recombination in HK swine with pH1N1

[gsgs]

http://evol.mcmaster.ca/~weilong/PDFs/HaoGene2011.pdf

claimed recombination in swine with pH1N1=***


PB2 , breakpoint 1197


1583+2886-->1809

>A/Sw/HK/NS1809/2009(H1N1/12/03
>A/Sw/HK/NS1583/2009(H1N1/10/22
---------................................................... 0 
......................................o..................... 1 
..................................................o......... 1 
............................................................ 0 
................................o........................... 1 
............................................................ 0 
.....................................................o...... 1 
............................................................ 0 
............................................o............... 1 
..........o................................................. 1 
............................................................ 0 
.................................o................o......... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................o............... 1 
............................................................ 0 
............................................................ 0 
.....................................................o...... 1 
................................o...............o........... 2 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
......................o..................................... 1 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
............................................................ 0 
-- 13 


 13 ( 2271 )+ 4 ( 2274 )+ 9 ( 2151 )+ 7 ( 1701 )+ 5 ( 1485 )+ 4 ( 1410 )+ 2 ( 982 )+ 4 ( 838 )+ 48 ( 13112 )

[gsgs]

Re: recombination in HK swine with pH1N1

                                        00000000000000000011111111112222222 00011111 000000001111111122 0000000001111 0000000111111 0000000000111 0000000 0000000  
                                        00011233455555678900111345670000111 11301567 012467992246678900 4466667790124 0002699012223 0133577899123 4455678 2233556  
                                        00979703124569910424378510262346368 67392084 590477154671412167 3300581381480 6699836544455 3813724924923 5959025 5556572  
                                        89917366457141411504439839931731737 87039033 169167078903166130 3457877974918 0978769035876 9966132755418 9254090 2447846  
-codon-position-------------------------2   2     12  1       12   22   1      11     12 1 1    2  2 2  12211  1    1   11            1 1 1 1           1  2 1 12  
---Index--------------------------------GAGTTATTAACCGATGAAACCGGCGGGCCAAGCGG GAACGACT GGCCCACGAAGACGACAC TCGGTGTTGCGAC GAAGAGTGGGGTG CTGGCAAGAAGTT GGGGGAC ACAAAGA  
   1 >A/******/index/2009/02/01         ................................... ........ .................. ............. ............. ............. ....... .......  
   2 >A/Sw/HK/NS1583/2009(H1N1)/10/22   AG...C..GG.T..CA.G..TA...........A. ...AA... .......AG.A..A..G. ....AA......T A..A....A.A.A T.A...G...... .A.AA.. ...G..G  
   3 >A/Sw/HK/2299/2009(H1N1)/10/22     --...C..GG.T..CA.G..TA...........A. ...AA... .......AG.A..A..G. ....AA......T A..A....A.A.A T.A...G...... .A.AA.. ...G..G  
   4 >A/Sw/HK/2995/2009(H1N1)/12/17     ......C......G....T....TAA..A..ATAA ......T. ...ATG.........T.T ....A......GT ...A....AAAC. .CA..GGAG..C. AAA.A.. G..GG..  
   5 >A/Sw/HK/2974/2009(H1N1)/12/17     ......CC....AG....T....TAA..A.GATAA ......T. A..ATG.........T.T ....A......GT ...A....AAAC. .CA..GGAG..C. AAA.A.. G..GG..  
   6 >A/Sw/HK/2886/2009(H1N1)/12/17     ......C......G....T....TAA..A..ATAA ......T. ...ATG.........T.T ....A......GT ...A....AAAC. .CA..GGAG..C. AAA.A.. G..GG..  
   7 >A/Sw/HK/2885/2009(H1N1)/12/17     ......C......G....TY...TAA..A..ATAA ......T. ...ATG.........T.T ....A......GT ...A....AAAC. .CA..GGAG..C. AAA.A.. G..GG..  
   8 >A/Sw/HK/2894/2009(H1N1)/12/17     ......C......G....T....TAA..A..ATAA ......TC ...ATG.........T.T ....A......GT ...A....AAAC. .CA..GGAG..C. AAA.A.. G..GG..  
   9 >A/Sw/HK/NS1809/2009(H1N1)/12/03   --AC..................A....T.....A. T.G..... ..T...T....GT..... C.AAA.C..TA.T .T.A..CAA.A.. ..A.T.G..G..C .A..AG. .TGG.A.  
  10 >A/Sw/HK/NS1810/2009(H1N1)/12/03   --AC..................A....T.....A. T.G..... ..T...T....GT..... CTA.A.C..TA.T .T.A..CAA.A.. ..A.T.G..G..C .A..AG. .TGG.A.  
  11 >A/Sw/HK/189/2010(H1N1)/01/07      ....C.....T.....G.........AT.T...A. .G...G.. .AT...T..T..A.G... C...A..CA...T ..GAGTC.A.A.. T.AA..G..GT.C .A..A.T ...G...