Multiz Alignments of 20 mammals (17 primates)
 

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Alignment block 1 of 36 in window, 77418096 - 77418228, 133 bps 
B D                     Human  ataaaaactgtggcctcacccatatgccag-aaaaagctgagtggggagccaagattt-ccaatgtagtg
B D                     Chimp  ataaaaactgtggcctcacccatatgccag-aaaaagctgagtggggagccaagattt-ccaatgtagtg
B D                    Bonobo  ataaaaactgtggcctcacccatatgccag-aaaaagctgagtggggagtcaagattt-ccaatgtagtg
B D                   Gorilla  ataaaaactgtggcctcacccatatgccag-aaaaagctgagtggggagccaagattt-ccaatgtagtg
B D                 Orangutan  aaaaaaactgtggcctcacccacatgccag-aaaaagctgagtggggagccaagattt-ccaatgtagtg
B D                    Gibbon  -------ctgtggcctcacccacatgccag-aaaaagctgagtggggagccaaaattt-ccagtgtagtg
B D                    Rhesus  --aaaaactgtagcctcacccacatgccag-caaaagctgagcagggagccaagattt-ccaatgtagtg
B D       Crab-eating macaque  --aaaaactgtagcctcacccacatgccag-caaaagctgagcagggagccaagattt-ccaatgtagtg
B D                    Baboon  --aaaaactgtagcctcacccacatgccag-caaaagctgagcagggagccaagattt-ccaatgtagcg
B D              Green monkey  --aaaaactgtagcctcacccacatgccag-caaaagctgagcagggagccaagattt-ccaatgtggtg
B D          Proboscis monkey  --aaaaactgtagcctcacccacatgccag-caaaagctgagcagggagccaagattt-ccaatgtagtg
B D  Golden snub-nosed monkey  --aaaaactgtagcctcacccacatgccag-caaaagctgagcagggagccaagatttcccaatgtagtg
B D               Mouse lemur  --aaaaactgtgaccccacccaaatcccagaaaaaggctaagtaggaagtcaagattt-ccaacctagtg
B D                  Bushbaby  --aaaagctgtgcccccacccacatgccag-cagagtctgagtgggaagtcaagattt-cccacccagtg
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D                   Tarsier  ======================================================================
B D           Squirrel monkey  ======================================================================
B D                  Marmoset  ======================================================================

                        Human  aagctgtgaggaggtactacaaaacccctactgggcaatgtaaagagggccaactaggaagctga
                        Chimp  aagctgttaagaggtactacaaaacccctactgggcaatgtaaagagggccaactaggaagctga
                       Bonobo  aagctgttaagaggtactacaaaacccctactgggcaatgtaaagagggccaactaggaagctga
                      Gorilla  aagctgttaagaggtactacaaaacccctactgggcaatgtaaagagggccaactaggaagctga
                    Orangutan  aagctgtgaagaggtactacaaaacccctactgggcaatgtaaagagggccaactaggaagctga
                       Gibbon  aagctgtgaagaggtactacaaaacccctactgggcaatgtaaagagggccaagtaggaagctga
                       Rhesus  aagctgtaaagaggtactacaaaacctctact-ggcaatgtaaagagggccaagtaggaagctgg
          Crab-eating macaque  aagctgtaaagaggtactacaaaacctctact-ggcaatgtaaagagggccaagtaggaagctgg
                       Baboon  aagctgtaaagaggtactacaaaacctctact-ggcaatgtaaagagggccaagtaggaagctgg
                 Green monkey  aagctgtaaagaggtactacaaaacctctact-ggcaatgtaaagagggccaagtaggaagctgg
             Proboscis monkey  aagctgtaaagacgtactacaaaacctctact-ggcaatgtaaagagggccaagtaggaagctgg
     Golden snub-nosed monkey  aagctgtaaagacgtactactaaacctctact-ggcaatgtaaagagggccaagtaggaagctgg
                  Mouse lemur  aagctgtgaagaggtactacaaatccactactgggtgatataaagaaggccaagaagggagctag
                     Bushbaby  aagctgtgaagaggtactgcaaacc--ctactgggtg-tacaaactagactgggaagggagctgg
                        Mouse  =================================================================
                   Tree shrew  =================================================================
                          Dog  =================================================================
                      Tarsier  =================================================================
              Squirrel monkey  =================================================================
                     Marmoset  =================================================================

Alignment block 2 of 36 in window, 77418229 - 77418232, 4 bps 
B D                     Human  aact
B D                     Chimp  aact
B D                    Bonobo  aact
B D                   Gorilla  aact
B D                 Orangutan  aact
B D                    Gibbon  aact
B D                    Rhesus  aact
B D       Crab-eating macaque  aact
B D                    Baboon  aact
B D              Green monkey  aact
B D          Proboscis monkey  aact
B D  Golden snub-nosed monkey  aact
B D           Squirrel monkey  aact
B D               Mouse lemur  aact
B D                  Bushbaby  aact
B D                     Mouse  ====
B D                Tree shrew  ====
B D                       Dog  ====
B D                   Tarsier  ====
B D                  Marmoset  ====

Alignment block 3 of 36 in window, 77418233 - 77418478, 246 bps 
B D                     Human  tttttccctgctgtccaggacatcccctcaccttcccactcctccgtcactaccatcagtggaaagcctg
B D                     Chimp  tttttccctgctgtccaggacatccccttaccttcccactcctccgtcactaccatcagtggaaagcctg
B D                    Bonobo  tttttccctgctgtccaggacatcccctcaccttcccactcctccgtcactaccatcagtggaaagcctg
B D                   Gorilla  tttctccctgctgtccaggacatcccctcaccttcccactcctccgtcactaccatcagtggaaagcctg
B D                 Orangutan  tttgtccctgctgtccaggacatcccttcaccttcccactcctccgtcactactatcagtggaaagcctg
B D                    Gibbon  tttgtccctgcagtccaggacatcccctcaccttcccactcctccgtcactaccatcagtgggaagtctg
B D                    Rhesus  tttgtccctactgtccaggacatcccctctccttcccactcctccgtcactaccatcagtggaaagcctg
B D       Crab-eating macaque  tttgtccctactgtccaggacatcccctctccttcccactcctccgtcactaccatcagtggaaagcctg
B D                    Baboon  tttgtccctgctgtccaggacatcccctctccttcccactcctccgtcactaccatcagtggaaagcctg
B D              Green monkey  tttgtccctgctgtccaggacatcccctctccttcccactcctccgtcactaccatcagtggaaagcctg
B D          Proboscis monkey  tttgtccctgctgtccaggacatcccctccccttcccactcctccgtcactaccatcagtagaaagcccg
B D  Golden snub-nosed monkey  tttgtccctgctgtccaggacatcccctctccttcctactcctccgtcactaccatcagtagaaagcccg
B D                  Marmoset  tttatctctgctgtccaggatatcccctcaccttaccactcctccatcactaccatcagtggaaagcctg
B D           Squirrel monkey  tttgtctctgctgtccaggatatcccctcaccttaccactcctccatcgctaccatcagtggaaagcctg
B D               Mouse lemur  tttgtctctgctggccagtatatcctgtcaccctctcacacctcc-ccaccaacatcaatggaaagcctg
B D                  Bushbaby  tttgtccctgttggccagtacatcccctcaccttctttcacctct-ccaccaccatcagcagaaagcctg
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D                   Tarsier  ======================================================================

                        Human  aatttgcaacatcacctcgtaacattacctgctgggaaagtgttgca-ggaggcctagtggaaagtagag
                        Chimp  aatttgcaacatcacctcataacattacctgctgggaaagcgttgca-ggaggtctagtggaaagtagag
                       Bonobo  aatttgcaacatcacctcgtaacattacctgctgggaaagcgttgca-ggaggcctagtggaaagtagag
                      Gorilla  aatttgcaacatcacctcataacattacctgctgggaaagtgttgca-ggaggcctggtggaaagtagag
                    Orangutan  aatt-------------------------tgctgggaaagtgttgga-ggaggcctagtggaaagtagag
                       Gibbon  aatttgc-------------aacattacctgctgggaaagtgttgga-ggaggcctggtggaaagtagag
                       Rhesus  aatttgcaacatcacctcataccatcacctgctgggaaagtgttgga-gaaggcctagtggaaagcagag
          Crab-eating macaque  aatttgcaacatcacctcataccatcacctgctgggaaagtgttgga-gaaggcctagtggaaagcagag
                       Baboon  aatttgcaacatcacctcataccatcacctgctgggaaactgttgga-gaaggcctagtggaaagcagag
                 Green monkey  catttgcaacatcacctcataccatcaccttctgggaaagtgttgga-gaaggcctagtggaaagcagag
             Proboscis monkey  aatttgcaacatcacctcataccattacctgctgggaaagtgttgga-gaaggcctagtggaaagcagag
     Golden snub-nosed monkey  aatttgcaacatcacctcataccattacctgctgggaaagtgttgga-gaaggcctagtggaaagcagag
                     Marmoset  attttgcaacatcacctcataccattacctgctgggatagtgtcggaaggaggcctagtggaaagtagaa
              Squirrel monkey  aatttacaacatcacgtcataccattacctgctgagatagtgttggagggaggcctagtgaaaagtagaa
                  Mouse lemur  aatttgcagattcatctcacactactctctgctcggttagtgtcaga-ggaggcctagtggaaagtaatg
                     Bushbaby  aatttgtaatatcatctcataccactctctgctgggttagtgtcaga-agaggcccagtggaaagcaatg
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================

                        Human  acttgcagcagcacccagggttaa-----------------------------------------caaga
                        Chimp  acttgcagcagcacccagggttaa-----------------------------------------caaga
                       Bonobo  acttgcagcagcacccagggttaa-----------------------------------------caaga
                      Gorilla  acttgcagcagcacccagggttaa-----------------------------------------caaga
                    Orangutan  acttgcagcagcacccagggttaa-----------------------------------------caaga
                       Gibbon  acttgcagcagcacccagggttaa-----------------------------------------caaga
                       Rhesus  acttgcagcagcacccagggttaa-----------------------------------------caaga
          Crab-eating macaque  acttgcagcagcacccagggttaa-----------------------------------------caaga
                       Baboon  acttgcagcagcacccagggttaa-----------------------------------------caaga
                 Green monkey  gcttgcagcagcacccagggttaa-----------------------------------------caaga
             Proboscis monkey  acttgcagcagcacccaaggttaa-----------------------------------------caaga
     Golden snub-nosed monkey  acttgcagcagcacccaaggttaa-----------------------------------------caaga
                     Marmoset  acttgcagcagcacccagggttaa-----------------------------------------caaga
              Squirrel monkey  acttgcatcagcacccagggttaa-----------------------------------------taaga
                  Mouse lemur  acttgcaacactacccagagttaataatacctccaccacagtgtcaaaagaaaccacttgttgggccaga
                     Bushbaby  acttgcagcaccacccaggattca---------ccccacagtgtcaaaagaaacacctggataatccaga
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================

                        Human  ccacctactcccacttaga----aagaagagt-actccctttctcttgtgtgttaattaagggcaatagg
                        Chimp  ccacctactcccacttaga----aagaagagt-actccctttctcttgtgtgtcaattaagggcaatagg
                       Bonobo  ccacctactcccacttaga----aagaagagt-actcccttcctcttgtgtgtcaattaagggcaatagg
                      Gorilla  ccacctactcccacttaga----aagaagagt-actccctttctcttgtgtgtcaattaagggcaatagg
                    Orangutan  ccaccttctcccacttaga----aagaagagt-actccctttctcttgtgtgtcaattaagggcaatagg
                       Gibbon  ccacccactcccacttaga----aagaagagt-actccctttctcttgtgtgtcaattaagggcaatagg
                       Rhesus  ccacccactcccacttaga----aagaagagt-actccctttctcttgtgtgtcagttaagggcaatagg
          Crab-eating macaque  ccacccactcccacttaga----aagaagagt-actccctttctcttgtgtgtcagttaagggcaatagg
                       Baboon  ccacccactcccacttaga----aagaagagt-actccctttctcttgtgtgtcagttaagggcaatagg
                 Green monkey  ccactcactcccacttaga----aagaagagt-actccctttctcttgtgtgt----------caatggg
             Proboscis monkey  ccacccattcccacttaga----aagaagagt-actccctttctcttgtgtgtcagttaagggcaatagg
     Golden snub-nosed monkey  ccacccactcccacttaga----aagaagagt-actccctttctcttgtgtgtcagttaagggcaatagg
                     Marmoset  ccacccacccccacataga----aagaagaac-atcccctttctcttgtgtgtcaattaagggcaatagg
              Squirrel monkey  ccacccacccccacgtaga----aaaaagaacaattccctttctcttgtgtgtcaattaagggcaatagg
                  Mouse lemur  aatcccatttccacctgaaaatgaggaggagc-accttcttattcttggatgtcaattgaggccagtagg
                     Bushbaby  aatccta-ttccacctggaaat-aggaggatc-atcttcttcctcttgggt-cccactgaggccagtgtg
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================

                        Human  aaatgagaattct
                        Chimp  aaatgagaattct
                       Bonobo  aaatgagaattct
                      Gorilla  aaatgagaattct
                    Orangutan  aaatgagaatgct
                       Gibbon  aaatgagaattct
                       Rhesus  aaatgagaattct
          Crab-eating macaque  aaatgagaattct
                       Baboon  aaatgagaattct
                 Green monkey  aaatgagaattct
             Proboscis monkey  aaatgagaattct
     Golden snub-nosed monkey  aaatgagaattct
                     Marmoset  aaatgaaaattct
              Squirrel monkey  aaatgaaaattcg
                  Mouse lemur  aaccaagagttct
                     Bushbaby  aaccaagactgcc
                        Mouse  =============
                   Tree shrew  =============
                          Dog  =============
                      Tarsier  =============

Alignment block 4 of 36 in window, 77418479 - 77419218, 740 bps 
B D                     Human  accttgaccagct-gtaataaaatag----ccccaactt--tctccttctgcattggtatcagagaaagc
B D                     Chimp  accttgacctgct-gtaataaaatag----ccccaactt--tctccttctgcattggtatcagagaaagc
B D                    Bonobo  accttgacctgct-gtaataaaatag----ccccaactt--tctccttctgcattggtatcagagaaagc
B D                   Gorilla  accttgacctgct-gtaataaaatag----ccccaactt--tctccttctgcattgatatcagagaaagc
B D                 Orangutan  accttgacctgct-gtaataaaatag----ctccaactt--tctccttctgtattggtatcagagaaagc
B D                    Gibbon  accttgacctgct-gtaataaaatag----ccccaactt--tctccttctgtattggtgtcagagaaagc
B D                    Rhesus  accttgacctgct-gtcataaaatag----ccccaactt--tctccttctgtattggtatcagagaaagc
B D       Crab-eating macaque  accttgacctgct-gtcataaaatag----ccccaactt--tctccttctgtattggtatcagagaaagc
B D                    Baboon  accttgacctgct-gtcataaaatag----ccccaactt--tctccttctgtattggtatcagagaaagc
B D              Green monkey  accttgacctgct-gtcataaaatag----ccccaactt--tctccttctgtattggtatcagagaaagc
B D          Proboscis monkey  accttaacctgct-gtcataaaatag----ccccaactt--tctccttctgtattagtatcagagaaagc
B D  Golden snub-nosed monkey  accttaacctgct-gtcataaaatag----ccccaactt--tctccttctgtattagtatcagagaaagc
B D                  Marmoset  actttgacctgctaataatgaaatagt--tccccacctt--tctcctgctgtattggtatcagagaaagc
B D           Squirrel monkey  actttgacctgctaataatgagatagt--tccccacctt--tctcctgttgtattggtatcagagaaagc
B D                  Bushbaby  acatctacctgctaccaataagacagtgacccccgaccccacctcctgctgcaatg------gagaaagc
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D                   Tarsier  ======================================================================
B D               Mouse lemur  ======================================================================

                        Human  ta----agaagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaacaaaagaaat
                        Chimp  ta----agaagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaagaaaagaaat
                       Bonobo  ta----agaagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaagaaaagaaat
                      Gorilla  ta----agaagttttaaataagatccatcatcttataatatgaaaatgtccaaatatcaacaaaagaaat
                    Orangutan  ta----agaagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaacaaaagaaat
                       Gibbon  ta----agaagttttaaataagatccatcatcttatgatatgaaaatgcccaaatttcaacaaacgaagt
                       Rhesus  ta----agaagttttatataagatccatcatcttataatatgaaaatgtccaaatttcaat-aaagaaat
          Crab-eating macaque  ta----agaagttttatataatatccatcatcttataatatgaaaatgtccaaatttcaat-aaagaaat
                       Baboon  ta----agaagttttatataagatccatcatcttataatatgaaaatgtccaaatttcaat-aaagaaat
                 Green monkey  ta----aaaagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaat-aaagaaat
             Proboscis monkey  ta----actagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaataaaagaaat
     Golden snub-nosed monkey  ta----agaagttttaaataagatccatcatcttataatatgaaaatgtccaaatttcaataaaagaaat
                     Marmoset  tt----agaaattttagatatgatccatcatcttataatatgaaaatgtccaaatttcaacaaaagaaat
              Squirrel monkey  ta----agaaattttagatgagatccatcatcttataatatgaaaatgtccaaatttcaacaaaagaaat
                     Bushbaby  caaagcaaaagcttaaaacaagatcaagtgtctt---atataaaatggtctagatttcaataaaataagc
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  cattcattataccaagaaccaggaagatctcaacctgaattttttaaaggcaatcaaaagatggcagtac
                        Chimp  cattctttataccaagaaccaggaagatctcaacctgaattttttaaaggcaatcaaaagatggcagtac
                       Bonobo  cattcattataccaagaaccaggaagatctcaacctgaattttttaaaggcaatcaaaagatggcagtac
                      Gorilla  cattcattataccaagaaccaggaagatctcaacctgaattttttaaaggcaatcaaaagatggcagtac
                    Orangutan  cattcattataccaagaaccaggaagctctcaacctgaattttttaaaggcaatcaaaagatggcagtac
                       Gibbon  cattcattataccaagagccaggaagatctcaacctgaattttttaaaggcaatcaaaagatggcagtac
                       Rhesus  tattcattataccgagaaccaggaagatatcaacctaaattttttaaaggcaatcaaacgatgccagtac
          Crab-eating macaque  tattcattataccgagaaccaggaagatatcaacctaaattttttaaaggcaatcaaacgatgccagtac
                       Baboon  tattcattataccgagaaccaggaagatatcaacctaaattttttaaaggcaatcaaacgatgccagtac
                 Green monkey  cattcattataccgagaaccaggaagatctccacctaaattttttaaaggcaatcaaacaatgccagtac
             Proboscis monkey  cattcattataccgagaaccaggaagatctcaacctgaattttttaaaggcaatcaaaagatgccagtac
     Golden snub-nosed monkey  cattcattatactgagaaccaggaagatctcaacctgaattttttaaaggcaatcaaaagatgccagtac
                     Marmoset  cattcattataccaagaaccaggaagatctcaacctgaactgtttaaaggcaatcaaaagattccaaaac
              Squirrel monkey  cattcattataccaagaaccaggaagatcgcaacctgaattttttaaaggcaatcaaaagatgagagaac
                     Bushbaby  tacttatcatgccaagaaccaggaagatctcaaactaaattttagaaagacaagtaaaagatgccagtgt
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  cactgccaaaaacacacaatggaaaaaggagagcctcataaataaatggtattggaagaactag------
                        Chimp  cactgccaaaaacacacaatgggaaaaggagagcctcataaataaatggtattggaagaactag------
                       Bonobo  cactgccaaaaacacacaatgggaaaaggagagcctcataaataaatggtattggaagaactag------
                      Gorilla  cactgccaaaaacacacaatgggaaaaggagagcctcataaataaatggtattggaagaactag------
                    Orangutan  cactgtcaaaaacacacaatggcaaaaggagagtctcataaataaatggtattggaagaactag------
                       Gibbon  ------caaaaacacacaatgggaaaaggagagtctcataaataaatggtattggaagaactag------
                       Rhesus  cactgccataaacacaccataggaaaaagagagtctcttaaataaatggtgttggaagaactag------
          Crab-eating macaque  cactgccataaacacaccataggaaaaggagagtctcttaaataaatggtgttggaagaactag------
                       Baboon  cactgccataaacacacaataggaaaaggagaatctcttaaataaatggtgttggaagaactag------
                 Green monkey  cactgccataaacacacaatgggaaaaggagagtctcttaaataaatggtgttggaagaactag------
             Proboscis monkey  cactgccataaacacacaatgggaaaaggagagtctcttaaataaatggtgttggaagaactag------
     Golden snub-nosed monkey  cactgccataaacacacaatgggaaaaggagagtctcttaaataaatggtgttggaagaactagatatac
                     Marmoset  cactgccaaaagcacaaaatggggaaaggagagtctcttaaataaatggtgttggaggaaatag------
              Squirrel monkey  cactgccaaaaacacacaatggggaaaggagagtctctt---taaatgttgttggaagaactag------
                     Bushbaby  tactgccaagaacacacaacagggaaaaggcagtctcctcaataaatggtattgagagaacagg------
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  atatacatatacagaagaatgaaattaggcccttatctc-------------------------------
                        Chimp  atatacatatacagaagaatgaaattaggcccttatctc-------------------------------
                       Bonobo  atatacatatacagaagaatgaaattaggcccttatctc-------------------------------
                      Gorilla  atatacatacacagaagaatgaaattaggcccttatctc-------------------------------
                    Orangutan  atatacatatacagtagaatgaaattaggcccttatctc-------------------------------
                       Gibbon  atatacatatacagaagaatgaaattaggcccttatctcatatatatatatatatatatatatatatata
                       Rhesus  atatacatatacagaagaatgaaattaggcccttatctc------------------------------a
          Crab-eating macaque  atatacatatacagaagaatgaaattaggcccttatctc------------------------------a
                       Baboon  atatacatatacagaagaatgaaattaggcccttatctc------------------------------a
                 Green monkey  atatacatatacagaagaatgaaattaggcccttatctc------------------------------a
             Proboscis monkey  atatacatagacagaagaatgaaattaggcccttatctc-------------------------------
     Golden snub-nosed monkey  atatacatatacagaagaatgaaattaggcccttatctc-------------------------------
                     Marmoset  atatacatatacagaagaatgaaattaggcccttatctc-------------------------------
              Squirrel monkey  atatacatatacagaagaatgaaatgaggcccttatctc-------------------------------
                     Bushbaby  atatacacatgaggaagaatgaaactgggcccttgtttt-------------------------------
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  -ata-tatgtacacaaactaacttaaaatgaaaaaaaagacataagtgtagaatcagaaactacaaaatt
                        Chimp  -ata-tatgtacacaaactaacttaaaatgaaaaaaa-gacataagtgtagaatcagaaactacaaaatt
                       Bonobo  -ata-tatgtacacaaactaacttaaaatgaaaaaaa-gacataagtgtagaatcagaaactacaaaatt
                      Gorilla  -ata-tatgtac----actaacttaaaatggaaaaaa-gacataagtgtagaatcagaaactacaaaatt
                    Orangutan  -ata-tatgtacacaaactaacttaaaatgaaaaaaa-gacataagtgtagaatcagaaactacaaaatt
                       Gibbon  tata-tatatacacaaactaacttaaaatgaaaaaaaagacataagtgtagaatcagaaactacaaaatt
                       Rhesus  tata-tatatacacaaactaatttaaaatgaaacaaa-gacgtaagtgtagagtcacaaactacaaaatt
          Crab-eating macaque  tata-tatatacacaaactaatttaaaatgaaacaaa-gacgtaagtgtagagtcacaaactacaaaatt
                       Baboon  tata-tatatacacaaactaatttaaaatgaaacaaa-gacgtaagtgtagagtcacaaactacaaaatt
                 Green monkey  tata-tatatacacaaactaatttaaaatgaaacaaa-gatgtaagtgtagagtcacaaactacaaaatt
             Proboscis monkey  -tta-tatatacacaaactaact-----tgaaacaaa-gacataagtatagagtcacaaactacaaaatt
     Golden snub-nosed monkey  -tta-tatatacacaaactagct-----tgaaacaaa-gacataagtatagagtcacaaactacaaaatt
                     Marmoset  -ata-tataca----------------atgaaataaa-gacgtaagtgtagaatcagcaactacaaaagc
              Squirrel monkey  -ata-tataca----------------atgaaacaaa-gacataagcctagaatcagcaactacaaaatt
                     Bushbaby  -ataccatatgcaaaaatcaactcaaaatggaggaaa-gacttaaatcca-agacgtgaactgtaaactt
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  agtagaataaaacatatgaggaaagctccatgacattggtctggacaaggactctttggatagga-tccc
                        Chimp  agtagaacaaaacatatgaggaaagctccatgacattggtctggacaaggactctttggatagga-tccc
                       Bonobo  agtagaataaaacatatgaggaaagctccatgacattggtctggacaaggactctttggatagga-tccc
                      Gorilla  agtagaataaaacatatgaggaaagctccatgacattggtctggacaaggactctttggatagga-tccc
                    Orangutan  agtagaataaaacatatgaggaaatctccatgacattggtctggacaaggactttttggatatga-tccc
                       Gibbon  agtagaataaaacacatgaggaaagctccatgacattggtctggacaaggactttttggatatga-tccc
                       Rhesus  agtagaataaaacatatgaggaaagctccacgtcattggtctggacaaggactttttcgatatga-tccc
          Crab-eating macaque  agtagaataaaacatatgaggaaagctccatgtcattggtctggacaaggactttttcgatatga-tccc
                       Baboon  agtagaataaaacatatgaggaaagctccatgtcattggtctggacaaggactttttggatatga-tccc
                 Green monkey  agtagaataaaacatatgaggaaagctccatgtcattggtctggacaaggactttttggatatga-tccc
             Proboscis monkey  agtagaatacaacatatgaggaaagctccatgtcattggtctggacaaggactttttggatatga-tccc
     Golden snub-nosed monkey  agtagaatacaacatatgaggaaagctccatgtcattggtctggacaaggactttttggatatga-tccc
                     Marmoset  actggaataaaacataggaggaaagctccatgacattggtctggacaatgactttttggatatgattccc
              Squirrel monkey  tctagaataaaacataggaggaaagctccatgacattgctctggacaatgactttttggatatga-tccc
                     Bushbaby  actggaagaaatcataggatgaaagatcta---cattactctaggcaggggcattttggatgtga-actc
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  caaagcacaggtgaaaaaactgaaaaaa-aaaa-----------------aaaaaaaa---aaaaa----
                        Chimp  aaaagcacaagtgaaaaaactgaaaaaa-caaa-----------------acaaaaca---aaaca----
                       Bonobo  aaaagcacaggtgaaaaaactgaaaaaa-caaa-----------------acaaaaca---aaaca----
                      Gorilla  caaagcacaggtgaaaaaacggaaaaaa--aaa-----------------gcaaaaaa---aaaca----
                    Orangutan  caaagcacaggtgaaaaaactgaaaaaa-acaa-----------------acaaaacaaacaaaca----
                       Gibbon  caaagcacaggtgaaagaactgaaagaa---------------------------------aaaaa----
                       Rhesus  caaagcgcaggtgaaaaaactgaaaaaaacaaa-----------------acaaaaca---aaaca----
          Crab-eating macaque  caaagcgcaggtgaaaaaactgaaaaaaacaaa-----------------acaaaaca---aaaca----
                       Baboon  caaagcgcaggtgaaaaaactgaagaaaacaaa-----------------acaaaaca---aaaca----
                 Green monkey  caaagcacaggtgaaaaaactgaaaaaaacaaa-----------------acaaaacaaacaaaca----
             Proboscis monkey  caaagcacaggtgaaaaaacggaa--------------------------aaaaaaaa---agaaa----
     Golden snub-nosed monkey  caaagcacaggtgaaaaaactgaaaaaaaaaaa-------------aaagaaaaaaaa---aaaaa----
                     Marmoset  caaagcacaggagacaaaactgaaaaaaaaaaatagacaaatggagatataccaaact---gaaaa----
              Squirrel monkey  caaagcacaggagacaaaactgaaaaaaaaaaatagacaaatgggaatataccaaact---gaaaaaaaa
                     Bushbaby  caaagcaaaggcaacaa--------------------------------------------aatca----
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  ----------------------------aaaaaaa-a-gccagacagatgggaatacaccaaactgagaa
                        Chimp  ----------------------------aaa---------cagacagatgggaatacaccaaactgagaa
                       Bonobo  ----------------------------aaacaaa-a---cagacagatgggaatacaccaaactgagaa
                      Gorilla  ----------------------------aacaaaa-aaaacagacggatgggaatacaccaaactgagaa
                    Orangutan  ----------------------------aataaaa-a-aacagacatatgggaatacaccaaactgaaaa
                       Gibbon  ----------------------------aaaaaaa-a---cagacagatgagaatacaccaaactgaaaa
                       Rhesus  ----------------------------aaaaaaaga---cagacagatgggaatacaccaagctgaaaa
          Crab-eating macaque  ----------------------------aaaaa---a---cagacagatgggaatacaccaagctgaaaa
                       Baboon  ----------------------------aaaaaa--a---cagacagatgggaatacaccaagctgaaaa
                 Green monkey  ----------------------------aaaaaa--a---cagacagatgggaatacaccaagctgaaaa
             Proboscis monkey  ----------------------------aaaaaa--a---cagacagatgggaatacaccaaactgaaaa
     Golden snub-nosed monkey  ----------------------------aaaaaa--a---cagacagatgggaacacaccaaactgaaaa
                     Marmoset  ----------------------------aaaaa---a---tagacaaatt-gtatgcatcaaactgaaaa
              Squirrel monkey  aatagacaaatgggaatataccaaactgaaaaa---a---tagacaaatg-gtatacaccaaactgaaaa
                     Bushbaby  ----------------------------aaa-----a---tagaaaaatgggattacagcaaattaaaaa
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  cattctgcatagcaaaggaaaacaaccaacaaaatgaagagacaacatatcaaataacagaaaatatttg
                        Chimp  cattctgcatagcaaaggaaaacaaccaacaaaatgaagagacaacatatcaaataacagaaaatatttg
                       Bonobo  cattctgcatagcaaaggaaaacaaccaacaaagtgaagagacaacatatcaaataacagaaaatatttg
                      Gorilla  cattctgcatagaaaaggaaaacaaccaacaaaatgaagagacaacatatcaaataacagaaaatatttg
                    Orangutan  cattctgcatagcaaaggaaaacaaccaacaaaatgaagagccaacatttcaaataacagaaaatatttg
                       Gibbon  cattctgcatagcaatggaaaacaaccaacaaaatgaagagacaacatatcaaataacagaaaatatttg
                       Rhesus  cattctgcatagcaaaggaaaa----cgacaaaacgaagagacaacctattgaataacagaaaatatttg
          Crab-eating macaque  cattctgcatagcaaaggaaaa----cgacaaaacgaagagacaacctattgaataacagaaaatatttg
                       Baboon  cattttgcatagcaaaggaaaa----cgacaaaacgaagagacaacctattgaataacagaaaatatttg
                 Green monkey  cattctgcatagcaaaggaaaa----cgacaaaacgaagagacaacctattgaataacagaaaatatttg
             Proboscis monkey  cattctgcatagcaaagaaaaa----caacaaactgaagagacaacctattgaataacagaaaatatttg
     Golden snub-nosed monkey  cattctgcatagcaaagaaaaa----caacaaaatgaagagacaacctattgaataacagaaaatatttg
                     Marmoset  tgttctacatagcaaaggaaaa----caacaaaataaagagacaacttatggaataacagaaaatatttg
              Squirrel monkey  tgttctacgtagcaaaggaaaacaatcaacaaaacgaaaagacagcttatggaataacagaaaatatttg
                     Bushbaby  gatac-gcacagcaaag-aggacaaccaacagagtgaagagacaacgcacagaatgggaggaaatatctg
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  caaaccatacatcctgataagaagttaatatcaaaaatacataagaaactcaaacaacttgacagtaaga
                        Chimp  caaaccgtacatcctgacaagaagttaatatcaaaaatacgtaagaaactctaacaacttgatagtaaga
                       Bonobo  caaaccatacatcctgacaagaagttaatatcaaaaatacgtaagaaactctaacaacttgatagtaaga
                      Gorilla  caaaccatacatcctgataagaagttaatatcaaaaatacgtaagaaactcaaacaacttgatagtaaga
                    Orangutan  caaaccatacatcctgataagaagttaatatcaaaaatacataagaaactcaaaaaactcgatagtaaga
                       Gibbon  caaactatacatcctgataagaagttaatatcaaaaatacataagaaactcaaacaactcgatagtaaga
                       Rhesus  caaaccgtacatcctgataagaagttaatatcaaaaatatgtaagaaactcaaacaactcaatagtaaga
          Crab-eating macaque  caaaccgtacatcctgataagaagttaatatcaaaaatatgtaagaaactcaaacaactcaatagtaaga
                       Baboon  caaaccgtacatcctgataagaagttaatatcaaaaatatgtaagaaactcaaacaactcaatagtaaga
                 Green monkey  caaaccatacatcctaataagaagttaatattaaaaatatgtaagaaactcaaacaactcaatagtaaga
             Proboscis monkey  caaaccgtacatcctgataagaagttaatatcaaaaatatgtaagaaactcaaacaactcaatagtaaga
     Golden snub-nosed monkey  caaaccgtacatcctgataagaagttaatatcaaaaatatgtaagaaactcaaacaactcaatagtaaga
                     Marmoset  caagccatacatcttgataagaagttaatatcaaaaatacataagaaactcaaacaactcagtagtaaga
              Squirrel monkey  caagccatacatcttgataagaagttagtatcaaaaatacataagaaactcaaacaactcagtagtaaga
                     Bushbaby  cacagcatgtatgc-aataaggaattaatttaaaaaatatataa-aaactcaaacaacccaataatagga
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  aaacaagagacatgacttaaaaatgagcaaagatcctaaatagacatttctcaaaaatagagtgactata
                        Chimp  aaacaagagacatgacttaaaaatgagcaaagatcctaaatagacatttctcaaaaatagggtgactata
                       Bonobo  aaacaagagacgtgacttaaaaatgagcaaagatcctaaatagacatttctcaaaaatagggtgactata
                      Gorilla  aaacaagagacatgacttaaaaatgagcaaagatcctaaatagacatttctcaaaaatagggtgacta-a
                    Orangutan  aaacaagagacatgacttaaaaattagcaaagatcctaaatagacattcctcaaaaatagggtgactata
                       Gibbon  aaacaatagacatgacttaaaaatgagcaaagatcctaaatagacatttctcaaaaatag-gtgactata
                       Rhesus  aaaccagagacatgacttaaaaatgagcaaagatcctgaatagacatttctcaaaaatagggtgactata
          Crab-eating macaque  aaaccagagacatgacttaaaaatgagcaaagatcctgaatagacatttctcaaaaatagggtgactata
                       Baboon  aaaccagagacatgacttaaaaatgagcaaagatcctgaatagacatttctcaaaaatagggtgactata
                 Green monkey  aaaccagagacatgacttaaaaatgagcaaagatcctgaatagacgtttctcaaaaatagggtgactata
             Proboscis monkey  aaaccagagacacgacttaaaaatgagcaaagatcctgaatagacatttctcaaaaatagggtgactata
     Golden snub-nosed monkey  aaaccagagacatgacttaaaaatgagcaaagatcctgaatagacatttctcaaaaatagggtgactata
                     Marmoset  aaacaagaaacacaatttaaaaataagcaaagatcccaaatagacatttcttaagaataaggtgac-ata
              Squirrel monkey  aaacaagagacacaatttaaaaatgagcaaagatcccaaatagacatttcttaagaatagggtgac-ata
                     Bushbaby  aaataagaaccacaacttaaaaatgggcaaagaaccagaatagacatttctcaaaagtagggtgacttta
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  tttt----------------------------------------------------------ac
                        Chimp  tttt----------------------------------------------------------ac
                       Bonobo  tttt----------------------------------------------------------ac
                      Gorilla  ttct----------------------------------------------------------ac
                    Orangutan  tttt----------------------------------------------------------ac
                       Gibbon  tttt----------------------------------------------------------at
                       Rhesus  ttta----------------------------------------------------------gc
          Crab-eating macaque  ttta----------------------------------------------------------gc
                       Baboon  ttta----------------------------------------------------------gc
                 Green monkey  tttaacaacttattatatatttcannnnnnnnnntttctcaaaaatagggtgactatatttgac
             Proboscis monkey  ttta----------------------------------------------------------ac
     Golden snub-nosed monkey  ttta----------------------------------------------------------ac
                     Marmoset  ttta----------------------------------------------------------ac
              Squirrel monkey  ttta----------------------------------------------------------ac
                     Bushbaby  gtta----------------------------------------------------------ac
                        Mouse  ================================================================
                   Tree shrew  ================================================================
                          Dog  ================================================================
                      Tarsier  ================================================================
                  Mouse lemur  ================================================================

Inserts between block 4 and 5 in window
B D                   Rhesus 33bp
B D                 Bushbaby 3bp

Alignment block 5 of 36 in window, 77419219 - 77419249, 31 bps 
B D                     Human  aacttattgtatatttcaaaataggtaaaag
B D                     Chimp  aacttattgtatatttcaaaataggtaaaag
B D                    Bonobo  aacttattgtatatttcaaaataggtaaaag
B D                   Gorilla  aacttattgtatatttcaaaataggtaaaag
B D                 Orangutan  aatttattgtatatttcaaaatagctaaaag
B D                    Gibbon  aacttactgtatatttcaaaatagctaaaag
B D       Crab-eating macaque  aacttattatatatttcaaaatagctaaaag
B D                    Baboon  aacttattatatatttcaaaatagctaaaag
B D              Green monkey  aacttattatatatttcaaaatagctaaaag
B D          Proboscis monkey  aacttattatata-ttcaaaatagctaaaag
B D  Golden snub-nosed monkey  aacttattatata-ttcaaaatagctaaaag
B D                  Marmoset  aacttac----tttttcaaaatagagaaaat
B D           Squirrel monkey  aacttactgtatttttcaaaatagtgaaaag
B D                  Bushbaby  aatttatcatacacctccaagtaactaaaag
B D                     Mouse  ===============================
B D                Tree shrew  ===============================
B D                       Dog  ===============================
B D                   Tarsier  ===============================
B D                    Rhesus  ===============================
B D               Mouse lemur  ===============================

Alignment block 6 of 36 in window, 77419250 - 77419478, 229 bps 
B D                     Human  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgaactgatggatacactaattaccct
B D                     Chimp  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgaactgatggatacactaattaccct
B D                    Bonobo  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgaactgatggatacactaattaccct
B D                   Gorilla  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgaactgatggatacactaattaccct
B D                 Orangutan  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgaattgatggatacactaattaccct
B D                    Gibbon  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgaactgatggatacactaattaccct
B D                    Rhesus  ---agatttgtaatgttcctaatgcaaagaaatgataaatgtttgagctgatggatacactaattacccc
B D       Crab-eating macaque  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgagctgatggatacactaattacccc
B D                    Baboon  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgagctgatggatacactaattacccc
B D              Green monkey  ---agatttgaaatattcacaacacaaagaaatgataaatgtttgagctgatggatacactaattaccct
B D          Proboscis monkey  ---agatttgaaatattcacaacac-aaaaaatgataaatgtttgagctgatggatacactaattaccct
B D  Golden snub-nosed monkey  ---agatttgaaatattcacaacacaaaaaaatgataaatgtttgagctgatggatacactaattaccct
B D                  Marmoset  ---aaatttgaaatattcacaacacaaagaaatattaaatgtttaagctgatgtacacaccaattaccct
B D           Squirrel monkey  ---agatttgaaatattcacaacacaaagaaatgttaaatgtttaagctgatggacacactaattaccct
B D                  Bushbaby  aggggatttgaaatatttgcaacacaaagatatgataaaaatttgcactgatgtatatactaattaccct
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D                   Tarsier  ======================================================================
B D               Mouse lemur  ======================================================================

                        Human  gatttgatca--------ttatacttggtatgcatgcatcaaaatatc--atgttccccataaatatgta
                        Chimp  gatttgatca--------ttatacttggtatgcatgcatcaaaatatcgtatgttccccataaatatgta
                       Bonobo  gatttgatca--------ttatacttggtatgcatgcatcaaaatatcatatgttccccataaatatgta
                      Gorilla  gatttgatca--------ttatacttggtatgcatgcatcaaaatatcatatgttccccataaatatgta
                    Orangutan  gatttgatcg--------ttatacttggtatgcatgcatcaaaatatc--atgtttcccataaatatgta
                       Gibbon  gatttgatca--------ttatacttggtatgcatgcatcaaaatatcatatgttccccataaatttgta
                       Rhesus  gatttgatca--------ttttacttggtatgcatgtattaaaatatcttatgttccccataaatattta
          Crab-eating macaque  gatttgatca--------ttttacttggtatgcatgtattaaaatatcttatgttccccataaatattta
                       Baboon  gatttgatca--------ttttacttggtatgcatgtattaaaatatcttatgttccccataaatattta
                 Green monkey  gatttgatca--------ttttacttggtatgcgtgtattaaaatatcatatgttccccataaatattta
             Proboscis monkey  gaattgatca--------ttatacttggtatgcatgtatcaaaatatcatatgttccccataaatattta
     Golden snub-nosed monkey  gaattgatca--------ttatacttggtatgcatgtatcaaaatatcatatgttccccataaatattta
                     Marmoset  gattttatca--------ttatacttagtattcatgtatcaaaat-----atgttccccataaatatgta
              Squirrel monkey  gattttatcagggtaaacttatact---tatgcatgtatcaaaat-----atgtt-cccataaatatgta
                     Bushbaby  gattttatca--------ttataattggtatgcatgaatcaaaatatcacttgtactccataaatatgga
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  caatttttatgtatcaat--aaaaacatacatgaacaggaaaaaattgtataggtg---taactatgaac
                        Chimp  caatttttatgtatcaat--aaaaacatacatgaacaggaaaaaattgtatagctg---taactatgaac
                       Bonobo  caacttttatgtatcgat--aaaaacatacatgaacaggaaaaaattgtatagctg---taactatgaac
                      Gorilla  caatttttatgtatcaat--aaaaacatacatgaacaggaaaaaattgtatagctg---taactatgaac
                    Orangutan  caatttttatgtatcaat--aaaaacatacatgaacaggaaaaaattgtatagcta---taactatgaac
                       Gibbon  caatttttatgtatcaat--aaaaacatacatgaacaggaaaaaattgtatagcta---taactgtgaac
                       Rhesus  caatttttatgtatcaat--aaaaacatacatgaacagg-aaaaattgtatagcta---taactatg-ac
          Crab-eating macaque  caatttttatgtatcaat--aaaaacatacatgaacagg-aaaaattgtatagcta---taactatg-ac
                       Baboon  caattttta-gtatcaat--aaaaacatacatgaacagg-aaaaattgtatagcta---taactatg-ac
                 Green monkey  caatttttatgtatcaat--aaaaacatacatgaacagg-aaaaattgtatagcta---taactatg-ac
             Proboscis monkey  caatttttatatatcaat--aaaaacatacatgaacagg-aaaaattgtatggctgtcctaactatg-ac
     Golden snub-nosed monkey  caatttttatatatcaat--aaaaacatacatgaacagg-aaaaattgtatggcta---taactatg-ac
                     Marmoset  taattttt-tgtatcaat--aaaaacatatatgaacaga-aaaaattgtatagcta---taaagatgaac
              Squirrel monkey  taacttttatgtatcaat--aaaaatatatatgaacaga-aaaaattgtatagcta---taaatatgaac
                     Bushbaby  taattattatgcaccaattaaaaaatagagattaaca---aaaaagtgcatagtta---taaatacaaac
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Tarsier  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  accactagtcattctgacttcagagaccatgctcttg
                        Chimp  accactagtcattctgacttcagagaccatgctcttg
                       Bonobo  accactagtcattctgacttcagagaccatgctcttg
                      Gorilla  accactagtcattctgacttcagagaccatgctcttg
                    Orangutan  accactagtcattctgacttcagagaccatgctcttg
                       Gibbon  actactagtcattctgacttcagagaccatgctcttg
                       Rhesus  accactagtcattctgactttagagaccatgctcttg
          Crab-eating macaque  accactagtcattctgactttagagaccatgctcttg
                       Baboon  accactagtcattctgactttagagaccatgctcttg
                 Green monkey  accactagtcattctgactttagagaccatgctcttg
             Proboscis monkey  accactagtcattctgacttcagagaccatgctcttg
     Golden snub-nosed monkey  accactagtcattctgacttcagagaccatgctcttg
                     Marmoset  accactagtcattcttattccacagaccctgctcttg
              Squirrel monkey  accactagtcattcttactccacagaccctgctctta
                     Bushbaby  accactaatcatt-tagcttcagagactatgctcttg
                        Mouse  =====================================
                   Tree shrew  =====================================
                          Dog  =====================================
                      Tarsier  =====================================
                  Mouse lemur  =====================================

Inserts between block 6 and 7 in window
B D             Green monkey 215bp

Alignment block 7 of 36 in window, 77419479 - 77419509, 31 bps 
B D                     Human  accactgtaatttttgctaacttttactcaa
B D                     Chimp  accactgtaatttttgctaccttttactcaa
B D                    Bonobo  accactgtaatttttgctaccttttactcaa
B D                   Gorilla  accactgtaatttttgctaccttttactcaa
B D                 Orangutan  accactgtaatttttgctaccttttactcaa
B D                    Gibbon  actactgtaatttttgctaccttttactcaa
B D                    Rhesus  accactgtaatttttgctaccttttactcaa
B D       Crab-eating macaque  accactgtaatttttgctaccttttactcaa
B D                    Baboon  accactgtaatttttgctaccttttactcaa
B D              Green monkey  accactgtaatttttgctaacttttactcaa
B D          Proboscis monkey  accacggtaaatcttgctaccttttactcaa
B D  Golden snub-nosed monkey  accactgtaaatcttgctaccttttactcaa
B D                  Marmoset  accactgtaatttttactgccttttactcaa
B D           Squirrel monkey  accactgtaatttttactgccttttactcaa
B D                  Bushbaby  accactgtaatttttgctcccttttacccaa
B D                     Mouse  ===============================
B D                Tree shrew  ===============================
B D                       Dog  ===============================
B D                   Tarsier  ===============================
B D               Mouse lemur  ===============================

Inserts between block 7 and 8 in window
B D                   Rhesus 102bp
B D                 Bushbaby 6bp

Alignment block 8 of 36 in window, 77419510 - 77419540, 31 bps 
B D                     Human  aaaagaaccattcatttcataaaataaaaat
B D                     Chimp  aaaagaaccattcatttcataaaataaaaat
B D                    Bonobo  aaaagaaccattcatttcataaaataaaaat
B D                   Gorilla  aaaagaaccattcatttcataaaataaaaat
B D                 Orangutan  aaaagaaccattcatttcataaaataaaaat
B D                    Gibbon  aaaagaaccattcatttcataaaataaaaat
B D                    Rhesus  aaaagaaacattcatttcataaaataaaaat
B D       Crab-eating macaque  aaaagaaacattcatttcataaaataaaaat
B D                    Baboon  aaaagaaacattcatttcataaagtaaaaat
B D              Green monkey  aaaagaaacattcatttcataaaataaaaat
B D          Proboscis monkey  aaaagaaacattcatttcataaaataaaaat
B D  Golden snub-nosed monkey  aaaagaaacattcatttcataaaataaaaat
B D                  Marmoset  aaaataaacattcatttcaaaaaacaaaaat
B D           Squirrel monkey  aaaataaacatttatttcaaaaattaaa---
B D                  Bushbaby  aaaaaaaaagttaatttcaaaa---------
B D                     Mouse  ===============================
B D                Tree shrew  ===============================
B D                       Dog  ===============================
B D                   Tarsier  ===============================
B D               Mouse lemur  ===============================

Alignment block 9 of 36 in window, 77419541 - 77419725, 185 bps 
B D                     Human  aaaaaagacatataaatggccaacaggtgtatt-ttaaaatgctcaatatcactaatcatcagggaaatg
B D                     Chimp  aaaaaagacatacaaatggccaacaggtgtatt-ttaaaatgctcaatatcactaatcatcagggaaatg
B D                    Bonobo  aaaaacgacatataaatggccaacaggtgtatt-ttaaaatgctcaatatcactaatcatcagggaaatg
B D                   Gorilla  aaaaaagacatataaatggccaacaggtgtatt-ttaaaatgctcaatatcactaatcatcagggaaatg
B D                 Orangutan  aaaaaagacatataaatagccaacaggtgtatt-ttaaaatgctcaatatcactaatcattagggaaatg
B D                    Gibbon  aaaaaagacatataaatggccaacaggtgtatt-ttaaaatgctcaatatcactaatcatcagggaaatg
B D                    Rhesus  aaaaaagacacataaatggccaacagatgtatt-ttaaaatgcccaaaatcactaatcatcagggaaatg
B D       Crab-eating macaque  aaaaaagacacataaatggccaacagatgtatt-ttaaaatgcccaaaatcactaatcatcagggaaatg
B D                    Baboon  taaaaagacacataaatggccaacaggtgtatt-tttaaatgcccaaaatcactaatcatcagggaaatg
B D              Green monkey  aaaaaagacacataaatggccaacaggtgtatt-ttaaaatgcccaaaatcactaatcatcagggaaatg
B D          Proboscis monkey  aaaaaagacatataaatggccaacaggtgtatt-ttaaaatgcccaaaatcactaatcatcagggaaatg
B D  Golden snub-nosed monkey  aaaaaagacatataaatggccaacaggtgtatt-ttaaaatgcccaaaatcactaatcatcagggaaatg
B D                  Marmoset  aaaaaagacatacaaatggccaagaagtatatt-ttaaaatgatcaatatcactaatcatcagataaatg
B D           Squirrel monkey  aaaaaagacatacaaatggccaacaagtatatt-ttaaaataatcaatatcactaatcatcagataaatg
B D                   Tarsier  aaaaaagacgtacaaatggtcaataggtaaaca-aaagagttttcagcatcattaatcatcagagacatg
B D                  Bushbaby  aaggaagctatacaagtagacaataggctcatgaaaaaaattctcaacaccactaatcatcagggaaatg
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D               Mouse lemur  ======================================================================

                        Human  taaattaaaaccacaatgagatgtcatctcatacctgttagaaca-cctattatcaaaaagacaaaga--
                        Chimp  taaattaaaaccacaatgagatgtcatctcatacctgttagaaca-cctattatcaaaaagaca--ga--
                       Bonobo  taaattaaaaccgcaatgagatgtcatctcatacctgttagaaca-cctattatcaaaaagaca--ga--
                      Gorilla  taaattaaaaccgcaatgagatgtcatctcatacctgttagaaca-cctattatcaaaaagaca--ga--
                    Orangutan  taaattaaaaacgcaatgagatgtcatctcatacctgttagaaca-gctattatcaaaaagacaaaga--
                       Gibbon  taaattaaaaccataaggagatgtcatctcatacctgttagaaca-gctattatcaaaaagacaaaga--
                       Rhesus  taaatttaaaccacaatgagatgtcatcttatacctcttagaaca-gctattatcaaaaagacaaaga--
          Crab-eating macaque  taaattaaaaccacaatgagatgtcatcttatacctcttagaaca-gctattatcaaaaagacaaaga--
                       Baboon  taaattaaaaccacaatgagatgtcatcttatacctcttagaaca-gctattatcaaaaagacaaaga--
                 Green monkey  taaattaaaaccacaatgagatgtcatcttatacctcttagaaca-gctattatcaaaaagacaaaga--
             Proboscis monkey  taaattaaaaccacagtgagatgtcatctcatacctcttagaaca-gcttttatcaaaaagacaaaga--
     Golden snub-nosed monkey  taaattaaaaccacagtgagatgtcatctcatacctcttagaaca-gcttttataaaaaagacaaaga--
                     Marmoset  taaattaaaaccatag-aaaatgtcatctaataccagcgagaaca-gctattatcaaaaagacaagga--
              Squirrel monkey  taaattaaaaccatagaaaaatgtcatctaataccagttagaaca-gctattatcaaaaagacaaaga--
                      Tarsier  taaattaaaatcacagtgagctatcatcttaaacctgttagaata-gctattatcaaaaattcaaaaa--
                     Bushbaby  tgaattaaaaacacagtgagatatcacttcacacctattagaacaggctattaccaaaaaaaaaaaaaaa
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  ======================================================================

                        Human  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
                        Chimp  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
                       Bonobo  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
                      Gorilla  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
                    Orangutan  -----------------taataggtgttggtgagaatgtattgaa-a-gggaatcctgtcatactgtt
                       Gibbon  -----------------taataggtgttggtgagaatgtattgaa-a-gggaaccctgtcacactgtt
                       Rhesus  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
          Crab-eating macaque  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
                       Baboon  -----------------taataggtattggtgagaacgtattgaa-a-gggaaccctgtcatactgtt
                 Green monkey  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgct
             Proboscis monkey  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
     Golden snub-nosed monkey  -----------------taataggtattggtgagaatgtattgaa-a-gggaaccctgtcatactgtt
                     Marmoset  -----------------taataggtgttggtaagaatgtattgaa-atgggaaccctgtcatactctt
              Squirrel monkey  -----------------taataggcattggtgagaatgtattgaa-aagggaaccctgtcatactctt
                      Tarsier  -----------------taacaggtattggctaggatatagagaa-aggggaactctagcacaccatc
                     Bushbaby  aaaaaagaaaagaaatgtaacaggtgttaccaaggaggtagagaaca-gggagccatggtagcctgtt
                        Mouse  ====================================================================
                   Tree shrew  ====================================================================
                          Dog  ====================================================================
                  Mouse lemur  ====================================================================

Alignment block 10 of 36 in window, 77419726 - 77420360, 635 bps 
B D                     Human  ggtggaaatgtaaattaagacagtcattatggaaaccagtataaaagtccctcaaaaaattaaaactaga
B D                     Chimp  ggtggaaatgtaaattaagacagtcattatggaaaccagtataaaagtccctcaaaaaattaaaactaga
B D                    Bonobo  ggtggaaatgtaaattaagacagtcattatggaaaccagtataaaagtccctcaaaaaattaaaactaga
B D                   Gorilla  ggtggaaatgtaaattaagacagtcattatggaaaccagtataaaagtccctcaaaaaattaaaactaga
B D                 Orangutan  ggtggaaatgtaaattaagacagtcattatggaaaccagtataaaagtccctcaaaaaattcaaactaga
B D                    Gibbon  ggtggaaatgtaaattaagatggtcattatggaaaccagtataaaagtccctcaaaaaattaaaactaga
B D                    Rhesus  ggtagaaatgtaaattaagatggtcattatggaaatcagtataaaagtctctgaaaaaattaaaactaga
B D       Crab-eating macaque  ggtagaaatgtaaattaagatggtcattatggaaatcagtataaaagtctctgaaaaaattaaaactaga
B D                    Baboon  ggtagaaatgtaaattaagacggtcattatggaaatcagtataaaagtctctgaaaaaattaaaactaga
B D              Green monkey  ggtggaaatgtaaattaagatggtcattatggaaatcagtataaaagtctctgaaaaaattaaaactaga
B D          Proboscis monkey  ggtagaaatgtaaattaagacagtca-tatggaaatcagtataaaagtccctgaaaaaattaaaactaga
B D  Golden snub-nosed monkey  ggtagaaatgtaaattaagacggtcattatggaaatcagtataaaagtccctgaaaaaattaaaactaga
B D                  Marmoset  ggtggaaatgtaaattaagacagtcatcatggaaagcagtacaaaaatccctcaaaaaattaaaactaga
B D           Squirrel monkey  ggtgaaaatgtaaattaagacagtcatcatggaaaccagtataaaagtctctcaaaaaattaaaactaga
B D                   Tarsier  ggtgggaatataaattaagacagccagtatggaaaccagcttaaaggtccctcaaaaatttaaaa-taat
B D               Mouse lemur  ggtaggaatgtacattaggatagccattatggaaattactataaaggttcctcaaaaaactaaaaataga
B D                  Bushbaby  ggtgggcg-gtacattagcacagccatcactgaaattagcataatgtttcgt-aaaaaattaaaaataga
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================

                        Human  actacaatatgatccagcaatctcagtgctggat------atggatctaaaggaaatgcaatcagtataa
                        Chimp  actacaatatgatccagcaatctcagtgctggat------atggatctaaaggaaatgcaatcagtataa
                       Bonobo  actacaatatgatccagcaatctcagtgctggat------atggatctaaaggaaatgcaatcagtataa
                      Gorilla  actacaatatgatccagcaatctcagtgctggat------atggatctaaaggaaatgcaatcagtataa
                    Orangutan  actacaatacgatccagcaatctcagtgctggat------gtggatctaaaggaaatgaaatcagtataa
                       Gibbon  actacagtatgatccagcaatctcagtgctggat------atggatctaaaggaaattaaatcagtataa
                       Rhesus  actacaatatgatccagcaatctcagtgctggat------atgtatctaaaggaaatgaaatcagtataa
          Crab-eating macaque  actacaatatgatccagcaatctcagtgctggat------atgtatctaaaggaaatgaaatcagtataa
                       Baboon  actacaatatgatccagcaatctcagtgctggat------atgtatctaaaggaaatgaaatcagtataa
                 Green monkey  actacaatatgatccagcaatctcagtgctggat------atgtatctaaagcaaatgaaatcagtataa
             Proboscis monkey  actacaatatgatccagcaatctcaatgctggat------atgtatct-aaggaaatgaaatcagtataa
     Golden snub-nosed monkey  actacgatatgatccagcaatctcaatgctggat------atgtatct-aaggaaatgaaatcagtataa
                     Marmoset  actacaatatgatccagcaatctcagtgctggac------atttatctaaaggaaatgaaatcagtacaa
              Squirrel monkey  actacaatatgatccagcaatctcagtgctggat------atgtatctaaaggaaatgaaatcagtagaa
                      Tarsier  actaccttaggattcagaaatctcgctgctggat------atgtatccaaaagaaattaaatcaaagtgt
                  Mouse lemur  actaccatatgagccagcaatctcactgttgagt------atatatccaaataaaatgaaataaatatgt
                     Bushbaby  agtaccatataaaccagcaatctcaccattgagtatacacatatatctaaagacaatggagccagaatgt
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  tgaagagatacgtatactcttatgttcatttgcagcattattgataataaccaagatatgtaatcaatct
                        Chimp  tgaagagataggtatactcttatgttcatttgcagcattattcataataaccaagatatgtaatcaatct
                       Bonobo  tgaagagataggtatactcttatgttcatttgcagcattattcataataaccaagatatgtaatcaatct
                      Gorilla  tgaagagatacgtatactcttatgttcatttgcagcattattcataataaccaagatacgtaatcaatct
                    Orangutan  tgaagagatacctatactcttatgttcatttgcagcattattcataataagcaagatatgtaatcaatct
                       Gibbon  tgaagagatacctatactcttatgttcatttgcagcattattcataataactaagatatgtaatcaatct
                       Rhesus  tgaagagatacctgtactcttatgttcatttgcagcattattcataataaccaagatatgtaatcagtct
          Crab-eating macaque  tgaagagatacctgtactcttatgttcaattgcagcattattcgtaataaccaagatatgtaatcagtct
                       Baboon  tgaagagatacctgtactcttatgttcatttgcagcattattcataataaccaagatatgtaatcagtct
                 Green monkey  tgaagagatacctgtactcttatgttcatttgcaacattattcataataaccaagatacgtaatcagtct
             Proboscis monkey  tgaagagatacccgtactcttatgttcatttgcagcattattcataataaccaagatatgtaatcagtct
     Golden snub-nosed monkey  tgaagagatacctgtactcttatgttcatttgcagcattattcataataaccaagatatgtaatcagtct
                     Marmoset  tgaagaagtatctgtactctcatgttca-ttgtagcattattcgtaataaccaacatatggaatcagcct
              Squirrel monkey  tgaagaagtatctgtactcttacattca-ttgta-cattattc---ataatcaacatacggaatcagcct
                      Tarsier  tgaagagaaattcgtac-cccacttttactt-cagtattatacataataaccaagatacggaatcagcct
                  Mouse lemur  tgaagtgatatctgtactcctatattca-ttgcagcattactcataataaccaaaacatggtatcaattt
                     Bushbaby  tgaagagacatccgtcctgctgtgttca-ctgcagcactgttcacaatgaccaagatggggaatcgacct
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  --g------t--ctatcagtgaatca---------atgttgctatgcttaaaaccttggtgtcctttcaa
                        Chimp  --g------tgtctatcagtgaatca---------atgttgctatgcttaaaaccttggtgtcctttcaa
                       Bonobo  --g------tgtctatcagtgaatca---------atgttgctatgcttaaaaccttggtgtcctttcaa
                      Gorilla  --g------tgtctatcagtgaatca---------atgttgatatgcttaaaaccttggtgtcctttcaa
                    Orangutan  --g------cgtctatcagtgaatca---------atgttgctatggttaaaaccttggtgtcctttcaa
                       Gibbon  --g------cgtctatcagtgaatca---------atgttgctatggctaaaaccttggtgtcctttcaa
                       Rhesus  --g------catctatcagtgaatca---------atgtcgctatggttgaaaccttggtgtccttacaa
          Crab-eating macaque  --g------catctatcagtgaatca---------atgtcgctatggttgaaaccttggtgtcctttcaa
                       Baboon  --g------catctatcagtgaatca---------atgtcgctatggttgaaaccttggtgccctttcaa
                 Green monkey  --g------catctatcagtgaatca---------atgtcgctatggttgaaaccttggtgtcctttcaa
             Proboscis monkey  --g------catctatcagtgaatgaatcaatgttatgttgctatggttgaaaccttggcatcctttcaa
     Golden snub-nosed monkey  --g------catctatcagtgaatgaatcaatgttatgttgctgtggttgaaaccttggcgtcctttcaa
                     Marmoset  --g------catctatcagtgaacca---------gtggtgctatggttgaagtgttggtgttctttcaa
              Squirrel monkey  --g------catctatcagtgaacca---------gtggtgccatggttgaagcattggtgttctttcaa
                      Tarsier  cag------tgacaatcaattaataa---------atggtgctacgatctgcctgttggcatccctccaa
                  Mouse lemur  --aagtgtccatcaatcaatgggtaa---------atggtgctaaggtttgaatgttggtgtcatttcaa
                     Bushbaby  --gagtgcccagcagtcaatggatga---------atggtgct--------aatgtcggtgtcccttcac
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  acttgagttgtacctaggc-----------------------------------------atccctgtga
                        Chimp  acttgagttgtacctaggc-----------------------------------------atccctgtga
                       Bonobo  acttgagttgtacctaggc-----------------------------------------atccctgtga
                      Gorilla  acttgagttgtacctaggc-----------------------------------------atccctgtga
                    Orangutan  acttgagttgtacccaggc-----------------------------------------atccctgtga
                       Gibbon  acttgagttgtacccaggc-----------------------------------------atcctggtga
                       Rhesus  actttagttgtacctaggc-----------------------------------------atccctgtga
          Crab-eating macaque  actttagttgtacctaggc-----------------------------------------atccctgtga
                       Baboon  actttagttgtacctaggc-----------------------------------------atccctgtga
                 Green monkey  actttagttgtacccaggc-----------------------------------------atccctgtga
             Proboscis monkey  actttagttgtacccaggc-----------------------------------------atccctgtga
     Golden snub-nosed monkey  actttagttgtacccaggc-----------------------------------------atccctgtga
                     Marmoset  acttcagttgtacttagga-----------------------------------------attcccgtga
              Squirrel monkey  actttagttgtatttagga-----------------------------------------attcctgtga
                      Tarsier  actttagttgtacccagtcaagcaacttcagc--------------aaggtggaactccaatccctgaga
                  Mouse lemur  actttagtttcacccaggcatgcaactccagcctgggagaacaacaagcatggaactccattccctgaga
                     Bushbaby  acttcagttttacccaggcatgcaactccagcctgggcgggcaacaagcgtgaaagtctgacccctgaga
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  gctggggctttggtagcaaccagcaaagctttgaagatatggctgctggcctgtgcttctccctcttttg
                        Chimp  gctggggctttggtagcaaccagcaaagctttgaagatatggctgctggcctgtgcctctccctcttttg
                       Bonobo  gctggggctttggtagcaaccagcaaagctttgaagatatggctgctggcctgtgcctctccctcttttg
                      Gorilla  gctggggctttggtagcaaccagcaaagctttgaagatatggctgctggcctgtgcctctccctcttttg
                    Orangutan  gctggggttttggtagcaaccagcaaagctttgaagatatggctgctggcctatgcctctccctcttttg
                       Gibbon  gctggggcttgggtagcaaccagcaaagctttgaagatatggctgccggcctgtgcctctccctcttttg
                       Rhesus  gctgaggcttgggtagcaaccagcagagttttgaagatatggctgctggcctgtgcctctccctctattg
          Crab-eating macaque  gctgaggcttgggtagcaaccagcagagttttgaagatatggctgctggcctgtgcctctccctctattg
                       Baboon  gctgaggcttgggtagcaaccaacaaagttttgaagatatggctgctggcctgtgcctctccctctattg
                 Green monkey  gctgaggcttgggtagcaaccagcaaagttttgaagatatggctgctggcctgtgcctctccctctatta
             Proboscis monkey  actgaggcttgggtagtaaccagcaaagttttgaagatatggctgctggtctctgcctctccctctattg
     Golden snub-nosed monkey  actgaggcttgggtagtaaccagcaaagttttgaagatatggctgctggtctctgcctctccctctgttg
                     Marmoset  gctggggcttgggtaaaaaccagcaaagctttgaggctacagctgctgacctgtgcctctccctgtattg
              Squirrel monkey  gctggagcttgggtaacaaccagcaaagctttgaggctacggttgctgacctgtgcctctgcctgtattg
                      Tarsier  gatggagcttgggctgcaaccaccaaagctgtggggacagggctgctgttttctgccttttccatagttg
                  Mouse lemur  gctggggcttggct-gcaaccagcaaagctgtgggggcagggccagtgtgcttttcctctcccaccattg
                     Bushbaby  ggtggggttaggct-gcaaccagcagagccgtgggggcagggccaccgtgccatgccactcccaccaccg
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  tattctggaagcacctaactca-----gttgatctcacaggctcaaagctggaggggaatttgcctccag
                        Chimp  tattctggaagcacctaactca-----gttgatctcacaggctcaaagctggaggggaatttgcctccag
                       Bonobo  tattctggaagcacctaactca-----gttgatctcacaggctcaaagctggaggggaatttgcctccag
                      Gorilla  tattctggaagcacctaacgca-----gttgatctcacaggctcaaagctggaggggaatttgcctccag
                    Orangutan  tattctggaagcacctaactca-----gttgatctcacaggctaaaagctggaggggaatttgcctccag
                       Gibbon  tattctggaagcgcctaactcg-----ggtgatctcgcaggctcaaagctggaggggaatttgcctccag
                       Rhesus  tattctggaagcacctaactca-----gttgatctcacaggctcaaagctggaggggaatttgcctcaag
          Crab-eating macaque  tattctggaagcacctaactca-----gttgatctcacaggctcaaagctggaggggaatttgcctcaag
                       Baboon  tattctggaagcacctaactca-----gttgatctcacaggctcaaagctggaggggaatttgcctcaag
                 Green monkey  tattctggaagcatctaactca-----gttgatctcacaggctcaaagctggagaggaatttgcctcaag
             Proboscis monkey  tactctggaaacaactagctca-----gttgatctcataggcccaaagcaggagggtaatttgcctccag
     Golden snub-nosed monkey  tattctggaagcaactaactca-----gttgatctcataggctcaaagcaggagggtaattagcctccag
                     Marmoset  tattctggaagtacccaaccca-----gttgatctcatagcctcaaaactggaggggaatttgcctccag
              Squirrel monkey  tattctggaagtacctaaccca-----gttgatctcacagactcaaaactggaggggaatttgcctccag
                      Tarsier  catcttgggcgcacata-cctg-----gttgattgattaagc--------ggaggggaatttgcctcacg
                  Mouse lemur  taatgtggaagcacataacttg-----tttgatttcacaggctcatagctagaaagaaatttgcctcagg
                     Bushbaby  taatttggaaagacataatttgtttattttaatttcataggctgacagctagcaagaaatttgccttaga
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  ataaatcatactttgaatctcatccat--aactgatttag-tga-tgtttagacaagac--tgcatttta
                        Chimp  ataaatcatactttgaatctcatccat--aactgatttag-tga-tgtttagacaagac--tggatttta
                       Bonobo  ataaatcatactttgaatctcatccat--aactgatttag-tga-tgtttagacgagac--tggatttta
                      Gorilla  ataaatcatactttgaatctcatccat--aactgttttag-tga-tgtttagacaagac--tggatttta
                    Orangutan  ataaatcgtactttgaatctcatccat--aactgatttagatga-tgtttagacaagac--tggattttg
                       Gibbon  ataaatcatactttgaatcttatccat--aactgatttagatga-tgtttacacaagac--tggatttta
                       Rhesus  ataaatcataccttgaatctcatccat--aactgatttagatgattttttagacaagac--tggatttta
          Crab-eating macaque  ataaatcataccttgaatctcatccat--aactgatttagatgattttttagacaagac--tggatttta
                       Baboon  ataaatcataccttgaatctcatccat--aactgatttagatgattttttagacaagac--tggattttg
                 Green monkey  ataaatcataccttgaatctcatccat--aactgatttagatga-tttttagacaagac--tggatttta
             Proboscis monkey  ataaatcatactttgaatctcatccat--aactgattgagatga-tacttagataaaac--tggatttta
     Golden snub-nosed monkey  ataaatcatactttgaatctcatccat--aactgattgagatga-tacttagacaaaac--tggatttta
                     Marmoset  ataaatcatacttcgaatctcatccat--aactgatttagatga-tgtttagacaagac--tggatttta
              Squirrel monkey  ataaatcatacttcgaatctcatccat--agctgatttagatga-tgtttagataagac--tggatttta
                      Tarsier  atgaat----gtttgaatctcag-gat--gtctg--ttggatga-catttgggtaagactttgaactgta
                  Mouse lemur  ataaatcataccttgaatctcacccac--atctgacttaaatta-tgtttagataagactctggacttta
                     Bushbaby  ataaatcattctttgaatctcatccacatatctga-ttacatga-tgtttggacaagactctgaatttta
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  gacttttgagttgacacttgaacaagttaagac--ttgggg--ctactgg----ggtgaaattactgtat
                        Chimp  gacttttgagttgacacttgaacaagttaagac--ttgggg--ctactgg----agtgaaattactgtat
                       Bonobo  gacttttgagttgacacttgaacaagttaagac--ttgggg--ctactgg----agtgaaattactgtat
                      Gorilla  gacttttgagttgacacttgaacaagttaggac--ttgggg--ctactgg----ggtgaaattactgtat
                    Orangutan  gacttttgagttgacacttgaacaagttaagac--ttgggg--ctactgg----ggtgaaattactgtat
                       Gibbon  gacttttgagttgacacttggacaggttaagac--ttgggg--ctactgg----ggtgaaattactgtat
                       Rhesus  gacttttgagttgacactggaacaagttaagac--tcaggg--ctattgt----ggtgaaattactatat
          Crab-eating macaque  gacttttgagttgacactggaacaagttaagac--tcaggg--ctattgt----ggtgaaattactatat
                       Baboon  gacttttgagttgacactagaacaagttaagac--tcaggg--ctattgt----ggtgaaattactatat
                 Green monkey  gacttttgagttaacacttgaacaagttaagac--tcgggg--ctattgt----ggtgaaattactatat
             Proboscis monkey  gacttttgcgttgacacttgaacaagttaagac--tcgggg--ctattgt----ggtgaaattactgtat
     Golden snub-nosed monkey  gacttttgagttgacacttgaacaagttaagac--tcgggg--ctattgt----ggtgaaattactgtat
                     Marmoset  gacttttgcattgacacttgaacaagttaagac--ccaggg--atatttg----ggtgaaattactgtgc
              Squirrel monkey  gacttttgcgttgacacttgaacaagttaagac--ccagga--atatttg----ggtgaaattactgtgt
                      Tarsier  gagtattgaactgatactataacaagttaagac--tttggggcctataga----gatgaaagcattgtgt
                  Mouse lemur  gacttttcagttgatgttggaacaagtt-------tggggg--ccactggaatgtatgacatgaatgtgt
                     Bushbaby  gaatttcgagttaatgatggaataagttaagactctgggga--cca--------tatgaaatgaatacga
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  tttgcatgtcagaagaacatgaatttgtggaggccatgggaagaatgctgtggtctgaatgttggtg--t
                        Chimp  tttgcatgtcagaagaacatgaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
                       Bonobo  tttgcatgtcagaagaacatgaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
                      Gorilla  tttgcatgtcagaagaacatgaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
                    Orangutan  tttgcatgtcagaagaacatgaatttgtggagaccatgggaagaatgctgtggtctgaatgttggtg--t
                       Gibbon  tttgcaagtcagaagaacatgaatttgtggaggccctgggaagaatgctgtagtctgaatgttggtg--t
                       Rhesus  tttgcatattagaagaacaggaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
          Crab-eating macaque  tttgcatattagaagaacaggaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
                       Baboon  tttgcttatcagaagaacaggaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
                 Green monkey  tttgcatatcagaagaacaggaatttgtggaggccatgggaagaatgctgtggtctaaatgttggtg--t
             Proboscis monkey  tttgcttatcagaagaacatgaatttttggaggccatgggaagaatgctgtggtctaaatgttggtg--t
     Golden snub-nosed monkey  tttgcttatcagaagaacatgaatttttggaggccatgggaagaatgctgtggtctaaatgttggtg--t
                     Marmoset  tttgcatgtcagaagaacatgaatttgggaaggctatgggcagaatgctgtggtctgaatgttggtg--t
              Squirrel monkey  tttgcatgtcagaagaacatgaatttgggaaggctatgggaagaatgttgtggtctgaatgttggtg--t
                      Tarsier  tttgcaagggacaagaatatgaatttttgtaggtcatgggagaattgttatggtctgaatgttggtgaat
                  Mouse lemur  tttgcatgtgacaagaacgtggatttgaggaggccaggggaggagtgctatggtctaaatgttggtg--t
                     Bushbaby  tttgtatacaagaagagcatggg-ctggggagcccaggggaggagtgct---------------------
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  ct-ccccaaaattcagatgttgt
                        Chimp  ct-ccccaaaattcagatgttgt
                       Bonobo  ct-ccccaaaattcagatgttgt
                      Gorilla  ct-ccccaaaattcagatgttgt
                    Orangutan  ct-ccccaaaattcagatgttgt
                       Gibbon  ctcccccgaaattcagatgttgt
                       Rhesus  gt-ccccaaaattcaggtgttgt
          Crab-eating macaque  gt-ccccaaaattcaggtgttgt
                       Baboon  gt-ccccaaaattcaggtgttgt
                 Green monkey  ct-ccccaaaattcaggtgttgt
             Proboscis monkey  ct-ccccaaaattcaggtgttgt
     Golden snub-nosed monkey  ct-ccccaaaattcaggtgttgt
                     Marmoset  ct-tctcaaaattcagatgttgt
              Squirrel monkey  ct-ccccaaaattcagatgttgt
                      Tarsier  at-gatccaaaatcatat-ctgt
                  Mouse lemur  cc-tctcaaaattcacatattat
                     Bushbaby  ---caccaaaattcatatgttgt
                        Mouse  =======================
                   Tree shrew  =======================
                          Dog  =======================

Alignment block 11 of 36 in window, 77420361 - 77420727, 367 bps 
B D                     Human  cccctgat----aattg----aatag-ttttaagaggtgaaggcttttggaaagtgattaagttgtgagg
B D                     Chimp  cccctgat----aatcg----aatag-ttttaagaggtgaaggcttttggaaagtgattaagttgtgagg
B D                    Bonobo  cccctgat----aatcg----aatag-ttttaagaggtgaaggcttttggaaagtgattaagttgtgagg
B D                   Gorilla  cccctgat----aatcg----aatag-ttttaagaggtgaaggcttttggaaagtgattaagttgtaagg
B D                 Orangutan  cccctgat----gatcg----aatag-ttttaagaggtgaaggttttcagaaagtgattaagttgtgagg
B D                    Gibbon  tccctgat----aatcg----aatag-ttttaagaggtgaaggcttttggagagtgattaagttgtgagg
B D                    Rhesus  accctgat----aatcg----aatag-ttttaagagttgaaggc-tttggaaagtgattaagttgtgagg
B D       Crab-eating macaque  accctgat----aatcg----aatag-ttttaagagttgaagac-tttggaaagtgattaagttgtgagg
B D                    Baboon  accctgat----aatcg----aatag-ttttaagagttgaaggc-tttggaaagtgattaagttgtgagg
B D              Green monkey  accctgat----aattg----aatag-ttttaagagttgaaggc-tttggaaagtgattaagttgtgagg
B D          Proboscis monkey  accctgat----aattg----aatagtttttaagagttgaaggcttttgaaaagtgattaagttgtcagg
B D  Golden snub-nosed monkey  accctgat----aatcg----aatagtttttaagagttgaaggcttttgaaaagtgattaagttgtcagg
B D                  Marmoset  aacctagtactcaattg----aatag-ttttaagagatgaaggcttttgaaaagtga-ttagttatgatg
B D           Squirrel monkey  aacctaat----aatcg----aatcg-ttttaagaggtgaaggcttttgaaaagtgatttagttgtgacg
B D                   Tarsier  aacccaat----atataccatgatag-ttttaagagatggagcatttaaggaagtaattaagttataaag
B D               Mouse lemur  aacctaatacccaatgt----gatag-ttttaagaggtggggcctttaaggaagtgattaagttgtgaga
B D                     Mouse  ======================================================================
B D                  Bushbaby  ----------------------------------------------------------------------
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================

                        Human  gctctgtcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct--g
                        Chimp  gctctgtcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct--g
                       Bonobo  gctctgtcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct--g
                      Gorilla  gctctgtcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct--g
                    Orangutan  gctctgtccttattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--tttttct--g
                       Gibbon  gctctgtcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct--g
                       Rhesus  gctctatcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct---
          Crab-eating macaque  gctctatcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct---
                       Baboon  gctctatcctctttgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct---
                 Green monkey  gctctatcctcattaatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct---
             Proboscis monkey  gctctatcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct---
     Golden snub-nosed monkey  gctctatcctcattgatgggatgagtgcctttataaaagaggttgaaaaaagctgtct--ttcttct---
                     Marmoset  gctctgtcctcattgatggaatgagtgcctttataaaagaagttg-aaaaagctgtct--atgttct--g
              Squirrel monkey  gctctgtcctcattgatgggatgagagcctttataaaagaagttg-aaaaagctatct--atgttct--g
                      Tarsier  gctctttcctaattaaaggaattagtgatcctataaaataaggtgaagagatccatctcattcgtcc--a
                  Mouse lemur  g--ttatcctcattaatggaactagtttccttatagaaaaggtcacagggggcttgct--tgcctttcca
                        Mouse  ======================================================================
                     Bushbaby  ----------------------------------------------------------------------
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  ccatgtgacgacacatccaccaagtgccaactatgaggaacaggacctcagcagataccaaatctgctgg
                        Chimp  ccatgtgaggacacatccaccaagtgccaactatgaggaacaggacctcagcagataccaaatctgctgg
                       Bonobo  ccatgtgaggacacatccaccaagtgccaactatgaggaacaggacctcagcagataccaaatctgctgg
                      Gorilla  ccatctgaggacacatccaccaagtgccaactatgaggaacaggacctcagcagataccaaatctgctgg
                    Orangutan  ccatgtgaggacgcatccaccaagtgccatctatgaggaacaggacctcagcagataccaaatctgctgg
                       Gibbon  ccatgtgaggatgcatccaccaagtaccatctatgaggaacaggacctcagcagataccagatctgctgg
                       Rhesus  ccttgtgaggatgcatccacaaagtgccatctgtaaggaacaagatctcagcagatacaaaatctgctgg
          Crab-eating macaque  ccttgtgaggatgcatccacaaagtgccatctgtaaggaacaagatctcagcagatacaaaatctgctgg
                       Baboon  ccttgtgaggatgcatccacaaaatgccatctgtaaggaacaagatctcagcagatacaaaatctgctgg
                 Green monkey  ccttgtgaggatgcatccacaaagtgccatctgtaaggaacaagatctcagcagataccaaatctgctgg
             Proboscis monkey  ccatgtgaggacgcatccacaaagtgccgtctatgaggaacaggatttcagcagataccaaatctgctgg
     Golden snub-nosed monkey  ccatgtgaggacgcatccacaaagtgccatctatgaggaacaggatctcagcagataccaaatctgctgg
                     Marmoset  ccatgtgaggacacatccacaaagtgccgtttataaggaacaggacctcagcagataccaaatctgcttg
              Squirrel monkey  ccatgtgaggacacatccacaaagccccatttatgaggaacaggacctcagcagataccaaatctgctgg
                      Tarsier  tcgtgtgaagacacacaaacaaggcatcctctgtgaggaatgggacctcaccagacaccaaatctgctgg
                  Mouse lemur  ccatgttaggacacaccaacaaggtaccatctatgaagaaaagaacctcactagacacca-atctgttgg
                        Mouse  ======================================================================
                     Bushbaby  ----------------------------------------------------------------------
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  tgccttgaccttagacttcacagcctccagaactgtaagcaataaatttctgttgtttgtaaattaccca
                        Chimp  tgccttgaccttagacttcacagcctccagaactgtgagcaataaatttctgttgtttgtaaattaccca
                       Bonobo  tgccttgaccttagacttcacagcctccagaactgtaagcaataaatttctgttgtttgtaaattaccca
                      Gorilla  tgccttgaccttagacttcacagcctccagaaccgtgagcaataaatttctgttgtttgtaaattaccca
                    Orangutan  tgccttgaccttagacttcacagcctccagaactgtgagcaataaatttctgttgtttgtaaattaccca
                       Gibbon  tgccttgaccttagacttcacagcctccagaactgtgagcaataaattcccgttgtttgtaaattaccca
                       Rhesus  tgccttgatcttagacttcacagcctccagaactgtgagcaataaatttctgttgtttgtaaattaccca
          Crab-eating macaque  tgccttgatcttagacttcacagcctccagaactgtgagcaataaatttctgttgtttgtaaattaccca
                       Baboon  tgccttgaccttagacttcacagcctccagaactgtgagcaataaatttctgttgtttgtaaattaccca
                 Green monkey  tgccttgaccttagacttcacagcctccagaactgtgagcaataaatttctgttgtttgtaaattaccca
             Proboscis monkey  tgccttgaccttagacttcacaacctccagaactgtcagcaataaatttctgttgtttgtaaattaccca
     Golden snub-nosed monkey  tgccttgaccttagacttcacaacctccagaactgtcagcaataaatttctgttgtttgtaaattaccca
                     Marmoset  tgctttgaccttagacttcacagcctccagaactataaggaataaatttctgttgtttgtaaatcacaca
              Squirrel monkey  tgccttgaccttagacttcacagcttccagaactgtaaggaataaatttctcttgtttgtaaatcaccca
                      Tarsier  caccttgaccttagatttcacagactccaggatggtaagccataaatttctgttgtttataaattgccca
                  Mouse lemur  tgacttgatcttcgatttca-------cagaactgtaagcaatagatttgggttg-ttataaattaccta
                        Mouse  ======================================================================
                     Bushbaby  ----------------------------------------------------------------------
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  gtatgaggttatttgttatagccttctgagtgggctaagaaaaatgaataaataaaatgtaacatataaa
                        Chimp  gtataaggttatttgttatagccttctgagtgggctaagaaaaatgaataaataaaatgtaacatataaa
                       Bonobo  gtataaggttatttgttatagccttctgagtgggctaag-aaaatgaataaataaaatgtaacatataaa
                      Gorilla  gtataaggttatttgttatagccttctgagtgggctaagaaaaatgaataaataaaatgtaacatataaa
                    Orangutan  gtataaggttatttgttatagccttctgagtgggctaagaaaaatgaataaataaaatgtaacatataaa
                       Gibbon  gtataaggttatttgttacagccttctgagtgggctaagaaaaatgaataaacaaaatgtagcatataaa
                       Rhesus  gtataaggttatatgttacagccttctgagtgggctaagaaaaatgaataaataaaatatagcatataaa
          Crab-eating macaque  gtataaggttatatgttacagccttctgagtgggctaagaaaaatgaataaataaaatatagcatataaa
                       Baboon  gtataaggttatttgttacagccttctgagtgggctaagaaaaatgaataaat-aaatatagcatataaa
                 Green monkey  gtataaggt----tgttacagccttctgagtgggctaagaaaaatgaataaataaaatatagcatataaa
             Proboscis monkey  gtataaggttatttgttatagccttctgagtgggtaaagaaaaatgaataaataaaatatagcatatgaa
     Golden snub-nosed monkey  gtataaggttatttgttatagccttctgagtgggtaaagaaaaatgaataaataaaatatagcatatgaa
                     Marmoset  gtataaggt--attattatggccttctgagtgggctaagaaaaacaaataaataaaatttggcagataaa
              Squirrel monkey  gtataaggt--attattatagccttctgagtgggctaagaaaaatgaatacataaaatttgtcagataaa
                      Tarsier  gtagaaggt-atctgctatagaagcctgaatgagttaagacaaatgaataaagaaaaggtggcatatgta
                  Mouse lemur  gtataaggtattttgttatagcagcttgaacgtactaag----acaaataaacaaaatgtggcatataca
                        Mouse  ======================================================================
                     Bushbaby  ----------------------------------------------------------------------
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  cacaatggaatactatttatccc-----------------------------------------------
                        Chimp  cacaatggaatactatttatccc-----------------------------------------------
                       Bonobo  cacaatggaatactatttatccc-----------------------------------------------
                      Gorilla  cacagtggaatactatttacccc-----------------------------------------------
                    Orangutan  cacaatggaatactatttatccc-----------------------------------------------
                       Gibbon  cacaatggaatactatttatccc-----------------------------------------------
                       Rhesus  cacaacagaatactatttagccg-----------------------------------------------
          Crab-eating macaque  cacaacagaatactatttagccg-----------------------------------------------
                       Baboon  cacaacagaatactatttagccc-----------------------------------------------
                 Green monkey  cacaacagaatactatttagccc-----------------------------------------------
             Proboscis monkey  cacaacagaacactatttagccc-----------------------------------------------
     Golden snub-nosed monkey  cacaacagaacactatttagccc-----------------------------------------------
                     Marmoset  cacaatagaatactatttagtcc-----------------------------------------------
              Squirrel monkey  cacaatagaatacgatttagccc-----------------------------------------------
                      Tarsier  cacaatggaatatgattcagcccaccctccaacaaaaataaaatcctgtaaaatcctgttgtttgcaaca
                  Mouse lemur  tataaggaaatattattcagctc-----------------------------------------------
                        Mouse  ======================================================================
                     Bushbaby  ----------------------------------------------------------------------
                   Tree shrew  ======================================================================
                          Dog  ======================================================================

                        Human  -------------------------------------------taaaaaa--
                        Chimp  -------------------------------------------taaaaaa--
                       Bonobo  -------------------------------------------taaaaaa--
                      Gorilla  -------------------------------------------taaaaaa--
                    Orangutan  -------------------------------------------taaaaaa--
                       Gibbon  -------------------------------------------taaaaaa--
                       Rhesus  -------------------------------------------taaaaaa--
          Crab-eating macaque  -------------------------------------------taaaaaa--
                       Baboon  -------------------------------------------taaaaaa--
                 Green monkey  -------------------------------------------taaaaaa--
             Proboscis monkey  -------------------------------------------tcaaaaa--
     Golden snub-nosed monkey  -------------------------------------------taaaaaa--
                     Marmoset  -------------------------------------------taaaaaa--
              Squirrel monkey  -------------------------------------------taaaaaa--
                      Tarsier  atatggataaaccgggaggacattaaatgaaataagccagccacagaaaa--
                  Mouse lemur  -------------------------------------------cccaaaata
                        Mouse  ====================================================
                     Bushbaby  ----------------------------------------------------
                   Tree shrew  ====================================================
                          Dog  ====================================================

Inserts between block 11 and 12 in window
B D                   Rhesus 100bp
B D      Crab-eating macaque 100bp
B D                   Baboon 99bp
B D             Green monkey 663bp
B D         Proboscis monkey 100bp
B D Golden snub-nosed monkey 100bp
B D                 Marmoset 100bp
B D          Squirrel monkey 100bp
B D                  Tarsier 12bp

Alignment block 12 of 36 in window, 77420728 - 77420753, 26 bps 
B D                     Human  taatctcacttaaatgtaaaaattta
B D                     Chimp  taatctcacttaaatgtaaaaattta
B D                    Bonobo  taatctcacttaaatgtaaaaattta
B D                   Gorilla  taatctcacttaaatgtaaaaattta
B D                 Orangutan  taatctcacttaaatgtaaaaattta
B D                    Gibbon  taatctcacttaaatgtaaaaattta
B D                    Rhesus  taatctcacttgaatgtaaaaattta
B D       Crab-eating macaque  taatctcatctgaatgtaaaaattta
B D                    Baboon  taatctcacttaaatgtaaaaattta
B D          Proboscis monkey  taatctcacttaaatgtaaaaattta
B D  Golden snub-nosed monkey  taatctcacttaaatgtaaaaattta
B D                  Marmoset  taatctcacttaaatgtaaaaattta
B D           Squirrel monkey  taatctcacttaaatgtaaaaattta
B D                   Tarsier  taatctcacttatatgt-aacatcta
B D               Mouse lemur  aaatcc--------tgtcaaatttta
B D                     Mouse  ==========================
B D                  Bushbaby  --------------------------
B D                Tree shrew  ==========================
B D                       Dog  ==========================
B D              Green monkey  ==========================

Alignment block 13 of 36 in window, 77420754 - 77420850, 97 bps 
B D                     Human  agaaactggaattcatagaagcagagagtagagtgg-----------ggccgaagtgtga--------tg
B D                     Chimp  agaaactggaattcatagaagcagagggtagagtgg-----------ggccgaagtgtga--------tg
B D                    Bonobo  agaaactggaattcatagaagcagagggtagagtgg-----------ggccgaagtgtga--------tg
B D                   Gorilla  agaaactggaattcatagaagcagagagtagagtgg-----------ggccaaagtgtga--------tg
B D                 Orangutan  agaaactagaattcatagaagcagagagtagagtgg-----------ggccgaagtgtga--------tg
B D                    Gibbon  agaaactggaattcatagaagcagagagtagagtgg-----------ggccgaagtgtga--------tg
B D                    Rhesus  agaaactagaattcatagaagcagaaggtagaatggtggttaccaggggccaaagtgtga--------tg
B D       Crab-eating macaque  agaaactaggattcatagaagcagaaggtagaatggtggttaccaggggccaaagtgtga--------tg
B D                    Baboon  agaaactggaattcatagaagcagagagtagagtggtggttaccaggggccaaagtgcga--------tg
B D          Proboscis monkey  agaaactggaattcatagaagcagagagtagagtggtggttaccaggggccaaagtgtga--------tg
B D  Golden snub-nosed monkey  agaaactggaattcatagaagcagagagtagagtggtggttaccagaggccaaagtgtga--------tg
B D                  Marmoset  agaaaatggaatttatagaagcagagagtagaatggtagctaccaggggccaaaatgtgatgtgtgtgtg
B D           Squirrel monkey  agaaaatggaattcatagaagtagagagtagagtggtggctaccaagggctgaaatgtga--tgtgtgtg
B D                   Tarsier  agaaagtggaatttatagaagcagagagcagaatggtgcttaccagagactgaggtgtgt-----gt-tg
B D                     Mouse  ======================================================================
B D                  Bushbaby  ----------------------------------------------------------------------
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D              Green monkey  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  tgtgtgttgcgggagggga----tggagagatattggtcaaaggagacaa
                        Chimp  tgtgtgttgcgggagggga----tggagagatattggtcaaaggagacaa
                       Bonobo  tgtgtgttgagggagggga----tggagagatattggtcaaaggagacaa
                      Gorilla  tgtgtgttgtgggagggga----tggagagatattggtcaaaggagacaa
                    Orangutan  tgtgtgttgcaggagggta----tggagagatattggtcaaaagagacaa
                       Gibbon  tgtgtgttgcgggagagga----tggaaagatattggtcaaaggagacaa
                       Rhesus  tgtgtgttgggggaggggg----tagagagatattggtcaaaggagacaa
          Crab-eating macaque  tgtgtgttgggggaggggg----tagagagatattggtcaaaggagacaa
                       Baboon  tgtgtgttgggggaggggg----tggagagatattggtcaaaggagacaa
             Proboscis monkey  tgtgtgttgggggagagg-------ggaaaatattggtcaaaggagac--
     Golden snub-nosed monkey  tgtgtgttgggggaggtg-------gggagatattggtcaaaggagac--
                     Marmoset  tgtgtgttaggggagggga----tggagagatattagctaaaggagacaa
              Squirrel monkey  tctgtgttagggga-ggga----tggagagatattagttaaaggagacaa
                      Tarsier  ggggtgggggggcaggggagaggtggtgagatattagtcaaagaatacag
                        Mouse  ==================================================
                     Bushbaby  --------------------------------------------------
                   Tree shrew  ==================================================
                          Dog  ==================================================
                 Green monkey  ==================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 14 of 36 in window, 77420851 - 77420991, 141 bps 
B D                     Human  aaattaaattatgtatgagaagtaagttcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D                     Chimp  aaattaaattatgtatgagaagtaagttcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D                    Bonobo  aaattaaattatgtatgagaagtaagttcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D                   Gorilla  aaattaaattatgtatgagaagtaagttcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D                 Orangutan  aaattaaattatatatgagaagtaagttcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D                    Gibbon  aaattaaattttatatgagaagtaagttcaagagatcttttgtataacatggtgtgtatagttaataata
B D                    Rhesus  aaatttaattaggtatgaaaagtaagatcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D       Crab-eating macaque  aaatttaattaggtatgaaaagtaagatcaagagatcttttgtacaacatggtgtgtatagttaataaca
B D                    Baboon  aaatttaattagatatgaaaagtaagatcaagatatcttttgtacaacatggtgtgtatagttaataaca
B D          Proboscis monkey  ----------------------------caagagatcttttgtacaacatggtgtgtatagttaataaca
B D  Golden snub-nosed monkey  ----------------------------caagagatcttttgtacaacatggtgtgtatagttaataaca
B D                  Marmoset  atactcaattagacatgagaagtaagttcaagagatcgtttgtacaacatggtgtacatagttaaaaaca
B D           Squirrel monkey  at----agttagacatgagaagtaagttcaagagatcttttgtacaacatggtgtgtatagttaaaaaca
B D                   Tarsier  aaatttaactagatatgaggaataagttcaagaactctataatacaacatg-----tctaaataacaaaa
B D                  Bushbaby  aacctaaatttcatttgaggaataagtttaagagatttattgtacaacatagtatctatagttaataaca
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D              Green monkey  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ccttatcatatacttgataattgtcaatagagattttaagtgatctcaccacaaaaagaagataagcatg
                        Chimp  ccttatcatatacttgataattgtcaatagatattttaagtgatctcaccacaaaaagaagataagcatg
                       Bonobo  ccttatcatatacttgataattgtcaatagatattttaagtgatctcaccacaaaaagaagataagcatg
                      Gorilla  ccttatcgtatacttgataattgtcaatagagattttaagtgatctcaccacaaaaagaagataagcatg
                    Orangutan  ccttattgtatacttgataattgccaatagagattttaagtgatctcaccacaaaaagaagataagcatg
                       Gibbon  ccttatcgtatacttgataattgtcaatagagattttaagtgatctcaccacaaaaagaagataagcatg
                       Rhesus  ccatct----------aaaaatgtcaatggagattttaagtgatctcaccacaaaatgaagataagcata
          Crab-eating macaque  ccatcttgtatacttgataattgtcaatggagattttaagtgatctcaccacaaaatgaagataagcata
                       Baboon  ccatcttgtatacttgataattgtcaatggagattttaagtgatctcaccacaaaatgaagataagcata
             Proboscis monkey  ccttcttgtatacttgataattgtcaatggagattttaagtgatctcaccacaaaaagaagataagcatg
     Golden snub-nosed monkey  ccttcttgtatacttgataattgtcaatggagattttaagtgatctcaccacaaaaagaagataagcatg
                     Marmoset  ccttattgtatacttgataatttgcaatagatattttaagtaatctcaccacaaaaataaggtaagcatg
              Squirrel monkey  ccttattgtatacttgataatttccaataggtattttaagtaatctcaccacaaaaagaagataagcata
                      Tarsier  c-----tgtatacttgaagcttactaagagagattttaagtgttcttaccacaaaaag----tatgcatg
                     Bushbaby  atataatctatactaaaacaatgccaagaaagattttaagagttacca-tacaaaaaaaaagt-------
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                 Green monkey  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  t
                        Chimp  t
                       Bonobo  t
                      Gorilla  t
                    Orangutan  t
                       Gibbon  t
                       Rhesus  t
          Crab-eating macaque  t
                       Baboon  t
             Proboscis monkey  t
     Golden snub-nosed monkey  t
                     Marmoset  t
              Squirrel monkey  t
                      Tarsier  t
                     Bushbaby  -
                        Mouse  =
                   Tree shrew  =
                          Dog  =
                 Green monkey  =
                  Mouse lemur  N

Inserts between block 14 and 15 in window
B D                  Tarsier 6902bp

Alignment block 15 of 36 in window, 77420992 - 77420998, 7 bps 
B D                     Human  gaggtaa
B D                     Chimp  gaggtaa
B D                    Bonobo  gaggtaa
B D                   Gorilla  gaggtaa
B D                 Orangutan  gaggtaa
B D                    Gibbon  gaggtaa
B D                    Rhesus  gaggtaa
B D       Crab-eating macaque  gaggtaa
B D                    Baboon  gaggtaa
B D          Proboscis monkey  gaggtaa
B D  Golden snub-nosed monkey  gaggtaa
B D                  Marmoset  aaagtaa
B D           Squirrel monkey  aaagtca
B D                  Bushbaby  gaagtga
B D                     Mouse  =======
B D                Tree shrew  =======
B D                       Dog  =======
B D                   Tarsier  =======
B D              Green monkey  =======
B D               Mouse lemur  NNNNNNN

Alignment block 16 of 36 in window, 77420999 - 77421124, 126 bps 
B D                     Human  tgcatatattaattaacttgatttaaccattccataatgtgtatgtatagataatgtgtgtgtgtttatg
B D                     Chimp  tgcatatattaattgacttgatttaaccattccatagtgtgtatgtatagataatgtgtgtgtgtttatg
B D                    Bonobo  tgcatatattaattgacttgatttaaccattccataatgtgtatgtatagataatgtgtgtgtgtttatg
B D                   Gorilla  tgcatatattaattaacttgatttaaccattccataatgtgtatatatagataatgtgtgtgtgtttatg
B D                 Orangutan  tgcatatattaattaacttgatttaaccattccataatgtgtatgtatagctaatgtgtgtgtgtttatg
B D                    Gibbon  tgcatatattaattaacttgatttaaccattccataatgtgtatgtatagataatgtgtgtgtgtttatg
B D                    Rhesus  tgcatatattaattaacttgatttaaccattccataatgtgtatgtatggataatatgagtgtgttta--
B D       Crab-eating macaque  tgcatatattaattaacttgatttaaccattccataatgtgtatgtatggataatatgagtgtgttta--
B D                    Baboon  tacatatattaattaacttgatttaaccatttcataatgtgtaggtatagataatatgagtgtgttta--
B D              Green monkey  tgcatatattaattaacttgattaaaccattccataatgtgtatgtatagataatatgaatgtgttta--
B D          Proboscis monkey  tgcatatattaattaacttgatttaaccatttcataatgtgtatgtatagataatgtgtgtgtgtttatg
B D  Golden snub-nosed monkey  tgcatatattaattaacttgatttaaccatttcataatgtgtatgtatagataatgtgtgtgtgtttatg
B D                  Marmoset  tacgtatattaattagcttgatttaattattccataatgcatatgtatagataatttgtatgtttttatg
B D           Squirrel monkey  tacatatattaatgagcttgatttaaccattccataatacatatgtatagataatttgtgtgtgtttatg
B D                  Bushbaby  ggcatatattaattacctggatttagctatttcacaatgtc-----------------------------
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D                   Tarsier  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  tatgtgtgtgtatatatatgtatacatcatttgttgtacaccataaatatatacaa
                        Chimp  tatgtgtgtatatatatatgtatacatcatttgttgtacaccataaatatatacaa
                       Bonobo  tatgtgtg--tatatatatgtatacatcatttgttgtacaccataaatatatacaa
                      Gorilla  tatgtgtgtgtatatatatgtatacatcatttgttgtacaccataaatatatacaa
                    Orangutan  tatgtgtg--tatatatatgtatacataatttgttgtacaccataaatatatacaa
                       Gibbon  tatgtgtatgtatatatatgtatacataat---ttgtacaccataaatatatacaa
                       Rhesus  tatgtgtg--tatatatatgtatacatcatatgttgtatgccataaatacatacaa
          Crab-eating macaque  tatgtgtg--tatatatatgtatacatcatatgttgtatgccataaatacatacaa
                       Baboon  tatgtgtg--tatatatatgtatacatcatatgttgtatgccagaaatacatacaa
                 Green monkey  tatgtgtg--tgtatatatgtatacatcatatattgtatgccataaatacatacaa
             Proboscis monkey  tatgtgtg--tgtatatatgtatacatcatatgttgtatgctataaatacatacaa
     Golden snub-nosed monkey  tatgtgtg--tgtatatatgtatacatcatatgttgtatgct----atacatacaa
                     Marmoset  tgtgtgtg--------tatttatacttcatatgttgggcaccataaatatatacaa
              Squirrel monkey  tgtgtgtg--------tatttatacctcatatgttgggcaccataaatatatacaa
                     Bushbaby  ----------catatatattaaaacatcatatgttgtgtaccataaatatatgcaa
                        Mouse  ========================================================
                   Tree shrew  ========================================================
                          Dog  ========================================================
                      Tarsier  ========================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 17 of 36 in window, 77421125 - 77421269, 145 bps 
B D                     Human  tcttcatttttcaattaaata--------tatat----------gcaacaaaataaataaattttaaaat
B D                     Chimp  tcttcatttttcaattaaata--------tatata--------tgcaacaaaataaataaattttaaaat
B D                    Bonobo  tcttcatttttcaattaaata--------tatat----------gcaacaaaataaataaattttaaaat
B D                 Orangutan  tcttcatttttcaattaaata--------tatata--------tgcaacaaaataaataaattttaaaat
B D                    Gibbon  tcttcatttttcaattaaata--------tatat----------gtaacaaaataaataaattctaaaat
B D                    Rhesus  tcttcatttttcagttaaata--------tatat----------gcaacaaaataaataca--ctaaaat
B D       Crab-eating macaque  tcttcatttttcagttaaata--------tatat----------gcaacaaaataaataca--ttaaaat
B D                    Baboon  tcttcatttttcagttaaata--------tatat----------gcaacaaaataaataca--ttaaaat
B D              Green monkey  tcttcatttttcagttaaata--------tatat----------gcaacaaaataaataca--ttaaaat
B D          Proboscis monkey  ttttcatgtttcaattaaata--------tatat----------gcaacaaaataaataaattttaaaat
B D  Golden snub-nosed monkey  ttttcatttttcaattaaata--------tatat----------gcaacaaaataaataaattttaaaat
B D                  Marmoset  tcttcatttttcaattaaaaa--------tatatacatatatttgcaacaaaataaatacattttaaaat
B D           Squirrel monkey  tattcatttttcaattaaaaatatatttttatatatatatgtttgcaacaaaataaataaattttaaaat
B D                  Bushbaby  ccttcatttctcaattaaaaa--------taaat----attttctaatgaaaatacatagattttaaaat
B D                     Mouse  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D                   Gorilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D                   Tarsier  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccacagta
                        Chimp  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
                       Bonobo  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
                    Orangutan  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
                       Gibbon  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
                       Rhesus  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
          Crab-eating macaque  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
                       Baboon  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
                 Green monkey  aaaacagatgtcagtactgagatgacaaagaggttacaataatctgagaaattttaaagcagccatggta
             Proboscis monkey  aaaacagatgtcagtactgagatgacaaagaggtgacaataatctgagaaattttaaagcaaccatggta
     Golden snub-nosed monkey  aaaacagatgtcagtactgagatgacaaagaggctacaataatctgagaaattttaaagcaaccatggta
                     Marmoset  aaaacagatgtcagtactgagatgacagacaggttccaattatctgagaaattttaaagcagccatggca
              Squirrel monkey  aaaacaaatatcagtactgagatgacaaacaggttccaattatgtgagaaattttaaagcagccatggca
                     Bushbaby  aaaa---aggtcaggaccaagatgaaaaagatgttagaattttttgatagtttttgaaacactgatgaaa
                        Mouse  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                      Gorilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
                      Tarsier  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  aaaatgattaaatgagcaattac
                        Chimp  aaaatgattaaatgagcaattac
                       Bonobo  aaaatgattaaacgagcaattac
                    Orangutan  aaaatgattaaatgagcaattac
                       Gibbon  aaaatgattaaatgagcaattac
                       Rhesus  aaaatgattaaatgagcaattac
          Crab-eating macaque  aaaatgattaaatgagcaattac
                       Baboon  aaaatgattaaatgagcaattac
                 Green monkey  aaaatgattaaatgagcagttac
             Proboscis monkey  aaaatgattaaatgagcaattac
     Golden snub-nosed monkey  aaaatgattaaatgagcaattac
                     Marmoset  aaaataattaaataagcggttat
              Squirrel monkey  aaaataattgaataagcagttat
                     Bushbaby  ataatgattaaatgaaaatttat
                        Mouse  =======================
                   Tree shrew  =======================
                          Dog  =======================
                      Gorilla  NNNNNNNNNNNNNNNNNNNNNNN
                      Tarsier  =======================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNN

Alignment block 18 of 36 in window, 77421270 - 77421294, 25 bps 
B D                     Human  aaaaatacttgaaa---------------caa--caacaac--a
B D                     Chimp  aaaaatacttgaaa---------------caa--caacaac--a
B D                    Bonobo  aaaaatacttgaaa---------------caa--taacaac---
B D                 Orangutan  aaaaatgcttgaaa---------------caa--caacaac--a
B D                    Gibbon  aaaaatgcttgaaa---------------caa--caacaac--a
B D                    Rhesus  aaaaatgcttgaaa---------------caa--caacaac---
B D       Crab-eating macaque  aaaaatgcttgaaa---------------caa--caacaac---
B D                    Baboon  aaaaatgcttgaaattacccagtttgttgtta--caacaac---
B D              Green monkey  aaaaatgcttgaaa------------cagcaa--caacaac---
B D          Proboscis monkey  aaaaaagcttgaaa---------------caa--caacaacaaa
B D  Golden snub-nosed monkey  aaaaaagcttgaaa---------------caa--caacaacaaa
B D                  Marmoset  aaaaattcttgaaa---------------caa--caaaaac---
B D           Squirrel monkey  aaaaatccttgaaa---------------caa--caaaaaa---
B D                   Tarsier  aaaaatgcttgaaa---------------taa--aaaaaat---
B D                  Bushbaby  aaacatacttcaaa---------------taaattaaaaat---
B D                     Mouse  ============================================
B D                Tree shrew  ============================================
B D                       Dog  ============================================
B D                   Gorilla  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 19 of 36 in window, 77421295 - 77421317, 23 bps 
B D                     Human  aaaaactagaaaagctcagcaaa
B D                     Chimp  aaaaactagaaaagctcagcaaa
B D                    Bonobo  -aaagctagaaaagctcagcaaa
B D                 Orangutan  aaaaactagaaaagctcagcaaa
B D                    Gibbon  aaaaactagaaaagctcagcaaa
B D                    Rhesus  --aaactagaaaaactcagcaaa
B D       Crab-eating macaque  --aaactagaaaaactcagcaaa
B D                    Baboon  --aaactagaaaaactcagcaaa
B D              Green monkey  --aaactagaaaaactcagcaaa
B D          Proboscis monkey  aaaaactagaaaagctcagcaaa
B D  Golden snub-nosed monkey  gaaaactagaaaagctcagcaaa
B D                  Marmoset  -----ctagaaaagctcagc---
B D           Squirrel monkey  -----ctagaaaagctcagc---
B D                   Tarsier  -------agaaaacctcagccat
B D                  Bushbaby  ---atataaaacagcttc-----
B D                Tree shrew  aaaaattagaaaacttcagtcaa
B D                     Mouse  =======================
B D                       Dog  =======================
B D                   Gorilla  NNNNNNNNNNNNNNNNNNNNNNN
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 19 and 20 in window
B D                Orangutan 1bp
B D                   Gibbon 1bp

Alignment block 20 of 36 in window, 77421318 - 77421380, 63 bps 
B D                     Human  aaa---aaaaaaaaa-gatataaagaagaacaaaatggggaatttggaaatgaaaacgctgtaactg
B D                     Chimp  aaa---aaaaaaaaaagatataaagaagaacaaaatggggaatttggaaatgaaaacactgtaactg
B D                    Bonobo  aaa---aaaaa-----gatataaagaagaacaaaatggggaatttggaaatgaaaacactgtaactg
B D                   Gorilla  aaa---aaaaaaaaa-gatataaagaagaacaaaatggggaatttggaaatgaaaacgctgaaactg
B D                 Orangutan  aaa---aaaaaaaaa-ggtataaagaaaaacaaaatggggaatttggaaatgaaaatgctgtaactg
B D                    Gibbon  aaa---atatatata-tatataaagaagaacaaaatggggaatttggaaatgaaaatgctgtaactg
B D                    Rhesus  -aatgtaaaaaaaaa-gatataaagaagaacaaaatggagaatttggaaatgaaaatgctgtaactg
B D       Crab-eating macaque  -aatgtaaaaaaaaa-gatataaagaagaacaaaatggagaatttggaaatgaaaatgctgtaactg
B D                    Baboon  -aatgtaaaaaaaaa-gatataaagaagaacaaaatggggaatttggaaatgaaaatgctgtaactg
B D              Green monkey  -aatgt--aaaaaaa-gatataaagaagaacaaaatggggaatttggaaatgaaaatgttgtaactg
B D          Proboscis monkey  -aata-aaaaaaaaa-gatataaagaagaacaaaatggggaatttggaaatgaaaatgctgtaactg
B D  Golden snub-nosed monkey  -aata-aaaaaaaaa-gatataaagaagaacaaaatggggaatttggaaatgaaaatgctgtaactg
B D                  Marmoset  --a---aaaaataaa-gatataaagaagaacaaaatggaagatttggatgtaaaaatgctgtaactg
B D           Squirrel monkey  -aa---aaaaataca-gatataaagaagaacaaaatggaaaatttggaaataaaaatgctgtaattg
B D                   Tarsier  -------aaatagaa-gctataaagaagaaacaaatgtggattttggaaattaaaatatagtaaca-
B D                  Bushbaby  -------aaaaaata-gatgtaaagaaaaaccaaatagaaatgttggaactgaaaacacaataatgg
B D                Tree shrew  -----atgaatagga-aatatgcagaagaactaaataaaaattttggaactaaaagtattaa-----
B D                     Mouse  ===================================================================
B D                       Dog  ===================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 20 and 21 in window
B D             Green monkey 178bp
B D                 Marmoset 1bp

Alignment block 21 of 36 in window, 77421381 - 77421384, 4 bps 
B D                     Human  taac
B D                     Chimp  taac
B D                    Bonobo  taac
B D                   Gorilla  taac
B D                 Orangutan  aaac
B D                    Gibbon  aaat
B D                    Rhesus  aaat
B D       Crab-eating macaque  aaat
B D                    Baboon  aaat
B D          Proboscis monkey  aaat
B D  Golden snub-nosed monkey  aaat
B D                  Marmoset  aaat
B D           Squirrel monkey  aaat
B D                   Tarsier  -aat
B D                  Bushbaby  aaat
B D                Tree shrew  taac
B D                     Mouse  ====
B D                       Dog  ====
B D              Green monkey  ====
B D               Mouse lemur  NNNN

Alignment block 22 of 36 in window, 77421385 - 77421923, 539 bps 
B D                     Human  --atatatttcagtaaatggaatcaaaagcaccaattaaa----ag---agatt-----------tattt
B D                     Chimp  --atatatttcagtaaatggaatcaaaagcaccaattaaa----ag---agatt-----------tattt
B D                    Bonobo  --atatatttcagtaaatggaatcaaaagcaccaattaaa----ag---agatt-----------tattt
B D                   Gorilla  --atatatttcagtaaatggaatcaaaagcaccaattaaa----ag---agatt-----------tattt
B D                 Orangutan  --atatatttcagtaaatggaatcaaaaacaccaattaaa----ag---agatt-----------tattt
B D                    Gibbon  --atatatttcagtaaatggaatcaaaagcaccagttaaa----ag---agatt-----------tattt
B D                    Rhesus  --atatatttcagtaaatggaatcaaaagcaccaatt-aa----ag---agatttgaaga--gtatattt
B D       Crab-eating macaque  --atatatttcagtaaatggaatcaaaagcaccaatt-aa----ag---agatttgaaga--gtatattt
B D                    Baboon  --atatatttcagtaaatggaatcaaaagcaccaatt-aa----ag---agatttgaaga--gtatattt
B D              Green monkey  --atatatttcagtaattggaatcaaaagcaccaatt-aa----ag---agatttgaaga--gtatattt
B D          Proboscis monkey  --atatatttcagtaaatggaatcaaaagcactaattaaa----ag---agatttgaaga--gtatattt
B D  Golden snub-nosed monkey  --atatatttcagtaaatggaatcaaaagcactaattaaa----ag---agatttgaaga--gtatattt
B D                  Marmoset  --aaatgtttcagtaaatggaatcaaaagcaccaattaaa----agacaagatttgaaga--gtatattt
B D           Squirrel monkey  --aaatatttcagtaaatggaatcaaaagcaccaattaaa----agacaagatttgaaga--gtatattt
B D                   Tarsier  --aaatagttcagtaaatgaactcaaaaacatcaacaaaactatag---agattaggaga--gtatatat
B D                  Bushbaby  --aaatagttcagtaactgtacgcaaaagcgccagttgaa----ag---agattagaacactgtactttt
B D                Tree shrew  ataaataaat-agtaaat-aactcaaaagcatccatgaaa-gacag---agata-taaga--gtagattt
B D                     Mouse  ======================================================================
B D                       Dog  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  taaaac---att--gcca---------------aattatatgctgtctacaagaaacccacttcaaataa
                        Chimp  taaaac---att--acca---------------aattatatgctgtctacaagaaacccacttcaaataa
                       Bonobo  taaaac---att--acca---------------aattatatgctgtctacaagaaacccacttcaaataa
                      Gorilla  taaaac---att--acca---------------aattatatgctgtctacaagaaacccacttcaaataa
                    Orangutan  taaaac---att--acca---------------aattatatgctgtgtacaagaaactcacttcaaataa
                       Gibbon  gaaaac---att--acca---------------aattatatgctgtgtagaagaaactcacttcaaataa
                       Rhesus  taaaag---att--acca---------------aattatatgctgtctacaagaaactcacttcaaataa
          Crab-eating macaque  taaaag---att--acca---------------aattatatgctgtctacaagaaactcacttcaaataa
                       Baboon  taaaag---att--acca---------------aattatatgctgtctacaagaaactcacttcaaataa
                 Green monkey  taaaag---att--acca---------------aattatatgctatctataagaaactcacttcaaataa
             Proboscis monkey  taaaag---att--acca---------------aattatatgctgtctataagaaactcacttcaaataa
     Golden snub-nosed monkey  taaaag---att--acca---------------aattatatgctgtctataagaaactcacttcaaataa
                     Marmoset  taaaac---att--acta---------------aattatatgctttctacaagaaacccacttcaaatga
              Squirrel monkey  gaaaac---att--acca---------------aattatatgctttctacaagaaacccacttcaaataa
                      Tarsier  ttattcttaata--gcca---------------aattatattctgtctacaagaaac-----tccaatat
                     Bushbaby  taaatc---actagactacatactggtatatataactatatgctgtatataagaaattcatttcaagtac
                   Tree shrew  taaaaa---gtg--acaa---------------aactatatattctctataattaacttacttcaaataa
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  aacaacataagcagatcagcagtaaaaatatggaaaaag----at-----atttaaacatttattggagg
                        Chimp  aacaacataagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttattggagg
                       Bonobo  aacaacataagcacattaacagtaaaagtatggaaaaag----at-----atttaaacatttattggagg
                      Gorilla  aacaacataagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttattggagg
                    Orangutan  aacaacataagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
                       Gibbon  aacaacataagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttattggagg
                       Rhesus  aacaacattagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
          Crab-eating macaque  aacaacattagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
                       Baboon  ---aacattagcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
                 Green monkey  aactacatttgcagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
             Proboscis monkey  ---aacataaacagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
     Golden snub-nosed monkey  ---aacataaacagattaacagtaaaagtatggaaaaag----at-----atttaaacatttatcagagg
                     Marmoset  aacaatataagctgattaatagtaaaagcatgaaaaaagatagat-----atttaaacatttatcagagg
              Squirrel monkey  aacaacataggctgattaacagtaaaaacatgagaaaagataaat-----atttaaacatttattagagg
                      Tarsier  gacaacacaggcagattaaaagaaaaaggatggaaaaag----at----cacagaaacacatattacagg
                     Bushbaby  ca---------------agaagtaaaagaatggcaaaag----atagatcatgtaaatgtgaatcagagg
                   Tree shrew  aacaaaataggcatattggaagtta------------------at-------------------------
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  gaagcaggagtagtaatattagcataagataaagt-agactttggaaaaaaataaagtttactagtgaca
                        Chimp  gaagcaggagtagtaatattagcataagataaagt-agactttggaaaaaaataaagtttactagtgaca
                       Bonobo  gaagcaggagtagtaatattagcataagataaagt-agactttggaaaaaaataaagtttactagtgaca
                      Gorilla  gaaacaggagtagtaatattagcataagataaagt-agactttgaaaaaaaataaactttactagtgaca
                    Orangutan  gaagcaggagtagtaatattagcataagataaagt-agactttgg-aaaaaataaaatttactagtgaca
                       Gibbon  gaagcaggagtagtaatattagcataagataaagt-agactttgg-aaaaaataaaatttactagtgaca
                       Rhesus  gaagcaggagtagtaatattagcataagataaagt-atactttgg-aaaaaataaaatttactagtgaca
          Crab-eating macaque  gaagcaggagtagtaatattagcataagataaagt-atactttgg-aaaaaataaaatttactagtgaca
                       Baboon  gaagcaggaatagtaatattagcataagataaagt-atactttgg-aaaaaataaaatttactagtgaca
                 Green monkey  gaagcaggagtagtaatattagcgtaagataaagt-atactttgg-aaaaaataaaatttactagtgaca
             Proboscis monkey  gaagcaggagtagtaatattagcataagataaagt-atactttgg-aaaaaataaaatttactagtgaca
     Golden snub-nosed monkey  gaagcaggagtagtaatattagcataagataaagt-atactttgg-aaaaaataaaatttactagtgaca
                     Marmoset  gaagcaggagtagtaatattagcataagataaagt-ggactttgg-aaaaaataaaatttactagtgaca
              Squirrel monkey  gaagcaggagtcgtaaccttagcataagataaagt-ggactttgg-aaaa---aaaatttacgagtgaca
                      Tarsier  aaagcaggaatagttgtattaatataagataaagt--gactttgt-aaataagaaaatttaccagagata
                     Bushbaby  aaagcaggcatggttatattaataaacaatgaaatgggactttgg-ataa---aaaatttaccagagact
                   Tree shrew  --agaaggagtagcta-----------aacaaagt-atactttgg-aaaaatgaaaatttactagaaaca
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  gaaaggga---cattatataatgataaaacagttaaactaacaag----aaaaaaatatcaatcctaaat
                        Chimp  gaaaggga---cattatagaataataaaacagttaaactaacaag----aaaaaaatatcaatcctaaat
                       Bonobo  gaaaggga---cattatataataataaaacagttaaactaacaag----aaaaaaatatcaatccaaagt
                      Gorilla  gaaaggga---cattatatagtgataaaacagttaaactaacaag----aaaaaaatatcaatcctaaat
                    Orangutan  gaaaggga---cattatataatgataaaacagttaaactaacaag----aaaaaaatatcaatcccaaat
                       Gibbon  ggaaggga---cattatataatgataaaacagttaaactaacaag----aaaaaaatatcaatcctaaat
                       Rhesus  aaaaggga---cattacataatgataaaac----aaactaacaag----aaaaaaatatcaatcctaaat
          Crab-eating macaque  aaaaggga---cattacataatgataaaac----aaactaacaag----aaaaaaatatcaatcctaaat
                       Baboon  aaaaggga---cattacataatgataaaac----aaactaacaag----aaaaaaagatcactcctaaat
                 Green monkey  aaaaggga---cattacataatgataaaac----aaactaacaag----aaaaaaatatcaatcctaaat
             Proboscis monkey  gaaaggga---cattatataatgataaaac----aaactcacaag----aatacaatatcaatcctaaat
     Golden snub-nosed monkey  gaaaggga---cattatataatgataaaac----aaactcacaag----aaaacaatatcaatcctaaat
                     Marmoset  aaaaggga---cattatataacgataaagcagttaaactaacaag-aaaaaaaaaatcccaatcctaaat
              Squirrel monkey  aaaaggga---cattatataatgataaagcaggtaagctaataagaaaaaaaaaaatcccaatcctaaat
                      Tarsier  gaaaggga---cattatataatgataaaatggtcaattctacaag--------acataccaactctaaat
                     Bushbaby  tacagggacttcattatacagtg--------------------------aaaaaattactcatcccataa
                   Tree shrew  aaaaagga---cattatataacaataaaaaaggccaatccaccaa----gaagatataccaattctaatt
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  gcatatgcaccaaacaatacagatgcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
                        Chimp  tcatatgcaccaaacaatacagatgcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
                       Bonobo  gcatatgcaccaaacaatacagatgcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
                      Gorilla  gcatatgcaccaagcaatacagatgcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
                    Orangutan  gcatatgcaccaaacaatacagatgcaaactagatgaagcaaaaactgatagaaac-t---agaaggaga
                       Gibbon  gcatatgcaccaaacaatacagatgcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
                       Rhesus  gcatatgcaccaaaaaatagagaagcaaattagatgaagcaaaaactgatag-aac-t---agaaggaga
          Crab-eating macaque  gcatatgcaccaaaaaatagagaagcaaattagatgaagcaaaaactgatag-aac-t---agaaggaga
                       Baboon  gcatatgcaccaaacaatagagaagcaaattagatgaagcaaaaactgatag-aac-t---agaaggaga
                 Green monkey  gcatatgcaccaaataatagagaagcaaattagatgaagcaaaaattgatag-aac-t---agaaggaga
             Proboscis monkey  gcatatgcaccaaacaatagagaagcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
     Golden snub-nosed monkey  gcatatgcaccaaacaatagagaagcaaactagatgaagcaaaaactgatag-aac-t---agaaggaga
                     Marmoset  gcatatgcaccaaacaacagagatgcaaattatatgaagcaaaaactgatag-aactt---agaaggaaa
              Squirrel monkey  gcatatgtaccaaacaacagagatgcaaattatatgaagcaaaaactggtag-aactt---agaaggaaa
                      Tarsier  gtctatgtatcaaacaacagagcggcaaaatacatgaaacaaaacttgacag-aac-tgaaagaaaaaaa
                     Bushbaby  gaagacacacaaacctccacaaatttaaaa----------aaaaaagtatgt-tat-t---tgatgacga
                   Tree shrew  atgtatgccccaaacaacagaggagtaagatatatgaagtaaaaacagatag-agc-a---aaaaagaga
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  aagaggcaaatctggaattatagttaagaacttc----aacccc-ctttctcaacaattgatacaacaac
                        Chimp  aagaggcaaatctggaattatagttaagaacttc----aacccc-ctttctcaacaattgatacagcaac
                       Bonobo  aagaggcaaatctggaattatagttaagaacttc----aacccc-ctttctcaacaattgatacagcaac
                      Gorilla  aagaggcaaatctggaattatagttaagaacttc----aacacc-ctttctcaacaattgatataacaac
                    Orangutan  aagaggcaaatctggaattatagttaagaacttc----aacacc-ctttctcaacaattgatacaacaac
                       Gibbon  aagaggcaaatctggaattatagttaagaacttc----aacacc-ctttctcaacaattgata---caac
                       Rhesus  aagaggcaaatctggaattatagttaagaacttc---aaacacc-ctttctcaacaattgatacaacaac
          Crab-eating macaque  aagaggcaaatctggaattatagttaagaacttc---aaacacc-ctttctcaacaattgatacaacaac
                       Baboon  aagaggcaaatctggaattatagttaagaacttc---aaacacc-ctttctcaacaattgatacaacaac
                 Green monkey  aagaggcaaatctggaattatagttaagaacttc---aaacacc-ctttcccaacaattgatacaacaac
             Proboscis monkey  aagaggcaaatctggaattatagttaagaacttc---aaacacc-ccttctcaacaattgataccacaac
     Golden snub-nosed monkey  aagaggcaaatccggaattatagttaagaacttc---aaacacc-ccttctcaacaattgataccacaac
                     Marmoset  aagaaggaaatctggaattacagttaagaacttc----aaaccc-ctttctcaacagttgatagaacaac
              Squirrel monkey  aagaagcaaatctggaattacagtttagaacttc----agcaca-ttttctcaacagttgatagaacaac
                      Tarsier  gagagaaacatgtacaattatagttaaagacctt----aacatc-ccttcttaacaattgataaaacaac
                     Bushbaby  tggagtgacatgagga-----aggtaagaacatctctgaacatc-c-------agaaatgctagaat-gc
                   Tree shrew  aagaaacaaatctaaaatta----taaaaattta----aacatctctttcttaacattcattagaac---
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  taaagagaa----------------------------------aaatcagtgatgaga-acttacaga--
                        Chimp  taaagagaa----------------------------------aaatcagtgatgaga-acttacaga--
                       Bonobo  taaagagaa----------------------------------aaatcagtgatgaga-acttacaga--
                      Gorilla  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
                    Orangutan  taaagagaa----------------------------------aaatcagtgatgaga-acttacaga--
                       Gibbon  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
                       Rhesus  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
          Crab-eating macaque  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
                       Baboon  taaagagaa----------------------------------aaatcagtggtgaga-acatacaga--
                 Green monkey  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
             Proboscis monkey  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
     Golden snub-nosed monkey  taaagagaa----------------------------------aaatcagtggtgaga-acttacaga--
                     Marmoset  taaagag-a----------------------------------aaatcagtggtgaga-actcaaagt--
              Squirrel monkey  taaaggg-a----------------------------------aaatcagtggtgaga-acttaaaaa--
                      Tarsier  taatgag-a----------------------------------aaatctgtaaagagataggaaaact--
                     Bushbaby  taaagaaaatattacacaattcccattgtgctttcaacttcttaattcagagg-aata-atctccaga--
                   Tree shrew  -agagagaa----------------------------------aaatcagtga--gga-tctagaagaat
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  -caactaaatca--aca----agatctaatcaccatttacagaacatttcactcaacaa--tagcagaaa
                        Chimp  -caactaaatca--aca----agatctaatcaccatttacagaacatttcactcaacaa--tagcagaaa
                       Bonobo  -caactaaatca--aca----agatctaatcaccatttacagaacatttcactcaacaa--tagcagaaa
                      Gorilla  -caactaaatca--aca----agatgtaatcaccatttacagaacatttcactcaacaa--tagcagaaa
                    Orangutan  -caactaaatca--aca----agatctaatcagcatttacagaacatttcactcaacag--tagcagaaa
                       Gibbon  -caactaaatca--aca----acatctaatcaccatttacataacatttcactcaacaa--tagcagaaa
                       Rhesus  -caactaaatca--aca----agatgtaatcaccgtttacagaacatttcactcaacga--tagcagaaa
          Crab-eating macaque  -caactaaatca--aca----agatgtaatcaccgtttacagaacatttcactcaacga--tagcagaaa
                       Baboon  -caactaaatca--aca----agatttaatcaccgtttacagaacatttcactcaacga--tagcagaaa
                 Green monkey  -caactaaatca--aca----agatctaatcaccatttacagaacatttcactcaacga--tagcagaaa
             Proboscis monkey  -caactaaatca--aca----agatctaatcaccatctacagaacatttcactcaacaa--tagcagaaa
     Golden snub-nosed monkey  -caactaaatca--aca----agatctaatcaccatctacagaacatttcactcaacaa--tagcagaaa
                     Marmoset  -caatgaaatca--aca----agatctaatcagcatttacagaatttttcactcaacaa--tagcagaat
              Squirrel monkey  -caatgaaatca--aca----agatctaatcagcatttacagaatttttcactcaacaa--tagcagaat
                      Tarsier  -caaccacatcc--cca----acatctaagcaacatttatagaactttccactcaacat--gatcagaat
                     Bushbaby  -ctagaaaattaggaca----aa----aatcaacattaacaaactgattctcttaaccagtttgatgaaa
                   Tree shrew  tcaatacaacca--ccaaaggagatctaatcaacat-tattgaatatttcacccaacaa--tagcagaat
                        Mouse  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ac-----ctattcaactatctata-gaa
                        Chimp  ac-----ctattcaactatctata-gaa
                       Bonobo  ac-----ctattcaactatctata-gaa
                      Gorilla  ac-----ctattcaactatctata-gaa
                    Orangutan  ac-----ctattcaactatctata-gaa
                       Gibbon  ac-----ctattcaactatctata-gaa
                       Rhesus  ac-----ctattcaactatctata-gaa
          Crab-eating macaque  ac-----ctattcaactatctata-gaa
                       Baboon  ac-----ctattcaactatctata-gaa
                 Green monkey  ac-----ctattcaactatttata-gaa
             Proboscis monkey  ac-----ctattcaactatctata-gaa
     Golden snub-nosed monkey  ac-----ctattcaactatctataggaa
                     Marmoset  ac-----caattcaaaaatctata-gaa
              Squirrel monkey  ac-----caattcaacaatctata-gaa
                      Tarsier  acatattcttttcaaatgcctatg-aaa
                     Bushbaby  at-----atttcaaattgtatatg-aaa
                   Tree shrew  atacagtcttttcaaatatccatg-gaa
                        Mouse  ============================
                          Dog  ============================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 22 and 23 in window
B D                 Bushbaby 61bp

Alignment block 23 of 36 in window, 77421924 - 77421968, 45 bps 
B D                     Human  cataaagtaaaatagataacat-agccacaaaacacatttccacaa
B D                     Chimp  cgtaaagtaaaatagataacat-agccacaaaacacatttccacaa
B D                    Bonobo  cgtaaagcaaaatagataacat-agccacaaaacacatttccacaa
B D                   Gorilla  cataaagtaaaatagataacat-agccacaaaacacatttccgcaa
B D                 Orangutan  cataaagtaaaatagataacat-agccacgaaacacatttccacaa
B D                    Gibbon  cataaagtaaaatagataacat-agccgcaaaacgcatttccacaa
B D                    Rhesus  caaaaagtgaaacagataatat-agccacaaaacacatttccacaa
B D       Crab-eating macaque  caaaaagtgaaacagataatat-agccacaaaacacatttccacaa
B D                    Baboon  caaaaagtgaaacagataatat-agccacaaaacacatttccacaa
B D              Green monkey  caaaaagtgaaacagataatat-agccacaaaacacatttccacaa
B D          Proboscis monkey  aaaaaagtaaaatagataatat-agccacaaaacacatttccacaa
B D  Golden snub-nosed monkey  aaaaaagtaaaatagataatgt-agccacaaaacacatttccacaa
B D                  Marmoset  cataaagtaagatagataatat-agccacaaaatgcatttccacaa
B D           Squirrel monkey  cataaagtaagatagataatac-aaccacaaaattcatttccacaa
B D                   Tarsier  cataaaccaagacggattatataaaccacaaaacaagtctccacaa
B D                Tree shrew  ------taaaaatagatcatattggtcattaaaaaa---tccacat
B D                     Mouse  ==============================================
B D                  Bushbaby  ==============================================
B D                       Dog  ==============================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 24 of 36 in window, 77421969 - 77421992, 24 bps 
B D                     Human  atttaaaa-caagagtatattctct
B D                     Chimp  atttaaaa-caagagtatattctct
B D                    Bonobo  atttaaaa-caagagtatattctct
B D                   Gorilla  atttaaaa-c--gagtatattctct
B D                 Orangutan  atttaaag-caagagtatattctct
B D                    Gibbon  atttaaag-caagagtatgttctct
B D                    Rhesus  atttaaaagcaagagtatattctct
B D       Crab-eating macaque  atttaaaagcaagagtatattctct
B D                    Baboon  atttaaaagcaaaagtatattctct
B D              Green monkey  atttaaaagcaagaatatattctct
B D          Proboscis monkey  attgaaaagcaagagtatattctct
B D  Golden snub-nosed monkey  attgaaaagcaagagtatattctct
B D                  Marmoset  atctaaaagcaagagtgtattctct
B D           Squirrel monkey  atttaaaagcaagagtgtattctct
B D                   Tarsier  atttaaaggaatgagtatattttct
B D                Tree shrew  atataaaagaaaggctgttttca--
B D                       Dog  atataaaa-----cgtgtgttttct
B D                     Mouse  =========================
B D                  Bushbaby  =========================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 25 of 36 in window, 77421993 - 77422041, 49 bps 
B D                     Human  gaccacagtgaaataaaactggaaa-------------gacaacaagaaaatttc---------------
B D                     Chimp  gaccacagtgaaataaaactggaaa-------------gacaacaagaaaatttc---------------
B D                    Bonobo  gaccacagtgaaataaaactggaaa-------------gacaacaagaaaatttc---------------
B D                   Gorilla  gatcacagtgaaatgaaactggaaa-------------gacaacaagaaaatttc---------------
B D                 Orangutan  gaccacagtgaagtaaaactggaaa-------------gacaacaagaaaatttc---------------
B D                    Gibbon  gaccacagtgaaataaaactggaaa-------------gacaacaagaaaatttc---------------
B D                    Rhesus  gaccacagtgaaataaaactggaac-------------aacaacaagaaaatttc---------------
B D       Crab-eating macaque  gaccacagtgaagtaaaactggaac-------------gacaacaagaaaatttc---------------
B D                    Baboon  gaccacagtgaaataaaactgaaac-------------gacaacaagaaaatttc---------------
B D              Green monkey  gaccacagtgaaataaaactggaac-------------gacaacaagaaaatttc---------------
B D          Proboscis monkey  gaccacagtgaaataaaactggaac-------------gacaacaagaaaatttc---------------
B D  Golden snub-nosed monkey  gaccacagtgaaataaaactggaac-------------gacaacaagaaaatttc---------------
B D                  Marmoset  gaccacagtgaaatgaaactggaag-------------gataataagaagatttc---------------
B D           Squirrel monkey  gaccacagtgaaataaaactggaag-------------gataacaagaaaatttc---------------
B D                   Tarsier  gaccacaatggaatcaatgtagaaa-------------aataataag---atccc---------------
B D                  Bushbaby  gaacacaa-gaaagaaggctttaaa-------------tttagcgggcaagtttt---------------
B D                Tree shrew  gcccacaatggaatcaaactagaaa-------------gataacaggaaaatctccatttagaaatgctg
B D                       Dog  tgccacgatgaaatctaactagaaaccaataaaattaggatagcaagaaaatatg---------------
B D                     Mouse  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  -----------a-------aaatat
                        Chimp  -----------a-------aaatat
                       Bonobo  -----------a-------aaatat
                      Gorilla  -----------a-------aaatat
                    Orangutan  -----------a-------aaatat
                       Gibbon  -----------g-------aagtat
                       Rhesus  -----------a-------aaatat
          Crab-eating macaque  -----------a-------aaatat
                       Baboon  -----------a-------aaatat
                 Green monkey  -----------a-------aaatat
             Proboscis monkey  -----------a-------aaatac
     Golden snub-nosed monkey  -----------a-------aaatac
                     Marmoset  -----------a-------aaatat
              Squirrel monkey  -----------t-------aaatat
                      Tarsier  -----------a-------aaacat
                     Bushbaby  -----------agttccacatccat
                   Tree shrew  agagactgacgg-------aaatat
                          Dog  -----------a-------aaacac
                        Mouse  =========================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 25 and 26 in window
B D               Tree shrew 225bp

Alignment block 26 of 36 in window, 77422042 - 77422341, 300 bps 
B D                     Human  ttgaaaatgctggaagac----------------------------------aggaaga------tatta
B D                     Chimp  ttgaaaatgctggaagac----------------------------------aggaaga------tatta
B D                    Bonobo  ttgaaaatgctggaagac----------------------------------aggaaga------tatta
B D                   Gorilla  ttgaaaatgctggaagac----------------------------------aggaaga------tatta
B D                 Orangutan  ttgaaaatgctggaagac----------------------------------aggaaga------tatta
B D                    Gibbon  ttgaaaatgctggaagac----------------------------------aggaaga------tatta
B D                    Rhesus  ttgaaaatgctggaagaa----------------------------------aggaaga------tatta
B D       Crab-eating macaque  ttgaaaatgctggaagaa----------------------------------aggaaga------tatta
B D                    Baboon  ttgaaaatgctggaagaa----------------------------------aggaaga------tatta
B D              Green monkey  ttgaaaatgctggaagag----------------------------------aggaaga------tatta
B D          Proboscis monkey  ttgaaaatgcttgaagag----------------------------------aagaagg------tacta
B D  Golden snub-nosed monkey  ttgaaaatgcttgaagag----------------------------------aggaagg------tacta
B D                  Marmoset  ttgaaaatgctggaaggg----------------------------------aggaaga------tatta
B D           Squirrel monkey  ttgaaaatgctggaaggg----------------------------------aggaaga------tatta
B D                   Tarsier  ttggaaaggatggaaggcta--------------------------------aagaaaa------tatca
B D                  Bushbaby  ttgtcaatgc---aagattt--------------------------------attaagatcattctaatg
B D                Tree shrew  ttcaatatgttggaggactaaagaaaggggatcatggcataactagactctgtgggagg------tactc
B D                       Dog  ttggaaattctggaaaact---------------------------------aaatcaa------tatta
B D                     Mouse  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ctcaatttccaattcattttcaacttctgtttt---tgcaggagaataa----------tctc----t--
                        Chimp  ctcaatttccaattcgttttcaacttctgtttt---tgcaggagaataa----------tctc----t--
                       Bonobo  ctcaatttccaattcgttttcaacttctgtttt---tgcaggagaataa----------tctc----t--
                      Gorilla  ctcaatttccaattcattttcaacttctgtttt---tgcaggagaataa----------tctc----t--
                    Orangutan  ctcaatttccaattcgttttcaacttctgtttt---tgcaggagaataa----------tctc----t--
                       Gibbon  ctcaatttccaatttgttttcaacttctgtttt---tgcaggagaataa----------tctc----t--
                       Rhesus  ctcaattaccaatttgctttcaatttctgtttt---tgcaggggaataa----------tctc----t--
          Crab-eating macaque  ctcaattaccaatttgctttcaatttctgtttt---tgcaggggaataa----------tctc----t--
                       Baboon  ctcaatttccaatttgctttcaatttctgtttt---tgcaggggaataa----------cctc----t--
                 Green monkey  ctcaatttccaatttgctttcaatttctgtttt---tgcaggggaataa----------tctc----t--
             Proboscis monkey  ctcaatttccaatttgtttttaatttctgtttt---tgcaggagaataa----------tctc----t--
     Golden snub-nosed monkey  ctcaatttccaatttgtttttaatttctgtttt---tgcaggagaataa----------tctc----t--
                     Marmoset  ttcaattaacaattaattttcaacttct-tttt---tgcaggagaatga----------tctc----c--
              Squirrel monkey  ttcaattaccaatttgttttcaagttat-tttt---tgc---agaatga----------tctc----c--
                      Tarsier  ctcaatcctcattttgttctttaacctt-ttta---tccaggagaacaa----------tcgc----c--
                     Bushbaby  cataaatttcaggttagactaa---cctggttt---gtgaggaaaaaaaccaaactgactctcaaatc--
                   Tree shrew  atctctctctctctctctctctctctctctctctcatgcataagtacac----------actc----ttt
                          Dog  ttcaatatccattttgcttttaatttatgtatt-----aaggagagtag----------tctc----c--
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ------------------------------------------------------gcactagaaaat-tag
                        Chimp  ------------------------------------------------------gcactagaaaat-tag
                       Bonobo  ------------------------------------------------------gcactagaaaat-tag
                      Gorilla  ------------------------------------------------------gtactagaaaat-tag
                    Orangutan  ------------------------------------------------------gcactagaaaat-tag
                       Gibbon  ------------------------------------------------------gcactagaaaat-tag
                       Rhesus  ------------------------------------------------------gcactagaaaat-tag
          Crab-eating macaque  ------------------------------------------------------gcactagaaaat-tag
                       Baboon  ------------------------------------------------------gcactagaaaat-tag
                 Green monkey  ------------------------------------------------------gcactagaaaat-tag
             Proboscis monkey  ------------------------------------------------------gcactagaaaat-tag
     Golden snub-nosed monkey  ------------------------------------------------------gcactagaaaat-tag
                     Marmoset  ------------------------------------------------------acactggaaaat-tag
              Squirrel monkey  ------------------------------------------------------acactggaaaac-tag
                      Tarsier  ------------------------------------------------------acactagaaaat-tga
                     Bushbaby  ------------------------------------------------------gcattacaaaat----
                   Tree shrew  catgaacaaagaataaaattaaacaaaaaatattaagtaattgaattccaagacacattagaagatagaa
                          Dog  ------------------------------------------------------acactagaaaac-agg
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  aac---------------------------------------------------aaatatctagtatgtc
                        Chimp  aac---------------------------------------------------aaatatctagtatgtc
                       Bonobo  aac---------------------------------------------------aaatatctagtatgtc
                      Gorilla  aat---------------------------------------------------aaatatctagtatgtc
                    Orangutan  aac---------------------------------------------------aaatatctagtatgtc
                       Gibbon  aac---------------------------------------------------aaatatctagtatgtc
                       Rhesus  aac---------------------------------------------------aaatatctagtatgtc
          Crab-eating macaque  aac---------------------------------------------------aaatatctagtatgtc
                       Baboon  aac---------------------------------------------------aaatatctagtatgtc
                 Green monkey  aac---------------------------------------------------aaatatctagtatgtc
             Proboscis monkey  aac---------------------------------------------------aaatatctagtatgtc
     Golden snub-nosed monkey  aac---------------------------------------------------aaatatctagtatgtc
                     Marmoset  aac---------------------------------------------------aaatatctagtatgtc
              Squirrel monkey  aac---------------------------------------------------aaatatcgagtatgtc
                      Tarsier  aacaaatatcaacattagaaaac--aatctcaagatacactggtagat--cagaaaatatcaagtagatc
                     Bushbaby  agc---------------------------------------------------aaccacctg-------
                   Tree shrew  aga---------------------------------------------------aaacatcaagtaggtt
                          Dog  gga-aaaatcaacagtaatgaactaaatcccaacatacacaagaagatagtagaatatttctagtaggtc
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  attaatggtc-ccagtgtatgact----------------gatggatagat---g-g-------------
                        Chimp  attaatggtc-ccagtgtatgact----------------gatggatagat---g-g-------------
                       Bonobo  attaatggtc-ccagtgtatgact----------------gatggatagac---g-g-------------
                      Gorilla  attaatggtc-ccagtgtatgact----------------gatggatagat---g-g-------------
                    Orangutan  attaatggtc-ccagtgtatgact----------------gatggatagac---g-g-------------
                       Gibbon  attcatggtc-ccagtgtatgact----------------gatggatagat---g-g-------------
                       Rhesus  atcaatggtc-ccagtgtatgact----------------gatggatggat---g-g-------------
          Crab-eating macaque  atcaatggtc-ccagtgtatgact----------------gatggatggat---g-g-------------
                       Baboon  atcaatggtc-ccagtgtatgact----------------gatggatggat---g-g-------------
                 Green monkey  atcaatggtc-ccagtgtatgact----------------gatggatggat---g-g-------------
             Proboscis monkey  atcaatggtc-ccagtgtatgact----------------gatggatggat---g-g-------------
     Golden snub-nosed monkey  atcaatggtc-ccagtgtatgact----------------gatggatggat---g-g-------------
                     Marmoset  attaatggtc-ccagtgtatgact----------------gagggatggat---gta-------------
              Squirrel monkey  attaatggtc-ccagtgtatgact----------------gatggatggat---gta-------------
                      Tarsier  atacatggtc-gcatagtatgactattggatgggtgggtagatggatggat---g-gata---aacagga
                     Bushbaby  ---agtggtc-ccagaggataact----------------gatagatggat---g-aacaggtggcggat
                   Tree shrew  cttaatagacttttgaatatgact----------------gactgatggatcaag-g-------------
                          Dog  tttaagtgtc-ccagagtatgact----------------gataagtggtt---g-g-------------
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ---tgta------tagatgtattt--------------------------------tactttttacactg
                        Chimp  ---tgta------tagatgtattt--------------------------------tactttttacactg
                       Bonobo  ---tgta------tagatgtattt--------------------------------tactttttacactg
                      Gorilla  ---tgta------tagatgtattt--------------------------------tactttttacacta
                    Orangutan  ---tgta------tagatgtattt--------------------------------tactttttacactg
                       Gibbon  ---tgta------tagacatattt--------------------------------tactttttacactg
                       Rhesus  ---tgta------tagatgtattt--------------------------------tactctttacactg
          Crab-eating macaque  ---tgta------tagatgtattt--------------------------------tactctttacactg
                       Baboon  ---tgta------tagatgtattt--------------------------------taccctttacactg
                 Green monkey  ---tgta------tagatgtattt--------------------------------tactttttacactg
             Proboscis monkey  ---tgca------tagatgtattt--------------------------------tactttttacactg
     Golden snub-nosed monkey  ---tgca------tagatgtattt--------------------------------tgctttttacactg
                     Marmoset  ---taga------tagatgtattt--------------------------------tactccttacactg
              Squirrel monkey  ---taga------tagatgtattt--------------------------------tactccttacactg
                      Tarsier  ggatgaa------cagatgaactgacagacagatggacagataaaaaatggatggatactcttcacactg
                     Bushbaby  gtacgga------cgggtggcttt--------------------------------cactcttcacgtta
                   Tree shrew  ---tataaatggttgtgtgtttta--------------------------------tacccttcacatta
                          Dog  ------g------tagatggatat----------------------------------cccttcacattg
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  caccactacc---ttgtgattttatg--tcttttatccccagttga-ttatgagttacttggagaagggc
                        Chimp  caccactacc---ttgtgattttatg--tcttttatccccagttga-ttatgagttacttggagaaggtc
                       Bonobo  caccactacc---ttgtgattttatg--tcttttatccccagttga-ttatgagttacttggagaaggtc
                      Gorilla  caccactacc---ttgtgattttatg--tcttttatccccagttga-ttatgagttacttggagaagggc
                    Orangutan  caccactacc---ttgtgattttatg--tcttttatccccagttga-taatgagttacttggagaaaggc
                       Gibbon  caccactacc---ttgtgattttata--tctcttatccccagttga-ttatgagatacttggagaagggc
                       Rhesus  caccactacc---ttgtgactttatg--tcttttatccgcagttga-ttatgagttatttggagaagggc
          Crab-eating macaque  caccactacc---ttgtgactttatg--tcttttatccgcagttga-ttatgagttatttggagaagggc
                       Baboon  caccactacc---ttgtgactttatg--tcttttatccgcagttga-ttatgagttatttggagaagggc
                 Green monkey  caccactacc---ttgtgactttatg--tcttttatccgcagttga-ttatgagttatttggagaagggc
             Proboscis monkey  caccactacc---ttgtgactttatg--tcttttaaccgcagttga-ttatgagttatttggagaagggc
     Golden snub-nosed monkey  caccactacc---ttgtgactttatg--tcttttaaccgcagttga-ttatgagttatttggagaagggc
                     Marmoset  agtcacttcc---tcgtaattttatg--tcttttatctccagttta-ttatgtgttatttggagaaggac
              Squirrel monkey  cgtcactacc---tcataattttatg--tcttttatctccagttga-ttatgagttatttggagaaggac
                      Tarsier  cacgactccc---ttctgcgtgtatt--ttttttatccccggtaga-ttgtgaattatttggagaaggat
                     Bushbaby  caccactaac---ttgtg--tttatg--tcttttatccacagttgacccatgaattcttgggagaaagac
                   Tree shrew  taccactactacattgtgcttatacagctcttttgttcccaattga-ttatgaattctctgtagaaggaa
                          Dog  tactattatc---ttgtgcttgtatt--tcttttctgcccagttgt-ttataagctctctggaagaacag
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ctataatg-acaaatcttctctcttttttctttgtacc-agtgctttgaacatggtaa
                        Chimp  ctataagg-acaaatcttctctcttttttcttcgtacc-agtgctttgaacatggcaa
                       Bonobo  ctataagg-acaaatcttctctcttttttcttcgtacc-agtgctttgaacatggcaa
                      Gorilla  ctataagg-acaaattttctctcttttttctttgtacc-agtgctttgaacatggtaa
                    Orangutan  ctataagg-acacatcttctctctttcttctttgtacc-agtgctttgaacatggtaa
                       Gibbon  ctataagg-acaaatcttctctctttcttctttgtacc-agtgctttgaacatggtag
                       Rhesus  ctataagg-acaaatcttctctctctcttctttgtacc-agtgctttgaacatggtaa
          Crab-eating macaque  ctataagg-acaaatcttctctctctcttctttgtacc-agtgctttgaacatggtaa
                       Baboon  ctataagg-acaaatcttctctctctcttctttgtacc-agtgctttgaacatggtaa
                 Green monkey  ctataagg--caaatcttctctctctcttctttgtacc-agtgctttgaacatggtac
             Proboscis monkey  ctagaagg-acaaatcttctctctctcttctttgcacc-agtgctttgaacatggtaa
     Golden snub-nosed monkey  ctataagg-acaaatcttctctctctcttctttgtacc-agtgctttgaacatggtaa
                     Marmoset  ttataagg-acagatcttctctcttttttctttgtacc-agtgttttgaacatggtaa
              Squirrel monkey  ttataagg-acagatcttctctctttttcctttgtacc-agtgttttgaacatggtaa
                      Tarsier  ctttaaaaaataatttttttctgtttcttctttgtatc-actgccttgaacaaagtgg
                     Bushbaby  ccctaaag-agaaatcttctc--tttcttctttgtacc-agtgccttgaacacaggga
                   Tree shrew  ctata----ataaatcttctt--ttccttctttgtacc-agtgctttaaatacagtga
                          Dog  cactaagg-agaaattttgtctctttcttctttgtaccaaatgtcttgagcacagtgg
                        Mouse  ==========================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 26 and 27 in window
B D                      Dog 168bp

Alignment block 27 of 36 in window, 77422342 - 77422374, 33 bps 
B D                     Human  ttattcagaaattatag----ttgagtttaatgactg
B D                     Chimp  ttattcagaaattatag----ttgagtttaatgactg
B D                    Bonobo  ttattcagaaattatag----ttgagtttaatgactg
B D                   Gorilla  ttattcagaaattatag----ttgagtttaatgactg
B D                 Orangutan  ttattcagaaattatag----ttgagtttaatgactg
B D                    Gibbon  ttattcagaaattatag----ttgagtttaatgaccg
B D                    Rhesus  ttattcagaaattatag----ttgagtttaatgactg
B D       Crab-eating macaque  ttattcagaaattatag----ttgagtttaatgactg
B D                    Baboon  ttattcagaaattatag----ttgagtttaatgactg
B D              Green monkey  ttattcagaaattatag----ttgagtttaatgactg
B D          Proboscis monkey  ttattcagaaattatag----ttgagtttaatgactg
B D  Golden snub-nosed monkey  ttattcagaaattatag----ttgagtttaatgactg
B D                  Marmoset  ttattcagaaattatagtttattgagtttaacgactg
B D           Squirrel monkey  ttattcagaaattatag----ttgagtttaatgactg
B D                   Tarsier  tcactcagaaattataa----ctgggtttaataattg
B D                  Bushbaby  tcactcagaagttataa----ctgagcttaatgattg
B D                Tree shrew  ccactcagaa-ttatac----ttgaatttaataatta
B D                       Dog  ttttttaaaaactataa----ttgagttgaataattg
B D                     Mouse  =====================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 27 and 28 in window
B D               Tree shrew 199bp

Alignment block 28 of 36 in window, 77422375 - 77422525, 151 bps 
B D                     Human  --------cttaattgactgatcatttgaatgag-----tta-----tagacatagagaatccacttatg
B D                     Chimp  --------cttaattgactgatcatttgaatgag-----tta-----tagacatagagaatccacttatg
B D                    Bonobo  --------cttaattgactgatcatttgaatgag-----tta-----tagacatagagaatccacttatg
B D                   Gorilla  --------cttatttgactgatcatttgaatgag-----tta-----tagacatagagaatccacttatg
B D                 Orangutan  --------cttaattgactgatgatttgaatgag-----tta-----tagacatagagaatccacttatg
B D                    Gibbon  --------cttaattgactgatcatttgaatgag-----tta-----tagacatagagaatccacttagg
B D                    Rhesus  --------cttaattgactgatcatttgaatgaa-----tta-----tagacatagacaatccacttatg
B D       Crab-eating macaque  --------cttaattgactgatcatttgaatgaa-----tta-----tagacatagacaatccacttatg
B D                    Baboon  --------cttaattgactgatcatttgaatgaa-----tta-----tagacatagacaatccacttatg
B D              Green monkey  --------cttaattgactgatcatttgaatgag-----tta-----tagacatagacaatccacttatg
B D          Proboscis monkey  --------tttaattgactgatcatttgaatgaa-----tta-----taggcatagacaatctacttatg
B D  Golden snub-nosed monkey  --------tttaattgactgatcatttgaatgaa-----tta-----tagacatagacaatctacttatg
B D                  Marmoset  --------cttaat----tgatcatttgaatgag----ttta-----tagacatagagaatccacttatg
B D           Squirrel monkey  --------cttaattgactgatcatttgaatgag----ttta-----cagacatagagaatccacttatg
B D                   Tarsier  -----------------------------atgaa-----tta--------atgtagagtattcatttatg
B D                  Bushbaby  --------attcattaactgataattggaatgaattagttta-----tagacacagatgattcattcaca
B D                Tree shrew  --------cttaattaattgaacatttgagtgaattacctta-----tagacacacagaattaacttatg
B D                       Dog  attaattaattaatccattgatcacttgaatgaa-----ttagtttctagccatagagaattcatttatg
B D                     Mouse  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  aatggaccaat--ga-g-gttg-----------acctttgaagc--------------------------
                        Chimp  aatggaccaat--ga-g-gttg-----------accgttgaagc--------------------------
                       Bonobo  aatggaccaat--ga-g-gttg-----------accgttgaagc--------------------------
                      Gorilla  aatggaccaat--ga-g-gttg-----------accattgaagc--------------------------
                    Orangutan  aacggaccaat--ga-g-gttg-----------acctttgaagc--------------------------
                       Gibbon  aatggaccaat--ga-g-gttg-----------acctttgaagc--------------------------
                       Rhesus  aatggaccaat--ga-g-gttg-----------atctttgaagc------------------actgagat
          Crab-eating macaque  aatggaccaat--ga-g-gttg-----------atctttgaagc------------------actgatat
                       Baboon  aatggaccaat--ga-g-gttg-----------atctttgaagc------------------actgatat
                 Green monkey  aatggaccaat--ga-g-gttg-----------atctttgaagc------------------actgatat
             Proboscis monkey  aatggaccaat--ga-g-gttg-----------atctttgaagc--------------------------
     Golden snub-nosed monkey  aatggaccaat--ga-g-gttg-----------atctttgaagc--------------------------
                     Marmoset  aatgaaccaat--ga-g-gttg-----------acctttgaagc--------------------------
              Squirrel monkey  aatgaaccaat--ga-g-gttg-----------acctttgaagc--------------------------
                      Tarsier  aatgaaccaat--tagg-gttg-----------acctct-aagc--------------------------
                     Bushbaby  aattaaccaat--ta-gcattg-----------atctctgaagc--------------------------
                   Tree shrew  aatgaaccagttaaa-a-gctg-----------actacttaaagaagattatgatgataataaataaaaa
                          Dog  aataaaccaatt-ca-a-gttgatgaaccaattacctttaaaac--------------------------
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  -------------------------------acttatataaatgtttcatta--------gt--------
                        Chimp  -------------------------------acttatataaatgtttcatta--------gt--------
                       Bonobo  -------------------------------acttatataaatgtttcatta--------gt--------
                      Gorilla  -------------------------------acttataaaaatgtttcacta--------gt--------
                    Orangutan  -------------------------------acttatataaatgtttcatta--------gt--------
                       Gibbon  -------------------------------actgataaaaatgtttcatta--------gt--------
                       Rhesus  atgaggttgat-----------ctttgaagtactgatataaatgtttcatta--------gt--------
          Crab-eating macaque  atgaggttgat-----------ctttgaagcactgatataaatgtttcatta--------gt--------
                       Baboon  atgaggttgat-----------ctttgaagcactgatataaatgtttcatta--------gt--------
                 Green monkey  atgaggttgat-----------ctttgaagcactgatatcaatgtttcatta--------gt--------
             Proboscis monkey  -------------------------------actgatataaatgtttcatta--------gt--------
     Golden snub-nosed monkey  -------------------------------actgatacaaatgtttcatta--------gt--------
                     Marmoset  -------------------------------actgatataaatgtttcatta--------gt--------
              Squirrel monkey  -------------------------------actgatataaatgtttcatta--------gt--------
                      Tarsier  -------------------------------atgcacgta---------------------t--------
                     Bushbaby  -------------------------------actgccatcgatgtttcattaattactttat--------
                   Tree shrew  ataataataatgaaaaagctgactactaagtataactgtaattgctttacaa--------attattttca
                          Dog  -------------------------------actgccaa----gtttcataa--------attactttac
                        Mouse  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  tctcaactaatctctttttataaag--gaaacacatgtgaaaggagtgg
                        Chimp  tctcaactaatctctttttataaag--gaaacacatgtgaaaggagtg-
                       Bonobo  tctcaactaatctctttttataaag--gaaacacatgtgaaaggagtg-
                      Gorilla  tctcaactaatctctttttataaag--gaaacacatgtgaaaggagtgg
                    Orangutan  tctcaactaatctctttttataaag--taaacacatgtgaaaggagtga
                       Gibbon  tctcaactaatctctttttataaag--gaaacacatgtgaaaggaatgg
                       Rhesus  tctcaactaacctctctttacaaagaaaaaacacatgtgaaaggagtgg
          Crab-eating macaque  tctcaactaacctctctttacaaagaaaaaacacatgtgaaaggagtgg
                       Baboon  tctcaactaacctctctttacaaag--gaaacacatgtgaaaggagtgg
                 Green monkey  tctcaactaacctctctttataaag--gaaacacatgtgaaaggagtgg
             Proboscis monkey  tctcaactaacctctctttataaag--gaaacacatgtgaaaggagtag
     Golden snub-nosed monkey  tctcaactaacctctctttataaag--gaaacacatgtgaaaggagtag
                     Marmoset  tctcaactcatctctttttata---------------tgaaatgagtag
              Squirrel monkey  tctcaactaatctctttttata---------------tgaaatgagtgg
                      Tarsier  tctcaactaatatctttccataaag--aaaacacatgtgaaaggagtgg
                     Bushbaby  tgtcaactaattcctttacataaag--aacacgtctgtgaaatgcgggg
                   Tree shrew  ttttagctgatctctttctacaaag--gatacaattgtgaaattagtgg
                          Dog  tcttggtcaaaatcttttcataaag--gacacatgtgtgaaatgaatga
                        Mouse  =================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 28 and 29 in window
B D                  Tarsier 729bp

Alignment block 29 of 36 in window, 77422526 - 77422556, 31 bps 
B D                     Human  aaaataagaacaaaggcaaagaagccaacaa
B D                     Chimp  aaaataagaacaaaggcaaagaagccaacaa
B D                    Bonobo  aaaataagaacaaaggcaaagaagccaacaa
B D                   Gorilla  aaaataagaacaaaggcaaagaagcaaacaa
B D                 Orangutan  aaaataagaacaaaggcaaagaagccaacaa
B D                    Gibbon  aaaatcagaacagaggcaaagaagccaacaa
B D                    Rhesus  aaaataagaacaaaagcaaagaagccaacaa
B D       Crab-eating macaque  aaaataagaacaaaagcaaagaagccaacaa
B D                    Baboon  aaaataagaacaaaagcaaagaagccaacaa
B D              Green monkey  aaaataagaacaaaagcaaagaagccaacaa
B D          Proboscis monkey  aaaataagaacaaaagcaaagaaaccaacaa
B D  Golden snub-nosed monkey  aaaataagaacaaaagcaaagaagccaacaa
B D                  Marmoset  aaaataagaacaaaggtaaagaagctgacaa
B D           Squirrel monkey  aaaataagaacaaaggcaaagaagccaacaa
B D                   Tarsier  acaaaaagaacaaaggcaaagaagctaatat
B D                  Bushbaby  aaaacaagaacaaaagaaaaaagtcatacaa
B D                Tree shrew  aaaacaagaacaaaacaaaataagccaataa
B D                       Dog  gaaatcaaatccaagcaaaagaagccaataa
B D                     Mouse  ===============================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 29 and 30 in window
B D                 Bushbaby 59bp

Alignment block 30 of 36 in window, 77422557 - 77422623, 67 bps 
B D                     Human  atatgccaagcacaggaatttgtaattaaacttgaatcttccacacagtctggt------------tgca
B D                     Chimp  atatgccaagcacaggaatttgtaattaaacttgaatcttccacacagtctggt------------tgca
B D                    Bonobo  atatgccaagcacaggaatttgtaattaaacttgaatcttccacacagtctggt------------tgca
B D                   Gorilla  atatgccaagcacaggaatttgtaattaaacttgaatcttccacacagtctggt------------tgca
B D                 Orangutan  atatgtgaagcacaggaatttgtaattaaacttgaatcttccacacagtctggt------------tgca
B D                    Gibbon  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacacagtctggt------------tgca
B D                    Rhesus  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacgcagtctggt------------tgca
B D       Crab-eating macaque  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacgcagtctggt------------tgca
B D                    Baboon  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacgcagtctggt------------tgca
B D              Green monkey  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacgcagtctggt------------tgca
B D          Proboscis monkey  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacgcagtctggt------------tgca
B D  Golden snub-nosed monkey  atatgtcaagcacaggaatttgtaattaaacttgaatcttccacgcagtctggt------------tgca
B D                  Marmoset  at-----aagcacaggaatttgtaattaaatttaaatcttccagacagtctggt------------tgca
B D           Squirrel monkey  ataagtcaagcacaggaatttgtaattaaatttaaatcttccagacagtctggt------------tgca
B D                   Tarsier  atgtgccaagcacaggcatttgaaactagacttaaaccttt----cagtctgat------------catc
B D                Tree shrew  atgtgctgaactcaaacatttttaactaaacttaaattttcctgacagtctact------------cata
B D                       Dog  atgtgccaaacacaagcatttataatcaaacttacagctttctgacagtaggatcagatatacacacaca
B D                     Mouse  ======================================================================
B D                  Bushbaby  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  catggaaaa
                        Chimp  catggaaaa
                       Bonobo  catggaaaa
                      Gorilla  catggaaaa
                    Orangutan  catggaaaa
                       Gibbon  catggaaaa
                       Rhesus  catggaaaa
          Crab-eating macaque  catggaaaa
                       Baboon  catggaaaa
                 Green monkey  catggaaaa
             Proboscis monkey  catggaaaa
     Golden snub-nosed monkey  catggaaaa
                     Marmoset  catgcaaaa
              Squirrel monkey  catgcaaaa
                      Tarsier  tatgcaaaa
                   Tree shrew  cacacaaat
                          Dog  cacacacaa
                        Mouse  =========
                     Bushbaby  =========
                  Mouse lemur  NNNNNNNNN

Inserts between block 30 and 31 in window
B D                 Marmoset 148bp
B D          Squirrel monkey 144bp

Alignment block 31 of 36 in window, 77422624 - 77422751, 128 bps 
B D                     Human  atatggtcagtt----aatcatattttaatgtttaccaaaagggtatccaggacttcagatttaatataa
B D                     Chimp  atatggtcagtt----aatcatattttaatgtttaccaaaagggtatccaggacctcagatttaatataa
B D                    Bonobo  atatggtcagtt----aatcatattttaatgtttaccaaaagggtatccaggacctcagatttaatataa
B D                   Gorilla  atatggtcagtt----aatcatattttaatgtttaccaaaagggtatccaggacctcagatttaacataa
B D                 Orangutan  atatggtcagtt----aatcatattttaatgtttaccaaaagggtatccaggacctcagatttaatataa
B D                    Gibbon  atatggtcagtt----aaccatattttaatgtttaccaaaagggtatccaggagctcagatttaatataa
B D                    Rhesus  atatggtcagtt----aaccacattttaacatttaccgaaagggtatccaggaccttagatttaatataa
B D       Crab-eating macaque  atatggtcagtt----aaccacattttaacatttaccgaaagggtatccaggaccttagatttaatataa
B D                    Baboon  atatggtcagtt----aaccacattttaacatttaccgaaagggtatccaggaccttagatttaatataa
B D              Green monkey  atatggtcagtt----aaccacattttaacatttgccaaaagggtatccaagaccttagatttaatataa
B D          Proboscis monkey  atatggtcagtt----aaccacattttaacatttaccaaaagggtatccaggaccttagatttaatataa
B D  Golden snub-nosed monkey  atatggtcagtt----aaccacattttaacatttaccaaaagggtatccaggaccttaggtttcatataa
B D                  Marmoset  atatgatcagttaaccaaccacattttgacatttacaaaaagaggatccaggacctcagatttaatgtga
B D           Squirrel monkey  atatgatcagttaaccaaccacattttaacatttacaaaaagagtatccaggacctcagatttaatatga
B D                   Tarsier  atattgtcagtt----aacaatatactatcattt-tttaaatgataccattgacttta--tgtgatgtgt
B D                Tree shrew  atgtgatcagtc----aaccatatttaatcatttttttaaaagtataccactgactcatatataatatga
B D                       Dog  atatggtc--------aaacaaattttattatttagaaaaaggataatactgtcctcggatttcctatga
B D                     Mouse  ======================================================================
B D                  Bushbaby  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ataaatcaaatgatgttactctcaaataaaagtatatactcagaatatgatgatagaagctt
                        Chimp  ataaatcaaatgatgttactctcaaataaaagtatatactcagaatatgattatagaagctt
                       Bonobo  ataaatcaaatgatgttactctcaaataaaagtatatactcagaatatgattatagaagctt
                      Gorilla  ataaatcaaatgatgttactctcaaataaaagtatatactcagaatatgatgatagaagctt
                    Orangutan  ataaatcaaatgatgttactctcaaataaaagtatctactcagaatatgatgatagaagctt
                       Gibbon  ataaatctaatgatgttactctcaaataaaagcatatactcagattatgatgatagaagctt
                       Rhesus  ataaatcaaatgatgtcactgtcaaataaaagtatatactcagaatatgatgatagaagctt
          Crab-eating macaque  ataaatcaaatgatgtcactgtcaaataaaagtatatactcagaatatgatgatagaagctt
                       Baboon  ataaatcaaatgatgtcactgtcaaataaaagtataaactcagaatatgatgatagaagctt
                 Green monkey  ataaatcaaatgattttactgtcaaataaaagtatatactcagaatgtgatgatagaagctt
             Proboscis monkey  ataaatcaaatgatgttactgtcaaataaaagtatatactcagaatatgatgatagaagctt
     Golden snub-nosed monkey  ataaatcaaatgatgttactgtcaaataaaagtatatactcagaatatgatgatagaagctt
                     Marmoset  ataaatcaagtgatgttactgtcaaataaaactacatactcaggatatgatgatagaagctt
              Squirrel monkey  ataaatcaaatgatgttactgtcaaataaaactacatagtcaggatataatgatagaagctt
                      Tarsier  gtaaatcaaatgatgtaactgtcaaataaaagtacatactcaggatatgatcatagaagctt
                   Tree shrew  aaaagtgaaattatttaactaccaacaaaaagaataaactcaggatatgatgatcgaatctt
                          Dog  atgaatctaat--tataactgccaaatgaaagtgcatattcaggctatgatgatggaagcat
                        Mouse  ==============================================================
                     Bushbaby  ==============================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 31 and 32 in window
B D               Tree shrew 1282bp

Alignment block 32 of 36 in window, 77422752 - 77422994, 243 bps 
B D                     Human  atagttaggtcacaggaagtgatagtctcagtaggttctgctggtcagagtacatgtggaacatggtgac
B D                     Chimp  atagttaggtcacaggaagtgatagtctcagtaggttctgctggtcagagtacatgtggaacatagtgac
B D                    Bonobo  atagttaggtcacaggaagtgatagtctcagtaggttctgctggtcagagtacatgtggaacatagtgac
B D                   Gorilla  atagttaggtcacaggaagtgatagtctcagtaggttctgctggtcagagtatatgtggaacatggtgac
B D                 Orangutan  atagttaggtcacaggaagtgatagtcccagtaggttctgctggtcagagtacatgtggaacatggtgaa
B D                    Gibbon  atagttaggtcacaggaagtgatagtcccagtaggttctgctggtcagagtacatgtggaacatagtgac
B D                    Rhesus  ataattaggtcacaggaagtgatagtcacagtagtctctgctggtcagcgtacatgtggaacatggtgac
B D       Crab-eating macaque  ataattaggtcacaggaagtgatagtcacagtagtctctgctggtcagcgtacatgtggaacatggtgac
B D                    Baboon  ataattaggtcacaggaagtgatagtcacagtagtctctgctggtcagagtacatgtggaacatggtgac
B D              Green monkey  ataattaggtcacaggaagtgatagtcacagtagtctctgctggtcagagtacatgtggaacatg-----
B D          Proboscis monkey  atagttaggtcacaggaagtgatagtcacagtaagctctgctggtcagagtacatgtggaacatggtgac
B D  Golden snub-nosed monkey  atagttaggtcacaggaagtgatagtcacagtaagctctgctggtcagagtacatgtggaacacggtgac
B D                  Marmoset  atctttaggtcacaggaagtgatagtcccagtttgctctgctggtcagagtacatgtggactatgatgac
B D           Squirrel monkey  atcgttaggtcacaggaagtgatagtcccagtttgctctgctggtcagagcacatgtggactatgatgac
B D                   Tarsier  aggattagaacacaggaagtgatggcatcacagactcttgcttgtcagtggatatgtggaacatagtg--
B D                       Dog  atggttagatcacaggaagtga------cggtaggctctactagtcagagcacatgtgaaacataatgat
B D                     Mouse  ======================================================================
B D                  Bushbaby  ======================================================================
B D                Tree shrew  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  caattttgttccttcatttaaagatgcaaatta-taaactctagtatgtttcagggaaatgtgacctgct
                        Chimp  caattttgttgcttcatttaaagatgcaaattaataaactgtagtatgtttcagggaaatgtgacctgct
                       Bonobo  caattttgttgcttcatttaaagatgcaaattaataaactgtagtatgtttcagggaaatgtgacctgct
                      Gorilla  caattttgttgcttcatttaaagatgcaaattaataaactctagtatgtttcagggaaatgtgacctgct
                    Orangutan  caattttggtgcttcatttaaagatgcaaattaataaactctagtatgttttagggaaatgtgacctgct
                       Gibbon  caattttggtgcttcatttaaagatgcaaattaataaactctggtatgttttagggaaatgtgacctgct
                       Rhesus  caattgtggtgcttcatttaaagatgtaaattaataaactctagtatgttttagggaaatgtgacctgct
          Crab-eating macaque  caattgtggtgcttcatttaaagatgtaaattaataaactctagtatgttttagggaaatgtgacctgct
                       Baboon  caattgtggtgcttcatttaaagatgtaaattaataaactctagtatgttttagggaaatgtgacctgct
                 Green monkey  -----gtggtgcttcatttaaagatataaattaataaactctagtatgttttagggaaatgtgacctgtt
             Proboscis monkey  caattttggtgcttcatttaaagatgtaaattaataaactctagaacattttagggaaatgtgacctgct
     Golden snub-nosed monkey  caattttggtgcttcatttaaagatgtaaattaataaactctagaacattttagggaaatgtgacctgct
                     Marmoset  aaattttattgttttatttaaagatgcaaattaataaactctagtatgttttagggaaatttgacctgct
              Squirrel monkey  aaatttcattgttttatttaaagatgcaaattaataaactctagtatgttgtagggaaatgtgacctgct
                      Tarsier  --------gtgcttcatttaaagacataaattaataaactgcagtgtgctttagggaaatgtgatctgga
                          Dog  cacttttggcacatcatttaaagatatatactaataaactctagcatgttttaagg-aatgtgagttaaa
                        Mouse  ======================================================================
                     Bushbaby  ======================================================================
                   Tree shrew  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaattcatgag-------------gg
                        Chimp  tggtaaaaggt-ttgaactatattatttaagtaacag-ttgtaagaattcatgag-------------ag
                       Bonobo  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaattcatgag-------------ag
                      Gorilla  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaattcatgag-------------gg
                    Orangutan  ttgtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaattcgtgag-------------gt
                       Gibbon  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaattcatgag-------------gg
                       Rhesus  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaatttgtgag-------------gg
          Crab-eating macaque  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaatttgtgag-------------gg
                       Baboon  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaatttgtgag-------------gg
                 Green monkey  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaatttgtgag-------------gg
             Proboscis monkey  tggtaaaaggt-ttgaactatattatttaagtaatag-ttgtaagaatttgtgag-------------gg
     Golden snub-nosed monkey  tggtaaaaggt-ttgagctatattatttaagtaatag-ttgtaagaatttgtgag-------------gg
                     Marmoset  tggtaaaagatcttgagctatattatttaagtaatag-ttgtaagaattagtcag-------------gg
              Squirrel monkey  tggtaaaagatcatgaactatattatttaagtaatag-ttgtaagaattagtgat-------------gg
                      Tarsier  cagtaaaaagtcttcaactatatcatttaagtaatag-ttgagagaatgagtgagaatagaaattcgcaa
                          Dog  tggtaaaaggtcctgaactacatcattcaagcaatggattgagagaattagtgag-------------ac
                        Mouse  ======================================================================
                     Bushbaby  ======================================================================
                   Tree shrew  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ga-aagtacaaaaattgtcatttagtatttggaaggc-----agtcatgtaaata
                        Chimp  ga-aagtacaaaaattgtcatttagtatttggaaggc-----agtcatgtaaata
                       Bonobo  ga-aagtacaaaaattgtcatttagtatttggaaggc-----agtcatgtaaata
                      Gorilla  ga-aagtacaaaaattgtcatttagtatttggaaggc-----agtcatgtaaata
                    Orangutan  ga-aagtacaaaaattgtcctttagtatttggaaggc-----agtcatgtaaata
                       Gibbon  ga-aagtacaaaaattgtcgtttagtatttggaaggc-----tgtcatgtaaata
                       Rhesus  ga-aaatacaaaaattgtcctttagtatttggtaggc-----agtcatgtaaata
          Crab-eating macaque  ga-aaatacaaaaattgtcctttagtatttggtaggc-----agtcatgtaaata
                       Baboon  ga-aaatacaaaaattgtcctttagtatttggtaggc-----agtcatgtaaata
                 Green monkey  ga-aaatacaaaaattgtgctttagtatttggtaggc-----agtcatgtaaata
             Proboscis monkey  ga-aaatacaaaaattgtcctttagtatttggaaggc-----agtcatgtaaata
     Golden snub-nosed monkey  ga-aaatacaaaaattgtcctttagtatttggaaggc-----agtcatgtaaata
                     Marmoset  ga-aaatataaaaattgtctttcagtacttggaaggc-----agtcaggtaaata
              Squirrel monkey  ga-aaata-----------------------gaaggc-----agtcaggtaaata
                      Tarsier  ga-aaatctgtgaatcgtcttttagcacttgaaaggc-----agtcatgtaaata
                          Dog  aagaaatcca------------------ttaaaaggcatatgaattatctaaata
                        Mouse  =======================================================
                     Bushbaby  =======================================================
                   Tree shrew  =======================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 32 and 33 in window
B D                      Dog 75bp

Alignment block 33 of 36 in window, 77422995 - 77423226, 232 bps 
B D                     Human  agggagaaaattctgcaggaattaaa-ttgtaaggatatgctaggaagac-------agtttat------
B D                     Chimp  agggagaaaattctgcaggaattaaa-ttgtaaggatatgctagggagac-------agtttat------
B D                    Bonobo  agggagaaaattctgcaggaattaaa-ttgtaaggatatgctagggagac-------agtttat------
B D                   Gorilla  agggagaaaattctgcaggaattaaa-ttgtaaggatatgctagggagag-------agtttat------
B D                 Orangutan  atggagaaaattctgcagaaattaaa-ttgtaaggatatgctagggagac-------agtttat------
B D                    Gibbon  agggagaaaattctgcaggaattaaa-ttgtaaggatatgctagggagat-------agtttat------
B D                    Rhesus  agggaaaaaattctgcaggaattaaa-ttgtaaggatatgctagagagac-------agtttat------
B D       Crab-eating macaque  agggaaaaaattctgcaggaattaaa-ttgtaaggatatgctagagagac-------agtttat------
B D                    Baboon  agggaaaaaattctgcaggaattaaa-ttgtaaggatatgctagagagac-------agtttat------
B D              Green monkey  agggaaaaaaatctgcaggaattaaa-ttgtaaggatatgctagagagag-------agtttat------
B D          Proboscis monkey  agggaaaaaattctgcaggaattaaa-ttgtaaggatatgctagagagac-------agttgat------
B D  Golden snub-nosed monkey  agggaaaaaattctgcaggaattaaa-ttgtaaggatatgctagagagac-------acttgat------
B D                  Marmoset  agggataaaattctgtagaaattaaa-ctgtaatgatatgctagggagag-------agtttat------
B D           Squirrel monkey  ggggagaaaaatctgtagaaattaaa-ctgtaatgatatgcta---agag-------agtttat------
B D                   Tarsier  a--gagcaatttgtgcaggaattaaacttataataacatgctagggagacattgctgagttcaacaccag
B D                     Mouse  ======================================================================
B D                  Bushbaby  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ------tttattttattt-ttt--------atttttgttttgtttgtgttttgaggcagagtctttctct
                        Chimp  ------cttattttattt-ttt--------atttttgttttgtttgttttttgaggcagagtcttgctct
                       Bonobo  ------cttattttattt-ttt--------atttttgttttgtttgttttttgaggcagagtcttgctct
                      Gorilla  ------tttattttattt-ttt--------atttttgttttgtttgttttttgaggcagagtcttgctct
                    Orangutan  ------tttattttattt-ttt--------atttttgttttgtttgttttttgaggcagagtctttttct
                       Gibbon  ------tttattttattt-ttt--------atttttattttgtttg----ttgaggcagagtcttgctct
                       Rhesus  ------tttattt------tttggttttgtttttttgttctgtttgttttttgaggcagagtcttgctct
          Crab-eating macaque  ------tttattt------ttttgttttg-ttttttgttctgtttgttttttgaggcagagtcttgctct
                       Baboon  ------tttattttttttgttttgttttg-ttttttgttctgtttgttttttgaggcagagtcttgctct
                 Green monkey  ------tttattttattt-ctttgttttg-ttttttgttttgtttgttttttgaggcagagtcttgctct
             Proboscis monkey  ------tttattttattt-ttttgttttg-ttttttgttttgtttgttttctgaggcagcgtcttgctct
     Golden snub-nosed monkey  ------tttattttattt-ttttgttttg-ttttttgttttgtttgttttttgaggcagtgtcttgctct
                     Marmoset  -------ttatttttttc-ttt--------att-----------------ttgatatgggatcttgctct
              Squirrel monkey  -------ttatttg-----ttt--------att-----------------ttgaggtggagtcttgttct
                      Tarsier  aaagagtttctttggatt-ttttgt-----ttgtttgttttgttt---ttctgaagtagaatctcact-t
                        Mouse  ======================================================================
                     Bushbaby  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  tgtcgctcaggctggagtgcaatggcacaatctccgctcactgcaacctccgcctcccaggttc------
                        Chimp  tgtcgctcaggctggagtgcaatggcacgatctctgctcactgcaacctccacctcccaggttc------
                       Bonobo  tgtcgctcaggctggagtgcaatggcacgatctccgctcactgcaacctccacctcccaggttc------
                      Gorilla  tgtcgctcaggctggagtgcaatggcacgatctccgctcactgcaacctccgcctcccaggttc------
                    Orangutan  tgtcgcccaggctggagtgcaatggcacgatatccgctcactgcaacctccgcctcccaggttc------
                       Gibbon  tgtcacccaagctggattgcaatggcaccatctctgctcactgcaacctctgcctcccaggttc------
                       Rhesus  tgtcacccaggctggagtgcaatggcatgatttctgctcactacaacctccgcctcccaggttc------
          Crab-eating macaque  tgtcacccaggctggagtgcaatggcatgatttctgctcactacaacctccgcctcccacgttc------
                       Baboon  tgtcacccaggctggagtgcaatggcatgatttctgctcactacaacctccgcctcccaggttc------
                 Green monkey  tgtcacccaggctggagtgcaatgacacgatttctgctcactgcaacctccgcctcccaggttc------
             Proboscis monkey  tgtcgcccaggctggagtgcaatggcacgatttctgctcactgcaacctccgcctcccaggttc------
     Golden snub-nosed monkey  tgtcgcccaggctggagtgcaatggcacgatttctgctcactgcaacctccgcctcccaggttc------
                     Marmoset  tatcccccaggctagagtgcaatggtacaatctcagctcactgcaacctccgcctctcaggttcaagtga
              Squirrel monkey  tgtcccctaggctggagtgcaatggcacgatctcagctcgctgcaacctctgcctctcaagttc------
                      Tarsier  catcacccaggctggagtgcagtggcacactcaaggc-cactgcagcctcgacctgctgggctc------
                        Mouse  ======================================================================
                     Bushbaby  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ---------------------------------------------------------aagcaattctcct
                        Chimp  ---------------------------------------------------------aagcaattctcct
                       Bonobo  ---------------------------------------------------------aagcaattctcct
                      Gorilla  ---------------------------------------------------------aagcaattctcct
                    Orangutan  ---------------------------------------------------------aagcaattctcct
                       Gibbon  ---------------------------------------------------------aagcaattctcct
                       Rhesus  ---------------------------------------------------------aagcaattctcct
          Crab-eating macaque  ---------------------------------------------------------aagcaattctcct
                       Baboon  ---------------------------------------------------------aagcaattctcct
                 Green monkey  ---------------------------------------------------------aagcaattctcct
             Proboscis monkey  ---------------------------------------------------------aagcaattctcct
     Golden snub-nosed monkey  ---------------------------------------------------------aagcaattctcct
                     Marmoset  tactactgcctcagcctcccgagtgctgggattgcaggcatgagtattgaatctttcaagtgatactact
              Squirrel monkey  ---------------------------------------------------------aagcgatactact
                      Tarsier  ---------------------------------------------------------aggtgatccttct
                        Mouse  ======================================================================
                     Bushbaby  ======================================================================
                   Tree shrew  ======================================================================
                          Dog  ======================================================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  gcctc-agcctccctagtagctgggattacaggtgcctgccacca
                        Chimp  gcctc-agcctccctagtagctgggattacaggtgcctgccacca
                       Bonobo  gcctc-agcctccctagtagctgggattacaggtgcctgccacca
                      Gorilla  gcctc-agcttccctagtagctgggattacaggtgcctgccacca
                    Orangutan  gcttc-agcctccctagtagctaggattacaggtgcctgccacca
                       Gibbon  gcctc-agcctccctagtagctgggattacaggtccctgccacca
                       Rhesus  gcctc-cgcctccctagtagctgggattacaggcgcctgtcacca
          Crab-eating macaque  gcctc-cgcctccctagtagctgggattacaggcgcctgtcacca
                       Baboon  gcctc-ggcctccctagtagctgggattacaggcgcctgtcacca
                 Green monkey  gcctc-agcctccctagtagctgggattacaggcgcctgtcacca
             Proboscis monkey  gcctc-ggcctccctagtagctgggattaaaggcgtctgtcacca
     Golden snub-nosed monkey  gcctc-ggcctccctagtagctgggattaaaggcgtctgtcacca
                     Marmoset  gcctc-agcctcccgagtagctgggattacaggagcctggcacca
              Squirrel monkey  gcctc-agcctcccgagtagctgggattacaggagcctgccacca
                      Tarsier  gcctcaagtcatccaagtagccagaattacaagtgcatgctacca
                        Mouse  =============================================
                     Bushbaby  =============================================
                   Tree shrew  =============================================
                          Dog  =============================================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Inserts between block 33 and 34 in window
B D             Green monkey 507bp

Alignment block 34 of 36 in window, 77423227 - 77423320, 94 bps 
B D                     Human  cgcctagctaatttt---tgtatttttagtaaagacagggtttcaccatgttggccaggctggtctcgaa
B D                     Chimp  cgcctggctaatttt---tgtatttttagtaaagacagggtttcaccatgttggccaggctggtctcgaa
B D                    Bonobo  cgcctggctaatttt---tgtacttttagtaaagacagggtttcaccatgttggccaggctggtctcgaa
B D                   Gorilla  cgcctggccaatttt---tgtatttttagtagagatggggtttcaccatgttggtcaagctggtcttgaa
B D                 Orangutan  cgcctggctaatttt---tgtatttttagtaaagacagggtttcaccatgttggccaggctggtctcgaa
B D                    Gibbon  cgcctggctaatttt---tgtatttttagtagagacagggtttcaccatgttgaccaggctggtctcaaa
B D                    Rhesus  cgcccggctaatttt---tgtatttttagtaaagacggggttttgccacgttggccaggctggtcttgaa
B D       Crab-eating macaque  cgcccggctaatttt---tgtatttttagtaaagacggggttttgccatgttggccaggctggtcttgaa
B D                    Baboon  cgcccggctaatttt---tgtatttttagtaaagacggggttttgccatgttggccaggttggtcttgaa
B D          Proboscis monkey  cgcccggctaatttt---tgtgtttttagtaaagatggggttttgccatgttggccaggctggtcttgaa
B D  Golden snub-nosed monkey  cgcccggctaatttt---tgtgtttttagtaaagatggggttttgccatgttggccaggctggtcttgaa
B D                  Marmoset  tgcacagc---tttt---tgtatttgtagtagagacagagtgttgccatgttggccaggctggtttcgaa
B D           Squirrel monkey  tgcacggc---tttt---tgtatttttagtagagacagggtatcgccatgttggccaggctggtttcaaa
B D                   Tarsier  cgcccagctaattttttatttatttattgtagaggcgaggtctcaccctgttgcccgggctggtcttgaa
B D                     Mouse  ======================================================================
B D                  Bushbaby  ======================================================================
B D                Tree shrew  ======================================================================
B D                       Dog  ======================================================================
B D              Green monkey  ======================================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

                        Human  ctcctgacctca--tgatcttctcgcctc
                        Chimp  ctcctgacctca--tgatctgctcgcctc
                       Bonobo  ctcctgacctca--tgatctgctcgcctc
                      Gorilla  ctcctgacgtcaggtgatctgcccgcctc
                    Orangutan  ctcctgacctca--tgatctgctcgcctt
                       Gibbon  ctcctgacctca--tgatctgctcgcctc
                       Rhesus  ctcctgaccttg--tgatctgcccgcctt
          Crab-eating macaque  ctcctgacctcg--tgatctgcccgcctt
                       Baboon  ctcctgacctca--tgatctgcccgcctt
             Proboscis monkey  ctcctgacctca--tgatctgcccgcctt
     Golden snub-nosed monkey  ctcctgacctca--tgatctgcccgcctt
                     Marmoset  ctcttgacctca--tgatctgcccaggtc
              Squirrel monkey  ctcctgacctca--tgatctgcccatgtc
                      Tarsier  cctgtgggctcaggcaatcctcttgcctc
                        Mouse  =============================
                     Bushbaby  =============================
                   Tree shrew  =============================
                          Dog  =============================
                 Green monkey  =============================
                  Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 35 of 36 in window, 77423321 - 77423369, 49 bps 
B D                     Human  ggcctcccaaagtgctgggattacaggcatgagccaccgtgcccagcca
B D                     Chimp  ggcctcccaaagtgctgggattacaggcatgagccaccgtgcccagcca
B D                    Bonobo  ggcctcccaaagtgctgggattacaggcatgagccaccgtgcccagcca
B D                   Gorilla  ggcctcccaaagtgctgggattacaggcgtgagccaccacgcttagcca
B D                 Orangutan  ggcctcccaaagtgctgggattacaggcatgagccaccgtgcccagcca
B D                    Gibbon  ggcctcccaaagtgctgggattacaggcatgagccaccgtgcccagcca
B D                    Rhesus  ggcctcccaaagtgctgagattacaggcgtgagccaccatgcccagcaa
B D       Crab-eating macaque  ggcctcccaaagtgctgagattacaggcgtgagccaccatgcccagcaa
B D                    Baboon  ggcctcccaaagtgctgagattacaggcgtgagccaccgtgcccagcaa
B D              Green monkey  ggcctcccaaagtgctgagattacaggcgtgagccaccatgcccagcaa
B D          Proboscis monkey  ggcctcccaaagtggtgagattacaggcgtgagccaccgtgcccagcaa
B D  Golden snub-nosed monkey  ggcctcccaaagtggtgagattacaggcgtgagccaccgtgcccagcaa
B D                  Marmoset  agccccccaaagtgctgggattgcaggcatgagccaccatacccggcca
B D           Squirrel monkey  agcccctcaaagtgctgggattgcaggcatgagccaccacacccgacca
B D                   Tarsier  agcctcccaaagtgctggcatgacaggcttgaaccactgcaccctgcc-
B D                     Mouse  =================================================
B D                  Bushbaby  =================================================
B D                Tree shrew  =================================================
B D                       Dog  =================================================
B D               Mouse lemur  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Alignment block 36 of 36 in window, 77423370 - 77423383, 14 bps 
B D                     Human  acagtttattttaa
B D                     Chimp  acggtttattttaa
B D                    Bonobo  acggtttattttaa
B D                   Gorilla  aaaat---acctaa
B D                 Orangutan  acagtttattttaa
B D                    Gibbon  acagtttattttaa
B D                    Rhesus  acagtttattttaa
B D       Crab-eating macaque  acagtttattttaa
B D                    Baboon  acagtttattttaa
B D              Green monkey  acagtttattttaa
B D          Proboscis monkey  acagtttattttaa
B D  Golden snub-nosed monkey  acagtttattttaa
B D                  Marmoset  acaatttattttaa
B D           Squirrel monkey  acaatttattttaa
B D                       Dog  accattagtttcaa
B D                     Mouse  ==============
B D                  Bushbaby  ==============
B D                Tree shrew  ==============
B D                   Tarsier  --------------
B D               Mouse lemur  NNNNNNNNNNNNNN

View table schema

Go to Cons 20 Mammals track controls

Data last updated: 2015-04-14

Description

This track shows multiple alignments of 20 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all twenty species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

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

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

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.

See also: lastz parameters and other details and chain minimum score and gap parameters used in these alignments.

Missing sequence in the assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below).

OrganismSpeciesRelease dateUCSC versionalignment type
HumanHomo sapiensDec. 2013GRCh38/hg38reference species
ChimpPan troglodytesFeb. 2011GSAC 2.1.4/panTro4Syntenic net
BonoboPan paniscusMay 2012Max-Planck/panPan1Reciprocal best net
GorillaGorilla gorilla gorillaMay 2011WTSI gorGor3.1/gorGor3Reciprocal best net
OrangutanPongo pygmaeus abeliiJul. 2007WUGSC 2.0.2/ponAbe2Syntenic net
GibbonNomascus leucogenysOct. 2012GGSC Nleu3.0/nomLeu3Syntenic net
Proboscis monkeyNasalis larvatusNov. 2014PMFGC Charlie1.0/nasLar1Reciprocal best net
Golden snub-nosed monkeyRhinopithecus roxellanaOct. 2014Rrox_v1/rhiRox1Reciprocal best net
Green monkeyChlorocebus sabaeusMar. 2014VGC Chlorocebus_sabeus 1.1/chlSab2Syntenic net
Crab-eating macaqueMacaca fascicularisJun. 2013WashU 5.0/macFas5Syntenic net
RhesusMacaca mulattaOct. 2010BGI CR 1.0/rheMac3Syntenic net
BaboonPapio anubisMar. 2012Baylor Panu_2.0/papAnu2Syntenic net
Squirrel monkeySaimiri boliviensisOct. 2011Broad/saiBol1Reciprocal best net
MarmosetCallithrix jacchusMar. 2009WUGSC 3.2/calJac3Syntenic net
TarsierTarsius syrichtaSep. 2013WashU 2.0.1/tarSyr2Syntenic net
Mouse lemurMicrocebus murinusJul. 2007Broad/micMur1Reciprocal best net
BushbabyOtolemur garnettiiMar. 2011Broad/otoGar3Reciprocal best net
Tree shrewTupaia belangeriDec. 2006Broad/tupBel1Reciprocal best net
DogCanis lupis familiarisSep. 2011Broad/canFam3Syntenic net
MouseMus musculusDec. 2011GRChm38/mm10Syntenic net

Table 1. Genome assemblies included in the 20-way Conservation track.

Downloads for data in this track are available:

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the value of the score. The conservation wiggles 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.

Pairwise alignments of each species to the human genome are displayed below the conservation histogram 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.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in 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 human 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 human 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 human sequence at those alignment positions relative to the longest non-human sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

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 (Table 2).

Gene TrackSpecies
Known Geneshuman, mouse
Ensembl Genes v78baboon, bushbaby, chimp, dog, gorilla, marmoset, mouse lemur, orangutan, tree shrew
RefSeqcrab-eating macaque, rhesus
no annotationbonobo, green monkey, gibbon, proboscis monkey, golden snub-nosed monkey, squirrel monkey, tarsier
Table 2. Gene tracks used for codon translation.

Methods

Pairwise alignments with the human genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.

An additional filtering step was introduced in the generation of the 20-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies.

type of net alignmentSpecies
Syntenic Netbaboon, chimp, dog, gibbon, green monkey, crab-eating macaque, marmoset, mouse, orangutan, rhesus
Reciprocal best Netbushbaby, bonobo, gorilla, golden snub-nosed monkey, mouse lemur, proboscis monkey, squirrel monkey, tarsier, tree shrew
Table 3. Type of Net alignment

The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 20-way alignment (msa_view). The 4d sites were derived from the Xeno RefSeq gene set, filtered to select single-coverage long transcripts.

This same tree model was used in the phyloP calculations, however their background frequencies were modified to maintain reversibility. The resulting tree model for all species.

PhastCons Conservation

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. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, 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).

The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements (http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

Conserved Elements

The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".

Credits

This track was created using the following programs:

  • Alignment tools: 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, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; 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 as of March 2007.

References

Phylo-HMMs, phastCons, and phyloP:

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

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

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

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

Blastz:

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

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