Multiz Alignments of 8 Species
 

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Alignment block 1 of 84 in window, 14092957 - 14093190, 234 bps 
B D  Stickleback  cgaagtcagtaatgtcatgagtgaagtaagtgactgaacgttaaaaaaaagagagagggggggggggggg
B D         Fugu  c------------------------------------acgtgagaag-----------------------
B D    Tetraodon  c------------------------------------acgtgaaaaaaaaaa-----------------t
         Medaka  ======================================================================
B D    Zebrafish  ======================================================================

     Stickleback  gtccacagattccggagagtgtatgacttcaaaacc------------------acacagtcaatgac--
            Fugu  gctcccatagttgggatggagagtgatttaaaacccccagcggcgcttaatgtgaccca-tcaatgacac
       Tetraodon  gctcatatatttaggatgcggggtgatttaaaatgc---------ctgagtgtgaccca-tcaatgacac
          Medaka  ======================================================================
       Zebrafish  ======================================================================

     Stickleback  --aacggtctcacaaactaaacaagacgcacgcgcgaccagccgctgtaacctt--gcgtgcatccatgt
            Fugu  aaaacgctctaacca--caagtaa----cacgcacacctg---gatgtaacctttgctgagtctcc----
       Tetraodon  --ggcgctcttccca--caaaagaaaggcacccccacctg---gatgtaacctctggcgcgtctccgtgt
          Medaka  ======================================================================
       Zebrafish  ======================================================================

     Stickleback  cagctccataagaggatgcgagtgccaaccaatgcgttgtatgccaca
            Fugu  --gctccg---------gcaaaacacaatcgg-------aagaacaaa
       Tetraodon  cagctccg---------gcaaagcgcaaccggcttgc--cagaacaaa
          Medaka  ================================================
       Zebrafish  ================================================

Alignment block 2 of 84 in window, 14093191 - 14093221, 31 bps 
B D  Stickleback  ctgccgaagga------------------agtgcaagtgttatctcc-------------------ga
B D         Fugu  ---caggaggaggcttcggggtattcatcggcagtctgatgtttaaca------------------gg
B D    Tetraodon  ---caggagga------------------agcttcggggtatttatcagcagtctgctgtttcatcgg
          Medaka  ctcacaaaggg------------------ggggtcgaagttgtcccc-------------------ga
B D    Zebrafish  ====================================================================

Alignment block 3 of 84 in window, 14093222 - 14093477, 256 bps 
B D  Stickleback  tagaagaaaaacaa------------------caagaag--aaaaacaacaacaatagcgc--aacttgt
          Medaka  cagaggaaa--------------------------------------------------------cttgt
B D    Tetraodon  cagaggcaacgttc----aagttgctgtgatgc-------------------------aaa--aacttgt
B D         Fugu  caaaggcaacattcaagt----tgatctgacgcaaaaaa--aagaagaaaagaaaaaaaaa--aacttgt
B D    Zebrafish  -------------------------tgggagacaaacagacaagaacaaaaacaacaacaatggactaat

     Stickleback  gcagccgcattgtgcttttggttgagccgcac--atgtcaacttccaggcat-tccagcactgccgac-t
          Medaka  gcacccgcattatgcgttacgctgcgccgcgc--atttcaacttccacgcat-tccagcacactctgc-t
       Tetraodon  gcagccgcatc---------------ccgaattgaattcaactt-cgcgcat-tccagcacagccggc-t
            Fugu  gcagccgcatt---------------ctgtac--aattcaactt-cacgcat-tccagcacagccggc--
       Zebrafish  a-atcagcttt---------------aaccac------caactg-aatacatagctagcacagcaggaat

     Stickleback  ctgacgccggacaacggcggcgccttttccctcgctggccaagaccgc-------tccaccgaggcgcaa
          Medaka  c---caccagcacacggc--------------cgcaaacgcgagcagc-------tgcgt----gcgcaa
       Tetraodon  cggacggcaccgaagagc----------cgatctgtggccagaactga---gcggagcgc----aggcaa
            Fugu  aggat--------agagc----------cgatccgtggccaaaactgc-------agcgc----aggcaa
       Zebrafish  cagatgg------aggac---------------actgattaagtcagctgattcgagcgt----acgctg

     Stickleback  gtcgtttttgtaaaaaataaag--caaagcaactctctttctctactgttatagttg-aactcacgcgcg
          Medaka  ------------------aggg--aacagccactcttgcccgcgtcaaacttagtgatgacaaacccacc
       Tetraodon  -acatgatcccaa-----cagg--------acctctctt----------------tgtaaccc-------
            Fugu  -acacgattctaa-----gagg--aatcccacctctctttttc------------tgtaaccca------
       Zebrafish  ----ccattgcaa-----aaggtaaacaaacacacacatcctcgcacat------gacaactcacatggc

     Stickleback  cgtgacacatga
          Medaka  tttcacactt--
       Tetraodon  ----acacttgc
            Fugu  ----acacttga
       Zebrafish  ata-acacataa

Alignment block 4 of 84 in window, 14093478 - 14093521, 44 bps 
B D  Stickleback  gca--catgcggctttagggcaacaccac-----aacgc------agccgccgccgc
B D         Fugu  acacgcgtgtgac------gtgcctccat-----atcatcttta-acttacgacagc
B D    Tetraodon  acacacgtgtgac------gtgcctccat-----atcatctttacagttacggcagc
          Medaka  -----cacacggc-------caacaccaccgaccaccac------aacccccaccgc
B D    Zebrafish  =========================================================

Alignment block 5 of 84 in window, 14093522 - 14093596, 75 bps 
B D  Stickleback  cgcctccccgcacaccacgccccgtctccacggcaacgcgcg-----gcg-------------ctcac-c
          Medaka  g-----cacgcacaccacgccc-gtctgtacagcagca-gca-----gcagcagcatcccagtctcac-c
B D    Tetraodon  c------------accacgccc-gtctgccccgaaccatccggagctgag-------------ctcac-c
B D         Fugu  c------------accacgccc-gtctggacagacacatccg-----gtg-------------ctcac-c
B D    Zebrafish  ---cgcctcccctgacatgctc--------tggcgcccccca-----ggggaggcgcgc----ctcacac

     Stickleback  tttaaagacgctggcac-agaggct
          Medaka  tttaaaaacgccgggac-acaggct
       Tetraodon  tttgaggacatctgcac-agaggcc
            Fugu  tttaatgacatctgcac-agaggcc
       Zebrafish  tttgaaaacccctgctctattggct

Alignment block 6 of 84 in window, 14093597 - 14093949, 353 bps 
B D  Stickleback  gtacagggtgaagatcaggtgcagcttgacaatcatc---ttctcttgtccttcgcgattctgttacgtc
B D         Fugu  ggagaggatgaagatcaggtactgcttgggagtcatg---ttctct----cttctc----------cgtc
B D    Tetraodon  ggagaggaggaagatcaggtactgcttgggagtcatattcttctct----cttctc----------cgtc
          Medaka  gcagaggaggaagatcaggtgctgctggacaatcatc---ttctc-----cttcacaat---gttacgcc
B D    Zebrafish  ======================================================================

     Stickleback  ga-----cagtcccgtcgcgctggtctcggt----------------------ctctcttgggcagtctc
            Fugu  gacactccactccactcgcgtctctgtcagg----------------------ctgcttcgctccttcgc
       Tetraodon  ga-----cactccactcgcgtctctgtcagg----------------------ctgtttcttccct--gc
          Medaka  aa-----cactccactcaggctcgactctgtttttttcgactctgttttttttctctctctctctctctc
       Zebrafish  ======================================================================

     Stickleback  ttctcctc--------gggatggacttatccaggtaaatggcgcagtttcggacagaccggagtcacatg
            Fugu  ccctcgtc--------gcgctgcacttatccaggt-aacggcgcagtttgtgagagagcggagttgcacg
       Tetraodon  tcctcgtc--------gtgatgcacttatccaggt-aacggcgcagctgctggcggagcggagttccacg
          Medaka  tgctcttctgtctcacaggatggacctgtccggctaaacggcgcagtttgtggctgaccggagttgcatt
       Zebrafish  ======================================================================

     Stickleback  gatgaactcttgcctttttttctttccagagaagtcgcggtgtatttctctttttttcttgcagatcctg
            Fugu  gatggagtctaccc---------ctccagcgaagtc-ttgtgtgtct----------ctcgcagatccga
       Tetraodon  gacggagtcttccc---------ctccagcgaagtc-tggtgcgtct----------cacgcagatccga
          Medaka  gataaactctggctgctgtct-------aaggagtcccagtgtttct-----------------------
       Zebrafish  ======================================================================

     Stickleback  ggagggagggagggggggagggatgtgatgactgtag----------cggcagagatgctcgtcggcaaa
            Fugu  cggcggcgcccggcg----------------ctgtgg---agcaggacggcagcgatgctcgtcagcaaa
       Tetraodon  cggcggcgagcggtg----------------ctgtgg---agcaggacggcagcgatgctcgtcagcaaa
          Medaka  -----gtgcgcagtgaaggggactgtgatcactgtggtgaggcaggacggcggggatgctcgtcggcaaa
       Zebrafish  ======================================================================

     Stickleback  gtgcagctcctgcctccctttattgcctttctctttgactcgctgcagaga
            Fugu  gtgcagctcctgcctccctttattgcctttctctttgactcgctgcagaga
       Tetraodon  gtgcagctcctgcctccctttattgcctttctctttgactcgctgcagaga
          Medaka  gtgcagccactgcttccctttattgcctttcactttgactcgctgcagaga
       Zebrafish  ===================================================

Alignment block 7 of 84 in window, 14093950 - 14093993, 44 bps 
B D  Stickleback  gcaagagtcccgcccacgctttttgactaatgaa-ggcgcctcac
          Medaka  gcaagagtcccgcccacgctttttgactaatgaa-gacgcttcac
B D    Tetraodon  gcaagagtcccgcccacgctttttgactaatgaa-gacaatccac
B D         Fugu  gcaagagtcccgcccacgctttttgactaatgaa-gacaattca-
B D    Zebrafish  gcaagtgctcgctctac---tattgattaatgactggcac-----

Inserts between block 7 and 8 in window
B D   Tetraodon 293bp
B D        Fugu 373bp

Alignment block 8 of 84 in window, 14093994 - 14094173, 180 bps 
B D  Stickleback  ---caatggaggagaacacctccaaatagttgcgatccg--tggta--------aaac-tgtcgaaacaa
          Medaka  ---caat---ggcaaacaacgaacaacacttctgatcta--tggt-------------------aaacat
B D    Tetraodon  ---gagt---ggagagccacacc------ttctgttccacctggtacaccaagtaaacatgctgaaaggg
B D    Zebrafish  ctgcaga---gccaagctctgccaactaattggcattca--ttgt------------cccgttt-----c
B D         Fugu  ======================================================================

     Stickleback  ttaca---ccgtggcacactcgggt----tactatttttaca-----gccatttcgagaggggggcatcg
          Medaka  ttaca---cggt-atgcactc----------ctacttttacac----atccattccagaaataaaaacca
       Tetraodon  ggacaactctgttgcagagctgggcagggagttgtgtgcatactccacccatgcctggagggggaccttg
       Zebrafish  ttact---ctttagggtgattggtcatctagcgattttttaaa----agtgtctttccagacacacgtcg
            Fugu  ======================================================================

     Stickleback  gtaatcctct-gttaagtttcgggag---ggtgatttggaaaatgtcactgcacgcctctgcaggagtgt
          Medaka  gcattaatctggtttatgatcaggac---agtca---gaaaaatgcaaaagcagtcatc-----------
       Tetraodon  gcagtctgat-cttcggctgcagaagctagctca---gaggagtggaatgtcatccctctg---------
       Zebrafish  aaa--------tttccactgaagggg---aactaaatagacactgtaaaaaactg------tgtgattat
            Fugu  ======================================================================

Inserts between block 8 and 9 in window
         Medaka 3725bp

Alignment block 9 of 84 in window, 14094174 - 14094391, 218 bps 
B D  Stickleback  ------------ggtgtcagtctaggccaatcctaaaaaaaaaacaactat--------aaaatat----
          Medaka  ------------ggggtaaatctagtttc-tcttaaaaaaaaactgaagac--------aa---------
B D    Zebrafish  acatgttttaaagcaattagttgactgta--cttaaaaattgagtaaagactttgccttaaattattaag
B D    Tetraodon  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  ---atgttccaaccacacgtcctctctg-atgtaaaaggcaacaataatgatgctctctctcctccgtgt
          Medaka  ----tgctgtaaggacagtttattcatgtatttttaacacaagcatgagattgatttcccaatg--aaac
       Zebrafish  tacatgaactaaaaacgctgtttgttta-atgtacttattaaaaat--------------------tagc
       Tetraodon  ======================================================================
            Fugu  ======================================================================

     Stickleback  ttgacttaaccgtgagagtgcagaaaatccatgcca-gtgatttaatgtattaaaatatgcccttagcta
          Medaka  ttgtgttaacc-tgtgcataaagccaaactttgttttgtttttcagcatatcaaactacaaa-------a
       Zebrafish  tttttttcattgtgggc-----gcaaatccatgtca-atggtttaatacatttaaatgagtttta----a
       Tetraodon  ======================================================================
            Fugu  ======================================================================

     Stickleback  gcagagttaatttaacactt---------ttagacagttttgaaca
          Medaka  acaatgtagagtttacgtct---------tttggcaactctaaa--
       Zebrafish  atggaaccatttaaatggttcaataaatgtaaaatagtttttaata
       Tetraodon  ==============================================
            Fugu  ==============================================

Alignment block 10 of 84 in window, 14094392 - 14094476, 85 bps 
B D  Stickleback  gccgcccccagaaccattacagcttta-------ttagcag-acgcacaagcctgcagtcgacattagac
          Medaka  ----------gacctatactagaccca-------ggagctg-gcatacaaacctgaagtaaatactaaac
B D    Zebrafish  gccttccactgaacaagttaagctataaaggtttggaacagcataaataatcataattgcaattttaact
B D    Tetraodon  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  actgcaca-tttgacactcgttat
          Medaka  ----cgta-taaaataaccatcac
       Zebrafish  ----tgaactatcccactctctat
       Tetraodon  ========================
            Fugu  ========================

Alignment block 11 of 84 in window, 14094477 - 14094523, 47 bps 
B D  Stickleback  cgctc-tgtaaattctagaattcaaaatgatct----cttggaaatacgaag
          Medaka  tgcaaacatcaactctttacctcgaaaacatttgcagctttggcctccatgg
B D    Tetraodon  ====================================================
B D         Fugu  ====================================================
B D    Zebrafish  ====================================================

Alignment block 12 of 84 in window, 14094524 - 14094595, 72 bps 
B D  Stickleback  tttt-------aagaaaaaagacagcacgcaatggccaaagacagacctgccaatgttgtgtgaatgcac
          Medaka  tttttcaaatgcagtgaacagacagcatgaagcacaaagagaaagagcggctgatgtttctcataaaggc
B D    Tetraodon  tctt-------caaaaagaggactgcatgcagtgagtaaacaaagatgggcagctgccgtt---------
B D         Fugu  ======================================================================
B D    Zebrafish  ======================================================================

     Stickleback  ggtaattcc
          Medaka  agttgcctt
       Tetraodon  ---------
            Fugu  =========
       Zebrafish  =========

Alignment block 13 of 84 in window, 14094596 - 14095925, 1330 bps 
B D  Stickleback  ctcagaggacgtgacct-ggcatccgcacgcgtgccaggaatcagtgcacaggggtataggggaggttaa
          Medaka  tttaacggttgtgatct-ggcatctaggtgcatgtcagaaatgactgcacaagca---atgggaggttaa
B D    Tetraodon  ctcagaggccgcgaacc-cgtgtctggttgtgagtcagaaacccatgcacaggtg--cagctcgggttaa
B D         Fugu  ctcggaggctgtgaccctcacgtctgggcgtgagtcacacacccttgcacaggtg--cagcttgggttaa
B D    Zebrafish  ======================================================================

     Stickleback  cgggctcctggacatccctcttccttcaaaggctcctatgat---cagtgcacgtgagtgtgaccatccc
          Medaka  tgggctgctggacatccctcttccttcaaaggttcccaggaggaacagagaa-atgagtgtgaccatccc
       Tetraodon  tgggctcccagacatccctcttccttcaaag-------tggtg--caaaaaa-atgagtgtgaccgtccc
            Fugu  tgggctcccagacatccctcttccttcaaag-------tggtg--caaagaa-atgagcgtgaccatccc
       Zebrafish  ======================================================================

     Stickleback  taaagacagaggtg--------ggaggagagcagctgctccagccagggatggttttctgagctcagcgc
          Medaka  taaagacagaggtgag---gtggggagtggatagcagctccagccagggatcattttctaagccgatcgt
       Tetraodon  taaagacagaggtgagcgaaagaggaggaggcaatggctccagccggggatcgttttctaagcccattgg
            Fugu  taaagacagaggtgagcgaaggaggaggaggcagcagctccagccggggatcgttttctaagcccattgc
       Zebrafish  ======================================================================

     Stickleback  aaggattttacacatggtttaacatgctgccggtcgaatttgcttcaattttgcacagtggccttccaca
          Medaka  aaggattttacacatggtttaacattctgctgggtgaatttggttcaattttgcacagtggccttcaatg
       Tetraodon  aaggattttacacatggtttaacatgctgccagtcgaatttggttcaatttcgcacagtggccctctttg
            Fugu  caggattttacacatggtttaacatgctgccagtcgaatttggttcaattttgcacagcggccctctttg
       Zebrafish  ======================================================================

     Stickleback  ccactcccactttaaatcaaattgctgaaatggctgtatca-cctgagaaaaatgtgcaaaaaaatatat
          Medaka  ccactcccacttcaaatcacactgctgacttggccaagcca-cctgtg---------------aacaggt
       Tetraodon  ccactcccacttcaaatcaaattgccgacctgtgcccgccg-actgcc---------------gaaagct
            Fugu  ccactcccacttcggatcaaattgctgacctgtgcgcaccgaactgcc---------------aaaagct
       Zebrafish  ======================================================================

     Stickleback  tcctgcttttaaatcctc-agcttttttgacagcagaaa--------------------tatatgtaaat
          Medaka  tcggtcctaaaacacctctagatttatctatatgggata--------------------aaattgtaatt
       Tetraodon  g----cttttttccc-----------cctccatcagtaa--------------------aaagct--gtt
            Fugu  gccctcttttttcccccc----ttttcctcctttagcagccttctccctcaccgggagcaaaac------
       Zebrafish  ======================================================================

     Stickleback  ggattgtgacactca-ttatctaaacaagcaatcccttggatgactcatttccattcccaacccag----
          Medaka  caataattacaaacactcatcttaacacactatcagatggatcaccaattattaaaatagaatgggaggg
       Tetraodon  aaagttttccagtttgttatttaaa-------------aaatacatca--gtc-----------------
            Fugu  aaagttctgca-----tcatt------------------gatgcatcattgcc-----------------
       Zebrafish  ======================================================================

     Stickleback  --acattgatgt-------gttttttcacacattctaatccatcacagcgtct--------cgggccgat
          Medaka  ataaattaatggaggcagagcttttttgcatgttgtgatcaattat-gcttttaatcaaaacgggtcgaa
       Tetraodon  --gaattgatg--------gttt---------tcattgtcaa-cacagaattt--------attattgaa
            Fugu  --aaagcaaga--------gtttatttac-tgtatttgtcta-cgcgggttct--------gcagctgat
       Zebrafish  ======================================================================

     Stickleback  tgggggccttttacaaagacgtgcgctcttttacttttgcatgctgatgttgcgttttggccttttaact
          Medaka  gaggaacttcttacttagatgggctctttttcactgagggatgctgatgctgcgattcagccttttaact
       Tetraodon  taca--tgtattattaa--------------------------------atgtgtttatttctgtgagtc
            Fugu  tcagattgtcgtgttca--------------------------------tcgtgattaagtcttggaact
       Zebrafish  ======================================================================

     Stickleback  ttgaacc----atgcacatcgctaatccctgcggaaccatcgttgcctttc--aacagtaaaccttgaag
          Medaka  tggaaccatgtatgcacatctctaaccccagtggagccattgatgcctttctgaactgtaaaccttgaag
       Tetraodon  --------------cgtgtttcaggcttctgggttagaaacat----ctgttgaggagttagccttggag
            Fugu  g----------tcgcacgtctgaatttccagtgtgaccattgttgtattcctgaagagagagccttgaag
       Zebrafish  ======================================================================

     Stickleback  gactcaacactcttgtgtgacatacattctcaataca----taatataattctaagc--tacgaaacaaa
          Medaka  gactgagtgctcttgtgtgacatacattctctttacaactcacttataattcggagcagaactatacaaa
       Tetraodon  gactgaatgctcttgtgtgacacacatacttggtacagctcacttaccattcagagcagaactatacaaa
            Fugu  gactgagtgctcttgtgtgacatacattctagattcagctctcttaccattcggagcacaatgatacaaa
       Zebrafish  ======================================================================

     Stickleback  gtcaattaccatgaggaatgagtgttcatcaatcaatccctagggtactgaaggtcaattcctcatcatt
          Medaka  gccaattaccatgagg-atgagggtaaag-aatcaatcccatgtgtcctgaaggtcagattctcgtcatt
       Tetraodon  gccaattaccacgagg-acggtggtaagg-aatcaatcccatgtgtcctgaaggtcaattcctcgtcatt
            Fugu  gccaattacccagagg-atggtggtaagg-aatcaatccctcgtgtcctgaaggtcaattctctgtcaat
       Zebrafish  ======================================================================

     Stickleback  tcattagatctttgagtgtag-aattctactcatgcgccttttaaacagcgagaatttattgaccatgtg
          Medaka  tcattagatctttgtgagtag-aattctactcatgcacctttttaacagcgagaatttattgaccatgtg
       Tetraodon  tcattagatctttgagaggagaaaacccacatgtgcgcctcttaaacagggataatttattgatcaggtg
            Fugu  tcattagatctttgaggggag-aattctgcacatgcgcctattaaactgcaataattcatcgatcaggtg
       Zebrafish  ======================================================================

     Stickleback  ggttcagcagaaaaggcttgaggtgctgacacagatctgtgatgcagagaagcactttctcctttgcttt
          Medaka  ggttcagcaaaaaaagcagggggtgctgacacagatctctaatgcagaggagctcattcccctttgcatt
       Tetraodon  ggttcagcaggacaacacaggcttgctga-------ctgtgaaacagaag----------------tgtt
            Fugu  ggtgcggcaggcaaacacaggc-tgctga-------ttgtaaaccaggaga--------------atgtt
       Zebrafish  ======================================================================

     Stickleback  taactctgggacattacactg-----cacactatgctctgcatcatttcgaat-----attgtgtgcatt
          Medaka  tatctctggggcattatattgcaatccattctgtactttgtataatttaaaatccccagttgtgtgcaat
       Tetraodon  catctctcggaca--------------------------gcatcattttaaa------------------
            Fugu  tcgctcctgggcagaatgctatacacccctcaatactttgtatcgtttaacat-----------------
       Zebrafish  ======================================================================

     Stickleback  gtgggtctt---aaagtcacgggcggccacagtatacccttgaattccgttgataataca----------
          Medaka  gccagatttaacaaggtcac---caggcacact----cctctactacctgttatggcatataaaaaatat
       Tetraodon  ----------------cccc---cgtct---------gctgaagtccaacagat----------------
            Fugu  ----------------cccc---ccacc---------cccggactccaactgattttcca----------
       Zebrafish  ======================================================================

     Stickleback  --gagt--ttccactaaagattagaatacaagattctaggagag--------aatacaaaaaaaggcaaa
          Medaka  ctgagttattctact----tctggcctgcaaagtgcaaagaaaa--------gaatccaaacaaagc--a
       Tetraodon  -------------------attaaatctcaac--gtgaggagaaatgagaagaaatcaattccaaacaat
            Fugu  --------ttttgcta---attaaatctgaacatataaggagaaat------aaatcaattctaaacaaa
       Zebrafish  ======================================================================

     Stickleback  aaagaatagtttagg------ctcagctgagtcacattaatatgcattaccctgt-cactgatagcattt
          Medaka  aaggcagagtcaagg------ctgaggcaactttcat---tatgcattaactcat-cactgatagctctc
       Tetraodon  aacaaagggcgaaaaagt---caataccgaggtacatttatatgcaaaaatatgc-atttgatagcattt
            Fugu  agcagagggcaaaggtgtgtgctctactgagttgcatttataggcaaaaatgggctttttgatagcattt
       Zebrafish  ======================================================================

     Stickleback  aatcctccgggttgattgaaaa-------acaactcatccagacacactcggtgcacaatccatttcagg
          Medaka  acccctccttcctgatcaaaac-------gca----------gcaatttcactgcgcagtccattccagg
       Tetraodon  aattcttctcaacagctgaaaatgttcaaaca--ctgtgtgttcacactatgtgcacaaaccgagtg---
            Fugu  aattttcctcaacaattgaaaatgttcagac---------ggacacactacatgcacgatccatttg-gg
       Zebrafish  ======================================================================

     Stickleback  atgggcctgaatggcagc-agtcgtgaaggctgaatgcttt-atgtaaatgag--------------aaa
          Medaka  gtggacatgaatgacag--aatcaacaa-----aatgcttc-acatgaacaat--------------gaa
       Tetraodon  -cgagcctgaatggcagcgagccacggacgctgaaagctccagcgtaaatgttcaaccgcaggtgacaaa
            Fugu  cagagcctgaatggcggc-agtcacgagtgctgaaagcccccatgtaaatggt-----------------
       Zebrafish  ======================================================================

     Stickleback  gtgctgcacacaggatcagtacatgggttgtgtcaatctttttgtcatttacacaataaacaca
          Medaka  ccactaaacactggatacggatgtggattg----attattaatgtacccaaagcaatttacact
       Tetraodon  gtgcctcacacggaatcctcatatcagctgtcagaccttttttat---ttcagcgggaaaccca
            Fugu  ---cctcgcacagaatcatcatctcagctttctcaccttttacat---ttcagcaaaaaaccca
       Zebrafish  ================================================================

Inserts between block 13 and 14 in window
B D   Tetraodon 143bp

Alignment block 14 of 84 in window, 14095926 - 14095982, 57 bps 
B D  Stickleback  ttatcatgtccaaataagatttaatattggagattttacattacattttcagacaag
          Medaka  ataatacacaaaagctagataaacaattgaagtttttgtttggcttctt--------
B D         Fugu  gcaggatgcaaaagaaagacctttaaagggaga------------------------
B D    Zebrafish  ttggcatgtctaaataaaatctaaaaaggaggttttagttttttgctgactgatatg
B D    Tetraodon  =========================================================

Inserts between block 14 and 15 in window
         Medaka 29924bp

Alignment block 15 of 84 in window, 14095983 - 14096047, 65 bps 
B D  Stickleback  atagacgttaataaaactacgactttgaagtaacagccttgatattttgtctcacttgcagacca
B D    Zebrafish  acacgcgatagtggaaacgcggct----aatctaagccttagtgtttt---tcaattgcagattg
B D    Tetraodon  =================================================================
         Medaka  =================================================================

Alignment block 16 of 84 in window, 14096048 - 14096132, 85 bps 
B D  Stickleback  cattttactttttatgaacggagatttaaaggtgaaaccgcatgaaagtgccttttcttttagtaacttg
B D    Tetraodon  cattttgctttccaaaaaaaaaaagaaaaaag-aaagaagtttgaaatatcttttcctttaactgattgg
B D    Zebrafish  aatttaactatgtgt-------------attgtgtaagtttctggaatttttggttataattttgatgta
         Medaka  ======================================================================

     Stickleback  ca-------------tttcctaaattat
       Tetraodon  ca-------------attcctaaattat
       Zebrafish  cattgtaaatagtgtatttctatgtttt
          Medaka  ============================

Alignment block 17 of 84 in window, 14096133 - 14096186, 54 bps 
B D  Stickleback  --tacataaaaactccacatgtaaaggtcaccatgaccggcattgtacaatattgt
          Medaka  --tacactacaatccatcttttaaatgttaccaaaactgtcactgtcatatgttgt
B D    Tetraodon  -------------------------------cgcgattgttctcgccctgtggtgg
B D    Zebrafish  aacaaaccaacattttatacataattgacgctgtaactatgctttttaaaaattgt

Inserts between block 17 and 18 in window
         Medaka 27bp

Alignment block 18 of 84 in window, 14096187 - 14096250, 64 bps 
B D  Stickleback  attcactcgtata-ttagtttat--atgagatatattggt--atcgatatgtattgacagtaaagataa
B D    Tetraodon  attttcttttgta-acagaaaatgaatcagatcaataact--ataaatacatgtt-ataataaaaatga
B D    Zebrafish  -attttttatgtatttagatttttattctagtgtgtaattgcattgtaatgtaca-acggtaa------
         Medaka  =====================================================================

Alignment block 19 of 84 in window, 14096251 - 14096298, 48 bps 
B D  Stickleback  ttg--taaatgatttaagatacttgagataatgtaca----------ttttttgccaaag
B D    Zebrafish  ctgactagat-atactagataatttatttcctgtacaactatcctgctatttttgtaaag
B D    Tetraodon  ============================================================
         Medaka  ============================================================

Alignment block 20 of 84 in window, 14096299 - 14096333, 35 bps 
B D  Stickleback  ttgttcaccaaagagctttaacaattca---gtcttca
B D    Tetraodon  ttgcttaaaagaatgcttgaaaaattca---attttaa
B D    Zebrafish  --gtgtaataaacagatgaaaaaaatcatacattt---
         Medaka  ======================================

Alignment block 21 of 84 in window, 14096334 - 14096360, 27 bps 
B D  Stickleback  accgtgaaatgtcttaccttcaacctt
B D    Tetraodon  at-----aattcttcactttttttctg
B D    Zebrafish  actgtaaaatatttttacatttacatt
         Medaka  ===========================

Alignment block 22 of 84 in window, 14096361 - 14096405, 45 bps 
B D  Stickleback  caaacagaagtttaattctgagttaagagattgatgtttgtagta
B D    Zebrafish  tgaactaggc----------aggtaagggttaactaggcaggtta
B D    Tetraodon  =============================================
         Medaka  =============================================

Alignment block 23 of 84 in window, 14096406 - 14096662, 257 bps 
B D  Stickleback  ggggactccacagtcctactgggagactttaatgcgcatgtgggcaacgatggagata---agagaggcg
B D    Tetraodon  ggaggttcccttgtcttcctaagcgactttaatgctcacgttggcagtgatagtgaaacctgaagaagtg
B D    Zebrafish  -ggagctctatcgttttactgtgaaactttagtgcccacat-ggcagtgatag------ctggagaggcg
         Medaka  ======================================================================

     Stickleback  tg-attgggaggaacggcctccctgatctgaacctgagcagtcgtttgatattggacttctgtgccagtc
       Tetraodon  tt-attgggaataatagcccccctgctctgaactcaagtggtgttctgttgttggacagatgtgctcgtt
       Zebrafish  tgttttgggtggaatggcctccctagtatgaatctgagtggtgttatgttgttgagcttctgtgctagtt
          Medaka  ======================================================================

     Stickleback  acggattgtccataacaaacaccatgttcaaacttaaggacgt-----tcataggtgtacctggtaccag
       Tetraodon  ataggttgtcc-ttacaaccatcgtgttcagacataaaggtgt-----ccata-------tttgcaccaa
       Zebrafish  acagtttgtccgaaacgaacaccatgttcaagcataggggtgtgaaacccaggttactagtgggtagtac
          Medaka  ======================================================================

     Stickleback  agcaccctaggccaaagatcgatgatcaattttgta-atcgtattgtc-------aggccgcat
       Tetraodon  gacaccttaaaaccaat-tcgacgattaactttgtg-gttgtgtcattgaatttggggccgtat
       Zebrafish  acagcaatagagcaaat---agaaatacatattatacatattataattcaatttcatacagcat
          Medaka  ================================================================

Alignment block 24 of 84 in window, 14096663 - 14096843, 181 bps 
B D  Stickleback  gttttggacactcgggtaaagag-----aggggcagaggtgtgaactgatcaccatctggtggtgagctg
B D    Tetraodon  gtccttgacactcaggtaaaaggggggtgggggcagagctgtcaaccaatcgccacctggtggtgagttg
B D    Zebrafish  gtcttggtcactcgggtaaagag-----aggggcaaagctgtcaactgatcaccacctggtggtgagtta
         Medaka  ======================================================================

     Stickleback  ggtcagagaattgggggtgaag------------------------------------------tgggaa
       Tetraodon  gctccgatggtggaggaggatgcttgtcagacctggcaggcccagctgtgttgagagggttggctgggaa
       Zebrafish  gatccactggcaagggggaaagctggacagacctggtaggcccaagcgtattgtgagggtcctctaggaa
          Medaka  ======================================================================

     Stickleback  catctggaggaggccctagtccaaaagattttcaactcacacctccggcggagcttctcgcacattcctg
       Tetraodon  cgcctggcagagtctcctgttagaaggagcttcaactctcacctccagaagaactttgaccatgttccag
       Zebrafish  cttcttgctgaaccccaagtcagagggattttcaattctcacctccggaagagctttgaccagatcccga
          Medaka  ======================================================================

     Stickleback  tggaggtaggcgacatcg
       Tetraodon  aggaggtgggggacat--
       Zebrafish  gggaggctggagacatgg
          Medaka  ==================

Inserts between block 24 and 25 in window
B D   Tetraodon 57282bp

Alignment block 25 of 84 in window, 14096844 - 14096963, 120 bps 
B D  Stickleback  aaccagagtggtgtatgttc-aaaacttgactgcaactgaggaggttgtcggg-----------------
B D    Tetraodon  agccaaggtagtta---------aaaaaaact--ccttgg------tggcaag-gccccgg---------
B D         Fugu  --------------atcccc-caagctgaact--caccgaggtagttagcaagcgcctcggcagaaatgt
B D    Zebrafish  agactgagtggtccatgttctccgactttatt---gttaatgcagccgtgagaagctgtggtcgta----
         Medaka  ======================================================================

     Stickleback  ----cggtggaaggaacactttgaggaactcctgaatccaactactctttggtagaggtggagctg----
       Tetraodon  ----gggtggatgaaatcagccccggaggctctggatgttgtagggctttggatgttgtagggctgtcat
            Fugu  gtcagggtggatgagatccgcc---------atgagtacctctagtctgtggctgttgtgggacggtctc
       Zebrafish  ----aggtcggtggtgcctgtcggggtggc----aatccacaaacccggtggtgga--------------
          Medaka  ======================================================================

     Stickleback  ----gaggc------t
       Tetraodon  ggctgacacaactctg
            Fugu  gcttgagatacctcgg
       Zebrafish  ----------------
          Medaka  ================

Inserts between block 25 and 26 in window
B D   Zebrafish 522bp

Alignment block 26 of 84 in window, 14096964 - 14097057, 94 bps 
B D  Stickleback  caacattgcatggaagtctggaacagtgccacaagaggcacagaccgggatggtggtacttttcttcaaa
B D    Tetraodon  caatattgcggggacgtctggggcagtgccactggattggcagaccagggtggtggtccctctttttaag
B D         Fugu  cagcatcgtgtgctggttcagaacagtgtctctggagtggcaaaccggggtggtggtaccgccttataaa
B D    Zebrafish  caacatcgcattgaggtcggggacagtatctttggactgggcaactggggtggtggttcccatttttaag
         Medaka  ======================================================================

     Stickleback  aagggggaccacagagtgtgtgcc
       Tetraodon  atgggggaccgaagggtgtgttcc
            Fugu  aaggaga----------gtgttcc
       Zebrafish  aaatgggaccggagggtaagctcc
          Medaka  ========================

Alignment block 27 of 84 in window, 14097058 - 14097267, 210 bps 
B D  Stickleback  aattatagaggtatcgccctactcagccccagtggtaaagtctactccaaggtgctggaaaggaggcttc
B D    Tetraodon  aactatagaaggatcaaactcctcagccatcctggtacggtctattcagtggtactagagagaagggtcc
B D         Fugu  aactacagaggggtcacatttcccagcctccctgggaagatcgatgccagggtactggagaggagaattt
B D    Zebrafish  agctgaagagatgtc------ctcagcctccatgcaagagtctatttcagcgtactggagaggaggatct
         Medaka  ======================================================================

     Stickleback  ggccgatggtcgaaccaaggattgaagaggaacaatgtggggttt-ttttgga------acgacggacca
       Tetraodon  gtcggatagtccaacctcagattcagaaggagcaatctggttttcatcttggacgtggaaccgtggacca
            Fugu  ggctgatagtcgaacc---gattcagaaggaacaacct--ctcctatcatgga-----------atacca
       Zebrafish  agctgacggttgaatc-------caggaggaacaatgcggattcggtccaggccagggttcattggagca
          Medaka  ======================================================================

     Stickleback  gctctttactcttgcaaggaccatgaggggggcctgggagtatgctcatccagtctacatgtgttttgtg
       Tetraodon  gctctacggcctcagcagggtccttaagggtgcatggaagtttgcccaaccaatccacctacgttttgtg
            Fugu  gctctttaccctccacagggtgctcggggggtcaggggagtttacccagccactcggctgttgtcctgtt
       Zebrafish  gctctacattctctctagggtgctggagggttcataggagtaagcccaaccagtccacatgtgttccgtt
          Medaka  ======================================================================

     Stickleback  gacctgg
       Tetraodon  gatttg-
            Fugu  gactt--
       Zebrafish  gatttag
          Medaka  =======

Inserts between block 27 and 28 in window
B D   Tetraodon 589bp

Alignment block 28 of 84 in window, 14097268 - 14097308, 41 bps 
B D  Stickleback  aggaggcgtatgacccggtcccccgagagatattttctgtt
B D         Fugu  ------catcaaaccaggaccttc-------accctgtact
B D    Tetraodon  =========================================
         Medaka  =========================================

Alignment block 29 of 84 in window, 14097309 - 14097408, 100 bps 
B D  Stickleback  -ggaacaagagccagttgagatggtttgggcatctggtgaggatgcccccatggcgcctcactag--aga
B D         Fugu  -ggggcggtttgctgccgag-tgggaaccagcacctccaaggctgaggctgtgattccccacaggaaaag
B D    Tetraodon  gaaactaaaccaccgtcggg-tggctgggttctctcttagagatgccttctggacgcctccctgg--tgg
B D    Zebrafish  ------agaagtcagctgaggtggctcgagcatctgcttcagatgcctcctggacgcctacctag--aga
         Medaka  ======================================================================

     Stickleback  ggtatttcaggcacagccagctgggaa--------gaggcc
            Fugu  ggtgttttg-------ccctctgcaggttgttggagaggtc
       Tetraodon  ggtgttcaggtcacgtccctctggtag--------gaggcc
       Zebrafish  ggtgttccaggcatgtccttccgcaag--------aaggcc
          Medaka  =========================================

Alignment block 30 of 84 in window, 14097409 - 14097466, 58 bps 
B D  Stickleback  gcggggaggacccaggactagggggagagactatatcgctacactggcctgggaacgc
B D    Tetraodon  -ctgggaagacccaggacatgctggagtgactatgtctctcagctagcctgggaatgc
B D    Zebrafish  tcgtggaagacccaggacaagctgaagggactatgtctttcagctggcctgggaacgc
         Medaka  ==========================================================

Alignment block 31 of 84 in window, 14097467 - 14097508, 42 bps 
B D  Stickleback  tgttg---ttcgtctaaatgaaaaagtgcaaaccaaagtaaaggg
B D    Tetraodon  cttgggattccccctagaaaagctagaggaaatagctggagagag
         Medaka  =============================================

Alignment block 32 of 84 in window, 14097509 - 14097555, 47 bps 
B D  Stickleback  tttgtccaagttactcatcagctgactcgctgggcgagcagagcttg
B D    Tetraodon  agtttgggagtccctgcttagactgctccccccgcgacccggccccg
         Medaka  ===============================================

Alignment block 33 of 84 in window, 14097556 - 14097590, 35 bps 
B D  Stickleback  ttctaccgaggcgaacgattacgttacacattccc
B D    Zebrafish  aatca-----atgaactattgaatgagcaataaca
B D    Tetraodon  ===================================
         Medaka  ===================================

Alignment block 34 of 84 in window, 14097591 - 14097866, 276 bps 
B D  Stickleback  atgccaaatttggctttaa------ttagagagcacaaaacgaag--ggtagaaccaatagtgcatga--
B D    Tetraodon  atcacaaagttttactaaa------tttttcgccataaaaaaaaa--aaaaaaacgtttttaggggga--
B D    Zebrafish  acaccagtttgttttctcagcattttcaaaggacgcaacacaaagataatgaaactagcacagggtagct
         Medaka  ======================================================================

     Stickleback  aaagtcctatatttttttgatttcacaatcaatgcacttgatgagtttaacccgatactttaaatc--ca
       Tetraodon  tcattacttaatattcttcatgttg----------actgcgtgatttt----------------------
       Zebrafish  aaggtac----ttttattcaatttgtaagcctgg-attgcaaaaggtt---catgtatttttaagcatca
          Medaka  ======================================================================

     Stickleback  cctggttt----gaacaagatgtacagtatacaactctgcatttataaatcacgttg---cacatatttg
       Tetraodon  tttttttt----taacaaattg---agt-cagatcactgcactattaaacaa---------actgagtta
       Zebrafish  ttttgcatagcataatcaattg---att-ccaagatcgtcattaa-agatgccattggttcaagaagtta
          Medaka  ======================================================================

     Stickleback  aaaatgcttctaatatgc----------atgccggctgt--tgggattcagagatatcaggaacttagtt
       Tetraodon  caaacaggtctgtgatgt----------tatctgccttt--tgtgctcggca------aaaggcttaatg
       Zebrafish  aaatgttctctgatatctacataatatgtatgtggctttgataagatcaagaaaatctctagaaatagtt
          Medaka  ======================================================================

     Stickleback  tcaca------ctaatgagctcccaaaacaccc
       Tetraodon  tt---------ttaaggaggttacaacacaaac
       Zebrafish  ttatatgcacttttattactccataaagtaccc
          Medaka  =================================

Inserts between block 34 and 35 in window
B D   Zebrafish 154bp

Alignment block 35 of 84 in window, 14097867 - 14098007, 141 bps 
B D  Stickleback  ttaattaatgaattcattcaatttaattaaaaatcactcacaaaagcaaggcagtttgatgccta-cctt
B D    Tetraodon  ctactgcaaaagtccacagacctggtttttattctac---caaaagaaagttaggaaaataatt------
B D    Zebrafish  ttaagttttaaattagtcaggtttaattaatatttatgcataaaaacaagttaatcaactttttagcatt
         Medaka  ======================================================================

     Stickleback  gcgggagtctaacagctatgttttacacatta---ggaatac--tcaatacttaacgctaatgtt-----
       Tetraodon  -cgaaaataaatcacct---------gcatta---gtactaccatcagtcctgcaagtcactgcttggtt
       Zebrafish  ttagcaattaaataggt---------acatagaacaaaacac--aaaaagctttttattgatgtg-----
          Medaka  ======================================================================

     Stickleback  ----------actgag-atgaga
       Tetraodon  ttttaaaagcattgca-atgata
       Zebrafish  ----------tctgagtatgaaa
          Medaka  =======================

Alignment block 36 of 84 in window, 14098008 - 14098110, 103 bps 
B D  Stickleback  cttttaatctagtcctttatcaaatata---------------tcatcgagagattt--agttttgaaag
B D    Tetraodon  atgtcaatttattcctctgtgaa---------------------cacctgtgtaatg--tgttataatat
B D    Zebrafish  --cttattttacctacttggaaagtgtgctctctaatataaacccatcagagtactgttaaccttaata-
         Medaka  ======================================================================

     Stickleback  gtttcctggtaaactc-----agctgcagtgtgtaatatcttttattttgttatt
       Tetraodon  ttcaatttatttgctc-----aacaataatgtttaatatcttttatgttcttagt
       Zebrafish  --ctgttaaacaagtcacaagagctgttgtggataggataaattataatt-----
          Medaka  =======================================================

Alignment block 37 of 84 in window, 14098111 - 14098171, 61 bps 
B D  Stickleback  agtattttattaattaaagtgataagacaaa----gtcatactct---accgcattattacataaaac
B D    Zebrafish  a--aacttgacaaacaggctgataagatatattgtgttgtatttttagaccataatgtcaaagaaaac
B D    Tetraodon  ====================================================================
         Medaka  ====================================================================

Alignment block 38 of 84 in window, 14098172 - 14098280, 109 bps 
B D  Stickleback  tagaacggttaaatgtctaaca----ttctaccagacaatatacagt-acagtt------actgtaccat
B D    Tetraodon  taacacagtaaattgtgttaac----ccctgctaataaacatcaaat-gttctt------tcagttttat
B D    Zebrafish  cactggggtaattcttctcagaggtttgctgtgagaaaaaagagagtcattatttagaaaacagcctcct
         Medaka  ======================================================================

     Stickleback  gcatggatggtttgtcccatt--aatgtgtcactttctttacattctttttt
       Tetraodon  ttttgatttgtctgactcatttgcatctttgatttcctgaatattggatttt
       Zebrafish  ttattagcagttagttttatt------ttttagtgttttagtgttactttac
          Medaka  ====================================================

Alignment block 39 of 84 in window, 14098281 - 14098512, 232 bps 
B D  Stickleback  cttgaagtaaaagaggttacaaatagcaacatgctaaggaaaatgggtcttaatcagcatcacatttaga
B D    Zebrafish  ctttacttcgaagaaagcacacccaaaggttggccatggtgagactgtcttcag----------------
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================

     Stickleback  caaacaccaatatg--tccgtccacaaatacattttgttattctgcatcctgcttctgtg---taatgat
       Zebrafish  -aaactgcagtttggcttcgtctacactcatg---------cctgcctgcttgttgtatgaattgatgat
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  gtgttgcaagacaaagatgaagacgagta--tttagagttaatg---ccatttttctagaattatgcaaa
       Zebrafish  gtgctgcagaccaaagacacaaacaattaatcttacaatgaaaaaatacacttttaaccaacttttaaaa
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  tgtgtctctattttttaatgg-aactactgcag
       Zebrafish  aatccctttattcatcaggggtcaccacagcgg
       Tetraodon  =================================
          Medaka  =================================

Alignment block 40 of 84 in window, 14098513 - 14098771, 259 bps 
B D  Stickleback  ttcatggatgcatggtgactttccagactgcggtacaaccagctctccatatgagccttttatgatccag
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================

     Stickleback  tgtgtctcctacatcaagttgtatgatgtcagtgctccactgggaaataacccctgctctcagctttgta
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  ctggctaaactttaacaacatgttgtattgagagagtatgttccccatccctttaagaacacaattccat
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  ctattcacagccttatcgacaggacattgggacccgctacaattggtaa
       Tetraodon  =================================================
          Medaka  =================================================

Alignment block 41 of 84 in window, 14098772 - 14098867, 96 bps 
B D  Stickleback  tggattttctgtaccaaaga-----acatgtaagtcagctctctgtggatttcattacatgcggcagcag
B D    Tetraodon  tggttatcctccaacagagaggcctacgtgcaccatagctatcacttatctactttctgtggaccaacag
         Medaka  ======================================================================

     Stickleback  tattaatccttcatgttgtctgcaggtgtat
       Tetraodon  t--tatgcctgtacacagtcagcaggtgtgt
          Medaka  ===============================

Inserts between block 41 and 42 in window
B D   Tetraodon 17bp

Alignment block 42 of 84 in window, 14098868 - 14098882, 15 bps 
B D  Stickleback  acatcacacttaatc
B D    Tetraodon  ===============
         Medaka  ===============

Alignment block 43 of 84 in window, 14098883 - 14099008, 126 bps 
B D  Stickleback  tcagcatcaaatgtacacaaattatacttacagcgtgccacgtcacaattattatgcacgctggtatgga
B D    Tetraodon  tcaacaggcaggggatagaaactaaag------------accccagagagaaaatacatgtaggtatgga
         Medaka  ======================================================================

     Stickleback  gaataaaagtgctaccatatgctcgtttaatctgatcagtgatcttaactaaagaa
       Tetraodon  gaggacatgtggaatctggcgatcaccaaatccaagtaagagacttatctaaaaga
          Medaka  ========================================================

Alignment block 44 of 84 in window, 14099009 - 14099253, 245 bps 
B D  Stickleback  catactctttatgtctgccatatgctgccaacaagctgatacgttagtgagctggatgagtgacaataaa
         Medaka  ======================================================================

     Stickleback  atcaaaagtaattcagctttgtgaggcaatgtcacagagagtaatgaagggaaaccaaaggccctttagt
          Medaka  ======================================================================

     Stickleback  aacattagacagtcattacacaaagagcgttcagattgggtttgctggaggttaattctttataatgctg
          Medaka  ======================================================================

     Stickleback  taaatcccactgatttatcttgttgacctactcct
          Medaka  ===================================

Alignment block 45 of 84 in window, 14099254 - 14099308, 55 bps 
B D  Stickleback  taatgtaaaaaacat-gaattaaaagtcacactagata-gtgtggctaaacttgtgg
B D    Zebrafish  tgatgtgagaaatattgaattaattactgaattaattacatgcatttaaatt-----
B D    Tetraodon  =========================================================
         Medaka  =========================================================

Alignment block 46 of 84 in window, 14099309 - 14099439, 131 bps 
B D  Stickleback  caactaaaagtatttccctatcacaatgac--agtgttgttggagggtacagatgacagtgaacctcact
B D    Tetraodon  ccattaaaagtaactgtttaatacaataat--cattcaattaaaaatcccttgtagcagctgccatcact
B D    Zebrafish  -catttgaaaggcttgctttgtgtaatgcttaaagctagttaatga-----tgcaacatttaacc-cac-
         Medaka  ======================================================================

     Stickleback  gaatggaattgaaaac---------taaatgttatcaaagga-taattgaacgaaagaccat-taatgtg
       Tetraodon  gatttggatcaaggaa---------aacatgtttgcggttgg--aatttaaccaaaggcca---------
       Zebrafish  -atttatggtgagaaatcacttttgaatatataattaattggacaattttat--aagaacatatcatgtg
          Medaka  ======================================================================

     Stickleback  tgca
       Tetraodon  --ca
       Zebrafish  agaa
          Medaka  ====

Alignment block 47 of 84 in window, 14099440 - 14099543, 104 bps 
B D  Stickleback  atttggttaaatcgatagttcag-acatcc--agcagtttgtcggaatttttcgtctctcttcacttttc
B D    Tetraodon  attcgttctaattggtgctccagcgcatcc--tccagt-----ggagtttttattttcccttcagccatt
B D    Zebrafish  ---taattaaacactgaattaattacatttaaaccaattgattagaatgatttgcttagtttgatgtat-
         Medaka  ======================================================================

     Stickleback  cagtcagaaactaaaaccaatagttaattcattacca
       Tetraodon  ctgcaatagcccacaaacaatagtgacctcagcacaa
       Zebrafish  ----------cgaatagtaaaaactagtttgatactt
          Medaka  =====================================

Alignment block 48 of 84 in window, 14099544 - 14099611, 68 bps 
B D  Stickleback  taatcatgatcctatgattaaattgagcaagtaaactaagagct-tttacttatagct---tcatctgag
B D    Zebrafish  ttttgat-------taattaaattgaatacatttcctttgaattgcttgattacaactagttaataaaac
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================

     Stickleback  gg
       Zebrafish  ta
       Tetraodon  ==
          Medaka  ==

Alignment block 49 of 84 in window, 14099612 - 14099790, 179 bps 
B D  Stickleback  gattgtatg-taacactg-tacaaataaattacacacttaattaaaagacaaattaatagtaattaaatg
B D    Tetraodon  gaatgtgtg-tattattg-taaacataacacacaatctcttttaaaagctcaaattgaactaattaggta
B D    Zebrafish  aattgtataccaatactgatataaaataattatgaatacatcactgaatgcattttataacaatgtatca
         Medaka  ======================================================================

     Stickleback  tgcagtgtaaaacatctac-caaatgagtcctcaactaaagccaaacatgatcactctgcggagtaacac
       Tetraodon  cactaaataaagaaggtacactaatatg-----aattgcgtgcaacggtgtccaattt-tgaggaatttt
       Zebrafish  tgtgaggattaacatattcattcgtgaa---ttaattaaatttaattacattctatt--aaatgtattgc
          Medaka  ======================================================================

     Stickleback  ttgttctgggttttactctgatactcttatctgggtagctaa
       Tetraodon  ttttttttaaatttatttttataattctattt----------
       Zebrafish  ttagtcggatgtttat----acaggtttatcattgatgatag
          Medaka  ==========================================

Alignment block 50 of 84 in window, 14099791 - 14099932, 142 bps 
B D  Stickleback  -------gtaaa------ttgaaacgcatcccaggaaaaca-atgtt-------------------ctca
B D    Tetraodon  -------gtaaa------atggagggcagtaggggaaaaca-atgta-------------------gcag
B D    Zebrafish  ataatttgtgaatatatcattaaatacatcttataagaacatatgttagtattaaccctctaccgcacac
         Medaka  ======================================================================

     Stickleback  attacaa-caggtaca-gtacaatatgcagctcaagattattgag-------------------------
       Tetraodon  atcacaatctgttctg-gaataaaaaaagacccattcttattctg-------------------------
       Zebrafish  attatgg-cagatctataaaaaacaaatatttgactgtttttcttttctaaaaatgactttacttgaagt
          Medaka  ======================================================================

     Stickleback  -----aatagaacaacctacaaggaaaaactgcaaacacaattataatatgtaatgaaagttgagat
       Tetraodon  ------acagaaaaacacagaaaagaattctgctgaaatttaaataatgtattgtgcatattaatat
       Zebrafish  gctgtaaaaaaaaaaaataggaaaaaatttt---aaaaaatgtatgaaatgttgccaaatgtagaat
          Medaka  ===================================================================

Alignment block 51 of 84 in window, 14099933 - 14100044, 112 bps 
B D  Stickleback  ttttcttggagcaaactattgtgtaaatagctgtacattaatccctagaacccctattatctaatgttgc
B D    Zebrafish  tttccttataattaataattgtgttgtttgttttgatttaattggt-gttgccgtattataagttttaac
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================

     Stickleback  cttcagttttcaagtga----tctgacatgtattacaactcctgct
       Zebrafish  acagaacttttaaatgacaccttaaacaaactttccaacaactgat
       Tetraodon  ==============================================
          Medaka  ==============================================

Alignment block 52 of 84 in window, 14100045 - 14100259, 215 bps 
B D  Stickleback  gggagagtttgtgctggagtaaaatatttcagcacaatttcatgtggaagtgcttacaaggatatccagc
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================

     Stickleback  acagcaccacagtgtactgttgtattatttgtactagttgcatcacattactgagcagaacctcggtatg
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  ggtcattaattgcaaacagaatgtacatacaccgtaagagaacagatcccggttttctagagaaactaca
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  agggg
       Tetraodon  =====
          Medaka  =====

Alignment block 53 of 84 in window, 14100260 - 14100361, 102 bps 
B D  Stickleback  aaaccgagtcaccgttgggccaaaagaggagcactgtaattactgtat------tgcacagttccagt--
B D    Tetraodon  agacagag----------------gcagcggcgtgagaa-gaatttgtttttagtgtcccactcaagagt
          Medaka  --------tcatctttgggcccgggcagatgtgtggtaattagtgtatcattagtgcacagcttcaga--

     Stickleback  tgtgtggagctg---------gatcaacgctggccttttgtcttaactt
       Tetraodon  tgtgtgtagtaa---------aatcatccctgactgtttttcttcattt
          Medaka  -gcgaagagctataataacttaatcaatagtggccttttgtcttaactt

Alignment block 54 of 84 in window, 14100362 - 14100572, 211 bps 
B D  Stickleback  tgcaaaccagacctctgttcaagggcccactcctcccctgtgggactacggtggcacattcaagcagacg
          Medaka  cacaggcaaaggatgttttcaagggtacaatccgttcctgtgggg-------gccacagtcaaac-----
B D    Tetraodon  ======================================================================

     Stickleback  ctgccctccccacctctctaccctcgctgattcaaacaaaaccaagtgccctgggtatgcagagggaaat
          Medaka  -tcagctcttcatcgctccatccgtggatatactatcaaagccgggtgccct----atgcagagtgcaga
       Tetraodon  ======================================================================

     Stickleback  gctttatattagggcccacgttcaccatagcccacagcagctggtgttctcacagaccactgcatggaca
          Medaka  gcttt---------ctcacatctgtgatagcccacagcagctggtgttctcacagaccactgcatggaaa
       Tetraodon  ======================================================================

     Stickleback  a
          Medaka  a
       Tetraodon  =

Alignment block 55 of 84 in window, 14100573 - 14100678, 106 bps 
B D  Stickleback  tgggccgatttcagagatttagcaac------------cctgactgtgc--ttat----tggggccagaa
          Medaka  tgggacgatttcag-gatttagctgcccgtggtggattcctcactctgcaattat----cagggcaagaa
B D    Zebrafish  taggtcgcttctatagacttaccggc------------cctgactgtgg--caataaaacagtgtgagaa
B D    Tetraodon  ======================================================================

     Stickleback  tcactttgatatggacttgcacaagattaacagccagagtcccttgtctcgatt
          Medaka  tcactttgttatggcaatgcacaagattaaca-ctgaggtttttagccctgact
       Zebrafish  ata----gattcagagattttcaaaatgcatagctatactcccttaaatcgatt
       Tetraodon  ======================================================

Alignment block 56 of 84 in window, 14100679 - 14100766, 88 bps 
B D  Stickleback  ttgttacgt-------gttgccgcagtgattgtcattatgcttttaca------------gctatttaat
          Medaka  gtgtggtgttaacatcaatgttgcagtctttgttgtcataatgttacatgaaaaaaaaatgcaggtagct
B D    Tetraodon  ======================================================================

     Stickleback  gttgtatttgaacagaagattcaagctcggataataa
          Medaka  gtttgcattgaactgtggataactgctctggtgataa
       Tetraodon  =====================================

Inserts between block 56 and 57 in window
         Medaka 1776bp

Alignment block 57 of 84 in window, 14100767 - 14100931, 165 bps 
B D  Stickleback  aatagttatcccattgggaagaaaatggcatagtttccctacgcattaaataccgatcccggtcacgtca
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================

     Stickleback  acacagaagagcatttatcttattaataacaaactggtcggtactcgactctattggtgctgaccaagtc
       Tetraodon  ======================================================================
          Medaka  ======================================================================

     Stickleback  agtgcatcacttaaaactccaaggt
       Tetraodon  =========================
          Medaka  =========================

Alignment block 58 of 84 in window, 14100932 - 14101042, 111 bps 
B D  Stickleback  cattgcatcacatacatcgaaaagtgagaagg-gacagtatttagtagctctaacgtgagcctgaatgaa
B D    Zebrafish  cataacaacaagtac-------agcgaaaagatggcaacatctaac--------tatgaggctaaaagaa
B D    Tetraodon  ---------------atcgtcaactgaacatg-agcagtggcaaatctttgtggcgtgggctcgcacaga
         Medaka  ======================================================================

     Stickleback  ac--tcatatta----tagcatgtgctatgc-------tacatca------aaatatgtga
       Zebrafish  aacgtcagtttc----taaagtcttggaagcagacaattacatgggtacaaaattaag---
       Tetraodon  aa--tcatattaatgccggtatatattatgc-------aacataa----------------
          Medaka  =============================================================

Alignment block 59 of 84 in window, 14101043 - 14101110, 68 bps 
B D  Stickleback  aacctgaaaaagagaacaattaaaaaacaacacatctggtgtctatcagcttcaatgagaaaagatga
B D    Tetraodon  caccggaaaaaaaaaaaaaaagaaaaatcaccattatggtgtc--tcagat-ttatgagacaaaataa
B D    Zebrafish  agcacaaaacgaagagcaatcaaggaacaacacagctgagatatatgactc-tacccagcaattacaa
         Medaka  ====================================================================

Alignment block 60 of 84 in window, 14101111 - 14101184, 74 bps 
B D  Stickleback  gttacaatt-ttgagaagcattgcaccacctctttagtagtctgacacggcaagcactaccaaaagtttt
          Medaka  gtggcatctgtcaggaagaagtacagatctatggaggtaattcaatct--cagacgctaccaaaagtttt
B D    Tetraodon  ---------ttttaaaggcatgactttagcatgacagtag---gaggcagcctgtcccaccagaggttcc

     Stickleback  gaca-c
          Medaka  gataac
       Tetraodon  gacc-c

Alignment block 61 of 84 in window, 14101185 - 14101248, 64 bps 
B D  Stickleback  ttggggagctgtgttatacacagaattatgatgccagtgtctcatagctcatcagtactctcag
B D         Fugu  ttggatagctgcctcatagacaga------acgcaaaga-------tctcatcagcactcctac
B D    Tetraodon  ttggatcgctgccttatcaacaga------atgcagggatccctcgtctcatcagcactcctac
          Medaka  ttggaaaggcgtgttatacacaaacctatgatgccagtgtctcaaagctcatcagcaatctcag

Alignment block 62 of 84 in window, 14101249 - 14101362, 114 bps 
B D  Stickleback  cacctcctttgcttatcttcgcataactaca--catcctggtcatgtttcct------ttctcctcctga
          Medaka  cacctcctttgcttatctttgcataactaca--catcctggtcatgtttctt------ttctcctcctga
B D    Tetraodon  cagctcctttgcttctctttgcataactacatccatcctggtgatgtttcct------ct---ctcctga
B D         Fugu  ccgctcatttgcctctctttgcataactacatacatcctggtcatgtttcct------tt---ctcagga
B D    Zebrafish  cacctcctatggtcatcttagaataataata--cataataatcaagttctcttgaaggttcttttcttat

     Stickleback  ccatctgttccctgctg-ccaatc----------------------ttctgagtgtgccagtttc-tgcc
          Medaka  ccatctgttccctgctg-ccaatc----------------------ttctgaatgtgccagcttc-tgcc
       Tetraodon  ccatctgttgggtggtg-cgaatg----------------------ttgtgaacatgccagcgtc-agtg
            Fugu  ccatctgttccctgctg-ccaatc----------------------ttctgagtctgccagcctc-cgcc
       Zebrafish  caaaatgctctaaactgaccaattcaaatggtctttatggattggattctgaccttgttggattcttgcc

     Stickleback  t-------------------------------------------------------------ctaca
          Medaka  t-------------------------------------------------------------ctaca
       Tetraodon  tcacagagatagagagagagagagagagagagagagagagagagagagagagagagagagagagaga
            Fugu  t-gtaaacacacacacacacacacacacacacacacacacacacacacacacacacacacacacaca
       Zebrafish  t-------------------------------------------------------------ccaca

Alignment block 63 of 84 in window, 14101363 - 14101502, 140 bps 
B D  Stickleback  tc----------ctctccctactgagccaatctgagtattgatatcatattctccctctttc----ctct
          Medaka  tc----------ctctcccaactgagtgaatctttgtattgatatcatattctccctc--tc----cact
B D    Tetraodon  tg----------gttgtggtggtgagtgaatcttagcactgatgtgatattctctcgttgtctgtgttcc
B D         Fugu  cacacacacactctttccctgctgagtcgatcttagcactgatgttatgttctcacctt-------cttc

     Stickleback  tctctctgtttctgtcatctctcttt----------ctctctctc-------tctcacacacacacacac
          Medaka  tccttctgcttctgtcaccattcttttcagttttcactctcgccc-------tctcctccacaaacacac
       Tetraodon  gttctctgcgtccggtatactttttt----------cttttacatggagacaacgcagacacacacacac
            Fugu  cttctcggcatctgacatgcttttat----------cttttacac-------actcaggcagacccatgt

     Stickleback  acacacacacac------acacacgctg--------------------aagtcctta
          Medaka  acatatgcacataagtagacacacaacgtctgaaatgtaacagactgcaagtcctta
       Tetraodon  acacacacacacacacacacacacacac--------------------aag------
            Fugu  gcacacacacaca--------------------------------------------

Inserts between block 63 and 64 in window
B D   Tetraodon 94bp
B D        Fugu 482bp

Alignment block 64 of 84 in window, 14101503 - 14101574, 72 bps 
B D  Stickleback  taagtatggcagaattgcatg--agcagtttgtgat--cttgaagactgtagaaattggcatcaggctgt
          Medaka  aaagtttggc-----tgcatgcaaacagttttaaattgctctccgcttcctagtattgtaataaaatgtc
B D    Zebrafish  tgaatgtgattttattatatg--cgatatttgtaat--tctttaaattattcaaatatagcttaggctat
B D    Tetraodon  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  atgttg
          Medaka  attgtt
       Zebrafish  tttatc
       Tetraodon  ======
            Fugu  ======

Alignment block 65 of 84 in window, 14101575 - 14101659, 85 bps 
B D  Stickleback  aaaatatggcaactaatattcttcagcatat------------atgaggattaatatttgttataaaact
          Medaka  tggacatgg--aataacaatcacaagtatattgaggaactgtcacaagcatttacatttacaagaaaaa-
B D    Tetraodon  aaaatgtgctaatcaaaataaaactgcaaac------------atttgcagcaatattttttgtggcact
B D    Zebrafish  gaaatatgac-actattgtt-ttgagcctcc------------aaaagtggacatgtttataaaagttt-
B D         Fugu  ======================================================================

     Stickleback  gtagtttta---------------tta----catattatttaaagt
          Medaka  aaagt-------------------tta----aagatttttaaatgt
       Tetraodon  gtactttgaatgtttgcattaaagtta----cacataaagcaattt
       Zebrafish  gtccttttt---------------ttatgtccacgtttttagaagt
            Fugu  ==============================================

Alignment block 66 of 84 in window, 14101660 - 14101693, 34 bps 
B D  Stickleback  aataacgtcgatc--aattaataatc------aatttcttta
          Medaka  ctttgtatcgctt--tgt-----atc------atttttttta
B D    Tetraodon  ttgtttgtcaatttgagttgacaagcttgcaaagcttttcta
B D         Fugu  ==========================================

Inserts between block 66 and 67 in window
         Medaka 669bp

Alignment block 67 of 84 in window, 14101694 - 14101735, 42 bps 
B D  Stickleback  atgagcg-tagtagtaaaaaatgtttaaattttgttaacttta
B D    Tetraodon  ttgagagccaaaattaaaagcagttggaatgtttctgacctta
         Medaka  ===========================================
B D         Fugu  ===========================================

Alignment block 68 of 84 in window, 14101736 - 14101739, 4 bps 
B D  Stickleback  aaaa
         Medaka  ====
B D         Fugu  ====

Alignment block 69 of 84 in window, 14101740 - 14101921, 182 bps 
B D  Stickleback  aaaattgtatgcatagtacaagca-ggtaacttaaatttcacaggatgtaccaa--------ttctatca
B D    Zebrafish  gaaatacccacagtgaaacggttatataaatttaaatatt------------ag--------tttaaata
B D    Tetraodon  --acttgtttctttaaaactgtta-atatgcttatctattccaatctgcttcagagtccagttaccagta
         Medaka  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  tatctaattgtgattcaga----gtcccatagtgaaag--------aatgaccacaaatcggatgtcaaa
       Zebrafish  catttatagtggttttaaatatcttttaatatgtaaagtagagttcaaattcaacaaactgaataaaaca
       Tetraodon  tatctcaaggaaaatcaaa---------atggtaaaag----------ttacca------gaatgtctca
          Medaka  ======================================================================
            Fugu  ======================================================================

     Stickleback  ggg----------------tgcaaaaa---ttagaaatgaaatgatacaatgcatgtttaaatgtacaat
       Zebrafish  agtcttcgtttttagtttatttaaaaacaattacaaatgaagtaattcaactcacaattaaatg-atctc
       Tetraodon  gat----------------tttcgaaa----tagatatcagaacatatgacac-----caaatgggtaac
          Medaka  ======================================================================
            Fugu  ======================================================================

     Stickleback  catatgcatgtt
       Zebrafish  attgagtgat--
       Tetraodon  cgtgaacacttt
          Medaka  ============
            Fugu  ============

Alignment block 70 of 84 in window, 14101922 - 14102011, 90 bps 
B D  Stickleback  caaacgcaatagttctgactcataataactcatagttc---tgctcccaag-------tattgatgtaag
B D    Zebrafish  ggaataataaaggtaaaactttaattgaatgatcagtcaagtgttttccaatgaaatctgttaaaataag
B D    Tetraodon  ======================================================================
         Medaka  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  agtgactc----cagcagcagagaaaggcgagga
       Zebrafish  agtcctacaaaacaggaacaaagacactcatgaa
       Tetraodon  ==================================
          Medaka  ==================================
            Fugu  ==================================

Alignment block 71 of 84 in window, 14102012 - 14102058, 47 bps 
B D  Stickleback  aagaatgtttctttatgatttcataa-------agccattattatc------agctgatt
B D    Tetraodon  aagaatgttggttttggattataaaattgttttagttattaacatctgttctagttgaaa
B D    Zebrafish  acgaaatgtgattgtcaattgtat--------------tttttatt------agatggtt
         Medaka  ============================================================
B D         Fugu  ============================================================

Inserts between block 71 and 72 in window
B D   Zebrafish 1522bp

Alignment block 72 of 84 in window, 14102059 - 14102140, 82 bps 
B D  Stickleback  ctacactaggcctatactcatgaac-------ctgacgttacgat---acctaactaacattct------
B D    Tetraodon  gttgaataggcaatagctggagagcatgtctgctgatgaaatgatcaaatcttcatgtcattatgtggca
         Medaka  ======================================================================
B D         Fugu  ======================================================================
B D    Zebrafish  ======================================================================

     Stickleback  -----tatatggctcaactcaacaccatgacaa
       Tetraodon  atatatttatagtttacataaattccatgataa
          Medaka  =================================
            Fugu  =================================
       Zebrafish  =================================

Alignment block 73 of 84 in window, 14102141 - 14102174, 34 bps 
B D  Stickleback  tttctgacaaaat-attcctcttgtttgtgccatt
B D    Tetraodon  attacgttgatatcatttgattaatatgtaacatt
B D    Zebrafish  tttcagctcaaat-attccacttttttttgttttt
         Medaka  ===================================
B D         Fugu  ===================================

Alignment block 74 of 84 in window, 14102175 - 14102233, 59 bps 
B D  Stickleback  -aatttaaaacccaacct--------tattgtctcccaaagc--acattactgtacctgtttctctaaag
          Medaka  -agttcaaaacatgacct--------tatttccacctgcagc--acaacagcgtacctgttcctcaatgg
B D    Tetraodon  ---ggtaaacatcaattt--------tatctgctccttg-----gcatcagtgtgtttacttctgaagag
B D    Zebrafish  aacccaaaaactcaaactactactcacattactactctaaacaaacttcaatagagctggtgttaaaaat
B D         Fugu  ======================================================================

     Stickleback  -
          Medaka  -
       Tetraodon  -
       Zebrafish  g
            Fugu  =

Alignment block 75 of 84 in window, 14102234 - 14102295, 62 bps 
B D  Stickleback  gcctctacact-----ccacacacctctac---------------------gtatccactcttgtg----
          Medaka  gcctctgcact-----tgatgcttc-ctgcatgagccaacggc------tggcgtccactcaagtg----
B D    Zebrafish  gcctatatgctaacaatgataaaactttac-------aatagcatgttttaatacttacacatctgactt
B D    Tetraodon  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  tattaat--aagaactccactgct
          Medaka  tgttaa-----gaactctgctgca
       Zebrafish  tgttgatcagagatctctcctttt
       Tetraodon  ========================
            Fugu  ========================

Inserts between block 75 and 76 in window
B D   Zebrafish 130bp

Alignment block 76 of 84 in window, 14102296 - 14102389, 94 bps 
B D  Stickleback  tgcctcaggcatt-taaaaggaatgactaacacactctttgcaaaccactgaaagactgctgtaaaatat
          Medaka  cgcctcaggcttt---acaggaatgactaatacactctc--caaaccgctgaaagacggctgtaaaacat
B D    Zebrafish  tgccacaggtgcaataaatggaatcacttccagaaatgttgcaaatcaactaaagttcacagtgcaagaa
B D    Tetraodon  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  ctctgcccaaacagagtgatgcag------------a
          Medaka  ctccagccaaacag--tgatgcaggttggtgtggtta
       Zebrafish  atctaagaaaatactgtgaatcaa------------a
       Tetraodon  =====================================
            Fugu  =====================================

Alignment block 77 of 84 in window, 14102390 - 14102477, 88 bps 
B D  Stickleback  aatac-----tctatg---------gtcaacacattctacagtttgcaaatgatcattatattgagatta
          Medaka  catgcctccatccatg-------catttaccagacgctgtaacctgctgaccggtggagcttcgaaattt
B D    Zebrafish  aatac-ttgatttataaaaataacattgcacatttgtaatagtaaactcaacattataattattaactat
B D    Tetraodon  ======================================================================
B D         Fugu  ======================================================================

     Stickleback  ttatcgtgtttggacaggctttgctgttttat
          Medaka  tattatagcttaaaaaaaatgt----ttctca
       Zebrafish  atacagggcttg--------------------
       Tetraodon  ================================
            Fugu  ================================

Alignment block 78 of 84 in window, 14102478 - 14102601, 124 bps 
B D  Stickleback  tcatataagcatcagacatattgttatata--------------agttatatataagttactactaagtc
          Medaka  ataaaaaaacatcagccctttttgta------------------------------gctaccaccaagta
B D         Fugu  tcacatgagcatcagctccac-----------------------------------attatcaccaagaa
B D    Zebrafish  --acattaacacccgccaaatgcgtgaagattttgcctggggcgggttacacagacaccctcactagcca
B D    Tetraodon  ======================================================================

     Stickleback  aa------at---tttaaagaacatctttttcatg----agttttgttttgg---gaaaaaaagtgggat
          Medaka  aa------ata--tttgaaaaac-----tttccaa----agtcttgttttgg----agagaaagtggaat
            Fugu  aaaaatatata--tataaaaaatac---tttcata----agttttgttaaggagggaaaaaaagtgcaat
       Zebrafish  tg------ttggctgttgaaaatagtttatttaaatgtcagtactgttttgt--cactaaatattagaat
       Tetraodon  ======================================================================

     Stickleback  tcaatcagtgcaat
          Medaka  ttcattactgcata
            Fugu  tccatccgtacatt
       Zebrafish  t---tttgtttaag
       Tetraodon  ==============

Alignment block 79 of 84 in window, 14102602 - 14102683, 82 bps 
B D  Stickleback  ttgcattactaatatataattcatacatggatgaaaatttcatcaaggaaacatgatgactgaggtac--
          Medaka  atgcacaactgatacataattcatgcagaaataaaaatttaatcaagaaaacatgatgactgaggtac--
B D         Fugu  atgcataagtgctgcataattaataagtaaataaacttttgatcaaggcaacatgatcactgaggtacag
B D    Tetraodon  ======================================================================

     Stickleback  ---acgcaattacaagc
          Medaka  ---acgcaattacaagc
            Fugu  tagatgcaattgcgtac
       Tetraodon  =================

Inserts between block 79 and 80 in window
B D        Fugu 1bp

Alignment block 80 of 84 in window, 14102684 - 14102753, 70 bps 
B D  Stickleback  tttgctcacttcaaagtaaagtaaactgatatgaataagtta---aacctacggaaatatgcattcaggc
B D         Fugu  ttaactagcttcaaagtaaaacaaaccaatatgaataaatgatggtacataatgaaacaagtattcaggc
B D    Tetraodon  tctgctagcttcaaagtataacaaactgatatgaataaatgatggtacataagaaaatatctattctggc
          Medaka  tttgctcacatcaaagtgaaataaactgatataaataagtgatggtatgtaaggaagca--cattcgagc

     Stickleback  taa-----
            Fugu  tac-----
       Tetraodon  taa-----
          Medaka  taatggat

Alignment block 81 of 84 in window, 14102754 - 14102816, 63 bps 
B D  Stickleback  gttgtataatgat----gtttttggtcaagcaagtttaaccactgacaaattaat--acag--aataaaa
          Medaka  gctccacaaaaat--ccaaactttatcagg-atattttcttacaggcaaactacc--tcaattcttaaaa
B D    Tetraodon  gttctgtaaggat----gtttttaggcaacagaaccatcatacagcctgataaatcagcagtgcgta---
B D         Fugu  gttctataatgat----gtttttggtcaacagaactgtcgtactgccactttagtctgtggtgcata---
B D    Zebrafish  attatacattcacaccagccttttgtaaaa-aggtaacctcaccaactattgacctggca-tacataaaa

     Stickleback  g--
          Medaka  c--
       Tetraodon  ---
            Fugu  ---
       Zebrafish  cag

Inserts between block 81 and 82 in window
B D   Tetraodon 142bp

Alignment block 82 of 84 in window, 14102817 - 14102865, 49 bps 
B D  Stickleback  aacatgtt---------gatggtcagacttttacacttatccagaatttaaaagggca
          Medaka  ggggaact---------gctgttcaaa-tattacacttcatctgaatctaaaagtcca
B D         Fugu  --gaagctttgattggggttctttggattttcactct---------------------
B D    Zebrafish  ---------cgcatgtgtaacgtaaaacttttaaaaatgcaaagaatttaaaaaggaa
B D    Tetraodon  ==========================================================

Inserts between block 82 and 83 in window
B D        Fugu 558bp

Alignment block 83 of 84 in window, 14102866 - 14102901, 36 bps 
B D  Stickleback  cttatgctggttcatctcctgaaaagctttgtcaga------------
          Medaka  cttct--tggtttgaggactg--gatctttttcaga------------
B D    Zebrafish  ------------tgtatattg----acctttttaaatattttgatcca
B D    Tetraodon  ================================================
B D         Fugu  ================================================

Inserts between block 83 and 84 in window
         Medaka 2706bp

Alignment block 84 of 84 in window, 14102902 - 14102956, 55 bps 
B D  Stickleback  ccacttccaggtcatcagac-cgtgcaccctaactagggcacggtttgccgaccgg
B D    Zebrafish  tttgttgactgtgtgcaggcacgagctccacagatactgtatg---tgcagactgt
B D    Tetraodon  ========================================================
         Medaka  ========================================================
B D         Fugu  ========================================================

View table schema

Go to Conservation track controls

Data last updated at UCSC: 2007-03-27

Description

This track shows a measure of evolutionary conservation in 8 vertebrates, including mammalian, bird, and fish species, based on a phylogenetic hidden Markov model, phastCons (Siepel et al., 2005). Multiz alignments of the following assemblies were used to generate this track:

  • stickleback (Feb. 2006 (Broad/gasAcu1), gasAcu1)
  • medaka (Oct 2005, oryLat1)
  • fugu (Oct 2004, fr2)
  • tetraodon (Feb 2004, tetNig1)
  • zebrafish (Mar 2006, danRer4)
  • chicken (May 2006, galGal3)
  • mouse (Feb 2006, mm8)
  • human (Mar 2006, hg18)

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a "wiggle" (histogram), where the height reflects the size of the score. Pairwise alignments of each species to the stickleback genome are displayed below as a grayscale density plot (in pack mode) or as a "wiggle" (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

The conservation wiggle can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Checkboxes in the track configuration section allow excluding species from the pairwise display; however, this does not remove them from the conservation score display. To view detailed information about the alignments at a specific position, zoom in the display to 30,000 or fewer bases, then click on the alignment.

Gap Annotation

The "Display chains between alignments" configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the stickleback genome or a lineage-specific deletion between the aligned blocks in the aligning species.
  • Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

  • Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
  • Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the stickleback genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the stickleback sequence at those alignment positions relative to the longest non-stickleback sequence. If there is sufficient space in the display, the size of the gap is shown; if not, and if the gap size is a multiple of 3, a "*" is displayed, otherwise "+" is shown.

Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:

  • No codon translation: The gene annotation is not used; the bases are displayed without translation.
  • Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
  • Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen:

Gene TrackSpecies
Known Geneshuman, mouse
Ensembl Genesstickleback, medaka, fugu
RefSeq Geneschicken, zebrafish
Genscan Gene Predictionstetraodon

Methods

Best-in-genome pairwise alignments were generated for each species using lastz, followed by chaining and netting. The pairwise alignments were then multiply aligned using multiz, following the ordering of the species tree diagrammed above. The resulting multiple alignments were then assigned conservation scores by phastCons, using a tree model with branch lengths derived from the ENCODE project Multi-Species Sequence Analysis group, September 2005 tree model. This tree was generated from TBA alignments over 23 vertebrate species and is based on 4D sites.

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Note that, unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size, so short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. (2005).

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

Credits

This track was created using the following programs:

  • Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
  • Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
  • Conservation scoring: PhastCons, phyloFit, tree_doctor, msa_view by Adam Siepel while at UCSC, now at Cold Spring Harbor Laboratory
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; genePredToMafFrames by Mark Diekhans, UCSC
  • Tree image generator: phyloPng by Galt Barber, UCSC
  • Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community.

References

Phylo-HMMs and phastCons:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Phylogenetic Tree:

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200