melanogaster  GATTGAG---GATTC-CGCACTCCTAATCCTTTGAC--TTTC-AGTTTGACTT----------TCGCTCC-CAAGGATCG-------------------------------CCGCTAG--
       simulans  GATTGAG---GATTC-CGCACTCCTAATCCTTTGAC--TTTC-AGTTTGACTT----------TCGCTCC-CAAGGATCG-------------------------------CCGCTAG--
      sechellia  GATTGAG---GATTC-CGCACTCCTAATCC---------------TTTGACTT----------TCGCTCC-CAAGGATCG-------------------------------CCGCTAG--
         yakuba  GATTCAG---GATTC-CGCACTCCTAATCCTTTGAC--TTTC-AGTTTGACTT----------TCGCTCC-CAAGGATCG-------------------------------CCGCTAG--
         erecta  GATTCAG---GATTC-CGCACTCCTAATCCTTTGAC--TTTC-AGTTTGACTC----------TCGCTCC-CAAGGATCG-------------------------------CCGCTAG--
      ananassae  ATCCCCG---GATTC-TGTTGCCTTAATCCTTTGAC----------------T----------TCGCCAC-C------CG-------------------------------ATTTAAG--
  pseudoobscura  GATCCAGCCAGATCC-TGC---TCTAATCCTTTGAC--TCTC-TCCGTGGCTT---------------------------------------------------------------AG--
     persimilis  GATCCAGCCAGATCC-TGC---TCTAATCCTTTGAC--TCTC-TCCGTGGCTT---------------------------------------------------------------AG--
        virilis  GGTCACT---GATCCGCGC---TTTAATCCTTTGAC--TTTC-GGCTCAGCCC----GACACTTGGCTTAGTGCGAATCGTTTGCTGCCAATGCTGGTTAACTGGC-----TGGCTAGCT
     mojavensis  GGTCACT---GATCCGCGC---ATTAATCCTTTGACTTTTTC-GGCTCATCCCGACGGACAGTTGGCTTAGCGCGAATCG--------CAAAGGCAGCGCGGCAGCGACAGCGGCTAGAG
      grimshawi  GGTCACT---GATCCGCGC---TCTAATCCTTTGAC--TTTCGGGCTCAGCCC----AACACTTGGCTTAGTCCGAATCAGTT----------------------------TGGCTGGCC
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRBBBBBBBBB

                 
   melanogaster  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCTCGGCTCTACGCATCCCAAAAACTCGGCAATTAA-------------C----GCGGCTGA
       simulans  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCTCGGCTCTACGCATCCCAAAAACTCGGCAATTAA-------------C----GCGCCTGA
      sechellia  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCTCGGCTCTACGCATCCCAAAAATTCGGCAATTAA-------------C----GCGGCTGA
         yakuba  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCTCGGCTCTACGCGTCCT-AAAACTCGGCAATTAA-------------C----GCGGCTGA
         erecta  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCTCGGCTCTACGCATCCC-AAAACTCGGCAATTAA-------------C----GCGGCTGA
      ananassae  --------------TCCC-----ACTTTCCGGAAAGTGTGCTGGCTTACTTTGGTTCCGCTC----TTCGGCAGGACAACTTTTTGGTAATTAAGATGTTAAGGCCCC----GTGGTCCT
  pseudoobscura  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCT-----------ATCC---AAAGTTGGTAATTAA-------------CATTTGCGCCCGA
     persimilis  --------------TCCG-----GCTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCT-----------ATCC---AAAGTTGGTAATTAA-------------CATTTGCGCCCGA
        virilis  GGCTGGCTGGTTTCTTGGC----CTTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCT-----------ATCC---AAAGTTGTTAATTAA-------------CATTTGCGCGCA-
     mojavensis  CACTGGTTAGTTTTTCCG-----ATTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCT-----------ATCC---AAAGTTGATAATTAA-------------CATTTGCTCGCA-
      grimshawi  TCCTCAACGTCGTATTCGCGCTTTTTTTCCGGAAAGTG---TGGCTTACTTTGGTTCCGCT-----------ATCC---AAAGTTGGTAATTAA-------------CATTTGCTCGCA-
        Summary  BBBMMMMMMMMMBBBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBMMM

                 
   melanogaster  -------------------TTCGCCCGA-------------------------------------------------------------------AGTCCA--GAATCCTAAATCC----
       simulans  -------------------TTCGCCCGA-------------------------------------------------------------------AGTCGA--GAATCCTAAATCC----
      sechellia  -------------------TTCGCCCGA-------------------------------------------------------------------AGTCGA--GAATCCTAAATCC----
         yakuba  -------------------TTCGCCCGAAGTCCGACTCCG---TAGTTC-----------------GGAGCTCGGAGTCCACATCCCACATCCCAAATTCT--AAATCCTAAATCC----
         erecta  -------------------TTCGCCCGA-------------------------------------------------------------ATCCCGAATCCC--AAATCCTAAGTCC----
      ananassae  -------------------TGTGGGCGT-------------------------------------------------------------------GGTCCTTGAACCCTTGAATTC----
  pseudoobscura  ATATTCGGTGCAGCCTGGACCGGCCCAG--CCCGGCCCCGACTTAGTGCCTTTTTCCTGCGTGCGTGGGCGTGGGCGTGTGTGC-----------TGTCCT--TCGCCCGAAACCCAAAG
     persimilis  ATATTCGGCCCAGC-----CCGGCCCGG--CCCGGCCCCGACTTAGTGCCTTTTT-CTGCGTGCGTGGGCGTGGGCGTGTGTGC-----------TGTCCT--TCGCCCGAAACCCAAAG
        virilis  ---------------------------------------------------------------------------------------------------------GCCCCGGGCGAG---
     mojavensis  ---------------------------------------------------------------------------------------------------------ATGCGGAACGTG---
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  MMMMMMMMMMMMMMMBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBMMMMMMMMMBBBBBBBBRRRRRRRRR

                 
   melanogaster  -------------------------CGA----------TCTCTTC-----------------TA-------------TGGGTGGGT---ACCGCGCAAAAGGGTTTAGTTTTAATTAGTC
       simulans  -------------------------CGA----------TCGCTTC-----------------TA-------------TGGGTGGGT---ACCGCGCAAAAGGGTTTAGTTTTAATTAGTC
      sechellia  -------------------------CGA----------TCGCTTC-----------------TA-------------TGGGTGGGT---ACCGCGCAAAAGGGTTTAGTTTTAATTAGTC
         yakuba  -------------------------CGA----------TCGGTTC-----------------TA-------------TGGGTGGGT---ACCGCGCAAAAGGGTTTAGTTTTAATTAGTC
         erecta  -------------------------CGA----------TCGGTTC-----------------TA-------------TGGGTGGGT---ACCGCGCAAAAGGGTTTAGTTTTAATTAGTC
      ananassae  -------------------------CTA----------TCCTTACGCTCGAAGAAGGAGATGCA-------------TAGG-GTGT---CCTGCCAAAAAGGGTTTAGTTTTAATTAGCT
  pseudoobscura  ACGAGGAGGATCTCGGGAAAGTGGGCGA----------GCGATTG-----------------TT-------------GAGGGAGGCGCGGCCGTTCGAAAGGGTTTAGTTTTAATTATCT
     persimilis  ACGACGAGGATCTCTGGAAAGTGGGCGA----------GCGATTG-----------------TT-------------GAGGGAGGCGCGGCCGTTCGAAAGGGTTTAGTTTTAATTATCT
        virilis  -------------------------CGA----------TCGATTC-----------------GCTCATCAGGCGACATCGGGCGAG---ACGGGGCGAAGGGGTTTAGTTATAATTAACT
     mojavensis  -------------------------CGAGGGGCGTTTGTTGTTTC-----------------GC-------------TCGAAGGCA---ACGACTCAAACGGGTTTAGTTATAATTAACT
      grimshawi  ------------------------------------------------------------------------------------------------AAAGGGGTTTAGTTATAATTAACG
        Summary  MMMMMMMMMRRRRRRRRRBBBMMMMMMMMMMMMMMMMMMBBRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  GACTTTGGACGCGCCT----------------------CAT------------------------C-GAAA-TGGTCACCGAAGATTGGGAG------------GACGTGAG--------
       simulans  GACTTTGGACGCGCCT----------------------CAT------------------------C-GAAA-TGGTCTCCGAAGATTGGGAG------------GACGAGAG--------
      sechellia  GACTTTGGACGCGCCT----------------------CAT------------------------C-GAAA-TGGTCACCGAAGATTGGGAG------------GACGAAAG--------
         yakuba  GACTTTGGACGCGCCT--------------------------------------------------------TGG-----GAAGATTGGAAA--------GATTGGGAAGAG--------
         erecta  GACTTTGGACGCGCCT----------------------CAT------------------------C-GAAA-TGGTCTCCGAAGATTGGAA-------------GGCGAGAG--------
      ananassae  GACTTTAGACTCGCCT----------------------CGTTCCTCAAAAAGTAACAATTTTTGGT-GAAA-GTGCCGGAAAATGTTGGAAA---ATCGTAGGCGTAAAGGG--------
  pseudoobscura  GACTTTGGACGCGCCCGTGACCGAGTTTTCACGGATCACAG------------------------C-GAAAGTGATCACAAAACACTTTAAGCAGATCCT----GAAAAGGGTTCGCGAT
     persimilis  GACTTTGGACGCGCCCGTGACCGAGTTTTCACGGATCACAG------------------------C-GAAAGTGATCACAAAACACTTTAAGCAGATCCT----GAAAAGGGTTCGCCAT
        virilis  GACTTTAGACGCGCCT----------------------C---------------------------------------------------------------------------------
     mojavensis  GACTTTAGACGCGCCT----------------------TG-------------------------CC-----------------------------------------------------
      grimshawi  CACTTTGGACGCGCCT--------------------------------------------------------------------------------------------------------
        Summary  BBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBRRRRRRRRRMMMM

                 
   melanogaster  TCACG-------GGGGGCGGGGCGATTTGGGA--AGTTT-CAAAACATTCAAATCGAACGAAAATCAG-----------------TGCGCTATAATTTAG----AAAAATT---------
       simulans  TCAC--------GGGGGCGGGGCGATTAGGGA--AGTTT-CAAAACATTCAAATCGAACGAAAATCAGTGGATCCATAGCCTTTTTGCGCTATAATTTAGAAAAAAAAATTATAGGAACT
      sechellia  TCAC--------GGGGGCGGGGCGATTAGGGA--AGTTT-CAAAACATTCAAATCGAACGAAAATCAGTGGATCCATAGCCTTTTTGCGCTACAATTTAG--AAAAAAATTATAGGAACT
         yakuba  TCAC--------GGAGGCGGGGCGATTAGGGA--AGTTT-CAAAACATTCAAATCGAACAAAAATCTGTGGAACAATCGGTTTTTTGCGCTATGAATTAG----TAAAATTGAAAGATGC
         erecta  TCAC--------GGGGGCGGTACCATTAGGGA--AGTTT-CAAAACATTCAAATCGAACGAAAATCTGTGGATCAATCGGTTTTTTGCGCTATGAATTAT----AATAATTAATAGGGGC
      ananassae  TTGTGTGCGAAAGGGGGCGAGGCGATTAGTGAAGAGTTT-CAAAACATTTAAATCT----AAATTGAGGAGAAACATAAA-----TAGCCTTCGATTGGG----AAAAACACACAATAGT
  pseudoobscura  TCGT--------GGGGGAGGAGCGTTTTGAGA--AGTTTGCAAAACATTCAAAC---ACTAA---------------------------TTTTGTATTGA----AACAATGCTGTAATCT
     persimilis  TCGT--------GGGGGAGGAGCGTTTTGAGA--AGTTTGCAAAACATTCAAAT---GCTAA---------------------------TTTTGTATTGG----AACAATGCTGAAATCT
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  MMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBRRRRRRRRRBBBBRRRRRRRRRRRR

                 
   melanogaster  --------------AATAG-----------------------------------------------------------------------------------------------------
       simulans  TGTAATTAATAATAAATAG--------------------------------------------TTCACGCACTCGATTCGCACATTGGGAAACTACTGCTTTAGAAACACTATTATTTAT
      sechellia  TGTAAATAATAATAAATAGTTTACGCACTCGATTCGCACATTGGGAAACTACTGTTTTAGAAA-----------------------------------------------CACTATTTAT
         yakuba  TG------ATAATAAAAAA-----------------------------------------------------------------------------------------------------
         erecta  TG------ATAATAAATAA-----------------------------------------------------------------------------------------------ATATTT
      ananassae  TGTCACTGAGGA--AATGG-----------------------------------------------------------------------------------------------------
  pseudoobscura  TTTATGAAATGAACAATCA-----------------------------------------------------------------------------------------------------
     persimilis  TTTATGAAATGAACAATCA-----------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBBRRRRRRRRRBB

                 
   melanogaster  ---------------------------------------------------AAACTGGT------AATAAAAGAATTAA----------------------AAATGTTTA----------
       simulans  GCTAGATTTTTTATTAAA-------------------------------TAAAACCAAT------GACAAAAGAATTAA----------------------AAATGTTTA----------
      sechellia  GCTAGATTTTTTATTAAA-------------------------------TAAAACCTAT------GACAAACAAATTAA----------------------AAATGTTTA----------
         yakuba  -------------------------------------------------TAAGAAGTATTTACTCTAAAGAGTGATTGTTTCCCATTCTT------------------------------
         erecta  ATTTAGTCTACAAGAATAAAGGCACCTTGAAACCTTCGATTCGAACTATTAGCAACTATTTTTTTTACCAAAAAATTGGTTTCAACGCTGCACAAAAGCCTTAATGTATA----------
      ananassae  -------------------------------------------------GAAGAGATTT----------------TTGGATTCAGAGTCTCCGGAATGGGATATGGTTTAGATTTTAAAT
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  BBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR

                 
   melanogaster  TAATATTTATATGTATAT--------------TTAT------------------------GGAGT-------------------GTGCAGCTGGAATAATATTAAGATTAAAGTGTTCGA
       simulans  AAATAGTTTTATGTATAT--------------TTAG------------------------GGAGT-------------------GTGCAGCTGGAAAAATATTAAGATTAAAGTGG----
      sechellia  TAATATTTTTATGTATAT--------------TTAG------------------------GGAGT-------------------GTGCAGCTGGAATAATATTAAGATTAAAGTGG----
         yakuba  ---TGTTTATCCATTTAT--------------CCAT-------------------AAGGGAAAGTAT------------CATATGTGCTATTGAGAAAAAATGTTTATTAAAGTGTTCGA
         erecta  TAACATTTATGTATTTATGGAGTGTTTCGGTACTATTCTTTGTT-----AATCCAAAGAGGAAATAT------------CATTGATGCAACCGGAATGATATAAAGATTAAAGTGTTCGA
      ananassae  CAATTCTTTTAAAGTAAT--------------CTTGTTTTTTTGCTAGAAATAGTTAGTGGAAGTACTTAAAATTATAATCTTATTTCAAATATCATAATATATTTGTTGAAAAAA--AA
  pseudoobscura  ----------------------------------------------AGGATCTGCAATCTGGGGT-------------------TTCCATAAAGAGTAA---------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBRRRRRRRR

                 
   melanogaster  TATAACAAGAAGATAACACAAATGGCTAAACACTG---------AGAAAGTAA----------------------------------------AATGCAGATAGAAACCATACGAATCTC
       simulans  -----------------GCAAATGGCTAAGCACTA---------AGAAAGG----------------------------------------------------------ATACGAATCTC
      sechellia  -----------------GCAAATGGCTAAGCACTA---------AGAAAGG----------------------------------------------------------ATACGAATCTC
         yakuba  TATAACAAGAAGATAAGATAATTTGC-------------------------------------TTGCTTACTTGCTGGCTTA--------AGTAATACAGATAGAAACCATACGAATCGG
         erecta  TTTAACAAGAAGGTAACATAAATGGCTAAACACTA---------AGAAAGGAA-----TACATTTATTTAATTGTTTATTTA------TTTATAAGCGAGATAGAAACCATACGAAACTG
      ananassae  TACAAAAAGGAGGAAAAGTGAA-AGTTCGGAACTATCTGCTTGGAGAAGGGGAGGAACTCTAATGCATTAGGCATTGATTAAAAATACTTGTTAAACAAAATAAAATCTTTAAAAACACT
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RBRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMBBMMMMMMMMMBBRRRRRR

                 
   melanogaster  TTTAGTTATA-ATGATCTCCTCCGTTAGT-TTAATCAAATTCAC-AATTTCCGCCAAT---------AAAAGCCCATAAGA---------------------------------------
       simulans  TTAAGTTTTA-ATGATCTCCTCCGTTAGT-TTAATCAAATTCAC-CATTTTCGCCAAT---------AAAAGCCCATAAAA---------------------------------------
      sechellia  TTAAGTTTTA-ATGATCTCCTCCGTTAGT-TTAATC-AATTCAC-CATTTCC--------------------------------------------------------------------
         yakuba  TTAAGTATTT-TTGATCGCCAGCGTTAGT-TTAATCGAATTCAC-TGTTTCCGCCAAT---------AAAACCCCATGAAA---------------------------------------
         erecta  TTGCGTATTA-TTGATCCCCACCGTTAGT-TTAATCGAATTTAG-TA-TTCCGCCAAT---------AAAACCCCAGAAAA---------------------------------------
      ananassae  TGATAAAATATATAATTTAAGCCATAAAA-TTAAAACAGTTTATATATTTGAGCCCCTTTAAGATTGAAAACCCCCTAAAG---------------------------------------
  pseudoobscura  ---------------CCTTTCTCGTTCGTATCAAGC--GTTGAA-AAGGCTCGCCAAG---------AGACACCCCTAAAGCCCTGGAGTACTCCTTCGAAAACAGTACATATCGCCATA
     persimilis  ---------------CCTTTCTCGTTCGTATCAAGC--GATGAA-AAGGCTTGCCAAG---------AGACACCCCTAAAG---------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBMMMMMMMMMMMMMMMMMMBBBMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRR

                 
   melanogaster  -ACTTGGGAGAATTTCCCAAAAACTGCCGCCGCTGTCATTTAATTTGGTGATTAAGTTTTATTAAATGTTGCAACTGG-----CG---AAGAGCGGCAAATGCCGCGTAATCCCCC-T-C
       simulans  -TGTTGGCAGAATTTCCCAAAAACTGCCGCCGCTGTCATTTAATTTGGTGATTAAGTTTTATTAAATGCTGCAACTGG-----CG---AAGAGCGGCAAATGCCGCGTAATCCCCC-T-C
      sechellia  --GTTGGCAGAATTTCCCAAAAACTGCCGCCGCTGTCATTTAATTTGGTGATTAAGTTTTATTAAATGCTGCAACTGG-----CG---AAGAGCGGCAAATGCCGCGTAATCCCCC-T-C
         yakuba  -CCTCTG-AGAATGGGCCAAAAACTGCCGCCGCTGTCATTTAATTTGGTGATTAAGTTTTATTAAATGTTGCAACTGG-----CG---AAAAGCGGCAAATGCCGCGTAATCCCCCCT-C
         erecta  -CCTCTG-AGAGTTTCCCAAAAACTGCCGCCGCTGTCATTTAATTTGGTGATTAAGTTTTATTAAATGTTGCAACTGG-----CA---AAAACCGGCAAATGCCGCGTAATCCCCCTT-C
      ananassae  --------AGCCTCTCCATAGAAGCCCTTTCCTTTTCATTTAATTTGCTGATTAAGTTTTATTAAATGTTGCAACTGGCTGACCA---AAAAGCAACAAATGCCGCTTAATTCCCCTT-C
  pseudoobscura  CCCGTTGCCCATCCTCCC-----TTGCCCATGTTGTCATTTATTTTTGTGATTAAGTTTTATTAAATGTTGCCACCGG-----GT---AAAAGTGGCAAATGCCGCGTAATACCCT-C-A
     persimilis  -CCGTAGCCCATCCTCCC-----TTGCCCATGTTGTCATTTATTTTTGTGATTAAGTTTTATTAAATGTTGCCACCGG-----GT---AAAAG---------------------------
        virilis  -------------------------------------TTTCATATATGGTATTA-TTGTTATTAAATATTGCGATTGC-----CG---------TGGAAATG----------CCCC-T-A
     mojavensis  ---------------------------------TTTAATTTATTTTTGCTATTA----TTATTAAATGTTGCGCTTGC-----CG---------GGAAAATGCCGCGTAATACCCC-T-A
      grimshawi  -------------------------------------------TTTTGCGTTTA----TTATTAAATGTGGCGATTGT-----CGTTT-----TTGGGAAAGCCGCGAAATACCCC-TCA
        Summary  RRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMM

                 
   melanogaster  ------------------GCCCAAAACAAAACCCCAGG--A------CG-ACACACACGAAA----------------------------AAAG-AAGAAACCGAAGCGAAACCTCCCGA
       simulans  ------------------GCCCAAAACAAAACCCCAGG--A------CG-ACACACACGAAA----------------------------AAAG-AAGAAACCGAGGCGAAACCTCCGCA
      sechellia  ------------------GCCCAAAACAAAACCCCAGG--A------CG-ACACACACGAAA----------------------------AAAG-AAGAAACTGAGGCGAAACCTCCGCA
         yakuba  ------------------GCCCAAAACAAAACCCCAGG--A------CACACACACACGAAA----------------------------AAAG-ATGAAACCAAAGCGAAACCTCCGGA
         erecta  ------------------GCCCAAAACAAAACCCCAGGACA------CACACACACACGAAA----------------------------AAAG-AAGAAACCGATGCGAAACCTCCGGA
      ananassae  AAACCGAGCAGAAATAAAATCAAAAAAAAAAAATAAAG--A------AT-ATATATACAATATATATTCTGGTAGATGGCTGGTAGATGTGAGA-CGGGAACCGGGACCCGGGACCCGGA
  pseudoobscura  ------------------TCCTTGGCCACATCCATATG--G------CC-ATGGGTATGTCT----------------------------ATGG-CTGGAAAC----CAAAACGTGCGGA
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------G---------AAACCAGAAG--C------CG-----ATGCCTAA----------------------------ACCG-AAAATACCGA----AAG-CCGTGCG
     mojavensis  ------------------G---------AAACCAGTAG--C------CG-----CTGCCTAA----------------------------GCCGAAAAATACCAA----AAATTCGTGCG
      grimshawi  ------------------G---------AAACCAGAGG--CCCGAAACG-----GACCGAAA----------------------------ATCG-AAAATGCCAA----AA--CCCTGCG
        Summary  MMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  CCGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTCGGCTGGTC---------------------AGATGGA-----TGGG----------------------------
       simulans  CCGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTCGGCTGGTC---------------------AGATGGA-----TGGG----------------------------
      sechellia  CCGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTCGGCTGGTC---------------------AGATGGA-----TGGG----------------------------
         yakuba  CCGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTCGGCTGGTC---------------------AGATGGA-----TGGG----------------------------
         erecta  CCGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTCGGCTGGTC---------------------AGATGGA-----TGGG----------------------------
      ananassae  CCGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTTGGTCAGGG---------------------AGATGGA-----TGGGCTGACAG--TTTTTGGG-----------
  pseudoobscura  -CGAGTGTCAAATTAATTAAAATGTCAGCGAAATATGTTCAATTGTTGGCCTGCTGCTGGCTGGCTGGCTGGATGGAGATGGA-----TGGATGGCTAGGATAGATGGGCTGACAGCTCT
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ACGAGTGTCAAATTAATTAAAATGTCAGCAAAATATGTTCAATTGTTGTTTGTTG-----CACGCTG----TTGGGAGATGGA-----TGAC----------------------------
     mojavensis  ACGAGTGTCAAATTAATTAAAATGTCAGCAAAATATGTTCAATTGTTGTTTGTTG----TCCCGCTGGTTTTTTGGAGATGGATGACA--------------------------------
      grimshawi  ACGAGTGTCAAATTAATTAAAATGTCACCAAAATATGTTCAATTGTTGTTTGTTT-----GCCGCTG--TTATGGGAGATGGA-----TGAC----------------------------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRR

                 
   melanogaster  ---------ATCGAA-----------------------------------------------ATC--GGATTCG------GGATTGGGAATCGGGCTTAACTT-----CGGCTGGCTGTC
       simulans  ---------ATCGAA-----------------------------------------------ATC--GGATTCG------GGATTGGGAATCGGGCTTAACTT-----CGGCTGGCTGTC
      sechellia  ---------ATCGAA-----------------------------------------------ATC--GGATTCG------GGATTGGGAATCGGGCTTAACTT-----CGGCTGGCTGTC
         yakuba  ---------ATCGAA-----------------------------------------------ATC--GGATTCG------GGATTGGGAATCGGGCTTAACTT-----CGGCTGGCTGTC
         erecta  ---------ATCGAA-----------------------------------------------ATCGGGGATTCG------GGATTGGGAATCGGGCTTAACTT-----CGGCTGGCTGTC
      ananassae  --AATCGGAATTGGA-----------------------------------------------ATT--GGAATCGAAAATCGGATTCAGAATTGGGTTTAACTT-----CGGTATG--GTC
  pseudoobscura  CCGCTCGGCATAGGA-----------------------------------------------ATA--GGAATAG------GAATC-GGAATCGGATTCTGTTTCTCGGCTGCTGCCTGTC
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ---------AGTTGCCTCCACGCCTGGCCAC--------------------------------------------------------------GACTT---TT-----GGGCTAACTGTC
     mojavensis  ---------------------------------------------------------------------------------------------GGCTT---TT-----GGGCTAACTGTC
      grimshawi  ---------AGTTGCCTGCTTGCCTCGACTCAACTCGAGTCGACTCGACTCGGATCGGATCG-------------------------------GACTT---TT-----GGGCTAACTGTC
        Summary  RRRRBBBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  AAACAGTTTTTGCC-GTAGCTGGGCATAG--C-C----GGAAGGAAGGAAA--AGTCGGAAAATTGTGA--------AAGGGACGGCGAGAG--------AGCGCCCTAAGCAGCGG---
       simulans  AAACAGTTTTTGCC-GGAGCCGGGCATAG--C-C----GGAAGGAAGGAAA--AGTCGGAAAATTGTGA--------AAGGGACGGCGAGAG--------AGCGCCCTAAGCAGCGG---
      sechellia  AAACAGTTTTTGCC-GGAGCCGGGCATAG--C-C----GGAAGGAAGGAAA--AGTCGGAAAATTGTGA--------AAGGGACGGCGAGAG--------AGCGCCCTAAGCAGCGG---
         yakuba  AAATAGTTTTTGCCAGGAGCAGGGCATAG--C-CGGAAGGAAGGAAGGAAA--AGTCGGAAAATTGTGAAAATTGTGAAAGGACGGCGAGAG--------AGCGCCCTAAGCAGCGG---
         erecta  AAACAGTTTTTGCCCAGAGCCGGGCATGG--C-CGGAAGGAAGGAAGGAAA--AGTCGGAAAATTGTGA--------AAGGGACGGCGAGAG--------AGCGCCCTAAGCAGCGG---
      ananassae  CTGCAGGGCCTGCC---TGCCTGTCAGAGATC-C-------------------TGTCCGGAAGCCGAGG--------GAGAGTGGGGTATGG--------TATGCCCTAAGCAGTAGCA-
  pseudoobscura  AAACTGCATTGACA---------ATATTG--G-C---AGGAAGGCCGGAAG--CGACAGCACA----GG--------AAGAGC-------AG--------ATAGCTCTAAGCAGCAGCCG
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  AAACTGCATTGACA---ATATTGGCATTT--C-C-------AGGC--------ACACAGCTAGGCGGAC--------GGGACACAGGAAGAGCC------CCCGCCCTAAGCAGCCG---
     mojavensis  AAACTGCATTGACA---ATATTGGCATTT--TGC-------AGGCAGATACGGATACAGATAGGCGGAC--------GGTATACAGGAAGAGCC------CCCGCCCTAAGCAGCCG---
      grimshawi  AAACTGCATTGA---------------------C-------AGGC--------GGACG-------GGGA--------AGGACACAGGAAGAGCCTCCCATCCTGCCCTAAGCAGCAG---
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBRRRRRRRRRBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBRRRRRRRR

                 
   melanogaster  -----------------G----------------------TTTTTC--CCAAAA-------AC----GG---GGATCC-------------TCTGTTGTCATATTTTCAATT--------
       simulans  -----------------G----------------------TTTTTC--CCAAAA-------AC----GG---GGATCC-------------TCTGTTGTCATATTTTCAATT--------
      sechellia  -----------------G----------------------TTTTTC--CCAAAA-------AC----GG---GGATCC-------------TCTGTTGTCATATTTTCAATT--------
         yakuba  -----------------G----------------------TTTTTC--CCAAAA-------AC----GG---GGATCC-------------TCTGTTGTCATATTTTCAATT--------
         erecta  -----------------G----------------------TTTTTC--CCAAAA-------AC----GG---GGATCC-------------TCTGTTGTCATATTTTCAATT--------
      ananassae  -----------------G----------------------GATATC--CAGGAT-------AT----AGCCAGGATTTTGACCAGTGTGTGTGTGTTGTCATATTTTCAATT--------
  pseudoobscura  GACAGTAGCAGACCCCTG----------------------TCCGGCATCCAAAA-------TCCATTGA---GGACCC-------------TCTGTTGTCATATTTTCAATT--------
     persimilis  ---------------------------------------------------------------------------------------------TGTTGTCATATTTTCAATT--------
        virilis  -----------------G----------------ACGACCCCTGTC--CAAGAG----------------------------------------ACTCTCCCTCCCTCTCTC------TC
     mojavensis  -----------------GACGTACGTACGTACGTACGACCCCTGTC--CGAGAGGTTTTCT--------------------------------CACTCTCCCACTCTCTCTCGCACAGTT
      grimshawi  -----------------C---------CGTACCAGCGAACCCTGTT--CCGGAA------C--------------------------------GACTGTCCAGTCATAAGTG--------
        Summary  RMMMMMMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBRRRRRRRRRBBB

                 
   melanogaster  --TTGCAAT--------------------------------CT-GCCTGTCACTCAT---------------TGTCCGACTTTGTCCGATTTTC----CGGGTGTGCTGGTGTGCTGG--
       simulans  --TTGCAAT--------------------------------CT-GCCTGTCACTCAT---------------TGTCCGACTTTGTCCGATTTTC----CGGGTGTGCTGGTGTGCTGG--
      sechellia  --TTGCAAT--------------------------------CT-GCCTGTCACTCAT---------------TGTCCGACTTTGTCCGATTTTC----CGGGTGTGCTGGTGTGCTGG--
         yakuba  --TTGCAAT--------------------------------CT-GCCTGTCACTCAT---------------TGTCCGACGTTGTCCGATTTTC----CG--------GGTGTGCTGG--
         erecta  --TTGCAAT--------------------------------CT-GCCTGTCACTCAT---------------TGTCCGACTTTGTCCGATTTTC----CGGGTGTGCTGGTGTGCTGG--
      ananassae  --TTGCGATTTCGCCTTTTTGCCTTTTGCCTTTTCGGCCTGCC-GGCTGTCATTCAT---------------TGTCCGATTT---------------------------GTGT-CTGG--
  pseudoobscura  --TTGTAAT--------------------------------TC-GCACGGCTTTCCC-ATTTTGACCATTT-TCTCTCTCTCTCTCTCTCTCTG----TGTGTGTGTGTGTCTGCTGG--
     persimilis  --TTGTAAT--------------------------------TC-GCACGGCCTTCTCAATTTTGACCATTTCTCTCTCTCTCTCTCTGAGTGTG----TGTGTGTGTGTGTCTGCTGG--
        virilis  TCTGTCCAC--------------------------------CC-AGATAAGACCCAT---------------TC-----CGTTGTCATATTTTCAATTTCGATATTCGCACGGGCTGC--
     mojavensis  TCTGGACAC--------------------------------CCAAAATAAGACCCAT---------------TG-----CGTTGTCATATTTTCAATTTCGTTATTCGCATGGGCTGCTC
      grimshawi  -ACGGACAC--------------------------------CC-AGATAAGACCCAC---------------TG-----CGTTGTCATATTTTCAATTTCGATATTCGCACAAG--GC--
        Summary  BBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBBRRRRR

                 
   melanogaster  ------------------------TGTTTGGCAATCTCATGCTCATTGCCATTT----CCCCCTCCCGATTTTCCG---------ATTTT--------CCGAGTTCCCGTTTAACGTTTA
       simulans  ------------------------TGTTTGGCAATCTCATGCTCATTGCCATTT----CCCCCTCCCGATTTTCCG---------AATTTCCGAGTCCCCGAGTTCCCGTTTAACGTTTA
      sechellia  ------------------------TGTTTGGCAATCTCATGCTCATTGCCATTT----CCCCCTCCAGATTTTCCG---------ATTTTCCGAGTCCCCGAGTTCCCGTTTAACGTTTA
         yakuba  ------------------------TGTTTGGCAATCTCATGCTCATTGCCATTTCC--CCCCCACCCGATTTTCCG---------ATTTCCCGATTTTCCGAGTTCCCGTTTAACG----
         erecta  ------------------------TGTTTGGCAATCTCATGCTCATTGCCATTTTC--CCTCCCCC----------------------TACCCATTTTCCGATTTCCCGTTTAACG----
      ananassae  ------------------------TGTTTGGCAATCTCATGCTCAT-----TTT----CCGCCCCC-------------------------------------ATCCAGTCCAG------
  pseudoobscura  ------------------------TGTTTGGCAATCTCATTCTCAT------------CCCCCGTC-AAATATGTA---------ACT------------------CTGTCCGACGACGA
     persimilis  ------------------------TGTTTGGCAATCTCATTCTCAT------------CCCCCGTCAAAATATGTA---------GCT------------------CTGTCCGACGACGA
        virilis  ------------------------TGCTGGTGCGTGTTTTGTTAACTACCCGGCCT--GCCCG---------------------GTCTACCC---------GCTGCCCGCT---------
     mojavensis  TGTGTGTGTGTGTGTGTGTGTGTGTGCGTGTGCGTATGTTATTTGCTACCCGCTCTCGACCCG---------------------------------------------------------
      grimshawi  ------------------------TGCTGGTACATA--TTGTCAGCTACCCGCT----ACCCC-------------CACTACAAGGCTACCCCTCAAAGCATCTATCCGCT---------
        Summary  RRRRMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRBBBBBBBBRRRRRRRR

                 
   melanogaster  -ACGTTTCCCATT-----TCCCATTTC------------CCATTTCGCATTTG-CCCAACCCCCATCAAAACGGG-ACTGTG-------------------TGTTT---TTGTGTGTCCG
       simulans  -ACGTTTCCCATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  -ACGTTTCCCATT-----TCGCATTTC------------C--------------CTCAACCCCCATCAAAACGGG-CCTGTG-------------------TGTTT---TTGTGTGTCCG
         yakuba  -----------TT-----TAACGTTTC------------CCATTTCGCATTTTCCTCAACCCCCATCAAAACTGGCACTGTG-------------------TGTTT---TTGTGTGTTCG
         erecta  ----TTTCCCATT-----TCGCATTTC------------GCATTTCGCATTTTCCTCAACCCCCATCAAAACGGG-AGTGTG-------------------TGTTT---TTGTGTGTCCG
      ananassae  -------------------TCCAGTCC------------ACAACAAGGAC----ACCAACCCCCGTCAGAAAATA-------------------------------------TCCTTCAG
  pseudoobscura  GGGGCTCCTCAT-------CCTCATCC------------ACATCGACATCATCTCTCTATTCCCATTCAAAGTCC-GCTGC--------------------TTTTG---TTGTTTGTCCG
     persimilis  GGGGCTCCTCAT-------CCTCATCCTCATCCACATCGACATCGACATCATCTCTCTATTCCCATTCAAAGCCC-GCTGC--------------------TTTTG---TTGTTTGTCCG
        virilis  -------------CGTAATCTCATACG------------TTATACAGGCCG------AACCCCCGTCAATA------------------------------GTTTT---GAGGGTTGCCG
     mojavensis  ---------------------------------------------------------AACCCCCATCAATA------------------------------GTTTT---GAGGGTTGCCG
      grimshawi  -------------CGTAATCTCATACG------------ATATAGAGGCCG------AACCCCTGTCAATATATG-TATATGTGTGTGTGTGTGTGTGTGTGTATTGCGGAGGGTTGCCG
        Summary  RBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBBRRRRRRRRRBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TTAATGTGCATTTGACATTT-------------------GGCGAAATGAGAATCT-GGGCAAATGATACGGATTTATGGCAAATTTGTCGAGCGATTTGTGTCGATTTACATG-AGTGCC
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  TTAATGTGCATTTGACATTT-------------------GGCGAAATGAGAATCT-GGGCAAATGATAGGGATTTATGGCAAATTTGTCGAGCGATTTGTGTCGATTTACATG-AGTGCC
         yakuba  TTAATGTGCATTTGACATTT-------------------GGCGAAATGAGAATCT-GGGCAAATGATACGGATTTATGGCAAATTTGTCGAGCGATTTGTGTCGATTTACATG-AGTGCC
         erecta  TTAATGTGCATTTGACATTT-------------------GGCGAAATGAGAATCT-GGGCAAATGATACGGATTTATGGCAAATTTGTCGAGCGATTTGTGTCGATTTACATG-AGTGCC
      ananassae  TTAATGTGCGTTTGACATTTTTCTTTTTTTTTTTTTCCGGGCAAAATGAGAATCC-GGGCAAATGATTCGGATTTATGGCAAATTTGTCGAACGATTTGTGTCGATTTACATGAAGTGGC
  pseudoobscura  TTAATGTGCATTTGACATTTT------------------TGCGAAATGAGAATCT-GGGCAAATGATTTGGATTTATGGCAAATTTGTCGAGCGATTTGTGTAGATTTACACG-AGTGCC
     persimilis  TTAATGTGCATTTGACATTTT------------------TGCGAAATGAGAATCT-GGGCAAATGATTTGGATTTATGGCAAATTTGTCGAGCGATTTGTGTAGATTTACACG-AGTGCC
        virilis  TTAATGTGCATTTGACATTT--------------------GTGAAATGAGAATCT-GGGCAAATGATTCGGATTTATCGCAAATTTGTCGAGCGATTTATGTCGATTTACATG-AGTGCC
     mojavensis  TTAATGTGCGTTTGACATTT--------------------GTGAAATGAGAATCT-GGGCAAATGATTCGGATTTATAGCAAATTTGTCGACTGATTTATGTCGATTTACATG-AGTGCC
      grimshawi  TTAATGTGCATTTGACATTT--------------------GTGAAATGAGAATCTCGGGCAAATGATTCGGATTTATCGCAAATTTGTCGAGCGATTTGTGTCGATTTACATG-AGTGCC
        Summary  BBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  -AAA-GCCAAGTGGCCACTCAA------GGCT--GCC----ACATGGGAT----GT-------CGAGCGGA---------TTGGTACCGAAACGCT-GCC--CAACTCGAGCTGTTATGT
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  -AAA-GCCAAGTGGCCACTCAA------GGCT--GCC----ACATGGGAT----GT-------CGAGCGGA---------TTGGTACCGAAACGCT-GCC--CAACTCGAGCTGTTATGT
         yakuba  -AAA-GCCAAGTGGCCACTCAA------GGCT--GCC----ACATGGGAT----GT-------CGAGCAGATTGGGA---TTGGTGCCGAAACGCTGGCC--TAACTCGAGCTGTTATGT
         erecta  -AAA-GCCAAGTGGCCACTCAA------GGCT--GCC----ACATGGGAT----GT-------CGAGCGGATT-------TTGTACCCAAAACGCTGGCC--CAACTCGAGCTGTTATGT
      ananassae  -AGA-GCCAAGTGGCCACTCCACTTATTGTTT--GCCATGGATATGGGATAAGGAT-------ATATGGGATAGGGATGTGTGCTCCCGAATGTCCTGCC-----------ATGTTATGT
  pseudoobscura  -AAA-GCCAAGTGGCCACTTGA------GGATAGGAC----ACACACACA----GC-------ACACAGGACA-------CAGGACCCAGGACAT--GCCAACGGTTACGGGTGTTATGT
     persimilis  -AAA-GCCAAGTGGCCACTTGA------GGATAGGAC----ACACACACA----GCACACAGGACACAGGACA-------CAGGACCCAGGACAT--GCCAACGGTTACGGGTGTTATGT
        virilis  -AAATGCCAAGTGGCCACTTGA------GGAC--GGC----A------------------------------------------------------------------------------
     mojavensis  -AAATGCCAAGTGGCCACTCGA------GGAT--GCC----A------------------------------------------------------------------------------
      grimshawi  AAAATGCCAAGTGGCCACTTGA------GGAT--GGC----A-------------------------------------------------------GCCAACGGC------------AA
        Summary  BBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBRRRRRRRRRBBBBRRRRRRRRRRRRRRRRRRBBBBRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  TAATGATACCCGCCGACCT-------CGACAAGAGGAGGTCCTTTTT-----CTGAC--TC---TGACGGACAGTTGACAGCGGACCAGATGGGTTGGCTCCGTCTCGAAGGCGATTCAT
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  TAATGATAC---CCGACCT-------CGACAA---GAGGTCCTTTTT-----CTGAC--TC---TGACGGACAGTTGACAGCGGACCAGATGGGTTGGCTCCTTCTCGAAGGCGATTCAT
         yakuba  TAATGATAC---CCGACCT-------CGACAA---GAGGTCCTTTTT-----CTGAC--TC---TGACGGACAGTTGACAGCGGTCCAAATGGGTTGTCTCCTTCTTGAAGTTCATTCCT
         erecta  TAATGATAC---CCGACCTCGGTACCCGACAA---GAGGTCCTTTTT-----CTGAC--TC---TGACGGACAGTTGACAGCGGTCCGGATGGGTTGTCTCCTTCTCGAAGGCGATTCCT
      ananassae  TAATGAGGC---GAG-----------GGATAA---GAA----------------TAC--TCGAGTGATGGACAGCTGACAG-GATCAAGAAG-----------TCTCTGGATATCTTAAA
  pseudoobscura  TAATGATGC---CCCTCATGC-----CGAGGA---CCGGGCCCAGCCTGAAGCTGACAGCC---AGACAGACAGTTGACA----------------------------------------
     persimilis  TAATGATGC---CCCTCATGC-----CGAGGA---CCGGGCCCAGCCTGAAGCTGACAGCC---AGACAGACAGTTGACA----------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  CAACAGCAC---CAGGCAAA------CAAGAG---GAGGTCCTTCTT-----CTGTT--TT---T-------------------------------------------------------
        Summary  BBBBBBBMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBMMMMMMMMMBBBMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMM

                 
   melanogaster  GACCACCTTTTTGGACAGACTTGTGGATGGGATTTTGGGAATTATACCAATTATTCAAGTAGCGGCAGTTGAGTTGCGTAATTTCAGCAGTATA---------------AAATTTATAAT
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  GGCCACCTTTTC-GACGGACTTGTGGATGGTATTTTGGAAATTATTTCAATTAT----GTTCAAGCAGTTGATTTGCGCAATTTCAGTGGTATAT------------GTATAATTTCAAT
         yakuba  GGTCACCTTTTC-AACGGACTTGTGGATGGGATTTTGGGAATTATTCAATTT--------------AGTAGAGTTGCGCAATTGTCGCTTTTAAATAAA--------TTAAAATTATAAA
         erecta  GGCCACCTTTTC-ATCGGACTTGTGGATGGGA-TTTGGGAATTATTCTAATTATTCTGCCAGCAGCAGTGGAGTTGCGCAATTTCAGCCGTACGCCGAACGCCGTTTTTGAAACCATATA
      ananassae  GGTTTCTTTTTT---------------------TCAGGACATTA---------------------------ATTTACA-----------------------------TCAAAATTATAAT
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  -------------------------------------------------------------------------------------------------------------AAATTCATTAA
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  MMMBBBBBBRRRRRRRRRBBBBBBBBBRRRRRRRRRBBBBRRRRRRRRRRRRRRRRRRRRRRRRRRRBRRRRRRRRRBBRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMBMMMM

                 
   melanogaster  CTAGTTGGAT------CAGAGGAAACTG----CTAGACGGCTAGTTGATAGTATATAAATTCC-----------------------ATTTGTATTCTCCATTTTGCCTATT---TAACTA
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  ATAGTTGGCT------CAGAGGAAACCG----CTAGAC-----------AGAATATAAATTCT-----------------------ATTTGTATTCTCCATTTTGCCTATT---TAACTA
         yakuba  CTAGTTGGTT------CGGAGGAAACTATCTACTTAACGGACA------ATAATGATAATTCTATAAAATATGTGAAACGATAATAATTGGTATTCTCCATTTTGCCTATGC--TTACTT
         erecta  ATTATTGGTT------TGGAGGAAGCTGTCCACCAAACGGATA------ATAATAATAGTTCTGTAAAATATGTGCAACGATAATAATTGGTATTCTCCATTTTGCCGATTTCATTTTTT
      ananassae  -TTGTTTTCT------TGAATAAGAGTG----CCTAAAGTGCC-------------TAGTTTT------TTCTTCAAAAAATAGCCATAAATATTAGCCT--------------TGACTT
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  TTTATTGGATTTCAACTACAGCAAGTTGTTTTTCTTAAATGCA--------AATACTTATTCA---------------------TTTTTTGTATTTTTCATT------------TGATTC
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  MMMMMRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRBRRRRRRRRRBBBBBRRRRRRRRRMMMMMMMMMM

                 
   melanogaster  AATAACCCAAC-TTTACTGACCTTCAAGAATTATTTGCAACTTTTATTACTCCTTTGAC----AAAACGCCAAGATA---CAAGGAACTCGTATCCTTTCATTGAAGAG----AAGAC-G
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  AATAACCCAAC-TTTACTTACCTTCAAGAAATACTTGCAACTTTTATTACTCCTTTGAC----AAAACGCCAAGATA---CAAGGAACTCGTATCCTTTCATTGAAGAG----AAGAC-G
         yakuba  AAGAATCCAACTTTTACTCACCTTCAAGAAATATTTGCCACTTTTATTACTCCTTTGAC----GAAACGCTAGGAAA---CAATGAGCTCTTATCCTTTCATTGAAGAG----AAGAT-G
         erecta  -----TTTAACTTTTAGTTACCTTCAAGAAGGACTGGCCAGTTTTATTACTCCTTTGGC----AAAACGCTAGGACA---CAAAGAACTCTTATCCTTTCATTGAAGAG----AGGAA-G
      ananassae  --------AACCTTAACTTTTCTTAAAAAA------------------ACTCTTTTAAA----AAAAAACAATGGAAGGGTAAAAAA----------TTCATTGAACAGTCTCAGGAC--
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  -----------------------------------------------------TTTGAG----GGACGCCTTAGAAA---CAATGGAGGGAGAAGACCTCTCCGGAAAC----AAAATTG
        virilis  AATACCAAAAG-TTTACAAATTCTCTACAA---TATGTGAATTTTGTTTATCTTCTTACATGAAATACGCCATGCCC---CCAAGCA----------TTTAT-----------AGGAT-C
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  MMMMMMMMBBRRRRRRRRRBBBRRRRRRRRRRRRRRRRRRBBRRRRRRRRRBBMMMMMMMMMMMMMMMMMMRRRRRRRRRBBRRRRRRRRRRRRRRRRRRBBBMMMMMMMMMBBBBRRRR

                 
   melanogaster  CTAACATTGCATGAACACAAC-----------------AATTTCCGCGGAATATTCGAGTTAATTTTGAGATTCTCCCTACAGTTTCCTTACAGTT--TCTTTGACACTTTCCT---ATT
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  CTAACATTGCATGAACGCA-------------------AATTTCCGCGGAATATTCGAGTTAATTTTGCGATTCTCCCTACAGTTTCCTTACAGTT--TCTTTGACACTTTCCT---ATT
         yakuba  CTAACATTGCATGAACGCA-------------------AATTTCCGCGGAATATGCGAGTTAATTTTGCGATTTTCCCTACAGTTCCCTTACAGTT--TCTTTGCCACTTTCCT---ATT
         erecta  CTAACATTGCATGAACGCA-------------------AATTTCCGCGGAATATTCGAGTTAATTTTGCGATTTTGCCAACAGTTTCCTTACAGTT--TCCTTGGCACTTTCCC---ATT
      ananassae  CTAACATTACATGATGGAA-------------------TATTTCCGCGAAAAATAAGAGTTAATTTTCCGCAACTCCTT--AGTTTTC-----------------AACTTTTTC---TTT
  pseudoobscura  ---------------------------------------------------------------------------------AGTTCCATTAGAGTTAATTTTTGCAACTTTCGCTGGATA
     persimilis  CCAAAATTGCATGATGGTACCATAGATAATGGATAATAGATTTCGAAGGAAAGTCAGAGTTCCATTAGAGTTAATTTTTGC------------------------AACTTTCGCTGGATA
        virilis  CT---ACTGCAC--ACGCC-------------------CATTT------ATCACTTCAGTTTTTTT--------TCCCTAAATTTGTTATATTGTT--TCTTT--TATGTTCGCCACATT
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRRRRBBBBBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBRRRRRRRRRBMMMMMMMMMBBBBBBBBBBBBBRRRRRRRRRBBRRRRRRRRRBBBBBBBBBBBBBB

                 
   melanogaster  TTGCCGAGAGCGCGCAAGTCA----AGGACACTTTCCCGCTAACTCTT-------GCCAATC----CCTTCCTTCTTTGC------------------------------------AATC
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  TTCCCGAGAGCGCGCAAGTCA----AGGACACTTTCCCGCTAACTCTT-------GCCAATC----CCTTCCTTCTTTGC------------------------------------AATC
         yakuba  TTCCCGAGAGCGCTCGAGTCA----AGGACACTTTCCCGCTAACTCTT-------GCCAATC----CCTTCCATCCTTGC------------------------------------AATC
         erecta  TTCCCGAGAGCGCGCAAGTCA----AGGACACTTTCCCGCTAACTCTT-------GCCAATC----CCTTCCATCCTTGC------------------------------------AATC
      ananassae  TTTC-----GCACCAAAGTCA----AGGACACTTTCCCGGCAACTCTTCCACCCGGACAATCATTGCCTTTCATCCTTTCCTTTC------C-----TTTTTTTTGTCATATATTTATTT
  pseudoobscura  TTTCCCTCTGGGCGAAAGTCA----AGGACACTTTCCCGCTAACTCTT-------AACCCTC---GCACTTCACCTCTTCCTTCCACCAGGC-----TGGGCCAGGCCAGCCCTTTCATC
     persimilis  TTTCCCTCTGGGCGAAAGTCA----AGGACACTTTCCCGCTAACTCTT-------AACCCTC---GCACTTCACCTCTTCCTTCCGCCAGGCCAGGGCAGGCCAGGCCAGCCCTTTCATC
        virilis  TTAC-------GCGCAAATTATGCTAAGAAGTTGCCTTGTTTATTGTT-------TCCTCTT----TACTCGCTGTTTGC----------------------------------TTTATT
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBMMMMMMMMMBBBBBBBMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMBMMMMMMM

                 
   melanogaster  CTTCCATTTATTTT---------------------------------------------CCCTTCCTGTTTTCCGGCTAACT---C--CACTGCT--------------GCTT---ATAT
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  CTTCCATTTATTTG---------------------------------------------CCCTTCCTGTTTTCCGGCTACCT---C--CACTGCT--------------GCTT---ATAT
         yakuba  CTTCCATTTATTTT---------------------------------------------CCCTTCCTGTTTTCCGGCTAACT---C--CACTGCC--------------GCTT---ATAT
         erecta  CTTCCATTTATTTG---------------------------------------------CCCTTCCTGTTTTCCGGCTAACTCCAC--CACTGCC--------------GCTT---ATAT
      ananassae  TTTGTATTTATTTTATTTCTCCGTTGCTTAGGGTTCTGTTCGCGCTGTTGATA-TTTGCCCTTTCCTGTTTTCTGGCTAACT---C--CTCCACTCTCCCACT-----GGCTT---ATAT
  pseudoobscura  CTTGTGTCTATCTT---------------------CAGAGGTTTCTGTTGATATTTTTCCCTTTTCCTGTTTCTGGCTAAGT---CAGCGCTGCTCCTTCCTTTCCTGGGCTT---ATAT
     persimilis  CTTGTGTCTATCTT---------------------CAGAGGTTTCTGTTGATATTTTTCCCTTTTCCTGTTTCTGGCTAAGT---CAGCGCTGCTCCTTCCTTTCCTGGGCTT---ATAT
        virilis  ACTGTGTTTTTTTT----------------------------------------------TTCTCTAGTTGTTTGTTTACTG---C--CTTTTTT--------------ATTTTGCTTGA
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  --------------------------------------------------------------------------------------------------------------------ATGT
        Summary  MMBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBB

                 
   melanogaster  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGCAAAAA--AAAA---AAAGTGAAAAGAGTGGGAGG--------------------------------GGGT-------------
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGC----A--AAAA---AAAGTGAAAAGAGTGGGAGG--------------------------------GGGT-------------
         yakuba  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGCAAAAA--AAAA-----AGTGAAAAGAGTGGAAGG--------------------------GGGTGTGGGT-------------
         erecta  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGCAAAAA--AAAA---ACAGTGAAAAGAGTGGGAGG--------------------------------AGGT-------------
      ananassae  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGCAAAAA--AAAA----------AAAAACAACAAGC--------------------------------AAGC-------------
  pseudoobscura  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGCACAAA--AAAACAAACAGGAGAAAGAGAAGGAGAAAGGTGGATAAAAAACGGATGGAAGGGTGTGCGGGT--------GTGGG
     persimilis  AACGTTGCGTTTTGTTAAACAAACCATAAAAATTTGCACAAA--AAAACAAACAGGGGAAAGAGAAGGAGAAAGGTGGATAAAAAACGGATGGAAGGGTGTGCGGGTGTGCGGGCGTGGG
        virilis  AACTTTGTTTGTTTTTTAGCAAGCCATAAAAATTTGCAAAAAGCACAA-----CCACAATTGACTTAA----------------------------------------------------
     mojavensis  -----------------AGCAAGCCATAAAAATTTGCAAAAAGCACAA-----TGTCTGTTGACTTGGAGT--------------------------------GGGT-------------
      grimshawi  AACTTTGCGTTTTGTTAAGCAAGCCATAAAAATTTGCAAAAAGCACAA------------------------------------------------------------------------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMRR

                 
   melanogaster  ----------GTTCATGCCCGAGCAAATCCTTTTTTTTTGCCCT----------TTGTC-------CTTTTTGCCGGCG---------CTGTTGTTGTTGGTGTTGTTGTTCGGTTTTGG
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  ----------GTTCATGCCCGAGCAAATCC--TTTTTTTGCCCT----------TTGTC-------CTTTTTGCCGGCG---------CGTTTGTTGTTGGTGTTGTTGTTCGGTTTTGG
         yakuba  ----------GTTCATGCCCGAGCAAATCC---TTTTTTGCCCT----------TTGTC-------CTTTTTGCCGGCG---------CTGTTGT------TGTTGTTGTTCGGTTTTGG
         erecta  ----------GTTCATGCCCGAGCAAATCC---TTTTTTGCCCT----------TTGTC-------CTTTTTGCCGGCG---------CTGTTGTTGTTGCTGTTGTTGCTCGTTTTTGG
      ananassae  ----------CTTCATGGTTGAACAAATCC---TTTGCTGCCTT----------TTGTC-------CTGGCT--CGTCC---------TGGCTGGTCCTGGCTTCGCGG--AGTTTTTCG
  pseudoobscura  ATGTGGCCCGCTTCATGCTTGAGCAAATCC---TTTTG---CCA----------TTGTC-------CTTTTTG---------------------------------------------GG
     persimilis  ATGTGGCCCGCTTCATGCTTGAGCAAATCC---TTTTG---CCA----------TTGTC-------CTTTTTG---------------------------------------------GG
        virilis  ----------CATTTTGCT---------------------CTCTCGAGTTGTTGTTGTTGCATTTGCTCTTTAACAGCTTTGCTAAAGTTGTTTTTGTTGTTGCTGTTGTTCAATTTAGC
     mojavensis  ------GTCTCGTCATGCTTGAGTGAATCC---TTCCTGCCCGTCGCTCAGTTGTTGTT-------CTTTATAACAGCC---------GTGTTTTCGTTTCTACT---------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRRRRRRBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBMMMMMMMMMBBBBBBBRRRRRRRRRBBBBBBBMMMMMMMMMRRRRRRRRRBBBRRRRRRRRRBBBBBRRRRRRRRRBBB

                 
   melanogaster  CGAAAAATGTTCAACTG------------TCGCGGAGTTGCGAGTTGAGTTCTGAA------GTCAACAA----CAATGGT-AGGTATGT-------------ATGCAGGTGTGTGTTTG
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
      sechellia  CGAAAAATGTTCAACTG------------TCGCGGAGTTGCGAGTTGAGTTCTGAA------GTCAACAA----CAATGGT-AGGTATGT-------------ATGCAGGTGTGTGCTTG
         yakuba  CGAAAAATGTTCAACTG------------TCGCGGAGTTGAGAGTTGAGTTCTGAA------GTCAACAA----CAATGGT-AGGTATGA-----------------AGGTGTGTGCTTG
         erecta  CGAAAAATGTTCAACTG------------TCGCGGAGTTGAGAGTTGAGTTCTGAA------GTCAACAA----CAATGGT-AGGTATGT-----------------AGGTGTGT-----
      ananassae  CAAA--------------------------------------------------------------------------------------------------------------------
  pseudoobscura  CGGAAAATGCTCGAATG------------TCGCGGAGTT-CTAGCCCTGTTCTGTG------GAGTTCAA----CAATGGCAAGGTAAGTGTCTGTGTGTGCCATGTATCTGTGTGTTTG
     persimilis  CGGAAAATGCTCGAATG------------TCGCGGAGTT-CTAGCCCTGTTCTGTG------GAGTTCAA----CAATGGCAAGGTAAGTGTCTGTGTGTGCCATGTATCTGTGTGTTTG
        virilis  GCCAAAATATACAATTAGCGTTTTGTTGTTGTTTTATTTCTCCGTTCAATTCTGTCATTAATGTACACATGTAATAATAAT-AGATAATT-------------ATAAATGTGT-------
     mojavensis  --CAGAGAAAACAAAAA------------TACTTCAACCGCCTTAGGAGTTTTGAAGTCGGCGTCAACAT----TA--AAT-AGGCAAGT-------------GTTCATATTCGCGAATT
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  BBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBMMMMMMMMMBBBBBBBRRRRRRRRRBBBBRRRRRRRRRBBBBBBBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRR

                 
   melanogaster  GTTATAG-AGTGGGTGGTGAGGGCACTGAGAATAAATACGACCACATT--CCAATGAATTCCTAAATTCC-------------------------------------TAAAGTGTTGGTC
       simulans  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACATT--CCATTAA-----TAAATTCT-------------------------------------TGAAGTAGTGGTC
      sechellia  GTTATAG-AGTG---GGTGAGGGCACTGAGAAAAAATACGACCACATT--CCATTAA-----AAAATTCC-------------------------------------TAAAGTAGTGGTC
         yakuba  GCTATAGAAGTG---GGTGAGGGCACTGAGAAAAAAATCGA-CACATTTGCGAAC-------CGAATTTCCATAAATAAGTCGGGAACTTACCCATTAAAGAGATGCTGAAGTATTGGAC
         erecta  GCTAAAGGAGTG---GGTGAGGGCACTGAGAGAAAATACGACCACATTGGCCATT-------CGGCTCCC---------------------------------GCACTGAAGCGCTGCAC
      ananassae  ------------------------------------------------------------------------------------------------------------------------
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  -GTGTGTGTGTG---GGTG-----------------------------------------------------------------------------------------------------
      grimshawi  ------------------------------------------------------------------------------------------------------------------------
        Summary  RRRRRRRRRRBBBBBRRRRRRRRRMMMMMMMMMBBRRRRRRRRRBRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRMMMMMMMMMMMMMMMMMMBRRRRRRRRRRR

                 
   melanogaster  TATATTAATTAATATT---TATTTGTGTAAGTCACCTTAGAGGATTTGTAGATTGTCAAA---------AGACGCATAGAATTTAGTATA--------ATATACTGTTCATATTATTTGC
       simulans  TATATTAATTAATATT---TA-TTGTGTTAGTCAGTTTAGAGGTTTTGCAGATTGTCAAA---------AGACGCATAGAATTTAG------------------------TATTGTTTGC
      sechellia  TATATTAATTAATATT---TATTTGTGTAAGTCACTTTAGAGGTTTTGCAGATTGTCAAA---------AGACGCATAGAATTTAG------------------------TATTTTTTGC
         yakuba  TAAATTTATGAATATTTGCTATTTAGACAT-----TTAAAACAATTAATTGATTCTCAGAAACATATGGGGAGGGTTATAAAATGTTTAT--------AAAA--------TGTTATTGGC
         erecta  TAAGTTAGTTAATATT---TATTTGTATATATCAGCTTAGAGAAATGGTAGATTATCAAA---------GGACTCCCATAAATTATTGGTTGTGGGAAACAT--------TACTATTTGC
      ananassae  ------------------------------------------------------------------------------------------------------------------------
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  -----------------------------------------------------------------------------------------------------------------TATTAGT
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  -----------------------------------------------------------------------------------------------------------------TGTGTGT
        Summary  RRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRMMMMMMMMMBMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMRRRRRRRRRMMMMMMMMMBBBB

                 
   melanogaster  ATGTGAC-ATTGTATAGGCAGAT--ATTTTTT-TGCAGT-G--CCTGAAGGAGTTGCCT---TT----------------------GAGTTTGGCAATTGTTTGGTTTACTGAATGCGCC
       simulans  ATGTGAC-ATTATATGGGCAGAT--ATTTTTTCTGCAGT-G--CCTGAAGGAGTTGCCT---TT----------------------GAGTTTGGCAATTGTTTGGTTTACTGAATGCGCC
      sechellia  ATGTGAC-ATTATATGGGCAGAT--ATTTTT--TGCAGT-A--CCTGAAGGAGATGCCT---TT----------------------GAGTTTGGCAATTGTTTGGTTTACTGAATGCGCC
         yakuba  ATGTGGC-ATTATATAAACAGAT--ATTTTT--TGCAGT-G--CCCGAAGGAGTTGCCT---TT----------------------GAGTTTGGCAATTGTTTGGTTTACTGAATGCGCC
         erecta  ATGTGTC-ATTAGATAATCGG----TTTTTT--TGCAGT-G--CCTGAAGGAGTTGCCT---TT----------------------GAGTTTGGCAATTGTTTGGTTTACTGAATGCGCC
      ananassae  ---CGACGACGACGAAGTCAACA--ATGGTA--GGTAAA-G--TGCGAAGGAGTTGCCT---TC----------------------GGGTTTGCCAATTGTTTGGTTTACTGAATGCGCC
  pseudoobscura  ---------------------------CATT--CGAGAC-G--AGCGAAGGAGTTGCCG---TTTTCGTTGCCGT-TGCCGCTGCCGCGCTTGGCAATTGTTTGGTTTACTGAATGCGCC
     persimilis  ---------------------------CATT--CGAGAC-G--AGCGAAGGAGTTGCCT---CTGCCGCTGCCGC-TGCCGCTGCCGCGCTTGGCAATTGTTTGGTTTACTGAATGCGCC
        virilis  GTGTGCC-TTAGTGTGGGTTGGTTGGCTGGC--TGCATTCG--GGCGAAGGAGTTGGAT---TCCTTGTCTTGCT-----CGTTGTCGGTTTTGCAATTGTTGGGCTTGCTGAATGCGCC
     mojavensis  ---------TGGTATTGCCTGGTTGGTTAGC--TGCATTCAGCGCCGAAGGAGTTGGCTTGCTCTTGGTCTTCCT-TCCACGTTGTCGGTTTTGCAATTGTTAGGTTTGCTGAATGCGCC
      grimshawi  GTGTGAC-TTGG--TTGGCTGGCTGGTTGGC--TGCATTCA--CGCGAAGGAGTTGGCT---ACCTTGGCATCCTTTCCCGGTTGTTGGTTTTGCAATTGTTAGGTTTGCTGAATGCGCC
        Summary  BBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBBBBBBBMMMMMMMMMBBBBBBBBBBBBRRRRRRRRRRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGCCGCTTGA--GTGTTGCCAAAACCCCACCCGCCACGAAGTTTCAT-CCCCATTTTCCGCCC--------ACTTTCC-
       simulans  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGCCGCTTGA--GTGTTGCCAAAACCCCACCCGCCGCGAGGTTTCAC-CCCCATTTTCCGCCC--------ATTTTCC-
      sechellia  ATAAAATCGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGCCGCTTGA--GTGTTGCCAAAACCCCACCCGCCGCGAGGTTTCAC-CACCATTTTCCGCCC--------ATTTTCC-
         yakuba  ATAAAAACGTCCACGGAATTCGCAATCGCAATCACCTTTTGTGCCGCTTGA--GTGTTGCCAAAACCCTACCCGCCACGAAGTTTCAC-CCCCATTTTCCGCCC--------ATTTTCC-
         erecta  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGCCGCTTGA--GTGTTGCCAAAACCCCACCCGCCACAAAGTTTCAC-CCCCATTTTCCGCCC--------ATTTTCC-
      ananassae  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTCCTGCCAGAGTGTGTTGCC----------------------TTTTT-CCCCTTTTTTTA--C--------ACTTTTT-
  pseudoobscura  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGCCGTTTGA--GTGTTGTTG---------------------------CCTCAGCTCCTGGCC--------CTCTCCCG
     persimilis  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGCCGTTTGA--GTGTTGTTG---------------------------CCTCAGCTCCTGGCC--------CTCTCCC-
        virilis  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGTTGTTTGA--GTGTCGTTC-------------------GTTGTTGTTTGTTGTTGTTGTTGGTTGTTGTTTGTTGT-
     mojavensis  ATAAAAACGTCAACGGAATTCACAATCGCAATCACCTTTTGTGTTGTTTGA--GTGTTGCCA-------------------GTTGTTG-TTGTTGTTGTTGTTG--------TTGTTAT-
      grimshawi  ATAAAAACGTCAACGGAATTCGCAATCGCAATCACCTTTTGTGTTGTTTGA--GTGTTGCTT------------------GGTTGTTG-CCATTGTTGTTGTTG--------CTGTTGT-
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBBRRRR

                 
   melanogaster  -----------ATCCACCTTTGCCGCGGCTCCT--TGT-------------G-AATGCAAAATGGAATGACAGCCGGCAAGGACGTTGCTGACAAACC----CGAAACGCGAAAATGTCA
       simulans  -----------ATCCACCTTTGCCGCGGCTCCT--TGT-------------G-AATGCAAAATGGAATGACAGCCGGCAAGGACGTTGCTGACAAACC----CGAAACGCGAAAATGTCA
      sechellia  -----------ATCCACCTTTGCCGCGGCTCCT--TGT-------------G-AATGCAAAATGGAATGACAGCCGGCAAGGACGTTGCTGACAAACC----CGAAACGCGAAAATGTCA
         yakuba  -----------ATCCACTTTTGCCGCGGCTCCT--TGT-------------G-AATGCAAAATGGAATGACAGCCGGCAAGGACGTTGCTGACAAACC----CGAAACGCGAAAATGTCA
         erecta  -----------ATCCACCTTTGCCGCGGCTCCT--TGT-------------G-AATGCAAAACGGAATGACAGCCGGCAAGGACGTTGCTGACAAACC----CGAAACGCGAAAATGTCA
      ananassae  -----------TTCCACTTTTTCCGCGGCTCCTTGTGT-------------G-AATGCAAAATGAAATGACAGCCGGCAAGGACGTTGCTGACAACACGAAACAAAACGCGAAAATGTCA
  pseudoobscura  GCCCTCTCCCTGGCCTTCTTC---TGGGCTCCT--TGT-------------G-AATGCAAAATGGAATGACAGCCGGCAAGGACGTTGCTGACAAAGC----CCAAACGCGAAAATGTCA
     persimilis  -----------GGCCTTCTTC---TGGGCTCCT--TGT-------------G-AATGCAAAATGGAATGACAGCCGGCAAGGACGTTGCTGACAAAGC----CCAAACGCGAAAATGTCA
        virilis  -----------TGCT---------------------GG---------------AATGCAAAC--AAATGACAG-CAGCAAGGACGTTGCTGACAAAGC----C-AAACGCGAATATGTCA
     mojavensis  -----------TGCT---------------------GT-------------GCAATGCAAAC--AAATGACAG-CAGCAAGGACGTTGCTGACAAAGC----C-AAACGCGAAAATGTCA
      grimshawi  -----------TGCT---------------------GTCCGTGTAGTTGTTGCAATGCAAAC--AAATGACAG-CAGCAAGGACGTTGCTGACAAAGC----C-AAACGCGAAAATGTCA
        Summary  RRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

                 
   melanogaster  GCAAACAGGGCCAAGAAA---GGTTGCAAGCGGGAAATGG-------------CGGGGACAGCGGGAAAAC---------G-TAAAGGGGGAATGGCAGTTGAGCA-CTTGCAG------
       simulans  GCAAACAGGGCCAAGAAA---GGTTGCAAGCGGGAAATGG-------------CGGGG-CAGCGGGGAAGC---------G-GAAAGGGGGAATGGCAGTTGAGCA-CTTGCAG------
      sechellia  GCAAACAGGGCCAAGAAA---GGTTGCAAGCGGGAAATGG-------------CGGGGACAGCGGGAAAGC---------G-GAAAGGGGGAATGGCAGTTGAGCA-CTTGCAG------
         yakuba  GCAAACAGGGCCAAGAAA---GGTTGCACGCGGAAACTGA-------------CGGGGAAAGCGGGAAAGCCGGGAAATGGAAAAGGGGGGAATGGCAGTTGAGCA-CTTGCAG------
         erecta  GCAAACAGGGCCAAGAAA---GGTTGCAGGCGGCGAATGGCGGGGGATGTGGCCGGGGAAAACGGGAAAGCCGGAAAATGG-AAAGGGGCGAGTGGCAGTTGAGCA-CTTGCAG------
      ananassae  AAAAAAAAAAAAAAGAAA---------------------------------------AACAGTAAGAAAG----------A-AAAAGGGAAAATGGCAGTTGAGCA-CTTGCAGTTGAGC
  pseudoobscura  GCGAACATGGCCAAGAAAAAGGCTTGTGTGCGG----CGG-------------TCGGGGCGTTTGTGTTGT---------G------------------TTGAGCATTTTGCAG--CCAT
     persimilis  GCGAACATGGCCAAGAAAATGGCTTGTGTGCGG----CGG-------------TCGGGGCGTTTGTGTTGT---------G------------------TTGAGCA-TTTGCTG--CCAT
        virilis  GCGGGCA-ATTCAAGAGA---GGGTGTTGGCTGTGTGTGTGTGTGTGTGTG--------------------------------------------GCGGGCCAGGA-CTTGCAG------
     mojavensis  GCGCACA-ATTCAAGTGA---GGGT--------------------------------------------------------------------------------A-CCTGCAG------
      grimshawi  GCGCACA-ATTGAAGAGC---GGGTT-------------------------------------------------------GTGGTGGTAGGGCAGAAGGTGTAGA-CCTGCTG------
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBRRRRRRRRRMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRR

                 
   melanogaster  -----CCCCGG--------AAAGGATTACTTTGC----------AAC--------------GGGAGGC---G---CGAA------------------------TAAATAAA-CAACA-AC
       simulans  -----CCCCGG--------AAAGGATTACTTTGC----------AAC--------------GGGAGGC---G---CGAA------------------------TAAATAAA-CAACA-AA
      sechellia  -----CCCCGG--------AAAGGATTACTTTGC----------AAC--------------GGGAGGC---G---CGAA------------------------TAAATAAA-CAACA-AC
         yakuba  -----CCCCGG--------AAAGGATTACTTTGC----------AAC--------------GGGAGGC---G---CGAA------------------------TAAATAAA-CAACA-AC
         erecta  -----CCCCGG--------AAAGGATTACTTTGC----------AAC--------------GGGAGGC---G---CGAA------------------------TAAATAAA-CAACA-AC
      ananassae  CACCCCTCCGG--------AAAGGATTACTTTACTTCCCAGTGAAGG--------------GGGGGGCTCTG---CAAA------------------------TAAATAAA-CAACACAC
  pseudoobscura  CGCCACCCAGGACCCTGCCAAAGGATTACACCA-----------GGCCGGGGGGGGGAGGGGGGGGGT---GCTCCGAAGGAGGCATTCAGCTGAAGGCAGTTCAAATAAA-CAACA-AC
     persimilis  CGCCACCCAGGACCCCGCCAAAGGATTACACCA-----------GGC--------------GGAGGGT---GTTCCGAAGGAGGCATTCAGCTGAAGGCAGTTCAAATAAA-CAACA-AC
        virilis  -------CCGG--------AAAGGATTATTTTGC----------AAA--------------AGACGGG---C---ACAG------------------------TAAATAAATCGGCA-A-
     mojavensis  -------CCGG--------AAAGGATTATTTTGC----------GAA--------------AGGCTGA---C---GAAG------------------------TAAATAATTCAATG-A-
      grimshawi  -------CCGG--------AAAGAATTATTTTGC----------AAA--------------AGGCTGC---T---GAAG------------------------TAAATAAATCAACA-A-
        Summary  RBBBBBBBBRRRRRRRRRBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMBBBBBBBBBRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBB

                 
   melanogaster  C------GAACACGA-AACGTTTTGCATACGGAA---CTCGACT-TTGGGGGTAGCCCAATGTA---ATCATGCTAAGCATACAAACGAGCCTGGGGAAACTTGCGA-----TGTCTGTA
       simulans  C------GAACACGA-AACGTTTTGCATACGGAA---CTCGACT-TTGGGGGTAGCCCAATGTA---ATCATGCTAAGCATACAAACGAGCCC--GGAGACTTGCAC-----TGTCTGTA
      sechellia  C------GAACACGA-AACGTTTTGCATACGGAA---CTCGACT-TTGGGGGTAGCCCAATGTA---ATCATGCTAAGCATACAAACGAGCCC--GGAAACTTGCAC-----TGTCTGTA
         yakuba  C------GAACACGA-ACCGTTTTGCATAC-GAA---CTCGAC--TTGGGGGTAGCCCAATGTA---ATCATGCTAAGCATACAAACGAGCTT--GA-AACTTGCAC-----GGTATTTG
         erecta  C------GAACACGA-AACGTTTTGCATAC-GAA---CTCGACT-TTGGGGGTAGCCCAATGTA---ATCATGCTAAGCATACAAACGAGCCC--GACAATTTGCAC-----TGTCCTCA
      ananassae  C------GAACACGA-AACGTTTTGCATACCGAA---CTTG-------------GTCCAATGTA---ATCATGCTAAGCATACAAACGAGTGC-------CTTTCGCAAGGATAATGGTG
  pseudoobscura  CGAAACTGAACACGT-AACGTTTTGCATACAAAAAGCCACGGCTCCCCCATGCAACCCCATGCA---ATCATGCTAAGCATACAAACAA-------------------------------
     persimilis  CGAAACTGAACACGT-AACGTTTTGCATACAAAAAGCCACGGCTCCCCCATGCAACCCCATGCA---ATCATGCTAAGCATACAAACAA-------------------------------
        virilis  -------GAACAA-----------------------------------------------------------------------------------------------------------
     mojavensis  -------GGACAA-----------------------------------------------------------------------------------------------------------
      grimshawi  -------ACCCAA--AATC-CTCAGCGCATCGAA---TTATGC--ATGCCCTTAAACCAATATCTATCTCATATTAAAT---TAAAAGA-----------GTTGAAC------ATTTTTA
        Summary  BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRBBBBBRRRRRRRRRRRRRRRRRR

                 
   melanogaster  AGGACCCAGGCT-TACCCTGTTTCAAGAACTT-TTG---------GCAA----TA-----CGATCCTAAGTATGTTATGT-TTCAGA-----CTTATGA------------TAAAACTAG
       simulans  AGGACCTGGGGGATACCCTGTTTCAAGAACTT-TTG---------GCAA----TA-----CGATCCTAACT-TGTTATGT-TTCAGA-----CTTATGG------------TAAAACTGG
      sechellia  AGGACCTGGGGGATACCCTGTTTCAAGAACTT-TTG---------GCAA----TA-----CGATCCTAACTATGTTATGT-TTCAGA-----CTTATGG------------TAAAACTGG
         yakuba  AAGACCTAGGGA-TACCCTGTTTTAAGAACAT-TTGATTTACTTTTCAATTTATA-----CGATCCTAACTATTTTCTGG-TTCGGA-----TTAATGGTAGACATACACTTAGAACTAT
         erecta  AGCACCCAGGGA-TACCCTGTTTCAAGAACTTGTTGTATTACTTTGCAATTC-TA-----CGA------------------TTCGCG-----TTAATGTTACAAATGGGCTTAAAACTAT
      ananassae  AGGACTTCAGGA-TATCCTGGATGGTATTATT-TTGCCTTAATT-TCAA----GG-----GGATTTCGGTT-TGAGAAAC-TTAAGATACTTCTTATGG------------CAAGACC--
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  AAAAT--------GATCATA----AATAACAT-CTAAATTGTT--GCAA----AATTGATCACTTTTGACTGTTAAATATATTTGAA-----ACTATGG------------TAAATT---
        Summary  BBBBBMMMMMMMMMBBBBBBBBBBBBBBBBRRRRRRRRRMMMMMMMMMRRRRRRRRRRRRRRRRRRBBRRRRRRRRRBBRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMBBRRR

                 
   melanogaster  GTGCTGGAAGGATTAATAACAGAACACATTGAATTAAAGTGTCACATATGAACAAGAAAACTCACA-------------CTTAACACTTTTAA---GATAATCAATAGGCATTTGTCCTA
       simulans  GTGCTGGAAAGATTTATCACA--------------------TTAATATTG-----------------------------ATATTGATT--------GATATTCAACAGGCATTTGTCCTA
      sechellia  GTGCTGGAAAGATTTATCGCAGAGCACATTGAATTAAAGTGTTAACAATGTACAAGAAAGCTTACACTTCTAAAAAAAAAGTATGACTCTTAA---GATATTCAACAGGCATTTGTCCTA
         yakuba  GCAATAGAAGGGTGTTTTATACAGCTCATTGAATAAAAATGATAATAATGAACAATAT---------TGGTTACACAAGATAATGACTTTGAAATATGTATTAACCAGGCAACTGTCTAA
         erecta  GCAATAGAAGGATTTTTCATAGAGCTCGCTGAATAAAAATGTTAATAATGAACAAATTAAATTACTATAATTATAGATTACAATCACTTCAAA----TTATTCAGCAGGCATCTGTCTGT
      ananassae  -TGCTTAGAAGACTTTTTCTAAAACTAAATCGGGAAAACCTCAAAAAATC----------------------------------------------------------------------
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  -AAATAAGAAGTTTCATTTC---------TTGAAATGAATGCAAATAGTTGATA--------------TCTTTATAATTATTATATCTTTAAT---GAACTTTAATTGAAATAAAAGTTG
        Summary  RRRRRRBMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMBBBMMMMMMMMMRRRRRRRRRRRRRRRRRRBBMMMMMMMMMRRRRRRRRR

                 
   melanogaster  GCCCATTG-------TTATA-ACAATTA------------TCTTACAATTGCATAATG-----------------AAATGCATGG-------TATTTTTATTT------GTCCATTGTCT
       simulans  AGCCATTA-------TTATA-ACAATTA------------TAACACATTTGTATAAGG-----------------AAGTGCATGG-------TATTTTGAATT-------TCAACTGTCT
      sechellia  GCCCATTA-------TTATA-AGAATTA------------TATTACAATTACATAATG-----------------AAATGCATTG-------TATTTTTATTT------CTCCTCAGTCT
         yakuba  ACTTTTGA-------TTATA-ACGAACA-----------------CAATTCAATCATC-----------------TTCTGCATGGA------TACT------------------------
         erecta  ATAGTTTGTATATCTTTATACATGGATAGCCGGGATTATGTATTCCTATTTGTCCACC--------------CGTTTCTGTTTCAC------TATTATTATTTT----ATTTGAGTGTAG
      ananassae  ---------------TCATA-ATTATTA------------TATCCCACCTCCTGAATT-----------------TAAAAAATCAAAATTCTTATTTTGATTTTG---ACTTATCCCTCC
  pseudoobscura  ------------------------------------------------------------------------------------------------------------------------
     persimilis  ------------------------------------------------------------------------------------------------------------------------
        virilis  ------------------------------------------------------------------------------------------------------------------------
     mojavensis  ------------------------------------------------------------------------------------------------------------------------
      grimshawi  ATCAACTGATC----TTTAA-AAAATTG------------CATATCTTTTGTTCAATAAATGTTGAGCTAAACGTTAAAGTAACC-------CATTATTAATTTGAACAATTATTTCAAG
        Summary  RRRRRRRRRMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRRR

                 
   melanogaster  CCGCATTTTTTGTCATATACCCAAC----ATAC--------CCTACTATACCTTAGAAAACACCACAGAAATGGCAGCCCCC----------GTCACC----TGTGACTGTGCGAAGTG
       simulans  CTTAATTTTTTTTCCTATACCCAAC----ATAC--------CCCACTATACCCTAGAAAACACCACAGAAATGGCAGCCCCC----------GTCACC----TGTGACTGTGCGAAGTG
      sechellia  CTTAATTTTTTGCCCTATACCCAAC----ATAC--------CCCACTATACCCTAGAAAACACCACAGAAATGGCAGCCCCC----------GTCACC----TGTGACTGTGCGAAGTG
         yakuba  -----CATTATCCCCTACACCATTC----ATGC--------CCCACTATACCCTGGAAACCACCACTGAAATGGCAG-CCCC----------GTCACC----TGTGACTGTGCGAAGTG
         erecta  CCCAGTATACTCCCCAATACCATTC----ATAC--------CCTACAATACCCTGGAAAACTCGACAGAAATGGCAG-CCCC----------GTCACC----TGTGACTGTGCGAAGTG
      ananassae  CCT---------CCATAAGCCCCTCCATTACAC--------CCTCTGATACCCTCTAAAA-AAAATAAAACCCAAAACCCCCCCCTAAAGAAGTCTCCAATGTGTGATTGTGTGAAGAG
  pseudoobscura  -----------------------------------------------------------------------------------------------------------------GGAGGG
     persimilis  -----------------------------------------------------------------------------------------------------------------GGAGGG
        virilis  -----------------------------------------------------------------------------------------------------------------------
     mojavensis  -----------------------------------------------------------------------------------------------------------------------
      grimshawi  CTTAATAATTGATCACATGCCTTAT----ATACCTATTCGACCTACTATGCTCTGTAATTCAAGAGATTAATGATTTCGATT----------TGCGCT----CTGCATTATAC-GCATA
        Summary  RRRRRRRRRRRRRRRMMMMMMMMMBMMMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBMMMMMMMMMBBBBBBBBMMMMMMMMMRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBB