melanogaster  GATTTTTGTCCCCATC-CAATGGACATTCGTGGGATTCCAGAAAGCATCTTTTTAAGTTGTCAGTTCGAATTGGAAATTGC----GGGAAAGGAAG------------GGAACTGGT---
       simulans  GATTTTTGTCCCCATC-CAATGGACATTCACGGGATTCCAGAAAGCATCTTTTCAAGTTGCCAGTTCGAATTGGAAATTGC----GGGAAAGGAAG------------GGAACTGGT---
      sechellia  GATTTTTGTCCCCATC-CAATGGACATTCGCGGGATTCCAGAAAGCATCTTTTCAAGTTGCCAGTTCGAATTGGAAATTGC----GGGAAAGGAAG------------GGAACTGGT---
         yakuba  GATTTTTGTCCCCATC-CAATGGACATTCGCGGGATTCCAGAAAGCATCTTTTCAACTTGCCAGTTCGAATCTGAAATTGA----GGCA----AAG------------GGAACTGGTTGT
         erecta  GATTTTTGGCCCCATC-CAATGGACATTCGCGGGATTCCAGAAAGCATCTTTTCAAGTAGCCAGTTCGAATTGGAAATTGA----GGAA----AGG------------AGAACTGCT---
      ananassae  GATTTTTGTCCCCGTC-CAATGGACATACGCCGGATTCCAGAAAGCAACTTTTAATGCTGCCAATGGGGATGGGAGGATGG----GAGG----ATG------------GGGGCTTGG---
  pseudoobscura  GATTTTTGTCCCCATC-GAATGGACATGCTCGGGATTCCAGAAAGCATCTTTTAATGTTTCGAGGCTGGAATGAAGATGGGTTCTGCCACAACCAGAGTCGCAGTCGCAGATCTGAT---
     persimilis  GATTTTTGTCCCCATC-GAATGGACATGCTCGGGATTCCAGAAAGCATCTTTTAATGTTTCGAGGCTGGAATGAAGATGGGTTCTGCCACAATCAG------------AGATCCTCT---
        virilis  GATTTTTGTCCC-----CAGCGGACATACCTCAAATTCCAAAACGCAGCATTT-AATTCTTCATTGCAG-TCGCAGCTTGG---------AGCTGG------------------------
     mojavensis  GATTTTTGTCCC-----CAGCGGACATTTCTGACATTCCAAAAACCCGC------AGTCTTCAATGC-----------------------------------------TGCATTGCA---
      grimshawi  GAGTTTTGTCCCCAAAGCAGCGGACATACCGAAAATTCCAAAATGCAGCATTT-AATTCGGCAGT-CGG-CAGGTTCTTGG---------AGCCTG------------CCAACTATT---
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBRRRRRRRRR

                 
   melanogaster  -TCGATGGATGGATGGATGGATGTTTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGCCC----A------AAAAAAA---------A
       simulans  -TCGTTGGATGGATGGATGGATGTTTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGCCC--------------AAAA---------A
      sechellia  -TCGTTGGATGGATGGATGGATGTTTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGCCC-------------AAAAA---------A
         yakuba  TTGGATGGATGGATGGATGGATGTTTCGTCAACGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGTCC-------------ACAAAAAAATAAAAA
         erecta  ---------TGGATGGATGGATGTTTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGTCG-------------AAAAA----------
      ananassae  -----------------GGCATGCCTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGCCC----AAGACGGAAGAAAA---------A
  pseudoobscura  ----------GGATGGA-GGATGACTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGCAGC-------------CAC-A---------A
     persimilis  -----------GATGGA-GGATGACTCGTCAGCGGCTGTC----------TGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGCAGC-------------CACAA---------A
        virilis  ----------------------------------CTTGTC-------AGTGGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGGCTGGGCGGACAGAAAAGTGAA---------C
     mojavensis  -TCTATATATCTTTGA--------GTTGTC-TCCGCTGTC-------TCGGGCCGTTTGTCAAGCTGTCATATGCTTGTCGCACGCTGGACCCGAAAACACACACACACA---------C
      grimshawi  -ACTGTGGGCTGTGGA-------------------TTGTCAAACCCTTTTGGCCGTTTGTCAAACTGTCATATGCTTGTCGCACGCTGCCC-----AATGTGGAACCACA---------A
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRB

                 
   melanogaster  AAACGCA-----------GGTCCAACTCC----AATATATTAGCTGAAATTTTAATTACCAACTGC-GACTT-----------GAA------GCGGACTCAGAAGCACTCAGAAAAATTT
       simulans  AAATGCA-----------GGTCCAACTCC----AATATATTAGCTGAAATTTTAATTACCAACTGC-GACTT-----------GAA------CCGGAC----AAACACTCAGAAAAATTA
      sechellia  AAACCCA-----------TGTCCAACTCC----AATATATTAGCTGAAATTTTAATTACCAACTGC-GACTT-----------GAA------CCGCAC----AAACACTGAGAAAAATTT
         yakuba  AAACACT-----------GCTCCAACTCC----AATATATTAGCTGAAATTTTAATTACC------------------------AA------CCGGAC----ATGCACTCGGAAAAATTA
         erecta  -----------------------AACTGC----AATATATTAGCTGAAATTTTAATTACCAACTGC-GACTT-----------GAA------CCGGAC----ATGCACTAAGAAAAATGA
      ananassae  AACTGAA-----------GCTTCAACCTC----AATATATTAGCTGAAATTTTAATTACCAACTGCAGACTC-----------AAA------ACTGGG----ATACACAAGGAAATAATA
  pseudoobscura  AAACCAT-----------GCCTCATCCTC----GATATATTAGCTGAAATTTTAATTACCAACGGG-GGCTG-----------GAA----------------------------------
     persimilis  AAACCAT-----------GCCTCATCCTC----GATATATTAGCTGAAATTTTAATTACCAATGGG-GGATG-----------GTAAGGGGGCTGGAA----------------------
        virilis  GAGGACA-------GCA-GCCTTCGCCTG--GATATATATTAGCAGAAATTTTAATTACCGACTG-------------------------------------------------------
     mojavensis  ACACACACACTGATGTATGTATATACCTGAAGATATATATTAGCAGAAATTTTAATTACTAACTGA-AGTTTTTTGTGCCGCT---------------------GCATTCGG--------
      grimshawi  AAAAACT-----------GAACGAGGCTG--GAGATATATTAGCTGAAATTTTAATTACCTGCTGC-AGGTT------------------------------------------------
        Summary  BBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBMMMMMMMMMBBBBBBBBBRRRRRRR

                 
   melanogaster  TAAGCAATAACACACGCCAAACGAATAAATATAAATATACTAAAGGGCAAATATTCATAAAGAACGTTACAGTTTTTAAAATTTG-GTTTTGCCTTT------------GTTTAAATAAT
       simulans  TTAACAAAAACACATGTCAAACGAATTAAAATAAATATACTAAAGGGCAAATATTCACAAGGGGCGTTAAAGTTTTTCAAC-----ATTTTGTCTTT------------GTTTGAATAAT
      sechellia  GAAACAATAACAAATGTCAAACGAATAAATATAAATATACTAAAGGGCAAATATTCACAAAGAACGTTAAAGTTTTTCAACTTTGGGTTTTATCTTT------------GTTTAAATAAT
         yakuba  TCAACAATAATGCATACCAAGCCACT---TGCAAGTTTC--------CAAGT-----TAAAGAATGAACAATTTGTTGAACTGTGGCATGTGCTTTTTGATT-TTTAAATTATAGATTAT
         erecta  TTGGCAATAACACATACCAATT---------------------------AAT-----TAAAGAACAGCCCATTTGCTCAACTGTGGTATGTGCCTTTTGATT-TATTTATATTCGATTAT
      ananassae  TGGGTAGT----------------------------------------------TCTCGAAG---------GTTTTTCTTTTTTAAAATATAATTTAAGGTGAGAAGAAGTCTAAGCATG
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRBBBMMMMMMMMMBMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRBBRRR

                 
   melanogaster  ATTAAT-----TATTTTATTTAAATGAAATCTCAGCTAA----GAGCTATGTTTTTTAAGTGTGAATCTGAGACTGGTCCTGCTGACGCCACTC--GACTGTCCGCAAAATCTTTTTCAT
       simulans  ACCAAT-----TT----TTTTAAATAAAATCTCAGCTAA----GAGCTATGTTTTTTAAGTGTGAATCTGAGACTGGTCCTGCTGACGCCACTC--GACTGCCCGCAAAATCATTTTCG-
      sechellia  ATGAAT-----TGATAATTTAAAAAAAAATCTCAGCTAA----GAGCTATG-TTTTTAAGTGTGAATCTGAGACTGGTCCTGCTGACGCCACTC--GACTGCCCGCAAAATCATTTTCG-
         yakuba  ATGAAT-----AATAAATTC--ACTAAAACCTCAATATA----GTACT-TATTTTCGAAGTGTAACCCTGAGAC----------GACGCCACTC--GACTGTCCGCAAAATCTTTTTCG-
         erecta  ATAAAT-----AATACATTT--ACTGAAGCCTCA--AGA----GAACT-TTTTCTTTAAGTGTGAATCTGAGACTGGTCCTGCTGACGCCACTC--GACTGTC--CAGCAGCTTTTTGG-
      ananassae  AAGAATGACCATATCACCTTTATAAGAAACTTCCTTTAATGTTACACTATTTTCTCTCAGTGCCAATCTGAACCTGGTCCTGCTGACGCCACTCAAAACTTGCCTCAAAGCCCTTGGC--
  pseudoobscura  -----------------------------------------------------------------------GACTGGTCTCGCTGACGCCACTG--GAACTT-------GGCTTTTGGG-
     persimilis  -----------------------------------------------------------------------GACTGGTCTCGCTGACGCCACTG--GAACTT-------GGCTTTTGGG-
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------AGTTTTTTTTT-
        Summary  RRRRRRRRRRRRRRRRRRRRRRRRBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TTTTTTCTGCTGACATGGC-----AAATATTTTCCATGCGGAGCATTATAAAAGTTTAATTGATTGATTTATA-----CG--TGGGG-AGTTGTCA-GGGAGAT-G--------------
       simulans  TTTTTTCTGCTGGCACGGC-----AAATATTTTCCATGCGGAGCATTATAAAAGTTTAATTGATTGATTTATA-----CG--TGGGG-AGTTGTCA-GGAAGAT-G--------------
      sechellia  TTTTTTCTGCTGGCACGGC-----AAATATTTTCCATGCGGAGCATTATAAAAGTTTAATTGATTGATTTATA-----CG--TGGGG-AGTTGTCA-GGGAGAT-G--------------
         yakuba  TTTTTTTTGCTGGCATGGC-----AAATATTTTCCATGCGGAGCATTATAAAAGTTTAATTGATTGATTTATA-----CG--TGGGG-AGTTGTCACGGGGGAT-G--------------
         erecta  TTTTTTCTGCCGGTATGGC-----AAATATTTTCCATGCGGAGCATTATAAAAGTTTAATTGATTGATTTATA-----CG--TGGGG-AGTTGTCA-GGGGGAT-G--------------
      ananassae  TTTTTGCCTCTGGCATCGC-----AAATATTTTCCATGCGGAGCATTATAAAAGTTTAATTGATTGATTTATA-----CG--TGGGG-AGTTGTCA-AGAGGTTGG--------------
  pseudoobscura  GCTTTTTTTTCAGC---GA-----AAATATTTTCCATGCTGGGCATTATAAAAGTTTAATTGATTGATTTATATATTTCG--GTGGA-AGTTGTCA-AGGCGGC-A--------------
     persimilis  GGCTTTTTTTCAAC---GA-----AAATATTTTCCATGCTGGGCATTATAAAAGTTTAATTGATTGATTTATATATTTCG--GTGGA-AGTTGTCA-AGGCGGC-A--------------
        virilis  TTTTTGTGGAAGGCATTGA-------ATATTTTTCATGCCAAGCTTTTTCAAAATTTAATTGATTGATTTATT-----TT--GGAGA-AGTTGCCA-TGCAGCA-G-----------TTG
     mojavensis  ---------------------------------------GAAGTTTTATAAAAATTTAATTGATTGATTTATT-----TTGAGGCGA-AGTTGTCA-TACGGGA-GAGTGGCTCAGCTCG
      grimshawi  TTTGTTTGGGTTGGTTTGGTTTGCGCATATTTTCCATGC---GCTTTATAAAAATTTAATTGATTGATTTATT-----TTGCAGAGACAGTTGTCA-AGCGACA-GTCTGTCAGAGATC-
        Summary  BBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMM

                 
   melanogaster  -------------CCAATC----------------GCTCTGCGGTAGTTCGTTGCCGACT----------------------------------TTGAGGA---------CCCT------
       simulans  -------------CCAATC----------------GCTCTGCGGTAGTTCGTTGTCGACT----------------------------------TTGAGGA---------CCCT------
      sechellia  -------------CCAATC----------------GCTCTGCGGTAGTTCGTTGCCGACT----------------------------------TTGAGGA---------CCCT------
         yakuba  -------------CCAATC----------------GCTCTGCGGTGGTTCGTTGCCGACT----------------------------------CCGAGGA---------GCCCTTGAGC
         erecta  -------------CCAATC----------------GCTCTGCGGTAGTTCGTTGCCGACT----------------------------------CAGAGGA---------CCCT------
      ananassae  -------------CCCGGC----------------ACTCTGCGGTAGTTCCTGGCTTTTT----------------------------------ATGAAGA---------CGCT-GCAGC
  pseudoobscura  --------------------------------------CTGCGGTAGTTCCTTGCCTGCTCCTCCGGTATGCAGTCGGGTCTGGTCTGGTCTGGTTGAGAG-------------------
     persimilis  --------------------------------------CTGCGGTAGTTC----------------------------------------------------------------------
        virilis  TCTGTACTCTG--CTGCTCCGTTCT----------GCACTGCGGTAGTTC------------------------------------------------GGGC------------------
     mojavensis  GCTGGGCTCCGGACTGGACTGGACT----------GGACTGCGGTAGTTC------------------------------------------------GGCCTCAGGTAG----------
      grimshawi  -TTTGGCTCCT--GTTCCCGGGACTCGAGTCCCGAACACTGCGGTAGTTC------------------------------------------------AGGC------------------
        Summary  MRRRRRRRRRBBBBBBBBMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRBBBBBRRRRRRRRRMMMMMMMMMMMMMM

                 
   melanogaster  --TTGAGGT---CTTAGGTAGGTGGTCAATGGAATACCT--------------------TGGCTGACAAATCAATTTCGA---ATAGC------GATCCTGC------------------
       simulans  --TTGAGGT---CTTAGGTAGGTGGTCAATGGAATACCT--------------------TGGCTGACAAATCAATTTCGA---ATAGC------GATCCTGC------------------
      sechellia  --TTGAGGT---CTTAGGTAGGTGGTCAATGGAATACCT--------------------TGGCTGACAAATCAATTTCGA---ATAGC------GATCCTGC------------------
         yakuba  CGTTGAGAT---CTTAGGTAGGTGGTCAATGGAATACCT--------------------TGGCTGACAAATCAATTTCGT---ATAGC------GATCCTGC------------------
         erecta  --TTGAGGT---CTTAGGTAGGTGGTCAATGGAATA-CT--------------------TGGCTGACAAATCAATTTCGA---ATAGC------GATCCTGC------------------
      ananassae  CATCGGGGTC--CTTAGGTAGGTGGTCAATGGAATACCTTGGCATCCCGTGCGGTTGGATGGCTGACAAATCAATTTCGT---ATTGCTGAGGAGATCCT-T------------------
  pseudoobscura  ---------CCACTTGGGTAGGTGGTCAATGAAATGCTTTGGCATTTCGTGCGGT----TTGCTGACAAATCAATTTCGT---ATTTC------TATCGGGTCACAGCGAGGGGGAGAGA
     persimilis  ---------CCACTTGGGTAGGTGGTCAATGAAATGCTTTGGCATTTCGTGCGGT----TTGCTGACAAATCAATTTCGT---ATTTC------TATCGGGTCGCAGCGAGG--------
        virilis  ---------------AGGTAGGTGGTCAATGAAAAACTTCGGCATTTAGTGCGG-----CTTTTGACAAATCAATTGCGC---GT----------------------CGAGCTGTCGC--
     mojavensis  -------------TTAGGTAGGTGGTCAACGGAA-----------------CAG-----AATTTGACAAATCAATTGAG----GT----------------------TGAGC--------
      grimshawi  ---------------AGGTAGGTGGTCAATGAAAAACTTTGGCATTTAGTGCGG-----CTTTTGACAAATCAATTTCGCATTGT----------------------CGAGCAAAGAC--
        Summary  MMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBMMMMMMMMMMMMMMMMMMRRRR

                 
   melanogaster  -----GGCAGGCGCAGTGCGGAGC--------------------------GGCT-AAGCCGAGCTAAGAGTCCTGTAAACTGTCTCAATAGCAACGCCCCGACGATTGT-GCCT------
       simulans  -----GGCAGGCGCAGTGCGGAGC--------------------------GGCT-AAGCCGAGCTAAGAGTCCTGTAAACTGTCTCAATAGCAACGCCCCGACGATTGT-GCCC------
      sechellia  -----GGAAGGCGCAGTGCGGAGC--------------------------GACT-AAGCCGAGCTAAGAGTCCTGTAAACTGTCTCAATAGCAACGCCCCGACGATTGT-GCCC------
         yakuba  -----GGCAGGCGCAGTGCGGAGC--------------------------GGCT-AAGCCGAGCTAAGAGTCCTGTAAACTGTCTCAATAGCAACGCCCCGGCGATTGT-TGCGATCC--
         erecta  -----GGCAGGCGCAGTGCGGAGC--------------------------GGCT-AAGCCGAGCTAAGAGTCCTGTAAACTGTCTCAATAGCAACGCCC---------------------
      ananassae  -----GGAGGGCGCATTGCAGAGC--------------------------GGCT-AAGCCGAGCTAAGTGTCCTGTAAACTGTCTCAATAACAACGCCCCGGCAATTGT-CCTTTCCCGA
  pseudoobscura  GGAGAGGGAGAGGGAGAGCGGAGC--------------------------GGCT-AAGCCGAGCTAAGTGTCCTGTAAACTGTCTCAATAGCAACGCCCAGACAATTGT-CCCT------
     persimilis  -----GGGAGAGGGAGAGCGGAGC--------------------------GGCT-AAGCCGAGCTAAGTGTCCTGTAAACTGTCTCAATAGCAACGCCCAGACAATTGT-CCCT------
        virilis  ------ACAGACG-------AGAC--------------------------AAATAAAGCCGAAGTAAATGCATTGTAAACTGTCTCAATAGTAACGCCT--ACAATGGC-CCGA------
     mojavensis  --------------------AGGC--------------------------AGCGAAAGCCGAGCTAAATGCACTGTAAACTGTCTCAATAGTAACGCCT--ACAATGGG-C---------
      grimshawi  -----GAGAGACG-------GGACGGGACAAGAGGAGAGGAGAGATGAGAAACTAAAGCCGAGCTAAATGCTCGGTAAACTGTCTCAATAGTAACGCCC--ACAATGGGACCGG------
        Summary  RRRRRBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBB

                 
   melanogaster  --GCTCC------T-TGTAAG---------------------------CCGCTCAGCTGGAGATAGAAATCCTGGCGGTCC----TGAAAGGAGCT-GGC--ACAATGG-CCAGGAGAAA
       simulans  --GCTCC------T-TGTAAG---------------------------CCGCTCAGCTGGAGATGCAAGTCCTGGCGGTCC----TGAAAGGAGCT-GGC--ACAATGG-CCAGGAGAAA
      sechellia  --GCTCC------T-TGTAAG---------------------------CCGCTCAGCTGGAGATGCAAGTCCTGGCGGTCC----TGAAAGGAGTT-GGC--ACAATGG-CCAGAAGAAA
         yakuba  -TGCTCC------T-TGTAAG---------------------------CCGCTCAGCTGGAGATGGAAGACCTGGCGGTCCG--GTGAAAGGAGCT-GGC--ACAATAG-CCAGGAGATA
         erecta  --GCTCC------T-TGTAAG---------------------------CCGCTCAGCTGGAGATAGAAGACCTGGAGGTCC----TGAAAGGCGCT-GGC--ACAATGG-CCAGGAGAGA
      ananassae  TTGTTCTGTCCAGT-TGTAAGCC-----------------------GTCCGCCCAGCTGGAGATTGTAGAGCGGACGG-CT----TGAAAGGAGCCGGGG--ACAATGG-TCAGGAGATC
  pseudoobscura  --ACTCC------T-TCTAATCCTACTG-CT---------------TTCTTCCCAGCTGGACTT-----------CGGCGC----TG----------GGC--ACAATGGCCCGGGGGGGA
     persimilis  --ACTCC------T-TCTAATCCTACTG-CT---------------TTCTTCCCAGCTGGACAA-----------CGGCGC----TG----------GGC--ACAATGGCCCGAGGGGGA
        virilis  -TACCCT------T-TCTAATCCCTGGACCAGGCACAGGCCCAGGCACAGGCACAGCTGGATCT------------AGCCCGGTTTG-AAAGGACT-TAC--ACAA-AA-CGGGCGGTGG
     mojavensis  --ACTCT------TCTCTAATCCCGGGCGCAG--------------ACTGGCACAGCTGGACTT------------AACCC----------GGACT-TGG--ACAACAA-CGGGCGGCAA
      grimshawi  -TACTCC------T-TCTAATCCCCGGGGA----------------CCAGGCACAGCTGGATCT------------AACCCGGTTTGCAAAGGACT-TTGCAACAA-AA-TGGG------
        Summary  BBBBBBMMMMMMMMMBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TGCGTCCTTTC-TTTTGGG------TCACC---GC----------ACATCGGGTC--AAACAGGATCAATCACCGGAATCGC--------TCCCTGATCCGCAGGATCATGCGCGAAAAT
       simulans  TGCGTCCTTTC-TTTTGGG------TCACC---GC----------ACATCGGGTC--AAACAGGATCAATCACCGGAATCGC--------TCCCTGATCCGCAGAATCATGCGCGAAAAT
      sechellia  TGCGTCCTTTC-TTTTGGG------TCACC---GC----------ACATCGGGTC--AAACAGGATCAATCACCGGAATCGC--------TCCCTGATCCGCAGAATCATGCGCGAAAAT
         yakuba  TGCGTCCTTTC-TTTTGGG------TCACC---GC----------ACATCGGGTC--AAACAGGATCAATCACCGGAATCGC--------TCCCTGATCCGCAGGATCATGCGCGAAAAT
         erecta  TGCGTCCTTTC-TTTCGGG------TCACC---GC----------ACATCGGGTC--AAACAGGATCAATCACCGGAATCGC--------TCCCTGATCCGCAGGATCATGCGCGAAAAT
      ananassae  TGCTTTCTTTA-TTTCGGG------TCACC---GC----------ACATCGGG-C--AAACAGGATCAATCACCGGAATCGCTCCCTGATTCCCTGATCTCCAGGATCATGCGCGAAAAT
  pseudoobscura  TCTGCCCTTTG-AGTCGGG------TCACCGCAGC----------ACATCCAG-C--AAACAGGATCAATCACCGGAATCCC--------T----------CAGGATCATGCGCGAAAAC
     persimilis  TCTGCCCTTTG-AGTCGGG------TCACCGCAGC----------ACATCCAG-C--AAACAGGATCAATCACCGGAATCCC--------T----------CGGGATCATGCGCGAAAAC
        virilis  CCTTTGTTGCT-CTTAGAG-CCGCCTCACC---GCATCTTGGCGAATATCCCA-C--AAACAGGATCAATCAGCAAAAACA----------CTGTGATCCTCAGGATCATGGGCAAAAAT
     mojavensis  CCTTTGTTGCC-TTTAGAG-CCGCCTCACC---GC------------ATCCCA-CA-AAACAGGATCAATCAGCAAGAATG---------TCTCTGATCCTGCGGATCATGCGCGAAAAT
      grimshawi  TCATTGTTGTTGTCTAGTGTCCGCCTCACC---GCATCTTGCCAAATATTCCA-CACAAACAGGATCAATCAGCAACAACA---------ACGCTGATCCTGAGGATCATGCGCGAAAAT
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TAGTGCAAACTTA--------------CTT------G-GACGCA--------------------------------GCAGGTAGCA------CGGAG---CACGGA-----GCTGACCGG
       simulans  TAGTGCAA----A--------------CTT------G-GACGCA--------------------------------GCAGGTAGCA------CGGAG---CTAGGA-----GCTGACCGG
      sechellia  TAGTGCAA----A--------------CTT------G-GACGCA--------------------------------GCAGGTAGCA------CGGAG---CAAGGA-----GCTGACCGG
         yakuba  TAGTGCAA----A--------------CTT------G-GACACA--------------------------------GCAGGT----------AGAAG---CACGGA-----GCTGACCGG
         erecta  TAGTGCAA----A--------------CTC------G-GACGCA--------------------------------GCAAGTAGCAGGTAGCAGGAG---CAAGGA-----GCTGACCGG
      ananassae  TGGTGCAA----A--------------CTCTCCTCGG-GACACG--------------------------------CCAGGTAGCC----------------GGGA-----GCTGACCGG
  pseudoobscura  TAGTGCAA----A--------------CTTCAGAAGA-GACGCG--------------------------------CCAGGTAGGC------CCAAG---GCAGGC---CTGCTGACCGG
     persimilis  TAGTGCAA----A--------------CTTCAGAAGA-GACGCG--------------------------------CCAGGTAGGC------CCAAG---GCAGGC---CTGCTGACCGG
        virilis  TAGTGCAA----A---TTTAAAGGCTCTTC------G-GGCTTG---------------------GGTAATGTCGTGCAGGTAGGG------CTTTTAC-TCTGACCGCTCGCTGACCGG
     mojavensis  TAGTGCAA----AATGTTGAGAATCCTTTT------GAGACTTGCGAATCGAGAAGATGGTAGATGGTAGAGC--TGCAGGTAGAG------CTGGG-----TGACCGCTCGCTGACCGG
      grimshawi  TAGTGCAA----A---TTTAAAGG---TTC------A-GGAATACAGGAATAGAGGAATACAGGCAGCAACGAC-TGCAGGTAGTG------CCACCAAGTTTGACCGCTCGCTGACCGG
        Summary  BBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBRRRRRRRRRBBBBBBRRRRRRRRRBRRRRRRRRRBRRRRRRRRRBBBBBBBBBB

                 
   melanogaster  AAAATCCGATCGAAGGGATTATAATTCCA---GCCAGGCA----G-----CAGCCCTA--CATATC-CTT--CT----CG-------------TTTCCCGCTTG------CTTTGCGACA
       simulans  AAAATCCGATCGAAGGGATTATAATTCCC---GCCAGGCA----G-----CAGCCTTA--CATATC-CTT--CTATCCCG-------------TTTCCCGCTTG------CTTTGCGACA
      sechellia  AAAATCCGATCGAAGGGATTATAATTCCA---GCCAGGCA----G-----CAGCCCTG--CATATC-CTT--CT----CG-------------TTTCCCGCTTG------CTTTGGGACA
         yakuba  AAAATCCGATCGAAGGGATTATAATTCCA---GCCAGCCA----G----GCAGGCCTA--CATATC-CTT--CT----CGAACACATCC----TTTCCCGCTTG------TTTTGCGACA
         erecta  AAAATCCGATCGAAGGGATTATAATTCCA---GCCAGGCA----GACCTACAGGGCTATGTATATC-CCT--CT----CG-------------TTTCCCGCTTG------TTTTGCGACA
      ananassae  AAAATCCGATCGAAGGGATTATAATTCTAAGGGGCATGCA----G----GCAGGCTAG--GATATC-CTTAACT----CGCAACCGTCCTGTGTTTC---CTTA------TTTTGCGACA
  pseudoobscura  AAAATCCGATCGAAGGGATTATAATTCCT---GGCAGGCT----G----GCAGGCAGG--CAGGCCTCGC--CT----CG-------------CCTCTTGTT---------TTTGCGACA
     persimilis  AAAATCCGATCGAAGGGATTATAATTCCT---GGCAGGCTGGCAG----GCAGGCAGG--CAGGCCTCGC--CT----CG-------------CCTCTTGTT---------TTTGCGACA
        virilis  AAAATCCGATCGAAGGGATTATATTTCTT---GCCAAA------------------GG--CGGTCC-TTC--TA----CGCTCCTTCCGCT--CTTAGGGTCCGGCTTGTTTGTACGACA
     mojavensis  AAAATCCGATCGAAGGGATTATAATTCTT------------------------------------C-CTC--TT----CGC------------CTTTGGGTTTG----CTTTCCACGACA
      grimshawi  AAAATCCGATCGAAGGGATTATAATTCCT---GGCGAGCA----G-----CAG--CAG--CAGCTC-TCC--TT----C--------------CTCTACGCCCATTGTCTGTGTGCGACA
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBRRRRRRRRRBBBBBBBBBBBBBBBRRRRRRRRRBBMMMMMMMMMBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBB

                 
   melanogaster  ATTAAGGCAAATATTTTGCGTACTAATTAAGCATGGCTCAA----------GAGCA---------------CCGG----AATCGTGGGCG-------GATTTGCAT-------------A
       simulans  ATTAAGGCAAATATTTTGCGTACTAATTAAGCATGGCTCAA----------GAGCA---------------CCGG----AATCGTGGGCG-------GATTTGCAT-------------A
      sechellia  ATTAAGGCAAATATTTTGCGTACTAATTAAGCATGGCTCAA----------GAGCA---------------CCGG----AATCGTGGGCG-------GATTTGCAT-------------A
         yakuba  ATTAAGGCAAATATTTTGCGTACTAATTAAGCACGGCTCAA----------GAGCA---------------CCGG----AATCGTGGGCG-------GATTTGCAT-------------A
         erecta  ATTAAGGCAAATATTTTGCGTACTAATTAAGCAAGGATCAG----------GAGCA---------------GCGG----CATCGTGGGCG-------GATTTGCAT-------------A
      ananassae  ATTAAGGCAAATATTTTGCGTACTAATTAAGCACGGATCTC----------GAGGA---------------CCCT----GA-AGGAGGAG-------GATTTGCAT-------------A
  pseudoobscura  ATTAAGGCAAATATTTTGCGTACTAATTAAGCACGGCCTAAGCCCGGGAAGGATCC---------------CCGGGCCAGATCAAGGGCTCTCGGGCGATTTGCAT-------------A
     persimilis  ATTAAGGCAAATATTTTGCGTACTAATTAAGCACGGCCTAAGCCCAGGAAGGATCC---------------CCGGGCCAGATCAAGGGCTCTCGGGCGATTTGCAT-------------A
        virilis  ATTACGGCAAATATTTTGCGTACTAATTAAGCACGGCTTAAGCCGTG------------------------CTGA----ATTTTGA--TG-------AATTTGCATACAGCGTTTTTGGA
     mojavensis  ATTACGGCAAATATTTTGCGTACTAATTAAGCAGGGCTCAAGCCGGAGCCAGAGCCGGATTGTTCGGCAGTCTGG----AGTCTGA---A-------AATTTGCATACAGCA----CGGA
      grimshawi  ATTAAGGCAAATATTTTGCGTGTTAATTGAGCATGGCTCAAATCCAACTCAAACTCAGGCAGCGA------CTCG----AGCC------G-------CATTTGCATACTGAGTTTTTGGA
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBRRRRRRRRRRRRRRRR

                 
   melanogaster  TGGCGCGTCGGATTTGCAGCC-ATTACCC------TTTTGTTGGCC---AAAGGATTTGTCCGTGGGCGTTGCATT----------TTCCT------CCGGCTTATCGAA----GATCGA
       simulans  TGGCGCGTCGGATTTGCAGCC-ATTACCC------TTTTGTTGGCC---AAAGGATTTGTCCGTGGGCGTGGCATT----------TTCCC------TCGGCTTATCGAA----GATCGA
      sechellia  TGGCGCGTCGGATTTGCAGCC-ATTACCC------TTTTGTTGGCC---AAAGGATTTGTCCGTGGGCGTTGCATT----------TTCCT------TCGTCTTATCGAA----GATCGA
         yakuba  TGGCGCGACGGATTTGCAGCC-ATTACCC------TTTTGTTGGCC---AAAGGATTTGCCCGTGGGCGTTGCATT----------TTCCT------CCGGCTTATCGAA----CTTCGA
         erecta  TGGCGCGACGGATTTGCAGCC-ATTACCC------TTTTGTTGGCC---AAAGGATTTGGCCGTGGGCGTGGCATT----------TTCCT------CCGGCTTATCGAA----GATCGA
      ananassae  TGGCGCGACGGATTTGCAGCC-ATTACCC------TTTTGTTGGCA---AAAGGATTTGCCCGGGGGCGTTGCGTT----------TTCCT------CCGGCTTATCGGG----GACTGG
  pseudoobscura  TGGCGCGACGGATTTGCAGCC-ATTACCC------TTTTGTT-GCC---AAAGGATGTGCCGGAGGGCGTTGCGTT----------TTCCG------CCGGCTTATCGGG----G-----
     persimilis  TGGCGCGACGGATTTGCAGCC-ATTACCC------TTTTGTT-GCC---AAAGGATGTGCCGGAGGGCGTTGCGTT----------TTCCG------CCGGCTTATCGGG----G-----
        virilis  TAGCGCATCGGATTTTCAGCC-ATTACCC------TTTTGTT-GCC---AAAGGATTTGCCAGTAGGCGTTTAGTT--------------G------TGC-----TGCGG----GAACAG
     mojavensis  TAGCGCATCGGATTTGCAGCA-ATTACCCT-----TTTTGTT-GTC---AAAGGATATGCCGGTGGGCGTTACGTTTG--------TCCCG------TACAGGAATGCGAGCACGAACAT
      grimshawi  TAGCGCATCGGATTTGCAGCCAATTACCCTTTTTGTTTTGTT-GGCCAAAAAGGATTTGGCAGTGGGCGTTGCAACTAGAAACATTTCCCGACAATTTCCCGGAACTGAA----GGACAA
        Summary  RRBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBRR

                 
   melanogaster  TC----------CTCG-----CTCCTTCCGGGAACT------CGCATCCGTCACGCACCGATCGCTGGAC------------TGTTTTGGCC----------------------CTGGG-
       simulans  TC----------CTCG-----CTCCTTCCGGGAACT------CGCATCCGTCACGCACCGATCTCTGGAC------------TGTTTTGGCC----------------------CTGGA-
      sechellia  TC----------CTCG-----CTCCTTCCGGGAACT------CGCATCCGTCACGCACCGATCGCTGTAC------------TGTTTTGGCC----------------------CTGGA-
         yakuba  TC----------CTCGGCAGTATCCTTCCGGGAACT------CGCATCCGTCACGCACCGATCG--------------------------------------------------CTGAG-
         erecta  TC----------CTCG-----CTCCTTCCGGGAACT------CGCATCCGTCACGCACCGATCTCTGGAC------------TGTTTTGGTC----------------------CTGGG-
      ananassae  GCCGAAGGACCTCCCG-----TCCTTTCCCGGAACTGCGTTCCGCATCCGTCACGCACCGATCG-----C------------ATCTCTGGCC----------------------CTGGGA
  pseudoobscura  -C----------CTCG-CCGTCACTTCCCGGAAACC------CA---CCGTCACGCTCCGATCGCATATCACGTCAGGCTCTGGCTCTGACCGTGGGTCCGTCT----------CTGGG-
     persimilis  -C----------CTCG-CCGTCACTTCCCGGAAACC------CA---CCGTCACGCTCCGATCGCATATCACGTCA------GGCTCTGACCGTGGGTCCGTCTCTGGGCTGGGCTGGG-
        virilis  TT----------C------------TTCTTGGAAC-------ATAAATTTTCACGCTTCTTTCG----GT------------ATTTTTGTGT----------------------CTG---
     mojavensis  TG----------CTTG----ACAATTTCCCAGAAC------AAAAATCCTTCACGCTTCAGTC---------------------------------------------------------
      grimshawi  CC----------C----------------------------TCACAGTCGTCACGCTTCAGTCG--TAAT------------ATGTCTGTGT----------------------------
        Summary  RRRRRRRBBBBBBBBBBMMMMMMMMMBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBMMMMMMMMMRRRRRRRRRMMMMMMMMMBMMM

                 
   melanogaster  ------AAGTGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTGAGCGTGAAATTTGTGC-CATCCTTT-TGCGTGGGATC---GGTTAAGCAAAGGAGTGTCATAGAAATGG
       simulans  ------AAGTGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TGAAGCGTGAAA-TTGTGC-CATCCTTT-TGCGTGGGATC---GGTTAAGCAAAGGAGTGCCATAGAAATGG
      sechellia  ------AAGTGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTAAGCGTGAAA-TTGTGC-CATCCTTT-TGCGTGGGATC---GGTTAAGCAAAGGAGTGCCCTAGAAATGG
         yakuba  ------AAATGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTGAGCGTGAAA-TTGTGC-CATCCTTT-TGCTTGCGATC---GGTTAAGCAAAGGAGTGCCGTAGAAATGG
         erecta  ------AAATGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTGAGCGTGAAA-TTTCGC-CATCC-TT-TGCGTGGGACC---GGTTAAGCAAAGGAGTGCCGTGGAAATGG
      ananassae  AACTGAAAATGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTGAGCGTGAAA-TGGTCTACATCCTTTAGGTGTGGGATC---GGTTAAGCAAAGGAGTGTCCGGCCAGTGG
  pseudoobscura  --CTGGGAATGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTGAGCGTGAAA-TTTT-T-CATCCTTCGTTCTCGGGTTC--GGGTTAAGCAAAGGAGT--------AGGCG
     persimilis  --CTGGGAATGATATGCAAATATTGACAC-CCATCATTTTTCAATAT-TTGAGCGTGAAA-TTTT-T-CATCCTTCGTTCTCGGGTTC--GGGTTAAGCAAAGGAGT--------AGGCG
        virilis  ------GAATGATATGCAAACATTGACAG-ACATCATTTTTCAATAT-TTGAGCGTGAG--------------TCT-GGCCCGTCACGTCTGCTTAGGCAAGGGAGT-------------
     mojavensis  ----------GATATGCAAATATTGACAGAAAATCATTTTTCAATTTCTCAAGCGTGAA-------------------------------------------------------------
      grimshawi  ------AAATGATATGCAAATATTGACAG-ACATCATTTTTCAATAT-TTGAGCGTGAA-------------ATTT-GGTTCCTGGCA--GGGTTAAGCAAAGGAGT-------------
        Summary  MMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  GTGAAATTCTG-TTCAAGGCTGTTTTGTA--------TAAT-GAAAATTGATGAATTGCC-----ATT-CTGTCTATTTTTCG--AGGTCATTG----------CAA--GCCGTTTTTCA
       simulans  GTGAAATTCTG-CTCAAGGCTGTTTTGTA--------TAAT-GAAAATTGATGAATTGCC-----ATT-CCATCCATTTTTCG--AGGTCATCG----------CAA--GTTGTTTTTCA
      sechellia  GTGAAATTCTG-CTCAAGGCTGTTTTGTA--------TAAT-GAAAATTGATGAATTGCC-----ATT-CCATCCATTTCT-G--AGGTCATCG----------CAA--GCTGTTTTTCT
         yakuba  GTGAAATTCTG-CTCAAGGCTGTTTTGTA--------CAAT-GAAAATTGATGAATTGCC-----GTTGCTGGCCATTTTCCG--AGGTCATCG----------CAA--GCCGTTTTTCA
         erecta  GTGAAATTCTG-CCCAAGGTCGTTCTGTG--------TAAT-GAAAATTGATGAATTGCC-----ATT-CTGTCCATTTTCCG--AGGTCATCG----------CAA--GCCGTTTTTCA
      ananassae  GAGAAATTGCG-CTCAAGGTTTCCAAGGA--------TAATGGAAAAAAAATGAATTGCC-----GTT-TCTACAATATTTCG--AGGTCATCGTTTTGCGAGACGA--ACTG-TTCAAA
  pseudoobscura  CAGAGACACTGTCTCAAGGCCGACTG----------------GACAATGGACCAATTCCCTGGAGGTC-GTTTCTCTGTTTAG----------G----------GAA--GCTG--TTTGA
     persimilis  CAGAGACACTGCCTCAAGGCCGACTG----------------GACAATGGACCAATTCCCTGGAGGTC-CTTTCTCTGTTTAG----------G----------GAA--GCTG--TTTGA
        virilis  -CGCCATTTCG-TTCAAGGCCGAGTTTAGCTATTCTTCAAG-GCTATTTGAAAAGCAATTCTAACGAT-TT---------CCGTTAGATCATAA----------CAA-------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  -CCAAATTCTA-TTCAAGGCCAAGCTGAG--------CAAC-GAAAACTGAGAA-----------AAT-GT---------TCG--AGGTCATTG----------CAAGAGTC--TTTTCT
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBBBBB

                 
   melanogaster  GGGGCGTTACCGAAGTCGACTCTCTGCTGAGCATGGCGAATTGAAGTTCA------------TAAAT-------ATTTTGCCTATCAACCTTTTCTCGATT--------GATGTGAAAAA
       simulans  TGGGGGTTACCGAAGTCGACTGTCTGCTG-------------------------------------------------AGCATAGCGA--------------------------------
      sechellia  TGGGCGTTTCCGAAGTCGACTGTCTGCTGA------------GCATGGCGAATTGAAGTTCATATAT-------ATTTTGCATATCAACCTTTTCTCGATT--------GAAAGAAAGGA
         yakuba  GGGGCGGTGCCGAAGTCGACTGTCTGCTGA------------GCATGGCGAATCGAAGTTCATAAAT-------ATTTTGCCTA-------TTTCACG-----------AAATGAAAGGA
         erecta  GGGGCGGTTCCGAAGTCGACTATCTGCTGA------------GCATGGCGAATCGAAGTTCATAAAT-------ATTACGCCTATTAACCTTTTCACGTTCTGCA----AAATGGAAGGA
      ananassae  GGGGCGTTTCTAAAGTCGAATGTCCGCTGA------------GCGAAGCGAATTCGTTTTCATAAATATATGCAATTTTATTTAAAAAT--------------------TATCCAAAGGA
  pseudoobscura  GGGGCGGTGCCGAAGTCGACTGCCAAAGGAGCGTAACAAATT-------------------ATGAACCATTGCCATAAGGTATGAAAA---TTTAATAGTTTTAA-TACATCCGTATAGA
     persimilis  GGGGCGGTGCCGCAGTCGACTGCCAAAGGAGCGTAACAAATT------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  CGAGCGT------AGTAAATT---------------------------------AAAATGTATATATACTCAG-ATATTGTATTTAAAATATTTAAAAGTAATAAATGAAGATTAAAATA
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRMM

                 
   melanogaster  TATTTAATTATTCACTAGTTGATACTAGACGAACTAACAAATGC---CTT-TATTGTATTGAAATAGTTGGCGATGAAAAGTATATATATTT-TTCAAATATTTAAGC--TTGGTTGGTA
       simulans  -----------------ATTGA---------AGTTCATAAAT-----ATT-TTGCATATCAACAT-TTTCTCGATTGAAAGAAATGAAAG------------------------------
      sechellia  AA--GGATGTAACAATGATGGA---------AATTTTAGAATGC---GTT-TAGTGTTTTAAAATAGTTTGCGCTGGATAATAGTAATAGAT-ATAATATTACCAATA--TTGTT---AA
         yakuba  -----------------TTTCA---------AATTCGTACAGCA---GTCGCTATGAAGAAGGATGACTAGCAGTAGACAAACTT----TGTATTAGGAGATTTAAGA------------
         erecta  -----------------TTTCA---------CGTTTGTACAGTT---TTC-TAATGAAATAGCATGGCTAG--ATAAACAGATATTAGATATGTTTGCATATTTAA--------------
      ananassae  -----------------TTCGA-----------TTTATAAATTT---CTA-CCAAGTGTC-GCTTAGGGATCGACTAAGAATAGGTAAAGGAATAGACATGCACAG--------------
  pseudoobscura  TATATATTTTGAGACAGACCAA---------GAGCGGAATATTT---GCA-TCTAATTTCATAATAATTATCATCGCGGTGAATTTTTTTAC-TTTCCAGGACTAAAAAATTAGCCTGTA
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  TAGAAAATAATT-----TTTAA---------CACTAAAAGAGGTTAACTA-CTGCACTTGCTACTATTTGCTGATAAATATTAATAATACACAATCCTAAAATTTGGA------------
        Summary  MMMMMMMMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRBRRRRRRRRRBMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRMMM

                 
   melanogaster  GTCCTTTATGTAAAATGTTTCAATCCCTTCCCT--C----AAGTAT----AAATTGTA----CAAAATAT--------------TTGATGCAGGAAT--ACGCCT---------------
       simulans  ---------------------GGCAACATAAAT--C----AAGTAT----AATATGTA----CAATATAT--------------TTAATGCTGGAATACACGCCT---------------
      sechellia  ATCCCTTTCATA------TTTAACAACATAAAT--C----AAGTAT----AATCTGTA----CAAAATAT--------------TTAATGCAGAAAT--ACGCCT---------------
         yakuba  ------------------TATTACAATATG----------AAATAT----------------AAATATAT--------------TTA---------------------------------
         erecta  -------------------ATAACAAAATGGAA--GTTAAGAATAT----AGTTTCTCAATAAAATACCT--------------TTAA-----AAGT--GCGCCTCGAGTTTGGGGGTTT
      ananassae  ----------------------------------------AGGCAC----AGATTTCT----AAA----------------------------GAGG-----------------------
  pseudoobscura  GGCCTGTGTAGATCTCTTCCTCAT----------------ACTTAG----AATTTGT-----AAAAATAC--------------TCAA--------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------TATTATTATATTAATTGC----AAATATTGTTAACTTTCAATCCTAAAATTTTGTAATTGATCTTAATATTGTAAGAGT-----------------------
        Summary  MMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMM

                 
   melanogaster  ------------------------TTTCATTTCTTATTTCTGTATCATT-TAT---------TACCATTTATTTAT-T---------------------CC-TGACTCATCATAATGGTC
       simulans  ------------------------TTTCA-TTCTTATTTCTTTATCATT----------------------CCTAT-T---------------------CC-TGACTCATCATAATGGTC
      sechellia  ------------------------TTTCA-TTCTTATTTCTTTATCATT----------------------CCTAT-T---------------------CC-TGACTCATCATAATGGTC
         yakuba  -------------------------------------------------------------------------TAT-T---------------------CC-TGACTCATCAT-------
         erecta  TATAACTTGTATAACTCAGAGAACTTCTA-CCCATACTTTTTAATAAAA--------------ATGGGACTATCAT-T---------------------CCATGACTCATCAT-------
      ananassae  ------------------------CTCCA-TTATTAAGTTCTTTTGATG----------------------GCCATGT---------------------CC-TGACTCATCATTTTGGGC
  pseudoobscura  ---------------------------------------------------------------------------------------------------CC-TGACTCATTATCCTCCCC
     persimilis  ---------------------------------------------------------------------------------------------------CC-TGACTCATTATCCTCCCC
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------TTTC--TTTTCAGTTTCCAATAATTGTATTCCCAAAAATTGCATTCAATCAT-TTGATCAATCTTCTTTAATATTTC-AAGCTTATTAT-------
        Summary  MMMRRRRRRRRRMMMMMMMMMRRRRRRRRRBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBMMMMMMM

                 
   melanogaster  GCATATTTCGATTCGTTTC-GATTC-----ACTTGCTAA------------TCGCATTATT-CACTTG-----------CCAGAATGAGAAGAATAGGG------------TCTGCCAA-
       simulans  GAATATTTCAATTCGTTTC-GATTC-----ACTTGCTAA------------TCGCCTTATT-CACTTG-----------CCAGAATGCGAAGAATAGGG------------TCTGCCAA-
      sechellia  GCATATTTCGATTCGTTTC-GATTC-----ACTTGCTAA------------TCGCATTATT-CACTTG-----------CCAGAATGGGAAGAATAGGG------------TCTGCCAA-
         yakuba  -----TTTCGATTCGTTTC-GATTCGATTTACTTGCTAA------------TCGCATTATT-CACTTG-----------CCGGAAT----------------------------------
         erecta  ---TATTTCGATTCGTTTC-GATTC-----ACTTGCTAA------------TCGCATTATT-CACTTG-----------CCAGAATTGGGAGAATTG-----------------GCCAA-
      ananassae  TCATATCCCAGCCCCCACAGGATTC-----ACTTGCTAA------------TCGCAATG----ACTGG-----------CCAGGGGGATGAGGGTTTGGGTGACCTAATACTCGACCGA-
  pseudoobscura  TTGTATTTCAACCCGTTTC-AGTTG-----GCATTCC--------------TCAGCCTATT-CCTTCGTATTCCCCTCCCCAGACCGTGATTCGGTGAG-----CTAATACCCAACCAAT
     persimilis  TTGTATTTCAACCCGTTTC-AGTTG-----GCATTCC--------------TCAGTCTATTCCCTTCGTATT-------CCAGACCGTGATTCGGTGAG-----CTAATACCCAACCAAT
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ---TTTTAAGACTCTATTC-AAGTT-----ATTCACAAACTCGCTGAGCTTTATCATTATTTTATTTT-----------AAATATTATAAAGATATACT---------------------
        Summary  MMBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBRRRRRRRRRBBRRRRRRRRRMMMMMMMMMBBBBMMMM

                 
   melanogaster  ------------AG------TTACCAGTTAATATGCGCAACATTTCCGCCTCCAAACTGACACCCAATCTGCC---CGAAAAGATC-----GAAATGCTTCCGTTT------------TT
       simulans  ------------AG------GTACCAGTGAATATGCGCAACATTTCCGCCTCCAAACTGACACCCAATCTGCC---CGAAAAGATC-----GAAATGCTTCCGTTT------------TT
      sechellia  ------------AG------TTACCAGTGAATATGCGCAACATTTCCGCCTCCAAACTGACACCCAATCTGCC---CGAAAAGATC-----GAAATGCTTCCGTTT------------TT
         yakuba  ---------------------------------GGCGCATCATTTCCGCCTCCAAACTGACACCCAATCTGCC---CGAAAAGATC-----GAAATGCTTCCGTTT------------TT
         erecta  ------------AG------TTAGCAGTGAATATGCGCAGCATTTCCGCCTCCAAACTGACACCCAATCTGGC---CGAAAAGATC-----GAAGTGCTTCCGTTT------------TT
      ananassae  ------------AGCGAAACTTGCCAAGGAATATGCGCAACATTTCCGCAACCAAACTGACACCCAATCTGCC---CCAAAAGATC-----GAACTGCTTCCG-----------------
  pseudoobscura  TCGAAAGCCTAGAG------TTACCAGTAAATAGGTCCAACATTTCCGGAAGCAAACTTCCACTCAATCTGGTATACGAAAAGATC-----GAAATGTTTCCGCTTATCAGATAGTTTTT
     persimilis  TCGAAAGCCTAGAG------TTACCAGTAAATAGGTCCAACATTTCCGGAAGCAAACTTCCACTCAATCTGGTATACGAAAAGATC-----GAAATGTTTCCGCTTATCAGACAG---TA
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------ACATATAATATATATTC---ACCAACCCGTTTCCCTTTCTTGTGTGCAGGCAGCTTTTCAGTTAATTCTTTATTTC------------TT
        Summary  MMMMMMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBRRRRRRRRRMMMMMMMMM

                 
   melanogaster  GGCGGATTCAT---------GTC-GCCTTCCGGAAGCGAGAACTCATCTT-----TGG-GGCA-------GGACACGCGG---------CGCTGACAG----------------------
       simulans  GGCGTATTCAT---------GTC-GCCTTCCGGAAGCGAGAAATCATCTT-----TGG-GGCA-------GGACACGCGG---------CGCTGAC------------------------
      sechellia  GGCGTATTCAT---------GTC-GCCTTCCGGGAGCGAGAAATCATCTT-----TGG-GGCA-------GGACACGCGG---------CGCTGACAG----------------------
         yakuba  GGCGGCTTCGT---------GTC-TCCTTCCGGAAGCCAGAAATCATCTT-----TGG-GGCA-------GGACACGCGG---------CGCTGACAG----------------------
         erecta  GGCGGATTCAT---------GTC-TCCTTCCGGAAGCCAGAAATCATCTT-----TGG-GGCA-------GGACACGCGG---------CGCTGACAG----------------------
      ananassae  --------------------------CTTCCGGAGGCGAGAAATCATCTTCGGGGCGG-GGCG-------GGGCAGGCGG---------CGCTGACAGACGGACAAGGCTGACTGGCTGA
  pseudoobscura  TTTTTTTTTTT---------GTC-TCTTGGCGGAAGCGAGAAATCATCTT-----CGG-GGGGGCAGAC-GGGCACGCGG---------CGATGACAG----------------------
     persimilis  TTTTTTTTTTT---------GTC-TCATGGCGGAAGCGAGAAATCATCTT-----CGG-GGGGGCAGAC-GGGCACGCGG---------CGATGACAG----------------------
        virilis  -------TCAT---------GACAGCGTTCCGGAAAAG--GAGTCGTCTT-----TGC-AGCAGCAAACAGGGATCGCAG-CAGTCTGACGATGACAG----------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  GGCGAATTCATGCATGAATCGACAATGTTCCGGAAAATACAAATCATCTT-----TGCTGGCAGTTAGCAGGGATCGCTGTCAGTCTGGCGATGACAG----------------------
        Summary  BBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBRRRRRRRRRMMMMMMMMMRRRRRRR

                 
   melanogaster  -CGCATAACAGGACATAGTCGAG--TCTGAAATCGCAGACAGAC--A----------------------------------------ACGAGACATGGGGCATATGCTAT----------
       simulans  -------ACAGGACACAGTCGAG--TCTGAAATCGCAGACAGAC--A----------------------------------------ACGAGACATGGGGCATATGC--T----------
      sechellia  -CGCATAACAGGACACAGTCGAG--TCTGAAATCGCAGACAGAC--A----------------------------------------ACGAGACATGGGGCATATGC--T----------
         yakuba  -CGGATAACAGGACATA---------CAGGA----CAGATAGAC--A----------------------------------------ACCAGACGTGGGGCATATGC--TGGCAGCTATA
         erecta  -CGGATAACAGGACACAGTCGTG--TCTGGAGTCGCAGACAGAC--A----------------------------------------ACCAGACGTGGGGCATATGC--C----------
      ananassae  CAGGATAACAGGAGCCAG--GAC--ACCGAATGCGCAGACAG-------------------------------------------------GACATGGGGCATATGC--T----------
  pseudoobscura  -GGCACAACAGGATACAA---------AAAAGGCGCAGACAGAC--ACCAGACACGGACCCTGACCCCC-------GACCCCGGACCCCGAGACATGGGGCATATGC--T----------
     persimilis  -GGCATAACAGGATACAA---------AAAAGGCGCAGACAGAC--ACCAGACACGGACCCCGACCCCCGACCCCGGACCCCGGACCCCGAGACATGGGGCATATGC--T----------
        virilis  ---GATAACAGAAAAACAGGGCATG---------CCGGGCAGAT--G-------------------------------------------GGACGTGAAAAATATGT--T----------
     mojavensis  ----------------------------------GCGCACAGATAGA-------------------------------------------GGACACGAGGAATATGT--T----------
      grimshawi  ---GATAACAGACAAGCAGAGAG-----------CCGGCCTGAA--A-------------------------------------------GGACATGGAAAATATGT--T----------
        Summary  RRBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRR

                 
   melanogaster  ---ATATCCTGGCAGGATAATCGACGCTAAATAGCGGCACGCGACCAACATTTTCCGGCCGGC---------GAG-------TATGATTATG------ATTT------------------
       simulans  ---ATATCCTCGCAGGATAATCGACGCTAAATAGCGGCACGCGACCAACATTTTCCGGCCGGC---------GAG-------TATGATTATG------ATTT------------------
      sechellia  ---ATATCCTTGCAGGATAATCGACGCTAAATAGCGGCACGCGACCAACATTTTCCGGCCGGC---------GAG-------TATGATTATG------ATTT------------------
         yakuba  CGAGTATCCTGGCAGGATAATCGACGCTAAATAGCGGCACGCGACCGACATTTTCCGGCCGGC---------GAG-------TATGAATATG------ATTT------------------
         erecta  ---ATATCCTGGCAGGATAATCGACGCTAAATAGCGGCACGCGACCGACATTTTCCGGCCGGC---------GAG-------TATGAATATG------ATTT------------------
      ananassae  ----------GGGAGGATAATCGACGTTAAATAGCGGCACGCGACCAACATTTTCCGGCAGTCTATGAGTATGAG-------TATGAATATG------ATTT------------------
  pseudoobscura  ----------GGCAGGATAATCGACGCTAAATAGCGGCACGCGGCCAACATTTTCCGGACTGC---------CAG-------TATGAATATG------ATTT------------------
     persimilis  ----------GGCAGGATAATCGACGCTAAATAGCGGCACGCGGCCAACATTTTCCGGACTGC---------GAG-------TATGAATATG------ATTT------------------
        virilis  ----------CTCTGGATAATAGACGCTAAATAGCGGCACGCGTCGCACATTTTCCGG-CAGC---------AAG-CGGGTATATGAATATGAA----ATTTGGAA-----CGGAATCGA
     mojavensis  ----------CGCAGGATAATAGACGCTAAATAGTGACACGCGTCGCACATTTTCCGG-CAGC---------TAG-CGGCTTTATGAATATAGAATCGATTTGAGATAT-GCCAAACAGA
      grimshawi  ----------CGCAGGATAATAGACGCTAAATAGCGGCACGCGTCGCACATTTTCCGG-CAGC---------AAGTCGGGCATATGAATATGGA----ATTTGAAACGGAACGCAATCGT
        Summary  RRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRBRRRRRRRRRRRRRRRRRRMMM

                 
   melanogaster  ------------GATCGAAATCG----------GGACAAAA----CGACGACTTCTTGTCA-----------------------GC-------------------------------GGG
       simulans  ------------GATCGAAATCG----------GGACAAAA----CGACGACTTCTTGTCA-----------------------GC-------------------------------GGG
      sechellia  ------------GATAGAAATCG----------GGACAAAA----CGACGACTTCTTGTCA-----------------------GC-------------------------------GGG
         yakuba  ------------GATCGAAATCG----------GGACAAAA----CGACGACTTCTTGTCA-----------------------GT-------------------------------GGG
         erecta  ------------GATCGAAATCG----------GGACAAAA----CGCCGACTTCTTGTCA-----------------------GC-------------------------------GGG
      ananassae  ------------TATCGAGTTCG----------GGACAAAA----CGCCGACTTCTCGCCG-----------------------GG-------------------------------AAG
  pseudoobscura  ------------GATCGAGATC-----------TAACAAAA----CGCTGACTTCTTGTCGAACACGCAGCACGCGAGGC----GC-------------------------------GAG
     persimilis  ------------GATCGAGATC-----------TAACAAAA----CGCTGACTTCTTGTCGAACACGCAGCACGCGAGGTCGCGGC-------------------------------GAG
        virilis  AAATGAAAACGCGATTGATATCGTAGAGCGACTGAACAAAG----TGTTGACTTCTTGTTA-----------------------ACAACGAA-------------------------AGG
     mojavensis  TAGAGAGAGACAGAGAGAGAGAG-AGAGAGAGAAGACAAAGAATATGTTGACTTCTTGTTA-----------------------ACAAAAAAAAAAAAAAAAAAAGGAAGGAGGAACAGG
      grimshawi  AAAGGAAATCCAGATCGAAATCG-AAAAAGA-AAAATAAA-----TGTTGACTTCTTGTTA-----------------------ACACCAAACAAA---------------------AGG
        Summary  MMMMMMBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBB

                 
   melanogaster  CCGA------------------ACA------------AG---------GA-----AAAACC-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTTGCTGGGCGTTTTT----C
       simulans  CCGA------------------ACA------------AG---------GA-----AAAACC-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTTGCTGGGCGTTTTT----C
      sechellia  CCGA------------------ACA------------AG---------GA-----AAAACC-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTTGCTGGGCGTTTTT----C
         yakuba  CCGA------------------ACA------------AG---------GA-----AAAACC-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTGGCTGGGCGTTCTTCGCCT
         erecta  CAGA------------------ACA------------AG---------GA-----AAAACC-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTTGCTGGGCGTTTT-----C
      ananassae  CCGC------------------CAA------------GGCCTGAGGGTGA-----AATGCCAAGGGCTCATTATGGAAAATAATTTCATAATTCGTGGGGT------------------T
  pseudoobscura  GCGC------GAGGC-------GAG------------GG---------GT-----GAAACG-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTAGC---------------A
     persimilis  GGGTCGGGGGTAAGC-------GAG------------GG---------GT-----GAAACG-----CTCATTATGGAAAATAATTTCATAATTCGTGGGGTAGC---------------A
        virilis  ACGA---GGGGTGAT-------AC--------------G---------GA-----CAAACG-----CTCATTATGGCAAGTAATTTCATAACTCGTGGGGC-------------------
     mojavensis  ACGA---GGGGTGAT-------ACAAA----------AG---------GA-----CACACG-----CTCATTATGGGAAATAATTTCATAACTTCTGGGGAGTGGGATGGAGAGG----G
      grimshawi  ACGA---GGGGTGATGACGAGGACGAAGACGGGGTCGAG---------GACAATGCACACA-----CTCATTATGGAAAATAATTTCATAACTCGCGGGGAGCCGAGCTGAGCCG----A
        Summary  BBMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRR

                 
   melanogaster  GCC---------TGTCACCCCT-CTGTG----------------------------------TCCTTGACAATGTGTGAAC----AACA----------TAAAAGGGGGTTGCTTTCGC-
       simulans  GCC---------TGTCACCCCT-CTGTG----------------------------------TCCTTGACAATGTGTGAAC----AACA----------TAAAAGGGGGTTGCTCGCGC-
      sechellia  GCC---------TGTCACCCCT-CTGTG----------------------------------TCCTTGACAATGTGTGAAC----AACA----------TAAAAGGGGGTTGCTTGCGC-
         yakuba  GTC---------TGTCACCCCTCCTGCG----------------------------------TCCTTGACAATGTGCG-------AACA----------TAAAAGGGGGTTGCTCTCGTG
         erecta  GCC---------TGTCACCCCT-CTGCG----------------------------------TCCTTGACAAAGTGCG-------AACA----------T-AAAGGGGGTTGCT-TCGC-
      ananassae  GCT---------TGTCACCCCT-CCGCGACTCGGCGACTCAGCGACTCCGAGACTCGACGACTCCTTGACAATGTGCGAACTGTGAACA------------GAAGGGGGTTG--------
  pseudoobscura  AC-----------GGCAGCCCT-CCAGG----------------------------------AACG-------------------AACA------------GAAGGGGGTTGC-------
     persimilis  AC-----------GGCACCCCT-CCAGG----------------------------------GTCG-------------------AACA------------GAAGGGGGTTGC-------
        virilis  ------------TGGCACCCTT-CGGTG----------------------------------GCGGCAACGTTGCATGAAC----AACA---TGCAACACGCAAACGGTTTGC--GCCT-
     mojavensis  GAGAGGGGGTTGTTGCA---------AG----------------------------------GCGTCAACGTTGCACGAAC----AGCAACTTGCAACACGCAAGCGCT-----------
      grimshawi  GCCGAGT-----TGCCACCCTT-CACAG----------------------------------GCGACAACATGCAACATGC----GACG---TGCAACACGCAAACGGTTTGC--GCCT-
        Summary  RRRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBMMMMMMMMMBMMMMMMMMMBBBBBBBBBBBBBBBBBRRRRRRR

                 
   melanogaster  T-------TGGTGTTGCTATAA-TTTTATGAGCGATTTCGTTTATTAATATGTTAGCCAATGTT---------GGC------CGAGGGTTAATAGGCCCACGACTCTAG--T--------
       simulans  T-------TGGTGTTGCTATAA-TTTTATGAGCGATTTCGTTTATTAATATGTTAGCCAATGTT---------GGC------CGAGGGTTAATAGGCCCACGACTCTAG-TT--------
      sechellia  T-------TGGTGTTGCTATAA-TTTTATGAGCGATTTCGTTTATTAATATGTTAGCCAATGTT---------GGC------CGAGGGTTAATAGGCCCACGACTCTAGTTT--------
         yakuba  C-------TGGTGTTGCTATAA-TTTTATGAGCGATTTCGTTTATTAATATGTTAGCCAATGTT---------GGCTAAGGGCGAGGGTTAATAGGCCCACGACTCTAG--TTTTTTTTT
         erecta  T-------TGGTGTTGCTATAA-TTTTATGAGCGATTTCGCTTATTAATATGTTAGCCAATGTT---------GGC------CGAGGGTTAATAGGCCCACGACTCTAG--T--------
      ananassae  T-------TGGTGTGGCTATAA-TTTTATGAGCGATTTCGTTTATTAATATGTTAGCCAATGTT---------GGC-----------------------------------T--------
  pseudoobscura  T-------CGGTGTGGCTATAATTTTTGTGAGCGATTCCATTATTTAATATGTGGCCCAATGCT---------GCA------CG---------------------------T--------
     persimilis  T-------CGGTGTGGCTATAATTTTTGTGAGCGATTCCATTATTTAATATGTGGCCCAATGCT---------GGA------CG---------------------------T--------
        virilis  TCAGCTACTGGTGTGGCTATAA-TTTTATGAGCGATTTCATT-ATTAATACGTTACATTATGTAACCGAAAAAGGA------TAAGGGAAAGTGCAACCATCAGTGGCG--T--------
     mojavensis  --------TGGTGTGGCTATAA-TTTTATGAGCGATTTCATT-ATTAATATGTTACGTAGTGCAA--GCAGCAGGA------GCTGGGGCAGCAGGAGCAGCAGGGGCA--T--------
      grimshawi  TTGA----TGGTGTGGCTATAA-TTTTATGAGCGATTTCATT-ATTAATATGTTACGT-------------AAGGA------TAAAAGGGGCAACAAGCAGCAGT--CG--T--------
        Summary  RRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMM

                 
   melanogaster  -TTT-------------------TTCGGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAT-T-------------TCCC----------------------------CATC
       simulans  -TTT-------------------TTCGGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAT-T-------------TCCC----------------------------CATC
      sechellia  -TTT-------------------TTCGGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAT-T-------------TCCC----------------------------CATC
         yakuba  CTTT-------------------TTTGGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAT-T-------------TCCC----------------------------CATT
         erecta  -TTT-------------------TTCGGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAT-T-------------TCCC----------------------------CCTC
      ananassae  --------------------------GGCACGTGG----CAGGAAGGCGTTATGTTTA--------CATAT-------------TCCC----------------------------CGAC
  pseudoobscura  --------------------------GGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAC-TAACCCCCTCTCCGTCCC----------------------------CATT
     persimilis  --------------------------GGCACGTGG----CAGGAAGGCGTTATGTTTA--------CAC-TTTCCCCCTCCCCGTCCC----------------------------CATT
        virilis  -CGTGGGCGACGTCGGCTCGGCATGTGGCACGTGC----CAGGAAGGCGTTATGTTTACATTCAG-CAC-T-------------TGGCC----------CGGCAGTGGCTGCCGGGTGTT
     mojavensis  -----------------GTGGCACGTGGCACGTGG----CAGGAAGGCGTTATGTTTACACAAAG-CAC-T-------------TGCCCACTCTGCCAGCAGGAGCAGCTACTGGGCGTT
      grimshawi  -CAGCCTTGGCGTCGCAACGGCACGTGGCACGTGGCAGACAGGAAGGCGTTATGTTTACATTCAGTCAC-T-------------TGCC-----------CACCACTTGCCACTGGGCGTT
        Summary  MMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBRRRRRRRRRMMMMMMMMMBBMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBB

                 
   melanogaster  CGCCGA--------------------------------------------TG
       simulans  CGCCGA--------------------------------------------TG
      sechellia  CGCCGA--------------------------------------------TG
         yakuba  CGGCGA--------------------------------------------TG
         erecta  CGCCGA--------------------------------------------TG
      ananassae  CACCGACTACCGACCCACGACCTCTGAGCCCCCACCCAGCCACCGTCTGGTG
  pseudoobscura  CATAGA--------------------------------------------TG
     persimilis  CATAGA--------------------------------------------TG
        virilis  CTTAGA--------------------------------------------TT
     mojavensis  GCGAGA--------------------------------------------TT
      grimshawi  CAGCGA--------------------------------------------TT
        Summary  BBBBMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBB