p0 e0 f0 h0 s1 maxl=45 #differences 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 PB2 PB1 PA HA NP NA M NS ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1 >Index_of this file 0 2 43 46 26 30 11 23 14 16 17 38 42 38 56 13 24 28 55 15 21 18 33 21 73 53 33 171 171# 29 1704 5864 1:>Index_of this file 2 >Index_B(indices) 2 0 43 46 28 28 13 25 16 16 19 38 43 38 58 13 23 26 55 15 23 20 33 21 73 52 33 173 173# 29 1704 5864 2:>Index_B(indices) 3 >A/Gs/Guangdong/1/96(H5N1) 43 43 0 21 19 69 36 54 55 55 59 77 84 77 91 53 65 66 93 54 25 43 62 26 81 88 44 322 322# 54 1704 5811 3:>A/Gs/Guangdong/1/96(H5N1) 4 >Index_C(Hongkong/1997) 46 46 21 0 24 70 39 57 58 58 60 78 85 78 96 56 68 69 94 57 30 46 63 25 84 91 47 335 335# 57 1704 5811 4:>Index_C(Hongkong/1997) 5 >Index_D(Hongkong/2000) 26 28 19 24 0 52 19 37 38 38 42 62 68 62 78 37 50 52 79 37 6 26 47 11 62 77 28 240 240# 40 1704 5858 5:>Index_D(Hongkong/2000) 6 >Index_A(Qinghai) 30 28 69 70 52 0 39 51 36 28 40 60 65 60 78 37 49 48 73 15 47 46 59 45 96 76 61 295 295# 50 1704 5864 6:>Index_A(Qinghai) 7 >Index_E(Henan/16/2004) 11 13 36 39 19 39 0 22 23 25 24 43 51 43 65 22 35 37 64 24 14 9 30 16 66 62 24 186 186# 31 1704 5852 7:>Index_E(Henan/16/2004) 8 >Index_F(Vietnam,Thailand) 23 25 54 57 37 51 22 0 37 39 40 57 61 57 73 34 45 45 68 38 32 28 10 32 84 74 43 253 253# 43 1704 5875 8:>Index_F(Vietnam,Thailand) 9 >Index_G(East Java 2003) 14 16 55 58 38 36 23 37 0 24 22 28 36 28 42 22 37 37 62 23 33 28 47 33 87 66 47 212 212# 36 1704 5899 9:>Index_G(East Java 2003) 10 >Index_H(Japan-Korea 2003) 16 16 55 58 38 28 25 39 24 0 28 47 55 47 64 25 39 36 67 13 33 32 45 33 86 66 49 231 231# 39 1704 5858 10:>Index_H(Japan-Korea 2003) 11 >Index_I(Yunnan 2003) 17 19 59 60 42 40 24 40 22 28 0 46 52 46 62 23 37 38 65 27 37 29 46 37 83 64 46 236 236# 40 1704 5887 11:>Index_I(Yunnan 2003) 12 >Index_J(Indonesia1-human) 38 38 77 78 62 60 43 57 28 47 46 0 52 0 69 47 59 58 83 47 57 45 62 55 106 86 59 317 317# 54 1704 5934 12:>Index_J(Indonesia1-human) 13 >Index_K(Indonesia2-bird,swine) 42 43 84 85 68 65 51 61 36 55 52 52 0 52 78 55 60 69 94 54 63 52 68 62 109 90 71 363 363# 61 1704 5893 13:>Index_K(Indonesia2-bird,swine) 14 >Index_L(Indonesia1-human same as J) 38 38 77 78 62 60 43 57 28 47 46 0 52 0 69 47 59 58 83 47 57 45 62 55 106 86 59 317 317# 54 1704 5934 14:>Index_L(Indonesia1-human same as J) 15 >Index_M(Bali 2007) 56 58 91 96 78 78 65 73 42 64 62 69 78 69 0 60 75 73 96 65 73 67 81 73 127 97 89 424 424# 72 1704 5899 15:>Index_M(Bali 2007) 16 >Index_N(Hunan 2004) 13 13 53 56 37 37 22 34 22 25 23 47 55 47 60 0 21 17 42 24 32 30 44 32 82 50 44 209 209# 35 1704 5858 16:>Index_N(Hunan 2004) 17 >Index_O(Mongolia-2008) 24 23 65 68 50 49 35 45 37 39 37 59 60 59 75 21 0 37 61 36 45 39 54 44 93 30 52 268 268# 45 1704 5881 17:>Index_O(Mongolia-2008) 18 >Index_P(Vietnam 2005) 28 26 66 69 52 48 37 45 37 36 38 58 69 58 73 17 37 0 37 35 47 43 53 45 95 66 59 276 276# 47 1704 5893 18:>Index_P(Vietnam 2005) 19 >Index_Q(Vietnam-2008) 55 55 93 94 79 73 64 68 62 67 65 83 94 83 96 42 61 37 0 64 74 70 78 72 115 88 86 416 416# 71 1704 5910 19:>Index_Q(Vietnam-2008) 20 >Index_R(raccoondog) 15 15 54 57 37 15 24 38 23 13 27 47 54 47 65 24 36 35 64 0 32 31 46 32 83 65 48 223 223# 38 1704 5840 20:>Index_R(raccoondog) 21 >Index_S(Hubei 1997) 21 23 25 30 6 47 14 32 33 33 37 57 63 57 73 32 45 47 74 32 0 21 42 9 56 72 22 217 217# 37 1704 5858 21:>Index_S(Hubei 1997) 22 >Index_T(chukar) 18 20 43 46 26 46 9 28 28 32 29 45 52 45 67 30 39 43 70 31 21 0 36 23 69 66 27 214 214# 36 1704 5864 22:>Index_T(chukar) 23 >Index_U(Thailand 2008) 33 33 62 63 47 59 30 10 47 45 46 62 68 62 81 44 54 53 78 46 42 36 0 40 92 83 51 297 297# 50 1704 5869 23:>Index_U(Thailand 2008) 24 >Index_V(Vietnam 2003) 21 21 26 25 11 45 16 32 33 33 37 55 62 55 73 32 44 45 72 32 9 23 40 0 65 71 28 218 218# 37 1704 5852 24:>Index_V(Vietnam 2003) 25 >Index_W(Shanxi/2/2006) 73 73 81 84 62 96 66 84 87 86 83 106 109 106 127 82 93 95 115 83 56 69 92 65 0 112 51 485 485# 82 1704 5887 25:>Index_W(Shanxi/2/2006) 26 >Index_X(Vietnam 2009) 53 52 88 91 77 76 62 74 66 66 64 86 90 86 97 50 30 66 88 65 72 66 83 71 112 0 75 414 414# 70 1704 5887 26:>Index_X(Vietnam 2009) 27 >Index_Y(Jilin 2002) 33 33 44 47 28 61 24 43 47 49 46 59 71 59 89 44 52 59 86 48 22 27 51 28 51 75 0 288 288# 47 1639 5838 27:>Index_Y(Jilin 2002) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 281 #differences in total to index #differences in total to index , considering only polymorphisms that occur more than once in this table #differences in total to index, where defined #differences in total to index, where defined, considering only polymorphisms that occur more than once in this table 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 00000000000000000111111111111111112222222222222222222222333333333333333333334444444444444444444444444445555555555555555555555555566666666666666666666666677777777777777777777888888888888888889999999999999999000000000000000000011111111111122222222222222223333333333334444444444444444444555555555555566666666666666667 12233333444555688012333445567778990000123345566667778999000011222233467789990001111122333355566666667890111233333344456667778899900011111123344566777889900012222355666667779001233555677889990012333457778999000111222223334456700112223578800033555667888990122266789990113344566678899999000113444688811222334445778890 02912456268147914570256140224571582467021738901780398569045618178969991840134670578906245846912567894028024312346702354783595915906912456876956136678230725813469503025781475270845238489581240687036844577036678345012341252432479062587060203736137062457392103608432585381736514642512467039059058313617036135789170356 -codon-position------------------------------1121212 1 1 2 1 1 1 2 12 1 122 12 2 12 1 2 1 21221 12 2 1 2 12 1 1 211 12 2 2 1 2 1 12 2 2 1 1 12 12 1 1 1 2 1 1 1 2 1 2 2 12 2 1 12 12 1 2 1 1 1 2 1 1 1 2 21 1 2 1 1 22 211 1 2 ---Index-------------------------------------ACTGTAGTTATTGTCCGACTTCCCAAACCGTGTATAGATTCAACATCGCGATGGCATGCCATCGAACCCATTGTCGAAGCTCGATAACAGCACAGAAAGTCCAACGAAGAGAGCCATATGGGGGCCTGCGGGCAAGCCCCTCGGACGTAAATTAACGGAGGCAGGACACCGTTTACGAGATATAGATAAGGCACACTGCACGTGTGAGCAAAGAGAAAAGCATTAGACTTGGGATGCGCGCTTAAAAGGAGAACCTTTCTCCTCCCGGGGCTGTCAATGTGAGACATGCATAAAAGCAGGTCCCGGGTCTAGAA 1 >Index_of this file .......................................................................................................................................................................................................................................................................................................................... 0 0 , 0 0 1:>Index_of this file 2 >Index_B(indices) .................................................................................................G.......A................................................................................................................................................................................................................ 2 2 , 2 2 2:>Index_B(indices) 3 >A/Gs/Guangdong/1/96(H5N1) ........C..................T...A.C.G......T............G........G.....C...........A..T........TG.G........G....G.......A...................TC..AG...TG..C....A....G..C..T...........................C........A.C..G.....................A...........G.G..C.............T......T...........A.......CC..G..........A........ 43 43 , 43 43 3:>A/Gs/Guangdong/1/96(H5N1) 4 >Index_C(Hongkong/1997) ..C........C......T.......G....A.C.G.G....T............G......T...................A..T.......TTG.G........G....G............................C..AG...TG..C....A....G..C..T.........A.................C........A.C........................AC.....A....G.G........C..............T.A.........A.......CC..G..........A........ 46 46 , 46 46 4:>Index_C(Hongkong/1997) 5 >Index_D(Hongkong/2000) ...................................G......T............G........G.................A...........TG..........G....G...............................A....T........A....G..C..T....................................A.C........................A.............GA......................T...........A.......CC..G..........A........ 26 26 , 26 26 5:>Index_D(Hongkong/2000) 6 >Index_A(Qinghai) ...................CC....................G..C........AT..........................A...............G...T.G.AG......T............A.......G..................G.......T....A..T...A....A..........A....C................G.................C..........T......A.....................T.....G........................C............. 30 30 , 30 30 6:>Index_A(Qinghai) 7 >Index_E(Henan/16/2004) ...................................G...................G........G.................A..........T.................G......................G........A........................................................................................A.........................................................C..............A........ 11 11 , 11 11 7:>Index_E(Henan/16/2004) 8 >Index_F(Vietnam,Thailand) .T.................................G......................T.....G.T.T.............AG...T.......................G......................................G...........................A..............T..........................T.....................C.........G.....................T...............C.....TT.......A.C..G... 23 23 , 23 23 8:>Index_F(Vietnam,Thailand) 9 >Index_G(East Java 2003) ...............TA........................G.....A.....................................................T....G...........................G..A......................A....................................................................................................TC.................A......A................A......... 14 14 , 14 14 9:>Index_G(East Java 2003) 10 >Index_H(Japan-Korea 2003) ...................C.....................G...............T..............A........................G........G...................A.......GA...............................G.T.............................G...............................................A...........................G..A....................A.............. 16 16 , 16 16 10:>Index_H(Japan-Korea 2003) 11 >Index_I(Yunnan 2003) ................A........................G.........A.........................................T............T...........................G..T...............G......T.........A.................G......T.......................A.....A......................A.A..............................G................................ 17 17 , 17 17 11:>Index_I(Yunnan 2003) 12 >Index_J(Indonesia1-human) ...............TAC.......................G.....A.........A.......G.........A.............A...T...GTC.T........A............A..........G..A....A....................T.......................................AA..........C.....................AT.............GTT..C...TC.................A.....CAT....G..........AA........ 38 38 , 38 38 12:>Index_J(Indonesia1-human) 13 >Index_K(Indonesia2-bird,swine) ....C....G.....TA...........T..........C.G.....A......T......C....T.................C.G......T...C.C.T......A........G.............A.G...AT......T..........A......C..........C.......C.A.......................................T......A..........................T..TC.............G.......TG.A.....G..T.......A......A.. 42 42 , 42 42 13:>Index_K(Indonesia2-bird,swine) 14 >Index_L(Indonesia1-human same as J) ...............TAC.......................G.....A.........A.......G.........A.............A...T...GTC.T........A............A..........G..A....A....................T.......................................AA..........C.....................AT.............GTT..C...TC.................A.....CAT....G..........AA........ 38 38 , 38 38 14:>Index_L(Indonesia1-human same as J) 15 >Index_M(Bali 2007) C.....AC.....CTTA.....A.C.........C......G...C.A...........T...A.......C...............T........C....TG...G.......T......A........A...G..A.T.T..................A..........CC.............C...A.G......GT....A............G......A..........TT......G................TC...AA...........CA..G...A.G..............A.TCT.G... 56 56 , 56 56 15:>Index_M(Bali 2007) 16 >Index_N(Hunan 2004) .......C.........................G................................................................T......AG...........................G.........................T...................G.................T..A.................A.......................................C..................................................G... 13 13 , 13 13 16:>Index_N(Hunan 2004) 17 >Index_O(Mongolia-2008) .......C...............T.........G......................C........................................C.C.....A...........G..A...TT..................................T...................G........A...........A......TT..A.....................................A........C.................C....................T..T........G... 24 24 , 24 24 17:>Index_O(Mongolia-2008) 18 >Index_P(Vietnam 2005) .......C..C......................G..................................T....A.............T.........GT.T....AG...........C.........A.....G.......A........C........T........T......A...G.................T..A.................A..........A.....................................A.......................G.........T.......G... 28 28 , 28 28 18:>Index_P(Vietnam 2005) 19 >Index_Q(Vietnam-2008) .T.....C..C.T..................A.G..A..A.........A..A..............TT....A...GA..A.....TG.........T....G.AG...A.......C.........A.....G.......A........C.......AT...............A.A.G..G.G.G.........AT..A......T........G.A.G......C.....C......A...G.............C.....A..A.................................T.A...TCG... 55 55 , 55 55 19:>Index_Q(Vietnam-2008) 20 >Index_R(raccoondog) ...................C.....................G..C....................................A...............G........G...................A.......G..................................T...................A.......................................C.................A.....................T.....G........................C............. 15 15 , 15 15 20:>Index_R(raccoondog) 21 >Index_S(Hubei 1997) ...................................G...................G........G.................A............G..........G....G...............................A.............A....G..T..T....................................A.C........................A..............A..................................A.......CC..G..........A........ 21 21 , 21 21 21:>Index_S(Hubei 1997) 22 >Index_T(chukar) ..............................C....G.....G.....A.......G........G.................A..........T.....C...........G...............................A...........................................................T.....................A......A...................................A.....................C..............A....T... 18 18 , 18 18 22:>Index_T(chukar) 23 >Index_U(Thailand 2008) .T.................................G..C.......T...........T.....G.T.T.......G.....AG...T.....T...G.............G.............................T........G...........................A..............T..........................T.................A...C.........G..................C..T......G........C.....TT.A.....A.C..G... 33 33 , 33 33 23:>Index_U(Thailand 2008) 24 >Index_V(Vietnam 2003) ...................................G...................G..........................A............G.G........G....G...............................A.............A....G..C..T.........A..........................A.C........................A......................C..............T...................CC.............A........ 21 21 , 21 21 24:>Index_V(Vietnam 2003) 25 >Index_W(Shanxi/2/2006) ...A.G...............T...G...AC....GA......TC...TA.....G....G...G.T.......A....A..A.......TCTT.G...C....TA.C.GTGA..CC.........CAA...T...A......A..........G..A....G.TT..T.T....................T..........C..AGC.....G..GG.A..CG........A..A...........AA..G....C.......A........C........A.......CC..GT.......T.........G 73 73 , 73 73 25:>Index_W(Shanxi/2/2006) 26 >Index_X(Vietnam 2009) ...A...C.............T.T........CG......T...............C......A.....G......................T....T.C.....A...........G..A...TT...A.............AG.AC.....G......T......G.......T.G.GGG.......A...........A......TT..A.A........G..TT.........A.....GGG....A........CT......A.........C....................T..T........G.G. 53 53 , 53 53 26:>Index_X(Vietnam 2009) 27 >Index_Y(Jilin 2002) ...A.................T........C....G..............G....G........G...............G.A........C.T.G...C....TA.....G..........A.........T..........A...........T.AG...G..T......................................A...........................A...............----------......A.................A.......CC..G..........A.......G 43 43 , 33 33 27:>Index_Y(Jilin 2002) ---Index-------------------------------------ACTGTAGTTATTGTCCGACTTCCCAAACCGTGTATAGATTCAACATCGCGATGGCATGCCATCGAACCCATTGTCGAAGCTCGATAACAGCACAGAAAGTCCAACGAAGAGAGCCATATGGGGGCCTGCGGGCAAGCCCCTCGGACGTAAATTAACGGAGGCAGGACACCGTTTACGAGATATAGATAAGGCACACTGCACGTGTGAGCAAAGAGAAAAGCATTAGACTTGGGATGCGCGCTTAAAAGGAGAACCTTTCTCCTCCCGGGGCTGTCAATGTGAGACATGCATAAAAGCAGGTCCCGGGTCTAGAA -codon-position------------------------------1121212 1 1 2 1 1 1 2 12 1 122 12 2 12 1 2 1 21221 12 2 1 2 12 1 1 211 12 2 2 1 2 1 12 2 2 1 1 12 12 1 1 1 2 1 1 1 2 1 2 2 12 2 1 12 12 1 2 1 1 1 2 1 1 1 2 21 1 2 1 1 22 211 1 2 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111 00000000000000000111111111111111112222222222222222222222333333333333333333334444444444444444444444444445555555555555555555555555566666666666666666666666677777777777777777777888888888888888889999999999999999000000000000000000011111111111122222222222222223333333333334444444444444444444555555555555566666666666666667 12233333444555688012333445567778990000123345566667778999000011222233467789990001111122333355566666667890111233333344456667778899900011111123344566777889900012222355666667779001233555677889990012333457778999000111222223334456700112223578800033555667888990122266789990113344566678899999000113444688811222334445778890 02912456268147914570256140224571582467021738901780398569045618178969991840134670578906245846912567894028024312346702354783595915906912456876956136678230725813469503025781475270845238489581240687036844577036678345012341252432479062587060203736137062457392103608432585381736514642512467039059058313617036135789170356