Multiz Alignments of 46 Vertebrates
 

Capitalize exons based on show bases
Place cursor over species for alignment detail. Click on 'B' to link to browser for aligned species, click on 'D' to get DNA for aligned species.
Alignment block 1 of 46 in window, 57862972 - 57862994, 23 bps 
B D          Human  a--cccgagag-----gcagaggttg--cagt
B D          Chimp  a--cccgagag-----gcagaggttg--cagt
B D      Orangutan  a--cccgagag-----gcggaggttg--cagt
B D         Rhesus  a--cctgagag-----gcagaggttc--cagt
B D         Baboon  a--cctgagag-----gcagaggttc--cagt
B D       Marmoset  a--cccaagag-----gcggaggttg--cagt
B D         Alpaca  a-------------------------------
B D            Cow  a-------------------------------
B D        Megabat  acc-----------------------------
B D        Opossum  g--actgtaagaatttgtagagattgtccatt
B D         Lizard  ================================
B D          Shrew  ================================
B D            Cat  --------------------------------
B D        Tarsier  ================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ================================
  D        Wallaby  ================================
B D    Stickleback  ================================
B D        Lamprey  ================================
B D         Medaka  ================================
B D        Chicken  ================================
B D    Zebra finch  ================================
B D       Hedgehog  ================================
B D      Tetraodon  ================================
B D     Tree shrew  ================================
B D            Rat  --------------------------------
         Microbat  --------------------------------
B D         Tenrec  ================================
         Squirrel  ================================
B D         Rabbit  ================================
B D           Pika  ================================
B D       Platypus  ================================
B D            Dog  ================================
B D  X. tropicalis  ================================
B D          Sloth  --------------------------------
B D     Rock hyrax  ================================
          Dolphin  --------------------------------
B D       Elephant  ================================
B D     Guinea pig  --------------------------------
B D          Mouse  ================================
B D    Mouse lemur  --------------------------------
         Bushbaby  --------------------------------
B D          Horse  --------------------------------

Alignment block 2 of 46 in window, 57862995 - 57863030, 36 bps 
B D          Human  -------gagctgagatcacaccactgcactccagcctaggtg
B D           Pika  -------gagctgggaacatgc-------ctctctcatgggca
B D          Chimp  -------gagctgagatcacaccactgcactccagcctaggtg
B D      Orangutan  -------gagccgagatcacaccactgcactccagcctaggtg
B D         Rhesus  -------gagccgagatcacaccactgcactccaccctaggtg
B D         Baboon  -------gagccgagatcacaccactgcactccaccctaggtg
B D       Marmoset  -------gagcttagatggcaccactgcactccaccctgggca
B D        Opossum  gataaaggagttt-----------cttcactt-----------
B D         Lizard  ===========================================
B D          Shrew  ===========================================
B D         Alpaca  -------------------------------------------
B D            Cat  -------------------------------------------
B D        Tarsier  ===========================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ===========================================
  D        Wallaby  ===========================================
B D    Stickleback  ===========================================
B D        Lamprey  ===========================================
B D         Medaka  ===========================================
B D        Chicken  ===========================================
B D    Zebra finch  ===========================================
B D       Hedgehog  ===========================================
B D      Tetraodon  ===========================================
B D     Tree shrew  ===========================================
B D            Rat  -------------------------------------------
         Microbat  -------------------------------------------
B D         Tenrec  ===========================================
         Squirrel  ===========================================
B D         Rabbit  ===========================================
B D       Platypus  ===========================================
B D            Dog  ===========================================
B D  X. tropicalis  ===========================================
B D          Sloth  -------------------------------------------
B D     Rock hyrax  ===========================================
          Dolphin  -------------------------------------------
B D            Cow  -------------------------------------------
B D       Elephant  ===========================================
B D     Guinea pig  -------------------------------------------
B D          Mouse  ===========================================
B D    Mouse lemur  -------------------------------------------
         Bushbaby  -------------------------------------------
B D          Horse  -------------------------------------------
B D        Megabat  -------------------------------------------

Inserts between block 2 and 3 in window
B D          Pika 135bp

Alignment block 3 of 46 in window, 57863031 - 57863074, 44 bps 
B D          Human  acagagtgagattc---catc------tcaaaaaaaaaaaaaaaaaa---------------------ga
B D       Marmoset  acagagtga-attc---cacc------tcaaaaaaaaaaacaaaaac-------aaa-----------aa
B D         Baboon  acagagtgagattc---catc------tcaaaaaaaaaaaaaaaaaa---------------------ga
B D         Rhesus  acagagtgagattc---catc------tcaaaaaaaaaaaaaaag-------------------------
B D      Orangutan  acagagtgagattc---catc------tcaaaaaaaaaaaaa--------------------------ga
B D          Chimp  acagagtgagattc---catc------tcaaaaaaaaaaaaaaaaaa-------aaa-----------ga
          Microbat  ----------act----gatcgatgtctcaggtgaggataaaaaaaaaatttt-----------------
B D        Megabat  -----------tt----catc----------------------------tttt-----------------
B D            Cow  ---------actt----catc----------------------------tttt-----------------
B D         Alpaca  ---------actt----catc----------------------------tttt-----------------
B D          Horse  ----------------------------catc-----------------tttt-----------------
B D          Shrew  -------------------------ccccaaaataaaataaatagaataaaat-----------------
B D    Mouse lemur  ------------------aaa------ttaaatgataagaaataaatg-tcttaaaacttcaccttttaa
          Bushbaby  -----------------caaa------ttaaacaataagaaataaaag-tcttagaacttcaccttttaa
B D        Opossum  ------tgaagttcactctac------ttaggaaaacacaaa----------------------------
B D         Lizard  ======================================================================
B D            Cat  ----------------------------------------------------------------------
B D        Tarsier  ======================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D            Rat  ----------------------------------------------------------------------
B D         Tenrec  ======================================================================
         Squirrel  ======================================================================
B D         Rabbit  ======================================================================
B D           Pika  ======================================================================
B D       Platypus  ======================================================================
B D            Dog  ======================================================================
B D  X. tropicalis  ======================================================================
B D          Sloth  ----------------------------------------------------------------------
B D     Rock hyrax  ======================================================================
          Dolphin  ----------------------------------------------------------------------
B D       Elephant  ======================================================================
B D     Guinea pig  ----------------------------------------------------------------------
B D          Mouse  ======================================================================

             Human  taaa
          Marmoset  cag-
            Baboon  aaag
            Rhesus  ----
         Orangutan  taaa
             Chimp  taaa
          Microbat  ----
           Megabat  ----
               Cow  ----
            Alpaca  ----
             Horse  ----
             Shrew  ----
       Mouse lemur  aag-
          Bushbaby  aag-
           Opossum  ----
            Lizard  ====
               Cat  ----
           Tarsier  ====
         Armadillo  NNNN
         Zebrafish  ====
           Wallaby  ====
       Stickleback  ====
           Lamprey  ====
            Medaka  ====
           Chicken  ====
       Zebra finch  ====
          Hedgehog  ====
         Tetraodon  ====
        Tree shrew  ====
               Rat  ----
            Tenrec  ====
          Squirrel  ====
            Rabbit  ====
              Pika  ====
          Platypus  ====
               Dog  ====
     X. tropicalis  ====
             Sloth  ----
        Rock hyrax  ====
           Dolphin  ----
          Elephant  ====
        Guinea pig  ----
             Mouse  ====

Inserts between block 3 and 4 in window
         Microbat 1814bp
B D       Megabat 1bp
B D           Cow 1bp
B D        Alpaca 1bp
B D         Horse 12bp
B D         Shrew 3bp

Alignment block 4 of 46 in window, 57863075 - 57863148, 74 bps 
B D          Human  aaagaatatcag-ttttttt--cct-ctattttca-tatcaattagcttgtcttt-----------ctgt
B D          Chimp  aaagaatatcag-ttttttt--cct-ctattttca-tatcaattagcttgtcttt-----------ctgt
B D      Orangutan  aag-aatatcag-ttttttt--cct-ctactttca-tatc-attagcttgtc-tt-----------ctgt
B D         Alpaca  aaaggata--ca-gtatttt--cct-tcatgttta-tagtggttag-----cttt-----------ctac
B D            Cow  aaagaata--ca-gtattcc--cct-ccatattaa-tcgtggttagcttgtcttt-----------ttat
B D        Megabat  aaagaattc------tcccc--cct-cattattta-tatcgaatagcttgtcttc-----------ctgt
          Microbat  aaagaatgc-aa-tattttt--cct-ccacattta-tattgacttgcttgttttt-----------ctct
B D          Shrew  ataaaatagtgt-gcgtttc--ctt-ccatgtttg-tgttgattagcttgtcttt-----------ctat
           Dolphin  ----------ca-gtctttt--cct-ccatattta-tagtggttagcttttcttt-----------ctat
B D            Dog  ---------------ttttt--cct-ccatat----------ttagtttgctttt-----------ctcc
B D          Horse  ---------------ttttt--cct-ccatattta-tattggttagtttgtcttt-----------atct
B D        Tarsier  -------------tttgttt--ttt-tcattttcattattgattaacttgtcttt-----------ctat
B D    Mouse lemur  --------------ttttgt--ctt-gcattttta-atttgagtagcttttcttc-----------ctat
          Squirrel  ----------------ttct--tct-ccattttca-ttttggttagcttaccttt-----------ctat
B D     Guinea pig  ---------tgc-tccattt--tctaccatcttca-tcttggttagcttatgttt---------------
B D            Rat  ------------attttgtt--tct-ccatatttg-ttctagtttgcttgtctttacctctccctgccct
B D         Rabbit  -------------------t--ttt-ccccattta-tgttgattagcttggcctt-----------ct--
           Gorilla  ----aatatcag-ttttttt--cct-ctattttca-tatcaattagcttgtcttt-----------ctgt
B D         Rhesus  ----aatatgagtttttttt--cct-ctattttcc-tatcaattagcttgtcttt-----------ctgt
B D         Baboon  ----aatatgag-ttttttttccct-ctattttcc-tatcaattagcttgtcttt-----------ctgt
B D       Marmoset  ----aatgtcag--tttttt--ccc-ctattttta-tattgattagcttgtcttt-----------ctat
          Bushbaby  ----aata-cag-ttttttt--ctt-ccattttta-aattgattagtttgt---------------ctgt
B D          Sloth  aaagaaatgaag-tttttcc--cct-ccatattca-cact--ctggc-------------------ttgt
B D        Opossum  -----------------tcc--act-ccatatacc-tgtc--tcaatttattatt-----------ca--
B D         Lizard  ======================================================================
B D            Cat  ----------------------------------------------------------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D         Tenrec  ======================================================================
B D           Pika  ======================================================================
B D       Platypus  ======================================================================
B D  X. tropicalis  ======================================================================
B D     Rock hyrax  ======================================================================
B D       Elephant  ======================================================================
B D          Mouse  ======================================================================

             Human  tga--------g----tatcgttcatgagtct
             Chimp  tga--------g----tatcgttcatgagtct
         Orangutan  tga--------g----tatcg-tcatgagtct
            Alpaca  tga--------g----tataattcatgagttt
               Cow  tgg--------g----tataattcgtgattct
           Megabat  tga--------g----tgtaattcatgagact
          Microbat  tga--------gtatatataattcatgagtct
             Shrew  tgc--------g----tgtaagttgtaaatct
           Dolphin  tgg--------g----tataattcgtgagtct
               Dog  tga--------a----tgtaagtcatgagtct
             Horse  tga--------g----tgtaatccatgagtct
           Tarsier  tga--------g----tgtcattcatgaatct
       Mouse lemur  tag--------g----tatcattcatgagtct
          Squirrel  tga--------g----tattaggcatgagtct
        Guinea pig  -----------c----ttattgtcataaatct
               Rat  ggactaggtaca----tttttaccaccagact
            Rabbit  -----------a----tattatttatgagtct
           Gorilla  tga--------g----tatcgttcatgagtct
            Rhesus  tga--------g----tatcgttcatgagtct
            Baboon  tga--------g----tatcgttcatgagtct
          Marmoset  tga--------g----catcattcatgagtct
          Bushbaby  taa--------a----tatcacacatgagttt
             Sloth  tgg--------g----tctagtttatgagtct
           Opossum  --------------------------------
            Lizard  ================================
               Cat  --------------------------------
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ================================
           Wallaby  ================================
       Stickleback  ================================
           Lamprey  ================================
            Medaka  ================================
           Chicken  ================================
       Zebra finch  ================================
          Hedgehog  ================================
         Tetraodon  ================================
        Tree shrew  ================================
            Tenrec  ================================
              Pika  ================================
          Platypus  ================================
     X. tropicalis  ================================
        Rock hyrax  ================================
          Elephant  ================================
             Mouse  ================================

Inserts between block 4 and 5 in window
B D     Orangutan 663bp
B D           Dog 3bp

Alignment block 5 of 46 in window, 57863149 - 57863154, 6 bps 
B D          Human  gcc-------------------------------------------------------------------
B D          Sloth  gca-------------------------------------------------------------------
B D          Shrew  atg-------------------------------------------------------------------
           Dolphin  gta-------------------------------------------------------------------
B D            Dog  gta-------------------------------------------------------------------
B D          Horse  ata-------------------------------------------------------------------
B D        Megabat  aca-------------------------------------------------------------------
B D            Cow  gta-------------------------------------------------------------------
B D         Alpaca  gta-------------------------------------------------------------------
B D         Rabbit  gta-------------------------------------------------------------------
B D            Rat  acattcccagtccttgtgcttcatcatgggtttggtttgttctgaggcagtgtctcagcccagttgtcgc
B D     Guinea pig  ata-------------------------------------------------------------------
          Squirrel  ata-------------------------------------------------------------------
B D    Mouse lemur  gca-------------------------------------------------------------------
          Bushbaby  aga-------------------------------------------------------------------
B D        Tarsier  gca-------------------------------------------------------------------
B D       Marmoset  gca-------------------------------------------------------------------
B D         Baboon  gca-------------------------------------------------------------------
B D         Rhesus  gca-------------------------------------------------------------------
B D          Chimp  gcc-------------------------------------------------------------------
           Gorilla  gcc-------------------------------------------------------------------
B D         Lizard  ======================================================================
B D            Cat  ----------------------------------------------------------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D        Opossum  ----------------------------------------------------------------------
B D     Tree shrew  ======================================================================
         Microbat  ----------------------------------------------------------------------
B D         Tenrec  ======================================================================
B D           Pika  ======================================================================
B D       Platypus  ======================================================================
B D  X. tropicalis  ======================================================================
B D     Rock hyrax  ======================================================================
B D       Elephant  ======================================================================
B D          Mouse  ======================================================================
B D      Orangutan  ======================================================================

             Human  ------------------------gac
             Sloth  ------------------------gac
             Shrew  ------------------------aac
           Dolphin  ------------------------cac
               Dog  ------------------------cac
             Horse  ------------------------tac
           Megabat  ------------------------ta-
               Cow  ------------------------cat
            Alpaca  ------------------------cag
            Rabbit  ------------------------gac
               Rat  tgctggcttcctgactgagctgccaag
        Guinea pig  ------------------------aag
          Squirrel  ------------------------aac
       Mouse lemur  ------------------------gac
          Bushbaby  ------------------------gaa
           Tarsier  ------------------------gtc
          Marmoset  ------------------------gac
            Baboon  ------------------------gac
            Rhesus  ------------------------gac
             Chimp  ------------------------gac
           Gorilla  ------------------------gac
            Lizard  ===========================
               Cat  ---------------------------
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ===========================
           Wallaby  ===========================
       Stickleback  ===========================
           Lamprey  ===========================
            Medaka  ===========================
           Chicken  ===========================
       Zebra finch  ===========================
          Hedgehog  ===========================
         Tetraodon  ===========================
           Opossum  ---------------------------
        Tree shrew  ===========================
          Microbat  ---------------------------
            Tenrec  ===========================
              Pika  ===========================
          Platypus  ===========================
     X. tropicalis  ===========================
        Rock hyrax  ===========================
          Elephant  ===========================
             Mouse  ===========================
         Orangutan  ===========================

Alignment block 6 of 46 in window, 57863155 - 57863168, 14 bps 
B D          Human  cattttag-------gttgaa
           Gorilla  cattttag-------gttgaa
B D          Chimp  cattttag-------gttgaa
B D         Rhesus  cattttag-------gctgaa
B D         Baboon  cattttag-------gctgaa
B D       Marmoset  cattttag-------gttgaa
B D        Tarsier  catccttg-------gttgaa
          Bushbaby  tatcctag-------atagag
B D    Mouse lemur  catcccag-------gtagag
B D            Rat  cagctggg-------attaga
B D     Guinea pig  ca----ag-------gttgaa
          Squirrel  tattttag-------gatgag
B D         Rabbit  cattttag-------gtaaat
B D           Pika  cattttaacccctgcatcaaa
B D         Alpaca  catcttag-------attaaa
B D            Cow  caccttag-------attaag
B D        Megabat  ---attag-------gttaag
          Microbat  ---gttag-------gttaag
B D          Horse  catcttag-------gttaa-
B D            Dog  catcttag-------gttaag
           Dolphin  caccttag-------attaac
B D          Shrew  cttcatag-------attaag
B D          Sloth  catcttaa-------gttaag
B D        Opossum  ------------------aaa
B D         Lizard  =====================
B D            Cat  ---------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  =====================
  D        Wallaby  =====================
B D    Stickleback  =====================
B D        Lamprey  =====================
B D         Medaka  =====================
B D        Chicken  =====================
B D    Zebra finch  =====================
B D       Hedgehog  =====================
B D      Tetraodon  =====================
B D     Tree shrew  =====================
B D         Tenrec  =====================
B D       Platypus  =====================
B D  X. tropicalis  =====================
B D     Rock hyrax  =====================
B D       Elephant  =====================
B D          Mouse  =====================
B D      Orangutan  =====================

Inserts between block 6 and 7 in window
B D           Rat 41bp
B D        Rabbit 745bp

Alignment block 7 of 46 in window, 57863169 - 57863190, 22 bps 
B D          Human  tatttcctca-aaggctatttta
B D          Sloth  catttcttca-aaggctattttt
B D          Shrew  tatttactca-gaagctattata
           Dolphin  tagttcctca-aaggctgtttta
B D            Dog  tatttcctca-aaggcgatttta
B D          Horse  tatttcctga-aaggctatttta
          Microbat  tatttcctca-aaggctatttta
B D        Megabat  tattttctca-aaggctacttta
B D            Cow  tagttcctca-aaagctgttttg
B D         Alpaca  tagttcctca-aaggctgtttta
B D           Pika  tatttactccctaaactatttta
          Squirrel  catttcctca-aaggccattttg
B D     Guinea pig  cattttctca-aaggctgttttg
B D            Rat  catctcttga-aagactagttta
B D          Mouse  tatctcttta-aagactagttta
          Bushbaby  catttcctca-aaggctatttta
B D        Tarsier  tatttcctaa-aaggctatttta
B D       Marmoset  tatttccccc-aaggctatttta
B D         Baboon  tatttcccca-aaggctattttg
B D         Rhesus  tatttcccca-aaggctattttg
B D          Chimp  tatttcctca-aaggctatttta
           Gorilla  tatttcctca-aaggctatttta
  D        Wallaby  ---------------------ta
B D        Opossum  tgatgcctaa-aatagta-----
B D         Lizard  =======================
B D            Cat  -----------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  =======================
B D    Stickleback  =======================
B D        Lamprey  =======================
B D         Medaka  =======================
B D        Chicken  =======================
B D    Zebra finch  =======================
B D       Hedgehog  =======================
B D      Tetraodon  =======================
B D     Tree shrew  =======================
B D         Tenrec  =======================
B D         Rabbit  =======================
B D       Platypus  =======================
B D  X. tropicalis  =======================
B D     Rock hyrax  =======================
B D       Elephant  =======================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNN
B D      Orangutan  =======================

Inserts between block 7 and 8 in window
B D         Mouse 192bp

Alignment block 8 of 46 in window, 57863191 - 57863211, 21 bps 
B D          Human  tagtttctgaa---ttt--aatct---tt
           Gorilla  tagtttctgaa---ttt--aatct---tt
B D          Chimp  tagtttctgaa---ttt--aatct---tt
B D         Rhesus  tagtttcggaa---ttt--aatct---ta
B D         Baboon  tagtttcggaa---ttt--aatct---ta
B D       Marmoset  tagtttctgca---ttt--aatct---ta
B D        Tarsier  tagtttctgga---ttt--aatct---ta
          Bushbaby  tggttcctgga---ttt--aatct---ta
B D            Rat  ----------ggccttt--gatttgtctt
B D          Mouse  tagtttataggtttttt--tatttgtctt
B D     Guinea pig  tagtttctggg---ttt--aatct---ta
          Squirrel  tagtttctggg---att--aatct---tt
B D           Pika  --atttctgga---ttt--aaagt---ta
B D         Alpaca  tagtcactgga---ttt--aatct---ta
B D            Cow  taatttctgga---ttt--tattt---ta
B D        Megabat  tagtttctaga---ttt--aatcg---ta
          Microbat  tagtttctgaa---ttt--aatct---ta
B D          Horse  tagtttctgaa---ttt--aatct---ta
B D            Dog  cagtttctgga---ttt--aatct---ta
           Dolphin  taatttctgga---ttt--aattt---ta
B D          Shrew  tagtttatgga---ttt--aatc------
B D          Sloth  tagtttctgga---ttt--aatct---ta
  D        Wallaby  caatttctgga---ttttaaatct---aa
B D        Opossum  cagtttctgga---gtttaaatct-----
B D         Lizard  =============================
B D            Cat  -----------------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  =============================
B D    Stickleback  =============================
B D        Lamprey  =============================
B D         Medaka  =============================
B D        Chicken  =============================
B D    Zebra finch  =============================
B D       Hedgehog  =============================
B D      Tetraodon  =============================
B D     Tree shrew  =============================
B D         Tenrec  =============================
B D         Rabbit  =============================
B D       Platypus  =============================
B D  X. tropicalis  =============================
B D     Rock hyrax  =============================
B D       Elephant  =============================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Orangutan  =============================

Inserts between block 8 and 9 in window
B D           Rat 1bp
B D         Mouse 1bp
B D    Guinea pig 1bp
         Squirrel 225bp

Alignment block 9 of 46 in window, 57863212 - 57863263, 52 bps 
B D          Human  --ttttaagggaaca----tttttaggttctatttaggactatagt----------aatt---aatgtaa
           Gorilla  --ttttaagggaaca----tttttaggttctatttaggactatagt----------aatt---aatgtaa
B D          Chimp  --ttttaagggaaca----tttttaggttctatttagaactatagt----------aatt---aatgtaa
B D         Rhesus  --ttttaagggaaca----tttttaggttctatttaggactatagt----------aatt---aaagtaa
B D         Baboon  --ttttaagggaaca----tttttaggttctatttaggactatagt----------aatt---caagtaa
B D       Marmoset  --ttttaagggaaca----tttttaggttatatttaggactacagt----------aatt---aaagtaa
B D        Tarsier  --ttttatgggagcg----tttttaggttccatttaaggctatggt----------actt---aagttaa
          Bushbaby  --ttttaagagaact----tttttagggtccctttaggactacagt----------attc---a------
B D            Rat  --tttcaagagaat------------gttctctttaagctaacagt----------attt---aaattaa
B D          Mouse  --tttcaagagaa--------------ttctctttaagctagcagt----------attt---aaattaa
B D     Guinea pig  --ctttaagggagca----tttttaggttccatttga--tggaagt----------attt----------
          Squirrel  --ttttaaatgagca----tttttaggttctgtttag---gatagt----------attt--------aa
B D           Pika  --ttttaagagaa-a----tttttagattttgttttaactacatgt----------a-------------
B D         Alpaca  --ttttaagggagcat---ttcttaggttctgtttaggactgcttt----------tttt---aatttaa
B D            Cow  --ttttaaaggagctt---ttcttagcttctgtttaggacagcagt----------attt---aaattaa
B D        Megabat  --ttttaagggagcat---tttttaa--gctgtttagggctgtgat----------atat---aa-----
          Microbat  --ttttaagggaacat---tttttagcttttgtttagggcttcggt----------attt---aaattaa
B D          Horse  --ttttaagagagcat---tttttagcttctgtttaggactgcagt----------gttt---aa-----
B D            Dog  --atttaagggaacat--atttttagcttctgtgtaggactgcaat----------atat---aa-----
           Dolphin  --ttttaagggaacgt---ttcttagcttctatttaggacagcagt----------attt---aaattaa
B D          Shrew  ---tttaagggaaca----tttatagcttctgt-taggactttagtattcatactaattt---aaattaa
B D          Sloth  --ttttgagggagcat---tttttaggttccatttagga-------------------------------
  D        Wallaby  --tttccagaggtgatttttttttaggttctgtttaggattatgat---------tattt---tagacaa
B D        Opossum  aatttccagagtt------ttttcagattctgctcaggattataat----------atttttaaa-----
B D         Lizard  ======================================================================
B D            Cat  ----------------------------------------------------------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D         Tenrec  ======================================================================
B D         Rabbit  ======================================================================
B D       Platypus  ======================================================================
B D  X. tropicalis  ======================================================================
B D     Rock hyrax  ======================================================================
B D       Elephant  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Orangutan  ======================================================================

             Human  t
           Gorilla  t
             Chimp  t
            Rhesus  t
            Baboon  t
          Marmoset  t
           Tarsier  t
          Bushbaby  -
               Rat  c
             Mouse  t
        Guinea pig  -
          Squirrel  t
              Pika  -
            Alpaca  t
               Cow  t
           Megabat  -
          Microbat  t
             Horse  -
               Dog  -
           Dolphin  t
             Shrew  t
             Sloth  -
           Wallaby  t
           Opossum  -
            Lizard  =
               Cat  -
         Armadillo  N
         Zebrafish  =
       Stickleback  =
           Lamprey  =
            Medaka  =
           Chicken  =
       Zebra finch  =
          Hedgehog  =
         Tetraodon  =
        Tree shrew  =
            Tenrec  =
            Rabbit  =
          Platypus  =
     X. tropicalis  =
        Rock hyrax  =
          Elephant  =
       Mouse lemur  N
         Orangutan  =

Inserts between block 9 and 10 in window
B D       Megabat 2bp
         Microbat 453bp
B D         Horse 6bp
B D           Dog 6bp
B D         Shrew 12bp

Alignment block 10 of 46 in window, 57863264 - 57863291, 28 bps 
B D          Human  ta-ataatcaataattgc------tacctactctg
           Gorilla  ta-ataatcaataattgc------tacctactctg
B D          Chimp  ta-ataatcaataattgc------tacctactctg
B D         Rhesus  ta-atactcaataattgc------tacctactctg
B D         Baboon  ta-atactcaataattgc------tacctactctg
B D       Marmoset  t--------aataattgc------tacctactctg
B D        Tarsier  a--------aatagctgc------tacttaatctg
          Bushbaby  ---------aatagtttg------tac--------
B D            Rat  c--------aatatttgc-------acttaatcta
B D          Mouse  c--------aacatttgt-------actt----ta
B D     Guinea pig  ------------atttgc------tacttaatttg
          Squirrel  t--------aatatttgc------cacttaatctg
B D           Pika  ------------atctg------------------
B D         Alpaca  t--------aatacttgc------cacttagtctg
           Dolphin  t--------aatactttccacttacacttagtctg
B D            Cow  t--------aatacttgccacttacacttagtctg
B D          Horse  t--------aatacgtgc------cacttaatctg
B D            Dog  g--------aatacttgc------cacttaatctg
          Microbat  t--------aaaacttgc------cacttg-tctg
B D        Megabat  t--------aatacttcc------cacttgatctg
B D          Shrew  t--------aat------------catttaatctg
B D          Sloth  --------------------------------ctg
  D        Wallaby  --------taaaacttta------tatttaaca--
B D        Opossum  -aaataaagcacatttta------aatttttaatg
B D         Lizard  ===================================
B D            Cat  -----------------------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ===================================
B D    Stickleback  ===================================
B D        Lamprey  ===================================
B D         Medaka  ===================================
B D        Chicken  ===================================
B D    Zebra finch  ===================================
B D       Hedgehog  ===================================
B D      Tetraodon  ===================================
B D     Tree shrew  ===================================
B D         Tenrec  ===================================
B D         Rabbit  ===================================
B D       Platypus  ===================================
B D  X. tropicalis  ===================================
B D     Rock hyrax  ===================================
B D       Elephant  ===================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Orangutan  ===================================

Inserts between block 10 and 11 in window
         Bushbaby 7bp
B D        Alpaca 1bp
          Dolphin 1bp
B D           Cow 1bp
B D         Horse 1bp
B D           Dog 1bp
         Microbat 1bp
B D       Megabat 1bp
B D         Shrew 1bp
B D         Sloth 19bp

Alignment block 11 of 46 in window, 57863292 - 57863337, 46 bps 
B D          Human  ---tatgttgaagc-taaatccccaaattaagttttaatactagtatctt
B D        Opossum  aaaaaaattaaaacatataaccccatgctaaaaataaaaatcagttg---
  D        Wallaby  ---tatcttgatgc-gtcatattta---caaatttaaaaatcat------
B D          Shrew  ---tttattaaagt-taagtatcgaagttaaattcacgagttaaatttac
B D        Megabat  ---tttattgaacc-taaatccccaaattaagtttaaatactaatatctt
          Microbat  ---tttattgaagt-taaattcc--aattaagtttaaatactaatatctt
B D            Dog  ---tttattgaagc-taaatccccaaattaagtttaaatactaatatctt
B D          Horse  ---ttcattgaagc-taaatctccaaa------ttaaatactaatatcct
B D            Cow  ---tttattgaaac-tgagtccccaagttaagtttaagtactgataactt
           Dolphin  ---tttattgaaac-taagtccccaagttaagtttaaatactaatatctt
B D         Alpaca  ---tttattgaaac-taagccaccaaattaagtttaa------atatctt
B D           Pika  ---tgtattaaagc-taaagccccagattaggtttaagtatttgaatatt
B D         Rabbit  ---tatattaaagc-taaatctccaaattaagtttaaatatttga-----
          Squirrel  ---tatattgagag-taaatccccagattaggtttaa--------atttt
B D     Guinea pig  ---tata-tgaaat-gaaatccccaaagtaag------tcctagtatctt
B D          Mouse  ---tatattaaaac-taaatgctcatactaagcatat-------------
B D            Rat  ---tgtattaaaac-taaatgcctatattaagcatattttgtagtatttt
B D        Tarsier  ---tatattgaagc-taaatcgccaaataaagttttaaaactaacatct-
B D       Marmoset  ---tatattgaagc-taaatccccaaattaatttttaatgctagtatctt
B D         Baboon  ---tatattgaagc-taaatccccaaattgagttttaatactagcatctt
B D         Rhesus  ---tatattgaagc-taaatccccaaattgagttttaatactagcatctt
B D          Chimp  ---tatgttgaagc-taaatccccaaattaagttttaatactagtatctt
           Gorilla  ---tatgttgaagc-taaatccccaaattaagttttaatactagtatctt
B D       Platypus  -----------agt-taattcacataatcagctttcaactctactgtatt
B D         Tenrec  -----------------------caaaccaggtgttaa------------
B D         Lizard  ==================================================
B D            Cat  --------------------------------------------------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ==================================================
B D    Stickleback  ==================================================
B D        Lamprey  ==================================================
B D         Medaka  ==================================================
B D        Chicken  ==================================================
B D    Zebra finch  ==================================================
B D       Hedgehog  ==================================================
B D      Tetraodon  ==================================================
B D     Tree shrew  ==================================================
B D  X. tropicalis  ==================================================
B D          Sloth  ==================================================
B D     Rock hyrax  ==================================================
B D       Elephant  ==================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ==================================================
B D      Orangutan  ==================================================

Inserts between block 11 and 12 in window
B D       Tarsier 1bp

Alignment block 12 of 46 in window, 57863338 - 57863449, 112 bps 
B D          Human  ttac-------cttactaat-ttctattaa----a--------tttaaggct--gaaaaaaatctt----
           Gorilla  ttac-------cttactaat-ttctattaa----a--------tttaaggct--gaaaaaaatctt----
B D          Chimp  ttac-------cttactaat-ttctattaa----a--------tttaaggct--gaaaaaaatctt----
B D         Rhesus  ttac-------cttactaat-ttgtattaa----a--------tttaaggct--gaaaaaagtctt----
B D         Baboon  ttac-------cttactaat-ttgtattaa----a--------tttaaggct--gaaaaaagtctt----
B D       Marmoset  ttac-------cttactaat-ttgtattaa----attt----ctttaaggct--gaaaaaaaacgt----
B D        Tarsier  ttac-------tttactagt-ttgtattaa----attt----atttaaaact--gaaaaaact-------
B D            Rat  tcc--------cttactagt-ttgtattaa----a--------tttaagact--aaaagaa---------
B D     Guinea pig  tcct-------ctttttagt-ttgtattaagtttg--------tttaaggtc--aaaaaat---------
          Squirrel  tcc--------ccaactagt-ttgtattaa----a--------tttaagtta--aaaaaaa---------
B D           Pika  ttgc-------cttactggt-ttatagtaa----a--------tttatgacttaaaaaaaaac-------
B D          Horse  ttac-------ctttctagt-ttgtattaa----atat----atttaaggcc----aaataatc------
B D            Dog  ttac-------t-----agt------ctta----ctat----atttaaggcc--caaaacactt------
          Microbat  ttcg-------cttactaat-ttgtgttaa----atat----atttaag-gc--cacaaaac--------
B D        Megabat  ac---------cttactagt-ttgtagtaa----atat----attaaagcgt--gaaaaaacct------
B D          Shrew  --------------------------------------------ttaaggca--aaaaatccttt-----
B D            Cat  ------------ttactagt-tggtgcttg----atat----atttaaggct--caaaaaactttatttt
B D            Cow  ------------tgactagt-gtgtattga----atat----attttaggct--aaaaatacc-------
           Dolphin  ------------ttactagc-ttgtattaa----atat----atttaaggct--gaaaatacc-------
B D         Alpaca  ------------ttactacc--------------------------------------------------
B D         Rabbit  ------------ctactagt-ttgtattaa----a--------tttaagaatt-aaaaaaact-------
B D          Mouse  --------------------------ataa----a--------tttaaggct--aaacaga---------
          Bushbaby  ----------------------------------a--------tgtaagaca--aaaaaaaagcct----
B D         Tenrec  --ac-------cttactggg-atgtgctca----atcg-----tttaaagca--taaggaa---------
B D       Elephant  ------------------------tattaa----aaat-----tttaaggca--gaaaaaaaaaaaaaaa
B D     Rock hyrax  -tac-------cttcctaat-ttgtattaa----aatt-----tttaaggca--gaaacaa---------
B D          Sloth  -taa-------attaacttt-acatactta----caac-----ttttataaa--actaaaa---------
  D        Wallaby  ttacag-----ttcagtaattttgtatcca----aatt----gctcaaaggg--gaaaaaaatccc----
B D        Opossum  ----tga----ttcaacagttttatatcag----aatt----gtttgaaggg--aacgaaaatccc----
B D       Platypus  ------taccctttatcatt-cttgattcc----agtgtcccaccaaaagaa--aaagaagtccta----
B D         Lizard  ======================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Orangutan  ======================================================================

             Human  -atttttt---------agc---ttaatagga-----------tcttt-------gtcctatt-cagaag
           Gorilla  -atttttt---------agc---ttaatagga-----------tcttt-------gtcctatt-cagaag
             Chimp  -atttttt---------agc---ttaatagga-----------tcttt-------gtcctatt-cagaag
            Rhesus  -atttttt---------agc---ttaatagga-----------tcttt-------gtcctttt-cagaag
            Baboon  -atttttt---------agc---ttaatagga-----------tcttt-------gtcctttt-cagaag
          Marmoset  -atttttt---------agc---ttaatagga-----------tcttt-------gccctatt-cagaca
           Tarsier  --ttcttt---------agt---ttaatggta-----------ttctt-------atcctatt-tggaaa
               Rat  --tttttt---------tac---ttgataaga-----------ttctt-------attct-tt-cagaaa
        Guinea pig  --tatttt---------ggc---ttaataggt-----------tacat-------gtcctact-cagaaa
          Squirrel  ------------------aa---ttaatagga-----------tcctt-------atcct-at-tcaaaa
              Pika  --tttttt---------agt---ttagtagga-----------ttctt-------------tt-ttgaaa
             Horse  -tttttgt---------agc---ttaatagga-----------tcctt-------atcctatt-cagaaa
               Dog  -ttttctt---------agg---ctaataaga-----------tcc-t-------ttcctatt-cagaaa
          Microbat  -ttttatt---------agc---ttaatagaa-----------ttttt-------atcctgtt-tagaaa
           Megabat  -ttttttc---------agc---gtaatagaa------------tttt-------atcctatt-cag-aa
             Shrew  -tattttt---------atc---ttagtagaa-----------ttc-t-------atccaatt-cggaaa
               Cat  attttttt---------agc---ttagtgaga-----------tcctt-------ttcctatc-tagaaa
               Cow  -ctttttt---------gac---ttaataaga-----------tctat-------atcctatt-cagaaa
           Dolphin  -tttttgg---------ggcggtttaatagga-----------tccat-------ttcctatt-cagaaa
            Alpaca  -------------------------------------------------------------tt-cagaaa
            Rabbit  --tatttt---------agt---ttagaagga-----------tcctt-------aacctatt-ctgaaa
             Mouse  -----ttt---------tac---ctagtaaga-----------ttttt-------attct-tt-cagaaa
          Bushbaby  -tgtttta---------agc---ataatacaa-----------tctta-------atcccatg-tagaaa
            Tenrec  -------------------------------------------tccct-------gccctgtt-tgagaa
          Elephant  acctttct---------agc---ataatagaa-----------tccc---------tcctgtt-taggaa
        Rock hyrax  --cttttg---------agc---ataatagaa-----------tccct-------gttctgtt-taggaa
             Sloth  --ctttttttttttttaaac---ttaatagga-----------tcctt-------atcttgtt-caggaa
           Wallaby  -tacttta---------cac---ctagtaagttgttggttttttttta-------accctgtt-taggag
           Opossum  -ttattta---------aac---ctaataaga-----------tttttttttaaatttttctt-taggag
          Platypus  -ttcactt---------aat---tcaactagt-----------tttta-------atccaattaaagaaa
            Lizard  ======================================================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ======================================================================
       Stickleback  ======================================================================
           Lamprey  ======================================================================
            Medaka  ======================================================================
           Chicken  ======================================================================
       Zebra finch  ======================================================================
          Hedgehog  ======================================================================
         Tetraodon  ======================================================================
        Tree shrew  ======================================================================
     X. tropicalis  ======================================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Orangutan  ======================================================================

             Human  ttttgagttatttacattatttta----ct-------agtg
           Gorilla  ttttgagttatttacgttatttta----ct-------agtg
             Chimp  ttttgagttatttacattatttta----ct-------agtg
            Rhesus  tttctagctatttacattatttta----ct-------agtg
            Baboon  tttctagctatttacattatttta----ct-------agtg
          Marmoset  tttccagttatttacattatttta----ct-------agtg
           Tarsier  tttcaagttatttatgttacttta----tt-------aatg
               Rat  cttctatttatttgcattagtggggggggt-------ggc-
        Guinea pig  ttacatgttatttatattattttattagt--------gaa-
          Squirrel  tttcaagttatttaccttatctta-----------------
              Pika  tttcaagggttttatgttatttta-----ttattgacaac-
             Horse  tttcaaattatttacattatttta----tt-------agtg
               Dog  tttcaggttatttacattactttt----tt-------agtg
          Microbat  ttttaagttatttacattatttta----tt-------agtg
           Megabat  tttcgag-tatagacattatttta----tt-------a---
             Shrew  acctcagttatttacattatttta----tt-------aatg
               Cat  tttcagattatttacattatttta----tt-------agtg
               Cow  tttcaggttacttacattat--------tt-------agtg
           Dolphin  tttcaagttatttacattatttta----tt-------agtg
            Alpaca  tttcaagctatttacattattttc----tt-------agtg
            Rabbit  tttcaagtgattcacattatttta-----tta-----ggt-
             Mouse  tttcaatttatttgcattagtgggggggg--------gac-
          Bushbaby  ttcc-aggtatttatgttattttt----cc-------aatg
            Tenrec  tttcaagttatttcac----ttta----tt-------agtg
          Elephant  tttcaagtta----------ttta----tt-------agca
        Rock hyrax  ttttaag--------------tta----tt-------agtg
             Sloth  tttcaagttatttcta-----tta----tt-------aatg
           Wallaby  tttaaagtgacaagtgatatttta----tc-------agtg
           Opossum  ttcaaagtgacaaatgacatttaa----c--------agtg
          Platypus  tttaaaggcattatcattg----------------------
            Lizard  =========================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  =========================================
       Stickleback  =========================================
           Lamprey  =========================================
            Medaka  =========================================
           Chicken  =========================================
       Zebra finch  =========================================
          Hedgehog  =========================================
         Tetraodon  =========================================
        Tree shrew  =========================================
     X. tropicalis  =========================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Orangutan  =========================================

Inserts between block 12 and 13 in window
B D       Tarsier 319bp
B D         Horse 2bp
B D           Dog 2bp
         Microbat 2bp
B D         Shrew 2bp
B D           Cat 2bp
B D           Cow 2bp
          Dolphin 2bp
B D        Alpaca 2bp
B D       Opossum 2bp

Alignment block 13 of 46 in window, 57863450 - 57863487, 38 bps 
B D          Human  a-aaatat----aaa------ac-c------aa-------------------------------------
           Gorilla  a-aaatat----aaa------ac-c------aa-------------------------------------
B D          Chimp  a-aaatat----aaa------ac-c------aa-------------------------------------
B D         Rhesus  a-aaatat----aaa------ac-c------aa-------------------------------------
B D         Baboon  a-aaatat----aaa------ac-c------aa-------------------------------------
B D       Marmoset  a-aaatac----aaa------ac-a------aa-------------------------------------
B D        Tarsier  a-aaacat----aaa------ac-c------aa-------------------------------------
B D      Orangutan  ----------------------------------------------------------------------
          Bushbaby  a-aaatatttagaag------tc-c------cc-------------------------------------
B D            Rat  a-aaaagc----aat------ct-t------aa-------------------------------------
B D          Mouse  a-aaaacc----aat------ct-t------aa-------------------------------------
B D     Guinea pig  a-acatat----aaa------ac-t------ga-------------------------------------
B D         Rabbit  aaacctag----aaa------at-c------ac-------------------------------------
B D           Pika  atacatag----aaa------at-c------ac-------------------------------------
B D         Alpaca  a-acacgc----aac------ac-c------aa-------------------------------------
           Dolphin  a-acacat----aagtgatgaac-c------aa-------------------------------------
B D            Cow  a-acacat----aacttaagaac-c------aa-------------------------------------
B D          Horse  a-acacat----aac------ac-c-------a-------------------------------------
B D            Cat  a-acacat----aac------gc-----------------------------------------------
B D            Dog  a-acacat----aac------ac---------a-------------------------------------
          Microbat  a-acacat----aac------ac-c------aa-------------------------------------
B D        Megabat  a-acac------aac------ac-c------aa-------------------------------------
B D          Shrew  g-atagat----aac------ac-tgcaaaaga-------------------------------------
B D         Tenrec  ------------aaa------at-c------ag-------------------------------------
B D       Elephant  ------------aac------acac------ac-------------------------------------
B D     Rock hyrax  ------------aaa------acgc------actaattctcagtgcctctctatttgctctctgaggaaa
B D          Sloth  ------------aaa------acac------aa-------------------------------------
  D        Wallaby  -gaaaaat----aaa------gc-t------ag-------------------------------------
B D        Opossum  a-ataaat----aaa------at-t------ag-------------------------------------
B D       Platypus  -------------------------------aa-------------------------------------
B D         Lizard  ======================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  ----------------------------------------------------------aa-aa---cagt
           Gorilla  ----------------------------------------------------------aa-aa---cagt
             Chimp  ----------------------------------------------------------aa-aa---cagt
            Rhesus  ----------------------------------------------------------aa-aa---cagt
            Baboon  ----------------------------------------------------------aa-aa---cagt
          Marmoset  ----------------------------------------------------------aa-aa---aaag
           Tarsier  ----------------------------------------------------------aa-aa----agt
         Orangutan  ----------------------------------------------------------------------
          Bushbaby  ----------------------------------------------------------aa-a--------
               Rat  ----------------------------------------------------------aacct---aagc
             Mouse  ----------------------------------------------------------aacca---aaac
        Guinea pig  ----------------------------------------------------------aa------aaaa
            Rabbit  ----------------------------------------------------------aa--t---cagt
              Pika  ----------------------------------------------------------aa--a---aaaa
            Alpaca  ----------------------------------------------------------aa--aaaaaaat
           Dolphin  ----------------------------------------------------------aa--a---gagt
               Cow  ----------------------------------------------------------aa--a----agt
             Horse  ----------------------------------------------------------aa--a---aagt
               Cat  ----------------------------------------------------------aa--a---aagt
               Dog  ----------------------------------------------------------aa--a---aagt
          Microbat  ----------------------------------------------------------aa-ta---aact
           Megabat  ----------------------------------------------------------aa--a---aagt
             Shrew  ----------------------------------------------------------aa--a---aagt
            Tenrec  ----------------------------------------------------------gt--g---aaat
          Elephant  ----------------------------------------------------------ac--a---aagt
        Rock hyrax  cttttgctttattttgaactctcttctctgctagcctcctcccccagacttcaaactaaa--g---aagt
             Sloth  ----------------------------------------------------aaacaaaa--a---aagt
           Wallaby  ----------------------------------------------------------tg--a-------
           Opossum  ----------------------------------------------------------tg--a-------
          Platypus  ----------------------------------------------------------aacaa---aggg
            Lizard  ======================================================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ======================================================================
       Stickleback  ======================================================================
           Lamprey  ======================================================================
            Medaka  ======================================================================
           Chicken  ======================================================================
       Zebra finch  ======================================================================
          Hedgehog  ======================================================================
         Tetraodon  ======================================================================
        Tree shrew  ======================================================================
     X. tropicalis  ======================================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  t-tattagttgtaatg-----
           Gorilla  t-tattagttgtaatg-----
             Chimp  t-tattagttgtaatg-----
            Rhesus  t-tatccattgtaatg-----
            Baboon  t-tatccattgtaatg-----
          Marmoset  tttatca--------g-----
           Tarsier  t-tgtcagttgtaatg-----
         Orangutan  --tatcagttgtaatg-----
          Bushbaby  t-tatcacttatagag-----
               Rat  t-tatcacttgttttg-----
             Mouse  t-tatcatttgttttg-----
        Guinea pig  t-cattctttgttatg-----
            Rabbit  t-cattacttacaatg-----
              Pika  t-catcatttata--------
            Alpaca  t-catcagttgtaacg-----
           Dolphin  t-catcagttgtaata-----
               Cow  t-catcacttgtgctg-----
             Horse  t-catcagttataatg-----
               Cat  t-catcag-------------
               Dog  t-catcagttgtaacg-----
          Microbat  t-tgttcattgcaatg-----
           Megabat  t-tctcaattgtaatg-----
             Shrew  t-catcttttctaa-------
            Tenrec  t-agtaacttcttatg-----
          Elephant  t-aataagttgtaatg-----
        Rock hyrax  t-aataaattgtaatg-----
             Sloth  t-catcagttgtcatg-----
           Wallaby  t-tgccagtattaatg-----
           Opossum  t-tgctagtattaatg-----
          Platypus  t-catacaatattactaagag
            Lizard  =====================
         Armadillo  NNNNNNNNNNNNNNNNNNNNN
         Zebrafish  =====================
       Stickleback  =====================
           Lamprey  =====================
            Medaka  =====================
           Chicken  =====================
       Zebra finch  =====================
          Hedgehog  =====================
         Tetraodon  =====================
        Tree shrew  =====================
     X. tropicalis  =====================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNN

Inserts between block 13 and 14 in window
          Dolphin 162bp
B D           Cow 22bp

Alignment block 14 of 46 in window, 57863488 - 57863513, 26 bps 
B D          Human  g-t--agt-------------------------------tctcattc--------------------t--
           Gorilla  g-t--agt-------------------------------tctcattc--------------------t--
B D          Chimp  g-t--agt-------------------------------tctcattc--------------------t--
B D         Rhesus  g-t--ag------------------------------------------------------------t--
B D         Baboon  g-t--ag------------------------------------------------------------t--
B D       Marmoset  g-t--agt-------------------------------tttcattc--------------------t--
B D        Tarsier  t-t--agt-------------------------------tcttatac--------------------t--
B D      Orangutan  gtt--agt-------------------------------tctcattc--------------------t--
          Bushbaby  g--------------------------------------ccttattc--------------------t--
B D            Rat  a-cc-aac-------------------------------actc---------------------------
B D          Mouse  a-ca-aac-------------------------------tctc---------------------------
B D     Guinea pig  g-t--agt-------------------------------tctt---------------------------
B D         Rabbit  a-t--agt-------------------------------tctcattc--------------------t--
B D           Pika  ----------------------------------------------------------------------
B D         Alpaca  --t--agc-------------------------------tctcattc--------------------t--
           Dolphin  g-t--agt-------------------------------tctcattc--------------------t--
B D            Cow  a-t--agttgattta-------------------cagtgtctcagtc--------------------tac
B D          Horse  g-t--agt-------------------------------tctcattc--------------------t--
B D            Cat  ------gt-------------------------------tttcattc--------------------t--
B D            Dog  g-t--agt-------------------------------tctcattt--------------------t--
          Microbat  g-t--agt-------------------------------tctcattc--------------------t--
B D        Megabat  a-t--agt-------------------------------tctcattc--------------------t--
B D          Shrew  ------------------------------------------cattc--------------------t--
B D         Tenrec  g-t--att-------------------------------taaaaatc--------------------t--
B D       Elephant  g-t--agt-------------------------------tcgcatcc--------------------t--
B D     Rock hyrax  g-c--tgt-------------------------------tctcatcc--------------------t--
B D          Sloth  g-t---gt-------------------------------tctcattc--------------------t--
  D        Wallaby  ----------actaatcttcttttctcctcgactcctctcccctctc--------------------c--
B D        Opossum  --------------------------------atcagtttctctttcccttactcacctctcccctgc--
B D       Platypus  ---aaagt-------------------------------tctcactc--------------------t--
B D         Lizard  ======================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  ------------------------------------------------tatgg-ccaatgc
           Gorilla  ------------------------------------------------tatgg-ccaatgc
             Chimp  ------------------------------------------------tatag-ccaatgc
            Rhesus  ------------------------------------------------tatga-ccaatgc
            Baboon  ------------------------------------------------tatga-ccaatgc
          Marmoset  ------------------------------------------------tatgg-ccaatgc
           Tarsier  ------------------------------------------------tgtgg-ccagtgc
         Orangutan  ------------------------------------------------taaggcccaatgc
          Bushbaby  ------------------------------------------------tatgg-ccagtgc
               Rat  -------------------------------------------------atga-cctgtgc
             Mouse  -------------------------------------------------atga-cctgtgc
        Guinea pig  -------------------------------------------------acaa-ccagtgc
            Rabbit  ------------------------------------------------tatgg-ccagtac
              Pika  -------------------------------------------------acag-cccatgc
            Alpaca  ------------------------------------------------tatgg-ccggtgc
           Dolphin  ------------------------------------------------tatgg-ctagtgc
               Cow  agcaaagtgatttagttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttt-cagattc
             Horse  ------------------------------------------------tatgg-cccgtgc
               Cat  ------------------------------------------------tatgg-ccagtac
               Dog  ------------------------------------------------tatgg-ctggtat
          Microbat  ------------------------------------------------tatgg-ccagtgc
           Megabat  ------------------------------------------------tatgg-ctagtgc
             Shrew  ------------------------------------------------ta-----------
            Tenrec  ------------------------------------------------tttgg-ccagtac
          Elephant  ------------------------------------------------tatgg-ccagtac
        Rock hyrax  ------------------------------------------------tgtga-ctggtac
             Sloth  ------------------------------------------------tatgg-ctggtac
           Wallaby  ------------------------------------------------caaag-ccaggac
           Opossum  ------------------------------------------------tagga-ccattgc
          Platypus  ------------------------------------------------agtta-ttacccc
            Lizard  =============================================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  =============================================================
       Stickleback  =============================================================
           Lamprey  =============================================================
            Medaka  =============================================================
           Chicken  =============================================================
       Zebra finch  =============================================================
          Hedgehog  =============================================================
         Tetraodon  =============================================================
        Tree shrew  =============================================================
     X. tropicalis  =============================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 14 and 15 in window
B D        Alpaca 1bp
          Dolphin 1bp
B D           Cow 1bp
B D         Horse 1bp
B D           Cat 1bp
B D           Dog 1bp
         Microbat 1bp
B D       Megabat 1bp
B D         Shrew 645bp
B D        Tenrec 1bp
B D      Elephant 1bp
B D    Rock hyrax 1bp
B D         Sloth 5bp
  D       Wallaby 7bp
B D       Opossum 1bp

Alignment block 15 of 46 in window, 57863514 - 57863537, 24 bps 
B D          Human  -c-ttttttttaatgc------------agtaaaacaa
           Gorilla  -c-ttttttttaatgc------------agtaaaacaa
B D          Chimp  -c-ttttttttaatgt------------agtaaaacaa
B D         Rhesus  -c-ttttttttaatgt------------agtaaaataa
B D         Baboon  -ctttttttttaatgt------------agtaaaataa
B D       Marmoset  -c--tttttttaatgc------------agaacaataa
B D        Tarsier  -cttttctttttgtgc------------ggtaaaataa
B D      Orangutan  -ctttttttttaatgc------------agtaaaacaa
          Bushbaby  -c-cgtctttttatg-------------agta-actta
B D            Rat  -cttttctttttagac------------tatg-----a
B D          Mouse  -cttttcattttagac------------aatg-----a
B D     Guinea pig  -cttttctttttaggc------------agtg-----a
B D         Rabbit  -cttttctttttatgc------------agta-----a
B D           Pika  -attttctttttatgc------------agtg-----a
B D         Alpaca  --ctttctttttatgc--------------ag-----g
           Dolphin  --ttttctttgtatgc---------------a-----g
B D            Cow  --tttccattgtaggtcattacaagatactga-----g
B D          Horse  --ttttctttttatgt------------agta-----g
B D            Cat  --tt-------tatgc------------agta-----g
B D            Dog  --tt-actctgtatgt------------agta-----g
          Microbat  --ttttctttttatgc----------------------
B D        Megabat  --ttttctttttatgc------------aata-----g
B D       Hedgehog  --ctctctctctttgt------------agta-----a
B D         Tenrec  --ttttccttttatgc------------atta-----g
B D       Elephant  --ttttcccattatga------------atta-----g
B D     Rock hyrax  --ttttcgttttatgt------------gtta-----a
B D          Sloth  --ttttctttttatgc------------aata-----g
  D        Wallaby  -ttttccatttgctga------------atta-----c
B D        Opossum  -ttttccctctgcctc------------attacaataa
B D       Platypus  atggtgctttcactgc------------attagagtaa
B D         Lizard  ======================================
B D          Shrew  ======================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================
B D    Stickleback  ======================================
B D        Lamprey  ======================================
B D         Medaka  ======================================
B D        Chicken  ======================================
B D    Zebra finch  ======================================
B D      Tetraodon  ======================================
B D     Tree shrew  ======================================
B D  X. tropicalis  ======================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 15 and 16 in window
B D       Opossum 80bp
B D      Platypus 4bp

Alignment block 16 of 46 in window, 57863538 - 57863593, 56 bps 
B D          Human  ----------------------aatagacatttatctagcg-a------acatcccttttcaa-------
           Gorilla  ----------------------aatagacatttatctagcg-a------acatcccttttcaa-------
B D          Chimp  ----------------------aatagacatttatctagcg-a------acatccctgttcaa-------
B D         Rhesus  ----------------------aatagacatttatctagtg-a------acttccctttccaa-------
B D         Baboon  ----------------------aatagacatttatctagtg-a------acatccctttccaa-------
B D       Marmoset  ----------------------aatagacatttatctagtg-a------acatcc---------------
B D        Tarsier  ----------------------aataggcttttatctagtg-a------atatcccttt-caa-------
B D      Orangutan  ----------------------aatagacatttatctagcgaa------acatcccttttcaa-------
          Bushbaby  ----------------------aatggccttt--cccaggg-a------ccatcccctt-----------
B D            Rat  ----------------------aagacatttttcc----------------------tttcaa-------
B D          Mouse  ----------------------aagacatttttcc----------------------tttcaa-------
B D     Guinea pig  ----------------------aatacatatttccccagtg-c------acagct-ttctcaa-------
B D         Rabbit  ----------------------aatggactcttaactagta-a------attgcc-ttttcaa-------
B D           Pika  ----------------------aatggacacttacctaata-c------atcacc-ctttcaa-------
B D         Alpaca  ----------------------aataga---ttaccta-tg-a------acatcc--gcccta-------
           Dolphin  ----------------------aataga---ttacccagtg-a------acatcc--cc-cga-------
B D            Cow  ----------------------tgtagt---gtagtcagtg-a------acatcc--cctcaa-------
B D          Horse  ----------------------aataga---ttatccagtg-a------acatcc--ccccaa-------
B D            Cat  ----------------------aataga---ttatccagtg-a------aca-cc--ccccaa-------
B D            Dog  ----------------------gataaa---ttacccagtg-a------acattc--ccccaa-------
          Microbat  ---------------------------a---ttacccagtg-a------atatcc--ccct---------
B D        Megabat  ----------------------aataga---ttacccagtg-a------acat-c--gcct---------
B D       Hedgehog  ----------------------aatagt---ttagccagag-a------acaccc--cctcga-------
B D         Tenrec  ----------------------aatgcatctgctctcaatg-a------ac---a-ccttcag-------
B D       Elephant  ----------------------aatacacattttcccagtg-a------acccct-cctccaa-------
B D     Rock hyrax  ----------------------aatgcatcttttctcagtg-a------accctg-cccctga-------
B D          Sloth  ----------------------aataagtatttacccagtg-a------acatct-caaccag-------
  D        Wallaby  ----------------------aataactgttctccaggcc-atcttctacctccccacccaaagcccta
B D       Platypus  aattagaatttcactgccgaatagtaattagttacctgaag-a------attcac--ctttaa-------
B D         Lizard  ======================================================================
B D          Shrew  ======================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D        Opossum  ======================================================================
B D     Tree shrew  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  ----actataggg------------tc-aaagtgaagga
           Gorilla  ----actataggg------------tc-aaagtgaagga
             Chimp  ----actataggg------------tc-aaagtgaagga
            Rhesus  ----agtataggg------------tc-aaagtgaagga
            Baboon  ----agtataggg------------tc-aaagtgaagga
          Marmoset  ---------------------------------------
           Tarsier  ----agtacaggg------------t-ggaaatgagtga
         Orangutan  ----agtataggg------------tcaaaagtgaagga
          Bushbaby  ---------------------------------------
               Rat  ----agaacaagg------------t-gtgagtgaagga
             Mouse  ----agaacaagg------------t-ataaatgaagga
        Guinea pig  ----agtacaatg------------t-gaaacagaaggg
            Rabbit  ----agtacaaag------------t-gaaaatgaagga
              Pika  ----aggacatag------------t-gaaaatgaagaa
            Alpaca  ----cgtatgagg------------t-gataattaaggt
           Dolphin  ----agtacaagg------------t-gata---aaggg
               Cow  ----agcacaagg------------t-gataattaaagg
             Horse  ----agtacaagg------------t-gataattaaagg
               Cat  ----agtgcaaga------------t-gataattaaagg
               Dog  ----agtacaaga------------t-gataattaaagg
          Microbat  ----catacacgg------------g-gataattaaagg
           Megabat  ----agtacaaga------------g-gataattaaagg
          Hedgehog  ----actacaagg------------t-aaaaatgataca
            Tenrec  ----agtccaaag------------g-------------
          Elephant  ----agtacaagg------------g-------------
        Rock hyrax  ----agtacaagg------------g-------------
             Sloth  ----agtacaaagtgaaaatgaagca-------------
           Wallaby  tctcagtatttga------------t-gtcagtgatgaa
          Platypus  ----at---------------------------------
            Lizard  =======================================
             Shrew  =======================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  =======================================
       Stickleback  =======================================
           Lamprey  =======================================
            Medaka  =======================================
           Chicken  =======================================
       Zebra finch  =======================================
         Tetraodon  =======================================
           Opossum  =======================================
        Tree shrew  =======================================
     X. tropicalis  =======================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 16 and 17 in window
B D      Marmoset 168bp
         Bushbaby 347bp
B D           Rat 11bp
B D         Mouse 11bp
B D    Guinea pig 12bp
B D        Alpaca 12bp
          Dolphin 20bp
B D           Cow 16bp
B D         Horse 11bp
B D           Cat 11bp
B D           Dog 11bp
         Microbat 11bp
B D       Megabat 11bp
B D      Hedgehog 7bp

Alignment block 17 of 46 in window, 57863594 - 57863614, 21 bps 
B D          Human  ttc---tt-------ttg--------a-----------taatgat-agaat
  D        Wallaby  ttt---ttaaggtgcttg--------a-----------taattgg-agaat
B D          Sloth  ttc---tt-------ttgaggtcctga-----------tagtgag-agaat
B D     Rock hyrax  ttc---tt-------ttgaggctctga-----------tagtga---gaac
B D       Elephant  ttc---tt-------ttgaagccttga-----------tagtgag-ggaac
B D         Tenrec  ttc---tg-------ttgaatctgtga-----------taataag-atact
B D       Marmoset  -tc---tt-------ttg--------a-----------taatgat-agagt
B D          Mouse  -tt---tg-------ttg--------a-----------taatgat-agaac
B D            Rat  -ttg--tg-------ttg--------a-----------tagtggt-agagc
B D   Kangaroo rat  -tt---tt-------ttg--------a-----------ccatgat-aaaat
B D     Guinea pig  -tc---tg-------ttg--------a-----------t-gtgac-agact
B D          Shrew  ttc---tt-------ttg--------a-----------taatgat-tgagt
B D       Hedgehog  ttc---ct-------ctg--------g-----------taataat-agaac
B D        Megabat  ttc---tt-------ttg----------------------atgat-gggac
          Microbat  ttc---tt-------ttg----------------------atgat-agaat
B D            Dog  ttc---tt-------ttg--------g-----------tagtgat-agaat
B D            Cat  ttc---tt-------ttg--------g-----------taatgat-aaaat
B D          Horse  ttc---tt-------act--------a-----------taatgat-agaat
B D            Cow  ttt---tt-------ttg--------c-----------taatgat-agaat
           Dolphin  ttc---tt-------ttg--------a-----------taatgat-agaat
B D         Alpaca  ttc---tt-------ttg--------a-----------taatgat-agaat
B D           Pika  ttc---at-------ttg---------------------------------
B D         Rabbit  ttc---tt-------gtgatg--atga-----------tgatgat-agaat
B D      Orangutan  ttc---tt-------ttg--------a-----------taatgataaaaat
B D        Tarsier  ttc---tt-------ttg--------aggttcatttggtaatgat-aga--
B D         Baboon  ttc---tt-------ttg--------a-----------taatgat-agaat
B D         Rhesus  ttc---tt-------ttg--------a-----------taatgat-agaat
B D          Chimp  ttc---tt-------ttg--------a-----------taatgat-agaat
           Gorilla  ttc---tt-------ttg--------a-----------taatgat-agaat
B D        Opossum  ---------------ctg--------a-----------tgattgg-agaat
B D       Platypus  ---ccatt-------gta--------g-----------taatgat-gaac-
B D         Lizard  ===================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ===================================================
B D    Stickleback  ===================================================
B D        Lamprey  ===================================================
B D         Medaka  ===================================================
B D        Chicken  ===================================================
B D    Zebra finch  ===================================================
B D      Tetraodon  ===================================================
B D     Tree shrew  ===================================================
B D  X. tropicalis  ===================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ===================================================

Inserts between block 17 and 18 in window
B D       Megabat 4360bp

Alignment block 18 of 46 in window, 57863615 - 57863709, 95 bps 
B D          Human  -----atgtgtttgat--------catttgagtttaaagactatgggaaagga-a---------------
B D       Platypus  agctggtggggctgatctttgaagcatttgagttctgtcattaagctcgggga-t---------------
B D        Opossum  -----ttgagtttga---------catttgagttcagaaatttcagtgaaaca-t---------------
  D        Wallaby  -----atgagtttga---------catttgagttcagaaatttcagggaagca-t---------------
B D          Sloth  -----atgtgtttgat--------catttgcatttagaggctatggaaaagca-t---------------
B D     Rock hyrax  -----atgtgtttcat--------catttcaccatatagactacgaaaaaaca-t---------------
B D       Elephant  -----atgtgtttcat--------catg--accttacagactatgaaaaaaca-t---------------
B D         Tenrec  -----atatatttgat--------tgtttgaccttagagatgaaggaaacaga-t---------------
B D          Shrew  -----gcatac-------------------attttagaggctatgggaaggtg-t---------------
B D       Hedgehog  -----atgtatttgat--------catttgagtttagagactatggaaaagca-t---------------
B D        Megabat  -----atgtgtttgat--------ca-ttgagtttagagactatgggaaagca-tttttttggtggaggg
          Microbat  -----atctgtttgat--------catttgagtttagagactatgggaaagca-t---------------
B D            Dog  -----atgtgtttgaa--------cattggagtttagagactatgagaaag-------------------
B D            Cat  -----atgtgtttgaa--------catctgaatttagagactatgggaaagca-t---------------
B D          Horse  -----acgtgtttgat--------catttgagtttagagactatgggaaagca-t---------------
B D            Cow  -----atatgtttgat--------catttgaggttagagacaatgggaaagca-t---------------
           Dolphin  -----atatgtttgat--------catttgagtttagagacaatgggaaagca-t---------------
B D         Alpaca  -----atatgtttggt--------catttgattttagagacaatgggaaagga-t---------------
B D           Pika  ------tttg----at--------catttaagtctagagattgtgggaaagcatt---------------
B D         Rabbit  -----atttg----ct--------catttaagtctagagattgtgggaaagca-t---------------
B D     Guinea pig  -----acttg----at--------catttaagcttggaagct-tgggaaagca-c---------------
B D   Kangaroo rat  -----atctg----ac--------ctttgcagtttagaca----gagaaagaa-t---------------
B D            Rat  -----atttgtttcat--------ca-ttgagtttggagattatgggagagca-c---------------
B D          Mouse  -----atttgtttcat--------catttgagtttggcgattatgggaaagca-t---------------
B D        Tarsier  -----atgtgtttgat--------cagttaagtttagagacaacgggaaagca-t---------------
B D       Marmoset  -----atgtgtttgat--------catttgagtttaaagactat-ggaaagca-g---------------
B D         Baboon  -----atgtgtttgat--------catttgagtttaaagactatgggaaagga-a---------------
B D         Rhesus  -----atgtgtttgat--------catttgagtttaaagactatgggaaagga-a---------------
B D      Orangutan  -----atgtgtttgat--------catttgagtttaaagactatgggacagga-a---------------
           Gorilla  -----atgtgtttgat--------catttgagtttaaagactatgggaaagga-a---------------
B D          Chimp  -----atgtgtttgat--------catttgagtttaaagactatgggaaagga-a---------------
B D         Lizard  ======================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ======================================================================

             Human  -----ttgataa--ga-ttatttaaatactc-acg--------aaagtgc-tt-tggca-ttc-cactaa
          Platypus  -----tgaagat-----cttattatttacct-aat---------aagtac-tt-tagga-ttg-cttctg
           Opossum  -----ttaggaagtgg-ttatttatttactt-att-ttcacattaaatgc-tt-tagaagttg-cttttt
           Wallaby  -----ttaggaaatgg-ttgtttatataatc-catctctacattaagtgc-tt-tagaa-tttgcttttt
             Sloth  -----ttaataa-caa-ttatttatacactc-act---------aagtgc-tt-tagca-ttc-ctttta
        Rock hyrax  -----ttagtga-caa-gtatttatatactc-act---------ttttgt-tt-cagca-ttc-atttta
          Elephant  -----ttagtag-taa-ttatttatatac-c-act---------aaatgt-tt-tagca-ttc-atttta
            Tenrec  -----tta-tga-tca-ttatctatacactc-act---------aaatgt-ttgcaata-ttc-ctttta
             Shrew  ------cagtaa-gga-ctatttaagcatgc-acg--------caagtgt-tg-caaca-t---------
          Hedgehog  ------taataa-tga-ttacttatatactc-atc--------aaagtgc-tt-taaca-tcc-ct----
           Megabat  aagcattaataa-tga-ttatttatacactc-ac---------taagtgc-tt-taaca-ttc-ctttga
          Microbat  -----ttaataa-tga-ttatttatacactc-act--------taagtgc-tt-taacg-ttc-ctttga
               Dog  ------taataa-tga-ttatttatacac-c-act--------gaagtgt-tt-tatca-tac-ctttga
               Cat  -----ttaataa-cga-ttatttattcactc-act--------aaagtgc-tt-taaca-ttc-ctttga
             Horse  -----ttaataa-tgatttatttatgcactc-act--------aaaatgc-tt-taaca-ttc-ctttga
               Cow  -----ttaataa-tga-ttatttacacactc-act--------gaagtgc-tt-taaca-ttc-ctgtga
           Dolphin  -----ttaataa-tga-ttatttatacattc-gct--------gaagtgc-tt-taacc-ttc-ctttga
            Alpaca  -----ttaatag-tga-ttat----atactc-gct--------gaagtgcttt-taaca-ttc-ctttga
              Pika  -----tttgtag-tga-ttatttatatactt-gct--------caagtgc-tt-tagca-ctc-cattta
            Rabbit  -----tcgataa-tga-----ttataccctc-act--------aaagtgc-tt-tagca-ccc-cattta
        Guinea pig  -----ttgatga-t-------ttacatgctc-act--------aaagtgc-ct--agca-ttc-cactga
      Kangaroo rat  -----t---taa-tgg-ttatttagtcactc-att--------aaggtgc-tt-taaca-ttt-tattta
               Rat  -----ttgataa-cgg-ttacggagacactcgacc--------agagtgc-tt-cagct-ttc-catttg
             Mouse  -----ttgataa-tgg-tcacttagacactcaacc--------aaagtgc-tt-cagca-ttc-cattta
           Tarsier  -----ttgataa-tga-ttatttatacactc-act--------aaagtgc-tt-tagca-ttc-cattta
          Marmoset  -----ctgataa--ga-t-------atactc-acg--------aaagtgc-tt-tgaca-ttc-cactaa
            Baboon  -----ttgataa--ga-ttatttacatactc-acg------aaaaagtgc-tt-tggca-ttc-cactaa
            Rhesus  -----ttgataa--ga-ttatttacatactc-acg-------aaaagtgc-tt-tggca-ttc-cactaa
         Orangutan  -----ttgataa--ga-ttatttaaatactc-acg--------aaagtgc-tt-tggca-ttc-cactaa
           Gorilla  -----ttgataa--ga-ttatttaaatactc-acg--------aaagtgc-tt-tggca-ttc-cactaa
             Chimp  -----ttgataa--ga-ttatttaaatactc-acg--------aaagtgc-tt-tggca-ttc-cactaa
            Lizard  ======================================================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ======================================================================
       Stickleback  ======================================================================
           Lamprey  ======================================================================
            Medaka  ======================================================================
           Chicken  ======================================================================
       Zebra finch  ======================================================================
         Tetraodon  ======================================================================
        Tree shrew  ======================================================================
     X. tropicalis  ======================================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Bushbaby  ======================================================================

             Human  -------------------------------------t-gcta
          Platypus  -------------------------------------t-gtgg
           Opossum  -------------------------------------c-atag
           Wallaby  -------------------------------------c-gtag
             Sloth  -------------------------------------t-gcta
        Rock hyrax  -------------------------------------t-gaca
          Elephant  -------------------------------------t-gcca
            Tenrec  -------------------------------------t-gcta
             Shrew  -------------------------------------------
          Hedgehog  ---------------------------------------tcta
           Megabat  -------------------------------------t-gcta
          Microbat  -------------------------------------t-gcta
               Dog  -------------------------------------t-actc
               Cat  -------------------------------------t-gcta
             Horse  -------------------------------------t-gcta
               Cow  -------------------------------------tggcgt
           Dolphin  -------------------------------------t-gcta
            Alpaca  -------------------------------------t-ggta
              Pika  -------------------------------------t-ctta
            Rabbit  -------------------------------------t-gtta
        Guinea pig  -------------------------------------t-acta
      Kangaroo rat  tttatttaaatgaaaatatgaaaaccaaaagattcttt-attc
               Rat  -------------------------------------t-gttc
             Mouse  -------------------------------------t-gttc
           Tarsier  -------------------------------------t-gtta
          Marmoset  -------------------------------------g-gcta
            Baboon  -------------------------------------t-gcta
            Rhesus  -------------------------------------t-gcta
         Orangutan  -------------------------------------t-gctg
           Gorilla  -------------------------------------t-gcta
             Chimp  -------------------------------------t-gcta
            Lizard  ===========================================
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ===========================================
       Stickleback  ===========================================
           Lamprey  ===========================================
            Medaka  ===========================================
           Chicken  ===========================================
       Zebra finch  ===========================================
         Tetraodon  ===========================================
        Tree shrew  ===========================================
     X. tropicalis  ===========================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
          Bushbaby  ===========================================

Alignment block 19 of 46 in window, 57863710 - 57863747, 38 bps 
B D          Human  ttct--------ctttt-----a---agcac-a--tttt---cctatg-aagtgtgtgcgg-----
B D          Chimp  ttct--------ctttt-----a---agcac-a--tttt---cctatg-aagtgtgtgcgg-----
           Gorilla  ttct--------ctttt-----a---agcac-a--tttt---cctatg-aagtgtgtgcag-----
B D      Orangutan  ttct-------cctttt-----a---agcac-cattttc---cctatg-aagtgtgtgcag-----
B D         Rhesus  ttct--------c--tt-----a---agcac-a--tttt---cctatg-aagtgtgtgcag-----
B D         Baboon  ttct--------c--tt-----a---agcac-a--tttt---cctatg-aagtgtgtgcag-----
B D       Marmoset  ttct--------ctttt-----a---agcac-a--tttt---cctatc-aagtgtttgcag-----
B D        Tarsier  tttt--------ctatt-----a---agcac-a--cttt---cctaag-atgtat-----------
B D          Mouse  tgtt---------tgtt-----g---agcac-a--tttt---cctgtg--agtgt-----------
B D            Rat  tgtt---------tgtt-----g---agcac-a--cttc---cctgtg--agcat-----------
B D   Kangaroo rat  ttttcctattttccttt-----t---agcac-c--tttt---cttttg-aagtgt-----------
B D     Guinea pig  tttt--------ctgct-----a---agcac-a--tttt---cctgtg-aagtgt-----------
B D         Rabbit  ttct--------ct--t-----a---cacac-a--tttt---cctctg-aagcat-----------
B D           Pika  ctgt--------ctgct-----a---tgcac-a--cttt---cctatc-aagtgt-----------
B D         Alpaca  ttct--------ttgtt-----a---agcac-a--tttt---cctatg-aagtgt-----------
           Dolphin  tttt--------ttgtt-----a---agcac-a--tttt---cctatg-aactgt-----------
B D            Cow  tttt--------ttgtt-----a---agcac-a--tttt---cctatg-aagtgt-----------
B D          Horse  ttct--------ctgtt-----a---agcac-a--tttt---cctgtg-aagtgt-----------
B D            Cat  ttct--------ctgtt-----a---agcac-a--tttt---cctatg-aagtgt-----------
B D            Dog  ttgt--------ctgtt-----a---agcac-a--tttt---ccaatg-aagtgt-----------
          Microbat  ttct--------ctgtt-----a---agcac-a--tttt---cctatg-aagtgt-----------
B D        Megabat  ttct--------ctgtt-----a---agcac-a--tttt---cttatg-aagtgt-----------
B D       Hedgehog  ttct--------ctgtt-----a---agtac-a--tttt---cctatg-aag--------------
B D          Shrew  ---t--------ctgct-----a---tttag-a--cttt---cctata-aagtat-----------
B D         Tenrec  cttt--------ctgtt-----t---gcctc-a--tttg---cctatg-aagtgt-----------
B D       Elephant  tttt--------ctgtt-----------cac-a--tttt---cctatg-aagtgt-----------
B D     Rock hyrax  tttt--------ctgtt-----c---agcac-c--attt---cctatg-cagtgt-----------
B D          Sloth  gtct--------ctgtt-----a---agcat-a--tttt---cctatg-aag-gt-----------
  D        Wallaby  ttat--------ctatgc-aaaa---agcatga--tttg---actaaa-aaatatct---------
B D        Opossum  tttt--------ctttc-----aaagagcac-a--atttgactccaaa-aaacat-----------
B D       Platypus  ttct--------gtcttcaaaaa---gccat-g--cttt---ccatt-------------------
B D        Chicken  ttct--------ccgca-----a---gccaa-a--tttc---catgtgaaaatat------ttcca
B D         Lizard  ==================================================================
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ==================================================================
B D    Stickleback  ==================================================================
B D        Lamprey  ==================================================================
B D         Medaka  ==================================================================
B D    Zebra finch  ==================================================================
B D      Tetraodon  ==================================================================
B D     Tree shrew  ==================================================================
B D  X. tropicalis  ==================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ==================================================================

Alignment block 20 of 46 in window, 57863748 - 57863784, 37 bps 
B D          Human  tt--g-cagttg-cct--acacca-t-------g--tcaatgc--ctgctgg--ttt
B D         Lizard  tg--g-cagttgccct--gtgttact-------a--tcgggccatttgctgct-ttg
B D    Zebra finch  tt--c-tagttg-cct--atgttact-------a--tcagcca--ctgctgt--ttg
B D        Chicken  -------agttg-cct--gtgttact-------a--tcagtcc--ctgctgc--ttg
B D       Platypus  tt--a-cattag-act--gtatcact-------c--tcagtgc--cttctga--ttt
B D        Opossum  ctcag-catata-ccc--ttatca-t-------c--c---tac--ttgttga--ttt
  D        Wallaby  tg--g-catttg-ccc--ttctta-c-------c--ctacttg--ttgcttt--gtt
B D          Sloth  tt--g-cagttg-ccc--acacca-t-------g-ctctatgc--ct-ctgg--ttt
B D     Rock hyrax  tt--t-cacttg-ctt--aca-ca-t-------g--gcattgc--ctgctag--ttt
B D       Elephant  tt--t-cggttg-ctc--aca-ca-t-------g--tcaatgc--ctgctgg--ttt
B D         Tenrec  tt--t-cagttg-gcc--acaccg-t-------g--tcaatgc--ctacttg--ttt
B D          Shrew  tt--g-ctgttt-ccc--acacca-g-------g--cctatgc--ctgctgg--ttt
B D       Hedgehog  -t--g-cagctg-cct--gtatct-t-------g--tcagtat--ctgctgg--tat
B D        Megabat  tt--g-cagttg--cg--acacta-t-------g--tcaatgt--ctgatgg--ttt
          Microbat  tt--g-tagctg-ccc--acacca-t-------g--tcaatgc--ctgctgg--ttt
B D            Dog  tt--g-cagttg-ccc--atacca-t-------g--tcaatgc--ctgctag--ttt
B D            Cat  tt--g-cagttg-ccc--atacca-t-------g--tcaatgc--ctgctgg--ttt
B D          Horse  tt--g-cagttc-ccc--acacca-t-------g--tcagtgc--ctgctgg--ttt
B D            Cow  tt--g-tagttg-cac--agaccg-t-------g--tcaatgc--ctgctgg--ttt
           Dolphin  tt--g-tagttg-cac--acacca-t-------g--tcagtgc--ctgctgg--ttg
B D         Alpaca  tt--g-tcgttg-tac--atacca-t-------g--tcaatgc--ctgctgg--ttt
B D           Pika  tt--g-cagttg-cct--acagta-t-------g--tcaatgc--ctgct----gtt
B D         Rabbit  tt--g-cacttg-cct--acacca-t-------g--tcaatgc--ctgct----ggt
B D     Guinea pig  tt--g-cagttg-cct--ccacca-t-tcagtgt--tcagtgc--ctgct-t--gtt
B D   Kangaroo rat  tt--g-ctattg-cct--acacca-t-------g--tgagtgt--ctgtt-g--gtt
B D            Rat  ta--g-caattg-tat--acatcg-t-------g--ttggtgc--ctgcggg--gtt
B D          Mouse  ta--g-cagttg-gat--atgcca-ggtca---g--tcagtgc--ctgctgg--gtt
B D        Tarsier  tt--g-cagttg-cct--acacca-t-------g--t--agac--ctgctgg--ttt
B D       Marmoset  tt--g-cagttg-cct--acacca-t-------g--tcaatgc--ctgccgg--ttt
B D         Baboon  tt--g-cagttg-cct--acactg-t-------g--tcaatgc--ctgccgg--ttt
B D         Rhesus  tt--g-cagttg-cct--acactg-t-------g--tcaatgc--ctgccgg--gtt
B D      Orangutan  tt--gccagttg-ccttaccacca-t-------ggtccaatgc--ctgctggctttt
           Gorilla  tt--g-cagttg-cct--acacca-t-------g--tcaatgc--ctgctgg--ttt
B D          Chimp  tt--g-cagttg-cct--acacca-t-------g--tcaatgc--ctgctgg--ttt
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  =========================================================
B D    Stickleback  =========================================================
B D        Lamprey  =========================================================
B D         Medaka  =========================================================
B D      Tetraodon  =========================================================
B D     Tree shrew  =========================================================
B D  X. tropicalis  =========================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  =========================================================

Inserts between block 20 and 21 in window
B D      Platypus 6bp
B D       Opossum 6bp
  D       Wallaby 3bp

Alignment block 21 of 46 in window, 57863785 - 57863828, 44 bps 
B D          Human  ttcctgctgtgaagt------ttttcctt--------t----------acata---cacag---------
B D          Chimp  ttcctgctgtgaagt------ttttcctt--------t----------acata---cacag---------
           Gorilla  ttcctgctgtgaagt------ttttcctt--------t----------acata---cacag---------
B D      Orangutan  tccttgctgtgaagt------ttttccct--------tt--------accata---tacag---------
B D         Rhesus  ttcctgctatgaagt------ttttcctt--------t----------acata---tacag---------
B D         Baboon  ttcctgctatgaagt------ttttcctt--------t----------acata---tacag---------
B D       Marmoset  ttcctgttgtgaagt------ttttcctt--------t----------acata---tacag---------
B D        Tarsier  ttccccttctgaagta---tgtgttcctt--------t----------atata---tacag---------
B D          Mouse  ttccccctatgaagta---tctgttcttt--------t----------tcata---caaag---------
B D            Rat  ttccacctatgaagta---tctgttcttt--------t----------tcata---caaag---------
B D   Kangaroo rat  ttccctccataaagta---tctgttcctt--------t----------atatg---cacac---------
B D     Guinea pig  ttcttcctatgaatta---tctgttcctt--------t----------acata---cgcag---------
B D         Rabbit  ttttccctacgaagta---tctatttctt--------c----------acata---tatag---------
B D           Pika  ttttccctgtgaggta---tctgttcctt--------t----------acaca---cacag---------
B D         Alpaca  ttcc-cctgtgaaata---tctgttcttt--------c----------acata---cagag---------
           Dolphin  ttcctcctgtgaagta---tccgttcttt--------t----------atata---cagag---------
B D            Cow  ttccctctgtgaagta---tctgttcctttataa---t----------atata---cagag---------
B D          Horse  ttccccttgtgaagta---tctgttcctt--------t----------acata---cagag---------
B D            Cat  ttccccctgtgaaccg---tctgttcctt--------t----------acata---cagag---------
B D            Dog  ttacccctgtgaactc---tctgttcctt--------t----------acata---cagaa---------
          Microbat  ttccccttgtgaagtt---tctgttcctt--------t----------acata---cagag---------
B D        Megabat  ttcccgttgtgaagta---tctgttcctt--------t----------acata---cagag---------
B D       Hedgehog  ttacccctgtgaatta---tctgtttctt--------t----------acata---caaat---------
B D          Shrew  ttccccctgtgaagta---tccatttctt--------c----------acata---cagag---------
B D       Elephant  caccccctgtgaagta---tctgttcctt--------t----------acata---catag---------
B D     Rock hyrax  tacctccactgaagta---tcttttcctt--------t----------acata---catag---------
B D          Sloth  -tcccccgataaag-------tgttcctt--------c----------acgta---cacag---------
  D        Wallaby  tttcctatattatttc---cctgtttcct--------t----------aaaga---aacat---------
B D        Opossum  tttactatattatttac--cctgtttcct--------t----------aaaga---aacat---------
B D       Platypus  tttcccatctgatttc---cttgtaagct--------ttaaaaaaaaaacatg---caaaaacacccaac
B D        Chicken  ctgacttcccaggctgc-atctgcctctg--------c----------aagga---cacaa---------
B D    Zebra finch  tttactctc-----------ctgcctcgg--------g----------aagaa---tacag---------
B D         Lizard  tttactctgtttcccccgatcttcctcggtttccataa----------aggga---ttaag---------
B D           Fugu  ttcagcctttgtgtt----tctttttttt--------c----------atctggcccagaa---------
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D         Tenrec  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ======================================================================

             Human  --------------attc-atgaaa
             Chimp  --------------attc-atgaaa
           Gorilla  --------------attc-atgaaa
         Orangutan  --------------attc-atgaaa
            Rhesus  --------------attc-atgaaa
            Baboon  --------------attc-atgaaa
          Marmoset  --------------attc-atgaaa
           Tarsier  --------------attt-atgaaa
             Mouse  --------------attttatgaaa
               Rat  --------------attttacgaaa
      Kangaroo rat  --------------agattataaaa
        Guinea pig  --------------attt-------
            Rabbit  --------------attt-atgaag
              Pika  --------------attt-attaaa
            Alpaca  --------------attt-atgaaa
           Dolphin  --------------attt-atgaaa
               Cow  --------------attt-atgagc
             Horse  --------------attt-atgaaa
               Cat  --------------attt-atgaaa
               Dog  --------------attt-atgaaa
          Microbat  --------------attt-atgaaa
           Megabat  --------------attt-atgaaa
          Hedgehog  --------------attt-at--ga
             Shrew  --------------attt-atggga
          Elephant  --------------atgt-ctcaaa
        Rock hyrax  --------------attt-ctaaaa
             Sloth  --------------actt-ctgaaa
           Wallaby  -------------caact-ttgaaa
           Opossum  -------------caact-ttgaaa
          Platypus  aaaaaacaaccccaactt-ttgaaa
           Chicken  --------------actt-gacaaa
       Zebra finch  --------------gctg-ggagaa
            Lizard  --------------gcag-ggaata
              Fugu  --------------a----------
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  =========================
       Stickleback  =========================
           Lamprey  =========================
            Medaka  =========================
         Tetraodon  =========================
        Tree shrew  =========================
            Tenrec  =========================
     X. tropicalis  =========================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNN
          Bushbaby  =========================

Inserts between block 21 and 22 in window
B D         Sloth 228bp
  D       Wallaby 8bp
B D       Opossum 1bp

Alignment block 22 of 46 in window, 57863829 - 57863897, 69 bps 
B D          Human  gag-tttatg-----g--tg--taga----tgatctgaaactaaacagga---cacat-tttc----ata
B D         Lizard  ggc-ttcta--------------ata----atggtc---atccattgtca---ctgggatttg----gag
B D    Zebra finch  ggg-ttaaat-----c--ca--taga----aatgccgaggtgcagcagga---ctggt-ttgg----aaa
B D        Chicken  ggg-ttaaat-----c--tg--caga----aaggccgcgatgcagcagcacccctggt---------aaa
B D       Platypus  tag-ttaaaa-----g--agcctgga----agtcctggacctaaacaggg----tcac-tttc----a--
B D        Opossum  cag-ttaaca-----g--tt--caga----agatctgagataaaatggtt---ctcat-tttc----aaa
  D        Wallaby  gaa-ctta-------g--tg--taga----acttccgagacaaattggtt---ctcat-tttc----aga
B D       Elephant  gaa-ttcatg-----g--tg--tcga----tgatctgaaaccaaacaaga---ctcat-tttc----ata
B D     Rock hyrax  gaa-ttcatg-----g--tg--tcag----tgatctgaaaccaaacaaga---ctcat-tttc----ata
B D          Shrew  aag-ttcttg-----g--tg--tgaa----tgatccgaaacccagcaggt---ctcat-ttcc----ata
B D       Hedgehog  aag-ttc--a-----g--tg--tgga----tagtctgaaatccagtagaa---cttat-tttc----ata
B D        Megabat  cag-tttatg-----g--tg--tgga----tgatctgaaactcaacagga---ctcat-tttc----aca
          Microbat  gag-tccctg-----g--tg--tgga----tgatctgaaacccaccggga---ctcat-cctc----ata
B D            Dog  gag-ttcatg-----a--tg--ttga----tgatctgaaacccaacagga---ct-at-tttt----gta
B D            Cat  gag-ttcatg-----g--tg--caga----tgatctgaaacccaacagga---ct-at-tttc----gta
B D          Horse  gag-ttcata-----g--tg--tgga----tgatctgaagtccaacagga---ctcat-tttc----ata
B D            Cow  gac-ttcatg-----g--tg--tgga----tgatcagaaacccaccagga---ctcat-tttc----ata
           Dolphin  gag-ttcatg-----g--tg--tgga----tgatcagaaacccaacagga---ctcat-tttc----ata
B D         Alpaca  gag-ttcagg-----g--tg--taga----tgatcagaaacccaacagga---tgcat-tttc----ata
B D           Pika  gag-ttca-------g--tg--taga----tgatctgaaaccaaacaaga---ctgat-tttcat--at-
B D         Rabbit  gaa-ttca-------g--gg--taaa----tgatctgaaactaagcagga---ctcat-tctc----at-
B D     Guinea pig  ------------atgg--ta--taga----tgatctgaaaacaaacagga---ttcat-tttt----at-
B D   Kangaroo rat  aac-ttcatg-------------------------------------agt---gccat-tt------ga-
B D            Rat  gag-ctcatggtatag--ta--taga----tgatctgaaactaaacaggg---gtcat-tttc----at-
B D          Mouse  gag-ctcatggtatag--ta--taga----tgatctgaaactaaacaggg---gtcat-tttc----at-
B D        Tarsier  gag-ttcatg-----g--tg--taga----ttatctgaaatcaaacagga---ctcat-tttc----ata
B D       Marmoset  gag-tttatg-----g--ta--caga----ttatctgaaaccaaacagga---cacat-tttc----ata
B D         Baboon  gag-tttatg-----g--tg--taga----tggtctgaaactaaacagga---cacat-tttc----ata
B D         Rhesus  gag-tttatg-----g--tg--taga----tggtctgaaactaaacagga---cacat-tttc----ata
B D      Orangutan  gagttttatg-----g--tg--taga----tgatctgaaactaaacagga---cacat-tttc----ata
           Gorilla  gag-tttatg-----g--tg--taga----tgatctgaaactaaacagga---cacat-tttc----ata
B D          Chimp  gag-tttatg-----g--tg--taga----tgatctgaaactaaacagga---cacat-tttc----ata
B D           Fugu  ggg-ttaaca-----ggctg--tgaattcttgattgccaactcccaggat---cgtat-ctcctgtaact
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D         Tenrec  ======================================================================
B D  X. tropicalis  ======================================================================
B D          Sloth  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ======================================================================

             Human  cactttagtacca----tt-t-gaaga
            Lizard  tcattgagtttcatgggtc-t-gtgcc
       Zebra finch  tgactgagtgcca----tc-t-gcaca
           Chicken  tgacccagtgcca----tc-t-gcaca
          Platypus  -aaacgagtgcca----tc-t-aaata
           Opossum  tcatcaattgtca----ta-t-gaaga
           Wallaby  tcatcaagtgtca----ta-t-gaaga
          Elephant  aaatttagagcag----tt-t-gaaca
        Rock hyrax  taatttagagcaa----tt-t-ggaca
             Shrew  taactt-atgcca----ctgt-ggaac
          Hedgehog  taatttaatgcca----cttt-gaaaa
           Megabat  taatttagtgcca----tt-t-gaaca
          Microbat  taatttggtgcca----tt-t-gaaca
               Dog  tacttcagtgcca----gt-t-gaaca
               Cat  taatttagtgcca----gt-t-gaaca
             Horse  tgatttagtgcca----tt-t-gaaca
               Cow  taatttagtgcca----gt-t-gaaca
           Dolphin  taatttagtgcca----gt-t-gaaca
            Alpaca  taattcagtgcca----gt-t-gaaca
              Pika  -acttcagagcca----ct-t-gaaca
            Rabbit  -acttgagagcca----tt-t-gaaca
        Guinea pig  -gttctaatgcca----tt-t-ggact
      Kangaroo rat  ------------------------atc
               Rat  ------------------------atg
             Mouse  ------------------------atg
           Tarsier  tactttactacca----tt-t-aaaca
          Marmoset  cactttaatatca----tt-t-gaaca
            Baboon  cactttagtacca----tt-t-gaaca
            Rhesus  cactttaatacca----tt-t-gaaca
         Orangutan  cactttagtacca----tt-tggaaca
           Gorilla  cactttagtacca----tt-t-gaaca
             Chimp  cactttagtacca----tt-t-gaaca
              Fugu  caaatcagggcca----tc-t-g----
         Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNN
         Zebrafish  ===========================
       Stickleback  ===========================
           Lamprey  ===========================
            Medaka  ===========================
         Tetraodon  ===========================
        Tree shrew  ===========================
            Tenrec  ===========================
     X. tropicalis  ===========================
             Sloth  ===========================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNN
          Bushbaby  ===========================

Alignment block 23 of 46 in window, 57863898 - 57863925, 28 bps 
B D          Human  c----tctgggtgtca-g------ttgttgctgggacct
B D          Chimp  c----tctgggtgtca-g------ttgttgctgggacct
           Gorilla  c----tctgggtgtca-g------ttgttgctgggacct
B D      Orangutan  c----tctgggtgtca-g------ttgttgctgggacct
B D         Rhesus  c----tccgggtgtca-g------ttgttgctgggacct
B D         Baboon  c----tccgggtgtca-g------ttgttgctgggacct
B D       Marmoset  c----tctgggtgtca-g------ttgttgctgggacct
B D        Tarsier  c----tctgggtgtca-g------ttgttgctgggacct
B D          Mouse  t----ttttaatgtca-t------ttgttgctgggacct
B D            Rat  t----tcttaatgtca-t------ttgttgctgggacct
B D   Kangaroo rat  c----tgtgaatatcagt------ttgttgctggaacct
B D     Guinea pig  t----tctgagtgtca-g------tggttgctgggacct
B D         Rabbit  c----ttctagtgtca-g------ttgttgctgggacct
B D           Pika  c----ttttggtgtca-g------ttgttgttgggacct
B D         Alpaca  c----tctgggtgtcg-g------ttgttgctgggacct
           Dolphin  c----tctgggtgctg-g------ttgttgctgggacct
B D            Cow  c----tctgggtgtcg-g------ttgttgctgggacct
B D          Horse  c----tctgggtgtca-g------ttgttactgggacct
B D            Cat  c----actgggtgtca-g------ttgttgctgggacct
B D            Dog  c----actgggtgtca-g------ttgttgctgggacct
          Microbat  c----tctgcgtgtcg-g------ttgttgctgggacct
B D        Megabat  c----tctgggtgtca-g------ttgttgctgggacct
B D       Hedgehog  a----tcagggtgtca-g------tagttgctgggacct
B D          Shrew  gtttctctgggtgtca-g------tggttactgggacct
B D     Rock hyrax  c----ttatggtgtca-g------ttgttgctgggacct
B D       Elephant  c----tcttggtgtca-g------ttgttgctgggacct
  D        Wallaby  c-----atgagtgtca-g------ttgttgctgggacct
B D        Opossum  c----cct-agtgtca-g------ttgttgctgggacct
B D       Platypus  c----actgggtgtca-g------ttgttgctgggacct
B D        Chicken  c------tggctgccc-g------gtgctgctgggacct
B D    Zebra finch  c------tggctgtca-g------tcgttgctgggacct
B D         Lizard  c---------ccctac-g------tattttttctatcct
B D  X. tropicalis  c----cctgggtgtca-g------ttgctgtcaggacct
B D           Fugu  c----gctgggcgtat-gcctgccttccccccctggcct
        Armadillo  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D      Zebrafish  =======================================
B D    Stickleback  =======================================
B D        Lamprey  =======================================
B D         Medaka  =======================================
B D      Tetraodon  =======================================
B D     Tree shrew  =======================================
B D         Tenrec  =======================================
B D          Sloth  =======================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  =======================================

Alignment block 24 of 46 in window, 57863926 - 57863952, 27 bps 
B D          Human  gtttttgactctga-tgaa----cc-tttactg
B D          Chimp  gtttttgactctga-tgaa----cc-tttactg
           Gorilla  gtttttgactctga-tgaa----cc-tttactg
B D      Orangutan  gtttttgactctga-tgaa----cc-tttactg
B D         Rhesus  gtttttgactctga-tgaa----cc-tttactg
B D         Baboon  gtttttgactctga-tgaa----cc-tttactg
B D       Marmoset  gtttttgactctgt-tgaa----cc-tttactg
B D        Tarsier  gtttttgactctgt-tgaa----cc-tttgctg
B D          Mouse  gtttttgactcttt-tgaa---ccc-tttgctg
B D            Rat  gtttttgactctgt-tgaa---ccc-tttgctg
B D   Kangaroo rat  gtttttgactctgt-tgaa----cc-tttgctg
B D     Guinea pig  gtttttgactctgt-tgaa----cc-tttactg
B D         Rabbit  gtttttgactctgt-tgaa----cc-tttactg
B D           Pika  gtttttgactctgt-tgaa----cc-ttttctg
B D         Alpaca  gtttttgactctct-tgaa----cc--ttactg
           Dolphin  gtttttgactctgt-tgaa----cc-tttactg
B D            Cow  gtttttgactctgt-tgaa----cc-tttactg
B D          Horse  gtttttgactctgt-tgaa----cc-tttactg
B D            Cat  gtttttgactctgt-tgaa----cc-tttactg
B D            Dog  gtttttgactttct-caaa----cc-tttactg
          Microbat  gtttttgactctgt-tgaa----cc-tttgctg
B D        Megabat  gtttttaactctgt-tgaa----cc-tttgctg
B D       Hedgehog  gtttttaactctgt-tgaa----cc-tttactg
B D          Shrew  gtttttga--ctgt-tgaa----cc-tttactg
B D       Elephant  gtttttgactctgc-tgaa----cc-tttactg
B D     Rock hyrax  gtttttgactctgcttgaa----cc-tttactg
         Armadillo  gtttttgactctgc-tgaa----cc-tttactg
  D        Wallaby  gtttttgactctgc-tgaa----cc-tttgctg
B D        Opossum  gtttttgactctgc-tgaa----cc-tttgctg
B D       Platypus  gtttttggctgtgc-tgaa----tc-tttactg
B D        Chicken  gtttttgcctccac-tgaa----cc-tttactg
B D    Zebra finch  gtttttgcctccgc-tgaa----cc-tttactg
B D         Lizard  ttctttgactcctt-ggaa----ccttttgctc
B D  X. tropicalis  gtttttgactccag-tgaa----tt-tattctg
B D           Fugu  -------actgcac-tcaaaggctc-tctgt--
B D      Zebrafish  =================================
B D    Stickleback  =================================
B D        Lamprey  =================================
B D         Medaka  =================================
B D      Tetraodon  =================================
B D     Tree shrew  =================================
B D         Tenrec  =================================
B D          Sloth  =================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  =================================

Alignment block 25 of 46 in window, 57863953 - 57863986, 34 bps 
B D          Human  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D          Chimp  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
           Gorilla  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D      Orangutan  gtttgtggtttgtctgg-cc-------atcacatgacttcaatct
B D         Rhesus  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D         Baboon  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D       Marmoset  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D        Tarsier  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D          Mouse  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D            Rat  g-ttgtggtttgtctgg-tc-------atcacatgacttc--tct
B D   Kangaroo rat  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D     Guinea pig  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D         Rabbit  a-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D           Pika  a-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D         Alpaca  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
           Dolphin  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
B D            Cow  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
B D          Horse  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
B D            Cat  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
B D            Dog  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
          Microbat  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
B D        Megabat  g-ctgtggtttgtctgg-cc-------atcacatgacttc--tct
B D       Hedgehog  g-ctgtggtttgtctgg-ct-------atcacatgacttc--tct
B D          Shrew  g-ctgtggtttgtctgc-cc-------atcacatgacttc--tct
B D       Elephant  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D     Rock hyrax  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
         Armadillo  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
  D        Wallaby  g-ttgtggtttgtctgg-cc-------atcacatgatttc--tct
B D        Opossum  g-ttgtggtttgtctgg-cc-------atcacatgatttc--tct
B D       Platypus  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D        Chicken  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D    Zebra finch  g-ttgtggtttgtctgg-cc-------atcacatgacttc--tct
B D         Lizard  t-ttgtggtttgtctgg-ct-------atcacatgatttc--ttt
B D  X. tropicalis  g-ttatggtttgtctggccc-------atcacatgacttc--tct
B D           Fugu  g-ctgtggtttgcccag-cccc-----atcacgtgacttc--tct
B D    Stickleback  g-ctgtggtttgcccgg-ccct-----gtcacgtgacttc--tct
B D         Medaka  g-ctgcggtttgcccag-cccc-----atcacgtgacttc--tct
B D      Zebrafish  g-ctgtggttagccctg-cccttacgggtcatgtgacttc--tct
B D        Lamprey  =============================================
B D      Tetraodon  =============================================
B D     Tree shrew  =============================================
B D         Tenrec  =============================================
B D          Sloth  =============================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  =============================================

Inserts between block 25 and 26 in window
B D     Orangutan 1bp

Alignment block 26 of 46 in window, 57863987 - 57864115, 129 bps 
B D          Human  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
          Bushbaby  ----------------cc-----------cttcatttccagtaagctgtttgagc----agga-gtgagt
B D          Chimp  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D      Orangutan  a--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----aggaggtgagt
B D         Rhesus  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D         Baboon  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D       Marmoset  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D        Tarsier  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D          Mouse  g--aaaattccccctcct-----------cttcatttccagtaaactgtttgagc----aggc-gtgagt
B D            Rat  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----aggc-gtgagt
B D   Kangaroo rat  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----tgga-gtgagt
B D     Guinea pig  g--aaaattccccctcct-----------cttcatttccagtaaactgtttgagc----agga-gtgact
B D         Rabbit  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D           Pika  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D         Alpaca  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagt----agga-gtgagt
           Dolphin  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagt----agga-gtgagt
B D            Cow  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagt----agga-gtgagt
B D          Horse  g--aaaattccccctccc-----------cttcatttccagtaaattgtttgagt----agga-gtgagt
B D            Cat  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagt----agga-gtgagt
B D            Dog  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagt----agga-gtgagt
          Microbat  g--aaaattccccctccc-----------cttcatttccagtaaactatttgagt----agga-gtgagt
B D        Megabat  g--aaaattccccctcct-----------cttcatttccagtaaactgtttgagt----agga-gtgagt
B D       Hedgehog  g--aaaattccccctccc-----------cttcatttccagt-aattgtttgagc----agga-gtgagt
B D          Shrew  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D       Elephant  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
B D     Rock hyrax  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
         Armadillo  g--aaaattccccctccc-----------cttcatttccagtaaactgtttgagc----agga-gtgagt
  D        Wallaby  g--aaaattccccctccc-----------ctccatttccagtaaactgtttgaac----agga-gtgagt
B D        Opossum  g--aaaattccccctccc-----------ctccatttccagtaaactgtttgaac----agga-gtgagt
B D       Platypus  g--aaaattccccctccc-----------ctccatttccagtaaactgtttgaac----agaa-gtgagt
B D        Chicken  g--aaaattccccctccc-----------ctccatttccagtaaactgtttgaac----agga-gtgact
B D    Zebra finch  g--aaaattccccctccc-----------ctccatttccagtaaactgtttgaac----agga-gtgact
B D         Lizard  gcacaaattcc----ccc-----------ctccatttccagtaaactgtttgaac----aggg-atgagt
B D  X. tropicalis  g--aaaattccccctcct-----------ctccatttccagtaaactgtttgaac----agca-gtgact
B D           Fugu  g--aaattgccccctcccttctcctccttctttatttccagtaaactgtttgaaaggaggggg-gtgagt
B D    Stickleback  g--aaaatgccccctccctcctcctcattctttatttccagtaaactgtttaaaaggaggggg-gtgagt
B D         Medaka  g--aaagtgccccctccctcctcctccctttttatttccagtaaactgtttgaacggaggggg-gtgagt
B D      Zebrafish  g--aagctccctcctccccctgcctccccccgtgtttccagt-aactg-ctgaaagga-gggg-ctgagt
B D        Lamprey  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D         Tenrec  ======================================================================
B D          Sloth  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  caca-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcagcgtggactc
          Bushbaby  caga-gtgaaaccagcttccc-tgta----accacaaggcttgttaaa-gaatttg-tcaacgtggactc
             Chimp  caca-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
         Orangutan  cacaggtgaaaccagcttcccttgtaaaccaacagaggctttgttaaaggaatttgttcaacgtggactc
            Rhesus  caca-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
            Baboon  caca-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
          Marmoset  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
           Tarsier  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
             Mouse  caga-gtgaaaccagcttccc-tgta----accacagggcttgttgaa-gaatttg-tcaacgtggactc
               Rat  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
      Kangaroo rat  caga-gtgaaaccagcttccc-tgta----accacagggcctgttaaa-gaatttg-tcaacgtggactc
        Guinea pig  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
            Rabbit  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
              Pika  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
            Alpaca  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
           Dolphin  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
               Cow  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
             Horse  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
               Cat  caga-gtgaaaccagcttccc-tgta----accaca--gcttgttaaa-gaatttg-tcaacgtggactc
               Dog  caga-gtgaaaccagcttccc-tgta----accgcagggcttgttaaa-gaatttg-tcaacgtggactc
          Microbat  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
           Megabat  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
          Hedgehog  caga-gtgaaaccagcttccc-tgta----accacagagcttgttaaa-gaatttg-tcaacgtggactc
             Shrew  caga-gtgaaaccagcttccc-tgta----accacagggcctgttaaa-gaatgtg-tcagcgtggactc
          Elephant  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
        Rock hyrax  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
         Armadillo  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtgtactc
           Wallaby  caga-gtgaaaccagcttccc-tgta----accacagggcttgttcaa-gaatttg-tcaacgtggactc
           Opossum  caga-gtgaaaccagcttccc-tgta----accacagggcttgttcaa-gaatttg-tcaacgtggactc
          Platypus  caga-gtgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
           Chicken  caga-ctgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
       Zebra finch  caga-ctgaaaccagcttccc-tgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
            Lizard  caga-atgaaaccagcttccc-tgca----accacaggagttgttaaa-gaatttg-tcaacgtggactc
     X. tropicalis  caga-gtgaaaccatctttccttgta----accacagggcttgttaaa-gaatttg-tcaacgtggactc
              Fugu  caga-gtaaaaccagcttccc-ttta----accaca--gcttgttaaa-gaatttg-tcaacgtggactc
       Stickleback  caga-gtaaaaccagcttccc-ttca----accgca--gcttgttaaa-gaatttg-tcaacgtggactt
            Medaka  caga-gtaaaaccagcttccc-ttta----accgca--gcttgttaaa-gaatttg-tcaacgtggactc
         Zebrafish  cagt-cttcaaccagcttccc-tttg----accaca--gcttgttaaa-gaatttg-tcaacgtggactc
           Lamprey  ======================================================================
         Tetraodon  ======================================================================
        Tree shrew  ======================================================================
            Tenrec  ======================================================================
             Sloth  ======================================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  tag--ag--ggttt-gca--tt-----
          Bushbaby  tag--ag--ggttt-gca--tt-----
             Chimp  tag--ag--ggttt-gca--tt-----
         Orangutan  taggaag--ggttt-gca--tt-----
            Rhesus  tag--ag--ggttt-gca--tt-----
            Baboon  tag--ag--ggttt-gca--tt-----
          Marmoset  tag--ag--ggttt-gca--tt-----
           Tarsier  tag--ag--ggttt-gca--tt-----
             Mouse  tag--ag--ggttt-gca--tt-----
               Rat  tag--ag--ggtgt-gca--tt-----
      Kangaroo rat  tag--ag--ggttt-gca--tt-----
        Guinea pig  tag--ag--ggttt-gca--tt-----
            Rabbit  tag--ag--ggttt-gca--tt-----
              Pika  tag--ag--ggttt-gca--tt-----
            Alpaca  tag--ag--ggttt-gca--tt-----
           Dolphin  tag--ag--ggttt-gca--tt-----
               Cow  tag--ag--ggttt-gca--tt-----
             Horse  tag--ag--ggttt-gca--tt-----
               Cat  tag--ag--ggttt-gca--tt-----
               Dog  tag--ag--ggttt-gca--tt-----
          Microbat  tag--ag--ggttt-gca--tt-----
           Megabat  tag--ag--ggttt-gca--tt-----
          Hedgehog  tag--ag--ggttt-gca--tt-----
             Shrew  tag--ag--ggttt-gca--tt-----
          Elephant  tag--ag--ggttt-gca--tt-----
        Rock hyrax  tag--ag--ggttt-gca--tt-----
         Armadillo  tag--ag--ggttt-gca--tt-----
           Wallaby  tag--ag--ggttt-gta--tt-----
           Opossum  tag--ag--ggtttggta--tt-----
          Platypus  tag--ag--ggtct-gta--tt-----
           Chicken  aag--ag--ggttt-gta--tt-----
       Zebra finch  gag--ag--ggttt-gta--ct-----
            Lizard  caa--ag--gg----------------
     X. tropicalis  tag--ag--ggctt-gtagctt-----
              Fugu  agg--ag------t-gca--t-----t
       Stickleback  -tt--gg------t-gca--ttttttt
            Medaka  agg--gg------t-gca--gttgcat
         Zebrafish  cag--ggtg------------------
           Lamprey  ===========================
         Tetraodon  ===========================
        Tree shrew  ===========================
            Tenrec  ===========================
             Sloth  ===========================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 26 and 27 in window
B D     Orangutan 1bp
B D        Lizard 12431bp
B D        Medaka 4522bp
B D     Zebrafish 42499bp

Alignment block 27 of 46 in window, 57864116 - 57864155, 40 bps 
B D          Human  aagctttgcag-taactg-ttatgg--tttgtgt---tgcgtca-gga
          Bushbaby  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D          Chimp  aagctttgcag-taactg-ttatgg--tttgtgt---tgcgtca-gga
B D      Orangutan  aagctttgcagttaactgtttatgg--tttgtgt---tgcgtcaggga
B D         Rhesus  aagctttgcag-taactg-ttatgg--tttgtgt---tccgtca-gga
B D         Baboon  aagctttgcag-taactg-ttatgg--tttgtgt---tctgtca-gga
B D       Marmoset  aagctttgcag-taactg-ttatgg--tttgtgt---tgcttca-gga
B D        Tarsier  aagctttgcag-taactg-ctatgg--ttcatct---tgtgtca-gga
B D          Mouse  aagctttgcag-caacga--tatgg--tttgtgt---tgtgtca----
B D            Rat  aagctttgcag-cagcta-ctatgg--ttagggt---tgt-tca----
B D   Kangaroo rat  aagcttggcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D     Guinea pig  aggccttgcag-taactg-ctatgg--tttatgt---tgcatta-gga
B D         Rabbit  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D           Pika  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D         Alpaca  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
           Dolphin  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D            Cow  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D          Horse  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D            Cat  aagctttgcag-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D            Dog  aagctttgcag-taacta-ctatga--tttgtgt---tgcgtca-gga
          Microbat  aagctt----------tg-ctatgg--tttgtgt---tgtgtca-gga
B D        Megabat  aagctttgccg-taactg-ctatgg--tttgtgt---tgcgtca-gga
B D       Hedgehog  aagctttgcaa-tagctg-ctatgg--tttgtat---tgcgtca-gtg
B D          Shrew  aaacttcgcag-taactg-cgttgg--tttgtat---tgcgtca-gga
B D       Elephant  aagctttgcag-taacta-ttacgg--tttgtgt---tgggtca-gga
B D     Rock hyrax  aagctttgcag-taactt-ctatgg--tttgtgt---tgcatca-gga
         Armadillo  aagccttgcag-taactg-ctacgg--tttttgt---tgcatca-gga
B D          Sloth  atg-cttgcag-taactg-ctatgggttttttgt---tgcatca-gga
  D        Wallaby  aaacttggctg-taactg-ctttg------------------------
B D        Opossum  aaacttggctg-taactg-ctttg------------------------
B D       Platypus  ccactttgctg-taactg-ctatag--tttgtat---tgcgtca-ggg
B D        Chicken  aaactaagctg-caactg-cttcgg--tttgcgt---tgcgtca-gga
B D    Zebra finch  caactgagctg-cagccg-cct-gc--cttggct---tgtggca-gtg
B D  X. tropicalis  aagtgagtttg-gaactg-ctgtgg--ttaacag---tgtgtca-gga
B D    Stickleback  gtgcgtttgtg-tgtcgg-tgggcg--tgtgcgtgcatgcgtcc-gga
B D         Lizard  ================================================
B D      Zebrafish  ================================================
B D        Lamprey  ================================================
B D         Medaka  ================================================
B D      Tetraodon  ================================================
B D     Tree shrew  ================================================
B D         Tenrec  ================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 27 and 28 in window
B D   Stickleback 3940bp

Alignment block 28 of 46 in window, 57864156 - 57864223, 68 bps 
B D          Human  gttccacagaaaagcttcctgc-----ttgca-gg-a-----tctct--tgcttgtttgcaaagagttaa
          Bushbaby  gttccatagaaaagcttcctgc-----tctca-gg-g-----tctct--tgcctgtttgcaaagagttaa
B D          Chimp  gttccacagaaaagcttcctgc-----ttgca-gg-a-----tctct--tgcttgtttgcaaagagttaa
B D      Orangutan  gttccacagaaaagcttcctgc-----ttgcaggg-a-----tctct--tgcttgtttgcaaagagttaa
B D         Rhesus  gttccacagaaaagcttcctgc-----tcgca-gg-a-----tctct--tgcttgtttgcaaagagttaa
B D         Baboon  gttccacagaaaagcttcctgc-----tcgca-gg-a-----tctct--tgcttgtttgcaaagagttaa
B D       Marmoset  gttccacagaaaagctttctgt-----ttgca-gg-a-----tctct--tgcttgtttgcaaagagttaa
B D        Tarsier  gtttcacagaaaagcttcccac-----tctca-gg-g-----tctct--tgcttgcctgtaaagagttaa
B D          Mouse  gttcctgggaaaagcttcctcc-----tctca-gg-a-----tcttt--tgcttatttgcattaagt---
B D            Rat  --tcctgggaaaagcttcctcc-----tttca-gg-a-----tctct--tgcttattagccttgagttaa
B D   Kangaroo rat  gttccacagagaagcttcctgc-----tctca-gg-a-----tctct--tgtgtgcttgtctagagttaa
B D     Guinea pig  ggtccacaga-aagctgtctgc-----tctca-gg-a-----tctc---agccagtttgtgcagagttat
B D         Rabbit  gttccacaaaaaagcttcctgc-----tctca-gg-a-----tctct--tgcttgtttgcatagagttaa
B D           Pika  gttccacagaaaagcttgctgc-----tctca-gg-a-----cctct--tgcttgtttgcatagagttga
B D         Alpaca  gttccacagaaaagcttcctgc-----tctca-ga-c-----tctct--tgcgtgtttgcaaagggtta-
           Dolphin  gttccacagaaaagcttcctgt-----tctca-ag-a-----tctct--tgcttgtttgcaaagggttaa
B D            Cow  gttccacagaaaagcttcctgc-----tttca-ag-a-----tccct--tgcttgtttgcaaagggttaa
B D          Horse  gttccacagaaaagcttcctgc-----tctca-ag-a-----tctct--tgcttgtttgcaaagggttaa
B D            Cat  cttccacagaaaagcttcctgc-----tctca-ag-a-----tcttt--tccttgtttgcaaagggttaa
B D            Dog  cttccacagaaaagcttcctgc-----tctca-ag-a-----tcttt--tccctgtttgcaaagggttaa
          Microbat  gttccacagaaaagcttccggc-----tctca-tg-a-----tctct--tgcttgtttgcaaagggttaa
B D        Megabat  gttccacagaaaggcttcctgc-----tctcc-tg-a-----tcttt--tgcttgtttgcaaagggttaa
B D       Hedgehog  gttctacagaaac-tttcttgt-----tccta-ag-a-----cttgt--tgcttt----cagaatgctaa
B D          Shrew  cttccacagaaaagcttcctgc-----tccca-gg-t-----gctct--tgctcttttgctaagggttaa
B D     Rock hyrax  attctagaggaaagcttcctgc-----tccca-ga-a-----tctct--tgtttgtaggcaaagagttaa
B D       Elephant  attctacaggaaagcttcctgg-----tcccg-ag-a-----tctcc--tgtttgtaggcaaagagttaa
B D         Tenrec  gttctacc-gaaagcttcgcgg-----tcgag-ag-a----gtctct--tgtttgtaggc--cgcgttaa
         Armadillo  gttccacagaaaagcttcctgc-----tctca-gg-a-----tctct--agcttatttacaaagagttaa
B D          Sloth  gttccacagaaaagcgtcctgc-----tctca-gg-a-----ttttttgtgcttgtttacaaagagttaa
  D        Wallaby  gttccatagaacaacttcctgc-----cattg-gg-aacagatcact--tacttgtttgcaaagagttaa
B D        Opossum  gttccatagaacaacttcctgccatttttatc-aa-a-----tcact--tacttgtttacaaagagttaa
B D       Platypus  gttccatagaacaacttcccgc-----tccca-gg-c-----tcagt--ttcttgcttgtgaggagttaa
B D        Chicken  gttccaccaaacaacttcctgc-----tcggg-ga-g-----gcggc--ttctcgtctgcaaggagttaa
B D    Zebra finch  cttccatcgagccccttcctat-----tcccg-aa-g-----g-------------ctgcaaggggttaa
B D  X. tropicalis  gtt-------agatgttctttt-----aatca-gaca-----tggga--tacttgtctgcaatgagttaa
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  actgatcaac-tt
          Bushbaby  actgataaac-at
             Chimp  actgatcaac-tt
         Orangutan  actaatcaac-tt
            Rhesus  actgataaac-tt
            Baboon  actgataaac-tt
          Marmoset  actgataaac-tt
           Tarsier  actgataagc-tt
             Mouse  att----------
               Rat  act----------
      Kangaroo rat  actgatcaac-tt
        Guinea pig  accgagcaac-tt
            Rabbit  gctgataaac-tt
              Pika  actgatcagc-tt
            Alpaca  -------aac-tt
           Dolphin  actgatcaac-tt
               Cow  actgatcaac-tt
             Horse  actgataaac-tt
               Cat  actgataaac-tt
               Dog  actgataaac-tt
          Microbat  actggtaagt-gt
           Megabat  cctgataa---ac
          Hedgehog  actgataaag-tt
             Shrew  actgacaaac-cc
        Rock hyrax  actggcaggcatt
          Elephant  actgatggat-tt
            Tenrec  actgataaacata
         Armadillo  actgataaat-tg
             Sloth  actgataaat-ta
           Wallaby  actgatgaac-tt
           Opossum  actgatgaac-tt
          Platypus  gctggtgaat-tt
           Chicken  agcgatgaac-tt
       Zebra finch  a------------
     X. tropicalis  actgttgaac-tt
            Lizard  =============
         Zebrafish  =============
       Stickleback  =============
           Lamprey  =============
            Medaka  =============
         Tetraodon  =============
        Tree shrew  =============
       Mouse lemur  NNNNNNNNNNNNN

Inserts between block 28 and 29 in window
B D   Zebra finch 6635bp
B D X. tropicalis 2636bp

Alignment block 29 of 46 in window, 57864224 - 57864320, 97 bps 
B D          Human  ta---------ccata------gtgaaca-tgagaga---cacatg----------ttaaacaca-cttc
          Bushbaby  ta---------ccatc------atgaaca-ttagaga---cacatg----------ttaaacata-tttc
B D          Chimp  ta---------ccata------gtgaaca-tgagaga---cacatg----------ttaaacaca-cttc
B D      Orangutan  ta---------ccata------gtgaaca-tgagaga---cacatg----------ttaaacaca-cttc
B D         Rhesus  ta---------ccgta------gtgaata-tgagaga---cacatg----------ttagacaca-cttc
B D         Baboon  ta---------ccgta------gtgaata-tgagaga---cacatg----------ttaaacaca-cttc
B D       Marmoset  ta---------ccata------gtgaaca-tgagaga---cgcatg----------taaaacaca-tttc
B D        Tarsier  ta---------tcata------atgaaca-tcagaga---cacatg----------ttaaacaca-----
B D          Mouse  --------------------------------agaaa---tgttca----------ttctaggc------
B D            Rat  --------------------------------ttaga---tgctca----------ttcaaggc----tc
B D   Kangaroo rat  ta---------tcata----------------ataaa---ccttaagagtgatgtgttcaacaca-tttc
B D     Guinea pig  ta---------tgata------gtgaaca-ggagaga---cacgtg----------ttgaacaca-actc
B D         Rabbit  ta---------ccata------atgaaca-ttagaga---cacatg----------ttaaacaca-tttc
B D           Pika  ca---------ctgta------gtgaaca-tttgagc---cccatg----------ctaaacata-tttc
B D         Alpaca  ta---------ccgtg------atgcaca-ttagcga---cacatg----------tttaacaca-tttc
           Dolphin  ta---------ccata------atgaaca-ttagaga---cacatg----------ttaaacaca-ttta
B D            Cow  ta---------ccata------ataaaca-ttagaga---caca------------ttaaaccca-ttta
B D          Horse  ta---------ccata------atgaaca-ttagaga---cacacg----------ttaaacaca-ttta
B D            Cat  ta---------ccata------atgaacatggggaga---cacacg----------ttaaacaca-tttc
B D            Dog  tg---------ccata------atgaaca-gtagaga---cacatg----------ttaaacact-tttc
          Microbat  tg---------cctta------atgagca-tcagaga---cacc------------ttaaacacattttt
B D        Megabat  ta---------ccata------aggaaca-ttagaga---cacttg----------ttaaacaca-tttc
B D       Hedgehog  ta---------ctata------gtaagca-actggaaacatac---------------taac-ca-tttc
B D          Shrew  tg---------ccatgatgaatgttagca-tcagtgaagtttcacg----------gttaa---g-tgcc
B D     Rock hyrax  ta---------ccgta------ctgaaca-ttgaaaa---cacatg----------ttgaa-----ctcc
B D       Elephant  ta---------ccata------atgacca-ttggaaa---cacatg----------ttaaacatg-cttc
B D         Tenrec  gagagagaaggatgag------atgaaca-ctggaaa---tacatg----------ttaagcaca-cttc
         Armadillo  ta---------ctgta------atgaaca-ctggagg---cacatg----------ttaaacaca-tttc
B D          Sloth  ta---------cccta------acgaaca-ttggagg---caca-------------taaacaca-tttc
  D        Wallaby  -----------cggta------gtgagca-ttggtga---cacatg----------ttaaacaca-tctt
B D        Opossum  -----------cggta------gtgagca-ttggtg----cacatg----------ttaaataca-tctt
B D       Platypus  tg---------ctaga------gtgaaca-tttgaga---cac--g----------ttaagccca-tctt
B D        Chicken  tg---------cgata------gtggcag-t--ggga---cacatg----------agaaagcca-tctc
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  -tttatcatt-a----aaggcgttgtcaaaac---------taccaagaattagtgtagtt-----tctc
          Bushbaby  -tctatcatt-a----aaggtgttgtcagagc---------taccaag-cttactgtagtt-----tttc
             Chimp  -tttatcatt-a----aaggcgttgtcaaaac---------taccaagaattagtgtagtt-----tctc
         Orangutan  -tttatcatt-a----aaggcgttgtcaaaac---------taccaagaattagtgtagtt-----tctc
            Rhesus  -tttatcatt-a----aaggcattgtcaaaac---------taccaagaattagtgtagtt-----tctc
            Baboon  -tttatcatt-a----aaggcattgtcaaaac---------taccaagaattagtgtagtt-----tctc
          Marmoset  -tttatcatt-a----aaggcgttgtcaaagc---------taccagttattacggtagtt-----tctc
           Tarsier  -tttatcatt-a----aaggcagtgtcaaagc---------caccaaggcttactgtagtt-----tctt
             Mouse  -----tcatt-c----gaggtcttgtca--------------------------tgtagat------ctc
               Rat  -attatcatt-a----gaagccttgtc---------------------------tgtagat------cgc
      Kangaroo rat  -tttatcttt-a----aaggccatgtcaaatc---------taccaaggcttactgtaactgaactgtac
        Guinea pig  -tttatcatt-a----aaggcactatcaaagc---------taccacggcttattgtagtt-----tctc
            Rabbit  -tttatcatt-c----aaggcgttgtcagaac---------taccaatgcttactgtagtt-----tctc
              Pika  -tttatcatt-t----aaggcgttgtcagagc---------taccagtgcttactgtagtt-----tctc
            Alpaca  -tttatcattta----aaggccgagtcaaagc---------taccggggctcactgtagtt-----tctc
           Dolphin  -tttatcactta----aaggctgtgtcaaagc---------taccaaggcttattgtagtt-----tctc
               Cow  ttttatcattta----aaggctgtgtcaaagc---------taccaaggcttattgtaatt-----tctc
             Horse  -tttatcattta----aaggccgtgtcaaagc---------taccaagacttactgtagtt-----tctc
               Cat  -tttatcgtt-------aggccccgttaaagc---------taccagggcttactgtagtt-----tctc
               Dog  -tttatcgttt-----aaaggcgtgtcaaagc---------taccagggcttactgtagtt-----tctc
          Microbat  -tttatcatgta----aagg-----------------------ccaaggcttactgtagtt-----tctc
           Megabat  -tttatcattta----aaagccctgtcaaagt---------taccaaggcttattgtagtt-----tctc
          Hedgehog  -attatcattta----aaaaccaagtaaaaac---------tagcaagatttagtgtagtt-----tctt
             Shrew  -cttatcttgta----aaggccaggtcaaaac---------taccaagacactctatagtt----ctctc
        Rock hyrax  -tttatcatt-a----aaggcattgtcaaagc---------taccaagacttactgtcctt-----tctc
          Elephant  -tttatcatt-a----aaggcgttgtcaaagc---------taccaaggcttgctgtagtt-----tctc
            Tenrec  -tttatcatt-a----aaggcgttgtcaaaac---------taccacggcttactgtagtt-----tctc
         Armadillo  -tttgt----------gttgctttgtcaaagg---------tactaaggtttaatgtagtt-----tctc
             Sloth  -tttat----------gtggcattgtcagagc---------tactaaggtttaatgtag-t-----tctc
           Wallaby  -tctagcatc-actctaaggcgttgtccaagg---------gcgatagctttaccaggatt-----tctc
           Opossum  -----------t----atggcattgtccaagg---------gagatagctttaccagggtt-----tctc
          Platypus  -tctagcatg-actttaaggcgtcgtcaaggcagatagcttttccacagcctgctggagtt-----tctc
           Chicken  -tccagcact-g------------ctgagagc---------tcccgtgccttgagctggat-----tgct
            Lizard  ======================================================================
         Zebrafish  ======================================================================
       Stickleback  ======================================================================
           Lamprey  ======================================================================
            Medaka  ======================================================================
       Zebra finch  ======================================================================
         Tetraodon  ======================================================================
        Tree shrew  ======================================================================
     X. tropicalis  ======================================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  ttttcat
          Bushbaby  ttttcag
             Chimp  ttttcat
         Orangutan  ttttcat
            Rhesus  ttttcat
            Baboon  ttttcat
          Marmoset  ctttcag
           Tarsier  ttttcag
             Mouse  ctttcag
               Rat  ctttcag
      Kangaroo rat  ctttcac
        Guinea pig  ctttgag
            Rabbit  ctttcaa
              Pika  ctttcag
            Alpaca  ttttcag
           Dolphin  ttttcag
               Cow  ttttcag
             Horse  ttctcag
               Cat  ttttcag
               Dog  ttttcag
          Microbat  ttttcag
           Megabat  tttacag
          Hedgehog  ttttcag
             Shrew  ttttcag
        Rock hyrax  ttttcag
          Elephant  ttttcag
            Tenrec  ttttcag
         Armadillo  ttttcag
             Sloth  ttttcag
           Wallaby  ttttcag
           Opossum  ttttcag
          Platypus  ttttcag
           Chicken  tttccat
            Lizard  =======
         Zebrafish  =======
       Stickleback  =======
           Lamprey  =======
            Medaka  =======
       Zebra finch  =======
         Tetraodon  =======
        Tree shrew  =======
     X. tropicalis  =======
       Mouse lemur  NNNNNNN

Inserts between block 29 and 30 in window
B D       Chicken 798bp

Alignment block 30 of 46 in window, 57864321 - 57864349, 29 bps 
B D          Human  -aatcaac-------------------------caaccaca-cccaataatgttta
          Bushbaby  -aatcaac-------------------------caaccaca-cccagtaatgttta
B D          Chimp  -aatcaac-------------------------caaccaca-cccaataatgttta
B D      Orangutan  -aatcaac-------------------------caaccaca-cccaataatgttta
B D         Rhesus  -aatcaac-------------------------caaccacaccccaataatgttta
B D         Baboon  -aatcaac-------------------------caaccacaccccaataatgttta
B D       Marmoset  -aatcaac-------------------------caaccaca-cccaataacgttta
B D        Tarsier  -agtcaac-------------------------caaccaca-cccaaaaatgttta
B D          Mouse  -atcccac-------------------------caaccaca-c-------------
B D            Rat  -atcctac-------------------------caaccaca-cacagtgacattta
B D   Kangaroo rat  -agtgaac-------------------------ctactaca-cccagtagggctta
B D     Guinea pig  aaatcaac-------------------------cagccgta-cccagtaacattta
B D         Rabbit  -aatcaac-------------------------caacccca-cccaatagcattta
B D           Pika  -aatcaac-------------------------ctacccca-ccctgtaacattta
B D         Alpaca  -aatcaag-------------------------cagccaca-cccaacaacgttaa
           Dolphin  -aatcacc-------------------------caaccaca-cccaacaacgttaa
B D            Cow  -aatcaac-------------------------caaccaca-cccaacaacgttaa
B D          Horse  -aatcaac-------------------------catccaca-cccaataacattta
B D            Cat  -aatcaa-----------------------------ccaca-cccaacaacgttta
B D            Dog  -aatcaa-----------------------------ccaca-cccaacaacattta
          Microbat  -aatcatc-------------------------caaccaca-cccaagaacattta
B D        Megabat  -aatcaac-------------------------caaccaca-cccaacaacaatta
B D       Hedgehog  -aatcaac-------------------------cagccaca-ct---caacgttta
B D          Shrew  -aaccaac-------------------------caaccaca-c----caacattta
B D     Rock hyrax  -aaacaac-------------------------caaccaca-cccagaaatgttta
B D       Elephant  -aatcaac-------------------------cagccaca-cccaaaaacgttta
B D         Tenrec  -aatcaaa-------------------------gaaccaca-cccaata--gctta
         Armadillo  -aatctac-------------------------caaccaca-cccaac---gttaa
B D          Sloth  -aa--tgc-------------------------caacccca-cccaacaatgttca
  D        Wallaby  -aaacaaaggactcgat------ccccttttggccaccaca-cccagtcac-----
B D        Opossum  -aaacaaaggacttgat------ccccttttggccaccaca-cccagttgc-----
B D       Platypus  -aaacaaagtacaaagtacgagactccatttggccaccacg-cccggcctcgctcg
B D         Lizard  ========================================================
B D      Zebrafish  ========================================================
B D    Stickleback  ========================================================
B D        Lamprey  ========================================================
B D         Medaka  ========================================================
B D        Chicken  ========================================================
B D    Zebra finch  ========================================================
B D      Tetraodon  ========================================================
B D     Tree shrew  ========================================================
B D  X. tropicalis  ========================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 30 and 31 in window
B D           Rat 218bp

Alignment block 31 of 46 in window, 57864350 - 57864427, 78 bps 
B D          Human  gtttttgaaaaggcgg---gcctggtagatagtct--ttcacagttggctcatgattttatca-----ca
          Bushbaby  gtttttgaaatggcaggcagcctgctagatcttct--ttcttagctggttcaggattttacca-----ca
B D          Chimp  gtttttgaaaaggcgg---gcctggtagatagtct--ttcacagttggctcatgattttatca-----ca
B D      Orangutan  gtttttgaaaaggcgg---gcctggtagatagtct--ttcacagttggctcatgattttatca-----ca
B D         Rhesus  gtttttgaaaaggcgg---gcctggtagatagtct--ttcatagttggctcatgattttatca-----ca
B D         Baboon  gtttttgaaaaggcgg---gcctggtagatagtct--ttcatagttggctcatgattttatca-----ca
B D       Marmoset  gtttttgaaaaggcgg---gcctgatagatagtct--ttcacagttggctc-tgattttatca-----ca
B D        Tarsier  gttttttaaaaggaag---gcctgctagatctcct--ttcatagctggttcatgattttacca-----ca
B D          Mouse  -------------aca---gccagtgaca---t----------------tcaggattttgttg-----ct
B D   Kangaroo rat  gtttttgaaaaggcaa---gcctgctaca---tct--tccatagctggctcatgactttacca-----ca
B D     Guinea pig  gtttttgaaaagtcca---gcctgctaga---tct--ttcttagctggctcgtgattttacca-----ca
B D         Rabbit  ttttttgaaaaggcag---gtcagctagatcttct--ttcgtagctgcctcatgattttacca-----ca
B D           Pika  gattttgaaaaggcag---gcctgctaga---tct--ttcatagctggctcatgattttacca-----ca
B D         Alpaca  gtttttgaaaagacag---gcctgctagatcttct--ttcagagctggctcatgattttacca-----ca
           Dolphin  gtttttgaaaaggcag---gcctgctagatcttct--ttcagagctggctcataattttacca-----ca
B D            Cow  gtttgtgaaaaggcag---gcctgctagatcttct--ttcagagctggctcatgattttacca-----ct
B D          Horse  gtttttgaaaagacag---gcctgctagatcttct--ttcagagctggctcatgattttacca-----ca
B D            Cat  gtttttgaaaagacag---gcctgctagatcttct--ttcagcactggctcatgattttacca-----ca
B D            Dog  gtttttgaaaagacag---gcctgctagatcttct--ttcagagctggctcatgattttacca-----ca
          Microbat  gtttttgaaaaggcag---gcc-------ttttcttctttcgagctggctcatgattttacca-----ca
B D        Megabat  gtttttgaaaaggcag---gcc-------ttttct--ttcagagctggctagtgattttacca-----ca
B D       Hedgehog  actttttaaaaagcag---gcctgttctatcttct--ttcagaactggctcatgattttacca-----ca
B D          Shrew  ttttttgaaaaggcag---gcctgctagctcttgt--ttcagagccggctcacgattttacca-----ca
B D     Rock hyrax  gtttttgaaaagccag---gccagctaggtcttct--ttcagcgct-gctcgtgattttacca-----cg
B D       Elephant  gtttttgaaaagccaa---gccagctagatctgct--ttcagcactggctcatgattttacca-----ca
B D         Tenrec  gtttttgaaacggctg---gcca-ctagatcttct--ttcagtactggctcatgattttacca-----ca
         Armadillo  gtttttgaaaaggcag---acctgctagatcttct--ttcagcactggttcatgattttacca-----ca
B D          Sloth  atttttgaaaaggcag---gcctactagatcatct--ttcagtgtgagctcatgattttacca-----ca
  D        Wallaby  ----------aggcag---acatgctgtcttcttt--ttcactgc---------acagtaaga-----ca
B D        Opossum  ----------acgcag---acatgctctcttcttg--ttcagtgcaa---taggacagtaaca-----tt
B D       Platypus  tattttgaaaaggcca---gccgactagatcttct--ttctggacaagattggagatgtaatattggcta
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D            Rat  ======================================================================
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  aagtaccatcaaaattaa-------
          Bushbaby  aagtactatcaaaattaa-------
             Chimp  aagtaccatcaaaattaa-------
         Orangutan  aagtaccatcaaaattaa-------
            Rhesus  aagtaccatcaaaattaa-------
            Baboon  aagtaccatcaaaattaa-------
          Marmoset  aggtaccatcaaaattaa-------
           Tarsier  aagcaccatcaaaattaa-------
             Mouse  taacatc------------------
      Kangaroo rat  aagtgccatcaagattaa-------
        Guinea pig  aagtatcagcaagattaa-------
            Rabbit  aagtaccatgaagattaa-------
              Pika  aagtaccatgaagatta--------
            Alpaca  aagtaccatcaagattaa-------
           Dolphin  aagtgccatcgagattaa-------
               Cow  aagtaccatcaagattaa-------
             Horse  aagtaccatcaagattaa-------
               Cat  aagtaccatcaagattaa-------
               Dog  aagtacaatcaagattaa-------
          Microbat  aagtaccatcaagattaa-------
           Megabat  aagtaccatcaagattaa-------
          Hedgehog  aagtaccatcaagattaa-------
             Shrew  aagtgccatcaccatgaa-------
        Rock hyrax  aag---cgtcaagattaa-------
          Elephant  aagtaccatcaagattaa-------
            Tenrec  aagtaccatcaagattaa-------
         Armadillo  aagtaccattaagattaa-------
             Sloth  aagcaccatcaagattta-------
           Wallaby  tcacacaatccagactaa-------
           Opossum  tcacacaatccagactaa-------
          Platypus  aaatctgacccaggccattcattac
            Lizard  =========================
         Zebrafish  =========================
       Stickleback  =========================
           Lamprey  =========================
            Medaka  =========================
           Chicken  =========================
       Zebra finch  =========================
         Tetraodon  =========================
        Tree shrew  =========================
               Rat  =========================
     X. tropicalis  =========================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 31 and 32 in window
B D         Mouse 200bp

Alignment block 32 of 46 in window, 57864428 - 57864476, 49 bps 
B D          Human  gcaatt-------t---taagtgg----------tcttgatg-gattctgttacag--------------
          Bushbaby  gcaatt-------t---taagtggtc--------ttttggcg-gactcttgtgcag--------------
B D          Chimp  gcaatt-------t---taagtgg----------tcttgatc-gattctgttacag--------------
B D      Orangutan  gcaatt-------t---taagtgg----------tcttgatg-gattctgttacag--------------
B D         Rhesus  gcaatt-------t---taagtgg----------tcttgatc-gattctgttacag--------------
B D         Baboon  gcaatt-------t---taagtgg----------tcttgatc-gattctgttacag--------------
B D       Marmoset  gcagtt-------t---taagtgg----------ccttgatc-aattctgttacag--------------
B D        Tarsier  gcaatt-------t---aaagtggtc--------tcttgatg-gatactgttgcag--------------
B D            Rat  gcttcc-------c---taagtggtc--------tttaaatgagattctgttatgg--------------
B D          Mouse  ----cc-------t---taagtggtc--------ttttaatgagaatccattatag--------------
B D   Kangaroo rat  gcaatt-------t---tacgtggtc--------tcttgatg-tattctgttgcag--------------
B D     Guinea pig  gcaatt-------t---tcagtggta--------tcttgatg-gattctcttgcag--------------
B D         Rabbit  gcaatg-------t---taagtggtc--------tcttgatg-gattttgttgtgg--------------
B D         Alpaca  gcaatt-------t---taagtggtctc------ttttgaag-gattctgttgcag--------------
           Dolphin  gcaatt-------t---taagt-gtctc------ttttgaag-gattctgttgcaa--------------
B D            Cow  gcaatt-------c---caagtggtctc------ttttgaag-gattctgttgcag--------------
B D          Horse  gcaatt-------t---taagtggtctc------ttttgaag-gattctgttgcag--------------
B D            Cat  gcaatt-------t---taagtggtctc------ttttgaag-gattctgttgcag--------------
B D            Dog  gcaatt-------t---taagtggtctc------ttttgaag-gattctgttgcag--------------
          Microbat  gcaatt-------t---tcagtggtctc------tcttgaag-gattctgttgcag--------------
B D        Megabat  gcaatt-------t---taagtggtctc------ttttgaag-gattctgttggag--------------
B D       Hedgehog  gcaatt-------t---taagtgctctct-----ttttgaaa-gattctcttgcag--------------
B D          Shrew  gcaatt-------c---taagtggtctgt--ctctcttgaag-gactctagtgcag--------------
B D     Rock hyrax  gcaatt-------t---taagtggtctc------ttttgaag-gagtctgtctca---------------
B D       Elephant  gcaatt-------t---taactggtcgc------ttttgaag-gagtctgtcccag--------------
B D         Tenrec  gcaatt-------t---tatatgacctc------ttttgaag-gattctgtttcc---------------
         Armadillo  gcaatg-------t---taagttgtgtc------ttttgaag-ggggttgttgcag--------------
B D          Sloth  gcaa----------------------ct------ttttgaag-gattctgttgcag--------------
  D        Wallaby  gtaatc-------t---gtagcagtag-------tacgtaaa-tattcttgtaaaa--------------
B D        Opossum  gaaatc-------tatgtcagtggtacatgcacatctttata-aaacctattacat--------------
B D       Platypus  gtaattatctggat---caagtggactactacg-ttttgagg----tctgtggcagattcaatatggcag
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D     Tree shrew  ======================================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  -------------------------------------gatattttgactat
          Bushbaby  -------------------------------------gatattttggccac
             Chimp  -------------------------------------gatattttgactat
         Orangutan  -------------------------------------gatattttgactat
            Rhesus  -------------------------------------gatattttgactat
            Baboon  -------------------------------------gatattttgactat
          Marmoset  -------------------------------------gatatttagacaat
           Tarsier  -------------------------------------gatatttcaactat
               Rat  -------------------------------------aatatctcaacctt
             Mouse  -------------------------------------aatatctcaactat
      Kangaroo rat  -------------------------------------aatatttcaactat
        Guinea pig  -------------------------------------aatatttcaactct
            Rabbit  -------------------------------------ggtatttcaactgt
            Alpaca  -------------------------------------gatgttgcgactac
           Dolphin  -------------------------------------gatattgcaactac
               Cow  -------------------------------------gatattgcgactac
             Horse  -------------------------------------gatatcaagtctgc
               Cat  -------------------------------------gatattgcgactac
               Dog  -------------------------------------gatattgcgactgc
          Microbat  -------------------------------------gatattgcgactga
           Megabat  -------------------------------------gatattgtatctaa
          Hedgehog  -------------------------------------aatatcgctactac
             Shrew  -------------------------------------gattttgcatctgc
        Rock hyrax  ----------------------------------------------actat
          Elephant  ----------------------------------------------actac
            Tenrec  ----------------------------------------------actac
         Armadillo  -------------------------------------gatttttcagctac
             Sloth  -------------------------------------gattttttgactac
           Wallaby  -------------------------------------catactgtgattat
           Opossum  -------------------------------------gtagttgtagat--
          Platypus  tggtttacgtagaaaatatcaaacaccctcaaggtgggatatttggactc-
            Lizard  ===================================================
         Zebrafish  ===================================================
       Stickleback  ===================================================
           Lamprey  ===================================================
            Medaka  ===================================================
           Chicken  ===================================================
       Zebra finch  ===================================================
         Tetraodon  ===================================================
        Tree shrew  ===================================================
              Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
     X. tropicalis  ===================================================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 33 of 46 in window, 57864477 - 57864528, 52 bps 
B D          Human  t-cgcac----agt-----taggtgt--cg-gtac----------caaaggtc--ac-ttac-ttgcact
B D        Tarsier  t-agcac----agt-----taagatt--tg-gtac----------caaaggtc--ac-ttac-ttgcgtt
B D       Marmoset  t-tgcacagttagt-----taggttt--gg-ggac----------taaagg-------ttac-ttgcagt
B D         Baboon  t-cgcgc----agt-----taggtgt--gg-gtac----------caaaggta--ac-ttac-ttgcatt
B D         Rhesus  t-cgcgc----agt-----taggtgt--gg-gtac----------caaaggta--ac-ttac-ttgcatt
B D      Orangutan  t-cgcac----agt-----taggtgt--cg-gtac----------caaaggtc--ac-ttac-ttgcact
B D          Chimp  t-cgcac----agt-----taggtgt--cg-gtac----------caaaggtc--ac-ttac-ttgcact
          Bushbaby  t-agcac----act-----taaattt--tg-gtac----------cggtggtc--ac-ttgc-ttgcatt
B D     Tree shrew  t-agcgc----agt-----tagttttagcg-ctac---------tcaaaggtc--ac-ttac-ttgaatt
B D            Rat  t-gggac----agt-----taaattt--ga-gtaa----------caaagg-------------------
B D          Mouse  t-gggat----agt-----taagttt--ga-gtac----------agaagg-------------------
B D   Kangaroo rat  t-agaat----agt-----tggtttt--tg-ctat----------caaagg------------tagcatt
B D     Guinea pig  a-ggtgc----agt-----tgggttt--tg-atac----------caaaagtc--ac-ttac-ttacatt
B D         Rabbit  t-agtac----aat-----taga-----------------------------------------------
B D         Alpaca  t-agcac----agt-----tagcttt---g-gtac---------acaaaggtc--ac-ttac-ttgcatt
           Dolphin  t-agcac----agt-----tagcttt--tt-gtac---------acaaaggtc--ac-ttac-ttgcatt
B D            Cow  t-agctc----agt-----tagcttt--gg-gtac---------ataaaggtc--gc-tta-----catt
B D          Horse  t-agcac----agt-----tagcttt---g-gtac---------ataaaggtc--ac-ttac-atgcatt
B D            Cat  t-agcac----att-----tagcttt---a-gtac---------acaaaggtc--ac-t-----tgcatt
B D            Dog  t-agcac----att-----tagcttt---g-gtac---------acaaaggtc--ac-t-----tgcatt
          Microbat  c-agtag----ag------tggcttt---g-gtac---------atgaaagtc--ac-tgac-ttgcatt
B D        Megabat  ctagcaa----agt-----tagctct---g-gtac---------acagaggtc--ac-ttac-ttgcatt
B D       Hedgehog  t-aggac----aat-----tattttt---a-gtac----------taaaggcc--ac-tgac-ttatatg
B D          Shrew  t-tgcac----aat-----cctcatt---g-gtac----------caaaggtc--acttaac-ttgtctc
B D     Rock hyrax  t-agcac----agt-----caggctt--tt-gtat----------caaaggtta-ac-tttg-ttgcact
B D       Elephant  t-agcac----aat-----taggctt--tc-gtac----------caaaggtt--ac-tttc-ttgcttt
B D         Tenrec  t-agcac----agt-----taggctt--ctggtac----------caaaggtta-ct-tttc-ttgcttt
         Armadillo  t-aacac-------------aggttt--tg-ggac----------caaaggtc--ac-ttactttgcatt
B D          Sloth  t-aacac----agt-----taggttt--tg-attc----------caacggtc--ac-ttac-ttgcgtt
B D        Opossum  t-aacct----agtgattatagtttt--ag-attc---------ccagaagttgcac-t-----------
B D       Platypus  c-agcac----aga-----cattgtt--ac-ggattcctgttttcaaatagtc--ac-ttgg-tggcctt
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  ttgt----tcatc
           Tarsier  ttgt----tca-c
          Marmoset  ttgt----tcatc
            Baboon  ttat----tcatc
            Rhesus  ttat----tcatc
         Orangutan  ttgt----tcatc
             Chimp  ttgt----tcatc
          Bushbaby  ttgt----tcagc
        Tree shrew  -------------
               Rat  -------------
             Mouse  ----------aag
      Kangaroo rat  ttgg----tcagc
        Guinea pig  tggagt--tcagc
            Rabbit  -------------
            Alpaca  tggt----tgaac
           Dolphin  tggt----tcaac
               Cow  tggt----tcaac
             Horse  tggt----tcaac
               Cat  gggc----tcaac
               Dog  gggc----tcaac
          Microbat  tggt----tccac
           Megabat  tggc----tggac
          Hedgehog  tggt----taaac
             Shrew  tggt----tcaac
        Rock hyrax  gggt----ttaac
          Elephant  tggt----tcaac
            Tenrec  tggt----tcaac
         Armadillo  tgat----tcaac
             Sloth  tgat----tcaaa
           Opossum  ----gtagtcata
          Platypus  tact----ttaac
            Lizard  =============
         Zebrafish  =============
           Wallaby  =============
       Stickleback  =============
           Lamprey  =============
            Medaka  =============
           Chicken  =============
       Zebra finch  =============
         Tetraodon  =============
              Pika  NNNNNNNNNNNNN
     X. tropicalis  =============
       Mouse lemur  NNNNNNNNNNNNN

Inserts between block 33 and 34 in window
B D           Rat 393bp
B D        Rabbit 379bp
B D       Opossum 371bp

Alignment block 34 of 46 in window, 57864529 - 57864567, 39 bps 
B D          Human  aagaaaaggtagcacttagagt-aatt-ctggagttgt------------ga--t-
B D          Chimp  aagaaaaggtagcacttagagt-aatt-ctggagttgt------------ga--t-
           Gorilla  aagaaaaggtagcacttagagt-aatt-ctggagttgt------------ga--t-
B D      Orangutan  aagaaaaggtagcacttagagt-aatt-ctggagttgt------------ga--t-
B D         Rhesus  aagaaaaggtagcacttagagt-aatt-ctggagttgt------------aa--t-
B D         Baboon  aagaaaaggtagcacttagagt-aatt-ctggagttgt------------aa--t-
B D       Marmoset  aagaaaaggtagcacttagagt-aa----tgtagttgt------------ga--t-
B D        Tarsier  aagaaaaggtagcatgtagaat-aatt-ctgtagttgt------------ag--t-
          Bushbaby  aagaaagggtagcgctgtgagg-actt-ccatagttgt------------ag--t-
B D     Tree shrew  ----ctaagtaatgcttagaat-ggtt-ttgcagtttt------------ag--t-
B D          Mouse  aaagaaaggtaatacttaaactg---------------------------------
B D   Kangaroo rat  aaggaaatgtagcatttaaaat--gtt-tggtagttaa------------aa--t-
B D     Guinea pig  aagaaagagtaacatttaaaaa--gtt-cagtggctat------------aa--t-
B D         Alpaca  aagagaagat---acttaaaac-agtt-ctatagttgt------------ag--t-
           Dolphin  aagaaaaggtagcacttaaaat-agtt-ctgtagttgt------------ag--t-
B D            Cow  aagaaaaggtagcacttaaaat-agtt-atgtagttgt------------agttt-
B D          Horse  aagaaaaggtagcagttaaaat-agtt-ctgtagttgt------------ag--t-
B D            Cat  aacataaagtaacacttgaaat-agtt-ctgtagttgt------------ag--t-
B D            Dog  aagaaaaggtagcacttgaaat-agtt-ctatagttgt------------ag--t-
          Microbat  aagaaaaggtcgcatttaaagc-aatt-ctgt------------------------
B D        Megabat  aagaaaaggtagcacttaaagt-agtg-ctgtagctgt------------ag--t-
B D       Hedgehog  aagaaagggtatcatttaaaat-catt-ctgttgttct------------ag--t-
B D          Shrew  acgataagatagcatttaaaat-agtt-ctgtagttgt------------ag--t-
B D     Rock hyrax  aagaaaaggtagcacttaaaac-agttgctgtag-tta------------tg--t-
B D       Elephant  aagaaaaggtagtgcttaaaat-agttgctgtagtttg------------ag--c-
B D         Tenrec  aagaaaaggtcgcacataaaat-agct-ctatagttac------------aa--t-
         Armadillo  tagaaaaggtagcacttaaaat-agtt-ctgtagttgt------------ag--t-
B D          Sloth  gagaaaaggtagtacttcaaat-agtt-ctgtggttgg------------ag--t-
B D        Opossum  acacatagaaggcatttaata--agtt-ctgttaactg------------ac--t-
B D       Platypus  aaggaaagagaatactttaaat-agtt-ccctggtctccaaggagctccaag--tt
B D         Lizard  ========================================================
B D      Zebrafish  ========================================================
  D        Wallaby  ========================================================
B D    Stickleback  ========================================================
B D        Lamprey  ========================================================
B D         Medaka  ========================================================
B D        Chicken  ========================================================
B D    Zebra finch  ========================================================
B D      Tetraodon  ========================================================
B D            Rat  ========================================================
B D         Rabbit  ========================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ========================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 34 and 35 in window
B D         Mouse 210bp
         Microbat 126bp
B D       Megabat 135bp

Alignment block 35 of 46 in window, 57864568 - 57864590, 23 bps 
B D          Human  -gtctaagc-----a-----------cacttagca-tgatt-
B D          Chimp  -gtctaagc-----a-----------cacttagca-tgatt-
           Gorilla  -gtctaagc-----a-----------cacttagca-tgatt-
B D      Orangutan  -gtctaagc-----a-----------cacttagca-tgatt-
B D         Rhesus  -gtctaagc-----a-----------cacttagca-tgatt-
B D         Baboon  -gtctaagc-----a-----------cacttagca-tgatt-
B D       Marmoset  -atctaagc-----a-----------cacttaact-tgatt-
B D        Tarsier  -gtctaagc-----t-----------tacttaaca-tgatt-
          Bushbaby  --tctatgt-----a-----------catttagct-tgata-
B D     Tree shrew  -atctaagc-----a-----------cacttagca-tgatt-
B D     Guinea pig  -ttctgagt-----------------cacttaaca-tgatt-
B D   Kangaroo rat  -ttctcagc-----a-----------cacgtagca-tgatt-
B D          Mouse  -tt----ga-----a-----------cactcaacattgact-
B D         Rabbit  -ttttcagc-----aagaaaaggtagcacttagaa-tagtt-
B D         Alpaca  -ttctaagc-----a-----------catttagca-tgatt-
           Dolphin  -ttctaagc-----a-----------cacttagca-tgaat-
B D            Cow  -ttttaagc-----a-----------catgtagca-t-agt-
B D          Horse  -ttctaagt-----a-----------tacttagca-tgatt-
B D            Cat  -ttctaagctacaca-----------cac----ca-t-----
B D            Dog  -ttctaagc-acaca-----------tacttagca-tgttt-
          Microbat  -ctctaaac-----a-----------cacttagca-tgact-
B D        Megabat  -ctctaaac-----a-----------cacttagca-tgatt-
B D       Hedgehog  -ttctaagc-----a-----------tatttagca-tgggt-
B D          Shrew  -ttctaagc-----a-----------ca------------t-
B D     Rock hyrax  -ttctaagc-----a-----------catttaaca-tgatt-
B D       Elephant  -ttctaagc-----a-----------catttagca-tgatt-
B D         Tenrec  -ttcaaagc-----a-----------catttatag-tgatt-
         Armadillo  -ttccaagc-----a-----------cacttagca-tgatt-
B D          Sloth  -ttccagac-----a-----------cacttagca-tgatt-
B D        Opossum  -gattaagc-----a-----------ca--ggaca-ttatt-
B D       Platypus  gttcagaaa-----a-----------aatt---ca-caactt
B D         Lizard  ==========================================
B D      Zebrafish  ==========================================
  D        Wallaby  ==========================================
B D    Stickleback  ==========================================
B D        Lamprey  ==========================================
B D         Medaka  ==========================================
B D        Chicken  ==========================================
B D    Zebra finch  ==========================================
B D      Tetraodon  ==========================================
B D            Rat  ==========================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ==========================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 35 and 36 in window
B D  Kangaroo rat 239bp
B D        Rabbit 35bp
B D           Dog 196bp
B D      Hedgehog 1bp
B D         Shrew 1bp

Alignment block 36 of 46 in window, 57864591 - 57864622, 32 bps 
B D          Human  tata-gtgg---aat-tctt---------------------------cg---------------tg----
B D          Chimp  tata-gtgg---aat-tctt---------------------------cg---------------tg----
           Gorilla  tata-gtgg---aat-tctt---------------------------cg---------------tg----
B D      Orangutan  tata-gtgg---aat-tctt---------------------------ca---------------tg----
B D         Rhesus  tata-gtgg---aat-tctt---------------------------ca---------------tg----
B D         Baboon  tata-gtgg---aat-tctt---------------------------ca---------------tg----
B D       Marmoset  taca-gtgg---aat-tctt---------------------------ca---------------tg----
B D        Tarsier  tata-gtgg---aat-tctt---------------------------ta---------------tg----
          Bushbaby  tagg-gtaa---aag-tctt---------------------------ca---------------tg----
B D     Tree shrew  tatg-gtag---aat-tctt---------------------------ca---------------tgcttg
B D     Guinea pig  tatgtgtag---aat-tctt---------------------------ca---------------tg----
B D          Mouse  t------ag---aat-tttt---------------------------ca---------------tg----
B D         Alpaca  taga-gtgg---aat-tctt---------------------------aa---------------tg----
           Dolphin  tatg-acgg---aat-tctt---------------------------aa---------------ta----
B D            Cow  tatg-gtgg---aat-tctt---------------------------aa---------------tg----
B D          Horse  tatg-gtgg---aat-tctt---------------------------aa---------------tg----
B D            Cat  tatg-gtgg---aat-tcttatgcctcattttaatttactttctcaaaa---------------tg----
B D            Dog  tatt-gtgg---aat-tctt---------------------------aa---------------ta----
          Microbat  tatg-gtgg---aat-tctt---------------------------aa---------------tg----
B D        Megabat  tatg-atgg---aat-tctt---------------------------aa---------------tg----
B D       Hedgehog  tata-gtgg---aat-tttt---------------------------ta---------------ta----
B D          Shrew  tata-gtag---aat-tttt---------------------------aa---------------tg----
B D         Rabbit  -atg-ctgg---aat-tctt---------------------------ca---------------tg----
B D   Kangaroo rat  -atg-atgg---aat-tctt---------------------------ca---------------tg----
B D     Rock hyrax  tatg-gtgg---ttt-tcct---------------------------aa---------------tg----
B D       Elephant  tatg-gtgg---tat-tcgt---------------------------aa---------------tg----
B D         Tenrec  tatg-gtggaatttt-tttt---------------------------aatgatgaaatttttactg----
         Armadillo  tatg-gtgg---aat-tctt---------------------------aa---------------tg----
B D          Sloth  tatg-gtgg---aat-tctt---------------------------aa---------------tg----
B D        Opossum  tatg-ttgg---aag-cctt---------------------------ag---------------tg----
B D       Platypus  aatg-atgg---aatgtttt---------------------------ca---------------tt----
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D      Tetraodon  ======================================================================
B D            Rat  ======================================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  cccc--------------cttttactt
             Chimp  cccc--------------cttttactt
           Gorilla  cccc--------------cttttactt
         Orangutan  cccc--------------cttttactt
            Rhesus  -ccc--------------cttttactt
            Baboon  -ccc--------------cttttactt
          Marmoset  cctc--------------cttttattt
           Tarsier  -ctc--------------cttttattt
          Bushbaby  cctc--------------cct----tt
        Tree shrew  cttt--------------ctttttctc
        Guinea pig  tctc--------------cttttcttt
             Mouse  gctt--------------ctt----tt
            Alpaca  cctc--------------attttactt
           Dolphin  cctc--------------attttattt
               Cow  cctc--------------attttattt
             Horse  cctc-------------------attt
               Cat  cctc--------------attttattt
               Dog  cctc--------------attttattt
          Microbat  cctc--------------attttattt
           Megabat  cctc--------------attttattt
          Hedgehog  ttga--------------tctttattt
             Shrew  ccac--------------tttttcatt
            Rabbit  cttc--------------cttttattt
      Kangaroo rat  cctc--------------cttttgctt
        Rock hyrax  cctc--------------ttt--attt
          Elephant  cctc--------------------ttt
            Tenrec  tctc--------------ttttaattt
         Armadillo  cctc--------------tttttattt
             Sloth  cctc--------------ttctcattt
           Opossum  ttcccaatctaaagaaagcttttatt-
          Platypus  t--------------------------
            Lizard  ===========================
         Zebrafish  ===========================
           Wallaby  ===========================
       Stickleback  ===========================
           Lamprey  ===========================
            Medaka  ===========================
           Chicken  ===========================
       Zebra finch  ===========================
         Tetraodon  ===========================
               Rat  ===========================
              Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNN
     X. tropicalis  ===========================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 36 and 37 in window
B D      Hedgehog 3157bp

Alignment block 37 of 46 in window, 57864623 - 57864658, 36 bps 
B D          Human  gctt-tctctagaa----------gcat-ttac---------------t---------------------
B D          Chimp  gctt-tctctagaa----------gcat-ttac---------------t---------------------
           Gorilla  gctt-tctctagaa----------gcat-ttac---------------t---------------------
B D      Orangutan  gcttctctctagaa----------gcat-ttac---------------t---------------------
B D         Rhesus  gctt-tctctagaa----------gcat-ttac---------------t---------------------
B D         Baboon  gctt-tctctagaa----------gcat-ttac---------------t---------------------
B D       Marmoset  gctt-tctcgggaa----------gcat-ttac---------------t---------------------
B D        Tarsier  gctc-----aggaa----------gctt-ttatattcttaattgtaggt---------------------
          Bushbaby  gtct-tctcagaaa----------gctt-ttac---------------t---------------------
B D     Tree shrew  ctct-tctcaggaa----------gcag-ttac---------------t---------------------
B D          Mouse  gttg-tctcaagaa----------actt-tttc---------------t---------------------
B D   Kangaroo rat  gctt-tctcaagag----------gtat-ttac---------------t---------------------
B D     Guinea pig  gcat-tctagggaa----------gctt-tgac---------------t---------------------
B D         Rabbit  cctt-tctcaggaa----------gcat-ttac---------------t---------------------
B D         Alpaca  gctt-tctcaggaa----------ggtt-ttac---------------t---------------------
           Dolphin  gctt-tctcaggaa----------gatt-tcac---------------t---------------------
B D            Cow  gctt-tctcgggaa----------ggtt-tcac---------------t---------------------
B D          Horse  gttc-tctcaggaa----------actt-ttac---------------t---------------------
B D            Cat  actt-tctcaggaa-----------------ac---------------t---------------------
B D            Dog  gctt-tcccaggaa----------actt-ttac---------------t---------------------
          Microbat  gctt-tctcaggaa----------actt-ttac---------------t---------------------
B D        Megabat  gctt-tctcaggaa----------gctt-ttac---------------t---------------------
B D          Shrew  actt-tctcagaaa----------actt-tttc---------------t---------------------
B D     Rock hyrax  gctg-tctcaggaa----------gctt-ttac---------------t---------------------
B D       Elephant  gctt-tctcaggaa----------gctt-ttac---------------t---------------------
B D         Tenrec  gctt-cctcagaga----------gatt-ttac---------------t---------------------
         Armadillo  gctt-tctcaggaa----------gctt-ttgc---------------t---------------------
B D          Sloth  gctt-tctcaggaa----------gctt-ttgc---------------t---------------------
B D        Opossum  gcat-tttgaagggaagggaacctgcat-ttat---------------taagtgcctactatgtgccatg
B D       Platypus  gttt-tcccaggaa----------gtttaatac---------------t---------------------
B D         Lizard  ======================================================================
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D            Rat  ======================================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  --ttatt----ttgaactct--
             Chimp  --ttatt----ttgaactct--
           Gorilla  --ttatt----ttgaactct--
         Orangutan  --ttatt----ttgaactct--
            Rhesus  --ttatt----ttgaactc---
            Baboon  --ttatt----ttgaactc---
          Marmoset  --ttact----ttgaactgt--
           Tarsier  --ttattttgattgaactct--
          Bushbaby  --ttatt----ctgaacttt--
        Tree shrew  --ttctt----ttgaagtcc--
             Mouse  --taata----ctaaattgt--
      Kangaroo rat  --ctatt----ttgaactct--
        Guinea pig  --ttatt----ctgaattct--
            Rabbit  --ttatt----ttgaactgt--
            Alpaca  --ttatt----ttgaattct--
           Dolphin  --ttatt----ttgaattct--
               Cow  --ttatt----ttgaattct--
             Horse  --ttatt----ttgaactct--
               Cat  --ttatt----ttgaactct--
               Dog  --ttatt----ttgaactct--
          Microbat  --ttatt----t----------
           Megabat  --ttatt----ttgaactcc--
             Shrew  --tt---------gaactct--
        Rock hyrax  --ttact----ttcaactct--
          Elephant  --ttatt----ttgaactct--
            Tenrec  --ttgtt----tttaactct--
         Armadillo  --ttatt----ttgaactct--
             Sloth  --ttatt----ttgaactct--
           Opossum  cactgtg----ctaagcact--
          Platypus  --tggaa----tctaggtcctc
            Lizard  ======================
         Zebrafish  ======================
           Wallaby  ======================
       Stickleback  ======================
           Lamprey  ======================
            Medaka  ======================
           Chicken  ======================
       Zebra finch  ======================
          Hedgehog  ======================
         Tetraodon  ======================
               Rat  ======================
              Pika  NNNNNNNNNNNNNNNNNNNNNN
     X. tropicalis  ======================
       Mouse lemur  NNNNNNNNNNNNNNNNNNNNNN

Inserts between block 37 and 38 in window
B D        Alpaca 3bp
          Dolphin 3bp
B D           Cow 3bp
B D         Horse 3bp
B D           Dog 3bp
         Microbat 232bp
B D       Megabat 1bp
B D    Rock hyrax 4bp
B D      Elephant 1bp
B D        Tenrec 2bp
B D         Sloth 2bp

Alignment block 38 of 46 in window, 57864659 - 57864694, 36 bps 
B D          Human  t---t----------tgccac-c-tcactcgcagactt----taatctttctccc
B D        Opossum  ---ttaaaa-----atattac-c-tcatttgaatacag---ctattatatctcct
B D          Sloth  tccct----------cctcac-c-ccactcccagactt----taatctttcttct
         Armadillo  --cct----------ccccac-c-ccactcccaggctt----taatctttcttct
B D         Tenrec  tccct----------tccagc-ttcttccccaaacttt----aattttttccccc
B D       Elephant  -ctct----------t-aagc-ctcctcccccaggctt----cattctttctcct
B D     Rock hyrax  tctct----------tccagc-ctcctcccccagactt----tagtctttctcc-
B D        Megabat  ---ct----------ccctac-a-ctattcccagacttttattaatctttcttca
          Microbat  ---tt----------cgccac-c-ccactcccagactt---tttatctttctttg
B D            Dog  ---ct----------cggtac-c-tcactcccagactt---ttaatccttatttg
B D          Horse  ---ct----------tgccac-c-tcactcccagactt---ttagtctttattcg
B D            Cow  ---ct----------ctccat-t-ccactcccagactt---ttgatctttcttcc
           Dolphin  ---ct----------tgcccc-t-ccactcccagactt---ttaatctttcttca
B D         Alpaca  ---ct----------tgcctc-t-ccactcccagactt---gtaatctttcttcc
B D         Rabbit  tctct----------taccac-c-ccacacctagcctt----taatcttttctcc
B D     Guinea pig  tctct----------caccac-c-ctactcctgaactt----gagtccttctc--
B D   Kangaroo rat  tctct----------agccac-a-ccgctcccagactt----tactctcatt---
B D          Mouse  ccttt----------ggccactc-ccattcccagattt----gactgtttc----
B D     Tree shrew  tctct----------caccac-c-ccactcccagactt----taatctttct---
          Bushbaby  tcttt----------ctccac-c-ccactcctagtctc----taatctttttcct
B D        Tarsier  tctct----------tgctcc-c-ccactcccaaactt----taatcgttctccc
B D       Marmoset  t---t----------tgccac-c-tcactcacagactt----taaactttctccc
B D      Orangutan  t---t----------tgccac-c-tcactcacagactt----taatctttctccc
           Gorilla  t---t----------tgccac-c-tcactcgcagactt----taatctttctccc
B D          Chimp  t---t----------tgccac-c-tcactcgcagactt----taatctttctccc
B D  X. tropicalis  ----t----------tgtcat-a-tcagtgtca----t----taatcattcc---
B D       Platypus  --------gttgttattccac-t-cttctcccac---------------------
B D          Shrew  --------------------------------tatctc---tcctttctttctct
B D         Baboon  ----t----------tgctac-c-tcaatcacagactt----taatctttctccc
B D         Rhesus  ----t----------tgctac-c-tcactcacagactt----taatctttctccc
B D         Lizard  =======================================================
B D            Cat  -------------------------------------------------------
B D      Zebrafish  =======================================================
  D        Wallaby  =======================================================
B D    Stickleback  =======================================================
B D        Lamprey  =======================================================
B D         Medaka  =======================================================
B D        Chicken  =======================================================
B D    Zebra finch  =======================================================
B D       Hedgehog  =======================================================
B D      Tetraodon  =======================================================
B D            Rat  =======================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 38 and 39 in window
B D       Opossum 4bp
B D         Sloth 1bp
        Armadillo 1bp
B D        Tenrec 1bp
B D      Elephant 1bp
B D    Rock hyrax 1bp
B D       Megabat 1bp
         Microbat 1bp
B D           Dog 1bp
B D         Horse 1bp
B D           Cow 1bp
          Dolphin 1bp
B D        Alpaca 1bp
B D        Rabbit 2bp
B D         Mouse 5bp
B D         Shrew 1bp

Alignment block 39 of 46 in window, 57864695 - 57864716, 22 bps 
B D          Human  tt-ttaatttcttct--attt--cttt
B D          Chimp  tt-ttaatttcttct--attt--cttt
           Gorilla  tt-ttaatttcttct--attt--cttt
B D      Orangutan  tt-ttagtttcttct--attt--cttt
B D         Rhesus  tt-ttaatttcttct--attt--cttt
B D         Baboon  tt-ttaatttcttct--attt--cttt
B D       Marmoset  tt-tcggtttcttct--gttt--cttt
B D        Tarsier  ttctctggcttttct--attt--cttt
          Bushbaby  tt-tctggctcttca--attt--cttt
B D     Tree shrew  tt-tctggcttttct--attt--cttt
B D          Mouse  tt-tctgactcttct--tct-------
B D            Rat  tc-ccggatttgact--ctt-------
B D   Kangaroo rat  tt-tctggcttttct--attt--ctgt
B D     Guinea pig  -t-tttgactttttt--tct-----tt
B D         Rabbit  tt-tctggctcttct--gttt--attt
B D         Alpaca  tt-tcggactcttctctattt--cttt
           Dolphin  tt-tctgactcttctcatttt--cttt
B D            Cow  tt-tccgactcttct--gttt--cttt
B D          Horse  tt-tctgactcttctctgttt--cttt
B D            Dog  tt-tctgagtcttctctattt--cttt
          Microbat  tt-tcttgctcttctctattt--cttt
B D        Megabat  tt-tctgactctt---tattt--catt
B D          Shrew  tc-tctttctttcatctgctg--cttt
B D     Rock hyrax  tt-cctgggtctcct--attt--cttt
B D       Elephant  tt-cctgggtcttct--attt--cttt
B D         Tenrec  tt-agtaggtcttcc--attt--cttt
         Armadillo  tt-tctgggtctttc--gtttttcttt
B D          Sloth  tt-tctgagtctttc---tttgacttt
B D        Opossum  -c-tttgtttatttc--attt--tcta
B D       Platypus  tt-cccagccctcct---ttt--ct--
B D  X. tropicalis  tt-attatttcttct--attt--gcat
B D         Lizard  ===========================
B D            Cat  ---------------------------
B D      Zebrafish  ===========================
  D        Wallaby  ===========================
B D    Stickleback  ===========================
B D        Lamprey  ===========================
B D         Medaka  ===========================
B D        Chicken  ===========================
B D    Zebra finch  ===========================
B D       Hedgehog  ===========================
B D      Tetraodon  ===========================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 39 and 40 in window
B D         Shrew 1123bp
B D       Opossum 3bp

Alignment block 40 of 46 in window, 57864717 - 57864744, 28 bps 
B D          Human  aactcatt-cccata-ttatcaaca----------------------------------a--------gg
B D          Chimp  aactcatt-cccata-ttatcaaca----------------------------------a--------gg
           Gorilla  aactcatt-cccata-ttatcaaca----------------------------------a--------gg
B D      Orangutan  aactcattccccatatttatcaaca---------------------------------------------
B D         Rhesus  aactcatt-cacata-ttatcaaca----------------------------------a--------gg
B D         Baboon  aactcatt-cacata-ttatcaaca----------------------------------a--------gg
B D       Marmoset  aacttatt-ccca-a-ttatcaacaaactgtcaaataggaaattatctaattatcaaata--------gg
B D        Tarsier  gccccttt-gccata-ttatcaact----------------------------------aacctgaccgg
          Bushbaby  aacccatt-ccacta-ttaccacct----------------------------------a----------
B D     Tree shrew  aatccatt-gctata-ttattaact----------------------------------gactacgcagg
B D          Mouse  -attcagt-tgtata-gcattaat------------------------------ggaact--------tg
B D            Rat  -tcttggt-tctctg-gcc------------------------------------gacca--------gg
B D   Kangaroo rat  aactcatt-cctaca-gtg---------------------------------------------------
B D     Guinea pig  aatccatt-cctatg-gtattaact-------------------------taagtgaact--------gg
B D         Rabbit  aactcatt-cctata-attttaac--------------------------taactgaaca--------gg
B D         Alpaca  aacccattgtttata-gtagtatta-----------------------actaactaaaca--------gg
           Dolphin  aacccatt-cttata-gtagtatt--------------------------------aaca--------gg
B D            Cow  aacccatt-cttaga-atggtatt--------------------------------aatg--------gg
B D          Horse  aacccatt-cttata-gtagtatta-----------------------actaaatgaacg----------
B D            Dog  aatctatt-tttata-gtggtatta-----------------------gctaactggac-----------
          Microbat  aacccatt-cttata-a---tagta-----------------------actaactgaatg--------gg
B D        Megabat  aacctatt-cctata-attgtatta-----------------------actaactgaaga--------at
B D     Rock hyrax  aacccttc-cccaga-atattaacc--------------------------gactgggta--------ag
B D       Elephant  aacccttt-cccata-gtatta------------------------------actgagta--------gg
B D         Tenrec  aacccttc-cctgta-atattaact--------------------------gactgatca--------gg
         Armadillo  aatcctac-cctata-gtattaact--------------------------gattgaaca--------gg
B D          Sloth  aacccttc-cctaca-gtcttaact--------------------------gtttgaaca--------ag
B D        Opossum  atcccttt-tctttg-ctcttaact--------------------------atgctgaaa--------ag
B D       Platypus  accttatt-tcctca-tagcgaact---------------------------gttggaca--------ag
B D  X. tropicalis  agcttgtt-atggta-tttctcata-------------------------------------------gg
B D         Lizard  ======================================================================
B D          Shrew  ======================================================================
B D            Cat  ----------------------------------------------------------------------
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  aa-
             Chimp  ga-
           Gorilla  aa-
         Orangutan  ---
            Rhesus  aa-
            Baboon  aa-
          Marmoset  aa-
           Tarsier  aa-
          Bushbaby  ---
        Tree shrew  ga-
             Mouse  aa-
               Rat  aa-
      Kangaroo rat  ---
        Guinea pig  aa-
            Rabbit  ac-
            Alpaca  aa-
           Dolphin  aa-
               Cow  aa-
             Horse  ---
               Dog  ---
          Microbat  ac-
           Megabat  ta-
        Rock hyrax  aa-
          Elephant  aa-
            Tenrec  aa-
         Armadillo  aa-
             Sloth  aa-
           Opossum  aa-
          Platypus  aa-
     X. tropicalis  aaa
            Lizard  ===
             Shrew  ===
               Cat  ---
         Zebrafish  ===
           Wallaby  ===
       Stickleback  ===
           Lamprey  ===
            Medaka  ===
           Chicken  ===
       Zebra finch  ===
          Hedgehog  ===
         Tetraodon  ===
              Pika  NNN
       Mouse lemur  NNN

Inserts between block 40 and 41 in window
B D X. tropicalis 9077bp

Alignment block 41 of 46 in window, 57864745 - 57864786, 42 bps 
B D          Human  agatag--ttgcaa-tgtgatgcaagc-tgtt-aaat--gaatggccag
B D          Chimp  agatag--ttgcaa-tgtgatgcaagc-tgtt-aaat--gaatggccag
           Gorilla  agatag--ttgcaa-tgtgatgcaagc-tgtt---at--gaatggccag
B D      Orangutan  ----ag--ttgcaa-tgtgatgcaagcgtgttcaaat--gaatggctaa
B D         Rhesus  agacag--ttgcaa-tgtgatgcaagc-tgtt-aatt--gaatggtcaa
B D         Baboon  agacag--ttgcaa-tgtgatgcaagc-tgtt-aatt--gaatggtcaa
B D       Marmoset  agatag--ttgcaa-tgtgttgcaagc-ctgt-aaat--gaatggccag
B D        Tarsier  agatag--gtgcaa-c-tgat-caagc-tgct--aat--gaatggccac
          Bushbaby  -----a--ctgaac-aggaat----gc-tgct-gaat--gaattgccac
B D     Tree shrew  agatag--ttgcagctcggatgcaagc-tcct-gaat--gaatggccac
B D          Mouse  agatag--ttgtgg-cttgatgcaagt-ctca-gaat--ggatggtcac
B D            Rat  agttag--tagtga-cttgatgcaagc-tgca-gaat--gcatagccac
B D   Kangaroo rat  ---taa--ttgcaa-cttaatatgtgg-ct----act--gaatggccac
B D     Guinea pig  agataa--ttagaa-tttgatacaagc-tgat-gaat--gaatgagtg-
B D         Rabbit  agatag--t-gcaa-cttgacgcaagc-tg-----ct--gaatggccac
B D         Alpaca  agag----ttgcaa-tttgatgcaagc-tgcc-aagt--gaa-------
           Dolphin  agagag--tcgcaa-tttgattcaaac-tgcc-aaat--aaatggccac
B D            Cow  agagagttttgcag-ttcgacacaaaa-tgcc-gaat--gaatgaccat
B D          Horse  agagag--ttgcaa-cttggtgcaaac-tgct-gcat--gaatgggcac
B D            Dog  -aggag--ttgcag-cttgatgcaagc-tgct-gaat--gaatggccac
          Microbat  aaagag--ctataa-cttgatgcaaat-tatg-gaat--gaatggtctc
B D        Megabat  agagag--ttacaa-cttgatgcaaac-tgct-gaat--gaatggccac
B D     Rock hyrax  agatag--ctgcag-cttgctgtagg--ggct-gact------gaccac
B D       Elephant  agatag--ttgcga-cttgatctaag--tgct-gact------ggccac
B D         Tenrec  agacag--ttgcat-cttgctgcaag-----------------------
         Armadillo  agatag--ctgcaa-cttggtgcaagc-tgct-gaatgtgaatggcaac
B D          Sloth  agatag--ctgcaa-cttgatgcaagc-tgct-gaatgtggaaggccac
B D        Opossum  aaagac--ttgata-tttcatacagcc-cact-gaat--gggtggccac
B D       Platypus  gaatcg--ttgggg-tttg---cagtc-tgcc-gaat--gggtggccat
B D         Lizard  =================================================
B D          Shrew  =================================================
B D            Cat  -------------------------------------------------
B D      Zebrafish  =================================================
  D        Wallaby  =================================================
B D    Stickleback  =================================================
B D        Lamprey  =================================================
B D         Medaka  =================================================
B D        Chicken  =================================================
B D    Zebra finch  =================================================
B D       Hedgehog  =================================================
B D      Tetraodon  =================================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  =================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 42 of 46 in window, 57864787 - 57864812, 26 bps 
B D          Human  t-gggaaac--------ttgtctt----ctc--aa--catac-a
B D          Chimp  t-gggaaac--------ttgtcgt----ctc--aa--cgtac-a
           Gorilla  t-gggaaac--------ttgtctt----ctc--aa--cgtac-a
B D      Orangutan  tagggaaac--------ttgtctt----cct--cacccatac-a
B D         Rhesus  t-gggaaac--------ttgtctt----ctc--ac--catac-a
B D         Baboon  t-gggaaac--------ttgtctt----ctc--ac--catac-a
B D       Marmoset  t-gagaaac--------ttgtctt----ctc--ac--catac-a
B D        Tarsier  t-gggaaat--------ctcactg----ctc--at--tgtgc-a
          Bushbaby  t-gggaaac--------ttgtctg----ctc--ac--tgtgc-a
B D     Tree shrew  c-gtgaaac--------ttgtcta----cta--at--tgtgc-a
B D          Mouse  t-gggaaggaaggctgtctgtctg----ctcctag--tctat--
B D            Rat  t-gggaagg--------ctgtctg----ctcctgg--tatac--
B D   Kangaroo rat  t-ggaaag---------ctatttt----ttc-------------
B D     Guinea pig  t-ggaaac---------ttatctg----ctc--at--tttgc--
B D         Rabbit  t-gagaag------------tctg----ctc--at--tgtgct-
B D         Alpaca  ------------------tgtctg----ttt--gttgtgtgc-a
           Dolphin  t-gggaaac--------ttgtctg----ctc--gt--cgtgc-a
B D            Cow  t-gggaaac--------ttgtctg----ctc--at--tgtgc-a
B D          Horse  t-gggaaac--------ttgtttg----ctc--gt--tgtgc-a
B D            Cat  t-gggaaac--------ttaacta----ctc--at--tgtac-a
B D            Dog  t-aggaaac--------atatcta----ctc--ag--cgtgc-a
          Microbat  t-aggaaa---------ttgtcta----ttc--at--catac-a
B D        Megabat  t-agaaaa---------ttttctg----ctc--at--tgtgc-a
B D     Rock hyrax  t-gagatac--------tggtctg----ctc--ac--tgtgc-a
B D       Elephant  c-gggaaac--------ttgtctg----ctc--ac--tgtgc-a
B D         Tenrec  ---------------------ctt----ctg--ac--tgtgc-a
         Armadillo  t-tggaaac--------ttgtcag----ctc--at--tatac-a
B D          Sloth  t-gggaagc--------ttgtttg----ctc--a----------
B D        Opossum  -caggaaac--------ttgtctg----tac--at--catac-a
B D       Platypus  -caggagac--------ttgtctgcacactc--ac--tgtac-a
B D         Lizard  ============================================
B D          Shrew  ============================================
B D      Zebrafish  ============================================
  D        Wallaby  ============================================
B D    Stickleback  ============================================
B D        Lamprey  ============================================
B D         Medaka  ============================================
B D        Chicken  ============================================
B D    Zebra finch  ============================================
B D       Hedgehog  ============================================
B D      Tetraodon  ============================================
B D           Pika  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D  X. tropicalis  ============================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 42 and 43 in window
B D  Kangaroo rat 1704bp

Alignment block 43 of 46 in window, 57864813 - 57864867, 55 bps 
B D          Human  ttccc--aagtgc-----------a-ttt-ctttt-tacatgcgc--atttctgtatttag-cc-t-tgt
B D          Chimp  ttccc--aagttc-----------a-ttt-ctttt-tacatgcgc--atatctgtatttag-cc-t-tgt
           Gorilla  ttccc--aagttc-----------a-ttt-ctttt-tacatgcgc--atttctgtatttag-cc-t-tgt
B D      Orangutan  ttgccaaaagttc-----------atttt-ctttt-tacatgtgc--atttctgtatttag-cc-tntgt
B D         Rhesus  ttccc--gagttc-----------a-ttt-ctttt-tacatgcac--attactgtatttag-cc-t-tgt
B D         Baboon  ttccc--aagttc-----------a-ttt-ctttt-tacatgcac--attactgtatttag-cc-t-tgt
B D       Marmoset  ttccc--aaattc-----------a-ttt-ctttt-tacatgtgc--atttctgtatttat-cc-t-tgt
B D        Tarsier  ttcct--gagttc-----------a-ttt-atttt-tatatgtga--gtttctgtatttct-cc-t-cat
          Bushbaby  tttct--gaggcc-----------a-ttt-gtttt-tacatgttc--gtttctgtatttag-tc-t-tgt
B D     Tree shrew  ttcct--taatcc-----------a-tttgttttt-tatatgtgc--atttc------taa-cc-t-tgt
B D          Mouse  -tcct--gagtcc-----------t-gct-ctttt-----------------------------------
B D            Rat  -tcct--gagtcc-----------g-ttg-ctttt-c-tgtgtgctagtttatgtgtt------------
B D     Guinea pig  ttcct--gagtcc-----------a-ttt-attgt-cacatgtgc---attttgtatttaa-tc-t-tat
B D         Rabbit  ttctt--gtttcc-----------a-ttt-atttt-c-catgtgc--atttctgcatttac-cg-t-tat
B D           Pika  ttcct--gttttc-----------g-ttt-atgtc-cacgtgtgc--acctctgcattgaa-ca-t-tgg
B D         Alpaca  tcccc--gaatcc-----------g-ttt-gtttt-tacatgttc--atttctatacttaa-cc-a-tgt
           Dolphin  ctcct--gaaccc-----------g-ttt-atttt-tacacgttc--gtttctgtatttaa-cc-a-tgt
B D            Cow  ttcct--aaatcc-----------g-ttt-gttct-tacctgttc--atttctgtatttaa-tc-a-ctt
B D          Horse  ctcct--gaatcc-----------a-ttt-gtttt-tgtgtatgc--atttctgtatttaa-cc-a-tgt
B D            Cat  ttcct--gaatcc-----------a-ttt-gcttt-taaatatgc--atttcagtatttaa-cc-a-tct
B D            Dog  ttcct--aaatct-----------a-ttt-gattt-tacatgggt--gtttctgtatttaa-tc-a-tgt
          Microbat  ttcct--gaatca-----------t-ttt-gtttt-tagttgtgc--atttctgtatt------------
B D        Megabat  ttcct--cagtct-----------g-acg-ttttt-tacatgtgc--atttctatatttaa-cc-a----
B D     Rock hyrax  ttcat--gcatcc-----------a-ttg-gtttt-tacatgtgc--gtgtctgcatg-aa-ccat-ctt
B D       Elephant  ttcct--gaatcc-----------a-ttt-gtttt-tacatgtgc--gtttctgcaat-ag-cc-t-tgt
B D         Tenrec  gtcct--gaatcc-----------a-ttt-gttttctgcatgtat--gtttctgtgtt-aa-cc-a-tgt
         Armadillo  ttcgc--aaagcc-----------g-tgt-gcttt-tacatgtgc--atttctgtaat-taatc-t-tct
B D          Sloth  --------------------------tgt-gtttt-tacatgggc--att------------cc-t-tgt
B D        Opossum  ttcct--gaagtctgacgca-gcta-gtt-gtttc-tacatatgc--atttccatttttaa-cc-c-tgt
B D       Platypus  ttcct--aaagtctgatgcattcgt-tgt-gtttc-tacatgtgc--aattccat-tttaa-cc-c-ttt
B D         Lizard  ======================================================================
B D          Shrew  ======================================================================
B D      Zebrafish  ======================================================================
  D        Wallaby  ======================================================================
B D    Stickleback  ======================================================================
B D        Lamprey  ======================================================================
B D         Medaka  ======================================================================
B D        Chicken  ======================================================================
B D    Zebra finch  ======================================================================
B D       Hedgehog  ======================================================================
B D      Tetraodon  ======================================================================
B D  X. tropicalis  ======================================================================
B D   Kangaroo rat  ======================================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

             Human  c-acctt
             Chimp  c-acctt
           Gorilla  c-acctt
         Orangutan  c-acctt
            Rhesus  c-acctt
            Baboon  c-acctt
          Marmoset  c-acctt
           Tarsier  c-atcct
          Bushbaby  c-atctt
        Tree shrew  c-atctt
             Mouse  -------
               Rat  -------
        Guinea pig  taatctt
            Rabbit  c-atctt
              Pika  c-atctt
            Alpaca  c-atc-t
           Dolphin  c-atc-t
               Cow  c-atc-t
             Horse  c-atc-t
               Cat  c-atc-t
               Dog  c-att-t
          Microbat  c-atc-t
           Megabat  t-atc-t
        Rock hyrax  c-atctt
          Elephant  c-atctt
            Tenrec  g-atctt
         Armadillo  c-ctctt
             Sloth  c-atctt
           Opossum  t-atctt
          Platypus  c-attgt
            Lizard  =======
             Shrew  =======
         Zebrafish  =======
           Wallaby  =======
       Stickleback  =======
           Lamprey  =======
            Medaka  =======
           Chicken  =======
       Zebra finch  =======
          Hedgehog  =======
         Tetraodon  =======
     X. tropicalis  =======
      Kangaroo rat  =======
       Mouse lemur  NNNNNNN

Inserts between block 43 and 44 in window
B D         Mouse 381bp
B D           Rat 655bp

Alignment block 44 of 46 in window, 57864868 - 57864909, 42 bps 
B D          Human  tagctagact----tacttatctaaaaaataaattt--aggctgggca
B D          Chimp  tagctagact----tacttatctaaaaaataaattt--aggctgggca
           Gorilla  tagctagact----tacttatctaaaaaataaattt--aggctgggca
B D      Orangutan  tagctagact-nnntacttatttaaaaaataaattt--aggctgggca
B D         Rhesus  tagctagact----tacttatttaaaaaataaattt--aggccaggca
B D         Baboon  tagctagact----tacttatttaaaaaataaattt--aggccaggca
B D       Marmoset  tagctagact----tactcatttgaaaaataaattt---ggccgggag
B D        Tarsier  tatccagatt--------catttaaaaaataaattt--a---------
          Bushbaby  cagccaga------catttattttaaaaataaattt--aa--------
B D     Tree shrew  caaaaagact----tttttttt--------------------------
B D     Guinea pig  tagtcagact----ta---acttaaa----------------------
B D         Rabbit  caaccagact----tacttatttaagaagtaaattt--ag--------
B D           Pika  caaccagact----tacttatggaaaaagtaaattt--ta--------
B D         Alpaca  cgaccaaact----t--ttattttaaaaataaatttaa----tgaata
           Dolphin  tggccagact----t--ttattttaaaaataaattt------------
B D            Cow  ggggcagact----t--ttattttaaatataaatgtaa----------
B D          Horse  cagccagact----t--ttatttaaaaaataaattt------------
B D            Cat  cagccagact----t--ttctttaaaaagtaaattt------------
B D            Dog  caaccaggct----t--tttttaaaa----------------------
          Microbat  cgg-cagact----t--ttatttaaataattaattt------------
B D        Megabat  cagccagact----t--tcatttaatgaatacattt------------
B D     Rock hyrax  gtgccagacg----gacttactgaaaaagttactgt--ag--------
B D       Elephant  gtgccaggct----gacttattgaaaaaattaattt--ag--------
         Armadillo  gggccagact----tatttacttaaaaaacaaattt--ag--------
B D          Sloth  gggccagatt----tattttctt-aaaaataacttt--ag--------
B D        Opossum  ggaccagaat---gtggtaacttaaaaacagaatct--g-gtggaata
B D       Platypus  aggttaggttgtgctaagaataagagaaatagagtc------------
B D         Lizard  ================================================
B D          Shrew  ================================================
B D      Zebrafish  ================================================
  D        Wallaby  ================================================
B D    Stickleback  ================================================
B D        Lamprey  ================================================
B D         Medaka  ================================================
B D        Chicken  ================================================
B D    Zebra finch  ================================================
B D       Hedgehog  ================================================
B D      Tetraodon  ================================================
B D            Rat  ================================================
B D         Tenrec  ================================================
B D  X. tropicalis  ================================================
B D          Mouse  ================================================
B D   Kangaroo rat  ================================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 44 and 45 in window
         Bushbaby 201bp
B D    Tree shrew 353bp
          Dolphin 23bp
B D           Cow 8bp
B D           Cat 37bp
B D    Rock hyrax 1bp
B D      Elephant 782bp
B D       Opossum 140bp
B D      Platypus 195bp

Alignment block 45 of 46 in window, 57864910 - 57864942, 33 bps 
B D          Human  ca-atggctcacgactgtaatcccagcattttgg
B D          Chimp  ca-atggctcacgactgtaatcccagcattttgg
           Gorilla  ca-attgctcacgcctgtaatcccagcattttgg
B D      Orangutan  cagatggctcacgcctgtaatcccagcattttgg
B D         Rhesus  ca-atggctcacgcctgtaatcccagcactttgg
B D         Baboon  ca-atggctcacgcctgtaatcccagcactttgg
B D       Marmoset  tg-gtggctcatgcccttaatcctagtactttgg
B D         Rabbit  -----gagcc--------------ggcattgtgg
B D           Pika  -----agttcactgttgt------ggcattgcgg
B D         Alpaca  ca--------------------------------
B D          Horse  -a-atg----------------------------
          Microbat  -a-atggccca-----------------------
B D        Megabat  -a-a------a-----------------------
B D         Lizard  ==================================
B D          Shrew  ==================================
B D            Cat  ==================================
B D        Tarsier  ----------------------------------
        Armadillo  ----------------------------------
B D      Zebrafish  ==================================
  D        Wallaby  ==================================
B D    Stickleback  ==================================
B D        Lamprey  ==================================
B D         Medaka  ==================================
B D        Chicken  ==================================
B D    Zebra finch  ==================================
B D       Hedgehog  ==================================
B D      Tetraodon  ==================================
B D        Opossum  ==================================
B D     Tree shrew  ==================================
B D            Rat  ==================================
B D         Tenrec  ==================================
B D       Platypus  ==================================
B D            Dog  ----------------------------------
B D  X. tropicalis  ==================================
B D          Sloth  ----------------------------------
B D     Rock hyrax  ==================================
          Dolphin  ==================================
B D            Cow  ==================================
B D       Elephant  ==================================
B D     Guinea pig  ----------------------------------
B D          Mouse  ==================================
B D   Kangaroo rat  ==================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ==================================

Inserts between block 45 and 46 in window
B D        Rabbit 103bp
B D          Pika 3bp
         Microbat 211bp
B D       Megabat 12bp

Alignment block 46 of 46 in window, 57864943 - 57864971, 29 bps 
B D          Human  ga------ggctgaggcgggtggatcacctgaggt
B D          Horse  -----------------------------------
B D         Alpaca  -----------------------------------
B D           Pika  gaactaccatctgtgatgcttgcgtcctttgtggg
B D       Marmoset  ga------ggctgaggcaggcagatcac--gaggt
B D         Baboon  ga------ggtcaaggcgagtggatcacctgaggt
B D         Rhesus  ga------ggtcaaggcgagtggatcacctgcggt
B D      Orangutan  ga------ggccgaggcgggtggatcacctgaggt
           Gorilla  ga------ggccgaggcgggtggatcacctgaggt
B D          Chimp  ga------ggctgaggcgggtggatcacctgaggt
B D         Lizard  ===================================
B D          Shrew  ===================================
B D            Cat  ===================================
B D        Tarsier  -----------------------------------
        Armadillo  -----------------------------------
B D      Zebrafish  ===================================
  D        Wallaby  ===================================
B D    Stickleback  ===================================
B D        Lamprey  ===================================
B D         Medaka  ===================================
B D        Chicken  ===================================
B D    Zebra finch  ===================================
B D       Hedgehog  ===================================
B D      Tetraodon  ===================================
B D        Opossum  ===================================
B D     Tree shrew  ===================================
B D            Rat  ===================================
         Microbat  ===================================
B D         Tenrec  ===================================
B D         Rabbit  ===================================
B D       Platypus  ===================================
B D            Dog  -----------------------------------
B D  X. tropicalis  ===================================
B D          Sloth  -----------------------------------
B D     Rock hyrax  ===================================
          Dolphin  ===================================
B D            Cow  ===================================
B D       Elephant  ===================================
B D     Guinea pig  -----------------------------------
B D          Mouse  ===================================
B D   Kangaroo rat  ===================================
B D    Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
         Bushbaby  ===================================
B D        Megabat  ===================================

View table schema

Go to Cons 46-Way track controls

Data last updated at UCSC: 2009-08-31

Description

This track shows multiple alignments of 46 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all species (vertebrate) and two subsets (primate and placental mammal). The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters for each species set (vertebrates, placental mammals, and primates). Thus, in regions in which only primates appear in the alignment, all three sets of scores will be the same, but in regions in which additional species are available, the mammalian and/or vertebrate scores may differ from the primate scores. The alternative plots help to identify sequences that are under different evolutionary pressures in, say, primates and non-primates, or mammals and non-mammals.

The species aligned for this track include the reptile, amphibian, bird, and fish clades, as well as marsupial, monotreme (platypus), and placental mammals. Compared to the previous 44-vertebrate alignment (hg18), this track includes 2 new species and 5 species with updated sequence assemblies (Table 1). The new species consist of two assemblies: baboon (papHam1) at 5.3X coverage and wallaby (macEug1) at 2X coverage. The elephant, opossum, rabbit, tetraodon, and zebrafish assemblies have been updated from those used in the previous 44-species alignment.

UCSC has repeatmasked and aligned the low-coverage genome assemblies, and provides the seque