melanogaster TTGATTTGGCCACCCGTGGCGGCT----------CTGTCACAGATGCC---------TCAATTTGCATCTATCGAATGGTTTACATGGCTCTAAAAAG-----GTACCTCGATGGGTTGG
simulans TTGATTTGGCCACCCGTGGCGGCT----------CTGTCACAGATGCC---------TCAATTTGCATCTATCAAATGGTTTACATGGCTCTAAAAAG-----GTCCCTCGATGGGTCG-
sechellia TTGATTTGGCCACCCGTGGCGGCT----------CTGTCACAGATGCC---------TCAATTTGCATCTATCAAATGGTTTACATGGCTCTAAAAAG-----GTCCCTCGATGGGTCG-
yakuba TTGATTTGGCCACCCCTGGCGGCT----------CAGTCACAGATGCC---------TCAATTTGCATCTATCAAATGGTTTACATGGCTCTAAGGAAGCCATGTTCCTCGATGAGTCG-
erecta TTGATTTGGCCACCCGTGGCGACT----------CCGTCGCAGATGCC---------TCAATTTGCATCTATCAAATGGTTTACATGGCTCTAAAAAAG----GCCCCTCCATGGGTC--
ananassae TTGATTT-----------------------------------------------------------------------------------------------------------------
pseudoobscura TTGATT-GGCCACCC---------------------------------------------------------------------------------------------------------
persimilis TTGATT-GGCCACCC---------------------------------------------------------------------------------------------------------
virilis TCGATT------------GCGGTTCCGACTAGCCATATCGAGATTACCACGGAGGAC---------------------------------------------------------------
mojavensis TCGATT------------GCGGTTCTGCTTGGCCATATCACAAATG--------------------------------------------------------------------------
grimshawi TCAATT------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TCACAATG-TGGTGGCCTCTCAACATTGCAAGGCTCTTACTTGTGAATTATTAAGT--TATTAACTGCTGCGATGTAAGTCATGGCAGTTTCTGTTTTCTTTATAGGATATATATAGGAA
simulans --CCAATGTTGGTGGCTTCTCAACATTGCGAGGCTCTTACTTGTGAATTATTAAAT----GTAACTACAGCGATATAAGTCATGGCAGTTTCTGTTTTCTTTATAGGAGGTA--------
sechellia --CCAATG-TGGTAACTTCTCAACATTGCAAGGCTCTTACTTGTGAATTATTAAAT----GTAACTACAGCGATATAAGTCATGGCAGTTTCTGTTTTCTTTATAGGAGGTA--------
yakuba ---------CCGTGGTGCCTTGGCATTGCAATGCGCTTGCTGGTGAATTATTAAGTGTAAGTAACTACTGCGATATAAGTCATGGCCGTAGCTCTTCGGCACCTGGCA------------
erecta ----------------GCCTTAACATTGCAATGCTCTTACTTGTGAATTATTAAGT----GTAACTACTGCGATATAACTCATGGCAGTTTCGGTTCGGT--------------------
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis ------------------------------------------------------------------------ATATAAAAAATTCCAGTTAATTTCTTCTATATAATGTATA--------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBRRRRRRRRB
melanogaster GGATTAAAGGAGGCATGTACAAT-------AATATGAGTATGATTTA-----GCTCAAATTCCAAATAT------GATAAAAGTACA-AAGCATACGATAATATAATCAAATTACGCTGA
simulans -ACTTAA------CATG-----T-------AATTTGAATACCAACGA-----GCTCAAGTTGCAAATAT------GAATAAAGTATG-TATATTAC----ACATGATCAAATTTAGCTGG
sechellia -ACTTAA------CATG-----T-------AATATGAATACCAACGA-----GCTCAAGTTGCAAAT-----------------------------------ATGATCAAATTTAGCTGA
yakuba -AATTGG------CATATATTAT-------ATAATGAATATCAAGGA-----GCCCGAATTGCAAATAT------GATCAAAGACCATTATTGTACCATCTTACAATTAAATGTTGTTGA
erecta --TTTAG------GATGCAACAT-------AGTATGAGTACCAACGA-----GCCCAAATTGCAAATACTCGTAGGATCAAAG-----TATTACAC------ATGATGGTATATGATT--
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis -TATATA------CATAAATATTTTACTGT------GATGCAAGTGATATATACTTAAGATACAA----------TATAAAAGCGCATCCTTTCAT----------TCCTACTA------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRRRMMMMMMMMMMMMMMMMBBBBBBMMMMMMMMB
melanogaster CAATCACGATAATG--TTC-------------TTGTAGTAGTATTTGTG-------TAAT------------ATTTATGTTTTTTTAAGATAAGAAACGGTAATAAAATCCA--------
simulans CAATCATGATAATG--TTCCTG-GTTAACTCGTTGTATTATCCTTTCTCAAAA---TAAA------AATCAGATATGTGCAACAACAAGTTAAGGAATGGTAATAAAATCAAATTAATTA
sechellia CAATCATGATAATG--TTCCTG-GTTATCACGTTGTAATATCCTTTCTCAAAAGCTTAAATGGTTTTATCAGATATGTATAACAAAAAGTTAAGAAATGGTAATAAAATCAAATTAGTTA
yakuba C----------ATGGACTCCTT------GACTCCATGTTATCTTTTTGCATGTATCCAAA---------CTGCGGTGCATTTTTGCAAAG-AAGAAAGGCTAATGAGATCAAATTAATTG
erecta -----------ATG--CTCCTTTATCAAGACGGCTTGCTATCCTTTTGCAATTATTCCAG---------CTG----ATAATGTTGC----------AGGGTAATAACATCAAATGAATTA
ananassae ---TCTAGCTAGTG--TTTGTG-------------TATTATAATTT--------------------------ATATATGTTTTAATAATT-AAATTATCATAATTAAGGCTAATAA--TA
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis ------------------------TAATAGTGATATGATATATGGT----------TATC------------CATCATACTACTTTCAATGTGTAATCCATAATGAAATCCATCAA--TA
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary RRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMRRRRRRRRBBBBBBBRRRRRRRRRRRRRRRRRRR
melanogaster ----------CGTAAGTGT-AAAAAATG--GATGCCCTAATCT-------ATGCCATGATGTG----TTCTACTTT-CGAGATTTCGCCTCTG-----------------------CCCT
simulans GAATTATCTTCGTGAGTCTAAAAAAATG--GAAA---TAATCT-------ATGCCAAGATGTG----TCCTACTTT--GAGATTTCGCCCCTG-----------------------CCCT
sechellia GAATTATCTTTGTGAGTGTAAAAAAATG--GATGGCCTAATCT-------ATGCCATGATGTG----TCCTACTTT--GAGATTTCGCCCCTG-----------------------TCCT
yakuba GAATAATCTACGAAAAG-T-AAAAAATGGAGATGCCCTAATCT-------ATCCCATGATGCCA---ATCTGCTTT--------------CTG-----------------------CCCT
erecta GAATTATCTACGTCAGGTT-AAAAAATG--GATGCCCTAATCT-------ATGCCCTGATCTTCTGTTTCTGCTTC--GAGATTCCGCCACTG-----------------------CCCT
ananassae AAACTATTT-----------GAAAAACA----------AATTT-------AT---------------TAATAGTCC--------------TTG-----------------------CTCT
pseudoobscura --------------------------------------------------------------------------------CCTTCGATGTCTG-----------------------GCCA
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis TGCTTATTTATGCAAATTTCCAGCCATA--GATACAATAGTATCTCAAAGATACTGAGTAGCT----TTTTA-TTCACGCACTTCTGCCGCTGCCCAGGTACATCTCTCTAACTCTCCCT
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary RRRRRBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster --CATTGATGGTT---TCCCGGGGCTACTTGGCCCAAAAATCCCGGCCGTCCAAAAAGA------CGATCCT-------TAAAAAAGAAACCGC-TAATCATTGG----G-CCGCACAAA
simulans --CATTGATGGTT---TCCCGGGGCTACTTGGCCCAAAAATCCCGGCCGTCCAAAAAGA------TGATCCT-------TAAAAAAGAAACCGC-TAATCATTGG----G-CCGCACAAA
sechellia --CATTGATGGTT---TCCCGGGGCTACTTGGCTCAAAAATCCCGGCCGTCCAAAAAGA------TGATCCT-------TAAAAAAGAAACCGC-TAATCATTGG----G-CCGCACAAA
yakuba --CATTGATGGTT---TCCC-GGGCTACTTGGCCCAAAAATCCCGGCCGGCCAAAAAGA------CGATCC--------TAAAAAAGAAACCGC-TAATCATTGG----G-CAGCACAAA
erecta --CATTGATGGTT---TGCC-GGGGTACTTGGCCCAAAAGTCCCTGCCGTCCAAAAAGA------CGATCC--------TAAAAAAGAAACCGC-TAATCATCGG----G-CAGCACAAA
ananassae --TCTTAG----T---TCCC------ACT----CCAATATCCTTCGCCGCCCGACAAAC------CATTTTTTTTTTTGTAAAAAAGAAACCGC-TAATCATTGA----G-CCTCACAAT
pseudoobscura TCCATTGATGATTGTACTCC-AGTTTCCAATTCCCTAAAACCAGAGACATGCCATAAGA---------TCC--------TAAAAAAGAAACCGC-TAATCATTTC----GCCCACACAAA
persimilis --CATTGATGATTGTACTCC-AGTTTCCAATTCCCTAAAACCAGAGACATGCCATAAGA---------TCC--------TAAAAAAGAAACCGC-TAATCATTTC----GCCCACACAAA
virilis ---------------------------------------------------------------------CCC-------TAAAAAAGAAACCGCATGATTATGCG----C-CCACACAAT
mojavensis --CGTTCCCATTT---CGCC-TACTTATCCGGCCATTCAGCAACTGCCGTCCACTGCCAGCTTCCCGATCCC-------TAAAAAAGAAACCGCATGATTATGCG----C-CCGCACAAT
grimshawi --------------------------------------------------------------------------------AAAAAAGAAACCAC-TAATTATGCGACCAA-CCACACAAT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster GAGCGGACAATCGCTC-------ACCTAATTATTTGGCCCGATTGTGAGGAGC--GGACAGTCGGCTCGTGGACGCTTTTTGTGGCC--------TCTTTTTG-TT-------------T
simulans GAGCGGACAATCGCTC-------ACCTAATTATTTGGCCCGATTGTGAGGAGC--GGACAGTCGGCTCGTGGACGCTTTTTGTGGCC--------TCTTTTTG-TT-------------T
sechellia GAGCGGACAATCGCTC-------ACCTAATTATTTGGCCCGATTGTGAGGAGC--GGACACTCGGCTCGTGGACGCTTTTTGTGGCC--------TCTTTTTG-TT-------------C
yakuba GAGCGCACAATCGCTC-------GCCTAATTATTTGGCCCGATTGTGAGGAGC--GGACTGCCGGCTCGTGGACGCTTTTTGTGGCC--------TCTTTTTG-TT-------------T
erecta GAGCGGACAACCGCTC-------ACCTAATTATTTGG-GCGATTGTGAGGAGC--GGACAGTCGGCTCGTGGACGCTTTTTGTGGCC--------TCTTTTTG-TT-------------T
ananassae GGCAGGACAATCGCTC-------ACCTAATTATTCGTCCTGATTGTCGCTGCCCAGGACTCACGGCTCGTGTAGACTTTTTGTGGCC--------TCTTTTTGTTT-------------T
pseudoobscura GAGGGAACAATC-CTCTGGCCAAACCTAATTATTTGACTCAATTGTGAGCCCC--G-------GGCTCGTGGACACTTTTTGTGGCC--------TCTTTTTG-TTCCCTACACGACACT
persimilis GAGGGAACAATC-CTCTGGCCAAACCTAATTATTTGACTCAATTGTGAGCCCC--G-------GGCTCGTGGACACTTTTTGTGGCC--------TCTTTTTG-TTCCCTACACGACACT
virilis ATCCG-ACAATGGTTC-------ACCTAATTATTTGGCTCG----------------------TGCTCTGCTCTGTTTTTTTTTGTTTTGTTTTGTTTTTTTG-TT---TGT-----TGT
mojavensis ATGCA-ACAATGGCTC-------ACCTAATTATTTGGCTCG----------------------------------CGTTTTTTTGTT--------CGTTTTTG-TT---CG------GGC
grimshawi ATCCG-ACAATGGTTC-------ACCTAATTATTTGGCTCAATTGTAGGTGGCTCTTGTTGTTTGTTATTGTCTG--TTTTTTTGTTT-------TTTTGTTG-TT---TGTCCGACACT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CGACAAAAAGCGAGCCAATTTTTTTTCTTTCTGGGCCACTTTGTTGCTCTTTTTATGAGTTTTTT--------CCATTGTCAG-TTTTTCCG-GGCCTGTCTCGCAGCCC----TCGAT-
simulans CGACAAAAAGCGAGCCAATTTTTTTTCTTTCTGGGCCACTTTGTTGCTCTTTTTATGAGTTTTTT--------CCATTGTCAC-TTTTTCCG-GGCCTGCCCAGCAGCCC----TCGAT-
sechellia CGACAAAAAGCGAGCCAATTTTTTTTCTTTCTGGGCCACTTTGTTGCTCTTTTTATGAGTTTTTT--------CCATTGTCAC-TTTTTCCG-GGCCTGCCCAGCAGCCC----TCGAT-
yakuba CCACAAAAAGCGAGCCAA--TTTTTTCTTTCTGGGCCACTTTGTTGCTCTTTTTATGAGTTTTTT--------CCATTGTCAC-TTTTTCAG-GGCCTGCCTCGCGGCAC----TCGAT-
erecta CGACAAAAAGCGAGCCAA-TTTTTTTCTTTCTGGGCCACTTTGTTGCTCTTTTTATGAGTTTTTT--------CCATTGTCAC-TTTTTCCG-GGCCTACCTCGCGGCCC----TCGAA-
ananassae TGAAAAAAAGCGAGCCAA-TTTTTTTCTTTCTGGGCCACTTTGTTGCTCTTTTTATGAGTTTTTT--------CCATTGTCAT-TTTTT------------GAACGACCC----TCGAT-
pseudoobscura CGACAAAAAGCGAGCCAA--TTTTTTTTTTGTAGACCACTTTGTTGCTCTTTTTATGAGTTTTTTCCATTGT-CCATTGTCACTTTTTTCCACGGCCTGTACTCCGACCTGGCAGCGAT-
persimilis CGAC-AAAAGCGAGCCAA--TTTTTTTTTTGTGGACCACTTTGTTGCTCTTTTTATGAGTTTTTTCCATTGTCCCATTGTCAC-TTTTTCCACGGCCTGTGCTCCGACCTGGCAGCGAT-
virilis CGACAAAAAGCGAGCCAA--TTTTT--------AAACGATTTGTCTCTCTTTTTATGAGTTTTTT--------CCATTGTGCG-CATTTTTA----------------------GCTGT-
mojavensis CGACAAAAAGCGAGCCAA--TTTTT--------AAACGATTTGTTTCTCTTTTTATGAGTTTTTT--------CCATTGTGCG-CATTTTTA----------------------GCTGTT
grimshawi CGACAAAAAGCGAGCCAG--TTTTT--------AAACGATTTGTTTCTCTTTTTATGAGTTTTTT--------CCATTGTAGG-CATTTTTA----------------------CCAGT-
Summary BBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ------TCC-CGCGATGCCTGCCCTACAAACCTCCTAATTACGGCAGTT------------AGTCGTTGTCC-----GGGACA-GGAGAGTAT---------------------------
simulans ------TCC-CGCGATGCCTGCCCTACAAACCTCCTAATTACGGCAGTT------------AGTCGTTGTCC------GGACA-GGAGAATAT---------------------------
sechellia ------TCC-CGCGATGCCTGCCCTACAAACCTCCTAATTACGGCAGTT------------AGTCGTTGTCC------GGACA-GGAGAATAT---------------------------
yakuba ------TCC-CGCGATGCCTGCCCTACAAACCTCCTAATTACGGCAGTT------------AGTCGTTGTCC------GGAGA-GGAGGACATGCGGACATGCGGACATACGGACAAGCG
erecta ------TCC-CGCGATGCCTGCCCTACAAACCTCCTAATTACGGCAGTT------------AGTCGTTGTCC------GGGCA-GCAGGACATGCGGACATGCGGACAT-----------
ananassae ------CCCGGGCAGTGCCTACGCTACAAACCTCCTAATTACAGCAATTGC-------CCCGGTCCTTGCCC----CGGGTCACACAGGACAT---------------------------
pseudoobscura ------CCT-CGCTG---CTGCCCTACAAACATCCTAATTACGGCAGTT------------AGTCGTTGTTC---------CA-GAAGGGA-----------------------------
persimilis ------CCT-CGCTG---CTGCCCTACAAACATCCTAATTACGGCAGTT------------AGTCGTTGTTC---------CA-GAAGGGA-----------------------------
virilis ------GTT-CG------CTGCTCTACAAACCTCCTAATTGCGGCAATTG--------CCGAGTCCTT----------------CGCGTTC-----------------------------
mojavensis TAGCTGTTT-GG------CTGCTCTACAAACCTCCTAATTGCGGCAGTT---------CCGACTCCTTGTCC--CTGGCTGCC-CTAGCTG-----------------------------
grimshawi ------GTT-CG------CTGCTCTACAAACGTCCTAATTGCGGCAGTTAGTTGTTGTTAGAGTCCTTGTGCTGCCTGGTGCC-TGGTGTC-----------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBB
melanogaster -----GCGGAA-GGACA--TGCG----TGAGTTTATTGCCCGCTCGAATTTCCACTAAAAATTGGGCCGAA----AAAAAAACAACTAGGTAG-------GACTA--GGAACTGCAAACT
simulans -----GCGGAA-GGACA--TGCG----TGCGTTTATTGCCCGCTCGAATTTCCACTAAAAATTGGGCCGGA----AAAAAAAAAACTAGGTAG-------GACTA--GGAACTGGAAACT
sechellia -----GCGGAA-GGACA--TGCG----TGCGTTTATTGCCCGCTCGAATTTCCACTAAAAATTAGGCCGG-----AAAAAAAAAACTAGGTAG-------GACTA--GGAACTGGAAACT
yakuba GACACGCGGAA-GGACC--TGCG----TCCGTTTATTGCTCGCTCGAATTTCCACTAAAAATTGGGCCGGA--------AAAAAACTAGGTAG-------GACTAGGGGAACGGGAAACT
erecta -----GCGGAA-GGACT--TGCG----TGCGTTTATTGCACGCTCGAATTTCCACTAAAAATTGGGCCGAA------AGAAAAAACTAGGTAG-------GACCA--GGAACTGGAAACT
ananassae -----GCGTAC-GGACAGGGGCG----AGGGTTTATTGCGCGCTCGCATTTCCACTAAAAATTGGACCGAGGCAAAAAAAAAAAAATTCCTAG-------GCCCG--GAA----------
pseudoobscura -----CCTGGA-CTGCA-------------GTTTATTACGCGCTCGAATTTCCACTAAAAATTGGACCGAA----------AAAACTAGGTAG-------AGTCC--CG-----------
persimilis -----CCTGGA-CTACA-------------GTTTATTACGCGCTCGAATTTCCACTAAAAATTGGACCGAA----------AAAACTAGGTAG-------AGTCC--CG-----------
virilis -----CGCGTA-CGTCG--TGCG---TCCTTTTTATTGAGCGCTCGCATTTCCACTAAAAATTGTGCCAT----TCCATTCTTAGCCAGGTAGTTGCCGC--------------------
mojavensis -----CAGGCAGCGTCG--TGCGCGTCCCTTTTTATTGCGCGAACGCATTTCCACTAAAAATTGTGCCAT------------------------------------------------TT
grimshawi -----CTGAGA-CGTCG-CCTCGTGAGTTCTTTTATTGCGCGCTCGCATTTCCACTAAAAATTGTGCCAT----TCAAGTCCT---TAGGTAG--------------------------T
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AGCAAAGCGGACGCGCCTTTTTATTGGTGCACCTTCGGCGGA---------------ACCGCAGGATAACAGCAGTAAAAGCGACGACGAGGACAC-----------AAGGATCCTCGAA
simulans AGCAAAGCGGACGCGCCTTTTTATTGGTGCACCTTCGGCAGA---------------ACCGCAGGATAACAGCAGTAAAAGCGACGACGAGGACAC-----------AAGGATCCTCGAA
sechellia AGCAAAGCGGACGCGCCTTTTTATTGGTGCACCTTCGGCGGA---------------ACCGCAGGATAACAGCAGTAAAAGCGACGACGAGGACAC-----------AAGGATCCTCAAA
yakuba AGCGAAGCGGACGCGCCTTTTTATTGGTGCACCTTCGGCGGA---------------ACCGCAGGATAAGAGCAGTAAAAGCGACGACGAGGACAC------------AGGATCCTCGAA
erecta AGCAAAGCGGACGCGCCTTTTTATTGGTGCACCTTCGGCGGA---------------ACCGCAGGATAAGAGCTGTAAAAGCGACGACGAGGACAC-----------AAGGATCCTCGAA
ananassae ---GATCCGGACGCGCCTTTTTATTGGTGCACCTTCGACGGA---------------ACCGCAGGACAACACACACACAC---------AGGGGAC-----------AAGGATCTATAAG
pseudoobscura --------GGACGCGCCTTTTTATTGGTGCACCTTCGCCGGAACTGAGAGCGCGACGACCGCAGAACAACGGCGAC-----CGGCGATGAGGATGCTGCTCCCGAGGATGCGTCCTGGCC
persimilis --------GGACGCGCCTTTTTATTGGTGCACCTTCGCCGGAACTGAGAGCGCGACGACCGCAGAACAACGGCGAC-----CGGCGATGAGGATGCTGCTCCCGAGGATGCATCCTGGCC
virilis --------AGACGCGCCTTTTTATTGGTGCACCTTCGGCGAAAATCGGAGTG--ACAACCGCAGTCCAA------------CGGCGAG--------------------------------
mojavensis AGGTAGACGAACGCGCCTTTTTATTGGTGCAACTTCAGCCGAAAATTGTGCG--ACAACCGCAGCCCAACAGCGA---------------------------------------------
grimshawi TGTTTGACGAACGCGCCTTTTTATTGGTGCACCTTCGGCGAAAATCGGAGCGCAACAACCGCA---------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ATCG----------------AG------------AGCGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTTTG-GCCGACCGATTTTTGTGCCCG-G-
simulans ATCG----------------AG------------AGCGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTCTG-GCCGGCCGATTTTTGTGCCCG-G-
sechellia ATCG----------------AG------------AGCGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTCTG-GCCGGCCGATTTTTGTGCCCG-G-
yakuba ATCG----------------AG------------AGCGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTCTG-GCCGTCCGATTTTTGTGCCCG-G-
erecta ATCG----------------AG------------AGCGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTTCGCGTCCGCTGATTTTTGTGCCCGTT-
ananassae GTCGTCGTGTCGTGGCTGGAAA------------ATGTAGTGCGCTGCTTTTAGAAAAC-------TAGATCAGTTTTTTG---------TTCTA-TTTGCTCGATTTTTGTGCTCT-G-
pseudoobscura ATGGC---------------AG------------GACGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTCTA---------ATTTTTGTGCCCT-GC
persimilis ATGGC---------------AGGACGACGATGACGACGACCTCGCTGC-ATTAGAAAAC-------TAGATCAGTTTTTTG---------TTCTA---------ATTTTTGTGCCCT-GC
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis ---------------------------------------------------------------------------TTTTTGGTAAAGATTTTTGA-G--------TTTTTGGTCCCG-T-
grimshawi ---------------------------------------------TAT-ATTAGAAAAAATATGCGTGGGTCCTT---------------GTTGC-G---------TTTTGGTCCCG-T-
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBB
melanogaster --TGCTCTC-----TTTACG--------GTTTATGGCCG---CGTTCC-----------------------------------CATTTCCCAGCTTCTTTGTT---CCGGGCTCAGAAAT
simulans --TGCTCTC-----TTTACG--------GTTTATGGCCC---CGTTCC-----------------------------------CATTTCCCAGCTCCTTTGTT---CCGGGCTCAGAAAT
sechellia --TGCTCTC-----TTTACG--------GTTTATGGCCC---CGTTCC-----------------------------------CATTTCCCAGCTCCTTTGTT---CCGGGCTCAGAAAT
yakuba --TGCTCTC-----TTTACG--------GTTTATGGCCT---TGTTTCC---ATTTCGTCATTTTTCCATTTTTCTATTTTTCCATTTCCCAGCTCCTTTGTG---CCGGGCAAAGAAAT
erecta --TGCTCTC-----TTTACG--------GTTTATGGCCC---CGTTTCCATTATTTCGTCATTTTTCCA--------------CATTTCCCAGCTCCTTTGTG---CCGCTCAAAGAAAT
ananassae --C-TTCGC-----TTTATG--------GTTTATGGTCCTCGCTTTTC-----------------------------------CATTTCCCAGTTCCATTGT------------------
pseudoobscura CCTGCTCTC-----CTTATG-CTTTATTGTTTATGGTCC---ATTTCC--------------ATTTCCATTTT----------CATTT-CCACTCCCATTGTTTGGCCGCAAAACAAACT
persimilis TCTGCTCTC-----CTTATG-CTTTATTGTTTATGGTCC---ATTTCC--------------ATTTCCATTTT----------CATTT-CCACTCCCATTGTTTGGCCGCAAAACAAACT
virilis ---------TTTATGGTATGGGCT----CGTTTTGGTAC---CATTTT----------------------------------------------TCTGTTGTT---TGCGGCAAAGAAAT
mojavensis --TTTGC--TTTTTGTTATG---------TTTGTGGCA---------------------------------------------------------------------------AAGAAAT
grimshawi --TTCGC--TTAAATTTATG-GCTGCAACGTTTTGGTCC---CGCTTC---------------------------------------------GTTCATTGTTTG-TGTGGCAAAGAAAT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster CTGTAT-GGAA-TTAT---------------------------------GG-----TATATGCAGATTTTTAT-----GGGT--CCCGGC--GATCCGG--------TTCGCGGA-----
simulans CTGTAT-GGAA-TTAT---------------------------------GG-----TATATGCAGATTTTTAT-----GGGT--CCCGGC--GATCCGG--------TTCGCGGA-----
sechellia CTGTAT-GGAA-TTAT---------------------------------GG-----TATATGCAGATTTTTAT-----GGGT--CCCGGC--GATCCGG--------TTCGCGGA-----
yakuba CTGTAT-GGAA-TTAT---------------------------------GG-----TATATGCAGATTTTTAT-----GGGT----CGCC--GATCTAG--------TTCGCGGA-----
erecta CTGTAC-GGAA-TTAT---------------------------------GG-----TATATGCAGATTTTTAT-----GGGT----CGCC--GATCCGG--------TTCGCGGA-----
ananassae -TGTAC-AAAA-TTAT---------------------------------GGTC---TATATGCAGATTTTTATGTCCCGGGA----CGGT--GATCTAG--------TTCGCGGA-----
pseudoobscura CCGGACGGGAA-TTAT---------------------------------GGTATGGTATATGCAGATTTTTAT-----GGGCACTCGGGT--GATCTAG--------TTCGCGGA-----
persimilis CCGGACGGGAA-TTAT---------------------------------GGTATGGTATATGCAGATTTTTAT-----GGGCACTCGGGT--GATCTAG--------TTCGCGGA-----
virilis GGTTCA-GGAA-TTAT---------------------------------GG-----TATATGCAGATTTTTAT-----GGGC----CGT---GCGCTGT--------TTCGCGGAATT--
mojavensis GGTTCA-AGAACTTATTTCCTCAACATATACATGTATACAATATATAGATG-----TTTATGCAGATTTTTAT-----GGGC---TCGTA--GCGTCGTATGGTTCGTTCGCGGAATTTT
grimshawi GGTTCA-AAAA-TTAT------------------------------GGCAG-----TTTATGCAGATTTTTAT-----GGAC----CGTGTTTCGCTGTTGAGGC--TTCGCGGAAAT--
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ------ACGG--GAGTGTCCTGCCGCGAGAGGTCCTCGCCGGCGATCCTTGT------------CGC-CCGTA--TTAGGAAAGTAGATCACG---TTTTTTGTTCCCATTGTGCGCTTT
simulans ------ACGG--GAGTGTCCTGCCGCGAGCGGTCCTCGCCGGCGATCCTTGT------------CGC-CCGTA--TTAGGAAAGTAGATCACG---TTTTTTGTTCCCATTGTGCGCTTT
sechellia ------ACGG--GAGTGTCCTGCCGCGAGAGGTCCTCGCCGGCGATCCTTGT------------CGC-CCGTA--TTAGGAAAGTAGATCACG---TTTTTTGTTTCCATTGTGCGCTTT
yakuba ------ACGG--GAGTGTCCTGCCGCGA--GGACCTCAGCAGCGATCCTCGT------------CGC-CCGTA--TTAAGAAAGTAGATCACG---TTTTTTGTTCCCATTGTGCGCTTT
erecta ------ACGC--GAGTGTCCTGCCGCGA--GGACCTCAGCGGCGATCCTTGT------------CGG-CCGTA--TTAAGAAAGTAGATCACG---TTTTTTGTTCCCATTGTGCGCTTT
ananassae ------ACGA-CCAATGTCCTGCCGCGAGTGGTCCT------CTATTTTTGG------------------GTA--TTAGGAAAGTAGATCAAG---TTTTTTGTTTTCATTGTTTGATTT
pseudoobscura ------ATGGGCGCGTATCCTGTAGCGCTGGGACCTCGAC--CGGCCCTCGGAGGATGTCTGTATGT-CTATA--TTAGGAAAGTAGATCAAG---TTTTTTGTTCCCTTTGTGCGCTTT
persimilis ------ATGGGCGCGTATCCTGTAGCGCTGGGACCTCGAC--CGGCCCTCGGAGGATGTCTGTATGT-CTATA--TTAGGAAAGTAGATCAAG---TTTTTTGTTCCCTTTGTGCGCTTT
virilis ------CCGT--CCGTGTCCTGTTGTG---------------CATTCCGAGG--------------ACCCGTAT-TTAGGAATGTAGATCAAAG--TTTTTTGTTTTCATTGTGGCATTT
mojavensis CATTTGCTGT--CCATGTCCTGTCGCG---------------CATTCCGAGG--------------A-CCGTATATTAGGAATGTAGATCAAAAACTTTTTTGTTTTCATTGTTTCATTT
grimshawi ------TCGG--CCGTGTCCTGTCGTG---------------CATTCCGAGG--------------A-CCGTA--TTAGGAATGTAGATCAATG--TTTTTTGTTTCCATTGT-GCATTT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBMMM
melanogaster TTTC-GCTGCGCTA-G--TTTTTTTCCCCGAACC----------CAGCG-----------AACTGCTCTAATTTTTTAATTCTTCACGGCTTTTCATTGGG--------CT--CCTGGAA
simulans TTTC-GCTGCGCTAGT--TTTTTTTCCCCGAACC----------CAGCG-----------AACTGCTCTAATTTTTTAATTCTTCACGGCTTTTCATTGGG--------CT--CCTGGAA
sechellia TTTC-GCTGCGCTA-T--TTTTTTTCCGCGAACC----------CAGCG-----------AACTGCTCTAATTTTTTAATTCTTCACGGCTTTTCATTGGG--------CT--CCTGGAA
yakuba TTTC-GCTGCGCCA-C--TTCTTTTCCCCGAACC----------CAGCG-----------AACTGCTCTAATTTTTTAATTCTTCACGGGTTTCCATTGCGACGAAAAACA--GGAGGAA
erecta TTTC-GCTGCGCCA-G--TTCTGTTCCCCGAACC----------CAGCG-----------AACTGCTCTAATTTTTTAATTCTTCACGGACTTTCATTGGG--------CT--CCTGGAA
ananassae TTTC-GCTGCGCTA-G--TTTTTTTCCCAGAACC----------CCGGG-----------AACTGCTCTAATTTTTTAATTCTTCACGGCTTTTCGTAGAG------TGCT--CCTGAAA
pseudoobscura TTTC-GCTGCGCTA-G--TTTTTTTCCCCGAACG----------CAGCA-----------AACTGCTCTAATTTTTTAATTCTTCACGGGTTTTTATTGTG--------CT--CCTGGAA
persimilis TTTC-GCTGCGCTA-G--TTTTTTTCCCCGAACG----------CAGCA-----------AACTGCTCTAATTTTTTAATTCTTCACGGGTTTTTATTGTG--------CT--CCTGGAA
virilis TTTCGGCTGCGCTA-G--TTTTTTTCCCCGAAGC----------CCCTGTACCG------GAATGCTCTAATTTTTTAATTCTTCACGCGTTTTTA----------TGACC--GCCGGAA
mojavensis TTTC-GCTGCGCTA-G--TTTTTTTCCCCGAAGCCAGAAAAATGCCGAGTGCCGACTGCCGACTGCTCTAATTTTTTAATTCTTCACGGGTTTTTA----------TGGCCGGGCCGGAA
grimshawi TTTC-GCTGCCCTA-GTTTTTTTTTCCCCGAAGC----------CAAAGC----------GACTGCTCTAATTTTTTAATTCTTCACGGGTTTTTA----------CGATC--GCTGGAA
Summary MMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AAA-------CG--CGG--------------------------------------ACAAGGTTATAAC----------------------------------------------------
simulans AAA-------CG--CGG--------------------------------------ACAAGGTTATAGC----------------------------------------------------
sechellia AAA-------CG--CGG--------------------------------------ACAAGGTTATAGC----------------------------------------------------
yakuba AAA-------CA--CGG--------------------------------------ACAAGGCTATC------------------------------------------------------
erecta AAA-------CA--CGC--------------------------------------ACAAGGCTAGCTCTAG-------------------------------------------------
ananassae AAAATA---TAT--CTT--------------------------------------ACAAGGTTAGC------------------------------------------------------
pseudoobscura AAACTACGGTCT--TCC--------------------------------------ACAAGGTTAGAGC----------------------------------------------------
persimilis AAACTACGGTCT--TCC--------------------------------------ACAAGGTTAGAGC----------------------------------------------------
virilis AAA-------CA--GTGGAAAAC-ATGAAAAT--------------CGTTTTC-CACAAGGTTACTTAGCACCATTTATACAGAGTCCGCCTCCGCCTCCTGCTCTGCCTCTGCCTCTGC
mojavensis AAA-------CGTTTTGGAAAAC-ATGAAAACGCACAGAGCGCGAACGTTTTCTCACAAGGTTACTTAGCACCATTTATA----------------------------------------
grimshawi AAA-------CA--GTGGAAAACAACGAAAACTCACTGAAC-----CGTTTTCTCACAAGGTTACTCAGCACCATTTATTCCAATATAGCCAGAGAGCCTCG--------------CTGC
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRRRRRRRR
melanogaster -GCTCTACT------------TACCTG-CAATTGTGGCCATAACTCGCAC----------------TGCT---CT-CGTTTTTAAG---------ATCCGTTTGTT----------TGTG
simulans -GCTCTACT------------TACCTG-TAATGGTGGCCATAACTCGCAC----------------TGCT---CT-CGTTTTTAAG---------ATCC----GTT----------TGTG
sechellia -GCTCTACT------------TACCTG-TAATGGTGGCCATAACTCGCAC----------------TGCT---CT-CGTTTTTAAG---------ATCC----GTT----------TGTG
yakuba -GCTCTACTGACACTTACCCGTACCTG-TAATGGTGGCCAAAACTCGCCC----------------TGCT---CT-CGTTTTTAAG---------ATCC----GCT----------TGTG
erecta GACTCTACTGGCA--------TACCTG-TAATGGTGTCCATAACGCGCAC----------------TGCT---CT-CGTTTTTAAG---------ACCC----GTT----------TGTG
ananassae -GTTCTACT------------TACCTGTTAATTATGG-----------------------------------------------------------------------------------
pseudoobscura -GTTCTAGT------------TACCTGTTAATTGTGGCCATAACTCACATTCACGTCCGCATTCAGTGCT---CT-CATTTTTAAG---------ATAT----GTTCTTT--TCTCTGTG
persimilis -GTTCTAGT------------TACCTGTTAATTGTGGCCATAACTCACATTCACGTCCGCATTCAGTGCT---CT-CATTTTTAAG---------ATAT----GTTCTTTTCTCTCTGTG
virilis CACTCTACT------------TACCTGTTAATTGTGGCCATAATTCCCAA----------------CGTTCAGCCACATTTTTAAG---------ATAT----TTT----------TAT-
mojavensis -----TGCG------------CATATATAGA--GTAGTC-----TCCCGG----------------CTTT--GCC-TATTT--------------ACCT----GTT----------AAT-
grimshawi CGCTCTACT------------TACCTGTTAATTGTGGGCATAATTCAGTG----------------TTTTTAACA-CAGTTCTCAACATCCATCCATAT----TTT----------TAT-
Summary RBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TT----------TG-----TTTGTCCG------CGATGGCATTCACGTTTTTACGAGCTCGT----------TCCTTCGG----------GTCCAAAATTATGCCAGTTTG-TTTTGT--
simulans TT----------TG-----TTTGTCCG------------------CGTTTTTACGAGCTCGT----------TCCTTCGGTTCCAACCATGTCCAAAATTATGCCAGTTTGTTTTTGT--
sechellia TT----------TG-----TTTGTCCG------------------CGTTTTTACGAGCTCGT----------TCCTTCGGTTCCAACCATGTCCAGAATTATGCCAGTTTGTTTTTGT--
yakuba TTTC--------TG-----CTTGTCCGCGATGGCGATGGCATTCACATTTTTATGAGCTCGT----------TCC-TCGGGCCCAACTACGTCTAA-A-TATGCCAGTTTG-TTTTGT--
erecta TT-----------------CGTCTCTGGAAAGTAGATGGCATTCACATTTTTATGAGTTCGT----------T--------CCCAACTACGGCTAAGA-TATGCCAGTTTG-TTTTGT--
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura TTTTCTGTTCTGTT-----CTTTTCCG------CTACGGCATTCATATTTTTATGAGGCTGT----------TCCTTCGG--CCGGGCCTGGCATAAATTATTTGAATTTG-TTTTTCCA
persimilis TTTTCTGTTCTGTT-----CTTTTCCG------CTACGGCATTCATATTTTTATGAGGCTGT----------TCCTTCGG--CCGGGCCTGGCATAAATTATTTGAATTTG-TTTTTCCA
virilis ------------TAGGGCGTG---------------------------------------------------------------------------------------------------
mojavensis ------------TGTGGCCAT-------AATTCAGTGCGCAGCCACGTTTTTACCAACT-------------------------------------------------------------
grimshawi ------------TAG--------------------GGCGTGTCCATTTGTTTGCCCATTTGTTAACGATCGT------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ----CTCTGG------CAATTATTGGAAATTTCATTGGGTCGATT------------------------TCGCTGCCTTCCTTGCTCTTCCCTTGAG-AAAAGTGAATAGGTTGTGCCAT
simulans ----CTCTGG------CAATTATTGGAAATTTCATTGGGTCGATTG---------------GGTCGATGTCGCTGCCTTCCTTCCTCTTCCCTCGGG-AAAAGTGAATAGGTTGTGCCAT
sechellia ----CTCTGG------CAATTATTGGAAATTTCATTGGGTCGATTG---------------GGTCGATGTCGCTGCCTTCCTTCCTCTTCCCTCGGGAAAAAGTGAATAGGTTGGGCCAT
yakuba ----CTCTGG------CAATTATTGGAAATTTCATTGGGTCGACTG------CGTCGATTGAGT-------GATTCCTTCCCT-----------GGG-GAAAGCGAATAGGTTGGGCCAT
erecta ----CTCCGG------CAATTATTGGAAATTTCATTGGGTCGATTGGGTAGATGTCGATTGGGTCGATGTCGATGCCTTCCCT----------CGGG-AAAAGTGAATAGGTTGTGCCAT
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura TTTGCTCTGAAATTGTCCATTATTGGAAA-------------------------------------------------------------------------------------------
persimilis TTTGCTCTGAAATTGTCCATTATTGGAAA-------------------------------------------------------------------------------------------
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBMMMMMMMMBBBBBRRRRRRRRBBBBBBBBBBBBBBRRRR
melanogaster AAAAATCGCTGCTCCTGAAGACCAAATGAAATGGATTTGT-GTAAGC-ATTAAAAACGCGAGGCAAGCCCCAAGATTCCTCCACTG-CTTTTTTTATATTGCCCACTGCTAAATGCAGCT
simulans AAAAATCGCTGCTCCTGGAGACCAGA-GAAATGGATTTGT-GTAAGCAATTAAAAATGCGAGGCAAGCCCCAAGATTCCTCCACTG-CTTTTTTTATATTGCCCACTGCTAAATGCAGCT
sechellia AAAAATCGCTGCTCCTGGAGACCAGA-GAAATGGATTTGT-GTAAGC-ATTAAAAATGCGAGACAATCCCCAAGATTCCTCCACTGTTTTTTTTTATATTGCCCACTGCTAAATGCAGCT
yakuba AAAAATCGCAGCTCATGGA-CCCAGT-GAAATGGATTTGT-GTAGAA-------------------TGCCCCAGTTTCATTCGCGG--CTTCTCTACATT-GCTACTGCTAAATGCAGCT
erecta AAAAATCGCTGCTCTTGGA----GAT-GAAATG---CTGTAGTAGTA-------------------TGCCAAAGCTTCATT--CTG--CTTTTTTATTTT-CTCACTGCTAAATGCAGCT
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary RRRRBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBMMMMMMMMBBBRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AATTC----------GTCGATTGTTT------------------------------------------------------AAAAATTAAATTACTTATGTTGCCATTCATA-----CAT-
simulans AATTC----------GTCGATTGTCTGAAAAGCGTTCTTCAAGCTGAAGCACTTTTTTATGATG---------TTTGCTAGAAAATTAAATTACTTATCTTGCCATTCATA-----CAT-
sechellia AATTC----------GTCGATTGTCTGAAAAGCGTTCTTCAAGCTGAATCACTTTTTTATGATG---------TTTGCTAGAAAATTAAATTACTTATGTTGCCATTCATA-----CATC
yakuba AATTCGAGTCGCTAAGTCGATTGTCTGAAAAGTGTTCTCTAAGCTGAAGCACTTTTTTATGATGTTTGCGATGTTTGCTGGAAAATTAAATTACTTATGTTGC----CATA-----CAT-
erecta AATTT----------GTCGATTGTCTGAAAAGTGTTCTCTAAGCCGAAGCACTTTTTTATGATG----------TTGCTAGAAAATGAAATCACTTATGTTGC----CATA-----CAT-
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis -------------------------------------------------------------------------------------------------TGCTGCGCTTCCTAGGGCCCAT-
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBRRRRRRRRRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster -CCCCTCACATTTTATGGCCATTTGA--GTGCGGGGTGCACA--GTTCTGTCTTAAGTGGCGGATGGAAACCAC-----CACATTTACTCGAG-----GGATGATGTGCT----------
simulans CCCCCTCACATTTTATGGCCATTTGA--GTGCGGGGTGCAAA--GTTCTGTCTTAAGTGGCGGATGGAAACCAC-----CACATTTACTCGAG-----GGATGATGTGCT----------
sechellia CCCCCTCACATTTTATGGCCATTTGAGTGTGCGGGGTGCAAA--GTTCTGTCTTAAGTGGCGGCTGGAAACCAC-----CACATTTACTCGAG-----GGATGATGTGCT----------
yakuba -CCCCAGACATTTTATGGCCATTTGA--GTGCGGGGTGCGCA--GCTCTGGCTCAAGTGGAGGATGGAAACCAC-----CACATTTATTCGGG-----GGATGATGTGCTCTAATACCTA
erecta -CCCCAGGCATTTTATGGCCATTTGA--GTGCGGGGTGCGCA--GTTCT-GCTTAAGTGGCGGATGGAAACCAC-----CACATTTATTCGAG-----GGATGATGTGCT----------
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis -ACCCTTACACCCCATGACCC----A--GCCCCCTGTGCACACTGTTTTGGCTTGATTGACGCTGATAGGGCACGTGTTGGCAATTATTTGAGCATAAACATGAAAAGCT----------
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ------------------------------------------------------------------------------------------------------------------------
Summary BBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster ----CTAATATCTCCTCATCAAAT------GGGATGGT-----TTCT--------ATGGAAA----GGCAAAATCGTTGTAAAGTGAGGCGGAGTTAAAAA---ATACC----TTGTTA-
simulans ----CTAATACCTCCTCATCAAAT------GGGTTGGTCTCTACTCT--------ATGGCAG----GGCAAAATCTTTGTAAAATGAGGCGGAGTTAAAAA--CATACC----ATGTTA-
sechellia ----CTAATACCTCCTCAACAAAT------GGGATGGT-----CTCT--------ATGGCAG----GACAAAATCTTTGTAAAATGAGGCGGAGTTAAAAA--CATACCTAAAATGTTA-
yakuba ATACCTAATACCTCCTCATCAAACGGGCTGGGGATGGT-----CTCTT----CGTATGGAGAGTGTGGCGAGATCTTAG-AAAGCGAGGCGGAGTTAAAAA-----GCC----AAGTTA-
erecta ----CTAATACCTCCTCATCAAAT------GGGATGGT-----CTCTT----CGCATGGAGA--GTGGCAAACTCTTGGAAAAGTGAGGCGGAGTTAAAAA-----GCC----GTGCT--
ananassae ------------------------------------------------------------------------------------------------------------------------
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ----------TCTTCTGGTCAAAT------CAGATGAC-----TTCTTGTTGAGCACGCCAA-----ACAGGCTCTCA-----GCGTGACT----------TACAGACT----GCCTTA-
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi -----------------------------------------------------------------------------------GTGAAACCGAATTGACAATACATACG----CCATTAT
Summary BBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBB
melanogaster ------TAGCCTTTTTAAAATAACACAAGAT----------------CGTTCGAATTGACTAGAAATATCAAAGTCTTTTTGTATTGAAGCGAGTGT--------------AGT------
simulans ------TAGCC-TTTTGAAATATTACAAGAT----------------TGTTAGAATTGTCTGGAAATGTCAATATCCTTTTTTATTTAAGCGTGTGT--------------AGT------
sechellia ------TAGCC-TTTTGAAATATTACAAGAT----------------TTTTAGAATTGTCTGGAAATGTCAATATCATTTTTTATTTAAGCGTGTGTCAATATATAACAGCAGT--AAAA
yakuba ------TAGCT-TTCTGAAATATGTAAGGATATAAAACATGGATATATATATATATTGACAAGAAATACCAAAGACCTCTTGCATTTAAGCGAGTGC--------------AGC------
erecta -------------------ATATAACAAGATTTTTGATATTCAGTTATGTATATATGGACAAGAAATATCAAAGACCTTAT---------------------------------------
ananassae -------------TTTAAAATATTATAGTAC----------------TCTTC--CTCGAGGAAAAATATTA--------TTTTACTCGAGTCATAAA--------------AATCTGAAA
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ---------------------ACAAATTGGT---------------------------AT------CATTAA---------------------------------------AAT------
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ATACGT-------------ATGTAAACAGAT---------------------------ACAAGATACATAAACACACACACACATATATACAC------------------AAT------
Summary BBBBBBBBBMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBBBBBBMMMMMMMMBBBBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBB
melanogaster ---------CTCAATTTAT----GCTTAATT---------------------TTAAGAA-ATACATCTCTTTAT---------TAG-----CCCCAAAATGA--AAC-AAATGGTCTACT
simulans ---------CTCAATATAT----GCTTATTTAAGCTTAAATGCGCATATAAATTAATAAAGTATACCTTTTTAT---------TAG-----CACCAAAATGA--AACAAAATGGTATAGT
sechellia ATAT----ATGCAATATAT----GCTTACTTAAGCTCAAATGAACATATAAATTTATAA----------TATAT---------TAG-----CACCAAAATGA--AAC-AAGTGGCATACT
yakuba ---------CCAAATATATACATACGTACCTATT------------------TCCATAT-GTATATTGCTTTAT-----------------TACTCTAATGGTCTAC-AAATGGTCTACT
erecta ----------CAAATATGT-------TGCCT--------------------------------------TTTAT-----------------CCTCGAAATGA--AAC-AAATGCTCTACT
ananassae CTTTTGGATAACAACATAT----ATATATTT---------------------TTGTTTA----------TTTAT---------TAGATAGAGACTATACCTA--AAT-TTATACTATATA
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis ---------TTGGCCAGAA------ATGTTTA--------------------TTAAAAA-AATATTAAGTTCGT---------GAA-----GCTCAAGAGCT--AGC-CATTGATCACTT
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi ---------CTTAATACAA----TGAAATTTA--------------------TCGAATA-AAATTTTCATACGTATTTCTAACAAA-----CCCTTAAATTT--AGA-AAATGGGCTTCT
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBMMMMMMMMMMMMMMMMBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster AATTAAGCAAGTCAACAGAATTTTTATGCAATTA-TTCAAAAT---GAAATAATATATACATA--AGATGTTTTTG------GGAATCTGTCATG---GGGTTTC----TGAAATAGGTT
simulans AATTTAGCAAGTCAACAGATTATTTAAGCTTTTA-GTCAAAAT---GAAATAATATATATGTG--CGTATTTTTTT------AANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
sechellia AATTCAGCAAGTCAACAGATTATTTAACCAATTA-TTCAAAAT---GAAATAATATATATGTG--TGTTTTTTTTT------AAAATCTGGCATGT--GGATTTC----TAAAATAGA-T
yakuba AATTTAGCAAGTCGGAAGATTATTTCAGCAATAA-TTCAAAAG---AAAATAAAATATACCTA--TG---CCGTTG------AAAATGTGCCAA----GGGGTTT----CAAAATAGA-T
erecta AATTTGGCAAGTCAAAAGATCAGTTCAGCAATTA-TTCAAAAG---AACATAAAATATGCGTA--TA---TTTTTG------GGAATGTACCAG----TGCTTTC----CAAAATAGA-T
ananassae AATATAAAAACTATATATTTTATTT-AGTTTTTA-TT-ACCAG---GAAATCATATAGAAGTT--TATGC------------------------------TTTTT----TTACAAATT-T
pseudoobscura ------------------------------------------------------------------------------------------------------------------------
persimilis ------------------------------------------------------------------------------------------------------------------------
virilis TGCT-----AATTGA------AATTCAGTTT----TTCAAATA---AAAAGTATATATATATA--AAATCTCTATG--------------------------------------------
mojavensis ----AAGCAAATC--------AATTCAGTTTGTG-TGCAATTATCCTAAAATACACGCGAAAA--AGTTGCCCAAA----------------------GAAATTTGGTGAAAATTATT-T
grimshawi TTCT-GGCAAGTG----------TTATATTTATATTTTTACTA---TTGGATATGTATAAATGTTTGTTCTTTATGCACTGTAAATTCTGGAATGCCTGGATTTTAGATGAAATTGGT-T
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBMMMMMMMMBBBRRRRRRRRBBRRRRRRRRMMMMMMMMRRRRRRRRBBBBB
melanogaster T----GCCAAACAAATTTTAAGTA----TAAATGTATA-----CATATG--TCAA---CTAATAAAT-TTAGCAAATAAAAT---GTACCTGCAAGTAT--------------------C
simulans NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
sechellia T----GCCAAACAAATTGTAAGTA----TATATTTATACATATCATATG--TCAA---CTAATAAAT-TTAGCAAATAAAAC---GTACCTGCAA-------------------------
yakuba T----TAAAAGAAAATTATGAGCA----CATGTGCA----------------CAA---CTAATAAGG-TTCGCATGTAAAAC---TCACCTGCTTAGAT--------------------C
erecta T----GCCAAACAAAT------------------------------------CAA---CTAATAACT-TT--------------------------------------------------
ananassae T----ATCATAAAACTTTTATGTATTTTTAAGTGTTGGCCTATT--------TTA---GGAATGATT-TT-----------------ACTACCAA-------------------------
pseudoobscura -----------------------------------------------------------------------------------------------GTATTTAAAGCCGTTTTGATCCTCT
persimilis -----------------------------------------------------------------------------------------------GTATTTAAAGCCGTTTTGATCCTCT
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis T----GACAGAAATCTTTATAGAA--------TGTTTAAGAAATATTTTATTCAA---ATATAAAAATTTCGTAA----------ATAACTGAGA-------------------------
grimshawi TCCTAGCCAGAGCACTTCTTTGAG-ACACCATTGTTTGCCGGACAGCTGACCGGATGGGTATGGAGG-ATCGTGAAGTTATCGGCATAGTTGCGT-------------------------
Summary BBBRRRRRRRRBBBMMMMMMMMBBBBBBBMMMMMMMMBBBMMMMMMMMRRRRRRRRBRRRRRRRRBBBBRRRRRRRRRRRRRRRRBBBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBMM
melanogaster TATAAATTTATTGGACCAATTTTGTGTAAAAAACTGAACTG------------------GCAC------------TCTTC------------------------CCAAGAATG--GGACT
simulans NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCATT------------------------GTAAAAAAG--GGGCT
sechellia TATACATTTATTGGATCAA--TTATGTAAAAAACTGAGCTG------------------GCAC------------TCTTC------------------------CAAAGAATG--GGACT
yakuba TATGAATTTA----AAAAA--CTGTTGTAAATCCTGCGTTG------------------GCAC------------TCTTC------------------------CCAAAAATG--CGTCT
erecta ----AATTTA----AAAAA--CTG--GGCAATCCTGAGTTG------------------GCAG------------TCTTC------------------------CCAAGAATG--GCTCC
ananassae TTTGTGTTTTTTGGCCAAA--ATACTTAAATTAATTAACTG------------------A------------------TT------------------------TAAACAAT------TT
pseudoobscura TGTATGTTTG-TGGCTTAA--CTTT-------------TTG------------------GCTC------------GCTTC----TGCA----------AGATCGCAAAGAATG--GGAAC
persimilis TGTATGTTTG-TGGCTTAA--CTTT-------------TTG------------------GCTC------------GCTTC----TGCA----------AGATCGCAAAGAATG--GGAAC
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis -------------GATAAA--TTCT-CTAAATTAAAGAGTAT--ATATTAAAATAGCTGCACTG--------------------------------------------------------
grimshawi -------------GGCAAA--T-----TGAATTTGGCACTGTCGGCACCCAAATAGCAGGCACCATAGGCGCTACTCTTGGTGATGCACACCAGCTTGAGATTGTAATCGATGCTCATCT
Summary MMMMMMMMMMMMMMRRRRRRRRBRRRRRRRRBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
melanogaster TCGAGGACTCCT----TGCTGAA----TCACTTACTCAACCC-ATTCCAACTCATCCAAT-CCGCGC--AATCATCATAAATT-TTGGCCTTTTTGTTGTAATTGTTTTATGGCAGAAAT
simulans TCCAAGAGGATGAGATCGGTGGA----TCATT---TCTAACC-ACCC--ACTCATC--AT-CGGC-----ATCATCATAA----TTAGTCTTTGTGTAATGGTTAT---------GAGAA
sechellia TCGAGGACTCCG----TGCTGAA----TCACTTACTCAACCC-ATCCCAACTCATCCAAT-CCGCGC--AATCATCATAAATT-TTGGTCTTTTTGTTGTAATTGTTTTATGGCAGAAAT
yakuba GCGAGGACTCCG----CGCTGAA----TCACTTACTCAACCC-ATC----------CCGT-TCGCGC--AATCATCATAAATG-TTGGTCTTTTTGCTGTAATTGTTTTATGGCAGAAAT
erecta TCGAGGATTTCG----GGCTGAA----TCACTTACTCAACCC-GTCG------ATTCCGT-CCGCGC--AATCATCATAAATTCTCGGTCTTTTTGCTGTAATTGTTTTATGGCAGAAAT
ananassae GTGAGGC---------TCATGGA----TGACAGA---GACCC-CTTC---------TAATGCCTCAC--AATCATCATAAATTGTTGCCATTTTTGGCGTAATCGTTTTATTACACAAAT
pseudoobscura TGGAAAATGCTT----TGTTCGG----TCTCTCACCCTCCCCGATCC------------------------------------------------------ATTATTTTATGGCGGAT--
persimilis TGGAAAATGCTT----TGTTCGG----TCTCTCACCCTCCCCGATCC------------------------------------------------------ATTATTTTATGGCGGAT--
virilis ------------------------------------------------------------------------------------------------------------------------
mojavensis ------------------------------------------------------------------------------------------------------------------------
grimshawi TCGAGATCTCCC----TGGTGAAAGCGTCCTTCATCAGATTC-C---------AACTGCT-CCACACGGAGCCAACGCAGA---------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBRRRRRRRRBBBBBMMMMMMMMBBBBBBBMMMMMMMMBBBBBBBBB
melanogaster TACTCAATCATCA-AGCATAATTCCCT----CGTTTTCGC
simulans TAATC-ATCATCA-AGCATAAT--CCT----CG--TTCGC
sechellia TACTCAATCATCA-AGCATAATTCCCT----CGTTTTCGC
yakuba TACTCAATCATCA-AGCATAATTCCCT----CGTTTTCGC
erecta TACTCAATCATCA-AGCATAATTCCCT----CGTTTTCGC
ananassae TACTCAATCATCA-ATCATAATTCCGTTTGCCGTTTTC-C
pseudoobscura ------ATCATGGCAGTACAATTTGCT----CGGCATTTT
persimilis ------ATCATGGCAGTACAATTTGCT----CGGCATTTT
virilis ----------------------------------------
mojavensis ----------------------------------------
grimshawi ----------------------------------------
Summary BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
hb