Multiz Alignments of 5 Mammals

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Alignment block 1 of 72 in window, 59339 - 59613, 275 bps B D Malayan flying lemur cctgcgggatttcgatttgtttcggggtggaatcatcaaagctttattgatgccttccttggtttcccag B D Mouse ====================================================================== B D Human ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur gggctggaaacagctctacacttatgtaaataatgtcatcctgcccggtcaccgaggttcaaaatatcaa Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gtaaccatgggaaaggagggaactcagagaaatgcatgctaagaaaaaaaccaaaaaacaaaaaactggt Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctttaaaagtttttctaaagcttgtgcaggtttaggtcccagcagggcttcagtgcggctcactg Mouse ================================================================= Human ================================================================= Tree shrew ================================================================= Guinea pig ================================================================= Alignment block 2 of 72 in window, 59614 - 59620, 7 bps B D Malayan flying lemur cagcacc B D Human cagcacc B D Mouse ======= B D Tree shrew ======= B D Guinea pig ======= Alignment block 3 of 72 in window, 59621 - 59631, 11 bps B D Malayan flying lemur ---cacatcacagc B D Tree shrew ---cactcctaaga B D Human cccaacatcacagc B D Mouse ============== B D Guinea pig ============== Alignment block 4 of 72 in window, 59632 - 59661, 30 bps B D Malayan flying lemur ctcccc-aacccatgctgttaag---gagccact B D Tree shrew ctcccc-aaagaacactacaacc---cagccttc B D Human ctcccctgatctatgatgctaag---ta-cctag B D Guinea pig cttcct-tgaccatggggtgaggatagagcca-- B D Mouse ================================== Alignment block 5 of 72 in window, 59662 - 59864, 203 bps B D Malayan flying lemur tttga-----ggctggtaatgtcc--tttggctccagaatccctagggt--tggggtcagagctcaggca B D Tree shrew tcagacctatggctggcaatgtcc-----agctccagaatcctgaaggtgtcaggatcaaagctcaggca B D Human ttaga-----ggctgggggtgtgtcatttggctccagaatccctaggat--tggggtcagagttcagaga B D Mouse tctga-----gcctgacagtggtg--tttggctct-ggactcccaaggt--tgggctcagagctccagca B D Guinea pig --tgc-----agctgggggtggcc--tttggctctagaattcatagggc--tggggtccaagctcaggta Malayan flying lemur gc---ttccagaaacagagcag-caccacttaacctctgcccttctaccttcct-----------gccc- Tree shrew gc---ttcctgaaacagaatagacaccacttgaactctgcccctccactttcct-----------gcctt Human gc----------------------------taaaccctgccctcccaccttccctcagagagggagccc- Mouse gtgggtttcaggggcacagatgctgctgtttaa--------cctacacctcccg----------agcttc Guinea pig gt---ttctagaaacagagcagcttcggctgaaa-tctg-ctttgcacctccct-----------gcctg Malayan flying lemur -----------------------aggca--ggggcaggcctgagccgctgtttgcaggatggctttaatc Tree shrew ccaccaccccccttttccgcaaggggga--ggggcaagcctgagctcctatttgcatgctagccttgatc Human ---------------------agggcgg--gaggcagacctgagcatctgtttgt-ttatggccttaatc Mouse cttggagctcgcagac-----agagggcagggggcgggacccagctgctgtttac-agattgcctgggtc Guinea pig tcagggccttg-----------gggggc--ggggcagggcctg--cgctttttgc--------------- Malayan flying lemur ctgcctgtggcggagcctgtacccactgtgtttacctgcctat Tree shrew ctgcttggggcggagcctgggcc-------------------- Human ctgcctg-agtggaacctgt--caatgctgctcacttgcctct Mouse ttgcagggggaggagcctgttc--------------------- Guinea pig ---------------cctgtcc--------------------- Alignment block 6 of 72 in window, 59865 - 60552, 688 bps B D Malayan flying lemur ggcagagcctgtccgcgctctgtttacctgcctgtggcagagcctgtccacactctgtttacctgcctat B D Tree shrew ---------------------------------------------------acactgtttacctgc---- B D Mouse --------------------------------------------------aacaccggtttcctgc---- B D Guinea pig ------------------------------------------------------cagcctcattgc---- B D Human ---------------------------------------------------------------------- Malayan flying lemur ggcggagcctgaccccactctgtttacc------------tgcct---tcgctgggccccaaagcctctt Tree shrew ----------------------tttact--------------------------ggccccaaggcccttg Mouse ----------------------ctttct---------tggtacctg--tggctaaacttccagtcccgtt Guinea pig ----------------------cttattgctgtggggtggagcctgccccgctgtgctccctgacccact Human ---------------------------------------------------------------------- Malayan flying lemur gtgtgcaacagctgcagagtcagcca-gagttatcccagcacaaaggttgctgg-------------ccc Tree shrew gtgtgcaccagctgcagagtcagccctgcaccagcccagttccaaggtc-ccag-------------cac Mouse ct---------------------gcctgaggtaacccagagccgaggttgcctg---accactg---cat Guinea pig gc---------------------ccc-----tactccactgccccagtcatgtatgtgccacaggcacac Human ---------------------------------------------------------------------- Malayan flying lemur tctgggccctactgcc-------------tgctgcgttgtcccg--------gcag-------gagccag Tree shrew tt-----cccattgcc-------------caggactttcttccc--------ggag-------aagccag Mouse ct-----gctgctgcc-------------cagggctttgttcaacttcctgtgggaacgcttcaagtca- Guinea pig tt-----gctgcttccgtgctcctgcactcagggcttggttcccc-------agga-------aagtcag Human ---------------------------------------------------------------------- Malayan flying lemur agtcagccaaggccactgaccactggagccactgtaggag----------tccacagtatggccagtcgg Tree shrew agtcagccaaggccactgaccacaggagccatggtagg-g----------cctgagatggggccagtcag Mouse agtcgtctgaccctgttgatcgctggaatcatggtaggaatgatagggggtctgtgagaccgccagtaga Guinea pig agccagccgaggccagcaacagctgtagccatggtaaggg---------------------gcccatag- Human ---------------------------------------------------------------------- Malayan flying lemur tccagcagggctgagtccaggctgggtgtgtgagcagggtgtgggaggacaaagttagaccaagtctggg Tree shrew tacagc-gcgatgtgtctgggatgggcctgtgagc-tggtttgggagggcactattgggccaagtctgaa Mouse tacagc-cggctgtgtccaggctgcatctgtgagccaagtgagggaaggtaaagtcagaccaaggctggg Guinea pig -----------tgtggccaggccgggcctgtgagccaggtgtgtgtgg-------------------ggg Human ---------------------------------------------------------------------- Malayan flying lemur gccactg-aggagaccacccaggaccctctcaaattggacctgaggctctggggaggtgctgggatgtgg Tree shrew gccagggtaggaaggctatagggactctcttgaattggacttgaggctttgtgg-ggtactgggatgata Mouse gccatca-gaggggccactggggatc--ccccaagtgaacttggggaac------ggt--tggggtgtta Guinea pig ggcagca-atggg-----------------ccaggtg-----------------------tggggctata Human ---------------------------------------------------------------------- Malayan flying lemur gcagaggtgcaggagaggaaggcctgggatggactcca-gcacctttacttggcttctttgtgagcttgg Tree shrew aggtgtgtatgagagagaaaggtctgggttggactgca-gtgccttcacttgtttgctgtgtaaacttgg Mouse gaagagatatgaaagtggaaggcttgggctgacctcttaatgccttcactgggcttctgtgtgaacttag Guinea pig gggaaggtgcg-----ggccatattgggctggactctt-tcgcctttattaagcggct------------ Human ---------------------------------------------------------------------- Malayan flying lemur ggaagtaatctcacctctctgagcctcagtttctgctcctgaaaatgggagtactattacctatttcacg Tree shrew agaagttacttcacctctctgaac--cattttctgctcctaaaaatggaagcaatctgtcctattttagg Mouse ggaag-accctgactgctctgagccttaattttgacagct-aaaagaagactaatgt--cctgtttcgtg Guinea pig ----------------ctgtgagcctcagttttgggtgctgaaaatggggataatgtcacttatttcatg Human ---------------------------------------------------------------------- Malayan flying lemur gcctgactgcaaggtctaaatgaggtgtgatatataaaggatgcca-gcacagtgccctg---------- Tree shrew gcattactataaagctcaaataggacaggacatggagaagatccca-gcacagtgctggggaacaccagg Mouse acattattgtaagatct-aataagccaggacacacagaagacccaccgtatctggctggctatacagtgg Guinea pig tcattattgtaaggtctcaatgagataggatgcaaagg---------gtcatttgctgac---------- Human ---------------------------------------------------------------------- Malayan flying lemur ---------------agtcttgtccctaggaccccatggc-tgtgagctagcagccaggagg--act--g Tree shrew tttccagcagatggcaatcttgcccctgagactctatgccttgtgggatcaaggccaggaag--gct--g Mouse tgtgcagaaaacatgattctgattccca-----------------ggctagaggctaagatgctacc--a Guinea pig --------aggtgggagtctcatctccagcattc--tggc-tgtgggccagaggccagctgggtacatgg Human ---------------------------------------------------------------------- Malayan flying lemur -----ctatagggtctcccaga-c Tree shrew cacctctgtggagtctcccaga-c Mouse -----ccatggaacacctaaggg- Guinea pig -----ccctggggcccctcacg-- Human ------------------------ Alignment block 7 of 72 in window, 60553 - 60843, 291 bps B D Malayan flying lemur atgcccctttcctgctggagaagcctggtggaaaagctgaaggccagtcccaagtcctttctgggccacc B D Mouse ataccccttccctgccag--------------------ggaagtcagaccccagccctt-----gcctcc B D Guinea pig ---ccccttccctgatag----gcctggtaggaaagctgaggaccaggctctagccctccttgggccacc B D Human ---------------------------------------------------------------------- B D Tree shrew ====================================================================== Malayan flying lemur ggggccagatcactcagccccgttcc-ggctgtcccacctgg-----------------tggagtgcact Mouse agcgccttctcctccagccctttctcagaccgccctactta------------------tctgctgggcc Guinea pig atgcccagctcacacagcccccttcccagttgccctactcagttacaccccccaccccctttgctgagct Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Malayan flying lemur gt-cctgga------gcaagggcaggag---cccctggtcctgttttctcaggctccaccc------ttg Mouse at-ccataatgcgcacctggagcaggaattgacccgagtcctggcttatcaggatttgtccttgtctttg Guinea pig ctgccagagggtgc-cccagagcaggaa---gcccgaggcctgctttctcgggctgcattc------ttg Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Malayan flying lemur atcatatctattcccttttgcctaagaatgggcagaact--------tatt------taaatctgctcat Mouse atcccatctatcgctttggccttcagaatgggcagaattcc---caccatt------ctgacctg----- Guinea pig acctcatctgtccccctgcacctaccaatgggcaggattctgcatgccatctacccacagagcag----- Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Malayan flying lemur ccatgtgaggggtcacaggacatgacaacaggaagccctacacatagccacagggcttc Mouse ------gagtgatcaa---agatagcattaggatg--ctgggtgtgggctgccagcttc Guinea pig ------gaggagtcaagggagataagaacgggtggccctgtgcatggacactcggcccc Human ----------------------------------------------------------- Tree shrew =========================================================== Alignment block 8 of 72 in window, 60844 - 61277, 434 bps B D Malayan flying lemur agagcttc-tgggtgtgtttaatcttcccagtggccct-----gagaggtgactatggcagagaagagc- B D Tree shrew agagcttcctgcaggtgttcaaacttcccag-------------agaggccatcagagctaagagatgcc B D Mouse tgagcagc-cggtgctgtttgatcttcctagtggcccttgacctaagaaccatagtagccaaagggagct B D Guinea pig aattcctc-cagtgatgtttgctcttcctagcggccct--------gatccacagtggattcagggaga- B D Human ---------------------------------------------------------------------- Malayan flying lemur tgagctcagagc--------tgtggcctcagcctccagttctgctatagtg---gtagcgg----gg--g Tree shrew tgaactttgcac--------tgtggcctcattctcctgtc--actacactg---ttggaggagaggg--g Mouse ggggctctctgtgctgtggccatgtcctctcctctttgtg--tctacggggtttggggttg----gt--g Guinea pig gaagcccaaggttccatg--catggcctcagccaccca-a--tctgaaaag---ggggtgg----gtagg Human ---------------------------------------------------------------------- Malayan flying lemur ctgtgatgggacagcgggacagcggtcagggcggcccgtggctgcttatctgctcatacctggttttttt Tree shrew cggacacaggaccatg----aatggttgggtcagc----------tgacctgctcagatctgactttttt Mouse atgtgacat-acagag-----------aggacagt----gactgcttgcctactgagacctggctttctt Guinea pig atgtggcatcacaggggga-tgcagctaggacag---------------ctgctgagacctggctgcttc Human ---------------------------------------------------------------------- Malayan flying lemur cc-tggcacaggtccacaggtacaa-ggagttaagtttgaaaactgggcgaggacctatggctgctgccc Tree shrew ccctgacacaggtccatggctacaaaggggtcaagttccaaaactgggcgaggacctatggctgttcccc Mouse cc-tggtataggtccatgggtacaaaggggtccagttccaaaactgggcgaagacctatggctgcagtcc Guinea pig cc-tggcacaggtccaggggcacaaaggcttctagttccaaaactgggtgaaaacctactgctgctgcct Human ---------------------------------------------------------------------- Malayan flying lemur agagatgcactgtcagcccacatccatggaggggatcagagaggtgtgtg----tcagcacagcgcccgt Tree shrew agagatgtactatcagcccacgtctgtggaggagatcagagaggtgagtgc---ccacctcagc------ Mouse agagatgtactaccagcccacatcagtgggggaggtcagagaggtaggtgcccatgaacaccac------ Guinea pig ggagatgtactaccagtcggcatcggtggaggaggtccgagaggtgagtg----tgagctccac------ Human ---------------------------------------------------------------------- Malayan flying lemur gatgg----cccggtcctgtagaccacagc-ctggccccaaagaggaggcggg-----gaccccacctgg Tree shrew -atgg----cctggcacaatagaccacagctctggccctagggaggaggcagggtgatggaccttccaga Mouse -atgggctgcccggc-ctgcag-ccacaaccctcgctct--ggaagacgctgg-atgtgaggcttcctg- Guinea pig -at------cccg----ctcag-ggactgccctggctcc----aagagtctgg-agatggaacttcctgg Human ---------------------------------------------------------------------- Malayan flying lemur gctaagatcctgcccctagccaagaac------------------ttgatgaag----------tcggct Tree shrew gctaaactcctacccatggcccagaactgccaaccaggtgacttgtgaataaaa----------gcagct Mouse --------------------------ctggc--------------ctggttggg---------------t Guinea pig gcc-agatcccattcctagctcagaactggc--------------tgggctgagctctggggattccgct Human ---------------------------------------------------------------------- Malayan flying lemur aactcca-ggccc Tree shrew aaatataggggtc Mouse aaaggca-aggct Guinea pig aaaccca-ggtcc Human ------------- Inserts between block 8 and 9 in window B D Mouse 1bp B D Guinea pig 170bp Alignment block 9 of 72 in window, 61278 - 61424, 147 bps B D Malayan flying lemur ctgtcccctctctcccctgctctggcttcgctcagcagccacattacaacatagtgtgcccatgttagtg B D Tree shrew ttgtcccttctcac--------------cacccagcagccacatcacaactttctgtaccca-------- B D Mouse ttcttcctgctttccccagctccaggtctgctccgcagcc-tgttgtaatgttctatgccca-------- B D Human ---------------------------------------------------------------------- B D Guinea pig ====================================================================== Malayan flying lemur tgcccgccacctccaatctgtacagcaacatgccattgatggcctggcttgcgtttcccgc---tcagat Tree shrew -------------------------caatacacc----agggcctagc-agctttcattgcaattcagac Mouse ---------cttcaagcctatacagcagtataccaggggcagccatgtctacactcacctc---tccaac Human ---------------------------------------------------------------------- Guinea pig ====================================================================== Malayan flying lemur ctcttccctg Tree shrew tgcatctcca Mouse ctgacctctg Human ---------- Guinea pig ========== Inserts between block 9 and 10 in window B D Mouse 1746bp Alignment block 10 of 72 in window, 61425 - 61488, 64 bps B D Malayan flying lemur agctgcagatt---------tctctcgccgtatgactcaaacacctcacaaatatggccaggaccacgtt B D Tree shrew aactgcagacccacaaaggacctcttattctttgactcaaagacattacaagcttagatacctcaaagtt B D Mouse ====================================================================== B D Human ---------------------------------------------------------------------- B D Guinea pig ====================================================================== Malayan flying lemur ttt Tree shrew ttt Mouse === Human --- Guinea pig === Inserts between block 10 and 11 in window B D Tree shrew 1165bp Alignment block 11 of 72 in window, 61489 - 63228, 1740 bps B D Malayan flying lemur gattttttttgccttcaacctattccacctcatgttcccatctctgcacagggtcccagttgcttaagtt B D Mouse ====================================================================== B D Human ---------------------------------------------------------------------- B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur aaaagccaggaagtgggtcacggtccctcctttacccttgtctcatgtcagcaactttgccttagagttt Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ccagaacccatggccttctctccagggccactgtcaccctcttgcccggccaccctttgttcctcatccg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctgtgacgtggggggccccttcctggcgtccctgcttctgttctttcctcccccaaatgcactttccaca Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cttggcaggagtaacgtccttacatgtaagctgaactgggttacgtccctgcttcaagcccttcagaggt Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gtcctgttgtttgtgggacaaaaccttcactcctgactcccaggccgtgccccttgggggcctgtcacct Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ccctaaggtgcctctctccctggctcgctacccagccacgtgattctcccttcagttcacagagcaaacc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tggctccttccggcctcagtgcctttgccctctctgttcccctgcctggaatgcccatctctcactaggt Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cccttccagggtcaacttcacctcctcagaagcattcccaggccaccgtatctgaagcatgtctccaagt Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ttctctgtcccagctccttgtttattgccgtcaccatgtattcataatttgcaactgttctgtcaacttg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur aacattttctcgcctttgacatcctccctcataaggacgtccacctgtgcttgtgtcactctctcttgta Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tcctcagcaccagaagcactgtgcccagcactcaggaagcacctaataaatatctgttggatgaatgagt Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gaatgggtagacgaatgaatgaatgaacaggacccaacttctgtctttaaaaggcgtggggtcttgtacc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gaagacagacattcatgcaactaacttcctaggatgcaggtgctgtttcaccagcactagcagtgtacag Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur aagacggtggtaaccattctgagtgtgagtggatgtgaagagaaagcacgtgtgcatgtgcacaagcgcg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggcatgggtgacgctgcgtgtgtgtgagcgtgggcacgggtgacatgcacgagcgtgggcacaggtgacg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cgtgcatgtgcgcgagcgtgggcatgggtgacgctgcgtgtgtgtgagcgtgggcacgggtgacatgcac Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gagcgtgggcacaggtgacgcgtgcatgtgcgcgagcgtgggcatgggtgacgctgcgtgtgtgtgagcg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tgggcacgggtgacatgcacgagcgtgggcacgggtgatacgtgcatgtgcgcgagcgtgggcacgggtg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur agtgcgtgtgtgatggtggccagaggacagcggcactaacagtaacagtcacccccgtcagcaccgtggc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cttcctatccattctcatcaatgtgaggtggtgatcactagccccattttacaggggagcacactgaggc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tcagagaggctttgtaattttcccatatcagtaagtgtcagagccaggattcaaatcaggtgttgtctga Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggtcaaagccaccaacttctcatgcagtgaaagctccctgaaggaaattggtcattgagctggccctgga Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggaagaatgagttcatccgggtgctggggagggctccatgagtgaggggagtgggagaccgtctggaagg Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ttgtggtgtgaaatgcaaggccagtgtccatggtgcagacatgacggtgttggagcatca Mouse ============================================================ Human ------------------------------------------------------------ Tree shrew ============================================================ Guinea pig ============================================================ Alignment block 12 of 72 in window, 63229 - 63419, 191 bps B D Malayan flying lemur tgcaattatttattcattcagtaatcatcagagactccctacttgtgctgggcctggggtaggcactgaa B D Tree shrew tgcatttatttattcacactatg----ttagagacctcctatgtatgcagagcctgcaggaggctct-aa B D Mouse ====================================================================== B D Human ---------------------------------------------------------------------- B D Guinea pig ====================================================================== Malayan flying lemur gatacaaagtcagatccagccactgttcctggcctctgggaatcttccttctaggctggaggcag-ctgg Tree shrew gatacaaagtcaaaatcagccactgtccctgg-----aggaaccttcattctagtgtggggacagactgg Mouse ====================================================================== Human ---------------------------------------------------------------------- Guinea pig ====================================================================== Malayan flying lemur aggttgtaggccaaggtcggaagcccaaatcttatcctgcggacact--ggact Tree shrew aggtcct---ccgagg-----ggcctgagtcctatcctgaggactctagggcac Mouse ====================================================== Human ------------------------------------------------------ Guinea pig ====================================================== Alignment block 13 of 72 in window, 63420 - 63592, 173 bps B D Malayan flying lemur ccttagaagggtgtgcgctggtgaagaatgtgattgggtt-gcctttagcaaagcctccagctgcagggg B D Tree shrew cctgggaagactttactctggcaaagcacgtcattgaatttgcctttaggaaagcctcagagtgcagtga B D Guinea pig ccccggaaggctttgcattggtgaagactgggaccaggtttgcatct--gaaagtctggagctgcagcag B D Mouse ====================================================================== B D Human ---------------------------------------------------------------------- Malayan flying lemur ccagaacgaaccggagccctg--ggactttggg-gggttccttggttctccatcctggctcccttcctgg Tree shrew g-agaatggaccagagccctg--ggacacagagagggctccttggtcctccatcccagctcact-cctgg Guinea pig g-aggatgaaccagagccacgcagtacagtagg-agtttccttggtcttctgtactggttcacctctagg Mouse ====================================================================== Human ---------------------------------------------------------------------- Malayan flying lemur cccttttctcttgttctctctcatggagtggccagca-------------- Tree shrew cctttttctctcactttctttc-tggaatggctggca-------------- Guinea pig cccacatctccagctctttcc--tgggcagcctggttcctgtgagccacct Mouse =================================================== Human --------------------------------------------------- Alignment block 14 of 72 in window, 63593 - 64025, 433 bps B D Malayan flying lemur cagcagc--ctgga-gctagg-------------------------------ctgggc------------ B D Tree shrew caacagc--ctgga-gccagggagaggccttggaggcctgggtgtgtaccgcctgggctgaccacactcc B D Mouse cagcagcctctgcaggctatg-------------------------------ccagg------------- B D Guinea pig --gcgccccctgca-gccagg-------------------------------ccagat------------ B D Human ---------------------------------------------------------------------- Malayan flying lemur ------------------ccccatg---cactctgcatgcctctt----gagaaaagcctgagtca--tg Tree shrew ctacaggccaggcctggaccctgtg---tgctct-caggccgcctcaagaaggaagtcctgactca--ta Mouse ------------------ccctgaagtcccccct---ggcttcctctctgagcagggccttactgactgg Guinea pig ------------------ccctgca---cactct---ggcctc--ctcgggaaaaggcttgactta--gg Human ---------------------------------------------------------------------- Malayan flying lemur cgttgtctcggctggtgctggttctagccaggcagcagaataagcgagcgaaggcagtgggtagtgacca Tree shrew ctgtgtcctggcaggtgctggccctcgccaggcagcagaacaagcgggtgaaggtggtgggcggaggcca Mouse cattgacttggcaggtgctggccctggcccggcagcagaacaagaaagtgaaggtggtgggtggcggcca Guinea pig ttatcatcttgcaggtgctggccctagccaggcaacagaacaagcgcgtgaaggttgtgggcagaggcca Human ---------------------------------------------------------------------- Malayan flying lemur ctcaccc-cagacatcgccagcactgaaggcttgatgatgcacacaggcaagatgaactgggtcctccag Tree shrew ctcaccctcggacatcgcctgcaccgatggcttcatgatccacatgggcaagatgaaccgagtcctccag Mouse ctcgccttcagacatcgcctgcaccgatggcttcatgattcacatgggcaagatgaaccgggttctccag Guinea pig ctccccctccgacattgcctgaacagagggcatcatgatccacaggggcaagatgaaccggatcctccag Human ---------------------------------------------------------------------- Malayan flying lemur gtcctcaga--gctggacagcc------------------------------ttagcctttaacccagac Tree shrew gtacttagaatgcttgactccccacttctacctgtccccgggtcctgctttctcagcctccgccccagat Mouse gtact-ggcgcccctgacacccctcctcagcccatgcccaggctgagtggcttcagtctacgtcccagac Guinea pig gtac-------------cgcaccacctttgcc--tgccc------------------------------- Human ---------------------------------------------------------------------- Malayan flying lemur ccggtctagaaactccttagcccctccttgagccctcatcctctccctgccc------------------ Tree shrew cctaggtcagagtcccttagtctttccctcagtccttgtccttgctctgcccttgagtccccagagaaat Mouse tctattcacgacatctccaatgtttgcctcagcccttagcttctccctgttc------------------ Guinea pig ------catgacatc----atgct---------ccttgact----------------------------- Human ---------------------------------------------------------------------- Malayan flying lemur ----caa-----------------gttcccagagtgacaccccaattcctggccggccc-ctgaacaccc Tree shrew atttcaatttttccctgcccttgtgtccccaaagaaatatcctgatttctagtcctccc-ctgagcacc- Mouse ----tgg-----------------gtcctcagggtgatgcccagatctctggccttcctgctgaacaact Guinea pig -----------------------------------------------------catcct--tgagagccc Human ---------------------------------------------------------------------- Malayan flying lemur ttcagctgaaccctccctgggtactc--aggcctcttgtcaggtctgcctagccccttgagaccacagag Tree shrew -tcaccagaaccctcccctggctctctcaggcctcttgtcaggcctgctcacccccttgaagccaaggag Mouse gtcacctgagcctccccttggattgctcaggccacttgtcaagtctacttggccctttgtggcctcagag Guinea pig ctttcctgaacctgtcc-aggcttgctcatgcaa---gtcagatctgcctggcctcctgtag-ctatgag Human ---------------------------------------------------------------------- Malayan flying lemur atgatgtccaccccc-----------------------ctctcc Tree shrew aggatgcccactcccacccccacctccccagtccccctcacccc Mouse agaatctccc----c-----------------------atctcc Guinea pig aaaatgtcctgtgac-----------------------cccttc Human -------------------------------------------- Alignment block 15 of 72 in window, 64026 - 64670, 645 bps B D Malayan flying lemur tgccagaggctcctctccacttctctacaataggagccaaaagtcagcaccccgacccccgcaaaaggta B D Tree shrew tgccagagcctcctctccacttctctaggacagg-gctgaaagtcag-gccctga-----------agga B D Human tgccagagccccctctccacttctcaggagcaagagcagtgagcagg-gccccga---------aagata B D Mouse tgctgtagcttctgttcttcctcctttaaagaggtgcacagaaacag-gctccca--------cagagta B D Guinea pig ttctagcgctccctctccactttgttatagcagaagtgatgaatcag-gtagaat--------cagag-- Malayan flying lemur gactcacaatgaccaatccagaagggcccaaagtggcacttagctagtttcacagagagagaaactgaag Tree shrew gacacacagggacgaattccgaagggcc-gaagtgccatttagctatttgtacaaataaggaaac--aag Human gactcaccatgacaaatacagaaaggtgcaaggtggcatttagctgactttacagat-gaggaactaagg Mouse gact----------aatccagtagaacccaaagtagcactgagccaggctcacaaatagggaaa-tggag Guinea pig -----------------ccagatgtgagcaaagtgacacgaggctagttttacacatggggaaactaagg Malayan flying lemur atcagagagggcaagtgactcacctgaggtcacacagtggatcagaaacagagctgggcatggactcagg Tree shrew atcagagagggcgagtggcttgcct-agttcacacagtc------aagcagagctgaacacagtctcggg Human atcagagagggtgagtgatttgcctggggtcgcagagccaatcagcagcagggctgggcacagactcagg Mouse atcagagacaggcagtgacttgcccatggtcacacag-caaacaacagcaaagctggacccggacttagg Guinea pig atcag----agtcagtgacttgcctggcatcacacagtcaaaggacagcaaagctgggagcaggcccagg Malayan flying lemur attgacgctatctctgtgctggaatattgtccatgcaatccagccagca-----cctgtgcatgccc--c Tree shrew accgataccagcttcatgctgggtcactggctatg--gttcagccagcatgaggcgagtgctcccccgac Human actgatgccaactctgtgctcagttactgtccatgcaattgagccagtac----ctggtgagtgccc--c Mouse attgctgctagcttcctattggaatactatccatgcagttcagctagcac-------------------c Guinea pig gccaacagcagagctatgcagggctgaagtctgtgtgattcagcccacat-------------------a Malayan flying lemur caggtgcctgccagcaa-tca-gggtgccagaca-------------ttaggactcctgtcctcatccac Tree shrew cccatgcctgccagtgagtcc-gggtgcgagacaggtgt-ggtgcccttagga-tcctatcctcacctgc Human caggtgcctgccagcgagtca-gggtgccggacaggtgt-gctgc--atgttactcccattctcacctgc Mouse cgcttgcctaacagggactcaggagcccag---agatgt--gtgc--ttaggactccagccctcaccttc Guinea pig tg---gcctgacagcaacaca-gagcccaggacaaatgtccgtgt--atcagtctcccg-tctcacccac Malayan flying lemur tggggctagctcaccc-agctagg-----atttttatcagataacctcccctccccccagccctcctagc Tree shrew tgggaatagctcccctgaactgct-----gtttttggcagatgagctccccttctcccaggcctgctaag Human tggggccagcttccctcagctgta-----atttttgccagataatctccccttcctctatgcctgctag- Mouse agggcctggctcccctgagctgag--------ttccacagaatgctttcccctccccgcagccaaccagc Guinea pig agggcctgctgcaccgagcctgagccgtcatttttcccagacgacct--ccctcgccccagcgcactagc Malayan flying lemur agaggttctgggttcctctctcctatttctttattcgctcaggctgatggtctccaacctttagaaaacc Tree shrew agaggttctgggtttctctcttct-----tttatctgctcaggctgacaatctttacctcttagaaaata Human aaaggctctgggattctctctgctatttccttatttgctcaggctgatggtctctaacttgtagaaaaca Mouse --agtacctaagtttctcta---------------ctgtgctggtgttta-ctccaactgacaggaa--- Guinea pig -----gtctgggtttctctcggcgatttcctt-ctttctcatgatgccaatctccacctcttagaga--- Malayan flying lemur ctcca-ccaagacatcagtcatggcagtaattaactctgattgctaattagtgaggattgggctccagca Tree shrew gccgagccaagacatcagtcacggcagtaattagcattgatggctaattagtgaggattgggtccttgca Human tctcagctgagacatcagtcatggtggtaatgaactctgattgctaattagtgaggattgggctccagca Mouse -----------acattagtcacggccatgattaaccctgatagctaattagtgaggactgggctccggca Guinea pig -----------acatcagtcatggctgtaatcacctctaattgctaattagca-----tgggttcctgtg Malayan flying lemur attcattttaccaagctctgtgctccgggtcaatgaaatgagctcgtgctctggagccagacagatgtgg Tree shrew attgattttcctgagctctgtgctctgggtcagtggaatgagcatgtgcttgggagtcagacagctatgg Human atcgatttcaccgagctctgtgccccgggtccatggaatgcgcttgtgctttggagtcagacagatgtgc Mouse attgattttcc-aagctctgtgcccctggcggctgaatgaacca-gtgctttgtacttgggtggatatgg Guinea pig attgattttcctgctttctgtgctcc--actcctggagtga------gctctgctctggagtg------- Malayan flying lemur attcccaactcagttccaccatcg------atatttgtgtgac---cttgggc Tree shrew atcctcagctctgttcagcctcca------atgtttgtgtaac---cttggac Human cttctcatctcagttccaccactg------atgtttgtgtgac---cttgggc Mouse cttccggtcccagctctgccaccgaccgccctgtttacatgac---cttggac Guinea pig -----aggctcagttctgccactg------ctgtttgtgtgactaatttaaat Inserts between block 15 and 16 in window B D Mouse 734bp Alignment block 16 of 72 in window, 64671 - 64899, 229 bps B D Malayan flying lemur aggtgacttcaagtcccaga-tctcagtctcctccctgcaaaatggaaagaatgttcctccctcccatgg B D Tree shrew aagtgacttcaagtccctgaaccccaacctctttcctgtgaggtacagagatggtttctatgggccaggg B D Human aagtgatttcaagtcccaga-cctcagtcccctccctgtaaagtggagagaccattcccacagcccaggg B D Guinea pig gagtgacttccaggcctgga-tcctgctctga-ccctgtgaagggcagagac--ttcctttctcctaggg B D Mouse ====================================================================== Malayan flying lemur ctgccatggggatctcatgacatggcccccttgtccacatggcaggcaccaaatagatgtcatgtctccc Tree shrew ccgctatggggatctcatgacaagggtc--ttgtccacatgacaggtatcaattgaatgttaaggctccc Human ctgccatggggatctcatgacatagtacccttgtccatatggcaggcaccaaacagacagtacgtctctt Guinea pig ctgttcctacttcctcaggacgcagcatcctggtccccacggcaggtgccaaaatgatgtcccatgtctg Mouse ====================================================================== Malayan flying lemur cccttccccttccagtgcttaggtctt------------------cccagggtgagaata---------- Tree shrew cct---cctttccagttcttagaccttgactagat-------ctccccacggagagagta---------- Human cctct-cccttccagctcttagtctttgcctaggtcctcacacctcccagggtgagaata---------- Guinea pig cccttcccctcccaagtctcagtctttgcccagag-------tttctcagaggacaaatagaaatggaat Mouse ====================================================================== Malayan flying lemur --agtggagaattt--------ggactccctctagcc--------------------------------- Tree shrew --ggtggagactct--------gaactccatccagccgaagcacaggtgctgtaacgaaaggccctgctt Human --agtggagaattt--------gaagtccatctagca-aagtcaagaccctatgggagtacgccctcttt Guinea pig gcagaggggaactctgcagaaggagccctcaccagcc----------------------agcccct---- Mouse ====================================================================== Malayan flying lemur -------------------ctacaca-----gaggactctcac---------ct---- Tree shrew aggttggggc--------gttgcacattatcgaggacactcct------gctct---- Human ggttggtgactttgtgcaactacaca-----aagcaatcctgg---------ct---- Guinea pig -------------------ccacacagccttgtggagacttacagcgcagctccacca Mouse ========================================================== Alignment block 17 of 72 in window, 64900 - 64929, 30 bps B D Malayan flying lemur tcccag--gt---------------------aggggtag--gag-------------------------- B D Tree shrew tcttag--tt---------------------gggtggaa--aag------------ctctactgagtgga B D Human tcccag--tctgggcggtggtgggagcacaggggtggag--gaatgctagacccagctcagcccagtgaa B D Mouse tcccag--ag---------------------aggcgtggctggg-----------------------aag B D Guinea pig tcccagtcac---------------------gggagtgg--ggg-----------------------gat Malayan flying lemur ----gataa--------------------------tgcatc Tree shrew catggacaaatctct------------------tctccatc Human cttgggccagtctctcctcctccctgtgcctcatcttcacc Mouse caagggcc--------------------------------- Guinea pig gaaggacc--------------------------------- Inserts between block 17 and 18 in window B D Tree shrew 32bp B D Human 140bp Alignment block 18 of 72 in window, 64930 - 64938, 9 bps B D Malayan flying lemur ---gggctacag B D Tree shrew ---gggttacag B D Human ---gggcaacca B D Mouse caggcgtgg--- B D Guinea pig --agcgtgg--- Inserts between block 18 and 19 in window B D Tree shrew 154bp Alignment block 19 of 72 in window, 64939 - 65317, 379 bps B D Malayan flying lemur cctgactccttccaacctgtgctggt--ctcctgcaggtggacaaggagaag---caggttgctgtgaag B D Tree shrew cccagcttcttccaga-tgtgctggt--ctcttgcaggtggacaaggagaagaagcaggtgaccgtggag B D Human cctggctcctcccggcctacactggt--ctcttgcaggtggatgaggagaagaagcaggtgaccatggag B D Mouse cctaactcttcccagcctgtgacggtggctcttacaggtggacaaggagaagaagcaggtcacagtggaa B D Guinea pig cctggatcctctgagcctaccctggt--ctcctgcaggtggacaagaagaataagcaggtgacggtggag Malayan flying lemur gccggcatcctcctggctgacctgcacccacagctggacaagcatggcctggccctgtccaagtaagagc Tree shrew gctggcatccttctagctgaactgcacccacagctggacaagcatggcctagctctgtccaagtaagagc Human gctggcatcctcctggccaacctgcacccacagctggatgagcatggcctggccctgtccaggtaagagc Mouse gccggtatcctcctgactgacctgcacccacagctggacaagcatggcctggccctgtctaagtaagagt Guinea pig actggcatcctgctggctgagctgcactcgcagctggacaagcacggcctgtccctgtccaagtaagaga Malayan flying lemur ccct-ct----gccattcttgggtgggccatggctgcttg---ccaacccttgccccagcctgggctgga Tree shrew ccct-at----cgcatacctgggtgggccagggctgc-ta---ccacctcctagcctggtttcaactgga Human ccatgct----gccactcctgggtgggccaagaccacctgc--ccaccccccatccttgcct-ggctgga Mouse ccct-ccaccagccccacctggggaaggaacggcctcttctctcctctctctg----------gaccaca Guinea pig cccg-cc------------------------------------cctccctctg---------------ca Malayan flying lemur cactca-gaatctggcaggagctttcaagga----cacttcccaggtgca---ccc--cttctctgggtc Tree shrew cactcagggatctggaaagggcctgagagga----gtgcttccaggagta---ccc--cttctcgaggtc Human cactcaaggatctgtcaggagccacagagga----gcgcctcccagtgtgcacccc--tttctctgggct Mouse ctctcaagggtct-------gccattgagacccgcacacttcttggggcgcatcccctctcctcagagct Guinea pig ctcctgggaa-------------------------gcacttcttaggatgcatccc--tttctctgggct Malayan flying lemur ccctttttccccc-ttggggtgcc-tgtctccccatcccccat----------------------ggaat Tree shrew cttgctcttcct----------cc-tgtctccccatcacccatgaattcaaaggctgttgtg-tgggaat Human cctgttcttccccattgtggtgcc-tatctccccatcccccatgggttcaggggctgttgtgttgggaat Mouse ctgcctttcctac-tcatgttgccatacttctcattgccccatgagttaagag-----------gggaac Guinea pig ctgctgcccgccc-ccgaggtgcc-tatctcctatt-ccacatggatttgggg-cccttgag-tgggaat Malayan flying lemur aga-aaaaacaggccagagaggggctgagcattaaataaaaatcctgaa-caggggtgggacaaccatgg Tree shrew agacagaaacagactggagatgagctaagcattaaataacaattcaaaagggggggggggataactatga Human agaaagaaataggccagagatgagatgagcattaaataatagtctcaaa-cagaaatgggacaaccctgg Mouse agatccaagtttagcagagtt---ttaagcaatg-------gttttgaa-ccagaatcagaccattaagg Guinea pig ggaatgaaagagaccagagctgagctaagcagtaagta--catcttgaa-cgtggctgagataatcatgg Malayan flying lemur actaagtc Tree shrew atcagg-- Human attaagtc Mouse actgagtc Guinea pig attaagtc Inserts between block 19 and 20 in window B D Guinea pig 27bp Alignment block 20 of 72 in window, 65318 - 65632, 315 bps B D Malayan flying lemur attctgaa-------aacttgca----------acaaataactccaaggatacaaacacaaggatatgca B D Tree shrew -ttctgaa-------aacttgca----------aca---aaattctagggtccaaacacaaagatatgca B D Human attctgaa-------aacttgca----------acaaacaactccagggatccaaatacaagaaaatgcc B D Mouse tttccaaaaggactcaacttacacctggtaatgatatacaactacacagcccaacacataaagataggca B D Guinea pig ====================================================================== Malayan flying lemur aaataagcacccaga-gaaacaggtgagcacagtgactgagccgcatggtccc---gttgtacctaccac Tree shrew gactaagcgctcagaggaaaaaaaagaacctgacaattagaccacaggcttcc-tggcattcttctctgt Human aa-taaaccctcaga-ggaacagaagaccctgatgactgagccccagggtttcctggcatgcctatccat Mouse aaaaacacctctgga-ggggtgggagagcaaggtg---------------------gtccttcctgtgat Guinea pig ====================================================================== Malayan flying lemur agcttcccttgtgcctccgtccacatc--------tgggtcattgctcagggttaatatcaggggatttc Tree shrew ggtttcacttgtccctccattcaaagtggagggagtgagtcgttgctcagatttaatatcaggata---c Human ggcttcacttgttcctccatccaaaca---tggtgtcagcgattgctcaggtttaatatcaggggatttc Mouse ggtttt-cttgtccctccatccaaatt------catttctcattgtcca-ccttagtgctaggggc-tgc Guinea pig ====================================================================== Malayan flying lemur caccaaaacaggagcaa--tgcagccaaagaagtgaatctctaactgtgggattt--------------- Tree shrew cattcaaacaggtgcaa-gcaaagcgaaagaagtgaatct----ctgcaggacttttgagcagtagaaac Human ctttgaaacaggagcaaaacacagccaaaggagtgaatctctaactgcagaattt--------------- Mouse catcaacatagcagtcaagtgtggctaatgaggtaactctgtgact---gaattt--------------- Guinea pig ====================================================================== Malayan flying lemur -----caaccattggcaccaggtgac--aggcgttttggacattggggt-agcaatcgcttcacagctgg Tree shrew agtgacaaccattagacacag-------aggtgattagaacattggggt-agcagtttctccacaactgg Human -----caaccattagaaacaggtgacagagctgtttggagcagtgaggtgagcaatctccttgcagctgg Mouse -----tatccaggagaaagcactggc--agatgttt-gaacatgagtgt-agaaatctcactgcagctgg Guinea pig ====================================================================== Malayan flying lemur aaatcacacccgtggaagc Tree shrew aaattacactcatggaaac Human gaatcatacccatggaaac Mouse -aattaaccctgtggagtc Guinea pig =================== Inserts between block 20 and 21 in window B D Tree shrew 911bp Alignment block 21 of 72 in window, 65633 - 65638, 6 bps B D Malayan flying lemur ctgtgg B D Human ctgtag B D Mouse ctgtgg B D Tree shrew ====== B D Guinea pig ====== Inserts between block 21 and 22 in window B D Mouse 275bp Alignment block 22 of 72 in window, 65639 - 65995, 357 bps B D Malayan flying lemur ggccctgagcacttttctttcagccttacaaaaaagtaacctggatcactcaacatgttaaccaactagt B D Human ------------------ttggtcttcacgtgggggtggcctgcatgccttagc---------------t B D Mouse ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tttttttttttccccct-----attctgtttccttgttctcgtgctgcccactgg-gacttcccgttcta Human ttcttatcacaggcccttgggcatcatgactcct----------ctgcactctggaaaccctctgttctg Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ---tttcatagaacgagggctgcccag--attcatgaattgcaaatagcatccagttacatctgtaactc Human gcctctctaaaggccatggcaacgcaaacatttatagagtgtctaccacgtgcag----------gccct Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur actttgtcttttgaca---------gcactcaacccaggggtccctcctgcagggagcctgttctgattc Human gttcaggccttggagaggcaaagatgaacaaagccca--gaccccacaagcaaggagct----------- Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tctccctctcccacctcccctgcctgccgagg------ctggatgcggagctcccttgggacccactgac Human ----------------------cctagcaaggggccacatagacgagga---------------actggc Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur aagcataacatgg-----taggatcggtgtcagcagag Human aggcatcacacagagcaataggttcaatgtcagtgaag Mouse ====================================== Tree shrew ====================================== Guinea pig ====================================== Inserts between block 22 and 23 in window B D Human 46bp Alignment block 23 of 72 in window, 65996 - 66038, 43 bps B D Malayan flying lemur gggacttccttattacactgccaacactgtcctgggactctct B D Mouse =========================================== B D Human =========================================== B D Tree shrew =========================================== B D Guinea pig =========================================== Alignment block 24 of 72 in window, 66039 - 66044, 6 bps B D Malayan flying lemur ctctcc B D Tree shrew ctctcc B D Mouse ====== B D Human ====== B D Guinea pig ====== Alignment block 25 of 72 in window, 66045 - 66045, 1 bps B D Malayan flying lemur t B D Mouse = B D Human = B D Guinea pig = Alignment block 26 of 72 in window, 66046 - 66697, 652 bps B D Malayan flying lemur gatttctcagagggtcagataaacaacttggtcttggcctggtgacgtagaacttcagcaccagagacct B D Human aatgtgtgagagggtaagaataggaac---------------------agaatcccttcaggggggaccc B D Mouse ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur ccattctggtctggtctgcggagcctagtgcaggagctcagtccaaaccagtggcctcctatacattcta Human ccgggttg-------------------------------------------------------------- Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tctaacagtcccaaaagatgactgggtatt-accaaaaagaagagggatgaggaggggttccaggcagag Human ------agccccaaaagatgattaggtattaaccagcaagaggagaggag-ggaggaatctcaggcagag Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggaacacatgagccaaaacccaggagagaggaagcgtgtagggtgtgcaggtgcctgtgagcagacagtg Human ggagccgcagtaacaaggcccaggagagggacagagtgtgaggtgtgcagg-acctggaagcaaacggcg Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggacagagcccatgatcaatgacagcagaaagagacgtgttcttagtaattacgggcattagcatgttgg Human gaa-acagcccttgaccaatgacaacaggaggagacgtgttcttcttaattacgggcatcagctcctggg Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur -------------tgtcctgtgtaagctctgtgtctgtcctcccctgggga--ctgtccttcacaagtgg Human ccctgaagcattcttgcccatctaagatgtgtccctgtcctcccctaggggccctgtcctcctcaagtgg Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctgcctacacgaggcccatctgcctctccagagggaattgggatgtcccatcctttatgtctt-gagggc Human ctcctgggatgaggcccatctgcctctccaaaggcagctgggatgtcccatcctgtatgtcctagggggc Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctcctgggcccgcagctctgaggatgctgggggactgtt-ggaagaggatgggagccacacagctgagtc Human tgcctgggactgcagttccaaggatgctggggcgctgttgggaagaggaag-----------gctg---c Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur acgcatgcgctggacatgctctctgacttcaccatcacaccaaccctgtgggg-gagaatcaggacccca Human atgcggggtctggacgccgtctttggtttaaccgtcacatcagccctgtggggaaaggatgagagtctca Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur -ttacagatgaggagacagaggtctgaggcaaaggtgttacc Human cttacaggcacagaagccagaatcttacccaaagatgttata Mouse ========================================== Tree shrew ========================================== Guinea pig ========================================== Inserts between block 26 and 27 in window B D Human 487bp Alignment block 27 of 72 in window, 66698 - 67181, 484 bps B D Malayan flying lemur caaagtcacgtggtggggaggctcgcagcacctcgtgtgtcatgcaccagatggggccagatggaagtgt B D Mouse ====================================================================== B D Human ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tgctttgccccccatggatttatcaccccacaccccctgggtgacagagatgcaaaggttactcaaagcc Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur catctcttctgagcagtgagagaccctgaagtggttaatctcccaccagaaccctcaagcgagaggcagc Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ccttccttgggaaattaaccctgaattgtggttctcttccagaccaggaagttacaggaagagaacaaag Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gtggggttatagtttaacagtataagctggtaactttcagtgaaactagccagatgacattccagtaagg Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur caattaagtggtcttatcaacacaagcttgatcttagcaaacattctttctccatccggaaattttccag Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tatctttatatttcaatcagtaactagtctgtccttgggccagcaaccttgctgcgccacaaat Mouse ================================================================ Human ================================================================ Tree shrew ================================================================ Guinea pig ================================================================ Alignment block 28 of 72 in window, 67182 - 67670, 489 bps B D Malayan flying lemur ctttatcttac---------------aacagaggctttgtagcctgaggaaaatttccagtcctcc-aca B D Human cctcattttacccagctcctgttcaaaatggagtcgttctgg-----------ttcacacgcctctgaca B D Mouse ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur aagtcgatatttgaaactgcaaggctttggaaaaccaggccctgtaaagtacatttgctttacagtatat Human aagtca-----tgcagctggaaggctccg-------agacttt-----gtgtgtttggtgc--------- Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tccacacagaagggccattgctaagggcaggcagcagcacagagaagaccccagcccca-gagcagacag Human ------caggcggggca-----------gggcaacatgatggtgaag--cccagctctaggagcagtcgg Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur acag-gtgctcttctgcttcacaatcgtcttagctggtgttcaggttccttgacccctcagggctgcaga Human cctgagcgtgagcctgcctctaccttgcaccagctgttaggcaagtgccttg-tgcctcggggccacagc Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gtccccatctagaaaatgggtctgtaaaacaggggtatttagaggagcggatgagttcaagatgcctcat Human atcctgccttagaaaacaggtctctaaaataggggtattcagagg-gctggtgagttagagatgcccctt Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gtagtatgtgctcaataaacattatctctcttcattttcttggctctgttaaggtgtggctcca-ggact Human gtagtgtg-gttcagtaaacgtcagcctccttcatt---ctggctttgtcaaggcctcgcttcagggact Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctgaaaaggggacctgtcccctcctc-----atctccaccctgtt-gaggccaaagtct--tccttcctt Human ccggacatgg--cctttctcctccccttgttatctccactctctcagggaccaaagtctaattcttcctt Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cccggtgggtctctctcccgaggagc Human ccaattgactccttttcactgaaagc Mouse ========================== Tree shrew ========================== Guinea pig ========================== Inserts between block 28 and 29 in window B D Human 1374bp Alignment block 29 of 72 in window, 67671 - 67722, 52 bps B D Malayan flying lemur ggatgagttcaagatgcctcatgtagtatgtgctcaataaacattatctctc B D Mouse ==================================================== B D Human ==================================================== B D Tree shrew ==================================================== B D Guinea pig ==================================================== Alignment block 30 of 72 in window, 67723 - 67912, 190 bps B D Malayan flying lemur ttcattttcttggctctgtcaaggtgtggctccaggactctgaaaaggg--gacctgtctcctcctcatc B D Tree shrew tttactttccaatgtctatcaatgcctcactccatgattctggtcatggcctgcctctccccttgttatc B D Mouse ====================================================================== B D Human ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tccaccctgttgaggccaaagtcttccttccttcccggtgggtctctctccccaggtaccttgctt---- Tree shrew tccatcttttcagggcc------------------cagaagccctccctccctaggggccttgcttttat Mouse ====================================================================== Human ====================================================================== Guinea pig ====================================================================== Malayan flying lemur -catctactttaacaaggttctaagcatatttccatatcactcttcagtctctgtat Tree shrew ccacttcttttaacatggtccttagcttatttccaagctactgtgtagtccccctat Mouse ========================================================= Human ========================================================= Guinea pig ========================================================= Inserts between block 30 and 31 in window B D Tree shrew 2bp Alignment block 31 of 72 in window, 67913 - 68321, 409 bps B D Malayan flying lemur tagtctgtttctgttgcttataacaaaatatctgaaactgggtgatttgtaagaaaacagtttcagaggc B D Mouse ====================================================================== B D Human ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tgggaagtccaaagtccaagggacacatctggtgagggtcttctttggtggtggctttatggcagtgcag Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gggtctcacatggtagaaagttgtggagcagaaagagactcgcctctcacatgctccccttttaaagccc Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tcagagccatgcctatgaccaccattgttaatccattcactacagcagggtcctgcaacctaatcacccc Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ttcaaggctccacctttcagtgaccataataggatttcccactctcttaacagtcacaatggggattgag Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cttctaatatatggactttgggggacacaattcaatcaacccacagcaggttcatgcac Mouse =========================================================== Human =========================================================== Tree shrew =========================================================== Guinea pig =========================================================== Alignment block 32 of 72 in window, 68322 - 68469, 148 bps B D Malayan flying lemur ttcctggagatggaaagctatgtgatgatttgat-ggacggtctttgt-tggtatttgggtcattctcac B D Tree shrew ttcatggagaagagacgtcacattatggtgcgattagtcagcctctttctcacatgtggatcctttatat B D Mouse ====================================================================== B D Human ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur ttgcactgttg----taaacagcactatgactaacatcttcatgtgtgcacctttccgtgtgccagagga Tree shrew ttt-----ttgccattaagaaatgctgtgatgaacatcttcatgcacgagtgcttctgcatgctgcagca Mouse ====================================================================== Human ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gctccctagggccc Tree shrew tttctcaagggcag Mouse ============== Human ============== Guinea pig ============== Alignment block 33 of 72 in window, 68470 - 68639, 170 bps B D Malayan flying lemur agtctctgggatcctcctccaacattctggtattttcagaaggggcaatgtcaccaactaacccaaccga B D Tree shrew aatttctatgatccttt---aacatccaggtatttttggaagagacaatattgtcaactaa-ccaacaaa B D Human aatatctgagatcttcttttcacattctggcattttcagaagaggcattatcacccactaaccccaccaa B D Mouse ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tgtggataacgagacctgagaagacaggaaggcaag-gggtgggtgggggaaggtgagaaaagactggag Tree shrew tgtggccaaagagacaagaataggcaggaaggt----gagtgggtggg-------aagggaaggct--ag Human catggacaaatagatgagagtagccaggagggtgagtgggtgggtgagggaaggctagaagaggcttgtg Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctcctttccttctcttcctgttgtgccggcg Tree shrew tttctttcatcctctttctgttctgctaggg Human tgtccttcaccctctccccattcagccaggg Mouse =============================== Guinea pig =============================== Inserts between block 33 and 34 in window B D Tree shrew 224bp Alignment block 34 of 72 in window, 68640 - 68662, 23 bps B D Malayan flying lemur tagct-caggcctcctctcctctc B D Tree shrew tagca-aatacttgtttgcttctc B D Human cagcaccaggtctcatcttctctc B D Mouse ======================== B D Guinea pig ======================== Inserts between block 34 and 35 in window B D Human 270bp Alignment block 35 of 72 in window, 68663 - 68697, 35 bps B D Malayan flying lemur cattaag----ctacgactgggatgtctcagagaaggct B D Tree shrew ctttaagtaaacaaggacttggatgtctcagagaaatct B D Human ctttaag----ttagggctgagatgactcagaaagtt-- B D Mouse ======================================= B D Guinea pig ======================================= Inserts between block 35 and 36 in window B D Tree shrew 258bp Alignment block 36 of 72 in window, 68698 - 68842, 145 bps B D Malayan flying lemur cctgaggactagggtttttt-acctcct----cactctccaccctcgaccctgagatccagacatgtcat B D Tree shrew cctgagaagtaagacttttg-aagtcctgatctacctttcattcctgaccctaagatccaggcatgtctt B D Human cctgggaagtaagattttttaaactcctgatccgctcttcgtccttgaccttgagatc--ggcaggtctt B D Mouse ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tctgatccctgcc------ctacacgcctcctgcaggg----------cactgctctcctttaggggtct Tree shrew tttaatttctgcc----tgcaccatgcctgccactggggaaggtggtgtactgcgcccccttagaggtct Human tctaattcctgcccccatggtgcacgcctgccaaggga----------tacaggattcctttcatgatct Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggc---cctaagcacacagaagcttcccc Tree shrew ggttctcctgtgtacacacaagcctcttc Human tgtcctcctgtgcacatggaagcctccca Mouse ============================= Guinea pig ============================= Alignment block 37 of 72 in window, 68843 - 69057, 215 bps B D Malayan flying lemur ttcttccttctagggcctgggacaccaggctgagggacaggggctccacccaggaggccccaggagcttc B D Tree shrew tcatttattctagggcctggaacaccaggccaagggatatgcactttgtcttggaggtcccaggaactcc B D Human ttattccttctagggcctggaacgccaggctgagggatgaggcctttctcctggag----------cccc B D Mouse ttcagcattctggg--cttgaaccccagtctaagaagcttag-ctttctcctagggctctgaggaagctg B D Guinea pig ====================================================================== Malayan flying lemur ggaaggtttctgagcagtggaggtgatggggcctcccctcctcctccttcccttgcagctcagggacgtt Tree shrew taaat-tttctgagtagaagagatggcaggactcctcttacttcccctt-------ggttcagggagatt Human tgaaggtttctgagcaggagaggtgacagggc--ctcctcctcctcctt--------------------t Mouse tgtaggtttcccagtaggacaagtttctg---ctctctctcccctccttttcttctag------------ Guinea pig ====================================================================== Malayan flying lemur cccacctgttcagacctttctggaatatttatttgtgcgacttgaaccaggtcagttccacagagacttt Tree shrew ctcacctcctcagacctttctgggatgttcatttgtgccatttgaacctggtcagttccatgagaatttt Human ctcatctccccaaacctttctgggatgtttatttgtgagatctgaaccaggctggttccatgaggatgtt Mouse ctcacctacacagacc-tgcggggatatttatttgtgtgtttagaaccaggacagtaccatgag------ Guinea pig ====================================================================== Malayan flying lemur ----------------------------------------------------gcagg Tree shrew tttttttttgagaggtttttgctatagggcgtgtgcgctcgccagacagacagcaag Human ----------------------------------------------------gcagg Mouse --------------------------------------------------------- Guinea pig ========================================================= Inserts between block 37 and 38 in window B D Tree shrew 221bp Alignment block 38 of 72 in window, 69058 - 69673, 616 bps B D Malayan flying lemur ccttgatgggctgggtac---agaggagcattagcaggagcatcttggcctttggtaggcagagatg--- B D Tree shrew ctttgataagctgagtaa---agacacatgttagcagtagcat-ttggccttttgttggtggagaaga-- B D Human ccttggtaggctgggtacctaagagaagtcttagcaggagaattttggcctttggtttgtggagagggta B D Mouse tcttagtaggttgggagc---agaagagtctcagccagaccat-gtggct----gtgcttggagaaga-- B D Guinea pig ====================================================================== Malayan flying lemur ----------tcggatggaggatggag--------gaaaggggtattg-tgggctgcagaga-ccccgca Tree shrew --tactgttttcagaaggaggatgtag--------gaaagaagcattg-cagtctacagaca-ccccatg Human tttattgttggcagatggaggttggaggaaaggaagaaaggggtgttg-tgggctgcagaggcccccaga Mouse -----tgccttcgggagatgggaaggg--------gagaggggtgctgttaagttgtagaga-cctcaaa Guinea pig ====================================================================== Malayan flying lemur gctggg-caggcaggcctcctctcagacctgcactgtgt-tcccccagcacatctgacaggtcactgaga Tree shrew gctgggacacccaagtctcct---agac-tggactgt---ttccctgcctcatctgacaggccg-taaga Human gccagg-caggcaggcctcccctcagccctgaaccatgtcgccactgggtcatctaacaggccacttaga Mouse gattaaacatataggcttccctgcaaac-tggcccatgtcccaaccagctaatctgatggtccatggaga Guinea pig ====================================================================== Malayan flying lemur tgaggcaactgaggcccagagaggagaa-gggccagccaagtaacat-agcgaggtcattgtagactgat Tree shrew caaggaaacagaagcctggagagaagagctggtcagcca-----cac-actgaggtcgtggtgga----t Human tgaggaaactgagaccccgagagaagac-aggcaggccacatcacacaagctaagtcatagcaga----t Mouse tcaggaaacagggaccaagagacat----aggctgatca-----ca--agctgggccatcaaagg----- Guinea pig ====================================================================== Malayan flying lemur tggggatgaggacccaggtaggagatgaataaactcttctgctctgagggccctt----gcacctcagtc Tree shrew ttgggcagaggaccca--caggaaatga-tcaatatttctgctc----------------catctgcg-- Human ttgggatgagaacccagacagca-ctgaataaacttttctgccctgaggggcctc----gcacctcaatc Mouse taaaggggaattctcagacagaaggagaac-----cttttgcccagaggagcatctatgtcatctttg-- Guinea pig ====================================================================== Malayan flying lemur c-----------aggtgggcctaccgtcctaggaa-gcctaactcatctcttgtgtccctcttgctccct Tree shrew ----------------gtgcccgttgtcctaatgg------------ctcttgtgtccctcttgctccct Human tgatgtgcctgggagtgtgcctgctgccccgggaa-gcctaactggtctcttgtgtcctttttgct---t Mouse ----------------gctcccattgtcctgagaaaacctaactgatctgtgacgtccctcttgtt-cct Guinea pig ====================================================================== Malayan flying lemur cctgctgagccaagcctgggagcagtgtcagaggtgatggcagttggtgtcactgaatccagaacacaca Tree shrew cctgctgagcca-gcctgggagccgtgtcagatgtgaccgcagcgggtgtcatcgggtccggaacacaca Human cttgctgagcccagcctgggcatagtggtagatgtgactgcagctggcgtcgttgggtctggaatgcaaa Mouse cctgctgagcccagtctgggagccgtgtctgatgtgacggttggtggcgtcattgggtctggaacacata Guinea pig ====================================================================== Malayan flying lemur acatggggatcaggcacagcatcccggccacccaggtgagtccacctgcttccctgtactccactgactt Tree shrew acacggggatcaaacacggcat-ctggccacgcatgtgagtccac------------------ctgactg Human acatgggaatcaggcctggcaccccggccagccaggtgagtccac------------------ctgcttc Mouse acaccgggatcaagcacggtatcctggccacccaggtgagt-cgc------------------ctgtgtc Guinea pig ====================================================================== Malayan flying lemur ccagggggagtggaggttagagtgagct-cctcacctggctcctgggagatcaggtgctcaacggcaagg Tree shrew ccagtgagcagagggctttaag-gagctgcagtacctgggcagtggggggctagttgctccatggcaa-t Human cc------------------------ct------------------------------------gcag-t Mouse c-------------------------at------------------------------------gcag-g Guinea pig ====================================================================== Malayan flying lemur gttggcttggctctgggtgggctttgagcccag Tree shrew gcaggctcggcactgcgtgggtctccagcccag Human gctggctcagctctgtgggggcctcatacccag Mouse gtaggtacagctccataaaggcctcagg----- Guinea pig ================================= Inserts between block 38 and 39 in window B D Tree shrew 352bp Alignment block 39 of 72 in window, 69674 - 70264, 591 bps B D Malayan flying lemur cccaggt-gttccctctgaca-cgactcaacaggtggcctccagcaatagcatttccttctctaagcccc B D Human cccagctggccccctttggcagagatgcaacaggtgccctccaggtatgtcactgccttctctgg----- B D Mouse ------------------------------cagatgccccccagaagtaccacttcttcccctaaacg-- B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur ctctgtccagacaggcacagtg-gcacgggagccgcatgcatgtcgatgccctaacagctaca-agtgcc Human -------ctgacagtcacgatgaggaagggaccctgctgcatgtcggtgctctgacagttgcacagtgcc Mouse -------ttatcaggcctgaag-------gagccccaggtttatcagcgct----------ca-ag---- Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cccccacctccgcctctcggaagcctcaatgccaccacgtgggaagaggcaggca------------agg Human ctcccaccttcgtctcttaggagcttcactgccaccctgtgggaagggatgggcagggatggggtgcagg Mouse ---ccatccccacctctgcacatcctcaaaggcagcacaaggcaaggggcaggc-------------agg Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ccaggggtgccgtccctgt-------------------------ggggatggggccatccaggttagcaa Human gaaggggtgccatctccactgaagatctgagccagagctgtgcaggggatggggctgtccaggttagcag Mouse gcaggggcaataactccttggaagttataatcaggagccagggagggggtgggactacc--------cta Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gtgggtggaggggccgggacaggcgccggggctaccttaggcagagcccagtacaggtgggcctgggatc Human gtgcagggaggggtcaggatag---------------------gagcccagtgcttgtggacctggaacc Mouse ggggaggcagagcccgggggtg---------------------ggg---------ggtgggaataggggc Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur c--------------ccacctgagctgcactgaaaa-catttcttaaacttc-----atgagagtccagt Human c--------------ctaccttatagtcattaaaaagcatttcttacacttc-----acaagagacca-t Mouse catctgtggcagagtctacctgtccttcaacaaaaaccacatcttaaacttcattcgatgagaatccagt Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ttggggaactggttaagagcac-agctttgggagtcggacctgggtttggaacctggctctgctagtcac Human ttggggaactggttaagagcac-aggtctgggactcagccctgggttcaaagcctggctccaccactcac Mouse ttggggaactgtttaagaatactaactcggagactcaagcctgaa-tcgtaacctatatc--ccgctccc Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tgggtatgtagacttaggtaagct-gtttatcttccacggaaatctctgt--aaaatcttcacctaaagt Human tgggtgtggaatgcacatttggtt-gcttagcttctctggacatccctgtaaaaaagcatcacccccaat Mouse t-ggtatgtgcacacctgtagactcccttagcttctgggtgcattgctgtcaaaaatcttcagctaaaat Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gaggagcataa-cctcaactca-tgaagagtaaagg-----ggtccgtgcatgttacacgcgtggccagc Human ggggagagcaatcctcaactcgttgaagaggaactt-----agatagcacatgttacatgtgtggccaac Mouse gaagaa------tttcagctca----agagttaaggtcacaagttagcactcattaaatg-gtgtctggc Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cacgcaacag-ccagagggtgcctgcgtcagggg Human cagaggacaattcagcggatgcctgtgtcaggag Mouse cacaaggcaattcagagg-caccttcatcaggag Tree shrew ================================== Guinea pig ================================== Inserts between block 39 and 40 in window B D Human 32bp Alignment block 40 of 72 in window, 70265 - 70270, 6 bps B D Malayan flying lemur cggcct B D Tree shrew cagtat B D Human caatat B D Mouse cagcct B D Guinea pig ====== Inserts between block 40 and 41 in window B D Mouse 116bp Alignment block 41 of 72 in window, 70271 - 70310, 40 bps B D Malayan flying lemur ttggaggggcttctccagggactaggctgggccgcaaggg--------------- B D Tree shrew ttagaggggctttcttatgaaccaggctgggcttccatgg--------------- B D Human taggaggggcttcctctctg-ccaggctgggcctccctggagcaggctgctgggg B D Mouse ======================================================= B D Guinea pig ======================================================= Inserts between block 41 and 42 in window B D Tree shrew 300bp Alignment block 42 of 72 in window, 70311 - 70666, 356 bps B D Malayan flying lemur tgtctgcacagagactggctgccc-catgttgagagggagtggg---cccctgtgc-----cagggccgc B D Human tgcttg--cagaggctggctgctcatttgtcggagacgtacaagacactcctgtgctggtgcagtggtgc B D Mouse ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur acctgcagcttaggctgtgctctctgtcgcccacgcagtcccatccatgctgg---------------gg Human acacac----tcagctgtgctttctttctcctgtatgagcccatttgcactaggggccatgtggctttgg Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tcaccacagcatcgtggctgtatgcaggggattaagctttcaatccagctccaccatcgtaatctgtgtg Human cccctggagcatcatggctaagtgctggg------------------gctccaccactattgtctgtgta Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur acatggagcgagtccctttacctttgcctgcctcagtttgctcacctgaaagatgggaatgattatgata Human acctggggcaggtctctttacctctggctacctcagtttgcttacctggaaaataggaatgctcatgata Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gcaacgcatgtgaggtgcagggaagaatgtacacagttagtgctcaataaatgtctgtgatggattttgc Human gccatgcatgtgagggacttagaagagtgtatacagttagtgcccaataagtgtttatgatgg-ttttgc Mouse ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ttgtaagatgaggccctttccagagcccac Human ttataagacaagcccttttccagagcccac Mouse ============================== Tree shrew ============================== Guinea pig ============================== Alignment block 43 of 72 in window, 70667 - 70842, 176 bps B D Malayan flying lemur actctgtgct---gttgtagaagcttcagcactgccaggggttggaccacgtggatcacctaagtaccct B D Tree shrew actctgtgctcccaccgtggaagcttcagcactgctgaagactggaccacagggatcacctggagtttat B D Human acttggtgct---gacttagaagcttcagcattgccaggggttagaccacatgggtcatctaagtttcct B D Mouse ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur cccaactagcca----------------cccaagcgatggct----------------ccaccttctgc- Tree shrew cccacctaacca----------------tacaagtgatggct----------------ctaccttctgcc Human ctcgactacacaaatttcctcttggttctgcatacgtttcctctcaactaagcataccctgccttctcca Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur --------------------------agcagacactg---agcgtgactcctgggagccgggtcccatgt Tree shrew atggttc---tgaagacaggcagctgatcaaacacattacagtgtaactcctgggagctgggttccttgt Human ggggttctgatgaaggcaagcagccaagcaaacactg-tctgactgacttctaggagtttgaccccaggt Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gctccaggctcagag----------acccaaagaaaatagc Tree shrew agttcaggctcagagca--------acacaaaacaaacaat Human agtccaggctcagagcagcactgagaccaaaagcaaacagc Mouse ========================================= Guinea pig ========================================= Inserts between block 43 and 44 in window B D Human 342bp Alignment block 44 of 72 in window, 70843 - 70877, 35 bps B D Malayan flying lemur cacagagccatttctaaggaatgcactttgttttt B D Tree shrew ctaaaagccatttctatgaaacata---------- B D Mouse =================================== B D Human =================================== B D Guinea pig =================================== Alignment block 45 of 72 in window, 70878 - 71265, 388 bps B D Malayan flying lemur ------tttatttgtactt-ttaaactccatgatgggacacctaattcacagtgactatcccttaaaact B D Tree shrew ------------------------acttcacaaaggtaagcctaattcacagtcactactccttaaa-ct B D Human tttgtttttatttgtatttcttgaattctgtgaagggaaacctaattcccagtgactgctccttaaaact B D Mouse ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur cactgtgttttctcatcagcatcgtatgcacactct---tgctacttggccttctcctgctccctgtttt Tree shrew cactttgctttctcatcagcaccatattcccattttggttgctatttgtcaatatgctcctccctctttt Human cactctgctttctcttgggcatcacatacacaccctcgttgctccttgcccttctcctcctccctctttt Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur cactgcaaaagcctcaaataaccaacaggccagatgggggc-tgctgaagggtga-----agcccaggaa Tree shrew caccacgaagtcctcaaagaaccaccaggcaatagtaggacattctgcaggtggggcatgagccaggaaa Human catcacaaaatcctcaaaaaatcaccaggcaagacgggagcatctgaggggatgg-----ggctgcggaa Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggggaaagac--aggccattg-tgtccttcatttttgaccccgcccctagttaagtggctttgcagcaag Tree shrew ggggaaagactgaaaacattgatgcaaatcatttttgacccctcccataggccagaggctttgcacaaaa Human ggggaaggactgaggccattcgcatccatcattcttgcgccctccc--aggtaagaggctttgcagcaaa Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur gcata-gagagat-tgtgcgccctgatttgcaggtacctggagccctttgtggacattgtcattttc--- Tree shrew gcacatgaggatt-tgttggacctgacattcaggttcttgaggccctccatggacataatggttatcaca Human gcata-gagggatgtgtgggtcctgat-------tccccagagcccagcatggacattctcatttcc--- Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ttcttgaggctgg-----gttcacaa---aacagtccagtggtgac------------atgat-----ag Tree shrew cccaaggaatttg-----ctgcccaagagaacagcaaactggtaactgggagtggagaacaat------g Human tcctcaaagctgggttcactgcccga---gggagcccagtggtaactgagggtgaaggatgacatgagag Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ctgccctgctcctca---gt Tree shrew ttgagacactctccaagtgt Human ccacccccttcctcaagatt Mouse ==================== Guinea pig ==================== Alignment block 46 of 72 in window, 71266 - 71347, 82 bps B D Malayan flying lemur tgggcccagtcctagtccactaaccaggaattatgtcaagctggttgcctgggatttttacaaaatgatc B D Tree shrew tggcccctgttctggtctataatccagga-ctatgtcatgctggttgctttgg-tttctat--------- B D Human tggccccagtcctagtccactatccaggacttatgtcaaatcggttgcctcag-tttctacaaaatgatc B D Mouse tgagcccagctct-ttccaccatctaggactggtgtcaagatgatcatgtcag-ttgctacacactggtc B D Guinea pig ====================================================================== Malayan flying lemur agcagagtatga Tree shrew -gcagaatatga Human agcaaagtatga Mouse gtcaggggataa Guinea pig ============ Inserts between block 46 and 47 in window B D Human 181bp Alignment block 47 of 72 in window, 71348 - 71403, 56 bps B D Malayan flying lemur caataattctgagaggtcacatatcaagatgcacacaagattcacaggccacttct B D Tree shrew aaataatcctgagtggccacagatcaaaatgcacatgggatatactagccatttct B D Mouse aactaac--------atcacccataaaaatgcacataggatttattggttactttt B D Human ======================================================== B D Guinea pig ======================================================== Alignment block 48 of 72 in window, 71404 - 71441, 38 bps B D Malayan flying lemur cttaggaggctcagctgag---------caggcctgggaac-cagtgg B D Tree shrew cttaggaagcccagctgag---------caagcctaggaac-ca---- B D Human ctcgggagcctgaggcaggagaatcgcttgaacctgggaga-cagtgg B D Mouse ctttggaagccccattgag---------caggtctggaaatgcagggg B D Guinea pig ================================================ Inserts between block 48 and 49 in window B D Human 214bp Alignment block 49 of 72 in window, 71442 - 71500, 59 bps B D Malayan flying lemur gacaagcagctattttattttacacattataccggtggcagcca------------gcaaggggcggggg B D Tree shrew ----------------attccacacattccaccaatggcagaga------------acgaggggaagaag B D Mouse ----agggcttattctgtgttaca-gccatgcagatggcaattatattggctatttgtgtgggggggggg B D Human ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur c Tree shrew a Mouse c Human = Guinea pig = Inserts between block 49 and 50 in window B D Mouse 628bp Alignment block 50 of 72 in window, 71501 - 71551, 51 bps B D Malayan flying lemur ttgacatctgtcgtgtctaccgtgcagcaggcaggcagctgcgtgctcagc B D Tree shrew ctaacacgtttaatatctattatccaccaggcagttagtcgcatgcttggt B D Mouse =================================================== B D Human =================================================== B D Guinea pig =================================================== Alignment block 51 of 72 in window, 71552 - 71625, 74 bps B D Malayan flying lemur atattctcccattagatc-tcaccaca--cctctgagatattatta-ctattatcccaatttcacagaca B D Tree shrew atattctactactcggtcctcactaaaaccctctgagatagtttta----tcatcccaattttacaggta B D Human atattccctcattttatcctcacctca----------atagttataactattatctccattttacaaacg B D Mouse ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur --gaaacaga Tree shrew aggaaatgca Human aggaaac--- Mouse ========== Guinea pig ========== Alignment block 52 of 72 in window, 71626 - 71666, 41 bps B D Malayan flying lemur gaggctgaggaacg-tgcccaaggtcacacagctagtaaata B D Tree shrew gaggctgaatagca-tggagaaggtcacataactcaaacata B D Human -aggctgaataaca-cacccgaggtcatacagctagcaaaga B D Mouse gaggcagaggatcagccgtcaaggtcacgggagcagtcaatg B D Guinea pig ========================================== Alignment block 53 of 72 in window, 71667 - 71952, 286 bps B D Malayan flying lemur cagtgcccaccctttattg--tttcctggat-cctgctggagtgtttcacaggccagctctcattcactg B D Tree shrew tagagcccaccctctattaaaggttcttgat-cctgttg---tgtttcacaggccagctctcattcagtg B D Human cagtgcctgttgcgcattg--gtttctggat-cctgtggaagtgttttgcaggccagctctcatttgctt B D Mouse cagagcccacccttcacag--gcctctagatgccta-cgaagcatctcacaggcaagctagcttccaagg B D Guinea pig cagtg-ccacccttcccgg--gctcc---aggcctagcaagatgcctcaca-gccggctctcactcactg Malayan flying lemur ctctggatcttacacaaaatttagtttttacaggaatcattctgatgccctcactcccac------agat Tree shrew tcctggatcttaggcaaaacccagtctttgtaaaaatcattgtgatgtgctccctcccac------agat Human ccctggatcttagacaaaagctagcttttgtaaaactcattctgatgccctcaccc-------------t Mouse ctctgaatctccggcagggtccaggcttc-----aaccatggagtcgccccctctcctctcacctcagcc Guinea pig ctcctgg-cccagacagagtccggctgtcttagaaattgctgtgacagcctcactccctc-------gca Malayan flying lemur ggtcacca--tgccccatttctgccagatcctcctctctggtctctgttcactgttaatcagaattagtt Tree shrew ggccacca--tgccccatttctgccaacttctcctctctggtctttggtcactgttaatcagaattagtt Human gctccccaggtgccccatttctgccaatttcctatctctggtctttgctcactgttaatgagaattagtt Mouse ggccacag--tgacctgtttctgtcag------ctctctggt-------cactgttaatcaggattagtt Guinea pig ggccacca--ag-ccattttctgccagcttctcctctctcgtctccgc-caacgttaatgagaatttgtt Malayan flying lemur cagctttatctgttctctcaccctgag-caccagccaccaaccacacatgtcaaaagcaatttccatcca Tree shrew ccactttatctgttctctctccctgagcccccagtcaccaactacacatgtcaagagcaatttccatcca Human cagctttatgtgttctctcaccccaagctcctggccaccaactgcacatgtcaaaagcaatttccatcaa Mouse cagctggagctaccct-ctctcctgagcaaccaaccaccaactgcccgtgtcagaagcaatttccatcca Guinea pig ccgctggagctgctctgccaccctgcgc-tccttccgccagctccgcaagtcagaagcaatttccctcca Malayan flying lemur aattagcaggtagcggca Tree shrew aattagcaggtagtggag Human aattagcaggtagcggag Mouse aattagcaggtagcagca Guinea pig ga-tagcatgt-gtggca Inserts between block 53 and 54 in window B D Mouse 3bp B D Guinea pig 562bp Alignment block 54 of 72 in window, 71953 - 72143, 191 bps B D Malayan flying lemur tgtggagaagttacttaagcagc--------------------------------------------aat B D Tree shrew tgtggagaag-tacttcaacagc--------------------------------------------aac B D Human tgtgaag----tgcttaaacagc--------------------------------------------gtc B D Mouse cacagagaag-gtcctcagcagctgagagagagagagagagagagagagagagagagagagagagagaga B D Guinea pig ====================================================================== Malayan flying lemur gaaagaggtttcctctggaattggggctgagggggaggacgctgca-ttaatcatcagtttccaatggag Tree shrew gaaagaggttcctctggaaacctttgctaagggcaaagatgcagaagttcatcaccagtttcctactgcg Human aagagaggtttcctctgga---gatgccagggg--aaggtgtagaagtcagtcatcagatttccactggg Mouse gagagagaacccttctgga------------agtagggaccatggagacctccatcagtttgcagccgag Guinea pig ====================================================================== Malayan flying lemur cctcctagtctttgcagaaacccaaaggctcctgcttgggtgaggctgagtaggggaatcaattc-ctca Tree shrew catcctaatctttgtagaaacccaaagtttctaggttggatatggccaaggaggagagtctagtt-cttc Human caccctggtctttgcagaaacccaaagacatctggctgggtgtggctgaataggaggatctagtt-ccga Mouse cgccttaatgctctcagaaacac-tatatttctggttagatgaggctagccgagaggatgtatttcctgg Guinea pig ====================================================================== Malayan flying lemur gggtag-tgggtccctgaaagaggggaa Tree shrew caggag-tgagttctcaaatg------- Human aggtggatgggcacgtggatgaggggag Mouse gggtag-agtgtccctattgaagaggaa Guinea pig ============================ Inserts between block 54 and 55 in window B D Mouse 112bp Alignment block 55 of 72 in window, 72144 - 72299, 156 bps B D Malayan flying lemur agacccagcttccctgacatgttgcccaggagg---agcaacaggcagagacaggctgcggggccctggc B D Tree shrew agactcagtttggctcacatatggcccaggagagctgacagcaggcagagagaatctgcagggcctggct B D Human gga--cagcttggccaacacattgcccaggaaa---agcaataggcagagaagtgcc-tgggaccctggc B D Mouse ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur tctggaccacgtgtcgggacagctgggccggcccaaccccagatgtgcacacacacagtctccctccctc Tree shrew cccaagccaggtgatagaacaccaggtctggaccatcctcacatgcatgcatg--------tcctcactt Human tc--------------------ctgggctggcctgaccccagatgcacacaca--------tcctcattt Mouse ====================================================================== Guinea pig ====================================================================== Malayan flying lemur tgccctcccgagcaccttc Tree shrew tactttcccccacaccttc Human tgtcttcccaaggcccttc Mouse =================== Guinea pig =================== Inserts between block 55 and 56 in window B D Human 18bp Alignment block 56 of 72 in window, 72300 - 72301, 2 bps B D Malayan flying lemur ac B D Tree shrew ac B D Mouse == B D Human == B D Guinea pig == Inserts between block 56 and 57 in window B D Tree shrew 119bp Alignment block 57 of 72 in window, 72302 - 72730, 429 bps B D Malayan flying lemur ggggggggggggggggnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn B D Mouse ====================================================================== B D Human ====================================================================== B D Tree shrew ====================================================================== B D Guinea pig ====================================================================== Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnngggggggggggggggg Mouse ====================================================================== Human ====================================================================== Tree shrew ====================================================================== Guinea pig ====================================================================== Malayan flying lemur ggggggggg Mouse ========= Human ========= Tree shrew ========= Guinea pig ========= Alignment block 58 of 72 in window, 72731 - 72746, 16 bps B D Malayan flying lemur ctttgcagcccagtct B D Human ccttgaagcctagtct B D Mouse ================ B D Tree shrew ================ B D Guinea pig ================ Alignment block 59 of 72 in window, 72747 - 72797, 51 bps B D Malayan flying lemur c-tctcagagctccgccaggcagagaaagc-tcgctgcatcctgactgtgagg B D Human cctcttagagctgccctgggcagaggaggccttgctgcatcctgactgtgagg B D Mouse -ccctcaagccatctccaggcagaggaggc-taactgcttcttgactgtgagg B D Tree shrew ===================================================== B D Guinea pig ===================================================== Inserts between block 59 and 60 in window B D Mouse 38bp Alignment block 60 of 72 in window, 72798 - 72801, 4 bps B D Malayan flying lemur ccca B D Tree shrew cttg B D Human ccca B D Mouse ccca B D Guinea pig ==== Inserts between block 60 and 61 in window B D Human 5bp Alignment block 61 of 72 in window, 72802 - 72846, 45 bps B D Malayan flying lemur tgcaatg----gtgggc-----ccccctctgctgggggctgctgcc-tggacatg B D Tree shrew tgcgatg----atgccc-----catcctctcgtgagggctgatgcc-ca------ B D Mouse tgtgatgtcacatgatcatggactctctctgtggagagctgataccatg------ B D Human ======================================================= B D Guinea pig ======================================================= Alignment block 62 of 72 in window, 72847 - 73135, 289 bps B D Malayan flying lemur gccttgctttccccactcccc--tttttctctcccccgagactgagaccc-----------ccctcccag B D Tree shrew -----------cccattcatc--tttgtctctcctgtgagactgagagcc-----------ctcagcttg B D Mouse ------gttt-tcctctcacccattcctccccaccccacccccaattcccagaatg-----ccctctaag B D Guinea pig gccctgcctt-tcctctctcc--tttctctctcctccaacactgagccccactgtggccatgcctctagg B D Human ====================================================================== Malayan flying lemur tg-ccacagtagacccggctggg-aagtcccct--atggccagataatggtggtcttccaggaataggct Tree shrew tg---acagtagacctagctagccaagtctcaa--gtggccagatgatggtagatttctgggagtaggtg Mouse tagtagcagtagacttggctagg-aagcagtgtgactggcca------tgttgacccccaggggtagatg Guinea pig ggattccag------tggccagg-ggctaggat---------------------cctctggggatgggtg Human ====================================================================== Malayan flying lemur gtccctg--gcctccctccagaggaca--cggggaagtgatggcgatggccacgggcctc-tgatgtgtg Tree shrew ataccta--gcctcactct-gaggacaaatggggaatgaagggcaatggctgtgggtattatgaggtgtg Mouse ctatcta--gcctctgtcctaaggacaagccagaaagtg-tggtgataactgagcgggctctaaagtgtg Guinea pig ctgcccactaccttcttgctgagccctgccctg--agtg-cagcg------------------------- Human ====================================================================== Malayan flying lemur actcctctcccactgccaggtgatagcactgaccctgctgacggccgacagggtcatcctggagtgctcc Tree shrew gttcttctac-actgccaggtggtggcgttgaccctgctgacagccagcggaaacattctggagtgctcg Mouse acacctctcccactgccaggtggtggccctgaccctgatgaaggctgatggaacagttctggaatgttct Guinea pig -------tccctctgccaggtggtggcactgacactgatgacagctgatggggtcattctggagtgctcc Human ====================================================================== Malayan flying lemur aagcccagcaatgcagaggtgttccaggcca Tree shrew gagaccaacaatgcagaggtgttccaggctg Mouse gagtcaagtaatgcagatgtgttccaggctg Guinea pig gagtccagccacccaga--tgttccaggcaa Human =============================== Alignment block 63 of 72 in window, 73136 - 73154, 19 bps B D Malayan flying lemur tgcaggagcacctgggctg B D Tree shrew cgcgagttcacctgggctg B D Human tgcatgggcagcgg---tt B D Mouse caagggtgcacctgggctg B D Guinea pig cgcgggtgcacctgggctg Alignment block 64 of 72 in window, 73155 - 73581, 427 bps B D Malayan flying lemur ctggggggtcatcctcactgtcaccttgcagtgcatgccccagttccacttgcaggagacatccttcccc B D Tree shrew ccttggagtcatcctcaccatcaccctccagtgtgtgccccagttccacttgcaggagacatccttcccc B D Human ctgggaggataacccaggtcccctcatgcagtgttgggccca---ccccctgtggggaactgatgcccac B D Mouse cctgggtgttatcctcactgtcaccctgcagtgtgtgccacagttccaccttctggagacatcctttcct B D Guinea pig ---------------------------------------------------------------------- Malayan flying lemur tcaatcctgaaagaggta------ctttcctcg---ccactgctcagcctcagaaaataagtggagggcc Tree shrew tcaaccctgaaagaggtaccggtcccttgctca---ccactgctcagcctcagaaaatacatgaaggatc Human ttaagc---------atagcctccctttccccatctctactgttctttcccatgaca---atgagacccc Mouse tcgaccctcaaggaggtacttgtctttggctct---ccatttcccagcatcagaaaacaaatagaggtcc Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ttagcaagtg-----------------------ctcatgggtcttcaggaccct--gactggtggg--tg Tree shrew ttgacacatgggccgcccccccaccaacagcctctcacggctcctcagtctccc----ctaatgga---a Human tcaggttgtg----------------acagtagaccctggctcttcaggccccctgaattggggca---a Mouse tgacaaaggg----actcagcctcggacagtt-cccacggacctctggtgccct--gagaggtccggttg Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ggggtctgaccttgccaccccttccttcaccctagggata-ctgtggccaggacccttctgagcagggca Tree shrew aggtactgaccttgccatcccttccctggtcctagggatatttgtggccagaacccttttgggcagatca Human gggagatgacctcaccaccctttccttggccctggggaca-ctgtggccaggacccttctgagcaggtca Mouse gaggtcttatttcaccagaccttccttggcccaagagaga-c--tggtcagaaccctggtggg-----ct Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gagagaaccagaggccgagaggacctgcag-gggtggcagaggtatgggcaagaaagggggttgggtaga Tree shrew gtgataccc--------agagcagctacagcgggtggcaaagctgtgggcaagaaggg------------ Human gtga-acct--------ggaggaactgcaggaggtagcagaggcatgggcaggaaaaggggttgagtaga Mouse gcaaaaccc--------agaagcacctcag-aacttactggcatgtgggtgtggaaggggtttgggcaga Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gacttacttgctcaggagagg-------agtgtgagcttactgc-ccccagagggcattcactctcaact Tree shrew gacttgc---cccaggaggca-------gatgtgagctgactatgcattggagggtgttaactctcaagt Human gacttgc---cacaggagacatgaggctggtgtgagctgccgct-cctgggagggcattaaccctcagct Mouse gagctgc---ctcaggacaaa--------gtgtggactagctgt-tcttag-gggcattaactcctaccg Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gcactgagcc--agaggatatgcccagaactgccttgataatggttccttcacag Tree shrew ------agcc-tttaggatatgcccaggatggtctttataaagcattttctatga Human gcactgagccccagaggatatgcctgggattccctttataatggtttcttcacag Mouse gtcctg-----taaaggacatgcc-agggcttccttaccatggatggcaccacag Guinea pig ------------------------------------------------------- Inserts between block 64 and 65 in window B D Mouse 49bp Alignment block 65 of 72 in window, 73582 - 73718, 137 bps B D Malayan flying lemur caaggtggatggagtaacttttagtcttg-ctgggtgcccaaggttgcatgcaaggtatttggatctgga B D Tree shrew c-agatgcatggagtaactttcatgtttg-ttggttgcctca--ttatttgtaggatatttggatctgag B D Human caaggtgggtggagtcattttcaggcttatttggctgcttaaggtgacatgcagggtatttggatctgga B D Mouse ====================================================================== B D Guinea pig ---------------------------------------------------------------------- Malayan flying lemur tgatggggggcagaaaggatgacttgtaattgatagcagtattgttttgaataaatgaaaatcagtgt Tree shrew tgatgaggagaaggaggaaggactgttaattagtagcagtgct-tcttgagtgaatgaaaaacagtgt Human taacgggggg------------cttgtaatttatagcagtgct-ttttgaatgaatgaaaaacagtgt Mouse ==================================================================== Guinea pig -------------------------------------------------------------------- Inserts between block 65 and 66 in window B D Human 616bp Alignment block 66 of 72 in window, 73719 - 74314, 596 bps B D Malayan flying lemur tggatggatggttagatggttgggtgggtggatggatggatgg-ttaatggatggtcatatggatggatg B D Tree shrew tagctggatagataaat----------------------------------------------------- B D Human tggatggatggacaaatggatggatggatggatgaagggatggatgaagggatggatgcatggatggatg B D Mouse ====================================================================== B D Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gatagttacatggacggatggatggacagttacatggatggatggatggatggttggatggatggaag-- Tree shrew ---------------aaatggatggataggtacttgagtagatggactggtggttgga------------ Human aagggatggatggatggatggatggacggatggatggatggatggatagctggatggataaagggaagga Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur -----gatgggtggatggatagatggatggttggatggttagacagatggttagatggatggttggatag Tree shrew -------------------------------cggatgattaggtagatgaatggatagatgggtggacga Human tggatgatggatggatggttggatggatgaagggatggatggacggatgaagagatgggagaatggatga Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ttggatggatggatggat--------ggatgtatagatggcaggcatgtagcaggcctgaagtgcctgga Tree shrew ttggatggatggatagat------------------------gacactcaatagggctgaaatgtctgaa Human -tggatggatagatagatgaagagatggatggatgggtgggtggtatgcagcatacctgaagtgcctgga Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur aggcctggatgtatcgctggtaatcactaagctataggattcaaatctatagttccaagtcccttggagt Tree shrew ------------atcactgatatttactaaattataggagtcaaatctattgttccaagttcttgggagt Human -atcctagatccattcttcatattcactaagccataggactcaaatctatggtttcaagttccttgaagt Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ttgggtccttccatagtcaccttgtc-----attcaatatgggtagaccctctgcaaaaatggtgtttgc Tree shrew ttggattcttccatagctaccttatc-----atttgatatgaacatatcatctgcatagatgaagttgg- Human ttgggctcttctctagtcatattgaataaggattcaatatgagcagatcctctgtgcagatggagttggc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur agtgatgtgaacagtgctgacccaacacagttaaggtgaagatcatgggctttggaatcaaatggacctg Tree shrew agtgatgtgagcataatagacccaacatggttaagatgaagattatgggctttggaatcaaatagactca Human aataatttgagcagtactgactcaa------gaagatgaagatcatgggctttgaaatcaaatgaaccca Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gccttgaatgctggctctgccacttctacactgtgaccttgagccagtcatttaaccttgctgagcctta Tree shrew acctttactgctggttctgacacttctaaattgtgacctttgaccactcatttaatcttactgagcctta Human attttgaatgctggctctgcaattcctaagctgtgagcgtgtgccagtcatttaatcctgctgagcctta Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gtttcctcatctaaaatgtg--ttaataatgtctaccttaattg-ttgaatataaggatt Tree shrew atttgctcatctaacaagagaattaataatgcttaccttacagt-attaatctgaggatt Human gtttcctcatctacggagagtgttaataatgtctaccttaaagtattgaatctgaggatt Mouse ============================================================ Guinea pig ------------------------------------------------------------ Alignment block 67 of 72 in window, 74315 - 74329, 15 bps B D Malayan flying lemur aaatcagatgacgca B D Tree shrew aaatcagatgataca B D Mouse =============== B D Human --------------- B D Guinea pig --------------- Inserts between block 67 and 68 in window B D Tree shrew 332bp Alignment block 68 of 72 in window, 74330 - 75572, 1243 bps B D Malayan flying lemur ttgcagatagatctgccatatgacccagctatcccactgctgggaatatacccagaggaatggaaatcat B D Mouse ====================================================================== B D Human ---------------------------------------------------------------------- B D Tree shrew ====================================================================== B D Guinea pig ---------------------------------------------------------------------- Malayan flying lemur caagtcaaaggtatacctgttccccaatgttcattacagcactctacaatagccaagagttggaaccagc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ccaaatgtccatcatcggatgagtggatacggaaaatgtggtatatctacacaatggaatactactcagc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur tataaaaacgaatgaaatactgccatttgcaacannnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaattcacacacacacacacac Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur acacaaaaaaaaaaaatcccggggagggaagaagatataacaactacaattacttgaagttgatacgaca Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur agcaaacagaaaggacattgttgggtgggaggggggagagggaagagggagggaggtttcggtgatgggc Mouse ====================================================================== Human ---------------------------------------------------------------------- Tree shrew ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur cacaataatcaaccacattgtatatcgacaaaataaaataaaaaatttaaaaa Mouse ===================================================== Human ----------------------------------------------------- Tree shrew ===================================================== Guinea pig ----------------------------------------------------- Alignment block 69 of 72 in window, 75573 - 75618, 46 bps B D Malayan flying lemur aaatcagatgacgcattcaaagtgtctcattctgtatgaaaacatg B D Human aagccagataatacatgtaaagcatctagtttagtgttcaaacatg B D Mouse ============================================== B D Tree shrew ============================================== B D Guinea pig ---------------------------------------------- Alignment block 70 of 72 in window, 75619 - 75670, 52 bps B D Malayan flying lemur -ctcctgtggcacccaggaggggataaatggaaactatgattatctagtacct B D Tree shrew -cctccatggcacccagtaggtgctaaatggaaactattattacctagcactt B D Human ccccgcatggcactcagtaggtgacaaacagaaac--ttgttttctagccccc B D Mouse ===================================================== B D Guinea pig ----------------------------------------------------- Inserts between block 70 and 71 in window B D Tree shrew 225bp Alignment block 71 of 72 in window, 75671 - 76054, 384 bps B D Malayan flying lemur catctaaaatccttcccactagaatttctaatccattaagcacagagccaaagccttaaatttggaagtc B D Tree shrew tacctgctggccccaccactggaatttctaatgcactaaactgtagggcaaaggctttaatccaaaaggg B D Human agtctaaaatccttcccactggaatttctaatactttaagacttggggcaaagaccttcactccagaagc B D Mouse ====================================================================== B D Guinea pig ---------------------------------------------------------------------- Malayan flying lemur cccctactcagaagcatgagcgtggcagaaatcttcccccagaattcccagatggtggctgagaaagtga Tree shrew cccttactcaaaggcattatt-tggtggaaag-tcctcccagaattctcagcaggtggctgggaaagtga Human cccctcctcagaggcatgagtttggggaaaatctttacccagaactcccaactggtggttgaaaaagtga Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur cttcacagctccaggggacaccgcattgatccctggggtaccagtgctgagcctgcat-----------g Tree shrew ttccatagctctaggctatccaacatt-accccagcagcacctatgctgagtctgcacaggacatgcacg Human ttccacagttcccgggg-tacagcatggatccctgaggtgccaatgctgggcctgcag-----------a Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ggccatttagcaaatgagctgcctgatgccttggcccaaggagca-ggacaagttcaggacaagggcgtt Tree shrew ggccatttaccaattgaacgaccta--gccctggtttaagagcgc-gggtaagtccaggacaagg-cttc Human aatcattcagcaaatgagatgcctgatgtcttagcccaagagagtggggcaagttcaggacaagagcatt Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ccctagaattgattggccatgacagggcgtggctgg-gccagagggccccaggacggcaggggcagggag Tree shrew tcaaataattgtttgggcagtacaaagcgcagttaaagccaaggagcctcatgaagactgagacgggg-- Human ccgtagaattgttgggctttgaaaaggcatgcctga-gccagggagccccgtgaggaaaggggcagggag Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gaggacaccagaacaaggaagggatgctggatgcccactggtccaca Tree shrew gagaacactggaatgagga-gggatg-tagatatccactggtccaca Human gaggacactggaatgaggaagggaggctggatgttcactggcccaca Mouse =============================================== Guinea pig ----------------------------------------------- Inserts between block 71 and 72 in window B D Tree shrew 153bp Alignment block 72 of 72 in window, 76055 - 77043, 989 bps B D Malayan flying lemur caattcctcct-----------------------------------------------gcagctgttgaa B D Tree shrew caatcccttctcctccattctcctctcaggatcttgggcacacacgcacacgtgcccagcatgagtttaa B D Human cggctccacct-----------------------------------------------ggagccgtccca B D Mouse ====================================================================== B D Guinea pig ---------------------------------------------------------------------- Malayan flying lemur g--------------------------------------------------------------------- Tree shrew gccaccgggtccaggactcgaaccgcagtcgactacgtgggagtccagcgacatagctattacgccaact Human g--------------------------------------------------------------------- Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur --------actctgaagcctttggcgcccccttgggcctgcctcggccaacc-ccagtccccagacaagt Tree shrew gctggcccgctctgagctcttaaaggccactttagttgtgcctcaaccagccaccatcccccagaccagt Human --------actctgagctttttggggtgaccttgggtgtgcttcaaccagccacagtccctcagagcagt Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gctaaggggcccatgtaggccacttgttcatgccaagcagtgttttaaaagcattct-acgctctgccca Tree shrew gctaagtggctgatctaggccattcattca-------cag-gatttaaaagcattct-acagtctgccca Human gccaaggggttcaccaaggccacttgttcacaccaaacagggtttaaaaggcattttcatattctgccca Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gtgccaggcaggctgattgagagctatcgtggaggtg-----------------------------agcc Tree shrew gtgccaggtatactgattgagagctacaatggggagagcatttgggagctaaatgacctaggaaataacc Human gtgccaggcatgctgattgagagggattgtggatttggcatttggggctcatatgacccatgggctcacc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur cctggggccacgcaacagcacggtgagctccc--------accgtgaggacagaagag------------ Tree shrew cctacagccatgaaagaacattctgagattccttttagtaactgtgaagatggaaaagagactttcttat Human ttgagagccatgaaataccattctgagctccc--------accatgaagacggaagag--attttcctcc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ----------ctgctgctgtccttggcgcttctctgc--tactcct----gggtga-ccactccattcc- Tree shrew aacccttatgcctctgtttttcttggcctttcctttccctattcctcatgaggtgaatcactccat---- Human agccctcatgcctctgttgatcgtggcctttcccctctctgcctgtcag-gagtga-acgctccctcctg Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur accacgcaccaggatgtggcaggta-cgccact-gaggtgcagccc----aggaatccttctcag-ccta Tree shrew --------cctggatgtggcagggaacctcacttgaggtgcaatcc----aggggtccttctcgggccta Human gctatgcagcagaatgtggcagggactcccaca-gaggtgcaacccagggagggacctttgtcaggcctg Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur tgctgggcagcccaggtgcccctttcttctctccgaca---------------gcctgcatctctcctcc Tree shrew tgctgaacaactc-gatggccctttcttcgttcaatca----cccctgggggagcctgcctctctccccc Human tgctgggcagccc-agtgaccctttcttctcctcaacagtcccctccaggacagcctgcatctctccccc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur t-agcagcgaccgccatcctctctgccccacagagtcctcctgcc-----ctggactaactacagaggag Tree shrew tgagcagctatcagcatcctctctgcctctcagtgccctcctact-----atggattggctacaaaaaag Human tcagcagctcctgccgtcatctctgcccttcagggtccttctggcctggactggactggctgcagaagtg Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ataaaaga-tcctcaacttttct-atccctgctgcctctgaagcaagcacaccagcccgtctcagttaaa Tree shrew gtaatagaatctccaactttcctcatcactgctgcctccaaatgaagtacaccaactcttctaaactaag Human ataatagg-tcttttgcttggctcattcctgctgtctctgaaccaagtacaccagcctttctcagttaaa Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur gggtgtttaacagacgggacattgcagagatgatgcacagcgggaggtctcagggcagccc-ccttggtc Tree shrew gaatttttaatggatgggaaattatggaaatgacatgcaa-gggaggttacaggacaccccatcctagtc Human cggtttctaacatacagggaattatggaaatagcatgcagcgaggggtcccagagcagcccgtcttggtc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur cctgctctgatgttaagcacattcgctgatgtggttaatggaagt--tcatgggtttagagc-------- Tree shrew cctactctgaggttaagcttatgtgctgatatagctggttgaaggcaccatagttttggagctgagcatc Human tgtgcactgaggttaagctc-tgcgc----gtggactcgtgaaggaacttcagccttagagctgggcctc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur -----------------------------ttgggtttgaagctgaagacagtgtccagtgaagatggcct Tree shrew caggactggcagc-tagtcagcctgcctttggggtttcaaattgaaggcagtgtccagtgaagatggcct Human caggaccagcagaggagccagcctgcccttggggcttgaagttgaaggcagtatccagtgcagagggcct Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ggccaggcactagagaaacagtccacctcagccatcaggtccaaagaggcctggcagag----------- Tree shrew -gcctggagctgaagaaataattcatgtcaatcaccagacccaaagaagcctggcagagaggaccaagac Human acccaggagctaaagaaataattc----------------------aagcctggcagagacggccgaggc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur -------atggccaaggtcagcaacgtgggcaggaggtttggaagaggcaggaacaga--gggcacagtc Tree shrew aaagaccatgaccgagagcagcaatatgggaaggaggtttggaagaggccagggtagggtggtcatatct Human aaagaccatgcctcaagtccggaacatgggaaggaggtgtggacgaggct-gggcagagtgagcatggcc Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur tgggagacacccg-aaggcttagatgaggaac-------------------------------------- Tree shrew ggagaggcacccatggggctgagatgtagagccaagtctattgtctta------gggtatatgttcaaga Human tggagaggatcctaggggctggaatacagagccaagtccattttctcagggtcc------atgttcaaga Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur --------------------aataggacttggccgctgagcatgggggcaagggaggagg-gggaggcgt Tree shrew gacaactaggatgaggacttaatcgcacttagcaacagagtgtgggggtgagggagtaggaggaaggagt Human ggtatttaggatgaggaaccaacaggactcggcagctgagtgt-gtggtgaggtggcaggaaggaagagt Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur cagggacagtggggccacagcaaaggtggggaccctaggaggctcagcaggtgtggg------------- Tree shrew caggagtgatgaagctaccaccaa----gagaatctaggaggctcaacaggtacgggggaccaagttatt Human caaggatgatggggccaccatcag--tagagaatccaggaggctcggca-----ggggcaacaaggtgat Mouse ====================================================================== Guinea pig ---------------------------------------------------------------------- Malayan flying lemur ----------------cagcatttggagggg Tree shrew agttcagttttgtaacctgagttttgaggta Human tgtttcctttgggaacttgagttc-gagggg Mouse =============================== Guinea pig -------------------------------

Data schema/format description and download

Go to 5-way Mammal track controls

Data last updated at UCSC: 2016-05-04

Downloads for data in this track are available:

Multiz alignments (MAF format), and phylogenetic trees
PhyloP conservation (WIG format)
PhastCons conservation (WIG format)

Description

This track shows multiple alignments of 5 species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 5 species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

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

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

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data, and both were run with the same parameters.

UCSC has repeatmasked and aligned all genome assemblies, and provides all the sequences for download. For genome assemblies not available in the genome browser, there are alternative browser views in the preview genome browser. The species aligned for this track include 5 genome sequences.

Organism Species Release date UCSC
version alignment type

Malayan flying lemur Galeopterus variegatus Jun. 2014 (G_variegatus-3.0.2/galVar1) Jun. 2014 (G_variegatus-3.0.2/galVar1) reference

Tree shrew Tupaia belangeri Dec. 2006 (Broad/tupBel1) Dec. 2006 (Broad/tupBel1) Reciprocal Best Net

Human Homo sapiens Dec. 2013 (GRCh38/hg38) Dec. 2013 (GRCh38/hg38) Syntenic Net

Mouse Mus musculus Dec. 2011 (GRCm38/mm10) Dec. 2011 (GRCm38/mm10) Syntenic Net

Guinea pig Cavia porcellus Feb. 2008 (Broad/cavPor3) Feb. 2008 (Broad/cavPor3) Syntenic Net

Table 1. Genome assemblies included in the 5-way Conservation track.

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the malayan flying lemur genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Note that excluding species from the pairwise display does not alter the the conservation score display.

To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.

Gap Annotation

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

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

Genomic Breaks

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

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

Base Level

When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the malayan flying lemur sequence at those alignment positions relative to the longest non-malayan flying lemur sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".

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

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

Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2). Species listed in the row labeled "None" do not have species-specific reading frames for gene translation.

Gene Track Species

UCSC Known Genes Human, Mouse

NCBI RefSeq gene annotations Malayan flying lemur

Ensembl genes v83/Dec. 2015 Tree shrew, Guinea pig

Table 2. Gene tracks used for codon translation.

Methods

Pairwise alignments with the Malayan flying lemur genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. All pairwise alignment and chaining parameters are the same for all pairs. See also: nematode 5-way alignment parameters. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.

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

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The nematode tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 5-way alignment (msa_view). The 4d sites were derived from the NCBI RefSeq gene set of Malayan flying lemur, filtered to select single-coverage long transcripts.

PhastCons Conservation

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

The phastCons parameters were tuned to produce approximately 70% conserved elements in the Malayan flying lemur NCBI RefSeq gene coding regions. This parameter set (expected-length=45, target-coverage=0.3, rho=0.3) was then used to generate the nematode and caenorhabditis conservation scoring.

PhyloP Conservation

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

Conserved Elements

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

Credits

This track was created using the following programs:

Alignment tools: lastz (formerly blastz) and multiz by Bob Harris, Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
Tree image generator: phyloPng by Galt Barber, UCSC
Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC

The phylogenetic tree is based on Kiontke et al. (2007).

References

Phylo-HMMs, phastCons, and phyloP:

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

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

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

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

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

Chain/Net:

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

Multiz:

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

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

Blastz:

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

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

Phylogenetic Tree:

Kiontke K, Barrière A, Kolotuev I, Podbilewicz B, Sommer R, Fitch DH, Félix MA. Trends, stasis, and drift in the evolution of nematode vulva development. Curr Biol. 2007 Nov 20;17(22):1925-37. PMID: 18024125