Multiz Alignments of 30 Vertebrates
 

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Alignment block 1 of 255 in window, 57795963 - 57795973, 11 bps 
B D          Mouse  gtcctgtgc-----tc
B D            Dog  -cctcgagc-caggca
B D            Cat  -cccctcgcacaggca
B D          Horse  --cgctcgc-------
B D       Hedgehog  accgtgcgc-----tc
B D          Shrew  tccttcggc-----tc
B D     Tree shrew  gccgtgcgc-----ta
          Bushbaby  gctgtgcgc-----tc
B D       Marmoset  gcagtgccc-----tc
B D         Rhesus  gcggtgcgt-----tc
B D      Orangutan  gctgtgcgc-----ta
B D          Chimp  gctgtgcgc-----ta
B D          Human  gctgtgcgc-----ta
            Rabbit  ----------------
        Guinea pig  gcc-------------
B D            Rat  gtcttgtgt-----tc
B D            Cow  ================
B D         Tenrec  ================
        Armadillo  ================
         Elephant  ================
B D    Stickleback  ================
B D      Zebrafish  ================
B D  X. tropicalis  ================
B D       Platypus  ================
B D        Opossum  ================
B D        Chicken  ================
B D         Lizard  ================

Alignment block 2 of 255 in window, 57795974 - 57796014, 41 bps 
B D          Mouse  -ctctttagtctggt--------------------------------tttttaatttttttttcctcact
B D            Rat  ----tttagtctgct--------------------------------tttcaaagttctt---ccttcca
        Guinea pig  --------------------------------------------------tgagtttccc---cggcaca
            Rabbit  ------------------------------------------------------------------caca
B D          Human  -gcgttagccgcctg--------------------------------tggttcagttcc----ccgcaca
B D          Chimp  -gcgttagccgcctg--------------------------------tggttcagttcc----ccgcaca
B D      Orangutan  -gcattagccgtctg--------------------------------tggttcagttcc----ccgaaca
B D         Rhesus  -gcgttagccgcctg--------------------------------tggttcagttcc----ctgcaca
B D       Marmoset  -gcgttagcctcctg--------------------------------tggttcagttcc----cggcaca
          Bushbaby  -gcgttagcggtgcg--------------------------------tggctccattct----ccgcatg
B D     Tree shrew  -gctttcgctgcgtg--------------------------------tggttactttct----ccgcaca
B D          Shrew  -accttcgaccgcttggtgcactagcttttagccactcaagg----tcggttatgtcca----ctgcac-
B D       Hedgehog  -gctttagccggctgaa---aataactttaagtaacttaaagaaactcggctacacact----c------
B D          Horse  ----tttggccgcgtg-------------------------------tggttacactct----ctgcac-
B D            Cat  -atcgtcgaccccttg-------------------------------tgcgtaacttct----cggcgc-
B D            Dog  -atcttcga--tgttgg------------------ctgggag----ctgcttaacttct----ccgcga-
         Armadillo  cgttttagtcatgtg--------------------------------tggctaagttct----ccgcaca
B D            Cow  ======================================================================
B D         Tenrec  ======================================================================
         Elephant  ======================================================================
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  -----gcac
               Rat  -----gcat
        Guinea pig  -----ggat
            Rabbit  -----ccgt
             Human  -----cggc
             Chimp  -----cggc
         Orangutan  -----cgtc
            Rhesus  -----cggc
          Marmoset  -----cggc
          Bushbaby  -----ctgt
        Tree shrew  ccgcgcagc
             Shrew  ---------
          Hedgehog  ---------
             Horse  ---------
               Cat  ---------
               Dog  ---------
         Armadillo  -----tggc
               Cow  =========
            Tenrec  =========
          Elephant  =========
       Stickleback  =========
         Zebrafish  =========
     X. tropicalis  =========
          Platypus  =========
           Opossum  =========
           Chicken  =========
            Lizard  =========

Inserts between block 2 and 3 in window
B D         Shrew 4bp
B D      Hedgehog 3bp
B D         Horse 7bp
B D           Cat 7bp
B D           Dog 7bp

Alignment block 3 of 255 in window, 57796015 - 57796220, 206 bps 
B D          Mouse  ctggcct-ctgctaggatcctgc-ttgac--t-gaggtttagcccctcactgc-----------------
B D            Rat  ccggctt-ctgcgaggatcctgc-ttggc--c-aaggtttagcctctcacggg-----------------
        Guinea pig  gcggcctcctgcctagatcctgc-gttgc--t-aagcgctgg-cttgcgctcc-----------------
            Rabbit  gcggtc--ctgccttgagcccgt-atggc--c-tcagcttggacaagcctggc-----------------
B D          Human  gtggccc-gtgcctcgagcctgt-gtggc--t-agtggttggccggtccacct-----------------
B D          Chimp  gtggccc-gtgcctcgagcctgt-gtggc--t-agtggttggccggtccacct-----------------
B D      Orangutan  gtggccc-ctgactcgagcctgc-gtggt--t-agtggttggccggtccatct-----------------
B D         Rhesus  gtggccc-ctgcctcgagcctgt-gtggc--t-agtggttagccggtccacct-----------------
B D       Marmoset  gtggccc-ctaccttgagcctgc-gtggc--t-agtggttggccagtccacctg----------------
          Bushbaby  gtgaccc-cgccctc-agcctga-gtggc--taaggggctggctggcgctccca-gacgagccc-----a
B D     Tree shrew  gcggcta-ctgcctcgagcctgc-tcgac--t-aagggttgaccccacgatcctagacgagc--------
B D          Shrew  cctggcc-ctgctgggagcccaa-ggggc--t-atggttt-gacccgagtctttgattaaatca------
B D       Hedgehog  tgagccc-ctgcctggaccgtga-gctgc--t-ggggtttgggcctgagcttctggatgagtc-------
B D            Dog  gcggcca-cagcctggagcctgc-gtggc--t-agggtttgcctccgcgctctcgaatgaacccaccaga
B D            Cat  acggcca-gggactggagcctgt-gtggc--t-acggtttggccccgcgcttctggatgaccccatcaga
B D          Horse  --ggccc-gcgcgtcgaggatgc-gtggc--t-aagctttggctccacgctcctgcatgaaccccctaga
B D            Cow  ttggtgt-ccacttggaggtaacagtggcctc-catctctggctcc-tgctcgtg---------------
         Armadillo  atggtct-ctgcctcgagcctgc-gtggc--g-agcgacaggccca-cgttcctgtgtgaat--------
          Elephant  ------------------cctgc-ttggc--g-agggttcgccctg-agctcccggatgaac--------
B D         Tenrec  ======================================================================
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  -----------t---ggactaaccac------ttcgggcg-----gggtacgggaagg---agtctctt-
               Rat  -----------g---gcactaaccat------ttcggtcg-----gggtacgggaagg---agtatcct-
        Guinea pig  -----------a---ggactggccactggaggtccgcgcgaagctggctatagagtgg---acctccttg
            Rabbit  ----------aa---ggggcggccgc------gccagacc-----cgcagccagaggg---gtctcccg-
             Human  -----ggactgg---ggggtcgccgc------aggaagct-----ggcggtaggagga---acctccct-
             Chimp  -----ggactgg---ggggtcgccgc------aggaagct-----ggcggtaggagga---acctccct-
         Orangutan  -----ggactgg---ggggtcgccgc------aggaagct-----ggcggtaggagga---acctccct-
            Rhesus  -----gtaccgg---tgggccaccgc------aggaagtt-----ggcggtaggagga---acctccct-
          Marmoset  ----gggggtgg---ggggctgccgc------gggaagct-----ggcggtaggagga---gcctccct-
          Bushbaby  cggtgggggcgg---gggggcgccgc------gggaaacc-----tgcggctgcaggaccggcctcccc-
        Tree shrew  -----ccaatgg---agggacgccgc------aggaagtc-----cgattccggaggg---gcctctct-
             Shrew  ------tctggg---gagctagtcgc------ag-----------aatggggaagggg---ctctctac-
          Hedgehog  ----------------cagtagccgc------cgg----t-----acccgggaatggg----tctcctc-
               Dog  aactgcgttgggggcggggtagtccc------ag-----------gggcagcagaggg---gtctccac-
               Cat  ggctgcgttagg---aggctagtcac------gg-----------agacacaagaagg---gtcaccac-
             Horse  gactgctgtggg---gagctaggtgc------gg-----------gggcaggagaggg---gtctccac-
               Cow  ------tttagt---cgctcagtttc-----------------------------gtg---tccgactc-
         Armadillo  -----ccactgg---ggaa-caccgc------ggggagcc-----agccgcccaaggg----------c-
          Elephant  -----ttagtgg---ggggccgccgc------gggaagcc-----gagcgcaggaggg----------c-
            Tenrec  ======================================================================
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Opossum  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  -----------------------gtcc-----------ttacac------ctcaagcgcctcctccactc
               Rat  -----------------------gtcc-----------ttacac------cccaaggagagtctcc---t
        Guinea pig  ggcctcagtgggcgtcatcctgggcct-----------tcgcac------ctctggcccggcctctgctc
            Rabbit  -----------------------ggccggaacaacgg-ccgcgc------ctctggctcggcctgcccgc
             Human  -----------------------ggccttaacagtggcccccac------ctgtggctcgggctccccgc
             Chimp  -----------------------ggccttaacagtggcccccac------ctgtggctcgggctccccgc
         Orangutan  -----------------------ggccttaacagtggcccccac------ctgtggctcgggctccccgc
            Rhesus  -----------------------gaccttaacaggggcccccac------ctgttgcttgggctccccgc
          Marmoset  -----------------------ggccttaacagtggccctcac------ctgtggctcgggctccccgt
          Bushbaby  ------------------------actttaacaacagcccccca------ccttggctctgctgccaggc
        Tree shrew  -----------------------ggccttaatagtggtccccac------ttctagtttggcagaccctg
             Shrew  ------------------ctagctgtt---acaat-gcatccat------ctatgactct-ttacccccc
          Hedgehog  ------------------ctgacgaca---acagtggtctccac------ctctgg-----------ttc
               Dog  ------------------ctggcggtc---acagtggcctccac------ctctggctcggtctcccctt
               Cat  ------------------ctggcggtc---gcagtggcccccatctccggctcggtctct------ccta
             Horse  ------------------ctggcggta---acagtggcctccat------ctctggctgggtctccccta
               Cow  ------------------tttgcgacc-----------------------ctttggctaggtctccccta
         Armadillo  --------------------------------------ccccac------ttcgggttcggcctcc----
          Elephant  --------------------------------------ccctgc------ctctggttcggactccccgt
            Tenrec  ======================================================================
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Opossum  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  gactt------------------------------------------c-tccccatcctga--gtgaact
               Rat  accct------------------------------------------t-tccccatccttt--gtgaact
        Guinea pig  agcctcctggtctctcc--cactggcccacctttccatatctgcgcgc-tcctcacttgga--gtagact
            Rabbit  aagctccaggtctccgc--gaccggcctaccttctcacacctgcgcgc-tcgcagcctaac--gcgccct
             Human  aacctcctggtttcttt--ggccggcctatcttctcacacctgcgctc-tcgccacctggc--atggact
             Chimp  aacctcctggtttcttt--ggccggcctatcttctcacacctgcgctc-tcgccacctggc--atggact
         Orangutan  aacctcttggtttctct--ggccggcctgtcttctcacacctgcgctc-tcgccacctggc--atggacc
            Rhesus  aacgtcctggtttctct--ggccggcctaccttctcacacctgcgctc-tcgccacctggc--atggact
          Marmoset  aacctcctggtttctct--ggcgggcctaccttctcacacctgcgctc-tctccacctggc--atggatt
          Bushbaby  cacctccaggtttcttc--ggcccgccagccttcttacacctgcgcttgtcaccagcccgg--attgacg
        Tree shrew  aacctc-tggtctctcc--aatgggcctactttctcacacctg---------------------tggact
             Shrew  aaactcctcacc--tct-----------cccttcttacacctgc-----------cctagtcaacgggct
          Hedgehog  tatttcctcgtc--tggaagaaaggcctaccttcttactcctgcgct--------cttggcacctggttt
               Dog  aacctcctggtc--tctcggatcggcctaccgact--cacctgcgctc-tagctacctagc--ataggct
               Cat  aacctcctggtctttcc--gaggggcctaccatctcacacctgtgctc-tcgccacctggc--ataggct
             Horse  aacctcctcgtccctcc-gagggggcctaccttctcatgtctgcgctc-tcgccacctggc---taggct
               Cow  ----ttctcatctctcc--aacgggcctaccttctcacacctgcgctc-tggtctctcggc--gtaggat
         Armadillo  -----ctgcgtctctcc--aa-----------------------------cacctcctggt--gtggcct
          Elephant  gacctccgcatctctcc--agtgggcctacctgtttacacctgcgctc-tcaccacctggc--gtggact
            Tenrec  ======================================================================
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Opossum  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  ggaaggagatagaatttgtgga-------------caagattctgacag-tcccc-aaaggtc--agcat
               Rat  gaaaggaggtagaatttgtgga-------------caagattctgacag-tcccc-aaaggtc--agcat
        Guinea pig  gaaaagaagtaa---ctgaggt-------------ccccact-tgacgc-ctcct-gaaggcc--cacag
            Rabbit  gaagggaggtggaaccagcgggtgac-cagagagccccgctcctgacag-ccctt-ggaggcc--tgcgg
             Human  gaagtgaggtagaatcggcaggtgacacaga----tcctctcctgacag-tcccc-agaggcc--cgcat
             Chimp  gaagtgaggtagaatcggcaggtgacacaga----tcctctcctgacag-tcccc-agaggcc--cgcat
         Orangutan  caagtgaggtagaatcggcaggtgacacaga----tcctctcctgacag-tcccc-agaggcc--cgcat
            Rhesus  gaagtgaggtagaatcggcaggtgacacaga----tcatctcctgacag-tcccc-agaggcc--cgcat
          Marmoset  gaagttaggtagaatcggcaggtgacacaga----ttctct------------cc-ggtggcc--ctctc
          Bushbaby  cgacgtagatagaatcttcgggcgaccaag-------ctctcttggcgg-ctggc-ggaggcc--tgcac
        Tree shrew  gaagtgaggtggaatcggctggtgacaaaga----a-ctctcctgacag-aaccc--gaggcc--tgcag
             Shrew  ggacagaggtagtacagtagcactgtagcac----tgctttcccgacag-tccat-ggaggcc--tcagt
          Hedgehog  ggagtgaagtggcataggtgggtgactgcgt----ggttcacctgccag-tccct-ggagacc--ttcat
               Dog  ggagtgaggtatcatcctcctgtaatagcgt----ccatctccggacag-cccca-ggaggcc--cgcag
               Cat  ggagtgaggtagcccctgccggtaatag-gt----tcttctccagacag-cccct-ggaggcc--cgcat
             Horse  ggagtgaggtaggatgggccggcaacaacat----tcctctccttgcagcccccc-ggagccc--tgcag
               Cow  gtagtgctgtaagatccgctggtaacagaca----tcctctcttgacaa-cctct-tgaagct--tgcct
         Armadillo  ggagtggggcagggtcggtaggtgccagcgc----tcctctcctggcag-ccctttcgaggctagcatat
          Elephant  ggcatggggtaggatcggccggtgatagcgc----tcccctcctgacag-cctcttggaagct--cgtat
            Tenrec  ======================================================================
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Opossum  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  gacaggtag
               Rat  gccagatag
        Guinea pig  ggcaggtta
            Rabbit  gaccggcca
             Human  gacagattt
             Chimp  gacagattt
         Orangutan  gacagattt
            Rhesus  gacagattt
          Marmoset  gacagattt
          Bushbaby  gacagatta
        Tree shrew  gtcagggta
             Shrew  gatacatta
          Hedgehog  gatgagtta
               Dog  gaccggcta
               Cat  gacgggcaa
             Horse  gacagacta
               Cow  gacaggcta
         Armadillo  aat----ca
          Elephant  gacagggtg
            Tenrec  =========
       Stickleback  =========
         Zebrafish  =========
     X. tropicalis  =========
          Platypus  =========
           Opossum  =========
           Chicken  =========
            Lizard  =========

Alignment block 4 of 255 in window, 57796221 - 57796278, 58 bps 
B D          Mouse  t--tctcagt-------------------catcc----------------------------ct------
          Elephant  t--cctaaga------------------------------------ccagtat---------ct------
         Armadillo  t--tctaaga------------------------------------ctccttt---------cc------
B D            Cow  t--tctaaga-------------------ac---cct---------caccatg---------gccaccat
B D          Horse  t--tctaaga-------------------ag---ccc---------ccttcca---------a-------
B D            Cat  t--tctaaga-------------------ac-cactg---------cccctcg-----------------
B D            Dog  t--tctaaga-------------------ataccccc---------ccccccg---------acacacac
B D       Hedgehog  t--tttaacacacacacacacacacacacacacactca----cacgcgccacg---------accacccc
B D          Shrew  -----------------------------agacactt-----------cgact---------tccatctg
B D     Tree shrew  t--tctaag--------------------cacctctc---------cacccccag-------gt------
          Bushbaby  t--gctaaga-------------------c--ctcgt--------gtccccca---------gt------
B D       Marmoset  t--gctaaga-------------------caactccc---------caccccc---------gt------
B D         Rhesus  t--gctaaga-------------------caactccc--------tcacccct---------gt------
B D      Orangutan  t--gctaaga-------------------caactccc--------tcacccct---------gt------
B D          Chimp  t--gctaaga-------------------caactccc--------tcacccct---------gt------
B D          Human  t--gctaaga-------------------caactccc--------tcacccct---------gt------
            Rabbit  t--tctgaga-------------------cgcccc-----------cagccca---------gt------
        Guinea pig  ttatttaaaa-------------------tacccc-----------ca--------------cc------
B D            Rat  t--tctcagt-------------------catcct-----------catgcccaggagctccct------
B D       Platypus  t--cctcggt-------------------gttccccaaagagccggggccctg---------gca-----
B D         Tenrec  ======================================================================
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  -----taagggt--cg-tgcc--a-cttgttctct---gagagctctaacct--ccaac
          Elephant  -----taaccggttgg-cgccc-a-cctcccacct---a-gattcttaactt-------
         Armadillo  -----taatgga--gg-cgcct-gccctcccgtcc---g-ga-----------------
               Cow  caa--agacggt--gg-cgctc-a-cctcccacct---a-gagttttaactt-------
             Horse  -----tgacggt--gg-cgccc-a-cctcccaccc---a-gagttttaactt-------
               Cat  -----taacggt--ggcccccc-a-cctcccacct---g-gagttttaactt-------
               Dog  acacctgacggt--gg-ccccc-a-cctctcacct---a-gagttctacctt-------
          Hedgehog  cga--agacggt--gg-tatcc-a-ccttccacttacaa-gagttttaactt-------
             Shrew  caa--ggacagt--gg-cggtc-a-tttctcacct---a-gagctttaactt-------
        Tree shrew  -----aaacagc--gg-cacttaa-attcccatct---a-gagtcttaattt-------
          Bushbaby  -----agacggt--gg-ctccc-g-cctcccaccc---a-gattcttaactt-------
          Marmoset  -----gcaccgt--gg-cgccc-g-cctcccactt---a-gggttttaactt-------
            Rhesus  -----gcacggt--gg-cg-cc-g-cctcccacct---a-tagtcttaactt-------
         Orangutan  -----gcacggt--gg-cgccc-g-cctcccacct---a-tagtcttaactt-------
             Chimp  -----gcacggt--gg-cgccc-g-cctcccacct---a-tagccttaactt-------
             Human  -----gcacggt--gg-cgccc-g-cctcccacct---a-tagccttaactt-------
            Rabbit  -----caacggc--gg-cgcc----cctgccacct---g-gagccctaactc-------
        Guinea pig  -----tatgtat--ac-tgcg--g-c--gcccccc---tccacccataatttaagcatc
               Rat  -----tgatggt--cg-tgccc-g-ctggctacct---tagagccctaacct--gtaat
          Platypus  -----atacggc--gg-cgccc-------------------------------------
            Tenrec  ===========================================================
       Stickleback  ===========================================================
         Zebrafish  ===========================================================
     X. tropicalis  ===========================================================
           Opossum  ===========================================================
           Chicken  ===========================================================
            Lizard  ===========================================================

Alignment block 5 of 255 in window, 57796279 - 57796324, 46 bps 
B D          Mouse  tttaattt-gacaaatt--catct---------------cttccccaaaagg------tgt-------cc
B D            Rat  ttcatttttgacaagtc--catct---------------cttccccaagagg------tgt-------cc
        Guinea pig  attaatta-gatagccc--tattt---------------ctt-cgcaagaag------tctcc---tccc
            Rabbit  --cgcttctgaggggtc--ggtcg---------------ttccctcaaagag------gaaccgggtctt
B D          Human  --caattctgagatgtc--catcg---------------ttccccggaggag------gtc-----tcct
B D          Chimp  --caattctgagatgtc--catcg---------------ttccccggaggag------gtc-----tcct
B D      Orangutan  --caattctgagacgtc--catcg---------------ttccccggaggag------gtc-----t-ct
B D         Rhesus  --caattctgagacgtc--catcg---------------ttccctagaggag------gtc-----tcct
B D       Marmoset  --caattctgagacgtc--catcg---------------ttcccctgaggag------gtc-----tcct
          Bushbaby  --taaagttgagacggc--cgtcc---------------ttcccccaaggagaagtccatc-----tcct
B D     Tree shrew  --gaattctgaga---------cg---------------ttcctccaaagag------gtc-----ttct
B D          Shrew  --caatttctaggcgtc--tgtca-----------gtccctctttctc--cg------ttc-----ccct
B D       Hedgehog  --ctattcctagacg-c--tgtct-----------ttagctcccccaa--at------atc-----tctt
B D            Dog  --cagttcggaggcgtc--tgttc-----------ccccctcccgcc---aa------gtt-----tcct
B D            Cat  --caattctgaggcatc--tgtcc-----------ctcctcccctcctagaa------gtc-----tctt
B D          Horse  --cagttctgagatgtc--cgttcctccccccccacccccccccccccataa------gtc-----tcct
B D            Cow  --aaattctgagatgtc--tgcct---------------tccccccagagaa------gcc-----ttct
         Armadillo  --------------gtg--gatga---------------accctccaaagag------ctc-----tcct
          Elephant  --caatcctgagacgtc--tgtca---------------tctccgtaaaagg------gtc-----tcct
B D        Opossum  ------tttgacccaacataattg---------------tttcctt------------ctc-----ttcc
B D       Platypus  -------------------------------------tttcatctcaacccg------atc-----tctt
B D         Tenrec  ======================================================================
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  tcggtct----
               Rat  tcggtct----
        Guinea pig  tcagccc----
            Rabbit  tgggccc----
             Human  cgggccc----
             Chimp  cgggccc----
         Orangutan  cgggccc----
            Rhesus  agggccc----
          Marmoset  cgggtcc----
          Bushbaby  t--cccc----
        Tree shrew  cag--cc----
             Shrew  tcg-ccc----
          Hedgehog  cag-ccc----
               Dog  caa-ctc----
               Cat  caa-ccc----
             Horse  cggtccc----
               Cow  cgg-ccc----
         Armadillo  cgc-ccc----
          Elephant  agt-ccc----
           Opossum  ttgttcc----
          Platypus  tcccctcatcc
            Tenrec  ===========
       Stickleback  ===========
         Zebrafish  ===========
     X. tropicalis  ===========
           Chicken  ===========
            Lizard  ===========

Inserts between block 5 and 6 in window
        Armadillo 1bp

Alignment block 6 of 255 in window, 57796325 - 57796397, 73 bps 
B D          Mouse  c--------------tacccacttaa--agttattcaaa-ccgag-accaa-agcttctgt----tcgct
B D       Platypus  --------------------------ctaaccgcccacagatagg-attaaatgatctcat----tggcc
B D        Opossum  c--------------tttccccataa---------------tctg-gtttaatattttaat----ttgac
B D         Tenrec  c--------------ttccccctcgg--agtcactc-----tcag-actaaacgctctcat----ttgct
          Elephant  c--------------ttcccctctgg--agtcagtcata-ttcgg-accgaacgctctcat----ttgct
         Armadillo  t--------------tttcactttag--agtcactgtta-ctcggaacaaaacgctttcat----ctgct
B D            Cow  c--------------ttctcccttca--agtctctcgta-ttcag-accaaaagctttcgt----ttgct
B D          Horse  c--------------ttcccccttcg--agtatctcata-agcgg-accaaacgctttcat----ttgct
B D            Cat  c--------------ttctcccttcg--agtctctcaaa-ttcag-accaaacgctttcat----ttgct
B D            Dog  c--------------ttcctcctt----agtctctc-ta-ttcag-actaaacgctttcat----ttgct
B D       Hedgehog  c--------------atccctctccac-agtctctcaaa-tttgg-atccaaggatgtcat----ttgct
B D          Shrew  tccaaatctcaggaggtttctctttag-tgtctctcata-ttcgg-accgacagattccat----ttgct
B D     Tree shrew  c--------------cttccccctcg--agt-----------cag-accaaacgctttcatttgcttgct
          Bushbaby  c--------------tttcctcttcg--agtcacccata-ttcag-actaaccgctttcat----ttgtt
B D       Marmoset  c--------------ttctcccttcg--aatcattcata-ctcag-ataagactctttcat----ttgtt
B D         Rhesus  c--------------ttctcccttcg--agtcattcata-ttcag-aacaaacgctttcat----ttgtt
B D      Orangutan  c--------------ttctcccttcg--agtcattcata-ttcag-accaaacgctttcat----ttttt
B D          Chimp  c--------------ttcccccttcg--agtcattcata-tgcag-accaaacgctttcat----ttgtt
B D          Human  c--------------ttctcccttcg--agtcattcaca-ttcag-accaaacgctttcat----ttgtt
            Rabbit  c--------------gtcccgtttgg--agtcactcgca-ttggg-gccacacactttcat----gtgct
        Guinea pig  c--------------taccctctttg--agttactcata-ttcag-accaaccgctttcct----ttgct
B D            Rat  c--------------tacccacttaa--agtcattcaaa-ccaag-accaa-agcttccgt----ttgct
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  tattcagcattttt--atcagcttgatt
          Platypus  tattcagcatattt--tcgggtttgatt
           Opossum  tattcaatatatat--tttgttttgatt
            Tenrec  tattcagcattttc--accagtctcatt
          Elephant  tactcagcattttt--accagtctgatt
         Armadillo  gattcagcattttttaccctgtctgatt
               Cow  tattcagcattttt--aagagcctgatt
             Horse  tattcagcattttt--atgagcctgatt
               Cat  tattcagcattttt--atcagcccgatt
               Dog  tattcagcattttt--atcagcctgatt
          Hedgehog  tattcagca-tttt--ctcagcctgatt
             Shrew  tattcagca-tttt--atcagcctgatt
        Tree shrew  tattcagcattttt--actagcttgatt
          Bushbaby  tattcagcattttt--accagcctgatt
          Marmoset  tattcagca-tttt--accagcctgatt
            Rhesus  tattcagca-tttt--accagcctgatt
         Orangutan  tattcagca-tttc--accagtctgatt
             Chimp  tattcagca-tttt--accagcctgatt
             Human  tattcagca-tttt--accagcctgatt
            Rabbit  tattcagcattttt--accggcccaatt
        Guinea pig  aattcagcatttta--accagacttatt
               Rat  tattcagcattttt--atcagcttgatt
       Stickleback  ============================
         Zebrafish  ============================
     X. tropicalis  ============================
           Chicken  ============================
            Lizard  ============================

Alignment block 7 of 255 in window, 57796398 - 57796560, 163 bps 
B D          Mouse  tt-gcactctgtttgcg--gcgcccc-tggga-agacgtcaaacactcttattc-attg-tatttagtca
B D        Chicken  tt-gctctttgcgtgcggcttaccgc-ctggc-aggtattacgcgggcgttgct-gttg-tggtagg--g
B D       Platypus  ttcaccgtcggtgggac--ttaccac-tggggcagatgttaaatattcatttcc-attg-tatttagcca
B D        Opossum  -----------tttgag--ttccaat-tgggc-tgatgttaaatattcatttcc-attgttatttagtaa
B D         Tenrec  tt-gctgtctgtttacg--ctgctcc-tggga-agatgtcaaacacccattttc-attg-tatttagtca
          Elephant  tt-gcagtctgtctacg--ctgccct-tggga-agatgtcaaacacccattttc-attg-tatttagtca
         Armadillo  tt-attgtctgtttgcg--cggccccttggga-agaagtcaaacaccca-tttc-attg-tatttagtca
B D            Cow  tt-g----ctgtttgcg--ctgcccc-tggga-aggtgtcaaacacctcttttc-attg-tatttagtca
B D          Horse  tt-gctgtctgtttgtg--ctgcccc-tggga-aggtgtcaaacacccattttc-attg-tatttagtca
B D            Cat  gt-gtcgtctgtttgcg--ctgctcc-tggga-aggtgtcaaactcccattttc-attg-tatttagtca
B D            Dog  tt-gttgtctgtttgcg--ctgccgc-cggaa-aggtgtcaaacatccattttc-attg-tatttagtca
B D       Hedgehog  tt-gctgcctgtttgcg--ctgcccc-cggga-aggtgtcaaacacctatttttgattg-tctttagtca
B D          Shrew  tt-tccgtctgtttgca--ctgcccc-ttgga-aggtgtcaaatgcccattttcaattg-tatttagtca
B D     Tree shrew  tt-gctgtctgtttgtg--ctgcccc-tggga-agatgtcaaacacccattttc-attg-tatttagtca
          Bushbaby  tt-gctgtctgtttgtg--tggctcc-tggga-tgatgtcaaacacccattttc-attg-tatttagtca
B D       Marmoset  tt-gctgtctttttgtg--tcgcttc-tggga-agatgtcaaacacccattttc-gtgg-tatttagtca
B D         Rhesus  tt-gctgtctttttgtg--cctcttc-tggga-agatgtcaaacacccattttc-attg-tatttagtca
B D      Orangutan  tt-gttgtctttttg-g--ccgcttc-tggga-agatgtcaaacacccattttc-attg-tatttagtca
B D          Chimp  tt-gctgtctttttgtg--ccgcttc-tggga-agatgtcaaacacccattttc-attg-tatttagtca
B D          Human  tt-gctgtctttttgtg--ccgcttc-tggga-agatgtcaaacacccattttc-attg-tatttagtca
            Rabbit  tt-gttgtctgtctgtg--cggccc---ggga-ggatgtcaaacccccattttc-cttg-tgttc-gtca
        Guinea pig  tg-gttgtgtatttgcg--ccggtcc-tggga-agatgtcaaacacccgttttc-tttg-tatttagtca
B D            Rat  tt-gtgat--gtttgag--gcgccct-tggga-agacgtcaaacactcctattc-attg-tatttagtca
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D         Lizard  ======================================================================

             Mouse  cccaggtgcggagccagccagaaacagacggcggaaggagtttccc-ggactgagctgtcactcaccg-g
           Chicken  accaggtgctgagcacgtccgcgagaggcagcggaaag-gccgccg-gccccgcgctgtccgtcatct-c
          Platypus  tccaggtgccgagcatgcctgcg-gagagaacggaaggagcttgcg-ggattttgctgtcggtcccag-t
           Opossum  tccaggtgcggagctctcctaaaagagagaacggaaggagttaccg-ggattatactgtctgttacca-t
            Tenrec  cccaggtgcagagcaa-tctgaaagagacaacggaaggagtttccc-ggcctgcgctgtcgctcaacg-g
          Elephant  cccaggtgcagagcaagtctgaaagagacaacggaaggagcttccc-ggacagcgctgtcgctcaacg-a
         Armadillo  cccaggtgcggagctagcccgagagagacagcggaaggagttcccc-gagccgcgctgctactcaccg-a
               Cow  cccaggtgcagagcgagattgagagagacagcggaagaactttccc-ggactgtgctgtcactcaacg-g
             Horse  cccaggtgccgagcaggcttgaaagagtcagcggaaggac-ttacc-ggaccgcactgtcgctcactg-g
               Cat  cccaggtgcagagcaagcttgaaagagacagcggaaggactttccc-ggactgcactgtcgctcagct-g
               Dog  cccaggtgcagagcaagcttgaaagagacagcggaagaactttccc-ggactgcactgtcgctcagca-g
          Hedgehog  cccaggtgcggggagagcctgccaaggacggcggaaggactttccc-cgacttcgctgtcgctcagcgcg
             Shrew  ctcaggtgcggagccagcctgaaagagacagcggaaggactttccc-ggactacagtgtcgctcagca-g
        Tree shrew  cccaggtgcggagcaagcctg--agagacagcggaaggagttgccc-ggattgggctgtcgctcacga-c
          Bushbaby  cccaggtggggagccagcccgaaagggacggcggaaggagtttccc-ggactgcgctgtcgctctccg-g
          Marmoset  cccaggtggggggccagcctgaaagagatagcggaaggagtttcct-ggactgccctgccgctcaccg-g
            Rhesus  cccaggtggggagccagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtagctcaccg-a
         Orangutan  cccaggtggggagccagcctgagagagacagcggaaggagtttcct-ggactgcgctgtcgctcactg-a
             Chimp  cccaggtggggagctagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtcgctcaccg-a
             Human  cccaggtggggagctagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtcgctcaccg-a
            Rabbit  ctcaggtgcggagacggaccgagagagacagcggaaggagtttccc-gggctgtgccgtcgctcaccg-t
        Guinea pig  tccaggtgcggagccagcctgaaaaagacagcggaaggaattttcc-ggactgcgctgccgctcacag-g
               Rat  cccaggtgcggagccagccagaaacagacggcggaaggagtttccccggactgagctgccactcaccg-g
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
            Lizard  ======================================================================

             Mouse  cctgcaccaattacaacgcagattgctcgcgg
           Chicken  ccgcggccactggcggggctgc----------
          Platypus  tttgcaccaatcgcaagggcgcctttccgtga
           Opossum  ctacagccaatctcaaagtcttcttctttgag
            Tenrec  ctcgtccctatcagcgcgcagattgccctggg
          Elephant  ctctcaccaatcgcagcacagagtgccctcgg
         Armadillo  gccgcaccaatcaccgcgcagctcgccctccg
               Cow  gccaaaccaatcatcacgcaggttgcctccgg
             Horse  cccgcaccaatcaccacgctgcttgtcctcgg
               Cat  gccgcaccaatcaccacgcagcttgccctcgg
               Dog  cccgcaccaatcaccacgcagcttgacctcgg
          Hedgehog  gccacaccaatcaccgcacggctggccctcgg
             Shrew  gtcacaccaatcggcgcacagtgtgccccagg
        Tree shrew  cctgctccaatcactacgctgcttgccctcag
          Bushbaby  atcgcaccaatcaacacgcagcttgcgcttgg
          Marmoset  cccgtaccaatcaccacgcagctcgccctcag
            Rhesus  cccgcaccaatcaccacgcagcttgccctcgg
         Orangutan  cccgcaccaatcaccacgcagcttgccctcgg
             Chimp  cccgcaccaatcaccatgcagcttgccctcgg
             Human  cccgcaccaatcaccatgcagcttgccctcgg
            Rabbit  cgggcgccaatcaacacgcagttttctctcgg
        Guinea pig  cctgcaccaatcaccaagcagttcgccctcgg
               Rat  cctgcaccaattacaacgcagattgcccgcgg
       Stickleback  ================================
         Zebrafish  ================================
     X. tropicalis  ================================
            Lizard  ================================

Inserts between block 7 and 8 in window
B D       Chicken 72bp

Alignment block 8 of 255 in window, 57796561 - 57796627, 67 bps 
B D          Mouse  gcccacctcttt-tggggtgtgtcacaagtgagtgatag-a--ctgagcc-gcccggccct-gctcagcc
B D            Rat  gcccacctcttt-tggggtgtgtcacaagtgagtgatag-a--ctgagcc-gcccggccct-acacagcc
        Guinea pig  gcccgcctcttt-aggggtgtgtccctagtgagtgatag-a--cagagccttcccggccca-gctcagcc
            Rabbit  gcccgcctctttggggggcgtgtccctagtgagtgatag-a--cggagcc-gcccggccct-gctcagcc
B D          Human  acccgccccttt-tagggcgtgtccccagtgagtgatag-a--cggagcc-gccctgccct-gctcagcc
B D          Chimp  acccgccccttt-tagggcgtgtccccagtgagtgatag-a--cggagcc-gccctgccct-gctcagcc
B D      Orangutan  acccgccccttt-tagggcgtgtccccagtgagtgatag-a--cggagcc-gccctgccct-gctcagcc
B D         Rhesus  acccgccccttt-tagggcgtgtccccagtgagtgatag-a--ctgagcc-gcccggcccc-gctcagcc
B D       Marmoset  gcccgcctcttt-gagggcgtgtccccagtgagtgatag-a--cggagcc-gcccggccct-gctcagcc
          Bushbaby  gcccgcctcttt-gggggcgcgtctctagtgagtgatag-a--ctgagcc-gcccggccct-gctcagcc
B D     Tree shrew  gcccgcctcttt-gggggcgtgtccctagtgagtgatag-a--cggagcc-gcccggccca-gatcagcc
B D          Shrew  gccctcctcttt-gtgggcgtgtccctagtgagtgatag-a--cggagcc-gcccggcccc-actcagcc
B D       Hedgehog  accctcctctccggggggcgtgtcgctcgtgagtgatag-a--cggagcc-gcccggcccc-gcgcagcc
B D            Dog  gccctcctcttt-gagggcgtgtccctggtgagtgatag-a--cggagcc-gcccggccca-gctcgggc
B D            Cat  accctcctcttt-gagggcgtgtccctggtgagtgattg-a--cggagcc-gcccggccca-gctcaggc
B D          Horse  accctcctcttt-gggggcgtgaccctaatgagtgatag-a--cggagtc-gcccggcccc-gctcagcc
B D            Cow  gccctcctcttt-gggggcgtgcccctagtgagtgatag-a--cggagcc-gcccggcccc-gctcagcc
         Armadillo  gcccgcctc-cc-gagggcgtgtccccagtgagtgatag-a--cggcgcc-gcccggcccc-gctcagcc
          Elephant  gcccgcctcttt-gggggcgtgtccctagtgagtgatag-a--cggagcc-gcccggcccc-gctcgacc
B D         Tenrec  gcccgcctcttt-gggggcgtgtccctagtgagtgatagcc--cgaagcc-gcccggccccgggtcaacc
B D        Opossum  tcccgcctcctt-gggggtgggccactagtgattgatag-g--cagagac-acccctccca-actcagcc
B D       Platypus  tcccgccttttt-gggggcgcggccctggtgactgatag-g--cagggtc-gcccggccca-gcccggcc
B D           Fugu  gctcacttcgtc-aggg--gtgtccttggtgtctggttg-gctctgggct-gcccggcggg-ccatggcg
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  cag
               Rat  cag
        Guinea pig  cag
            Rabbit  cag
             Human  cag
             Chimp  cag
         Orangutan  cag
            Rhesus  cag
          Marmoset  cag
          Bushbaby  cag
        Tree shrew  cag
             Shrew  cag
          Hedgehog  cag
               Dog  cag
               Cat  cag
             Horse  cag
               Cow  cag
         Armadillo  cag
          Elephant  cag
            Tenrec  cag
           Opossum  cag
          Platypus  cag
              Fugu  ccg
       Stickleback  ===
         Zebrafish  ===
     X. tropicalis  ===
           Chicken  ===
            Lizard  ===

Alignment block 9 of 255 in window, 57796628 - 57796685, 58 bps 
B D          Mouse  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcagcccggcacaga
B D            Rat  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcagccgggcacaga
        Guinea pig  cccacgttgctgc-tga-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
            Rabbit  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D          Human  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D          Chimp  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D      Orangutan  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D         Rhesus  cccacgttgctgc-tta-gattgaaatg-----cagaactcacgtctctttcatcggggcacaga
B D       Marmoset  cccacgttgcagc-tta-gattgaaatg-----cagaactcaagcctctttcaccggggcacaga
          Bushbaby  cccacgttgctgc-ttg-gattgaaatg-----cagagctcaagcctctttcatcggggcacaga
B D     Tree shrew  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D          Shrew  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D       Hedgehog  cccacgttgctgcttta-gattgaaatg-----cagaactcaagcctctttcatcagggcacaga
B D            Dog  cccacgttgctgc-tta-gattgaaatg-----cagaactctagcctctttcatcggggcacaga
B D            Cat  cccacgttgctgc-tta-gattgaaatg-----cagaactctagcctctttcatcggggcacaga
B D          Horse  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcggggcacaga
B D            Cow  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcagcggggcacaga
         Armadillo  cccacgctgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcagggcacgga
          Elephant  cccacgttgctgc-tta-gattgaaatg-----cagaactcaagcctctttcatcccggcacaga
B D         Tenrec  cccacgttgctgc-ttaggattgaaatg-----cagaactcaagcctctttcatccccgcacaga
B D        Opossum  cccactttactgc-tta-gattgaaatg-----cagaactcatacctctttcatcagggcacaga
B D       Platypus  cccacgttgctgc-ttg-gattgaaatg-----cagaactcaaacctctttcatcgggacacgga
B D        Chicken  cccacgttgcc-c-tga-ggttgaaatg-----cagaactcaaggctctctcgccgggaagtaga
B D           Fugu  gcccggatgttgc-tga-ggttgatctggcgctccgggggcgggccgcctcgaggctggccccga
B D    Stickleback  =================================================================
B D      Zebrafish  =================================================================
B D  X. tropicalis  =================================================================
B D         Lizard  =================================================================

Alignment block 10 of 255 in window, 57796686 - 57796713, 28 bps 
B D          Mouse  cttccttttactctttcc---tttggcac-tc--
B D            Rat  cttccttttactctttcc---tttggcac-tc--
        Guinea pig  cttctttttactctttcc---ttt-gcac-tc--
            Rabbit  cttccttttactccttcc---ttttgcac-tc--
B D          Human  cttccttttacttcttcc---ttttgccc-tc--
B D          Chimp  cttccttttacttcttcc---ttttgccc-tc--
B D      Orangutan  cttccttttacttcttcc---ttttgccc-tc--
B D         Rhesus  cttccttttacttcttcc---ttttgcac-tc--
B D       Marmoset  cttccttttacttcttcc---ttttgcac-tc--
          Bushbaby  cttccttttactccttcc---ttttgccc-tc--
B D     Tree shrew  cttccttctactccttcc---ttttgcac-tc--
B D          Shrew  cttccttttactctttcc---ttttgcac-tc--
B D       Hedgehog  cttccttttacttcttcc---tttagctc-tc--
B D            Dog  cttccttttactccttcc---ttctgctc-tc--
B D            Cat  cttccttttactccttcc---ttttgcac-tc--
B D          Horse  cttccttttactccttcc---ttttgcac-tc--
B D            Cow  cttccttttactccttcc---ttttgcac-tc--
         Armadillo  cttccttttactccttcc---tttcgtac-tc--
          Elephant  cttccttttactccttcc---ttttgcac-tc--
B D         Tenrec  cttccttttactccttcc---ttttgcacttc--
B D        Opossum  cttccttttattcctttc---tctttaag-tt--
B D       Platypus  cttcctttttctcctttcccactttacgt-c---
B D        Chicken  tttcctcgtagtcctttt---ttcctcgc-cccc
B D    Stickleback  ==================================
B D      Zebrafish  ==================================
B D  X. tropicalis  ==================================
B D         Lizard  ==================================

Inserts between block 10 and 11 in window
B D       Opossum 1bp

Alignment block 11 of 255 in window, 57796714 - 57796766, 53 bps 
B D          Mouse  ttgtcgcctcctcccgggaagaagc-caaggcaccctcggc---ttggagcag-------cgac
B D            Rat  ttgtcgcctcctcccggggagaagc-caaggcacccgcggc---ttggagcag-------cgac
            Rabbit  tcgccgcctcctcccggggagaagc-ggaggcaccggcggc---ccggggcag-------cgac
B D          Human  tcgcctcctcctcctgggaagaagc-ggaggcgccggcggtcggccgggatag-------caac
B D          Chimp  tcgcctcctcctcctgggaagaagc-ggaggggccggcggtcggccgggatag-------caac
B D      Orangutan  tcgcctcctcctcctgggaagaagc-ggaggcgccggcggtcggccgggatag-------caac
B D         Rhesus  tcgcctcctcctcctgggaagaatc-ggaggcgccggcggtccgcccgggtag-------caac
B D       Marmoset  tcgcctccacctcctgggaagaagc-ggaggcgccggcggc---tcggggtag-------caac
          Bushbaby  ttgcctcctcctcctgggaagaagc-ggaggcaccggcagc---ccggggtaa-------ccac
B D     Tree shrew  tcgccgcctcctcccggggagaagc-cgaggccccggcggc---cccgggcag-------cgac
B D          Shrew  tcgccgcctcctctcggggtgaagc-ggaggcaccggcggc---ccagagctg-------cgat
B D       Hedgehog  tcgccgcctcctcccgcggcgaagc-gga------ggcggc---cggggacag-------cggc
B D            Dog  tcgccgcctcctcccgggaagaagc-ggaggcaccggcggt---ccggggcag-------cggc
B D            Cat  tcgccgcctcctcccgggaagaagc-ggaggcaccggcggc---ccggggcag-------cgac
B D          Horse  tcgccgcctcctcctggggagaagc-ggaggcaccggcggc---ccggggcag-------cgac
B D            Cow  tcgccgcctcctccgggggagaagc-ggaggcaccggcggc---ccggggcag-------cagc
         Armadillo  tcgccgcctcctccccgggagaagc-agaggcaccggcggc---ccggggcac-------cgac
          Elephant  tcgccgcctcctctcggggagaagc-ggaggcaccggcggc---ccggggcaa-------ccat
B D         Tenrec  tcgccgcctcctctcggggagaagcgggaggcttcggcggc---ccagggcaa-------ttat
B D        Opossum  tttctgtctgctcctgggatcaatc-ggagggacccgtggc---cagagctagaggagacagaa
B D       Platypus  ctagagtctcctcc-ggggaaagca-ggagggaccggtggc---ccgggagac-------cggg
B D        Chicken  ctgctatctcctc--ggcggcaagc-agggag--------------------------------
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ================================================================
B D      Zebrafish  ================================================================
B D  X. tropicalis  ================================================================
B D         Lizard  ================================================================

Inserts between block 11 and 12 in window
B D       Chicken 913bp

Alignment block 12 of 255 in window, 57796767 - 57796834, 68 bps 
B D          Mouse  aggccgg------ctcagtgagaacaagaaaaaagtttc-----------tttctgggagtgcggaactg
B D       Platypus  ggggtggggggttgtcgccgaggcgccggtgaaagtttcttttttctttttttttgcaagccagga----
B D        Opossum  atatcga------agcactaaggagatagcgaaaatttg-----------ttcttggaattctagagtc-
B D         Tenrec  aggccggg----ttccactgaggccgtgcgaaaagtttc-----------tttctgggagaacagaactg
          Elephant  aggccgg------tccactgaggccgtgcgaaaagtatc-----------tttctgggagaacggaacag
         Armadillo  agaccgg------gccactgcggccgtgcgagaagtttc-----------cttctgggattgcggaactg
B D            Cow  acgacgg------gccactaaggccacacgaagagtttc-----------tttctgggagcgcggaactg
B D          Horse  aggccgg------gccactgaggccgtgagaaaagtttc-----------tctctgggagtgcggaactg
B D            Cat  gagccgg------gccactgaggctgtgcgaaaagttac-----------tttttgggagtgcggaactg
B D            Dog  aagccgg------gccactggggctgtgcgaaaagtttc-----------tttttgggagttcggaactg
B D       Hedgehog  cggacgg------gccaccgaggccgcgcagaaggtctc-----------tccctgggagcgcggagccg
B D          Shrew  agaccgg------gtcactgaggccgagcgaaaagtttc-----------tttctgggagtgtcgaactg
B D     Tree shrew  aggccgg------tccactgaggccgtgcgaaaagtttc-----------tttctgggagtgtggaactg
          Bushbaby  aggctgg------gccactgaggccacggtaaaagtttc-----------ttcctgggagtgcggaactg
B D       Marmoset  aggccgg------gccattgcggccctgcggaaagtttc-----------tgtctggttgtgcggaactg
B D         Rhesus  aggccgg------gccactgaggcggtgcggaaagtttc-----------tgtctgggagtgcggaactg
B D      Orangutan  aggccgg------gccgctgaggcggtgcggaaagtttc-----------cgtctgggagtgcggaactg
B D          Chimp  aggccgg------gccactgaggcggtgcggaaagtttc-----------tgtcttggagtgcggaactg
B D          Human  aggccgg------gccactgaggcggtgcggaaagtttc-----------tgtctgggagtgcggaactg
            Rabbit  aggccgg------gctaccgaggccgtgcgtcaagtttc-----------tttctggaagtgcgggac-a
B D            Rat  aggccgg------cccagtgagagcaaggaaaaagtttc-----------tttctgggagtgcggaactg
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  gggccgggttggtgt-
          Platypus  gggctccgcggagac-
           Opossum  ---tcttattggtgtc
            Tenrec  gagcccggttggtgt-
          Elephant  gggcccggttggtgt-
         Armadillo  gggccctgtcgctgt-
               Cow  gggcccggttggtgt-
             Horse  gggcccggtcggtgt-
               Cat  gggtcccgttggtgt-
               Dog  gggcccctttggtgt-
          Hedgehog  gggcgcggcgggtgt-
             Shrew  gggccccgtggctgt-
        Tree shrew  gagccgggttggtgt-
          Bushbaby  gggcccagttggtgt-
          Marmoset  gggccgggttggtgt-
            Rhesus  gggccgggttggtgt-
         Orangutan  ggtccgggttggtgt-
             Chimp  gggccgggttggtgt-
             Human  gggccgggttggtgt-
            Rabbit  gggccgggctggtgt-
               Rat  gggccgggttggtgt-
        Guinea pig  NNNNNNNNNNNNNNNN
       Stickleback  ================
         Zebrafish  ================
     X. tropicalis  ================
           Chicken  ================
            Lizard  ================

Alignment block 13 of 255 in window, 57796835 - 57796891, 57 bps 
B D          Mouse  actgctc-agagcaATGGgtgagtggctgatggggga-cgttg-tcagatccg-------a---------
B D            Rat  actgctc-ggagcaATGGgtgagtgactg-cggggga-cgttg-tcagaaccg-------a---------
            Rabbit  acggctc-ggagcaATGGgtgagtggctg-cgggggc-cgctg-tcagagcgg-------c---------
B D          Human  actgctc-ggagcaATGGgtgagtggcgg-cggggga-ctctg-tcagagccg-------ggaag-----
B D          Chimp  actgctc-ggagcaATGGgtgagtggcgg-cgggaga-ctctg-tcagagccg-------ggaag-----
B D      Orangutan  actgctc-ggagcaATGGgtgagtggcgg-cggggga-ctctg-tcagagccg-------ggaag-----
B D         Rhesus  actgctc-ggagcaATGGgtgagtggcgg-cggggga-ctctg-tcagagccg-------ggaag-----
B D       Marmoset  actgctc-ggagcaATGGgtgagtggcgg-tggaaga---ctg-tcggagccg-------cgaag-----
          Bushbaby  actgctc-ggagcaATGGgtgagtggcgg-cgggcga-ctctg-tcaaagccg-------tgaag-----
B D     Tree shrew  actgctc-ggagcaATGGgtgagtggcgg-cggggga-cgctg-tcagagcgg-------agaa------
B D          Shrew  actgctc-ggagcaATGGgtgagtggcgg-cggggac--gctg-tcagcgccg-------ggaag-----
B D       Hedgehog  cctgccc-ggagcgATGGgtgagcggcgg-cgagggc-ggctg-tcagcgcc------------g-----
B D            Dog  actgctc-ggagcaATGGgtgagtggcgg-cggggaa-cgctg-tcagagccg-------gggag-----
B D            Cat  actgctc-ggagcaATGGgtgagtggcgg-cggggga-cgctg-tcagagccg-------ggaag-----
B D          Horse  actgctc-ggagcaATGGgtgagtggcgg-cggggga-cgctg-tcagagtcg-------gcaag-----
B D            Cow  actgctc-ggagcaATGGgtgagtggcgg-cagggta-cgctg-tcagagccg-------ggaaa-----
         Armadillo  gctgctc-ggagcaATGGgtgagcggcgg-cggggga-cgctg-tcagagccc-------gggag-----
          Elephant  actgctc-ggagcaATGGgtgagtggcgg-cgaggga-cgctg-tcagagccggggaggagggag-----
B D         Tenrec  actgctt-ggagcaATGGttgagtggcgg-cggggga-cgctgttcagacccg-------ggcag-----
B D        Opossum  cccgctc-aaagcaATGGgtaagtggttg-c---------ctg-ttgtatccg-------cgaaatattc
B D       Platypus  cgtgctctggagctATGGgtgagtgggtg-c-------------ccgggagcg-----------------
B D           Fugu  actgcac-acaacaGGGCtgcagtggctg-cgagcatttgttg-tcaaataca-------aacaa-----
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  --------------ggaggg
               Rat  --------------ggaggg
            Rabbit  --------------ggcgga
             Human  --------------ggaggg
             Chimp  --------------ggaggg
         Orangutan  --------------ggaggg
            Rhesus  --------------ggaggg
          Marmoset  --------------ggaggg
          Bushbaby  --------------ggaggg
        Tree shrew  --------------ggaggg
             Shrew  --------------ggaggg
          Hedgehog  --------------ggcggg
               Dog  --------------ggaggg
               Cat  --------------ggaggg
             Horse  --------------ggaggg
               Cow  --------------ggaggg
         Armadillo  --------------ggaggg
          Elephant  --------------ggaggg
            Tenrec  --------------ggaggg
           Opossum  agtgctgtcagactgggtgt
          Platypus  --------------gggggc
              Fugu  --------------gg----
        Guinea pig  NNNNNNNNNNNNNNNNNNNN
       Stickleback  ====================
         Zebrafish  ====================
     X. tropicalis  ====================
           Chicken  ====================
            Lizard  ====================

Alignment block 14 of 255 in window, 57796892 - 57796925, 34 bps 
B D          Mouse  aggg------a--------gcgagca----ggcg----agggc------------------------tag
B D            Rat  aggg------a--------gcgagca----ggcg----agggc------------------------tag
            Rabbit  cg--------------------------------------------------------------------
B D          Human  aggg------a--------gcgagcg----ggcaagggaggga------------------------ggg
B D          Chimp  aggg------a--------gcgagcg----ggca----aggga------------------------ggg
B D      Orangutan  aggg------a--------gcgagcg----ggca----aggga------------------------ggg
B D         Rhesus  aggg------a--------gcgagcg----ggcgagggaggga------------------------ggg
B D       Marmoset  aggg------a--------gcgagcg----agag----aggga------------------------ggg
          Bushbaby  aggg------a--------gcgagcg----ggcg--------a------------------------ggg
B D     Tree shrew  aggg------a--------gcgagcg----ggag--------a------------------------ggg
B D          Shrew  aggg------a--------gagagcg----ggc--------ga------------------------ggg
B D       Hedgehog  aggg------a--------gggagcg----ggc--------gg------------------------gag
B D            Dog  aggg------a--------aggagaa----ggcg----aggga------------------------ggg
B D            Cat  aggg------a--------accacag----ggtg----aggga------------------------ggg
B D          Horse  aggg------a--------gcgagct----ggc--------ga------------------------ggg
B D            Cow  aggg------a--------gcgagcg----ggc--------ga------------------------ggg
         Armadillo  cggg------c--------gcgagcg----agcg----ggcga------------------------ggg
          Elephant  aggg------a--------gcgagcgagcgagcg----agcgagcgggcgggcgggcgggcgcgggaggg
B D         Tenrec  aggg------a--------gcgagcg-----gct----cgcga---------------------gaaagg
B D        Opossum  gggg------a--------aaaagtg----gcgg----ggggt------------------------ggg
B D       Platypus  aggg------gcacctcttgcgggct----gtc-----agaga------------------------gga
B D           Fugu  ----------g--------gtgggtg----ggca------gga------------------------aag
B D    Stickleback  agaaaataaag--------aagtgcg----agcg------gga------------------------ggg
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  agggagg-----gag
               Rat  agggagg-----gag
            Rabbit  ---------------
             Human  agggagg-----gag
             Chimp  agggagg-----gag
         Orangutan  agggagg-----gag
            Rhesus  agggagg-----gag
          Marmoset  agggagg-----gag
          Bushbaby  agggagg-----gcg
        Tree shrew  agggagg-----gag
             Shrew  agggagg-----gag
          Hedgehog  gcggagg-----g--
               Dog  agggagg-----gag
               Cat  agggagg-----gag
             Horse  agggagg-----gag
               Cow  agggagg--------
         Armadillo  aggga-------ggg
          Elephant  agggagggctc-ggg
            Tenrec  agggagggcgcgggg
           Opossum  ggggagg-----ag-
          Platypus  aagaggg-----g--
              Fugu  aggggg---------
       Stickleback  agtgac---------
        Guinea pig  NNNNNNNNNNNNNNN
         Zebrafish  ===============
     X. tropicalis  ===============
           Chicken  ===============
            Lizard  ===============

Inserts between block 14 and 15 in window
B D       Opossum 718bp
B D      Platypus 1bp

Alignment block 15 of 255 in window, 57796926 - 57797001, 76 bps 
B D          Mouse  ct----g--aggcgcgccacc----gcg------------ct--gtattgactcag-actg-cgtccgt-
B D            Rat  ct----g--aggcgcgccacc----gcg------------ct--ctattgactcag-accg-cgtcccta
            Rabbit  ----------ggcgttccgct----g--------------------attgactttg-ctcg--gttactg
B D          Human  cgcgagg--gcgcgcgccact----aggcgctc--acattct--ctattgactttg-ctcg-tgttccta
B D          Chimp  cgcgagg--gcgcgcgccact----aggcgctc--acattct--ctattgactttg-ctcg-tgttccta
B D      Orangutan  ctcgagg--gcgcgcgccact----aagcgctc--acattct--ctattgactttg-ctcg-tgttccta
B D         Rhesus  tgcgagg--gcgcgcgccact----aggcgctc--acattct--ctattgactttg-ctcg-tgttccta
B D       Marmoset  cgagagg--gcgcgcgccact----aagcgctc--acatttt--ctattgactttg-ctcg-tgttccta
          Bushbaby  cgcaagg--gcgcgcgccact----aagggctc--gcactcttcttattgactttg-ctcg-tgttccta
B D     Tree shrew  cgcgagg--gcgcgcgccacc----gagcgctc--acactctccttattgactttg-ctcg-tgttcgta
B D          Shrew  cgccagg--gcgcgcaccact----gagcgctc--gcactttacttattgactttg-ctcg-tgttccta
B D       Hedgehog  ----agg--gcgcgcacccct----gagcgctc--acacgctccttattgactttg-ctcg-tgttccta
B D            Dog  cgcgagg--gcgcgcaccgct----gagcgctc--acactcttcttattgactttg-ctcg-tgttccta
B D            Cat  agcgagg--gcgcgcaccact----gagcgctc--acactcttcttattgactttg-ctcg-tgtttcta
B D          Horse  cgcgagg--gcgcgcactact----gagcgctc--gcactctccttattgactttg-ctcg-tgttcata
B D            Cow  ---gagg--gcgcgcaccact----gagcgctc--acactctccttattgactttg-ctca-tgttccta
         Armadillo  agcgagg--gcgcgcaccgct----gagcgctc--accctcgtcttattgactttg-ctcg-tgtttcta
          Elephant  cgcgagg--gcgcgcaccact----gagcgctc--aaactctccttattgactttg-ttcg-tgttccta
B D         Tenrec  cgcgagg--gc-tgcgtcgctcatggggcgcttcgcacccctctttatggactttgcctcg-agtctctt
B D       Platypus  cgggcga--gccagcgcagct----g---gctg-------------gttgagtttg-ttcg-tgttcttc
B D           Fugu  ----gagaactacttgtcacttttaatatgtta--agaatcca-ggcgcgccctcg-tttg-tgtggccg
B D    Stickleback  ----cgg--ctgcgtcccgc--------cgctt--ggaa--------gcagctcag-tttgatttcacag
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  c--gagctgt--------------------aagcaccctcc---aagggtcagt-ggcg
               Rat  c--gagttgt--------------------atgcacacgcc---aagggtcagc-ggct
            Rabbit  c--tgggtgt--------------------aggactgcgcc---aagggccagc-ggcg
             Human  c--aagttgt--------------------aggaacacgct---aagggtcagc-ggcg
             Chimp  c--aagttgt--------------------agaaacacgct---aagggtcagc-ggcg
         Orangutan  c--aagttgt--------------------aggaacacgct---aagggtcagc-ggcg
            Rhesus  c--aagttgt--------------------aggaacacgct---aagggtcagc-ggcg
          Marmoset  c--aagttgt--------------------aggaacacgct---aagggtcagc-ggcg
          Bushbaby  c--aagttgt--------------------aggaacacgct---aagggtcaac-ggcg
        Tree shrew  c--aagttgt--------------------aggaacacgct---gagggtcagc-ggcg
             Shrew  c--aagttgt--------------------aggaacacgct---aagggtcagt-ggcg
          Hedgehog  c--acgttgt--------------------agcaacacgcc---aagggtcagc-ggcg
               Dog  c--aagttgtt-------------------aggaacgcgct---aagggtcag--ggcg
               Cat  c--aagttgtt-------------------aggaacacgct---aagggtcag--ggcg
             Horse  c--aagttgt---------------------aggacccgct---aagggtcggc-gtcg
               Cow  c--aagttgt--------------------aggaacacgct---aagggtcagc-ggct
         Armadillo  c--acgttgt--------------------aggaactcgct---gagggtcagc-ggcg
          Elephant  c--aaatagt--------------------aggaacgctct---aagggtcagc-ggtg
            Tenrec  tcaaagttgt--------------------gggtaccacccgtaaggggtcagctggtg
          Platypus  c--gagttgtt-------------------agggacacgtt---gagggtccgt-agcg
              Fugu  c--gcgtagcccctggccaccttaaaacgaagtctccctcc---gagggtaaac-g---
       Stickleback  a--gcgagaccgttgact--------------tcacacttc---atgt--------gtg
        Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ===========================================================
     X. tropicalis  ===========================================================
           Opossum  ===========================================================
           Chicken  ===========================================================
            Lizard  ===========================================================

Inserts between block 15 and 16 in window
B D         Shrew 1bp
B D           Dog 1bp
B D           Cat 1bp
B D         Horse 1bp
B D           Cow 1bp

Alignment block 16 of 255 in window, 57797002 - 57797077, 76 bps 
B D          Mouse  gaaag-g-gttctg--tga--g-------a-gc----ca--------ctgggt---gacaa-tt-gatgc
B D            Rat  aaaag-g-gtgctg--tgg--g-------a-gc----ta--------ccgagt---ggcag-tt-gatgc
            Rabbit  cacggcg-gtccgg--tgt--gcgc-gccg-gc----tg--------ctgggc---tgctg-tt-gatgc
B D          Human  cacagca-gttcaa--tgt--gaac-gctg-gc----ta--------ctgggt---ggctg-tt-gatgc
B D          Chimp  cacagca-gttcaa--tgt--gaac-gctg-gc----ta--------ctgggt---ggctg-tt-gatgc
B D      Orangutan  cacagca-gttcaa--tgt--gaac-gctg-gc----ta--------ctgggc---ggctg-tt-gatgc
B D         Rhesus  cacagca-gttcaa--cgt--gaac-gctg-gc----ta--------ctgggt---ggctg-tt-gatgc
B D       Marmoset  cacagga-gttcaa--tgt--gaac-gctg-gc----ta--------ctggct---ggcta-tt-gatgc
          Bushbaby  catagca-gttcag--tct--gaat-actg-gc----ta--------ctgggt---cactg-tt-gatgc
B D     Tree shrew  cacagca-gttcag--cct--gaac-tctg-gc----ta--------ccgggt---tgctg-tt-gatgc
B D          Shrew  -gcagca-gttcag--tct--g-----att-gc----ta--------ct-------ggcta-ctaggtgc
B D       Hedgehog  -acggca-gctgcg--tct--gcac-cctg-gc----tacctacagcct-------ggctg-ct-gatgc
B D            Dog  -acggca-gttcagtgtgt--gaac-gctg-gc----ta--------ctgggt---tgctg-tt-gatgc
B D            Cat  -acagca-gttcagt-tct--gaac-gctg-gc----ta--------ctgggt---tgctg-tt-gatgc
B D          Horse  -acagca-gttcag--tct--gaac-gctg-gc----tc--------ctgggt---tgctg-tt-catgc
B D            Cow  -gcagct-gttcag--tct--gaac-gctg-gc----ta--------ctgggttgctgctg-tt-gatgc
         Armadillo  cacagca-gtcgcg--tct--gaac-gccg-gc----tg--------ctgggt---tgttg-tc-cttgc
          Elephant  cacagca-gttcat--tct--gatt-gctg-gt----tg--------ctgcgt---tgttg-tt-gatgc
B D         Tenrec  cacagcacgttctt--tcttgaatc-tcggagt----ag--------ctgggt---ttttgatc-gatgc
B D       Platypus  ----------------------aag-gcca-gcccatcg--------tccggc---tgtcc-tt-aaggt
B D    Stickleback  -gatgtg-tttcta--ttt--gagctggag-ga----gc--------ctgtgt---gtgtg-tt-tat-t
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  cat-tttgcg-a-ttt-----aagggaagag--ggccgtggcattgg
               Rat  cat-ttcccg-a-tttt----aacagacgag--ggccgtggcactgg
            Rabbit  gggagtcctg-a-tttt----aaacagcgca--g--cgtggcatcag
             Human  cat-tttctg-a-tttt----aagagaaggg--agctgtggcatcag
             Chimp  cat-tttctg-a-tttt----aagagaaggg--agctgtggcatcag
         Orangutan  cat-tttctg-a-tttt----aagagaaggg--agctgtggcatcag
            Rhesus  cat-tttctg-a-tttt----aagagaaggg--agctgtggcatcag
          Marmoset  cat-tttctg-a-tttt----aagagaaggg--aactatggcatcag
          Bushbaby  tat-tttctg-a-tttt----aagagaaggg--agctgtgccatcag
        Tree shrew  cat-tttctg-attttt----aagaggcggg--agctgaggctgcag
             Shrew  cgt-tt---------tt----ccgagaagtg--agcgctggcattag
          Hedgehog  ccc-tt---------tg----gagaggaggg--agtggtggcatcag
               Dog  cat-tttctg-a-tctt----aaaacaaggg--agcggtggcatcag
               Cat  cat-tttctg-a-tttt----aaaagaaggg--agcggtggcatcag
             Horse  cat-tttctg-a-tttt----aggagaatag--aggggtggcatcgg
               Cow  cat-tttttg-a-tttc----aagactaggg--agcggtggcatcag
         Armadillo  cat-tttctg-g-ttct----aagggaaggg--cgctgtggcatcag
          Elephant  cgt-tttctg-a-tttt----aagaggaagg--agctgtggtatcag
            Tenrec  tat-tttctgaa-tttt----aagaaaaagggaagctgtgccatgcc
          Platypus  cac-tcggcg-g------------ggaatag--agatgc----tagg
       Stickleback  tat-tttatg-c-tgatggaggggaggacag--gacagggggatagg
        Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ===============================================
     X. tropicalis  ===============================================
           Opossum  ===============================================
           Chicken  ===============================================
            Lizard  ===============================================

Alignment block 17 of 255 in window, 57797078 - 57797151, 74 bps 
B D          Mouse  cgaat-ctcgcagctccagtgtcaat-cca---agttt----------------tgtt--------gcac
B D            Rat  cgagt-ctctcaaccccagtgtcaat-cca---agttt----------------tgtt--------gcac
            Rabbit  agagc-cccgcagccccggtggcaat-cca---agccg----------------tgtttcccacgcgcgc
B D          Human  cgagc-ccctcagcccgagtagcaaa-cca---agttt----------------tgtt--------tcac
B D          Chimp  cgagc-ccctcagcccgagtagcaaa-cca---agttt----------------tgtt--------tcac
B D      Orangutan  cgagc-cccgcagcccgagtagcaaa-cca---agttt----------------tgtt--------tcac
B D         Rhesus  c--gc-cccgcagccccagtagcaaa-cca---agttt----------------tgtt--------tcac
B D       Marmoset  caagc-cccgcagcccccgtagcaaa-cca---agttt----------------tgct--------tcac
          Bushbaby  cgagc-gccacagccccagtagcaaa-cca---agttt----------------tgtt--------tcac
B D     Tree shrew  tgaac--ccgcagccctggtagcaaa-ctactggggtt----------------tgtt--------tctc
B D          Shrew  caagc-cccgcggccccagcgacg---cca---aattt----------------tgtt--------tcac
B D       Hedgehog  caggt-cccgcggccccaatgagggatcga---ttttt----------------ttat--------tctc
B D            Dog  caagc-cctgtagcctcggtggcgga-cca---agttt----------------tgtt--------tcac
B D            Cat  caagc-tccgcagtcttagtggagga-cca---agttt----------------tgtt--------tcac
B D          Horse  caagc-cctccagccctagaggcgga-cca---agttt----------------tgtt--------tca-
B D            Cow  caagc-cccgc-gccccggtggcgga-cca---aattt----------------tgtt--------tcgc
         Armadillo  cgagc-cccgcagccccggtggcaga-cca---agttt----------------tgtt--------gcac
          Elephant  cgagc-cccgcaaccccagtggcaga-cta---agttt----------------tgtt--------tcac
B D         Tenrec  cgagt-cccccacccccagtggcaga-cca---agttt----------------tgtt--------tcag
B D       Platypus  cgatcgcccgaatgatcactggcacg-gtg---ggttttctgctctctccccgctctc--------tccc
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  acgtgtt---tacac-ttg-caag------c---------------------------aaaacag-----
               Rat  acgtgtt---tacac-ttg-caag------c---------------------------aaaacag-----
            Rabbit  acgcacg---gacgc-tcg-caaa------c---------------------------aaaacag-----
             Human  acgcgcg---cacac-atg-caaa------c---------------------------aaaacaggaaaa
             Chimp  acgcgcg---cacac-atg-caaa------c---------------------------aaaacag-----
         Orangutan  acgcgcg---cacac-atg-caaa------c---------------------------aaaacaggaaaa
            Rhesus  acgcgcg---cacac-acg-caaa------c---------------------------aaaacaggaaaa
          Marmoset  acgcgcg---catac-aca-caaa------c---------------------------aaaacag-----
          Bushbaby  agacgct---cacgc-atg-caaa------c---------------------------aaaacagaaaaa
        Tree shrew  ctacgcg---cacac-acg-caaa------c---------------------------aaaacag-----
             Shrew  atactcg---tccac-acg----g------c---------------------------acaa-aa-----
          Hedgehog  gtgtccg---ctcac-ccg-caaa------c---------------------------tcaacag-----
               Dog  ataaact---cacacaact-caga------acaggaaaaaaccaaaccaaaccaaaacaaaacaa-----
               Cat  gtagact---cacac-act-caga------acgtgagggg------------------aaaaaaa-----
             Horse  atacaca---cacac-acg-caaa------c---------------------------aaaacag-----
               Cow  gtacacagggtacaa-aag-ccaa------cc--------------------------aagaaaa-----
         Armadillo  acacgcg---catac-atg-ccaa------c---------------------------aaaacag-----
          Elephant  acacacg-------------caga------c---------------------------aaaacag-----
            Tenrec  acacatg---taacc-aaaccaaa------c---------------------------caaacca-----
          Platypus  ccgcgct---tcccg-ccc-caaaggggcgc---------------------------aaaacct-----
        Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Opossum  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  -----aacaaa
               Rat  -----aacaaa
            Rabbit  -ccaaaacaac
             Human  gaaaagaaaag
             Chimp  gaaaagaaaag
         Orangutan  gaaaagaaaag
            Rhesus  caaaacaaaac
          Marmoset  -gagggaaaaa
          Bushbaby  aaagagagaaa
        Tree shrew  ----------g
             Shrew  -----cgga--
          Hedgehog  -----cggt--
               Dog  -----ccaaac
               Cat  -----acaaac
             Horse  -----aaaaaa
               Cow  -----aaaaag
         Armadillo  -----aga---
          Elephant  -----aaaa--
            Tenrec  -----aaat--
          Platypus  -----aa----
        Guinea pig  NNNNNNNNNNN
       Stickleback  ===========
         Zebrafish  ===========
     X. tropicalis  ===========
           Opossum  ===========
           Chicken  ===========
            Lizard  ===========

Inserts between block 17 and 18 in window
B D      Hedgehog 8bp

Alignment block 18 of 255 in window, 57797152 - 57797221, 70 bps 
B D          Mouse  aacacc--------------------cccc-ccccagcttt-ctctggactgcgtct--aaccccgc---
B D            Rat  aacacc--------------------ccccgccccagtttt-ccctaggctgcgtct--aacccctc---
            Rabbit  aacccc-----------------aaactct-ctctagctttgccctacgcttggtcc--agctgcgcg--
B D          Human  aaaaca---aacaacaacaaataaaacacc-ctctagcttc-ccctagactttgttt--aactggccg--
B D          Chimp  aaaaca---aacaacaacaaataaaacacc-ctctagcttc-ccctagactttgttt--aactggccg--
B D      Orangutan  aaaacaaacaacaacaacaaataaaacacc-ctctagcttc-ccctagactttgttt--aactggccg--
B D         Rhesus  aaaaca---aacaacaac-aacaacacacc-ctctagcttc-ccctagactttgttt--aactgcccg--
B D       Marmoset  aaagca-----------------------c-ctctagcttc-tcctagactttgttt--aactgcccg--
          Bushbaby  aaaatc-----------------------c-ctctagcttc-ccctagactttgtct--aacagcaca--
B D     Tree shrew  aaaatc-----------------------c-ctctagcttc--cctggac-ttgtct---actgcgcg--
B D       Hedgehog  --------------------aagaagtacc-cggtagttac-gtccagaccttgtct--cagggcgca--
B D            Dog  ---------------------------caa-ccgtagtttc-tcctagaccttgcct--aattgcgcc--
B D            Cat  ---------------------------aaa-ctgtagtttc-ttctagaccttgtct--aatcgcgcg--
B D          Horse  ---------------------------aac-ctgtggtttt-ccctggcccttgtct--aatcgcgca--
B D            Cow  ---------------------------a----------------ctagactttgtct--aattgcgca--
         Armadillo  ----------------------------ac-cgccggcttc-ccctagaccccgcct--aactgcgcc--
          Elephant  ----------------------------at-ctctagcttc-tcctagaccttgtct--gactacg-g--
B D         Tenrec  ----------------------------tt-ctctagttt----ctagccttagtct--gtttgcg-c--
B D       Platypus  ---------------------------------atcgtttc-taaaaggggttgctctggagagagcggg
B D          Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  -----------------------a---------gaagggaggggtaagg-------------------cg
               Rat  -----------------------t---------gaagggaggggtaagg-------------------cg
            Rabbit  -----------ggtcttcgggcgg---------ggcgcgggggaggggg-------------------cg
             Human  -----------ggtctccagaagg---------aacgctggggatggga-------------------tg
             Chimp  -----------ggtctccagaagg---------aacgctggggatggga-------------------tg
         Orangutan  -----------ggtctccagaagg---------aacgctggggatggga-------------------tg
            Rhesus  -----------ggtctccagaagg---------aaagctggggatggga-------------------tg
          Marmoset  -----------ggtctccaggagg---------aacgctggggatggga-------------------tg
          Bushbaby  -----------ggtcttcaagagg----------gtgctgggagcggtc-------------------tg
        Tree shrew  -----------gctcctcagcctg-----------cagtaggggtgggg-------------------tg
          Hedgehog  -----------ggtccccaggctg---------ggcgcagggggtccagtggggctgggggagggggag-
               Dog  -----------ggtccccaggccg---------ggcgctggggctcaag-------------------c-
               Cat  -----------ggtctccaggcgg---------ggcgctggggctcaag-------------------g-
             Horse  -----------ggtccccgggcgg---------ggcgctagggatcaag-------------------g-
               Cow  -----------ggtccctaggcgg---------ggcgctggggatcaaa-------------------g-
         Armadillo  -----------agtccccaggcga---------ggcgctggggctcgag-------------------c-
          Elephant  -----------ggtcctcgggtgg---------ggcgccgggattgagg-------------------a-
            Tenrec  -----------gatcccggggggg---------gg----gggggggggg-------------------c-
          Platypus  aggaggagattggcccttaggaagcgagaggaaggaggaggagaggagg-------------------cg
             Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
        Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       Stickleback  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Opossum  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  gtggaagg
               Rat  gtggagag
            Rabbit  ggggcggg
             Human  ggtggaga
             Chimp  ggtggaga
         Orangutan  ggtggaga
            Rhesus  ggtggaga
          Marmoset  agt--aaa
          Bushbaby  ggagggaa
        Tree shrew  ggggaggg
          Hedgehog  --------
               Dog  --------
               Cat  --------
             Horse  --------
               Cow  --------
         Armadillo  --------
          Elephant  --------
            Tenrec  --------
          Platypus  ggggagaa
             Shrew  NNNNNNNN
        Guinea pig  NNNNNNNN
       Stickleback  ========
         Zebrafish  ========
     X. tropicalis  ========
           Opossum  ========
           Chicken  ========
            Lizard  ========

Inserts between block 18 and 19 in window
B D         Human 4bp
B D         Chimp 4bp
B D     Orangutan 4bp
B D        Rhesus 4bp
B D      Marmoset 4bp
         Bushbaby 4bp
B D    Tree shrew 105bp
B D      Hedgehog 2bp
B D           Dog 2bp
B D           Cat 2bp
B D         Horse 2bp
B D           Cow 2bp
        Armadillo 2bp
         Elephant 1bp
B D        Tenrec 8bp

Alignment block 19 of 255 in window, 57797222 - 57797284, 63 bps 
B D          Mouse  gagcaagggccgagtgt-tttggtaccaggcaggca-------aagaggggcgc-gct---------gga
B D            Rat  gagcaggggctgggcgt-tcttgtgtcgggcaggga-------acgaagggcgc-gct---------gga
            Rabbit  gagc--ggcccgagagc-ttccgtgcggagccggcc-------agcgggtgcgc-gtt---------cag
B D          Human  gagc--ggctcaaggac-tttagtgaggagcaggcg-------agaaggagcac-gtt---------cag
B D          Chimp  gagc--ggctcaaggac-tttagtgaggagcaggcg-------agaaggagcgc-gtt---------cag
B D      Orangutan  gagc--ggctcaaggac-tttagtgaggagcaggcg-------agaaggagcgc-gtt---------cag
B D         Rhesus  gagc--ggctcaaggac-tttagtaaggagcaggcg-------agaaggagcgc-gtt---------cag
B D       Marmoset  gagt--ggcccaagaaa-tttagtgaggagcaggct-------acaagcagcgc-gtt---------tag
          Bushbaby  gagc--agcctaaggac-tttagtgcgcagcaggcg-------agaaggagcgt-gtt---------cag
B D     Tree shrew  ---------------------------gagcagg------------------------------------
B D       Hedgehog  gagc--gttccaaggac-ttgagctccgaactggct-------aagagaagcgg-gttc--------cag
B D            Dog  tagc--ggcccaaagacttttagcgccgagcagccg-------agaaggagccg-gttg--------cag
B D            Cat  tagc--ggcccaaagac-tttagcgccgagaaggcg-------agaaggagcct-gttg--------cag
B D          Horse  cagc--ggcccaaagac-tttagcgacgaccaggcg-------agaaggggccg-gtcg--------ctg
B D            Cow  gagc--ggcccaaggac-attagcgccgagtgggcg-------agaaggagccgctttg--------tag
         Armadillo  gagc--agcccaaggac-tcgagctccgagcaggcg-------ggaaggagcc--gtcg--------cag
          Elephant  aagt--agcccaaggac-tttaggtcccagcaggcg-------agaaggaggcg-gttg--------cag
B D         Tenrec  gaga--agtccaaggtc-ttca-gtccaagtaggcg-------agaaggagccg-gtgg--------cag
B D       Platypus  gaga--aggaagaagac-gagaaggaggaggaggaggaggaaaagaaggaggaa-gacaaggaatcccaa
B D          Shrew  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  g-cctcagaacc
               Rat  g-tgtcaggacc
            Rabbit  g-agtcgagacc
             Human  g-cgtcaagacc
             Chimp  g-cgtcaagacc
         Orangutan  g-tgtcaagacc
            Rhesus  g-cgtcaagacc
          Marmoset  g-catcaagacc
          Bushbaby  g-cgtcaagacc
        Tree shrew  ------------
          Hedgehog  g-agccaaaacc
               Dog  g-cgtcaagact
               Cat  g-cgtcaagacc
             Horse  g-catcaggacc
               Cow  g-cgtcaagacc
         Armadillo  g-cgtcaagacc
          Elephant  g-cgtcaagacc
            Tenrec  gatatcaggatc
          Platypus  g-ccgtaggacc
             Shrew  NNNNNNNNNNNN
        Guinea pig  NNNNNNNNNNNN
       Stickleback  ============
         Zebrafish  ============
     X. tropicalis  ============
           Opossum  ============
           Chicken  ============
            Lizard  ============

Inserts between block 19 and 20 in window
B D      Hedgehog 32bp

Alignment block 20 of 255 in window, 57797285 - 57797312, 28 bps 
B D          Mouse  ------gattt------ccccgcc-tgcttcgg--agagtttt
B D            Rat  ------gattt------ccccgcc-tgcttcgg--agagttta
            Rabbit  ------gattc------ccccgcc-tggttcgg--agactt--
B D          Human  ------gattt------ctccccc-tgcttcgg-gagactttt
B D          Chimp  ------gattt------ctccccc-tgcttcgg-gagactttt
B D      Orangutan  ------gattt------ct---cc-tgcttcgg-gagactttt
B D         Rhesus  ------gattt------cccctcc-tgcttcgg-gagac-ttt
B D       Marmoset  ------gattt------cccgtcc-tgcttcgg-aggactttt
          Bushbaby  ------tattt------ctccgtc-tgcttcgg--agactttt
B D     Tree shrew  ----------------------------------------tct
B D          Shrew  ------gattt------ccccgccagtcttaga--agaccttt
B D       Hedgehog  ------cacct------ctccctcctgctcctg--agac--tt
B D            Dog  ------gattt------ccccgcc-tgcttcgg--aggctttt
B D            Cat  ------gatct------ccttgcc-cgcttcgg--agactttt
B D          Horse  ------gattt------cccagcc-tgcttcgg--agactttt
B D            Cow  ------gactt------cctcgcc-tgcttcgg--aggcttct
         Armadillo  ------gattt------ccccgac-tacaccg-----------
          Elephant  ------aattt------ccctgcc-tgcttcag--agactttt
B D         Tenrec  ------gattt------ccctgct-tgcttcag--agtttttt
B D       Platypus  gagggcgatctcattgcctccgtc-tgcctaggcaataccc--
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ===========================================
B D      Zebrafish  ===========================================
B D  X. tropicalis  ===========================================
B D        Opossum  ===========================================
B D        Chicken  ===========================================
B D         Lizard  ===========================================

Alignment block 21 of 255 in window, 57797313 - 57797354, 42 bps 
B D          Mouse  aagtgtccggagttgc--cctgggtct-------------------------------------------
B D            Rat  gagtgtcccgagttgc--cctgggtctgtctctctctctctctctctctctctctctctctctctctctc
            Rabbit  ------------tctc--gctg------------------------------------------------
B D          Human  gaacgctcggagaggc--ccggcatctcacca--------------------------------------
B D          Chimp  gaacgctgggagaggc--ccggcatctcacca--------------------------------------
B D      Orangutan  gaacactcggagaggc--ccggcatctcacca--------------------------------------
B D         Rhesus  gaacgctcggagaggc--cctgcgtctcacca--------------------------------------
B D       Marmoset  gaacgcttggagaggc--cctgagtctcacca--------------------------------------
          Bushbaby  gaacactcagagctgc--cctgcttagcacca--------------------------------------
B D     Tree shrew  ga-------------c--cc--------------------------------------------------
B D          Shrew  gaactcccgaagctgccaccgccgtctcaccaac------------------------------------
B D       Hedgehog  gaattctgggagctgc--tcagcgcctcgcca--------------------------------------
B D            Dog  gagcacttggagcggc--cttgcttctcacca--------------------------------------
B D            Cat  gaacacttggagcggc--cctgtgtcccacca--------------------------------------
B D          Horse  gaacgctcggagcggc--cctgcgtct----a--------------------------------------
B D            Cow  gaacactcggagaggc--cctgcgtctcacca--------------------------------------
         Armadillo  -agcgcctggggcggc--cctgag----------------------------------------------
          Elephant  gaacactcggagcgtc--cctgcgtctcaccc--------------------------------------
B D       Platypus  -----cgccgcctcgc--tctgcctttctccc--------------------------------------
B D         Tenrec  ======================================================================
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  -----------------ctcttcttgtttgttgt
               Rat  tctctctctctctctctctctccttgtttgtagt
            Rabbit  -----------------ctttgctggtcagttgc
             Human  -----------------ctttacttggccgtagg
             Chimp  -----------------ctttacttggccgtagg
         Orangutan  -----------------ctttacttggctgtagg
            Rhesus  -----------------ctttacttggttgtagg
          Marmoset  -----------------ctttacttggctgtagg
          Bushbaby  -----------------ccacacttgactggagc
        Tree shrew  ----------------------------------
             Shrew  -----------------ttgaatttgcctg----
          Hedgehog  -----------------ctcaatttgtttg----
               Dog  -----------------ctttatttgcttg----
               Cat  -----------------ctttctttgcttg----
             Horse  -----------------ttttattagcggc----
               Cow  -----------------ctttatttgcttg----
         Armadillo  ------------------tttacttgtttgtcgt
          Elephant  -----------------ttttatttgcctatcac
          Platypus  -----------------cctgaggggcct-----
            Tenrec  ==================================
        Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
       Stickleback  ==================================
         Zebrafish  ==================================
     X. tropicalis  ==================================
           Opossum  ==================================
           Chicken  ==================================
            Lizard  ==================================

Inserts between block 21 and 22 in window
B D         Shrew 22bp
B D      Hedgehog 18bp
B D           Dog 18bp
B D           Cat 141bp
B D         Horse 11bp
B D           Cow 18bp

Alignment block 22 of 255 in window, 57797355 - 57797397, 43 bps 
B D          Mouse  tgggaatcgcaaagtaggagcgagg-------------------------tctgg---ccg---cagctt
          Elephant  ggcctccggctcccctggaatgactaggggc--------------g--cgaccag--actgcgccgtc-g
         Armadillo  ggccgctggcccgacgggaacgagggagggc--------------acccgacccg--gctg---cggc-g
B D            Cow  --------------cggtaatgagggaggagg-------------gtctgactca--accc---cggt-g
B D          Horse  --------------ccagaatgcgggaggtggtg-----------gtctgactct--agcg---cgat-g
B D            Dog  --------------ccggaacggggtggggggagggagggagggtgtccgattcg--acct---tagt-g
B D       Hedgehog  --------------cggaaatgagagagggcggg-----------tcttgacccc---------------
B D          Shrew  --------------cagaatgaaaggaggggcca-----------tcctgaccccgacctt---cggt-t
B D     Tree shrew  ------------------------------------------------------g--acct---tggc-c
          Bushbaby  ggcctcaagcac-gcaggaatcagggagggc--------------atctagccgg--acct---tggc-g
B D       Marmoset  ggcctctggcaccgcaggaatgagggagggg--------------gtccgattgg--accg---tgac-a
B D         Rhesus  ggcctccggcacggcaggaatgagagagggg--------------gtccgattgg--accg---tgac-c
B D      Orangutan  ggcctccggcacggcaggaatgagggagggg--------------atccgactgg--accg---tgac-g
B D          Chimp  ggcctccggcacggcaggaatgagggagggg--------------gtccgattgg--accg---tgac-g
B D          Human  ggcctccggcacggcaggaatgagggagggg--------------gtccgattgg--acag---tgac-g
            Rabbit  ggccactcccgcggcaggaacgagggaaggg--------------gtcctcctgg--accg---cggcaa
B D            Rat  tgggaatcgcaaagcaggagcgagg-------------------------tctgg---tct---cagctt
B D       Platypus  -------------ccgggcttgttcgacagg--------------atgctactcc---tgc---cggc-t
B D         Tenrec  ======================================================================
B D            Cat  ======================================================================
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  gttt
          Elephant  cctt
         Armadillo  cttt
               Cow  attt
             Horse  gttt
               Dog  gttt
          Hedgehog  ----
             Shrew  agtt
        Tree shrew  actt
          Bushbaby  cttt
          Marmoset  g-tt
            Rhesus  gttt
         Orangutan  gttt
             Chimp  gttt
             Human  gttt
            Rabbit  gtct
               Rat  gttt
          Platypus  cccc
            Tenrec  ====
               Cat  ====
        Guinea pig  NNNN
       Stickleback  ====
         Zebrafish  ====
     X. tropicalis  ====
           Opossum  ====
           Chicken  ====
            Lizard  ====

Alignment block 23 of 255 in window, 57797398 - 57797434, 37 bps 
B D          Mouse  tga--gacgtttgg-------ctcag-g--------ccggaa---cagtctgg--ttt----------cg
B D       Platypus  gga--gtcacttggaaagccccgggccg--------cgggga---taat---------------------
B D            Rat  t---------tgag-------ctcag-g--------ctggag---cagtctgg--ttt----------tg
            Rabbit  ttgccggggggggg-------ggggg-g--------gggggg---gaatctgg--ttt----------gc
B D          Human  ggg--gccgttcgg-------ctatgtt--------caggga---ccatatgg--ttt----------gg
B D          Chimp  ggg--gccgttcgg-------ctatgtt--------caggga---ccatatgg--ttt----------gg
B D      Orangutan  ggg--gctgttcgg-------ctatgtt--------caggga---ccatatgg--ttt----------gc
B D         Rhesus  cgg--gccgttcgg-------ctatgtt--------ccggga---ccgtatgg--ttt----------gg
B D       Marmoset  ggg--cccgttcgg-------ctttgtt--------caggaa---tcgtttgg--ctt----------gg
          Bushbaby  ggg--gccgttc-g-------ctatgtt--------cgggaac--ccgtatgg--ttt----------gg
B D     Tree shrew  ggg--gccgttaga-------caatgtt--------agggga---ccggatgg--ttt----------gg
B D          Shrew  tgg--gtggttggg-------ctaagct--------tcggaagacccgtagaagttcc----------gg
B D       Hedgehog  -----acggtccag-------ctgggct--------cgaga----ccgtcgcg--tct----------gg
B D            Dog  ggg--gctgttggg-------caaggct--------cgggga---cagtaggg--ttt----------gg
B D          Horse  ggg--gtcgtttgg-------ctgggct--------caagga---ccgaatga--ttt----------gg
B D            Cow  gag--gccgttcct-------caaggct--------cgggga---ccgtatgg--ttt----------gg
         Armadillo  ggg--gccgttcgg-------cgaggtt--------cgaaga---ccgtcctg--tttggggggaggggg
          Elephant  tgg--gctgttcgg-------cgaggtt--------cgtggt---tcgtatgg--ttt----------gg
B D           Fugu  tga--ggttttggg-------tttggat--------cagagg---t--taaag--ttt----------ac
B D         Lizard  ------------------------------------ctgagg---ctgttagg--aat----------tg
B D        Chicken  -------------------------gcggaggtcggaagggg---ctgcgggg--act----------tc
B D         Tenrec  ======================================================================
B D            Cat  ======================================================================
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Stickleback  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================

             Mouse  -
          Platypus  -
               Rat  -
            Rabbit  -
             Human  -
             Chimp  -
         Orangutan  -
            Rhesus  -
          Marmoset  -
          Bushbaby  -
        Tree shrew  -
             Shrew  -
          Hedgehog  -
               Dog  -
             Horse  -
               Cow  -
         Armadillo  -
          Elephant  -
              Fugu  a
            Lizard  -
           Chicken  -
            Tenrec  =
               Cat  =
        Guinea pig  N
       Stickleback  =
         Zebrafish  =
     X. tropicalis  =
           Opossum  =

Inserts between block 23 and 24 in window
B D      Platypus 266bp
B D         Shrew 3bp

Alignment block 24 of 255 in window, 57797435 - 57797468, 34 bps 
B D          Mouse  gggc----------aac------------------cccagtcct-ta-----taga-agggt--------
          Elephant  ggac----------agc------------------ccctgtcct-tg-----atcc-ggggc--------
         Armadillo  gggc----------aga------------------ccctgttct-tg-----accc-aggag--------
B D            Cow  tgaa----------agc------------------ccgggtcct-ta-----gtcc-caggc--------
B D          Horse  ggaa----------agc------------------cggggtcct-ta-----gtcc-ggggc--------
B D            Dog  gaaa----------agc------------------ccaggttcc-cc-----gccg-ggggt--------
B D       Hedgehog  ggac----------agc------------------ccgcgtctg-ta-----gtct-gggacgcgtgtca
B D          Shrew  gaaa----------agc------------------ccgggtctt-ga-----ctcc-ggatc--------
B D     Tree shrew  ggac----------agc------------------tccagacgt-ta-----gcct-ggggc--------
          Bushbaby  ggaca---------agc------------------cccagacgt-ca-----tttctggggg--------
B D       Marmoset  ggac----------agc------------------ccctgtcgt-ta-----gtac-aggac--------
B D         Rhesus  ggac----------agt------------------cccagtcgt-ta-----gtac-gggac--------
B D      Orangutan  ggac----------agc------------------cccagtcgt-ta-----gtac-gggac--------
B D          Chimp  gaac----------agc------------------cccagtcgt-ta-----gtac-gggac--------
B D          Human  ggac----------agc------------------cccagtagt-ta-----gtag-gggac--------
            Rabbit  ggac----------agc------------------cttggacgtccg-----ttgg-ggggc--------
B D            Rat  g--------------------------------------------------------agggt--------
B D       Platypus  gggc----------aag------------------gccagggct-tg-----gaca-ggggg--------
B D        Chicken  ----gggaacttcggcc------------------ccgggtccc-tt--------c-ccggc--------
B D         Lizard  ----tggcagttggagt------------------ccaaaacac-ttggagggccc-cagtt--------
B D           Fugu  ggat----------aaatgcggtcacaaaatagaccccagtgat--------------------------
            Medaka  -----------------------------------aagcgtgat--------------------------
B D    Stickleback  ------------------ccaagccc---attaaactatgtggt--------------------------
B D         Tenrec  ======================================================================
B D            Cat  ======================================================================
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Opossum  ======================================================================

             Mouse  ----------gt---cataa
          Elephant  ----------gagtgagttc
         Armadillo  ----------gggttggttc
               Cow  ----------gggtgcctcc
             Horse  ----------gggtgcaacc
               Dog  ----------gggtgcatct
          Hedgehog  gtctgtctgtcggcgtgtcg
             Shrew  ---------cctgtgctccc
        Tree shrew  ----------gggtgcgttc
          Bushbaby  ----------gggtgcgtcc
          Marmoset  ----------gggtgcgttc
            Rhesus  ----------gggcgcgttc
         Orangutan  ----------cggtgcgttc
             Chimp  ----------gggtgcgttc
             Human  ----------gggtgcgttc
            Rabbit  ----------gcgtgcgtgc
               Rat  ----------gt---cataa
          Platypus  ----------ggcagag---
           Chicken  ----------g---------
            Lizard  ----------t---------
              Fugu  --------------------
            Medaka  --------------------
       Stickleback  --------------------
            Tenrec  ====================
               Cat  ====================
        Guinea pig  NNNNNNNNNNNNNNNNNNNN
         Zebrafish  ====================
     X. tropicalis  ====================
           Opossum  ====================

Inserts between block 24 and 25 in window
B D      Platypus 35bp

Alignment block 25 of 255 in window, 57797469 - 57797488, 20 bps 
B D          Mouse  ccct--gccc---ctgg-----------ac---------------gctctt
          Elephant  gccc-tgccc---ccag-----------ac---------------gcgcgc
         Armadillo  gcct-tcttc---ccgg-----------ac---------------gcgcgc
B D            Cow  gcct-tgccc---cctg-----------ac---------------gcgcgc
B D          Horse  gccc-tgccc---cctg-----------at---------------gggcgc
B D            Dog  accc-agccc---cctg-----------ac---------------gtgggc
B D       Hedgehog  gcct-gtcct---ccgg-----------gtgcgtagtgtgtgtgcgcgcgc
B D          Shrew  gccc-tacct---ccca-----------cccccaaa---------gcgcac
B D     Tree shrew  gctc-tgccc---cggg-----------ac---------------gcgcac
          Bushbaby  tcccttgttc---ccga-----------ac---------------gcgcac
B D       Marmoset  gccc-agtcc---ccgg-----------ac---------------gcgcag
B D         Rhesus  gccc-agtcc---ccgg-----------ac---------------gcgcag
B D      Orangutan  gccc-agtcc---ccgg-----------ac---------------gcgtag
B D          Chimp  gccc-agtcc---ccgg-----------at---------------gcgtag
B D          Human  gccc-agtcc---ccgg-----------at---------------gcgtag
            Rabbit  cccctggcccaagccgg-----------tg---------------ccccag
B D            Rat  cact--gccc---ctgg-----------aa---------------gctctt
B D        Chicken  gccc---tcc---ccgg-----------tt---------------------
B D         Lizard  gccc---atg---cctg-----------cctt-------------------
B D           Fugu  -----cattt---ccgtaaatatccatagg---------------------
B D    Stickleback  -----ttaac---ccgg-----------tt---------------------
            Medaka  -----ttaat---ctcgcgggatc----tt---------------------
B D         Tenrec  ===================================================
B D            Cat  ===================================================
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ===================================================
B D  X. tropicalis  ===================================================
B D       Platypus  ===================================================
B D        Opossum  ===================================================

Alignment block 26 of 255 in window, 57797489 - 57797504, 16 bps 
B D          Mouse  ggaggc----cgagtgg-cag-------
B D         Tenrec  ------------------cag-------
B D        Opossum  ggaaga----agggtgatctg-------
          Elephant  ggaggc----cgagtgg-caa-------
         Armadillo  ggaagc----cgggtgg-cag-------
B D            Cow  ggaggc----cgagtgg-caa-------
B D          Horse  ggaggc----cgagtgg-caa-------
B D            Dog  ggaggc----cgagtgg-taa-------
B D       Hedgehog  ggaggc----cgagcgg-cca-------
B D          Shrew  ggaaga----atcgcgg-caa-------
B D     Tree shrew  ggaggc----cgggtgg-cag-------
          Bushbaby  tgaggt----cgagtgg-cag-------
B D       Marmoset  ggaggc----ccagtgg-cag-------
B D         Rhesus  ggaggc----ccagtgg-cag-------
B D      Orangutan  ggaggc----ccagtgg-cag-------
B D          Chimp  ggaggc----ccagtgg-cag-------
B D          Human  ggaggc----ccagtgg-cag-------
            Rabbit  gggggg----caagcgg-cag-------
B D            Rat  ggaggc----cgagtgg-cag-------
B D        Chicken  --gggcgcaacaggtgc-cgg-------
B D         Lizard  agaggcgccttgagtgc-ccg-------
B D           Fugu  -----------------tcagg--gtag
B D    Stickleback  -----------------ttaaa--gcag
            Medaka  -----------------tcagactgaag
B D            Cat  ============================
       Guinea pig  NNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ============================
B D  X. tropicalis  ============================
B D       Platypus  ============================

Inserts between block 26 and 27 in window
B D        Lizard 16bp
B D          Fugu 5bp
B D   Stickleback 17bp

Alignment block 27 of 255 in window, 57797505 - 57797537, 33 bps 
B D          Mouse  gcggctgtcccaa--------------gcag-t-tggtgc-----------g------cgttgtgg
B D         Tenrec  gcagctgtcccaa--------------gcgg-c-gagtgc-----------g------cgtccccg
B D        Opossum  acagttgtcac-a--------------gtga-t-ctgtgt-----------g------tgttcctg
          Elephant  gcggctgtcccaa--------------gcgg-c-gggtgc-----------g------cgtccccg
         Armadillo  acggctgtcccaa--------------gcgg-c-gggtgc-----------g------cgtccccg
B D            Cow  gcggttgtcccaa--------------actg-t-gggtgc-----------g------cgtccccg
B D          Horse  gcggctgtcccaa--------------actg-c-gggtgc-----------g------cgttcccg
B D            Dog  ccggctgtcccaa--------------actg-c-cggggc-----------g------cgtccccg
B D       Hedgehog  gcgacctccccga--------------acag-c-gagtgc-----------g------cgtccccg
B D          Shrew  gctgctgtcccga--------------actg-cggggtgc-----------g------cgtccctg
B D     Tree shrew  gctgctgtcccaa--------------gcag-c-gggtgt-----------g------cgtccccg
          Bushbaby  gcagctgtcccaa--------------gccgcc-gggtgc-----------gc-----cgtccccg
B D       Marmoset  gcggctgtcccaa--------------gcag-c-gtgtgc-----------g------cgtctccg
B D         Rhesus  gcggctgtcccaa--------------gcag-c-gggtgc-----------g------cgcccctg
B D      Orangutan  gcggctgtcccaa--------------gcag-c-gggtgc-----------g------cgtccctg
B D          Chimp  gcggctgtcccaa--------------gcag-c-gggtgc-----------g------cgtccctg
B D          Human  gcagctgtcccaa--------------gcag-c-gggtgc-----------g------cgtccctg
            Rabbit  ggggctgtcccaa--------------gcgg-c-gggtgc-----------g------cgtccccg
B D            Rat  gctgctgtcccaa--------------gcag-t-tggtgc-----------g------cgttgtgg
B D       Platypus  gcagctgtcccaataacgcgcgcgtgtgtgg-c-gtgtgt-----------gattgtgtgtgcgtg
B D           Fugu  -gtgtgta-----------------------tt-ttgacc-----------g------tgctgcag
B D    Stickleback  -gggttgg-----------------------tc-acgatcacggtctcattg------ttccgccg
        Guinea pig  ------------a--------------gcgg-c-ggttgc-----------g------cgtccctg
B D        Chicken  -------tcctga--------------gc-a-c-cgcgca-----------g------tgtccgac
B D         Lizard  -------ttctga--------------g--g-c-ttctcc-----------t------tgtttgcc
B D            Cat  ==================================================================
B D      Zebrafish  ==================================================================
B D  X. tropicalis  ==================================================================

Inserts between block 27 and 28 in window
B D          Fugu 11bp
B D   Stickleback 5bp

Alignment block 28 of 255 in window, 57797538 - 57797549, 12 bps 
B D          Mouse  cgcgc------------------------tctgtgc-------
B D         Lizard  tcc----------------------------------------
B D        Chicken  ggcca------------------------tgtgtgt-------
        Guinea pig  cgcgc------------------------tgtgtgt-------
B D       Platypus  tgtgg------------------------tgtgtgc-------
B D            Rat  cgcgc------------------------tctatgg-------
            Rabbit  cgcgc------------------------tttgtgt-------
B D          Human  cgcgc------------------------tgtgtgt-------
B D          Chimp  cgcgc------------------------tgtgtgt-------
B D      Orangutan  cgcgc------------------------tgtgtgt-------
B D         Rhesus  cgcgc------------------------tgtgtgt-------
B D       Marmoset  cgcgc------------------------tgtgtgt-------
          Bushbaby  cgcgc------------------------tgtgtgt-------
B D     Tree shrew  cgctc------------------------cttgtgt-------
B D          Shrew  cgcgc------------------------cgtgtgt-------
B D       Hedgehog  cgcgc------------------------cgtgtgt-------
B D            Dog  cgcgc------------------------cgcgtgt-------
B D          Horse  cgtgc------------------------cgtgtgt-------
B D            Cow  cgcgc------------------------cgtgtgt-------
         Armadillo  cgcgc------------------------cgtgtgt-------
          Elephant  cgcgc------------------------cctgtgt-------
B D        Opossum  tgcgcgcgcgagcgcgcgcgttgtttgcgtttatgt-------
B D         Tenrec  cgcgc------------------------cttgtgt-------
B D    Stickleback  -------------------------------tgtgtttttgtt
B D           Fugu  ---------------------------------tctcctctgt
B D      Tetraodon  ---------------------------------cgttcttggt
B D            Cat  ===========================================
B D      Zebrafish  ===========================================
B D  X. tropicalis  ===========================================

Alignment block 29 of 255 in window, 57797550 - 57797808, 259 bps 
B D          Mouse  tcct-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGAAGGC
B D         Tenrec  tcgt-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGTTGGGAGGAGTGTTTGTGAACGGGAGGC
B D        Opossum  tc-t-----tttgcagAGCCAGCTTTCGGGGAGGTCAACCAGCTGGGAGGGGTATTCGTGAACGGGAGGC
          Elephant  tcgt-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGTTGGGAGGAGTGTTTGTGAACGGGAGGC
         Armadillo  tcgt-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGGCGGC
B D            Cow  tcgt-----tttgcagAGCCAGCCTTTGGGGAGGTAAACCAGTTGGGAGGAGTATTCGTGAACGGGAGGC
B D          Horse  tcat-----tttgcagAGCCAGCCTTTGGGGAGGTGAACCAGCTGGGAGGAGTATTCGTGAACGGGAGGC
B D            Dog  tcgt-----tttgcagAGCCAGCCTTTGGGGAGGTGAACCAGCTGGGAGGAGTATTCGTGAACGGGAGGC
B D       Hedgehog  tggtc----tttgcagAGCCGGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTTGTCAACGGGAGGC
B D          Shrew  tcat-----tttgcagAGCCAGCCTTTGGGGAGGTGAACCAGCTGGGAGGAGTATTCGTGAACGGGAGGC
B D     Tree shrew  tcgt-----tttgcagAGCCTGCCTTTGGGGAGGTGAACCAGCTGGGAGGAGTGTTTGTAAACGGGAGGC
          Bushbaby  ttgt-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGGAGGC
B D       Marmoset  tcgt-----tttttagAGCCAGCTTTCGGGGAGGTGAACCAGCTGGGTGGAGTGTTCGTGAACGGGAGGC
B D         Rhesus  tcgt-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGGAGGC
B D      Orangutan  tcat-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGGAGGC
B D          Chimp  tcat-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGGAGGC
B D          Human  tcat-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGGAGGC
            Rabbit  tggt-----tttgcaaAATCGGGCTTCGGGGAGGTGAACCAGCTGGGATGAGTGTTCGTGAACCGGAGGC
B D            Rat  tcct-----tttgcagAGCCAGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGAAGGC
B D       Platypus  tcgc-----cttgcagAGCCGGCCTTCGGGGAGGTGAACCAGCTGGGCGGCGTGTTCGTCAACGGCCGGC
        Guinea pig  tcct-----ttcgcgtAGCCTGCCTTCGGGGAGGTGAACCAGCTGGGAGGAGTGTTCGTGAACGGAAGGC
B D        Chicken  gcttg----cttgcagAACCCGCCTTCGGGGAGGTGAACCAGCTCGGGGGGGTGTTCGTCAACGGGAGGC
B D         Lizard  -cttc----cttgcagAGCCGGCCTTCGGGGAGGTGAACCAGCTGGGCGGCGTCTTCGTCAACGGGCGCC
B D  X. tropicalis  tctc-----tttgcagAACCCGCTTTCGGGGAAGTGAACCAGCTGGGCGGCGTGTTTGTGAATGGGAGGC
            Medaka  ---------tttctagAGCAAACCTATGGAGAGGTGAACCAGCTTGGCGGCGTTTTCGTCAATGGGCGAC
B D    Stickleback  tcca-----acaccagAGCCAGCCTTCGGTGAGGTGAACCAACTCGGCGGTGTTTTCGTGAACGGCAGGC
B D           Fugu  ttgttttgggcaccagAACCTGCCTTCGGCGAGGTCAACCAGCTCGGCGGTGTTTTCGTGAACGGCAGGC
B D      Tetraodon  tctcctttgacaccagAACCTGCCTTCGGCGAGGTCAACCAGCTCGGCGGGGTCTTCGTGAACGGCAGGC
B D      Zebrafish  --------------agAGCCAGCCTTTGGGGAGGTGAACCAACTAGGCGGTGTTTTTGTCAACGGAAGAC
B D            Cat  ======================================================================

             Mouse  CGCTGCCCAACGCCATTCGGCTTCGCATCGTGGAATTAGCCCAACTGGGCATCCGACCTTGTGACATCAG
            Tenrec  CGCTGCCTAACGCCATCCGGCTTCGTATCGTGGAACTGGCCCAACTGGGCATTCGACCGTGTGACATCAG
           Opossum  CTTTACCCAACGCCATCAGACTCCGCATCGTGGAACTGGCCCAATTGGGCATCCGACCCTGTGACATCAG
          Elephant  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
         Armadillo  CACTGCCCAACGCCATCCGGCTTCGCATAGTGGAACTGGCCCAACTGGGCATCCGGCCGTGTGACATCAG
               Cow  CGCTGCCCAACGCCATCCGGCTTCGCATAGTGGAGCTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
             Horse  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
               Dog  CGCTGCCCAACGCTATCCGGCTTCGTATCGTGGAACTGGCCCAACTGGGCATCAGACCGTGTGACATCAG
          Hedgehog  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
             Shrew  CCCTGCCTAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCCTGTGACATCAG
        Tree shrew  CGCTGCCCAACGCCATCCGGCTTCGCATAGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
          Bushbaby  CGCTGCCCAACGCCATCCCGCTTCGCATAGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
          Marmoset  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCCTGTGACATCAG
            Rhesus  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
         Orangutan  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
             Chimp  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
             Human  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
            Rabbit  CGCTTGCCAACGCCCTCCGGCTTTCCATCGTGGAACTGGTCTTTTTGGGCATTTTATCCTGTGACATTAC
               Rat  CGCTGCCCAACGCCATTCGGCTTCGCATCGTGGAATTAGCCCAACTGGGCATCCGACCTTGTGACATCAG
          Platypus  CGCTGCCCAACGCCATCCGGCTCCGCATCGTGGAGCTGGCCCAGCTCGGGATCCGGCCCTGCGACATCAG
        Guinea pig  CGCTGCCCAACGCCATCCGGCTTCGCATCGTGGAACTGGCCCAACTGGGCATCCGACCGTGTGACATCAG
           Chicken  CCCTGCCCAACGCCATCCGGCTCCGGATTGTGGAACTGGCACAGCTGGGGATCAGGCCCTGCGACATCAG
            Lizard  CTCTGCCCAACGCCATCCGGCTCCGGATCGTGGAGCTGGCCCAGCTGGGCATCCGGCCCTGCGACATCAG
     X. tropicalis  CTCTGCCCAATGCCATCCGCCTGCGGATCGTGGAGCTGGCGCAGCTGGGCATCCGGCCGTGCGATATCAG
            Medaka  CCCTGCCCAATGCCATCCGGTTAAGAATAGTGGAACTGGCGCAGCTCGGGATCAGGCCCTGCGACATAAG
       Stickleback  CGCTGCCGAACGCGATCCGGCTCAGGATAGTGGAGCTGGCCCAGCTCGGGATTCGACCCTGTGACATCAG
              Fugu  CGCTCCCCAACGCCATCAGACTCCGGATAGTGGAGCTGGCCCAACTCGGGATCCGGCCCTGTGACATCAG
         Tetraodon  CGCTGCCCAACGCCATCCGCCTCCGGATAGTGGAGCTGGCCCAGCTCGGGATCCGGCCCTGCGACATCAG
         Zebrafish  CCCTACCCAATGCCATCCGGCTCAGGATAGTAGAGTTGGCCCAGTTGGGCATCAGGCCTTGTGACATCAG
               Cat  ======================================================================

             Mouse  CCGCCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGCTACAACGAGACCGGTTCGATT
            Tenrec  CCGCCAGCTACGGGTCTCGCACGGCTGTGTCAGCAAGATCCTGGCGCGCTACAACGAGACGGGTTCGATC
           Opossum  CCGGCAGTTAAGAGTGTCCCATGGCTGTGTCAGTAAGATACTGGCGCGCTACAATGAGACTGGCTCCATC
          Elephant  CCGTCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGCTACAACGAGACAGGCTCGATC
         Armadillo  CCGCCAGCTGCGGGTCTCGCACGGCTGCGTCAGTAAGATCTTGGCGCGCTACAACGAGACGGGCTCGATC
               Cow  CCGCCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGCTACAATGAGACAGGCTCGATC
             Horse  CCGCCAGCTACGGGTCTCACACGGCTGCGTCAGCAAGATCCTGGCGCGCTACAACGAGACAGGCTCGATC
               Dog  CCGCCAGCTACGGGTCTCACACGGCTGCGTCAGCAAGATTCTGGCGCGCTACAACGAGACGGGCTCGATC
          Hedgehog  CCGCCAGCTCCGGGTGTCCCACGGCTGCGTCAGCAAGATCCTGGCGCGCTACAACGAGACGGGCTCGATC
             Shrew  CCGCCAGCTACGGGTCTCGCACGGCTGCGTCAGTAAGATCCTGGCGCGCTACAACGAGACGGGCTCGATC
        Tree shrew  CCGCCAGTTAAGGGTCTCTCACGGCTGCGTCAGCAAGATCTTGGCGCGCTACAACGAGACAGGCTCGATC
          Bushbaby  CCGCCAGCTACGGGTCTCGCACGGCTGCGTGAGCAAGATCCTGGCGCGCTACAACGAGACGGGTTCGATC
          Marmoset  CCGCCAGCTACGGGTCTCACACGGCTGTGTCAGCAAGATCCTGGCGCGCTACAACGAAACAGGCTCGATC
            Rhesus  CCGGCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGATACAACGAGACGGGCTCGATC
         Orangutan  CCGCCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGATACAACGAGACGGGCTCGATC
             Chimp  CCGCCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGATACAACGAGACGGGCTCGATC
             Human  CCGCCAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCCTGGCGCGATACAACGAGACGGGCTCGATC
            Rabbit  CCGCCAACTACGAATCTCGCTTGGTTGCGTCATC-AGATCCTGGACCGCTACAACAAGATCGGTTCCATC
               Rat  CCGACAGCTACGGGTCTCGCACGGCTGCGTCAGCAAGATCTTGGCGCGCTACAACGAGACCGGTTCGATT
          Platypus  CCGCCAGCTGCGGGTGTCCCACGGCTGCGTGAGCAAGATCCTGGCGCGCTACAACGAGACGGGCTCCATC
        Guinea pig  CCGCCAACTCCGGGTCTCGCACGGTTGCGTCAGCAAGATCTTGGCGCGCTACAAAGAGACGGGCTCGATC
           Chicken  CCGCCAGCTCCGCGTTTCCCACGGCTGTGTGAGCAAAATCCTGGCTCGCTACAACGAGACCGGCTCCATC
            Lizard  TCGCCAGCTGCGGGTCTCGCACGGCTGCGTGAGCAAGATCCTGGCCCGCTACAACGAGACGGGCTCCATC
     X. tropicalis  TAGGCAGCTGCGAGTGTCGCACGGATGTGTCAGCAAGATTCTAGCGCGGTACAACGAGACCGGCTCCATC
            Medaka  CCGGCAGCTGCGAGTCTCTCATGGCTGCGTGAGCAAGATTTTAGCGAGATACAACGAGACTGGCTCCATC
       Stickleback  CAGGCAGCTACGCGTCTCCCACGGCTGCGTCAGCAAGATCCTGGCCCGCTACAACGAAACCGGCTCCATC
              Fugu  CAGGCAGTTGCGGGTCTCCCACGGCTGCGTCAGCAAGATTCTAGCGCGCTACAACGAGACCGGCTCCATC
         Tetraodon  CAGGCAGCTGCGGGTCTCCCACGGCTGCGTCAGCAAGATTCTAGCGCGCTACAACGAGACGGGCTCCATC
         Zebrafish  CAGGCAGCTCCGCGTCTCCCACGGCTGCGTGAGCAAGATTCTGGCTCGGTACAACGAAACCGGCTCAATA
               Cat  ======================================================================

             Mouse  TTGCCGGGAGCTATTGGGGGGAGCAAGCCCCGGGTCACCACCCCTACTGTGGTG
            Tenrec  TTGCCAGGGGCCATCGGGGGCAGCAAGCCCCGGGTCACCACCCCCACCGTGGTG
           Opossum  TTACCTGGGGCCATTGGGGGCAGCAAACCTCGGGTTACCACCCCCACAGTAGTG
          Elephant  TTGCCAGGGGCCATTGGGGGCAGCAAGCCCCGGGTCACCACCCCCACCGTGGTG
         Armadillo  TTGCCGGGGGCTATCGGAGGTAGCAAGCCTCGGGTCACAACCCCCACTGTGGTG
               Cow  TTGCCAGGAGCCATTGGGGGCAGCAAGCCTCGGGTCACCACCCCCACCGTGGTG
             Horse  TTGCCAGGAGCCATTGGGGGCAGCAAGCCCCGGGTCACCACCCCTACCGTGGTG
               Dog  TTGCCAGGAGCCATTGGGGGCAGCAAGCCCCGAGTTACCACCCCCACCGTGGTG
          Hedgehog  TTGCCCGGAGCCATCGGAGGCAGCAAACCCCGGGTCACCACCCCCACCGTGGTG
             Shrew  TTGCCCGGAGCTATAGGGGGCAGTAAGCCTCGGGTCACCACCCCCACCGTGGTG
        Tree shrew  TTGCCAGGAGCCATCGGGGGCAGCAAGCCCCGGGTCACTACCCCCACAGTAGTG
          Bushbaby  TTGCCAGGAGCCATCGGGGGCAGCAAGCCCCGAGTCACCACCCCTACAGTGGTG
          Marmoset  TTGCCAGGAGCCATCGGGGGCAGCAAGCCCCGGGTCACTACCCCCACCGTGGTG
            Rhesus  TTGCCTGGAGCCATCGGGGGCAGCAAGCCCCGGGTCACTACCCCCACCGTGGTG
         Orangutan  TTGCCAGGAGCAATCGGGGGCAGCAAGCCCCGGGTCACTACCCCCACCGTGGTG
             Chimp  TTGCCAGGAGCCATCGGGGGCAGCAAGCCCCGGGTCACTACCCCCACCGTGGTG
             Human  TTGCCAGGAGCCATCGGGGGCAGCAAGCCCCGGGTCACTACCCCCACCGTGGTG
            Rabbit  TTTGCCGGATCCATCCGGGGCACCAAGGCTCGGGTTACCACTCCCTCCGTGGTG
               Rat  TTGCCGGGAGCTATCGGGGGAAGCAAGCCCCGGGTCACCACCCCTACTGTAGTG
          Platypus  CTGCCGGGGGCCATCGGCGGCAGCAAGCCCCGCGTCACCACCCCCACCGTGGTC
        Guinea pig  TTGCCTGGAGCGATTGGGGGCAGCAAGCCGCGGGTCACCACTCCCACCGTGGTG
           Chicken  CTACCGGGGGCTATCGGAGGCAGCAAGCCGCGGGTCACCACCCCCACGGTGGTT
            Lizard  CTGCCGGGGGCCATCGGGGGCAGCAAGCCCCGCGTCACCACCCCGACGGTGGTC
     X. tropicalis  CTGCCGGGGGCCATCGGGGGCAGCAAGCCCAGGGTCACTACCCCCACTGTGGTC
            Medaka  TTGCCCGGTGCCATCGGTGGAAGCAAGCCACGGGTCACGACGCCGAACGTGGTT
       Stickleback  CTCCCGGGGGCCATCGGGGGCAGCAAGCCGCGGGTCACCACGCCCACCGTGGTC
              Fugu  CTCCCCGGGGCCATCGGAGGCAGCAAGCCGCGCGTCACCACACCCACCGTCGTC
         Tetraodon  CTCCCCGGGGCCATCGGAGGCAGCAAGCCGCGCGTCACCACACCCACCGTCGTC
         Zebrafish  CTTCCCGGTGCAATCGGCGGCAGTAAACCGAGGGTCACGACCCCAAACGTAGTC
               Cat  ======================================================

Alignment block 30 of 255 in window, 57797809 - 57797835, 27 bps 
B D          Mouse  AAACACATCCGGACTTACAAGCAGA-GG
B D            Rat  AAACACATCCGGACTTACAAGCAGA-GG
        Guinea pig  AAGCACATCCGGACCTACAAGCAGA-GG
            Rabbit  AACTGCGACCTGACCTACCCTTCAA-GT
B D          Human  AAACACATCCGGACCTACAAGCAGA-GA
B D          Chimp  AAACACATCCGGACCTACAAGCAGA-GA
B D      Orangutan  AAACACATCCGGACCTACAAGCAGA-GA
B D         Rhesus  AAACACATCCGGACCTACAAGCAGA-GG
B D       Marmoset  AAGCACATCCGGACCTACAAGCAGA-GG
          Bushbaby  AAACACATCCGGACCTACAAGCAGA-GG
B D     Tree shrew  AAACACATCCGGACCTACAAGCAGA-GG
B D          Shrew  AAGCACATCCGGACCTACAAGCAGA-GG
B D       Hedgehog  AAGCACATCCGGACCTACAAGCAGAGGG
B D            Dog  AAGCACATCCGGACCTACAAGCAAA-GG
B D            Cat  AAACACATCCGGACCTACAAGCAAA-GG
B D          Horse  AAGCACATCCGGACCTACAAGCAGA-GG
B D            Cow  AAGCACATCCGGACCTACAAGCAGA-GA
         Armadillo  AAACACATCCGGACCTACAAGCAGA-GG
          Elephant  AAACACATCCGGACCTACAAGCAGA-GG
B D         Tenrec  AAACACATCCGGACCTACAAGCAGA-GG
B D        Opossum  AAACATATCCGGACCTACAAGCAGA-GG
B D       Platypus  AAACACATCCGGACCTACAAACAGA-GG
B D        Chicken  AAACATATCCGGACCTACAAACAAA-GG
B D         Lizard  AAGCACATCCGGACCTACAAGCAGC-GC
B D  X. tropicalis  AAACACATACGGACTTACAAGCAGA-GG
            Medaka  AAAAATATCAGGGAATACAAACAGA-AC
B D    Stickleback  AAGCACATACGGACATACAAGCAGA-GG
B D           Fugu  AAGCACATACGGACATACAAGCAGA-GG
B D      Tetraodon  AAGCACATTCGGACATACAAGCAGA-GG
B D      Zebrafish  AAGCACATTAGGACTTACAAGCAAC-GG

Inserts between block 30 and 31 in window
         Elephant 2469bp

Alignment block 31 of 255 in window, 57797836 - 57797954, 119 bps 
B D          Mouse  GA-CCCAGGCATCTTCGCTTGGGAGATCCGGGACCGCCTGCTG-GCGGATGGCGTGTGCGACAAGTAC-A
B D            Rat  GA-CCCAGGCATCTTTGCTTGGGAGATCCGGGACCGCCTGCTG-GCGGATGGCGTGTGCGACAAGTAC-A
        Guinea pig  GA-CCCCGGCATCTTCGCCTGGGAGATCCGCGACCGCCTGCTG-GCCGACGGCGTGTGCGACAAGTAC-A
            Rabbit  GA-CTCGGGTATCATCACCTGGGAGATCCTGGACTGTCTGCTG-GATGACTGAGTGTGTGACAAAAAA-A
B D          Human  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAGTAC-A
B D          Chimp  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAGTAC-A
B D      Orangutan  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAGTAC-A
B D         Rhesus  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGTGTGTGCGACAAGTAC-A
B D       Marmoset  GA-CCCTGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGTGTGTGCGACAAGTAC-A
          Bushbaby  GA-CCCTGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAGTAC-A
B D     Tree shrew  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCCGACGGCGTATGCGACAAGTAC-A
B D          Shrew  GA-CCCGGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCTGACGGCGTGTGCGACAAGTAC-A
B D       Hedgehog  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGATCGCCTGTTG-CCCGACGGCGTGTGTGACAAGTACAA
B D            Dog  GA-TCCTGGCATCTTTGCCTGGGAAATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGTGACAAGTAC-A
B D            Cat  GACCCCTGGCATCTTTGCCTGGGAAATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAGTAC-A
B D          Horse  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGATCGCCTGCTG-GCAGACGGCGTGTGCGACAAATAC-A
B D            Cow  GA-CCCCGGCATCTTCGCCTGGGAGATACGGGACCGCCTGCTG-GCGGACGGCGTGTGTGACAAGTAC-A
         Armadillo  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAGTAC-A
          Elephant  GA-CCCCGGCATCTTCGCCTGGGAGATTCGGGACCGCCTGCTGTGCTGACGGCGTGTGTGACAAGTAC-A
B D         Tenrec  GA-CCCCGGCATCTTTGCCTGGGAGATTCGGGACCGCCTGCTG-GCGGACGGCGTGTGCGACAAATAC-A
B D        Opossum  GA-CCCAGGAATCTTTGCCTGGGAGATACGCGATCGTTTGTTA-GCAGACGGTGTGTGTGACAAGTAC-A
B D       Platypus  GA-CCCCGGCATCTTCGCCTGGGAGATCCGGGACCGGCTGCTG-GCCGACGGGGTGTGCGACAAGTAC-A
B D        Chicken  GA-TCCGGGCATCTTCGCCTGGGAGATCCGGGATCGCCTGCTG-GCCGACGGCGTGTGCGACAAGTAC-A
B D         Lizard  GA-CCCGGGCATCTTCGCCTGGGAGATCCGCGACCGCCTCCTG-GCCGACGGCGTGTGCGACAAGTAC-A
B D  X. tropicalis  GA-CCCGGGCATCTTCGCTTGGGAGATCAGGGACAGGCTGCTG-GCAGATGGGGTGTGCGACAAGTAC-A
            Medaka  GA-CCCCGGGATCTTTGCCTGGGAGATTCGGGACAGGCTTTTG-GCAGACGGCGTTTGTGACAAGTAC-A
B D    Stickleback  GA-CCCGGGGATTTTTGCCTGGGAGATCCGGGACAGGCTACTC-GCCGACGGGGTTTGCGACAAGTTC-A
B D           Fugu  GA-CCCGGGGATTTTTGCCTGGGAGATCCGGGACAGGCTACTC-GCCGACGGGGTTTGTGATAAGTTC-A
B D      Tetraodon  GA-CCCGGGGATTTTTGCCTGGGAGATCCGGGACAGGCTACTC-GCCGACGGGGTTTGTGATAAATTC-A
B D      Zebrafish  GA-CCCTGGTATTTTCGCATGGGAGATTCGAGACAGACTGCTC-GCGGACGGCGTATGTGATAAATTT-A

             Mouse  -ACGTGCCCTCGGTGAGTTCCATCAGCCG-TATTCTGCGCAACAAGATCGGCAA
               Rat  -ACGTACCCTCTGTGAGTTCCATCAGCCG-GATTCTGCGCAACAAGATCGGCAA
        Guinea pig  -ACGTGCCCTCGGTGAGTTCCATCAGCCG-CATTCTGCGCAACAAGATCGGCAA
            Rabbit  CACGTGCCTTCCGTGAGCTCCTTCAGCCTCCAGTCTGTGCAACAAGATCTGTAA
             Human  -ATGTGCCCTCCGTGAGCTCCATCAGCCG-CATTCTGCGCAACAAGATCGGCAA
             Chimp  -ATGTGCCCTCCGTGAGCTCCATCAGCCG-CATTCTGCGCAACAAGATCGGCAA
         Orangutan  -ACGTGCCCTCCGTGAGCTCCATCAGCCG-CATTCTGCGCAACAAGATCGGCAA
            Rhesus  -ACGTGCCCTCCGTGAGCTCCATCAGCCG-TATTCTGCGCAACAAGATCGGCAA
          Marmoset  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATTCTGCGCAACAAGATCGGCAA
          Bushbaby  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATTCTGCGCAACAAGATCGGCAA
        Tree shrew  -ACGTGCCCTCTGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
             Shrew  -ACGTGCCTTCGGTGAGCTCCATTAGCCG-CATCCTGCGCAACAAGATCGGCAA
          Hedgehog  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
               Dog  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
               Cat  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
             Horse  -ACGTACCCTCGGTGAGCTCCATCAGCCG-CATCCTGCGTAACAAGATCGGCAA
               Cow  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATACTGCGCAACAAGATCGGCAA
         Armadillo  -ACGTGCCTTCGGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
          Elephant  -ATGTGCCCTCGGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
            Tenrec  -ACGTGCCTTCGGTGAGCTCTATCAGCCG-TATCCTGCGCAACAAGATCGGCAA
           Opossum  -ACGTTCCTTCAGTCAGTTCCATCAGCCG-AATCCTGCGCAACAAGATTGGTAA
          Platypus  -ACGTGCCCTCCGTCAGCTCCATCAGCAG-GATCCTGCGCAACAAGATCGGGAA
           Chicken  -ACGTGCCGTCGGTCAGCTCTATCAGCCG-CATCCTCCGCAACAAGATCGGAAA
            Lizard  -ACGTGCCCTCGGTGAGCTCCATCAGCCG-CATCCTGCGCAACAAGATCGGCAA
     X. tropicalis  -ACGTCCCCTCGGTCAGCTCCATCAGCCG-GATCCTACGGAATAAGATCGGGAA
            Medaka  -ACGTCCCGTCTGTTAGTTCGATCAGCAG-GATTTTACGCAACAAGATTGGGAA
       Stickleback  -ACCTCCCCTCCGTCAGCTCCATCAGCCG-GATCCTCCGCAACAAGATCGGGAA
              Fugu  -ATCTGCCCTCTGTCAGCTCCATCAGCCG-GATCCTGCGCAACAAGATCGGGAA
         Tetraodon  -ATCTGCCCTCCGTGAGCTCCATCAGCCG-GATCCTGCGCAACAAGATCGGGAA
         Zebrafish  -ATTTGCCCTCTGTCAGCTCAATTAGTAG-GATTCTCCGCAACAAGATCGGGAA

Alignment block 32 of 255 in window, 57797955 - 57798073, 119 bps 
B D          Mouse  CTTGGCCCAGCAGGG------TCATTACGACTCATACAAGCAG---CA-CCA------------------
B D            Rat  CTTGGCCCAGCAGGG------TCACTACGACTCCTATAAGCAG---CA-CCA------------------
        Guinea pig  CTTGGCCCTGCAAAG------CCATTATGATTCGTACAAGCAG---CA-CCA------------------
            Rabbit  CTTGGCCCAGCAGGG------CCACTACGACTCCTACAAGCAG---CA-CCA------------------
B D          Human  CTTGGCCCAGCAGGG------TCATTACGACTCATACAAGCAG---CA-CCA------------------
B D          Chimp  CTTGGCCCAGCAGGG------TCATTACGACTCATACAAGCAG---CA-CCA------------------
B D      Orangutan  CTTGGCCCAGCAGGG------TCATTACGACTCATACAAGCAG---CA-CCA------------------
B D         Rhesus  CTTGGCCCAGCAGGG------TCATTACGACTCATACAAGCAG---CA-CCA------------------
B D       Marmoset  CTTGACCCAGCAGGG------TCATTACGACTCGTACAAGCAG---CA-CCA------------------
          Bushbaby  CTTGGCCCAGCAGGG------TCATTACGATTCGTACAAGCAG---CA-CCA------------------
B D     Tree shrew  CTTGGCTCAGCAGGG------CCATTACGACTCCTACAAGCAG---CA-CCA------------------
B D          Shrew  CTTGGCCCAACAGAG------CCACTACGACTCCTACAAGCAG---CA-CCA------------------
B D       Hedgehog  CTTGGCCCAGCAGAG------CCACTACGACTCGTACCAGCAG---CA-CCA------------------
B D            Dog  CTTGGCTCAACAGGG------CCATTACGACTCGTACAAGCAG---CA-CCA------------------
B D            Cat  CTTGGCTCAACAGGG------TCATTACGACTCCTACAAGCAG---CA-CCA------------------
B D          Horse  CTTGGCCCAACAGGG------CCATTACGACTCATTCAAACAG---CA-CCA------------------
B D            Cow  CTTGGCCCAACAGGG------CCATTACGACTCCTACAAGCAG---CA-CCA------------------
         Armadillo  CCTGGCTCAGCAGAG------CCACTACGACTCGTACAAGCAG---CA-CCA------------------
          Elephant  CCTGGCCCAGCAGGG------CCACTACGACTCATACAAGCAG---CA-ACA------------------
B D         Tenrec  CCTGGCTCAGCAGGG------CCACTACGACTCCTACAAACAG---CA-CCA------------------
B D        Opossum  CCTGTCTCAGCAGAG------CCAGTACGACTCTTACAAACAG---CA-TCA------------------
B D       Platypus  CCTGGCCCAGCCGGG------CCACTACGACACCTACAAGCAG---CA-CCA------------------
B D        Chicken  CCTGTCCCAGCAGGG------CCACTACGAGTCCTACAAGCAG---CA-TCA------------------
B D         Lizard  CCTGGCGCAGCAGGGCGCCCACCACTTCGAGGCCTACAAGCAG---CA-CCACCATCACCACCACCACCA
B D  X. tropicalis  CCTGGCCCAACAGAA------CCACTATGAGAGCCACAAACAG---CACCCG------------------
            Medaka  CCTCTCTCAGCCTAA------CCAGTATGAAAGCAGCAAGCAAG--------------------------
B D    Stickleback  TCTGTCCCAGCAGAG------TCAATACGAGTCGGGGAAGCAGGCGCC-TCA------------------
B D           Fugu  TCTCTCCCAGCAGGG------CCAGTATGAGTCTGGGAAGCAGGCGCC-GCA------------------
B D      Tetraodon  TCTCTCCCAGCAGGG------CCAGTATGAGTCTGGGAAGCAGGCGCC-GCA------------------
B D      Zebrafish  TCTGTCTCAACAGAA------CCAGTACGAGTCGAGCAAACAGGCCTC-TCA------------------

             Mouse  ----------GCCCGCGCCGCAG-CCCGCGCTGCCCTACAACCACATTTACTCATA-------TCCCAGT
               Rat  ----------GCCAGCGCCGCAG-CCCGCGCTGCCCTACAACCACATCTACTCCTA-------CCCCAGT
        Guinea pig  ----------GCCGGCGCCACAG-CCTGCGCTGCCCTACAACCACATCTACTCGTA-------TCCTAGT
            Rabbit  ----------GCCGGCGCCGCAG-CCCGCGCTGCCCTACAACCACATCTACTCGTA-------CCCCAGC
             Human  ----------GCCGACGCCGCAG-CCAGCGCTGCCCTACAACCACATCTACTCGTA-------CCCCAGC
             Chimp  ----------GCCGACGCCGCAG-CCGGCGCTCCCCTACAACCACATCTACTCGTA-------CCCCAGC
         Orangutan  ----------GCCGACGCCGCAG-CCAGCGCTGCCCTACAACCACATCTACTCGTA-------CCCCAGC
            Rhesus  ----------GCCGACGCCGCAG-CCAGCGCTGCCCTACAACCACATCTACTCGTA-------CCCCAGC
          Marmoset  ----------GCCGGCACCGCAG-CCAGCGCTGCCCTACAACCACATCTACTCATA-------CCCCAGT
          Bushbaby  ----------GCCGGCGCCCCAG-CCAGCGCTGCCGTACAACCACATCTACTCGTA-------CCCCAGC
        Tree shrew  ----------GCCGGCGCCTCAG-CCAGCGCTGCCCTACAATCACATCTATTCGTA-------CCCCAGC
             Shrew  ----------ACCCGCGCCGCAG-CCTGCGCTGCCCTACAACCACATCTACTCGTA-------CCCCAGC
          Hedgehog  ---------GGCCCGCGCCGCAG-CCTGCGCTGCCCTAC-ACCACATCTACTCGTA-------CCCCAGC
               Dog  ----------GCCGGCGCCACAG-CCGGCGCTGCCCTATAACCACATCTACTCGTA-------CCCCAGC
               Cat  ----------GCCGGCGCCGCAG-CCGGCTCTGCCCTATAACCACATCTACTCGTA-------CCCCAGC
             Horse  ----------GCCGGCGCCGCAGCCCGGCGCTGCCCTATAATCACATCTACTCGTA-------CCCCAGC
               Cow  ----------ACCGGCGCCTCAG-CCGGCGCTACCCTATAACCACATCTACTCGTA-------CCCCAGC
         Armadillo  ----------GCCAGCGCCGCAG-CCCGCCCTGCCCTACAACCACATCTACTCTTA-------CCCCAGC
          Elephant  ----------GCCGGCGCCGCAG-CCCACGCTGCCCTACAACCACATCTATTCGTA-------CCCTAGC
            Tenrec  ----------GCCGGCGCCACAG-CCCGCGCTACCCTACAACCACATTTACTCCTA-------CCCCAGC
           Opossum  ----------GCCACCACCGCAG-CCCGCCTTGCCTTATAACCATATATATTCCTA-------TCCAAGT
          Platypus  ----------GCCCCCGCCGCAG-CCAGCCCTGCCCTACAACCCCATCTACTCCTA-------CCCCAGC
           Chicken  ----------GCCGCCCCCGCAG-CCGCCCCTGCCCTACAACCACATCTACTCCTA-------CCCCAGC
            Lizard  CCACCCCCAGGCCG-CCCCGCAG-ACCGCCCTGCCCTACAACCCGCTCTACTCCTA-------CCCCAGC
     X. tropicalis  ----------GCCGCCGCC-----TCCGCACTCCCTTACAACCACCTGTATTCCTA-------CCCCAGC
            Medaka  -----------CCTCCG-CGCAA-GCCGGGCTCCCCTACAACCACATTTACCCTTATTCCTACCCCAACA
       Stickleback  ----------CCCGCCGCCCCAA-GCAACGATACCCTACAACCACTTGTACTCGTA-------CCCGACG
              Fugu  ----------CCCACCTCCGCAG-CCAACGTTACCCTACAACCACTTATACTCATA-------CCCGACA
         Tetraodon  ----------C------CCGCAG-CCGGCCTTGCCCTACAACCACCTCTACTCCTA-------CCCGACC
         Zebrafish  ----------TCCTCAACCTCAA-CCCACCATACCCTACAACCACCTGTATTCGTA-------TCCAACT

             Mouse  CCCATCACGGCG---GCAGCAGCTAAGG
               Rat  CCCATCACGGCG---GCAGCTGCTAAGG
        Guinea pig  CCCATCACGGCG---GCGGCAGCCAAGG
            Rabbit  CCCATTACGGCGGCTGCGGCCGCCAAGG
             Human  CCTATCACGGCG---GCGGCCGCCAAGG
             Chimp  CCTATCACGGCG---GCGGCCGCCAAGG
         Orangutan  CCTATCACGGCG---GCGGCCGCCAAGG
            Rhesus  CCTATCACGGCG---GCGGCCGCCAAGG
          Marmoset  CCTATCACGGCG---GCGGCTGCCAAGG
          Bushbaby  CCCATCACTGCG---GCGGCCGCCAAGG
        Tree shrew  CCCATCACGGCG---GCGGCTGCCAAGG
             Shrew  CCCATCACGGCC---GCGGCCGCTAAGG
          Hedgehog  CCTATCTCGGCA---GCCACGGCCAAGG
               Dog  CCCATCACGGCG---GCCGCAGCTAAGG
               Cat  CCCATCACGGCG---GCCGCAGCTAAGG
             Horse  CCCATCACTGCG---GCCACCGCTAAGG
               Cow  CCCATCACGGCG---GCCGCCGCTAAGG
         Armadillo  CCCATCACGGCG---GCGGCCGCTAA-G
          Elephant  CCCATCACGGCG---GCGGCCGCCAAGG
            Tenrec  CCCATAACGGCG---GCGGCCGCCAAGG
           Opossum  CCCATTACTGCC---GCAGCAGCCAAAG
          Platypus  CCCATC---------GCCGCCGCCAAAG
           Chicken  CCCATCGCTGCC---GCGGGAGCCAAGG
            Lizard  CCCATCGCCGCC---TCGGGCGCCAAGG
     X. tropicalis  CCCAT---AGCG---GCAGGGGCCAAGG
            Medaka  CC-ATGTCGCCC---CCCAGCACCAAAA
       Stickleback  T---------------------CCAAAG
              Fugu  T---------------------CCAAAG
         Tetraodon  T---------------------CCAAAG
         Zebrafish  CCAATAGCAGCC---GCTGGGACTAAAG

Inserts between block 32 and 33 in window
B D      Hedgehog 1996bp

Alignment block 33 of 255 in window, 57798074 - 57798203, 130 bps 
B D          Mouse  TGCCTACACCACCTGGGGTGCCGGCCATCCCCGGATCGGTGGCCTTGCCGCGCACCTGGCCCTCC-TCTC
B D            Rat  TGCCCACACCACCTGGGGTGCCGGCCATCCCAGGATCCGTGGCCCTGCCGCGCACCTGGCCCTCC-TCTC
        Guinea pig  TGCCCACGCCACCCGGGGTGCCTGCCATCCCTGGCTCGGTGGCCATGCCGCGCACCTGGCCTTCC-TCGC
            Rabbit  TGCCCACGCCACCCGGGGTGCCCGCCATCCCCGGTTCGGTGGCCATGCCGCGCACCTGGCCCTCT-TCAC
B D          Human  TGCCCACGCCACCCGGGGTGCCTGCCATCCCCGGTTCGGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
B D          Chimp  TGCCCACGCCACCCGGGGTGCCTGCCATCCCCGGTTCGGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
B D      Orangutan  TGCCCACGCCACCCGGGGTGCCTGCCATCCCCGGTTCTGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
B D         Rhesus  TGCCCACGCCACCCGGGGTGCCTGCCATCCCCGGTTCGGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
B D       Marmoset  TGCCCACACCACCCGGGGTGCCTGCCATTCCCGGTTCGGTGGCCATGCCGCGCACCTGGCCTTCC-TCGC
          Bushbaby  TGCCCACGCCGCCCGGTGTGCCCGCCATTCCCGGTTCTGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
B D     Tree shrew  TGCCCACGCCACCCGGGGTGCCCGCCATCCCCGGCTCGGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
B D          Shrew  TGCCCACGCCGCCCGGCGTGCCCGCCATCCCCGGCTCCGTGGCCATGCCGCGCACCTGGCCCTCC-TCTC
B D       Hedgehog  GGCCCACGCCGCCCGGGGTGCCCGCCCTCCCCGGCTCGGTGGCCATGCCGCGCACCTGGCCCTCC-TCAC
B D            Dog  TGCCCACGCCTCCCGGGGTGCCTGCCATCCCCGGCTCGGTGGCCATGCCCCGTACCTGGCCCTCC-TCCC
B D            Cat  TGCCCACGCCGCCCGGGGTGCCAGCCATCCCCGGCTCGGTGGCCATGCCCCGTACCTGGCCCTCC-TCCC
B D          Horse  TGCCCACGCCACCCGGGGTGCCCGCCATCCCCGGCTCAGTGGCCATGCCGCGCACCTGGCCTTCC-TCCC
B D            Cow  TGCCCACGCCGCCGGGGGTGCCCGCCATCCCCGGCTCAGTGGCCATGCCGCGCACCTGGCCCTCC-TCGC
         Armadillo  TCCCCACGCCTCCCGGGGTACCCGCCATCCCGGGTTCAGTGGCCCTGCCGCGCACCTGG-CCTCT-TCGC
          Elephant  TACCCACGCCGCCCGGGGTGCCAGCCATCCCCGGCTCGGTGGCCATGCCGCGCACCTGGCCCTCCTTCGC
B D         Tenrec  TACCCACGCCGCCCGGGGTCCCAGCCATCCCCGGCTCGGTGGCTCTGCCGCGCACCTGGCCCTCC-TCGC
B D        Opossum  TACCCACTCCTCCCGGAGTGCCTGGAATTCCTGGCAACATGGCCATGCCTAGAACCTGGCCCTCT-TCGC
B D       Platypus  TGCCCACTCCGCCCGGGGTGCCCGCCCTGCCGGGCACCGTGGCCATGCCCCGCACCTGGCCCTCC-TCCC
B D        Chicken  TGCCCACGCCTCCGGGAGTGCCTGCCATCCCTGGTACCATGGCCATGCCTCGCACCTGGCCTTCG-TCCC
B D         Lizard  GGCACACCCCGCCCGGAGTGCCCACCCTCCACAGCGCCGTCCACCTGCCCCGCACCTGGCCCTCC-TCCC
B D  X. tropicalis  TGCCCACCCCTCCTGGAATGCCCTCCATCCCTGGCACCATGGGCATGCCAAGGACCTGGCCCTCT-TCCC
            Medaka  TGGGAAGCCCTCCCGGAGTACCAGTGACGCCGGGACATGTGAGCATATCCAGGGCTTGGCCTTCT-CCGC
B D    Stickleback  TGCAGACTCCCCCCGGCATGCCCACCATTCCTGGACACATGGCCATGCACAGGATATGGCCCTCC-TCGC
B D           Fugu  TGCCCAAT---CCCGGCATGCCAACCCTTCCCGGACACATGGCCATGCACAGGATATGGCCCTCC-TCGC
B D      Tetraodon  TGCCCAATCCCCCCGGCATGCCCACCCTTCCCGGACACATGGCCATGCACAGGATATGGCCCTCC-TCAC
B D      Zebrafish  TACCAACTCCGCCTGGCATGCCCACTCTTCCTGGACATATGGCAATGCATAGGATATGGCCTTCC-TCTC

             Mouse  ACTCC-GTCACGGACATTCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-aag-gagctcagagg
               Rat  ACTCC-GTCACCGACATCCT-GGGCATCCGT-TCCATCACCGACC---AAGgt-aag-gggctcggaag
        Guinea pig  ATTCT-GTCACCGACATTCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-aag-g-gctcagaga
            Rabbit  ACTCT-GTCACAGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-aag-g-gcacggagg
             Human  ACTCC-GTCACCGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagagg
             Chimp  ACTCC-GTCACCGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagagg
         Orangutan  ACTCC-GTCACCGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagagg
            Rhesus  ACTCC-GTCACAGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagagg
          Marmoset  ACTCC-GTCACTGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagaga
          Bushbaby  ACTCG-GTCACTGACATCCT-GGGGATTCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagagg
        Tree shrew  ACTCG-GTCACTGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-aag-g-gctcggg--
             Shrew  ACTCC-GTCACCGACATCCT-GGGCATTCGC-TCCATCACCGACC---AAGgt-agg-g-actctcggg
          Hedgehog  ACTCG-GTCACCGACATCCT-GGGCATTCGT-TCCATCACCGACC---AAGgt-aag-g-accccaggg
               Dog  ATTCC-GTCACCGACATCCT-GGGCATTCGC-TCTATCACCGACC---AAGgt-aag-g-gctcggggg
               Cat  ATTCC-GTCACCGATATCCT-GGGCATTCGC-TCCATCACCGACC---AAGgt-aag-g-gctcacggg
             Horse  ATTCCTGTCACCGACATCCTGGGGCATTCGCTTCCATCACCGACC---AAGgtaaag-g-gctcgaggg
               Cow  ACTCC-GTCACCGACATCCT-GGGCATTCGC-TCCATCACCGACC---AAGgt-aag-g-gcacggggg
         Armadillo  ACTCG-GTCACCGACATTCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-agg-g-gctcagggc
          Elephant  AATTCGGTCACCGATATACT-GGGCATCCGC-TCCATCACCGACC---AAGgt-aag-g-tctccaggg
            Tenrec  ACTCC-GTCACGGACATCCT-GGGCATCCGC-TCCATCACCGACC---AAGgt-ca--g-tctccgggg
           Opossum  ACTCT-GTCACGGATATCCT-GGGAATCCGC-TCCATCACAGACC---AAGgt-aaa-t----------
          Platypus  ACTCG-GTCACGGATATTTT-GGGGATCCGC-TCCATCACCGACC---CAGgt-aag-g-tc-----gg
           Chicken  ACTCG-GTGACGGACATCCT-GGGCATCCGC-TCCATCACGGACC---AAGgt-gag--------gagg
            Lizard  ACTCC-GTCACCGACATCTT-GGGCATCAGG-TCCATCACGGATC---AAGgt-aagag-cctctgaag
     X. tropicalis  ATTCG-GTTACAGACATCCT-TGGGATTCGC-TCCATCACCGACC---AAGgt-aag-a-a--------
            Medaka  ACACC-GTCAGTAACATCCT-GGGAATACGC-GCCTTCATGGATCCCACAGgt-gag-g-a--------
       Stickleback  ACTCG-GTGACAGATATTCT-GGGGATACGG-TCTATTACAGAGCAACAAAgt-aag-c-acggctg--
              Fugu  ACTCT-GTTACAGATATTCT-GGGGATTCGG-TCAATCACAGAGCAACAAAgt-aag-c-atggctg--
         Tetraodon  ACTCC-GTCACAGATATTCT-GGGGATCCGG-TCGATCACAGAGCAACAAAgt-aag-c-atggctg--
         Zebrafish  ATTCT-GTTACAGATATTCT-GGGCATTCGA-TCAATAACGGAGCAGCAAAgt-aag-c-atc------

Inserts between block 33 and 34 in window
B D       Chicken 9bp
B D        Lizard 2977bp
B D X. tropicalis 1292bp
           Medaka 661bp
B D     Zebrafish 2274bp

Alignment block 34 of 255 in window, 57798204 - 57798211, 8 bps 
B D          Mouse  --c----ag-------------------tg-tgc
B D            Rat  --c----ag-------------------tg-tgc
        Guinea pig  --c----cggact-t----gagg----atg-tgc
            Rabbit  --c----cgggcg-g----gtga----aag-tgt
B D          Human  --c----tgggcg-t----gtgg----atg-tgc
B D          Chimp  --c----tgggcg-t----gtgg----atg-tgc
B D      Orangutan  --c----tgggcg-t----gtgg----atg-tgc
B D         Rhesus  --c----tggtca-t----gtga----atg-tgc
B D       Marmoset  --c----agggcg-t----gtgg----atg-tgc
          Bushbaby  --c----tggacg-t----gtgg----atg-tgc
B D     Tree shrew  --------------------------------gc
B D          Shrew  --c----cggggg-a----tggaga-tgtg-cag
B D       Hedgehog  --c----caggcg-g----cgag-----------
B D            Dog  --c----cggacg-t----gtgg----gtg-tgc
B D            Cat  --c----cggatg-t----gtgg----acgttgc
B D          Horse  --c----ccgatg-t----gtgg----atg-tgc
B D            Cow  --c----cggata-t----ggga----ttg-tgc
         Armadillo  --c----ggggtg-tgcagatat----ata-tgc
          Elephant  --cccggagggt-------gtga----gtg-tgc
B D         Tenrec  --ttgcgggggtg-taagcgtga----gtg-tgc
B D        Opossum  --t----tggacc-g----tggc----gcg-cct
B D       Platypus  --c----cgggtg-a----ctcg----ggg-cga
B D        Chicken  --c----cgggcact----gagc----ttc-cgc
B D  X. tropicalis  -----------------------aacttag-cgc
B D    Stickleback  cat----gg-------------------------
B D           Fugu  cac----cgagc----------------------
B D      Tetraodon  cac----cgagc----------------------
           Medaka  ==================================
B D      Zebrafish  ==================================
B D         Lizard  ==================================

Inserts between block 34 and 35 in window
B D          Fugu 3403bp

Alignment block 35 of 255 in window, 57798212 - 57798229, 18 bps 
B D          Mouse  --------agagcggagtgggttcc---t
B D            Rat  --------taggcggagagcgttcc---t
        Guinea pig  --------acggc-----gtgtccc---c
            Rabbit  --------tcgga-----acctgcc---t
B D          Human  --------agcgt-----ctgcccc---c
B D          Chimp  --------agcgt-----ctgcccc---c
B D      Orangutan  --------agcgt-----ctgcccc---c
B D         Rhesus  --------agcgt-----ctgcttc---c
B D       Marmoset  --------agcat-----ctgcctc---c
          Bushbaby  --------agagc-----ctgaccc---c
B D     Tree shrew  --------agagc-----ttgcctc---c
B D          Shrew  --------agagc-----ttttttg---g
B D       Hedgehog  -----------------------tg---g
B D            Dog  --------agagc-----cttcctc---t
B D            Cat  --------agagt-----cttcctc---t
B D          Horse  --------agagc-----ctccctc---c
B D            Cow  --------agagc-----ttccctc---c
         Armadillo  --------agcgc-----cctccctagtc
          Elephant  --------agcgc-----ctcccct----
B D         Tenrec  --------cgcac-----ctcctct----
B D        Opossum  --------ggggc-----ctggaag----
B D       Platypus  --------gtcgc-----ttcactc----
B D        Chicken  --------gggac-----gtgcccc----
B D  X. tropicalis  --------agtct-----gggtgct---a
B D      Tetraodon  acagcggaggggt-----tatt-------
B D    Stickleback  agggcggttgcgt-----ttct-------
B D           Fugu  =============================
           Medaka  =============================
B D      Zebrafish  =============================
B D         Lizard  =============================

Inserts between block 35 and 36 in window
B D     Tetraodon 3bp
B D   Stickleback 5079bp

Alignment block 36 of 255 in window, 57798230 - 57798280, 51 bps 
B D          Mouse  gcacgc------gttc-----g--ggaaccccagtacct-tcggcct------c-t-agcgagtgtctat
B D            Rat  gcaagc------ggtc-----g--ggaatcccagtacct-tcggcct------c-t-atcgagtgtctat
        Guinea pig  agactc------ccgg-----g--ggaatcctattatct-gcggcct----gcc-t-ggcccgggtcgat
            Rabbit  gcgccc------ttgc-----gctgggaccccggcgtct-gcggcct-----cc-c-ggcccgggtccat
B D          Human  gcactc------tcgc-----g--gaggtcccagtatct-gcagcct------c-agggacactgtcttt
B D          Chimp  gcactc------tcgc-----g--gaggtcccagtatct-gcagcct------c-agggacactgtcttt
B D      Orangutan  gcactc------tcgc-----g--gaggtcccagtatct-gcggcct------c-agggacactgtcttt
B D         Rhesus  gcactc------cagc-----g--gaggtaccagtttct-gcggcct------c-cgggaccctgtcttt
B D       Marmoset  gcattc------ccgc-----g--gaggtcccactatct-gcggcct------c-tgggaccctgtcttt
          Bushbaby  gcaccc------ctgc-----g--gagagcccagtatctcgcggcct------c-c-ggcccgtgtctat
B D     Tree shrew  gcgccc------ct-c-----g--gggatcccagtatct-gcggcct------t-c-gagccgagctgaa
B D          Shrew  gagccc------tggt-----t--gg-ggtctggcccct-cgggtctccgagcc-caggcccgtgtccgt
B D       Hedgehog  atgcct---------------------gtgcaggcccct-tgggtct----------------tgaccgg
B D            Dog  gcaccc------tcgc-----t--ggtgtctccgtatct-gcggcct------c-ggggcccgcgcctat
B D            Cat  acaccc------tcgt-----t--ggtgtctcggtatct-gcggcct------c-cgagcccgcgtctat
B D          Horse  gcaccc------tagc-----t--ggggtttctctatct-gaggcct------c-cgggcccccgtccgt
B D            Cow  tcaacc------tctc-----t--ggggttaccgcatct-gcgtctc------caggggcccgcgtctgt
         Armadillo  cacccc------cagc-----g--ggggtccgggtatct-gcgtcct------c-tccggcggtgtcgat
          Elephant  ------------tcgc-----t--gaggttccagtatct-gaggcct------c-caggcctgagtatgt
B D         Tenrec  ------------tcgc-----g--gagataccgggatct-gaggccg------c-caggcccctgcccat
B D        Opossum  ---------------------g--gagggaatagtagca-acgatat------t-c-------atcttct
B D       Platypus  -------------ctc-----t--gggcctccgtcttct-------------------------------
B D        Chicken  ------------------------gtgattcgggtac---------------------------------
B D  X. tropicalis  acaggc------tctccgccaa--gcgtaaccattacct-gct--------------agtcagcaaccat
B D      Tetraodon  gtgcgtgatggatggc-----t--agagaaccagttctg-gctgccg------g-caggacaataatgc-
B D           Fugu  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D         Lizard  ======================================================================

             Mouse  ccc
               Rat  ccc
        Guinea pig  gcc
            Rabbit  ccc
             Human  ccc
             Chimp  ccc
         Orangutan  ccc
            Rhesus  ccc
          Marmoset  cct
          Bushbaby  ccc
        Tree shrew  cct
             Shrew  ctc
          Hedgehog  ttc
               Dog  ccc
               Cat  ccc
             Horse  ccc
               Cow  ccc
         Armadillo  ccc
          Elephant  tct
            Tenrec  gcc
           Opossum  cgc
          Platypus  ---
           Chicken  ---
     X. tropicalis  tcc
         Tetraodon  ---
              Fugu  ===
       Stickleback  ===
            Medaka  ===
         Zebrafish  ===
            Lizard  ===

Inserts between block 36 and 37 in window
         Elephant 1bp
B D      Platypus 790bp
B D       Chicken 1092bp

Alignment block 37 of 255 in window, 57798281 - 57798355, 75 bps 
B D          Mouse  ---a----ccacctgtggctctttt------cttttgg--aaacct--------aaggagtcttcc-ca-
B D        Opossum  ---c----tcatcctagcc-tttctttaagactttcaa--acagct--------ttagtgtcttccgca-
B D         Tenrec  ---a----ccacctggcct-ttttg------cctttgg--aaaa-t--------caggcgtccttc-tg-
          Elephant  ---a----tcacctgaggc-ttttg------cattt-g--aaac-t--------aaggagtcctcc-cg-
         Armadillo  ---a----ccacctgaggc-ttttt------cctttgg--aaacgt--------aagacattctcc-cg-
B D            Cow  ---a----ccacctgagac-ttttt------cctttgg--aaacgt--------caagagtcctcc-ca-
B D          Horse  ---a----ccaccggaggc-ctttt------cctttgg--aaatgt--------aagcagtcctcc-ca-
B D            Cat  ---a----ccacctgaggc-ttttt------cctttcg--aaact----------atgagtcctcc-cag
B D            Dog  ---a----ccacctgaggc-ttttt------cctttcg--aaacg---------aaggagtcctcc-ca-
B D       Hedgehog  ---a-----------------------------gttgg--aaaccg--------aaggactcctcc-ccg
B D          Shrew  ---acccactacgcgaggc-ttctc------tctttgg--aaacgc--------aaggagtcttcc----
B D     Tree shrew  ---g----ccatatgaggt-ttatt------cctttgg--aaatgt--------aaggagtcttcc-ca-
          Bushbaby  ---a----ccacctgaggc-ttttt------cctttgg--aaacgt--------aaggagtcttcc-ca-
B D       Marmoset  ---a----tcacctgaggc-ttttt------cctttgg--aaacgt--------aaggagtcttcc-ta-
B D         Rhesus  ---a----ccacctaaagc-ttttt------cctttgg--aaaagt--------aaggagtcttcc-ta-
B D      Orangutan  ---a----ccacctgaggctttttt------cctttgg--aaacgt--------aaggagtcttcc-ta-
B D          Chimp  ---a----ccacctgaggc-ttttt------cctttgg--aaacgt--------aaagagtcttcc-ta-
B D          Human  ---a----ccacctgaggc-ttttt------cctttgg--aaacgt--------aaggagtcttcc-ta-
            Rabbit  ---a----ccacccgaggc-ctttt------cctttgg--aaacga--------aaggcggcttcc-ca-
        Guinea pig  ---a----ccacttgaggc-ttttt------cctttgg--agtcat--------aaggagtcttcc-ca-
B D            Rat  ---a----ccacctgtggc-ctttt------cttttgg--aaacct--------aaggagtcgtcc-ca-
B D      Tetraodon  agga----ctgc-----gt-ttcac------cattcagccgaaagtccactttcaataggcctttt-ca-
B D           Fugu  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  --------------------------------g------------------------ggggtgt------
           Opossum  --------------------------------t------------------------ggggaattactgt
            Tenrec  --------------------------------ggggggcggcgcagtgggggtgggggtggtgc------
          Elephant  --------------------------------g-----------agaggggagggggaaggtgt------
         Armadillo  --------------------------------g------------------------ggggtgc------
               Cow  --------------------------------g------------------------ggggtgt------
             Horse  --------------------------------g------------------------ggggtgt------
               Cat  --------------------------------g------------------------ggggtgt------
               Dog  --------------------------------g------------------------ggggtgt------
          Hedgehog  ggtggtgtggtggagatggtggtggtggtggta------------------------gtggtgt------
             Shrew  ------------agggcggggggcgtgtgtgtg------------------------tgggggt------
        Tree shrew  --------------------------------g------------------------ggggtgt------
          Bushbaby  --------------------------------g------------------------ggggtgt------
          Marmoset  --------------------------------g------------------------ggggtgt------
            Rhesus  --------------------------------g------------------------ggggtgt------
         Orangutan  --------------------------------g------------------------ggggtgt------
             Chimp  --------------------------------g------------------------ggggtgt------
             Human  --------------------------------g------------------------ggggtgt------
            Rabbit  --------------------------------g------------------------gggggac------
        Guinea pig  --------------------------------g------------------------ggggtgt------
               Rat  --------------------------------g------------------------ggggtgt------
         Tetraodon  --------------------------------t------------------------gggatga------
              Fugu  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  --------------cctgatctcatta------------------acttgaaac
           Opossum  ctcgcgattgcccacctgatcccgttatagaacaggaagatttttattgggaag
            Tenrec  --------------cctgctctcatta------------------acttgaaat
          Elephant  --------------cctgctctcatta------------------acttgaaat
         Armadillo  --------------cctgatctcatta------------------acttgaaac
               Cow  --------------cctgatctcatta------------------acgtgaaat
             Horse  --------------cctgatctcatta------------------acttgaaat
               Cat  --------------cctgatctcatta------------------acttgaaat
               Dog  --------------cctgatctcatta------------------acttgaaat
          Hedgehog  --------------cctgatctcatta------------------acttg-aat
             Shrew  --------------cctgatctcatta------------------acttgaaat
        Tree shrew  --------------cctgatctcatta------------------acttgaagc
          Bushbaby  --------------cctgatctcatta------------------acttgaaac
          Marmoset  --------------cctgatctcatta------------------acttgaaac
            Rhesus  --------------cctgatctcatta------------------acttgaaac
         Orangutan  --------------cctgatctcatta------------------acttgaaac
             Chimp  --------------tctgatctcatta------------------acttgaaac
             Human  --------------tctgatctcatta------------------acttgaaac
            Rabbit  --------------cctgatctcatta------------------actcgaaac
        Guinea pig  --------------cctgatctcatta------------------acttgaaac
               Rat  --------------cctgatctcatta------------------acttgaaac
         Tetraodon  --------------tgcgtttgcaaac------------------actttgctc
              Fugu  ======================================================
       Stickleback  ======================================================
            Medaka  ======================================================
         Zebrafish  ======================================================
     X. tropicalis  ======================================================
          Platypus  ======================================================
           Chicken  ======================================================
            Lizard  ======================================================

Alignment block 38 of 255 in window, 57798356 - 57798408, 53 bps 
B D          Mouse  -------tcttgccc---ctctgttt----cc----ttgc--c------------acacacag-------
B D            Rat  -------tcttgccc---ctctgttt----cc----ttgccac------------acacacag-------
        Guinea pig  -------ttttgccc---ct-ggttt----cc----ttgc--c------------acacacag-------
            Rabbit  -------tcctgccc---ct--gctt----cc----ttgc--c------------acacacag-------
B D          Human  -------tcatgccc---ct-ggttt----cc----ttgc--c------------acacacag-------
B D          Chimp  -------tcatgccc---ct-ggttt----cc----ttgc--c------------acacacag-------
B D      Orangutan  -------tcatgccc---ct-ggttt----cc----ttgc--c------------acacacag-------
B D         Rhesus  -------tcatgccc---ct-ggttt----cc----ttgc--c------------acacacag-------
B D       Marmoset  -------gcttgccc---ct-ggttt----cc----ttgc--c------------acacacag-------
          Bushbaby  -------tcatgccc---ct-agttt----cc----tcgc--c------------acacacag-------
B D     Tree shrew  -------tcctgccc---ct-cgttt----cc----ttgc--c------------acacacag-------
B D          Shrew  -------tcatgccc---tt-ccttt----cc----ttgc--c------------acacacag-------
B D       Hedgehog  -------acatgcct---tt-ccttc----cc----ttg---c------------acaaacag-------
B D            Dog  -------tcatgccc---tc-tgttt----cc----ttgc--c------------acacacag-------
B D            Cat  -------tcatgccc---tc-cgttt----cc----ttgc--c------------acacacag-------
B D          Horse  -------tcatgccc---tt-cgttt----cc----ttgc--c------------acacacag-------
B D            Cow  -------tcatgccc---tt-cgttt----cc----ttgc--c------------acacacag-------
         Armadillo  -------tcctgccc---ct-cgttt----cc----ttgc--c------------acacacag-------
          Elephant  -------tcatgcct---ct-cgttt----cc----ttgc--c------------acacacag-------
B D         Tenrec  -------tcatgccc---ct-cgttt----cc----ttgc--c------------acccacag-------
B D        Opossum  -------cagtgctc---cc----tt----ct----ctgc--cttctctgtttgaaatcgctg-------
B D       Platypus  -------tcttgccccggcc-cgttttaaccg----tttt--c------------agctgcag-------
B D      Tetraodon  acctgttatatcccc---tt-taatc----ccccagctac--t------------acagacatatgtcac
B D           Fugu  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  ----tctccag--cc--tcatctcaaacta
               Rat  ----tttccag--cc--tcatctcaaacta
        Guinea pig  --tctctcctg--cc--tcatctcaaacta
            Rabbit  ----cctcctg--cc--tcatctcaaacta
             Human  ----tcttctg--cc--tcatctcaaacta
             Chimp  ----tcttctg--cc--tcatctcagacta
         Orangutan  ----tctcctg--cc--tcatctcaaacta
            Rhesus  ----tctcctg--cc--tcaactcaaacta
          Marmoset  ----tctcctg--cc--tcatctcaaacta
          Bushbaby  ----tctcctg--cc--tcatctcaaacta
        Tree shrew  ----tctccag--cc--tcatctcaaacta
             Shrew  ----tctcctg--cc--tcatctcaaacta
          Hedgehog  ----tctcctg--cc--tcatctcagactc
               Dog  ----tctcctg--cc--tcatctcaaacta
               Cat  ----tctcctg--cc--tcatctcaaacta
             Horse  ----tctcctg--cc--tcatctcaaacta
               Cow  ----tctactg--cc--tcatctcaaacta
         Armadillo  ----tctcctg--cc--tcatctcaaacta
          Elephant  ----tctcctg--cc--tcatctcaaacta
            Tenrec  ----tctcctg--cc--tcatctcaaacta
           Opossum  ----ttttttc--cccttcacctcaagct-
          Platypus  ----cccccag--cc--gttttgcagacac
         Tetraodon  tgcttctccagaccc--ttatcccaagttt
              Fugu  ==============================
       Stickleback  ==============================
            Medaka  ==============================
         Zebrafish  ==============================
     X. tropicalis  ==============================
           Chicken  ==============================
            Lizard  ==============================

Inserts between block 38 and 39 in window
B D      Platypus 6bp
B D     Tetraodon 616bp

Alignment block 39 of 255 in window, 57798409 - 57798514, 106 bps 
B D          Mouse  ccagacccataacataccccc---ccc-----cccaaacacatggttcgcatttt-ccaccct-cccccg
B D            Rat  ccagacccataacatcccccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
        Guinea pig  ccagacccataacat----cc---ccca---tccccaacacatggttcgcatttt-ccaccct-gccccg
            Rabbit  ccagacccataacat----cc---ccca---gccccaacacatggttcgcatttt-ccaccct-cccccg
B D          Human  ccagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
B D          Chimp  ccagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
B D      Orangutan  ccagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
B D         Rhesus  tcagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
B D       Marmoset  ccagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
          Bushbaby  ccagacccataacat--cccc---ccca---ttcccaacacatggttcgcatttt-ccaccct-cctccg
B D     Tree shrew  ccagacccataacat---ccccctccca---tccccgacacatggttcgcatttt-ccaccct-cccccg
B D          Shrew  ccagacccataacat---ccc---ccca---gccccaacacatggttcgcatttt-ccatcct-cccccg
B D       Hedgehog  ccagacccataacat---ccc---cccctatttccaaacacatggtttcctttttcccaccctacccccg
B D            Dog  ccagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
B D            Cat  ccagacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
B D          Horse  ccagacccataacat---ccc---ccca---tccctaacacatggttcgcatttt-ccaccct-cccccg
B D            Cow  ccagacccataacat----cc---ccca---tccccaacacatggttcgcatttt-ccaccct-cccccg
         Armadillo  ccaaacccataacat---ccc---ccca---tccccaacacatggttcgcatttt-ccacccg-ccccca
          Elephant  ccagacccataacat---ccc---ccca---gccccaacacatggttcacatttt-ccaccct-cccccg
B D         Tenrec  ccagaccctgaacat----cc---ccca---gccccgacacatggttcacatttt-ccaccct-cccccg
B D        Opossum  ----actcagcagac--tcct---tccc---aaccaaactcatgattcacatgct-ccttttc-cttttc
B D       Platypus  gagggtgcagggcat---------tcga---tcctcagcgtttggtacaaatttg-cagccct-cc----
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  cctctcgcgcact-----------------------c-------------------agcc-tca-gccgg
               Rat  cctctcgcgcact-----------------------c-------------------agcc-tca-gccgg
        Guinea pig  cctctcgcgccgc----g-----------------gc-------------------agtc-tca-gccgg
            Rabbit  cctctcgcgccgc----gccgcgccgcgccgcgccgc-------------------agcc-tca-gccgg
             Human  cctctcgcgccga----g-----------------gc-------------------agcc-tca-gcccg
             Chimp  cctctcgcgccga----g-----------------gc-------------------agcc-tca-gcccg
         Orangutan  cctctcgcgcgga----g-----------------gc-------------------agcc-tca-gcccg
            Rhesus  cctctcgcgccaa----g-----------------gc-------------------agcc-tca-gcccg
          Marmoset  cctctcgagccga----g-----------------gc-------------------ggcc-tca-gcccg
          Bushbaby  cctctcgcgccgc----g-----------------gc-------------------agtc-tcaggccgg
        Tree shrew  cctctctctcggc----t-----------------gc-------------------agcc-tct-gcccg
             Shrew  cctctcgcgccgc----c-----------------gc-------------------ggcc-tca-gactg
          Hedgehog  ctttttgggccgc----g-----------------gc-------------------ggccttca-gacag
               Dog  cctctcgcgccgc----g-----------------gc-------------------agcc-tta-gaccc
               Cat  cctctctcgccgc----t-----------------gc-------------------tgcc-tca-gaccc
             Horse  cctctcgcgccac----c-----------------gc-------------------agcc-tca-gaccg
               Cow  cctctcgcgccgc----g-----------------gc-------------------agcc-tcg-gacca
         Armadillo  ccccccgcgccgc----g-----------------gc-------------------agct-cca-gccgg
          Elephant  ccccctgcgccgcgccag-----------------gc-------------------agct-tca-ggctg
            Tenrec  ccccctgcgctgc----c-----------------gc-------------------ggcc-tcc-gtcag
           Opossum  tttctttctcctt----t-----------------gctttagaatttatcttctagaatt-tcg-tccaa
          Platypus  -----------------g-----------------gc----------------------c-tga-g----
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  gctagactgt-ttggag-ag-cg-
               Rat  gctagactgt-ttggag-ag-cg-
        Guinea pig  gct----tgc-tcacagcag-cg-
            Rabbit  gcttgctcac-tcggag-ag-cg-
             Human  gcttgctcac-ttggag-ag-tg-
             Chimp  gcttgctcac-ttggag-ag-tg-
         Orangutan  gcttgctcac-ttggag-ag-tg-
            Rhesus  gcttgctcac-ttggag-ag-ca-
          Marmoset  gcttgctcac-ttgaag-ag-ag-
          Bushbaby  gctcgcagaa-gcgcag-ag-cg-
        Tree shrew  gcttgctcactttggag-ag-cg-
             Shrew  gctcgctcgc-ttgcag-ag-cg-
          Hedgehog  actttttcgc-agagag-ag-ca-
               Dog  gctcgctcgc-ttggag-ag-cg-
               Cat  gttcgctcac-ttggag-ag-cg-
             Horse  gctcactcac-ttggag-agccg-
               Cow  gcctgctcac-ttggag-ag-cg-
         Armadillo  gctcgctcac-ttggag-ag-cg-
          Elephant  gctggctggc-ttggag-ag-cg-
            Tenrec  gcgggctacc-tcggag-cg-cg-
           Opossum  atttcgaatc-ccgtgc-ag-ca-
          Platypus  --------gc-gggggg-aa-tgg
              Fugu  ========================
         Tetraodon  ========================
       Stickleback  ========================
            Medaka  ========================
         Zebrafish  ========================
     X. tropicalis  ========================
           Chicken  ========================
            Lizard  ========================

Inserts between block 39 and 40 in window
       Guinea pig 1bp

Alignment block 40 of 255 in window, 57798515 - 57798548, 34 bps 
B D          Mouse  cagcctgg----cgatttgggga---gcacaag-aggaggcc
B D            Rat  cagcctgg----agatttgggga---gcacaag-agaaggcc
        Guinea pig  ttgcccga-g-ccgaccagaggc---gctgccc-gggagggc
            Rabbit  cggccggg-gccggacttggggc---tcagccc-gggaggcc
B D          Human  cggccggg-gctggacttggggc---gcagccc-gggaggcc
B D          Chimp  cggccggg-gctggacttggggc---gcagccc-gggaggcc
B D      Orangutan  cggccggg-gctggacttggggc---gcagcccggggaggcc
B D         Rhesus  cggctggg-gctggacttggggc---gcagccc-gggaggcc
B D       Marmoset  cgtcc-gg-gccggacttggggg---gcagccc-gggaggcc
          Bushbaby  cggcc--g-gccggacttgggga---gcagcccaggagggcc
B D     Tree shrew  cagccggg-gccggacttggggc---gcagccc-ggaaggcc
B D          Shrew  cggccagg-acccgacttgggga---gcagccc-agcaggcc
B D       Hedgehog  cgccccggcgccggacttgggggc--gcagccc-ggaaggcc
B D            Dog  cggcccgg-gtcggacttggggc---gcagccc-gggaggcc
B D            Cat  tggcccgg-gttggactgggggc---tcagccc-gggaggac
B D          Horse  cggccggg-gccggacttggggc---gcagccc-gggaggcc
B D            Cow  cggccggg-gccggacttgggga---gcagccc-gagaggcc
         Armadillo  cagccggg-gccggacttggggc---gcagccc-gggaggcc
          Elephant  cggcccgg-gctggacttgggac---ccagccg-gggaggcc
B D         Tenrec  cggccggg-gccggtc-gggggc---gcagccc-gggaggcc
B D        Opossum  taac-----tttagatttaaata---gcagggg-agaaggga
B D       Platypus  cggcctga-ggcgg----ggggaatggcaggtt-aaagag--
B D           Fugu  ==========================================
B D      Tetraodon  ==========================================
B D    Stickleback  ==========================================
           Medaka  ==========================================
B D      Zebrafish  ==========================================
B D  X. tropicalis  ==========================================
B D        Chicken  ==========================================
B D         Lizard  ==========================================

Inserts between block 40 and 41 in window
B D       Opossum 36bp

Alignment block 41 of 255 in window, 57798549 - 57798584, 36 bps 
B D          Mouse  ctag---caggct--tggggctgcgggttgt-aggtagccac
B D       Platypus  ----ccaccaggg--caggaaggcggcccgagacac-gcacc
B D            Rat  ctag---caggct--tggggctgcgggctgt-agatggccac
        Guinea pig  ccag---tcggct--tggggcagtcggcagc-agat-gcctc
            Rabbit  cgag---ccggcg--tggggctaccggctgc-aaac-gccgc
B D          Human  cgag---cctgct--tggggctgccggctgc-agac-tccgc
B D          Chimp  cgag---cctgct--tggggctgccggctgc-agac-tccgc
B D      Orangutan  cgag---cctgct--tggggctgccggctgc-agac-gccgc
B D         Rhesus  ggag---cctgct--tggggctgccggctgc-agac-gccgc
B D       Marmoset  tgag---cctgct--tggggctgccggctgc-agat-gccgc
          Bushbaby  cgagc--cctgcg--tggggctgcgagcggc-aggc-gccgc
B D     Tree shrew  cgag---ccggct--tggggctgcgggttgc-agag-gccgc
B D          Shrew  cgag---ccggcg--aggggctgccggcggc-agac-gccgc
B D       Hedgehog  cgag---cgggtg--tggggctgcgggctgc-cgac-gccgc
B D            Dog  tgag---ccggcg--tggggctgctggctgc-agac-accgc
B D            Cat  tgag---cgggcg--tggggctgccggttgt-agac-accgc
B D          Horse  cgag---ccggcg--tggggctgccggctgc-agac-accgc
B D            Cow  cgag---cgggcg--tggagctgccggctgc-agac-acggc
         Armadillo  ggag---caggcgt-gggggccgcaggcttc-agac-gccgc
          Elephant  ggag---ccggct--tggggccgccggctgc-agac-gccgc
B D         Tenrec  gagg---ccggcttgtggggctgcaggcagc-aggc-gacgc
B D           Fugu  ==========================================
B D      Tetraodon  ==========================================
B D    Stickleback  ==========================================
           Medaka  ==========================================
B D      Zebrafish  ==========================================
B D  X. tropicalis  ==========================================
B D        Opossum  ==========================================
B D        Chicken  ==========================================
B D         Lizard  ==========================================

Alignment block 42 of 255 in window, 57798585 - 57798638, 54 bps 
B D          Mouse  tgtcggc-----agcttgctcac--------------ga---------------------gtcag--atg
B D         Tenrec  tgcaggt-----tgcccgctcggtggtgggtgggtgagg---------------------gtcag--atg
          Elephant  tgcaggc-----acctcgctcgt--------------gg---------------------agcag--att
         Armadillo  tgcccgc-----agcttgctcgg--------------gc---------------------attag--atg
B D            Cow  ttcgggc-----ggcttgtttgg--------------gg-------------------------------
B D          Horse  tgcgggc-----ggcttgttcgg--------------gg---------------------atcag--atg
B D            Cat  tgcgggc-----agcttgtttgg--------------gg---------------------atcag--atg
B D            Dog  tgcgggc-----ggcttgtttgg--------------gg---------------------atcag--atg
B D       Hedgehog  tgcgggg-----agcttgtttgg--------------ggcggggggggggggagggcataatctg--ttg
B D          Shrew  tgcggac-----agcttgtttgg--------------gg---------------------atcac--ttg
B D     Tree shrew  tgccggc-----agcttgcttgg--------------gg---------------------atcag--atg
          Bushbaby  tgcgggc-----agcgtgcttgg--------------gg---------------------atcag--atg
B D       Marmoset  tgcaggcagagtagcttgcttgg--------------gg---------------------atcac--aga
B D         Rhesus  tgcgggcagagcagcttgcttgg--------------gg---------------------atcac---ta
B D      Orangutan  tgcgggcagagcagcttgcttgg--------------gg---------------------atcac---ta
B D          Chimp  tgtgggcagagcagcttgcttgg--------------gg---------------------atcac---ta
B D          Human  tgtgggcagagcagcttgcttgg--------------gg---------------------atcac---ta
            Rabbit  tgcgggc-----agcttgctccg--------------gg---------------------atcag--agg
        Guinea pig  tgg-agc-----agcttgcttgc--------------ga----------------------tcag--atg
B D            Rat  tgtccgc-----agcttgctcac--------------ga---------------------atcag--atg
B D       Platypus  cacaggc-----aactcgcctcg--------------ca---------------------agacc--ctc
B D         Lizard  tgcctgt-----tgtttgctctc--------------aa---------------------gtcagggatt
B D        Opossum  ----------------gtctcga--------------ct---------------------cccag--atg
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================

             Mouse  c----cgcagct------acg---------------agtccccgcacactc
            Tenrec  cggctggccggg------aag---------------agc-ccggcactagg
          Elephant  c----ggccgcg------agg---------------agt-ccggcgcacgg
         Armadillo  c----gccggcg------agg---------------agt-cgggcacgctg
               Cow  ------------------------------------agt-cggggactctg
             Horse  c----ggccgcg------agga--------------agt-cgggcaccctg
               Cat  c----ggccgcg------agg---------------agt-tgggcaccctg
               Dog  c----ggccgcg------agg---------------agt-cgggcaccctg
          Hedgehog  t----ggccgcg------aga---------------agt-cgggcgccctg
             Shrew  c----ggccccg------agg---------------agt-agggcacccag
        Tree shrew  c----cgctgcg------agg---------------agt-ctagcacgctg
          Bushbaby  a----ggccgcg------acg---------------agt-ac-gcgcgcag
          Marmoset  c----gcccggg------agg---------------agt-ccagcacgcgg
            Rhesus  c----ggccggg------agc---------------agt-ccagcacgcgg
         Orangutan  c----agccggg------aggagtccggccaggaggagt-ccagcacgccg
             Chimp  c----ggccggg------agaagtctggccgggaggagt-ccagtacgcct
             Human  c----ggccggg------agaagtctggccgggaggagt-ccagcacgcct
            Rabbit  c----ggt-gcg------agg---------------agg-ccggtgcgcgg
        Guinea pig  c----agcagct------aag---------------agt-cccatatgatg
               Rat  c----agcagct------acg---------------agt-cccgcacactc
          Platypus  c----cgtgctc------cgg---------------gcc-tgtgcacacta
            Lizard  t----cgcagga------aag---------------gca-tctcc------
           Opossum  c----agactcacatagcaag---------------agc-ttttca-----
              Fugu  ===================================================
         Tetraodon  ===================================================
       Stickleback  ===================================================
            Medaka  ===================================================
         Zebrafish  ===================================================
     X. tropicalis  ===================================================
           Chicken  ===================================================

Inserts between block 42 and 43 in window
B D      Platypus 1bp

Alignment block 43 of 255 in window, 57798639 - 57798738, 100 bps 
B D          Mouse  tggaaattgtatta---tt---att---c---tcggattc-------tggcaatcagggcaaa-tttgct
B D         Lizard  ttgaaattgcaggc---aa---atc---cacctccagttc-------tcgcaatcaggccaaa-tttgct
B D       Platypus  tggaatttgtagcg---tt---cgc---ctcctctcgtct-------tcgcaatcagaccaaa-tagact
B D        Opossum  ttgaaattgcaggg---tt---ccc---cttctcggattc-------tcgcaatcaggccaaa-tttgct
B D         Tenrec  gggaaatggcagag---tt---ctc---cttctcgggttc-------tggcaatcaggccaaa-tttgct
          Elephant  gggaaattgcagag---tt---ttc---cgtctcgggttc-------tggcaatcaggccaaa-tttgct
         Armadillo  tggaaattgcagtg---tt---cgc---cttcttgggttc-------tggcaatcaggccaaa-tttgct
B D            Cow  tagaaattgcagtattctt---ctt---g------cattc-------tggcaatcagaccaaa-tttgct
B D          Horse  tggaaattgcagta---tt---ctt---g------gattc-------tggcaatcagg-caaa-tttgct
B D            Cat  tggaaattgcagta---tt---ctt---g------gattc-------tggcaatcaggccaaa-tttgct
B D            Dog  tggaaattgcagta---tt---ctt---g------gattc-------tggcaatcaggccaaa-tttgct
B D       Hedgehog  tggaaatggcagtg---tt---ctt---g------gattc-------tggcaatcaggctaaa-tttgct
B D          Shrew  tagaaattgcagta---tt---cttcgag------gattc-------tggcaatcaggccaaa-tttgct
B D     Tree shrew  tggaaattgtagga---tt---ctt---cttctcggattc-------tggcaatcaggctaaa-tttgct
          Bushbaby  tggaaattgtagta---tt---ctt---ct--ttggattt-------tggcaatcaggccaaattttgct
B D       Marmoset  tggaaattgaagta---tt---ctc---c------cattt-------tggcaatcaggccaaa-tttgct
B D         Rhesus  tggaaattgaagta---ttcttctc---c------gattctggattgtggtaatcaggccaaa-tttgct
B D      Orangutan  tagaaattgaagta---tt---ctc---t------gattc-------tggtaatcgggccaaa-tttgct
B D          Chimp  tggaaattgaagta---tt---------c------gattc-------tggtaatcaggccaaa-tttgct
B D          Human  tggaaattgaagta---tt---ctc---c------gattc-------tggtaatcaggccaaa-tttgct
            Rabbit  tggaaattgtagta---tt---ctt---c---tcggatac-------tggcaatcagaccaaa-tttgct
        Guinea pig  tggaaattg---ta---gt---att---c---tcggattc-------tggcaatcaggctaaa-tttgct
B D            Rat  tggaaattgtatta---tt---att---c---tcggattc-------tggcaatcaggccaaa-tttgct
B D  X. tropicalis  -----------------------------ttctctgcctt-------gtgcaatcagactaaa-ttcacc
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D        Chicken  ======================================================================

             Mouse  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
            Lizard  cagacaggaagttcaaatgtcacctaattgctttcgttcttctgcttcac
          Platypus  caaacaggaagttcaaatgtcacctaattggtttcattcttatactccac
           Opossum  cagacaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
            Tenrec  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
          Elephant  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
         Armadillo  gaggcagaaagttcaaatgtcacctaattggtttcattcttatgcttcac
               Cow  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
             Horse  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
               Cat  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
               Dog  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
          Hedgehog  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
             Shrew  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcgc
        Tree shrew  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
          Bushbaby  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcag
          Marmoset  ccggcaggaagttcaaatgtcaactaattggtttcgttcttatgcttcac
            Rhesus  caggcaggaagttcaaatgtcacctaattggtttcgttcttatgcttcac
         Orangutan  caggcaggaagttcaaatgtcacctaattggtttcgttcttatgcttcac
             Chimp  caggcaggaagttcaaatgtcacctaattggtttcgttcttatgcttcac
             Human  caggcaggaagttcaaatgtcacctaattggtttcgttcttatgcttcac
            Rabbit  caggcaggaagttcaaatgtcacctaattggtttcgttcttatgcttcac
        Guinea pig  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcctcac
               Rat  caggcaggaagttcaaatgtcacctaattggtttcattcttatgcttcac
     X. tropicalis  cagacaggaagttcaaatgtcagataattggtttcattcttaggc-----
              Fugu  ==================================================
         Tetraodon  ==================================================
       Stickleback  ==================================================
            Medaka  ==================================================
         Zebrafish  ==================================================
           Chicken  ==================================================

Inserts between block 43 and 44 in window
B D       Opossum 248bp
B D X. tropicalis 2805bp

Alignment block 44 of 255 in window, 57798739 - 57798763, 25 bps 
B D          Mouse  ttcattttcctcggaaacggaggtc
B D            Rat  ttcattttcctcg----tcgcgctc
        Guinea pig  ttcattttcctcggaaacccaggtc
            Rabbit  ttcattttcctcggaaacggaggtc
B D          Human  ttcattttcctcggaaatggaggtc
B D          Chimp  ttcattttcctcggaaatggaggtc
B D      Orangutan  ttcattttcctcggaaatggaggtc
B D         Rhesus  ttcattttcctcggaaatagaggtc
B D       Marmoset  ttcattttcctcggaaatggaggtc
          Bushbaby  ttcattttcctcggaaaccgaggtc
B D     Tree shrew  ttcattttcctcggaaatggaggtc
B D          Shrew  ttcattttcctcggaaacagaggtc
B D       Hedgehog  ttcattttc----------------
B D            Dog  ttcattttcctcggaaacggaggtc
B D            Cat  ttcattttcctcggaaactgaggtc
B D          Horse  ttcattttcctcggaaaccgaggtc
B D            Cow  ttcattttcctcggaaacggaggtc
         Armadillo  ttcattttcctcagaaacggaggtc
          Elephant  ttcattttcctcggaaacggaggtc
B D         Tenrec  ttcattttcctcggaaatggaagtc
B D        Opossum  ttccttatactcggagtcttttccc
B D       Platypus  tttgttttccttaaccaggccggtc
B D         Lizard  tttgttttcctccaaagcggtggtc
B D           Fugu  =========================
B D      Tetraodon  =========================
B D    Stickleback  =========================
           Medaka  =========================
B D      Zebrafish  =========================
B D  X. tropicalis  =========================
B D        Chicken  =========================

Inserts between block 44 and 45 in window
B D        Lizard 1474bp

Alignment block 45 of 255 in window, 57798764 - 57798826, 63 bps 
B D          Mouse  tc-----ggtctct--------------------------------------------c--------tct
B D            Rat  tc-----tctctct--------------------------------------------c--------tct
        Guinea pig  ct-----ggttgct---agtaa-catgc-----ttgt----atctc------------c--------tct
            Rabbit  ccc---aagttactactagtaa-cttgc-----atga----ag---------------c--------tca
B D          Human  ccg---aagttactactagtaa-cttgc-----atgt----aa---------------c--------tca
B D          Chimp  ccg---aagttactactagtaa-cttgc-----gtgt----aa---------------c--------tca
B D      Orangutan  ccg---aagttactactagtaa-cttgc-----atgt----aa---------------c--------tca
B D         Rhesus  ccg---aagttactactagtaa-cttgc-----atgt----aa---------------c--------tca
B D       Marmoset  ccg---aagttactacta-----------------ct----aa---------------c--------tca
          Bushbaby  ccg---aagttactactagtaa-ctttctctctcttt----ct---------------c--------tcc
B D     Tree shrew  tca---aagttactactagtaa-cttac-----atgt----ag---------------c--------tca
B D          Shrew  ccg---acgttactactagtaa-cttgt-----atgt----tactg------------cgcagttgctca
B D       Hedgehog  -----------------------tgtgc-----atgt----gactg------------c---attgctta
B D            Dog  ccc---aagttactactagtaa-cttgc-----atgt----tgctgcattgctcattct---gggactca
B D            Cat  ccg---aagttactactagtaa-cttgc-----atgt----tactg------------c---attgctca
B D          Horse  ccg---aagttactactagtaa-cctgc-----atgt----tactg------------c---attgctca
B D            Cow  ccg---aagttactactagtaa-cttgc-----atgttagatagag------------c---attgctca
         Armadillo  cag---aagttactgcttgtag-cttgc-----atgc----ag---------------c--------tca
          Elephant  cag---aagttactactagtaa-cttgc-----atgt----ag---------------c--------tca
B D         Tenrec  ccg---aagttactactagtaa-cttgc-----atgt----ag---------------c--------tca
B D        Opossum  ccg--------------------ccccc-----ttgt---------------------c--------tct
B D       Platypus  caggaaagaaaactgctagtgaccctag-----atat----at---------------c--------tca
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  ctctc--------------tctctctctctctc-------tc------------tct-------------
               Rat  ctctc--------------tctctctctctctc-------tc------------tct-------------
        Guinea pig  ccccg--------------cctctgtctttctc-------tt------------cct-------------
            Rabbit  atccg--------------gctcgcgctctctc-------tc------------cct-------------
             Human  ttcccagacgaagtcatattcacattctctctc-------tc------------tct-------------
             Chimp  ttcccagacgaagtcatattcacattctctctc-------tc------------tct-------------
         Orangutan  ttcccagacgaagtcatattcacattctctctc-------tctgt--gtctctgtct-------------
            Rhesus  ttcccagatgaagtcatattcacattctctctc-------tc------------tct-------------
          Marmoset  ttcccagacgaggtcatattctctctctctctc-------tc------------tcc-------------
          Bushbaby  ctctc-----------tcctctctttctctcta-------tctcttggtctcggcct-------------
        Tree shrew  ttcagagaggaa-----------------tttt-------gt------------gct-------------
             Shrew  ttctaggactag-------ttttcttctttatt-------tc------------ttc-------------
          Hedgehog  ttctcacactga-------ttttctttat--tt-------cc------------ttt-------------
               Dog  ttttctgcttta-------tttctctctctctc-------tc------------tctctctctctctctc
               Cat  ttctgggactaa-------ttttctgctttatt-------tc------------tct-------------
             Horse  ttctgggactaa-------ttttctgctttatt-------tc------------tct-------------
               Cow  ttctgggacgaa-------ttttctgctttatt-------tc------------tct-------------
         Armadillo  ttgaatgaccaa-------ttttctgctttacttccctcttc------------tcc-------------
          Elephant  ttccgggactaa-------ttttctgctttatt----acttc------------tct-------------
            Tenrec  ttctgggactaa-------ttttctgctgtatt----acttc------------tca-------------
           Opossum  ccttagaactgt-------ttgctctcggtttt-------tc------------tcc-------------
          Platypus  gtcca-gacagc-------cccccccccccatt-------tt------------ttt-----------tc
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  -------ctctctctctctctctc---------------------------------cccttac-ct
               Rat  -------ctctctccccccccctct--------------------------------ctctccc-cc
        Guinea pig  -------tccttcccttattactcc--------------------------------cttccat-ct
            Rabbit  -------taacgt------------------------------------------------------
             Human  -------ctttctctctc---------------------------------------cattcac-tt
             Chimp  -------cttgctctctc---------------------------------------cattcac-tt
         Orangutan  -------ctctctctctc---------------------------------------cattcac-tt
            Rhesus  -------ctctctctcat---------------------------------------cattcac-tt
          Marmoset  -------ctctacctctc---------------------------------------ccc-------
          Bushbaby  -------ctctttctttcgtattcctcc-------------------------ccaaaattcacact
        Tree shrew  -------ttctcgctcac---------------------------------------agatca--tc
             Shrew  -------ctccctgacttaaaaaa---------------------------------aaatc-----
          Hedgehog  -------ctcctttatgtgaatat---------------------------------atata-----
               Dog  tctctgcctctctctttttcgtat---------------------------------cgctc-----
               Cat  -------ctccctttttttccaag---------------------------------cgccc-----
             Horse  -------ctctctct------------------------------------------ccctc-----
               Cow  -------ctttctcccgctctcct---------------------------------cctcc-----
         Armadillo  -------cgctctccctctcccccccccccacgcccccac----ccccagcgttctctcttt-----
          Elephant  -------ctctcttgatctag----------------------------tcgttctctattt-----
            Tenrec  -------cgcgcttgctctatctctcgc---------------------tcgctcttgattt-----
           Opossum  -------ttatct------------------------------------------------------
          Platypus  cctgtg-ctctctcgctccgacccgatgtgtcttcctcattttaccttttaaaaaaaaagt------
              Fugu  ===================================================================
         Tetraodon  ===================================================================
       Stickleback  ===================================================================
            Medaka  ===================================================================
         Zebrafish  ===================================================================
     X. tropicalis  ===================================================================
           Chicken  ===================================================================
            Lizard  ===================================================================

Inserts between block 45 and 46 in window
           Rabbit 73bp
B D         Shrew 6bp
B D      Hedgehog 6bp
B D           Dog 11bp
B D           Cat 11bp
B D         Horse 9bp
B D           Cow 15bp

Alignment block 46 of 255 in window, 57798827 - 57798879, 53 bps 
B D          Mouse  cccacc--------cacct-----cc-----------ctt-------------------------a----
        Guinea pig  ttcatt--------cttca-----tt-----------cttctttactcctgctgtgtccactctga----
B D            Rat  cctaac--------cactt-----tc-----------ctt-------------------------a----
B D          Human  ----------------tct-----aa-----------ctt-------------------------a----
B D          Chimp  ----------------tct-----aa-----------ctt-------------------------a----
B D      Orangutan  ----------------tct-----aa-----------ctt-------------------------a----
B D         Rhesus  ----------------tct-----aa-----------ctt-------------------------a----
B D       Marmoset  -------------------------------------ctt-------------------------a----
          Bushbaby  ----------------ttt-----ac-----------ctt-------------------------c----
B D     Tree shrew  ----------------ttt-----ac-----------ctt-------------------------a----
B D          Shrew  c---------------ttg-----ac----aggtatatat-------------------------agatt
B D       Hedgehog  c---------------ttt-----actttaatgtacactt-------------------------a---c
B D            Dog  c---------------ttt-----ac-----------ctt-------------------------a----
B D            Cat  c---------------ttt-----ac-----------ctt-------------------------a----
B D          Horse  t---------------ttt-----at-----------ctt-------------------------a----
B D            Cow  t---------------tct-----ac-----------ctt-------------------------a----
         Armadillo  ------------------------ac-----------ctg-------------------------a----
          Elephant  ------------------------ac-----------ctt-------------------------a----
B D         Tenrec  ----------------cctcgttgcc-----------ctt-------------------------a----
B D        Opossum  --caacttcttccacacct-----ag-----------act-------------------------a----
B D       Platypus  ----------------------------------------------------------------------
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================
           Rabbit  ======================================================================

             Mouse  acagacgtt------------aattatcaacccagtagt-------------------tgaggtgac
        Guinea pig  agagacatca--ccatcacaaaatgaccaagaccaaatg-------------------taagagggt
               Rat  acagacgtt------------aattatcaacccagtagt-------------------taaggtgac
             Human  acagacttca--c--------tgtatatatcttaggaag-------------------ggaagtggc
             Chimp  acagacttca--c--------tgtatatatcttaggaag-------------------ggaagtggc
         Orangutan  acagacttca--c--------tgtatatatcttaggaag-------------------ggaagtggc
            Rhesus  acagacttca--c--------tgtatatatcttagaaag-------------------ggaagtggc
          Marmoset  acagacttca--c--------cgtgtgtatcttaggagg-------------------ggaagtggc
          Bushbaby  acagactt---------------------------aagg-------------------gaaagtggc
        Tree shrew  acagacttca--c--------tatatctaccttaggaag-------------------ggaagtgac
             Shrew  atatactatagat--------tatacacaca-tag------------------------atatatgt
          Hedgehog  atacatttctaat--------aatatgtgt--tag------------------------aaagtgtc
               Dog  gccgacttcagtc--------tgtgtgtatcttag------------------------gaagtggc
               Cat  acagacttca--c--------tacttgtatcttag------------------------gaagtagc
             Horse  acagtcttca--c--------tatatatatcttag------------------------gaagtggc
               Cow  acagattttagca--------catatatatcctag------------------------gaagtggc
         Armadillo  acagagta----a--------aagatatatctcac------------------------a-agtggt
          Elephant  ccagacgt----c--------aatatctatctcag------------------------gcagtgga
            Tenrec  accgactt----c--------gatatatatcttaa------------------------gcagtggc
           Opossum  ccagagtcaaagc--------tgtgttttt-------------------------------------
          Platypus  -----cttcc--c--------gatgtgtggtttaggaaattaattttcataggcatatttaggtgat
              Fugu  ===================================================================
         Tetraodon  ===================================================================
       Stickleback  ===================================================================
            Medaka  ===================================================================
         Zebrafish  ===================================================================
     X. tropicalis  ===================================================================
           Chicken  ===================================================================
            Lizard  ===================================================================
            Rabbit  ===================================================================

Inserts between block 46 and 47 in window
B D         Human 25bp
B D         Chimp 25bp
B D     Orangutan 25bp
B D        Rhesus 25bp
B D      Marmoset 19bp
         Bushbaby 25bp
B D    Tree shrew 23bp
B D         Shrew 31bp
B D      Hedgehog 28bp
B D           Dog 29bp
B D           Cat 26bp
B D         Horse 26bp
B D           Cow 26bp
        Armadillo 25bp
         Elephant 25bp
B D        Tenrec 24bp
B D      Platypus 9bp

Alignment block 47 of 255 in window, 57798880 - 57799086, 207 bps 
B D          Mouse  -----aattgctag-gtgatt-----------cgctgttgtcc-----attcggctgc-------tgtc-
B D            Rat  -----aattgcttg-gtgatt-----------cgctgttgtcc-----tttcggctgc-------tgtc-
        Guinea pig  -----aa---------agaat-----------ccaagtgttct-----ttttcactgt-------tctca
            Rabbit  -----aagtgcatg-gcgact-----------ccatgccgtcc-----tttccac-gt-------tctt-
B D          Human  -----aaatgca-g-gcaatt-----------ccatgctg-tc-----cttttactgt-------tcttt
B D          Chimp  -----aaatgca-g-gcaatt-----------ccatgctg-tc-----cttttactgt-------tcttt
B D      Orangutan  -----aaatgca-g-gcaatt-----------ccatgctg-tc-----cttttactgt-------tcttt
B D         Rhesus  -----aaatgca-g-gcaatt-----------ccatgctg-tc-----cttttacggt-------tcttt
B D       Marmoset  -----aaatgca-g-gcgatt-----------ccatgccgttc-----tttttactgt-------tcttt
          Bushbaby  -----aaatggatg-gcgatt-----------ccaagctgttt-----tttctactgt-------tcttt
B D     Tree shrew  -----aaatgta-gagcgatt-----------ccatgctgttc-----attttattgt-------tcttt
B D          Shrew  ------tattcata-catcttagtgttatcaaccacactatactaatgtctttcctgt-------tcttc
B D       Hedgehog  ------aatgcagg-ggactt-----------ccacgctgccc-----tcttaaccgg-------acccc
B D            Dog  ------aatgcatg-gtgatt-----------tc-----atct-----tgtcctctct-------tcttt
B D            Cat  ------aatgcgtg-gtgatt-----------cc-----atct-----tgtcctctct-------tcttt
B D          Horse  ------aatgtatg-gcgatt-----------ccgtgctgtcc-----tgtcttctgt-------tcttt
B D            Cow  ------aatgcacg-gcgatt-----------ccacgctgtcc-----tctcttctgt-------tcttt
         Armadillo  -----aaatacgcg-gcacta-----------tcagggcatcc-----tttctggagt-------ctttc
          Elephant  -----aaatgcctg-acgatt-----------ccacgccttcc-----tttcttccgt-------ctttc
B D         Tenrec  -----------------------------------tggcttcc-----tttcctctgc-------cttcc
B D        Opossum  -----------------gatt-----------tcgcg-----c-----ttttagcagctaaagaatggtt
B D       Platypus  aactcagatg---g-gcgatt-----------tcttccttcct-----cccccccccc-------tttcc
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  tctg-----g-ttcc-----ccccagcctcctgctttcctt--a--------gggtcctc---------g
               Rat  tctg-----t-ctcc-----cccccccccccccagcctccg--g--------cttcccta---------g
        Guinea pig  cctg-----c-tttt-----cctaagccttcagctttcctttag--------ggtcctct---------t
            Rabbit  tcc----------------------------------------a--------gttctatc---------g
             Human  tcag-----t-tttc-----cctgagcctgccactttccttt-ggggtccccgggtcccc---------g
             Chimp  tcag-----t-tttc-----cctgagcctgccactttccttt-ggggtccccgggtcccc---------g
         Orangutan  tcag-----t-tttc-----tctgagcctgccactttccttt-g--------gggtcccc---------g
            Rhesus  tcag-----t-tttc-----cctgagcctgccactttccttt-g--------gggtcccc---------g
          Marmoset  tccg-----t-ttac-----cctgagctttccgctttccttt-g--------gggttctc---------g
          Bushbaby  cctg-----t-tttc-----cctgagcctgcggttttccttt-g-------------------------g
        Tree shrew  tccg-----tgtttc-----tctgagcctcctactttccttt-a--------gagtctcctgacccgggg
             Shrew  ctcc-------tttc-----ccagctcctgcaacttttcttt-c---------tgtctcc----------
          Hedgehog  ccccccccat-tttt-----ccagtgtccgctggttccccgt-a--------gggtctcc---------t
               Dog  cccg-----t-tttc-----cccaagcctgcggcttcccttt-a--------gggtcccc---------c
               Cat  cccc-----c-tttc-----cccacgcctgtggcttctcttt-a--------gtgtttcc---------t
             Horse  cccg-----t-ctct-----cccacgactgccacttcccttt-g--------gggtacgc---------g
               Cow  gccg-----t-tttc-----cccgcgcctgccgcttcccttt-a--------gggtccga---------c
         Armadillo  ctgg-----gtctcc-----cctgctcctgcctctttcctta-g--------aggttccc---------c
          Elephant  cccg-----tcttcc-----cctgcccctgccg-------------------------------------
            Tenrec  ccat-----ttgccc-----cctgcgcccacca-------------------------------------
           Opossum  catc-----t-ttcc-----cttcctccttctaacttcc----a--------g---ccgc---------a
          Platypus  cccc-----t-ttcctaccgccatcgccttttcattttcttc-g-----------ttcct---------g
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  ggaactaggaaacgc-tagtggttgcgtgccccttt----cctgc---------aaagtt--------tc
               Rat  agtactgggaaatgc-tagtggtcgccggccctttt----cctgc---------aaactt--------tc
        Guinea pig  ggtccctggcatttc-aagtg-------gaccacct----cctg--------------------------
            Rabbit  gagcccagggaccgc-gagtgaacgcctgcttatttagcacttgc---------acggtt--------tc
             Human  ggtccccgagaatgc-aagtggatatctatctagtt----cctgc---------atgttt--------ta
             Chimp  ggtccccgagaatgc-aagtggatatatatctagtt----cctgc---------atgttt--------ta
         Orangutan  gctccccgagaatgc-aagtggatatctatctagtt----cctgc---------atgttt--------tc
            Rhesus  ggtccccgagaatgc-aagtggatatctatctagtt----cctgc---------atgctt--------tc
          Marmoset  ggtccccaagaatgc-aagtggatatctatctagtt----tctgc---------acattt--------tc
          Bushbaby  ggtccccgagaatac-gagtggacatctgtctagtt----cct---------------------------
        Tree shrew  agtgtccgggaatgc-gagtggacgtctatctaggt----cgtgc---------atgttt--------tt
             Shrew  actctctgggaa--t-gcagggac----attgagtc----ccttc---------aagttt--------tc
          Hedgehog  ggtctccagcaactt-gagtggac----attaaccc----ctgt------------atgt--------ta
               Dog  -gtccttgggaatgc-atgcagac----atctagta----cctgc---------acattt--------tc
               Cat  ggtcccgggaaatgc-cagtggat----atctagta----cttgc---------acgttt--------tc
             Horse  ggtcccagggaaggc-aagtggaa----gtctagtc----ccggc---------atgttt--------tc
               Cow  agtcccagggaattc-tagtggac----atcccgtc----cctgc---------acgttt--------tc
         Armadillo  -gtctatgggaatgcagagcagacatc-tagttgtc----cctgc---------acgttt--------tc
          Elephant  -gtcctctggaatgc-gagcggacatt-tcgttgtc----cctga---------acgttt--------tc
            Tenrec  -gtccgctggaatgc-gagcggacagc-aagtagtt----cctga---------acgtttg-------tt
           Opossum  ggccc---------c-------------------------catac---------acattt--------tc
          Platypus  tattccaatccttgc-caaatgacattgaattgaga----ttggccgagcggaaacatttgggaaaactc
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  cagcag-tgtttttt----------tccttttctgtgccggaaccttgctctgtc--------ctggacg
               Rat  cagcag-tgttccccc------ccacccctttctctgctggaaccttattctgtc--------ctggacg
        Guinea pig  ----ag-tccttttc--------------tttcttacccctgactttgctgtgtc--------ctgagca
            Rabbit  ----ac-tggtgccg----------cccct--------------------------------------cg
             Human  -agcag-tgccaccccactgtttctttcctttctcacccctgaccttgcctagtc--------ctaagcg
             Chimp  -agcag-tgccaccccactgtttctttcctttctcacccctgaccttgcctagtc--------ctaagcg
         Orangutan  -agcag-tgccaccccactgttcctttcctttctcaccgctgaccttgcctagtc--------ctaagcg
            Rhesus  -agcag-tgccaccccactgttcctttcctttctcacccctgaccttgcctagtc--------ctaagcg
          Marmoset  -agcag-tgccaccccactgtt-ctttcctttctcacccctgaccttgcctagtc--------ctaagcg
          Bushbaby  --------------ccactgttcctttcctttctcacccctgaccttgccttgtc--------acgagcg
        Tree shrew  gagcag-tgccaccccactgttcctttcctttctcacccctgaccttgccgtgtt--------gagagcg
             Shrew  -actgggtgccaccccacggtctttttc--ttttcacccttgaccttgcagggtt------------gtg
          Hedgehog  -accgg--cccaccccatagttcctttccatcctcacccttgaccttgtggtgtg--------atgagtg
               Dog  -agcgg-tgccaccccactcttcctttcctttctcacccttgaccttgcggtgtc--------ttgagtg
               Cat  -agcgg-tgccaccccgctgttctcttcctttctcacccttgaccttgtggtgtc--------cccagtg
             Horse  -agggg-tgccaccccgctgttcctttcctttctcatccttgaccttgcggtgtc--------gtgagtg
               Cow  -agtgg-tgccaccccaccgttcctttcctttctcacccttgaccttgc-gtgtt--------gtgaatg
         Armadillo  -ggcgg-tg---ccccactgtttctttgctttctcacccctgacctaaccgggtc--------gcaagag
          Elephant  -ggcga-tgccaccccactgttcctttccattttcacctctgaccttgccgggtc--------gtcagcg
            Tenrec  -ggcga-tgccaccccactgttcgttcccatgctcacctctgacctcgccgggtc--------gtcagca
           Opossum  -------ttcc-tcccacgaccttttcccttgttga---tagaccagg-----------------gagtg
          Platypus  -aggaa--gttatct-----tctcccacgtccctcccccctg---ttgctaggtaaggttaaggggagcg
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  tctgttgtgattgttcagaaagat---ctcg
               Rat  tcttttctgactgttcagaaagat---ctcc
        Guinea pig  tcttttctgtggtgacagaaggat--gccca
            Rabbit  ccttttctgcataaccaggag------tccc
             Human  tcctttctgccttgtcagaaggat--tcccc
             Chimp  tcctttctgccttgtcagaaggat--tcccc
         Orangutan  tcctttctgcgttgtcagaaggat--tcccc
            Rhesus  tcctttctgcgttgtcagaaggat--tcccc
          Marmoset  tcctttctgcctagtc---aggat--tcccc
          Bushbaby  tcttttctgcgtagtcagaacgat--tctcc
        Tree shrew  tcttttctgcgtagtcaaacgtac--tctcc
             Shrew  tcttttctacttggtaagaaccat--tcccc
          Hedgehog  tcttttctactggataacaactat--tcctt
               Dog  tcttttctgcgtggtaagaacgat--tcccc
               Cat  tcttttctggttggtaagaaggat--tcccc
             Horse  tcttttctgcttggtaagaaccgt--tcccc
               Cow  tcttattctgctgcttaggatgat--tcccc
         Armadillo  tcttttctgcgcggtcaggacgac--tccct
          Elephant  tctttgctgcgtggtcaggatgac--tcctg
            Tenrec  tcttttctgcgtggccagaaggac--tcccg
           Opossum  tcttttctgtggggt-agattggc--tccca
          Platypus  tctcttgggccgtctctgagcagccaccccc
              Fugu  ===============================
         Tetraodon  ===============================
       Stickleback  ===============================
            Medaka  ===============================
         Zebrafish  ===============================
     X. tropicalis  ===============================
           Chicken  ===============================
            Lizard  ===============================

Alignment block 48 of 255 in window, 57799087 - 57799173, 87 bps 
B D          Mouse  gag-----------tgttctgtaccatacagtccggcttt----cccgggcgactt---gagtttgtttt
B D       Platypus  caa-----------atgcc----ggagcaaatcgggattg----tgccacggagga---aaataggcttt
B D        Opossum  gag-----------gtc-c----atgtcgatccgtgtttt----cttaggcg-------aagtttgtttt
B D         Tenrec  gag-----------ccctc----ttgctcggcccgacttc----cgctggagacct---gagtttgtttt
          Elephant  gaa-----------ccctt----ttgcctagtctggcttc----cgtaggagacct-----gtttgtttt
         Armadillo  gag-----------ccc------------ggctgggcttc----cgcaggagacca---gggtttatttt
B D            Cow  gcg-----------ccctt----atgctcagtcgggcttc----cgcaggagaccc---gagtttgtttt
B D          Horse  cag-----------ccgtc----ctgctcagtcgggcttc----cgcaggagaccc---ccgtttgtttt
B D            Cat  gagcaaccccccccccccc----cagctcagtc-ggcttc----tgc---agacca---gagtttgtttt
B D            Dog  gag-----------ctctc----ccgcacggttgggcttc----cgc---agacca---gagcttgtttt
B D       Hedgehog  gag-----------ccccc----atgatcagt------------------------aggaagtttgtttt
B D          Shrew  cag-----------tactt----atgctcagtctggcttc----tgcgggagactcaaggggtttgtttt
B D     Tree shrew  gag-----------ccctc----ctgcccagtcttgcttc----cgcaggagaccc---gagtttgtttc
          Bushbaby  ga------------ccctc----ctgcccagtccggcttc----cgcaggagacct---gagtttgtttt
B D       Marmoset  gag-----------ccctc----ctgcccagtccggcttc----agcaggagacct---gagtttgtttt
B D         Rhesus  gag-----------ccctc----ctgcccagtccggcttc----cgcaggagacct---gagtttgtttt
B D      Orangutan  gag-----------ccctc----ctgcccagtccggcttc----cgcaggagacct---gagtttgtttt
B D          Chimp  gag-----------ccctc----ctgcccagtccggcttc----cgcaggagacct---gagtttgtttt
B D          Human  gag-----------ccctc----ctgcccagtccggcttc----cgcaggagacct---gagtttgtttt
            Rabbit  cga-----------ctctc----ctgctcagtttgctttc----tgcgggagatcg---tagtttgtttt
        Guinea pig  gag-----------ccctc----ctgtccagtctggctac----tttaggagacct---ggctttgtttt
B D            Rat  cag-----------tgctccgcaccgtacagtctggcttt----cccaggagactt---gagtttgtttt
B D      Zebrafish  ggg-----------catac----tgtacgaggccgtgtacaacgtgtgggtcaatg---ggttttgtttg
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  cttttttattgta------------------------------------------------ctg------
          Platypus  c--tttcgcttcg------------------------------------------------cgg------
           Opossum  c--ttttactaaa------------------------------------------------ctg------
            Tenrec  ---ctttactgcggttttctttt--------------------------------ctttctttc------
          Elephant  c--ctttactgcg------------------------------------------------ttg------
         Armadillo  c--ttttactgcg------------------------------------------------ttg------
               Cow  c--ttttactgcg------------------------------------------------ttg------
             Horse  c--ttttactgcg------------------------------------------------ttg------
               Cat  c--ttttacttca------------------------------------------------tag------
               Dog  c--ttttacttca------------------------------------------------taa------
          Hedgehog  c--ttttactgag------------------------------------------------cag------
             Shrew  c--ttttactgcg------------------------------------------------ctgtttttt
        Tree shrew  c--ttttactgcg------------------------------------------------ttg------
          Bushbaby  c--ctttactaag------------------------------------------------ttg------
          Marmoset  c--ttttactgag---ttgtttt--------------------------------ttttttttt------
            Rhesus  c--ttttactgag--ttttttttttttttttttttttttttttttttttggttggttttttttt------
         Orangutan  c--ttttactgag--tttttttt--------------------------------ttttttttt------
             Chimp  c--ttttactgag---ttttttt--------------------------------ttttttttt------
             Human  c--ttttactgag----tttttt--------------------------------ttttttttt------
            Rabbit  c--ttttactgcg------------------------------------------------ttg------
        Guinea pig  c--ttttactgca------------------------------------------------t--------
               Rat  c-tttttattgca------------------------------------------------ctg------
         Zebrafish  cttttttatgacg------------------------------------------------tat------
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  ------tta--------------------------------a--ag---------------ataaaattt
          Platypus  ------tta--------------------------------c--ag------------------------
           Opossum  ------tta--------------------------------a--aa------------------------
            Tenrec  ------ttt--------------------------------t--aa------------------------
          Elephant  ------tttaaaaaaaaaaa---------------------a--aa------------------------
         Armadillo  ------tta--------------------------------a--aa------------------------
               Cow  ------tta--------------------------------a--aa-----------cagaataaaacaa
             Horse  ------tta--------------------------------a----------------------------
               Cat  ------tta--------------------------------aacaa-----------aacaatacaacaa
               Dog  ------tta--------------------------------accaa-----------aacaacacaacaa
          Hedgehog  ------tta--------------------------------a--aa-----------caaaacaaaacaa
             Shrew  tttttttta--------------------------------a--aa-----------aaaaac-------
        Tree shrew  ------tta--------------------------------a--aaccaaaccaaaccaaaacaaaaata
          Bushbaby  ------ttaaaaagggggcggtggggggtggggggagaagga--gg------------------------
          Marmoset  ------ttt--------------------------------t--gg------------------------
            Rhesus  ------tta--------------------------------a--gg------------------------
         Orangutan  ------tta--------------------------------a--gg------------------------
             Chimp  ------tta--------------------------------a--gg------------------------
             Human  ------tta--------------------------------a--gg------------------------
            Rabbit  ------tta--------------------------------a--aa---------------aaaaaaaaa
        Guinea pig  --------------------------------------------ag---------------ttaaaatat
               Rat  ------tta--------------------------------a--ag---------------ataaaattt
         Zebrafish  ------tta--------------------------------c--aa---------------attaacttt
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  ----aaaa
          Platypus  ----cccg
           Opossum  --------
            Tenrec  ----accg
          Elephant  ----aaag
         Armadillo  ----aacg
               Cow  ----aaca
             Horse  ----aaca
               Cat  caacaaga
               Dog  cagcagca
          Hedgehog  ----aaca
             Shrew  ----agca
        Tree shrew  ----aaca
          Bushbaby  --------
          Marmoset  --------
            Rhesus  --------
         Orangutan  --------
             Chimp  --------
             Human  --------
            Rabbit  ----aaaa
        Guinea pig  ----aaaa
               Rat  ----aaaa
         Zebrafish  ----agta
              Fugu  ========
         Tetraodon  ========
       Stickleback  ========
            Medaka  ========
     X. tropicalis  ========
           Chicken  ========
            Lizard  ========

Inserts between block 48 and 49 in window
B D     Zebrafish 98bp

Alignment block 49 of 255 in window, 57799174 - 57799285, 112 bps 
B D          Mouse  g--a---------------cattaggtt-c-tttctt-ggtatagggagaaa--aa-gaaa-gttaaaat
B D            Rat  g--a---------------cattaggct-c-tttctt-ggtattgggtgaaa--aa-gaaa-gttaaaat
        Guinea pig  g--a-----g---------tgttaactt-cttttctt-ggta---gggtaaa--aa-gaa---tcaaagt
            Rabbit  a--a----gg---------cgttaacct-c-tttctg-agta---gggagaa--aa-gag---taaaaat
B D          Human  -------------------cgttaactt-t-tttctt-ggta---gggagaa--aa-gaaa-gtctgaat
B D          Chimp  -------------------cgttaactt-t-tttctt-ggta---gggagaa--aa-gaaa-gtctgaat
B D      Orangutan  -------------------cgttaactt-t-tttctt-ggta---gggagaa--aa-gaaa-gtctaaat
B D         Rhesus  -------------------cgttaactt-t-tttctt-ggta---gggaaaa--aa-aaaa-gtctaaat
B D       Marmoset  -------------------cgttaac------ttctt-ggta---gggagaa--aa-taaa-gtctaact
          Bushbaby  -------------------cattaacttct-tttctt-ggta--ggggaaaa--aa-gaaa-gtctaaat
B D     Tree shrew  a--a----caaaaaaacctccttaactt-c-tttctt-gtta---gagagaa--aa-aaaatgtcaaaat
B D          Shrew  g--taa--tg---------tc-----------ttcctgggta---gggagaa--ga-gaaa-gtaaaaac
B D       Hedgehog  a--aaa--gg---------cctcgactt-c-tttctctggga---gtgagaa--aa-gaaa-gtaaaaat
B D            Dog  aggaaactgg---------cattgactt-c-tttctc-ggta---gggggag-----aaaa-gtaaaaat
B D            Cat  a--aaaccag---------cattagctt-c-tttctt-ggta---ggggta------aaaa-gtcaaaat
B D          Horse  a--aacacgg---------cgttaactt-c-tttctc-ggta---gggaaaa-----aaaa-gtcaaact
B D            Cow  t--aaaacag---------cgttaactt-c-tttctc-agta---gggagaa--aacaaag-tcaaaaat
         Armadillo  g------------------cgttaacgt-c-tttctt-ggta---gggagag------------------
          Elephant  g------------------cgttaactt-c-tttctt-gatg---gggagaa------aaa-gtcaaaag
B D         Tenrec  g------------------cattaacgt-c-tttctt-ggtt---gggagaa--aa-gaaa-atcagaat
B D        Opossum  -------------------ca--------t-cttcaa-gtca---aagtgacctca-aata-atagcaag
B D       Platypus  a------------------tattaactc-c-----cc-agaa---gacagag--cc-caga-gccaaag-
B D           Fugu  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  -gttttattc-gc---------------------------------cttattgcct-aactgctcag-tg
               Rat  -gtttcattc-cc---------------------------------ttaacttcttcaattgctcag-gg
        Guinea pig  -actttagac-gagg----a--ggagataagatag----------gctaccttctt-aatttctcag-tg
            Rabbit  -gctctccac-gcat----attgtaaatacttcaga---------gataccttctt-aatgtttcagccg
             Human  -gacctagat-gcag----aatttaaataatgtgtagata----gtccactttctt-aatttctcag-cc
             Chimp  -gacctagat-gcag----aatttaaataatgtgtagata----gtccactttgtt-aatttctcag-cc
         Orangutan  -gacctagat-gcag----aatttaaataatgtgtagata----gtccactttctt-aatttctcag-cc
            Rhesus  -gacctaaat-gcaa----aatttaaataatgcgtaaata----gtccactttctt-aatttctcag-cc
          Marmoset  -gtcctatat-gcag----aatttaaataatgtgtagata----gtccactttctt-aacatatcag-cc
          Bushbaby  -gcccttgat-aaat----atttaaaataatgagc--ata----gtctattttctt-aatttctcag-cc
        Tree shrew  -gccctacac-gcagacaaaatctaaataatgtagagata----gcctatcttctt-agtttctcag-tt
             Shrew  -cccttagac-gcag----aatttaagtaatgaagagataaagagtccatcttctt-aatcgcctag-cc
          Hedgehog  gcccccagatggtgg----aatcaatataatgaagagataccaagtctcccccttg-aattcctctg-tc
               Dog  -accctagac-acag----aatctaaataatatagaaata-agagcctaccgtttt-aatttcttag-cc
               Cat  -gtcctagat-gcag----aattaaaataatacagagata-agagcctacctttta-aatttgttgg-cc
             Horse  -gccctagac-gctg----aatttaaataaggcagagatacagagcctaccttct--aatttctcag-cc
               Cow  -gccctag------------atttaaataatacagagataaagagcctaccttctt-aatttctcag-cc
         Armadillo  ------------aag----aattcaaataatgcagagatagagaatttaccttctt-aacttctcag-tc
          Elephant  -gccttgaac-gcag----aattcaagtaatgc--agatagagagcctacctccct-aacttctcgg-tc
            Tenrec  -gccttgaac-ggag----aattcaaataatgc--agatagagagcctatctcctt--gcttgtcgt-tt
           Opossum  -gactgagga-gtgt----aa-----------------------gtccttcttttc-taactctctg-tc
          Platypus  -gccacttct-gccg----atctcaaatagcgcag---------ggtcgccgtttg-ggcgttt--g---
              Fugu  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  gaaagtttaagacaggc-aga-ggaaaattt-aaat
               Rat  gaaggtttaaga----c-aga-ggaaa-----aatt
        Guinea pig  taaagtttaaaaactga-agg-gga-------aaat
            Rabbit  tgaagtttaaaaagcgc-aga-ggaaa-----aatt
             Human  taaagttttaaaagtgt-aga-ggaaaaatt-aaat
             Chimp  taaagttttaaaagtgt-aga-ggaaaaatt-aaat
         Orangutan  taaagttttaaaagtgt-aga-ggaaaaatt-aaat
            Rhesus  tgaagttttaaaagtgt-gga-ggaaaaatt-aaat
          Marmoset  taaagttttaaaaatgt-agg-gggaaaatt-aaat
          Bushbaby  taaagtttataaagtgc-agg-ggaaaaatt-aaat
        Tree shrew  tgaagtttaaaaatcac-aaa-tgaaaaaat-gaaa
             Shrew  a-aaagtttaaaagtgc-aga-gaaaaaatt-aaat
          Hedgehog  agaaggtttaaaattga-agaggaaaaaact-aaat
               Dog  gaaagtttaaaaagtgc-agg-ggggaaatt-aagt
               Cat  aaaagtttaaaaagcac-aga-agaaaaatt-aaat
             Horse  aaaaggctaaaaagcac-aga-ggaaaaatg-aaat
               Cow  aagactttaaaaagagcgggg-ggaaaaatt-aaat
         Armadillo  caaagttttaaaagttc-aga-gtaaa-att-aaat
          Elephant  caaagatttaaaaagcc-aga-ggaaaaatt-aaat
            Tenrec  ta--------------c-aac-ggaaagatt-gaat
           Opossum  cata---tgaaaagacc-aga-gggacaattccatt
          Platypus  -------taatgggcaa-aga-gggaaaattcaatt
              Fugu  ====================================
         Tetraodon  ====================================
       Stickleback  ====================================
            Medaka  ====================================
         Zebrafish  ====================================
     X. tropicalis  ====================================
           Chicken  ====================================
            Lizard  ====================================

Alignment block 50 of 255 in window, 57799286 - 57799329, 44 bps 
B D          Mouse  ag--------------------g-aaagagaa-agatat-ttcctgtgctaatttcccgctttttga
B D       Platypus  ag--------------------g-aatgggga-gagtagatacctttaatgatttcctccttt----
B D        Opossum  tt--------------------g-ggtgcggt-agata----cctttaaatgttttctccttt----
B D         Tenrec  ag--------------------g-aaagggagaaaatag-tttctttaattatttcctgcctttctt
          Elephant  ag--------------------g-aaagggagaaaatag-cttctttaattatttcttgcctttttt
         Armadillo  ag--------------------g-agagggggaaaacg---tcctttaattatttcctgcctttctc
B D            Cow  ag--------------------g-aaaagggg-aaatag-ttcatttaattatttcctgcctttctc
B D          Horse  ag--------------------a-gacggggg-aaatag-ttcttttaattatttcctgcctttctc
B D            Cat  agga------------------t-gggggggg-gaatag-ttcctttaattatttcctgtctttctc
B D            Dog  aggagaaggtggtggtggtggtg-gggggggg-gaagag-ttcctttaattatttcctgcctttctc
B D       Hedgehog  agga------------------g-aagcagtg-aaatag-ttcttttaatta-------------ta
B D          Shrew  agga------------------a-agttgggg-gaatag-ttcctttaattatttcctgcctttctc
B D     Tree shrew  ta--------------------g-agtggggg-agttaa-ttcctttaattatttcccgagtttcag
          Bushbaby  ag--------------------g-aaaggagg-aaatag-ttcctttaattatttcctggctttctt
B D       Marmoset  ag--------------------g-aaagagga-aaatag-ttcttttaattacttcctgcctttctt
B D         Rhesus  gg--------------------g-aaaggggg-aaatag-tttctttaattacttcctgcctttctt
B D      Orangutan  ag--------------------g-aaaggggg-aaatag-ttgctttaattacttcctgcctttctt
B D          Chimp  ag--------------------g-aaaggggg-aaatag-tttctttaattacttcctgcctttctt
B D          Human  ag--------------------g-aaaggggg-aaatag-tttctttaattacttcctgcctttctt
            Rabbit  aa--------------------ataaaggggg-aaatag-ttcctttaattatttcctgcctttctc
        Guinea pig  ag--------------------a-caaaagac-aaatgg-ttcttctaattatttcctgctttttgc
B D            Rat  ag--------------------a-aaagagga-aaatat-ttccta-------gttttttttttttc
B D      Zebrafish  aa--------------------a-aaaaaaaa-aaaaat-ttaatgggtgtatttcccacgtattaa
B D           Fugu  ===================================================================
B D      Tetraodon  ===================================================================
B D    Stickleback  ===================================================================
           Medaka  ===================================================================
B D  X. tropicalis  ===================================================================
B D        Chicken  ===================================================================
B D         Lizard  ===================================================================

Inserts between block 50 and 51 in window
B D     Zebrafish 2013bp

Alignment block 51 of 255 in window, 57799330 - 57799377, 48 bps 
B D          Mouse  tgtt-cccaccaca-ctggcac-agttaccttttaa--agtaatt-aagcagtg----
B D            Rat  agtt-cccaccacc-ttggtgc-aattaccttttaa--agtaattaaaacagtg----
        Guinea pig  aatt-gccaacaca-ttggcac-aattatgtttttc--gataattaaagcagag----
            Rabbit  gatt-gccaacaca-ttggcac-aattatcttttta--agtaattaaagcaggg----
B D          Human  ggtt-gccaccaca-ttggcac-aattatcttttta--agtaattaaagcaggg----
B D          Chimp  ggtt-gccaccaca-ttggcac-aattatcttttta--agtaattaaagcaggg----
B D      Orangutan  tgtt-gccaccaca-ttggcac-aattatcttttta--agtaattaaagcaggg----
B D         Rhesus  ggtt-gccaccaca-ttggcac-aattatcttttta--agtaactaaagcaggg----
B D       Marmoset  ggtt-gccaccaca-ttggcac-aattatcttttta--agtaattaaagtagag----
          Bushbaby  ggtt-gcca-caca-ttggcac-aattatcttttta--agtaattaaggcaggg----
B D     Tree shrew  ggtt-atcaccaca-ctggcac-aatgatctttt------taatgaaagcagga----
B D          Shrew  agct-gccaccaca-ttggcac-aattatcttttta--agtaattaaagcagag----
B D       Hedgehog  atcc-accaccacc-ttggcacaaagtatcttttta--cacaattaagccagag----
B D            Dog  tgtt-gccaccaca-ttggtac-aattatcttttta--agtaattaaatcagag----
B D            Cat  tgtt-gtcaccaca-ttggcac-aattatcttttta--agtaattaaagcagag----
B D          Horse  ggtt-gccaccacg-ctggcac-aattatcttttta--agtaattaaagcagaa----
B D            Cow  agtc-gccaccaca-ttggcac-aattatcttttta--aataatt-aaccatag----
         Armadillo  agtt-gccaccaca-ttggcat-aattatctcttta--agtaattaatgtaggc----
          Elephant  ggtttgccaccaca-ttggcac-aattatctcttta--agtaattgaagtaggtaggc
B D         Tenrec  ggtt-------acacttatcac-aattatcgctttgttagtaattaaaatagtg----
B D        Opossum  -att-aacaccaca-tagacac-atttgcctcttgc--agtaactaaacaagag----
B D       Platypus  -att-aacaccaca-ttggcgc-aattgcctcttta--agtaatcgagccc-------
B D           Fugu  ==========================================================
B D      Tetraodon  ==========================================================
B D    Stickleback  ==========================================================
           Medaka  ==========================================================
B D      Zebrafish  ==========================================================
B D  X. tropicalis  ==========================================================
B D        Chicken  ==========================================================
B D         Lizard  ==========================================================

Alignment block 52 of 255 in window, 57799378 - 57799413, 36 bps 
B D          Mouse  ca-cga-tttcccatcttcttgtcctctgact---gc-aaat
B D       Platypus  ctcgct-tttcccctttcctcgctgtctggct---tcggaat
B D        Opossum  gcttaactttttcattcccttgttgtcgataa---ta-gaat
B D         Tenrec  ccctga-tttctcatcttcttgttttc----t---gt-gaat
          Elephant  ccttga-tttctca---tcttgttttc----t---at-gaat
         Armadillo  ccttga-tttctcatcttcttgtttccagatt---gt-ggat
B D            Cow  ccctga-tttctcatcttcttgttttctgact---gt-gact
B D          Horse  cgctga-tttctcatcttcttgttttctgact---gc-gaat
B D            Cat  -cctga-tttctcatattcttgttttctgact---gt-caat
B D            Dog  ccctga-tttctcatcttcttggatgctgacc---g---agc
B D       Hedgehog  ttctga-tttctcatcttcttgtttt----cc---at-gaat
B D          Shrew  ccctga-tttctcatcatcttgtttt----ct---gt-gact
B D     Tree shrew  ccccga-tttctcatctttttgttttctgact---gt-gaat
          Bushbaby  ttctga-tttctcatcttcttgttttctgact---gc-aaat
B D       Marmoset  ctctga-tttctcatcttcttgttttctgact---gc-aagt
B D         Rhesus  ctctga-tttctcatcttcttgttttctgact---gc-aagt
B D      Orangutan  ctctga-tttctcatcttcttgttttctgact---gc-aagt
B D          Chimp  ctctga-tttctcatcttcttgttttctgact---gc-aagt
B D          Human  ctctga-tttctcatcttcttgttttctgact---gc-aagt
            Rabbit  gcctga-tttctcatcttcttggtttctgatt---gt-gaat
        Guinea pig  ccttga-tttctcatattcttgttttctgcct---gt-gaat
B D            Rat  ca-cga-ttccccatcttcttgtcttctgactgcggc-gaat
B D           Fugu  -cacca-tttccctccttcttgccctttcact---gg-gaat
B D      Tetraodon  ==========================================
B D    Stickleback  ==========================================
           Medaka  ==========================================
B D      Zebrafish  ==========================================
B D  X. tropicalis  ==========================================
B D        Chicken  ==========================================
B D         Lizard  ==========================================

Alignment block 53 of 255 in window, 57799414 - 57799460, 47 bps 
B D          Mouse  tgac----------------aagag-caatg-ttctgggttatttggaactgg-----------------
B D       Platypus  ttacaagtttctct--a---aagca-caaat-tctcgtccgacccggagtcgg----gttggggcgaact
B D        Opossum  ttaaaggactctttta----aaaat-gtaac-tcttaacctcttcagagccagccaggttagggtgaaca
B D         Tenrec  ttacaagacccttctat---aagag-cccag-atttgtagtatttcgagccg------------------
          Elephant  ttacaagatccttc--t---aacag-cccag-ttttgtcttatttggagctgg-----------------
         Armadillo  ttacaagattcttc--t---aagag-cctagtttttttcttatttggaggtgg-----------------
B D            Cow  ttacaggatccttc--t---aaggg-cccag-ttttgtcttatttggagctgg-----------------
B D          Horse  ttacaagatccttc--t---aagag-atcag-ttttgtcttattctgaactgg-----------------
B D            Cat  ttacaagatccttc--t--aagaag-ctcag-ttttgtcttattcggggctgg-----------------
B D            Dog  ttacaagactcttc--ttctaggag-ctcag-ttttgtcttattcagagttgg-----------------
B D       Hedgehog  ttacaagatccttc--t---aagag-cttgg-ttttgccttattggcagcca------------------
B D          Shrew  taagatgatctttc--t---aaaag-cttac-ttttgtcatattcaaagctgg-----------------
B D     Tree shrew  ttag----------------aagag-cccag-ttttgtcctaattggagctgg-----------------
          Bushbaby  ttac----------------aagagccccag-ttttatcttattc-cagctag-----------------
B D       Marmoset  ttac----------------aagag-cccag-ttttgtcttatttggagctac-----------------
B D         Rhesus  ttac----------------aagac-cccag-ttttgtcttatttggagctac-----------------
B D      Orangutan  ttac----------------aagag-cccag-ttttgtcttatttggagctac-----------------
B D          Chimp  ttac----------------aagag-cccag-ttttgtcttatttggagctac-----------------
B D          Human  ttac----------------aagag-cccag-ttttgtcttatttggagctac-----------------
            Rabbit  ttcc----------------aagag-cccag-ttctgtcttactctgagctac-----------------
        Guinea pig  ttac----------------aagag-cca-g-ttctgtcttatttggagctca-----------------
B D            Rat  tgac----------------aagag-taaag-ctctgggttatttggaactag-----------------
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  ------ttggaacctta-g
          Platypus  gaatagcagaagctgca-c
           Opossum  gaacactggaagctgca-t
            Tenrec  ------------------g
          Elephant  ------ttggagcttta-g
         Armadillo  ------ttggagcttta-g
               Cow  ------ctggagtttta-g
             Horse  ------ttggagcttta-g
               Cat  ------ttggagcttta-g
               Dog  ------ttggagcttta-g
          Hedgehog  ------------------g
             Shrew  ------ttaaacatttc-g
        Tree shrew  ------ttgcagcttta-g
          Bushbaby  ------ttgaagctctacg
          Marmoset  ------ttggagccgta-g
            Rhesus  ------ttggagccgta-g
         Orangutan  ------ttggagccgtc-g
             Chimp  ------ttggagccata-g
             Human  ------ttggagccata-g
            Rabbit  ------ttgcagcttta-c
        Guinea pig  ------ctagagcttag-g
               Rat  ------ttggagactcg-g
         Tetraodon  ===================
       Stickleback  ===================
            Medaka  ===================
         Zebrafish  ===================
     X. tropicalis  ===================
           Chicken  ===================
            Lizard  ===================

Alignment block 54 of 255 in window, 57799461 - 57799598, 138 bps 
B D          Mouse  ttggagacg---ttgcccttgatttataggat--aagctgacctcactgacatttaaaggaagcccctgt
B D            Rat  ttggagacg---ttgcccttgatttataggat--aaactgacctcattgacatttaaaggaagcccctgt
        Guinea pig  ttggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
            Rabbit  ttggagaga-gttcgcccttgatttataggat--aaactgaccccactgacatttggaggaagcccctgt
B D          Human  ttggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D          Chimp  ttggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D      Orangutan  tt-gagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D         Rhesus  ttggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D       Marmoset  tt--ggaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
          Bushbaby  ttggagaga-gtttgcccttgatttataggat--aaactgaccccagtgacatttaaaggaagcccctgt
B D     Tree shrew  ttggaggga-gtatgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D          Shrew  ttggagagc-gtttgtccttgatttataggat--aaactgacctcactgacatgtaaaggaagcccctgt
B D       Hedgehog  ttggagaga-ttttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D            Dog  ttggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
B D            Cat  ttggagaga-gtttgcccttgatttataggat--aaactgacctcagtgacatttaaaggaagctcctgt
B D          Horse  ctggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaaggccctgc
B D            Cow  ttggagaga-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
         Armadillo  ttggagagt-gtttgcccttgatttataggat--aaactgacctcactgacatttaaaggaagcccctgt
          Elephant  ttggagaga-atttgcccttgatttataggatacaatctgacctcactgacatttaaaggaagctcctgt
B D         Tenrec  cgggagagt-gtttgcccttgatttataggct--aacctgacctcactgacatttaaaggaagcccctgt
B D        Opossum  tctgagggttgtttgcccttgatttataggat--aaactgacctcgctgacatttaaaggaaggtcctat
B D       Platypus  tctgagggctctttgcccctgatttataggag--aaactgacctcggtgacatttaaaggaagcgtctat
B D        Chicken  -tgggggcc-gttcgcccttgatttataggat--aaactgacctctctgacacggaaaggaagcccctat
B D         Lizard  ------------ttgcccttgatttataggag--aagctgaccttgctgacaccaaaaggaagcccctat
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================

             Mouse  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-gggggaatctcaatttcttaagataac-t
               Rat  tcgtgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
        Guinea pig  tcatgggaaagtgtgagatcagcagaaat-gaggctcaca-ggggg-atctcaatttcttaagataac-t
            Rabbit  tcatgggaaagtgtgagatcagcagaaatgggggcttgca-gggag-atctcaatttcttaagataac-t
             Human  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
             Chimp  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
         Orangutan  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
            Rhesus  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
          Marmoset  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
          Bushbaby  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
        Tree shrew  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
             Shrew  tcatgggaaagtgtgagatcagcagaaatgggggctcaca--gggg-atctcaatttc-taagataac-t
          Hedgehog  gcatgggaaagtgtacgatcagcagaattgggggctcgca-ggggg-atctcaatttcttaagataac-t
               Dog  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
               Cat  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
             Horse  gcatgggaaagtgtgagatcagcagaaaagggggctcgca-ggggg-atctcaatttcttaagataac-t
               Cow  tcatgggaaagtgtgagatcagcagaaatgggggcgcgca-ggggg-atctcaatttcttaagataac-t
         Armadillo  tcatgggaaagtgtgagatcagcagaaatgcgggctcgca-ggggg-atctcaatttcttaagataac-t
          Elephant  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-ggggg-atctcaatttcttaagataac-t
            Tenrec  tcatgggaaagtgtgagatcagcagaaatgggggctcaca-gggga-atctcaatttcttaagataactt
           Opossum  tcatgggaaagtgtgagatctgcaggaattggggctctct-gagag-atctcagtttcttaagtcatc-t
          Platypus  tcatgggaaagtgtgagatcagcagaaatgaggactcact-aaggg-agctcaatttcttaagacaac-t
           Chicken  tcatgggaaagtgtgagatcagcagaaaagggcactcacc-gagtg-ggctcaatttctcaagccagc-c
            Lizard  tcatgggaaagtgagagatcagccgaactgggagctcgccagagac-agctcggtttcctaagacatg-t
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================

             Mouse  tcagg
               Rat  ttaga
        Guinea pig  tcagg
            Rabbit  tcagg
             Human  tcaag
             Chimp  tcagg
         Orangutan  tcagg
            Rhesus  tcagg
          Marmoset  tcagg
          Bushbaby  tcagg
        Tree shrew  tcagg
             Shrew  ttagg
          Hedgehog  tcaga
               Dog  acagg
               Cat  tcagg
             Horse  tcagg
               Cow  tcagg
         Armadillo  tcaga
          Elephant  tcagg
            Tenrec  ttagg
           Opossum  gctgg
          Platypus  tcaag
           Chicken  ccatg
            Lizard  gcggg
         Tetraodon  =====
       Stickleback  =====
            Medaka  =====
         Zebrafish  =====
     X. tropicalis  =====

Inserts between block 54 and 55 in window
B D        Lizard 9686bp

Alignment block 55 of 255 in window, 57799599 - 57799651, 53 bps 
B D          Mouse  cttatgcccaccgactg-ccttttgtctgggac-tgcaaagaccag-ca------ggcagtt
B D            Rat  cttatgcccaccgattg-ccttttgtctgggac-ggcagcaaatag-cgtcagacagtagtt
        Guinea pig  cttgtgcccaccgactg-ccttttgtctgggaa-ggcagaaaagagtca------ggcagtt
            Rabbit  cttgtgcccaccgagtg-ccttttgtctgggaa-ggcaaggagaga-ca------ggcagtt
B D          Human  cttgtgcccaccgactg-ccttttgtctgggaa-ggcaaagacaga-ca------ggcagtt
B D          Chimp  cttgtgcccaccgactg-ccttttgtctgggaa-ggcaaagacaga-ca------ggcagtt
B D      Orangutan  cttgtgcccaccgactg-ccttttgtctgggaa-ggcaaagacaga-ca------ggcagtt
B D         Rhesus  cttgtgcccaccgactg-ccttttgtctgtgaa-ggcaaagacaga-ca------ggcagtt
B D       Marmoset  cttgtgcccactgactg-ccttttgtctgggaa-ggcaaaaacaga-ca------ggcagtt
          Bushbaby  cttgtgcccaccgactg-ccttttgtctggaaa-ggcaaagagaga-ca------ggcagta
B D     Tree shrew  catgtgcccaccgactg-ccttttgtctgggaa-ggcagag--aga-ca------ggcagtt
B D          Shrew  cttgtgcccaccgactg-tcttatgtctggaaa-ggcaaaaagaga-ca------ggcagtt
B D       Hedgehog  cttgtgcccagcaactg-tcttttgtctggcaa-ggcaaagagaaa-ct------ggaagtt
B D            Dog  cttgtgcccaccgattg-ccttttgtctgggaa-ggcaaagagaga-tt------ggcagtt
B D            Cat  cttgtgcccaccgattg-ccttttgtctgggaa-ggcaaagagaga-ct------ggcagtt
B D          Horse  cttgtgcccaccgattg-ccttttgtctgggaa-ggcaaagagaga-ct------ggcagtt
B D            Cow  cttgtgcccaccgattg-ccttttgtctgggaa-ggcaaggaaaga-ct------ggcagtt
         Armadillo  cttgtg-ccaccgactg-ccctttgtctgcgaa-ggcaaagagaga-ca------gacagtt
          Elephant  cttgtgcccaccaactg-ccttttgtctgggaa-ggtaa--agaga-ta------ggcagtt
B D         Tenrec  cttgtgcccaccgactacccttttgactgggaa-agcaactagaga-ca------ggcactt
B D        Opossum  ctgatgcccatcgacta-cattttgctacggaa-gacgaagagata-ta------gaaagcc
B D       Platypus  cttgtggtccccgaatg-tattttcctttggaa-agcgaggcgaga-ca------ggcagct
B D        Chicken  ttggtgcccctccagcg-------gtcgaagagctgctcagagccg-ct------cgcag--
B D      Tetraodon  ==============================================================
B D    Stickleback  ==============================================================
           Medaka  ==============================================================
B D      Zebrafish  ==============================================================
B D  X. tropicalis  ==============================================================
B D         Lizard  ==============================================================

Inserts between block 55 and 56 in window
B D      Platypus 1713bp
B D       Chicken 536bp

Alignment block 56 of 255 in window, 57799652 - 57799912, 261 bps 
B D          Mouse  gggaatc----------agtg--atggctttctggtac-aaaaataggagcacaatc-tacttctttgga
B D            Rat  gtgaatc----------agtc--atggcttcctggtac-aaaaatgggaacacaatc-tttgtctttgga
        Guinea pig  ttgtacc----------aa-a--acagtttcctggtgcaaaaaataggaacacaat-----ttcttggga
            Rabbit  ctggacc---------taaac--accccatcctggtgc-aaaaatgggaacacagtc-ta-atctttgag
B D          Human  ctggacc---------aaaac--acagtttcctggtgc---aaatggg-actcaatc-taattcttgggg
B D          Chimp  ctggacc---------aaaac--acagtttcctggtgc---aaatggg-actcaatc-taattcttgggg
B D      Orangutan  ctggacc---------aaaac--acagtttcctggtgc---aaatggg-actcaatc-taattcttgggg
B D         Rhesus  ctggacc---------aaaac--acagtttcctggtgc---aaatggg-actcaatc-caattcttgggg
B D       Marmoset  ttgaacc---------aaaac--acagtttcctggtgc---aaatggg-actcaatc-taattcttgagg
          Bushbaby  atggacc---------aaaac--acagtttcttggtgc---aaatggg-aatcaatc-tagttctttggg
B D     Tree shrew  ttagacc---------aaa----acagtttcctggtgc---aaatgggaacgcaatc-taattctttgga
B D          Shrew  ctgggca---------aaaac--acaatttcctggtac---aaaacggaatacaacc-taattctttgga
B D       Hedgehog  ggggggggggggaggcaaagc--acagcttcctggtgc---aaattggaacccaatc-taattatttgga
B D            Dog  ctttgcc---------aaaat--acggtttcctggtgc---aaattggaacacaatc-tgattctttgga
B D            Cat  ctgcgcc---------aaaac--atggtttcctggtgc---aaattggaacataatc-taatcctttgga
B D          Horse  cagcacc---------aaaac--actgtttcctggtgc---aaattagaacacaatc-taattctttgga
B D            Cow  ctgggcc---------aaaat--cctgtttcctggtgc---aaattggaacacaatcttaattcttcggc
         Armadillo  ctgggcc---------aaaac--acggtttcctggtgc---aaataggaatacaatc-taattatttgga
          Elephant  ctgggac---------aaaac--atggtttcctggtgc---aaataggaacacaatc-----taatgggt
B D         Tenrec  ctgggcc---------caaac--atgctttcttggtgc---aaataagaacacattc--aattctttagg
B D        Opossum  ctgagct---------ggaacagagagagcctcaatcc---aaatgagaacacgacc-taattaaattgt
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  --------gggggagac--agt----g-------------------------------------------
               Rat  --------gggggagacaaaat----g-------------------------------------------
        Guinea pig  --------gggggggtaatggt----g-------------------------------------------
            Rabbit  --------gggggaggcatggt----g-------------------------------------------
             Human  gtggtagaggaggagacatagt----g-------------------------------------------
             Chimp  gtggtagaggaggagacatagt----ga------------------------------------------
         Orangutan  gtggtagaggaggagacatagt----g-------------------------------------------
            Rhesus  gtggtagaggaggaaacatagt----g-------------------------------------------
          Marmoset  gtggtagaggaggagacatagt----g-------------------------------------------
          Bushbaby  gtt-----gggaaaaatatagt----g-------------------------------------------
        Tree shrew  g-------gagggaggcatagt----gaaaagacaaaagaaaagaaaagaagagaaaaggaaagaaaaaa
             Shrew  ------gagggggaagcatagt----g-------------------------------------------
          Hedgehog  ------gaaggggacccttaat----g-------------------------------------------
               Dog  ------gagggggaggaagggg----c-------------------------------------------
               Cat  ------aaggaggaggaatagt----t-------------------------------------------
             Horse  ------gagg-ggaggaataat----g-------------------------------------------
               Cow  ------gagggggaggcatagt----g-------------------------------------------
         Armadillo  -------gaggggaggtttagtggggg-------------------------------------------
          Elephant  -------gggggcggtcatagt---gg-------------------------------------------
            Tenrec  -------gggagagggcaaagt-gggg-------------------------------------------
           Opossum  --------gggggaaactcatt----c-------------------------------------------
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  ---------------------aga-----------ataagctgaca--gttgaaaagaaaactttccac-
               Rat  ---------------------aaa-----------ataggctgaca--gtagaaaaaaaaacttttcac-
        Guinea pig  ---------------------aca-----------aaaggctgaca-----gagatgaaaagtttt----
            Rabbit  ---------------------aaa-----------acagactgacagagttgcaaagaaaaattttctt-
             Human  ------aaaaaaaaaaaaaaaaaa-----------aaaggctgacagagtttaaaagaaaacttttcct-
             Chimp  -aaaaaaaaaaaaaaaaaaaaaaa-----------aaaggctgacagagtttaaaagaaaacttttcct-
         Orangutan  ----gaaaaaaaaaaaaaaaaaaa-----------aaaggctgacagagtttaaaagaaaacttttcct-
            Rhesus  ---------gaaaaaaaaaaaaaa-----------aaagactgacagagttgaaaataaaacttttctt-
          Marmoset  -----------------gaaaaaa-----------aaaggctgac--agttgaaaagaaaacttttcct-
          Bushbaby  -------------------gacga-----------aaaagctgacagaattgaaaagcaaacttttctt-
        Tree shrew  gaaaagaaagaagagaagaaaagg-----------aaaggttgacagagttgaaaagaaaacttttctt-
             Shrew  ---------------------aaa-----------aaagactgacagaattgaaaagaaaacttttttc-
          Hedgehog  --------------ggaaaaaaaa-----------aaagactgacagagttgaaaagaaaacttttctc-
               Dog  ---------------------ggg------------------gggagagttgaaaagacaaccgtgctt-
               Cat  ---------------------aaaaaaaaaaaaaaaaagactgacagatttgaaaagacaactgttctt-
             Horse  ---------------------aaa-----------aaagactgacagagttgaaaagaaaactttcctt-
               Cow  ---------------------aaa-----------aaagactgacagagttgaaaagaaaacctttctt-
         Armadillo  ---------------------gaa-----------aaaggctggcagagttgtaaagaaaacttttctt-
          Elephant  ---------------------aaa-----------aaagtctgacagagttgaaaagaaaactttttttc
            Tenrec  ---------------------aaa-----------aaagcctgatggagttgaaaagagaacttgtctt-
           Opossum  ----------------------aa-----------gggggtagacaaaatttaaaagaaag---ttctt-
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  ctctgggga-atcctgcaaccagaccaaatgtcaggtcgggaagaatcggat--ta-----tagaaggca
               Rat  ctctgcata-gtcctgcaaccagaccgaatgtcaggtagggaggaattggag--ta-----gagaaggca
        Guinea pig  ctctaggga-g-cctacaatcggaccaactatcagtcgaggaaatattggat--ta-----tagagaaga
            Rabbit  cttgagaga-t-tctgcagtcagaccaaatgtcagttggcaaaggattggct--ta-----ctggagaga
             Human  gcctaggga-t-cctaccatcagagcaaatgtcagttgggaaagtattggag--aa-----tggaaagga
             Chimp  gcctaggga-t-cctaccatcagagcaaatgtcagttgggaaagtattggag--aa-----tggaaagga
         Orangutan  gcctaggga-t-cctaccatcagagcaaatgtcagttgggaaagtattggag--aa-----tggaaagga
            Rhesus  gcctaggga-t-attaccatcagagcaaacgtcagttgggaaagcattggac--aa-----tggaaagga
          Marmoset  -cctaggga-t-tctcccatcagagcgaatgtcagctgggaaagtactggag--aa-----tggaaagga
          Bushbaby  gcctcagga-t-cctacaatcagactaaaggtcacttggaaaacgattggat--tg-----tggaaagga
        Tree shrew  ccccaggga-t-cttacagtcagaccaaaggtcagttggaaaggtattggat--t----------aagga
             Shrew  ccctaggga-c-cctacaaaaagaccatatggtagatgggaaag-attgg--------------------
          Hedgehog  aactaggaa-t-cctacagccagagcaaatatcagctaggaaagtactgggt--ta------gcaaagga
               Dog  ccctagggg-t-cctatagtcagaccaactatccgctggaaaagtagtggattata-----tggagagga
               Cat  ccccaggga-t-cctacaatcagaccaaatatcagttggaaaagtaatggagtata-----tggagagga
             Horse  ccctaggga-t-cctacaatcagaccaaatgtcagttggaaaagtattggct--ta-----tggagagga
               Cow  ccctaggga-g-cctacaatcagaccaaatgtcagtcggaaaagtattagat--ta-----tggagagaa
         Armadillo  ccctaggga-t-cctacaatcaggtcaaatgtcagttggaaaagtactggat--ta-----tggagaaga
          Elephant  ccccagggact-cctacaatcagagtaaatgtcagttgagacagtatcggat--ta-----tggtgagga
            Tenrec  ccctagggact-cccacaagcagagcaaatgccagtccagaaagtattggat--ta-----tggttcgat
           Opossum  ccacagaaa-t-c--atagttagactaagtgtcagttggcagtttctttgac--tagtgagcgaggaggg
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  gtggtgcctccacgtagat-actgt-tgtctgtttgtgatgtcacctttaaacaaa--------------
               Rat  gtgatgcttccgggtagataagtgt-tgtctatttgtgatgtcacttttaaacaag--------------
        Guinea pig  gcaactcttccctgttgct-attgc-tgatgattctggagactggctctaagcaac--------------
            Rabbit  gcaaatcttcatggcagat-acttg-tgttgactctgggtgccagctttaaacaag--------------
             Human  gcaacttttcctttcagat-attat-tg-tgattttggatgccagctttaaacaac--------------
             Chimp  gcaacttttcctttcagat-attat-tg-tgattttggatgccagctttaaacaac--------------
         Orangutan  gcaacttttccttttagat-attgt-tg-tgattttggatgccagctttaaataac--------------
            Rhesus  gcaacttttccttttagat-attgt-tg-tgattttggatgccagctttaaacaac--------------
          Marmoset  gcaactcttccttatagac-attgt-tg-tgattttcgatgccagctttaaacaac--------------
          Bushbaby  acaactcttccttgtagat-gt-------tgattctggatgtcagctttaaacaactagatttttagaca
        Tree shrew  acaactcttctttggagat-agtgtgct-tgattctgggtgccaactttaaac-ac--------------
             Shrew  gcaactctttatactaga-----------tgattctggatgccaactttaaacagc--------------
          Hedgehog  gcaactcagaagggtgga----tgt----tgattctgaatgccagctt---acagcataac---------
               Dog  gtaactcttcattctaga----tgt----tgattctggatgccagctttaaacgac--------------
               Cat  gcaactgttcgttctaga----tgt----tgattctggatgccagctttaaaca----------------
             Horse  gcaacttttcattctagat-gttgt----tgattctgcatgccagctttaaacaac--------------
               Cow  gcaacccttcgttctacat-atggt----tgattctgggtgccagctttaaacaac--------------
         Armadillo  gcacttcttcattctacct-c---t-tgttgacttggaatgccagctttaaacaag--------------
          Elephant  gcaactc--aattccagat-attgt-tgttaattctgagtgccagctttaaacaac--------------
            Tenrec  gcaactcttaattccagat-atggt-tgttgcttctgagtgccaacttcatacaac--------------
           Opossum  taaaatcttcatttt-----gatgt-a--ttgtttttaatactcgtgttcaa-aat--------------
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  -cag---gtttctgacaaatctgtgcatat-aagaaggtaatttct
               Rat  -cag---ggttctgacaaatctgtgcatgt-aaaagggtaatttct
        Guinea pig  -ttg---cttactgacaaatctgcgaacat-aaaacaaggatttgt
            Rabbit  -gtg---gtt-----------tgtgaacat-aaaatgatcatttct
             Human  -cca---gtttgtgacacatttgtgattataaaaatgatcatttct
             Chimp  -cca---gtttgtgacacatttgtgattataaaaatgatcatttct
         Orangutan  -cca---gtttgtgacaaatttgtgattataaaaatgatcatttct
            Rhesus  -cca---gcttgtgacaaatttgtgattataaaaatgatcatttct
          Marmoset  -cca---gattctgacaaatttgtgactat-aaaatgatgatttct
          Bushbaby  accacatatttttgacagatctgtgaatatgaa----atcattt-t
        Tree shrew  -tag---gtttctgacaaatttgtgaacac-caaatgataattt--
             Shrew  -----------ctaacaaatttgtatatgt-aaaataattattttt
          Hedgehog  -cta---ttttctgacaagtcttagagtac-aaaataatgatttct
               Dog  -ctg---ttctctgacaaatctatgaatat-aaaatgattatttct
               Cat  --tg---ttttctgacaaatccatgaacat-aagatgattatttct
             Horse  -ctg---ttttctgacaaatctgtgaatct-aaaatgattat----
               Cow  -ctg---ttttctgacaaatctatgaatat-aaaatgattatttct
         Armadillo  -ctt---gtttctgataactc--tgaacat-caca-----ccttct
          Elephant  -ctg---gtttttgacaaatttgtgaatat-agca-----ctttgt
            Tenrec  -cca---acttcagacacatttgtgactag-ag-------ctttct
           Opossum  -ttt---gcttgtgaaaaatc----aatat-tcca-----------
         Tetraodon  ==============================================
       Stickleback  ==============================================
            Medaka  ==============================================
         Zebrafish  ==============================================
     X. tropicalis  ==============================================
          Platypus  ==============================================
           Chicken  ==============================================
            Lizard  ==============================================

Inserts between block 56 and 57 in window
       Guinea pig 1bp
           Rabbit 1bp
B D         Human 2bp
B D         Chimp 2bp
B D     Orangutan 2bp
B D        Rhesus 2bp
B D      Marmoset 2bp
         Bushbaby 2bp
B D         Shrew 17bp
B D           Dog 17bp
B D           Cat 17bp
B D           Cow 16bp
        Armadillo 1bp
         Elephant 1bp
B D        Tenrec 1bp

Alignment block 57 of 255 in window, 57799913 - 57799989, 77 bps 
B D          Mouse  ccaagtgactgctc--t--ttg-aagcacctgta----tcagagggaagtg-tgt---------------
B D            Rat  ccaaatgaccgctc--t--ttg-aaacacctgta----tcagatgggagtg-tat---------------
        Guinea pig  caaaatgaacatcc--c--ttc-taagctcttta----tcagatgaaagtg-ttt---------------
            Rabbit  taaaatgatcaccc--c--ctc-aaagcactagg----tcacatggaagtg-ttt---------------
B D          Human  aaaaatgctcactc--t--ttt-aaagcactgtg----ttagatggaagtg-ttt---------------
B D          Chimp  aaaaatgctcactc--t--ttt-aaaacactgtg----ttagatgaaagtg-ttt---------------
B D      Orangutan  aaaaatgctcactc--t--ctt-aaagcactgtg----ttagatgaaagtg-ttt---------------
B D         Rhesus  aaaaatgatcactc--t--ctt--aagcactgtg----ttagatggacgtg-ttt---------------
B D       Marmoset  aaaaatgatcactc--t--ctt-aaagcact-tg----tcagatggaagtg-ttt---------------
          Bushbaby  agaaa---------------------------tg----tcagatggaagtg-ttt---------------
B D     Tree shrew  --------ttactc--c--ttc-aaagcactgca----tcagatggaagtg-ttt---------------
B D          Shrew  caaaaggattttca--t--ttc-tgag-------------------ga----------------------
B D       Hedgehog  caaaatcatgacca--ccatcc-tgtg-------------------aagtg-cat---------------
B D            Dog  caaaatgattgccc--t--ttcaaaagcactgtg----tcagatggaagta-ttt---------------
B D            Cat  caaaatgattgctc--c--ttc-aaagcactgtg----tcagatggaagta-ttt---------------
B D          Horse  ----atgatcaccc--c--gtg-gaagcactgtg----tcagatgcaaatg-ttt---------------
B D            Cow  caaaatgattgccctgc--ttt-gaagctcagta----tcagatggaagtgtttt---------------
         Armadillo  caaaatgattgccc--c--tta-gaagcactgtg----tcagatggaagtg-ttt---------------
          Elephant  taaaatgatcatcc--t--gtt-gaagcaccgtg----tcagatggaagta-ttt---------------
B D         Tenrec  cacagtggccatct--t--ttc-tgagcacagtg----tcagatggagata-ttt---------------
B D        Opossum  cttaatcattgctc--t--tta-acattccttcattgtttatatgtatatg-tatatatatatatagtta
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  ------aaaaccaagtataaacggcact--gtcaca-------cttc--
               Rat  ------aaaatcaagtataaaagacact--gtcaaa-------cttc--
        Guinea pig  ------aaaatcaaat---catagtttt--gtcaaatgtggtccttc--
            Rabbit  ------aaaaccaagttttaagtgccttgggtcaca-------cttc--
             Human  ------aaaatcaagttacaatggcttt--gccaaa-------c--c--
             Chimp  ------aaaattaagttacaatggcttt--gccaaa-------c--c--
         Orangutan  ------aaaatcaagttacaatggcttt--gccaaa-------cttc--
            Rhesus  ------aaaatcaagttacaatggcttt--gccaaa-------cttc--
          Marmoset  ------aaaatcaagttacaatggcttt--gtcaaa-------cttc--
          Bushbaby  ------aaaatcaagttacagtggcttt--gtcaaa-------cttt--
        Tree shrew  -------aaatccagttataatggcttt--atcaaa-------c--c--
             Shrew  --------aatcaagttatagtggcttt--gtcaaa---------tt--
          Hedgehog  ------ccaatcaggttgtagcagcgtt--gtcaaa-------tttt--
               Dog  ------aaactcaagttgtggtggcttt--gtcaaa-------cttc--
               Cat  ------aaaatcaagttgtagcggcttt--atcaaa-------cttc--
             Horse  ------aaaatcaagttgtagtggcttt--gtcaaa-------ttta--
               Cow  ------aagatc--gtagtagtagcttt--gtcaaa-------cttc--
         Armadillo  ------aaaatcaagttacagtagcttt--atcaaa-------catt--
          Elephant  ------aaaatcaagttccagtggcttt--gtcaaa-------cttc--
            Tenrec  -------aaatcaggttgccgaggcttg--gtcaaa-------cttg--
           Opossum  ctgggaagagttggggtggggggaggaa--gtctaa-------ttcttc
         Tetraodon  =================================================
       Stickleback  =================================================
            Medaka  =================================================
         Zebrafish  =================================================
     X. tropicalis  =================================================
          Platypus  =================================================
           Chicken  =================================================
            Lizard  =================================================

Inserts between block 57 and 58 in window
           Rabbit 2145bp
B D         Human 7bp
B D         Chimp 7bp
B D     Orangutan 7bp
B D        Rhesus 7bp
B D      Marmoset 7bp
         Bushbaby 7bp
B D    Tree shrew 7bp
B D         Shrew 7bp
B D      Hedgehog 7bp
B D           Dog 7bp
B D           Cat 342bp
B D         Horse 7bp
B D           Cow 7bp
        Armadillo 7bp
         Elephant 7bp
B D        Tenrec 7bp

Alignment block 58 of 255 in window, 57799990 - 57800050, 61 bps 
B D          Mouse  tatgcgcggagtccagaag-cagaactaga-----------tgaa----tgtagtc------------tt
        Guinea pig  tgcccataggacctggaga-taataatata----------ttgtg----tctagtc------------tt
B D            Rat  tatacatggggcccagaag-cagaattaga-----------tgca----tgcaatc------------tt
B D          Human  cacccataggacccaaaga-caaacataca----------ttgtt----tgtagcc------------tt
B D          Chimp  cacccataggacccaaaga-caaacataca----------ttgtt----tgtagcc------------tt
B D      Orangutan  cacccatgggacccaaaga-caaacataca----------ttgtt----tgtagcc------------tt
B D         Rhesus  catccataggacccaaaga-caaacataca----------ttgtt----tgtagcc------------tt
B D       Marmoset  cacccataggacccaaaga-caaaaataca----------ttgtt----tgtagcc------------tt
          Bushbaby  cacccaaagtacccaaaga-taaaaacatc----------atcttcaaatgtctcctctttgaaattatt
B D     Tree shrew  cacccgtagaccccatgga-cacaaatgca----------tttct----tggagcc------------tt
B D          Shrew  cacctatagaacccacaaattcaaaacaaa----------ctgct----gactgtt------------tt
B D       Hedgehog  catccctagagcccacaga-gaaaaacaaa----------ttgct----gatagtt------------tt
B D            Dog  cacccataggtcccaaaga-caaaaacaca----------ttgct----catagtc------------tt
B D          Horse  cacccataggtcccaaaga-caaaaacaca----------ttgct----tccagtc------------tt
B D            Cow  cacccatgggtcccaaaga-caa------a----------ctgct----cctagtt------------tt
         Armadillo  cacctatatgtaccaaaga-caaaaataga----------caacc----aggagtc------------tt
          Elephant  tacccacaggtaccaggca-caaaaataca----------ttcct----tgtaatc------------tt
B D         Tenrec  catccataggtgccaaaca-caaaaataca----------ttcct----ggtagcc------------tt
B D        Opossum  aatccgtgtcacttcaaaa-taaaattatgtgaagtgcctttgtc----tttaact------------tt
B D            Cat  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================
           Rabbit  ======================================================================

             Mouse  caa----atat---ct----------------------------ttt---t-----tc------------
        Guinea pig  caa----atat---tt----------------------------cct---t-----tt------------
               Rat  caa----atat---ct----------------------------ttt---t-----tc------------
             Human  cac----atat---ct----------------------------ctt---t-----ga----aactatac
             Chimp  cac----atat---ct----------------------------ctt---t-----ga----aactatac
         Orangutan  cac----atat---ct----------------------------ctt---t-----ga----aactatac
            Rhesus  cac----atat---ct----------------------------ctt---t-----ga----aactacac
          Marmoset  cac----caat---ct----------------------------ctt---t-----gaaactaactatac
          Bushbaby  caa----atat---ct----------------------------cctctat-----ga----aattactc
        Tree shrew  caa----atatcccct----------------------------ctt---t-----aa----aattaca-
             Shrew  cag----atat---ct----------------------------tat---tttttaaa----aattgcac
          Hedgehog  cat----a-ac---ct----------------------------ctc---ttctctaa----aactgtac
               Dog  caa----atat---ct----------------------------ttt---cttt--aa----aactgcac
             Horse  taa----gtat---ct----------------------------tcc---tttt--aa----aatggcac
               Cow  caa----atat---ct----------------------------tct---cttt--aa----aattgtac
         Armadillo  tca----atat---ct----------------------------tct---t-----aa----aattacat
          Elephant  caa----atac---ct------------------------------------------------------
            Tenrec  taaaattacac---ctgatctctctctctctctctctctctctctct---c-----tc----tctctctc
           Opossum  -------gtgt---ct----------------------------ctt---t-----ta----aa--gaag
               Cat  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================
            Rabbit  ======================================================================

             Mouse  --------------------------caat
        Guinea pig  --------------------------taaa
               Rat  --------------------------cccc
             Human  ctggtcactgaaaaatgccaataattcaat
             Chimp  ctggtcactgaaaaacgccaataattcaat
         Orangutan  ctggtcaatgaaaaatgccaataattcaat
            Rhesus  ctggacaccgaaaaatgccaataattcaat
          Marmoset  ctggtcactgaaaaatggcaatgattcaat
          Bushbaby  ctggccactgaaaaacaccagtgattcaat
        Tree shrew  ctggtttctttaaaataccaatgattcaat
             Shrew  ttggttattta-agatgacagtgatttgat
          Hedgehog  ttgattactaagagatgcaagcaattcact
               Dog  ttagtcatttaaggatggcagtgattcaag
             Horse  tttgtcacttaaagacgccagtgattcaat
               Cow  ttgctcacttaaagatgccgatgattcaac
         Armadillo  ttggtctcataaagat--------------
          Elephant  ------tctttgaaat--------------
            Tenrec  tctctctctctcacac--------------
           Opossum  tagactaatagaaaatgaat----------
               Cat  ==============================
         Tetraodon  ==============================
       Stickleback  ==============================
            Medaka  ==============================
         Zebrafish  ==============================
     X. tropicalis  ==============================
          Platypus  ==============================
           Chicken  ==============================
            Lizard  ==============================
            Rabbit  ==============================

Inserts between block 58 and 59 in window
        Armadillo 14bp
         Elephant 1646bp
B D        Tenrec 26bp

Alignment block 59 of 255 in window, 57800051 - 57800077, 27 bps 
B D          Mouse  atgcat--------aactgtagatatt----attattat
        Guinea pig  at-tacacttggtcacttaaagaagtc----a-----gt
B D            Rat  atatgca-------aactgtagatgtt----atgaaaat
B D          Human  attctc--------aaccccaggtatt----atagtaat
B D          Chimp  attctc--------aaccccaggtatt----atagtaat
B D      Orangutan  attctc--------aaccccaggtatt----atagtaat
B D         Rhesus  atgcac--------aaccctaggtatt----atagtaat
B D       Marmoset  atgcac--------aactccaagtatc----atagtaa-
          Bushbaby  atgcac--------aaccccaagtact----gtggtaat
B D     Tree shrew  atgcac--------aaccctgtatatt----gcggtaat
B D          Shrew  atgcac--------aactatatgtatt----gtggtaat
B D       Hedgehog  atacac--------aaccctaggcatt----gtggtaag
B D            Dog  aggcac--------acttctaggtatt----gtggtcat
B D          Horse  atgcac--------aaccctaagtatt----gtggtaat
B D            Cow  atgcac--------acctcttggtatt----gtggtaat
         Armadillo  atgtgc--------aaccttaggtgtc----atggcaat
          Elephant  atccac--------aaccctcagtatt----gtaataat
B D         Tenrec  atgcac--------aaacttcagcatt----gtggtaat
B D        Opossum  aagcat--------tgccttaggcttttagaatttttat
B D            Cat  =======================================
B D      Tetraodon  =======================================
B D    Stickleback  =======================================
           Medaka  =======================================
B D      Zebrafish  =======================================
B D  X. tropicalis  =======================================
B D       Platypus  =======================================
B D        Chicken  =======================================
B D         Lizard  =======================================
           Rabbit  =======================================

Inserts between block 59 and 60 in window
B D         Human 15bp
B D         Chimp 15bp
B D     Orangutan 15bp
B D        Rhesus 15bp
B D      Marmoset 11bp
         Bushbaby 15bp
B D    Tree shrew 15bp
B D         Shrew 15bp
B D      Hedgehog 15bp
B D           Dog 15bp
B D         Horse 15bp
B D           Cow 15bp
        Armadillo 15bp
         Elephant 15bp
B D        Tenrec 15bp

Alignment block 60 of 255 in window, 57800078 - 57800158, 81 bps 
B D          Mouse  tat------tt------ggtctgta---------------------tttcctt----------t--aaga
B D        Opossum  ---cgcttata------tttgtgta---------------------tgttgat----------t--ggaa
B D         Tenrec  aat------tt------tctttgca---------------------tctcc-t----------t--aaga
          Elephant  aat------tt------tctttgca---------------------tctccat----------t--aaga
         Armadillo  aat------tt------tctttgca---------------------tctccac----------t--aaga
B D            Cow  aat------tt------tctttgcg---------------------tctctat----------a--aaga
B D          Horse  aat------tt------tcttcgca---------------------tctctgt----------t--aaga
B D            Dog  aat------tt------tctttata---------------------tctctat----------taaaaaa
B D       Hedgehog  aac------tg------ccttttca---------------------tttgtgt----------t--agga
B D          Shrew  aaag-----tt------tctttgca---------------------tct-tat----------t--aagg
B D     Tree shrew  aat------tt------tctttgtg---------------------tctttat----------g--aaga
          Bushbaby  aat------tt------tctttcca---------------------tcttcat----------t--aaga
B D       Marmoset  aat------tt------tctttgca---------------------tctccaa----------c--aaga
B D         Rhesus  aat------tt------tctttgca---------------------tctccac----------c--aaga
B D      Orangutan  aat------tt------tctttgca---------------------tctccac----------c--aaga
B D          Chimp  aat------tt------tctttgca---------------------tctccac----------c--aaga
B D          Human  aat------tt------tctttgca---------------------tctccac----------c--aaga
            Rabbit  tat------tt------tctttgc----------------------ttttcta----------t--caga
        Guinea pig  gat------tt------ggtatgtacaacatactgtactatgtaggtttccttacatctccagc--aaga
B D            Rat  ctt------ttagggggggtctgta---------------------tctcctt----------t--aaga
B D            Cat  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  acagagagtttggca--gat-ggct----tggctttgctcttttt-tttttaaatgttaaa---------
           Opossum  accaaaagaattcct--gaa-cctc----taga--------tcctttccctaaagttttgaattattaaa
            Tenrec  actgaaagttcaact--aat-ggc--------------------------caaacacttca---------
          Elephant  acagaaaggataact--gat-ggct----tgac--------tcct-tttttaaacacttaa---------
         Armadillo  acagaaagataactg--aat-ggct----ttac--------tcct-tttcttaacacttaa---------
               Cow  gaataaaggatagtt--gac-agct----ttag--------ctcttttccaaaacacttaa---------
             Horse  acataaaggataact--gat-gattttacttac--------tcctgtttcaaaacacttaa---------
               Dog  acataaaggataact--gac-agct----ttac--------tcctttttcaaaacacttaa---------
          Hedgehog  atggaaagaataacg--gac-gatt----ttac--------tcctttttcaaaacacttga---------
             Shrew  acaataaggaaa------at-tatt----ttac--------tcctttttcaaaacaattaa---------
        Tree shrew  acagaaagggtaact--gatgggtt----ttac--------tcct-tttcttaatgcttaa---------
          Bushbaby  agagaaagggcaact--gat-ttct----ttac--------tcct-tttcttaacacttca---------
          Marmoset  acagaaagaataact--gat-gaca----ttac--------ac------cttaacacttaa---------
            Rhesus  acagaaagaataaca--gaa-agaa----aaaa--------at-----------aacttaa---------
         Orangutan  acagaaagaataact--gat-ggca----ttac--------ac------cttaacacttaa---------
             Chimp  acagaaagaataact--gat-ggca----ttac--------ac------cttaacacctaa---------
             Human  acagaaagaataact--gat-ggca----ttac--------ac------cttaacacttaa---------
            Rabbit  acagagaa---gatacgtat-ggct----tt-c--------ttgc-ttccttaacatttaa---------
        Guinea pig  aaagaaaa---ggta--act-gttt----taac--------tcct-tttcttaacacttaa---------
               Rat  acagaaagattggta--gat-ggtt----ttgc--------tccc-tttcttaacgttaaa---------
               Cat  ======================================================================
         Tetraodon  ======================================================================
       Stickleback  ======================================================================
            Medaka  ======================================================================
         Zebrafish  ======================================================================
     X. tropicalis  ======================================================================
          Platypus  ======================================================================
           Chicken  ======================================================================
            Lizard  ======================================================================

             Mouse  -----ttc
           Opossum  acgtcttt
            Tenrec  -----ctc
          Elephant  -----tag
         Armadillo  -----gtc
               Cow  -----ttc
             Horse  -----tcc
               Dog  -----ttc
          Hedgehog  -----ttc
             Shrew  -----ttt
        Tree shrew  -----ttc
          Bushbaby  -----ttc
          Marmoset  -----ttc
            Rhesus  -----ttt
         Orangutan  -----ttt
             Chimp  -----ttt
             Human  -----ttt
            Rabbit  -----ttc
        Guinea pig  -----ttt
               Rat  -----ttc
               Cat  ========
         Tetraodon  ========
       Stickleback  ========
            Medaka  ========
         Zebrafish  ========
     X. tropicalis  ========
          Platypus  ========
           Chicken  ========
            Lizard  ========

Alignment block 61 of 255 in window, 57800159 - 57800187, 29 bps 
B D          Mouse  -----------tactttcattt------tctt----------aacat--------tttatttca
B D            Rat  -----------tactttcattt------tctt----------tacac--------tttatttca
        Guinea pig  -----------tacttccattt------tctt----------aacat--------tttatttaa
            Rabbit  -----------tactttcgttt------g-tt----------aacgt--------tgtattcaa
B D          Human  -----------tactttcattt------tctt----------aacc-----------tatttca
B D          Chimp  -----------tactttcattt------tctt----------aacc-----------tatttca
B D      Orangutan  -----------tactttcattt------tctt----------aacc-----------tatttca
B D         Rhesus  -----------tactttcattt------tctt----------aacc-----------tatttca
B D       Marmoset  -----------tactttcattt------tctt----------aacc-----------gatttca
          Bushbaby  -----------tactttcattt------tctt----------aacct--------tttatttca
B D     Tree shrew  -----------cactttcattt------tctt----------aacat--------tttatttca
B D          Shrew  -----------ga---------------------------------------------------
B D       Hedgehog  -----------tac-----tcc------tctt----------agcat--------ttcactt--
B D            Dog  -----------taccttcattt------tctt----------aa-ct--------tttatttca
B D          Horse  -----------tactttcattt------tctt----------aatcg--------tctgtttca
B D            Cow  -----------cactttaattt------tcct----------aacct--------tttgtttca
         Armadillo  -----------cattttcagtt------tctc----------aatctatttccct---------
          Elephant  -----------tattttctgtt------tctt----------aacct-----------------
B D         Tenrec  -----------tacttgcactg------gttt----------gcact-----------------
B D        Opossum  -----------catttttattc------tcttcctctcgcaaagcca-----------------
B D      Zebrafish  ta---------ctttatcaattataaacttgt----------a---------------------
B D           Fugu  --cctttttctctttatcgttt----gctctc----------a---------------------
B D            Cat  ================================================================
B D      Tetraodon  ================================================================
B D    Stickleback  ================================================================
           Medaka  ================================================================
B D  X. tropicalis  ================================================================
B D       Platypus  ================================================================
B D        Chicken  ================================================================
B D         Lizard  ================================================================

Inserts between block 61 and 62 in window
B D         Shrew 63bp

Alignment block 62 of 255 in window, 57800188 - 57800222, 35 bps 
B D          Mouse  tt-ttttctttctga----------------------------tg----------ttttaaaa----aaa
B D            Rat  tt-ttctctatctga----------------------------tg----------cctaaaaa----aaa
        Guinea pig  tt-ttctcttccttg----------------------------tc----------cttaaaaa----aaa
            Rabbit  tt-cttttt----------------------------------------------------------aaa
B D          Human  tt-ttctctttcttg----------------------------ta----------tatacattttttaaa
B D          Chimp  tt-ttctctttcttg----------------------------ta----------tatatattttttaaa
B D      Orangutan  tt-ttctccttcttg----------------------------ta----------tatatatattttaaa
B D         Rhesus  tt-ttctctttcttg----------------------------ta----------tatacatatttgaaa
B D       Marmoset  tt-ttctctttcttgtatatatatatatacaaatatatatatata----------tatatatatttaaaa
          Bushbaby  tt-ttctctgtcttg----------------------------------------tatatgtttttaaaa
B D     Tree shrew  ca-tttttcttgtat----------------------------ta----------aaaaaaaagaatgac
B D       Hedgehog  ------------------------------------------------------------------aaaa
B D            Dog  ---------------------------------------------------------------ttaaaaa
B D          Horse  ---------------------------------------------------------------ttaaaaa
B D            Cow  ---------------------------------------------------------------ttgaaaa
         Armadillo  tt-ctttatttctca----------------------------ta----------ttaaaaa-agcaaaa
          Elephant  ----tttatttcttg----------------------------ta----------ttaaaaaaaaaaaaa
B D         Tenrec  ----tttattttcta----------------------------tatgtgtcggatttgaaaacagcagaa
B D        Opossum  -----ctctttctca----------------------------------------aaccctttctataaa
B D      Zebrafish  ttgtattctttcaga----------------------------tagatat-----cttaaaaaccacaat
B D           Fugu  ct-cactctttctaa----------------------------tca---------tttgtgggccgcgac
B D          Shrew  ======================================================================
B D            Cat  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  --------------------a-ccattct
               Rat  -------------------ga-acattct
        Guinea pig  --------------------a-catctcc
            Rabbit  --------------------a-accctct
             Human  --------------------c-tctttca
             Chimp  --------------------c-tctttca
         Orangutan  --------------------c-tctttca
            Rhesus  --------------------cttttttca
          Marmoset  --------------------c-tctttta
          Bushbaby  --------------------c-tctt---
        Tree shrew  --------------------c-tctctc-
          Hedgehog  --------------------a-aaat---
               Dog  --------------------a-aaaaaaa
             Horse  --------------------c-acacaca
               Cow  --------------------a-gtaaac-
         Armadillo  -----------------cacc-tct----
          Elephant  --------------------c-cct----
            Tenrec  gcagtagcaacaaaacccttc-tct----
           Opossum  --------------------g-cc-----
         Zebrafish  --------------------a-tt-----
              Fugu  --------------------t-ct-----
             Shrew  =============================
               Cat  =============================
         Tetraodon  =============================
       Stickleback  =============================
            Medaka  =============================
     X. tropicalis  =============================
          Platypus  =============================
           Chicken  =============================
            Lizard  =============================

Inserts between block 62 and 63 in window
B D           Dog 10bp
B D         Horse 13bp
B D          Fugu 13bp

Alignment block 63 of 255 in window, 57800223 - 57800289, 67 bps 
B D          Mouse  ttat-----------------aattc--taccattaac----a-attacggtatttc-------------
B D            Rat  ttac-----------------aattc--caccgttgac----a-atcgcggtatttc-------------
        Guinea pig  ataa-----------------gaccc--tgccattgcc----g-ctcatggtattca-------------
            Rabbit  ataa-----------------accccattcctactgat----a-cttgtggcattca-------------
B D          Human  ggaa-----------------aaccc--tgccactaac----a-cccatggcatgta-------------
B D          Chimp  ggaa-----------------aaccc--tgccactaac----a-cccatggcatgta-------------
B D      Orangutan  ggaa-----------------aaccc--tgccactaac----a-cccatggcatgta-------------
B D         Rhesus  ggaa-----------------aaccc--tgccactaac----a-cccatggcatgta-------------
B D       Marmoset  ggat-----------------aaccc--tgccactgac----a-cccatgacatgta-------------
          Bushbaby  -aac-----------------aaccc--tgccagt------------atggaataca-------------
B D     Tree shrew  ---t-----------------aaccc--tgccactgct----a-ctggaggcgttta-------------
B D          Shrew  ttag-----------------ccttt--tacccatgat----c-tttatggcattct-------------
B D       Hedgehog  tcat-----------------aactt--cacaagtgatactca-ttcacggcatttt-------------
B D            Dog  ctac-----------------aacct--tgccactgac----actggttggcattta-------------
B D          Horse  ctct-----------------aacct--taccactgac----a-taggtggcattta-------------
B D            Cow  ctat-----------------gacct--tacctctgac----a-ctggtggcactta-------------
         Armadillo  ctat-----------------aaccc--tgccactgac----a-cctgtagcttttc-------------
          Elephant  ctgt-----------------atccc--tgccactgcc----a-tttgtggggttta-------------
B D         Tenrec  cttt-----------------aaccc--tgccactgct----g-ttgttgcggggca-------------
B D        Opossum  -cag-----------------aattt--ta-gggtgat----g-gacaaattattca-------------
B D           Fugu  aattgtctcgttcagtccctcagcct--tgc----aat----a-actgcaggatacaagagctcacagtc
B D            Cat  ======================================================================
B D      Tetraodon  ======================================================================
B D    Stickleback  ======================================================================
           Medaka  ======================================================================
B D      Zebrafish  ======================================================================
B D  X. tropicalis  ======================================================================
B D       Platypus  ======================================================================
B D        Chicken  ======================================================================
B D         Lizard  ======================================================================

             Mouse  ---cag----aatta-ctatttaaaa-----acaatatgcatata-ac
               Rat  ---cag----acttagttatttaaaa-----agaataggcatata-cc
        Guinea pig  ---cag------------------------------------------
            Rabbit  ---cagtggcaata----------------------------------
             Human  ---tagtggta-------att-------------gcaag-attta-tt
             Chimp  ---tagtggta-------att-------------gcaag-attta-tt
         Orangutan  ---tagtggta-------att-------------gcaag-attta-tt
            Rhesus  ---tagtggca-------att-------------gcaag-atttattt
          Marmoset  ---gagtggta-------att-------------gcaag-attta---
          Bushbaby  ---tagtgtta-------att-------------gtaag-atttatgt
        Tree shrew  ---tagtggta-------att---------------------------
             Shrew  ----actggta-------ac------------------t-attta-tc
          Hedgehog  ------tgggt-------gt------------------t-actta-tt
               Dog  ---ctgcggta-------act-gt------------agt-cttta-tt
             Horse  ---cagcggta-------act-gt------------agt-atttg-tt
               Cow  ---cagtggta-------act-gt------------act-atttg-tt
         Armadillo  ---cagtggca-------att-------------gttgg-gttta-tt
          Elephant  ---gagtggta-------att-------------gtaaa-attta-tt
            Tenrec  ---gagtggtg-------gcg-------------gtgaa-atgca-tt
           Opossum  ---ttttcaca-------attccttattttcttataaat-acttc---
              Fugu  taatactgataccacagcaat-------------atact-atata---
               Cat  ================================================
         Tetraodon  ================================================
       Stickleback  ================================================
            Medaka  ================================================
         Zebrafish  ================================================
     X. tropicalis  ================================================
          Platypus  ================================================
           Chicken  ================================================
            Lizard  ================================================

Inserts between block 63 and 64 in window
       Guinea pig 43bp
           Rabbit 45bp
B D    Tree shrew 41bp
B D         Shrew 1bp
B D      Hedgehog 1bp
B D           Dog 1bp
B D         Horse 1bp
        Armadillo 29bp
         Elephant 132bp
B D        Tenrec 1bp
B D       Opossum 18bp

Alignment block 64 of 255 in window, 57800290 - 57800323, 34 bps 
B D          Mouse  tctaaattatatgcatata--------------tataaatatgcatat
B D            Rat  ctta------------------------------------------ct
          Bushbaby  tttgaatcatatgtaggtg--------------aca----ctgcaact
B D       Marmoset  ----agtcatatgcactta--------------tca-------catat
B D         Rhesus  tttaagtcatatgcacata--------------tca-------catgt
B D      Orangutan  tttaagttatatgcacata--------------tca-------catac
B D          Chimp  tttaagtcatatgcacata--------------tca-------catat
B D          Human  tttaagtcatatgcacata--------------tca-------catat
B D          Shrew  tttgagtcatatgcacatg-----------acctca-------cat--
B D       Hedgehog  cttgagtcaca--cacatg-----------accttg-------cat--
B D            Dog  tttaagttatgtgcacata-----------atctca-------cat--
B D            Cat  tctgagtcatatgcacata-----------acctca-------cat--
B D          Horse  tttgagtcatatgcacata-----------acctca-------cat--
B D            Cow  tttgagtcatatgcacata-----------acctca--------gt--
B D         Tenrec  tctaactcttatacacaca----------aacctta-------cgt--
         Armadillo  ------------------------------atttaa-------tgtgt
B D        Opossum  cctggctgacatacac--------------------------------
B D           Fugu  tatatatcgtgtgtgtgtgtgtgtgtgtgtgtgt--------------
         Elephant  ================================================
       Guinea pig  ================================================
B D     Tree shrew  ================================================
B D      Tetraodon  ================================================
B D    Stickleback  ================================================
           Medaka  ================================================
B D      Zebrafish  ================================================
B D  X. tropicalis  ================================================
B D       Platypus  ================================================
B D        Chicken  ================================================
B D         Lizard  ================================================
           Rabbit  ================================================

Inserts between block 64 and 65 in window
         Bushbaby 2bp
B D      Marmoset 2bp
B D        Rhesus 2bp
B D     Orangutan 2bp
B D         Chimp 2bp
B D         Human 2bp
        Armadillo 2bp

Alignment block 65 of 255 in window, 57800324 - 57800373, 50 bps 
B D          Mouse  aatt------------------------tagcaggcagaggcagaagcagagaaagtaaggaagtcc---
B D            Rat  tatt------------------------tagcaggcagtggc----------gatgtagggtagtcc---
            Rabbit  gatt------------------------tagtgtgtggagag-------ggagcatcagggtagtcc---
          Bushbaby  a-----------------------------aggcagagagct------agggtacccaggctaggc----
B D       Marmoset  a-----------------------------atgtgtagaggt------agagtatcaaggggagccc---
B D         Rhesus  a-----------------------------atgtgtagaggt------agagtatcaaggggagccc---
B D      Orangutan  a-----------------------------atgtgtagagat------agagtatcaaggggaaccc---
B D          Chimp  a-----------------------------atgtgtagaggt------agtgtatcaaggggagccc---
B D          Human  a-----------------------------atgtgtagaggt------agtgtatcaaggggagccc---
B D     Tree shrew  -att------------------------taatgtgctgagat------acagcagcaagggcagtcc---
        Guinea pig  ----------------------------------------gtagaggcaaagcttgcagagtagacc---
B D          Shrew  -act------------------------tattgtatggagct--------agtagcaagg----------