bio-maf 0.2.0 → 0.3.0

data/spec/bio/maf/parser_spec.rb

@@ -3,121 +3,6 @@ require 'spec_helper'
 module Bio
   module MAF
 
-    describe Header do
-      before(:each) do
-        @p = Parser.new(TestData + 't1.maf')
-      end
-
-      it "provides version information" do
-        @p.header.version.should == '1'
-      end
-      it "provides the scoring scheme" do
-        @p.header.scoring.should == 'humor.v4'
-      end
-      it "provides alignment parameters" do
-        @p.header.alignment_params.should =~ /humor.v4 R=30/
-      end
-
-      it "presents multiline parameters correctly" do
-        @p.header.alignment_params.should == "humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf"
-      end
-
-      it "provides arbitrary parameters"
-    end
-
-    describe Block do
-      describe "#find_gaps" do
-        it "finds a single 14-base gap" do
-          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
-          p.sequence_filter = { :only_species => %w(mm8 rn4 hg18 canFam2 loxAfr1) }
-          block = p.parse_block
-          gaps = block.find_gaps
-          gaps.size.should == 1
-          gaps[0][0].should == 34
-          gaps[0][1].should == 14
-        end
-      end
-      describe "#remove_gaps!" do
-        it "removes a single 14-base gap" do
-          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
-          p.sequence_filter = { :only_species => %w(mm8 rn4 hg18 canFam2 loxAfr1) }
-          block = p.parse_block
-          block.sequences.size.should == 5
-          block.text_size.should == 54
-          block.remove_gaps!
-          block.text_size.should == 40
-        end
-      end
-    end
-
-    describe Sequence do
-      before(:each) do
-        @parser = DummyParser.new
-      end
-
-      describe "#gapped?" do
-        it "is false for sequences with no gaps" do
-          line = "s human_unc 9077 8 + 10998 ACAGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          s.gapped?.should be_false
-        end
-        it "is true for sequences with gaps" do
-          line = "s human_unc 9077 8 + 10998 AC-AGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          s.gapped?.should be_true
-        end
-      end
-
-      describe "#text_range" do
-        it "returns 0...text.size for a spanning interval" do
-          line = "s human_unc 9077 8 + 10998 ACAGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          range = s.text_range(9077...(9077 + 8))
-          range.should == (0...(s.text.size))
-        end
-        it "returns 0...text.size for a gapped spanning interval" do
-          line = "s human_unc 9077 8 + 10998 AC--AGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          range = s.text_range(9077...(9077 + 8))
-          range.should == (0...(s.text.size))
-        end
-        it "handles a leading subset" do
-          line = "s human_unc 9077 8 + 10998 ACAGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          range = s.text_range(9077...(9077 + 2))
-          range.should == (0...2)
-        end
-        it "handles a trailing subset" do
-          line = "s human_unc 9077 8 + 10998 ACAGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          range = s.text_range(9079...9085)
-          range.should == (2...8)
-        end
-        it "handles a gap in the middle" do
-          line = "s human_unc 9077 8 + 10998 AC--AGTATT"
-          s = @parser.parse_seq_line(line, nil)
-          range = s.text_range(9078...(9077 + 8))
-          range.should == (1...(s.text.size))
-        end
-        it "errors on a range starting before" do
-          expect {
-            line = "s human_unc 9077 8 + 10998 ACAGTATT"
-            s = @parser.parse_seq_line(line, nil)
-            range = s.text_range(9076...(9077 + 8))
-          }.to raise_error
-        end
-        it "errors on a range ending after" do
-          expect {
-            line = "s human_unc 9077 8 + 10998 ACAGTATT"
-            s = @parser.parse_seq_line(line, nil)
-            range = s.text_range(9076...(9077 + 9))
-          }.to raise_error
-        end
-
-      end
-
-    end
-
     describe ParseContext do
       it "tracks the last block position"
     end
@@ -247,6 +132,20 @@ module Bio
             blocks = @p.fetch_blocks(fl).to_a
             blocks.size.should == 2
             blocks.collect {|b| b.offset}.should == [16, 3011]
+          end 
+          it "does not return empty blocks" do
+            fl = [[16, 1087]]
+            @p.sequence_filter = { :only_species => %w(jabberwocky unicorn) }
+            blocks = @p.fetch_blocks(fl).to_a
+            blocks.size.should == 0
+          end
+         it "takes a block argument" do
+            fl = [[16, 1087], [1103, 1908], [3011, 2027]]
+            n = 0
+            @p.fetch_blocks(fl) do |block|
+              n += 1
+            end
+            n.should == 3
           end
         end
         context "with 4K chunk size" do
@@ -287,6 +186,13 @@ module Bio
         end
       end
 
+      describe "#each_block" do
+        it "returns an Enumerator when called without a block" do
+          p = described_class.new(TestData + 'mm8_chr7_tiny.maf')
+          p.each_block.count.should == 8
+        end
+      end
+
       describe "sequence_filter" do
         before(:each) do
           @p = described_class.new(TestData + 'mm8_mod_a.maf')
@@ -309,6 +215,10 @@ module Bio
           }
           @p.parse_block.filtered?.should be_false
         end
+        it "does not return empty blocks" do
+          @p.sequence_filter = { :only_species => %w(jabberwocky unicorn) }
+          @p.parse_blocks.count.should == 0
+        end
       end
 
       context "at end of file" do
@@ -450,6 +360,56 @@ module Bio
         end
       end
 
+      describe ":join_blocks" do
+        it "returns joined blocks" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf',
+                         :join_blocks => true)
+          p.sequence_filter = {
+            :only_species => %w(mm8 rn4 oryCun1 hg18 panTro2 rheMac2 canFam2 loxAfr1 echTel1)
+          }
+          idx = KyotoIndex.open(TestData + "mm8_chr7_tiny.kct")
+          l = idx.find([GenomicInterval.zero_based('mm8.chr7',
+                                                   80082334,
+                                                   80082471)],
+                       p).to_a
+          l.size.should == 1
+          l.first.text_size.should == 210
+        end
+      end
+
+      describe ":remove_gaps" do
+        it "removes gaps from #parse_blocks" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf',
+                         :remove_gaps => true)
+          p.sequence_filter = { :only_species => %w(mm8 rn4) }
+          b = p.parse_blocks.first
+          b.text_size.should == 34
+        end
+        it "removes gaps from #parse_block" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf',
+                         :remove_gaps => true)
+          p.sequence_filter = { :only_species => %w(mm8 rn4) }
+          b = p.parse_block
+          b.text_size.should == 34
+        end
+      end
+
+      describe ":as_bio_alignment" do
+        it "returns bio-alignment objects" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf',
+                         :as_bio_alignment => true)
+          idx = KyotoIndex.open(TestData + "mm8_chr7_tiny.kct")
+          l = idx.find([GenomicInterval.zero_based('mm8.chr7',
+                                                   80082334,
+                                                   80082471)],
+                       p).to_a
+          l.size.should == 2
+          l.first[0][0].should == 'G'
+          l.first[0].id.should == 'mm8.chr7'
+        end
+      end
+
+
     end
 
   end

data/spec/bio/maf/tiler_spec.rb

@@ -4,6 +4,47 @@ module Bio::MAF
 
   describe Tiler do
 
+    describe "#reference=" do
+      it "takes a FASTARangeReader" do
+        t = Tiler.new
+        t.reference = FASTARangeReader.new((TestData + 'gap-sp1.fa').to_s)
+        t.reference.read_interval(0, 3).should == 'CCA'
+      end
+      it "takes an open file" do
+        (TestData + 'gap-sp1.fa').open do |fh|
+          t = Tiler.new
+          t.reference = fh
+          t.reference.read_interval(0, 3).should == 'CCA'
+        end
+      end
+      it "takes a FASTA literal" do
+        ref = File.read(TestData + 'gap-sp1.fa')
+        t = Tiler.new
+        t.reference = ref
+        t.reference.read_interval(0, 3).should == 'CCA'
+      end
+      it "takes a Pathname" do
+        t = Tiler.new
+        t.reference = TestData + 'gap-sp1.fa'
+        t.reference.read_interval(0, 3).should == 'CCA'
+      end
+      it "takes a path string" do
+        t = Tiler.new
+        t.reference = (TestData + 'gap-sp1.fa').to_s
+        t.reference.read_interval(0, 3).should == 'CCA'
+      end
+      it "takes a gzipped Pathname" do
+        t = Tiler.new
+        t.reference = TestData + 'gap-sp1.fa.gz'
+        t.reference.read_interval(0, 3).should == 'CCA'
+      end
+      it "takes a gzipped path string" do
+        t = Tiler.new
+        t.reference = (TestData + 'gap-sp1.fa.gz').to_s
+        t.reference.read_interval(0, 3).should == 'CCA'
+      end
+    end
+
     describe "#runs" do
       it "returns a uniform run properly" do
         a = Array.new(10, 'a')
@@ -57,6 +98,9 @@ module Bio::MAF
       it "returns the entire sequence" do
         check_range(0, 50)
       end
+      it "returns a sub-line fragment" do
+        check_range(0, 4)
+      end
       it "returns an entire line" do
         check_range(10, 20)
       end

data/test/data/chr22_ieq2.maf

@@ -0,0 +1,11 @@
+##maf version=1 scoring=autoMZ.v1
+a score=13668.000000
+s hg19.chr22              16054189 54 + 51304566 TCTGTGAAACCCACAGTAATGGGGCTGACATCCTCTGCCCTATGCAAGAGAGGT
+s ponAbe2.chrUn           13354616 54 + 72422247 TCTTTCAAACCCACAGTAATGGGGCTGACATCCTCTACCATATGCAAGAGAGGT
+q ponAbe2.chrUn                                  855489998999999899968899889893997969799999879999999989
+i ponAbe2.chrUn           N 0 C 0
+s panTro2.chrUn            7684562 54 + 58616431 TCTGTGAAACCCACAGTAATGGGGCTGACATCCTCTGCCCTATGCAAGAGAGAT
+q panTro2.chrUn                                  999999999999999999999999999999999999999999999999999999
+i panTro2.chrUn           C 0 I 146
+e turTru1.scaffold_109008    25049 1601 +    50103 I
+

data/test/data/gap-1.maf

@@ -0,0 +1,9 @@
+##maf version=1
+a score=20.0
+s sp1.chr1        10 13 +      50 GGGCTGAGGGC--AG
+s sp2.chr5     53010 13 +   65536 GGGCTGACGGC--AG
+s sp3.chr2     33010 15 +   65536 AGGTTTAGGGCAGAG
+
+a score=21.0
+s sp1.chr1        30 10 +      50 AGGGCGGTCC
+s sp2.chr5     53030 10 +   65536 AGGGCGGTGC

data/test/data/gap-filled1.fa

@@ -0,0 +1,6 @@
+>sp1
+CCAGGATGCTGGGCTGAGGGC--AGTTGTGTCAGGGCGGTCCGGTGCAGGCA
+>sp2
+**********GGGCTGACGGC--AG*******AGGGCGGTGC**********
+>sp3
+**********AGGTTTAGGGCAGAG***************************

data/test/data/mm8_chr7_tiny_slice1.maf

@@ -0,0 +1,9 @@
+##maf version=1
+a score=10542.0
+s mm8.chr7                 80082350 18 + 145134094 TGGAGGGCGGTCCCAGCA
+s rn4.chr1                136011801 18 + 267910886 CGGAGGGCGGTCCCAGCA
+
+a score=-33148.0
+s mm8.chr7                 80082368 12 + 145134094 TGAGAGGGCATG
+s rn4.chr1                136011819 12 + 267910886 TGAGAGGGCATG
+

data/test/data/mm8_chr7_tiny_slice2.maf

@@ -0,0 +1,10 @@
+##maf version=1
+a score=30120.0
+s mm8.chr7                 80082718 10 + 145134094 CAAAGGCAGC 
+s rn4.chr1                136012152 10 + 267910886 CAGAGGCAGC 
+s hg18.chr15               88557993 10 + 100338915 CTGAACCAGC 
+s panTro2.chr15            87960238 10 + 100063422 CTGAACCAGC 
+s rheMac2.chr7             69865091 10 + 169801366 CTGAACCAGC 
+s canFam2.chr3             56030954 10 +  94715083 TTGACCCAGC 
+s echTel1.scaffold_304651       922 10 -     10007 TCCATCCCAC 
+

data/test/data/mm8_chr7_tiny_slice3.maf

@@ -0,0 +1,10 @@
+##maf version=1
+a score=30120.0
+s mm8.chr7                 80082757 10 + 145134094 AAGAGATAAA 
+s rn4.chr1                136012191 10 + 267910886 AAGAGATAAA 
+s hg18.chr15               88558033 10 + 100338915 AAAAGATAAG 
+s panTro2.chr15            87960278 10 + 100063422 AAAAGATAAG 
+s rheMac2.chr7             69865131 10 + 169801366 AAAAGATGAG 
+s canFam2.chr3             56030983  6 +  94715083 ACAA----AG 
+s echTel1.scaffold_304651       962 10 -     10007 AAAAGATAAA 
+

data/test/data/mm8_chrM_tiny.maf

@@ -0,0 +1,1000 @@
+##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
+