Multiz Alignments of 35 Vertebrates
 

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Alignment block 1 of 344 in window, 56741761 - 56741771, 11 bps 
B D                 Mouse  gtc-----ctgtgctc--
B D                   Rat  gtc-----ttgtgttc--
            GCF_003668045  -tc-----ctgcgctc--
                   Beaver  gtt-----ctgcgctc--
B D            Guinea pig  gtt-----ctgggcaa--
B D                Rabbit  gtc-----c----ctg--
B D                 Human  gct-----gtgcgc----
B D                 Chimp  gct-----gtgcgc----
B D                Bonobo  gct-----gtgcgc----
B D               Gorilla  gct-----gtgcgc----
B D                Rhesus  gcg-----gtgcgt----
B D              Marmoset  gca-----gtgccc----
B D               Tarsier  gctcgcgcgcgcgc----
B D              Bushbaby  gct-----gtgcgc----
B D            Tree shrew  gcc-----gtgcgc----
B D  Malayan flying lemur  gcc---ttgagcgc----
B D                   Pig  ------------------
B D               Dolphin  ------------------
B D                 Sheep  ------------------
B D                 Horse  ------------------
B D      Chinese pangolin  ------------------
B D                   Dog  ------------------
B D    Hawaiian monk seal  ------------------
B D              Hedgehog  ------------------
B D                 Shrew  ------------------
B D              Elephant  gcg-----gtgcga--tc
B D                Tenrec  gta-----ttgtgc--tt
B D                  Pika  ==================
B D             Zebrafish  ==================
B D         X. tropicalis  ==================
B D                   Cow  ==================
B D               Opossum  ==================
B D               Chicken  ==================
B D              Squirrel  ==================

Inserts between block 1 and 2 in window
B D                Human 1bp
B D                Chimp 1bp
B D               Bonobo 1bp
B D              Gorilla 1bp
B D               Rhesus 1bp
B D             Marmoset 1bp
B D              Tarsier 1bp
B D             Bushbaby 1bp
B D           Tree shrew 2bp
B D Malayan flying lemur 24bp

Alignment block 2 of 344 in window, 56741772 - 56741811, 40 bps 
B D                 Mouse  ctctttagt--------ct--ggttttttaatttttttttcctcactgca
B D                   Rat  ---tttagt--------ct--gcttttcaaagttctt---ccttccagca
            GCF_003668045  -cctttagt--------cttggagtttaaaaattctc------cacaact
                   Beaver  -tctttggc--------cgc-gtgtgattaaattctc----cgctcacgt
B D            Guinea pig  --cttcaac--------cgcaggtgcctgagtttccc---cggcacagga
B D                Rabbit  -ccttgagc--------cc--g----------------------------
B D                 Human  agcgttagc--------cgc-ctgtggttcagttccc----cgcacacgg
B D                 Chimp  agcgttagc--------cgc-ctgtggttcagttccc----cgcacacgg
B D                Bonobo  agcgttagc--------cgc-ctgtggttcagttccc----cgcacacgg
B D               Gorilla  agcgttagc--------cgc-ctgtggttcagttccc----cgcacacgc
B D                Rhesus  cgcgttagc--------cgc-ctgtggttcagttccc----tgcacacgg
B D              Marmoset  cgcgttagc--------ctc-ctgtggttcagttccc----ggcacacgg
B D               Tarsier  cgcgctagc--------ggc-gtgtggttaagttccc----ggcacagcg
B D              Bushbaby  cgcgttagc--------ggt-gcgtggctccattctc----cgcatgctg
B D            Tree shrew  -gctttcgc--------tgc-gtgtggttactttctc----cgcacaccg
B D                   Pig  gacattggct------gtgc--cttgctttag------------------
B D               Dolphin  gacgttg----------tgc-gcttgctttag------------------
B D                 Sheep  gaagttggct------ttgc-gctcgctgtag------------------
B D                 Horse  cgctttggc--------cgc-gtgtggttacactctc----tgca-----
B D      Chinese pangolin  cgcattagc--------cat-gtgtggttatgttctt----tgca-----
B D                   Dog  ------------------------tgcttaacttctc----cgcg-----
B D    Hawaiian monk seal  agctttagc--------cgc-gtgtgcttaagttctc----cgca-----
B D              Hedgehog  cgctttagccggctgaa----aataactttaagtaac----ttaa-----
B D                 Shrew  caccttcgaccgcttggtgc-actagcttttagccac----tcaa-----
B D              Elephant  ------------------gc-ttgtagttaagttctc----ggtaca---
B D                Tenrec  ------------------gc-ttgtagttaatttctg----ggtaca---
B D                  Pika  ==================================================
B D             Zebrafish  ==================================================
B D         X. tropicalis  ==================================================
B D                   Cow  ==================================================
B D               Opossum  ==================================================
B D               Chicken  ==================================================
B D              Squirrel  ==================================================
B D  Malayan flying lemur  ==================================================

Inserts between block 2 and 3 in window
B D                  Pig 17bp
B D              Dolphin 18bp
B D                Sheep 13bp
B D               Tenrec 5bp

Alignment block 3 of 344 in window, 56741812 - 56741812, 1 bps 
B D                 Mouse  c
B D                   Rat  t
            GCF_003668045  g
                   Beaver  t
B D              Squirrel  c
B D            Guinea pig  t
B D                Rabbit  t
B D                 Human  c
B D                 Chimp  c
B D                Bonobo  c
B D               Gorilla  c
B D                Rhesus  c
B D              Marmoset  c
B D               Tarsier  c
B D              Bushbaby  t
B D            Tree shrew  c
B D                 Horse  c
B D      Chinese pangolin  c
B D                   Dog  a
B D    Hawaiian monk seal  t
B D              Hedgehog  a
B D                 Shrew  g
B D                Tenrec  c
B D                 Sheep  =
B D                  Pika  =
B D             Zebrafish  =
B D         X. tropicalis  =
B D                   Cow  =
B D               Opossum  =
B D               Chicken  =
B D              Elephant  -
B D                   Pig  =
B D               Dolphin  =
B D  Malayan flying lemur  =

Inserts between block 3 and 4 in window
B D                Horse 5bp
B D     Chinese pangolin 5bp
B D                  Dog 7bp
B D   Hawaiian monk seal 7bp
B D             Hedgehog 22bp
B D                Shrew 24bp

Alignment block 4 of 344 in window, 56741813 - 56741815, 3 bps 
B D                 Mouse  ctg
B D                   Rat  ccg
            GCF_003668045  gcg
                   Beaver  gcg
B D              Squirrel  gag
B D            Guinea pig  gcg
B D                Rabbit  atg
B D                 Human  gtg
B D                 Chimp  gtg
B D                Bonobo  gtg
B D               Gorilla  gag
B D                Rhesus  gtg
B D              Marmoset  gtg
B D               Tarsier  gtg
B D              Bushbaby  gtg
B D            Tree shrew  gca
B D                   Cow  ggc
B D                 Sheep  --c
B D                 Horse  gtg
B D      Chinese pangolin  gcg
B D                   Dog  gcg
B D    Hawaiian monk seal  gcg
B D              Hedgehog  tga
B D                 Shrew  cct
B D                Tenrec  atg
B D                  Pika  ===
B D             Zebrafish  ===
B D         X. tropicalis  ===
B D               Opossum  ===
B D               Chicken  ===
B D              Elephant  ---
B D                   Pig  ===
B D               Dolphin  ===
B D  Malayan flying lemur  ===

Inserts between block 4 and 5 in window
B D           Tree shrew 5bp

Alignment block 5 of 344 in window, 56741816 - 56741874, 59 bps 
B D                 Mouse  gcct-ctgctaggatcctg---------------cttgact---gag--------gtttag-cc------
B D                   Rat  gctt-ctgcgaggatcctg---------------cttggcc---aag--------gtttag-cc------
            GCF_003668045  gtcc-cagccagcatcctg---------------cttgact---gag--------gtttag-cc------
                   Beaver  cttc-ttgcctggaacctg---------------tgtgact---gag--------ggctgg-cc------
B D              Squirrel  atct-ctgcttggagcccaagttgacactgcgctcctggat---gagttcagtgtgctaag-tc------
B D            Guinea pig  gcctcctgcctagatcctg---------------cgttgct---aag--------cgctgg-ct------
B D                Rabbit  gcct-cagcttgga-caag---------------cctggc----aag--------gggcgg-ccgcgcca
B D                 Human  gccc-gtgcctcgagcctg---------------tgtggct---agt--------ggttgg-cc------
B D                 Chimp  gccc-gtgcctcgagcctg---------------tgtggct---agt--------ggttgg-cc------
B D                Bonobo  gccc-gtgcctcgagcctg---------------tgtggct---agt--------ggttgg-cc------
B D               Gorilla  gccc-gtgcctcgagcctg---------------tgtggct---agt--------ggttgg-cc------
B D                Rhesus  gccc-ctgcctcgagcctg---------------tgtggct---agt--------ggttag-cc------
B D              Marmoset  gccc-ctaccttgagcctg---------------cgtggct---agt--------ggttgg-cc------
B D               Tarsier  gctc-gtgcctcgggcctg---------------cgtggct---agg--------ggttgg-cc------
B D              Bushbaby  accc--cgccctcagcctg---------------agtggcta--agg--------ggctgg-ct------
B D            Tree shrew  gcta-ctgcctcgagcctg---------------ctcgact---aag--------ggttgaccc------
B D  Malayan flying lemur  gccc-ctgccccaaggctg---------------cgtgcct---gag--------ggttggccc------
B D                   Pig  ----------------cta------------------ggct---atg--------gtttga-cc------
B D               Dolphin  -----ctgcttggagtcta------------------ggct---agg--------gtttta-cc------
B D                   Cow  ctcc-atctctggctcct--------------------gct---cgt--------gtttag-tc------
B D                 Sheep  gttc-ctgcttggagccta------------------ggct---aat--------gtttga-cc------
B D                 Horse  gccc-gcgcgtcgaggatg---------------cgtggct---aag--------ctttgg-ct------
B D      Chinese pangolin  gtca-ctacctggagcctg---------------cgtggct---aac--------gtttgg-ct------
B D                   Dog  gcca-cagcctggagcctg---------------cgtggct---agg--------gtttgc-ct------
B D    Hawaiian monk seal  gcca-catcctggagtctg---------------cgtggct---aag--------gtttgg-cc------
B D              Hedgehog  gccc-ctgcctggaccgtg---------------agctgct---ggg--------gtttgg-gc------
B D                 Shrew  ggcc-ctgctgggagccca---------------aggggct---atg--------gttt-g-ac------
B D              Elephant  -----------ttagcctg---------------cttggc----gag--------ggttcg-cc------
B D                Tenrec  gtcc-ctgccttgaacctg---------------cgtggctggtgag--------g--------------
B D                  Pika  ======================================================================
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  -cctc------------------actgct--ggac----------------ta------------ac-c-
                      Rat  -tctc------------------acgggg--gcac----------------ta------------ac-c-
            GCF_003668045  -tctg------------------acggag--agac----------------ta------------at-c-
                   Beaver  -ctgc------------------gctcct--ggac----------------ta------------at-c-
                 Squirrel  ----a------------------gccgca--agag----------------gg------------gc-c-
               Guinea pig  --tgc------------------gctcca--ggac----------------tg------------gc-c-
                   Rabbit  gaccc------------------gcagcc--agag----------------gg------------gt-c-
                    Human  --ggt------------------ccacct--ggac----------------tg--------gggggt-c-
                    Chimp  --ggt------------------ccacct--ggac----------------tg--------gggggt-c-
                   Bonobo  --ggt------------------ccacct--ggac----------------tg--------gggggt-c-
                  Gorilla  --ggt------------------ccacct--ggac----------------tg--------gggggt-c-
                   Rhesus  --ggt------------------ccacct--gtac----------------cg--------gggggc-c-
                 Marmoset  --agt------------------ccacctgggggg----------------tg--------gggggc-t-
                  Tarsier  --cgc------------------gctcct--ggac-----------------------------------
                 Bushbaby  --ggc------------------gctccc--agacgagcccacggtgggggcg--------gggggg-c-
               Tree shrew  --cac------------------gatcct--agacgagcccaa--------tg--------gaggga-c-
     Malayan flying lemur  --caa------------------gctcct--ggacgatcccac--------ggg---gcctgggggg-g-
                      Pig  -cgccctcttcgcctcccctgcagctcct--ggat----------------ga------------ac-t-
                  Dolphin  -ccgt------------------gctcct--ggat----------------ga------------ac-t-
                      Cow  -gctc-----------------agtttcg--tgtc----------------cg------------ac-t-
                    Sheep  -ccgc------------------gttcct--ggat----------------ga------------ac-t-
                    Horse  -ccac------------------gctcct--gcat----------------ga------------ac-c-
         Chinese pangolin  -ccac------------------gctcct--agat----------------ga------------acac-
                      Dog  -ccgc------------------gctctc--gaat----------------ga------------ac-c-
       Hawaiian monk seal  -ccgc------------------gctcct--ggat----------------ga------------ac-c-
                 Hedgehog  -ctga------------------gcttct--ggat----------------ga------------gt-c-
                    Shrew  -ccga------------------gtcttt--gatt----------------aa------------at-ca
                 Elephant  -ctga------------------gctccc--ggat----------------gaacttagtggggggc-c-
                   Tenrec  -ttgc------------------gctctc--agat----------------gcacctactgggggac-c-
                     Pika  ======================================================================
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ---act-t
                      Rat  ---att-t
            GCF_003668045  ---atc-t
                   Beaver  ---att--
                 Squirrel  ---tcc-t
               Guinea pig  ---act-g
                   Rabbit  ---tcc-c
                    Human  ---gcc-g
                    Chimp  ---gcc-g
                   Bonobo  ---gcc-g
                  Gorilla  ---gcc-g
                   Rhesus  ---acc-g
                 Marmoset  ---gcc-g
                  Tarsier  --------
                 Bushbaby  ---gcc-g
               Tree shrew  ---gcc-g
     Malayan flying lemur  ---gcg-g
                      Pig  ---ccc--
                  Dolphin  ---ccc--
                      Cow  ---ctt--
                    Sheep  ---ctc--
                    Horse  ---ccct-
         Chinese pangolin  ---aaca-
                      Dog  ---cacc-
       Hawaiian monk seal  ---tacc-
                 Hedgehog  --------
                    Shrew  tct-----
                 Elephant  ---gcc-g
                   Tenrec  ---aca-g
                     Pika  ========
                Zebrafish  ========
            X. tropicalis  ========
                  Opossum  ========
                  Chicken  ========

Inserts between block 5 and 6 in window
B D                  Pig 23bp
B D              Dolphin 28bp
B D                  Cow 2bp
B D                Sheep 247bp
B D                Horse 27bp
B D     Chinese pangolin 27bp
B D                  Dog 30bp
B D   Hawaiian monk seal 35bp
B D             Hedgehog 11bp
B D                Shrew 15bp

Alignment block 6 of 344 in window, 56741875 - 56741983, 109 bps 
B D                 Mouse  cg-g-g---------------------------------cgg--ggtacgggaaggag-t---ctct---
B D                   Rat  cg-g-t---------------------------------cgg--ggtacgggaaggag-t---atcc---
            GCF_003668045  ca-g-g---------------------------------cag--ggtacaggaacggg-t---ctcc---
                   Beaver  ----------------------------------------gg--gacccgcggacggt-t---ctct---
B D              Squirrel  tg-g-c---------------------------------ctt--aacac--------------ctctggc
B D            Guinea pig  ga-g-gtccgcgcgaagctggctatagagtggacctccttgg--gcctcagtgggcgt-c---atcc---
B D                Rabbit  gg-g-c---------------------------------cgg--aacaacgg-------------cc---
B D                 Human  ca-g-g---------------------------------aagctggcggtaggaggaa-c---ctcc---
B D                 Chimp  ca-g-g---------------------------------aagctggcggtaggaggaa-c---ctcc---
B D                Bonobo  ca-g-g---------------------------------aagctggcggtaggaggaa-c---ctcc---
B D               Gorilla  ca-g-g---------------------------------aagctggcggtaggaggaa-c---ctcc---
B D                Rhesus  ca-g-g---------------------------------aagttggcggtaggaggaa-c---ctcc---
B D              Marmoset  cg-g-g---------------------------------aagctggcggtaggaggag-c---ctcc---
B D               Tarsier  -----g---------------------------------agcccactggaaggacgag-cccactcc---
B D              Bushbaby  cg-g-g---------------------------------aaacctgcggctgcaggac-c-ggcctc---
B D            Tree shrew  ca-g-g---------------------------------aagtccgattccggagggg-c---ctct---
B D  Malayan flying lemur  ga-g-g---------------------------------gggt-cgccgcgggacggg------tct---
B D                   Pig  cg-g-g---------------------------------tgg--------ggaagg--------------
B D               Dolphin  ag-g-c---------------------------------cgg--------gggagagg-t---ctcc-ac
B D                   Cow  cg-a-c---------------------------------c------------------------------
B D                 Horse  gg-g-g---------------------------------cag--------gagagggg-t---ctcc-ac
B D      Chinese pangolin  gg-g-c---------------------------------agg--------gggaagaa-t---ctcc-at
B D                   Dog  gg-g-g---------------------------------cag--------cagagggg-t---ctcc-ac
B D    Hawaiian monk seal  gg-a-g---------------------------------cag--------gagagggg-t---ctcc-ac
B D              Hedgehog  ggta-c---------------------------------ccg--------ggaatggg-t---ctcc-tc
B D                 Shrew  g--a-a---------------------------------tgg--------ggaaggggct---ctct-ac
B D              Elephant  cg-g-g---------------------------------aagccgagcgcaggagggc-c---cct----
B D                Tenrec  tg-gag---------------------------------aagccactgcccggacatc-c---cccc---
B D                 Sheep  ======================================================================
B D                  Pika  ======================================================================
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  -tgtcctt--------------------------------ac--a-------------------------
                      Rat  -tgtcctt--------------------------------ac--a-------------------------
            GCF_003668045  ttgtcctta-------------------------------ac--a-------------------------
                   Beaver  ttgtcttta-------------------------------ac--a-------------------------
                 Squirrel  tcggcctc--------------------------------ac--a-------------------------
               Guinea pig  tgggccttc-------------------------------gc--a-------------------------
                   Rabbit  ----------------------------------------gc--g-------------------------
                    Human  ctggccttaaca---------------------gtggccccc--a-------------------------
                    Chimp  ctggccttaaca---------------------gtggccccc--a-------------------------
                   Bonobo  ctggccttaaca---------------------gtggccccc--a-------------------------
                  Gorilla  ctggccttaaca---------------------gtggccccc--a-------------------------
                   Rhesus  ctgaccttaaca---------------------gtggccccc--a-------------------------
                 Marmoset  ctggccttaaca---------------------gtggccctc--a-------------------------
                  Tarsier  ctggccttaaca---------------------gtggctccc--a-------------------------
                 Bushbaby  cccactttaaca---------------------acagccccc--c-------------------------
               Tree shrew  ctggccttaata---------------------gtggtcccc--a-------------------------
     Malayan flying lemur  ctggccttagca---------------------gcagccccc--a-------------------------
                      Pig  -----------------------gtccagt---gttcccccc--a----tccccaccctgggtaacaacg
                  Dolphin  ctggtggaaacaaaggcctccatttctggcttggtctcgcct--aattctcctcgtc-------------
                      Cow  -----------------------ctttggctaggtctcccct--a----ttctcatc-------------
                    Horse  ctggcggtaaca---------------------gtggcctcc--a-------------------------
         Chinese pangolin  ccggaggtaaca---------------------gggtcctcc--a-------------------------
                      Dog  ctggcggtcaca---------------------gtggcctcc--a-------------------------
       Hawaiian monk seal  ctggcggtcaca---------------------gtggcctcc--a-------------------------
                 Hedgehog  ctgacgacaaca---------------------gtggtctcc--a-------------------------
                    Shrew  ctagctgttaca---------------------at-gcatcc--a-------------------------
                 Elephant  --------------------------------------------g-------------------------
                   Tenrec  ---------------------------------tccgcccccaag-------------------------
                    Sheep  ======================================================================
                     Pika  ======================================================================
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  -------cctcaag---cgcc-----------------tcctc--------cact---------------
                      Rat  -------ccccaaggagagtc-----------------tccta--------c------------------
            GCF_003668045  -------cctcaag---cttt-----------------tctcc--------ctttgcctctggtctttct
                   Beaver  -------cctcgagatcggtc-----------------tcacc--------g--------caacctcctg
                 Squirrel  -------gctacccactggtc-----------------tctct--------g------------------
               Guinea pig  -------cctctggcccggcc-----------------tctgc--------t--------cagcctcctg
                   Rabbit  -------cctctggctcggcc-----------------tgccc--------g--------caagctccag
                    Human  -------cctgtggctcgggc-----------------tcccc--------g--------caacctcctg
                    Chimp  -------cctgtggctcgggc-----------------tcccc--------g--------caacctcctg
                   Bonobo  -------cctgtggctcgggc-----------------tcccc--------g--------caacctcctg
                  Gorilla  -------cctgtggctcgggc-----------------tcccc--------g--------c-acctcctg
                   Rhesus  -------cctgttgcttgggc-----------------tcccc--------g--------caacgtcctg
                 Marmoset  -------cctgtggctcgggc-----------------tcccc--------g--------taacctcctg
                  Tarsier  -------cct---gatcggcc-----------------tctcc--------g--------aaa---cctg
                 Bushbaby  -------accttggctctgct-----------------gccag--------g--------ccacctccag
               Tree shrew  -------cttctagtttggca----------------gaccct--------g---------aacctc-tg
     Malayan flying lemur  -------cttctagctcgac------------------ctcct--------g--------caacctcgtc
                      Pig  gcctccatctctggcttggctttccttatttctcctcctttctcccacgagc----------------ct
                  Dolphin  -------tctccgacggg---------------------------------c----------------ct
                      Cow  -------tctccaacggg---------------------------------c----------------ct
                    Horse  -------tctctggctgggtctcccctaaacctcctcgtccctc-------c--------gagggggcct
         Chinese pangolin  -------cctgtggctccgtctcccctaaacctccttgcctct--------c--------gggcaggcct
                      Dog  -------cctctggctcggtctccccttaacctcctggtctct--------c--------ggatcggcct
       Hawaiian monk seal  -------cctgtggctcggcctcccattaacctcctggtctct--------c--------cgatcggcct
                 Hedgehog  -------cctctgg----------------------------t--------t--------ctatttcctc
                    Shrew  -------tctatgact------------------ctttacccc--------c--------caaactcctc
                 Elephant  -------cctctggttcggactccccgtgacctccgcatctct--------c--------ca--------
                   Tenrec  -------cttctggttctgcctcctgacgtcctccaggtctgt--------c--------c---------
                    Sheep  ======================================================================
                     Pika  ======================================================================
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  -----------------------------------cgacttc-tccccatcctgagtgaactggaag---
                      Rat  --------------------------------------cctt-tccccatcctttgtgaactgaaag---
            GCF_003668045  gtctctctgatcggcctatctt------------ctgagctc-tcctcatcctgagtggactgaaag---
                   Beaver  gtctgtctaaccaacctcccttcttaca-----cctacgctc-ccgccacctggagtgggctgaaag---
                 Squirrel  ---------acccacctaccttctcaca-----cctacgttc-ttgccacctggagtagtctggaat---
               Guinea pig  gtctctcccactggcccacctttccata-----tctgcgcgc-tcctcacttggagtagactgaaaa---
                   Rabbit  gtctccgcgaccggcctaccttctcaca-----cctgcgcgc-tcgcagcctaacgcgccctgaagg---
                    Human  gtttctttggccggcctatcttctcaca-----cctgcgctc-tcgccacctggcatggactgaagt---
                    Chimp  gtttctttggccggcctatcttctcaca-----cctgcgctc-tcgccacctggcatggactgaagt---
                   Bonobo  gtttctttggccggcctatcttctcaca-----cctgcgctc-tcgccacctggcatggactgaagt---
                  Gorilla  gtttctttggccggcctatcttctcaca-----cctgcgctc-tcgccacctggcatggactgaagt---
                   Rhesus  gtttctctggccggcctaccttctcaca-----cctgcgctc-tcgccacctggcatggactgaagt---
                 Marmoset  gtttctctggcgggcctaccttctcaca-----cctgcgctc-tctccacctggcatggattgaagt---
                  Tarsier  gtctctctgaccggcctaccttctcaca-----cctgcgctc-ttgccacctggagtggaccgaaga---
                 Bushbaby  gtttcttcggcccgccagccttcttaca-----cctgcgcttgtcaccagcccggattgacgcgacg---
               Tree shrew  gtctctccaatgggcctactttctcaca-----cctg-------------------tggactgaagt---
     Malayan flying lemur  gtctctccaatgggcctaccttctcaca-----cctgtgctc-tcgccacctggcatgaactgaagt---
                      Pig  acctt-----------------ctcaca-----cctacccgc-tggccacc---agtaagctggagt---
                  Dolphin  acctt-----------------ctcaca-----cctgggctc-tggccacctggcgtaggctggagc---
                      Cow  acctt-----------------ctcaca-----cctgcgctc-tggtctctcggcgtaggatgtagt---
                    Horse  acctt-----------------ctcatg-----tctgcgctc-tcgccacctggc-taggctggagt---
         Chinese pangolin  acctt-----------------ctcatacctgttctgcgctc-ttgtcgtctgacggagggtggagt---
                      Dog  accga-----------------ct--ca-----cctgcgctc-tagctacctagcataggctggagt---
       Hawaiian monk seal  accgt-----------------ctcaca-----cctgagctc-tcgccacctggcataggctggagtgag
                 Hedgehog  gtctggaagaaaggcctaccttcttact-----cctgcgctc-ttggcacc-----tggtttggagt---
                    Shrew  acctc-----------tcccttcttaca-----cctgc---c-ctagtcaa-----cgggctggaca---
                 Elephant  ---------gtgggcctacctgtttaca-----cctgcgctc-tcaccacctggcgtggactggcat---
                   Tenrec  ---------gtgggcctaccttgttaca-----cctgcgatc-tcaccacctggcgtggactgaagt---
                    Sheep  ======================================================================
                     Pika  ======================================================================
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  gagatagaatttgtggacaaga
                      Rat  gaggtagaatttgtggacaaga
            GCF_003668045  g-ggtagaatttgtagggaaga
                   Beaver  a-agtagaattggtgggtcaca
                 Squirrel  gaggtggaatcggtgggtaaca
               Guinea pig  gaagtaa---ctgaggtcccca
                   Rabbit  gaggtggaaccagcgggtgacc
                    Human  gaggtagaatcggcaggtgaca
                    Chimp  gaggtagaatcggcaggtgaca
                   Bonobo  gaggtagaatcggcaggtgaca
                  Gorilla  gaggtagaatcggcaggtgaca
                   Rhesus  gaggtagaatcggcaggtgaca
                 Marmoset  taggtagaatcggcaggtgaca
                  Tarsier  gaggtagaatgggcgggtgaca
                 Bushbaby  tagatagaatcttcgggcgacc
               Tree shrew  gaggtggaatcggctggtgaca
     Malayan flying lemur  aaggaagaatctgtgggtgac-
                      Pig  gtggtagtgtccgctggtgaca
                  Dolphin  gcggtaggacccgccggtaaca
                      Cow  gctgtaagatccgctggtaaca
                    Horse  gaggtaggatgggccggcaaca
         Chinese pangolin  gaggtaagatcggcccggaaca
                      Dog  gaggtatcatcctcctgtaata
       Hawaiian monk seal  gaggtatcatcccccggtaata
                 Hedgehog  gaagtggcataggtgggtgact
                    Shrew  gaggtagtacagtagcactgta
                 Elephant  ggggtaggatcggccggtgata
                   Tenrec  ggggtaggatcagccggtgctg
                    Sheep  ======================
                     Pika  ======================
                Zebrafish  ======================
            X. tropicalis  ======================
                  Opossum  ======================
                  Chicken  ======================

Inserts between block 6 and 7 in window
                  Beaver 9bp
B D             Squirrel 9bp
B D               Rabbit 12bp
B D                Human 9bp
B D                Chimp 9bp
B D               Bonobo 9bp
B D              Gorilla 9bp
B D               Rhesus 9bp
B D             Marmoset 9bp
B D              Tarsier 9bp
B D             Bushbaby 6bp
B D           Tree shrew 8bp
B D Malayan flying lemur 8bp
B D                  Pig 9bp
B D              Dolphin 9bp
B D                  Cow 9bp
B D                Horse 9bp
B D     Chinese pangolin 8bp
B D                  Dog 9bp
B D   Hawaiian monk seal 9bp
B D             Hedgehog 9bp
B D                Shrew 9bp
B D             Elephant 9bp
B D               Tenrec 12bp

Alignment block 7 of 344 in window, 56741984 - 56742076, 93 bps 
B D                 Mouse  ttc----tgacag-tcccc-aaaggtcagcatgacaggt----agt--tctcagtcatcc----------
B D                   Rat  ttc----tgacag-tcccc-aaaggtcagcatgccagat----agt--tctcagtcatcc----------
            GCF_003668045  ttctttttgacag-tcccc-aaaggtcagcattgcagga----agt--tctcagtcatct----------
                   Beaver  ttc----tgacag-ccctt-aaagaccagtatgacaggt----aat--tctaagacagct----------
B D              Squirrel  tcc----tgacag-ccccc-aaagtcctgcatggtcggt----tat--tctaagactccc----------
B D            Guinea pig  -ct----tgacgc-ctcct-gaaggcccacagggcaggt----tattatttaaaataccc----------
B D                Rabbit  tcc----tgacag-ccctt-ggaggcctgcgggaccggc----cat--tctgagacgccc----------
B D                 Human  tcc----tgacag-tcccc-agaggcccgcatgacagat----ttt--gctaagacaact----------
B D                 Chimp  tcc----tgacag-tcccc-agaggcccgcatgacagat----ttt--gctaagacaact----------
B D                Bonobo  tcc----tgacag-tcccc-agaggcccgcatgacagat----ttt--gctaagacaact----------
B D               Gorilla  tcc----tgacag-tcccc-agaggcccgcatgacagat----ttt--gctaagacaact----------
B D                Rhesus  tcc----tgacag-tcccc-agaggcccgcatgacagat----ttt--gctaagacaact----------
B D              Marmoset  t----------------cc-ggtggccctctcgacagat----ttt--gctaagacaact----------
B D               Tarsier  tcc----tgatag-tcccc-ggaggcctgcctggcaggt----aat--gctaagacagcc----------
B D              Bushbaby  tct----tggcgg-ctggc-ggaggcctgcacgacagat----tat--gctaagac--ct----------
B D            Tree shrew  tcc----tgacag-aaccc--gaggcctgcaggtcaggg----tat--tctaag--cacc----------
B D  Malayan flying lemur  tct----tgacag-cccct-agaagcctgcatgacgggt----cat--tctaag----------------
B D                   Pig  tcc----tgacag-cctag-cgaggcttgcacggcaggctatttat--tctaagaaccct----------
B D               Dolphin  tcc----tgatat-cccct-cgaggcttacaggacaggc----tat--tctaagaacgct----------
B D                   Cow  tct----tgacaa-cctct-tgaagcttgcctgacaggc----tat--tctaagaaccct----------
B D                 Sheep  tct----tgacaa-cctct-tgaagcttgcatgacaggc----tat--tctaagaaccct----------
B D                 Horse  tcc----ttgcagcccccc-ggagccctgcaggacagac----tat--tctaagaagccc----------
B D      Chinese pangolin  --c----tgacag-cccct-ggaggcctgtgtgacaggc----tat--tctgagaactcc----------
B D                   Dog  tcc----ggacag-cccca-ggaggcccgcaggaccggc----tat--tctaagaatacc----------
B D    Hawaiian monk seal  tcc----aggcag-cccct-ggaggcctgcatgacaggc----tat--tctaagaagcac----------
B D              Hedgehog  acc----tgccag-tccct-ggagaccttcatgatgagt----tat--tttaacacacatacacacacac
B D                 Shrew  tcc----cgacag-tccat-ggaggcctcagtga---------tac--attaagacactt----------
B D              Elephant  tcc----tgacag-cctcttggaagctcgtatgacaggg----tgt--cctaaga---------------
B D                Tenrec  ttc----tgacaa-cctgtaggaggcctgcatgacaggt----cat--tctaagg---------------
B D                  Pika  ======================================================================
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  ---------------------------------------------------c-------------tta--
                      Rat  -------------------t---------------catgcccaggagctccc-------------ttg--
            GCF_003668045  -------------------t---------------cacgtcccggagctccc-------------tca--
                   Beaver  -------------------t---------------catcctccccgcccggg-------------taa--
                 Squirrel  -------------------c---------------catcctt---------g-------------taa--
               Guinea pig  -------------------c---------------cacctat---------g-------------tat--
                   Rabbit  -------------------c---------------cagccca---------g-------------tca--
                    Human  -------------------ccc-----t-------cacccct---------g-------------tgc--
                    Chimp  -------------------ccc-----t-------cacccct---------g-------------tgc--
                   Bonobo  -------------------ccc-----t-------cacccct---------g-------------tgc--
                  Gorilla  -------------------ccc-----t-------cacccct---------g-------------tgc--
                   Rhesus  -------------------ccc-----t-------cacccct---------g-------------tgc--
                 Marmoset  -------------------ccc-------------caccccc---------g-------------tgc--
                  Tarsier  -------------------tcc-----tctggccccatctcc---------g-------------tga--
                 Bushbaby  -------------------cgt-----g-------tccccca---------g-------------tag--
               Tree shrew  -------------------tct-----c-------caccccc---------a-------------ggtaa
     Malayan flying lemur  ---------------------------a-------caacctg---------a-------------gac-a
                      Pig  -------------------ca------c-------caccacc---------a-------------atg--
                  Dolphin  -------------------caccatcac-------caccatc---------a-------------aag--
                      Cow  -------------------caccatggc-------caccatc---------a-------------aag--
                    Sheep  -------------------caccatggc-------caccatc---------a-------------aag--
                    Horse  ------------------------------------ccttcc---------a-------------atg--
         Chinese pangolin  -------------------c-------c-------acccccc---------a-------------ttg--
                      Dog  -------------------c-------c-------ccccccc---------cgacacacacacacctg--
       Hawaiian monk seal  -------------------c-------c-------ccctccc---------c----------cacccg--
                 Hedgehog  acacacacacactcacacgcgccacgac-------caccccc---------g-------------aag--
                    Shrew  ---------------------cgacttc-------catctgc---------a-------------agg--
                 Elephant  -------------------c-------c-------agtatct---------t-------------aac--
                   Tenrec  -------------------c-------c-------catctca---------g-------------aac--
                     Pika  ======================================================================
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  agggtcgtgcc--acttgttctctg--agagctctaacctccaac
                      Rat  atggtcgtgccc-gctggctacctt--agagccctaacctgtaat
            GCF_003668045  actgtcgttctc-acttgctacctt--agagtcctagactccaat
                   Beaver  acagtggcccct-gcctcccacct---acagtatt-------aac
                 Squirrel  acagtgctgc---gcttcccacct---agagtctt-------aac
               Guinea pig  actgcggcgcc--cccctccaccc---ataatttaagc----atc
                   Rabbit  acggcggcgcc---cctgccacct---ggagccct-------aac
                    Human  acggtggcgccc-gcctcccacct---atagcctt-------aac
                    Chimp  acggtggcgccc-gcctcccacct---atagcctt-------aac
                   Bonobo  acggtggcgccc-gcctcccacct---atagcctt-------aac
                  Gorilla  acggtggcgccc-gcctcccacct---atagtctt-------aac
                   Rhesus  acggtggcg-cc-gcctcccacct---atagtctt-------aac
                 Marmoset  accgtggcgccc-gcctcccactt---agggtttt-------aac
                  Tarsier  acggtggcgccc-gcctcccacct---agagtctt-------aac
                 Bushbaby  acggtggctccc-gcctcccaccc---agattctt-------aac
               Tree shrew  acagcggcacttaaattcccatct---agagtctt-------aat
     Malayan flying lemur  acggtggcgccc-acctcccacct---agagtctt-------aac
                      Pig  acggtggcgctc-accttccatct---agagtttt-------aac
                  Dolphin  acggtggcgctc-acctccagc-----agaactca-------agc
                      Cow  acggtggcgctc-acctcccacct---agagtttt-------aac
                    Sheep  acggtggcgctc-acctcccacct---agagtttt-------aac
                    Horse  acggtggcgccc-acctcccaccc---agagtttt-------aac
         Chinese pangolin  tcggtggcgccc-actttccacct---agagtttt-------aac
                      Dog  acggtggccccc-acctctcacct---agagttct-------acc
       Hawaiian monk seal  acggtgaccccc-acctcccacct---agagtttt-------aac
                 Hedgehog  acggtggtatcc-accttccacttacaagagtttt-------aac
                    Shrew  acagtggcggtc-atttctcacct---agagcttt-------aac
                 Elephant  cggttggcgccc-acctcccacct---agattctt-------aac
                   Tenrec  cagttggcgtcc-acttcccacct---ggagtctt-------aac
                     Pika  =============================================
                Zebrafish  =============================================
            X. tropicalis  =============================================
                  Opossum  =============================================
                  Chicken  =============================================

Alignment block 8 of 344 in window, 56742077 - 56742137, 61 bps 
B D                 Mouse  tttaattt-gacaaattcatct---------------cttc--cccaaaag------gtgt----cc---
B D                   Rat  ttcatttttgacaagtccatct---------------cttc--cccaagag------gtgt----cc---
            GCF_003668045  ttcaattctgagagctccatct---------------cttc--cccaagtg------gtgt----cc---
                   Beaver  ttcaactcggagaaatccatcg---------------cttc-gccaaagag------gtct----cc---
B D              Squirrel  ttccattctgaggtgttcaacg---------------ttcccacctagggg------gtct----cc---
B D            Guinea pig  attaatta-gatagccctattt---------------cttc---gcaagaa------gtct----cc---
B D                Rabbit  tccgcttctgaggggtcggtcg---------------ttcc--ctcaaaga------ggaa----ccggg
B D                 Human  ttcaattctgagatgtccatcg---------------ttcc-ccggaggag------gtct----cc---
B D                 Chimp  ttcaattctgagatgtccatcg---------------ttcc-ccggaggag------gtct----cc---
B D                Bonobo  ttcaattctgagatgtccatcg---------------ttcc-ccggaggag------gtct----cc---
B D               Gorilla  ttcaattctgagatgtccatcg---------------ttcc-ccggaggag------gtct----cc---
B D                Rhesus  ttcaattctgagacgtccatcg---------------ttcc-ctagaggag------gtct----cc---
B D              Marmoset  ttcaattctgagacgtccatcg---------------ttcc-cctgaggag------gtct----cc---
B D               Tarsier  ttcacttttgagatgtccatcg---------------ttct-tccaaggag------gtct----cc---
B D              Bushbaby  tttaaagttgagacggccgtcc---------------ttcc-cccaaggagaagtccatct----cc---
B D            Tree shrew  ttgaattctgaga-------cg---------------ttcc-tccaaagag------gtct----tc---
B D  Malayan flying lemur  ttcaattctgagacatcccccg---------------ttcc-cccaaagag------gtct----cc---
B D                   Pig  ttaaattctgagatgtctgtat---------------ttca-cccaaagaa------gtct----tc---
B D               Dolphin  ctctttcatcggggcacagact---------------tcct-ttta--------------c----tc---
B D                   Cow  ttaaattctgagatgtctgcct---------------tccc-cccagagaa------gcct----tc---
B D                 Sheep  ttaaattctgagatgtctgcct---------------tccc-ctcaaataa------cttt----tc---
B D                 Horse  ttcagttctgagatgtccgttcctccccccccccccccccc-cccccataa------gtct----cc---
B D      Chinese pangolin  tttaattctgagacgtcttt-----------------ctat-cgcaaacag------atct----tt---
B D                   Dog  ttcagttcggaggcgtctgttcc--------------cccc-tcccgccaa------gttt----cc---
B D    Hawaiian monk seal  ttaaattctgaggcgtctgtttt--------------cccc-tccccccaa------gtct----cc---
B D              Hedgehog  ttctattcctagacg-ctgtcttt-------------agct-cccccaaat------atct----ct---
B D                 Shrew  ttcaatttctaggcgtctgtcagt-------------ccct-ctttctccg------ttcc----cc---
B D              Elephant  ttcaatcctgagacgtctgtca---------------tctc-cgtaaaagg------gtct----cc---
B D                Tenrec  ttcaatccagagacgtcagtca---------------ctct-ctgaaaaag------gtctggggga---
B D               Opossum  tttgaccc-aacataattgttt---------------cctt-c--------------tctt----cc---
B D                  Pika  ======================================================================
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  tc----ggt-c-tc---------------tacccacttaaagt
                      Rat  tc----ggt-c-tc---------------tacccacttaaagt
            GCF_003668045  tc--ggggt-c-cc---------------tacccgcttaaagt
                   Beaver  tt----ggt-cacc---------------tccccacttagagt
                 Squirrel  tc----ggt-c-tc---------------tatcccctcctagt
               Guinea pig  tccctcagc-c-cc---------------taccctctttgagt
                   Rabbit  tctttgggc-c-cc---------------gtcccgtttggagt
                    Human  tc---gggc-c-cc---------------ttctcccttcgagt
                    Chimp  tc---gggc-c-cc---------------ttcccccttcgagt
                   Bonobo  tc---gggc-c-cc---------------ttctcccttcgagt
                  Gorilla  tc---gggc-c-cc---------------ttctcccttcgagt
                   Rhesus  ta---gggc-c-cc---------------ttctcccttcgagt
                 Marmoset  tc---gggt-c-cc---------------ttctcccttcgaat
                  Tarsier  tc----ggc-c-cc---------------ttccccctccgagt
                 Bushbaby  tt-----cc-c-cc---------------tttcctcttcgagt
               Tree shrew  tc----agc-c--c---------------cttccccctcgagt
     Malayan flying lemur  tc----ggc-c-gc---------------tttccccttcgagt
                      Pig  tc----agt-c-cc---------------ttcccctttggagt
                  Dolphin  ct----tcc-c-cc---------------ttctcccttcgagt
                      Cow  tc----ggc-c-cc---------------ttctcccttcaagt
                    Sheep  tc----ggc-c-cc---------------ttctcccttcgagt
                    Horse  tc----ggtcc-cc---------------ttcccccttcgagt
         Chinese pangolin  tt----agt-c-ct---------------ttcccccttcgagt
                      Dog  tc----aac-t-cc---------------ttcctccttag---
       Hawaiian monk seal  tc----aac-t-cc---------------ttcccccttagagt
                 Hedgehog  tc----agc-c-cc--------------atccctctccacagt
                    Shrew  tt----cgc-c-ctccaaatctcaggaggtttctctttagtgt
                 Elephant  ta----gtc-c-cc---------------ttcccctctggagt
                   Tenrec  gg----gga-g-gc---------------ttccccctcggagt
                  Opossum  tt----gtt-c-cc---------------tttccccataatct
                     Pika  ===========================================
                Zebrafish  ===========================================
            X. tropicalis  ===========================================
                  Chicken  ===========================================

Alignment block 9 of 344 in window, 56742138 - 56742195, 58 bps 
B D                 Mouse  tattcaaaccgagaccaaa-gcttctgt----t-cgcttattcagcatttttatcagcttgatt
B D                   Rat  cattcaaaccaagaccaaa-gcttccgt----t-tgcttattcagcatttttatcagcttgatt
            GCF_003668045  ctctcaaacccagaccaaa----------------gcttattcagcgtttttaccagcttaatt
                   Beaver  tactcatattcagaccaaacgcttttat----t-cgcttattcatcacttttaccagcctgata
B D              Squirrel  cattcatattcagaccaaaagctttcat----t-tgcttattcagcatttttagcagcctgat-
B D            Guinea pig  tactcatattcagaccaaccgctttcct----t-tgctaattcagcattttaaccagacttatt
B D                Rabbit  cactcgcattggggccacacactttcat----g-tgcttattcagcatttttaccggcccaatt
B D                  Pika  tgctcgcactcagaccgaaagcctccga----gttgctggctcagcacttgcgccggcctcacg
B D                 Human  cattcacattcagaccaaacgctttcat----t-tgtttattcagca-ttttaccagcctgatt
B D                 Chimp  cattcatatgcagaccaaacgctttcat----t-tgtttattcagca-ttttaccagcctgatt
B D                Bonobo  cattcatatgcagaccaaacgctttcat----t-tgtttattcagca-ttttaccagcctgatt
B D               Gorilla  cattcatattcagaccaaacgctttcat----t-tgtttattcagca-ttttaccagcctgatt
B D                Rhesus  cattcatattcagaacaaacgctttcat----t-tgtttattcagca-ttttaccagcctgatt
B D              Marmoset  cattcatactcagataagactctttcat----t-tgtttattcagca-ttttaccagcctgatt
B D               Tarsier  cactcatatccaaaccgaacgctttcat----g-tgtttattcagcatttttaccggcctgatt
B D              Bushbaby  cacccatattcagactaaccgctttcat----t-tgtttattcagcatttttaccagcctgatt
B D            Tree shrew  ca----------gaccaaacgctttcatttgct-tgcttattcagcatttttactagcttgatt
B D  Malayan flying lemur  cactcatattctgaccaaacattttcat----t-tgcttattcagcgtttttaccagcctggtt
B D                   Pig  ctctcaaattcagaccaaatgctttcat----t-tgcttattcagca--tttaacagcttgatt
B D               Dolphin  ctttcatattcagaccaaacgctttcat----t-tgcttattcagcatttttaacagcctgact
B D                   Cow  ctctcgtattcagaccaaaagctttcgt----t-tgcttattcagcatttttaagagcctgatt
B D                 Sheep  ctctcgtattcagaccaaaagctttcga----t-tgcttattcagcatttttaagagcccgatt
B D                 Horse  atctcataagcggaccaaacgctttcat----t-tgcttattcagcatttttatgagcctgatt
B D      Chinese pangolin  ccctcatattacgaccaaaggcttcctt----t-tgcttattcagcatttttatcagcctgatt
B D                   Dog  ----tctattcagactaaacgctttcat----t-tgcttattcagcatttttatcagcctgatt
B D    Hawaiian monk seal  ctctcatattccgaccaaatgatttcat----t-tgcttattcagcatttttatcagcttgatt
B D              Hedgehog  ctctcaaatttggatccaaggatgtcat----t-tgcttattcagca-ttttctcagcctgatt
B D                 Shrew  ctctcatattcggaccgacagattccat----t-tgcttattcagca-ttttatcagcctgatt
B D              Elephant  cagtcatattcggaccgaacgctctcat----t-tgcttactcagcatttttaccagtctgatt
B D                Tenrec  cactc----tcagactaaacgctctcat----t-tgcttattcagcattttcaccagtctcatt
B D               Opossum  ------------ggtttaatattttaat----t-tgactattcaatatatattttgttttgatt
B D             Zebrafish  ================================================================
B D         X. tropicalis  ================================================================
B D               Chicken  ================================================================

Alignment block 10 of 344 in window, 56742196 - 56742508, 313 bps 
B D                 Mouse  ttgcactctgtttgcg--gcgcccct--gggaagacgtc-aaacactct--tattc-at-----tg-tat
B D                   Rat  ttgtgat--gtttgag--gcgccctt--gggaagacgtc-aaacactcc--tattc-at-----tg-tat
            GCF_003668045  ttgcact--gtttgtg--gcgcccccgagggaagatgtc-aaacactca--taatc-at-----tg-tat
                   Beaver  ttgttgtctgtttgtg--ccgcccct--gggaagatgtc-aaataccca--tattc-at-----ta-ttt
B D              Squirrel  ttgctttctgcttgtg--cctccccccccccaagatgtc-aaataccca--ttttc-at-----tc-tat
B D            Guinea pig  tggttgtgtatttgcg--ccggtcct--gggaagatgtc-aaacacccg--ttttc-tt-----tg-tat
B D                Rabbit  ttgttgtctgtctgtg--cggccc----gggaggatgtc-aaaccccca--ttttc-ct-----tg-tgt
B D                  Pika  ctgctgtctgtgtgtg--ccgccccgg-ggagggacgtc-cgacacccattttttc-ct-----gg-tgt
B D                 Human  ttgctgtctttttgtg--ccgcttct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D                 Chimp  ttgctgtctttttgtg--ccgcttct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D                Bonobo  ttgctgtctttttgtg--ccgcttct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D               Gorilla  ttgctgtctttttgtg--ccgcttct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D                Rhesus  ttgctgtctttttgtg--cctcttct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D              Marmoset  ttgctgtctttttgtg--tcgcttct--gggaagatgtc-aaacaccca--ttttc-gt-----gg-tat
B D               Tarsier  ctgctgtc----tgtg--ccgcttct--gcgaagacgtc-aaacaccca--ttttt-at-----tg-tat
B D              Bushbaby  ttgctgtctgtttgtg--tggctcct--gggatgatgtc-aaacaccca--ttttc-at-----tg-tat
B D            Tree shrew  ttgctgtctgtttgtg--ctgcccct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D  Malayan flying lemur  tcgctgtctgtttgtg--ccgcccct--gggaagatgtc-aaacacctc--ttttc-attgtactg-tat
B D                   Pig  ttgctgtctgtttgcg--ctgcccct--gggaaggtgtc-aaacaccct--ttttc-gt-----tg-cat
B D               Dolphin  ttgctgtctgtttgcg--ctgcccct--gggaaggtgtc-aaacacctc--ttttc-at-----tg-tat
B D                   Cow  ttg----ctgtttgcg--ctgcccct--gggaaggtgtc-aaacacctc--ttttc-at-----tg-tat
B D                 Sheep  ttg----ctgtttgcg--ctgcccct--gggaaggtgtc-aaacacctc--ttttc-at-----tg-tat
B D                 Horse  ttgctgtctgtttgtg--ctgcccct--gggaaggtgtc-aaacaccca--ttttc-at-----tg-tat
B D      Chinese pangolin  ctgctgtctgtttgcg--ctgcctct--gggaaggtgtc-aaacaccca--ttttc-at-----tg-tat
B D                   Dog  ttgttgtctgtttgcg--ctgccgcc--ggaaaggtgtc-aaacatcca--ttttc-at-----tg-tat
B D    Hawaiian monk seal  ttgttgtctgtttgcg--ctgcccct--aggaaggtgtcaaaacaccca--ttttc-at-----tg-tat
B D              Hedgehog  ttgctgcctgtttgcg--ctgccccc--gggaaggtgtc-aaacaccta--tttttgat-----tg-tct
B D                 Shrew  tttccgtctgtttgca--ctgcccct--tggaaggtgtc-aaatgccca--ttttcaat-----tg-tat
B D              Elephant  ttgcagtctgtctacg--ctgccctt--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D                Tenrec  ttgctgtctgtttacg--ctgctcct--gggaagatgtc-aaacaccca--ttttc-at-----tg-tat
B D               Opossum  tt----------tgag--ttccaatt--gggctgatgtt-aaatattca--tttcc-at-----tgttat
B D               Chicken  ttgctctttgcgtgcggcttaccgcc--tggcaggtatt-acgcgggcg--ttgct-gt-----tg-tgg
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================

                    Mouse  tt-agtcacccaggtgcggagccagccagaaacagacggcggaaggagtttccc-ggactgagctgtcac
                      Rat  tt-agtcacccaggtgcggagccagccagaaacagacggcggaaggagtttccccggactgagctgccac
            GCF_003668045  tt-agtcacccaggtgcggagccggcctg----agacagcggaaggagtttcccagaactgagctgtcac
                   Beaver  tt-agtcacccaggtgcggagccagcctgcaaaagacagcggaaggagtttccc-ggactgcggtgtcac
                 Squirrel  tt-agtcacccaggtgcggagccagcctgaaaaagacagcggaaggagtttccc-ggaccgcgctgtcac
               Guinea pig  tt-agtcatccaggtgcggagccagcctgaaaaagacagcggaaggaattttcc-ggactgcgctgccgc
                   Rabbit  tc--gtcactcaggtgcggagacggaccgagagagacagcggaaggagtttccc-gggctgtgccgtcgc
                     Pika  cccagtcacccaggtgcggagacgg-tcgcaggagacggcggaaggagttttccggggccgcgctgtcgc
                    Human  tt-agtcacccaggtggggagctagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtcgc
                    Chimp  tt-agtcacccaggtggggagctagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtcgc
                   Bonobo  tt-agtcacccaggtggggagctagcctgaaagagacagcggaaggagtttccc-ggactgcgctgtcgc
                  Gorilla  tt-agtcacccaggtggggagctagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtcgc
                   Rhesus  tt-agtcacccaggtggggagccagcctgaaagagacagcggaaggagtttcct-ggactgcgctgtagc
                 Marmoset  tt-agtcacccaggtggggggccagcctgaaagagatagcggaaggagtttcct-ggactgccctgccgc
                  Tarsier  tt-agtcacccaggtggggagccagcctgagagagacggcggaaggagtttcct-ggactgcgctgtcgc
                 Bushbaby  tt-agtcacccaggtggggagccagcccgaaagggacggcggaaggagtttccc-ggactgcgctgtcgc
               Tree shrew  tt-agtcacccaggtgcggagcaagcctga--gagacagcggaaggagttgccc-ggattgggctgtcgc
     Malayan flying lemur  tt-agtcactcaggtgcggagccagcctgaaggagacagcggaaggagtttctc-gaactgcgctgtcgc
                      Pig  tt-agtcacccaggtgcagagcacgattgaaagagacagcggaaggactttccc-agactgtgctgtcgt
                  Dolphin  tt-agtcacccaggtgctgagcaagattgaaagagacagcggaaggactttccc-ggactgtgctgtcgc
                      Cow  tt-agtcacccaggtgcagagcgagattgagagagacagcggaagaactttccc-ggactgtgctgtcac
                    Sheep  tt-agtcacccaggtgcagagcgagattgaaagagacagcggaagaactttccc-ggactgtgctgtcgc
                    Horse  tt-agtcacccaggtgccgagcaggcttgaaagagtcagcggaaggac-ttacc-ggaccgcactgtcgc
         Chinese pangolin  tt-agtcacccaggtgcggatcaatcttgaaagagacagcggaaggactttccc-ggactgcgttgtcgc
                      Dog  tt-agtcacccaggtgcagagcaagcttgaaagagacagcggaagaactttccc-ggactgcactgtcgc
       Hawaiian monk seal  tt-agtcacccaggtgcagagcaagcttgaaagagacagcggaaggactttccc-ggactgcactgtcgc
                 Hedgehog  tt-agtcacccaggtgcggggagagcctgccaaggacggcggaaggactttccc-cgacttcgctgtcgc
                    Shrew  tt-agtcactcaggtgcggagccagcctgaaagagacagcggaaggactttccc-ggactacagtgtcgc
                 Elephant  tt-agtcacccaggtgcagagcaagtctgaaagagacaacggaaggagcttccc-ggacagcgctgtcgc
                   Tenrec  tt-agtcacccaggtgcagagcaa-tctgaaagagacaacggaaggagtttccc-ggcctgcgctgtcgc
                  Opossum  tt-agtaatccaggtgcggagctctcctaaaagagagaacggaaggagttaccg-ggattatactgtctg
                  Chicken  ta-gg--gaccaggtgctgagcacgtccgcgagaggcagcggaaag-gccgccg-gccccgcgctgtccg
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  tcaccg-gcctgcaccaattacaacgcagattgctcgcgggcccacctcttt-tgg-ggtgtgtcacaag
                      Rat  tcaccg-gcctgcaccaattacaacgcagattgcccgcgggcccacctcttt-tgg-ggtgtgtcacaag
            GCF_003668045  tcaccg-gcctgcaccaattacaacgcagattgccctcgggcccacctcttt-tgg-ggtgtgtcacaag
                   Beaver  tcaccg-gctcgcaccaatcaccacgcagtttgccctcgggcccgcctcttt-ggg-ggtgtgtccttaa
                 Squirrel  tcaccg-aacgacaccaatcatcacgcagcttgccctcggaccctcctcttt-ggg-ggtgtgcccttag
               Guinea pig  tcacag-gcctgcaccaatcaccaagcagttcgccctcgggcccgcctcttt-agg-ggtgtgtccctag
                   Rabbit  tcaccg-tcgggcgccaatcaacacgcagttttctctcgggcccgcctcttt-ggggggcgtgtccctag
                     Pika  tcaccg-gcctgcaccaatcaacacgcggcgtgctgccgggcccgcctcttg-gggaggcgtgtcccccg
                    Human  tcaccg-acccgcaccaatcaccatgcagcttgccctcggacccgccccttt-tag-ggcgtgtccccag
                    Chimp  tcaccg-acccgcaccaatcaccatgcagcttgccctcggacccgccccttt-tag-ggcgtgtccccag
                   Bonobo  tcaccg-acccgcaccaatcaccatgcagcttgccctcggacccgccccttt-tag-ggcgtgtccccag
                  Gorilla  tcaccg-acccgcaccaatcaccatgcagcttgccctcggacccgccccttt-tag-ggcgtgtccccag
                   Rhesus  tcaccg-acccgcaccaatcaccacgcagcttgccctcggacccgccccttt-tag-ggcgtgtccccag
                 Marmoset  tcaccg-gcccgtaccaatcaccacgcagctcgccctcaggcccgcctcttt-gag-ggcgtgtccccag
                  Tarsier  tcagcg-gcccgcaccaaccaccacgcagcttgtcctcgggcccgcctcttt-ggg-ggcgtgtccacag
                 Bushbaby  tctccg-gatcgcaccaatcaacacgcagcttgcgcttgggcccgcctcttt-ggg-ggcgcgtctctag
               Tree shrew  tcacga-ccctgctccaatcactacgctgcttgccctcaggcccgcctcttt-ggg-ggcgtgtccctag
     Malayan flying lemur  tcacgg-ggccgcaccaatcagcacgcagtttgccctcgggtccgcctcttt-aga-ggcgtgtccctag
                      Pig  tcagca-gactacaccaatcaccacgcagcttcctctcgggcccgcctctttgggg-ggcgtgtccctag
                  Dolphin  tcaacg-gaccaaaccaatcagcatgcagcttgccttcgggccctcctcttt--gg-ggcgtgtccctag
                      Cow  tcaacg-ggccaaaccaatcatcacgcaggttgcctccgggccctcctcttt-ggg-ggcgtgcccctag
                    Sheep  tcaacg-ggccaaaccaatcatcacgcaggttgcctccgggccctcctcttt-ggg-ggcgtccccctag
                    Horse  tcactg-gcccgcaccaatcaccacgctgcttgtcctcggaccctcctcttt-ggg-ggcgtgaccctaa
         Chinese pangolin  tcagcg-gaaagcaccaatcaccacgcagcttgccctcggaccctcctcttt-ggg-ggcgtgtccctag
                      Dog  tcagca-gcccgcaccaatcaccacgcagcttgacctcgggccctcctcttt-gag-ggcgtgtccctgg
       Hawaiian monk seal  tcagcg-gcccgcaccaatcaccacgcagcttgacctcgggccctcctcttt-gag-ggcgtgtccccag
                 Hedgehog  tcagcgcggccacaccaatcaccgcacggctggccctcggaccctcctctccgggg-ggcgtgtcgctcg
                    Shrew  tcagca-ggtcacaccaatcggcgcacagtgtgccccagggccctcctcttt-gtg-ggcgtgtccctag
                 Elephant  tcaacg-actctcaccaatcgcagcacagagtgccctcgggcccgcctcttt-ggg-ggcgtgtccctag
                   Tenrec  tcaacg-gctcgtccctatcagcgcgcagattgccctggggcccgcctcttt-ggg-ggcgtgtccctag
                  Opossum  ttacca-tctacagccaatctcaaagtcttcttctttgagtcccgcctcctt-ggg-ggtgggccactag
                  Chicken  tcatct-cccgcggccactggcggggctgcagggccgccgggccgccccc---ggg-ggcggg---ctcg
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  tgagtgatagactgagccgcccggccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                      Rat  tgagtgatagactgagccgcccggccctacacagcccagcccacgttgctgc-ttagattgaaatgcaga
            GCF_003668045  tgagtgatagactgagccgcccggccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                   Beaver  tgagtgatagacggagccgcccggccttgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                 Squirrel  tgagtgatagacggagccgcccggccctactcagcccagcccacgttactgc-ttagattgaaatgcaga
               Guinea pig  tgagtgatagacagagcctcccggcccagctcagcccagcccacgttgctgc-tgagattgaaatgcaga
                   Rabbit  tgagtgatagacggagccgcccggccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                     Pika  tgagtgatagacggagccgcccggccctgctcagcccagcccacgccgctgc-ttagattgaaatgcaga
                    Human  tgagtgatagacggagccgccctgccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                    Chimp  tgagtgatagacggagccgccctgccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                   Bonobo  tgagtgatagacggagccgccctgccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                  Gorilla  tgagtgatagacggagccgccctgccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                   Rhesus  tgagtgatagactgagccgcccggccccgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                 Marmoset  tgagtgatagacggagccgcccggccctgctcagcccagcccacgttgcagc-ttagattgaaatgcaga
                  Tarsier  tgagtgatagacggagccgcccggccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                 Bushbaby  tgagtgatagactgagccgcccggccctgctcagcccagcccacgttgctgc-ttggattgaaatgcaga
               Tree shrew  tgagtgatagacggagccgcccggcccagatcagcccagcccacgttgctgc-ttagattgaaatgcaga
     Malayan flying lemur  tgagtgatagacggagccgcccggccctgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                      Pig  tgagtgatagacggagccgcccgg-cccgttcagcccagcccacgttgctgc-ttagattgaaatgcaga
                  Dolphin  tgagtgatagacggagccgcccggccccgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                      Cow  tgagtgatagacggagccgcccggccccgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                    Sheep  tgagtgatagacggagccgcccggccccgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
                    Horse  tgagtgatagacggagtcgcccggccccgctcagcccagcccacgttgctgc-ttagattgaaatgcaga
         Chinese pangolin  tgagtgatagacggagccgcccggcccagctcaggccagcccacgttgctgc-ttagattgaaatgcaga
                      Dog  tgagtgatagacggagccgcccggcccagctcgggccagcccacgttgctgc-ttagattgaaatgcaga
       Hawaiian monk seal  tgagtgatagacggagccgcccggcccagctcaggccagcccacgttgctgc-ttagattgaaatgcaga
                 Hedgehog  tgagtgatagacggagccgcccggccccgcgcagcccagcccacgttgctgctttagattgaaatgcaga
                    Shrew  tgagtgatagacggagccgcccggccccactcagcccagcccacgttgctgc-ttagattgaaatgcaga
                 Elephant  tgagtgatagacggagccgcccggccccgctcgacccagcccacgttgctgc-ttagattgaaatgcaga
                   Tenrec  tgagtgatagcccgagccgcccggccccggtcaacccagcccacgttgctgc-ttagattgaaatgcaga
                  Opossum  tgattgataggcagagacacccctcccaactcagcccagcccactttactgc-ttagattgaaatgcaga
                  Chicken  ggagcggggggctgcggctcccggcccagcccggccctgcccacgttgcc-c-tgaggttgaaatgcaga
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  actcaagcctctttcagcccggcacagacttccttttactctttcctttggca--
                      Rat  actcaagcctctttcagccgggcacagacttccttttactctttcctttggca--
            GCF_003668045  actcaagcctctttctggccggcacagacttccttttactctttcctttggca--
                   Beaver  actcaagtctctttcatcggggcacagacttccttttactccttccttttgca--
                 Squirrel  actcaagcctctttcatcagggcacagacttccttttactccttccttttgca--
               Guinea pig  actcaagcctctttcatcggggcacagacttccttttactctttccttttgca--
                   Rabbit  actcaagcctctttcatcggggcacagacttccttttactccttccttttgca--
                     Pika  actcaagcctctttcatcggggcgcagacttccttttactccttccttttgca--
                    Human  actcaagcctctttcatcggggcacagacttccttttacttcttccttttgcc--
                    Chimp  actcaagcctctttcatcggggcacagacttccttttacttcttccttttgcc--
                   Bonobo  actcaagcctctttcatcggggcacagacttccttttacttcttccttttgcc--
                  Gorilla  actcaagcctctttcatcggggcacagacttccttttacttcttccttttgcc--
                   Rhesus  actcacgtctctttcatcggggcacagacttccttttacttcttccttttgca--
                 Marmoset  actcaagcctctttcaccggggcacagacttccttttacttcttccttttgca--
                  Tarsier  actcaagcctccttcaaccgggcacagacttccttttactccttccttttgca--
                 Bushbaby  gctcaagcctctttcatcggggcacagacttccttttactccttccttttgcc--
               Tree shrew  actcaagcctctttcatcggggcacagacttccttctactccttccttttgca--
     Malayan flying lemur  actcaagcctctttcatcggggcacagacttccttttactccttccttttgca--
                      Pig  actcaagcctctttcagcggagcacagacttccttttactccttccttttgca--
                  Dolphin  actcaagcctctttcatcggggcacagacttccttttactccttccttttgca--
                      Cow  actcaagcctctttcagcggggcacagacttccttttactccttccttttgca--
                    Sheep  actcaagcctctttcagcggggcacagacttccttttactccttccttttgca--
                    Horse  actcaagcctctttcatcggggcacagacttccttttactccttccttttgca--
         Chinese pangolin  actcaagcctctttcatcagggcacagacttccttttactccttccttttgca--
                      Dog  actctagcctctttcatcggggcacagacttccttttactccttccttctgct--
       Hawaiian monk seal  actctagcctctttcaacggggcacagacttccttttactccttccttctgca--
                 Hedgehog  actcaagcctctttcatcagggcacagacttccttttacttcttcctttagct--
                    Shrew  actcaagcctctttcatcggggcacagacttccttttactctttccttttgca--
                 Elephant  actcaagcctctttcatcccggcacagacttccttttactccttccttttgca--
                   Tenrec  actcaagcctctttcatccccgcacagacttccttttactccttccttttgca--
                  Opossum  actcatacctctttcatcagggcacagacttccttttattcctttctctttaa--
                  Chicken  actcaaggctctctcgccgggaagtagatttcctcgtagtccttttttcctcgcc
                Zebrafish  =======================================================
            X. tropicalis  =======================================================

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

Alignment block 11 of 344 in window, 56742509 - 56742571, 63 bps 
B D                 Mouse  ctcttgtcgcctcctcccgggaagaagccaaggcaccctcggc---------t-t-ggagcag-------
B D                   Rat  ctcttgtcgcctcctcccggggagaagccaaggcacccgcggc---------t-t-ggagcag-------
            GCF_003668045  ctctcgtcgcctcctcctggggagaagccgaggcagccgcgtc---------t-t-ggagcag-------
                   Beaver  ctcttgtcgcctcctcccggggagaagctgaggcaccagccac---------c-c-ggagcag-------
B D              Squirrel  ctctcgcctcctcctcccggggagaagctgaggtaccagcaac---------c-c-ggagcag-------
B D            Guinea pig  ctcgtgcctcctcctcccggggagaacctaagataccggcagc---------c-c-ggagcac-------
B D                Rabbit  ctctcgccgcctcctcccggggagaagcggaggcaccggcggc---------c-c-ggggcag-------
B D                  Pika  ctcttgccgcctcctcccggggagaacccgaggccccggcggc---------cgc-gggacag-------
B D                 Human  ctctcgcctcctcctcctgggaagaagcggaggcgccggcggt------cggc-c-gggatag-------
B D                 Chimp  ctctcgcctcctcctcctgggaagaagcggaggggccggcggt------cggc-c-gggatag-------
B D                Bonobo  ctctcgcctcctcctcctgggaagaagcggaggggccggcggt------cggc-c-gggatag-------
B D               Gorilla  ctctcgcctcctcctcctgggaagaagcggaggcgccggcggt------cggc-c-gggatag-------
B D                Rhesus  ctctcgcctcctcctcctgggaagaatcggaggcgccggcggt------ccgc-c-cgggtag-------
B D              Marmoset  ctctcgcctccacctcctgggaagaagcggaggcgccggcggc---------t-c-ggggtag-------
B D               Tarsier  ctctcgccgcctcctccggggaagacgcggaggcaccggcggt---------c-c-ggggtcg-------
B D              Bushbaby  ctcttgcctcctcctcctgggaagaagcggaggcaccggcagc---------c-c-ggggtaa-------
B D            Tree shrew  ctctcgccgcctcctcccggggagaagccgaggccccggcggc---------c-c-cgggcag-------
B D  Malayan flying lemur  ctctcgccgcctccacccggggagaatcggaggcactcgcggc---------c-g-ggggcag-------
B D                   Pig  ctctcgccgcctcctcccggggagaagcggaggcagcgacagg---------c-c---------------
B D               Dolphin  ctctcgccgcctcctcccggggagaagcggaggcaccagcggc---------c-cggggggag-------
B D                   Cow  ctctcgccgcctcctccgggggagaagcggaggcaccggcggc---------c-c-ggggcag-------
B D                 Sheep  ctctcgccgcctcctcccggggagaagccgaggcaccggcggc---------c-c-ggggcag-------
B D                 Horse  ctctcgccgcctcctcctggggagaagcggaggcaccggcggc---------c-c-ggggcag-------
B D      Chinese pangolin  ctctcgccgcctcctccaggggagaagccgaggcaccggcgac---------c-c-ggggcag-------
B D                   Dog  ctctcgccgcctcctcccgggaagaagcggaggcaccggcggt---------c-c-ggggcag-------
B D    Hawaiian monk seal  ctctcgccgcctcctcccgggaagaagcggaggcaccggctgc---------c-c-ggggcag-------
B D              Hedgehog  ctctcgccgcctcctcccgcggcgaagcgga------ggcggc---------c-g-gggacag-------
B D                 Shrew  ctctcgccgcctcctctcggggtgaagcggaggcaccggcggc---------c-c-agagctg-------
B D              Elephant  ctctcgccgcctcctctcggggagaagcggaggcaccggcggc---------c-c-ggggcaa-------
B D                Tenrec  ctctcgccgcctcctctcggggagaagcggaggcttcggcggc---------c-c-agggcaa-------
B D               Opossum  ttctttctgtctgctcctgggatcaatcggagggacccgtggc---------c-a-gagctagaggagac
B D               Chicken  cccctgctatctcctc--ggcggcaagcagggagcccggcgggcgagcgcggc-c-ggggcgg-------
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================

                    Mouse  cgacaggccgg
                      Rat  cgacaggccgg
            GCF_003668045  cgacaggtcgg
                   Beaver  cgacaggccgg
                 Squirrel  cgacaggtcgg
               Guinea pig  cgacaagccgg
                   Rabbit  cgacaggccgg
                     Pika  agccaggccgg
                    Human  caacaggccgg
                    Chimp  caacaggccgg
                   Bonobo  caacaggccgg
                  Gorilla  caacaggccgg
                   Rhesus  caacaggccgg
                 Marmoset  caacaggccgg
                  Tarsier  cgacaggccgg
                 Bushbaby  ccacaggctgg
               Tree shrew  cgacaggccgg
     Malayan flying lemur  cgacaggccgg
                      Pig  ---------gg
                  Dolphin  cgacacaccgg
                      Cow  cagcacgacgg
                    Sheep  cagcacgacgg
                    Horse  cgacaggccgg
         Chinese pangolin  cgacaggcctg
                      Dog  cggcaagccgg
       Hawaiian monk seal  cgacaagccgg
                 Hedgehog  cggccggacgg
                    Shrew  cgatagaccgg
                 Elephant  ccataggccgg
                   Tenrec  ttataggccgg
                  Opossum  agaaatatcga
                  Chicken  cgggaggtcgg
                Zebrafish  ===========
            X. tropicalis  ===========

Inserts between block 11 and 12 in window
B D              Chicken 15bp

Alignment block 12 of 344 in window, 56742572 - 56742606, 35 bps 
B D                 Mouse  ctcagtgagaacaaga---aaaaagtttctttctggga
B D                   Rat  cccagtgagagcaagg---aaaaagtttctttctggga
            GCF_003668045  cctagtgagagcaaga---gaaaagtttctttctggga
                   Beaver  gtcagtaagaccgtga---gaaaagtttctttctggga
B D              Squirrel  gccactgaggccgtga---gaaaagtttttttctggga
B D            Guinea pig  gccactgaggccagga---acaaagtttcttcctggca
B D                Rabbit  gctaccgaggccgtgc---gtcaagtttctttctggaa
B D                  Pika  gctaccgaggccgtgcgaagcaaagtttctttctggaa
B D                 Human  gccactgaggcggtgc---ggaaagtttctgtctggga
B D                 Chimp  gccactgaggcggtgc---ggaaagtttctgtcttgga
B D                Bonobo  gccactgaggcggtgc---ggaaagtttctgtcttgga
B D               Gorilla  gccactgaggcggtgc---ggaaagtttctgtctggga
B D                Rhesus  gccactgaggcggtgc---ggaaagtttctgtctggga
B D              Marmoset  gccattgcggccctgc---ggaaagtttctgtctggtt
B D               Tarsier  cccactaaggccgtga---gaaaagtttctttttggga
B D              Bushbaby  gccactgaggccacgg---taaaagtttcttcctggga
B D            Tree shrew  tccactgaggccgtgc---gaaaagtttctttctggga
B D  Malayan flying lemur  gccactgaggccttgc---gaaaagtttctttctggaa
B D                   Pig  gccactgaggccacga---gaaaagtttctttctggga
B D               Dolphin  gccactgaggccacgc---gaaaagcttctttctggga
B D                   Cow  gccactaaggccacac---gaagagtttctttctggga
B D                 Sheep  gccactaaggccacac---gaagagtttctttctggga
B D                 Horse  gccactgaggccgtga---gaaaagtttctctctggga
B D      Chinese pangolin  gccactgaagcggggc---gaaaagtttctttctggga
B D                   Dog  gccactggggctgtgc---gaaaagtttctttttggga
B D    Hawaiian monk seal  gccactgaggctgtgc---gaaaagtttctttttggga
B D              Hedgehog  gccaccgaggccgcgc---agaaggtctctccctggga
B D                 Shrew  gtcactgaggccgagc---gaaaagtttctttctggga
B D              Elephant  tccactgaggccgtgc---gaaaagtatctttctggga
B D                Tenrec  tccactgaggccgtgc---gaaaagtttctttctggga
B D               Opossum  agcactaaggagatag---cgaaaatttgttcttggaa
B D             Zebrafish  ======================================
B D         X. tropicalis  ======================================
B D               Chicken  ======================================

Alignment block 13 of 344 in window, 56742607 - 56742842, 236 bps 
B D                 Mouse  gtgcggaactgg---ggccgggttggtgt-actgctcagagcaatgggtgagtggctg----------at
B D                   Rat  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtgactg-----------c
            GCF_003668045  gtgcggaactgg---ggccgggttggtat-actgctcggagcaatgggtgagtggcgg-----------c
                   Beaver  gtgcggaactgg---ggcccggttggtgt-gctgctcggagcaatgggtgagtggcgg-----------c
B D              Squirrel  gtgtggaactgg---ggcccggttggtgt-actgttcggagcaatgggtgagtggcgg-----------c
B D            Guinea pig  gtgcagaactgg---ggccgggttggtgt-gctgctcggagcaatgggtgagtggctg-----------c
B D                Rabbit  gtgcgg-gacag---ggccgggctggtgt-acggctcggagcaatgggtgagtggctg-----------c
B D                  Pika  gcgcag-cctag---ggccggcttggggt-acggctcggagcaatgggtgagtggctg-----------c
B D                 Human  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                 Chimp  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                Bonobo  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D               Gorilla  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                Rhesus  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D              Marmoset  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------t
B D               Tarsier  gtgcggaactgg---ggccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D              Bushbaby  gtgcggaactgg---ggcccagttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D            Tree shrew  gtgtggaactgg---agccgggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D  Malayan flying lemur  ctgcggaactgg---ggcccggctggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                   Pig  gtgtggagcttg---ggccccgttggtgt-actgctcggagcaatgggtgagtggtgg-----------c
B D               Dolphin  gtgcggagctgg---ggcccggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                   Cow  gcgcggaactgg---ggcccggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                 Sheep  gtgcggaactgg---ggcccggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                 Horse  gtgcggaactgg---ggcccggtcggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D      Chinese pangolin  gtgcggaactgg---ggcccggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                   Dog  gttcggaactgg---ggcccctttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D    Hawaiian monk seal  gctcggaactgg---ggccccgttggtgt-atagctcggagcaatgggtgagtggcgg-----------c
B D              Hedgehog  gcgcggagccgg---ggcgcggcgggtgt-cctgcccggagcgatgggtgagcggcgg-----------c
B D                 Shrew  gtgtcgaactgg---ggccccgtggctgt-actgctcggagcaatgggtgagtggcgg-----------c
B D              Elephant  gaacggaacagg---ggcccggttggtgt-actgctcggagcaatgggtgagtggcgg-----------c
B D                Tenrec  gaacagaactgg---agcccggttggtgt-actgcttggagcaatgggtgagtggcgg-----------c
B D               Opossum  ttctagagtc-------tcttattggtgtccccgctcaaagcaatgggtaagtggttgcctgttgtatcc
B D               Chicken  gtggggatttagggcggccccggaggtgt-cccgctcggaggaatgggtgagtgctgg-------gatcc
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================

                    Mouse  ggggg-a-------cgt-tgtc-agatccg-------a--------------------------------
                      Rat  ggggg-a-------cgt-tgtc-agaaccg-------a--------------------------------
            GCF_003668045  gggga-a-------cgc-tgtc-agaaccg-------a--------------------------------
                   Beaver  ggggg-a-------cgc-tgtc-agaaccg-------a--------------------------------
                 Squirrel  ggggg-a-------cgc-tgtc-agaaccg-------a--------------------------------
               Guinea pig  ggggg-c-------tgc-tgtc-agagccg-------g--------------------------------
                   Rabbit  ggggg-c-------cgc-tgtc-agagcgg-------c--------------------------------
                     Pika  gggggcc-------cgc-tgtcaagagcgg-------c--------------------------------
                    Human  ggggg-a-------ctc-tgtc-agagccg-------g--------------------------------
                    Chimp  gggag-a-------ctc-tgtc-agagccg-------g--------------------------------
                   Bonobo  ggggg-a-------ctc-tgtc-agagccg-------g--------------------------------
                  Gorilla  ggggg-a-------ccc-tgtc-agagccg-------g--------------------------------
                   Rhesus  ggggg-a-------ctc-tgtc-agagccg-------g--------------------------------
                 Marmoset  ggaag-a---------c-tgtc-ggagccg-------c--------------------------------
                  Tarsier  ggggg-a-------cac-tgtc-agagccg-------g--------------------------------
                 Bushbaby  gggcg-a-------ctc-tgtc-aaagccg-------t--------------------------------
               Tree shrew  ggggg-a-------cgc-tgtc-agagcgg-------a--------------------------------
     Malayan flying lemur  ggggg-a-------cgc-tgtc-agagccg-------a--------------------------------
                      Pig  ggggg-a-------cgcttgac-agagcct-------g--------------------------------
                  Dolphin  ggggg-a-------cgc-tgtc-agaaccg-------g--------------------------------
                      Cow  agggt-a-------cgc-tgtc-agagccg-------g--------------------------------
                    Sheep  ggggt-a-------cgc-tgtc-agagccg-------g--------------------------------
                    Horse  ggggg-a-------cgc-tgtc-agagtcg-------g--------------------------------
         Chinese pangolin  ggggg-a-------cgc-tgtc-agagctg-------t--------------------------------
                      Dog  gggga-a-------cgc-tgtc-agagccg-------g--------------------------------
       Hawaiian monk seal  ggggg-a-------cgc-tgtc-agagccg-------g--------------------------------
                 Hedgehog  gaggg-c-------ggc-tgtc-agcgcc-----------------------------------------
                    Shrew  gggga-c--------gc-tgtc-agcgccg-------g--------------------------------
                 Elephant  gaggg-a-------cgc-tgtc-agagccggggaggag--------------------------------
                   Tenrec  ggggg-a-------cgc-tgtc-agagccg-------g--------------------------------
                  Opossum  gcgaa-atattcagtgc-tgtc-agactgg-------gtgtggggaaaaagtggcggggggtggggggga
                  Chicken  gcggg-g-------ggc-tgtc---------------a--------------------------------
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  ------------------------------ggagggagggagcga-------------------------
                      Rat  ------------------------------ggagggagggagcga-------------------------
            GCF_003668045  ------------------------------ggagggagggagtga-------------------------
                   Beaver  ----------------------ga----agggagggagggagcga-------------------------
                 Squirrel  ----------------------gaagggagggagggagggagcga-------------------------
               Guinea pig  ------------------------------agagggagggagcgg-------------------------
                   Rabbit  ------------------------------ggcgg-----------------------------------
                     Pika  ------------------------------ggagggagggaggga-------------------------
                    Human  ----------------------gaag----ggagggagggagcga-------------------------
                    Chimp  ----------------------gaag----ggagggagggagcga-------------------------
                   Bonobo  ----------------------gaag----ggagggagggagcga-------------------------
                  Gorilla  ----------------------gaag----ggagggagggagcga-------------------------
                   Rhesus  ----------------------gaag----ggagggagggagcga-------------------------
                 Marmoset  ----------------------gaag----ggagggagggagcga-------------------------
                  Tarsier  ----------------------caag----ggagggcgggagcgg-------------------------
                 Bushbaby  ----------------------gaag----ggagggagggagcga-------------------------
               Tree shrew  ----------------------gaag-----gagggagggagcga-------------------------
     Malayan flying lemur  ----------------------gaag----agagggagggagcga-------------------------
                      Pig  ----------------------gaag----ggagggagggagcaa-------------------------
                  Dolphin  ----------------------gaag----ggagggagggagcga-------------------------
                      Cow  ----------------------gaaa----ggagggagggagcga-------------------------
                    Sheep  ----------------------gaag----ggagggagggagcga-------------------------
                    Horse  ----------------------caag----ggagggagg----ga-------------------------
         Chinese pangolin  ----------------------gaag----ggagggagggagcga-------------------------
                      Dog  ----------------------ggag----ggagggagggaagga-------------------------
       Hawaiian monk seal  ----------------------gaag----ggagggagcgaacca-------------------------
                 Hedgehog  -------------------------g----ggcgggagggaggga-------------------------
                    Shrew  ----------------------gaag----ggagggagggagaga-------------------------
                 Elephant  ----------------------ggag----ggagggagggagcgagcgagcgagcgagcgagcgggcggg
                   Tenrec  ----------------------gcag----ggagggagggagcga-------------------------
                  Opossum  ggagagaatgagaagagggggagaga----ggagagagagagaga-------------------------
                  Chicken  ------------------------------agagagagggagccc-------------------------
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  ---gcaggcg--------agggctagagggaggga--------gctgaggcg------------------
                      Rat  ---gcaggcg--------agggctagagggaggga--------gctgaggcg------------------
            GCF_003668045  ---gcaggcg--------agggcgagagggaggga--------gctggggcg------------------
                   Beaver  ---gcgggcg--------agggagggagggaggga----gagcgagggcgcg------------------
                 Squirrel  ---gcgggcg--------agggagggagggaggga----gtgcgagggcgcg------------------
               Guinea pig  ---gcgagcg--------ggcgggcgcgcgagggc----gcgctcggaggag------------------
                   Rabbit  ---acgggcg--------ttccgctgattgacttt----gctcg--------------------------
                     Pika  ---gcgggcg--------ggccagggcgggagggc----gcccgcagaggcg------------------
                    Human  ---gcgggca----agggagggagggagggaggga----gcgcgagggcgcg------------------
                    Chimp  ---gcgggca--------agggagggagggaggga----gcgcgagggcgcg------------------
                   Bonobo  ---gcgggca--------agggagggagggaggga----gcgcgagggcgcg------------------
                  Gorilla  ---gcgggca--------agggagggagggaggga----gcgcgagggcgcg------------------
                   Rhesus  ---gcgggcg----agggagggagggagggaggga----gtgcgagggcgcg------------------
                 Marmoset  ---gcgagag--------agggagggagggaggga----gcgagagggcgcg------------------
                  Tarsier  ---gcgtgcgtgcgggcgggcgagggagggaggga----gcgagagggcgcg------------------
                 Bushbaby  ---gcgggcg------------agggagggagggc----gcgcaagggcgcg------------------
               Tree shrew  ---gcgg------------gagagggagggaggga----gcgcgagggcgcg------------------
     Malayan flying lemur  ---gcgggctaggaagggagggagggagggaggga----gcgcaagggcgcg------------------
                      Pig  ---gcgggcg--------agggagggagg--------------gagggcacg------------------
                  Dolphin  ---gcgggcg--------agggagggagggagggc----gcgcgagggcgcg------------------
                      Cow  ---gcgggcg--------agggagggagg--------------gagggcgcg------------------
                    Sheep  ---gcgggcg--------agggagggagg--------------gagggcgcg------------------
                    Horse  ---gcgagct--------ggcgagggagggaggga----gcgcgagggcgcg------------------
         Chinese pangolin  ---gcgagcg--------agcgagggagggaggga----gagcaagggcgcg------------------
                      Dog  ---gaaggcg--------agggagggagggaggga----gcgcgagggcgcg------------------
       Hawaiian monk seal  ---gagggcg--------agggaggaagggaggga----gcgcgagggcgcg------------------
                 Hedgehog  ---gcgggcg--------ggaggcggaggg--------------agggcgcg------------------
                    Shrew  ---gcgggcg--------agggagggaggga--------gcgccagggcgcg------------------
                 Elephant  cgggcgggcg--------cgggagggagggagggctcgggcgcgagggcgcg------------------
                   Tenrec  ---gcggtcg--------cgagaaaggagggaggcgcgggcgcgagggcgcg------------------
                  Opossum  ---gagagag--------agagagagagagagaga----gagagagagagagagagagagagagagagag
                  Chicken  --------cg--------tgc------------------ccgcgccgtcatg------------------
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  -----------------------------------cgccaccgcgctg------------tattgactca
                      Rat  -----------------------------------cgccaccgcgctc------------tattgactca
            GCF_003668045  -----------------------------------cgcaaccgcgctc------------tattgactca
                   Beaver  -----------------------------------cgccactgagcgcttacactctccttattgacttt
                 Squirrel  -----------------------------------cgccactgagcgctcacactctccttattgacttt
               Guinea pig  -----------------------------------cgcgctcg-gctc----------cgtgttgacttt
                   Rabbit  ----------------------------------------------------------------------
                     Pika  -----------------------------------c----------------------------------
                    Human  -----------------------------------cgccactaggcgctcacattctc--tattgacttt
                    Chimp  -----------------------------------cgccactaggcgctcacattctc--tattgacttt
                   Bonobo  -----------------------------------cgccactaggcgctcacattctc--tattgacttt
                  Gorilla  -----------------------------------cgccactaagcgctcacattctc--tattgacttt
                   Rhesus  -----------------------------------cgccactaggcgctcacattctc--tattgacttt
                 Marmoset  -----------------------------------cgccactaagcgctcacattttc--tattgacttt
                  Tarsier  -----------------------------------cgccactaagcgctcacactctccttattgacttt
                 Bushbaby  -----------------------------------cgccactaagggctcgcactcttcttattgacttt
               Tree shrew  -----------------------------------cgccaccgagcgctcacactctccttattgacttt
     Malayan flying lemur  -----------------------------------cgccactgagcgctcacactctccgtattgacttt
                      Pig  -----------------------------------cagcacagagcgcttacattctccttattgacttt
                  Dolphin  -----------------------------------caccactgagcgcttacactctccttattgacttt
                      Cow  -----------------------------------caccactgagcgctcacactctccttattgacttt
                    Sheep  -----------------------------------caccactgagcgctcacactctccttattgacttt
                    Horse  -----------------------------------cactactgagcgctcgcactctccttattgacttt
         Chinese pangolin  -----------------------------------caccactgagcgctcatactctccttattgacttt
                      Dog  -----------------------------------caccgctgagcgctcacactcttcttattgacttt
       Hawaiian monk seal  -----------------------------------caccactgagcgctcacactcttcttattgacttt
                 Hedgehog  -----------------------------------cacccctgagcgctcacacgctccttattgacttt
                    Shrew  -----------------------------------caccactgagcgctcgcactttacttattgacttt
                 Elephant  -----------------------------------caccactgagcgctcaaactctccttattgacttt
                   Tenrec  -----------------------------------cgccactgggcgctcgcaccctccttattgacttt
                  Opossum  agagagagagagagagagagagagagagagagatttgttgccggagagtcacaacttgcttattgacttt
                  Chicken  -----------------------------------tgccaccgcg---------gctccttattgacttt
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  gactgcgtccgt-cgagctg-taagcaccctccaagggtcagtggcg-gaaagggttct--gtgag-a--
                      Rat  gaccgcgtccctacgagttg-tatgcacacgccaagggtcagcggct-aaaagggtgct--gtggg-a--
            GCF_003668045  gaccgcgtccccaagagctg-tacgagcatgccaagggtcagcggcg-acaggggtgca--atggg-aac
                   Beaver  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcggcgcacagcagttca--atctg-atc
                 Squirrel  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcgacgcacagcagttca--atccg-aac
               Guinea pig  gctcttgttcctacaagttg-aaggaactggccaagggtcagaggcttgcggtggttcc--gtgcg-aac
                   Rabbit  ------gttactgctgggtg-taggactgcgccaagggccagcggcgcacggcggtccg--gtgtg-cgc
                     Pika  --ccccgctcccgctgag-----ggacttgggtgggttcctaccacgcgtcccgggac------tg-cgc
                    Human  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcggcgcacagcagttca--atgtg-aac
                    Chimp  gctcgtgttcctacaagttg-tagaaacacgctaagggtcagcggcgcacagcagttca--atgtg-aac
                   Bonobo  gctcgtgttcctacaagttg-tagaaacacgctaagggtcagcggcgcacagcagttca--atgtg-aac
                  Gorilla  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcggcgcacagcagttca--atgtg-aac
                   Rhesus  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcggcgcacagcagttca--acgtg-aac
                 Marmoset  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcggcgcacaggagttca--atgtg-aac
                  Tarsier  gctcgtgttcctacaagttg-taggagcacgctaagggtcagcggcgcatagcagttcc--gtctg-aac
                 Bushbaby  gctcgtgttcctacaagttg-taggaacacgctaagggtcaacggcgcatagcagttca--gtctg-aat
               Tree shrew  gctcgtgttcgtacaagttg-taggaacacgctgagggtcagcggcgcacagcagttca--gcctg-aac
     Malayan flying lemur  gctcgtgttcctacaagttg-taggaacacgctaagggtcagcggcgc---gcggttca--gtctg-aat
                      Pig  gttcatgttcctacaagttg-taggaacactctaagggtcagcggcgcacagcagttcc--gtctg-aac
                  Dolphin  gctcgtgttcctacaacttg-taggaacacgctaagggtcagcgacgcacagcagctca--gtctg-aac
                      Cow  gctcatgttcctacaagttg-taggaacacgctaagggtcagcggctcgcagctgttca--gtctg-aac
                    Sheep  gctcgtgttcctacaagttg-tgggaacacgctaagggtcagcggctcgcagcagttca--gtctg-aac
                    Horse  gctcgtgttcatacaagttg-tagg-acccgctaagggtcggcgtcgcacagcagttca--gtctg-aac
         Chinese pangolin  gctcgcgttcctacaagttg-taggaacacgccaagggtcatcggcatacagcagttca--gtctgaaac
                      Dog  gctcgtgttcctacaagttgttaggaacgcgctaagggtcag-ggcgcacggcagttcagtgtgtg-aac
       Hawaiian monk seal  gctcgtgttcctacaagttgttagaaacacgctaagggtcag-ggcacacagcagttca--gtatg-aac
                 Hedgehog  gctcgtgttcctacacgttg-tagcaacacgccaagggtcagcggcgcacggcagctgc--gtctg-cac
                    Shrew  gctcgtgttcctacaagttg-taggaacacgctaagggtcagtggcgcgcagcagttca--gtctg----
                 Elephant  gttcgtgttcctacaaatag-taggaacgctctaagggtcagcggtgcacagcagttca--ttctg-att
                   Tenrec  gctcgagttccttcaagttg-tgggaacacgttaagggtcagcggtgcacagcagttct--ttctg-atc
                  Opossum  gctcatgtttctacaagttg-taacaatgagttaaaggtcaacagtacagagtagagag--atcta-atg
                  Chicken  actcgtgtttctacacgtcg-ggacagcgcgccgaggggcag-agcggggaggaggaaa--agcta-a--
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  ----gcca--------ctgggtg-acaa---tt-gatgccat-t
                      Rat  ----gcta--------ccgagtg-gcag---tt-gatgccat-t
            GCF_003668045  tcccgcta--------cagggtg-gcag---tt-aatgccag-g
                   Beaver  gctggcta--------ctgggtt-gctg---tt-gatgccat-t
                 Squirrel  gctggcta--------ctgggtt-tctg---tt-ggtgccat-t
               Guinea pig  gctggcta--------ctgggtt-gctg---tt-gatgccat-t
                   Rabbit  gccggctg--------ctgggct-gctg---tt-gatgcgggag
                     Pika  gcctgcta--------ccggggtggctg---tg-gatgccccgt
                    Human  gctggcta--------ctgggtg-gctg---tt-gatgccat-t
                    Chimp  gctggcta--------ctgggtg-gctg---tt-gatgccat-t
                   Bonobo  gctggcta--------ctgggtg-gctg---tt-gatgccat-t
                  Gorilla  gctggcta--------ctgggtg-gctg---tt-gatgccat-t
                   Rhesus  gctggcta--------ctgggtg-gctg---tt-gatgccat-t
                 Marmoset  gctggcta--------ctggctg-gcta---tt-gatgccat-t
                  Tarsier  gtgggcta--------ccgggct-gcgg---tt-gatgccat-t
                 Bushbaby  actggcta--------ctgggtc-actg---tt-gatgctat-t
               Tree shrew  tctggcta--------ccgggtt-gctg---tt-gatgccat-t
     Malayan flying lemur  ggtagctg--------ctgggtg-gctg---ct-gatgccat-t
                      Pig  gatggcta--------ctggggt-gctgctttt-gatgccat-t
                  Dolphin  gcgggcta--------ctgggtt-gctgctgtt-gatgccat-t
                      Cow  gctggcta--------ctgggtt-gctgctgtt-gatgccat-t
                    Sheep  gctggcta--------ctgggtt-gctgctgtt-gatgccat-t
                    Horse  gctggctc--------ctgggtt-gctg---tt-catgccat-t
         Chinese pangolin  actggcta--------ctgggct-gctg---gc-gatgccat-t
                      Dog  gctggcta--------ctgggtt-gctg---tt-gatgccat-t
       Hawaiian monk seal  gctggcta--------ctgggtt-gctg---tt-gatgccat-t
                 Hedgehog  cctggctacctacagcctg-----gctg---ct-gatgcccc-t
                    Shrew  -attgcta--------ctg-----gcta---ctaggtgccgt-t
                 Elephant  gctggttg--------ctgcgtt-gttg---tt-gatgccgt-t
                   Tenrec  tccggtag--------ctgggtt-ctta---tc-gatgccat-t
                  Opossum  ggtgg-----------ctgagtg-atta---tt-aaagcaat-t
                  Chicken  --tgactg--------ctcggtttatta---tt-aatgttat-t
                Zebrafish  ============================================
            X. tropicalis  ============================================

Inserts between block 13 and 14 in window
B D              Opossum 189bp

Alignment block 14 of 344 in window, 56742843 - 56742890, 48 bps 
B D                 Mouse  ttgcga-ttt--aagggaagagggccgtggcatt-ggcgaatctcgc-ag----ctc
B D                   Rat  tcccga-ttt-taacagacgagggccgtggcact-ggcgagtctctc-aa----ccc
            GCF_003668045  ttttga-ttt-taa-----gagggccatggcacg-ggagagtcccgc-ag----ctc
                   Beaver  ttctga-tttttaagagaagggagccgaggcatc-agcgagccccgcaaa----ctc
B D              Squirrel  ttctga-ttt-taagagaaaggagctgtggcatt-ggcgagctctac-ag----ctc
B D            Guinea pig  ttctga-ttt-tgagaaaaggcagctgtggcatc-agcgagccccgc-ag----ctc
B D                Rabbit  tcctga-ttt-taa--acagcgcagcgtggcatc-agagagccccgc-ag----ccc
B D                  Pika  gcccg------------------ggcgtggcatc-gcagagtccccc-agtgccccc
B D                 Human  ttctga-ttt-taagagaagggagctgtggcatc-agcgagcccctc-ag----ccc
B D                 Chimp  ttctga-ttt-taagagaagggagctgtggcatc-agcgagcccctc-ag----ccc
B D                Bonobo  ttctga-ttt-taagagaagggagctgtggcatc-agcgagcccctc-ag----ccc
B D               Gorilla  ttctga-ttt-taagagaagggagctgtggcatc-agcgagcccctc-ag----cgc
B D                Rhesus  ttctga-ttt-taagagaagggagctgtggcatc-agc--gccccgc-ag----ccc
B D              Marmoset  ttctga-ttt-taagagaagggaactatggcatc-agcaagccccgc-ag----ccc
B D               Tarsier  ttctga-ttt-taagaggagggggctgcggcgtc-agcgagccccgc-ag----ccc
B D              Bushbaby  ttctga-ttt-taagagaagggagctgtgccatc-agcgagcgccac-ag----ccc
B D            Tree shrew  ttctgatttt-taagaggcgggagctgaggctgc-agtgaa-cccgc-ag----ccc
B D  Malayan flying lemur  ttctga-ttt-taagagaagggagttatggcatc-agcgagccccgc-ag----ccc
B D                   Pig  ttctga-ttt-caagaggagggagccaaggcatc-agcaacccccgc-ag----cgc
B D               Dolphin  ttctga-ttt-caagagtagggagaggttgcatc-agcaagccccgc-gg----tcc
B D                   Cow  ttttga-ttt-caagactagggagcggtggcatc-agcaagccccgc--g----ccc
B D                 Sheep  ttctga-ttt-caagactagggagcggtggcatc-agcaagccccgc--g----ccc
B D                 Horse  ttctga-ttt-taggagaatagaggggtggcatc-ggcaagccctcc-ag----ccc
B D      Chinese pangolin  ttctga-ttt-taagagaagggagaggtagcatcaagcaagccctgc-ag----tcc
B D                   Dog  ttctga-tct-taaaacaagggagcggtggcatc-agcaagccctgt-ag----cct
B D    Hawaiian monk seal  ttctga-tat-taaaggaagagagcggtggcatc-agcaagctccgt-ag----cct
B D              Hedgehog  t--------t-ggagaggagggagtggtggcatc-agcaggtcccgc-gg----ccc
B D                 Shrew  t--------t-tccgagaagtgagcgctggcatt-agcaagccccgc-gg----ccc
B D              Elephant  ttctga-ttt-taagaggaaggagctgtggtatc-agcgagccccgc-aa----ccc
B D                Tenrec  ttctga-ttt-taagagaagggagctgtggcatt-accgagtccccc-aa----ccc
B D               Chicken  atgcga-ccg-tgaggca---gaatcgcagcaga-atggatggccgc-ag----ccc
B D             Zebrafish  =========================================================
B D         X. tropicalis  =========================================================
B D               Opossum  =========================================================

Inserts between block 14 and 15 in window
B D              Chicken 630bp

Alignment block 15 of 344 in window, 56742891 - 56743019, 129 bps 
B D                 Mouse  cagtgtcaat-cca---agttttgttgca----cacgtgtttacac------tt--------gc------
B D                   Rat  cagtgtcaat-cca---agttttgttgca----cacgtgtttacac------tt--------gc------
            GCF_003668045  cagtgtcaat-cca---agttttgttgca----cacgtgtttacac------at--------gc------
                   Beaver  cagtggcatt-tca---agttttgt--------------ttcactc------ac--------gc------
B D              Squirrel  cagtggaaac-cca---agttttgt--------------tttacac------ac--------gc------
B D            Guinea pig  caggagcaat-ccc---aatttcatttca----cacacacacacac------ac--------ac------
B D                Rabbit  cggtggcaat-cca---agccgtgtttcc----cacgcgcgcacgc------acggacgctcgc------
B D                  Pika  ggggggccac-ccg---aggtgtgtttcg----cttgcgcgcacacaagccaacgaa-----gc------
B D                 Human  gagtagcaaa-cca---agttttgtttca----cacgcgcgcacac------at--------gc------
B D                 Chimp  gagtagcaaa-cca---agttttgtttca----cacgcgcgcacac------at--------gc------
B D                Bonobo  gagtagcaaa-cca---agttttgtttca----cacgcgcgcacac------at--------gc------
B D               Gorilla  gagtagcaaa-cca---agttttgtttca----cacgcgcgcacac------at--------gc------
B D                Rhesus  cagtagcaaa-cca---agttttgtttca----cacgcgcgcacac------ac--------gc------
B D              Marmoset  ccgtagcaaa-cca---agttttgcttca----cacgcgcgcatac------ac--------ac------
B D               Tarsier  cagtagcaaa-cca---agttttgtttcg----cacgcgcgcacac------at--------gc------
B D              Bushbaby  cagtagcaaa-cca---agttttgtttca----cagacgctcacgc------at--------gc------
B D            Tree shrew  tggtagcaaa-ctactggggtttgtttct----cctacgcgcacac------ac--------gc------
B D  Malayan flying lemur  cagtagcaaa-cca---agttttgttccg----tacacgcgcacac------ac--------tc------
B D                   Pig  cagtggcgga-cca---aattttgtttta----cacacaggcagac------ac--------gcagaaaa
B D               Dolphin  cagttgcgga-cca---aattttgtttca----catacacgcagac------ac--------gggg----
B D                   Cow  cggtggcgga-cca---aattttgtttcg----cgtaca-------------------------------
B D                 Sheep  cggt-gcgga-cca---aatt-------------------------------------------------
B D                 Horse  tagaggcgga-cca---agttttgtttca-atacacacacacacgc------------------------
B D      Chinese pangolin  cagtggcggg-cca---ggttttgtttcatctacacgcagacacac------------------------
B D                   Dog  cggtggcgga-cca---agttttgtttca----cataaactcacac------a-----------------
B D    Hawaiian monk seal  cagt-gcgga-cca---agttttgtttca----cacaaactcacgc------------------------
B D              Hedgehog  caatgagggatcga---tttttttattct----cgtgtccgctcac------cc--------gc------
B D                 Shrew  cagcgacg---cca---aattttgtttca----catactcgtccac------ac--------gg------
B D              Elephant  cagtggcaga-cta---agttttgtttca------------cacac------ac--------gc------
B D                Tenrec  cagtggcaga-cca---agttttgtttca------------gacac------at--------gt------
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  -----aagcaaaa---------cagaac---------------------aaa--------aac-------
                      Rat  -----aagcaaaa---------cagaac---------------------aaa--------aac-------
            GCF_003668045  -----aaacaaaa---------cagaac---------------------aaa--------aac-------
                   Beaver  -----aaagagaa---------cagaaa---------------------aaa--------aaa-------
                 Squirrel  -----acacacac---------gcaaac---------------------aaa--------aac-------
               Guinea pig  -----acacacac---------acacac---------------------aca--------cac-------
                   Rabbit  -----aaacaaaa---------cagcca---------------------a-a--------aca-------
                     Pika  -----agaacaaa---------cagaca---------------------aga--------acc-------
                    Human  -----aaacaaaa---------caggaa---------------------aag--------aaaagaaaag
                    Chimp  -----aaacaaaa---------cag--------------------------g--------aaaagaaaag
                   Bonobo  -----aaacaaaa---------caggaa---------------------aag--------aaaagaaaag
                  Gorilla  -----aaacaaaa---------caggaa---------------------aag--------aaaagaaaag
                   Rhesus  -----aaacaaaa---------caggaa---------------------aac--------aaaacaaaac
                 Marmoset  -----aaacaaaa---------cagg-----------------------------------agggaaaaa
                  Tarsier  -----aaaccaaa---------cagg------------------------------------aggaggga
                 Bushbaby  -----aaacaaaa---------cagaaa---------------------aaa--------aagagagaaa
               Tree shrew  -----aaacaaaa---------caggaa------------------------------------------
     Malayan flying lemur  -----agacaaaa---------caacaa---------------------ca-------------------
                      Pig  caaccaaacaaaaaaacccaaccagaaa---------------------aaa--------aga-------
                  Dolphin  -cggggggtaaaaaacgccaaccagaaa---------------------aaa--------aga-------
                      Cow  -cagggtacaaaagccaaccaagaaaaa---------------------aaa--------aga-------
                    Sheep  -----aaacaaaaaaaaaaaaaaaaaaa---------------------aaa--------aga-------
                    Horse  -----aaacaaaa---------cagaaa---------------------aaa--------aac-------
         Chinese pangolin  -----aaacgaaa---------cagaaa---------------------aat--------acc-------
                      Dog  -----actcagaa---------caggaaaaaaccaaaccaaaccaaaacaaa--------aca----acc
       Hawaiian monk seal  -----actcagaa---------caggaa---------------------aaa--------aaa----tcc
                 Hedgehog  -----aaactcaa---------cagcgg---------------------tgggggaaaaagaa-------
                    Shrew  -----caacaaaa---------cggagg---------------------agg--------gaa-------
                 Elephant  -----agacaaaa---------cagaaa---------------------aa-------------------
                   Tenrec  -----aaacaaaa---------caaaac---------------------aaa--------aca-------
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  --accc------------------ccc-ccccagctt--------------tctctgg------actgc-
                      Rat  --accc------------------cccgccccagttt--------------tccctag------gctgc-
            GCF_003668045  aaaaca------------------acc-cctcagctt--------------tccctga------actcc-
                   Beaver  aaat------------------------ctctagctt--------------cccctag------acgtt-
                 Squirrel  --------------------------t-ttccagctt--------------cccctag------acttt-
               Guinea pig  --accc------------gaaaaactc-ctccaggctaacaacagcgcgcatctcggg------acgca-
                   Rabbit  --acaa--------------------c-cccaaactc--------------tctctagctttgccctacg
                     Pika  --acta------------tcacccccc-cccaaactc--------------tccctcg------cccac-
                    Human  aaaacaaacaacaacaaataaaacacc-ctctagctt--------------cccctag------acttt-
                    Chimp  aaaacaaacaacaacaaataaaacacc-ctctagctt--------------cccctag------acttt-
                   Bonobo  aaaacaaacaacaacaaataaaacacc-ctctagctt--------------cccctag------acttt-
                  Gorilla  aaaaca---aacaacaaataaaacacc-ctctagctt--------------cccctag------acttt-
                   Rhesus  aaaacaaacaacaac-aacaacacacc-ctctagctt--------------cccctag------acttt-
                 Marmoset  aaagca--------------------c-ctctagctt--------------ctcctag------acttt-
                  Tarsier  aaaacaatc-----------------c-cttcagctt--------------cccctag------acttt-
                 Bushbaby  aaaatc--------------------c-ctctagctt--------------cccctag------acttt-
               Tree shrew  --aatc--------------------c-ctctagctt--------------ccctgga------ct--t-
     Malayan flying lemur  acaaga--------------------t-cttcagctt--------------cccctag------gc--t-
                      Pig  ------------------------------------------------------ctag------atctt-
                  Dolphin  ------------------------------------------------------ctag------acttt-
                      Cow  ------------------------------------------------------ctag------acttt-
                    Sheep  ------------------------------------------------------ctag------acttt-
                    Horse  ----------------------------ctgtggttt--------------tccctgg------ccctt-
         Chinese pangolin  -------------------------------tagttt--------------cccctag------aactt-
                      Dog  aaacca--------------------a-ccgtagttt--------------ctcctag------acctt-
       Hawaiian monk seal  aaacca--------------------a-ctgtagttt--------------ctcctag------acctt-
                 Hedgehog  --gtac--------------------c-cggtagtta--------------cgtccag------acctt-
                    Shrew  --ctcc--------------------c-cagtagttt--------------ccccaag------atctt-
                 Elephant  --------------------------t-ctctagctt--------------ctcctag------acctt-
                   Tenrec  -aaaat--------------------t-ctctagctt-----------------ctag------accta-
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ----g---tctaaccccgca-ga----agggagggg---------taagg-------------------c
                      Rat  ----g---tctaacccctct-ga----agggagggg---------taagg-------------------c
            GCF_003668045  ----g---tctaatagcgct-gg----ggggagggg--------ataaga-------------------a
                   Beaver  ----g---tctaatcccgcg-ggtctccgggagcggcgctggggatgaga-------------------c
                 Squirrel  ----g-----------cgcg-ggtctccgggagcggcgctggtgacgagt-------------------t
               Guinea pig  ----gcgatggagaccgggt-ggtggtggagaggagaggagaggagagga-------------------g
                   Rabbit  cttgg---tccagctgcgcg-ggtcttcgggcggggcgcgggggaggggg-------------------c
                     Pika  --cgg---acca-ccgcgcg-ggtctccgggacgggcgccggggagag----------------------
                    Human  ----g---tttaactggccg-ggtctccagaaggaacgctggggatggga-------------------t
                    Chimp  ----g---tttaactggccg-ggtctccagaaggaacgctggggatggga-------------------t
                   Bonobo  ----g---tttaactggccg-ggtctccagaaggaacgctggggatggga-------------------t
                  Gorilla  ----g---tttaactggccg-ggtctccagaaggaacgctggggatggga-------------------t
                   Rhesus  ----g---tttaactgcccg-ggtctccagaaggaaagctggggatggga-------------------t
                 Marmoset  ----g---tttaactgcccg-ggtctccaggaggaacgctggggatggga-------------------t
                  Tarsier  ----g---tctaactgcgcg-ggtctccaggcggggcgctggggatgggg-------------------t
                 Bushbaby  ----g---tctaacagcaca-ggtcttcaagagg-gtgctgggagcggtc-------------------t
               Tree shrew  ----g---tctac-tgcgcg-gctcctcagcc--tgcagtaggggtgggg-------------------t
     Malayan flying lemur  ----g---tctaagtgcgcg-ggtctccaggcggggccctggggatgggg-------------------t
                      Pig  ----g---tctaattgcgca-ggtcccaaggcggggcgctggggatcaag-------------------g
                  Dolphin  ----g---tctaattgcgca-ggtcccaaggcggggcgctggggatcaag-------------------g
                      Cow  ----g---tctaattgcgca-ggtccctaggcggggcgctggggatcaaa-------------------g
                    Sheep  ----g---tctaattgcgca-ggtccctaggcggggcgctggggatcaag-------------------g
                    Horse  ----g---tctaatcgcgca-ggtccccgggcggggcgctagggatcaag-------------------g
         Chinese pangolin  ----g---tcaaattgcgca-agtccccacgcggggctctggggatcaag-------------------g
                      Dog  ----g---cctaattgcgcc-ggtccccaggccgggcgctggggctcaag-------------------c
       Hawaiian monk seal  ----g---tctaattgctccaggcccccaggcggggcgctggggctcaag-------------------g
                 Hedgehog  ----g---tctcagggcgca-ggtccccaggctgggcgcagggggtccagtggggctgggggagggggag
                    Shrew  ----g---tctaattgctta-ggatcacagg---------agggaactag-ggggataggaaggggggga
                 Elephant  ----g---tctgactacgg--ggtcctcgggtggggcgccgggattgagg-------------------a
                   Tenrec  ----g---tctgtctgcgc--gatcc-cgggcgggggggggggggggggg-------------------g
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Opossum  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ggtggaagg
                      Rat  ggtggagag
            GCF_003668045  tgtggaggg
                   Beaver  ggtgctggg
                 Squirrel  ggtggtggg
               Guinea pig  aggagagga
                   Rabbit  gggggcggg
                     Pika  gaggacgga
                    Human  gggtggaga
                    Chimp  gggtggaga
                   Bonobo  gggtggaga
                  Gorilla  gggtggaga
                   Rhesus  gggtggaga
                 Marmoset  gagt--aaa
                  Tarsier  gggtgggga
                 Bushbaby  gggagggaa
               Tree shrew  gggggaggg
     Malayan flying lemur  ggggaggag
                      Pig  ---------
                  Dolphin  ---------
                      Cow  ---------
                    Sheep  ---------
                    Horse  ---------
         Chinese pangolin  ---------
                      Dog  ---------
       Hawaiian monk seal  ---------
                 Hedgehog  ---------
                    Shrew  ---------
                 Elephant  ---------
                   Tenrec  ---------
                Zebrafish  =========
            X. tropicalis  =========
                  Opossum  =========
                  Chicken  =========

Inserts between block 15 and 16 in window
B D                Human 4bp
B D                Chimp 4bp
B D               Bonobo 4bp
B D              Gorilla 4bp
B D               Rhesus 4bp
B D             Marmoset 4bp
B D              Tarsier 4bp
B D             Bushbaby 4bp
B D           Tree shrew 105bp
B D Malayan flying lemur 2bp
B D                  Pig 2bp
B D              Dolphin 2bp
B D                  Cow 2bp
B D                Sheep 2bp
B D                Horse 2bp
B D     Chinese pangolin 2bp
B D                  Dog 2bp
B D   Hawaiian monk seal 2bp
B D             Hedgehog 2bp
B D                Shrew 2bp

Alignment block 16 of 344 in window, 56743020 - 56743091, 72 bps 
B D                 Mouse  -----------gagcaa----gggc-cgagtgt-tttggtaccaggcaggcaaagaggggcgcg-ct-gg
B D                   Rat  -----------gagcag----gggc-tgggcgt-tcttgtgtcgggcagggaacgaagggcgcg-ct-gg
            GCF_003668045  -----------gagcaa----gggc-agaacgt-tttggtgccaagcaggcaaccaggga-gcg-ct-gg
                   Beaver  -----------gagcag---cggcc-caaggat-tttagtgccaagcaggcgaggaggggcgcg-tt-ca
B D              Squirrel  -----------gaggag---cggcc-catggac-tttt----------ggctaggaggggcgcg-tt-cg
B D            Guinea pig  -----------gaggagaggaggcc-caaggac-ttcaggatcgagg-ggcgatgtggggcgcg-tt-ca
B D                Rabbit  -----------gagc------ggcc-cgagagc-ttccgtgcggagccggccagcgggtgcgcg-tt-ca
B D                  Pika  -----------gagc------ggccgcgggctc-tttggtgcggagccggccagtccgagcgcg-tt-cg
B D                 Human  -----------gagc------ggct-caaggac-tttagtgaggagcaggcgagaaggagcacg-tt-ca
B D                 Chimp  -----------gagc------ggct-caaggac-tttagtgaggagcaggcgagaaggagcgcg-tt-ca
B D                Bonobo  -----------gagc------ggct-caaggac-tttagtgaggagcaggcgagaaggagcgcg-tt-ca
B D               Gorilla  -----------gaac------ggct-caaggac-tttagtgaggagcaggcgagaaggagcgcg-tt-ca
B D                Rhesus  -----------gagc------ggct-caaggac-tttagtaaggagcaggcgagaaggagcgcg-tt-ca
B D              Marmoset  -----------gagt------ggcc-caagaaa-tttagtgaggagcaggctacaagcagcgcg-tt-ta
B D               Tarsier  -----------gagc------ggcc-caagacc-ttgagcgaggagcagacgagaaggagcgct-ct-ca
B D              Bushbaby  -----------gagc------agcc-taaggac-tttagtgcgcagcaggcgagaaggagcgtg-tt-ca
B D            Tree shrew  -------------------------------------------gagcag---------------------
B D  Malayan flying lemur  -----------gaga------agcc-caaggac-tttggtgccgagcaggcgagaaggggcgcg-tt-ca
B D                   Pig  -----------gagc------ggcc-ccaggac-tttaaagctgagtaggcgagaaggagccta-ttaca
B D               Dolphin  -----------gagc------ggca-caaggac-tttagcgccgagtaggcgagaaggagccgc-ttgca
B D                   Cow  -----------gagc------ggcc-caaggac-attagcgccgagtgggcgagaaggagccgctttgta
B D                 Sheep  -----------gagc------ggcc-caaggac-attagcgccgagtgggcgagaaggagccgctttgca
B D                 Horse  -----------cagc------ggcc-caaagac-tttagcgacgaccaggcgagaaggggccgg-tcgct
B D      Chinese pangolin  -----------gaag------agcc-caagaac-ttttgcgtggagctggcgagaaggagccgc-ttgca
B D                   Dog  -----------tagc------ggcc-caaagacttttagcgccgagcagccgagaaggagccgg-ttgca
B D    Hawaiian monk seal  -----------tagc------agcc-cagagac-tttagcgccgagaagccaagaaggagctgg-ttgca
B D              Hedgehog  -----------gagc------gttc-caaggac-ttgagctccgaactggctaagagaagcggg-ttcca
B D                 Shrew  -----------gaga------ggcc-caatgac-ttcagcccgcagcaggcgagaaggagcgcg-ttgca
B D              Elephant  g----------aagt------agcc-caaggac-tttaggtcccagcaggcgagaaggaggcgg-ttgca
B D                Tenrec  ggcgctggtcagaga------agtc-caaggtc-ttca-gtccaagtaggcgagaaggagccgg-tggca
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  ag-cctcagaa----------------------------------ccgatt-----tcccc
                      Rat  ag-tgtcagga----------------------------------ccgatt-----tcccc
            GCF_003668045  ca-cgtcagga----------------------------------ccgatt-----tcccc
                   Beaver  gg-cgtcaaga----------------------------------ccgatt-----tcccc
                 Squirrel  gg-cgtcaaga----------------------------------cggatt-----tcccc
               Guinea pig  gg-cgtctgga----------------------------------cggatt-----tctcc
                   Rabbit  gg-agtcgaga----------------------------------ccgatt-----ccccc
                     Pika  gg-cgtccagg----------------------------------cctctcgctcgccgcc
                    Human  gg-cgtcaaga----------------------------------ccgatt-----tctcc
                    Chimp  gg-cgtcaaga----------------------------------ccgatt-----tctcc
                   Bonobo  gg-cgtcaaga----------------------------------ccgatt-----tctcc
                  Gorilla  gg-cgtcaaga----------------------------------ccgatt-----tctcc
                   Rhesus  gg-cgtcaaga----------------------------------ccgatt-----tcccc
                 Marmoset  gg-catcaaga----------------------------------ccgatt-----tcccg
                  Tarsier  gg-cttctgga----------------------------------ccgatt-----tcccc
                 Bushbaby  gg-cgtcaaga----------------------------------cctatt-----tctcc
               Tree shrew  -------------------------------------------------------------
     Malayan flying lemur  gg-cgtcaaga----------------------------------ccgatt-----tcccc
                      Pig  gg-cgtcaaga----------------------------------cctatt-----tcc-c
                  Dolphin  gg-cgtcgaga----------------------------------ccgatt-----tcccc
                      Cow  gg-cgtcaaga----------------------------------ccgact-----tcctc
                    Sheep  -g-cgtcaaga----------------------------------ccgact-----tcctc
                    Horse  gg-catcagga----------------------------------ccgatt-----tccca
         Chinese pangolin  gg-cgtcatgc----------------------------------cggatt-----tccta
                      Dog  gg-cgtcaaga----------------------------------ctgatt-----tcccc
       Hawaiian monk seal  gg-cgtcaaga----------------------------------ccgatt-----tcccc
                 Hedgehog  gg-agccaaaacccgacccccgcccccggcgccatccccccccccccacct-----ctccc
                    Shrew  gg-cgtcaaag----------------------------------ccgatt-----tcccc
                 Elephant  gg-cgtcaaga----------------------------------ccaatt-----tccct
                   Tenrec  ggatatcagga----------------------------------tcgatt-----tccct
                Zebrafish  =============================================================
            X. tropicalis  =============================================================
                  Opossum  =============================================================
                  Chicken  =============================================================

Alignment block 17 of 344 in window, 56743092 - 56743109, 18 bps 
B D                 Mouse  gcctgcttcgg-ag-agttt
B D                   Rat  gcctgcttcgg-ag-agttt
            GCF_003668045  gtctgcttcgg-ag-agttt
                   Beaver  gcctgcttcgg-ag-tcttt
B D              Squirrel  gcctgcttggg-ag-acttc
B D            Guinea pig  gccagcttctg-ag-aacct
B D                Rabbit  gcctggttcgg-ag-acttt
B D                  Pika  ggcggcccccg-ag-acttc
B D                 Human  ccctgcttcgggag-acttt
B D                 Chimp  ccctgcttcgggag-acttt
B D                Bonobo  ccctgcttcgggag-acttt
B D               Gorilla  ccctgcttcgggag-acttt
B D                Rhesus  tcctgcttcgggag-ac-tt
B D              Marmoset  tcctgcttcggagg-acttt
B D               Tarsier  gcctgc-tcgggaa-ccatt
B D              Bushbaby  gtctgcttcgg-ag-acttt
B D  Malayan flying lemur  gcctgctttgg-ag-acttg
B D                   Pig  gcctgcttcgg-ag-acttt
B D               Dolphin  gcctgcttcgg-ag-acttc
B D                   Cow  gcctgcttcgg-ag-gcttc
B D                 Sheep  gcctgcttcgg-ag-gcttc
B D                 Horse  gcctgcttcgg-ag-acttt
B D      Chinese pangolin  gcctgtttcgg-ag-acatt
B D                   Dog  gcctgcttcgg-ag-gcttt
B D    Hawaiian monk seal  gcctgcttcgg-ag-gcttt
B D              Hedgehog  tcctgctcctg-ag-ac--t
B D                 Shrew  gccagtcttgg-ag-acttt
B D              Elephant  gcctgcttcag-ag-acttt
B D                Tenrec  gcttgcttcag-agtttttt
B D               Opossum  gtccgttctgg-aa-agttt
B D            Tree shrew  --------------------
B D             Zebrafish  ====================
B D         X. tropicalis  ====================
B D               Chicken  ====================

Inserts between block 17 and 18 in window
B D               Rabbit 320bp
B D                 Pika 1bp

Alignment block 18 of 344 in window, 56743110 - 56743234, 125 bps 
B D                 Mouse  --taagtgtccggagttgccc----tgggtct--------------------------------------
B D                   Rat  --agagtgtcccgagttgccc----tgggtctgtctctctctctctctctctctctctctctctctctct
            GCF_003668045  --tgggtgccgggagctgccc----tgggtct--------------------------------------
                   Beaver  --tgaactttcggagcggccc----agcgccg--------------------------------------
B D              Squirrel  --agca---ctcgagcggccc----tgagtct--------------------------------------
B D            Guinea pig  --caaaagtccgagcgggggc----tgcgtct--------------------------------------
B D                  Pika  --cgggcgctcggaacagcctggagtgcgtct--------------------------------------
B D                 Human  --tgaacgctcggagaggccc----ggcatct--------------------------------------
B D                 Chimp  --tgaacgctgggagaggccc----ggcatct--------------------------------------
B D                Bonobo  --tgaacgctcggagaggccc----ggcatct--------------------------------------
B D               Gorilla  --tgaacgctcggagaggccc----ggcatct--------------------------------------
B D                Rhesus  --tgaacgctcggagaggccc----tgcgtct--------------------------------------
B D              Marmoset  --tgaacgcttggagaggccc----tgagtct--------------------------------------
B D               Tarsier  --tggaccctcgggacggctc----cgcgtct--------------------------------------
B D              Bushbaby  --tgaacactcagagctgccc----tgcttag--------------------------------------
B D            Tree shrew  ----------------------------gtct--------------------------------------
B D  Malayan flying lemur  --tgagcgctgggagcggccc----tgcgtct--------------------------------------
B D                   Pig  --tgaacactcggagaggctc----t-tgtct--------------------------------------
B D               Dolphin  --tgagcactcggagaggccc----tgcgtct--------------------------------------
B D                   Cow  --tgaacactcggagaggccc----tgcgtct--------------------------------------
B D                 Sheep  --tgaacactcggagaggccc----tgcgtct--------------------------------------
B D                 Horse  --tgaacgctcggagcggccc----tgcgt----------------------------------------
B D      Chinese pangolin  --tgaactctcggagcagccc----ttccttt--------------------------------------
B D                   Dog  --tgagcacttggagcggcct----tgcttct--------------------------------------
B D    Hawaiian monk seal  --tgaacacttggagcggccc----cgcgtct--------------------------------------
B D              Hedgehog  --tgaattctgggagctgctc----agcgcct--------------------------------------
B D                 Shrew  --tgaactcccgaagctgcac----cgcgtct--------------------------------------
B D              Elephant  --tgaacactcggagcgtccc----tgcgtct--------------------------------------
B D                Tenrec  --tggacactc-gagtgtccc----agcg-----------------------------------------
B D               Opossum  ggagaaagcct---atggccc----tacaact--------------------------------------
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================
B D                Rabbit  ======================================================================

                    Mouse  -------------------------------ctcttcttgtttgttgttggg-aatcgcaaagtaggagc
                      Rat  ctctctctctctctctctct---------ctctctccttgtttgtagttggg-aatcgcaaagcaggagc
            GCF_003668045  -------------------------------ttctacttgtttgtagctgga-acgcgcaaagcaggaac
                   Beaver  -------------------------------caccacttgttagtagccgtc-gcccgccgggcaagaat
                 Squirrel  -----------------cgc---------cacattacttgcctgtagcagcc-gccctc--accagggat
               Guinea pig  -------------------------------cagcattt-----tatttgct-gcccccaccgcaggaat
                     Pika  -----------------cgc---------ctctcggctggtccgcggcggct-gccctcgcatcaggaag
                    Human  -----------------cac---------cactttacttggccgtaggggcc-tccggcacggcaggaat
                    Chimp  -----------------cac---------cactttacttggccgtaggggcc-tccggcacggcaggaat
                   Bonobo  -----------------cac---------cactttacttggccgtaggggcc-tccggcacggcaggaat
                  Gorilla  -----------------cac---------cactttacttggccgtaggggcc-tccggcacggcaggaat
                   Rhesus  -----------------cac---------cactttacttggttgtaggggcc-tccggcacggcaggaat
                 Marmoset  -----------------cac---------cactttacttggctgtaggggcc-tctggcaccgcaggaat
                  Tarsier  -----------------ccc---------cact----ttgaccgtggcggcc-tctcgcccggcaggaac
                 Bushbaby  -----------------cac---------caccacacttgactggagcggcc-tccagcac-gcaggaat
               Tree shrew  -----------------gac---------cc---------------------------------------
     Malayan flying lemur  -----------------cac---------cactttacatgtctgtagcagccgcccttcacgacaggaat
                      Pig  -----------------cac---------cattttattcgtttatagccgcc-gcaggcaccaccagaat
                  Dolphin  -----------------cac---------cactacatttgtctgtagcggcc-tcaggcactgccagaat
                      Cow  -----------------cac---------cactttatttgcttgtatcggcc-gcaggcactgcggtaat
                    Sheep  -----------------cac---------cactttatttgcttgtatcggcc-gcaggcactgccgtaat
                    Horse  -------------------c---------tattttat-------tagcggcc-ataggcatcaccagaat
         Chinese pangolin  -----------------tac---------cattttatttgtttgtagcggcc-tcaggcagcaccataat
                      Dog  -----------------cac---------cactttatttgcttgtagtggcc-gcaggcaccaccggaac
       Hawaiian monk seal  -----------------cac---------cactttatttgcttgtagtggcc-gcagacaccactggaat
                 Hedgehog  -----------------cgc---------cactcaatttgtttgtggcggtc-tcaggcaccgcggaaat
                    Shrew  -----------------cac---------cacttgatttgcctgtagcggct-gcagtcacccccagaat
                 Elephant  -----------------cac---------ccttttatttgcctatcacggcc-tccggctcccctggaat
                   Tenrec  -------------------------------------------atcgc-gcc-atcagcgcctcaggacc
                  Opossum  -----------------tgctcttagttgtaatttgtttgcctat-gaagca-acagacg-aactggatt
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================
                   Rabbit  ======================================================================

                    Mouse  g-a-------------------------------------ggtctgg--ccgca-----gcttgttttga
                      Rat  g-a-------------------------------------ggtctgg--tctca-----gcttgtttt--
            GCF_003668045  g-a-------------------------------------ggtctgg--ccaca-----gcttgttccgg
                   Beaver  g-a--------g-------------ggagg--g-------ggtccga--ccaca-----gcttgtttggg
                 Squirrel  g-a--------g-------------aaagg--gat---tccaaccga--cccga-----gattgttttgg
               Guinea pig  g-a--------g-------------gaagg--ggt---ccgtgctga--cctca-----acttccacggg
                     Pika  c-agggatgtgg-------------ggagg--ggg---tccgcctggacccggg-----ggtcgtccggg
                    Human  g-a--------g-------------ggagg--ggg---tccgattgg--acagt-----gacggtttggg
                    Chimp  g-a--------g-------------ggagg--ggg---tccgattgg--accgt-----gacggtttggg
                   Bonobo  g-a--------g-------------ggagg--ggg---tccgattgg--accgt-----gacggtttggg
                  Gorilla  g-a--------g-------------ggagg--ggg---tccgattgg--accgt-----gacggtttggg
                   Rhesus  g-a--------g-------------agagg--ggg---tccgattgg--accgt-----gaccgtttcgg
                 Marmoset  g-a--------g-------------ggagg--ggg---tccgattgg--accgt-----gacag-ttggg
                  Tarsier  gaa--------g-------------ggagg--ggg---tccgactgc--gcctcagctgggctgtttggg
                 Bushbaby  c-a--------g-------------ggagg--gca---tctagccgg--acctt-----ggcgcttt-gg
               Tree shrew  ----------------------------------------------g--acctt-----ggccacttggg
     Malayan flying lemur  g-a--------g-------------ggagg--gcg---tccgaatgg--accgc-----ggcgatttggg
                      Pig  g-a--------g-------------ggagg--aggg--tttacctgg--accac-----gggaatttgag
                  Dolphin  g-a--------g-------------ggagg--aggg--tctgactcg--accgc-----ggtgatttgca
                      Cow  g-a--------g-------------ggagg--aggg--tctgactca--acccc-----ggtgatttgag
                    Sheep  g-a--------g-------------ggagg--aggg--tctgactca--accgc-----ggtgatttgag
                    Horse  g-c--------g-------------ggagg--tggtggtctgactct--agcgc-----gatggtttggg
         Chinese pangolin  a-a--------g-------------agaag--gggc--tcggattcg--acagc-----ggtagttt-ta
                      Dog  g-g--------ggtggggggagggagggag--ggtg--tccgattcg--acctt-----agtggtttggg
       Hawaiian monk seal  g-g--------g-------------gggag--gggg--tccgactcg--acctt-----agtggtttggg
                 Hedgehog  g-a--------g-------------agagggcgggt--cttgacccc--ac-------------------
                    Shrew  g-a--------a-------------ggagg--ggca--tctgacccg--acctc-----ggtagttt-gg
                 Elephant  g-a--------c-------------taggg--g-----cgcgaccag--actgcgcc--gtcgcctttgg
                   Tenrec  g-a--------c-------------ggggg--c-----tccgactcc--acc--------ccggctttga
                  Opossum  g-c--------a-------------ggagg--aggg--tgggagaat--gaagc-----agtcggatagt
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================
                   Rabbit  ======================================================================

                    Mouse  gacgtttggctc---------ag-gccggaacagtctggtttcg----g-g------------------
                      Rat  -----tgagctc---------ag-gctggagcagtctggttttg----g--------------------
            GCF_003668045  gctgtttggccc---------ag-gccgagactgtctggtttcg----g-g------------------
                   Beaver  gacgttcggcag---------tgttccgggactgtatattttgg----g-g------------------
                 Squirrel  gccgttcggcaa---------tg-ttcggggacctatggtttgg----g-g------------------
               Guinea pig  gctgttcagcga---------ag-tgcgggaccttagggttagg----g-g------------------
                     Pika  actgtgcgggccgtgtttgtagg-ggcagtggcgtccggtcctgctgcg-c------------------
                    Human  gccgttcggcta---------tgttcagggaccatatggtttgg----g-g------------------
                    Chimp  gccgttcggcta---------tgttcagggaccatatggtttgg----g-a------------------
                   Bonobo  gccgtttggcta---------tgttcagggaccatatggtttgg----g-a------------------
                  Gorilla  gccgttcggcta---------tgttcagggaccatatggtttgg----g-g------------------
                   Rhesus  gccgttcggcta---------tgttccgggaccgtatggtttgg----g-g------------------
                 Marmoset  cccgttcggctt---------tgttcaggaatcgtttggcttgg----g-g------------------
                  Tarsier  gccgctcggcca---------tgttcggggactgaatggtttgg----g-g------------------
                 Bushbaby  gccgttc-gcta---------tgttcgggaaccgtatggtttgg----g-g------------------
               Tree shrew  gccgttagacaa---------tgttaggggaccggatggtttgg----g-g------------------
     Malayan flying lemur  gccattcggcaa---------tgtttggggaccgtctggcttgg----g-g------------------
                      Pig  gccgttcctcaa---------ggctcggagatcctatggttcgg----g-g------------------
                  Dolphin  gccgttcctcaa---------ggctcggggaccttacggtttgg----t-g------------------
                      Cow  gccgttcctcaa---------ggctcggggaccgtatggtttgg----t-g------------------
                    Sheep  gccgttcctcaa---------ggctcggggaccgtatggtttgg----t-g------------------
                    Horse  gtcgtttggctg---------ggctcaaggaccgaatgatttgg----g-g------------------
         Chinese pangolin  gcggttcggcaa---------ggct-agcgatcttatgg-ctgg----g-g------------------
                      Dog  gctgttgggcaa---------ggctcggggacagtagggtttgg----g-a------------------
       Hawaiian monk seal  gccattgggcaa---------ggctcgggggcagtagggtttgg----g-a------------------
                 Hedgehog  --ggtccagctg---------ggctc-gagaccgtcgcgtctgg----g-g------------------
                    Shrew  gtggttgggcta---------agctcggagaccgtagagttcgg----gag------------------
                 Elephant  gctgttcggcga---------ggttcgtggttcgtatggtttgg----g-g------------------
                   Tenrec  gccgatcggcgt---------ggttcgtggagcatgtgatttgg----g-a------------------
                  Opossum  tcatttcagtga---------ggcttcggaaccatgcgatttga----a-gacccactttggtttaggg
                Zebrafish  =====================================================================
            X. tropicalis  =====================================================================
                  Chicken  =====================================================================
                   Rabbit  =====================================================================

Inserts between block 18 and 19 in window
B D              Opossum 86bp

Alignment block 19 of 344 in window, 56743235 - 56743277, 43 bps 
B D                 Mouse  gcaaccccag----tcctt------atagaagg-gtgt-----------------c---ataaccctgcc
B D                   Rat  ------------------------------agg-gtgt-----------------c---ataacactgcc
            GCF_003668045  gcagccacaa----tccta------tcaggagg-gtgt-----------------c---atagctctgtc
                   Beaver  acagccccag----tcgttagtc--aggggcgg-gtac-----------------g---ttagccctgcc
B D              Squirrel  acagtacaag----tggttagtc--aggggtgg-gtgc-----------------g---ttagttctgtc
B D            Guinea pig  acagcccccg----tcctaag----tcggggcg-gttc-----------------c---ttagcccggcc
B D                  Pika  tcagccccgg----gcccacgtcttggggggag-gtgc-----------------gcgtgtgggccggcc
B D                 Human  acagccccag----tagttagta--ggggacgg-gtgc-----------------g---ttcgcccagtc
B D                 Chimp  acagccccag----tcgttagta--cgggacgg-gtgc-----------------g---ttcgcccagtc
B D                Bonobo  acagccccag----tcgttagta--cgggacgg-gtgc-----------------g---ttcgcccagtc
B D               Gorilla  acagccccag----tcgttagta--cgggacgg-gtgc-----------------g---ttcgcccagcc
B D                Rhesus  acagtcccag----tcgttagta--cgggacgg-gcgc-----------------g---ttcgcccagtc
B D              Marmoset  acagcccctg----tcgttagta--caggacgg-gtgc-----------------g---ttcgcccagtc
B D               Tarsier  a-----cccg----cggttagcc--ccgggaga-gcgc-----------------t---ttcgccctgcc
B D              Bushbaby  acagccccag----tcgtcattc--tggggcgg-gtgc-----------------g---tcctccctgct
B D            Tree shrew  acagctccag----acgttagcc--tggggcgg-gtgc-----------------g---ttcgctctgcc
B D  Malayan flying lemur  acagcccccg----tcgttagtc--cggggcaa-gtgt-----------------g---tccgcccggtt
B D                   Pig  aaagcccggg----tccttagtc--ctaggc-g-gtgt-----------------a---tccgccttgcc
B D               Dolphin  aaagcccgggtccttccttagtc--cgaggcgg-gtgt-----------------a---tccgccttgta
B D                   Cow  aaagcccggg----tccttagtc--ccaggcgg-gtgc-----------------c---tccgccttgcc
B D                 Sheep  aaagcccggg----tccttagtc--ccaggcgg-gtgc-----------------c---tccgtcttgcc
B D                 Horse  aaagccgggg----tccttagtc--cggggcgg-gtgc-----------------a---accgccctgcc
B D      Chinese pangolin  aaagct-ggg----tccttagtc--ctgggtggtttgt-----------------a---gccaacct-tc
B D                   Dog  aaagcccagg----ttccccgcc--gggggtgg-gtgc-----------------a---tctacccagcc
B D    Hawaiian monk seal  aaagcccagg----tcccgagtc--ccgggtgg-gtgc-----------------a---tctgccctgcc
B D              Hedgehog  acagcccgcg----tctgtagtc--tgggacgc-gtgtcagtctgtctgtcggcgt---gtcggcctgtc
B D                 Shrew  aaagcccggg----tcttgactc--cggatcct-gtgc-----------------t---cccgccctacc
B D              Elephant  acagcccctg----tccttgatc--cggggcga-gtga-----------------g---ttcgccctgcc
B D                Tenrec  acagtccctg----tccctgtcc--cacggcta-gtgg-----------------g---ttcg-cctgcc
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================
B D                Rabbit  ======================================================================

                    Mouse  cctg
                      Rat  cctg
            GCF_003668045  atcg
                   Beaver  cccg
                 Squirrel  cccg
               Guinea pig  cctg
                     Pika  accc
                    Human  cccg
                    Chimp  cccg
                   Bonobo  cccg
                  Gorilla  cccg
                   Rhesus  cccg
                 Marmoset  cccg
                  Tarsier  cgcg
                 Bushbaby  cccg
               Tree shrew  ccgg
     Malayan flying lemur  cgcg
                      Pig  ccca
                  Dolphin  cctg
                      Cow  ccct
                    Sheep  ccct
                    Horse  ccct
         Chinese pangolin  ccct
                      Dog  ccct
       Hawaiian monk seal  ttct
                 Hedgehog  ctcc
                    Shrew  tccc
                 Elephant  ccca
                   Tenrec  ccca
                Zebrafish  ====
            X. tropicalis  ====
                  Opossum  ====
                  Chicken  ====
                   Rabbit  ====

Inserts between block 19 and 20 in window
B D             Hedgehog 6bp
B D                Shrew 6bp

Alignment block 20 of 344 in window, 56743278 - 56743286, 9 bps 
B D                 Mouse  gac----------gctctt-----------
B D                   Rat  gaa----------gctctt-----------
            GCF_003668045  gac----------actcgt-----------
                   Beaver  gac----------gctttc-----------
B D              Squirrel  gac----------actcac-----------
B D            Guinea pig  gac----------gcggac-----------
B D                  Pika  cgc----------gccctcgctgtgcaccg
B D                 Human  gat----------gcgtag-----------
B D                 Chimp  gat----------gcgtag-----------
B D                Bonobo  gat----------gcgtag-----------
B D               Gorilla  gat----------gcgtag-----------
B D                Rhesus  gac----------gcgcag-----------
B D              Marmoset  gac----------gcgcag-----------
B D               Tarsier  ggc----------gcgcac-----------
B D              Bushbaby  gac----------gcgcac-----------
B D            Tree shrew  gac----------gcgcac-----------
B D  Malayan flying lemur  gac----------gcgcac-----------
B D                   Pig  gac----------gcgcgc-----------
B D               Dolphin  gac----------acgcgc-----------
B D                   Cow  gac----------gcgcgc-----------
B D                 Sheep  gac----------gcgcgc-----------
B D                 Horse  gat----------gggcgc-----------
B D      Chinese pangolin  gac----------actcgc-----------
B D                   Dog  gac----------gtgggc-----------
B D    Hawaiian monk seal  gac----------gtcggc-----------
B D              Hedgehog  gtagtgtgtgtgcgcgcgc-----------
B D                 Shrew  aaa----------gcgcac-----------
B D              Elephant  gac----------gcgcgc-----------
B D                Tenrec  cac----------gcgcgc-----------
B D             Zebrafish  ==============================
B D         X. tropicalis  ==============================
B D               Opossum  ==============================
B D               Chicken  ==============================
B D                Rabbit  ==============================

Alignment block 21 of 344 in window, 56743287 - 56743347, 61 bps 
B D                 Mouse  ggaggccgagtgg----caggcgg-ctgtcccaag---------------cagttggtgcgcgttgtggc
B D                   Rat  ggaggccgagtgg----caggctg-ctgtcccaag---------------cagttggtgcgcgttgtggc
            GCF_003668045  ggaggccgagtgg----caggcgt-ttgtcccaag---------------aagcgggtgcgcgttgtcgc
                   Beaver  ggaggccgagtgg----caggcgg-cggtcccaag---------------cagcgggcgcgcgtccccgc
B D              Squirrel  --agtccaagtgg----caggcgg-ctgtcccaag---------------cggcgggtgcgcgtccccgc
B D            Guinea pig  ggaggccaagtgg----caggcag-ttgtcccaag---------------cggcggttgcgcgtccctgc
B D                  Pika  gggaagcgagcgg-gcacgggcggcctgtcccaag---------------cggcgggtgcgcgtccc--c
B D                 Human  ggaggcccagtgg----caggcag-ctgtcccaag---------------cagcgggtgcgcgtccctgc
B D                 Chimp  ggaggcccagtgg----caggcgg-ctgtcccaag---------------cagcgggtgcgcgtccctgc
B D                Bonobo  ggaggcccagtgg----caggcgg-ctgtcccaag---------------cagcgggtgcgcgtccctgc
B D               Gorilla  ggaggcccggtgg----caggcgg-ctgtcccaag---------------cagcgggtgcgcgtccctgc
B D                Rhesus  ggaggcccagtgg----caggcgg-ctgtcccaag---------------cagcgggtgcgcgcccctgc
B D              Marmoset  ggaggcccagtgg----caggcgg-ctgtcccaag---------------cagcgtgtgcgcgtctccgc
B D               Tarsier  ggaggccgggcgg----caggcag-ctgtcccaag---------------aggcgggtgcgcgtccccgc
B D              Bushbaby  tgaggtcgagtgg----caggcag-ctgtcccaag---------------cggcgggtgcgcgtccccgc
B D            Tree shrew  ggaggccgggtgg----caggctg-ctgtcccaag---------------cagcgggtgtgcgtccccgc
B D  Malayan flying lemur  ggaggccgacagg----caggcgg-ctgtcccaag---------------cggcgggtgcgcgtccccgc
B D                   Pig  ggagcccaagcag----caagcag-ctgtcccaaa---------------cagcgggtgcgcgtccccac
B D               Dolphin  ggaggccgagtgg----caagcgc-ttgtcccaaa---------------ctgcggatgcgcgtccccgc
B D                   Cow  ggaggccgagtgg----caagcgg-ttgtcccaaa---------------ctgtgggtgcgcgtccccgc
B D                 Sheep  ggaggccgagtgg----caagcgg-ttgtcccaaa---------------ctgtgggtgcgcgtccccgc
B D                 Horse  ggaggccgagtgg----caagcgg-ctgtcccaaa---------------ctgcgggtgcgcgttcccgc
B D      Chinese pangolin  ggaggccgagtgt----caagcga-ctgttccaaa---------------ctgcgggtgcgcgttcccgc
B D                   Dog  ggaggccgagtgg----taaccgg-ctgtcccaaa---------------ctgccggggcgcgtccccgc
B D    Hawaiian monk seal  ggaggccgagtgg----taaacgg-ctgtcccaaa---------------ctgccggtgcgcgtccccgc
B D              Hedgehog  ggaggccgagcgg----ccagcga-cctccccgaa---------------cagcgagtgcgcgtccccgc
B D                 Shrew  ggagatc--gcgg----caagctg-ctgtcccgaa---------------ctgcgggtgcgcgtccctgc
B D              Elephant  ggaggccgagtgg----caagcgg-ctgtcccaag---------------cggcgggtgcgcgtccccgc
B D                Tenrec  ggaggccgggtgt----caggcag-ctgtcccaag---------------cggcgggtgcgcgtccccgc
B D               Opossum  ggaggaagaagggtgatctgacag-ttgtcacagtgatctgtgtgtgttcctgtgcgcgcgcgagcgcgc
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================
B D                Rabbit  ======================================================================

                    Mouse  gcgctctgtgc-------
                      Rat  gcgctctatgg-------
            GCF_003668045  gcgctctgtgc-------
                   Beaver  gcgctatgtgt-------
                 Squirrel  gcgctgtgtgt-------
               Guinea pig  gcgctgtgtgt-------
                     Pika  gcgctgtgtgt-------
                    Human  gcgctgtgtgt-------
                    Chimp  gcgctgtgtgt-------
                   Bonobo  gcgctgtgtgt-------
                  Gorilla  gcgctgtgtgt-------
                   Rhesus  gcgctgtgtgt-------
                 Marmoset  gcgctgtgtgt-------
                  Tarsier  gcgctctgtgt-------
                 Bushbaby  gcgctgtgtgt-------
               Tree shrew  gctccttgtgt-------
     Malayan flying lemur  gcgctatgtgt-------
                      Pig  gcgcc-tgtgt-------
                  Dolphin  gcgccatgtgt-------
                      Cow  gcgccgtgtgt-------
                    Sheep  gcgccgtgtgt-------
                    Horse  gtgccgtgtgt-------
         Chinese pangolin  gcgcc--ctgt-------
                      Dog  gcgccgcgtgt-------
       Hawaiian monk seal  gcgccgtgtgt-------
                 Hedgehog  gcgccgtgtgt-------
                    Shrew  gcgccgtgtgt-------
                 Elephant  gcgccctgtgt-------
                   Tenrec  gcgccttgtgt-------
                  Opossum  gcgttgtttgcgtttatg
                Zebrafish  ==================
            X. tropicalis  ==================
                  Chicken  ==================
                   Rabbit  ==================

Alignment block 22 of 344 in window, 56743348 - 56743352, 5 bps 
B D                 Mouse  tcct-t
B D                   Rat  tcct-t
            GCF_003668045  tcct-t
                   Beaver  tcct-t
B D              Squirrel  tcct-t
B D            Guinea pig  tcct-t
B D                  Pika  tcgt-t
B D                 Human  tcat-t
B D                 Chimp  tcat-t
B D                Bonobo  tcat-t
B D               Gorilla  tcat-t
B D                Rhesus  tcgt-t
B D              Marmoset  tcgt-t
B D               Tarsier  tggt-c
B D              Bushbaby  ttgt-t
B D            Tree shrew  tcgt-t
B D  Malayan flying lemur  tcgt-t
B D                   Pig  tcgt-t
B D               Dolphin  tcgt-t
B D                   Cow  tcgt-t
B D                 Sheep  tcgt-t
B D                 Horse  tcat-t
B D      Chinese pangolin  cccc-t
B D                   Dog  tggt-t
B D    Hawaiian monk seal  tcgt-t
B D              Hedgehog  tggtct
B D                 Shrew  tcat-t
B D              Elephant  tcgt-t
B D                Tenrec  tcgt-t
B D               Opossum  ttct-t
B D         X. tropicalis  tctc-t
B D             Zebrafish  ======
B D               Chicken  ======
B D                Rabbit  ======

Alignment block 23 of 344 in window, 56743353 - 56743355, 3 bps 
B D                 Mouse  ttg
B D                   Rat  ttg
            GCF_003668045  ttg
                   Beaver  ttg
B D              Squirrel  ttg
B D            Guinea pig  tcg
B D                  Pika  tcg
B D                 Human  ttg
B D                 Chimp  ttg
B D                Bonobo  ttg
B D               Gorilla  ttg
B D                Rhesus  ttg
B D              Marmoset  ttt
B D               Tarsier  ttg
B D              Bushbaby  ttg
B D            Tree shrew  ttg
B D  Malayan flying lemur  ttg
B D                   Pig  ttg
B D               Dolphin  ttg
B D                   Cow  ttg
B D                 Sheep  ttg
B D                 Horse  ttg
B D      Chinese pangolin  ttg
B D                   Dog  ttg
B D    Hawaiian monk seal  ttg
B D              Hedgehog  ttg
B D                 Shrew  ttg
B D              Elephant  ttg
B D                Tenrec  ttg
B D               Opossum  ttg
B D               Chicken  ttg
B D         X. tropicalis  ttg
B D             Zebrafish  ===
B D                Rabbit  ===

Alignment block 24 of 344 in window, 56743356 - 56743356, 1 bps 
B D                 Mouse  c
B D                   Rat  c
            GCF_003668045  c
                   Beaver  c
B D              Squirrel  c
B D            Guinea pig  c
B D                  Pika  c
B D                 Human  c
B D                 Chimp  c
B D                Bonobo  c
B D               Gorilla  c
B D                Rhesus  c
B D              Marmoset  t
B D               Tarsier  c
B D              Bushbaby  c
B D            Tree shrew  c
B D  Malayan flying lemur  c
B D                   Pig  c
B D               Dolphin  c
B D                   Cow  c
B D                 Sheep  c
B D                 Horse  c
B D      Chinese pangolin  c
B D                   Dog  c
B D    Hawaiian monk seal  c
B D              Hedgehog  c
B D                 Shrew  c
B D              Elephant  c
B D                Tenrec  c
B D               Opossum  c
B D               Chicken  c
B D         X. tropicalis  c
B D               Lamprey  c
B D             Zebrafish  =
B D                Rabbit  =

Alignment block 25 of 344 in window, 56743357 - 56743386, 30 bps 
B D                 Mouse  agagccagccttcggggaggtgaaccagct
B D                   Rat  agagccagccttcggggaggtgaaccagct
            GCF_003668045  agagccagccttcggggaggtgaaccagct
                   Beaver  agagccagccttcggggaggtgaaccagct
B D              Squirrel  agagccagctttcggggaggtgaaccagct
B D            Guinea pig  agagccagccttcggggaggtgaaccagct
B D                  Pika  agagccagccttcggggaggtgaaccaact
B D                 Human  agagccagccttcggggaggtgaaccagct
B D                 Chimp  agagccagccttcggggaggtgaaccagct
B D                Bonobo  agagccagccttcggggaggtgaaccagct
B D               Gorilla  agagccagccttcggggaggtgaaccagct
B D                Rhesus  agagccagccttcggggaggtgaaccagct
B D              Marmoset  agagccagctttcggggaggtgaaccagct
B D               Tarsier  agaaccagccttcggggaggtgaaccagct
B D              Bushbaby  agagccagccttcggggaggtgaaccagct
B D            Tree shrew  agagcctgcctttggggaggtgaaccagct
B D  Malayan flying lemur  agaaccagccttcggggaggtgaaccagct
B D                   Pig  agagccagcctttggggaggtgaaccagct
B D               Dolphin  agagccagccttcggggaggtgaaccagct
B D                   Cow  agagccagcctttggggaggtaaaccagtt
B D                 Sheep  agagccagcctttggggaggtaaaccagtt
B D                 Horse  agagccagcctttggggaggtgaaccagct
B D      Chinese pangolin  agagccagcctttggggaggtgaaccagct
B D                   Dog  agagccagcctttggggaggtgaaccagct
B D    Hawaiian monk seal  agagccagcctttggggaggtgaaccagct
B D              Hedgehog  agagccggccttcggggaggtgaaccagct
B D                 Shrew  agagccagcctttggggaggtgaaccagct
B D              Elephant  agagccagccttcggggaggtgaaccagtt
B D                Tenrec  agagccagccttcggggaggtgaaccagtt
B D               Opossum  agagccagctttcggggaggtcaaccagct
B D               Chicken  agaacccgccttcggggaggtgaaccagct
B D         X. tropicalis  agaacccgctttcggggaagtgaaccagct
B D             Zebrafish  agagccagcctttggggaggtgaaccaact
B D               Lamprey  agaccagtcgttcggcgaggtgaaccagct
B D                Rabbit  ==============================

Alignment block 26 of 344 in window, 56743387 - 56743918, 532 bps 
B D                 Mouse  gggaggagtgttcgtgaacggaaggccgctgcccaacgccattcggcttcgcatcgtggaattagcccaa
B D                   Rat  gggaggagtgttcgtgaacggaaggccgctgcccaacgccattcggcttcgcatcgtggaattagcccaa
            GCF_003668045  gggaggagtgttcgtgaacggaaggccgctgcccaacgccattcgacttcgcatcgtggaattagcccaa
                   Beaver  gggaggagtgttcgtgaacggaaggccgcttcccaacgccatccggcttcgcatcgtggaactagcccaa
B D              Squirrel  gggaggagtgttcgtgaacggaaggccgctgcccaacgccatcaggcttcgtattgtggaactggcccaa
B D            Guinea pig  gggaggagtgttcgtgaacggaaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                Rabbit  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccag
B D                  Pika  gggaggagtgttcgtgaacgggagaccgctgcccaacgccatccggcttcgcatcgtggaactggcccag
B D                 Human  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                 Chimp  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                Bonobo  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D               Gorilla  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                Rhesus  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D              Marmoset  gggtggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D               Tarsier  gggaggagtgttcgtgaacggcaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D              Bushbaby  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatagtggaactggcccaa
B D            Tree shrew  gggaggagtgtttgtaaacgggaggccgctgcccaacgccatccggcttcgcatagtggaactggcccaa
B D  Malayan flying lemur  gggaggagtgttcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                   Pig  cggaggagtattcgtgaacgggaggccgctgcccaacgccatccggcttcgcatagtggaactggcccaa
B D               Dolphin  gggaggagtattcgtgaacgggaggccgctgcccaacgccattcggcttcgcatagtggagctggcccaa
B D                   Cow  gggaggagtattcgtgaacgggaggccgctgcccaacgccatccggcttcgcatagtggagctggcccaa
B D                 Sheep  gggaggagtattcgtgaacgggaggccgctgcccaacgccatccggcttcgcatagtggagctggcccaa
B D                 Horse  gggaggagtattcgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D      Chinese pangolin  gggaggagtattcgtgaacgggaggccgctgcccaacgccatccggcttcgtatcgtggaactggcccaa
B D                   Dog  gggaggagtattcgtgaacgggaggccgctgcccaacgctatccggcttcgtatcgtggaactggcccaa
B D    Hawaiian monk seal  gggaggagtattcgtgaacgggaggccgctgcccaacgccatccggcttcgtatcgtggaactggcccaa
B D              Hedgehog  gggaggagtgtttgtcaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                 Shrew  gggaggagtattcgtgaacgggaggcccctgcctaacgccatccggcttcgcatcgtggaactggcccaa
B D              Elephant  gggaggagtgtttgtgaacgggaggccgctgcccaacgccatccggcttcgcatcgtggaactggcccaa
B D                Tenrec  gggaggagtgtttgtgaacgggaggccgctgcctaacgccatccggcttcgtatcgtggaactggcccaa
B D               Opossum  gggaggggtattcgtgaacgggaggcctttacccaacgccatcagactccgcatcgtggaactggcccaa
B D               Chicken  cgggggggtgttcgtcaacgggaggcccctgcccaacgccatccggctccggattgtggaactggcacag
B D         X. tropicalis  gggcggcgtgtttgtgaatgggaggcctctgcccaatgccatccgcctgcggatcgtggagctggcgcag
B D             Zebrafish  aggcggtgtttttgtcaacggaagacccctacccaatgccatccggctcaggatagtagagttggcccag
B D               Lamprey  gggcggcgtcttcgtgaacgggcgaccgctgcccaacgcgatccgcctgcgcatcgtagagatggcgcag

                    Mouse  ctgggcatccgaccttgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                      Rat  ctgggcatccgaccttgtgacatcagccgacagctacgggtctcgcacggctgcgtcagcaagatcttgg
            GCF_003668045  ctgggcatccgaccttgtgacatcagccgccagttacgggtctcacacggctgcgtcagcaagatcctgg
                   Beaver  ctgggcatccgaccctgtgacatcagccgccagctaagagtctcgcacggctgcgtcagcaagatcctgg
                 Squirrel  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctctcacggctgcgtcagcaagatcctgg
               Guinea pig  ctgggcatccgaccgtgtgacatcagccgccaactccgggtctcgcacggttgcgtcagcaagatcttgg
                   Rabbit  ctgggcatccgaccgtgtgacatcagccgccagctacgagtctcgcacggctgcgtcagcaagatcctgg
                     Pika  ctgggcatccgaccgtgtgacatcagccgccagctgcgggtctctcatggttgcgtcagcaagatcctgg
                    Human  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                    Chimp  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                   Bonobo  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                  Gorilla  ctgggcatccgaccctgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                   Rhesus  ctgggcatccgaccgtgtgacatcagccggcagctacgggtctcgcacggctgcgtcagcaagatcctgg
                 Marmoset  ctgggcatccgaccctgtgacatcagccgccagctacgggtctcacacggctgtgtcagcaagatcctgg
                  Tarsier  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggttgcgtcagcaagatcctgg
                 Bushbaby  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtgagcaagatcctgg
               Tree shrew  ctgggcatccgaccgtgtgacatcagccgccagttaagggtctctcacggctgcgtcagcaagatcttgg
     Malayan flying lemur  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcacacggctgcgtcagcaagatcctgg
                      Pig  ctgggcatcagaccatgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                  Dolphin  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                      Cow  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                    Sheep  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagatcctgg
                    Horse  ctgggcatccgaccgtgtgacatcagccgccagctacgggtctcacacggctgcgtcagcaagatcctgg
         Chinese pangolin  ctgggcatcagaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagattctag
                      Dog  ctgggcatcagaccgtgtgacatcagccgccagctacgggtctcacacggctgcgtcagcaagattctgg
       Hawaiian monk seal  ctgggcatcagaccgtgtgacatcagccgccagctacgggtctcgcacggctgcgtcagcaagattctgg
                 Hedgehog  ctgggcatccgaccgtgtgacatcagccgccagctccgggtgtcccacggctgcgtcagcaagatcctgg
                    Shrew  ctgggcatccgaccctgtgacatcagccgccagctacgggtctcgcacggctgcgtcagtaagatcctgg
                 Elephant  ctgggcatccgaccgtgtgacatcagccgtcagctacgggtctcgcacggctgcgtcagcaagatcctgg
                   Tenrec  ctgggcattcgaccgtgtgacatcagccgccagctacgggtctcgcacggctgtgtcagcaagatcctgg
                  Opossum  ttgggcatccgaccctgtgacatcagccggcagttaagagtgtcccatggctgtgtcagtaagatactgg
                  Chicken  ctggggatcaggccctgcgacatcagccgccagctccgcgtttcccacggctgtgtgagcaaaatcctgg
            X. tropicalis  ctgggcatccggccgtgcgatatcagtaggcagctgcgagtgtcgcacggatgtgtcagcaagattctag
                Zebrafish  ttgggcatcaggccttgtgacatcagcaggcagctccgcgtctcccacggctgcgtgagcaagattctgg
                  Lamprey  ctgggcatcaggccgtgcgacatctcgcggcagctgcgcgtctcccacggctgcgtctccaagatcctgg

                    Mouse  cgcgctacaacgagaccggttcgattttgccgggagctattggggggagcaagccccgggtcacca-ccc
                      Rat  cgcgctacaacgagaccggttcgattttgccgggagctatcgggggaagcaagccccgggtcacca-ccc
            GCF_003668045  cgcgctacaacgagaccggctcgattttgcccggagccatcgggggcagcaaaccccgggtcacca-ctc
                   Beaver  cgcgctacaatgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
                 Squirrel  cgcgctacaatgaaacaggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacca-ctc
               Guinea pig  cgcgctacaatgagacgggctcgatcttgcctggagcgattgggggcagcaagccgcgggtcacca-ctc
                   Rabbit  cgcgctacaacgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacca-ccc
                     Pika  cgcgctacaacgagaccggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacga-ccc
                    Human  cgcgatacaacgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
                    Chimp  cgcgatacaacgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
                   Bonobo  cgcgatacaacgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
                  Gorilla  cgcgatacaacgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
                   Rhesus  cgcgatacaacgagacgggctcgatcttgcctggagccatcgggggcagcaagccccgggtcacta-ccc
                 Marmoset  cgcgctacaacgaaacaggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
                  Tarsier  cgcgctacaacgagacgggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacaa-ccc
                 Bushbaby  cgcgctacaacgagacgggttcgatcttgccaggagccatcgggggcagcaagccccgagtcacca-ccc
               Tree shrew  cgcgctacaacgagacaggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ccc
     Malayan flying lemur  cgcgctacaacgagacaggctcaatcttgccaggagccatcgggggcagcaagccccgggtcacca-cac
                      Pig  cgcgctacaatgagacaggctcaatcttgccaggagccatcgggggtagcaagcctcgggtcacca-ccc
                  Dolphin  cgcgctacaatgagacaggctcgatcttgccaggggccattgggggcagcaagcctcgggtcacca-ccc
                      Cow  cgcgctacaatgagacaggctcgatcttgccaggagccattgggggcagcaagcctcgggtcacca-ccc
                    Sheep  ctcgctacaatgagacaggctcgatcttgccaggagccattgggggcagcaagcctcgggtcacca-ccc
                    Horse  cgcgctacaacgagacaggctcgatcttgccaggagccattgggggcagcaagccccgggtcacca-ccc
         Chinese pangolin  cgcgctacaacgagacaggctcgatcttgccaggagccatcgggggcagcaagccccgggtcacta-ctc
                      Dog  cgcgctacaacgagacgggctcgatcttgccaggagccattgggggcagcaagccccgagttacca-ccc
       Hawaiian monk seal  cgcgctacaacgagactggctcgatcttgccaggagccattgggggcagtaagccccgagttacca-ccc
                 Hedgehog  cgcgctacaacgagacgggctcgatcttgcccggagccatcggaggcagcaaaccccgggtcacca-ccc
                    Shrew  cgcgctacaacgagacgggctcgatcttgcccggagctatagggggcagtaagcctcgggtcacca-ccc
                 Elephant  cgcgctacaacgagacaggctcgatcttgccaggggccattgggggcagcaagccccgggtcaccacccc
                   Tenrec  cgcgctacaacgagacgggttcgatcttgccaggggccatcgggggcagcaagccccgggtcacca-ccc
                  Opossum  cgcgctacaatgagactggctccatcttacctggggccattgggggcagcaaacctcgggttacca-ccc
                  Chicken  ctcgctacaacgagaccggctccatcctaccgggggctatcggaggcagcaagccgcgggtcacca-ccc
            X. tropicalis  cgcggtacaacgagaccggctccatcctgccgggggccatcgggggcagcaagcccagggtcacta-ccc
                Zebrafish  ctcggtacaacgaaaccggctcaatacttcccggtgcaatcggcggcagtaaaccgagggtcacga-ccc
                  Lamprey  ctcgctacaacgagacgggctccatcctgccgggagccatcgggggaagcaagccgcgcgtcacca-ccc

                    Mouse  ctactgtggtgaaacacatccggacttacaagcagagggacccaggcatcttcgcttgggagatccggga
                      Rat  ctactgtagtgaaacacatccggacttacaagcagagggacccaggcatctttgcttgggagatccggga
            GCF_003668045  ccactgtggtgaaacacatccggacttacaagcagagggacccgggcatcttcgcttgggagatccggga
                   Beaver  ccaccgtggtgaagcacatcagaacctacaagcagagggacccaggcatcttcgcctgggagatccggga
                 Squirrel  ccaccgtagtgaaacacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
               Guinea pig  ccaccgtggtgaagcacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccgcga
                   Rabbit  ccaccgtggtgaagcacatccggacctacaagcagagggacccgggtatcttcgcctgggagatccggga
                     Pika  ccacggtggtgaagcacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccgtga
                    Human  ccaccgtggtgaaacacatccggacctacaagcagagagaccccggcatcttcgcctgggagatccggga
                    Chimp  ccaccgtggtgaaacacatccggacctacaagcagagagaccccggcatcttcgcctgggagatccggga
                   Bonobo  ccaccgtggtgaaacacatccggacctacaagcagagagaccccggcatcttcgcctgggagatccggga
                  Gorilla  ccactgtggtgaaacacatccggacctacaagcagagagaccccggcatcttcgcctgggagatccggga
                   Rhesus  ccaccgtggtgaaacacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
                 Marmoset  ccaccgtggtgaagcacatccggacctacaagcagagggaccctggcatcttcgcctgggagatccggga
                  Tarsier  ctaccgtggtgaaacacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
                 Bushbaby  ctacagtggtgaaacacatccggacctacaagcagagggaccctggcatcttcgcctgggagatccggga
               Tree shrew  ccacagtagtgaaacacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
     Malayan flying lemur  ccaccgtggtgaaacacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
                      Pig  ccaccgtggtgaagcacatccggacctacaagcagagggatcccggcatcttcgcctgggaaatacggga
                  Dolphin  ccactgtggttaagcacatccggacctacaagcagagggaccccggcatcttcgcctgggagatacggga
                      Cow  ccaccgtggtgaagcacatccggacctacaagcagagagaccccggcatcttcgcctgggagatacggga
                    Sheep  ccaccgtggtgaagcacatccggacctacaagcagagagaccccggcatcttcgcctgggagataaggga
                    Horse  ctaccgtggtgaagcacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
         Chinese pangolin  ccaccgtggtgaagcacatccggacctacaagcagagggaccccggcatctttgcctgggagatccggga
                      Dog  ccaccgtggtgaagcacatccggacctacaagcaaagggatcctggcatctttgcctgggaaatccggga
       Hawaiian monk seal  ccaccgtggtgaagcacatccggacctacaagcaaagggaccctggcatctttgcctgggaaatccggga
                 Hedgehog  ccaccgtggtgaagcacatccggacctacaagcagagggaccccggcatcttcgcctgggagatccggga
                    Shrew  ccaccgtggtgaagcacatccggacctacaagcagagggacccgggcatcttcgcctgggagatccggga
                 Elephant  ccaccgtggtgaaacacatccggacctacaagcagagggaccccggcatcttcgcctgggagattcggga
                   Tenrec  ccaccgtggtgaaacacatccggacctacaagcagagggaccccggcatctttgcctgggagattcggga
                  Opossum  ccacagtagtgaaacatatccggacctacaagcagagggacccaggaatctttgcctgggagatacgcga
                  Chicken  ccacggtggttaaacatatccggacctacaaacaaagggatccgggcatcttcgcctgggagatccggga
            X. tropicalis  ccactgtggtcaaacacatacggacttacaagcagagggacccgggcatcttcgcttgggagatcaggga
                Zebrafish  caaacgtagtcaagcacattaggacttacaagcaacgggaccctggtattttcgcatgggagattcgaga
                  Lamprey  ccaacgtggtcaaccacatccgcacgtacaagcagcgagacccgggaatcttcgcgtgggaaatccgcga

                    Mouse  ccgcctgctggcggatggcgtgtgcgacaagtacaacgtgccctcggtgagttccatcagccgtattctg
                      Rat  ccgcctgctggcggatggcgtgtgcgacaagtacaacgtaccctctgtgagttccatcagccggattctg
            GCF_003668045  ccgcctgctggcggacggcgtgtgcgacaagtacaacgtgccctcggtgagttccatcagccggattctg
                   Beaver  ccgcctgctggcggacggcgtgtgcgacaagtacaacgtgccctcggtgagttccatcagccgcattctg
                 Squirrel  ccgcctgctggcggacggcgtgtgcgacaagtacaacgtgccctcggtgagttccatcagtcgcattctg
               Guinea pig  ccgcctgctggccgacggcgtgtgcgacaagtacaacgtgccctcggtgagttccatcagccgcattctg
                   Rabbit  ccgcctgctggcggacggcgtgtgtgacaagtacaacgtgccttcggtgagctccatcagccgcatcctg
                     Pika  ccgcctgctggcggacggcgtgtgcgacaagtacaacgtgccctcggtcagctccatcagccgcatcctg
                    Human  ccgcctgctggcggacggcgtgtgcgacaagtacaatgtgccctccgtgagctccatcagccgcattctg
                    Chimp  ccgcctgctggcggacggcgtgtgcgacaagtacaatgtgccctccgtgagctccatcagccgcattctg
                   Bonobo  ccgcctgctggcggacggcgtgtgcgacaagtacaatgtgccctccgtgagctccatcagccgcattctg
                  Gorilla  ccgcctgctggcggacggcgtgtgcgacaagtacaatgtgccctccgtgagctccatcagccgcattctg
                   Rhesus  ccgcctgctggcggacggtgtgtgcgacaagtacaacgtgccctccgtgagctccatcagccgtattctg
                 Marmoset  ccgcctgctggcggacggtgtgtgcgacaagtacaacgtgccctcggtgagctccatcagccgcattctg
                  Tarsier  ccgcctgctggcggacggcgtgtgcgacaagtacaacgtgccctcggtgagctccatcagccgcattctg
                 Bushbaby  ccgcctgctggcggacggcgtgtgcgacaagtacaacgtgccctcggtgagctccatcagccgcattctg
               Tree shrew  ccgcctgctggccgacggcgtatgcgacaagtacaacgtgccctctgtgagctccatcagccgcatcctg
     Malayan flying lemur  ccgcctgctggcagacggcgtgtgcgacaagtataacgtgccctcggtgagctccataagccgcattctg
                      Pig  ccgcctgctggcggatggagtgtgtgacaagtacaatgtgccctcggtgagctccatcagccgcatcctg
                  Dolphin  ccgcctactggcggacggcgtgtgtgacaagtacaacgtgccctcggtgagctctatcagccgcatcctg
                      Cow  ccgcctgctggcggacggcgtgtgtgacaagtacaacgtgccctcggtgagctccatcagccgcatactg
                    Sheep  ccgcctactggcggacggcgtgtgtgacaagtacaacgtgccctcggtgagctccatcagccgcatcctg
                    Horse  tcgcctgctggcagacggcgtgtgcgacaaatacaacgtaccctcggtgagctccatcagccgcatcctg
         Chinese pangolin  ccgcctgctggcggacggcgtatgtgacaagtacaatgtgccctcggtgagctctatcagtcgcatccta
                      Dog  ccgcctgctggcggacggcgtgtgtgacaagtacaacgtgccctcggtgagctccatcagccgcatcctg
       Hawaiian monk seal  ccgcctgctggcggacggcgtgtgtgacaagtacaacgtgccctcggtgagctccatcagccgcatcctg
                 Hedgehog  tcgcctgttggccgacggcgtgtgtgacaagtacaacgtgccctcggtgagctccatcagccgcatcctg
                    Shrew  ccgcctgctggctgacggcgtgtgcgacaagtacaacgtgccttcggtgagctccattagccgcatcctg
                 Elephant  ccgcctgctggctgacggcgtgtgtgacaagtacaatgtgccctcggtgagctccatcagccgcatcctg
                   Tenrec  ccgcctgctggcggacggcgtgtgcgacaaatacaacgtgccttcggtgagctctatcagccgtatcctg
                  Opossum  tcgtttgttagcagacggtgtgtgtgacaagtacaacgttccttcagtcagttccatcagccgaatcctg
                  Chicken  tcgcctgctggccgacggcgtgtgcgacaagtacaacgtgccgtcggtcagctctatcagccgcatcctc
            X. tropicalis  caggctgctggcagatggggtgtgcgacaagtacaacgtcccctcggtcagctccatcagccggatccta
                Zebrafish  cagactgctcgcggacggcgtatgtgataaatttaatttgccctctgtcagctcaattagtaggattctc
                  Lamprey  caagctgctcgccgacggcgtctgcgacaaatacaacgtgccctccgtgagctccatcagccgcatcctg

                    Mouse  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgactcatacaagc
                      Rat  cgcaacaagatcggcaacttg--------gcccagcagggtc------------tacg--tcctataagc
            GCF_003668045  cgcaacaagatcggcaacttg--------gcccagcaggccc----------actacgactcatacaagc
                   Beaver  cgcaacaagatcggcaacttg--------gcccagcaggggc----------attacgactcatacaagc
                 Squirrel  cgcaacaagatcggcaacttg--------gcccaacagggtc----------attacgactcatacaagc
               Guinea pig  cgcaacaagatcggcaacttg--------gcccagcaaagcc----------attatgattcgtacaagc
                   Rabbit  cgcaacaagatcggcaacttg--------gcccagcagggcc----------actacgactcctacaagc
                     Pika  cgcaacaagatcggcaacctg--------gcccagcagggcc----------attacgactcctacaagc
                    Human  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgactcatacaagc
                    Chimp  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgactcatacaagc
                   Bonobo  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgactcatacaagc
                  Gorilla  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgactcatacaagc
                   Rhesus  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgactcatacaagc
                 Marmoset  cgcaacaagatcggcaacttg--------acccagcagggtc----------attacgactcgtacaagc
                  Tarsier  cgcaacaagatcggcaacttg--------gcccagcagggtc----------actacgactcgtacaagc
                 Bushbaby  cgcaacaagatcggcaacttg--------gcccagcagggtc----------attacgattcgtacaagc
               Tree shrew  cgcaacaagatcggcaacttg--------gctcagcagggcc----------attacgactcctacaagc
     Malayan flying lemur  cgcaacaagatcggcaacttg--------gcccagcagggcc----------attacgactcatacaagc
                      Pig  cgcaacaagatcggcaacttg--------gcccaacagggcc----------attacgactcatacaaac
                  Dolphin  cgcaacaagatcggcaacttg--------gcccaacagggcc----------attacgactcatacaagc
                      Cow  cgcaacaagatcggcaacttg--------gcccaacagggcc----------attacgactcctacaagc
                    Sheep  cgcaacaagatcggcaacttg--------gcccaacagggcc----------attacgactcctacaagc
                    Horse  cgtaacaagatcggcaacttg--------gcccaacagggcc----------attacgactcattcaaac
         Chinese pangolin  cgcaacaaaatcgggaacttg--------gcccaacagggcc----------attacgactcatacaagc
                      Dog  cgcaacaagatcggcaacttg--------gctcaacagggcc----------attacgactcgtacaagc
       Hawaiian monk seal  cgcaacaagatcggcaacttg--------gctcaacagggcc----------attacgactcatacaagc
                 Hedgehog  cgcaacaagatcggcaacttg--------gcccagcagagcc----------actacgactcgtacaagc
                    Shrew  cgcaacaagatcggcaacttg--------gcccaacagagcc----------actacgactcctacaagc
                 Elephant  cgcaacaagatcggcaacctg--------gcccagcagggcc----------actacgactcatacaagc
                   Tenrec  cgcaacaagatcggcaacctg--------gctcagcagggcc----------actacgactcctacaaac
                  Opossum  cgcaacaagattggtaacctg--------tctcagcagagcc----------agtacgactcttacaaac
                  Chicken  cgcaacaagatcggaaacctg--------tcccagcagggcc----------actacgagtcctacaagc
            X. tropicalis  cggaataagatcgggaacctg--------gcccaacagaacc----------actatgagagccacaaac
                Zebrafish  cgcaacaagatcgggaatctg--------tctcaacagaacc----------agtacgagtcgagcaaac
                  Lamprey  cgcaacaagatcggcaacctgtcgcagccgcccaacgcgggcagctcctcgcactacgacggctccaagc

                    Mouse  agca-c---cagcccgcgccgcagcccgcgctgccctacaaccacatttactcatatcccagtcccatca
                      Rat  agca-c---cagccagcgccgcagcccgcgctgccctacaaccacatctactcctaccccagtcccatca
            GCF_003668045  agca-c---cagcctgcgccacagcccgcgctgccctacaaccacatctactcgtaccccagtcccatcg
                   Beaver  agca-c---cagccggcgccgcagcctgcgctgccctacaaccacatctattcgtaccctagtcccatca
                 Squirrel  agca-c---cagcccgcgccgcagcctgcgcttccctacaaccacatctactcataccccagtcccatca
               Guinea pig  agca-c---cagccggcgccacagcctgcgctgccctacaaccacatctactcgtatcctagtcccatca
                   Rabbit  agca-c---cagccggcgccgcagcccgcgctgccctacaaccacatctactcgtaccccagccccatta
                     Pika  agca-c---cagcccgcgccgcagcccgcgctgccctacaaccacatctactcgtaccccagccccatca
                    Human  agca-c---cagccgacgccgcagccagcgctgccctacaaccacatctactcgtaccccagccctatca
                    Chimp  agca-c---cagccgacgccgcagccggcgctcccctacaaccacatctactcgtaccccagccctatca
                   Bonobo  agca-c---cagccgacgccgcagccagcgctcccctacaaccacatctactcgtaccccagccctatca
                  Gorilla  agca-c---cagccgacgccgcagccagcgctgccctacaaccacatctactcgtaccccagccctatca
                   Rhesus  agca-c---cagccgacgccgcagccagcgctgccctacaaccacatctactcgtaccccagccctatca
                 Marmoset  agca-c---cagccggcaccgcagccagcgctgccctacaaccacatctactcataccccagtcctatca
                  Tarsier  agca-c---cagccggcgccgcagccggcgctgccctacaaccacatctactcgtaccccagccccatca
                 Bushbaby  agca-c---cagccggcgccccagccagcgctgccgtacaaccacatctactcgtaccccagccccatca
               Tree shrew  agca-c---cagccggcgcctcagccagcgctgccctacaatcacatctattcgtaccccagccccatca
     Malayan flying lemur  agca-c---cagccagcaccgcagcctacgctgccctacaaccacatctactcgtaccccagccccatca
                      Pig  agca-c---cagccggcaccgcagccggcgctgccctataaccacatctattcgtaccccagccccattt
                  Dolphin  agca-c---caaccggcgccgcagccggcgctgccctataaccacatctactcgtaccccagccccatca
                      Cow  agca-c---caaccggcgcctcagccggcgctaccctataaccacatctactcgtaccccagccccatca
                    Sheep  agca-c---caaccggcgccgcagccggcgctaccctataaccaccccccccccccccccacgcc-----
                    Horse  agca-c---cagccggcgccgcagccggcgctgccctataatcacatctactcgtaccccagccccatca
         Chinese pangolin  agca-c---cagcctgcaccgcagccggcgctgccctataaccacatctactcataccccagccccatca
                      Dog  agca-c---cagccggcgccacagccggcgctgccctataaccacatctactcgtaccccagccccatca
       Hawaiian monk seal  agca-c---cagccggcaccacagccggcgctgccctataaccacatctactcgtaccccagccccatca
                 Hedgehog  agca-c---cagcccgcgccgcagcctgcgctgccctacaaccacatctactcgtaccccagccctatct
                    Shrew  agca-c---caacccgcgccgcagcctgcgctgccctacaaccacatctactcgtaccccagccccatca
                 Elephant  agca-a---cagccggcgccgcagcccacgctgccctacaaccacatctattcgtaccctagccccatca
                   Tenrec  agca-c---cagccggcgccacagcccgcgctaccctacaaccacatttactcctaccccagccccataa
                  Opossum  agca-t---cagccaccaccgcagcccgccttgccttataaccatatatattcctatccaagtcccatta
                  Chicken  agca-t---cagccgcccccgcagccgcccctgccctacaaccacatctactcctaccccagccccatcg
            X. tropicalis  agcacc---cggccgccgcc----tccgcactcccttacaaccacctgtattcctaccccagccccatag
                Zebrafish  aggc-ctctcatcctcaacctcaacccaccataccctacaaccacctgtattcgtatccaactccaatag
                  Lamprey  agca-ggggcagtcgaccccgtcgggcgcccttccgtacaatcacatttacgcgtacccaagcgccatgg

                    Mouse  ---cggcggcagcagctaaggtgcctacaccacctggggtgccggccat---------------------
                      Rat  ---cggcggcagctgctaaggtgcccacaccacctggggtgccggccat---------------------
            GCF_003668045  ---ccgctgcggctgctaaggtgcctacaccacctggggtgcccgccat---------------------
                   Beaver  ---ccgcggcggccgccaaggtgcccacgccacctggtgtgcccgccat---------------------
                 Squirrel  ---cggcggctgccgccaaggtgcccacgccacccggggtgcccgccat---------------------
               Guinea pig  ---cggcggcggcagccaaggtgcccacgccacccggggtgcctgccat---------------------
                   Rabbit  cggcggctgcggccgccaaggtgcccacgccacccggggtgcccgccat---------------------
                     Pika  ---cggccgcggccgccaaggtgcccacgccacccggggtgcccgctct---------------------
                    Human  ---cggcggcggccgccaaggtgcccacgccacccggggtgcctgccat---------------------
                    Chimp  ---cggcggcggccgccaaggtgcccacgccacccggggtgcctgccat---------------------
                   Bonobo  ---cggcggcggccgccaaggtgcccacgccacccggggtgcctgccat---------------------
                  Gorilla  ---cggcggcggccgccaaggtgcccacgccacccggggtgcctgccat---------------------
                   Rhesus  ---cggcggcggccgccaaggtgcccacgccacccggggtgcctgccat---------------------
                 Marmoset  ---cggcggcggctgccaaggtgcccacaccacccggggtgcctgccat---------------------
                  Tarsier  ---cggcggcggccgccaaggtgcccacgcctcccggcgtgcccgccat---------------------
                 Bushbaby  ---ctgcggcggccgccaaggtgcccacgccgcccggtgtgcccgccat---------------------
               Tree shrew  ---cggcggcggctgccaaggtgcccacgccacccggggtgcccgccat---------------------
     Malayan flying lemur  ---cggcggcggccgccaaggtgcccacgccacccggggtgcccgccat---------------------
                      Pig  ---cagcggcc---gctaaggtgcccactccgcccggggtgcccgccat---------------------
                  Dolphin  ---cggcggccgcggctaaggtgcccacgccgcccggcgtgcccgccat---------------------
                      Cow  ---cggcggccgccgctaaggtgcccacgccgccgggggtgcccgccat---------------------
                    Sheep  ------cggccgccgctaaggtgcccacgccgccgggggtgccagccat---------------------
                    Horse  ---ctgcggccaccgctaaggtgcccacgccacccggggtgcccgccat---------------------
         Chinese pangolin  ---cggctgccgcggctaaggtgcccacgccgcccggggtgccagccat---------------------
                      Dog  ---cggcggccgcagctaaggtgcccacgcctcccggggtgcctgccat---------------------
       Hawaiian monk seal  ---cggcggccgcagctaaggtacccacgccgcccggggtgcctgccat---------------------
                 Hedgehog  ---cggcagccacggccaaggggcccacgccgcccggggtgcccgccct---------------------
                    Shrew  ---cggccgcggccgctaaggtgcccacgccgcccggcgtgcccgccat---------------------
                 Elephant  ---cggcggcggccgccaaggtacccacgccgcccggggtgccagccat---------------------
                   Tenrec  ---cggcggcggccgccaaggtacccacgccgcccggggtcccagccat---------------------
                  Opossum  ---ctgccgcagcagccaaagtacccactcctcccggagtgcctggaat---------------------
                  Chicken  ---ctgccgcgggagccaaggtgcccacgcctccgggagtgcctgccat---------------------
            X. tropicalis  ---cggcaggg---gccaaggtgcccacccctcctggaatgccctccat---------------------
                Zebrafish  ---cagccgctgggactaaagtaccaactccgcctggcatgcccactct---------------------
                  Lamprey  ------------ctcccaaggtgcccagccccgccgcgatgcccggggtaggagtcggggtcggggtggg

                    Mouse  ccccggatcggtggccttg
                      Rat  cccaggatccgtggccctg
            GCF_003668045  ccccggttccgtggctatg
                   Beaver  cccgggttcagtggccatg
                 Squirrel  ccccggctcggtggccatg
               Guinea pig  ccctggctcggtggccatg
                   Rabbit  ccccggttcggtggccatg
                     Pika  cccagcttcggtggccatg
                    Human  ccccggttcggtggccatg
                    Chimp  ccccggttcggtggccatg
                   Bonobo  ccccggttcggtggccatg
                  Gorilla  ccccggttcggtggccatg
                   Rhesus  ccccggttcggtggccatg
                 Marmoset  tcccggttcggtggccatg
                  Tarsier  ccccggctcggtggccctg
                 Bushbaby  tcccggttctgtggccatg
               Tree shrew  ccccggctcggtggccatg
     Malayan flying lemur  cccaggttcggtggccatg
                      Pig  cccagggtcagtggccatg
                  Dolphin  ccccggctcagtggccatg
                      Cow  ccccggctcagtggccatg
                    Sheep  ccccggctcagtggccatg
                    Horse  ccccggctcagtggccatg
         Chinese pangolin  ccccggctctgttgccatg
                      Dog  ccccggctcggtggccatg
       Hawaiian monk seal  ccccggctcggtggccatg
                 Hedgehog  ccccggctcggtggccatg
                    Shrew  ccccggctccgtggccatg
                 Elephant  ccccggctcggtggccatg
                   Tenrec  ccccggctcggtggctctg
                  Opossum  tcctggcaacatggccatg
                  Chicken  ccctggtaccatggccatg
            X. tropicalis  ccctggcaccatgggcatg
                Zebrafish  tcctggacatatggcaatg
                  Lamprey  catgggctccatgtgcatg

Alignment block 27 of 344 in window, 56743919 - 56743962, 44 bps 
B D                 Mouse  ccgcgcacctggccctcctctcactccgtcacggacattctggg
B D                   Rat  ccgcgcacctggccctcctctcactccgtcaccgacatcctggg
            GCF_003668045  ccgcgcacctggccctcctctcactctgtcaccgacatcctggg
                   Beaver  ccgcgcacctggccctcctcgcactctgtcaccgacatcctggg
B D              Squirrel  ccgcgcacctggccctcttcgcactctgtcaccgacatcctggg
B D            Guinea pig  ccgcgcacctggccttcctcgcattctgtcaccgacattctggg
B D                Rabbit  ccgcgcacctggccctcttcacactctgtcacagacatcctggg
B D                  Pika  cctcgcacctggccctcctcgcactccgtcaccgatatcctggg
B D                 Human  ccgcgcacctggccctcctcgcactccgtcaccgacatcctggg
B D                 Chimp  ccgcgcacctggccctcctcgcactccgtcaccgacatcctggg
B D                Bonobo  ccgcgcacctggccctcctcgcactccgtcaccgacatcctggg
B D               Gorilla  ccgcgcacctggccctcctcgcactccgtcaccgacatcctggg
B D                Rhesus  ccgcgcacctggccctcctcgcactccgtcacagacatcctggg
B D              Marmoset  ccgcgcacctggccttcctcgcactccgtcactgacatcctggg
B D               Tarsier  ccgcgcacctggccctcctcgcactcggtcaccgacatcctggg
B D              Bushbaby  ccgcgcacctggccctcctcgcactcggtcactgacatcctggg
B D            Tree shrew  ccgcgcacctggccctcctcgcactcggtcactgacatcctggg
B D  Malayan flying lemur  ccgcgcacctggccctcctcgcattctgtcaccgacatcctggg
B D                   Pig  ccgcgcacctggccctcctcccactccgtcaccgacatcctagg
B D                   Cow  ccgcgcacctggccctcctcgcactccgtcaccgacatcctggg
B D                 Sheep  ccgcgcacctggccctcctcgcactccgtcaccgacatcctggg
B D                 Horse  ccgcgcacctggccttcctcccattccgtcaccgacatcctggg
B D      Chinese pangolin  ccccgcacctggccctcctcccactccgtcaccgacatcctggg
B D                   Dog  ccccgtacctggccctcctcccattccgtcaccgacatcctggg
B D    Hawaiian monk seal  ccccgtacctggccctcctcccattccgtcaccgacatcctggg
B D              Hedgehog  ccgcgcacctggccctcctcacactcggtcaccgacatcctggg
B D                 Shrew  ccgcgcacctggccctcctctcactccgtcaccgacatcctggg
B D              Elephant  ccgcgcacctggccctcctcgcattcggtcaccgatatactggg
B D                Tenrec  ccgcgcacctggccctcctcgcactccgtcacggacatcctggg
B D               Opossum  cctagaacctggccctcttcgcactctgtcacggatatcctggg
B D               Chicken  cctcgcacctggccttcgtcccactcggtgacggacatcctggg
B D         X. tropicalis  ccaaggacctggccctcttcccattcggttacagacatccttgg
B D             Zebrafish  cataggatatggccttcctctcattctgttacagatattctggg
B D               Lamprey  cccagggcatggccctcgtcccactccgtgagcgacatcctggg

Alignment block 28 of 344 in window, 56743963 - 56743990, 28 bps 
B D                 Mouse  catccgctccatcaccg---accaaggtaag
B D                   Rat  catccgttccatcaccg---accaaggtaag
            GCF_003668045  catccgctccatcaccg---accaaggtaag
                   Beaver  catccgctccatcaccg---accaaggtaag
B D              Squirrel  catccgctccatcaccg---accaaggtaag
B D            Guinea pig  catccgctccatcaccg---accaaggtaag
B D                Rabbit  catccgctccatcaccg---accaaggtaag
B D                  Pika  catccgttccatcaccg---accaaggtaag
B D                 Human  catccgctccatcaccg---accaaggtagg
B D                 Chimp  catccgctccatcaccg---accaaggtagg
B D                Bonobo  catccgctccatcaccg---accaaggtagg
B D               Gorilla  catccgctccatcaccg---accaaggtagg
B D                Rhesus  catccgctccatcaccg---accaaggtagg
B D              Marmoset  catccgctccatcaccg---accaaggtagg
B D               Tarsier  catccgctccatcaccg---accaaggtagg
B D              Bushbaby  gattcgctccatcaccg---accaaggtagg
B D            Tree shrew  catccgctccatcaccg---accaaggtaag
B D  Malayan flying lemur  catccgctccatcaccg---accaaggtaag
B D                   Pig  tattcgctccatcaccg---accaaggtaag
B D                   Cow  cattcgctccatcaccg---accaaggtaag
B D                 Sheep  cattcgctccatcaccg---accaaggtaag
B D                 Horse  cattcgctccatcaccg---accaaggtaag
B D      Chinese pangolin  cattcgctccatcaccg---atcaaggtaag
B D                   Dog  cattcgctctatcaccg---accaaggtaag
B D    Hawaiian monk seal  cattcgctctatcaccg---accaaggtaag
B D              Hedgehog  cattcgttccatcaccg---accaaggtaag
B D                 Shrew  cattcgctccatcaccg---accaaggtagg
B D              Elephant  catccgctccatcaccg---accaaggtaag
B D                Tenrec  catccgctccatcaccg---accaaggtca-
B D               Opossum  aatccgctccatcacag---accaaggtaaa
B D               Chicken  catccgctccatcacgg---accaaggtgag
B D         X. tropicalis  gattcgctccatcaccg---accaaggtaag
B D             Zebrafish  cattcgatcaataacggagcagcaaagtaag

Inserts between block 28 and 29 in window
B D            Zebrafish 5411bp

Alignment block 29 of 344 in window, 56743991 - 56743992, 2 bps 
B D                 Mouse  ga-
B D                   Rat  gg-
            GCF_003668045  gc-
                   Beaver  g--
B D              Squirrel  g--
B D            Guinea pig  g--
B D                Rabbit  g--
B D                  Pika  g--
B D                 Human  g--
B D                 Chimp  g--
B D                Bonobo  g--
B D               Gorilla  g--
B D                Rhesus  g--
B D              Marmoset  g--
B D               Tarsier  g--
B D              Bushbaby  g--
B D            Tree shrew  g--
B D  Malayan flying lemur  g--
B D                   Pig  g--
B D                   Cow  g--
B D                 Sheep  g--
B D                 Horse  g--
B D      Chinese pangolin  g--
B D                   Dog  g--
B D    Hawaiian monk seal  g--
B D              Hedgehog  g--
B D                 Shrew  g--
B D              Elephant  g--
B D                Tenrec  g--
B D               Chicken  g--
B D         X. tropicalis  a-a
B D             Zebrafish  ===
B D               Opossum  ---

Inserts between block 29 and 30 in window
B D        X. tropicalis 1680bp

Alignment block 30 of 344 in window, 56743993 - 56743993, 1 bps 
B D                 Mouse  g-
B D                   Rat  g-
            GCF_003668045  g-
                   Beaver  g-
B D              Squirrel  g-
B D            Guinea pig  g-
B D                Rabbit  g-
B D                  Pika  g-
B D                 Human  g-
B D                 Chimp  g-
B D                Bonobo  g-
B D               Gorilla  g-
B D                Rhesus  g-
B D              Marmoset  g-
B D               Tarsier  g-
B D              Bushbaby  g-
B D            Tree shrew  g-
B D  Malayan flying lemur  g-
B D                   Pig  c-
B D                   Cow  g-
B D                 Sheep  g-
B D                 Horse  g-
B D      Chinese pangolin  g-
B D                   Dog  g-
B D    Hawaiian monk seal  g-
B D              Hedgehog  a-
B D                 Shrew  a-
B D              Elephant  t-
B D                Tenrec  t-
B D               Chicken  ag
B D             Zebrafish  ==
B D         X. tropicalis  ==
B D               Opossum  --

Inserts between block 30 and 31 in window
B D              Chicken 248bp

Alignment block 31 of 344 in window, 56743994 - 56744004, 11 bps 
B D                 Mouse  ctcaga-------ggcag
B D                   Rat  ctcgga-------agcag
            GCF_003668045  ctcaga-------ggcgg
                   Beaver  tccagagac--cgggcgg
B D              Squirrel  ctcagagac--ctagcgt
B D            Guinea pig  ctcagagac--cggactt
B D                Rabbit  cacggaggc--cgggcgg
B D                  Pika  cttgaaggt--ccgacgt
B D                 Human  ctcagaggc--tgggcgt
B D                 Chimp  ctcagaggc--tgggcgt
B D                Bonobo  ctcagaggc--tgggcgt
B D               Gorilla  ctcagaggc--tgggcgt
B D                Rhesus  ctcagaggc--tggtcat
B D              Marmoset  ctcagagac--agggcgt
B D               Tarsier  ctcggaggc--cgggcgt
B D              Bushbaby  ctcagaggc--tggacgt
B D            Tree shrew  ctcggg------------
B D  Malayan flying lemur  ctcagaggc--ctagtgt
B D                   Pig  tcaggggct--tg-----
B D                   Cow  cacgggggc--cg-----
B D                 Sheep  cccggggcc--cg-----
B D                 Horse  ctcgaggg---cc-----
B D      Chinese pangolin  ctcaggga---gg-----
B D                   Dog  ctcgggggc--cg-----
B D    Hawaiian monk seal  ctcaggggc--cg-----
B D              Hedgehog  ccccagggc--ca-----
B D                 Shrew  ctctcgggc--cg-----
B D              Elephant  ctccagggc--cgggggt
B D                Tenrec  ctccggggttgcgggggt
B D             Zebrafish  ==================
B D         X. tropicalis  ==================
B D               Opossum  ------------------
B D               Chicken  ==================

Inserts between block 31 and 32 in window
B D               Rabbit 2bp
B D                 Pika 2bp
B D                  Pig 9bp
B D                  Cow 10bp
B D                Sheep 10bp
B D                Horse 10bp
B D     Chinese pangolin 10bp
B D                  Dog 10bp
B D   Hawaiian monk seal 11bp
B D             Hedgehog 9bp
B D                Shrew 13bp
B D             Elephant 5bp
B D               Tenrec 11bp

Alignment block 32 of 344 in window, 56744005 - 56744209, 205 bps 
B D                 Mouse  tgtgcagagcggag--------tgggttcctgca-cgcgt-tcgggaaccccag-tacct-tcggcct--
B D                   Rat  tgtgctaggcggag--------agcgttcctgca-agcgg-tcgggaatcccag-tacct-tcggcct--
            GCF_003668045  agtgctgagcagag--------tgggttcctgca-cgctg-tcgggaaccccag-aacct-tcggcct--
                   Beaver  gaaggtgtgcaaag--------cctgttcccgcacctccc-gcggggatcccag-tgtct-gtagcct--
B D              Squirrel  caggacgtgcagag--------cctgtcttcgca-ccccc-gcggggatcccag-tgtct-gcggcct--
B D            Guinea pig  gaggatgtgcacgg--------cgtgtccccaga-ctccc-gggggaatcctat-tatct-gcggcctgc
B D                Rabbit  gaaagtgttcggaa--------cctgcctgcgcc-cttgc-gctgggaccccgg-cgtct-gcggcct-c
B D                  Pika  gagactagctgcgagcccctttcctgcccgctca-ccgcc-gaggggtccccag-tgcct----------
B D                 Human  gtggatgtgcagcg--------tctgcccccgca-ctctc-gcggaggtcccag-tatct-gcagcct--
B D                 Chimp  gtggatgtgcagcg--------tctgcccccgca-ctctc-gcggaggtcccag-tatct-gcagcct--
B D                Bonobo  gtggatgtgcagcg--------tctgcccccgca-ctctc-gcggaggtcccag-tatct-gcagcct--
B D               Gorilla  gtggatgtgcagcg--------tctgcccccgca-ctctc-gcggaggtcccag-tatct-gcagcct--
B D                Rhesus  gtgaatgtgcagcg--------tctgcttccgca-ctcca-gcggaggtaccag-tttct-gcggcct--
B D              Marmoset  gtggatgtgcagca--------tctgcctccgca-ttccc-gcggaggtcccac-tatct-gcggcct--
B D               Tarsier  gtagatgtgcggag--------tgcaccccc--------c-gcagcgatcccag-ggtct-gcggcct--
B D              Bushbaby  gtggatgtgcagag--------cctgaccccgca-cccct-gcggagagcccag-tatctcgcggcct--
B D            Tree shrew  --------gcagag--------cttgcctccgcg-cccc--tcggggatcccag-tatct-gcggcct--
B D  Malayan flying lemur  gtggatgcgcagag--------cctgcccccgca-cccccgcgggggaccccag-tattt-gcggcct--
B D                   Pig  -----tgtgctgag--------cctccctcctca-ccctc-tctagggtcttta-tattt-gg-------
B D               Dolphin  -----tgtgcagag--------cttcccgccgca-gcctc-tctggggtctctg-tatct-gcggcct--
B D                   Cow  -----tgtgcagag--------cttccctcctca-acctc-tctggggttaccg-catct-gc-gtct--
B D                 Sheep  -----tgtgcagag--------cttcgctccgca-ccctc-tcaggggttaccg-catct-gc-gcct--
B D                 Horse  -----tgtgcagag--------cctccctccgca-cccta-gctggggtttctc-tatct-gaggcct--
B D      Chinese pangolin  -----cgtccagag--------cc-ccctccaca-cccgc-gctggggtc-------ttt-gtggtct--
B D                   Dog  -----tgtgcagag--------ccttcctctgca-ccctc-gctggtgtctccg-tatct-gcggcct--
B D    Hawaiian monk seal  -----tgtgcagag--------cctccctctgca-ccctc-gctgatgtctctgttatct-gcggcct--
B D              Hedgehog  ----------------------------tggatg-cct---------gtgcagg-cgcct-tgggtct--
B D                 Shrew  -----tgcagagag--------cttttttgggag-ccctg-gttgg-ggtctgg-cccct-cgggtct--
B D              Elephant  -----tgtgcagcg--------cctcc--------ccttc-gctgaggttccag-tatct-gaggcct--
B D                Tenrec  -----tgtgccgca--------cctcc--------tcttc-gcggagataccgg-gatct-gaggccg--
B D               Opossum  --tttggaccgtgg--------cgcgcctggggc-ctgga-agggagggaatag-tagca-acgatat--
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  ct--ag--c-gag-tgtcta----------tccc-accacctgtggc--tctttt------cttttggaa
                      Rat  ct--at--c-gag-tgtcta----------tccc-accacctgtggc---ctttt------cttttggaa
            GCF_003668045  ct--gg--c-gag-tgtcta----------tccc-accacctgtggc---ttttt------cttttggaa
                   Beaver  ct--gg--c-cgg-tgtcta----------tccc-accacctgaggc----cttt------cttttggaa
                 Squirrel  cg--gg--ctcgg-tgtcca----------tccc-accacctgaggctttttttt------cctttggaa
               Guinea pig  ct--gg--c-ccg-ggtcga----------tgcc-accacttgaggc---ttttt------cctttggag
                   Rabbit  cc--gg--c-ccg-ggtcca----------tccc-accacccgaggc---ctttt------cctttggaa
                     Pika  ---------------gtcca----------accc-gccacccgaggc---ctttt------cctttggaa
                    Human  ca--gg--gacac-tgtctt----------tccc-accacctgaggc---ttttt------cctttggaa
                    Chimp  ca--gg--gacac-tgtctt----------tccc-accacctgaggc---ttttt------cctttggaa
                   Bonobo  ca--gg--gacac-tgtctt----------tccc-accacctgaggc---ttttt------cctttggaa
                  Gorilla  ca--gg--gacac-tgtctt----------tccc-accacctgaggc---ttttt------cctttggaa
                   Rhesus  cc--gg--gaccc-tgtctt----------tccc-accacctaaagc---ttttt------cctttggaa
                 Marmoset  ct--gg--gaccc-tgtctt----------tcct-atcacctgaggc---ttttt------cctttggaa
                  Tarsier  cc--gg--gcccg-tgtctg----------tccc-accacctgaggc--tttttt------cctttggaa
                 Bushbaby  cc---g--gcccg-tgtcta----------tccc-accacctgaggc---ttttt------cctttggaa
               Tree shrew  tc--ga--g-ccg-agctga----------acct-gccatatgaggt---ttatt------cctttggaa
     Malayan flying lemur  cg--gg--gccct-tgttta----------tccc-accacctgaggc---ttttt------cctttggaa
                      Pig  ----gg----cca-cgtcta----------tctc-accacctgaggc---ttttt------cctttggaa
                  Dolphin  ccgggggggcccg-cgtcta----------tccc-accgcctgaggc---ttctt------cctttggga
                      Cow  cc--aggggcccg-cgtctg----------tccc-accacctgagac---ttttt------cctttggaa
                    Sheep  cc--aggggcccg-cgtctg----------tccc-accacctgagac---gtttc------cctttggaa
                    Horse  cc--gg--gcccc-cgtccg----------tccc-accaccggaggc---ctttt------cctttggaa
         Chinese pangolin  cc--gg--ttctcgaatcta----------tcct-accacctgaggc---tttgt------cctttggaa
                      Dog  cg--gg--gcccg-cgccta----------tccc-accacctgaggc---ttttt------cctttcgaa
       Hawaiian monk seal  cc--gg--gcccg-ggtcta----------tccc-accacctgaggc---ttttt------cctttggaa
                 Hedgehog  tg--aa----cca-gttcag--------------------------------------------ttggaa
                    Shrew  cc--ga--gccca-ggcccgtgtccgtctcaccc-actacgcgaggc---ttctc------tctttggaa
                 Elephant  cc--ag--gcctg-agtatg----------ttctaatcacctgaggc---ttttg------cattt-gaa
                   Tenrec  cc--ag--gcccc-tgccca----------tgcc-accacctggcct---ttttg------cctttggaa
                  Opossum  tc--at--------cttctc----------gcct---catcctagcc---tttctttaagactttcaaac
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  acctaaggagtcttcc-cag------------------------g-------------------------
                      Rat  acctaaggagtcgtcc-cag------------------------g-------------------------
            GCF_003668045  acctaaggagtcttcc-cag------------------------g-------------------------
                   Beaver  acttcagtagtcttcc-cat------------------------g-------------------------
                 Squirrel  acgtaaggagacttcc-cag------------------------g-------------------------
               Guinea pig  tcataaggagtcttcc-cag------------------------g-------------------------
                   Rabbit  acgaaaggcggcttcc-cag------------------------g-------------------------
                     Pika  gcgtgaggaggcttcc-cag------------------------g-------------------------
                    Human  acgtaaggagtcttcc-tag------------------------g-------------------------
                    Chimp  acgtaaagagtcttcc-tag------------------------g-------------------------
                   Bonobo  acgtaaagagtcttcc-tag------------------------g-------------------------
                  Gorilla  acgtaaggagtcttcc-tag------------------------g-------------------------
                   Rhesus  aagtaaggagtcttcc-tag------------------------g-------------------------
                 Marmoset  acgtaaggagtcttcc-tag------------------------g-------------------------
                  Tarsier  acgtaaggagtcttcc-cag------------------------g-------------------------
                 Bushbaby  acgtaaggagtcttcc-cag------------------------g-------------------------
               Tree shrew  atgtaaggagtcttcc-cag------------------------g-------------------------
     Malayan flying lemur  acttcaggagtcttcc-cag------------------------g-------------------------
                      Pig  atgtaaggagtcttct-gag------------------------a-------------------------
                  Dolphin  acgtaaggggccctcc-cat------------------------g-------------------------
                      Cow  acgtcaagagtcctcc-cag------------------------g-------------------------
                    Sheep  acgtcaggagtcctcc-cag------------------------g-------------------------
                    Horse  atgtaagcagtcctcc-cag------------------------g-------------------------
         Chinese pangolin  ac-taaagagtccttc-cag------------------------g-------------------------
                      Dog  ac-gaaggagtcctcc-cag------------------------g-------------------------
       Hawaiian monk seal  ac-taaggagtcctcc-cag------------------------g-------------------------
                 Hedgehog  accgaaggactcctcc-ccg------------------------ggtggtggtggtggagatggtggtgg
                    Shrew  acgcaaggagt-cttc-cag------------------------ggcggggggcgt--------------
                 Elephant  ac-taaggagtcctcc-cgg-----------agaggggaggggga-------------------------
                   Tenrec  aa-tcaggcgtccttc-tgggggggcggcgcagtgggggtggggg-------------------------
                  Opossum  agctttagtgtcttccgcat------------------------g-------------------------
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ----------gggt-gt--------------------cctgatctcatta------------------ac
                      Rat  ----------gggt-gt--------------------cctgatctcatta------------------ac
            GCF_003668045  ----------gggt-gt--------------------cctgatctcatta------------------ac
                   Beaver  ----------gggt-gt--------------------cctgatctcatta------------------ac
                 Squirrel  ----------gggt-gt--------------------cctgatctcatta------------------ac
               Guinea pig  ----------gggt-gt--------------------cctgatctcatta------------------ac
                   Rabbit  ----------gggg-ac--------------------cctgatctcatta------------------ac
                     Pika  ----------ggggtgt--------------------cctgatctcatta------------------ac
                    Human  ----------gggt-gt--------------------tctgatctcatta------------------ac
                    Chimp  ----------gggt-gt--------------------tctgatctcatta------------------ac
                   Bonobo  ----------gggt-gt--------------------tctgatctcatta------------------ac
                  Gorilla  ----------gggt-gt--------------------tctgatctcatta------------------ac
                   Rhesus  ----------gggt-gt--------------------cctgatctcatta------------------ac
                 Marmoset  ----------gggt-gt--------------------cctgatctcatta------------------ac
                  Tarsier  ----------gggt-gt--------------------cctgatctcatta------------------ac
                 Bushbaby  ----------gggt-gt--------------------cctgatctcatta------------------ac
               Tree shrew  ----------gggt-gt--------------------cctgatctcatta------------------ac
     Malayan flying lemur  ----------gggt-gt--------------------catgatctcatta------------------gc
                      Pig  ----------gggt-ga--------------------cctgatctcatta------------------at
                  Dolphin  ----------gggt-gt--------------------cctgatctcatta------------------ac
                      Cow  ----------gggt-gt--------------------cctgatctcatta------------------ac
                    Sheep  ----------gggt-gt--------------------cctgatctcatta------------------ac
                    Horse  ----------gggt-gt--------------------cctgatctcatta------------------ac
         Chinese pangolin  ----------gagt-gt--------------------cctgatctcatta------------------ac
                      Dog  ----------gggt-gt--------------------cctgatctcatta------------------ac
       Hawaiian monk seal  ----------gggt-gt--------------------tctgatctcatta------------------ac
                 Hedgehog  tggtggtagtgggt-gt--------------------cctgatctcatta------------------ac
                    Shrew  --gtgtgtgtgggg-gt--------------------cctgatctcatta------------------ac
                 Elephant  ----------aggt-gt--------------------cctgctctcatta------------------ac
                   Tenrec  ----------tggt-gc--------------------cctgctctcatta------------------ac
                  Opossum  ----------ggga-attactgtctcgcgattgcccacctgatcccgttatagaacaggaagatttttat
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ttgaaactcttgcccctctgtttccttgc--c------------acacacag--tctccagcc--tcatc
                      Rat  ttgaaactcttgcccctctgtttccttgccac------------acacacag--tttccagcc--tcatc
            GCF_003668045  ttgaaactcttgcccctccgtttccttgccac------------acacacag--tctgcagcc--tcatc
                   Beaver  ttgaaactcatgcccct-tgtttccttgc--c------------acacacag--tcttctgcc--tcatc
                 Squirrel  ttgaaactcacgcccct-cgtttccttgc--c------------acacacag--tctccagcc--tcatc
               Guinea pig  ttgaaacttttgcccct-ggtttccttgc--c------------acacacagtctctcctgcc--tcatc
                   Rabbit  tcgaaactcctgcccct--gcttccttgc--c------------acacacag--cctcctgcc--tcatc
                     Pika  ttgaaactcctgcccct--gtttccttgc--c------------acacacag--tctcctgcc--tcatc
                    Human  ttgaaactcatgcccct-ggtttccttgc--c------------acacacag--tcttctgcc--tcatc
                    Chimp  ttgaaactcatgcccct-ggtttccttgc--c------------acacacag--tcttctgcc--tcatc
                   Bonobo  ttgaaactcatgcccct-ggtttccttgc--c------------acacacag--tcttctgcc--tcatc
                  Gorilla  ttgaaactcatgcccct-ggtttccttgc--c------------acacacag--tcttctgcc--tcatc
                   Rhesus  ttgaaactcatgcccct-ggtttccttgc--c------------acacacag--tctcctgcc--tcaac
                 Marmoset  ttgaaacgcttgcccct-ggtttccttgc--c------------acacacag--tctcctgcc--tcatc
                  Tarsier  tcgaaactcatgcccct-cgtttccttgc--c------------acacacag--tctcctgcc--tcatc
                 Bushbaby  ttgaaactcatgcccct-agtttcctcgc--c------------acacacag--tctcctgcc--tcatc
               Tree shrew  ttgaagctcctgcccct-cgtttccttgc--c------------acacacag--tctccagcc--tcatc
     Malayan flying lemur  ttgcaactcatgcccct-agtttccttac--c------------acacacag--tctcctgcc--tcatc
                      Pig  gtgaaattcatgccctt-cgtttccttgc--c------------acacacag--tctcctgcc--tcatc
                  Dolphin  gtgaaattcatgccctt-cgtttccttgc--c------------acacgcag--tctactgcc--tcatc
                      Cow  gtgaaattcatgccctt-cgtttccttgc--c------------acacacag--tctactgcc--tcatc
                    Sheep  gtgaaattcatgccctt-cgtttccttgc--c------------acacacag--tctactgcc--tcatc
                    Horse  ttgaaattcatgccctt-cgtttccttgc--c------------acacacag--tctcctgcc--tcatc
         Chinese pangolin  ttgaaattcgtgccctc-cgttttcttgc--c------------acacacag--tctcctgcc--tcatc
                      Dog  ttgaaattcatgccctc-tgtttccttgc--c------------acacacag--tctcctgcc--tcatc
       Hawaiian monk seal  ttgaaattcatgccctc-cgtttccttac--c------------acacacag--tctcctgcc--tcatc
                 Hedgehog  ttgaaattcatgccctt-ccttcccttgc--c------------acacacag--tctcctgcc--tcatc
                    Shrew  ttgaaattcatgccctt-cctttccttgc--c------------acacacag--tctcctgcc--tcatc
                 Elephant  ttgaaattcatgcctct-cgtttccttgc--c------------acacacag--tctcctgcc--tcatc
                   Tenrec  ttgaaattcatgcccct-cgtttccttgc--c------------acccacag--tctcctgcc--tcatc
                  Opossum  tgggaagcagtgctccc----ttctctgc--cttctctgtttgaaatcgctg--ttttttccccttcacc
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  tcaaactacca
                      Rat  tcaaactacca
            GCF_003668045  tcaaactgcca
                   Beaver  tcaaactacca
                 Squirrel  tcaaactacca
               Guinea pig  tcaaactacca
                   Rabbit  tcaaactacca
                     Pika  tcaaactacca
                    Human  tcaaactacca
                    Chimp  tcagactacca
                   Bonobo  tcaaactacca
                  Gorilla  tcaaactacca
                   Rhesus  tcaaactatca
                 Marmoset  tcaaactacca
                  Tarsier  tcaaactacca
                 Bushbaby  tcaaactacca
               Tree shrew  tcaaactacca
     Malayan flying lemur  tcaaactacca
                      Pig  tcaaactacca
                  Dolphin  tcaaacgacca
                      Cow  tcaaactacca
                    Sheep  tcaaactacca
                    Horse  tcaaactacca
         Chinese pangolin  tcaaactacca
                      Dog  tcaaactacca
       Hawaiian monk seal  tcaaactacca
                 Hedgehog  tcagactccca
                    Shrew  tcaaactacca
                 Elephant  tcaaactacca
                   Tenrec  tcaaactacca
                  Opossum  tcaagctact-
                Zebrafish  ===========
            X. tropicalis  ===========
                  Chicken  ===========

Alignment block 33 of 344 in window, 56744210 - 56744222, 13 bps 
B D                 Mouse  gacccataacata-
B D                   Rat  gacccataacatc-
            GCF_003668045  gacccataacat--
                   Beaver  gacccataacat--
B D              Squirrel  gacccataacat--
B D            Guinea pig  gacccataacat--
B D                Rabbit  gacccataacat--
B D                  Pika  gagccgtaacat--
B D                 Human  gacccataacat--
B D                 Chimp  gacccataacat--
B D                Bonobo  gacccataacat--
B D               Gorilla  gacccataacat--
B D                Rhesus  gacccataacat--
B D              Marmoset  gacccataacat--
B D               Tarsier  gacccataacat--
B D              Bushbaby  gacccataacat--
B D            Tree shrew  gacccataacat--
B D  Malayan flying lemur  gacccgtaacat--
B D                   Pig  gacccataacat--
B D                   Cow  gacccataacat--
B D                 Sheep  ga-ccataacat--
B D                 Horse  gacccataacat--
B D      Chinese pangolin  gacccataacat--
B D                   Dog  gacccataacat--
B D    Hawaiian monk seal  gacccataacat--
B D              Hedgehog  gacccataacat--
B D                 Shrew  gacccataacat--
B D              Elephant  gacccataacat--
B D                Tenrec  gaccctgaacat--
B D               Opossum  ------cagcag-a
B D             Zebrafish  ==============
B D         X. tropicalis  ==============
B D               Chicken  ==============

Alignment block 34 of 344 in window, 56744223 - 56744344, 122 bps 
B D                 Mouse  ccccc---ccc--cccaaacacatggttcgcattttccaccctcccccgcctc-tcgcgcact-------
B D                   Rat  ccccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgcact-------
            GCF_003668045  ---cc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgcact----c--
                   Beaver  --ccc---cccatctccaacacatggttcgcattttccaccctcccccgcctc-tcgcggcgc----g--
B D              Squirrel  ---cc---cccgtccccaacacatggttcgcattttccaccctcccccgcccc-tcgcgctgc----g--
B D            Guinea pig  ---cc---cccatccccaacacatggttcgcattttccaccctgccccgcctc-tcgcgccgc----g--
B D                Rabbit  ---cc---cccagccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----gcc
B D                  Pika  --ccc---cccagccctgacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----gc-
B D                 Human  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccga----g--
B D                 Chimp  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccga----g--
B D                Bonobo  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccga----g--
B D               Gorilla  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccga----g--
B D                Rhesus  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccaa----g--
B D              Marmoset  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgagccga----g--
B D               Tarsier  --ccc---gccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----a--
B D              Bushbaby  --ccc---cccattcccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----g--
B D            Tree shrew  --ccccctcccatccccgacacatggttcgcattttccaccctcccccgcctc-tctctcggc----t--
B D  Malayan flying lemur  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----g--
B D                   Pig  --ccc---tccatccctaacacatggttcgcattttccaccctcccccgcctc-tctcgctgc----g--
B D               Dolphin  --ccc---cccatccccgacacatggttcgcattttccaccctcccccgcctc-gcgcgccgc----c--
B D                   Cow  ---cc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----g--
B D                 Sheep  ---cc---cccatccccaacacatggttcgcattttccaccctcccccccccc-ccccccccc----c--
B D                 Horse  --ccc---cccatccctaacacatggttcgcattttccaccctcccccgcctc-tcgcgccac----c--
B D      Chinese pangolin  --tcc---cccacccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----a--
B D                   Dog  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----g--
B D    Hawaiian monk seal  --ccc---cccatccccaacacatggttcgcattttccaccctcccccgcctc-tcgcgccgc----t--
B D              Hedgehog  --ccc---cccatctccaacacatggttcgcattttccaccctaccccgcctctttgcgccgc----g--
B D                 Shrew  --ccc---cccagccccaacacatggttcgcattttccatcctcccccgcctc-tcgcgccgc----c--
B D              Elephant  --ccc---cccagccccaacacatggttcacattttccaccctcccccgcccc-ctgcgccgcgccag--
B D                Tenrec  ---cc---cccagccccgacacatggttcacattttccaccctcccccgcccc-ctgcgctgc----c--
B D               Opossum  ctcct---tcccaaccaaactcatgattcacatgctccttttccttttctttc-tttctcctt----t--
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  ----------------c-------------------agcctcag-ccg--ggctagactgt-ttggagag
                      Rat  ----------------c-------------------agcctcag-ccg--ggctagactgt-ttggagag
            GCF_003668045  ---------------gc-------------------ggccttag-ccg--ggctattctgc-ttggagag
                   Beaver  ---------------gt-------------------aaccgcag-ccc--ggcttgctcac-ttggagag
                 Squirrel  ---------------gc-------------------agcctcag--cg--ggctggctggc-ttggtgag
               Guinea pig  ---------------gc-------------------agtctcag-ccg--ggcttgctcac----agcag
                   Rabbit  gcgccgcgccgcgccgc-------------------agcctcag-ccg--ggcttgctcac-tcggagag
                     Pika  -----------tgctgc-------------------ctcctccgcccg--ggctggctcac-t--gagtg
                    Human  ---------------gc-------------------agcctcag-ccc--ggcttgctcac-ttggagag
                    Chimp  ---------------gc-------------------agcctcag-ccc--ggcttgctcac-ttggagag
                   Bonobo  ---------------gc-------------------agcctcag-ccc--ggcttgctcac-ttggagag
                  Gorilla  ---------------gc-------------------agcctcag-ccc--ggcttgctcac-ttggagag
                   Rhesus  ---------------gc-------------------agcctcag-ccc--ggcttgctcac-ttggagag
                 Marmoset  ---------------gc-------------------ggcctcag-ccc--ggcttgctcac-ttgaagag
                  Tarsier  ---------------gc-------------------cgcctcaa-ccg--gcctggctcgc-tcggaga-
                 Bushbaby  ---------------gc-------------------agtctcag-gcc--ggctcgcaga--gcgcagag
               Tree shrew  ---------------gc-------------------agcctctg-ccc--ggcttgctcactttggagag
     Malayan flying lemur  ---------------gc-------------------agcctcag-ccc--ggcttgctcac-ttggagag
                      Pig  ---------------gt-------------------agcctcag-accggcgctctctcgc-ttggagag
                  Dolphin  ---------------gc-------------------agcctcag-acc--agctcgctcac-ttggagag
                      Cow  ---------------gc-------------------agcctcgg-acc--agcctgctcac-ttggagag
                    Sheep  ---------------cc-------------------gcccc-----cc--cgccc-ccccc-ccggagag
                    Horse  ---------------gc-------------------agcctcag-acc--ggctcactcac-ttggagag
         Chinese pangolin  ---------------gc-------------------agcctcag-acc--ggcttgctcac-ttggagag
                      Dog  ---------------gc-------------------agccttag-acc--cgctcgctcgc-ttggagag
       Hawaiian monk seal  ---------------gc-------------------agccttag-acc--ggctcgctcac-ttggagag
                 Hedgehog  ---------------gc-------------------ggcctcag-aca--gactcgttcgc-agggagag
                    Shrew  ---------------gc-------------------ggcctcag-act--ggctcgctcgc-ttgcagag
                 Elephant  ---------------gc-------------------agcttcag-gct--ggctggctggc-ttggagag
                   Tenrec  ---------------gc-------------------ggcctccg-tca--ggcgggctacc-tcggagcg
                  Opossum  ---------------gctttagaatttatcttctagaatttcgt-cca--aatttcgaatc-ccgtgcag
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  -cg-cag-cctgg--c-gatt-tgggga-gcacaagaggagg
                      Rat  -cg-cag-cctgg--a-gatt-tgggga-gcacaagagaagg
            GCF_003668045  -gg-cag-cccgc--c-gact-taggga-gcagtgggggagg
                   Beaver  -cg-ccg-cccgg--ctgact-tggggc-gcagcccgggagg
                 Squirrel  -cg-ctg-cccgggcc-cact-tggggc-gcagccctggagg
               Guinea pig  -cgattg-cccgagcc-gacc-agaggc-gctgcccgggagg
                   Rabbit  -cg-cgg-ccggggccggact-tggggc-tcagcccgggagg
                     Pika  -cg-cgg-cc---gccgggct-tggggc-gcagcccgggagg
                    Human  -tg-cgg-ccggggctggact-tggggc-gcagcccgggagg
                    Chimp  -tg-cgg-ccggggctggact-tggggc-gcagcccgggagg
                   Bonobo  -tg-cgg-ccggggctggact-tggggc-gcagcccgggagg
                  Gorilla  -tg-cgg-ccggggctggact-tggggc-gcagcccgggagg
                   Rhesus  -ca-cgg-ctggggctggact-tggggc-gcagcccgggagg
                 Marmoset  -ag-cgt-cc-gggccggact-tggggg-gcagcccgggagg
                  Tarsier  -cg-cgt-tcggggccggact-tggggt-gcagcccgggagg
                 Bushbaby  -cg-cgg-cc--ggccggact-tgggga-gcagcccaggagg
               Tree shrew  -cg-cag-ccggggccggact-tggggc-gcagcccggaagg
     Malayan flying lemur  -cg-cgg-ccggggccggact-tggggc-agagcccgggagg
                      Pig  -cg-aga-cc---gctggact-tggggc-gcagcccgggagg
                  Dolphin  -cg-ccg-ccggggccggact-tggggc-gcagccggagagg
                      Cow  -cg-cgg-ccggggccggact-tgggga-gcagcccgagagg
                    Sheep  -cg-ggg-ccggggccgggctctggggc-gcagcctgagagg
                    Horse  ccg-cgg-ccggggccggact-tggggc-gcagcccgggagg
         Chinese pangolin  -cg-cgg-ccccggccggact-tgggga-gcagcccgggagg
                      Dog  -cg-cgg-cccgggtcggact-tggggc-gcagcccgggagg
       Hawaiian monk seal  -cg-cgg-cccgggtcggact-tggggc-gcagcccgggagg
                 Hedgehog  -ca-cggcccggggccggact-tgggggcgcagcccgggagg
                    Shrew  -cg-cgg-ccaggacccgact-tgggga-gcagcccagcagg
                 Elephant  -cg-cgg-cccgggctggact-tgggac-ccagccggggagg
                   Tenrec  -cg-cgg-ccggggccggtc--gggggc-gcagcccgggagg
                  Opossum  -ca-taa-ct----ttagatt-taaata-gcaggggagaagg
                Zebrafish  ==========================================
            X. tropicalis  ==========================================
                  Chicken  ==========================================

Inserts between block 34 and 35 in window
B D              Opossum 13bp

Alignment block 35 of 344 in window, 56744345 - 56744391, 47 bps 
B D                 Mouse  ccctagcaggct--tggggctgcgg-gttgtaggtagccactgtcggc-----ag
B D                   Rat  ccctagcaggct--tggggctgcgg-gctgtagatggccactgtccgc-----ag
            GCF_003668045  ccttagcgggct--tgggtctgcga-gctgcagat-gccactgccggt-----aa
                   Beaver  cccgagccggct--tggggctgccg-gctgcagat-gccgctgtccgc-----ga
B D              Squirrel  cccgagccgact--taaggttgccg-gcggcagat-gcggctacaggc-----aa
B D            Guinea pig  gcccagtcggct--tggggcagtcg-gcagcagat-gcctctg-gagc-----ag
B D                Rabbit  cccgagccggcg--tggggctaccg-gctgcaaac-gccgctgcgggc-----ag
B D                  Pika  -ccgaaccggcc--tggggttgccgagct-----t-gccgggctggac-----ag
B D                 Human  cccgagcctgct--tggggctgccg-gctgcagac-tccgctgtgggcagagcag
B D                 Chimp  cccgagcctgct--tggggctgccg-gctgcagac-tccgctgtgggcagagcag
B D                Bonobo  cccgagcctgct--tggggctgccg-gctgcagac-tccgctgtgggcagagcag
B D               Gorilla  cccgagcctgct--tggggctgccg-gctgcagac-tccgctgtgggcaaagcag
B D                Rhesus  cccgagcctgct--tggggctgccg-gctgcagac-gccgctgcgggcagagcag
B D              Marmoset  cctgagcctgct--tggggctgccg-gctgcagat-gccgctgcaggcagagtag
B D               Tarsier  cccgagcctgtt--tggggcggccg-gctgcagac-gccgctgcgggc-----gg
B D              Bushbaby  cccgagcctgcg--tggggctgcgg-gcggcaggc-gccgctgcgggc-----ag
B D            Tree shrew  cccgagccggct--tggggctgcgg-gttgcagag-gccgctgccggc-----ag
B D  Malayan flying lemur  cccgagccggca--tggggctgccg-gctgcagac-gccgctgcgggc-----ag
B D                   Pig  cccgagccgtcg--tggggctgccg-gctgcagac-actgctttgggc-----ag
B D               Dolphin  cccgagcaggcg--tggggctgccg-gctgcagac-actgctgcgggc-----ag
B D                   Cow  cccgagcgggcg--tggagctgccg-gctgcagac-acggcttcgggc-----gg
B D                 Sheep  cccgagcgggcg--tggagctgccg-gctgcagac-acggcttcgggc-----gg
B D                 Horse  cccgagccggcg--tggggctgccg-gctgcagac-accgctgcgggc-----gg
B D      Chinese pangolin  cccaggcaggcg--tggggctgccg-gctgcagac-actgctgcgagc-----aa
B D                   Dog  cctgagccggcg--tggggctgctg-gctgcagac-accgctgcgggc-----gg
B D    Hawaiian monk seal  cctgagcgggcg--tggggctgctg-gctgcagac-accgctgcggac-----ag
B D              Hedgehog  cccgagcgggtg--tggggctgcgg-gctgccgac-gccgctgcgggg-----ag
B D                 Shrew  cccgagccggcg--aggggctgccg-gcggcagac-gccgctgcggac-----ag
B D              Elephant  ccggagccggct--tggggccgccg-gctgcagac-gccgctgcaggc-----ac
B D                Tenrec  ccgaggccggcttgtggggctgcag-gcagcaggc-gacgctgcaggt-----tg
B D             Zebrafish  =======================================================
B D         X. tropicalis  =======================================================
B D               Opossum  =======================================================
B D               Chicken  =======================================================

Alignment block 36 of 344 in window, 56744392 - 56744453, 62 bps 
B D                 Mouse  cttgct-----------c-ac--------------ga-------------------gtc-----------
B D                   Rat  cttgct-----------c-ac--------------ga-------------------atc-----------
            GCF_003668045  cttgct-----------t-ac--------------cg-------------------atc-----------
                   Beaver  tttgct-----------t-gg--------------gg-------------------atc-----------
B D              Squirrel  cttgtt-----------tggg--------------gg-------------------att-----------
B D            Guinea pig  cttgct-----------t-gc--------------g--------------------atc-----------
B D                Rabbit  cttgct-----------c-cg--------------gg-------------------atc-----------
B D                  Pika  tttgtt-----------tggg--------------gg-------------------atc-----------
B D                 Human  cttgct-----------t-gg--------------gg-------------------atcactacggccgg
B D                 Chimp  cttgct-----------t-gg--------------gg-------------------atcactacggccgg
B D                Bonobo  cttgct-----------t-gg--------------gg-------------------atcactatggccgg
B D               Gorilla  cttgct-----------t-gg--------------gg-------------------atcactacggccgg
B D                Rhesus  cttgct-----------t-gg--------------gg-------------------atcactacggccgg
B D              Marmoset  cttgct-----------t-gg--------------gg-------------------atcac---------
B D               Tarsier  cttgat-----------c-cg--------------gg-------------------atc-----------
B D              Bushbaby  cgtgct-----------t-gg--------------gg-------------------atc-----------
B D            Tree shrew  cttgct-----------t-gg--------------gg-------------------atc-----------
B D  Malayan flying lemur  cttgct-----------t-tg--------------gg-------------------atc-----------
B D                   Pig  cttgtt-----------t-gg--------------gg-------------------atc-----------
B D               Dolphin  cttgtt-----------t-gg--------------gg-------------------atc-----------
B D                   Cow  cttgtt-----------t-gg-------------------------------------------------
B D                 Sheep  cttgtt-----------t-gg-------------------------------------------------
B D                 Horse  cttgtt-----------c-gg--------------gg-------------------atc-----------
B D      Chinese pangolin  ctagtt-----------t-gg--------------gc-------------------atc-----------
B D                   Dog  cttgtt-----------t-gg--------------gg-------------------atc-----------
B D    Hawaiian monk seal  tttgtt-----------t-gg--------------gg-------------------atc-----------
B D              Hedgehog  cttgtt-----------t-gg--------------ggcggggggggggagggcataatc-----------
B D                 Shrew  cttgtt-----------t-gg--------------gg-------------------atc-----------
B D              Elephant  ctcgct-----------c-gt--------------gg-------------------agc-----------
B D                Tenrec  cccgct-----------c-ggtggtgggtgggtgagg-------------------gtc-----------
B D               Opossum  cttactcttcaccaagat-aa--------------gt-------------------atagtctcgactcc
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  -aga--t--gc----cgcagctacgagt--ccccgcacactctggaaattgtat---tatta
                      Rat  -aga--t--gc----agcagctacgagt---cccgcacactctggaaattgtat---tatta
            GCF_003668045  -aga--t--gc----agcagctacgcgt---cccgcacgctgtggaaattgtat---tatta
                   Beaver  -aga--t--gc----ggcagttggaagt---cccgcacgatgtggaaattgtag---tattc
                 Squirrel  -aga--t--gt----gactgctagcagt---ctcctacgttgtggaaattgtaa---tattc
               Guinea pig  -aga--t--gc----agcagctaagagt---cccatatgatgtggaaattgtag---ta---
                   Rabbit  -aga--g--gc----gg-tgcgaggagg---ccggtgcgcggtggaaattgtag---tattc
                     Pika  -cca--g--gc----ggctgcgaggaggagatcggtgagcagtggaaattgtag---tg---
                    Human  gagaagt--ct----ggccgggaggagt---ccagcacgccttggaaattgaag---tatt-
                    Chimp  gagaagt--ct----ggccgggaggagt---ccagtacgccttggaaattgaag---tatt-
                   Bonobo  gagaagt--ct----ggccgggaggagt---ccagcacgccttggaaattgaag---tatt-
                  Gorilla  gagaagt--ct----ggccgggaggagt---ccagcaggccttggaaattgaag---tatt-
                   Rhesus  gagc---------------------agt---ccagcacgcggtggaaattgaag---tattc
                 Marmoset  -aga------c----gcccgggaggagt---ccagcacgcggtggaaattgaag---tatt-
                  Tarsier  -aga--t--gc----ggccgcgaggagc---tcggcgcgctgtggaaattgtag---tattc
                 Bushbaby  -aga--t--ga----ggccgcgacgagt---ac-gcgcgcagtggaaattgtag---tattc
               Tree shrew  -aga--t--gc----cgctgcgaggagt---ctagcacgctgtggaaattgtaggattcttc
     Malayan flying lemur  -aga--t--gc----ggtctcgaggagt---ccggcacgctggggaaaatgtag---tgttc
                      Pig  -tga--tgggc----ttcgaggagaagt---cgggcaccctgtggaaattgcag---tattc
                  Dolphin  -aga--t--gc----ggccgcgaggagt---cgggcacgctgtggaaactgcag---tgttc
                      Cow  -----------------------ggagt---cggggactctgtagaaattgcag---tattc
                    Sheep  -----------------------ggagt---cggggactctgtagaaattgcag---tattc
                    Horse  -aga--t--gc----ggccgcgaggagt---cgggcaccctgtggaaattgcag---tattc
         Chinese pangolin  -aga--t--gc----ggccgtgaggagt---cgggcaccctatggaaattgcag---tattc
                      Dog  -aga--t--gc----ggccgcgaggagt---cgggcaccctgtggaaattgcag---tattc
       Hawaiian monk seal  -aga--t--gc----ggccgcgaggagt---tgggcaccctgtggaaattgcag---tattc
                 Hedgehog  -tgt--t--gt----ggccgcgagaagt---cgggcgccctgtggaaatggcag---tgttc
                    Shrew  -act--t--gc----ggccccgaggagt---agggcacccagtagaaattgcag---tattc
                 Elephant  -aga--t--tc----ggccgcgaggagt---ccggcgcacgggggaaattgcag---agttt
                   Tenrec  -aga--t--gcggctggccgggaagagc---ccggcactagggggaaatggcag---agttc
                  Opossum  caga--t--gc----agactcacatagc--aagagcttttcattgaaattgcag---ggttc
                Zebrafish  ==============================================================
            X. tropicalis  ==============================================================
                  Chicken  ==============================================================

Alignment block 37 of 344 in window, 56744454 - 56744454, 1 bps 
B D                 Mouse  t
B D                   Rat  t
            GCF_003668045  t
                   Beaver  t
B D              Squirrel  t
B D            Guinea pig  t
B D                Rabbit  t
B D                  Pika  t
B D                Rhesus  t
B D               Tarsier  t
B D              Bushbaby  t
B D            Tree shrew  t
B D  Malayan flying lemur  g
B D                   Pig  t
B D               Dolphin  t
B D                   Cow  t
B D                 Sheep  t
B D      Chinese pangolin  t
B D              Elephant  t
B D                Tenrec  t
B D               Opossum  c
B D         X. tropicalis  t
B D    Hawaiian monk seal  -
B D                   Dog  -
B D                 Horse  -
B D              Marmoset  -
B D               Gorilla  -
B D                Bonobo  -
B D                 Chimp  -
B D                 Human  -
B D              Hedgehog  -
B D             Zebrafish  =
B D               Chicken  =
B D                 Shrew  -

Inserts between block 37 and 38 in window
B D             Elephant 3bp
B D               Tenrec 3bp
B D              Opossum 3bp

Alignment block 38 of 344 in window, 56744455 - 56744531, 77 bps 
B D                 Mouse  tctc---ggattc-------tggcaatcagggcaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                   Rat  tctc---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
            GCF_003668045  tctc---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
                   Beaver  tctc---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D              Squirrel  tctt---ggattc-------aggcaatcaggccaaattcgctcaggcaggaagttcaaatgtcacctaat
B D            Guinea pig  tctc---ggattc-------tggcaatcaggctaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                Rabbit  tctc---ggatac-------tggcaatcagaccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                  Pika  tctc---agattc-------tggcaatcagaccacatttgctcaggcaggaagttcaaatgtcacctaat
B D                 Human  -ctc---cgattc-------tggtaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                 Chimp  -------cgattc-------tggtaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                Bonobo  -------cgattc-------tggtaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D               Gorilla  -ctc---cgattc-------tggtaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                Rhesus  tctc---cgattctggattgtggtaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D              Marmoset  -ctc---ccattt-------tggcaatcaggccaaatttgctccggcaggaagttcaaatgtcaactaat
B D               Tarsier  tctc---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D              Bushbaby  tctt---ggattt-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D            Tree shrew  tctc---ggattc-------tggcaatcaggctaaatttgctcaggcaggaagttcaaatgtcacctaat
B D  Malayan flying lemur  tctc---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                   Pig  tctt---ggattc-------tggtaatcagaccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D               Dolphin  tctt---gcattc-------tggcaatcagaccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                   Cow  tctt---gcattc-------tggcaatcagaccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                 Sheep  tctt---gcattc-------tggcaatcagaccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                 Horse  --tt---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D      Chinese pangolin  tttt---ggattc-------tggcaatcaggtcaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                   Dog  --tt---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D    Hawaiian monk seal  --tt---ggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D              Hedgehog  --tt---ggattc-------tggcaatcaggctaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                 Shrew  --ttcgaggattc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D              Elephant  tctc---gggttc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D                Tenrec  tctc---gggttc-------tggcaatcaggccaaatttgctcaggcaggaagttcaaatgtcacctaat
B D               Opossum  tctc---ggattc-------tcgcaatcaggccaaatttgctcagacaggaagttcaaatgtcacctaat
B D               Chicken  tctc---cgcttt-------tcgcaatcaggccaaatgcgctcaggcaggaagttcaaatgtcacctaat
B D         X. tropicalis  tctc---tgcctt-------gtgcaatcagactaaattcacccagacaggaagttcaaatgtcagataat
B D             Zebrafish  ======================================================================

                    Mouse  tggtttcattcttatgc
                      Rat  tggtttcattcttatgc
            GCF_003668045  tggtttcgttcttatgc
                   Beaver  tggtttcattcttatgc
                 Squirrel  tggtttcattcttatgc
               Guinea pig  tggtttcattcttatgc
                   Rabbit  tggtttcgttcttatgc
                     Pika  tggtttcgttcttatgc
                    Human  tggtttcgttcttatgc
                    Chimp  tggtttcgttcttatgc
                   Bonobo  tggtttcgttcttatgc
                  Gorilla  tggtttcgttcttatgc
                   Rhesus  tggtttcgttcttatgc
                 Marmoset  tggtttcgttcttatgc
                  Tarsier  tggtttcattcttatgc
                 Bushbaby  tggtttcattcttatgc
               Tree shrew  tggtttcattcttatgc
     Malayan flying lemur  tggtttcattcttatgc
                      Pig  tggtttcattcttatgc
                  Dolphin  tggtttcattcttatgc
                      Cow  tggtttcattcttatgc
                    Sheep  tggtttcattcttatgc
                    Horse  tggtttcattcttatgc
         Chinese pangolin  tggtttcattcttatgc
                      Dog  tggtttcattcttatgc
       Hawaiian monk seal  tggtttcattcttatgc
                 Hedgehog  tggtttcattcttatgc
                    Shrew  tggtttcattcttatgc
                 Elephant  tggtttcattcttatgc
                   Tenrec  tggtttcattcttatgc
                  Opossum  tggtttcattcttatgc
                  Chicken  tgccttaattctgatgc
            X. tropicalis  tggtttcattcttaggc
                Zebrafish  =================

Inserts between block 38 and 39 in window
B D        X. tropicalis 2818bp

Alignment block 39 of 344 in window, 56744532 - 56744608, 77 bps 
B D                 Mouse  ttcacttcattttcctcggaaacggag-------------gtctc-------ggt----ctct-------
B D                   Rat  ttcacttcattttcctc-----------------------gtcgc-------gct----ctct-------
            GCF_003668045  ttcacttcattttcttcggaaacggaggttcgggttcctagtctc-------tct----ctct-------
                   Beaver  ttcacttcattttcctcggaaacggag-------------gtcct-------ggt----tactac-ta--
B D              Squirrel  ttcacttcattttcctcggaaacggag-------------gtccc-------gct----tactgc-ta--
B D            Guinea pig  ctcacttcattttcctcggaaacccag-------------gtcct-------ggt----tgctag-ta--
B D                Rabbit  ttcacttcattttcctcggaaacggag-------------gtccc-c----aagt----tactac-ta--
B D                  Pika  ttcacttcattttcctcggaaatggag-------------gtcctga----aagt----tattgcttt--
B D                 Human  ttcacttcattttcctcggaaatggag-------------gtccc-g----aagt----tactac-ta--
B D                 Chimp  ttcacttcattttcctcggaaatggag-------------gtccc-g----aagt----tactac-ta--
B D                Bonobo  ttcacttcattttcctcggaaatggag-------------gtccc-g----aagt----tactac-ta--
B D               Gorilla  ttcacttcattttcctcggaaatggag-------------gtcct-g----aagt----tactac-ta--
B D                Rhesus  ttcacttcattttcctcggaaatagag-------------gtccc-g----aagt----tactac-ta--
B D              Marmoset  ttcacttcattttcctcggaaatggag-------------gtccc-g----aagt----tactac-ta--
B D               Tarsier  ttcacttcattttcctcggaaaccgag-------------gtccc-c----aagt----tactac-caa-
B D              Bushbaby  ttcagttcattttcctcggaaaccgag-------------gtccc-g----aagt----tactac-ta--
B D            Tree shrew  ttcacttcattttcctcggaaatggag-------------gtctc-a----aagt----tactac-ta--
B D  Malayan flying lemur  ttcacttctttttcctcggaaacagag-------------gtccc-g----aagt----cactac-ta--
B D                   Pig  ttcacttcattttcctcggaaacggag-------------gtccc-a----aagt----tactac-ta--
B D               Dolphin  ttcacttcattttcctcggaaacggag-------------gtcct-g----aagt----tactac-ta--
B D                   Cow  ttcacttcattttcctcggaaacggag-------------gtccc-g----aagt----tactac-ta--
B D                 Sheep  ttcacttcattttcctcggaaacggag-------------gtccc-g----aagt----tactat-ta--
B D                 Horse  ttcacttcattttcctcggaaaccgag-------------gtccc-g----aagt----tactac-ta--
B D      Chinese pangolin  ttcacttcattttcctcggaaacggag-------------gtccc-g----aagt----tactac-ta--
B D                   Dog  ttcacttcattttcctcggaaacggag-------------gtccc-c----aagt----tactac-ta--
B D    Hawaiian monk seal  ttcacttcattttcctcggaaacggag-------------gtccc-g----aagt----tactac-ta--
B D              Hedgehog  ttcacttcattttc--------------------------------------------------------
B D                 Shrew  ttcgcttcattttcctcggaaacagag-------------gtccc-g----acgt----tactac-ta--
B D              Elephant  ttcacttcattttcctcggaaacggag-------------gtcca-g----aagt----tactac-ta--
B D                Tenrec  ttcacttcattttcctcggaaatggaa-------------gtccc-g----aagt----tactac-ta--
B D               Opossum  ttcacttttt--------gaaacagcgagt----------gagcc-a----aaatagaaaaccat-cg--
B D               Chicken  tgta-----ttttccttcgaagcggtg-------------gtccg-ggaaaacga----aacccc-gaag
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================

                    Mouse  -----ctctctctct--------------------c------tc-tctctctc-----------------
                      Rat  -----ctctctctct--------------------c------tc-tctctctc-----------------
            GCF_003668045  -----ctctctctct--------------------c------tc-tctctctc-----------------
                   Beaver  gt--aacttgtatat--------------------a------gc-tcattccg-----------------
                 Squirrel  gt-aactttgtaact--------------------t------gcatttagctg-----------------
               Guinea pig  ac-atgcttgta-at--------------------c------tc-tctccccg-----------------
                   Rabbit  gt-a-acttgcatga--------------------a------gc-tcaatccg-----------------
                     Pika  gt-a-acttacatgt--------------------a------gc-tcgttctg-----------------
                    Human  gt-a-acttgcatgt--------------------a------ac-tcattcccaga--------------
                    Chimp  gt-a-acttgcgtgt--------------------a------ac-tcattcccaga--------------
                   Bonobo  gt-a-acttgcgtgt--------------------a------ac-tcattcccaga--------------
                  Gorilla  gt-a-acttgcatgt--------------------a------ac-tcattcccaga--------------
                   Rhesus  gt-a-acttgcatgt--------------------a------ac-tcattcccaga--------------
                 Marmoset  -------------ct--------------------a------ac-tcattcccaga--------------
                  Tarsier  gt-a-acttgcatgt--------------------a------ac-tcattcccgga--------------
                 Bushbaby  gt-a-actt---tct--------------------c------tc-tctttctc-----------------
               Tree shrew  gt-a-acttacatgt--------------------a------gc-tca----------------------
     Malayan flying lemur  gc-a-tctt---tgt--------------------a------gc-tcattccaggattctctctctctct
                      Pig  gt-a-actta-aggt----tactg-----------c---atcgc-tcattctggga--------------
                  Dolphin  gt-a-acttgcgtgt----tacag-----------c---attgc-tcattctggga--------------
                      Cow  gt-a-acttgcatgttagatagag-----------c---attgc-tcattctggga--------------
                    Sheep  gt-a-acttgcatgt----tagag-----------c---attgc-tcattctggga--------------
                    Horse  gt-a-acctgcatgt----tactg-----------c---attgc-tcattctggga--------------
         Chinese pangolin  gt-a-acttgcatgt----tactgggactaattccc---gttgc-tcattctggga--------------
                      Dog  gt-a-acttgcatgt----tgctg-----------c---attgc-tcattctggga--------------
       Hawaiian monk seal  gt-a-acttgcatgt----tactg-----------c---attgc-tctttctggga--------------
                 Hedgehog  ------tgtgcatgt----gactg-----------c---attgc-ttattctcaca--------------
                    Shrew  gt-a-acttgtatgt----tactg-----------cgcagttgc-tcattctagga--------------
                 Elephant  gt-a-acttgcatgt--------------------a------gc-tcattccggga--------------
                   Tenrec  gt-a-acttgcatgt--------------------a------gc-tcattccggga--------------
                  Opossum  gtta-ttttgcctgg--------------------t------tc-tccttccagga--------------
                  Chicken  gt-t-tgctccctgt--------------------a------aa-ccttccac-----------------
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  -----------------------------------------tctctctc---------tctctc-----t
                      Rat  -----------------------------------------tctctctc---------tctctc-----t
            GCF_003668045  -----------------------------------------tctctctc---------tctctc-----t
                   Beaver  -----------------------------------------tctctctc---------tctctc-----t
                 Squirrel  -----------------------------------------attccggg---------ttcccc-----t
               Guinea pig  -----------------------------------------cctctgtc---------tttctc-----t
                   Rabbit  -----------------------------------------gctcgcgc---------tctctc-----t
                     Pika  -----------------------------------------gcgcgctc---------tctctc-----t
                    Human  --------------------------cgaagtcatattcacattctctc---------tctctc-----t
                    Chimp  --------------------------cgaagtcatattcacattctctc---------tctctc-----t
                   Bonobo  --------------------------cgaagtcatattcacattctctc---------tctctc-----t
                  Gorilla  --------------------------cgaagtcatattcacattctctc---------tctctc-----t
                   Rhesus  --------------------------tgaagtcatattcacattctctc---------tctctc-----t
                 Marmoset  --------------------------cgaggtcatattctctctctctc---------tctctc-----c
                  Tarsier  --------------------------agaattcat----------tctc---------tctctc------
                 Bushbaby  ------------------------------------tccctctctcctc---------tctttc-----t
               Tree shrew  ----------------------------------------------ttcagagaggaattttgt-----g
     Malayan flying lemur  ctctctctctctctctctctctctctctctctctctctctctctctctc---------tctctc-----t
                      Pig  --------------------------ctaa-----------ttttctgc---------tttatt-----t
                  Dolphin  --------------------------ctaa-----------ttttctgc---------tttatt-----t
                      Cow  --------------------------cgaa-----------ttttctgc---------tttatt-----t
                    Sheep  --------------------------ctaa-----------ttttctgc---------tttatt-----t
                    Horse  --------------------------ctaa-----------ttttctgc---------tttatt-----t
         Chinese pangolin  --------------------------ctaa-----------ttttctgc---------tttatt-----t
                      Dog  --------------------------ctca-----------ttttctgc---------tttatt-----t
       Hawaiian monk seal  --------------------------ctaa-----------ttttctgc---------tttatt-----t
                 Hedgehog  --------------------------ctga-----------ttttcttt---------at--tt-----c
                    Shrew  --------------------------ctag-----------ttttcttc---------tttatt-----t
                 Elephant  --------------------------ctaa-----------ttttctgc---------tttattac--tt
                   Tenrec  --------------------------ctaa-----------ttttctgc---------tgtattac--tt
                  Opossum  -------------------------actaa-----------ttttctgc---------tttattaccgtt
                  Chicken  -----------------------------------------cttctttc---------tgtttc-----t
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================

                    Mouse  ct----
                      Rat  ct----
            GCF_003668045  ct----
                   Beaver  ct----
                 Squirrel  tt----
               Guinea pig  tc----
                   Rabbit  cc----
                     Pika  ct----
                    Human  ct----
                    Chimp  ct----
                   Bonobo  ct----
                  Gorilla  ct----
                   Rhesus  ct----
                 Marmoset  ct----
                  Tarsier  ct----
                 Bushbaby  ct----
               Tree shrew  ct----
     Malayan flying lemur  ct----
                      Pig  ct----
                  Dolphin  ct----
                      Cow  ct----
                    Sheep  ct----
                    Horse  ct----
         Chinese pangolin  ct----
                      Dog  ct----
       Hawaiian monk seal  ct----
                 Hedgehog  ct----
                    Shrew  ct----
                 Elephant  ct----
                   Tenrec  ct----
                  Opossum  ct----
                  Chicken  ccgcct
                Zebrafish  ======
            X. tropicalis  ======

Inserts between block 39 and 40 in window
B D              Chicken 732bp

Alignment block 40 of 344 in window, 56744609 - 56744624, 16 bps 
B D                 Mouse  ctctctccc----------------------------------cttacct
B D                   Rat  ctccccccccctctct---------------------------ctccccc
            GCF_003668045  ctctctctctctctctctctct--ctctctctctc--------ctccctc
                   Beaver  ctgcccccc-----------------------------------------
B D              Squirrel  ctcctcccc-----------------------------------------
B D            Guinea pig  cttccttcccttttttctcccttccttctttcctt--------cttcctt
B D                Rabbit  ct------------------------------------------taacgt
B D                  Pika  ctctctctctctctctctct-----------------------ctcacac
B D                 Human  ttctctctc----------------------------------cattcac
B D                 Chimp  tgctctctc----------------------------------cattcac
B D                Bonobo  tgctctctc----------------------------------cattcac
B D               Gorilla  ttctctctc----------------------------------cattcac
B D                Rhesus  ctctctctctctctctctctctctctctctctctctctctcatcattcac
B D              Marmoset  ctacctctc----------------------------------ccc----
B D               Tarsier  cccccccaa----------------------------------cattctg
B D              Bushbaby  ctatctcttggtctcggcctctctttctttcg-----------tattcct
B D            Tree shrew  ttctcgctcacagat----------------------------ca-----
B D  Malayan flying lemur  ctctctctctctcgt----------------------------catttac
B D                   Pig  ctct--------------------------------------------cc
B D               Dolphin  ctctttgtcctccccctcct-----------------------cccccct
B D                   Cow  ctctttctc----------------------------------ccgctct
B D                 Sheep  ctctttctc----------------------------------ccgctct
B D                 Horse  ctctctctctccctcc---------------------------cctc---
B D      Chinese pangolin  ctctccctctttttcc---------------------------cctccct
B D                   Dog  ctctctctctctctctctctctctctctg--------------cctctct
B D    Hawaiian monk seal  ctctctctctctccc----------------------------cctctct
B D              Hedgehog  ttctcctttatgtgaa---------------------------tatatat
B D                 Shrew  tcctccctgacttaaa---------------------------aaaaaat
B D              Elephant  ctctctcttgatctag---------------------------tcgttct
B D                Tenrec  cacgcgcttgctctatctctcgc--------------------tcgctct
B D               Opossum  ttccgcttttct--------------------------------------
B D             Zebrafish  ==================================================
B D         X. tropicalis  ==================================================
B D               Chicken  ==================================================

Inserts between block 40 and 41 in window
B D               Rabbit 73bp
B D                 Pika 9bp
B D                Human 2bp
B D                Chimp 2bp
B D               Bonobo 2bp
B D              Gorilla 2bp
B D               Rhesus 2bp
B D              Tarsier 2bp
B D             Bushbaby 2bp
B D           Tree shrew 2bp
B D Malayan flying lemur 2bp
B D                  Pig 22bp
B D              Dolphin 23bp
B D                  Cow 23bp
B D                Sheep 23bp
B D                Horse 4bp
B D     Chinese pangolin 7bp
B D                  Dog 27bp
B D   Hawaiian monk seal 27bp
B D             Hedgehog 19bp
B D                Shrew 15bp
B D             Elephant 6bp
B D               Tenrec 6bp

Alignment block 41 of 344 in window, 56744625 - 56744628, 4 bps 
B D                 Mouse  c--cca
B D                   Rat  c--cta
            GCF_003668045  c--ctc
B D            Guinea pig  cttctt
B D                   Pig  t-----
B D               Dolphin  t-----
B D                   Cow  t-----
B D                 Sheep  t-----
B D                 Horse  t-----
B D      Chinese pangolin  c-----
B D                   Dog  c-----
B D    Hawaiian monk seal  c-----
B D              Hedgehog  g-----
B D                 Shrew  g-----
B D               Opossum  --ttca
B D                Rhesus  ======
B D              Marmoset  ------
B D               Gorilla  ======
B D                Bonobo  ======
B D                 Chimp  ======
B D                 Human  ======
B D                Tenrec  ======
B D               Tarsier  ======
B D            Tree shrew  ======
B D                  Pika  ======
B D             Zebrafish  ======
B D         X. tropicalis  ======
B D               Chicken  ======
B D              Elephant  ======
B D              Squirrel  ------
B D                Rabbit  ======
B D              Bushbaby  ======
                  Beaver  ------
B D  Malayan flying lemur  ======

Inserts between block 41 and 42 in window
B D              Opossum 172bp

Alignment block 42 of 344 in window, 56744629 - 56744677, 49 bps 
B D                 Mouse  cccacct---------------------ccctt---aac--agacgtta--att----------------
B D                   Rat  accactt---------------------tcctt---aac--agacgtta--att----------------
            GCF_003668045  ccctcctcacacctcccccttgc-----ccctt---aac--agacgtta--att----------------
                   Beaver  -ccacct---------------------cccat---tac--------------t----------------
B D              Squirrel  -ccacctcactttt--------------acctt---aacagagacatca--a-t----------------
B D            Guinea pig  tcctcctgctgtgtcca-----------ctctg---aag--agacat------c----------------
B D                  Pika  -----------------cacaca-----cacac---aac--ctaccata--t-t----------------
B D                 Human  --------------------tct-----aactt---aac--agacttca--c-t-gtatata--------
B D                 Chimp  --------------------tct-----aactt---aac--agacttca--c-t-gtatata--------
B D                Bonobo  --------------------tct-----aactt---aac--agacttca--c-t-gtatata--------
B D               Gorilla  --------------------tct-----aactt---aac--agacttca--c-t-gtatata--------
B D                Rhesus  --------------------tct-----aactt---aac--agacttca--c-t-gtatata--------
B D              Marmoset  ------------------------------ctt---aac--agacttca--c-c-gtgtgta--------
B D               Tarsier  --------------------ttt-----acatg---aac--agatttca--c-taatacata--------
B D              Bushbaby  --------------------cca-----aaatt---cac--acttttac--c-t-tcacaga--------
B D            Tree shrew  --------------------ttt-----acctt---aac--agacttca--c-t-atatcta--------
B D  Malayan flying lemur  --------------------ttt-----atctt---aac----acttca--c-tcatacata--------
B D                   Pig  --------------------ttt-----acctt---aat--atatatatata-t-atacatatatatttc
B D               Dolphin  --------------------ttt-----acctt---aac--agatttcacta-c-atatatg--------
B D                   Cow  --------------------tct-----acctt---aac--agattttagca-c-atatata--------
B D                 Sheep  --------------------ttt-----acctt---aac--agattttagca-c-atatata--------
B D                 Horse  --------------------ttt-----atctt---aac--agtcttca--c-t-atatata--------
B D      Chinese pangolin  --------------------ttt-----accat---aac--agacttca--c-t-atacgta--------
B D                   Dog  --------------------ttt-----acctt---agc--cgacttcagtc-t-gtgtgta--------
B D    Hawaiian monk seal  --------------------ttt-----atctt---aac--agacttca--c-t-atatgta--------
B D              Hedgehog  --------------------tac-----actta---cat--acatttctaat-a-atatgtg--------
B D                 Shrew  --------------------tat-----atatagattat--atactatagat-t-atacaca--------
B D              Elephant  ----------------------------acctt---acc--agacgtca--a-t---atcta--------
B D                Tenrec  --------------------cctcgttgccctt---aac--cgacttcg--a-t---atata--------
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Opossum  ======================================================================
B D               Chicken  ======================================================================
B D                Rabbit  ======================================================================

                    Mouse  --------------------------atcaaccca--gtagt-----tgaggtgac
                      Rat  --------------------------atcaaccca--gtagt-----taaggtgac
            GCF_003668045  --------------------------atcaaccct--gcagt-----tagggtgac
                   Beaver  --------------------------accactgca--atgat-----taagacaaa
                 Squirrel  --------------------------accactgca-tatgac-----gcagacaaa
               Guinea pig  --------------------------accatcacaaaatgac-----caagaccaa
                     Pika  --------------------------atctatcta--tcttg-----gaaagtggc
                    Human  tcttaggaagggaagtggca---tcagccactgca--gtgat-----ggagat---
                    Chimp  tcttaggaagggaagtggca---tcagccactgca--gtgat-----ggagat---
                   Bonobo  tcttaggaagggaagtggca---tcagccactgca--gtgat-----ggagat---
                  Gorilla  tcttaggaagggaagtggca---tcagccactgca--gtgat-----ggagat---
                   Rhesus  tcttaggaagggaagtggcc---tcagcaactgca--gtgat-----ggagat---
                 Marmoset  tcttaggaggggaagtggca---t------ctgca--gtgat-----ggaaat---
                  Tarsier  tcttggcaagagaagtggca---tcaaccacttgg--gcgag-----ggagac---
                 Bushbaby  cttaag---ggaaagtggcc---tcaacaactgcg--gtgat-----ggaaac---
               Tree shrew  ccttaggaagggaagtgaca---cccaccactgtg--gtgaa-----gacaa----
     Malayan flying lemur  ccgtgggaagagaggtggca---ccagccatggcg--gtgat-----ggagac---
                      Pig  tattag-----agagtggca---ctaaccatcgct--gtgat-----ggaggg---
                  Dolphin  tcttag-----gaagtggca---ccaactactgct--gtgat-----ggagag---
                      Cow  tcctag-----gaagtggca---ccaatcaccgct--aaaat-----gaaggg---
                    Sheep  tcctag-----gaagtggcg---ccaaccaccgct--ataat-----gaaggg---
                    Horse  tcttag-----gaagtggca---ccaaccaccgct--gtgat-----ggagcc---
         Chinese pangolin  tcttag-----gaagtggta---ctaaccacctct--ttgag-----ggagtc---
                      Dog  tcttag-----gaagtggcaccccccccccccgca--gggat-----ggaaac---
       Hawaiian monk seal  tcttag-----gaagtggca---ccaaccactgct--gtgat-----gggaac---
                 Hedgehog  t--tag-----aaagtgtca---ccagcaatcact--taagtac---tagata---
                    Shrew  ca-tag-----atatatgta---cacatatgcacg--ttcatacacatatata---
                 Elephant  tctcag-----gcagtggaa---ccgatcactgta--gtgat-----ggaaag---
                   Tenrec  tcttaa-----gcagtggca---tccaaccctgcg--gtggt-----ggaaag---
                Zebrafish  ========================================================
            X. tropicalis  ========================================================
                  Opossum  ========================================================
                  Chicken  ========================================================
                   Rabbit  ========================================================

Inserts between block 42 and 43 in window
B D                Human 1bp
B D                Chimp 1bp
B D               Bonobo 1bp
B D              Gorilla 1bp
B D               Rhesus 1bp
B D             Marmoset 1bp
B D              Tarsier 1bp
B D             Bushbaby 1bp
B D Malayan flying lemur 1bp
B D                  Pig 1bp
B D              Dolphin 1bp
B D                  Cow 1bp
B D                Sheep 1bp
B D                Horse 1bp
B D                  Dog 1bp
B D   Hawaiian monk seal 1bp
B D             Hedgehog 1bp
B D                Shrew 1bp
B D             Elephant 1bp

Alignment block 43 of 344 in window, 56744678 - 56744713, 36 bps 
B D                 Mouse  aattgc-taggtgat------t-----------cgct-gttgt--ccattcggctgc
B D                   Rat  aattgc-ttggtgat------t-----------cgct-gttgt--cctttcggctgc
            GCF_003668045  aattgc-ttgatgat------t-----------cgct-gttgt--cctttcggctgc
                   Beaver  a--tgc-atggtgat------t-----------ccat-gttgt--cctttctactgt
B D              Squirrel  a-------------t------t-----------atat-gccgt--cctttctactgt
B D            Guinea pig  a--tgt-aagagggtaaagaat-----------ccaa-gtgtt--ctttttcactgt
B D                Rabbit  aagtgc-atggcgac------t-----------ccat-gccgt--cctttccac-gt
B D                  Pika  -----a-gcggccac------t-----------ccctggccgt--cctttctactgt
B D                 Human  aaatgc-a-ggcaat------t-----------ccat-gctg---tccttttactgt
B D                 Chimp  aaatgc-a-ggcaat------t-----------ccat-gctg---tccttttactgt
B D                Bonobo  aaatgc-a-ggcaat------t-----------ccat-gctg---tccttttactgt
B D               Gorilla  aaatgc-g-ggcaat------t-----------ccat-gctg---tccttttactgt
B D                Rhesus  aaatgc-a-ggcaat------t-----------ccat-gctg---tccttttacggt
B D              Marmoset  aaatgc-a-ggcgat------t-----------ccat-gccgt--tctttttactgt
B D               Tarsier  aaatgcaa-ggcgat------t-----------ccat-gccg---tctttctaccgc
B D              Bushbaby  aaatgg-atggcgat------t-----------ccaa-gctgt--tttttctactgt
B D            Tree shrew  aaatgt-agagcgat------t-----------ccat-gctgt--tcattttattgt
B D  Malayan flying lemur  aaatgc-atggcggt------t-----------ccat-acggtcctctttctactgt
B D                   Pig  aaatgc-acagtgat------t-----------ccat-gctgt--cctcaattc--t
B D               Dolphin  aaattc-ac-gcgat------t-----------tcat-gctgt--cctcttttctgt
B D                   Cow  aaatgc-acggcgat------t-----------ccac-gctgt--cctctcttctgt
B D                 Sheep  aaatgc-acggcgat------t-----------ccac-gctgt--cctctcttctgt
B D                 Horse  aaatgt-atggcgat------t-----------ccgt-gctgt--cctgtcttctgt
B D      Chinese pangolin  aaatgc-atgacgat------t-----------tcat-gttgt--cctctcttcttt
B D                   Dog  aaatgc-atggtgat------t-----------tcat-cttgt--cctctcttctt-
B D    Hawaiian monk seal  aaatgc-agggtgat------t-----------tcat-cacgt--cctctcttctt-
B D              Hedgehog  aaatgc-aggggact------t-----------ccac-gctgc--cctcttaaccgg
B D                 Shrew  gtattc-atacatct------tagtgttatcaaccac-actat--actaatgtcttt
B D              Elephant  aaatgc-ctgacgat------t-----------ccac-gcctt--cctttcttccgt
B D                Tenrec  ------------------------------------t-ggctt--cctttcctctg-
B D             Zebrafish  =========================================================
B D         X. tropicalis  =========================================================
B D               Opossum  =========================================================
B D               Chicken  =========================================================

Alignment block 44 of 344 in window, 56744714 - 56744883, 170 bps 
B D                 Mouse  --tgt----c--tc-------tggt-tcccccc-agcctcc-tgctttcctta--------gggt--cct
B D                   Rat  --tgt----c--tc-------tgtc-tcccccc---ccccc-ccccaccctcc--------ggcttccct
            GCF_003668045  --ccc----ccgcc-------cgcc-cccctcccaggctcc-cgctttcctta--------gcgt--cct
                   Beaver  --tct----t--tt-------ggct-tctctgc------------tttttctg--------gggt--cct
B D              Squirrel  --ttt----c--cc-------cgga-gcctgcc---------cctttctttta--------gggt--ccc
B D            Guinea pig  --tct----c--ac-------ctgc-ttttcctaagccttcagctttccttta--------gggt--cct
B D                Rabbit  --tct----t--tc-------cag-------------ttct----------------------at--cgg
B D                  Pika  --tct----c--cc-------cagc-ctgctttttgcctca----------------------gt--ccg
B D                 Human  --tct----t--tt-------cagt-tttccctgagcctgccactttcctttggggtccccgggt--ccc
B D                 Chimp  --tct----t--tt-------cagt-tttccctgagcctgccactttcctttggggtccccgggt--ccc
B D                Bonobo  --tct----t--tt-------cagt-tttccctgagcctgccactttcctttg--------gggt--ccc
B D               Gorilla  --tct----t--tt-------cagt-t-------agcctgccactttcctttggggtccccgggt--ccc
B D                Rhesus  --tct----t--tt-------cagt-tttccctgagcctgccactttcctttg--------gggt--ccc
B D              Marmoset  --tct----t--tt-------ccgt-ttaccctgagctttccgctttcctttg--------gggt--tct
B D               Tarsier  --ttt----t--tc-------ccgt-gttccctgagcttgccgctttcctttg--------gggc--ccc
B D              Bushbaby  --tct----t--tc-------ctgt-tttccctgagcctgcggttttcctttg-----------------
B D            Tree shrew  --tct----t--tt-------ccgtgtttctctgagcctcctactttccttta--------gagt--ctc
B D  Malayan flying lemur  --tct----t--tc-------ccgt-tttccttgcgcctgccgctttcctttt--------gggg--ccc
B D                   Pig  --cct----t--tc-------ccgt-tttacccatacctgctgcttcccttta--------gagt--ccc
B D               Dolphin  --tct----t--tc-------ccgt-ttttcccgcgcctgccgcttcccttta--------gggt--ccc
B D                   Cow  --tct----t--tg-------ccgt-tttccccgcgcctgccgcttcccttta--------gggt--ccg
B D                 Sheep  --tct----t--tg-------ccgt-tttccccgcgcctgccgcttctcttta--------gggt--ccg
B D                 Horse  --tct----t--tc-------ccgt-ctctcccacgactgccacttccctttg--------gggt--acg
B D      Chinese pangolin  --gcc----a--tt-------ccgc------------ctgccgcttcccttta--------gggt--ctc
B D                   Dog  ------------tc-------ccgt-tttccccaagcctgcggcttcccttta--------gggt--ccc
B D    Hawaiian monk seal  ------------tc-------ctgg-tttccccaagcctgtggattcccttga--------gggc--ccc
B D              Hedgehog  --accccccc--cc-------ccat-ttttccagtgtccgctggttccccgta--------gggt--ctc
B D                 Shrew  --cctgttct--tc-------ctcc-tttcccagctcctgcaacttttctttc---------tgt--ctc
B D              Elephant  --ctt----t--cc-------ccgt-cttcccct---------------------------gccc--ctg
B D                Tenrec  --cct----t--cc-------ccat-ttgcccct---------------------------gcgc--ccg
B D               Opossum  tgtct----c--tccttagaactgt-ttgctctcggtttttctccttatctca--------actt--ctt
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  cg-ggaac---------taggaaacgctagtggttgcg----tgcccctttcctg----caaagttt-cc
                      Rat  ag-agtac---------tgggaaatgctagtggtcgcc----ggcccttttcctg----caaacttt-cc
            GCF_003668045  cg--gtac---------tgggaaatgccagtggctacc----ggtcccctttccg----caga-------
                   Beaver  ct-ggtcc---------tggg-aacgcgagtggactcc----tacctagttcctg----cagg-ttt-tc
                 Squirrel  ct-agtcc---------ccgggaa-acaagtggacgtg----tatctagttcttg----cacg-ggt-tc
               Guinea pig  cttggtcc---------ctggcatttcaagtgga-----------ccacctcctg----agtc-------
                   Rabbit  ag----cc---------cagggaccgcgagtgaacgcctgcttatttagcacttg----cacg-gtt-tc
                     Pika  ag--gtcc---------cagggactgccagcgaacacc----taaggaacttctg----cac--gtt-tc
                    Human  cg-ggtcc---------ccgagaatgcaagtggatatc----tatctagttcctg----catg-ttt-ta
                    Chimp  cg-ggtcc---------ccgagaatgcaagtggatata----tatctagttcctg----catg-ttt-ta
                   Bonobo  ca-ggtcc---------ccgagaatgcaagtggatata----tatctagttcctg----catg-ttt-ta
                  Gorilla  cg-ggtcc---------ccgagaatgcaagtggatatc----tatctagttcctg----catg-ttt-ta
                   Rhesus  cg-ggtcc---------ccgagaatgcaagtggatatc----tatctagttcctg----catg-ctt-tc
                 Marmoset  cg-ggtcc---------ccaagaatgcaagtggatatc----tatctagtttctg----caca-ttt-tc
                  Tarsier  ca-agtcc---------ccgatgatgcgagtggacgtc----tatctagttcctg----cacg-ttt-tt
                 Bushbaby  -g-ggtcc---------ccgagaatacgagtggacatc----tgtctagttcct----------------
               Tree shrew  ct-gacccggggagtgtccgggaatgcgagtggacgtc----tatctaggtcgtg----catg-ttt-tt
     Malayan flying lemur  ct-gcccc---------ccgggaatgcaagtggacatc----tctctagttcccg----cacg-ttt-tc
                      Pig  cc-aggcc---------ccagaaacatgagtgga--------catctagtctctg----aacg-ttt-tc
                  Dolphin  cc-agtcc---------ccgggaatgtgagtgga--------catctagtccctg----aacg-ttt-tc
                      Cow  ac-agtcc---------cagggaattctagtgga--------catcccgtccctg----cacg-ttt-tc
                    Sheep  cc-agtcc---------cagggaatgctagtgga--------catcccgtccctg----cacg-ttt-tc
                    Horse  cg-ggtcc---------cagggaaggcaagtgga--------agtctagtcccgg----catg-ttt-tc
         Chinese pangolin  cc-tgtcc---------ccgggaatgcgagtaga--------catctagtcattg----caca-ttt-tc
                      Dog  cc--gtcc---------ttgggaatgcatgcaga--------catctagtacctg----caca-ttt-tc
       Hawaiian monk seal  cc-agtcc---------ctggggatgcaagtgga--------catctagtacctg------ca-ttt-tc
                 Hedgehog  ct-ggtct---------ccagcaacttgagtgga--------cattaacccctgt-------a-tgt-ta
                    Shrew  c--actct---------ctgggaa--tgcaggga--------cattgagtccctt----caag-ttt-tc
                 Elephant  cc-ggtcc---------tctggaatgcgagcggacat-----ttcgttgtccctg----aacg-ttt-tc
                   Tenrec  cc-agtcc---------gctggaatgcgagcggacag-----caagtagttcctg----aacg-tttgtt
                  Opossum  cc-acacc---------tagactaccagagtcaa--------agctgtgtttttgatttcgcg-ctt-tt
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  -agcag-tgttt-ttt-------------------tccttttctgtgccggaacct-----tgctctgtc
                      Rat  -agcag-tgttc-ccc-------cc--------cacccctttctctgctggaacct-----tattctgtc
            GCF_003668045  --------------------------------------ttttttcagcctgaa-tt-----tgcgctgtt
                   Beaver  -agcgg-tgcca-ctc-------cactgttg--ctttcctttctcacccctgacct-----tgccgtgtc
                 Squirrel  -agcga-tgcca-ccc-------cactgttc--ctttcctttctcacccctgacct-----tgccgagtc
               Guinea pig  ---------------------------------cttttctttcttacccctgactt-----tgctgtgtc
                   Rabbit  -actgg-tgccg-----------------------cccctc-----------------------------
                     Pika  -agcgt-tgcca-------------------------gctt-----------------------------
                    Human  -agcag-tgcca-ccc-------cactgttt--ctttcctttctcacccctgacct-----tgcctagtc
                    Chimp  -agcag-tgcca-ccc-------cactgttt--ctttcctttctcacccctgacct-----tgcctagtc
                   Bonobo  -agcag-tgcca-ccc-------cactgttt--ctttcctttctcacccctgacct-----tgcctagtc
                  Gorilla  -agcag-tgcca-ccc-------cactgttt--ctttcctttctcacccctgacct-----tgcctagtc
                   Rhesus  -agcag-tgcca-ccc-------cactgttc--ctttcctttctcacccctgacct-----tgcctagtc
                 Marmoset  -agcag-tgcca-ccc-------cactgtt---ctttcctttctcacccctgacct-----tgcctagtc
                  Tarsier  -agcgg-ggcca-ccccacacctcaccgttc--ctttcctttctcacccctgacct-----tgccttgtc
                 Bushbaby  ---------------c-------cactgttc--ctttcctttctcacccctgacct-----tgccttgtc
               Tree shrew  gagcag-tgcca-ccc-------cactgttc--ctttcctttctcacccctgacct-----tgccgtgtt
     Malayan flying lemur  -agcgg-tgcca-ccc-------cattgttt--cttttctttctcacccctgacct-----tgccctgtc
                      Pig  -agcag-tgaca-ccc-------cactgttc--ctttcctttctcacccttgacct-----tgcagtgtc
                  Dolphin  -agtgg-tg---------------------c--ctttcctttctcacccttgacct-----tgc-gtgtg
                      Cow  -agtgg-tgcca-ccc-------caccgttc--ctttcctttctcacccttgacct-----tgc-gtgtt
                    Sheep  -agtgg-tgcca-ccc-------cactgttc--ctttcctttctcacccttgacct-----tgc-gtgtt
                    Horse  -agggg-tgcca-ccc-------cgctgttc--ctttcctttctcatccttgacct-----tgcggtgtc
         Chinese pangolin  -agtgg-tgtca-ccc-------cattgttc--ctttcctttctcacccttgacct-----tgctgtgtc
                      Dog  -agcgg-tgcca-ccc-------cactcttc--ctttcctttctcacccttgacct-----tgcggtgtc
       Hawaiian monk seal  -ggcgg-tgccacccc-------cactgttc--ctttcctttctcacccttgacct-----tgctgggta
                 Hedgehog  -accgg--ccca-ccc-------catagttc--ctttccatcctcacccttgacct-----tgtggtgtg
                    Shrew  -actgggtgcca-ccc-------cacggtct--ttttc--ttttcacccttgacct-----tgcagggtt
                 Elephant  -ggcga-tgcca-ccc-------cactgttc--ctttccattttcacctctgacct-----tgccgggtc
                   Tenrec  -ggcga-tgcca-ccc-------cactgttc--gttcccatgctcacctctgacct-----cgccgggtc
                  Opossum  -agcag---cta-aag-------aatggttcatctttcccttcctccttctaacttccagccgcaggccc
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ctggacgtctg-ttgtga--ttgttcagaaagatctc----------------
                      Rat  ctggacgtctt-ttctga--ctgttcagaaagatctc----------------
            GCF_003668045  ctgggtgtctt-ttctga--ctgctcagaaaaatccc----------------
                   Beaver  ccgagcgtctt-ttctgagcatggtcagaatgattct----------------
                 Squirrel  ctgag-gtct--ttctgc--gtggtcagaacgattcc----------------
               Guinea pig  ctgagcatctt-ttctgt--ggtgacagaaggatgcc----------------
                   Rabbit  ------gcctt-ttctgc--ataaccagga--gtccc----------------
                     Pika  ------gactt-ttctgc----aatcagaatggcatc----------------
                    Human  ctaagcgtcct-ttctgc--cttgtcagaaggattcc----------------
                    Chimp  ctaagcgtcct-ttctgc--cttgtcagaaggattcc----------------
                   Bonobo  ctaagcgtcct-ttctgc--cttgtcagaaggattcc----------------
                  Gorilla  ctaagcgtcct-ttctgc--cttgtcagaaggattcc----------------
                   Rhesus  ctaagcgtcct-ttctgc--gttgtcagaaggattcc----------------
                 Marmoset  ctaagcgtcct-ttctgc--ctagtc---aggattcc----------------
                  Tarsier  gtgagcgtctt-ttctgc--gtgatcagaacgattcc----------------
                 Bushbaby  acgagcgtctt-ttctgc--gtagtcagaacgattct----------------
               Tree shrew  gagagcgtctt-ttctgc--gtagtcaaacgtactct----------------
     Malayan flying lemur  atgagcttctt-ttctgc--gtggtcagaaggattcc----------------
                      Pig  atgagtgtctt-ttctgc--cggctaagaaccattcc----------------
                  Dolphin  gtg--tgtctt-ttctgc--tcgctaagaacgattcc----------------
                      Cow  gtgaatgtcttattctgc--t-gcttaggatgattcc----------------
                    Sheep  g----tgtcttattctgc--t-gctaaggatgattcc----------------
                    Horse  gtgagtgtctt-ttctgc--ttggtaagaaccgttcc----------------
         Chinese pangolin  atgagcgtctt-ttctgc--ttgctaagaacgattct----------------
                      Dog  ttgagtgtctt-ttctgc--gtggtaagaacgattcc----------------
       Hawaiian monk seal  gcaagtgtctt-ttctgc--ttggtaagaaccattcc----------------
                 Hedgehog  atgagtgtctt-ttctac--tggataacaactattcc----------------
                    Shrew  ----gtgtctt-ttctac--ttggtaagaaccattcc----------------
                 Elephant  gtcagcgtctt-tgctgc--gtggtcaggatgactcc----------------
                   Tenrec  gtcagcatctt-ttctgc--gtggccagaaggactcc----------------
                  Opossum  ccatacacatt-ttcttc--ctcccacgaccttttcccttgttgatagaccag
                Zebrafish  =====================================================
            X. tropicalis  =====================================================
                  Chicken  =====================================================

Inserts between block 44 and 45 in window
B D                  Pig 1bp
B D              Dolphin 1bp
B D                  Cow 1bp
B D                Sheep 1bp
B D                Horse 1bp
B D     Chinese pangolin 1bp
B D                  Dog 1bp
B D   Hawaiian monk seal 1bp
B D             Hedgehog 23bp
B D                Shrew 1bp
B D             Elephant 1bp
B D               Tenrec 1bp

Alignment block 45 of 344 in window, 56744884 - 56744926, 43 bps 
B D                 Mouse  ggagtg-ttctgtaccat---acagtccg-gctttcccggg-------cgacttg---------------
B D                   Rat  ccagtg-ctccgcaccgt---acagtctg-gctttcccagg-------agacttg---------------
            GCF_003668045  ccggcacccccgcaccct---acgatccg-acttctccggg-------aagcttg---------------
                   Beaver  ccgagc-cctcctacc------cggtcag-ccttccgcagg-------agacctg---------------
B D              Squirrel  cggagc-cctcctgct------cagtctg-gcttccgcagg-------agacctg---------------
B D            Guinea pig  cagagc-cctcctgtc------cagtctg-gctactttagg-------agacctg---------------
B D                Rabbit  cga--c-tctcctgct------cagtttg-ctttctgcggg-------agatcgt---------------
B D                  Pika  tga--c-cctccggtt------cagttgg-ccttctgggag-------agatctg---------------
B D                 Human  ccgagc-cctcctgcc------cagtccg-gcttccgcagg-------agacctg---------------
B D                 Chimp  ccgagc-cctcctgcc------cagtccg-gcttccgcagg-------agacctg---------------
B D                Bonobo  ccgagc-cctcctgcc------cagtccg-gcttccgcagg-------agacctg---------------
B D               Gorilla  ccgagc-cctcctgcc------cagtccg-gcttccgcagg-------agacctg---------------
B D                Rhesus  ccgagc-cctcctgcc------cagtccg-gcttccgcagg-------agacctg---------------
B D              Marmoset  ccgagc-cctcctgcc------cagtccg-gcttcagcagg-------agacctg---------------
B D               Tarsier  ctgagc-cctcctgcc------cggtccg-gcttccgcagg-------agacctg---------------
B D              Bushbaby  ccga-c-cctcctgcc------cagtccg-gcttccgcagg-------agacctg---------------
B D            Tree shrew  ccgagc-cctcctgcc------cagtctt-gcttccgcagg-------agacccg---------------
B D  Malayan flying lemur  ccgagt-cctcctgct------cagtacg-gcttccgcagg-------agacctg---------------
B D                   Pig  -tgagt-ccttctgtt------cagtcggagcttccgcagg-------agacctg---------------
B D               Dolphin  -cgagc-ccctgtgct------tagtcgg-gcttccgcagg-------agacccg---------------
B D                   Cow  -cgcgc-ccttatgct------cagtcgg-gcttccgcagg-------agacccg---------------
B D                 Sheep  -cgcgc-ccttacgct------cagtcgg-gcttccgcagg-------agacccg---------------
B D                 Horse  -ccagc-cgtcctgct------cagtcgg-gcttccgcagg-------agacccc---------------
B D      Chinese pangolin  -cgaac-ccttctgct------cagtctg-gcttccgcagg-------agacctg---------------
B D                   Dog  -cgagc-tctcccgca------cggttgg-gcttctgc----------agaccag---------------
B D    Hawaiian monk seal  -tgagc-cctcctgca------cagttgg-gcttccac----------agaccag---------------
B D                 Shrew  -ccagt-acttatgct------cagtctg-gcttctgcggg-------agactca---------------
B D              Elephant  -ggaac-ccttttgcc------tagtctg-gcttccgtagg-------agacct----------------
B D                Tenrec  -ggagc-cctcttgct------cggcccg-acttccgctgg-------agacctg---------------
B D               Opossum  -ggagt-gtcttttctgtggggtagattg-gctcccagaggtccatgtcgatccgtgttttcttaggcga
B D              Hedgehog  ======================================================================
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

Inserts between block 45 and 46 in window
B D                Shrew 3bp

Alignment block 46 of 344 in window, 56744927 - 56745260, 334 bps 
B D                 Mouse  agtttgttttcttttttattgta----------------------------------------------c
B D                   Rat  agtttgttttc-tttttattgca----------------------------------------------c
            GCF_003668045  agtttgttttc--ttttattgtg----------------------------------------------c
                   Beaver  agtttgttttc-tttttactgtg----------------------------------------------t
B D              Squirrel  tgtttgttttc--ttttactgcg----------------------------------------------c
B D            Guinea pig  gctttgttttc--ttttactgca----------------------------------------------t
B D                Rabbit  agtttgttttc--ttttactgcg----------------------------------------------t
B D                  Pika  agtttgttttc--ttttactgcg----------------------------------------------t
B D                 Human  agtttgttttc--ttttactgag----------------------------------ttttttttttttt
B D                 Chimp  agtttgttttc--ttttactgag---------------------------------tttttttttttttt
B D                Bonobo  agtttgttttc--ttttactgag----------------------------------ttttttttttttt
B D               Gorilla  agtttgttttc--ttttactgag-------------------------------------tttttttttt
B D                Rhesus  agtttgttttc--ttttactgagtttttttttgtttttttgtttttttggtttttttttttgtttttttt
B D              Marmoset  agtttgttttc--ttttactgag--------------------------------ttgtttttttttttt
B D               Tarsier  agtttgttttc--ttttactaag----------------------------------------------t
B D              Bushbaby  agtttgttttc--ctttactaag----------------------------------------------t
B D            Tree shrew  agtttgtttcc--ttttactgcg----------------------------------------------t
B D  Malayan flying lemur  agtttgttttc--tttctttgcg----------------------------------------------t
B D                   Pig  agtttgttttc--ttttactgca----------------------------------------------c
B D               Dolphin  aggttgttttc--ttttactgcg----------------------------------------------t
B D                   Cow  agtttgttttc--ttttactgcg----------------------------------------------t
B D                 Sheep  agtttgttttc--ttttactgcg----------------------------------------------t
B D                 Horse  cgtttgttttc--ttttactgcg----------------------------------------------t
B D      Chinese pangolin  agtttgttttc--ttttactgtg-----------------------------------------------
B D                   Dog  agcttgttttc--ttttacttca----------------------------------------------t
B D    Hawaiian monk seal  actttgttttc--ctttacttca----------------------------------------------t
B D              Hedgehog  agtttgttttc--ttttactgag----------------------------------------------c
B D                 Shrew  ggtttgttttc--ttttactgcg----------------------------------------------c
B D              Elephant  -gtttgttttc--ctttactgcg----------------------------------------------t
B D                Tenrec  agtttgtttt---ctttactgcg------------------------------gttttcttttctttctt
B D               Opossum  agtttgttttc--ttttactaaa----------------------------------------------c
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================
B D               Chicken  ======================================================================

                    Mouse  tg------------tt--------------------------aa----agataaaatttaaaagacatta
                      Rat  tg------------tt--------------------------aa----agataaaatttaaaagacatta
            GCF_003668045  tg------------tt--------------------------aa----aaataaaatctaaaagacatta
                   Beaver  tg------------tt--------------------------aa----aaaataaattaaaaaggcgtta
                 Squirrel  tg------------tt--------------------------aa----aaaataaat-aaaaaggcgtta
               Guinea pig  ag------------tt--------------------------aa----aatata-----aaagagtgtta
                   Rabbit  tg------------tt------------------------aaaa----aaaaaaaaaaaaaaaggcgtta
                     Pika  tg------------tt--------------atttaaaagaagaa----gaagaagaaaaaggaggtgcta
                    Human  tt------------tt---------------------------------------------aaggcgtta
                    Chimp  tt------------tt---------------------------------------------aaggcgtta
                   Bonobo  tt------------tt---------------------------------------------aaggcgtta
                  Gorilla  tt------------tt---------------------------------------------aaggcgtta
                   Rhesus  tt------------tt---------------------------------------------aaggcgtta
                 Marmoset  tt------------tt---------------------------------------------ttggcgtta
                  Tarsier  tg------------ttaaa---aaaaa-----------------------aaaaaaaaaaaaaggcgtta
                 Bushbaby  tg------------ttaaa---aagggggc------ggtggggg----gtggggggagaaggaggcatta
               Tree shrew  tg------------ttaaaaccaaaccaaaccaaaacaaaaata----aacaaacaaaaaaacctcctta
     Malayan flying lemur  tg------------ttgaa---aaagaaaa--gaaaagaaaaca----aaagaaaagaaaaaaggcttta
                      Pig  tg------------tt----------------aaaacagaacag----aacaaaacaaaaaacagcgtta
                  Dolphin  tg------------tt----------------aaaacgggacaa----aacaaaaca-aaaacagcgtta
                      Cow  tg------------tt----------------aaaacagaataa----aacaaaacataaaacagcgtta
                    Sheep  tg------------tt----------------aaaacagaataa----aacaaaacacaaaacagcgtta
                    Horse  tg------------tt----------------aaaacaaaaca-------------------cggcgtta
         Chinese pangolin  ta------------tt----------------ataacaacacaac-acaaca-caaacaaaccggtgtta
                      Dog  aa------------tt------------aaccaaaacaacacaacaacagcagcaaggaaactggcattg
       Hawaiian monk seal  aa------------tt-----------------aaacaaaacaacaacaacagcaaagaaactggcatta
                 Hedgehog  ag------------tt----------------aaaacaaaacaa----aacaaaacaaaaa--ggcctcg
                    Shrew  tgtttttttttttttt----------------aaaaaaaaac-----------agcagtaa--tgtc---
                 Elephant  tg------------tt-------------------------taa----aaaaaaaaaaaaaaaggcgtta
                   Tenrec  tc------------tt-------------------------t---------------taaaccggcatta
                  Opossum  tg------------tt--------------------------aa-------------------------a
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ggtt-c-tttcttggtataggg------ag---aaaaagaaa-gtt-aaaat----gtttt-attc-gc-
                      Rat  ggct-c-tttcttggtattggg------tg---aaaaagaaa-gtt-aaaat----gtttc-attc-cc-
            GCF_003668045  gctt-c-tttcttggtgtaagg------agaacaaaaagaaa-ttt-aaaat----gtttt-attc-ac-
                   Beaver  gctt-c-tgccttggta--ggg------ag----aaaagaaa-atc-aaact----gcttt-agga-gca
                 Squirrel  actt-c-tttcttggta--ggg------ag----aaaagaaa-gta-aaaat----gcggt-agac-ata
               Guinea pig  actt-cttttcttggta--ggg------ta----aaaagaa---tc-aaagt----acttt-agac-ga-
                   Rabbit  acct-c-tttctgagta--ggg------ag----aaaagagt-a---aaaat----gctct-ccac-gca
                     Pika  ccgt-c-tttcttcgta--ggg------ag----aaaagaaa-g----------------t-ccat-gta
                    Human  actt-t-tttcttggta--ggg------ag----aaaagaaa-gtc-tgaat----gacct-agat-gca
                    Chimp  actt-t-tttcttggta--ggg------ag----aaaagaaa-gtc-tgaat----gacct-agat-gca
                   Bonobo  actt-t-tttcttggta--ggg------ag----aaaagaaa-gtc-tgaat----gacct-agat-gca
                  Gorilla  actt-t-tttcttggta--ggg------ag----aaaagaaa-gtc-taaat----gacct-agat-gca
                   Rhesus  actt-t-tttcttggta--ggg------ag----aaaagaaa-gtc-taaat----gacct-agat-gca
                 Marmoset  ac------ttcttggta--ggg------ag----aaaataaa-gtc-taact----gtcct-atat-gca
                  Tarsier  actt-c-tttcttggta--gaa------ag----caaa-------------t----gccctaagag-gca
                 Bushbaby  acttct-tttcttggta-gggg------aa----aaaagaaa-gtc-taaat----gccct-tgat-aaa
               Tree shrew  actt-c-tttcttgtta--gag------ag----aaaaaaaatgtc-aaaat----gccct-acac-gca
     Malayan flying lemur  actt-c-tttcttggta--gggaacagaaa----aaaaaaaaagtg-aaaat----gccct-agac-gca
                      Pig  actt-a-tttctttgta--ggg------ag----aaaataaa-gtc-aaatt----gccct-agat-gca
                  Dolphin  actt-c-ttcctcggta--ggg------ag----aaaagaaa-gtaaaaaat----gccct-agac-gca
                      Cow  actt-c-tttctcagta--ggg------ag----aaaacaaa-gtcaaaaat----gccct-agat----
                    Sheep  actt-c-tttctcagta--ggg------ag----aaaacaaa-gccaaaaat----gccct-agac-gca
                    Horse  actt-c-tttctcggta--ggg------aa----aaa--aaa-gtc-aaact----gccct-agac-gct
         Chinese pangolin  actt-c-tttctaga-g--gag------aa----aag--aaa-atc-agatctaaattcct-ggac-aca
                      Dog  actt-c-tttctcggta--ggg------gg----aga--aaa-gta-aaaat----accct-agac-aca
       Hawaiian monk seal  actt-c-tttctcggta--ggg------gg----a-a--aaa-gcc-aaaat----gtctt-agac-aca
                 Hedgehog  actt-ctttctctggga--gtg------ag----aaaagaaa-gta-aaaat---gccccc-agatggtg
                    Shrew  -------ttcctgggta--ggg------ag----aagagaaa-gta-aaaac----ccctt-agac-gca
                 Elephant  actt-c-tttcttgatg--ggg------ag----aa---aaa-gtc-aaaag----gcctt-gaac-gca
                   Tenrec  acgt-c-tttcttggtt--ggg------ag----aaaagaaa-atc-agaat----gcctt-gaac-gga
                  Opossum  acat-c-ttc---------aag------tc----aaagtgac-ctc--aaat----------aata-gca
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  -------------------------------------cttattgcct----aactgctc--ag-tggaaa
                      Rat  -------------------------------------ttaacttctt---caattgctc--ag-gggaag
            GCF_003668045  -------------------------------------tcaatttactgcccagtttttc--ag-tgtaag
                   Beaver  g----aacttaaataatgcagagtt----agagagagcctatctttt---gaaattttc--ag-tataaa
                 Squirrel  g----aatttaaataatgcagagat----ag------cctaccttct---taatttctc--ag-cataaa
               Guinea pig  -----------ggaggagataagat----ag------gctaccttct---taatttctc--ag-tgtaaa
                   Rabbit  t----attgtaaatacttcaga---------------gataccttct---taatgtttc--agccgtgaa
                     Pika  g----aatcgaactaattcgga---------------gataacttgc---taatgtctcatagccctaat
                    Human  g----aatttaaataatgtgtagat----ag------tccactttct---taatttctc--ag-cctaaa
                    Chimp  g----aatttaaataatgtgtagat----ag------tccactttgt---taatttctc--ag-cctaaa
                   Bonobo  g----aatttaaataatgtgtagat----ag------tccactttgt---taatttctc--ag-cctaaa
                  Gorilla  g----aatttaaataatgtgtagat----ag------tccactttct---taatttctc--ag-cctaaa
                   Rhesus  g----aatttaaataatgcgtagat----ag------tccactttct---taatttctc--ag-cctgaa
                 Marmoset  g----aatttaaataatgtgtagat----ag------tccactttct---taacatatc--ag-cctaaa
                  Tarsier  g----aatttaaatgat---tacat----ag------tcgactttct---tcatttctc--aa-cccaag
                 Bushbaby  t----atttaaaataatgagc--at----ag------tctattttct---taatttctc--ag-cctaaa
               Tree shrew  gacaaaatctaaataatgtagagat----ag------cctatcttct---tagtttctc--ag-tttgaa
     Malayan flying lemur  g----aatttaagtagtgcggagatacagag------cctaccttct---taattcctc--gg-cctaga
                      Pig  g----aaattaaataatgcggagataaagag------cctacctcct---taatttctc--tg-ccaaaa
                  Dolphin  g----aatttaaataatgcagagataaagag------cctaccttct---taatttctc--ag-ccagaa
                      Cow  --------ttaaataatacagagataaagag------cctaccttct---taatttctc--ag-ccaaga
                    Sheep  g----aaattaaataatgcagagataaagag------cctatcttct---taatttctc--aa-ccaaaa
                    Horse  g----aatttaaataaggcagagatacagag------cctaccttc----taatttctc--ag-ccaaaa
         Chinese pangolin  g---------aaataatgcagagataaagag------cctactttct---taatttctc--ca-gcaaaa
                      Dog  g----aatctaaataatatagaaat-aagag------cctaccgttt---taatttctt--ag-ccgaaa
       Hawaiian monk seal  g----aatttaaagaatacagagat-cagag------cccaccgttt---taatttctt--ag-ccgaaa
                 Hedgehog  g----aatcaatataatgaagagataccaag------tctccccctt---gaattcctc--tg-tcagaa
                    Shrew  g----aatttaagtaatgaagagataaagag------tccatcttct---taatcgcct--ag-cca-aa
                 Elephant  g----aattcaagtaatgc--agatagagag------cctacctccc---taacttctc--gg-tccaaa
                   Tenrec  g----aattcaaataatgc--agatagagag------cctatctcct---t-gcttgtc--gt-ttta--
                  Opossum  a----ggactgaggagtgta---------ag------tccttctttt---ctaactctc--tg-tcca--
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  gttt-aagacaggcaga-g---g-----aaa-attt-aaataggaaag-----------------aga-a
                      Rat  gttt-aaga----caga-g---g-----aaa------aattagaaaag-----------------agg-a
            GCF_003668045  gttt-aagacgggcaga-g---g-----aaaaattt-aaataggaaag-----------------aggaa
                   Beaver  gttt-aaaaagtacaga-g---g-----aaa-aatt-aaatagcatag-----------------agg-g
                 Squirrel  gttt-aaaaagtgcaga-g---gggggaaaa-tact-aaataggaaag-----------------ggg-g
               Guinea pig  gttt-aaaaactgaagg-g---g-----aaa--------atagacaaa-----------------aga-c
                   Rabbit  gttt-aaaaagcgcaga-g---g-----aaa-aatt-aaataa---ag-----------------ggg-g
                     Pika  gttt-caaaagcacaga-g---g-----aga-aatt-aaatag---gg-----------------ggg-g
                    Human  gttt-taaaagtgtaga-g---g-----aaa-aatt-aaataggaaag-----------------ggg-g
                    Chimp  gttt-taaaagtgtaga-g---g-----aaa-aatt-aaataggaaag-----------------ggg-g
                   Bonobo  gttt-taaaagtgtaga-g---g-----aaa-aatt-aaataggaaag-----------------ggg-g
                  Gorilla  gttt-taaaagtgtaga-g---g-----aaa-aatt-aaataggaaag-----------------ggg-g
                   Rhesus  gttt-taaaagtgtgga-g---g-----aaa-aatt-aaatgggaaag-----------------ggg-g
                 Marmoset  gttt-taaaaatgtagg-g---g-----gaa-aatt-aaataggaaag-----------------agg-a
                  Tarsier  gttt-taaaagcgcaga-g---g-----aaa-aatt-aaataggaaag------------------gg-a
                 Bushbaby  gttt-ataaagtgcagg-g---g-----aaa-aatt-aaataggaaag-----------------gag-g
               Tree shrew  gttt-aaaaatcacaaa-t---g-----aaa-aaat-gaaatagagtg-----------------ggg-g
     Malayan flying lemur  gttt-aaaaagtgcaga-g---g-----aaa-aatt-gaataggaaaa-----------------gag-g
                      Pig  gctt-aaaatgagcaga-g---g-----aac-aatt-aaatagaaaaa-----------------ggg-g
                  Dolphin  gttt-aaaaagagcaga-g---g-----aaa-aatt-aaataggaaaa-----------------ggg-g
                      Cow  cttt-aaaaagagcggg-gg--g-----aaa-aatt-aaataggaaaa-----------------ggg-g
                    Sheep  cttt-aaaaagagcggg-gggtg-----gga-aatt-aaataggaaaa-----------------ggg-g
                    Horse  ggct-aaaaagcacaga-g---g-----aaa-aatg-aaatagagacg-----------------ggg-g
         Chinese pangolin  gtttaaaaaagtgcaga-g---g-----aaa-aaat-aaatggaaaag-----------------ggg-g
                      Dog  gttt-aaaaagtgcagg-g---g-----gga-aatt-aagtaggagaaggtggtggtggtggtggggg-g
       Hawaiian monk seal  gttt-aaaaagtgcagg-g---g-----aaa-aatt-aagtagggaaa-----------------agg-g
                 Hedgehog  ggtt-taaaattgaagagg---a-----aaa-aact-aaataggagaa---------------gcagt-g
                    Shrew  agtt-taaaagtgcaga-g---a-----aaa-aatt-aaataggaaag---------------ttggg-g
                 Elephant  gatt-taaaaagccaga-g---g-----aaa-aatt-aaataggaaag-----------------gga-g
                   Tenrec  -------------caac-g---g-----aaa-gatt-gaataggaaag-----------------gga-g
                  Opossum  -tat-gaaaagaccaga-g---g-----gac-aattccattttgggtg-----------------cgg-t
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ag---atatttcctgtgctaatttcccgctttttgatgtt-cccaccaca-ctggcac-agttacctttt
                      Rat  aa---atatttc-----ctagttttttttttttca--gtt-cccaccacc-ttggtgc-aattacctttt
            GCF_003668045  aa---atatttcctgtaaccatttcttggtttttga-ctt-tccacggca-tccgcac-aatgacctttt
                   Beaver  aa---atcgttcctttaattatttcctgccttttgcagtt-gccagcaca-ttggcac-aattacctttt
                 Squirrel  aa---atagttcctttaattatttcctgccttttgctgtt-gccaccaca-ttggcac-aattacctttt
               Guinea pig  aa---atggttcttctaattatttcctgctttttgcaatt-gccaacaca-ttggcac-aattatgtttt
                   Rabbit  aa---atagttcctttaattatttcctgcctttctcgatt-gccaacaca-ttggcac-aattatctttt
                     Pika  gg---ataactcctttaattatttcctgcctttctcg-tt-gccaccaca-ttggcac-aattatctttt
                    Human  aa---atagtttctttaattacttcctgcctttcttggtt-gccaccaca-ttggcac-aattatctttt
                    Chimp  aa---atagtttctttaattacttcctgcctttcttggtt-gccaccaca-ttggcac-aattatctttt
                   Bonobo  aa---atagtttctttaattacttcctgcctttcttggtt-gccaccaca-ttggcac-aattatctttt
                  Gorilla  aa---atagtttctttaattacttcctgcctttcttggtt-gccaccaca-ttggcac-aattatctttt
                   Rhesus  aa---atagtttctttaattacttcctgcctttcttggtt-gccaccaca-ttggcac-aattatctttt
                 Marmoset  aa---atagttcttttaattacttcctgcctttcttggtt-gccaccaca-ttggcac-aattatctttt
                  Tarsier  aa---atagttctggtaattatttcctgcctttcttggtt-gccaccaca-ttggcac-aattatc---c
                 Bushbaby  aa---atagttcctttaattatttcctggctttcttggtt-gcca-caca-ttggcac-aattatctttt
               Tree shrew  ag---ttaattcctttaattatttcccgagtttcagggtt-atcaccaca-ctggcac-aatgatctttt
     Malayan flying lemur  aa---atagttcctttaattatttcctgcctttcttggtt-gccaccaca-ttggcat-aattatctttt
                      Pig  aa---atagtttctttaatcattttctgtctttctcggtt-gccaccaca-ttggcac-aattatctttt
                  Dolphin  aa---atagttcctttaattgtttcctgcctttctcggtt-gccaccaca-ttggcac-aattatctttt
                      Cow  aa---atagttcatttaattatttcctgcctttctcagtc-gccaccaca-ttggcac-aattatctttt
                    Sheep  aa---atagttcatttaattatttcctgccttcctcagtt-gccaccaca-ttggcac-aattatctttt
                    Horse  aa---atagttcttttaattatttcctgcctttctcggtt-gccaccacg-ctggcac-aattatctttt
         Chinese pangolin  gagggatagtgcctttaattatttcctgcgtttctgggtt-gccaccaca-ttggcac-aattatctttt
                      Dog  ggggaagagttcctttaattatttcctgcctttctctgtt-gccaccaca-ttggtac-aattatctttt
       Hawaiian monk seal  ggggaatagttcctttaattgtttcctgcctttttctgtt-gccaccaca-ttggcac-aattatctttt
                 Hedgehog  aa---atagttcttttaatta-------------taatcc-accaccacc-ttggcacaaagtatctttt
                    Shrew  ga---atagttcctttaattatttcctgcctttctcagct-gccaccaca-ttggcac-aattatctttt
                 Elephant  aa--aatagcttctttaattatttcttgccttttttggtttgccaccaca-ttggcac-aattatctctt
                   Tenrec  aa--aatagtttctttaattatttcctgcctttcttggtt-------acacttatcac-aattatcgctt
                  Opossum  ag---ata---cctttaaatgttttctccttt-----att-aacaccaca-tagacac-atttgcctctt
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  aa--agtaatt-aagcagtg----cac-ga-tttccca--------------tcttcttgtcct-ctgac
                      Rat  aa--agtaattaaaacagtg----cac-ga-ttcccca--------------tcttcttgtctt-ctgac
            GCF_003668045  aa--agtaattaaagcagtg----ctt-ga-tttctca--------------tctccgtgtttt-ctgat
                   Beaver  ta--agtaattaaagcagag----ccctga-tttctca--------------tcttcttgtttt-ctgac
                 Squirrel  ta--agcaattaaagcaggg----ccctga-tttctta--------------tcttcttgtttt-ttgac
               Guinea pig  tc--gataattaaagcagag----ccttga-tttctca--------------tattcttgtttt-ctgcc
                   Rabbit  ta--agtaattaaagcaggg----gcctga-tttctca--------------tcttcttggttt-ctgat
                     Pika  ta--agcaattaaagca-gg----ccctga-ttcctcagctccttgctcctgtctcctggtttt-cggat
                    Human  ta--agtaattaaagcaggg----ctctga-tttctca--------------tcttcttgtttt-ctgac
                    Chimp  ta--agtaattaaagcaggg----ctctga-tttctca--------------tcttcttgtttt-ctgac
                   Bonobo  ta--agtaattaaagcaggg----ctctga-tttctca--------------tcttcttgtttt-ctgac
                  Gorilla  ta--agtaattaaagcaggg----ctctga-tttctca--------------tcttcttgtttt-ctgac
                   Rhesus  ta--agtaactaaagcaggg----ctctga-tttctca--------------tcttcttgtttt-ctgac
                 Marmoset  ta--agtaattaaagtagag----ctctga-tttctca--------------tcttcttgtttt-ctgac
                  Tarsier  ta--agtaattaaagcagga----ttctga-tttctca--------------tcttcttgtttt-ctgac
                 Bushbaby  ta--agtaattaaggcaggg----ttctga-tttctca--------------tcttcttgtttt-ctgac
               Tree shrew  ------taatgaaagcagga----ccccga-tttctca--------------tctttttgtttt-ctgac
     Malayan flying lemur  aa--agtaattaaagcagga----ccctga-tttctca--------------tcttcttgtttt-ctgac
                      Pig  aa--gataattaaagcataa----tcctta-tttgtca--------------tcttcttttttttttgac
                  Dolphin  ta--aataattaaagcatag----ccctga-tttctca--------------tcttcttgcttt-ctgac
                      Cow  ta--aataattaac-catag----ccctga-tttctca--------------tcttcttgtttt-ctgac
                    Sheep  ta--aataattaac-catag----ccctga-tttctca--------------tcttcttgtttt-----c
                    Horse  ta--agtaattaaagcagaa----cgctga-tttctca--------------tcttcttgtttt-ctgac
         Chinese pangolin  ca--agtaattaaagcagag----cactga-tttctca--------------tcttcttgtttt-ctgac
                      Dog  ta--agtaattaaatcagag----ccctga-tttctca--------------tcttcttggatg-ctgac
       Hawaiian monk seal  ta--agtaattaaagcagag----ccctga-tttctca--------------tcttcttgtttg-ctgcc
                 Hedgehog  ta--cacaattaagccagag----ttctga-tttctca--------------tcttcttgtttt-----c
                    Shrew  ta--agtaattaaagcagag----ccctga-tttctca--------------tcatcttgtttt-----c
                 Elephant  ta--agtaattgaagtaggtaggcccttga-tttctca-----------------tcttgtttt-----c
                   Tenrec  tgttagtaattaaaatagtg----ccctga-tttctca--------------tcttcttgtttt-----c
                  Opossum  gc--agtaactaaacaagag----gcttaactttttca--------------ttcccttgttgt-cgata
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  t---gcaaattgacaaga----------------g-caatgtt-ctgggttatttgg---------aact
                      Rat  tgcggcgaattgacaaga----------------g-taaagct-ctgggttatttgg---------aact
            GCF_003668045  t---gggaattgacaaga----------------g-taaagtt-ctgagttatttgg---------aact
                   Beaver  t-----gaatttacaaga----------------g-ctcagtt-ttgtcttatttgg---------agct
                 Squirrel  c---atgaatttacagga----------------a-tccagtt-ttgtcttatttgg---------agct
               Guinea pig  t---gtgaatttacaaga----------------g-c-cagtt-ctgtcttatttgg---------agct
                   Rabbit  t---gtgaatttccaaga----------------g-cccagtt-ctgtcttactctg---------agct
                     Pika  g---gtggatttccaagt----------------g-ctccact-ttgccttgctcggcggccgcctagcc
                    Human  t---gcaagtttacaaga----------------g-cccagtt-ttgtcttatttgg---------agct
                    Chimp  t---gcaagtttacaaga----------------g-cccagtt-ttgtcttatttgg---------agct
                   Bonobo  t---gcaagtttacaaga----------------g-cccagtt-ttgtcttatttgg---------agct
                  Gorilla  t---gcaagtttacaaga----------------g-cccagtt-ttgtcttatttgg---------agct
                   Rhesus  t---gcaagtttacaaga----------------c-cccagtt-ttgtcttatttgg---------agct
                 Marmoset  t---gcaagtttacaaga----------------g-cccagtt-ttgtcttatttgg---------agct
                  Tarsier  t---gcgaatttacaagc----------------g-ctcagtt-ttgtcttcttcgg---------agcg
                 Bushbaby  t---gcaaatttacaaga----------------gccccagtt-ttatcttattc-c---------agct
               Tree shrew  t---gtgaatttagaaga----------------g-cccagtt-ttgtcctaattgg---------agct
     Malayan flying lemur  t---gtgaatttacaaga----------------g-cccagtt-ttgttttattcgg---------agct
                      Pig  -----tgaatttacaaga---tcctta--taagag-ctcagtt-ttgtcttatttgg---------agct
                  Dolphin  t---gtgactttacaaga---tccttc--taagag-cctggtt-ttgtcttgttcgg---------agct
                      Cow  t---gtgactttacagga---tccttc--taaggg-cccagtt-ttgtcttatttgg---------agct
                    Sheep  t---gtgactttacagga---tccttc--taaggg-cccagtt-ttgtcttatttgg---------agct
                    Horse  t---gcgaatttacaaga---tccttc--taagag-atcagtt-ttgtcttattctg---------aact
         Chinese pangolin  t---gtgagtttacaaga---tccttt--taaaag-ctcagtt-ttgtcttatatgg---------agct
                      Dog  -----cgagcttacaagactcttcttc--taggag-ctcagtt-ttgtcttattcag---------agtt
       Hawaiian monk seal  t---gtgaatttacaaga---ttcttc--gaggag-ctcagtt-ttgtcttattcgg---------agct
                 Hedgehog  c---atgaatttacaaga---tccttc--taagag-cttggtt-ttgccttattggc---------agcc
                    Shrew  t---gtgacttaagatga---tctttc--taaaag-cttactt-ttgtcatattcaa---------agct
                 Elephant  t---atgaatttacaaga---tccttc--taacag-cccagtt-ttgtcttatttgg---------agct
                   Tenrec  t---gtgaatttacaaga---cccttctataagag-cccagat-ttgtagtatttcg---------agcc
                  Opossum  a---tagaatttaaagga---ctcttt--taaaaa-tgtaactcttaacctcttcag---------agcc
                Zebrafish  ======================================================================
            X. tropicalis  ======================================================================
                  Chicken  ======================================================================

                    Mouse  ggtt-----------------------ggaacctta-gtt
                      Rat  agtt-----------------------ggagactcg-gtt
            GCF_003668045  agtt-----------------------ggagcctta-ggt
                   Beaver  agtt-----------------------ggagcttta-gtt
                 Squirrel  agtt-----------------------ggggcttta-gtt
               Guinea pig  cact-----------------------agagcttag-gtt
                   Rabbit  actt-----------------------gcagcttta-ctt
                     Pika  actgga--------------------agcagctttt-aag
                    Human  actt-----------------------ggagccata-gtt
                    Chimp  actt-----------------------ggagccata-gtt
                   Bonobo  actt-----------------------ggagccata-gtt
                  Gorilla  actt-----------------------ggagccata-gtt
                   Rhesus  actt-----------------------ggagccgta-gtt
                 Marmoset  actt-----------------------ggagccgta-gtt
                  Tarsier  agtc-----------------------agagcttta-gtt
                 Bushbaby  agtt-----------------------gaagctctacgtt
               Tree shrew  ggtt-----------------------gcagcttta-gtt
     Malayan flying lemur  agtt-----------------------ggagcttta-gtt
                      Pig  ggtt------------------------gagcttta-gtt
                  Dolphin  ggtt-----------------------ggagcttta-ttt
                      Cow  ggct-----------------------ggagtttta-gtt
                    Sheep  ggct-----------------------ggagcttta-gtt
                    Horse  ggtt-----------------------ggagcttta-gct
         Chinese pangolin  ggtt-----------------------ggagcttta-gtt
                      Dog  ggtt-----------------------ggagcttta-gtt
       Hawaiian monk seal  ggtt-----------------------ggagcttta-gtt
                 Hedgehog  a------------------------------------gtt
                    Shrew  ggtt-----------------------aaacatttc-gtt
                 Elephant  ggtt-----------------------ggagcttta-gtt
                   Tenrec  g------------------------------------gcg
                  Opossum  agccaggttagggtgaacagaacactggaagctgca-ttc
                Zebrafish  ========================================
            X. tropicalis  ========================================
                  Chicken  ========================================

Alignment block 47 of 344 in window, 56745261 - 56745405, 145 bps 
B D                 Mouse  ggagacg---ttgcccttgatttataggataagctgacctcactgacatttaaaggaagcccctgttcat
B D                   Rat  ggagacg---ttgcccttgatttataggataaactgacctcattgacatttaaaggaagcccctgttcgt
            GCF_003668045  ggagatg---ctgcccttgatttataggataaactgacctcactgacattt-aaggaaggccctgtccgt
                   Beaver  ggagaga-gttcgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D              Squirrel  ggagaga-ctttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D            Guinea pig  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                Rabbit  ggagaga-gttcgcccttgatttataggataaactgaccccactgacatttggaggaagcccctgttcat
B D                  Pika  ggggaga-gttggcccttgatttataggataaactgacctccctgacatttagaggaaacccctgtgcct
B D                 Human  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                 Chimp  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                Bonobo  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D               Gorilla  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                Rhesus  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D              Marmoset  g--gaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D               Tarsier  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D              Bushbaby  ggagaga-gtttgcccttgatttataggataaactgaccccagtgacatttaaaggaagcccctgttcat
B D            Tree shrew  ggaggga-gtatgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D  Malayan flying lemur  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                   Pig  g--gcga-gtttgcccttgatttataggataaactgacctcactgacatttagaggaagcccctgttcat
B D               Dolphin  gaagaga-gtttgcccttgatttataggataaactgacctcactgacacttaaaggaagccccggttcat
B D                   Cow  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                 Sheep  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                 Horse  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaaggccctgcgcat
B D      Chinese pangolin  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D                   Dog  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D    Hawaiian monk seal  ggagaga-gtttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgttcat
B D              Hedgehog  ggagaga-ttttgcccttgatttataggataaactgacctcactgacatttaaaggaagcccctgtgcat
B D                 Shrew  ggagagc-gtttgtccttgatttataggataaactgacctcactgacatgtaaaggaagcccctgttcat
B D              Elephant  ggagaga-atttgcccttgatttataggataaactgacctcactgacatttaaaggaagctcctgttcat
B D                Tenrec  ggagagt-gtttgcccttgatttataggctaacctgacctcactgacatttaaaggaagcccctgttcat
B D               Opossum  tgagggttgtttgcccttgatttataggataaactgacctcgctgacatttaaaggaaggtcctattcat
B D               Chicken  -ggggcc-gttcgcccttgatttataggataaactgacctctctgacacggaaaggaagcccctattcat
B D             Zebrafish  ======================================================================
B D         X. tropicalis  ======================================================================

                    Mouse  gggaaagtgtgagatcagcagaaatgggggctcacagggggaatctcaatttcttaagataacttcaggc
                      Rat  gggaaagtgtgagatcagcagaaatgggggctcacaggggg-atctcaatttcttaagataactttagac
            GCF_003668045  gggaacgtgtgagatcagcagaaat-ggggctcacaggggg-atctcagtttcttaagataacttcaggc
                   Beaver  gggaaagtgtgagatcagca-aaatgggggctcacaggggg-atctcaatttcttaagataacttaaggc
                 Squirrel  gggaaagtgtgagatcagcagaaatggaagctcacaggggg-atctcaatttcttaagataacttcaggc
               Guinea pig  gggaaagtgtgagatcagcagaaat-gaggctcacaggggg-atctcaatttcttaagataacttcaggc
                   Rabbit  gggaaagtgtgagatcagcagaaatgggggcttgcagggag-atctcaatttcttaagataacttcaggc
                     Pika  gggaaagtgtgagatca