTTAACCATATGCCAGTGATGACGAGATGTGATCCGAGAAGGCACATTCCAAGGACATCATACCCCTATTGTACAAAAAGGACTACGATACGGAATAGTTCTTTTTATCGTATCAGAAGTATTTTTCTTTGCAGGCTTCTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACTCCTGAACTTGGGGGTTGCTGACCTCCTACCGGCATTATTCCTCTTAACCCATTAGAAGTGCCTCTACTCAACACCTCAGTCCTCCTAGCCTCCGGAGTATCTATTACTTGAGCCCATCATAGTTTAATAGAAGGTAATCGCAAACATATACTTCAAGCCTTATTCATTACAATCTCCTTAGGCGTATATTTTACGCTATTACAGGCCTCCGAATACTATGAGACATCTTTTACAATCTCCGATGGGGTATACGGATCTACCTTTTTTATAGCCACTGGATTTCACGGATTACACGTAATTATTGGCTCTACATTCCTCATCGTGTGCTTCCTCCGACAGCTATACTACC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      12582 529 -     16977 --AACTTCTTAACTATATACCAATGATGACGAGACATTATTCGAGAAAGCACATTTCAAGGTCACCACACAACCATTGTACAAAAAGGCCTACGATACGGCATAATCCTATTCATTGTGTCAGAAGTGTTCTTCTTTGCGGGTTTCTTCTGAGCCTTTTACCACTCAAGCCTAGCTCCAACTCCAGAACTAGGAGGCTGCTGACCACCAACAGGAATTAACCCTCTCAACCCCCTAGAAGTACCCTTACTAAATACATCAGTCCTTCTTGCCTCAGGAGTATCAATTACATGGGCACACCATAGCTTAATAGAAGGTCACCGAAAGCACATACTACAAGCCCTATTTATTACTATCGCTCTAGGCGTATACTTTACCCTCTTACAAGCCTCAGAATATTACGAAGCACCATTCACAATTTCCGACGGCATTTACGGCTCCACGTTCTTTGTAGCAACCGGATTCCATGGACTACACGTAATTATCGGCTCATCTTTCCTAATCGTCTGCTTCATACGTCAACTAAAATTTC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      11754 529 +     16266 --AATATCCTAACTATATTTCAATGATGACGAGATGTAGTTCGAGAAGGAACCTTCCAAGGCCACCATACACCTGTCGTGCAAGAAAGTTTACGATATGGTATAATTTTATTTATCACCTCTGAAGTATTATTCTTCACAGGTTTCTTCTGAGCCTTTTATCACTCCAGTCTAGCACCTACCCCTGAACTAGGAAGCTATTGACCTCCAGTAGGTGTCTACCCACTAAATCCACTAGAAGTACCGCTTCTAAATACATCAGTCCTCCTAGCTTCAGGAGTGACTATTACCTGAGCTCACCATAGCTTAATAGAAGGAAACCGTAAAAATATACTTCAAGCCCTCCTTATTACTATTCTCTTAGGAGTCTACTTCACACTTCTCCAAATGTTTGAGTACTATGAAGCATCCTTTACAATCTCCGATGGCATCTACGGCTCAACTTTCTTTGTAACCACAGGATTCCATGGCCTACACGTTATTATTGGCTCTACATTTCTCCTAACCTGCTTTATTCGCCAACTTAAATTCC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      8163 529 +     18297 --AATCTACTAACTATATATCAATGATGACGTGATATTATTCGAGAAAGCACCTTTCAAGGTCATCACACACCTTTTGTCCAAAAAGGTCTACGCTATGGAATAATCCTCTTTATTATCTCTGAAGTATTCTTTTTCGCCGGCTTCTTCTGAGCTTTCTACCATTCAAGTTTAGCCCCAACACCAGAGTTAGGTGGCTGCTGGCCCCCTACAGGAATTACTCCCCTAAACCCCCTGGAAGTCCCTCTATTAAACACCGCTATTCTCCTGGCCTCCGGAGTTACTATCACCTGAGCCCACCACAGCCTCATAGAAGGAAATCGAAAGCAAATAATTCAAGCACTATCCATCACGATCGCTCTAGGCATTTACTTTACACTTCTTCAAGCCTCGGAATATTATGAGACTCCATTTACTATTTCTGATGGAGTCTACGGCTCAACATTTTTTGTAGCCACGGGTTTCCATGGTCTTCATGTTATTATTGGCTCCACTTTCCTCATTGTTTGCCTACTACGTCAAGTAATGTTCC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117160247 529 + 174229318 --ATACTCCTGACAATATACCAATGATGACGAGACATTATCCGTGAAGGGACATTTCAAGGACACCATACCCCAGTAGTACAAAAGGGATTGCGATATGGAATAGTACTATTTATCTTATCAGAAGTTTTCTTCTTCATTGGCTTCTTCTGAGCATTTTATCACTCAAGCTTAGCCCCTACCCATGAATTAGGGGGTTGTTGACCCCCAACCGGAATTCATCCACTTAACCCACTTGAAGTCCCACTATTAAATACATCAATCCTACTAGCCTCAGGCGTATCGATCACATGAGCCCACCATAGTCTAATAGAAGGTAATCGAAAACAAATAATTCAAGCACTTACTATTACAATCCTCCTGGGTCTCTACTTCACTATTCTTCAAGCCATAGAGTACTATGAATCCCCTTTCACAATTTCTGATGGTATCTATGGGTCCACCTTTTTTGTAGCTACAGGATTTCACGGTTTACATGTAATTATTGGATCAACATTTTTAATTGTCTGCTTACTTCGACAATTCTACTTCC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                10069 529 +     16775 --ATACTTCTAGTCATGCTGCAATGATGACGAGACGTAGTCCGAGAAAGCACCTTCCAGGGCCACCACACCCCAACTGTCCAAAAGGGCCTACGATACGGAATAATCCTTTTCATTACATCAGAGGCCTTCTTCTTCCTAGGATTCTTCTGAGCCTTCTTCCACTCAAGCCTAGCCCCAACACCAGAACTGGGGGGCCAATGGCCCCCAACAGGAGTCAAACCCCTAAACCCCCTTGAAGTACCCCTACTAAATACAGCAATCCTCCTAGCCTCAGGAGTCACCGTTACATGGGCTCACCACAGCATCACAGAAGGAAACCGAAAACAAGCCATCCACGCACTAACTCTCACAATCCTCCTAGGATTCTATTTCACAGCCCTACAAGCAATAGAGTACCATGAAGCCTCCTTCTCAATCGCTGACAGCGTCTACGGCTCCACCTTCTTCGTCGCTACAGGGTTCCACGGACTACATGTAATCATTGGATCATCCTTTTTAACAGTTTGCCTCCTACGACTAATCAAATTCC
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random     10672521 529 - 171761319 --AATTCGCTCACCATGTACCAATGATGACGAGACATCGTACGAGAAGGCACCTTCCAAGGCCACCACACACCCCCTGTTCAAAAAGGCCTTCGTTATGGTATAATCCTTTTTATTACCTCTGAGGTGTTTTTCTTCCTTGGTTTTTTCTGAGCCTTCTACCACTCAAGCCTAGCCCCCACCCCGGAACTCGGAGGCTGCTGACCACCCACAGGCATTGTACCACTCAACCCCTTTGAGGTCCCCCTTCTTAACACAGCAGTCCTACTGGCATCAGGAGTAACAGTAACCTGAGCACACCATAGCATTATAGAAGGAGAACGAAAACAAGCAATTCACTCTCTAACCCTAACGATCCTATTAGGCTTCTACTTTACTTTCCTACAGGCAATAGAATACTACGAAGCTCCATTCACAATTGCCGACGGAGTTTATGGCTCGACCTTCTTTGTCGCCACTGGCTTCCACGGACTCCACGTTATCATTGGCTCTACCTTCCTAGCCATCTGCCTACTTCGTCAAATCCGATACC
+i tetNig1.chrUn_random    N 0 C 0
+s danRer4.chrM                 9881 529 +     16596 CTTATT--TTAACTATAATCCAATGATGACGAGACATTATTCGAGAAGGGACCTTTCAAGGCCACCATACCCCGCCCGTACAAAAAGGGTTGCGGTACGGTATAATCCTATTTATTACCTCAGAGGTATTTTTTTTCCTAGGATTTTTCTGAGCTTTTTATCATTCAAGTTTAGCCCCCACCCCTGAACTAGGGGGATGTTGACCACCCACAGGGCTAACAACTCTTGACCCATTTGAAGTGCCGCTCCTCAATACAGCTGTTTTGCTAGCATCCGGAGTAACAGTAACATGAGCACATCACAGCCTCATGGAAGGAGAACGAAAACAAGCCATTCAATCTCTTGCTCTTACAATTCTACTAGGATTGTACTTCACAGCACTTCAGGCTATAGAATACTATGAAGCCCCATTTACAATTGCAGACGGAGTATATGGCTCAACATTCTTTGTAGCTACAGGGTTTCATGGTCTACACGTTATTATTGGATCAACCTTTTTAGCTGTATGCCTTCTACGCCAAGTTTTATTTC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154   0 -   2855184 I
+
+a score=738151.000000
+s mm8.chrM                     9282 103 +     16299 ACTTCACATCAAAACATCACTTCGGATTTGAAGCCGCAGCATGATACTGACATTTTGTAGACGTAGTCTGACTTTTCCTATACGTCTCCATTTATTGATGAGG
+s rn4.chrM                     9259 103 +     16300 ACTTCACATCAAAACATCATTTCGGATTTGAAGCCGCAGCATGATACTGACACTTCGTAGATGTAGTTTGACTATTCCTATACGTTTCTATCTATTGATGAGG
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      9448 103 +     20791 ACTTTACATCGAACCACCACTTTGGTTTTGAAGCAGCCGCATGATACTGACACTTTGTAGATGTAGTCTGACTATTCCTATATGTATCAATCTATTGATGAGG
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    9883 103 +     16571 ACTTTACATCCAAACATCACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGTTTGACTATTTCTGTATGTCTCCATCTATTGATGAGG
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 9300 103 +     16554 ACTTCACATCCAAACATCACTTCGGCTTTCAAGCCGCCGCCTGATACTGACACTTCGTAGATGTAGTCTGACTATTTCTATATGTCTCTATTTACTGATGAGG
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr15            38011259 103 - 110119387 aCTTTACATCCAACCACCACTTTGGCTTTGAAGCCACTGCCTGATATTGGCACTTCGTAGATGTAGTGTGACTATTCTTATACGTCTCTATCTACTGATGAGG
+i rheMac2.chr15           I 6148 C 0
+s bosTau2.chrM                 9645 103 +     16338 ATTTTACTTCTAACCACCACTTCGGCTTTGAAGCCGGTGCCTGATACTGACATTTCGTAGACGTAGTCTGACTTTTCCTCTATGTTTCTATCTATTGATGAGG
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 9319 103 +     16727 ACTTCACATCAAACCACCACTTCGGATTTGAAGCCGCTGCATGATATTGACACTTTGTTGATGTAGTCTGGCTATTCTTGTATGTATCTATTTATTGATGAGG
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      13111 103 -     16977 ACTTCACATCTAGCCATCATTTCGGTTTTGAAGCCGCAGCTTGATACTGACACTTCGTAGACGTAGTCTGACTATTCCTATACGTTTCCATCTATTGATGAGG
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      12283 103 +     16266 ATTTTACATCCAACCATCACTTTGGCTTTGAAGCAGCTGCTTGATATTGACATTTCGTAGATGTAGTATGACTATTCCTCTATCTATCCATTTACTGATGAGG
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      8692 103 +     18297 ACTTCACTTCTAAACACCACTTTGGATTCGAAGCTGCTGCTTGATACTGACATTTTGTTGATGTAGTATGGCTATTCCTCTATGTCTCAATCTATTGATGAGG
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117160776 103 + 174229318 ACTTTACTTCCACACACCATTTTGGCTTTGAAGCAGCAGCTTGATACTGACATTTTGTAGACGTTGTATGACTATTCCTCTATGTATCCATCTATTGATGAGG
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                10598 103 +     16775 ACTTCACACCAAACCACCACTTCGGATTTGAAGCAGCAGCCTGATACTGACACTTCGTAGACATCATCTGACTCTTCCTCTACATATCCATATACTGATGAGG
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random     10673050 103 - 171761319 ACTTTACATCCGAACATCACTTCGGCTTCGAAGCAGCAGCCTGATACTGACACTTTGTAGATGTCGTCTGACTATTCCTCTACATCTCAATCTACTGATGAGG
+i tetNig1.chrUn_random    C 0 N 0
+s danRer4.chrM                10410 103 +     16596 ACTTCACATCAGACCACCACTTTGGTTTTGAAGCTGCCGCTTGATATTGACACTTCGTCGACGTAGTCTGACTATTCCTCTACGTATCAATCTATTGATGAGG
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154   0 -   2855184 I
+
+a score=857783.000000
+s mm8.chrM                     9385 254 +     16299 ATCTTA-CTCCCTTAGTA-T--AATTAATATAACTGACTTCCAATTAGTAGATTCTGAAT--AAACCCAGAAGAGAGTAATTAAC---CTGTACACTG----TTATCTTCATTAATATTTTATTATCCCTAACGCTAATTCTAGTTGCATTCTGACTCCCCCAAATAAATCTGTACTCAGAAAAAGCAAATCCATATGAATGCGGATTCGACCCTACAAGCTCTGCACGTCTACCATTCTCAATAAAATTTTTCTTGGTAGCAATTA
+s rn4.chrM                     9362 254 +     16300 ATCCTA-CTCCCTTAGTA-T--AAACAATACAACTGACTTCCAATCAGTTAATTCTGAAA--AAACTCAGAAGAGAGTAATTAAC---CTACCCATTA----TCATCACAATTAACATCACCTTATCCTTTATCCTCATTTCAATTGCATTCTGATTGCCTCAAATAAACTTATACTCCGAAAAAGCAAACCCATATGAATGTGGCTTCGACCCAACAAGTTCTGCACGCCTTCCTTTTTCAATAAAATTTTTCTTAGTAGCCATTA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182      9551 256 +     20791 GTCATA-CTCTTTTAGTA-TC-AACTAGTACAGCTGACTTCCAATCAGTTAGTTTTGGCT-CCAACCCAAAAAAGAGTAATAAAC---CTAATACTAG----TACTATTAATTAACACCACCATTTCCTTAGTCCTAGTTACAATTGCATTCTGACTCCCTCAATTAAATATCTATTCAGAAAAATCAAGCCCTTATGAATGCGGATTCGATCCCATAGGATCAGCACGACTCCCTTTCTCTATAAAATTTTTTCTAGTAGCCATTA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                    9986 254 +     16571 GTCTTA-CTCTTTTAGTA-T--AAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACA--ACATTCAAAAAAGAGTAATAAAC---TTCGCCTTAA----TTTTAATAATCAACACCCTCCTAGCCTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACATAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCCCGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                 9403 254 +     16554 ATCTTA-CTCTTTTAGTA-T--AAGTAGTACCGTTAACTTCCAATTAACTAGTTTTGACA--ACATTCAAAAAAGAGTAATAAAC---TTCGTCCTAA----TTTTAATAACCAATACCCTTCTAGCCCTACTACTGATAATTATCACATTCTGACTACCACAACTCAACAGCTACATAGAAAAATCTACCCCTTACGAATGTGGCTTCGACCCTATATCCCCCGCCCGCGTCCCCTTCTCCATAAAATTTTTCCTAGTAGCCATCA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr15            38011362 250 - 110119387 ATCCTA-CTCTTTTAGTA-T--AAACAGCACCATTGACTTTCAATCAACTAGTTTCGATA--ATATCTGAAACAGATT----AAC---CTGACACTAG----CCTTAGTAACCAACACCTTACTGACCCTACTAGTAATAATAATTACATTTTGACTTCCACAACTTAATATTTATATAGATAAATCCAGTCCCTATGAAGGCAGATTTGACCCAATAACCTCCAACCGCCTCCCCTTTTCCATAAAATTCTTCCTGGTAGCCATCA
+i rheMac2.chr15           C 0 n 0
+s bosTau2.chrM                 9748 255 +     16338 CTCCTA-TTCTTTTAGTATT--AACTAGTACAGCTGACTTCCAATCAGCTAGTTTCGGTC--TAGTCCGAAAAAGAATAATAAAT---TTAATACTAG----CCCTCCTGACCAATTTTACACTAGCCACCCTACTCGTCATCATCGCATTCTGACTTCCCCAACTAAATGTATACTCTGAGAAAACAAGCCCATACGAATGTGGATTTGACCCCATAGGATCAGCCCGCCTTCCCTTCTCTATAAAATTCTTTCTGGTAGCCATCA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                 9422 254 +     16727 ATCCTA-TTTCTTTAGTA-T--AACTAGTACAATTGACTTCCAATCAGTTAGCTCCAGAT--CAACCTGGAAAGAAGTAATAAAC---GTTATATTAA----CTTTGATAACTAATGTAACCCTAGCATCCTTACTTGTACTAATCGCATTCTGACTTCCCCAGCTAAATATCTATACAGACAAGACAAGCCCCTACGAATGTGGTTTTGACCCCATGGGATCTGCTCGCCTACCTTTCTCTATAAAATTTTTCCTAGTTGCCATCA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      13214 256 -     16977 CTCATG-CTCTATTAGTATT--AAGCAGTACAGTTGACTTCCAATCAACTAGATTCGGTA-TCAACCCGAAATAGAGCAATAAAC---ATTATAATTA----CACTATTCATCAACATATCCCTAGCCTCCTTACTGGTACTAATTGCATTCTGACTACCTCAGTTAAACACATACACAGAAAAATCAAGCCCATATGAATGCGGGTTTGACCCAATAGGGTCAGCCCGTCTACCCTTTTCCATAAAATTCTTTCTAGTAGCCATCA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      12386 256 +     16266 ATCCTA-TTTCTTTAGTA-TTAACTTAGTATAACTAACTTCCAATTAGTAGGCTTTGGTA--AATCCCAAAAAGAAATAATCAAC---CTTATAATCA----CGCTACTAACCAATACTATACTAACATCACTTATAGTTCTAATCGCATTTTGACTGCCCCAAACATACAATTACTCAGAGAAAACAAGTCCATACGAATGCGGCTTTGATCCAGTAGGCTCTGCTCGCTTACCATTCTCAATAAAATTCTTCTTAGTAGCTATCA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343      8795 254 +     18297 GTCTTA-ATTCTTT--TA-GTATATCAGTACAGATAACTTCCAATTATCTAGATCTAGTT--CAGTCTAGGAAAGAATAATTAAC---TTAATAATTACTATCACTATTAATGTATTCT----TAGCCTCACTTTTAGTATTAATTGCCTTTTGACTACCCCAACTGAATTTATACATCGAAAAATCAAGCCCCTATGAATGTGGCTTTGATCCAATAAACTCAGCCCGACTACCTTTCTCAATAAAATTTTTCCTTATCGCCGTTA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117160879 254 + 174229318 TTCCTA-TTTTTCTAGTA-T--AATTAGTACTACTGATTTCCAATCATTAAGTTCTGGGT--AATTCCAGAGAAAAATAATTAAT---CTCATAGTTA----CTCTTCTAGTAAATTCTCTCCTAGCTACAATCGTAATTATTATTGCCTTTTGACTTCCTCAACTATACTTGTACATAGAGAAGGCAAGCCCCTATGAATGTGGCTTTGACCCCTTAGGTTCGGCACGCCTGCCATTTTCAATGAAGTTTTTTCTAGTAGCAATTA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                10701 258 +     16775 ATCTTG-CTCTTCTAGTA-T--ACTCATTACAACTGACTTCCAATCTTTAAAATCTGGTA-TCAACCCAGAGAAGAGCAATGAACACACTTACATTTA----TACTCTCACTATCCTTTCTACTAAGCGCTGCACTAACTACTATAAACTTTTGACTAGCCCAAATAGCCCCAGACACAGAAAAACTGTCACCGTACGAATGCGGATTTGACCCACTAGGATCAGCCCGACTCCCATTCTCAATCCGATTCTTCCTAGTAGCCATCC
+i galGal2.chrM            C 0 C 0
+s danRer4.chrM                10513 260 +     16596 CTCATAGCCTTTCTAGTA-T--AACCAGTATAAATGACTTCCAATCATTTGGTCTTGGTGAAAAATCCAGGGAAAGGTAATGAATTTATTTGCAACTA----TTCTTATTATTATAACGACCTTATCATTGGTCTTAGCTCTAGTATCATTTTGACTACCACAAATGAACTCTGATACAGAAAAGCTATCACCATATGAATGCGGATTTGATCCACTAGGGTCCGCCCGCCTACCATTTTCATTACGATTTTTCTTAGTAGCAGTTT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154   0 -   2855184 I
+
+a score=5778556.000000
+s mm8.chrM                     9639 1652 +     16299 CATTTCTATTATTTGACCTAGAAATTGCTCTTCTACTTCCACTACCATGAGCAATTCA----AACAATTAAAACCTCTACTATAATAATTATAGCCTTTATTCTAGTCACAATTCTATCTCTAGGCCTAGCATATGAATGAACACAAAAAGGATTAGAATGAACAGAGTAAATGGTAATTAGTTTAA-A-A--AAAATTAATGATTTCGACTCATTAGATTATGATGAT-GTTCATAATTACCAATA-TGCCATCTACCTTCTTCAACCTCACCATAGCCTTCTCACTATCACTTCTAGGGACACTTATATTTCGCTCTCACCTAATATCCACATTACTATGCCTGGAAGGCATAGTATTATCCTTATTTATTATAACTTCAGTAACTTCCCTAAACTCCAACTCCATAAGCTCCATACCAATCCCCATCACCATCTTAGTTTTCGCAGCCTGCGAAGCAGCTGTAGGACTAGCCCTACTAGTAAAAGTTTCAAACACGTACGGAACAGATTACGTCCAAAATCTCAACCTACTACAATGCTAAAAATTATTCTTCCCTCACTAATGCTACTACCACTAACCTGACT---ATCAAGCCCTAAAAAAA---CCTGAACAAACGTAACCTCATATAGTTTTCTAATTAGTTTAACCAGCCTAACACTTCTATGACAAACCGACGAAAATTATAAAAACTTTTCAAATATAT---TCTCCTCAGACCCCCTATCCACACCATTAATTATTTTAACAGCCTGATTACTGCCACTAATATTAATAGCTAGCCAAAACCACCTAAAAAAAGATAATAACGTACTACAAAAACTCTACATCTCAATACTAATCAGCTTACAAATTCTCCTAATCATAACCTTTTCAGCAACTGAACtaattatattttatattttatttGAAGCAACCTTAATCCCAACACTTATTATTATTACCCGATGAGGGAACCAAACTGAACGCCTAAACGCAGGGATTTATTTCCTATTTTATACCCTAATCGGTTCTATTCCACTGCTAATTGCCCTCATCTTAATCCAAAACCATGTAGGAACCCTAAACCTCATAATTTTATCATTCACAACACACACCTTAGACG--CTTCATGATCTAACAACTTACTATGGTTGGCATGCATAATAGCATTTCTTATTAAAATACCATTATATGGAGTTCACCTATGACTACCAAAAGCCCATGTTGAAGCTCCAATTGCTGGGTCAATAATTCTAGCAGCTATTCTTCTAAAATTAGGTAGTTACGGAATAATTCGCATCTCCATTATTCTAGACCCACTAACAAAATATATAGCATACCCCTTCATCCTTCTCTCCCTATGAGGAATAATTATAACTAGCTCAATCTGCTTACGCCAAACAGATTTAAAATCACTAATCGCCTACTCCTCAGTTAGCCACATAGCACTTGTTATTGCATCAATCATAATCCAAACTCCATGAAGCTTCATAGGAGCAACAATACTAATAATCGCACATGGCCTCACATCATCACTCCTATTCTGCCTAGCAAACTCCAACTACGAACGGATCCACAGCCGTACTATAATCATGGCCCGAGGACTTCAAATGGTCTTCCCACTTATAGCCACATGATGACTGATAGCAAGTCTAGCTAATCTAGCTCTACCCCCTTCAATCAATCTA
+s galGal2.chrM                10959 1651 +     16775 TATTCCTTTTATTCGACCTAGAAATCGCCCTGCTTCTTCCCCTTCCATGAGCCATCCA----ACTTGCACACCCTATAATAACCCTTACTTGAGCCACCACTATCATCGCCCTCCTCACATTTGGTCTCATCTACGAATGAACTCAGGGCGGCTTAGAATGAGCAGAATAACAGAAAGTTAGTCTAA-C-T--AAGACAGCTGGTTTCGACCCAGCAAATTATAGACCC-ACCTATAACTTTCTT-A-TGTCTCCCCTACACTTCAGCTTCTATTCTGCATTCACATTCAGCAGCCTAGGACTAGCATTCCACCGAACACACCTCATCTCTGCCCTACTATGCCTAGAGAGCATAATACTATCCATATTCATCCCCCTCTCAATCTGACCAGTAGAAAACCAAACCCCATCATTCGCCCTTGTACCTATCCTAATACTAGCCTTCTCAGCATGCGAAGCTGGCACAGGCCTAGCCATACTAGTAGCTTCTGCACGAACACATGGCTCTGACCACCTACACAACCTAAACCTTCTACAATGCTAAAGATCATCCTACCAACAATCATACTCTTGCCCACAGCCCTCTT---ATCCCCAGCAAAATCCA---TATGAACTAACACCACAATATACAGCCTTCTAATCGCCTCGATCAGCCTACACTGACTAACCCCATCATACTACCCCACAAAAACCCTAACCCTCTGAA---CAGGCATAGACCAAATCTCAACTCCCCTCTTAGTACTCTCCTGCTGGTTTCTCCCCCTCATAATTATAGCTAGCCAAGGCCACCTACAACATGAACCCCACAAACGAAAACGAATATTCATCTCCACCTTAATCATCATCCAACCATTCATCATCCTAGCCTTCTCAGCAACTGAACTCATACTATTCTACATCTCATTCGAAGCAACCCTAATCCCAACCCTCATCTTAATCACACGCTGAGGAAACCAACCAGAACGACTTAGCGCAGGCATTTACCTTCTATTCTATACCCTAATTAGCTCTCTTCCCCTACTAGTCTCCATCCTCTACCTTCACACAAATACTGGAACCCTCCACCTACCCATTATCAAACTCACCCACCCCAACCTACCTG--CCTCCTGAACAAGCTTATTATCTAGCCTAGCTCTCCTAATAGCCTTTATAGTCAAAGCACCCCTATACGGACTACACCTATGACTGCCTAAAGCCCATGTAGAAGCACCAATCGCAGGCTCCATACTACTCGCTGCTCTACTACTAAAACTAGGCGGATATGGCATCATACGAGTCACCCTCCTAATGGAGCCCGTATCCAACTTCTTACACTACCCCTTCCTCACCCTAGCCCTATGAGGTGCCCTAATAACTAGCTCTATCTGCTTACGCCAAACAGACCTAAAATCCCTCATTGCCTACTCATCCGTAAGCCATATGGGCCTAGTCATCGCTGCAAGTATAATCCAAACCCAATGATCATTCTCAGGTGCAATAATCCTCATAATCTCCCATGGACTAACCTCTTCCCTTTTATTCTGCCTAGCAAACACAAACTACGAACGGACACACAGCCGCATTCTTATCCTGACACGAGGCCTCCAACCCCTCCTACCATTGATATCAGTATGATGATTACTAGCCAACTTAACCAACATGGCCCTGCCCCCAACCACCAACCTG
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117161133 1649 + 174229318 CATTTCTTCTATTTGACTTAGAAATTGCCCTGTTACTACCCCTACCATGAGCTATTCA----ACTGCCCAACCCGTTCATTATACTAGCACTATCTTACTGCCTTATTATCTTGCTCACAGCTGGCCTAGCCTATGAGTGGTTACAAAAAGGCCTAGAATGGGCCGAAT---AGGTATTTAATCTAA-T-T--AAGATAGTTGATTTCGACTCAACTAATCATGGTTTTAACCCATGACTACCTT-A-TAGAACAAATTAACCTAAATATAATCACAGCTTTTACTATTGCACTCATAGGAGTCCTAACCTATCGCTCACACCTAATATCTACCTTACTATGCCTAGAAGGAATAATACTATCACTATTTATTCTAATAGTATTATTAATTTCCCACTCCCATATAGTATCCATATCAATGGCACCTTTAATCCTACTAGTATTCTCTGCTTGTGAAGCAGGGGTTGGTTTGGCCTTGCTTGTGACCATCTCACATACCTATGGGAATGACTATGTTCAAAATTTAAATCTCCTACAATGCTAAAAATTTTAATACCTACTATTATATTAATCCCGCTAACTTGATT---CTCAAAAAAACCCTGAC---TATGGGTTAATACAACCTCATATAGCCTTATTATTGCCATTAGCAGCCTGATACTATTATATCATAGCATAGATATAGGTTACAATTTTAATGGTTCTT---TTTCTATAGATACCTTATCAGGACCTCTGCTAATTCTCTCTTGCTGACTACTTCCCTTAATAATTATAGCAAGCCAAAACCACCTAAATAAAGAATCACTCCTACGAAAAAAACTGTATATTACTTTATTAATTACTCTTCAACTATCACTAATTATAGCTTTCACCTCATCAGAATTAATTATATTCTATATTTTATTCGAAACAACTCTAATCCCAACCCTAATTATTATTACCCGCTGGGGTAATCAAAATGAACGACTTAACGCAGGACTTTACTTTTTATTTTATACATTAGTAGGATCACTCCCACTACTAGTAGCCCTACTAAACTTAAACTACAGCCTAGGATCCATACACATACTAACAAACTTTTTACTAATCAATACACTAGAAC--ATTCAACCTCTAGCACACTAATATGATACGCATGTATGACCGCTTTTATAGTCAAAATGCCACTATATGGGTTGCATCTTTGATTACCAAAAGCACATGTAGAAGCCCCCATTGCTGGATCCATAGTACTAGCTGCAATTCTACTAAAACTAGGGGGTTACGGCATTATACGAATTACAACATTCATCGAACCTATTACTATTCAATTATCCTACCCATTTATTATTTTATCTCTATGAGGGATAATTATAACAAGCTCAATCTGCCTACGTCAAACAGACCTAAAATCACTAATTGCCTACTCATCAGTTAGCCACATAGGCTTAGTAATCGTAGCAGCACTAATACAAACAACCCTTAGTTTTATAGGCGCCACTGTATTAATAATTGCCCATGGCTTGACATCTTCAATATTATTCTGCTTAGCCAATACTAACTATGAACGAATCCACAGTCGCACTATAATCCTAGCACGAGGGTTACAAATGATTCTACCACTAATATGCACATGATGATTGCTAGCTAGCCTAGCTAACCTAGCTTTACCTCCTTCAATTAATTTA
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343      9049 1649 +     18297 CTTTCCTTTTTTTCGACTTAGAAATTGCTCTTTTACTTCCACTACCATGAGCAATCCA----ATCAAATAACCTTATATTAATATTAAGTATAGCCTTGTTCTTAGTAGTAATCTTATCCCTTGGTCTCGCCTACGAATGAACCCAAAAAGGCTTAGAATGAATAGAAT---TGTTAGTTAGTTTAA-A-T--AAAATGAATGATTTCGACTCATTAGATTATGGTTCT-ACCCATAACTATC-ACA-TGCCCGTTATTTACATTAACCTTATTGCCGCCTTCTTTATAGCCTTTGTAGGTCTCTTAATTTACCGATCACACCTAATATCCTCACTATTATGCCTTGAAGGGATAATATTATCTCTATTTATCCTAAATTCAACCCTCGCTCTAAGCATGCATTTTACTTTATACTCAATGATACCCATTATCCTCTTAGTCTTCGCTGCATGTGAGGCTGCATTAGGCCTATCACTATTGGTTATAGTGTCAAACACCTACGGCCTAGACTATGTCCAAAACTTAAATCTCTTACAATGTTAAAACTTATTATCCCAACCCTTATATTGATCCCCTTAGCATGACT---CTCAAA---CAGCAAAAATTTATGAATCAATACTCTAATATATAGCTTCATACTCACCCCAATCAGCCTACTCTTACTTAATCAAACCTCTGACACAAGCCTAAACATATCTGTCCTAT---TTTTTTCTGACCCATTATCCACCCCTCTTATTATTCTTACCTCATGACTCCTACCATTAATACTTTTAGCTAGCCAATCTCATATATCTAAAGAATCAGAGATTCGAAAAAAATATTATAACACTATACTTATTATCCTCCAACTCTTTCTCTTCTTAACATTTTCAGCAACTGAAATAATACTATTTTATATTTTATTTGAATCAACACTGATTCCTACCCTAATTATTATTACCCGCTGAGGAAATCAAACTGAACGACTAAACGCAGGAGTCTATTTCCTCTTTTATACTCTTATAGGCTCGTTGCCTCTACTAATTGTTCTCATCTACATTTACAATAATTTAGGTACATTAAACCTCCTAATTATACCATATTATATTATACCC-TTACCATTTTTTATGATCCTCTAAACTATTATGGTTAGCCTGCATAATAGCCTTTATAGTTAAAATGCCCCTTTATGGTCTACACTTATGACTACCCAAAGCACATGCAGAAGCTCCTATCGCAGGGTCTATGGTTTTAGCTGCTATTCTCCTTAAATTAGGTGGGTACGGAATAATATGAATTACAATTTTTCTTGACCCAATTACCCTAAATATATCTTATCCATTCATAATACTATCCCTATGAGGTATACTAATAACTAGCTCAATCTGCCTGCGACAAACAGACTTAAAATCCCTCATTGCCTATTCATCTGTTAGCCATATAGCTTTAGTGATTGTAGCTATCCTTATTCAAACCCCTTGAAGCTTTATGGGTGCCTCCACCCTTATAATTGCACATGGCTTGACTTCCTCCATACTATTTACCCTAGCTAACACAAACTATGAACGTACTCACAGCCGTACTATAATTCTTGCTCGAGGTTTGCAAACCATACTCCCTGTAATAGCTTCATGATGAATTTTAGCCAGCCTAACCAATCTAGCTCTCCCCCCTACAATTAATTTA
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650      12642 1649 +     16266 CATTTCTCCTATTTGACCTAGAAATTGCATTACTCCTACCTTTACCCTGAGCCATCCA----AGCTAATAATACAAGTCTAACACTTTTGATATCATTTATATTAATCATTCTCTTAGCTATTGGCTTAGCCTATGAATGACTCCAAAAAGGCCTTGAATGAACCAAATA--TGGTACTTAGTTTAA-A-C--AAAACAAATGATTTCGACTCATTAAACTATGAATAT-A-TCATAATTACCAATA-TGCCCTACATTTACATAAATATTACACTAGCCTTCGTTATTTCACTCATTGGTACCCTCATATACCGCTCTCACCTAATATCTTCGTTACTATGCCTTGAAGGAATAATACTTTCACTATTTACCCTAAACGCACTATTATCCCTCAACATAAACTTCACATTATCTACTACAGTACCACTAATTCTACTAGTATTCGCAGCCTGTGAAGCTGCAGTAGGCTTGGCACTTCTTGTTATAATCTCCAATACCTACGGACTAGACTACGTACAAAACTTAAACCTACTTCAGTGCTAAAAACTATCTTACCAACAATCATACTTATTCCCCTTGCCTGATTTACCTCTAA---CAATATAG---TGTGAATTAATACTACTCTCTATAGCTTTGCAATTAGTCTAACTAGCCTCCACCTGCTCTACCAACCCCTTGACAATAGCCTAAACCTCTCCCCAGAAT---TCTTCTTAGACTCTCTATCTACCCCACTACTAATCCTTACTATTTGACTACTCCCTCTAATACTAATCGCCAGCCAATCCCATCTATCCTCCGGATCAACTTTTCAGAAAAAGTCCTATATCACTACAATTATCCTTTTACAAGTATCCCTAATTATAACATTTGCTGCTACAGACCTAATTCTACTGTACATTATATTTGAAACAACGCTTATCCCAACTATAGTTATCATTACTCGATGAGGAAACCAACTGGAACGATTAAACGCAGGGTCATACTTCCTATTCTATACCCTAATAGGATCTCTCCCCCTACTAGTAACCCTCATGCTAATCCAAAATACCCTAGGGTCATTGAACTTAATAATACTACCATACCTAATTAAACCCATTGACA--ACCTATGATCCACTAATATATTATGACTAACATGTACTATAGCCTTCATAGTAAAAATACCTCTATATGGTCTCCACCTATGATTACCAAAAGCTCATGTAGAAGCACCAATCGCTGGATCTATAGTATTGGCTGCCATTCTCTTAAAACTAGGAGGGTATGGGATACTACGAATCACCATCCTCTTGGATCCCCTAACAACACACATATATTATCCATTCCTCATACTATCACTATGAGGTATGGTCATATCTAGCTCCATCTGCTTGCGACAAACAGATATGAAATCCCTCATCGCTTATTCTTCAGTCAGCCACATAGCCTTAGTAATCATTGCTATTATACTTCAAACACCATGAAGTTTCATGGGGGCACTTACCCTAATAATCGCCCACGGCCTAACTTCCTCAATACTTTTCTGTCTAGCAAATTCAAACTACGAGCGCATTCACAACCGAACTATAATTTTAGCACGAGGCTTACAAACTCTTCTCCCACTAATAGCTACATGATGACTACTAGCTAGCTTAATTAACATGGCCCCACCACCCACTATTAATTTA
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239      13470 1650 -     16977 CATTCTTACTATTCGACCTAGAAATTGCATTACTACTTCCCCTCCCATGAGCCACACA----AGCAAATACTATAACACCTATACTAACGACagccctagtattaatcctactcctagccctaggtctagccTACGAATGACTACAAAAAGGACTAGAGTGAAACGAATA--TAGTAGCTAGTTTAACA-C--AAAATAATTGATTTCGACTCAATAGACTATGATTAA-CCTCATAGCTACCAA-A-TGCCATCAATCTACTTAAACATTATTATAGCATTCTCCATCGCCATAGTAGGAGTACTAGTATATCGCTCACACATAATATCATCCCTACTATGTTTAGAAGGCATAATACTATCCCTCTTTATCCTAAGCACCCTTATAATCCTAAGCATACACTTTACAATAGCTATGATAATACCAATTATTCTTATAGTATTTGCCGCATGCGAAGCAGCAGTAGGACTGGCTCTGCTAGTCATAGTATCCAACACATACGGCCTAGACCACGTCCAAAATCTTAACCTCCTGCAATGCTAAAACTAATTATACCCACTATTATACTCATCCCTCTAACATGACT---ATCAAAAAAGAACATAG---TCTGAATTAACTCAACCACACACAGCATTTTAATTAGCTTGATTAGTCTTTCCATGCTTTTCCAAACAACAGACTCCAATATAAACTTTTCTCTAATAT---TTTTCGCGGATCCTCTATCAACACCACTTATTATCTTAACAACTTGACTGCTCCCACTAATAATCATTGCCAGCCAATCTCACCTTATCAAAGAAACAACAACCCGCAAAAAACTATATATCTCTATACTAATTACTCTTCAAGCACTCTTAATCATAACATTTTCCGCCACAGAACTAATTCTATTTTACATCTTATTTGAAGCCACACTAATTCCAACCCTTATCCTCATCACACGATGAGGAAACCAAACAGAACGCCTGAACGCAGGATTCTACTTTCTATTTTATACATTAGCAGGATCCCTACCCCTCCTAGTAATCCTATTATATATGCAAAACACAATAGGCTCACTAAACATATTACTCATCCAGTATTTTCCCCAAACACTCACAC--ACACCTGAACAGCCAAACTTATATGATTAGCATGCATAATAGCATTCATAGTAAAAATACCACTATATGGCTTACACCTTTGACTACCAAAAGCACACGTAGAAGCACCAATCGCAGGATCAATAGTCCTGGCAGCTATTCTACTAAAGCTTGGCGGCTATGGCATAATACGAATCACAATAATTCTAGAACCAACTACAACATCCATGTCCTATCCATTCATAATACTTTCTCTATGAGGCATAGTAATAACAAGCGCAATTTGCCTACGACAAACGGACTTAAAATCACTAATTGCATACTCATCCGTAAGCCACATAGCTCTAGTAATTATAGCTATCCTAATCCAAACACCCTGAAGCTATATAGGCGCAACAGCCCTAATAATTGCCCACGGTCTCACATCATCAATACTATTCTGTCTAGCAAATACTAATTACGAACGAACTCACAGCCGCACCATAATTCTAGCCCGGGGTTTACAAACATTATTACCCCTAATAGCCTCATGATGACTACTAGCCAGCCTAACTAACCTAGCCCTACCCCCTACAATCAACTTA
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                 9676 1649 +     16727 CATTTCTGCTTTTCGACCTAGAAATTGCACTCCTACTCCCACTTCCCTGAGCGTCACA----AACCAACAAGCTAACAACAATACTTATCATAGCACTCCTACTAATCTCCCTCCTAGCTGCGAGCCTAGCGTATGAATGGACCGAAAAGGGGCTAGAATGAACCGAATA--TGATAATTAGTTTAA-G-CCAAAAACAAATGATTTCGACTCATTAGATTATGATTTA-TCTCATAATTATC---A-TGTCCATAGTATATATTAATATCTTTCTGGCATTCATTCTTTCTCTAATAGGTATACTTGTTTATCGATCACACCTAATATCATCGCTACTATGCTTAGAGGGCATAATATTATCACTATTTGTAATAATATCTGTAACTATTCTCAACAATCACCTCACATTAGCCAGCATGATACCAATCGTACTACTAGTATTTGCTGCCTGCGAAGCAGCATTAGGACTATCTCTACTAGTTATAGTATCTAACACCTACGGGACTGATTACGTACAAAACCTAAACCTTTTACAATGCTAAAAATTATCATCCCTACTATCATACTAATCCCCCTTACATGAAT---ATCAAAGCCTAACATAA---TCTGAATTAACACGACAACATATGGTTTGCTAATCAGCTTAATCAGCTTATTCTACCTAAACCAACCAAATGATAATACATTGAACTCCTCCTTAATAT---TTTTCTCTGATTCCCTATCGGCACCACTATTAGCACTCACAACATGACTTCTGCCCCTTATACTTATAGCAAGTCAACACCATTTATCAAAAGAACCCTTAACTCGAAAAAAACTATATATTTCAATACTAATTCTTCTCCAATTGTTCCTAATTATAACTTTCACAGCCTCTGAACTCATCTTCTTTTACATCCTATTTGAAGCAACACTGATTCCGACCCTGATCATTATTACCCGATGAGGAAATCAAACTGAACGACTAAACGCAGGACTCTACTTCTTATTTTATACTTTAATAGGATCCCTCCCACTCCTAGTAGCTCTCCTTTATATCCACAATTTCATGGGCTCCCTAAATTTTCTCATAATTCAATACTGAATCCAGCCTCTGCCAA--ACTCCTGATCTAATATTTTCCTATGACTGGCATGCATAATAGCATTCATAGTAAAGATACCTCTATACGGCCTCCACTTGTGACTACCAAAAGCACACGTAGAGGCCCCTATTGCCGGCTCCATAGTACTTGCCGCTGTACTCCTAAAACTAGGGGGCTATGGCATGATACGAATTACAACCCTACTAAATCCCCTGACCAATTTCATAGCATACCCCTTCATAATATTGTCTCTATGAGGCATAATCATAACAAGCTCTATCTGTCTCCGTCAAACAGATCTAAAATCCCTAATTGCATACTCCTCAGTTAGTCATATGGCACTGGTTATCGTAGCGGTTCTTATTCAAACACCATGAAGTTATATAGGTGCAACAGCTCTAATAATTGCCCATGGTTTAACATCCTCAATACTATTCTGCTTAGCCAACTCCAATTACGAACGAATCCATAGCCGTACTATAATTCTCGCACGAGGACTTCAAACTCTCCTTCCCCTAATAGCAGCCTGATGACTATTAGCAAGCCTCACAAATCTGGCTCTCCCTCCAACAATTAATCTT
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                10003 1650 +     16338 CATTCCTCTTATTTGACCTAGAAATTGCACTCCTCCTACCACTGCCATGAGCCTCACA----AACAGCAAATCTAAACACAATGCTTACCATAGCCCTCTTCCTAATTATCCTCCTAGCTGTAAGCCTAGCCTATGAGTGAACTCAAAAAGGACTAGAATGAACCGAATA--TGGTACTTAGTTTAA-A-AT-AAAATAAATGATTTCGACTCATTAGATTATGATTTA-ATTCATAATTACCAA-A-TGTCTATAGTATACATAAACATTATAATAGCATTCACAGTATCTCTTGTAGGACTACTAATATACCGATCCCACCTAATATCCTCCCTTCTATGCTTAGAAGGAATAATGCTATCCCTATTCGTTATAGCAGCCCTAACAATCCTCAACTCACATTTTACATTAGCTAGCATAATACCTATTATCCTACTAGTCTTCGCAGCCTGTGAAGCAGCCCTAGGTCTATCTCTACTAGTAATAGTATCAAATACATATGGTACTGATTATGTACAAAACCTCAACTTACTCCAATGCTAAAATACATTATTCCAACAATTATACTTATACCCCTAACCTGGTT---ATCAAAAAATAATATAA---TTTGGGTTAACTCCACAGCACACAGCCTTCTAATTAGCTTTACAAGCCTCCTCCTCATAAACCAGTTTGGCGACAACAGCCTTAATTTTTCACTACTAT---TTTTCTCCGACTCCCTATCCACTCCACTACTAATTTTAACCATATGGCTCCTCCCTCTAATACTAATAGCTAGCCAACATCATCTATCAAAAGAAAACCTAACCCGAAAAAAACTATTTATTACTATGCTGATCTCACTACAACTATTCCTAATTATAACCTTTACCGCCATGGAACTAATCTTATTTTATATTCTATTTGAAGCAACACTAGTCCCAACACTCATTATTATTACCCGATGAGGAAACCAAACAGAACGCCTAAACGCCGGACTCTATTTCCTATTCTATACACTAGCTGGCTCCCTACCCCTATTAGTCGCACTAATTTATATCCAAAACACAGTAGGATCCCTAAATTTCCTAATATTACAGTACTGAGTACAACCTGTTCATA--ACTCTTGATCTAATGTCTTCATATGACTAGCATGTATAATAGCTTTCATAGTAAAAATACCACTATATGGCCTCCACCTTTGACTACCTAAAGCTCACGTAGAAGCCCCCATCGCAGGCTCCATAGTCCTTGCAGCAGTTCTACTAAAACTAGGGGGGTACGGTATGCTACGAATCACACTAATTCTAAACCCTATGACCGACTTTATAGCATACCCATTCATTATACTCTCCCTATGAGGCATAATTATAACCAGCTCAATCTGCCTCCGTCAAACGGACCTAAAATCACTCATCGCATACTCCTCTGTAAGCCACATAGCACTCGTTATCGTAGCCATCCTTATCCAGACACCTTGAAGCTACATAGGAGCAACCGCCCTTATGATTGCCCACGGCCTCACATCCTCCATACTTTTCTGTCTAGCAAACTCAAACTACGAACGAATCCACAGCCGAACCATAATTCTAGCTCGAGGCCTACAAACGCTCCTTCCACTAATAGCCACCTGATGACTACTAGCAAGTCTAACCAACTTAGCTCTACCCCCAACAATCAACTTA
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34445352 1643 - 182086969 CACTCCTCCTCTTTGACTTAGAGATTGCTGTGCTACTACCCCTGCCATGAGCCCTTCA----AACAACCAACATGACGCTAATAATCAGCACAGCCCTTCTATTAGTTACCATTTCAATCCTAGGCTTGATTTATGAATGAGCCCCAAAAGGGTTAGACTGAGTTGAAT---TGGTAAGTAGTTTAA-GTC--AAAATAAATGATTTTGACTCATTAGATTATGATA---GACCATATTTACCAA-A-TGACCTCTATTAATATCATGATTATATTAGCATACACCATATCACTGCTAGGAGTGTTAGTCTATCAATCCCACCTAATATCATCCCTATTATGCCTAGAAGGCATAATACTATCAATATATATCATAAATACTCTTATAACTTTAAATATAGATTTCACTCTAGCATCCATAATACCCATTATTCTCCTAGTATTTGCTACCTGCGAAGCCGCAATGGGCCTTGCCTTACAAGTTTCAATCTCCAGTGCATATGGCCTAGATTGCATACAAAATCTAACTTTACTTCAATGCTAAAAATTATTATTCCAACAATTATACTGTTACTGATGATATGATT---CTCTAAAAATTCTATAA---TCTGAATCAACATGGTTATCCACAGCCTACTCATCAGCCTCATCAGCCTACTATTTTTTAACCAATTCAGCAAT-ACTCGTCCAACTTCTTATTAATAT---TT---TCTGACCTGCTGACATCACCCCTTCTAATCTTAACAGCCTGACTACTGCCTCTTATAATTCTAGCAAGCCATTATCACCTGTCCAATGAATCACCCCCATGAAAAAAATTATATATTTCTATATTGATTTCCCTACAGATGTTTTTAATCATGGCATTCACTGTCACAGAACTAATTATATTTTATATCCTCTTTGAAGCCACACTAGTTCCTACCCCAATTATCATCACTCACTGGGGCAACCAACCAGAACGCCTCAATGCAAGCTCATACTTCTTATTTTACACACTAGTAGGATCCCTTTCTTTACTTGTAACACTTGTTTATACTCAAAATACCTCAGGTTCACTAAATATGCTAGTAATAATACTTACTATCCAAGAGTTATTAA--CCTCCTGATCCAACAATCTTATATAACTAGCATGTATCATGGCCTTCATAGTAAAAATACCTCTATATGAACTTCACCTATGACTCTCCAAAGCCTATGTAGAAGCCCCTATTGCCAACTCAATAGTACTTGCAGCAGTACTCCTAAAGCTAGGCAGGTGCGGTGTAATACGGCTTACTCTTATCCTCAACCCCGTAACAGAACATATAGCCTACCCTTTCCTCATGTTGTTCCTATGAGGAATAGTTATGACAAGCTCTATTTGTCTATGACAAACTAATCTAAAATCACTTATTGCCTACTCTTTCATAAGCCACATAACACTTGTTATTATGGCTATCCTCATTCAGACCCATTGAAGCTTTAGAGATGCAATCACCCTTATAATTGCTCATGGACTCACTTCATCCTTACTCTTCTGCCTAGCAAATTCAAACTACGAGCGAGTCCATAGCCAAACCATATTGCTTACCCAAGGCCTTCAAACACTGCTCCCACTAATAGCCTCTTGATGATTTCTGGCAAATCTAACTAACCTTGTCTTACTCCCTACCATTAATCTA
+i rheMac2.chr5            M 987 C 0
+s panTro2.chrM                 9657 1645 +     16554 CCTTCCTATTATTTGACCTAGAAATTGCCCTCCTATTGCCCTTACCTTGAGCCCTACA----AACGGCCAACCTACCACTAATAGTCACATCATCCCTCTTATTAATTACTATCCTAGCCCTAAGCCTCGCCTACGAATGATTACAAAAAGGGTTAGACTGAACCGAAT---TGGTATATAGTTTAA-A-T--AAAACGAATGATTTCGACTCATTAAATTATGATA----ATCATATTTACCAA-A-TGCCCCTTATTTATATAAATATTATACTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTAATATCTTCCCTACTATGCCTAGAAGGAATAATACTATCACTGTTCATCATAGCCACCCTCATAACCCTCAATACTCACTCCCTCTTAGCCAATATTGTACCCATCACCATACTAGTCTTTGCTGCCTGCGAAGCAGCAGTAGGTCTAGCACTACTAGTTTCAATCTCTAACACATATGGCTTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCATCCCGACAATTATATTACTACCACTAACATGATT---CTCTAAAAAACGTATAA---TTTGAATCAACACAACCACTCACAGCCTAATTATCAGCACCATTCCCTTACTATTTTTTAACCAAATTAACAACAACCTATTCAGCTGTTCCCTGCCCT---TCTCCTCCGACCCCTTAACAACTCCCCTCCTAATATTAACTGCTTGACTTCTACCCCTCACAATCATAGCAAGCCAGCGCCACCTATCCAACGAACCACTATCACGAAAAAAACTCTACCTCTCCATGCTAATTTCCCTCCAAATCTCCTTAATTATAACATTCTCGGCCACAGAGCTAATTATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCCTGGCTATCATCACCCGATGGGGTAACCAACCAGAACGCCTGAACGCAGGTACATACTTCCTATTCTATACCCTAGTAGGCTCCCTCCCCCTACTCATCGCACTAATCTATACCCACAACACCCTAGGCTCACTAAATATCCTATTACTCACTCTTACAACCCAAGAACTATCAA--ACACCTGAGCCAACAACTTAATATGACTAGCGTACACGATGGCTTTCATGGTAAAAATACCCCTTTACGGACTCCACCTATGACTCCCTAAAGCCCATGTCGAAGCCCCTATTGCCGGGTCAATGGTACTTGCTGCAGTACTCTTAAAATTAGGTGGCTATGGCATAATACGCCTCACACTCATCCTCAACCCCCTAACAAAACATATAGCCTATCCCTTCCTCATGTTGTCCTTATGAGGTATAATCATAACAAGCTCCATCTGCCTGCGACAAACAGACCTAAAATCGCTCATTGCATACCCTTCAGTCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATCCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTGGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTC
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                   10240 1645 +     16571 CCTTCTTATTATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACA----AACAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATCCTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGCCGAAT---TGGTATATAGTTTAA-A-C--AAAACGAATGATTTCGACTCATTAAATTATGATA----ATCATATTTACCAA-A-TGCCCCTCATTTACATAAATATTATACTAGCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCATATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAGCTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCTATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCTACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAAACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCACTGACATGACT---TTCCAAAAAGCACATAA---TTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGCTGTTCCCCAACCT---TTTCCTCCGACCCCCTAACAACCCCCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGCCAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTCTATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAGAACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCACATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCACTAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACTCTCACTGCCCAAGAACTATCAA--ACTCCTGAGCCAACAACTTAATATGACTAGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACTTATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTACTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCACACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTACTATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACAGACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGTAGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTA
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182      9807 1649 +     20791 CATTTTTACTTTTTGACCTAGAAATTGCTCTCCTACTCCCACTCCCATGAGCCGCACAATTTAATAATTTAAACCT----AGTCCTCATCATAGCACTTATGTTAATCTCAATCTTAGCCCTTGGATTAGCCTACGAATGAATCCAAAAAGGACTAGAATGAGTTGAATA--TGATAATTAGTTTAG-T-T--AAAATAAATGATTTCGACTCATTAGACTATGGTAA--GACCATAATTATCAAAA-TGCCTTCAATCTATATTAATATTTTCCTAGCATTTATCCTAGCTCTTCTAGGCATACTAGTCTATCGATCCCATCTAATATCATCCCTTCTATGCCTAGAAGGCATAATACTCTCACTATTTGTTCTAATTACATTAACAGCCCTTAATACCCACTTCACACTATCATTTATATTTCCAATCATCCTACTAGTATTCGCAGCCTGTGAAGCAGCAGTTGGACTAGCTCTTCTAGTTATAGTCTCCAACACTTATGGAATAGACTATGTACAAAACCTAAATCTTCTACAATGCTAAAAACTATTATCCCCACAATCATACTTATTCCAACCGTATGGTG---ATCAAAACCCCATATAA---TTTGAATTAACGCAACAGTTTACAGCCTATTAATTAGCCTAACTACCCTCTCTCTACTTAATCAGCCAAGTGACACCAACCTAAACTTCTCAACCACAT---TTTTTTCAGATGCCTTATCCACTCCTCTCCTGATGTTAACGACCTGACTTCTTCCACTCATAATCTTAGCAAGCCAACATCACTTAGACAAAGAAACCTTAACCCGTAAAAAAATTTATATTTCTCTTTTAATTTCCTTACAAGTATTCCTAGTAATAACATTTTCAGCCACAGAATTTATCCTGTTTTATATTCTATTTGAAGCCACACTGATTCCCACTCTTATCATTATTACACGATGAGGTAATCAAACAGAGCGACTCAACGCAGGAACCTACTTCCTATTTTATACCCTCATAGGATCCCTCCCCCTTCTAGTGGCTCTAATTTATTTACAGAACTCTATAGGATCTCTAAACTTCCTCCTACTTCAACTTATAAATAAATCCATTACAA--CATCGTGATCAAACTCACTGATATGACTAGCATGCATAATAGCATTTTTAGTCAAAATACCCTTATATGGGCTTCACCTGTGATTACCAAAAGCTCACGTTGAAGCCCCCATCGCTGGCTCAATAGTCCTGGCAGCTATTCTACTTAAACTAGGCGGCTACGGAATAATACGCATTACCATCCTACTCAGCCCTATTACAGACTATATAGCCTACCCATTCCTCATACTCTCCCTCTGAGGCATAATTATAACCAGCTCTATCTGTCTCCGGCAAACAGACCTCAAATCACTCATTGCTTATTCATCAGTGAGCCACATAGCCCTAGTAATCGTAGCCATCCTTATTCAAACACCATGAAGCTTTATAGGCGCCACCGCTCTAATAATCGCACATGGCCTTACTTCCTCATTATTATTCTGCCTAGCCAATTCCAACTACGAGCGCATTCACAGCCGAACCATACTACTAGCCCGAGGCCTACAGACTATTCTTCCGCTAATAGCAGCATGATGACTAGTTGCTAGCCTTACCAACCTGGCCCTACCTCCAACTATTAATCTG
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                     9616 1653 +     16300 CATTTCTACTATTCGACCTAGAAATCGCCTTACTACTTCCCCTCCCATGAGCGATTCA----AACAACCAATACCACTACAATAATAGCAACTGCCTTTATTTTAGTCACTATTTTGTCTCTTGGCCTAGCCTACGAATGAACACAAAAAGGACTAGAATGAACAGAATAATTGGTAATTAGTTTAA-A-T--AAAATTAATGATTTCGACTCATTAGATTATGATAAT-AATCATAATTACCAACAATGACATCTGCTTTCCTAAATTTAACTATAGCCTTTACATTATCTCTACTAGGTACTTTTATATTTCGCTCCCACCTAATATCCACTCTCCTCTGCCTAGAAGGAATAATACTATCACTATTTGTCATAACTTCAACATCCACATTAAACTCCAACTCCATAATCTCCATAACCATCCCAATTACCATTCTAGTTTTTGCAGCCTGCGAAGCAGCAGTAGGTTTAGCCTTACTAGTAAAAATTTCAAATACTTACGGAACAGACTACGTACAAAACCTCAACCTTCTACAATGTTAAAAATTATTTTCCCATCTATCATACTCCTCCCACTAACATGACT---CTCAGCCAACAAAAAAA---TCTGAACCAATGTCACCTCCTACAGCTTTCTAGTGAGCCTATTAAGCTTATCACTCCTATGACAAAATGACGAAAATTACCTAAATTTCTCAGTTATAT---TCTCCTCCGATCCATTATCCACCCCACTAATCATTCTAACAACTTGACTCCTCCCACTAATAATGCTCGCTAGCCAAAATCACATAAAAAAAGAAAATATAATGCATCAAAAACTTTACATCTCAATACTTATTAGCCTCCAAATTTTACTCATCATAACATTCTCCGCAACAGAACTAATTTTATTTTATATCCTGTTCGAGGCCACTCTAATCCCAACACTAATTATCATTACACGATGAGGCAACCAAACAGAACGCTTAAATGCAGGAATTTATTTCCTGTTTTATACACTAATTGGCTCCATCCCACTCTTAATTGCCCTCATTTCAATCCAAAACTCAATAGGAACACTCAACTTCCTAATCCTTTCCCTCACAACACACCCCCTACCCT--CAACATGATCCAACACCATTCTATGACTAGCATGTATAATAGCATTTATAATCAAAATACCATTATACGGAGTCCATCTATGATTACCAAAAGCCCACGTAGAAGCTCCAATTGCAGGCTCTATAATTTTAGCAGCAATTCTCCTAAAGCTAGGGGGTTATGGGATAATACGAGTTTCCATCATTCTAGACCCCCTAACAAAATCTTTAGCCTACCCATTCATCATCCTCTCATTATGAGGCATAATTATAACTAGCTCAATCTGCCTACGCCAAACAGATCTAAAATCATTAATTGCTTACTCATCAGTAAGCCATATAGCCCTAGTCATCACAGCCATTATAATCCAGACACCATGAAGCTTCATGGGAGCCACAATACTAATAATCGCCCACGGCTTAACCTCATCACTCTTATTCTGCCTAGCAAACACCAACTACGAACGAATTCACAGCCGAACTATAATTATAGCTCGAGGATTACAAATAATCTTTCCATTGATAGCAACATGATGACTATTAGCAAGCTTAGCCAACCTAGCACTACCACCCCTAATTAACCTC
+i rn4.chrM                C 0 C 0
+s danRer4.chrM                10773 1653 +     16596 TATTCCCTTTATTTGACTTGGAAATTGCTCTCCTATTACCACTCCCATGAGGAGATCA----ACTTAATAACCCAATAGAAACTCTCTTTTGAGCTATAACAGTACTGATTTTGCTAACACTAGGACTAGCCTACGAATGAGCCCAAGGCGGCCTTGAATGAGCAGAGT---AGGGAGCTAGTCCAA-A-GA-AAGACCCTTGATTTCGGCTCAAATAATTGCGGTGTAAACCCGTAACTCCCTT-A-TGACACCCACGCACTTTAGTCTTAACGCAGCATTTATACTAGGCTTAGCAGGACTTACATTTCACCGTGTTCACCTCCTATCAGCATTATTATGTTTAGAAGGCATAATATTATCTTTATTTATTTCCATAGCCCTTTGAACTTTAAAAACAGAGTCAATAAGTTTATCCACAGCCCCTATACTACTACTAGCCTTTTCTGCCTGTGAAGCAAGTGCCGGCCTAGCACTCCTAGTAGCCACAGCTCGAACCCACGGATCTGACCACATAAAAAACCTTAATCTACTACAATGCTAAAAGTACTGATCCCCACTATTATGCTATTCCCTACAATCTGATT---ATCTTCATCAAAATGAC---TGTGAACAACTACAACAATAAACAGCTTTTTAATTGCCTTTATTAGCTTAACATGACTAAAATGAACCTCGGATACAGGGTGAAATGCTTCTAACTCGTACATAGCTGCAGACCCACTATCAACACCTCTTCTAGTACTAACCTGTTGACTTCTTCCATTAATGATTCTAGCTAGCCAAAATCACATCAACTCGGAGCCTGTAAACCGACAACGAATATACATTACACTTCTTGCCTCTTTACAAACTTTCATAATTATGGCGTTTGGCGCTACAAAAATCATTATATTCTACATTATATTCGAAGCTACACTTATCCCAACACTAATCATTATTACCCGATGAGGTAATCAAGCTGAGCGCCTTAACGCAGGTACTTACTTTCTTTTCTATACATTAGCAGGCTCTCTACCTCTTTTAGTAGCCCTCCTATTACTGCAACAATCAACAGGAACCCTATCAATACTAGTACTTCAGTACTCAGACCCACTTTTACTTA--ACTCTTGAGGACATAAAATCTGATGAGCCGGCTGCTTAATTGCATTCCTAGTAAAAATACCGCTATATGGGATACACCTTTGATTACCAAAAGCACATGTAGAAGCCCCTGTAGCAGGATCTATAATTCTAGCGGCAGTGCTACTAAAACTAGGAGGCTACGGTATGATACGAATAATAGTAATATTAGATCCTTTATCTAAGCAACTAGCATACCCGTTTATTATCCTTGCTCTATGAGGAGTAATCATAACAGGATTAGTTTGTCTACGACAAACAGACTTAAAATCGCTAATTGCCTATTCATCAGTAGGCCATATGGGACTAGTTGCAGGAGGAATTTTGATTCAAACCCCCTGAGGATTTACAGGAGCAATTATTTTAATAATCGCCCACGGACTAACCTCATCCGCCCTATTTTGCTTAGCTAACACATCGTATGAACGAACTCATAGCCGGACCATAATCCTCGCTCGAGGACTCCAGATAGTGCTACCGCTAGCAACAGTATGGTGATTTATTGCTAATCTGGCCAACCTAGCACTTCCACCTCTACCAAACTTG
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154    0 -   2855184 I
+
+a score=1795914.000000
+s mm8.chrM                    11291 679 +     16299 ATAGGAGAATTATTCATTACCATATCATTATTTTCTTGATCAAACTTTACCATTATTCTTATAGGAATTAACATTATTATTACAGGTATATACTCAATATACATAATTATTACCACCCAACGCGGCAAACTAACCAACCATATAATTAACCTCCAACCCTCACACACACGAGAACTAACACTAATAGCCCTTCACATAATTCCACTTATTCTTCTAACTACCAGTCCAAAACTAATTACAGGCCTGACAATAT-GTGAATATAGTTTACA-AAAAACATTAGACTGTGAATCTG-ACAACAGGAAATAA--ACCTCCTTATTCACCAAGA--------AAGAT-T---------GCAAGAACTGCTAATTC-ATGC-T-TCCATGTTTAAAA-ACATGGCTTTCTT--------ACTTTTATAGGATAATAG-TA-ATCCATTGGTCTTAGGAACCAAAAAC-CTTGGTGCAAATCCAAATAAAAG----TA------ATCAATA---------TTTTCACAA---CCTC---AA---TCTTATTAATCTTCATTCTTCTACTATCCCCAA---TCCT----------A----ATTTCAATATCAAACCTAA-TTAAACACATCAACTTCCCAC-------TGTACAC-CACCACATCAATCAAATTCTCCTTCATTATTAGCCTCTTACCCCTATTAATATTTTT-CCACAATAATATAGAATATATAATTACAACCTGGCACTGAGTCACCATAAATTCAATAGAACTTA
+s galGal2.chrM                12610 692 +     16775 ATAGCAGAACTAACAATTATAGTTGCCCTCTTCAACTGATCCTCCCCCACAATTATCTTAACCGGCACTGCAACACTCCTAACCGCCTCTTACACCCTCTACATACTACTCTCAACCCAACGAGGCACTCTTCCATCCCACATCACAACAACCCCCAACTCAAACACTCGAGAACATCTTCTCATAACCCTCCACATCATCCCCATACTAACACTCATCCTCAAACCAGAACTAATCTCAGGAACCCCTCTAT-GCAAACATAGTTTAAC-CCAAACATTAGATTGTGATTCTA-AAAATAGGAGTTTA-ACCCTCCTTGTTCGCCGAGGGGAGGCCCAAGCC-A---------GCAAGAACTGCTAATTC-CTGC-A-TCTGAGCTTTAAA-CCTCAGTCCCCTT-A------ACTTTTAAAGGATAAGAG-CA-ATCCGTTGGTCTTAGGAACCACCTAT-CTTGGTGCAAATCCAAGTAAAAG----TA------ATGGAGACTCCACTGCTCCTTAACA---CCCT---CA---CAACATTAACACTACTCACCCTCCTTACCCCTA---TTAT----------CCTTCCCC-------CCCTCCTAAATCTAAAAAA--CTCCC-CCAT------ATCCAT---CACCAAAACCATTAAAACCGCCTTCCTAATCAGCCTAATCCCAACAACAATCTTCAT-CCACTCAGGGGCAGAAAGCATTGCCACCCACTGAGAATGACAATTTATCCCCAACTTCAAGATCC
+i galGal2.chrM            C 0 C 0
+s monDom4.chrUn           117162782 683 + 174229318 CTAGGAGAACTCATAGTTATTATTTCATCATTCTCATGATCAAACTGATCCATCCTACTACTAGGATTAAACACAGTCATTACAGCCTTATATACACTATACATACTGATTACCTCCCAACGGGGTAAATTTACACACCACTTAAACCCACTTCATCCTACAATAACACGCGAACATATACTGATAACTCTCCATATACTACCACTCCTAATTATCTCATTAAATCCAAAATATATTTTAGGTACCACATTTT-GCAAATATAGTTTAAC-AAAAACATTAGATTGTGAGTCTA-AATATAGAAGTTTA-AACCTTCTTATATGCCGAGA--------AAGAC-T----------CAAGAACTGCTAACTC-TTGTAC-TCCATACCTAATA-GTATGGCTTTCTT--------ACTTTTAAAGGATAAAAG-CT-ATCCGTTGGTCTTAGGAACCAAAAAC-TTTGGTGCAACTCCAAATGAAAG----TA------ATTAATT---------TTACTTTAAACTCAAT---AA---TCCTATTATCTATCATCATGCTAGTATCACCT----CTAC----------TGTATAACATACTAATACCCCACAAAACAACTTATTTTCCA-ACCT-------ATTGT---AAAAACATAATTATAATA-GCTTTTATAACAAGCCTACCACCCATAATTATCTTTAT-ATTATACGGCCAAGAATCTGTTATTACAAATTGGCATTGATTTTCAATTACTACATTTAACATTT
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343     10698 677 +     18297 ATTGGAGAATTATTAATTATTTCATCATCATTTTCTTGATCAAATATCACTATACTATTTATAGGTCTAAATATATTAATAACCGCTTCTTATACCCTCTATATACTTATTATAACTCAACGAGGGAATGTAAATCCCCATATTAAATCTATACCACCCTCATTTACTCGAGAAAATACTCTAATAGCCCTTCACATACTTCCTCTACTTCTTCTAATGCTTAACCCCAAAATCATTATAGGACCAACTTTCT-GTAAATTTAGTTTAAT-AAAAACATTAGACTGTGACTCTA-AAATTAGGAGGTAA--AGCTCCAAATTTACCAAGA--------AAGAA-----------AAAAGAACTGCTAATTC-TTTA-T-ACCATCCGTAAAA-CTATGGCTTTCTT--------ACTTTTTTAGGATAGAAG-AA-ATCCGTTGGTCTTAGGAACCAAAAA--ATTGGTGCAACTCCAAATAAAAG----TA------ATTAATA---------TAGTATCTA---TCTT---TA---CTCTGTCATCCCTAATTATTCTTTTACTCCCGA---TCAT----------TATATCATTACTAAACTACCCTAACCCCAATTTA--CTGCC-ATCC-------TACGT---AAAACATGCAGTCTCTTACTCATTTTTTCTTAGTATTGTTCCTTTATTATTATTCACATCAACATATCCAGAAACAATA-ATTTCAAACTGACACTGAATATCAATTCACACCTTTAACTTAT
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_36650      14291 680 +     16266 ATCGGAGAATTACTTATTATCACAACATCATTTTCATGATCTAATCTCACCATTTTCCCTATAGGACTAAACGTATTAATTACTACAATATATACTCTCCACATAATAACCACAACTCAACGGGGAAAGACATCTCACCACGCTAAATCCATTAAACCTTCATTTACCCGAGAGAACACCTTAATAGCCCTCCATTTTCTACCCCTACTGCTCCTTTCCCTAAACCCCAAGATCATTCTAGGATTAACATATT-GCAGACATAGTTTAAC-CAAAACATTAGGTTGTGGACCTATAAATAAGAATTTAA--TCCTCTTTGTCTACCAAGA--------AAGAA-T---------TAAGGAACTGCTAATCC-CTTA-T-ACCTCATCTAATA-ATGTGGCTTTCTT-A------ACTTTTAAAGGGTAAGAG-CT-ACCCATTGGTCTTAGGCACCAAAAA--ACTGGTGCAACTCCAGATAAAAG----TA------ATCAACC---------TAATCCCAA---CCCT---AA---TACTAACATCACTAATCATTCTAACCCTACCCA---TTAT----------CACAACATTACTACAAAACAACAAGACAAATTGC--TTTCT-ATAT-------ATCAC---CAAAACAGCTGTAACCTACGCCTTCGCAATCAGTCTAATTCCAACTCTGTTATTTAT-TCAATCTAACCAAGAAGCCTATATCTCCAACTGACACTGAATAACAATCCACACCCTAAAGTTAT
+i loxAfr1.scaffold_36650  C 0 C 0
+s dasNov1.scaffold_23239      15120 679 -     16977 ATTGGAGAACTACTAGTAACCATAACAACATTCAAGTGATCCAACCTAACCATCCTAGCCCTGGGTCTAAACATATTAATCACAGCCTTATACTCCCTATACATACTCATTACTACACAACGAGGTAAATTCACCTACCATACCTATTCAATTAAACCAACATTCACCCGAGAAAGTACCCTGATACTAATACACCTCCTACCCATTATACTACTATCAATTAACCCAAAAATTATCCTCGGGCCCCTATACT-GTGGACATAGTTTACC-CAAAACTCTAGATTGTGAATCTA-GCAACAGAACATAA--AAATTCTTGTTCACCAAGA--------AAGAATT---------GCAGGAACTGCTAACTC-TTGC-C-CCCATACCTAAAA-ATATGGCTTTCTT--------ACTTTTATAGGATAACAG-TA-ATCCACTGGTCTTAGGAACCAGAAA--CTTGGTGCAAATCCAAATAAAAG----TA------ATTAACC---------TAATCATAC---CATT---TT---CTATTATTACTCTTACCATTCTAACTATCCCAA---TCAT----------AATGTCTTACACAAACAAATACAAAACCAAATCG--TACCC-CTAC-------CACGT---TACAACAACCGTGTCATATGCATTTATGACAAGCATAATTCCAACCATAATATTCCT-TCTATCAAACCAAGACTCCTACATTTCAAACTGGCACTGAATAACAATACAAACCATAAAACTAT
+i dasNov1.scaffold_23239  C 0 C 0
+s canFam2.chrM                11325 681 +     16727 ATCGGAGAACTATTTGTAGTGATATCCTCATTCTCATGATCCAACATTACTATTATCCTAATAGGAATTAACATTATCATCACCGCCCTATACTCACTTTATATATTAATCACCACACAACGTGGTAAATATTCCCACCATATCAAAAATATCAAACCATCATTCACACGAGAAAATGCCCTAATGACCTTGCACCTACTGCCCCTACTCCTCCTATCCCTTAACCCTAAAATTATTCTCGGTCCCATCTACT-GTAAGCATAGTTTAAC-AAAAACATTAGATTGTGAGTCTA-ACAATAAAAGCTCA-AACCTTTTTGCTTACCGAAA--------AAGTACT---------GCAAGAACTGCTAATTC-ATGC-T-CCCATGCATAAGA-ACATGGCTTTTTC-A------ACTTTTATAGGATAGAAG-TA-ATCCGTTGGTCTTAGGAACCAAAAA--ATTGGTGCAACTCCAGATAAAAG----TA------ATAAATA---------TATTTTCTT---CATG---CA---TAATCACAGCCCTAGTTATTCTTACTTTGCCCA---TCAT----------TATATCCTCTACTAAACTTTACAAGAATAAGCTA--TACCC-ATAC-------TATGT---AAAAACCGCTACTTCTTACGCGTTCATAATTAGCATAATTCCCACAATAATATTCAT-CTACTCAGGACAGGAAACAATCATTTCAAACTGGCATTGAATAACAATCCAAACTATAAAACTAT
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                11653 684 +     16338 ATTGGAGAACTATTTGTAGTAATGTCAACCTTTTCATGATCTAACATTACAATTATTCTAATAGGAGTAAATATAGTAATCACCGCCCTATATTCTCTATACATGCTAATTATAACCCAACGAGGAAAATATACCTACCACATTAATAATATCTCGCCTTCCTTTACACGGGAAAATGCACTCATATCATTACACATCCTACCCCTACTACTCCTAACCCTAAACCCAAAAATTATTCTAGGACCTCTATACT-GTAAATATAGTTTAAC-AAAAACATTAGATTGTGAATCTA-ACAATAGAAACTCATTACCTTCTTATTTACCGAAA--------AAGTA-T---------GCAAGAACTGCTAATTCTATGC-T-CCCATATCTAATA-GTATGGCTTTTTCGA------ACTTTTAAAGGATAGTAGTTT-ATCCGTTGGTCTTAGGAACCAAAAA--ATTGGTGCAACTCCAAATAAAAG----TA------ATAAACA---------TATTCTCCT---CACT---CT---CACTAGTTACTTTACTCTTACTAACTATACCCA---TTATAATAATAAGCTTTAACACCTAC-AAACCTTCCAA---------C--TACCC-ACTC-------TACGT---AAAAACAGCTATCTCATACGCCTTCATTACCAGCATAATTCCCACAATAATATTTAT-CCACTCAGGCCAAGAACTAATTATTTCAAACTGACACTGACTAACCATCCAAACTCTTAAATTAT
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34446995 678 - 182086969 GTGGAAGAACTCTTTGTGACTACGGCCTTATTCTCCTGATCAAATATCACTATTACGCTTACAGGACTTAATATACTAATTACAGCCCTTTACTCCCTGTATATGCTAATCTCAACACAACGAGGAACACTTTCATATTATATTAACAGTATGAAACCTTCCTTTACATGAGAAAACACATTAATACTTATACATCTTGTGCCTATCTTACTATTATCCTTAAACCCTAAAATTATTATGTGGTTTGCATGCT-GTAGCTATAGTTTACC-CAAAACATTAGATTGTGGATCTA-ACAATAGAAGCCTG-CAACTTCTTACCTACCAAGA--------AAGTA-T---------GCAAGAACTGCTAACTC-ATGC-C-CCGATGTTTAACA-ACATGGCTTTCTC-A------ACTTTTAAAGGATTAGAA-TT-ATCCGTTGGTCTTAGGAACCAAAAAC-ATTGATGTAACTCCAAATAAAAG----TA------ACAAACA---------TGTAT-CTT---CCAC---GG---CTATCACAGCCCTAATCCCCTTAATCCTACCGA---TTAC----------TGTTACCTTAGCCAACTTCTGCAAAATAGGCTCA--TACCC-AAAT-------TATGT---AAAAACATCTATCGCACGTGCCTTCATCATTAGCCTCATCCCAAAAACAATGTTTAT-ATGCACAGACCAAGAAGCCATTATCTC--ACTGACATTGAATGACGATCCAAACTCTCAAATTCT
+i rheMac2.chr5            C 0 C 0
+s panTro2.chrM                11302 681 +     16554 CTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAGCATAAAGCCCTCATTCACACGAGAAAACACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCT-GTAAATATAGTTTAAC-CAAAACATCAGATTGTGAATCTG-ACAACAGAGGCTCA-CGACCCCTTATTTACCGAGA--------AAGCT-T---------ATAAGAACTGCTAACTC-GTAT-T-CCCATGCCTAACA-ACATGGCTTTCTC-A------ACTTTTAAAGGATAACAG-TT-ATCCATTGGTCTTAGGCCCCAAAAAT-TTTGGTGCAACTCCAAATAAAAG----TA------ATAACCA---------TGTATGCTA---CCAT---AA---CCACCTTAGCCCTAACTTCCTTAATTCCCCCCA---TCCT----------CGGCGCCCTCATTAACCCTAACAAAAAAAACTCA--TACCC-CCAT-------TACGT---GAAATCCATTATCGCATCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCAT-ATGCCTAGACCAAGAAACTATTATCTCGAACTGACACTGAGCAACAACCCAAACAACCCAACTCT
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                   11885 681 +     16571 CTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTT-GTAAATATAGTTTAAC-CAAAACATCAGATTGTGAATCTG-ACAACAGAGGCTTA-CGACCCCTTATTTACCGAGA--------AAGCT-C---------ACAAGAACTGCTAACTC-ATGC-C-CCCATGTCTAACA-ACATGGCTTTCTC-A------ACTTTTAAAGGATAACAG-CT-ATCCATTGGTCTTAGGCCCCAAAAAT-TTTGGTGCAACTCCAAATAAAAG----TA------ATAACCA---------TGCACACTA---CTAT---AA---CCACCCTAACCCTGACTTCCCTAATTCCCCCCA---TCCT----------TACCACCCTCGTTAACCCTAACAAAAAAAACTCA--TACCC-CCAT-------TATGT---AAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCAT-GTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCT
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182     11456 680 +     20791 CTAGGGGAACTTCTTATCATTATGGCCTCCTTCTCATGATCTAACCTCACAATCATCCTGATAGGGACTAACGTCCTAATCACGGCCCTCTACTCCCTCTATATACTATCAACCACCCAACGAGGCAAATTCACGTATCACACAAACAACATTTCCCCTACATTCACCCGAGAAAATACTCTTATAGTACTTCACCTAGCCCCACTTCTTCTACTATCAATTAGCCCAAAAATCATCTTAGGCCCAATATTCT-GTAAATATAGTTTAAC-AAAAACATTAGATTGTGAGTCTA-ATAATAGGAGACCG-CACCTCCTTATCTACCGAGA--------ATGTC-T---------GCAAGAACTGCTAATTC-ATGC-T-CCCATGTCTAACC-CCATGGCTTTCTC-A------ACTTTTAAAGGATAGAAG-TA-ATCCGTTGGTCTTAGGAGCCAAAAA--ATTGGTGCAACTCCAAATAAAAG----TA------ATTAACT---------TATTCTCCA---CCTCTGTAG---CTGTATCAATTATTATTTTAGTCCT---CCCTA---TTGT----------GGCCTCTTTCACTAACATTTTTAA--TAGTCCTAACTACCC-TCAC-------TACGT---AAAAACTTCAGTATCTTATGCATTCACTATCAATCTCATTCCAACATTAATTTTCAT-CGCTACTAGTCAAGAAATAATAGTATCCAACTGACACTGAATAACAATTCACACCTTAAAATTAA
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                    11269 680 +     16300 ATAGGCGAGTTATTCATTGTTATAGCAACATTTTCCTGATCGAACCCCTCTATCATCCTTATAGCAACTAACATTGTCATCACAGGAATATACTCAATATATATGATTATCACAACCCAACGAGGAAAACTAACCAGCCACATAAACAACCTCCAACCTTCCCACACACGAGAATTAACACTCATAGCTCTACACATTATTCCCCTCATACTATTAACAATCAACCCTAAACTCATCACAGGCCTAACAATAT-GTAGATATAGTTTACA-AAAAACATTAGACTGTGAATCTA-ACAACAGGAAATCA--AATTCCTTATTTACCAAGA--------AAGTA-T---------GCAAGAACTGCTAATTC-ATGC-A-CCCATACCTAAAACATATGGCTTTCTT--------ACTTTTATAGGATAGAAG-TA-ATCCATTGGTCTTAGGAACCAAAAAC-CTTGGTGCAACTCCAAATAAAAG----TA------ATAAATA---------TAATAACAA---TCCT---AA---TCCTCATAATTCTTGATTTACTTACAACACCAA---TCAC----------A----TTTTCAATAACAATCTTAA-CCAAACTTATGTACTT-CCGT-------CATATGCTCATTACATCAATTAAATTCTCATTCCTCCTTAGCCTCTTACCTTTACTACTATTCTT-CCACCACAACACAGAATACATAATTACTAACTGACATTGACTAACTATTAATTCTATTAAACTTA
+i rn4.chrM                C 0 C 0
+s tetNig1.chrUn_random    108042749 712 - 171761319 ATAGGGGAACTAATGATTGTCACCTCCGTATTCGGCTGATCGTGATGAACTATCGCCCTAACGGGACTAGGAATATTAATTACCGCAAGCTATTCACTCTACATATTCCTTATAACCCAACGAGGCCCCCTCCCAAGCCACATCATAGCCCTAGAGCCCTCCCACACCCGAGAGCACCTACTAATCGCCCTCCACCTCCTCCCCCTACTCCTACTCATCCTAAAGCCAGAACTTATCTGAGGATGAGCCGTCT-GTAGACATAGTTTAAC-CAAAACATTAGATTGTGATTCTA-AAAACAGAGGTTAA-AACCCTCTTGTCCACCGAGA--------GAGGC-CTG--CTGCAGTGAAGACTGCTAATCT-TCAT-C-CCTTTGGTTAAACTCCAGAGCTCACTC-GCCAAAAGCTTTTAAAGGATAATAG-CTCATCCGTTGGTCTTAGGAACCAAAAACTCTTGGTGCAACTCCAAGTAAAAG-CTATGCACTCCACCCCCT---------TAATCATAA---CATC---AAGCCTTGTCATTATCTTCACCTTACTTATCTACCCAATCCTCAC----------CACACTCTCCCCAAGCCCCCAAAGCCCAGACTGA--GCCTT-AAAA-------CAAGT---CAAAACAGCAGTAAAACTAGCCTTCTTAGTCAGCCTTCTACCTCTTTTCCTCTTCCT-TAATGAAGGTGCTGAAGCCGTAATTACAAACTGAAGCTGAATGAACACCCACACATTTGACATTA
+i tetNig1.chrUn_random    N 0 C 0
+s danRer4.chrM                12426 699 +     16596 ATAGGAGAACTTATGATTATCACAGCCCTATTTAACTGATCTCCATGAACAATTATTATTACAGGAATAGGAACCTTAATTACAGCAAATTATTCACTTTATATATTTTTAACATCTCAACGAGGCTCAATCCCAGAACACATCACCAATCTTTCACCATCCCACACCCGAGAACATCTCTTAATGACTTTACACCTAATTCCTATCATCTTACTTATATTAAAACCAGAACTTATGTGAGGTTGATGTAACTAGTAAGTTTAGTTTAAAGTAAAATTTTAGATCGTGACTCTA-AAGATAGGGGTTAA-AGCCCCCTCACTCACCGAGG--------AAGAG-TAGGAAAACAGTAAATGCTGCTAATAT-TTAC-CAACCATGGTTAAACTCCATGGCTTCCTT-ACC----GCTTCTAAAGGATAATAG-TACATCCATTGGTCTTAGGAACCAAAAACTCTTGGTGCAACTCCAAGTAGAAGTTTATG------ACTGATA---------TGATCATAC---CTTT---AACATTAATCCTAATTTTCGC----------------AGTTTTAT----------CATACCCCTTATTAAAACCAAAAAGCTATTCAAA--ATCCA-ACAACTCTTTCCAAGC---TTGAAATGCTGTCCATGTATCTTTCTTAATTAGTCTTATCCCACTTACAATGATGCT-GTACAAAGAATCAGACCATGTTGTAATATGCTGAAGCTGAATAAATACACAAGCGTTTAACGTAG
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_96       2680154   0 -   2855184 I
+
+a score=3655161.000000
+s mm8.chrM                    11970 741 +     16299 AAATAAGCTTCAAAACTGACTTTTTCTCTATCCTGTTTACATCTGTAGCCCTTTTTGTCAC----ATGATCAATTATACAATTCTCTTCAT--GATATATACACTCAGACCCAAACATCAATCGATTCATTAAATATCTTACACTATTCCTGATTACCATGCTTATCCTCACCTCAGCCAACAACATATTTCAACTTTTCATTGGCTGAGAAGGGGTGGGAATTATATCTTTCCTACTAATTGG---------------ATGATGGTACGGACGAACAGACGCAAATACTGCAGCCCTACAAGCAATCCTCTATAACCGCATCGGAGACATCGGATTCATTTTAGCTA-TAGTTTGATT--------------TTCCCTAAACATAAACTCATGAGAACTTCAACAG-------------------ATTATATTCTCCAACAACAACGACAATCT---AATTCCACTT------ATAGGCCTATTAATCGCAGCTACAGGAAAATCAGCACAATTTGGCCTCCACCCATGACTACCATCAGCAATAGAAGGCCCTACACCAGTTTCAGCACTACTACACTCAAGTACAATAGTAGTTGCAGGAATTTTCCTACTGGTCCGATTCCACCCCCTCACGACTAATAATAACTTTATTTTAACAACTATACTTTGCCTCGGAGCCCTAACCACATTATTTACAGCTATTTGTGCTCTCACCCAAAACGACATCAAAAAAATCATTGCCTTCTCTACATCAAGCCAACTAGGCCTGATAATAGTGACGCTAGGAATAAACCAACCACACC
+s rn4.chrM                    11949 741 +     16300 CTATAAGTTTCAAAATTGACTATTTCTCAATCCTATTCCTATCAGTATCCCTATTCGTAAC----ATGATCAATTATACAATTCTCTTCAT--GATATATACACTCTGACCCCCACATTAACCGATTCATTAAGTACTTAATAATATTCCTGAATAACATACTAATCCTAACCTCAGCTAACAATCTATTCCAACTCTTTATTGGATGAGAAGGGGTAGGAATTATATCCTTCTTATTAATCGG---------------ATGATGATATGGCCTTGCAGACGCCAACACAGCGGCCCTCCAAGCAATCCTCTACAACCGAGTCGGAGACATTGGTTTCATCCTAGCTA-TAACCTGATT--------------CTGCCTAAACATAAACTCCTGAGAACTCCAACAA-------------------ATTTTCTTAACCAACACCAACAACAATCT---AGTCCCTCTC------ACAGGACTACTAATTGCAGCCACAGGAAAATCCGCCCAATTCGGACTTCATCCATGACTCCCATCAGCTATAGAAGGCCCAACTCCCGTCTCTGCCCTACTACACTCAAGCACAATAGTTGTAGCAGGGATCTTCCTAATAATCCGATTCCACCCCCTAACCTCAAACAATAGTACTATTATAACAGCCATACTATGTCTTGGTGCAATCACCACATTATTCACAGCAATCTGTGCTCTCACCCAAAACGACATCAAAAAAATCGTAGCTTTCTCAACATCCAGCCAACTAGGCCTTATAATAGTCACATTAGGGATTAACCAACCCTACC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     12136 741 +     20791 CAACCAGCTTTAAATTAGATTACTTCTCTATACTATTCACCCCAATTGCACTATTTGTTAC----ATGGTCTATCATAGAATTTTCCATAT--GATATATACACTCAGACCCTAAAATCAACCAATTCTTTAAATACCTACTCATATTTCTTATTACTATACTAATTTTAGTCACCGCTAATAATATATTTCAGCTATTTATTGGATGAGAGGGAGTGGGAATCATATCATTTCTCCTCATCGG---------------CTGATGACACGGGCGAACAGATGCCAATACTGCAGCCTTACAAGCAATCTTATACAACCGCATTGGAGATATTGGCTTTATTATAGCCT-TAGCCTGATT--------------TGCTATTAACCTCAACACATGAGAACTCCAACAA-------------------ATCTTTATTTTAGACAATAACATTACCAT---CCTCCCACTG------ATAGGATTAATTCTTGCCGCCACGGGCAAATCCGCACAATTTGGTCTACACCCATGACTCCCATCAGCTATAGAAGGCCCGACGCCCGTATCAGCCCTACTTCATTCTAGCACAATAGTAGTAGCTGGAGTTTTCCTCCTAATCCGCTTCTACCCCTTGCTAGAAAATAACAAAACTGCCCAAACATTAATCCTATGCCTAGGCGCAATTACTACCTTATTCACAGCCCTATGTGCCCTCACACAAAACGATATCAAAAAAATTGTAGCCTTTTCCACATCAAGTCAACTCGGACTAATAATGGTCACAATCGGAATTAACCAACCACACC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   12566 741 +     16571 CCCTAAGCTTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTAC----ATGGTCCATCATAGAATTCTCACTGT--GATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAG---------------TTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAGTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCT-TAGCATGATT--------------TATCCTACACTCCAACTCATGAGACCCACAACAA-------------------ATAGCCCTTCTAAACGCTAATCCAAGCCT---CACCCCACTA------CTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                11983 741 +     16554 CCCTGAGCTTTAAACTAGACTATTTCTCCATAACATTTATCCCCGTAGCACTGTTCGTTAC----ATGATCCATCATAGAATTCTCACTAT--GATATATAGACTCAGACCCCAACATCAACCAATTCTTCAAATACTTACTTATCTTCCTAATTACTATACTAATCCTAGTCACCGCTAACAACCTATTCCAACTCTTCATCGGCTGAGAAGGCGTAGGAATTATATCCTTTCTACTCATTAG---------------CTGATGGTACGCCCGAACAGATGCCAACACAGCAGCCATCCAAGCAATCCTATATAACCGTATCGGTGATATTGGTTTTGTCCTAGCCC-TAGCATGATT--------------TCTCCTACACTCCAACTCATGAGATCCACAACAA-------------------ATAATCCTCCTAAGTACTAATACAGACCT---TACTCCACTA------CTAGGCTTCCTCCTAGCAGCAGCAGGCAAATCAGCTCAACTAGGCCTTCACCCCTGACTCCCCTCAGCCATAGAAGGCCCTACCCCTGTTTCAGCCCTACTCCACTCAAGCACCATAGTCGTAGCAGGAATCTTCCTACTCATCCGCTTCTACCCCCTAGCAGAGAATAACCCACTAATCCAAACTCTCACGCTATGCCTAGGCGCTATCACCACCCTATTCGCAGCAGTCTGCGCCCTCACACAAAATGACATCAAAAAAATCGTGGCCTTCTCCACTTCAAGCCAACTAGGACTCATAATAGTTACAATCGGTATCAACCAACCACACC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34447673 748 - 182086969 CACTAAGCTTCAAACTAGACTACTTCTCCACAAAATTTACCCCAGTAGCACCACTCATTAC----CTGATCTATTATAGAATTCTCAATAT--GATATATAAATTCAGACCATAACATTCATCAATTTTTCAAG----TACTTATTTTCTTCATCACAATATTAATTCTGGTTACTGCCAACAACCTCTTTCAGCTCTTTATCAGATGGGAAGGTGTAGGAATCATGTCTTTCTTACTAATTAGTAAGAATTACTAATTCTGAAGGTATGGCAGAGCAGATGCTAATACAGCAGCCCTCCAAGCAGTCCTGTACAACCTCATCGGTGATATTGGCTTTATTTTAGCTA-TAGCATTGT-----------------TCATGTCCTCCAACACATGAGAATTTTAACAA-------------------ACATTTTTTCTAGAC-CTCACCCCCAACT---CCTTCCATTA------ATTAGCCTTCTCTTAGCAGCAGCAGAAAAGTCAGCTCAATTCGGCCTCCATCCCTGACTTCCATCTGCCATAGAAGGCCCAGCCCCAGTCTCAGCCCTACTTCACTCCAGCACTATAGTTGCAGCAGGAGTTTTCCTGCTCGTCTGCTTCTACCCTTTAATAGAAAATAACCTATAAATCCAAACCTTTACATTACGTCTGGTAGCTATTACTACCTTATTCACAGTCATCTGTGCTCTAACACAAAATGATATCCAAAAAATCATAGCATTCTCCCCCTCAAGCCATCTAGGCCTTATAATAGTCACAATTGGCATTAATCAGCCACACC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                12337 741 +     16338 CCCTCAGCTTTAAAATAGACTATTTCTCAATAATATTTATCCCAGTAGCACTATTCGTCAC----ATGATCTATTATAGAATTCTCAATAT--GATATATATACTCAGACCCCAATATTAACAAATTCTTCAAATATCTACTCCTATTCCTCATTACTATGCTCATCCTTGTAACCGCAAACAACCTCTTCCAGCTATTCATTGGCTGAGAAGGCGTCGGAATCATATCATTTCTACTCATCGG---------------ATGATGATACGGACGAGCAGATGCAAACACAGCAGCCCTACAAGCAATCTTATATAACCGCATCGGCGACATTGGTTTCATTTTAGCAA-TAGCATGGTT--------------CCTAACAAATCTCAATACCTGAGACCTCCAACAG-------------------ATCTTCATACTAAACCCAAGCG---ACTCAAACATACCCTTG------ATTGGACTAGCATTAGCTGCAACCGGAAAATCCGCCCAATTTGGCCTCCACCCGTGACTTCCCTCTGCAATAGAAGGCCCAACTCCCGTCTCAGCACTACTCCATTCAAGCACAATAGTGGTAGCAGGTATCTTCCTACTAATCCGTTTCTATCCCCTCACAGAAAACAATAAATACATCCAATCTATTACATTATGCTTAGGAGCCATTACCACACTATTTACAGCAATATGCGCCCTCACCCAAAATGACATTAAAAAAATCATCGCCTTCTCCACATCCAGTCAACTGGGCCTTATAATAGTAACTATTGGCATTAACCAACCTTACC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                12006 741 +     16727 CCATGAGTTTCAAATTAGACTACTTCTCAATAATCTTTGTACCTGTAGCCCTTTTTGTCAC----GTGGTCTATCATAGAATTCTCTATAT--GATATATACACTCCGATCCTTACATTAACCGGTTTTTCAAGTACCTTCTCTTATTCCTCATCACTATAATAGTCCTAGTTACCGCAAACAACATATTCCAACTATTCATTGGTTGAGAAGGAGTTGGCATTATATCATTCCTACTTATTGG---------------ATGATGGTACGGCCGAACCGATGCAAATACAGCCGCCCTACAAGCCGTCCTCTACAACCGTATTGGAGATGTAGGCTTCATTATAACCA-TAGCATGATT--------------TCTACTAAACTTAAACACATGAGACCTTCAACAA-------------------ATCTTCATTACGA---CAAACGATAATTTTAATCTGCCACTA------CTTGGCCTACTACTAGCAGCTACCGGTAAATCTGCTCAATTCGGCCTACATCCCTGACTCCCCTCAGCCATAGAAGGCCCCACTCCTGTATCAGCCCTACTTCACTCAAGCACAATAGTTGTAGCAGGAGTATTTCTTCTTATCCGCTTTCATCCACTAATAGAGCATAACCAAACTATTCAAACCCTCACTTTATGCTTAGGGGCCATTACTACACTATTTACCGCAATCTGCGCTCTTACACAGAATGATATCAAAAAAATTGTAGCGTTCTCTACCTCAAGCCAACTAGGCCTAATAATAGTAACAATTGGCATTAACCAGCCCTACT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      15799 738 -     16977 CACTTAGTTTTAAACTGGACTTCTTCTCAATTATCTTTGTATCCGTAGCCCTATTCGTAAC----CTGGTCAATTATAGAATTCTCACTAT--GATATATACACTCAGACCCCTACATCAATCAATTCTTCAAGTACTTACTACTATTCTTAATCACAATAATAATCTTAGTAACAGCAAACAACATATTCCAACTCTTCATCGGATGAGAAGGAGTGGGAATTATATCATTTCTACTTATCGG---------------CTGATGATATGGACGAACAGACGCCAACACCGCAGCCCTCCAAGCAATCCTATATAACCGAATTGGTGACATTGGCTTTATCTTAACCA-TAGCATGACT--------------CCTTCTCCACCTAAACTCATGAGACCTTCAACAA-------------------ATCTTTATACTCAAACCAACCA---ACCT---TCTCCCTCTA------TTAGGACTACTAGTAGCAGCAGCAGGAAAATCAGCCCAATTTGGACTACATCCATGACTCCCTTCAGCTATAGAAGGTCCTACCCCTGTATCAGCATTACTCCATTCAAGTACTATAGTTGTAGCAGGTATCTTCCTATTAGTACGTTTCTACCCACTAATACAAAATAACCCAACCATTCTGACAATAACCCTATGCCTAGGCGCCATCACCACCTTATTTACCGCCATCTGCGCCCTAACACAAAATGATATTAAAAAGATCATTGCCTTCTCAACCTCCAGTCAACTGGGCCTCATAATAGTAACTATTGGCATTAACCAACCCCATT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      14971 741 +     16266 CTATAAGCTTTAAATTAGACTTCTTTTCCCTAACATTCATGCCAATTGCACTTTTTATTAC----CTGATCAATTATAGAATTTTCACTAT--GATATATACACTCAGATCCCCATATTAACCGTTTCTTCAAATACCTCCTGTTATTCCTAATCACTATACTAATTTTGGTAAGCGCTAATAATCTACTGCAACTATTTATAGGCTGAGAAGGAGTTGGCATTATGTCCTTCCTGCTAATCAG---------------TTGATGACATGGACGAACAGACGCTAACACAGCAGCTCTACAAGCAATACTCTATAACCGCATTGGCGATATAGGCTTTATTATAATAA-TAGCCTGATT--------------TACTATCCATTTAAATTCTTGAGAGTTTCAACAA-------------------ATCTTCTTAACTAACCCCAAGAACACTAC---ACTCCCACTA------CTAGGTCTTCTCCTGGCCTCAGCAGGAAAATCAGCCCAATTCGGGCTTCATCCGTGACTTCCATCAGCCATAGAAGGTCCTACTCCAGTATCGGCACTCCTTCATTCCAGTACAATAGTTATAGCTGGAGTATTTACCCTCATCCGCTTTTACCCACTAATAGAAAATAACCTCACTATTCAAACTTCAACACTATGCCTAGGGGCCATTACTACTTTATTTACAGCTATCTGTGCTCTCACACAGAATGACATCAAAAAGATTATCGCACTCTCCACTTCCAGCCAACTAGGCTTAATAATAGTAACCATCGGCATTAATCAGCCACATC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     11375 738 +     18297 GTTTAAGCTTTAAACTTGACTACTTTTCCCTAATTTTCATCCCTGTAGCCCTCTACGTTAC----CTGATCAATTATACAATTCTCCGTAT--GATATATACACTCTGACCCTAACATTGACCGCTTTTTTAAATATCTTCTTCTATTCTTAATTACTATAATAATCTTAGTTACCGCTAATAATATATTTCAGCTATTCATTGGTTGGGAAGGTGTAGGAATTATGTCCTTTTTATTAATTGG---------------TTGGTGACATGGACGCTCAGACGCTAACACAGCAGCCCTCCAAGCTATTATCTTTAACCGAATTGGGGATGTAGGTCTAATTTTAGCTA-TAGCATGATT--------------TTTTAAAAACTTTAACTCCTGAGAATTTCAACAA-------------------ATCTTCTTACTAAACCCTCCCAATAATG------TTCCTTTA------CTTGGACTCCTCCTAGCAGCAATAGGCAAATCTGCACAATTTGGTCTACATCCCTGACTCCCCTCCGCAATAGAAGGCCCAACCCCAGTCTCAGCACTTCTTCACTCTAGCACTATAGTAGTAGCAGGAATTTTCTTACTAATTCGGTTTTATCCTCTTTACCAAAATAATAGTACGATACAGACATTAATTCTATGTGTAGGAGCCCTAACAACGCTATTCACAGCAGTCTGTGCCTTAACCCAAAATGATATTAAAAAGATTGTAGCATTCTCTACTTCAAGCCAATTAGGACTAATAATAGTTACCATCGGAATTAATCAACCTTACT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117163465 735 + 174229318 CAATAAGCTTCAAACTAGATTTCTTCTCAATTATCTTTATCCCCATTGCCCTGTATGTGAC----CTGATCTATCCTAGAATTTTCCTTAT--GGTATATACATTCTGATATTTTTATCCATAAATTCTTCAAATACTTAGTATCCTTCCTCCTAACAATAATTATTTTGGTCTCAGCTAACAACTTATTTCAGCTGTTCATTGGATGGGAGGGTGTTGGTATTATGTCCTTTCTACTAATTGG---------------CTGATGGTACGGACGCACAGATGCTAACACCGCAGCCTTACAAGCAATTATCTACAACCGAATTGGAGACATTGGCTTTATACTGACAA-TAGCATGACT--------------AATACTAAACAGCAACTCCTGAGAACTACAAAAC-------------------ATCTTCTC------CACTAACATAGACTT---TATCGCACTT------CTAGGCCTAATTATTGCTGCAACCGGAAAATCCGCCCAATTCGGCCTACATCCATGACTCCCTTCTGCAATAGAAGGCCCAACCCCTGTATCAGCCCTACTTCACTCAAGCACTATAGTAGTAGCAGGAATTTTCTTACTAATCCGCTTCCACCCCATGATAGAAAATAATCAAATAATTTTAACGACCATTCTATGTTTAGGGGCAATAACAACACTATTTACAGCAATCTGTGCAATTACACAAAATGATATTAAAAAAATTGTAGCATTCTCCACTTCAAGCCAATTAGGCCTAATAATAGTTACTGTAGGCCTAAATCAACCCCACT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                13302 738 +     16775 CCATCTCCCTAAAAATAGACATATACTCCATAATATTCTTCCCCATTGCACTATTTGTAAC----CTGATCCATCTTAGAGTTCGCAACAT--GATACATAGCATCCGAACCATTTATTACAAAATTCTTTACCTACCTACTCACCTTCCTCATCGCCATATTAACACTAACCATCGCAAATAACATATTCCTCCTATTTGTAGGATGAGAAGGAGTAGGAATCATGTCATTCCTTCTCATTGG---------------ATGATGACAAGGACGAGCTGAAGCCAACACAGCTGCACTACAGGCAATAATCTACAACCGAATCGGAGACATTGGCCTCATCCTAAGCA-TAGCATGACT--------------AGCCTCTTCCCTAAACACCTGAGAAATTCAACAA-------------------ATCACCCACCCAAAC-CAAACACCCACCC-----TCCCCCTC------CTTGGCCTAATCCTAGCCGCCACAGGAAAATCCGCTCAATTTGGCCTTCACCCATGACTTCCAGCAGCAATAGAAGGCCCAACCCCTGTCTCCGCCCTACTCCATTCCAGCACAATAGTAGTTGCTGGAATTTTTTTACTCATCCGCACCCACCCCTTCCTGTCATCCAATAAAACAGCCCTGACAACGTGCCTATGCTTAGGTGCTCTATCAACACTCTTTGCCGCAACATGCGCTCTCACTCAAAACGACATCAAAAAAATCATTGCCTTCTCCACTTCAAGCCAACTAGGCCTCATAATAGTCACAATTGGCCTAGACCTCCCCCAAC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_8452       13792 760 +     23823 AAGTAGGCTTCCTGGTAGACAGTCTGACGGCCATGATGATGGTCGTGGTGACTTTCGTATCGCTGATGGTGCAC------ATCTACACCATCGGTTACATGGCAGAGGATGAGGGCTACAACCGCTTCTTCTCCTACATCTCGCTGTTCACCTTCTCCATGCTCATGCTGGTCATGAGCAACAACCTGCTGCAGCTGTTCTTCGGCTGGGAGGCGGTGGGGCTGGTGTCGTACCTGCTCATCGG---------------CTTCTGGTTCAACAAGCCCACGGCCATCTTCGCCAACATGAAAGCCTTTCTGGTCAACCGCGTGGGCGACTTCGGCTTCATCCTGGGCATTGGCCTGATCGCGGCCTACGCGGGCACGCTGAACTACGGC----GAGATTTTCGCCAAGTCAGCCGAACTGGGCAGCATCGGCTTCCCCGGCACCGACTGGATGCT---GATCACCGTGGTCTGCATCTGCCTGTTCATCGGCGCCATGGGCAAGAGCGCACAGTTCCCGCTGCACGTGTGGTTGCCCGATTCGATGGAAGGCCCAACGCCCATCTCCGCGCTGATCCACGCCGCCACCATGGTGACGGCAGGCATCTTCATGGTGTCGCGCATGTCGCCGCTGTTCGAACTGTCGGACGCGGCGCTGAACTTCATCCTCGTGATCGGCGCCATCACAGCGCTGTTCATGGGCTTCCTGGGCATCATCCAGAACGACATCAAGCGCGTGGTGGCCTATTCCACACTGTCGCAGCTGGGCTATATGACCGTGGCCCTGGG-----------------
+i xenTro2.scaffold_8452   I 1675 I 17
+s tetNig1.chrUn_random    108043461 744 - 171761319 ACATTAGTCTTAAATTCGACCACTACTCTATCATCTTCACCCCCGTCGCCCTCTATGTGAC----CTGATCTATTTTAGAGTTCGCGTCCT--GATACATGCACGCCGACCCATTCATAAACCGATTTTTTAAGTACCTTCTAACCTTTCTCATCGCAATAATTATCCTAGTCACAGCCAACAATATGTTTCAACTGTTTATTGGGTGAGAAGGCGTAGGAATCATATCCTTCCTATTAATCGG---------------CTGATGGTACGCACGGGCTGACGCCAACACCGCAGCACTACAGGCAGTCCTATACAACCGAGTCGGAGACATCGGCCTAGTCTTCTCCA-TAGCCTGAAT--------------AGCCACTCATCTTAACTCCTGAGAAATCCAACAA-------------------ATCTTTTTTTCCTCAAAAGATATAGACCTGACCCTCCCCCTA------ATCGCCCTAATCCTAGCTGCAACAGGAAAATCAGCACAATTCGGACTTCACCCTTGACTGCCCTCTGCCATAGAGGGCCCCACACCGGTCTCTGCCCTACTACACTCCAGCACCATAGTTGTCGCAGGAATTTTCCTGCTAATTCGGACTAGCCCCCTAATAGAAAACAACCCCACAGCCCTAACACTATGTCTATGTCTAGGAGCCCTCACCACCTTGTTTACTGCCACATGCGCACTCACCCAAAACGACATCAAAAAAATCGTTGCTTTCTCAACCTCAAGCCAACTAGGCCTCATAATAGTGACCATCGGACTTAATCAACCCCAAC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                13125 744 +     16596 ACCTAAGTTTTAAATTTGACTACTATTCTGTGACTTTTACCTCAATCGCCTTATTCATCAC----CTGGTCAATTTTAGAATTTGCATCAT--GATATATAGCCTCTTATCCACAAAAAGAATTATTTTACAAATATTTACTTCTTTTTCTTATATCAATAATTATCTTAGTTACAGCCAACAATCTATTTCAACTATTTATTGGCTGAGAAGGGGTAGGAATCATATCATTTTTACTCATTGG---------------CTGATGATTTGGGCGGACAGAGGCTAACACAGCATCTCTACAGGCCGTAATCTACAACCGAATAGGAGACATTGGATTTATCTTAACCT-TAGCATGAAT--------------AGCAATATACCTCAACTCCTGAGACATTCAGCAA-------------------ATTTTCATTCTTTCAAAAGACTTCGACATGACCATTCCCCAA------ATTGGACTTATTATTGCAGCCACAGGGAAATCAGCCCAATTTACACTTCACCCCTGACTACCATCAGCCATAGAAGGCCCTACACCAGTATCTGCTTTACTTCACTCTAGCACTATGGTTGTAGCAGGGATTTTCCTTTTAATCCGTCTTCACCCAATTATAGAAACTAACAAGCTTGCACCAACAATCTGTCTATGCCTTGGAGCATTAACAACTCTATTTGCAGCAACCTGTGCTCTAACCCAAAATGATATCAAAAAAATCGTAGCTTTCTCAACATCAAGCCAACTAGGGCTAATGATAGTAGCAATTGGCCTAAACCAACCACATC
+i danRer4.chrM            C 0 C 0
+
+a score=759977.000000
+s mm8.chrM                    12711 121 +     16299 TAGCATTCCTACACATCTGTACC-CACGC-ATTCTTCAAAGCTATACTCTTTATATGCTCTGGCTCAATCATTCATAGCCTGGCAGACGAAC-AAGACATCCG-AAAAATAGGAAACATCACAAA
+s rn4.chrM                    12690 121 +     16300 TTGCTTTCCTCCACATTTGCACC-CATGC-ATTCTTCAAAGCCATATTATTCATATGCTCCGGATCAATCATCCATATCCTCAACGATGAAC-AAGACATTCG-AAAAATAGGCAATATAATAAA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     12877 121 +     20791 TGGCATTTCTCCACATCTGCACC-CACGC-CTTCTTCAAAGCTATGCTCTTTCTCTGCTCCGGCTCAATTATTCACAGCCTCAATGATGAAC-AGGATATCCG-AAAGATAGGCGGCCTATATAA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   13307 121 +     16571 TAGCATTCCTGCACATCTGTACC-CACGC-CTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAAC-AAGATATTCG-AAAAATAGGAGGACTACTCAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                12724 121 +     16554 TAGCATTCCTTCACATCTGCACC-CACGC-TTTCTTCAAAGCCATACTATTCATATGCTCCGGATCCATTATTCACAACCTCAATAATGAGC-AAGACATTCG-AAAAATAGGAGGATTACTCAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34448421 121 - 182086969 TAGCATTCCTTCACATCTGCACC-CATGC-CTTTGTTAAAGGTATATTATTTATATGTTTAGGATTCATCATCCATAGCCTCAATGATGAGC-AAGACATCTG-AAAAATAGGAGGGCTATTCAA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13078 121 +     16338 TAGCTTTCCTCCACATCTGTACC-CACGC-CTTTTTCAAAGCTATACTATTCATATGCTCCGGTTCCATTATTCACAGCCTAAACGACGAAC-AAGATATTCG-AAAAATAGGAGGCCTATTTAA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                12747 121 +     16727 TAGCCTTCTTACACATCTGCACT-CACGC-ATTTTTTAAAGCTATACTATTCATATGCTCAGGGTCAGTTATCCACAGCCTAAACGATGAAC-AAGACATTCG-AAAAATGGGTGGCCTATTTAA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      16537 121 -     16977 TAGCCTTTCTGCACATTTGCACC-CACGC-ATTTTTCAAAGCCATATTATTCATATGCTCTGGATCAATTATCCACAGCCTAAACAATGAAC-AGGACATTCG-AAAAATAGGTGGCTTACTAAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      15712 121 +     16266 TAGCCTTTATCCACATATGTACA-CACGC-ATTCTTCAAGGCAATACTATTTCTCTCCTCTGGCTCTATCATCCACAACCTAAACAACGAAC-AAGACATCCG-CAAAATAGGAGGACTCTATAA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     12113 125 +     18297 TAGCATTTATACATATCTGTACGCCATGCAATTCTTTAAAGCCATACTCTTTTTATGCTCAGGCTCTATTATTCATAACCTCAATAATGAGCGAAGACATCCGAAAAAATGGGAGGTCTATTTAA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164200 121 + 174229318 TAGCATTTTTACACATCTGTACA-CACGC-ATTCTTTAAAGCTATACTATTCCTATGCTCAGGGTCCATTATTCATAGCTTAAATGACGAAC-AGGATATTCG-AAAAATAGGCGGACTATTTCT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14040 121 +     16775 TAGCCTTCCTCCACATCTCAACC-CATGC-CTTCTTTAAAGCTATATTATTCCTATGCTCCGGCCTAATTATCCACAGCCTCAATGGAGAAC-AAGACATCCG-CAAAATAGGATGTCTACAAAA
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_8452       14569 121 +     23823 TGGCCGTGTTCCACCTGATGACG-CACGC-CTTCTTCAAGGCGCTGCTGTTCCTCGGCGCGGGCTCGGTCATCATGGGCATGCACCACAATC-AGGACATCCG-CTGGATGGGCGGTGTGCGCAA
+i xenTro2.scaffold_8452   I 17 N 0
+s tetNig1.chrUn_random    108044205 121 - 171761319 TTGCCTTCCTACACATCTGCACC-CATGC-ATTCTTCAAAGCAATACTATTCCTTTGCTCCGGCTCAATTATCCACAGCCTGAACGACGAAC-AAGACATCCG-AAAAATAGGAGGAATACACCA
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                13869 121 +     16596 TAGCATTTTTCCACATCTGCACT-CACGC-TTTTTTTAAAGCCATATTATTCTTATGCTCAGGGGCAATTATTCACAGTCTTAACAACGAAC-AAGACATCCG-TAAAATAGGGGGAACTTACCA
+i danRer4.chrM            C 0 C 0
+
+a score=213535.000000
+s mm8.chrM                    12832 57 +     16299 AATCATACCATTCACATCATCATGCCTAGTAATCGGAAGCCTCGCCCTCACAGGAAT
+s rn4.chrM                    12811 57 +     16300 AGCAATACCATTCACATCATCTTGTCTCATTATCGGAAGCCTAGCCCTTACCGGAAT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     12998 57 +     20791 GACTATACCCTTCACAGCCTCAGCCCTCACTATTGGCAGTCTGGCCCTCACAGGTAT
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   13428 57 +     16571 AACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAAT
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                12845 57 +     16554 AACCATACCCCTCACTTCAACCTCCCTCACCATTGGGAGCCTAGCATTAGCAGGAAT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34448542 57 - 182086969 GACTTTACCCCTTACTTCTTCTTCCTTTATTATTGGCAGCTTTGCACTTACAGGCAC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13199 57 +     16338 AGCCATGCCATTCACCACAACAGCCCTCATTGTTGGCAGTCTCGCACTAACAGGAAT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                12868 57 +     16727 AGTCCTTCCCTTCACCACAACCTCCCTTATTATCGGAAGCCTCGCATTAACAGGCAT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      16658 57 -     16977 AGCAATACCATTTACATCATCATGCCTAATAATTGGAAGCCTTGCATTAACAGGAAT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      15833 57 +     16266 AACAATACCTATTACCTCAACAGCTATCATTATTGGCAGCTTAGCACTCACCGGTAT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     12238 57 +     18297 ACTAATACCATTTACATCTTCTTCACTTACGATTGGTAGCCTAGCATTAACAGGCAC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164321 57 + 174229318 CATTCTACCTATTACATCATCTGCATTAATAACAGGCAGCCTAGCCCTAGTAGGCAC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14161 57 +     16775 AACCCTCCCAATAACCACCTCCTGCCTAACCATTGGCAACCTCGCTCTAATAGGAAC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_19023        322 57 +      3053 ACTCACACAAATCACCTTCTGAGCCTTAGTAGCTGACACCCTAATCCTCACATGAAT
+i xenTro2.scaffold_19023  N 0 I 912
+s tetNig1.chrUn_random    108044326 57 - 171761319 CTTAACCCCCTTTACCTCTTCCTGCTTAACAATCGGCAGCCTTGCCCTAACAGGCAC
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                13990 57 +     16596 CACCCTACCAATAACCACAAACTATTTGACCATCGGGAAAATAGCCCTTATGGGTAC
+i danRer4.chrM            C 0 C 0
+
+a score=661041.000000
+s mm8.chrM                    12889 134 +     16299 ACCATTCCTAACAGGGTTCTACTCAAAAGACCTAATTATTGAAGCAATTAATACC-TGCAACACCAACGCCTGAGCCCTACTAATTACACTAATCGCCACTTCTATAACAGCTATGTACAGCATACGAATCATTT
+s rn4.chrM                    12868 134 +     16300 ACCTTTCCTCACAGGATTCTATTCAAAAGATCTCATCATCGAAGCCATCAACACG-TGTAACACCAACGCCTGAGCCCTAATAATCACTTTAATCGCCACATCCATAACTGCTGTGTACAGCATACGGATCATCT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13055 134 +     20791 ACCATTCCTAACAGGCTTTTACTCAAAAGATCTAATTATTGAATCAGCAAACACG-TCTAATACCAACGCCTGAGCCCTTATCATCACTCTTATTGCCACATCCCTAACAGCTGTCTATAGCACTCGAATTATCT
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   13485 134 +     16571 ACCTTTCCTCACAGGTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATA-TCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                12902 134 +     16554 ACCCTTCCTCACAGGTTTCTACTCCAAAGACCTCATCATCGAAACCGCTAACATA-TCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCCACCTCTCTGACAAGCGCCTACAGCACCCGAATAATCC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34448599 134 - 182086969 GCCTTTCCTCACAGGCTTTTACTCT-AAGGCCTCATCATTGAAACCTCAAACACATTCATACACCAATGCCTGAGCCCTTTATATTACTCTTATTGCCAGTTTCTTGACAGCTGTTCATAATACCCATATTATTT
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13256 134 +     16338 ACCCTTCCTCACAGGATTCTACTCCAAAGACCTAATCATCGAAGCCGCCAACAAG-TCTTATACCAACGCCTGAGCCCTTCTAATAACATTAATTGCCACCTCTTTCACAGCTATTTACAGCACCCGTATTATTT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                12925 134 +     16727 GCCTTTCCTTACAGGATTCTACTCCAAAGACCTGATCATCGAGTCCGCTAACACG-TCGAATACCAACGCCTGAGCCCTCTTAATTACACTCGTTGCCACATCCCTAACCGCTGCCTACAGCACCCGAATTATAT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      16715 134 -     16977 ACCATTTCTAACAGGCTTCTACTCAAAAGACCTAATCATTGAATCAGCCAACACA-TCCTACTCAAACGCCTGAGCCCTCTTAATTACACTACTTGCCACCTCATTCACAGCATCATATAGTACACGACTAATCT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650      15890 134 +     16266 ACCATTCCTAACAGGGTTTTACTCAAAAGACCCAATTATTGAAACTGCTAACATA-TCCTACATCAACACCTGAGCACTACTAATTACTCTCATTGCCGTATCCATAACAGCAAGTTACAGTACCCGAATCATTT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     12295 134 +     18297 ACCTTTCCTCACAGGATTTTACTCAAAAGACCTAATTATTGAAGCTATAAATTTA-TCTCACATCAACGCCTGAGCCCTAATCTTAACTCTAATTGCAACCTCTATAACAGCTATCTACAGCACCCGAATTATCT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164378 134 + 174229318 CCCCTTCCTAGCTGGTTTTTACTCAAAAGACTCAATCATTGAAGCCATTAACACA-TCATATACAAATTCATGGGCCTTAATAATAACTCTTATTGCCACTTCTCTTACAGCCATCTATAGCCTACGAATTATTT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14218 134 +     16775 TCCATTCCTAGCAGGCTTCTACTCAAAAGACCTGATCATCGAAAACCTAAACACC-TCATACATCAATACCTGAGCCCTCTCACTTACACTACTTGCCACATCTTTCACTGCAACCTACAGCCTCCGCATAACCT
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random    108044383 134 - 171761319 CCCTTTCCTCGCCGGCTTTTTCTCAAAAGACGCCATCATTGAAGCCCTCAACACC-TCCTACCTAAACGCCTGAGCCCTTTCTCTCACCCTTCTGGCAACCTCCTTCACAGCCATCTACAGCTTGCGCGTTGTCT
+i tetNig1.chrUn_random    C 0 C 0
+s danRer4.chrM                14047 134 +     16596 CCCCTTCCTTGCAGGATTTTTCTCAAAAGACGCTATCCTAGAAGCAATAACCACC-TCCCATCTTAACGCCTGAGCCCTAACACTAACATTAATCGCCACATCATTTACCGCAGTTTATAGCTTCCGAATAATTT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_19023        379 912 +      3053 I
+
+a score=405230.000000
+s mm8.chrM                    13023 124 +     16299 ACTTCGTAACAATAACAAAACCGCGTTTTCCCCCCCTAATCTCCATTAACGAAAATGACCC-AGACCTCATAAACCCAATCAAACGCCTAGCATTCGGAAGCATCTTTGCAGGATTTGTCATCTC---
+s rn4.chrM                    13002 124 +     16300 ACTTCGTCACCATGACAAAACCACGATACTCCCCACTAATTACTATTAATGAAAACAACCC-AAACCTCATTAATCCAATCAAACGCCTAGCATTAGGAAGCATCCTAGCAGGCTTCCTTATCTC---
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13189 124 +     20791 TCTTCGCCCTCCTGGGTCAACCCCGTTACCCAGCCCTTATTATTATTAACGAAAATAACCC-TCTACTCATCAACTCTATTAAACGCCTTGCACTAGGAAGCATTTTTGCAGGATTCTTAATTTC---
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   13619 124 +     16571 TTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCC-CACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTAC---
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13036 124 +     16554 TCCTCACCCTAACAGGTCAACCTCGCTTCCCAACCCTCACCAACATTAACGAAAACAACCC-CACTCTGTTAAATCCCATTAAACGCCTAACCATTGGAAGCTTATTTGCAGGATTTCTCATTAC---
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34448733 124 - 182086969 TCTTCACTCTTATAGGACAACCTTGCTTCACAACTGTGGCTGCTATTAATGAAAATAACCC-CTTCCTAATTGACTCAATTAAGCACCTAACAATCGGCAGCATATTCACCGGATTCCTCATCAC---
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13390 124 +     16338 TTTTCGCACTTCTAGGACAACCCCGATTCCCTACCCTAGTTAATATTAACGAAAACAACCC-CCTTCTGATCAACTCTATCAAACGCTTACTAATTGGAAGCCTCTTCGCAGGATACATCATTTC---
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13059 124 +     16727 TCTTTGCTCTACTAGGCCAGCCCCGCTTCTCCCCTATAATCCTTATCAACGAGAATAATCC-TCTCCTAATTAACTCTATTAAACGACTCCTTATCGGAAGTGTATTTGCAGGGTATATTATCTC---
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239      16849 124 -     16977 ACTTTTCCTCACTAGGACCACCACGATATCTACCCCTCATCACCATTAATGAAAACAACCC-TAATCTCCTAAAACCGATCAAACGCCTAGCCCTAGGAAGCATTTTCGCGGGCTTCTTGATCTC---
+i dasNov1.scaffold_23239  C 0 N 0
+s loxAfr1.scaffold_36650      16024 124 +     16266 TCTTTGCTCTCCTTGGGCAACCACGATACCCCCCACTAACCCAAGTCAACGAAAATAACCC-GTATCTCGTCAACCCTATTAAACGATTAATCCTAGGCAGTATCTTCATGGGCTTCCTTATCTC---
+i loxAfr1.scaffold_36650  C 0 I 3
+s echTel1.scaffold_181343     12429 124 +     18297 ATTTCGCCCTAATAAACCAACCCCGATTTAACTCAATCATTACCATCAATGAGAATACTAT-AGACCTTATTAATCCTATTAAACGTTTAGTTATCGGAAGCATCCTAGCTGGATTCTTGATTTC---
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164512 124 + 174229318 ACTATGCCCTGCTAGGTAACCCACGTTTCTCTTCTATTTCACCAATTAATGAAAATAACCC-AAATTTAATTAACCCTATTATACGATTAGCTATAGGAAGCATTTTCGCAGGATTCTTAGTAAC---
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14352 124 +     16775 TACTAGTCCAAACAGGACACACACGAACCCCCAGCAATCACCCCATTAACGAAAACACCCC-CCCAGCCATTCTCCCAATCATACGACTAGCCCTTGGCAGCATTATAGCAGGCCTATTAATCTC---
+i galGal2.chrM            C 0 C 0
+s tetNig1.chrUn_random    108044517 127 - 171761319 TCTTCGTCTCTATAGGCCACCCTCGCTTTAACACCCTCTCCCCCATCAACGAAAACAACCC-CGCCGTAATTAACCCGATCAAACGACTAGCCTGAGGAAGCATCCTCGCTGGCTTACTAATCACCGC
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320903858 128 + 349519338 ACTTCGTATCCATAGGCCACCCTCGCTTTAATTCCCTTTCACCAATCAATGAAAATAACCCATGCTGTAATTAAACCTATCAAACGACTGGCATGAGGCAGCATTATTGCTGGCCTATTAATCACCAC
+i fr1.chrUn               N 0 C 0
+s danRer4.chrM                14181 121 +     16596 ACTTAGTCTGTTTAGGAAGCCCCCGACACAAGACCTACGAGACAATTGATGAAAA----CCACATTCCAACCAATACTATTCAACGGCTTGCCTGAGGAAGCATTATTGCAGG---ATTAATCATCTC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_19023        379 912 +      3053 I
+
+a score=247774.000000
+s mm8.chrM                    13147 116 +     16299 ATATAATATTCCA---CCAACCAGCATTCCAGTCCTCACAATACCA-TGATTTTTAAAAACCACAGCCCTAATTATTTCAGTATTAGGATTCCTAATCGCACTAGAACTAAACAACCTAA
+s rn4.chrM                    13126 116 +     16300 ACTAAATATTCCT---CCAACTAACATTCAAATTCTCACAATACCC-TGACATTTAAAAATAACAGCCCTACTTATTACAATCCTAGGATTTGCCATTGCCCTAGAACTTAACAATTTAA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13313 116 +     20791 CAACCTTATTACA---CCAAACAATGTCCCTCAAATAACTATACCC-CTATATATAAAAATAACTGCTCTATTTGTTACCATTATAGGCTTTACTATTGCAATAGAACTTAACCAACTCA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   13743 116 +     16571 TAACAACATTTCC---CCCGCATCCCCCTTCCAAACAACAATCCCC-CTCTACCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13160 116 +     16554 CAACAACATTCTC---CCCATATCTACTCCCCAAGTGACAATTCCC-CTTTACTTAAAACTTACAGCCCTAGGCGTTACTTCCCTAGGACTTCTAACAGCCCTAGACCTCAATTACCTAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34448857 116 - 182086969 CAACAGTATTATG---CTTGCTTCATCCCCCCAAACAACCATACCA-CTCCACCTGAAGCTCACAGCTCTAGGTGTGACGCTTTTAGGCTTCTCACTAGCAACGGAGCTTAATCCCATAA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13514 116 +     16338 CAACAATATTCCT---CCAACAACAATTCCCCAAATAACTATGCCC-TACTACCTAAAAACAACAGCCCTAATTGTTACAATCCTAGGCTTCATCTTAGCCCTAGAAATCAGTAATATAA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13183 116 +     16727 CCACAGCATCACA---CCCACTACCATCCCACAGATAACTATGCCT-CATTATCTAAAAATGACAGCCCTTGCAGTAACCACCTTGGGTTTCATCCTGGCACTAGAACTAAACCTTACCT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_1761       31149 116 +    197909 CAACTATATTCCA---CCCCTAATCACACAACAAACAACCATACCT-AACTACATAAAACTATCAGCACTTATTGTAACAATTATAGGATTCATGGTCGCCATAGAACTAAGTCATATCA
+i dasNov1.scaffold_1761   N 0 C 0
+s loxAfr1.scaffold_36650      16151 113 +     16266 AAATACTATCCCG---CACACAA---CACCCCAAATAACCATACCT-CCTCACTTAAAATTTATAGCCCTGGCTGTAACCTTACTAGGATTTACGGTAGCAACAGAACTTAACAACATAA
+i loxAfr1.scaffold_36650  I 3 N 0
+s echTel1.scaffold_181343     12553 116 +     18297 CTACAGCATCCCC---CCTACAAATTATCCCCTCATAACTATACCT-GCATATTTAAAAATAACCGCCCTAACCGTAACCGTACTAGGCTTCATTACCGCCACAGAGTTGAATATATTAA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164636 116 + 174229318 AATAAGCATCCCA---CCAATAACATCAATCACAATAACTATGCCA-GATATAATTAAATTATCAGCCCTACTAATCACCTTAGCAGGCTTAGCAATTGGTATAGAACTTAACTCTTTCA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14476 115 +     16775 ATCCCTAATCCTC---CCCCCTAAAACCCCTCCAATAACTATACCC-ACCATCACAAAAACTGCTGCCATCATTGTTACAACCCTAGGAATTATCCTAGCCCTAGAACTCTCAAGCCTA-
+i galGal2.chrM            C 0 I 27
+s tetNig1.chrUn_random    108044644 113 - 171761319 ---AAACATCCTA---CCAATAAAAACCCCCGTCATATCCATACCT-CCTCTCCTAAAACTAGCCGCCCTTGCTGTTACACTCCTTGGCCTCCTAACCGCCCTAGAACTAGCCTCCCTAA
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320903986 114 + 349519338 ---ACAACTTCTC---CCAACAAAAACACCCGTAATATCAATACCTATAGTTGTTAACACTTACTGCTCTTATCGTCACAATCTTAGGACTCCTAATTGCCCTAGAATTAGCTTCCTTAA
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                14302 116 +     16596 ---ATACACTATAATTCCTCTTAAAACACCCATTTTAACCATGCCT-ATTTATCTAAAATTGGCAGCCATTCTAGTAACTCTACTAGGTATTATCTTAGGACTAGAAATTAGTACGCTAG
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_19023        379 912 +      3053 I
+
+a score=7261.000000
+s mm8.chrM                    13263 108 +     16299 ---CCATAAAACTATCAATAAATAAAGCAAATCCATAT--TCATCCTTCTCAACTTTACTGGGGTTTTTCCCATCTATTATTCACCGCATTACACCCAT--AAAATCTCTCAACC
+s monDom4.chrUn           117164752 105 + 174229318 ---CTAATAAACTTA---TAAA-CTCAATAAAACATACT-ACTAACTTCTCAAATATATTAGGGTACTTCACTTACTTTACTCATCGAATTTACCCCCTAATAAATCTATATT--
+i monDom4.chrUn           C 0 C 0
+s echTel1.scaffold_181343     12669 108 +     18297 ---CAACGTACTTGAAATTC-T-CTACCCCCAATATATACTATAAATTTTCAAATCTACTAGGTTATTACCCTTCCATTATTCATCGTCTAATACCACAAACTAACTTAATTT--
+i echTel1.scaffold_181343 C 0 C 0
+s loxAfr1.scaffold_17571      30729 108 +     47616 ---CATGCAACTTAACATTCAA-ACAACCATCATATATA-TACAAATTCTCAAATATATTAGGATACTACCCACCTATTGTCCACCGACTTCTACCCTACCTAGGCCTTACTA--
+i loxAfr1.scaffold_17571  N 0 C 0
+s dasNov1.scaffold_1761       31265 108 +    197909 ---CACTAAATCTCAAACCAGA-ATACCCAAACCCCTTC-CACTCATTTTCTTCTTTACTAGGGTTTTACCCAAACATTATACATCGAATAACCCCATATTATGCTCTAATAA--
+i dasNov1.scaffold_1761   C 0 N 0
+s canFam2.chrM                13299 110 +     16727 ---CACAAGGACTCAAATTTAA-CTATCCTTCTAATTAC-TTTAAATTCTCCAGCCTCCTTGGCTACTATCCAACCATTATGCACCGCCTCACACCTAAAACAAGTTTAACCATT
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                13630 110 +     16338 ---CTAAAAATCTAAAATATCA-CTACCCCTCAAACGCC-TTCAAGTTCTCAACCTTGCTAGGGTATTTCCCCACAATTATACATCGCCTAGCTCCATACATAAATTTATCAATA
+i bosTau2.chrM            C 0 C 0
+s rheMac2.chr5             34448973 110 - 182086969 ---CTAATAGCCTTAAACCAAA-ATACCCATTACAGACA-TTCAACTTCTCCAACATACTAGGATTTTATTCAGCCACAATTCACCATACAACCCCCAACTTAGGCCTATTCCCA
+i rheMac2.chr5            C 0 C 0
+s panTro2.chrM                13276 110 +     16554 ---CCAGCAAGCTCAAAATAAA-ATCCCCACTATATACA-TTTCACTTCTCTAATATACTCGGATTCTACCCTAACATTATACACCGCTCGATCCCCTATCTAGGCCTTCTTACA
+i panTro2.chrM            C 0 C 0
+s hg18.chrM                   13859 110 +     16571 ---CCAACAAACTTAAAATAAA-ATCCCCACTATGCACA-TTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACG
+i hg18.chrM               C 0 C 0
+s oryCun1.scaffold_140182     13429 110 +     20791 ---GCCTTAGTCTAAAAATAACTACACAATCTCCATAC--TTTAACTTCTCAAACATACTAGGGTTCTTTCCAATGACAATTCATCGTATTCTACCCTATCTAAACCTTTCAGCT
+i oryCun1.scaffold_140182 C 0 C 0
+s rn4.chrM                    13242 108 +     16300 ---CACTAAATCTATCAATAAGCAAACCCACCAAACTA--TCATCATTCTCAACCTCCCTAGGCTACTACCCACCAATTATACCCCGAATTATTCCTCA--AAAAACTCTAAATT
+i rn4.chrM                C 0 C 0
+s galGal2.chrM                14618  82 +     16775 -----------------------------AATCCCCTC--ATAAACTTCTCCTCCTCCCTAGGCTACTTTAACCCCCTAACTCACCGAATTAGCCCCTCAATCCTCCTACATA--
+i galGal2.chrM            I 27 C 0
+s tetNig1.chrUn_random    108044757 111 - 171761319 CCACCAAACAAATCAAAACAAC-CCCTCACTTAACCCCA-CACCACTTCTCAAACATGCTGGGATTCTTCCCAAGTATCATCCACCGCCTCTCCCCTAAAATAAACCTTATTC--
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320904100 111 + 349519338 CCTCCAAACAACTTAAACCTAC-ACCACACCTGTCCCCC-CACCACTTCTCAAACATACTTGGCTTCTTCCCAACAATTGTACACCGTGCCTCTCCTAAAATTAATCTCATTT--
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                14418  95 +     16596 CTAATAAAATTAACAAAAACAC-TACCCCAGGAATTCCA-TTCCACTTTTCAATTTCACTAATCTTCTTTCCA---ATCCTTCACCGACTAATCCCTATA---------------
+i danRer4.chrM            C 0 I 109
+e xenTro2.scaffold_19023        379 912 +      3053 I
+
+a score=103897.000000
+s mm8.chrM                    13371 95 +     16299 TAAGCCTAAAAACATCCCTAACTCTCCTAGACTTGATCTGGTTAGAAAAAACCATCCCAAAATC-------CACCTCAACTCTTCACACAAA----CATAACC---ACT
+s rn4.chrM                    13350 91 +     16300 CTAGCTACAAATTATCCTTAAACCTACTAGACCTAATCTGATCAGAAAAGACAATCCCAAAATC-------AACCTCAA----TCACCCAAA----CCCAACT---ATC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13539 93 +     20791 --AGCCAAAACATAGCCACATTACTCCTAGATATGACCTGAACTGAAAAAGCGATCCCGAAAAA-------TATCTCAG----ACATTCAAATTTTCGCATCA---ACC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   13969 93 +     16571 --AGCCAAAACCTGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAAC-------AATTTCAC----AGCACCAAATCTCCACCTCC---ATC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13386 93 +     16554 --AGCCAAAACCTACCCCTACTTCTTCTAGACCTGACCTGACTAGAGAAACTATTACCTAAAAC-------AATTTCAC----AGTACCAAATCTCCGCTTCC---ATT
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449083 92 - 182086969 --AGCCAAAACCTGGCTTCACTTCTACTAGACCTAATTTGACTAGAAAAGTCTGTACCGAAGAC-------CATTACAC----CAT-CCAAATTTCAGCCTCC---ATT
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13740 93 +     16338 --AGCCAAAAATCAGCATCCTCCCTTCTAGACCTAATCTGACTAGAAGCCATCCTACCAAAAAC-------CATCTCAC----TCGCCCAAATAAAAGCATCT---ACC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13409 93 +     16727 --AGCCAGAAATCAGCATCTATACTTCTGGACTCCATCTGACTAGAAAACATCCTACCCAAATC-------AATCTCAT----ATTTCCAAATAAAATCTTCT---ACC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239         16 92 -     16977 TAAGCCAAAACCTAGC---ATCCCTTACAGTTATTCTCTGACTAGAAAAGTTAGCCCCAAAAAG-------CCTATCAC----AAATGCAGCTTTCAGCTTCC---ATA
+i dasNov1.scaffold_23239  N 0 C 0
+s loxAfr1.scaffold_17571      30837 92 +     47616 TAAGCCAAAATCTAGCAACAACTATTATAGACTTAATTTGACTAGAAAAAATAATCCCTAAAAA----------CCTAA----TAATTATGCAAAAAACAACC---GCC
+i loxAfr1.scaffold_17571  C 0 C 0
+s echTel1.scaffold_181343     12777 95 +     18297 TAAGCCATAAATTAGCCTCCACTGCCATGGACCTCATCTGATTAGAAAAACTTCTCCCTAAGAA-------TATCTCAT----TAATTAGTATTACAACAGCC---TCC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164857 98 + 174229318 CAGGCCAACGCATTGCTACCATACTAATTGATATAAACTGATATGAAAAAACAGGACCTAAAGGGCAGACTAATATCCA----TTCTTCAAT----ATCATCA---CTA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14700 98 +     16775 CCGGACAAAAAATTGCATCCCACTTAATCGACATAGCATGGTACAAAAAAATAGGCCCCGAAGG-------CCTTGCCA----ACCTTCATCTCACCATAACCAAAATC
+i galGal2.chrM            C 0 C 0
+s fr1.chrUn               320904211 95 + 349519338 TAGGACAAACAATTGCTACCCAAATTATTGACCTAACCTGACTAGAAAAAGTTGGACCCAAAAC-------AATTTCAT----CTATCAATACTCCCCTCATC---TCT
+i fr1.chrUn               C 0 I 4
+s tetNig1.chrUn_random    108044868 95 - 171761319 TAGGACAAACCATCGCCAGCCAAACCATCGACCTCACCTGACTAGAAAAAATTGGTCCCAAGGC-------AACCGCCA----ACCTAAACACCCCCCTCGTC---TCC
+i tetNig1.chrUn_random    C 0 I 4
+e xenTro2.scaffold_19023        379 912 +      3053 I
+e danRer4.chrM                14513 109 +     16596 I
+
+a score=77227.000000
+s mm8.chrM                    13466 44 +     16299 T----TAACAACC----------AACCAAAAAGGCTTAATTAAATTGTACTT----------TATATC
+s rn4.chrM                    13441 48 +     16300 TAAAATAATATCC----------AACCAAAAAGGACTAATCAAACTATATTT----------CCTATC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13632 44 +     20791 T----CCGTATCC----------TCACAAAAAGGCCTCATTAAACTCTACTT----------CCTATC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   14062 44 +     16571 A----TCACCTCA----------ACCCAAAAAGGCATAATTAAACTTTACTT----------CCTCTC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13479 44 +     16554 A----CCACCTCA----------ACCCAAAAAGGCATGATCAAACTTTATTT----------CCTCTC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449175 36 - 182086969 A----CCATATCT----------ACTCAGAACGGC----CTTAACTCTACTT--------------TC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13833 44 +     16338 C----TGGTCACA----------AACCAAAAAGGCCTGATCAAACTATATTT----------CCTCTC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13502 44 +     16727 C----TTATTTCA----------AATCAAAAAGGTCTCATCAAACTCTATTT----------CCTATC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239        108 44 -     16977 A----TCACATCC----------AATCAAAAAGGACTGATCAAACTATACTT----------CATATC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_17571      30929 57 +     47616 A-GCCTAGTATCTAAAAAAAAAAAATCAAAAGGGCCTAATAAAACTCTACTT----------CCTATC
+i loxAfr1.scaffold_17571  C 0 C 0
+s echTel1.scaffold_181343     12872 44 +     18297 A----TTATCTCT----------AACCAAAAAGGAATAATCAAATTTTATTC----------CCTAAC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164955 44 + 174229318 C----TTACTTCT----------ACTCAAAAAGGCCTAATTAAAGTTTACTT----------TATATC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14798 38 +     16775 T----CAACCACA----------CTCCACACAGGCCTAATTAAATCTTACCT----------------
+i galGal2.chrM            C 0 I 53
+s tetNig1.chrUn_random    108044967 39 - 171761319 -----TCAGCAAT----------GTCCAACAAGGCTCAATCAAAACAT--------------TATAGC
+i tetNig1.chrUn_random    I 4 N 0
+s fr1.chrUn               320904310 41 + 349519338 -----TTAGTAAC----------ATCCAACAAGGATCAATCAAGACATA------------CCTTGTC
+i fr1.chrUn               I 4 I 2
+s danRer4.chrM                14622 53 +     16596 ----TTAAGGACC----------ATCGAATAGCG-TCAATCAAGTCTTACCTAGCCGTCTTCCTTACC
+i danRer4.chrM            I 109 I 6
+e xenTro2.scaffold_19023        379 912 +      3053 I
+
+a score=81103.000000
+s mm8.chrM                    13510  86 +     16299 ATTCCTA---ATTAACATCATCTTAATTATTATCTTATAC---TCAAT--------------------TAATCT--CGAGTAATCTCGATAATAATAAAAATACCCGCAAACAA
+s rn4.chrM                    13489  86 +     16300 ATTTCTC---ATCACTATTTCACTAATTTTTATCTTACAC---ACACT--------------------TAATCC--CGAGTGATTTCAATAATAATAAAAATCCCCGCAAACAA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13676  86 +     20791 TTTCTTA---ATCTCT-TTACTCTTAGTACTAT-TTATTT---TAACC--------------------TAGCCCCACGAGTAATCTCAATAACAATAAAAATACTAACAAATAA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   14106  91 +     16571 TTTCTTC---TTCCCACTCATCCTAACCCTACTCCTAATCACATAACC--------------------TATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13523  91 +     16554 TTTTTTC---TTCCCTCTCATCTTAACCTTACTCCTAATCACATAACC--------------------TATTCCCCCGAGCAATCTCAATCACAATGTATACACCAACAAACAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449211  91 - 182086969 TTTTTTT---ATCCCATCCCTTCTAACCCTACTCCTAATTATCTAATC--------------------TATCATCCTGAGTAATTTCAATCACAACATAAATACTAACAAATAA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13877  83 +     16338 CTTCTTA---ATCACAATCCTTATCAGCATAATCTTATTT----------------------------AATTTCCACGAGTAATTTCTATAATAACCACAACACCAATTAATAA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13546  83 +     16727 GTTCATA---CTAACTATAATCCTCAGTCTACTAATCCTT----------------------------AATTACCACGGGTAACTTCCATGATAACCAACACACCAATTAATAA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239        152  87 -     16977 ATTTATT---ATCTCAATAACACTAGCTACTATACTAATC----ATTT--------------------AACGACCACGAGTAATCTCAATTACAATAAAAATGCTAACAAATAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_17571      30986  87 +     47616 ATTCCTC---CTATCAATTACACTAGGCTTGCTAATTGTC----CTAT--------------------AACGCTTTCGAGTAACCTCAATAACAATAAAAATACTAACAAACAA
+i loxAfr1.scaffold_17571  C 0 N 0
+s echTel1.scaffold_181343     12916  87 +     18297 TTTCCTA---TTTACCTTAACCCTAACTTTCCTTTTGATA----ATTT--------------------AACGCCCCCGAGTAATTTCTATCACAATAAAAACACTAACAAATAG
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117164999  85 + 174229318 CTTTCTG---ATCTCAATTACACT---TCCTCTAATATTC---GCATC--------------------TATGTCCACGAACAACTTCTAACACAACATAGATAGTAATAAATAA
+i monDom4.chrUn           C 0 C 0
+s fr1.chrUn               320904353 113 + 349519338 CTTCCTCACGACCCTTGCTCTATCAACCCTCGTTCTTCTTACCTAACT-GCTCGAAGAGCCCCCCGACCCAACCCCCGCACCAGCTCTAATACTACAAGCAACGTCAATAACAA
+i fr1.chrUn               I 2 C 0
+s danRer4.chrM                14681 104 +     16596 ----------ATTCTTAAAATAATAATACTGAAACTATACACTTAAATAGCACGAAGCACACCATAACTAAGACCTCGAGTAACCTCTAGTACAACAAACAAAGTCAGAAGCAA
+i danRer4.chrM            I 6 C 0
+e xenTro2.scaffold_19023        379 912 +      3053 I
+e galGal2.chrM                14836  53 +     16775 I
+
+a score=72627.000000
+s mm8.chrM                    13596 51 +     16299 AGATCACCCAGCTACTACCATCATTCAAGTAGCACAACTATATATTGCCGC
+s rn4.chrM                    13575 51 +     16300 TGACCACCCAGCCACCACTATCATTCAAGTAGCACAACTATAAATAGCCGC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13762 51 +     20791 AGATCAACCCGCAACAACCATCAATCAACTACCATAACTATACAACGCCGC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   14197 51 +     16571 TGTTCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13614 51 +     16554 TGTCCAACCAGTAACTACTACTAACCAACGCCCATAATCATATAAGGCCCC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449302 51 - 182086969 TGATCAACCAGCAACTACCATTAATCAGCACTCGTAACTGCACAAGGCAGC
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                13960 51 +     16338 AGACCACCCAGTTACAATAACTAATCAGGTACCATAACTGTATAAAGCCGC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13629 51 +     16727 TGATCAGCCTGTAACAACCACCAACCAAGTCCCATAACTGTACAGAGCCGC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239        239 51 -     16977 GGATCACCCAGCTAAAATCACCAACCATCCCCCATAAGTATATAAAGCAGA
+i dasNov1.scaffold_23239  C 0 C 0
+s echTel1.scaffold_181343     13003 51 +     18297 ACATCACCCCGATAATAATAGCATTCAATTTCCCCCACTATATAAAATTGA
+i echTel1.scaffold_181343 C 0 I 1
+s monDom4.chrUn           117165084 51 + 174229318 AATTCATCCTAACAAAGCTAAAGCTCATCCCCCACATCAATATAATAAAGG
+i monDom4.chrUn           C 0 C 0
+s fr1.chrUn               320904466 51 + 349519338 GACCCAGGCCCCCAATAGTAATACTCCCCCACCGCTAGAATATATAAGTGA
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                14785 51 +     16596 TACCCAAGCACAAATCACTAATATTTTTCCACCTGACGAATATATTATTGC
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_19023        379 912 +      3053 I
+e galGal2.chrM                14836 53 +     16775 I
+
+a score=74448.000000
+s mm8.chrM                    13647 214 +     16299 TACCCCAATCCCTCCTTCCAACATAACTCCA---------ACATCATCAACCTCATACATCAACCAATCTCCCAAACCATCAAGATTAATTAC---T---CCAA---CTTCATCA-TAATA-----ATTAAGCAC--ACAAATTAAAAAA--ACCTCTATAATCACCCCCAATACTAAAAAACCCAAAATTAATCAGTTAGATCCCC----AAGTCTCTGGATATTCCTCAGTAGCTATAGCAGTC
+s rn4.chrM                    13626 214 +     16300 AACCCCAATCCCCCCCTCCAACATAACCCCA---------ACATCATCAATCTCATACATTAATCAATCGCCTAGACTATCAAAATCAACTAA---C---TCCA---CCTTATTA-TTCAA-----ACTAAACAA--GTAGAACACTACC--AACTCCATAAAAAGCCCTAAAACAAAAAAACTAAAAATAAACCAATTAGACCCTC----AAGTTTCCGGATATTCCTCAGTAGCCATAGCAGTT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     13813 217 +     20791 CACCCCTATAGAATCCTCCCGGATTAATCCT---------ACCTCGTCCCCTTCAAAAACCACCCAATCCCCTATATTTTTAAAATCAACCACAATC---TCAA---CCCCATCACTCATC-----ACTATATAC--ACA-ACCAAGCCT--ACCTCTATTAACAACCCTAAAACGAATATACCCAAAATCATAACATTCGATCCTC----AAGTCTCAGGATACTCCTCAGTTGCCATCGCAGTA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   14248 217 +     16571 CGCACCAATAGGATCCTCCCGAATCAACCCT---------GACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACC---ACCA---CCCCATCATACTCT-----TTCACCCAC--AGC-ACCAATCCT--ACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCCCTGACCCCC----ATGCCTCAGGATACTCCTCAATAGCCATCGCTGTA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13665 217 +     16554 CGCACCAATAGGATCCTCCCGAATCAGCCCT---------GGCCCCTCCCCTTCATAAATTATTCAACTTCCCACGCTATTAAAATTTACCACAACC---ACCA---TCCCATCATACCCT-----TTTACCCAT--AAC-ACTAATCCT--ACCTCCATCGCCAGTCCTACTAAAACACTAACCAAAACCTCAACCCCTGACCCCC----ATGCCTCAGGATACTCCTCAATAGCCATAGCCGTA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449353 217 - 182086969 CACATATACAGAATCTTCAGGGAACAACCCT---------GCCCTCTCACCCTAAAAAATCCTCCAACTCTTTGTGCTATTAAAATCAATCATGATC---CTCG---CTCTATCGTGCTCA-----ACTATTCAC--AGA-ACCAGCATC--AACTCCATTATTGGTTCTCATAATAAGGCTCCTCAGATGTCAATACTCAACCCTC----ATGTTTCAGGATACTCCTCAGTAGCCATCGCCATG
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                14011 217 +     16338 AATCCCTATGGCCTCTTCACTAAAGAACCCA---------GAATCCCCTGTATCATAAATCACCCAATCCCCTAAACCATTAAACTCAAACACAACC---TCAA---CTTCTTTATCCTTT-----AATACATAA--TAG-ACCATAAAG--AACTCCATCAACAAGCCAGTAACAAATGCCCCTAAAACAGCCTTATTAGAAAGCC----AAATTTCAGGATACTGTTCTGTAGCCATAGCCGTT
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13680 217 +     16727 AATACCCATAGCCTCTTCACTAAAAAACCCA---------GAGTCCCCCGTATCATAGATCACTCAATCCCCTATTCCATTAAACTTTAATACTACC---TCCA---CCTCGTCATCCTTC-----AAAATATAG--CAA-GCAGTCAAC--AATTCAGACAACAAACCAGTAATAAAAGCCGCTAGAACAGCCTTATTTGAAACTC----ACACCTCAGGGTATTGCTCAGTAGCCATAGCAGTT
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239        290 220 -     16977 TCCACCAGCATAATCTTCACGAACAACATCC---------ATCCCATATCCCCCCAAGACAACCCAATCTTCTATATCTTTCAAACCACAAGAAATCAAGCCTA---CTTCACCGTCAACA-----ATCATTCAA--ACA-ATTATCGCA--ACCTCTACTAACAATCCAACAAATAACGCACTCAAAATAACAACGTTAGAACCCC----AAGCCTCAGGATACTCCTCAGTAGCCATAGCAGTA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_3823      111222 219 -    141669 CCCACCAGAATAATCCTCATAAAGAAACTCA---------ATTTCTTCACTATTAAAAACCATTCAATTCTCAAATTACTTGAA-----TCACAACC---TACCAACTCAAATACCCCACC-----TTTCAACAATCACA-ACAATAAAAGCCCCTCCATCAGCAACCCTATAAATAATGTGCCCAAAACTGTAACATTGGATCCCG----AACCCTCAGGATATTCTTCAGCAGCTATTGAAGTC
+i loxAfr1.scaffold_3823   N 0 N 0
+s echTel1.scaffold_181343     13055 201 +     18297 CCTGCTAG-ATAATCTTCCCGAATAAAACCA---------ACCTCCTCTCCACTAAATATTACTAAACTCTC------------------TGCACCC---CATATTTTTTCATCGCCCCCT-----TTTAAATAA--ACC-ACGATCAAA--CCCTCAGCTAATAGACCTAGACATAATGAACCTATAACAGTCGTACTCGACATCC----AAATCTCAGGGAACTCTTCAGTAGCTATAGCTGTA
+i echTel1.scaffold_181343 I 1 C 0
+s monDom4.chrUn           117165135 190 + 174229318 GACACCACTAAAATCTTGACCAATACAACTT---------ATTAC-------TGTGAAATCAATCAACTC-----AATATTAGAATCTA-CATAAGT---ATTA---CC------------------AAAGATAA--AGT-ATCAT-ATA--ATCTCTATAAGTAATACAAATAATAATATACAAAAAGCCAGGATATTTCCAACTC----AAGTCTCAGGGTATTCTTCTGTAGCCATAGCGGCA
+i monDom4.chrUn           C 0 C 0
+s fr1.chrUn               320904517 190 + 349519338 AACCCCGTCCATATCACCTCGAAAAACTGCATCTCAGTCTATCTC-------TCCAGAAAC---------CCCTCATCA-----------------C---ACCT---CTTCATCAAGGACCATATTTGTGTACAA--GAT-ACCAAAA----------ACAAAAAAAAAATATCCAAAAAAGAATAAAACCAC----CTGTCAACCTGTAGGCGCCTTAGGATCCTTATCTGCAGACAGCGCTGAC
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                14836 187 +     16596 AACCCCGCTTACATCAGCTCGAATAACAGAA---------AACTC-------TTTAAAAGCATCAA----CCGATATTAATAAA-----CCAGTGTC---ACCA---GTTAATAAAAACCC-------------A--GCC-GCCACAATT--------ACAACCAGACCATAAACCATAACACGTCAAAACACCACACGGTCACCCC----ACGCTTCAGGAAAAGGCTCGGCTGCTAGGGCCGCT
+i danRer4.chrM            C 0 C 0
+e xenTro2.scaffold_19023        379 912 +      3053 I
+e galGal2.chrM                14836  53 +     16775 I
+
+a score=1026410.000000
+s mm8.chrM                    13861 280 +     16299 GTATATCCAAACACAACCAACATCCCCCCTAAATAAATTAAAAAAA----CTATTAAACCTAAAAACGATCCACCAAACCCTA---AAACCATTAAACAACCAACAAACCCACTAACAATTAAACCTAAACCTCCATAAATAGGTGAAGGCTTTAATGCTAACCCAAGACAACCAACCAAAAATAATGAACTTAAAACAAAAATAT---AATTAT---T---CATTA--TTTCTACACAGCATTCAACTGCGACCAATGACATGAAAAATCATCGTTGT-AATTCAACTACAGAAAC--AC
+s rn4.chrM                    13840 280 +     16300 GTATACCCAAATACAACCAACATCCCACCCAAATAAATTAAAAATA----CTATTAAACCTAAAAACGAACCCCCAAACCCTA---AAACTATTAAGCACCCAATACATCCACTAACAATCAATCCAAACCCACCATAAATAGGTGAAGGCTTCAACGCCAACCCTAGACAACCAGTCAAAAACAGTAAACTTAAAATAAACATAT---AATTTG---T---CATTA--TTTCTACACAGCATTTAACTGTGACTAATGACATGAAAAATCATCGTTGT-AATTCAACTATAGAAAC--AT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     14030 277 +     20791 GTATACCCAAAAACTACCAACATCCCCCCTAAATAAATTAAAAACA----TCATTAAACCTAAAAATGAACCCCCGAAACTTA---AAACAATACCACACCCGACCCCACCACTAACAATCAACCCAAGCCCCCCATAAATTGGTGATGGCTTAGAAGAAAACCCAACAAACCCCATCACAAACATTACACTTAATAAAAACACTA---CGTATG---T---CATAG--TTCTCACATGGACTTGAACCATGACTAATGACATGAAAAATCATCGTTGT--TTTCAACTATAAGAAC----
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   14465 279 +     16571 GTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAA----CTATTAAACCCATATAACCTCCCCCAAAATTCA---GAATAATAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTCAACAGAAACAAAG---CATACA---T---CATTA--TTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGTTGT-ATTTCAACTACAAGAAC--A-
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                13882 279 +     16554 GTATACCCAAAAACAACCATTATTCCCCCCAAATAAATTAAAAAAA----CCATTAAACCTATATAACCTCCCCCATAATTCA---AAATGATGGCACACCCAACTACACCACTAACAATCAATACTAAACCCCCATAAATGGGAGAAGGCTTAGAAGAAAACCCCACAAACCCTATCACTAAACTCACACTCAATAAAAATAAAG---CATATG---T---CATTA--TTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGTTGT-ATTTCAACTACAAGAAC--A-
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449570 282 - 182086969 GTACAGCCATAAACAACCATCATACGACACAAATAAATGAAAAAAAAAATCCATCAACCCCATGAAAGCACCACCAAAATTCA---ACAAAATACCTCAACCCACAGCACCACTAATAATTAGCTGTAGACCTCCGT-AATAGGAGAAGGTTTTGAAGAGAAACCTACAAACCCTATAACCAAAAAGACACTTAAGAAAAATATAG---TATATG---C---CATTA--TTCCTACATGGACGATAACCGTGACTAATGACATGAAAAATCATCATTGT-ATTTAAACTATAAGAAG--G-
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                14228 282 +     16338 GTATAACCAAAAACTACCATCATACCTCCCAAATAAATTAAAAAGA----CCATCAACCCCAAAAAGGATCCACCAAAATTCA---ATACAATTCCACAGCCAACCCCACCACTCACAATTAACCCTAACCCCCCATAAATAGGTGAAGGTTTCGAAGAAAACCCCACAAAACCTATCACGAAAATAACGCTTAGAATAAATACAA---TGTATAGTAT---CATTA--TTCTTACATGGAATCTAACCATGACTAATGATATGAAAAACCATCGTTGT-CATTCAACTACAAGAAC--A-
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                13897 282 +     16727 GTATAACCAAATACTACTAATATACCCCCCAAATAAATTAAAAATA----CTATCAACCCTAAAAAAGAACCCCCAAAATTCA---GAACAATCGCACAACCAATCCCACCGCTAATAATTAGCACAAGCCCACCATAAATAGGAGATGGTTTAGTGGCAAAACCCACAAAACTCATCACAAAAACGATACTTAAAATAAATACAA---TGTATGTTAT---CATTA--TTCCTACATGGAATTTAACCATGACTAATGACATGAAAAATCATCGTTGT-ATTTCAACTATAAGAAC--A-
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239        510 279 -     16977 GTATAACCAAACACTACCAACATACCACCTAAATAAACCAAAAAAA----CCATTAATCCTAAAAAAGACCCTCCTAAACCCA---TAACAATACCACAACCCACCCCTCCACCAACAATCAACCCTAACCCCCCATAAATGGGAGACGGCTTTGAAGAGAAGCCAATAAAACTAATCACAAAAGCTACACTTAATAAAAAAACTA---TGTATA---T---CATTATGTTCCAGCATGGAGC-TAACCACGACCAATGATATGAAAAACCATCGTTGTAAATTCAACTACAAGAA-----
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650          2 283 +     16266 GTATAACCAAAAACCACTATCATCCCACCCAAATATACCAAAAATA----CAACCAGGCCCAAAAAAGACCCCCCAGAACCCATCCATTAAAAAACACATCCCAAGCCTCCACTCACAACCAAACTCATTCCCCCATAAACAGGGGAAGGCTTAGACGAAAAACCAATGAAACCTACCACATAAAGCACACTCATAATAAAAACAA---TATACA---T---CATTA--CTTCCACATGGACTCCTACCATGACTAATGATCTGAAAAACCATCGTTGT-ATTTCAACTATAGAAAT--AA
+i loxAfr1.scaffold_36650  N 0 C 0
+s echTel1.scaffold_181343     13256 280 +     18297 GTATAACCAAAAACCACCAGTATACCACCCAAATAAACCAAAAACA----CTATTAACCCCAAAAATGCCCCACCAAAATATA---GTACAACCCCACACCCAACCCCTCCCCCAATGATCAAGCCTAACCCACCATAAATAGGTGACGGCTTACAAGAAAATCCTACAAAACTGACTACAAATAGAACACTCATCAAAAATAAAA---TAAATT---T---CACAA--TTCTTGCTTGGGCATAAACCAAAACCTGTGGAATGAAACTCCACCGTTGT-TATTCAACTACAAAAAC--CT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117165325 277 + 174229318 GTATAACCAAACACTACTAACATACCCCCTAAATAAACTAAAAAAA----CTACAAGTCCTAAAAAAGAATCTTCAAAGTTAA---CTACTATAACACACCCCAAACCACCACTTGCAACTAAACTTAATCCTCCATAAACAGGAGAAGGTTTAGAAGAAAATGCCACAAACCCAAAAATCAAAAGCAAAGAAATAATAAAAATTA---TTATCA---T---TGTTA--TTTTAGCATGGATTTTAACCATAACCTATGGCATGAAAAACCATTGTTGT-GTTTCAACTACAAAAA-----
+i monDom4.chrUn           C 0 C 0
+s xenTro2.scaffold_18302          3 264 +      2726 ---------------ACCAACATCCCACCTAAATAAATTAAAAACA----AAACAAGAGATAAAAAGGAAGACCCCAATCCAA---CAATCACTCAACAACCCGCACCGGCAGCCACAACTAAACCCAGAGCAGCATAATAAGGAGAAGGGTTTGAAGCAACAGCTACTAACCCTAGTACTAAGCCTACTATAAAAAAAGAAACTA---TATAAA---T---CATAA--TTCCCATCAGGACTCTAACCAGAACCTGTGATCTGAAAAACCACTGTTGT-TCTTCAACTATGGAAAC--T-
+i xenTro2.scaffold_18302  n 912 I 1
+s fr1.chrUn               320904707 279 + 349519338 GAATAAATAAACACAACCAGTATGCCCCCCATATAAATCATTAACA----ACACCAAAGACAAGAAAGTCCCCCCGTGCAAAA---CTGAAGCCCCACAGCAAAGAAGTGCAACCAGCACCAAATTGAAAACTCCATAAAAAGGAGCAGGATTTGTAGACAACACAATTAT---CACAACCAACATCCCTAATAAAAGAAAAACAAGCGCATAAA---A---CATAG--TTTCTGCCAGGATTTTAACCAGGACCTATGGCGTGAAAAACCATCGTTGT-TACTCAACTACAAAAAC--A-
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                15023 281 +     16596 GAATAAGCAAACACTACAAGCATCCCACCTAAATAAATCAAAAAAA----GAATTAGAGACAAAAATGAACCCCCATAACTAA---CTAAAATTCCACATCCAACCCCTGCCACAACTACTAAACCAAATGCAGCAAAATAAGGAGCCGGATTAGAAGCAATAGCAATCATACCCCCAACTAGAGCTGCCATCAAA--AAAGACAA----ATAAA---ATGCCATAA--TTCTTACTCAGACTTTAACTGAGACCGGTGACTCGAAAAACCACTGTTGT-AGTTCAACTACAAGAACTGC-
+i danRer4.chrM            C 0 C 0
+e galGal2.chrM                14836  53 +     16775 I
+
+a score=2289633.000000
+s mm8.chrM                    14141 388 +     16299 C----TAATGA---CAAACATACGAAAAACACACCCATTATTTAAAATTATTAACCACTCATTCATTGACCTACCTGCCCCATCCAACATTTCATCATGATGAAACTTTGGGTCCCTTCTAGGAGTCTGCCTAATAGTCCAAATCATTACAGGTCTTTTCTTAGCCATACACTACACATCAGATACAATAACAGCCTTTTCATCAGTAACACACATTTGTCGAGACGTAAATTACGGGTGACTAATCCGATATATACACGCAAACGGAGCCTCAATATTTTTTATTTGCTTATTCCTTCATGTCGGACGAGGCTTATATTATGGATCATATACATTTATAGAAACCTGAAACATTGGAGTACTTCTACTGTTCGCAGTCATAGCCACAGCATTTA
+s rn4.chrM                    14120 388 +     16300 C----TAATGA---CAAACATCCGAAAATCTCACCCCCTATTCAAAATCATCAACCACTCCTTTATCGACCTACCGGCCCCATCTAACATCTCATCATGATGAAACTTCGGTTCTCTACTAGGAGTATGCCTCATAGTACAAATCCTCACAGGCTTATTCCTAGCAATACACTACACGTCTGATACCATAACAGCATTCTCATCAGTCACCCACATCTGCCGAGACGTAAACTACGGCTGACTAATCCGATACCTACAAGCCAACGGCGCCTCAATATTTTTCATCTGCCTATTCCTCCATGTGGGACGAGGACTATACTATGGATCCTACACTTTCCTAGAAACCTGAAACATTGGGATCATCCTACTATTTGCAGTCATAGCAACTGCATTCA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     14307 388 +     20791 C----TAATGA---CCAACATTCGCAAAACCCACCCCCTATTAAAAATTGTTAACCACTCCCTAATTGACCTTCCTGCTCCATCAAACATCTCTGCCTGATGAAACTTTGGCTCTCTACTAGGCCTGTGCCTTATAATTCAAATTTTCACTGGCCTATTCTTAGCCATACACTATACCTCTGACACAACAACAGCATTCTCATCAGTAACCCATATTTGCCGAGATGTTAACTATGGCTGACTTATCCGATACCTCCACGCTAACGGAGCATCTATATTCTTTATTTGCCTCTACATACACGTAGGCCGCGGAATCTACTATGGATCATACACATACCTAGAGACCTGAAACATTGGCATCATCCTCCTATTCGCAGTAATAGCCACAGCATTTA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   14744 388 +     16571 C----CAATGA---CCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGCAACAGCCTTCA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                14161 388 +     16554 C----CAATGA---CCCCGACACGCAAAATTAACCCACTAATAAAATTAATTAATCACTCATTTATCGACCTCCCCACCCCATCCAACATTTCCGCATGATGGAACTTCGGCTCACTTCTCGGCGCCTGCCTAATCCTTCAAATTACCACAGGATTATTCCTAGCTATACACTACTCACCAGACGCCTCAACCGCCTTCTCGTCGATCGCCCACATCACCCGAGACGTAAACTATGGTTGGATCATCCGCTACCTCCACGCTAACGGCGCCTCAATATTTTTTATCTGCCTCTTCCTACACATCGGCCGAGGTCTATATTACGGCTCATTTCTCTACCTAGAAACCTGAAACATTGGCATTATCCTCTTGCTCACAACCATAGCAACAGCCTTTA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34449852 384 - 182086969 C----TAATGG---CCAATATCTACAAAACACACCTGCtaataaaaattattaattattCATT----GATCATCCCACATCATCTAACATTTCTATATGATGAAACTTCGGCTCACTTTTAGGTGCCTGCCTAACCCTCCAAATCATTACAGGACTGTTTTTGGCCATGAACTACACATCAGACACCCCAACGGCCTTCTCTTCAGACGCTCATATCAGCTGAGATGTAAACTTCGACTGAATGGTTTGCTATTTCCATGCTAATGGCGCTTCAATATTTTTTATCTGCCTCTTCTTACATGTTGGCTGAGGTTTATGCCATGGATCATTTACATTTCTAGAAATGTGAAATATTGGCATCATCCTCCTACTCAAAACAATGGCAACAGCACTCA
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                14510 388 +     16338 C----TAATGA---CTAACATTCGAAAGTCCCACCCACTAATAAAAATTGTAAACAATGCATTCATCGACCTTCCAGCCCCATCAAACATTTCATCATGATGAAATTTCGGTTCCCTCCTGGGAATCTGCCTAATCCTACAAATCCTCACAGGCCTATTCCTAGCAATACACTACACATCCGACACAACAACAGCATTCTCCTCTGTTACCCATATCTGCCGAGACGTGAACTACGGCTGAATCATCCGATACATACACGCAAACGGAGCTTCAATGTTTTTTATCTGCTTATATATGCACGTAGGACGAGGCTTATATTACGGGTCTTACACTTTTCTAGAAACATGAAATATTGGAGTAATCCTTCTGCTCACAGTAATAGCCACAGCATTTA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                14179 388 +     16727 T----TAATGA---CCAACATTCGAAAAACCCACCCACTAGCCAAAATTGTTAATAACTCATTCATTGACCTCCCAGCGCCGTCTAACATCTCTGCTTGATGGAACTTCGGATCCTTACTAGGAGTATGCTTGATTCTACAGATTCTAACAGGTTTATTCTTAGCTATGCACTATACATCGGACACAGCCACAGCTTTTTCATCAGTCACCCACATCTGCCGAGACGTTAACTACGGCTGAATTATCCGCTATATGCACGCAAATGGCGCTTCCATATTCTTTATCTGCCTATTCCTACATGTAGGACGAGGCCTATATTACGGATCCTATGTATTCATAGAAACATGAAACATTGGAATTGTACTATTATTCGCAACCATAGCCACAGCATTCA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239        789 388 -     16977 C----TAATGA---CCAACATCCGTAAAAACCACCCACTCCTAAAAATCGTAAACCAATCATTCATTGACTTACCAACACCAACAAGCATTTCAGCATGATGAAACTTCGGTTCATTGCTGGGCATCTGCCTAGCAATGCAAATTCTTACAGGCTTATTCCTAGCAATACACTATACATCAGACACCATAACAGCCTTCTCATCTGTAACTCACATCTGCCGAGACGTAAACTATGGCTGATTAATTCGTTACCTACATGCCAACGGCGCATCCCTATTCTTCATATGCCTATACCTCCATATCGGCCGAGGCTTGTACTACGGCTCATACACCTTCCTAGAAACTTGAAACATCGGAATTATCCTATTATTCACCGTTATAGCCACAGCATTTA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650        285 392 +     16266 TCAAATAATGA---CCCACATTCGAAAATCTCACCCCTTACTTAAAATCATCAATAAATCCTTCATTGATCTACCTACCCCATCCAACATCTCAACATGATGAAATTTCGGCTCACTACTAGGAGCATGCCTAATTACCCAAATCCTAACAGGATTATTCCTAGCCATACATTATACACCCGACACAATAACTGCATTTTCATCTATATCCCATATTTGCCGAGATGTGAACTACGGCTGAATTATTCGACAACTACACTCAAACGGAGCATCCATTTTCTTCCTCTGCCTATACACACACATTGGACGAAACATCTACTATGGGTCCTACCTATACTCGGAAACTTGAAATACCGGCATTATATTACTACTAATCACCATAGCCACCGCCTTCA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     13536 388 +     18297 T----TAATGA---CCAACATCCGAAAAACCCACCCACTAGCCAAGATTATTAACAGTTCCTTCATTGATCTCCCAGCCCCAACCAACATCTCATCATGATGAAACTTCGGTTCTCTACTAGGTATTTGTTTAGTTCTACAGATCATTACAGGCCTATTTTTAGCTATGCACTATACATCAGACACAATTACAGCATTCTCATCAATTGCCCACATCTCTCGAGATGTAAACTACGGTTGATTAATCCGTTATTTGCATGCCAACGGAGCATCACTATTCTTTATCTGCTTGTATCTTCATATTGGCCGAGGAATCTATTACGGCTCCTATATATTCTCTGAGACATGAAACATTGGTATTATCCTCCTATTTGCTGTGATAGCCACTGCATTCA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117165602 388 + 174229318 T----TAATGA---CCAACCTTCGAAAAAACCACCCCCTAATAAAAATTATTAACCACTCATTCATTGACCTACCAGCCCCTTCCAATATCTCTGCTTGATGGAACTTTGGATCACTTTTAGGCATATGTTTAATTATTCAAATCCTAACAGGACTATTTCTAGCCATACATTATACATCAGACACTCTAACCGCTTTTTCATCAGTAGCACATATTTGCCGAGATGTTAACTACGGATGACTGATCCGAAATCTACATGCTAACGGAGCTTCAATATTCTTTATATGTTTATTCCTTCACGTAGGACGAGGAATTTACTATGGTTCCTACCTGTATAAAGAAACCTGAAACATCGGAGTGATTCTCATACTTACTGTAATAGCCACTGCCTTCG
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                14889 391 +     16775 C----TAATGGCACCCAACATTCGAAAATCCCACCCCCTACTAAAAATAATTAACAACTCCCTAATCGACCTCCCAGCCCCATCCAACATCTCTGCTTGATGAAATTTCGGCTCCCTATTAGCAGTCTGCCTCATGACCCAAATCCTCACCGGCCTACTACTAGCCATGCACTACACAGCAGACACATCCCTAGCCTTCTCCTCCGTAGCCCACACTTGCCGGAACGTACAATACGGCTGACTCATCCGGAATCTCCACGCAAACGGCGCCTCATTCTTCTTCATCTGTATCTTCCTTCACATCGGACGAGGCCTATACTACGGCTCCTACCTCTACAAGGAAACCTGAAACACAGGAGTAATCCTCCTCCTCACACTCATAGCCACCGCCTTTG
+i galGal2.chrM            I 53 C 0
+s xenTro2.scaffold_18302        268 388 +      2726 -------ATGGCACCAAACATTCGAAAATCTCATCCACTTATCAAAATTGTTAATAACTCATTTATTGACCTACCAACCCCATCAAACCTATCCTCGTGATGAAACTTCGGCTCCCTTCTAGGGGTCTGCTTAATTGCCCAGATCGCTACAGGTTTATTCCTAGCAATACACTACACAGCAGACACCTCTATAGCCTTCTCATCAGTCGCCCACATCTGCCGAGACGTTAACTACGGCTGACTAATCCGTAACCTTCACGCAAACGGCGCATCCTTCTTCTTTATCTGTATTTATCTACACATTGGCCGAGGGTTGTATTATGGATCATTCCTCTACAAAGAAACATGAAATATTGGAGTCATCCTCTTATTCCTAGTCATAGCCACTGCATTTG
+i xenTro2.scaffold_18302  I 1 C 0
+s fr1.chrUn               320904986 388 + 349519338 C----TAATGG---CCAGCCTACGCAAAACCCACCCCCTACTAAAAATCGTAAACGACATAGTAATTGACCTTCCTACCCCCTCAAACATTTCCGCCTGATGAAACTTTGGCTCTCTACTCGGATTATGCCTTATTACACAAATCATCACAGGACTGTTCCTTGCAATACACTACACATCCGACATCTCTACCGCCTTTTCATCCGTAGCCCACATTTGCCGAGACGTAAACTACGGCTGACTAATTCGCAATCTACACGCAAACGGTGCCTCATTCTTTTTTATTTGCTTATACTCCCACATCGGCCGAGGTCTTTACTATGGCTCTTACCTAAGTAAAGAAACCTGAAACGTAGGGGTAGTCCTCTTACTTTTAGTAATGGCCACCGCTTTCG
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                15304 388 +     16596 T----TAATGA---CAAGCCTGCGAAAAACACACCCAGTTTTAAAAATCGCTAATGACGCATTAGTTGATTTGCCAACGCCACTAAATATTTCAGCGTGATGAAATTTTGGATCTCTCCTTGGATTATGTCTTATTACACAAATTTTAACAGGACTATTTTTAGCAATACACTACACCTCAGACATCTCAACAGCATTTTCATCTGTTGTGCATATTTGCCGAGATGTAAATTTCGGCTGACTTATTCGGAGCATCCATGCCAATGGGGCTTCCTTCTTCTTCATCTGCCTGTATATTCACATCGCCCGAGGACTATATTACGGATCTTATCTTTATAATGAAACTTGAAACATCGGAGTAGTCCTGTTCTTACTTGTAATAATAACAGCTTTTG
+i danRer4.chrM            C 0 C 0
+
+a score=1831171.000000
+s mm8.chrM                    14529 256 +     16299 TAGGCTACGTCCTTCCATGAGGACAAATATCATTCTGAGGTGCCACAGTTATTACAAACCTCCTATCAGCCATCCCATATATTGGAACAACCCTAGTCGAATGAATTTGAGGGGGCTTCTCAGTAGACAAAGCCACCTTGACCCGATTCTTCGCTTTCCACTTCATCTTACCATTTATTATCGCGGCCCTAGCAATCGTTCACCTCCTCTTCCT-CCACGAAACAGGATCAAACAACCCAACAGGATTAAACTCAGA
+s rn4.chrM                    14508 256 +     16300 TGGGCTATGTACTCCCATGAGGACAAATATCATTCTGAGGAGCTACAGTAATTACAAACCTATTATCAGCTATCCCTTACATTGGGACTACCCTAGTCGAATGAATCTGAGGAGGCTTCTCAGTAGACAAAGCAACCCTAACACGCTTCTTCGCATTCCACTTCATCCTCCCATTCATTATCGCCGCCCTTGCAATTGTACATCTTCTTTTCCT-CCACGAAACAGGATCAAATAACCCCACAGGATTAAACTCCGA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     14695 256 +     20791 TGGGTTATGTCCTCCCATGAGGACAAATATCATTTTGGGGGGCAACCGTAATCACTAACCTCCTATCAGCAATCCCATATATCGGAACAACCTTAGTTGAATGAATCTGAGGAGGATTTTCAGTTGATAAAGCCACTCTTACCCGATTCTTCGCTTTTCACTTCATCTTGCCATTTATCATCGCAGCTTTAGTCTTAATTCACCTCCTCTTTCT-ACATGAAACTGGCTCCAACAACCCTACAGGAATTCCTTCAAA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   15132 256 +     16571 TAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTT-GCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                14549 256 +     16554 TGGGCTATGTCCTCCCATGAGGCCAAATATCCTTCTGAGGAGCCACAGTAATTACAAACCTACTGTCCGCTATCCCATACATCGGAACAGACCTGGTCCAGTGAGTCTGAGGAGGCTACTCAGTAGACAGCCCTACCCTTACACGATTCTTCACCTTCCACTTTATCTTACCCTTCATCATCACAGCCCTAACAACACTTCATCTCCTATTCTT-ACACGAAACAGGATCAAATAACCCCCTAGGAATCACCTCCCA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34450236 255 - 182086969 TAGGCTACGTGCTCCCATGAGGCCAGACATCATTCTGAGGCACTACAATAATTACAAATCTACTATCAGTCATCTCATATATTGGAACTGACCTAATGCAATAAATCTGAGGTGGGTTCTCAGTTGACAAAGCCACCCTTACACGATTCTTCGCTTTCCATTTCATCTTA-CCTTCATCTTTACAGCCCTAGCAGCTGTTCACCTTTTATTCCT-ACATGAAACAGGATCTAATAACGCTTCAGGGGTTTCATCAGT
+i rheMac2.chr5            C 0 C 0
+s bosTau2.chrM                14898 256 +     16338 TAGGATACGTCCTACCATGAGGACAAATATCATTCTGAGGAGCAACAGTCATCACCAACCTCTTATCAGCAATCCCATACATCGGCACAAATTTAGTCGAATGAATCTGAGGCGGATTCTCAGTAGACAAAGCAACCCTTACCCGATTCTTCGCTTTCCATTTTATCCTTCCATTTATCATCATAGCAATTGCCATAGTCCACCTACTATTCCT-CCACGAAACAGGCTCCAACAACCCAACAGGAATTTCCTCAGA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                14567 256 +     16727 TGGGCTATGTACTACCATGAGGACAAATATCATTTTGAGGAGCAACTGTAATCACTAATCTTCTCTCTGCCATCCCTTATATCGGAACTGACTTAGTAGAATGGATCTGAGGCGGCTTCTCAGTGGACAAAGCAACCCTAACACGATTCTTTGCATTCCATTTCATCCTCCCTTTCATCATCGCAGCTCTAGCAATAGTACACCTCCTATTTCT-ACACGAAACCGGATCCAACAACCCTTCAGGAATCACATCAGA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       1177 256 -     16977 TAGGTTATGTCCTACCATGAGGACAAATATCATTCTGAGGGGCCACAGTAATTACCAACCTATTATCTGCCATCCCCTACATTGGAACCGACCTAGTAGAATGAATCTGAGGTGGCTTCTCAGTAGACAAAGCAACTCTAACACGCTTCTTCGCCTTCCACTTCATCTTACCATTTATTATCACAGCACTCGTAGTAGTCCACCTGTTATTCCT-ACACGAAACAGGATCAAACAACCCCACAGGTATCTCGTCAAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650        677 256 +     16266 TAGGATATGTCCTTCCGTGAGGACAAATATCATTCTGAGGGGCAACCGTAATCACTAACCTTTTCTCAGCAATCCCTTATATCGGCACAAACCTAGTAGAATGAATCTGAGGAGGCTTTTCAGTAGATAAAGCAACCTTAAATCGATTTTTCGCCCTCCATTTCATTCTCCCATTTACTATAATTGCACTAGCAGGAGTACACCTAACCTTTCT-TCACGAAACAGGCTCAAACAATCCACTGGGCCTCACTTCAGA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     13924 256 +     18297 TAGGCTATGTACTTCCATGAGGTCAAATATCTTTTTGAGGTGCAACCGTTATTACTAACCTACTTTCAGCTATTCCTTATATTGGCTCCAATCTTGTTGAGTGAATTTGAGGGGGCTTCTCAGTAGATAAAGCTACATTAACCCGTTTTTTTGCATTTCACTTTATTTTACCATTTATTGTCACTGCCTTAGTAATTATTCATCTACTGTTCCT-CCACGAATCGGGCTCCAATAACCCTACAGGAATCATTTCAGA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117165990 256 + 174229318 TAGGCTATGTACTCCCATGAGGACAAATATCCTTTTGAGGGGCTACAGTTATTACTAACCTTTTATCAGCCATTCCATACATTGGTAATACTCTAGTAGAATGAATCTGAGGCGGATTTTCAGTTGACAAAGCTACATTAACTCGATTCTTCGCATTCCATTTTATTTTACCTTTCATTATCCTTGCATTAGTTATTGTTCACCTCCTATTCCT-ACATGAGACCGGATCAAATAATCCTACAGGAATTAACCCCAA
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                15280 256 +     16775 TGGGCTATGTTCTCCCATGGGGCCAAATATCATTCTGAGGGGCCACCGTTATCACAAACCTATTCTCAGCAATTCCCTACATTGGACACACCCTAGTAGAGTGAGCCTGAGGGGGATTTTCAGTCGACAACCCAACCCTTACCCGATTCTTCGCTTTACACTTCCTCCTCCCCTTTGCAATCGCAGGTATTACTATCATCCACCTCACCTTCCT-ACACGAATCAGGCTCAAACAACCCCCTAGGCATCTCATCCGA
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18302        656 256 +      2726 TCGGATACGTCCTCCCCTGAGGACAAATATCTTTCTGAGGGGCCACAGTAATTACTAATCTTCTCTCTGCTATTCCGTACATCGGAAACGTACTAGTCCAATGAATCTGGNGAGGATTCTCAGTAGACAACGCTACCTTAACCCGATTTTTTGCCTTCCACTTCCTCCTACCTTTCCTTATTGCAGGAGCCAGCATCCTCCACTTACTGTTCCTCCCATGAAACTGGATCAACAAACCCCACA-GACTAAACTCGGA
+i xenTro2.scaffold_18302  C 0 M 685
+s tetNig1.chrUn_random    103508045 256 + 171761319 TAGGCTACGTCCTCCCCTGAGGACAGATGTCTTTCTGAGGCGCAACCGTCATCACAAACCTCCTATCCGCTGTCCCTTACGTAGGAAATACCCTTGTTCAATGAGTCTGAGGCGGTTTCTCAGTTGACCACGCAACTCTCACCCGATTTTTTGCTTTCCACTTCCTACTGCCATTCATCGTCGCAGCCGCTGTCATTGTACACCTCATTTTCCT-TCACGAAACCGGCTCAAACAACCCCCTAGGATTAAACTCCGA
+i tetNig1.chrUn_random    N 0 C 0
+s fr1.chrUn               320905374 256 + 349519338 TAGGCTACGTTCTCCCATGAGGACAAATATCCTTCTGAGGCGCCACTGTAATTACAAACCTGCTCTCTGCTGTCCCCTACGTAGGAAACACGCTCGTTCAATGAGTATGAGGAGGCTTTTCAGTAGACAGCGCCACTCTAACACGATTCTTTGCCTTCCACTTCCTCCTCCCATTTATCGTTGCAGCCGCTGCCATCGTACATCTTATTTTTCT-TCACGAAACAGGCTCCAACAATCCCCTAGGACTTAATTCAAA
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                15692 256 +     16596 TGGGCTACGTCCTTCCATGGGGCCAAATATCATTCTGAGGGGCCACAGTAATTACTAACCTATTATCGGCCGTTCCTTACGTGGGAGATACCCTAGTGCAATGAATCTGAGGGGGATTCTCAGTAGACAATGCAACCCTTACACGATTCTTCGCATTCCACTTTTTATTACCATTTATTATCATCGCCATAGTTATTCTACACTTGCTATTTCT-CCACGAAACCGGATCAAATAACCCCCTTGGCCTAAACCCCAA
+i danRer4.chrM            C 0 C 0
+
+a score=1289207.000000
+s mm8.chrM                    14785 195 +     16299 TGCAGATAAAATTCCATTTCACCCCTACTATACAATCAAAGATATCCTAGGTATCCTAATCATATTCTTAATTCTCATAACCCTAGTATTATTTTTCCCAGACATACTAGGAGACCCAGACAACTACATACCAGCTAATCCACTAAACACCCCACCCCATATTAAACCCGAATGATATTTCCTATTTGCATACGC
+s rn4.chrM                    14764 195 +     16300 CGCAGACAAAATCCCATTCCATCCATATTATACAATTAAAGACCTCCTAGGTGTATTTATATTACTATTATTCCTAATAACCCTAGTACTATTCTTCCCAGACCTACTAGGAGACCCAGACAATTATACACCCGCTAACCCCCTCAACACCCCACCCCACATCAAACCAGAATGATACTTTCTCTTTGCCTACGC
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     14951 195 +     20791 CTCAGATAAAATCCCTTTCCACCCCTACTACACAATCAAAGACACCCTAGGTTTCCTTGTAGCCATTCTTCTCCTCCTTATTTTAGTCCTATTTTCACCAGACCTATTAGGAGACCCAGACAACTACACCCCTGCCAACCCCCTTAATACCCCTCCCCATATCAAACCAGAATGATACTTCCTATTTGCCTACGC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   15388 195 +     16571 TTCCGATAAAATCACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACAC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                14805 195 +     16554 CTCCGACAAAATTACCTTCCACCCCTACTACACAATCAAAGATATCCTTGGCTTATTCCTTTTCCTCCTTATCCTAATGACATTAACACTATTCTCACCAGGCCTCCTAGGCGATCCAGACAACTATACCCTAGCTAACCCCCTAAACACCCCACCCCACATTAAACCCGAGTGATACTTTCTATTTGCCTACAC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr5             34450491 195 - 182086969 CCCCGACAACATTACTTTCCACCCCTGCCATACAACCAAAGATATTTTAGGTTTGATTTTTCTCCTCTTCCTCCTGATAATTCTAGTACTATTTTTGCCTGACCTCCTGGGTGACCCAGATAACTAAGTACTAGCCAACCCCATCAACACCCCATCCCACATTAAGCCGGAATGGTACTTTTTGTTTGCCTATGC
+i rheMac2.chr5            C 0 N 0
+s bosTau2.chrM                15154 195 +     16338 CGTAGACAAAATCCCATTCCACCCCTACTATACCATTAAGGACATCTTAGGGGCCCTCTTACTAATTCTAGCTCTAATACTACTAGTACTATTCGCACCCGACCTCCTCGGAGACCCAGATAACTACACCCCAGCCAATCCACTCAACACACCCCCTCACATCAAACCCGAGTGATACTTCTTATTTGCATACGC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                14823 195 +     16727 CTCAGACAAAATTCCATTTCACCCTTACTACACAATCAAGGATATCCTAGGAGCCTTACTCCTACTCCTAATCCTAATATCACTAGTTTTATTTTCACCTGACCTATTAGGAGACCCAGATAACTACACCCCTGCAAACCCCCTAAACACCCCTCCACATATTAAACCTGAGTGATATTTTCTATTCGCCTATGC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       1433 195 -     16977 CATAGACACAATCCCATTCCACCCGTACTATACAATTAAAGATATCCTAGGCTTAATTCTCATAATCCTGCTTCTAATAACATTAGTTCTATTTTACCCAGACCTACTAGGAGACCCAGACAACTACACCCCAGCAAACCCACTGAACACTCCACCCCATATTAAACCAGAATGATATTTTCTATTTGCCTACGC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650        933 195 +     16266 CTCAGACAAAATCCCCTTTCACCCATACTATACCATTAAGGACTTCCTAGGATTACTTATCCTAATTTTACTTCTTCTACTCCTAGCCCTACTATCTCCTGACATACTAGGAGACCCTGACAACTACATACCAGCCGACCCACTAAATACTCCCCTACATATCAAGCCAGAGTGATATTTTCTCTTTGCTTACGC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     14180 195 +     18297 TTCTGATAAAATCCCCTTTCACCCTTACTATACAATTAAAGATCTTCTAGGCCTAATAGTTATAATTATATTTCTTCTTATATTAGTCCTATTTACTCCTGACCTTCTTGGAGACCCCGATAATTTTACCCCTGCTAACCCCTTAGTTACCCCACCCCATATCAAACCAGAATGATATTTTCTGTTTGCATATGC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117166246 195 + 174229318 CTCAGACAAAATTCCATTTCACCCCTACTACACTATCAAAGACGCCCTAGGCCTAATCCTTATACTTCTTATTTTAATATCACTAGCAATATTCTCACCCGACATACTAGGTGACCCAGACAATTTCTCACCAGCCAACCCATTAAACACTCCTCCACATATTAAACCAGAATGATATTTCCTATTTGCCTATGC
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                15536 195 +     16775 CTCTGACAAAATTCCATTTCACCCATACTACTCCTTCAAAGACATTCTGGGCTTAACTCTCATACTCACCCCATTCCTAACACTAGCCCTATTCTCCCCCAACCTCCTAGGAGACCCAGAAAACTTCACCCCAGCAAACCCACTAGTAACCCCCCCACATATCAAACCAGAATGATATTTTCTATTCGCCTATGC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_19023       1291 195 +      3053 CCCAGACAAAATCCCATTTCACCCATACTTTTCTTACAAAGACCTCCTGGGATTTCTAATTATACTAACCTCACTAACTCTCCTAGCAATATTTGCCCCGAACCTTCTAGGTGACCCAGAAAACTTCACCCCAGCCAATCCACTTGTTACCCCTCCACACATCAAGCCAGAATGGTACTTCCTGTTTGCCTATGC
+i xenTro2.scaffold_19023  I 912 C 0
+s tetNig1.chrUn_random    103508301 195 + 171761319 CACAGATAAAATTCCATTCCACCCCTACTTCTCCTACAAAGACCTTATTGGATTCACTGTCCTCCTCACAACACTTACAATGCTCGCCCTCTTCTCTCCCAACTACCTAGGAGACCCAGACAACTTCACCCCTGCTAACCCCCTAGTCACCCCCGCCCACATCAAACCAGAGTGGTACTTCCTATTTGCATACGC
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320905630 195 + 349519338 CGCAGACAAAATCCCATTCCACCCATACTTCTCTTACAAAGACCTCCTGGGCTTCACAATCATGCTCTCAGCCCTCGCAACACTCGCCCTATTCTCTCCAAACTACCTCGGAGACCCTGACAACTTCACACCAGCCAACCCTCTAGTTACCCCCGCCCACATTAAACCAGAATGGTATTTCCTATTTGCATACGC
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                15948 195 +     16596 CATGGATAAAATCCCCTTTCATCCTTATTTTTCAAATAAAGACCTCCTTGGTTTTGTAATTATATTATTTTCCCTCTCACTATTAGCACTATTCTCACCAAACCTCTTAGGAGATCCAGAAAATTTCACCCCTGCTAACCCTCTAGTAACACCTCCTCACATTAAACCAGAATGATATTTCCTATTCGCATACGC
+i danRer4.chrM            C 0 C 0
+
+a score=1644802.000000
+s mm8.chrM                    14980 278 +     16299 CATTCTACGCTCAATCCCCAATAAACTAGGAGGTGTCCTAGCCTTAATCTTATCTATCCTAATTTTAGCCCTAATACCTTTCCTTCATACCTCAAAGCAACGAAGCCTAATATTCCGCCCAATCACACAAATTTTGTACTGAATCCTAGTAGCCAACCTACTTATCTTAACCTGAATTGGGGGCCAACCAGTAGAACACCCATTTATTATCATTGGCCAACTAGCCTCCATCTCATACTTCTCAATCATCTTAATTCTTATACCAATCTCAGGAATTA
+s rn4.chrM                    14959 278 +     16300 TATTCTACGCTCCATTCCCAACAAACTAGGAGGGGTCGTAGCCCTAATCTTATCAATCCTAATCTTAGCCTTCCTACCATTCCTGCATACCTCAAAACAACGCAGCTTAACATTCCGCCCAATCACCCAAATCCTTTACTGAATCCTAGTAGCCAACCTCCTAGTCTTAACATGAATCGGAGGCCAACCAGTAGAACACCCATTTATCATTATTGGTCAACTAGCCTCCATCAGTTATTTTTCAATTATCCTCATTCTCATACCAATCTCTGGAATTG
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     15146 278 +     20791 TATCCTACGCTCTATTCCAAATAAGCTCGGAGGAGTCCTAGCTCTAGTCCTATCCATCCTTGTTCTAGCCTTCATCCCATTCCTTCATATGTCTAAACAACGTAGCATGATATTCCGACCCATTAGTCAAGTCCTATTCTGAGTTCTCGTCGCAGATCTTCTCACACTCACATGAATCGGGGGCCAGCCAGTAGAACACCCATTCATCACCATTGGACAAGTAGCATCTGTCCTCTACTTCACCACCATCCTTATTCTTATACCCCTCGCAAGCCTAA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   15583 278 +     16571 AATTCTCCGATCCGTCCCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                15000 278 +     16554 AATCCTCCGATCCATCCCCAACAAACTAGGAGGCGTCCTCGCCCTACTACTATCTATCCTAATCCTAACAGCAATCCCTGTCCTCCACACATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAACTGCTTTACTGACTCCTAGCCACAGACCTCCTCATCCTAACCTGAATCGGAGGACAACCAGTAAGCTACCCCTTCATCACCATCGGACAAATAGCATCCGTATTATACTTCACAACAATCCTAATCCTAATACCAATCGCCTCTCTAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr3             59791440 276 + 196418989 AATCTTATGATCCATCCCCAATAAACTAGGAGGTGTACTGGCCCTTCTATTATCCATTCTCCTTCTAGCAGTTGTTCCTGCACTCCACACATCCAAACAACAAAGCATAATATTCCACCCATTAAGGCAATATCTGTTCTGAATCTTACTCACCAACCTATTCACCCTCATATGGATTGGAGGACAGCCAAGAA--CATCCTTTCATTACCATTGGACAGATGGCATCTATGATATGTTTCTCTATTATTCTTGTTCTCGTACCACTCACTGCCCTAA
+i rheMac2.chr3            N 0 C 0
+s bosTau2.chrM                15349 278 +     16338 AATCTTACGATCAATCCCCAACAAACTAGGAGGAGTACTAGCCCTAGCCTTCTCTATCCTAATTCTTGCTCTAATCCCCCTACTACACACCTCCAAACAACGAAGCATAATATTCCGACCACTCAGCCAATGCCTATTCTGAGCCCTAGTAGCAGACCTACTGACACTCACATGAATTGGAGGACAACCAGTCGAACACCCATATATCACCATCGGACAACTAGCATCTGTCCTATACTTTCTCCTCATCCTAGTGCTAATACCAACGGCCGGCACAA
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                15018 278 +     16727 TATCCTACGATCCATTCCTAATAAATTAGGAGGTGTACTCGCCCTAGTATTCTCCATCCTAATCTTGGCATTCATTCCACTCCTCCACACATCTAAGCAACGCAGCATAATATTCCGGCCCCTTAGCCAATGCCTATTCTGACTTTTAGTCGCCGATCTTCTCACTTTAACATGAATTGGAGGACAACCAGTTGAGCACCCTTTCATCATTATCGGACAAGTCGCTTCAATCTTATATTTCACCATCTTATTGATCCTAATACCAACAGTTAGCGTTA
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       1628 278 -     16977 AATCCTACGATCTATCCCAAATAAACTAGGAGGAGTATTAGCCCTAGTTTGCTCAATCCTTGTCCTCGCCATCATCCCTTTACTACACACAGCAAAACAACGAAGCCTTATATTCCGTCCAATCAGCCAATGTCTATTTTGACTCCTAGCAGCCAACCTAATAATCCTTACATGAATCGGAGGCCAACCAGTCGAACACCCATTCATTATCATCGGACAAGTAGCATCTATTTCATACTTCACAATTATCCTGGTCCTCATACCAATTGCAGGCCTAA
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       1128 278 +     16266 CATCCTACGATCTGTACCAAACAAACTAGGAGGCGTCCTAGCCCTACTCCTATCAATTCTAATCCTAGGATTAATACCACTTCTCCATACATCCAAGCACCGAAGCATAATACTCCGACCTCTTAGCCAAGTCCTATTCTGAACTCTAACAATAGATTTACTAACACTTACATGAATTGGCAGCCAACCAGTAGAATATCCTTACATCATTATTGGTCAAATAGCCTCAATTCTATATTTCTCCATTATCCTAGCCTTCCTGCCAATTGCAGGAGTAA
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     14375 278 +     18297 TATCCTTCGTTCTATCCCAAACAAACTAGGAGGAGTCTTAGCCCTCGTAACCTCCATTTTAATCCTTGCATTTATTCCTCTTCTTCATACAGCCAAACAACGAAGTCTTATATTCCGCCCGCTAAGCCAAATTCTATTCTGAATCCTGGCAGCTGACCTATTAGCCCTAACATGAATTGGAGGCCAACCCGTTGAAGACCCTTACATTATTATTGGCCAATTAGCTTCAATCACATATTTCACTATTATTCTAGTAATTATACCCTTATCAGGGGTAA
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117166441 278 + 174229318 AATCTTACGATCAATTCCAAACAAATTAGGAGGAGTATTAGCTCTCTTAGCATCTATCTTAATCCTACTAATCATCCCACTGCTCCACACATCAAAACAACGAAGCCTAATATTCCGACCAATTTCACAAATCATATTCTGATCATTAGTAGCCAACCTTTTAACCCTTACATGAATTGGGGGACAACCAGTAGAACAACCTTTTATTATTATCGGTCAACTAGCCTCAATCCTATATTTTTCACTCATTATTATTTTTATACCATTAGCAGGTATGT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                15731 278 +     16775 CATCCTACGCTCCATCCCCAACAAACTTGGAGGTGTACTAGCCCTAGCAGCCTCAGTCCTCATCCTCTTCCTAATCCCCTTCCTCCACAAATCTAAACAACGAACAATAACCTTCCGACCACTCTCCCAAACCCTATTCTGACTTCTAGTAGCCAACCTTCTTATCCTAACCTGAATCGGAAGCCAACCAGTAGAACACCCCTTCATCATCATTGGCCAAATAGCATCCCTCTCTTACTTCACCATCCTACTTATCCTCTTCCCCACAATCGGAACAC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_19023       1486 278 +      3053 CATCCTCCGATCGATCCCAAATAAATTAGGCGGAGTCCTAGCCCTAGTCTTCTCAATTCTGATTCTGGCTCTAATGCCCCTCCTGCATACCTCTAAACAACGAAGCCTTATATTCCGACCACTCACACAAATCACCTTCTGAGCCTTAGTAGCTGACACCCTAATCCTCACATGAATCGGAGGACAACCAGTAGAAGACCCTTATATCATGATCGGCCAACTAGCCTCAGTAATTTACTTCGCCATCTTCCTGGTCTTAATCCCCACCATTGGATGAG
+i xenTro2.scaffold_19023  C 0 n 0
+s tetNig1.chrUn_random    103508496 278 + 171761319 CATCCTACGGTCAATTCCAAACAAACTAGGAGGAGTCCTAGCCCTGCTTGCATCCATCCTCGTCCTCATAGTAGTCCCCCTCCTCCACACTTCAAAACAACGAAGCCTTACTTTCCGACCCTTTACACAATTTCTATTCTGAACCCTAATTGCCGATGTTGCCATCCTCACCTGAATCGGAGGCATACCTGTTGAACACCCTTACGTAATCATTGGCCAGGCTGCTTCAATCCTCTACTTCTCCTTATTTCTAGTCCTAATACCAGCAGCAGGATGGC
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320905825 278 + 349519338 AATTCTACGGTCTATCCCCAATAAACTAGGAGGAGTCCTGGCCCTTCTTGCCTCAATCTTAATTCTTATAGTAGTTCCTTTCTTACACACCTCTAAACAACGAAGCCTAACATTCCGCCCACTATCACAATTCCTATTCTGAACCCTAATTGCCGACGTCGTCATCCTAACCTGAATTGGAGGCATACCCGTCGAACATCCTTACATTATTATCGGACAAATTGCCTCAGTACTTTACTTCTCTCTCTTCCTAATCTTGATGCCAATAGCCGGTTGAC
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                16143 278 +     16596 CATTCTACGATCTATCCCAAACAAACTAGGAGGTGTACTAGCTCTCTTATTTTCCATTTTAGTATTAATAGTAGTACCAATTTTACACACTTCTAAACAGCGAGGAATAGCATTCCGCCCAGTTACCCAATTTCTGTTCTGAACACTGGTAGCAGACATGCTTGTACTAACATGAATTGGAGGGATACCAGTAGAACACCCCTACATCATCATTGGACAAATAGCATCAATCTTATATTTTTCACTATTCTTAGTCTTATTCCCAATTACAGGGATTT
+i danRer4.chrM            C 0 C 0
+
+a score=405176.000000
+s mm8.chrM                    15258 160 +     16299 TCGAAGACAAAATACTAAAATTATATC-----------CATGTCTTGATAGTATAAA-C--ATTACTCTGGTCTTGTAAACCTGAAATGAAGAT---CTTCTCTTCTCAAGAC-----------------------------AT-------CA-AGAAGAAGGAGCTA----CT---CCCCACCAC-CAGCACCCAAAG-CTGGTATTCT-AA-TTAAACTACTT
+s rn4.chrM                    15237 162 +     16300 TTGAAGACAAAATGTTAAAATGAAATT-----------AATGTCCCGATAGTATAAA-A--ATTACTCTGGTCTTGTAAACCAAAAATGAAGAG---TCAGTCTTCTCAGGAC----------------------------AAT-------CA-AGAAGAAGGAACTAC---CT---CCCCACCAT-CAACACCCAAAG-CTGATATTCT-AC-TTAAACTACTT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     15424 153 +     20791 TCGAAAACAAAATCCTCAAATGA----------------AGGTCCCAGTAGTATAAA-C--ATTACTCTGGTCTTGTAAGCCAGGAATGGAGA----TAGTTCTCCCTGAGAC-----------------------------AT-------CA---GAGAAGAGGCTCC---TG---CCCCACCAT-CAGCACCCAAAG-CTGATATTCT-AC-TTAAACTACCC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   15861 159 +     16571 TTGAAAACAAAATACTCAAATGGGC--------------CTGTCCTTGTAGTATAAA-CT-AATACACCAGTCTTGTAAACCGGAGACGAAAA-----CCTTTTTCCAAGGACA---------------------------AAT-------CAGAGAAAAAGTCTTTA-----A---CTCCACCAT-TAGCACCCAAAG-CTAAGATTCT-AATTTAAACTATTC
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                15278 159 +     16554 TCGAAAACAAAATACTTGAATGAAC--------------CTGCCCTTGTAGTATAAA-CT-AATACACCGGTCTTGTAAACCGGAAACGAAAA-----CTTTCTTCCAAGGACA---------------------------AAT-------CAGAGAAAAAGTAATTA-----A---CTTCACCAT-CAGCACCCAAAG-CTAAGATTCT-AATTTAAACTATTC
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr3             59791716 156 + 196418989 TCAAGGATAAACTACTTAAATGAAA--------------CTGCCCTTATAGTATAAT-CC-AATACGCCAGTCTTGTAAACCAGAAATGGAGA-------GTCCCCCAGGGA-A---------------------------ACT-------CAGAGAAAAAGCATTCC----TG---CTTCACCAT-CAACACCCAAAG-CTGAGATTCT-AA-TTAAACTATTC
+i rheMac2.chr3            C 0 C 0
+s bosTau2.chrM                15627 160 +     16338 TCGAAAACAAATTACTAAAATGAAGAC------------AGGTCTTTGTAGTACATC-T--AATATACTGGTCTTGTAAACCAGAGAAGGAGAACAACTAACCTCCCTAAGAC------------------------------T-------CA---AGGAAGAAACTGC---AG---TCTCACCAT-CAACCCCCAAAG-CTGAAGTTCT-AT-TTAAACTATTC
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                15296 157 +     16727 TCGAAAACAACCTTCTAAAATGAAGA---------------GTCTTTGTAGTATAAT-C--ATTACCTTGGTCTTGTAAACCAAAAATGGAGAGTAACCGCCCTCCCTAAGAC------------------------------T-------CA---AGGAAGAAGCTCT---TG---CTCCACCAT-CAGCACCCAAAG-CTGAGATTCT-TC-TTAAACTATTC
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       1906 164 -     16977 TCGAGAATAAGCTCATAAAATGAAG--------------ACGTCCCAGTAGTATAAA-T--ATTACCATGGTCTTGTAAACCATAAATGAAGAATAACCA--CTTCCTAGGACA---------------------------ATT-------CA-AGGAGAGGATACTACACTAA---CCCCACCAT-CAACTCCCAAAG-CTGACATTCT-AA-TTAAACTACTC
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       1406 153 +     16266 TCGAAAACTACCTCATTAAGT-------------------AACCCCTATAGTATAAGAT--ATTACAATGGTCTTGTAAGCCATAAATGAAAG-----CCATTTTCTAAGGGTA----------------------------TT-------CAGGGAAGAGGTCCACT----TA---CCTCGCTAT-CAATACCCAAAA-CTGAAATTCT-TC-TTAAACTATTC
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     14653 184 +     18297 TTGAAAATAACCTTCTTAAATGAAGACT--------ACTAAGCTTATGTAGTATAAT-T--ATTACCATGGTCTTGTAAACCATAGATGAAAG-----CTCCCTTCCATAAGCACAAA-------------CAAAAAAAAATCC-------CAGCGGAAAACGACACT----CAGTCCCTACCCATCCAGCACCCAAAAGCTGATATTCTAGT-TTAAACTACCC
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117166719 176 + 174229318 ATGAAGACCATTTACTTGAACCAAAATTCCCATAGAACAAAGTCCAAGTAATTTAAT-A--AAAATACTGGCCTTGTAAGCCAGCAATGAAGG-AAATATACCTTCCTTAGACAT--------------------------CCT-------CA-AGAAGAAGGACTAA----CA---CCCTACCAT-CAACACCCAAAG-CTGATATTCT-AT-TTAAACTACTT
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                16009 164 +     16775 TAGAAAACAAAATACTCAACTACTAAA------------ATACTCTAATAGTTTATG-A--AAAACATTGGTCTTGTAAACCAAAAACTGAAG-ACTCCACCCTTCTTAGAGTA-----------------------------T-------CAGAAAAGGAGGGCTCAA---AC---CTCCATCTC-CAGCTCCCAAAG-CTGGTATTTTCAA-ATAAACTACTC
+i galGal2.chrM            C 0 C 0
+s xenTro2.scaffold_18302       1606 190 +      2726 TAGAAAACAAACTCCTCAACTGA----------------TAGTCCTGATAGCTTAAC-TT-AAAGCATCGGTCTTGTAAGCCGAAGACTGGAGGCTAACGCCCTCCTCAAGACTTTCATTTTTGGCAGTTGCCAGCCCNCAATT-------CGAGGAAGAAGGAATCAA---AC---CTCCACTAT-TGACCCCCAAAG-CCAACATTCT-AT-TTAAATTACCC
+i xenTro2.scaffold_18302  M 685 C 0
+s tetNig1.chrUn_random    103508774 164 + 171761319 TAGAAAACAAAACACTTCAATAACC--------------AAGCATTAGTAGCTCAGC-GTTAGAGCGCCGGTCTTGTAAACCGGACGCCGGAGGTTAGAGTCCTCCCTACTGC------------------------------T-------CAAAAAGGAAGGATTCTA---AC---CTCCACCGC-TGGCTCCCAAAG-CCAACATTCTCAG-TTAAACTACTT
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320906103 163 + 349519338 TAGAAAACAAAATACTAAACTAA-C--------------AAGCATTAGTAGCTCAGA-TTCAGAGCGTCGGTCTTGTAAACCGAATGTCGGGGGTTAAAGTCCCCCCTTATGC------------------------------T-------CAAAAAGAAGGGACTTCA---AC---CCCCACCAC-TGGCTCCCAAAG-CCAGCATTCTTAA-TTAAACTACTT
+i fr1.chrUn               C 0 C 0
+s danRer4.chrM                16421 171 +     16596 TAGAGAATAAGGCACTCCAATGAAG--------------CTGCCCTAGTAGCTTAGT-TTTAAAGCATCGGTCTTGTAATCCGAAGATCGGAGGTTAGACCCCTCCCTAGCGC------------------------------TAAATTACCAGAAAAGAGAGATTTTA---AC---TCACACCCC-TGACTCCCAAAG-CCAGGATTCTAAA-TTAAACTATTT
+i danRer4.chrM            C 0 N 0
+
+a score=-119632.000000
+s mm8.chrM                    15418  5 +     16299 CT---------------------------------------------------------TG-----------------------------------A
+s rn4.chrM                    15399  7 +     16300 CT---------------------------------------------------------TG---------------------------------TCA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     15577 39 +     20791 TC---------------------------------------------------------TGCTCTTTTACTTTAATAAAA-CTCAAGTACTTCATCA
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   16020 40 +     16571 TC---------------------------------------------------------TGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAA
+i hg18.chrM               C 0 C 0
+s panTro2.chrM                15437 40 +     16554 TC---------------------------------------------------------TGTTCTTTCATGGGGAAGCAAATTTAGGTACCACCTAA
+i panTro2.chrM            C 0 C 0
+s rheMac2.chr3             59791872 39 + 196418989 TC---------------------------------------------------------TGTATTCTTTTCGACATGCAT-TTTAACTACTATGTAA
+i rheMac2.chr3            C 0 C 0
+s bosTau2.chrM                15787  5 +     16338 CC---------------------------------------------------------TGA-----------------------------------
+i bosTau2.chrM            C 0 I 173
+s canFam2.chrM                15453  5 +     16727 CC---------------------------------------------------------TGA-----------------------------------
+i canFam2.chrM            C 0 I 1
+s dasNov1.scaffold_23239       2070  5 -     16977 CT---------------------------------------------------------TGA-----------------------------------
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       1559 61 +     16266 CCTGCAGGCAATCAACCCGCTATGTATATCGTGCATTAAATGCTTGTCCCCATACATAATG------------------------------------
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     14837  5 +     18297 CCC--------------------------------------------------------TG------------------------------------
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117166895  5 + 174229318 CT---------------------------------------------------------TGA-----------------------------------
+i monDom4.chrUn           C 0 C 0
+s galGal2.chrM                16173  5 +     16775 TC---------------------------------------------------------TGA-----------------------------------
+i galGal2.chrM            C 0 N 0
+s xenTro2.scaffold_18302       1796  5 +      2726 CT---------------------------------------------------------CGA-----------------------------------
+i xenTro2.scaffold_18302  C 0 C 0
+s tetNig1.chrUn_random    103508938  4 + 171761319 CT---------------------------------------------------------TG------------------------------------
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320906266  4 + 349519338 TT---------------------------------------------------------TG------------------------------------
+i fr1.chrUn               C 0 C 0
+s danRer4.chr11            47797944  4 +  52342180 TC---------------------------------------------------------TG------------------------------------
+i danRer4.chr11           N 0 C 0
+
+a score=-468235.000000
+s mm8.chrM                    15423  89 +     16299 GTAC--ATAAATT------------------------------------------------------T---------ACATAGT---------------ACAAC-A--------------GTACA------------------------------TTTAT----------G-------------------------------TAT-----AT-C------------------GTACAT-----TAAACTATTTTCCCCAA-GCAT---ATAAGCT-AGTACATTAA-------ATC
+s rn4.chrM                    15406  88 +     16300 GTAC--ATAAAAT------------------------------------------------------G---------ATATGG----------------ACATT-A--------------AAACA------------------------------TTTAT----------G-------------------------------TAT-----AT-C------------------GTACAT-----TAAATTATTTTCCCCAA-GCAT---ATAAGCA-TGTAATATAT-------ATC
+i rn4.chrM                C 0 I 1
+s oryCun1.scaffold_140182     15616 159 +     20791 GTACTGACAAATTACTAACACACTATGTAATTCGTGCATTAATGCTCGTCCCCATTAA---------A---------ATGTATT---------------ACAAC-A--------------ATAAA------------------------------TTCAT----------AACCAACATTCA--------------ACATATTATGCTTAAT-C------------------GTACAT-----AAATTCCTCATCCCCAT-GAATA--ATAAGCT-AGTACATTAC-------TGC
+i oryCun1.scaffold_140182 C 0 I 9
+s hg18.chrM                   16060  82 +     16571 GTAT--------T------------------------------------------------------G---------ACTCAC----------------CCATCAA--------------CAACC------------------------------GCTAT----------G-------------------------------TAT-----TT-C------------------GTACAT-----T-ACTGCCAGCCACCAT-GAAT---ATTGTAC-GGTACCATAA-------ATA
+i hg18.chrM               C 0 I 102
+s panTro2.chrM                15477  80 +     16554 GTAC--------T------------------------------------------------------G---------GCTCAT----------------TCATT-A--------------CAACC------------------------------GCTAT----------G-------------------------------TAT-----TT-C------------------GTACAT-----T-ACTGCCAGCCACCAT-GAAT---ATCGTAC-AGTACCAT-A-------TCA
+i panTro2.chrM            C 0 I 189
+s rheMac2.chr3             59791911  86 + 196418989 GTAC--------T------------------------------------------------------GACCATCAGCACTGAT----------------ACATT-A--------------ATACT------------------------------TTTAT----------G-------------------------------TAC-----TT-C------------------ATGCAT-----T-ACTGCTAGTCCCCAT-GAAT---AATATAT-AGTACTATC-----------
+i rheMac2.chr3            C 0 I 26
+s bosTau2.chrM                15965  87 +     16338 -----------------------------------------------------------------------------GTACATA---------------ACATT-A--------------ATGTA------------------------------ATAAA----------G------ACATA--------------ATATG-TAT-----AT-A------------------GTACAT-----TAAATTATATGCCCCAT-GCAT---ATAAGCA-AGTACATGAC-------CTC
+i bosTau2.chrM            I 173 C 0
+s canFam2.chrM                15459 104 +     16727 ------------------------------------------------------------------------------ACCCCT---------------ACATT-C--------------ATATA------------------------------TTGAA----------T---CACCCCTA--------------CTGTGCTAT-----GTCA------------------GTATCTCCAGGTAAACCCTTCTCCCCTC-CCCT---ATGTACGTCGTGCATTAATGGTTTGCCC
+i canFam2.chrM            I 1 C 0
+s dasNov1.scaffold_23239       2075 111 -     16977 --------ACACT------------------------------------------------------A---------ACATGC----------------ACAAT-ATAT-----------ATATA------------------------------TATAT----------ATACCAAACATAGCGCTATTTCGGCGCTATG-TAA-----TT-C------------------GTGCAT-----ACATTTATCTACCCCAT-ACAT---ATCATTA-TATACTAAC-----------
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       1620  99 +     16266 -----------------------------------------------------------------------------ATATATATTACTAACTATACTTAATCT-T--------------ACATAGA------------------------CCATACTAT----------G-------------------------------TAT----AAT-C------------------GTGCAT-----CACATTATTTACCCCAT-GCTT---ATAAGCA-AGTACTGTTT-------AAC
+i loxAfr1.scaffold_36650  C 0 I 1
+s echTel1.scaffold_181343     14842  64 +     18297 -----------------------------------------------------------------------------ATGTACA---------------AATTT-T--------------CAATA---------------------------------AT----------G-------------------------------TAT----TAT-C------------------GTGCAT-----ATATGTCTTTCCCCCAT----------------AGTACATTTT-------ATG
+i echTel1.scaffold_181343 C 0 I 1
+s monDom4.chrUn           117166900 138 + 174229318 -------------------------------------AAAAACAAAAAAAAACAAAAAAACGCGATTT---------GTATGCT---------------ATGTC-A--------------GTATTGaattttttaatattttaagatttttttgttttat----------g-------------------------------tat-----at-a------------------ttaCAT-----GGATTTATTTACCCCTA-GCAT---ATATCTA-TGTACAAGCT-------ACT
+i monDom4.chrUn           C 0 I 5
+s xenTro2.scaffold_18302       1801  83 +      2726 ------------------------------------------------------------AGCAAAGG---------ATATGCT---------------CTATA-T--------------ACATA-------------------------------CTAT----------G-------------------------------CTT-----AT-A------------------GAGCAT-----TAATTTTTTAACCCCAC-GAATAATATTTATA-GCTAAAATG-----------
+i xenTro2.scaffold_18302  C 0 C 0
+s tetNig1.chrUn_random    103508942  51 + 171761319 ------------------------------------------------------------------------------------------------------------------------TTGCA------------------------------TATAT----------G-------------------------------TAA-----TA-T------------------CACCAT-----GCATATATATTAACCATATAAT---AGGATG----------------------
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320906270  53 + 349519338 ---------------------------------------------------------------------------------------------------------------------ATAATACA------------------------------TATAT----------G-------------------------------TAT-----TA-T------------------CCCCAT-----TCATATATATTAAACAT-TAAT---ATAATG----------------------
+i fr1.chrUn               C 0 C 0
+s danRer4.chr11            47797948  91 +  52342180 -----------------------------------------------------------------------------------------------------------ACGGCCGGCGACAATTTA------------------------------TATGTCAATGTTTTAG-------------------------------TAA-----TT-TACAATTAAGACAGACATGCACTGT-----ATTGATACATTAATCAT-ACAT---AAAATG----------------------
+i danRer4.chr11           C 0 C 0
+
+a score=-705633.000000
+s mm8.chrM                    15512 107 +     16299 AATGGTTC--AGGT--------------------------CATAAAA-----T----AATCA----TCAAC-A-TAAATC-AATATA-----TA---------TACCATGAATATTATCTTA-----------------------AACACATTA----------------AACTA------------------------------AT------------GTTA----------TAAGGACA-TATCTGTGTTATCTG
+s rn4.chrM                    15495 103 +     16300 AATGATTT--AGGA--------------------------CATACAT-----T----TAAAC----TCAACTA-TAAATT-CACA--------A---------CAACATGTCTAT--TCTCA-----------------------AATACATTA----------------AGATA------------------------------AT------------GCTT----------ATTAGACA-TATCTGTGTTATTAG
+i rn4.chrM                I 1 C 0
+s oryCun1.scaffold_140182     15784 113 +     20791 CATAATCC--ACTT--------------------------AATACAT-----C----ACACATAATTCAACAA-AAAATC-GACC--------C---------AAACATGAATAT--TCTCA--------------------------CCAAAA----------------ATCTA------------------------------AT------------GATTGACT--TGACATTGGACATTAATTCCATAATTAA
+i oryCun1.scaffold_140182 I 9 C 0
+s hg18.chrM                   16244  87 +     16571 TGCAACTCCAAAGC--------------------------CACCCCT-----C----ACCCA----CTAGG-A------------------------------TACCAACAAACC--TACCC-----------------------------------------------------------------------------------AC------------CCTTAACA--GTACATAGTACA-TAAAGTCATTTACCG
+i hg18.chrM               I 102 I 1
+s panTro2.chr2a            84667382 123 + 114460064 AGTGATTTCTTAAT--------------------------CAACTAT-----C----ACACA----TCATC-A--TTATT-GGTT--------G---------TACAATAAGACC--TGCCC-CACA------------------TGAATATTG-----------------ACCAGTACTGT---------------------AAAT------------CCTTACTC--TTACATAGTACA-TATGTTCATTCATCT
+i panTro2.chr2a           n 189 I 313
+s rheMac2.chr3             59792023 167 + 196418989 AGAGATTTTATGACATTA----TAAGCTT----------GCTCCACA-----T----GCATA----TAAGC-A-ATTATT-AGCA--------ATTTCTTAACTATCATATATAA--TACTA-TACT------------------TACATATAG----------------AACTAGTTCCATATGAATATCGACCAGTACTCAAAGT------------TCTTAATA--TTACATAGTACA-ATCATTTGTTCATTG
+i rheMac2.chr3            I 26 I 1
+s bosTau2.chrM                16052  77 +     16338 --------------------------TAT-----A-GCAGTACATAA-----T----ACATA----TAATT-A-TTGACTGTACA------------------TAGTAC--ATTA--TGTCA------------------------------------------------AATTC------------------------------AT------------TCTTGATA--GTATATCTA-------------------
+i bosTau2.chrM            C 0 C 0
+s canFam2.chrM                15563  90 +     16727 --------------------------CAT----------GCATATAAGCATGT----ACATA----ATATT-A-TATCCT-TACA------------------TAGGACATATTA--ACTCA------------------------------------------------ATCTC------------------------------ATAATTCACTGATCTTTCAACA--GTA-ATCGA-------------------
+i canFam2.chrM            C 0 C 0
+s dasNov1.scaffold_23239       2186 119 -     16977 ----------------TATTATTAATCTT-----ACATAGTACATTC-----T----ATGTA----TAATC-A-CACATA-CACTTA---TCTA---------CCCCATACATAT--CATTA-------------------------TATACTA----------------ACT--------------------------------AT------------TATTAATC--TTACATAGTACATTCTATGTATAATCAC
+i dasNov1.scaffold_23239  C 0 I 54
+s loxAfr1.scaffold_36650       1720 106 +     16266 ----------------------------------------AATGTGT-----C-AAGTCATA----TTCAT-G-TAGATT-CACA------------------GGTCATGTTCTG--GTTCA-----------------------TGGATATTATTT--------ACCTACGATA------------------------------AA------------CCATAGTC--TTACATAGCACATTAAAGCTCTTGG---
+i loxAfr1.scaffold_36650  I 1 I 4
+s echTel1.scaffold_181343     14907  82 +     18297 ----------------------------------------AATCCCC-----C----CCTTT----TAAAT-T-TATTTC-CCCC------------------ATTCATATCTTG-------------------------------TAATATTACT--------------CAGTC------------------------------AA------------TGATACTCAATTAAATAA-----------TCTTAA---
+i echTel1.scaffold_181343 I 1 I 4
+s monDom4.chrUn           117167043 102 + 174229318 --------------------------------------ATTACTAAA-----T----ACATA----AAATT-A-TTAATC-------------G---------TACAATGATTTG--TACAG-TATA------------------CGGATATTCTTA--------ACCTAATATA------------------------------TA------------TCATAATC--TTACATAAGACA-------TATTATGAA
+i monDom4.chrUn           I 5 I 5
+s xenTro2.scaffold_18302       1884 111 +      2726 -----------------------AAATATCTAACATAGAGGATATGC-----T----CTATA----TACAT-ACTATGCT-TATA------------------GAGCATTAATTT--TTTAACCCCA------------------CGAATAATATTT--------AT---AGCTA------------------------------AA------------ATGAAATATCTAACATAGAGG-----------------
+i xenTro2.scaffold_18302  C 0 N 0
+s tetNig1.chrUn_random    103508993 119 + 171761319 ------------------------------------------TATAG-----T----ACATA----ATTAG-A-T-TAAT-CACTTAAAACTGG---------GGTTATACATAA--AGCAAGGATAACAAGTGAAAAAGGACATAAAACATAACTGGAACAG--ACAGAAATTT------------------------------ATAGAGAA------GCATGACA------------------------------
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320906323 125 + 349519338 ------------------------------------------CATAA-----CTAAGACATA----GTACT-A-TATATT-CACCTATAATTCC---------TATAACCCATAA--AGCAAGTACAGAAAACTAAAAATGCTA-AAAGCATGACTAGAAAAATCCCTAAAAATT------------------------------GTTGAAGA------ACTGAACG------------------------------
+i fr1.chrUn               C 0 C 0
+s danRer4.chr11            47798039  71 +  52342180 ------------------------------------------CATGC-----T-----CTAA----TTTTT-A-CATATG-CATGT--------------------------------GCAAGCATA------------------TACATATGTGTGGAT-----ACACACGTAT------------------------------GT------------GCTTTGTC------------------------------
+i danRer4.chr11           C 0 C 0
+
+a score=25648.000000
+s mm8.chrM                    15619 194 +     16299 ACATA-CACCATACA-GT-------CATAAACTCTT-----CTCTTCCATAT-----GACTATC----CC--CTT--CCCCA--------------------------------------------TTTG---------G-----TC---------------TATTAATCT-ACCATCC--------------------TCCGTGAA---ACCAACAACCC--GCCCA--CCAATG---CCCCTCTTCTCGCT----CCGGGCCCATTA-AACTTGGGGGTAGCT-AA-ACTGAAACTTTATCAGACATCTGGTTCTTACTTCAGGGCCAT---C
+s rn4.chrM                    15598 194 +     16300 ACATG-CACCATTAA-GT-------CATAAACCTTT-----CTCTTCCATAT-----GACTATC----CC--TGT--CCCCA--------------------------------------------ATTG---------G-----TC---------------TCTATTTCT-ACCATCC--------------------TCCGTGAA---ATCAACAACCC--GCCCA--CTCGTC---CCCCTCTTCTCGCT----CCGGGCCCATTC-GTCCTGGGGGTGACT-AT-ACTGAAACTTTACCAGGCATCTGGTTCTTACTTCAGGGCCAT---C
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     15897 202 +     20791 ACATA-GACCATCAA-ATCT----ACACACACCACTCAACCCTTACCCATAC-----GACTATC----CC--TCT--CCCCC--------------------------------------------AGTC---------C-----TC---------------TCACAACTT-ACCATCC--------------------TCCGTGAA---ACCAACAACCC--GCCCA--CCAAGG--ATCCCTCTTCTCGCT----CCGGGCCCATAA-AACTTGGGGGTTTCT-AA-TATGAAACTATAACTGGCATCTGGTTCTTACCTCAGGGCCAT----
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   16332 192 +     16571 ACATAGCACATTACA-GT-------CA-AATCCCTT-----CTCGTCCCCAT-----GGATGAC----CC--CCC--TCAGAT-------------------------------------------AGGG---------G-----TC---------------CCTTGACC--ACCATCC--------------------TCCGTGAA---ATCAATATCCC--GCACA--AGAGTG---CTACTCTCCTCGCT----CCGGGCCCATAA-CACTTGGGGGTAGCT-A--AAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCAT----
+i hg18.chrM               I 1 C 0
+s panTro2.chrM                15746 190 +     16554 ACATAGCACATTACA-GT-------CA-AACCCCTC-----CTCGCCCCCAC-----GGATGCT----CC--CCC--TCAGAT-------------------------------------------AGGA---------A-----TC---------------CCTTGGTC--ACCATCC--------------------TCCGTGAA---ATCAATATCCC--GCACA--AGAGTG-----ACTCTCCTCGCT----CCGGGCCCATAA-CATCTGGGGGTAGCT-A--AAGTGAACTGTATCCGACATCTGGTTCCTACCTCAGGGCCAT----
+i panTro2.chrM            I 189 C 0
+s rheMac2.chr3             59792191 193 + 196418989 ACATAGCACATTTCA-GT-------CA-AAACCACC-----CTTGCCAGCAT-----GGATATC----TC--CTA--CCAAAT-------------------------------------------TTTG---------G-----TC---------------TCTTAGTCT-ACCAACC--------------------TCTGAGAA---ATCATCATCCC--ACTTG--GGCATG---TAACCCTCCTCACT----CCAGGCCCGTAA-TACTTGGAGGTGACT-AT-ACTTCAACTGTACCTGGCATTTGGTTCTTACCTC-GGGTCAT----
+i rheMac2.chr3            I 1 C 0
+s dasNov1.scaffold_23239       2359 263 -     16977 ACATAGCACATTCTATGTATAATCACACATACATTT-----ATCTACCCCAT-----GCATATC----AC--ACC--CCAACTAAACCTACGCACAGACATAACGAGTACCAAGTTCTAACCGTACACTG---------A-----TCATCTCCAACCAAAATTCTCACTC--ACCAACT--------------------CCCGAGAA---ACCAGCAACCC--GCCAG--ACAAGT--ATCCCTCTGCTTGCT----CTGAGCCCATAA-ACCGTGGGGGTTTCT-ATACGTGAAACTTTATCTGGCATCTGGTTCTTTCTTCAGGGCCAT---C
+i dasNov1.scaffold_23239  I 54 C 0
+s loxAfr1.scaffold_36650       1830 191 +     16266 ACATAGCACATCACT-GA-------GA----AATCT-----CTAGTCACCAT-----GCATATC----AC--CTC--CAAT---------------------------------------------GGTT---------G-----TA---------------CCTTAACT--ACCTACC--------------------TCCGAGAA---ACCATCAACCC--GCCCATCTTCGTG---TCCCTCTTCTCGCT----CCGGGCCCATCA-ATTGTGGGGGTTTCT-AT-ACTGGATCTATACCTGGCATCTGGTTCTTTCTTCAGGACCAT---C
+i loxAfr1.scaffold_36650  I 4 C 0
+s echTel1.scaffold_181343     14993 190 +     18297 ACATAGCACATCTCT-GT-------CT----CCGTC-----CTTGTCAAATG-----GCGTATC----AC--CTC--CAAA---------------------------------------------TATC---------T-----TT---------------CATTAATC--ACCAAGC--------------------TTCGAGAA---ACCAACAACCC--GCTCGG-GTAATG---CCCCTCTTCTCGCT----CCGGGCCCATTA-ATCGTGGGGGTTTCTAAT-AATGAATTT-TATCAGACATCTGGTTCTTTCTTCAGGACCAT---C
+i echTel1.scaffold_181343 I 4 C 0
+s monDom4.chrUn           117167150 206 + 174229318 GCATA-GACATTGTATGCATGGTTCCACAGACTAAC-----TAACCTACCATTTCTAGCATATC----AT--CAC--CAAC---------------------------------------------GATA---------G-----TA---------------CCTCAGTC--CTCCCCT--------------------CACGAGAA---ACCACCATCCC--GCCAT--CTGAAGGTAAAACGTCCTTCAGA----GGAGATGCATGT-ATTGTGTCGG-ACCT-A--AGTTCCTTTCTAATGGGCCACTGGTTGCTACTTCAGGGTCAT---A
+i monDom4.chrUn           I 5 C 0
+s canFam2.chrM                15653 161 +     16727 --------------------------------------------------AT-----GCATATC----AC--TTAGTCC-----------------------------------------------AATA---------A-----GG---------------GCTTAATC--ACCATGC--------------------CTCGAGAA---ACCATCAACCCTTGCTCG--TAATG----TCCCTCTTCTCGCT----CCGGGCCCATACTAACGTGGGGGTTACT-AT-CATGAAACTATACCTGGCATCTGGTTCTTACTTCAGGGCCATAACC
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                16129 161 +     16338 --------------------------------------------------TT-----ATATATT----CC--TTA--CC-----------------------------------------------ATTA---------GATCACGA---------------GCTTAATT--ACCATGC--------------------CGCGTGAA---ACCAGCAACCC--GCTAG--GCAGGG--ATCCCTCTTCTCGCT----CCGGGCCCATAA-ACCGTGGGGGTCGCT-ATCCAATGAATTTTACCAGGCATCTGGTTCTTTCTTCAGGGCCAT---C
+i bosTau2.chrM            C 0 C 0
+s tetNig1.chrUn_random    103509112 201 + 171761319 GTATT-CAAGACCTA-AC-------ACTAAATC--------CATCAGTCAAG-----ATATACCAAGTAC--CCA--GCATCC-------------------------------------------CGTT---------A-----AA---------------ATCCAAAT--CCGATGT--------------------AGTAAGAACCGACCATCAGTTG--ATTTC--TTAATG--CATACTCTTATTGATAG--TGAGGGACAATC-GTTCTGAGGGTCGCA-CT-TCTTGAATTATTCCTGGCATTTGGTTCCTACTTCAGGGCCAT---G
+i tetNig1.chrUn_random    C 0 C 0
+s fr1.chrUn               320906448 201 + 349519338 AAATT-TAAGACCGA-AC-------AATAAACT--------CATCAGTCAAG-----ATATACCAGG-AC--TCA--ACACCC-------------------------------------------CGTA---------A-----AA---------------TACCAACTA-TTAATGT--------------------AGTAAGAACCGACCATCAGTTG--ATTTC--TTAATG--CATATTATTATTGAAGG--TGAGGGACAATA-ACAGTGGGGGTTTCA-CT-AAATGAACTATTCCTGGCATTTGGTTCCTACTTCAGGGCCAT---T
+i fr1.chrUn               C 0 C 0
+s danRer4.chr11            47798110 237 +  52342180 ACATG-TATGTACTG-GT-------TACATATTATG-----CATGTATTAGG-----ACATACTATGTATTATCA--CCATAT-------------------------------------------CATTATTTTAACCA-----TA---------------AAGCAGGTACATAATGTTTATATTATTCACCATATCAAGTGAGAGACCACCAATAATTT--A--TA--TAAATG--CATATCATGCATGATAGAATCAGGGACATCG-ATTTAAACGTTGTTA-AA-AAATGAACTATTCCTGGTATCTGGTTCAAATCTCACGTTCAT---C
+i danRer4.chr11           C 0 N 0
+
+a score=70787.000000
+s mm8.chrM                    15813 46 +     16299 AAATGCGTTATCG--CCCATACGTTCCCCTTAAATAAGACAT--CTCGAT
+s rn4.chrM                    15792 46 +     16300 AATTGGTTCATCG--TCCATACGTTCCCCTTAAATAAGACAT--CTCGAT
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     16099 46 +     20791 AAACCTAAGATCG--CCCACACGTTCCTCTTAAATAAGACAT--CTCGAT
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chrM                   16524 45 +     16571 AAAGCCTAAATAG--CCCACACGTTCCCCTTAAATAAGACAT--CACGA-
+i hg18.chrM               C 0 N 0
+s panTro2.chrM                15936 47 +     16554 GAAGTTCAAAAGACTCCCACACGTTCCCCTTAAATAAGACAT--CACGA-
+i panTro2.chrM            C 0 I 1
+s rheMac2.chr3             59792384 46 + 196418989 AAAACTAAGATTG--CCCACACGTTCGCCTTAAATAAGACAC--CTCGAT
+i rheMac2.chr3            C 0 C 0
+s dasNov1.scaffold_23239       2622 46 -     16977 TCACCTAAAACCG--TCCACTCATTCCCCTTAAATAAGACAT--CTCGAT
+i dasNov1.scaffold_23239  C 0 C 0
+s loxAfr1.scaffold_36650       2021 46 +     16266 TCACCTAAAATCG--CCCATTCTTTCCTCTTAAATAAGACAT--CTCGAT
+i loxAfr1.scaffold_36650  C 0 C 0
+s echTel1.scaffold_181343     15183 46 +     18297 TCACCTAAAATCG--CCCACTCTTTCCTCTTAAATAAGACAT--CACGAT
+i echTel1.scaffold_181343 C 0 C 0
+s monDom4.chrUn           117167356 43 + 174229318 ATACTGTTCATTG--CATCCAAACTGCTTTTTAA-GAGGCAT--TGCT--
+i monDom4.chrUn           C 0 I 3
+s canFam2.chrM                15814 46 +     16727 TTATTTACTCCAA--TCCTACTAATTCTCGCAAATGGGACAT--CTCGAT
+i canFam2.chrM            C 0 C 0
+s bosTau2.chrM                16290 46 +     16338 TCATCTAAAACGG--TCCATTCTTTCCTCTTAAATAAGACAT--CTCGAT
+i bosTau2.chrM            C 0 N 0
+s tetNig1.chrUn_random    103509313 45 + 171761319 --ACTTGGATCAT--TCCTCACACTTTCATCGACGCTGACATAAGTTAT-
+i tetNig1.chrUn_random    C 0 N 0
+s fr1.chrUn               320906649 46 + 349519338 --AATCGATTTAT--TCCTCATTCTTTCATCGACGCTGACATAAGTTGTT
+i fr1.chrUn               C 0 C 0
+
+a score=39116.000000
+s mm8.chrM                    15859 70 +     16299 ----GGTATCGGGT-CT--AATC-AGCCCA-----TGACCA--ACATAACTGTG--GTGTCATG-CATTTGGTATCTTTTTATTTT--GG
+s rn4.chrM                    15838 70 +     16300 ----GGTAACGGGT-CT--AATC-AGCCCA-----TGATCA--ACATAACTGTG--GTGATATA-CATTTGGTATTTTTTAATTTT--CG
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     16145 71 +     20791 ----GGACTAATGA-CT--AATC-AGCCCA-----TGCTCAC-ACATAACTGTG--ATGTCATG-CATTTGGTATTTTTAATTTTT--TG
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chr7                57270118 70 + 158821424 ----GGACTACCGA-CT---ATC-ACCCTA----TTAACCAG-TCACGGGAGCA--CTGTCACA-CATTTGGTATTTTTAACTTTT--G-
+i hg18.chr7               N 0 I 2
+s panTro2.chrM                15984 61 +     16554 ----GGATCACAGGTCT---ATC-ACCCTA----TTAACCAG-TCACGGGAGC---CTTCCATG-CATTTGGTATTTT------------
+i panTro2.chrM            I 1 n 1
+s rheMac2.chr3             59792430 70 + 196418989 ----GGACGAGTGA-CT---CTC-ACCCTA----TTAACCAG-TCACAGGAGCA--CTGTCATG-CATTTGGTATTTTTAACTTTT--G-
+i rheMac2.chr3            C 0 N 0
+s canFam2.chrM                15860 69 +     16727 ----GGACTAATGA-CT--AATC-AGCCCA-----TGATCAC-ACATAACTGTG--GTGTCATG-CATCTGGTATCTTTTAATTTT----
+i canFam2.chrM            C 0 N 0
+s dasNov1.scaffold_23239       2668 72 -     16977 ----GGACTTATGC-CA--TATT-AAACCG-----TGACCTT-GCATCCCCTTA-TCTGTCATA-CATTTGGTACCTTTTTTTTTG--GG
+i dasNov1.scaffold_23239  C 0 N 0
+s loxAfr1.scaffold_36650       2067 70 +     16266 ----GGATTAATGA-CT--AATC-AGCCCA-----TGATCATAACATAACTGTG--GTGTCATG-CATTTGGTATCTTTTTAATTT----
+i loxAfr1.scaffold_36650  C 0 N 0
+s echTel1.scaffold_181343     15229 74 +     18297 ----GGGTTAATGT-CT--AATCAAGCCCA-----TGCTCAC-ACATAACTGTG--GTGTCATG-CAGTTGGTATTTTTTTAATTTTTAG
+i echTel1.scaffold_181343 C 0 I 1
+s monDom4.chrUn           117167402 74 + 174229318 ----GTTTCGTTTA-CT--GTTT-GCCTCA-----TAATCGCGGCATCAGTTGAACTCAACAGG-CATGGGGTGGATTTTTTTTTG--GG
+i monDom4.chrUn           I 3 N 0
+s fr1.chrUn               320906695 83 + 349519338 GGTGGAGTTCATCA-GTGAGATA-ATCCCACATGCCGAGCGT-TCTCTCCACGG--GGGTCAGGTTATTTTTTCTCTCTTTCCTTT--CA
+i fr1.chrUn               C 0 C 0
+
+a score=-32971.000000
+s mm8.chrM                    15929 35 +     16299 C----CTACTT-------------------TCATCAACATAGCCGTC-AAGG--CATGAAA
+s rn4.chrM                    15908 34 +     16300 G----ATGCCT-------------------TCCTCAACATAGCCGTC-AAGG--CATG-AA
+i rn4.chrM                C 0 C 0
+s oryCun1.scaffold_140182     16216 40 +     20791 GG-TTATGCTT------------------GGACTCAACATGGCCGCG-GTGGGCCCTG-AC
+i oryCun1.scaffold_140182 C 0 C 0
+s hg18.chr7                57270190 31 + 158821424 ----GATGCTA------------------TCATTCACCATCACAG---AAGG--CCTG---
+i hg18.chr7               I 2 N 0
+s panTro2.chr2a            84667818 30 + 114460064 ----GA-GCTG------------------TGACTCAGCATGGGGG---AA-G--CCTGA--
+i panTro2.chr2a           I 313 I 4
+s rheMac2.chrX            101422069 32 + 153947521 ----GATGATG------------------TGATCCAACATGGCTGTC-AAGG--CCT----
+i rheMac2.chrX            N 0 C 0
+s echTel1.scaffold_181343     15304 35 +     18297 ----GATGCTG------------------TGATCCAACTAGGCCGTCTGAGG--CCTTA--
+i echTel1.scaffold_181343 I 1 I 4
+s fr1.chrUn               320906778 40 + 349519338 -ATTGACATTTCAGAGTGCAGCGCGTCAATGGTTCATCAAG--------------------
+i fr1.chrUn               C 0 C 0
+
+a score=-27643.000000
+s mm8.chrM                    15964 108 +     16299 GGACAGCACAC-AGTCTAGAC--GCACC-TACGGTGAAGAATCATT-----AGTCCGCAAAACCCAATCA----------CCTAAGGCTA-ATTA----TTCATGCTTGTT-----AGACATAAATGCTACTCAATA
+s echTel1.scaffold_181343     15343 105 +     18297 AGTCAAGTCT--ATTGTAGCT--GGACT-TCAATTGAAATATCCTT-----AATCCACATAA--ACATGA----------ATGTTAATTATTTAA----TTAATGCTTGTT-----AGACATAAA-GAGAAATCATA
+i echTel1.scaffold_181343 I 4 N 0
+s rheMac2.chrX            101422101  94 + 153947521 TGACAAAACTTGACTGTAGCT--GAACT-TAAATTGAAT-GTTATT-----TTCCCAAGTAA--AAACCA----------TAAGGTGTTAATTAA----TCTATGCTCAAT-----GGACATAA-------------
+i rheMac2.chrX            C 0 I 33
+s panTro2.chr2a            84667852  92 + 114460064 TGCCTAATCC--ATTGTAACT--GAACT-TACATTGAAT-ATTCCG-----GACTCACATAA--CAACCA----------TAAGGTTTTAATTAA----TTCATGCTTGAA-----GGACATAA-------------
+i panTro2.chr2a           I 4 N 0
+s hg18.chrX               101950202  94 + 154913754 TGACAAAACTTGACTGTAGTT--GAACT-TAAATTGAAT-GTTATT-----TTCCCAAACAA--AAACGA----------TAAGGTGTTAATTAA----TCCATGCTCAAT-----GGGCATAA-------------
+i hg18.chrX               N 0 N 0
+s oryCun1.scaffold_140182     16256  93 +     20791 CCGGGACACTT-ATTGTAGAC--GAGCA-CCTAATGAAG-ACCCTC-----CATCCTCATAATTATGAGC----------CGGGACATTCTTTTA-------ATGCTTGTC-----GGACATAAA------------
+i oryCun1.scaffold_140182 C 0 N 0
+s rn4.chrM                    15942 110 +     16300 GGTCAGCACAA-AGTCCTGTG--GAACCTTTTAGTTAAGGGTCATT-----TATCCTCATAGACAAAGCT----------CGAAAGACTATTTTA----TTCATGTTTGTA-----AGACATAAATATTTATAAATA
+i rn4.chrM                C 0 C 0
+s monDom4.chr4            336353929  99 + 430141050 -------------ATATAATCTAGGACC-TAACATAAAGTGCTGTTCTCAGAGTTCATGCAATTAAATGA------------GGATATTATATAA-------ATGATTTTA-----AGACATATTATATTATTAGAA
+i monDom4.chr4            N 0 C 0
+s fr1.chrUn               320906818  94 + 349519338 ------------------GTT--GAACA-TTT--------TTTCTT-----GGTTTACGGAA--ATGTTAATTAATGAATTAAGACATTATTTAAGAATTACATTATTGATATCAAGGACATAAATAATA-------
+i fr1.chrUn               C 0 C 0
+
+a score=-35064.000000
+s mm8.chrM                    16072 38 +     16299 CCA---------AATTTTAACTC-------T-----CCAAACCCCCC-----------ACCCCCTCCTC--------T
+s rn4.chrM                    16052 47 +     16300 CTG---------AA----AAATC-------TGTCAACAAACCCCCCC-----------ACCCCCTACACCTGAAACTT
+i rn4.chrM                C 0 C 0
+s hg18.chr8                77619431 34 - 146274826 CCA---------AT---TAAATC-------T-----GCAAGCCCCC------------ATCTCTGACTT--------T
+i hg18.chr8               N 0 I 14
+s panTro2.chr8             79213306 34 - 145085868 CCA---------AT---TAAATC-------T-----GCAAGCCCCC------------ATCTCTGACTT--------T
+i panTro2.chr8            N 0 I 14
+s rheMac2.chrX            101422228 47 + 153947521 CCATCATACATGAT---TAACTC-------T-----GCAAACTCCCT--------CTGATCCCCTACTT--------T
+i rheMac2.chrX            I 33 N 0
+s monDom4.chr4            336354028 47 + 430141050 -----TTAACACAT----ATATA-------T-----GTATATGCACTATTAAAAGATTATCATTTAAT----------
+i monDom4.chr4            C 0 C 0
+s echTel1.scaffold_123517       890 23 +      1275 ------------------AACTC-------C-----CCTACCCCCCT-----------ATTACT--------------
+i echTel1.scaffold_123517 N 0 C 0
+s fr1.chrUn               320906912 38 + 349519338 --------------ATACGATTCAACATCAT-----ACAATTTCACC-----------CCCTTCTTCT----------
+i fr1.chrUn               C 0 C 0
+
+a score=-19675.000000
+s mm8.chrM                    16110 54 +     16299 TAA-------------------------TGCCAAAC---CCCAAAAACACTAA-GAACTTGAAAGACATATAATATTAA-CTAT
+s rn4.chrM                    16099 54 +     16300 CAA-------------------------TGCCAAAC---CCCAAAAACATTAA--AGCAAGAATTAAATAAAACAAAAAGCTAC
+i rn4.chrM                C 0 C 0
+s hg18.chr8                77619479 61 - 146274826 TAA---------------ACATAC-TCTTGCCAAAC---CCCAAAAACAAGA---GACTAAAATGCAACCCAGTTTTGA-TTAT
+i hg18.chr8               I 14 N 0
+s panTro2.chr8             79213354 61 - 145085868 TAA---------------ACATAC-TCTTGCCAAAC---CCCAAAAACAAGA---GACTAAAATGCAACCCAGTTTTGA-TTAT
+i panTro2.chr8            I 14 N 0
+s echTel1.scaffold_123517       913 69 +      1275 TAATGTTTAGA-----TAATATGCATCTTGCCAAAC---CCCAAAAACAA-----AACTTAAAATAAATACCCGATTAA-GTA-
+i echTel1.scaffold_123517 C 0 N 0
+s monDom4.chr4            336354075 53 + 430141050 TAA-------------------------TTTTAAGCTGACATTAAATCAATG---ATCTGAAGACATATATTTACATTA-TT--
+i monDom4.chr4            C 0 C 0
+s fr1.chrUn               320906950 67 + 349519338 ----TTTTAAAAAAATTAACGTATACCCCCCCTACCCCCCCTACAAATAGGAGAGACCTTTAAGTTTGGAC-------------
+i fr1.chrUn               C 0 C 0
+
+a score=-9447.000000
+s mm8.chrM         16164 97 +     16299 CAAACCCT--ATGTCCTGATCAATTCTAGTAG----TTCCCAAAA------------TATGACTTATATTTTAGTACTTGTAAAAATTT----TACAAAATCATGTTCCGTGAACCAAA
+s rn4.chrM         16153 87 +     16300 TTAATTCTTAAAAGGCTTCTCCATTCTAGTAG----ACCACAAAA-----------TTTTAACTTAAATCTTAGCATTGGTAAAATTTCCCGACACAAAATC-----------------
+i rn4.chrM     C 0 N 0
+s monDom4.chr4 336354128 90 + 430141050 --------------------CCACCCAGGTGA----TGGAAGCAAGCATGaatttataataatttatatattattaagtgaatataatt----taaagtat-atattCATTAAACCCAA
+i monDom4.chr4 C 0 N 0
+s fr1.chrUn    320907017 73 + 349519338 CAAGCTCT------------CCACttaattaaatattcatcatat-----------tattatcatatattataatattataataatat-----aattatat------------------
+i fr1.chrUn    C 0 N 0
+