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  • #31
    Re: swine flu sequences (thread from h5n1experts)

    ---------------posted:2009/11/15---------------

    ******-mutations at the receptor binding domain (RBD) in HA



    Code:
       
                                     111111111111112222222222222222222222222222
                                     004455556667990000000000113333333333444444
                                     898901237890890123456789010123456789012345
                                     Y GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM 
                                     ------------------------------------------
>A/Lishui/01/2009/07                 - ..... ... ............. ..........R.... 
>A/Ekaterinburg/01/2009/             . ..... ... ............. ..........R.... 
>A/Omsk/01/2009/                     . ..... ... ............. ..........R.... 
>A/Finland/553/2009/05/10            . ..... ... ............. ..........R.... 
>A/Irkutsk/02/2009/                  . ..... ... ............. ..........R.... 
>A/Mexico/InDRE4487/2009/04/14       . ..... ... ............. ..........R.... 
>A/Mexico/4603/2009/04/19            . ..... ... ............. ..........R.... 
>A/Texas/17/2009/04/24               . ..... ... ............. ..........R.... 
>A/Zhejiang/DTID-ZJU01/2009/06       . ..... ... ............. ..........R.... 
>A/Singapore/TLL51/2009/06/14        . ..... ... ............. ..........R.... 
>A/Singapore/TLL10/2009/07/27        . ..... ... ............. ..........R.... 
>A/New York/05/2009/04               . ..... ... ............. ..........X.... 
>A/New York/25/2009/04/24            . ..... ... ............. ..........X.... 
>A/New York/08/2009/04/25            . ..... ... ............. ..........X.... 
>A/New York/13/2009/04/25            . ..... ... ............. ..........X.... 
>A/New York/34/2009/04/25            . ..... ... ............. ..........X.... 
>A/New York/33/2009/04/25            . ..... ... ............. ..........X.... 
>A/New York/18/2009/04/25            . ..... ... ............. ..........X.... 
>A/Delaware/05/2009/04/28            . ..... ... ............. ..........X.... 
>A/Texas/08/2009/04/24               . ..... ... ............. ..........X.... 
>A/Texas/20/2009/04/25               . ..... ... ............. ..........X.... 
>A/Mexico/4108/2009/04/02            . ..... ... ............. ..........X.... 
>A/California/12/2009/04/22          . ..... ... ............. ..........X.... 
>A/Singapore/ON903/2009/07/04        . ..... ... ............. ..........X.... 


>A/Arizona/04/2009/04/27             . ..... ... ............. .........B..... 
>A/South Carolina/09/2009/04/26      . ..... ... ............. .........B..... 

>A/Italy/172/2009/                   - ..... ... ............. .........E..... 
>A/Catalonia/387/2009/06/26          . ..... ... ............. .........E..... 
>A/Athens/893/2009/06/09             . ..... ... ............. .........E..... 
>A/Catalonia/S1120/2009/07/20        . ..... ... ............. .........E..... 
>A/Catalonia/S1165/2009/07/30        . ..... ... ............. .........E..... 
>A/Catalonia/S1209/2009/08/05        . ..... ... ............. .........E..... 
>A/Catalonia/S1205/2009/08/05        . ..... ... ............. .........E..... 
>A/Catalonia/S1199/2009/08/06        . ..... ... ............. .........E..... 
>A/Catalonia/S1222/2009/08/10        . ..... ... ............. .........E..... 
>A/Catalonia/S1227/2009/08/10        . ..... ... ............. .........E..... 
>A/Catalonia/S1215/2009/08/12        . ..... ... ............. .........E..... 
>A/Catalonia/S1249/2009/08/18        . ..... ... ............. .........E..... 
>A/Catalonia/S1260/2009/08/19        . ..... ... ............. .........E..... 
>A/Catalonia/S1265/2009/08/24        . ..... ... ............. .........E..... 
>A/Catalonia/S1269/2009/08/24        . ..... ... ............. .........E..... 
>A/Catalonia/S1272/2009/08/25        . ..... ... ............. .........E..... 
>A/Catalonia/S1273/2009/08/25        . ..... ... ............. .........E..... 
>A/Catalonia/S1300/2009/08/28        . ..... ... ............. .........E..... 
>A/Catalonia/S1304/2009/08/28        . ..... ... ............. .........E..... 
>A/Catalonia/S1333/2009/09/01        . ..... ... ............. .........E..... 
>A/Catalonia/S1331/2009/09/03        . ..... ... ............. .........E..... 
>A/Catalonia/S1350/2009/09/09        . ..... ... ............. .........E..... 
>A/Catalonia/S1379/2009/09/16        . ..... ... ............. .........E..... 
>A/Catalonia/S1453/2009/09/30        . ..... ... ............. .........E..... 
>A/Catalonia/S1490/2009/10/07        . ..... ... ............. .........E..... 
>A/Catalonia/S1545/2009/10/19        . ..... ... ............. .........E..... 
>A/Catalonia/S1592/2009/10/21        . ..... ... ............. .........E..... 
>A/Catalonia/S1606/2009/10/26        . ..... ... ............. .........E..... 
>A/Catalonia/S1637/2009/10/28        . ..... ... ............. .........E..... 
>A/Catalonia/S1641/2009/10/28        . ..... ... ............. .........E..... 
>A/Catalonia/378/2009/06/23          . ..... ... ............. .........E..... 
>A/Milan/83/2009/07/15               . ..... ... ............. .........E..... 
>A/Milan/80/2009/07/08               . ..... ... ............. .........E..... 
>A/Catalonia/S1183/2009/07/28        . ..... ... ............. .........E..... 
>A/Catalonia/S1182/2009/07/29        . ..... ... ............. .........E..... 
>A/Catalonia/S1254/2009/08/19        . ..... ... ............. .........E..... 
>A/Catalonia/S1286/2009/08/25        . ..... ... ............. .........E..... 
>A/Catalonia/S1237/2009/08/13        . ..... ... ............. .........E..... 
>A/Catalonia/S1248/2009/08/18        . ..... ... ............. .........E..... 
>A/Catalonia/S1479/2009/10/05        . ..... ... ............. .........E..... 
>A/Catalonia/S1605/2009/10/26        . ..... ... ............. .........E..... 
>A/Catalonia/S1236/2009/08/13        . ..... ... ............. .........E..... 
>A/Catalonia/S1478/2009/10/05        . ..... ... ............. .........E..... 
>A/Catalonia/S1587/2009/10/22        . ..... ... ............. .........E..... 
>A/Catalonia/S1436/2009/09/28        . ..... ... ............. .........E..... 
>A/Almati/01/2009/                   . ..... ... ............. .........E..... 
>A/New Jersey/01/2009/04             . ..... ... ............. .........E..... 
>A/Sapporo/1/2009/06/11              . ..... ... ............. .........E..... 
>A/Paris/2591/2009/05/01             . ..... ... ............. .........E..... 
>A/Hong Kong/2369/2009/06/11         . ..... ... ............. .........E..... 
>A/California/25/2009/06/15          . ..... ... ............. .........E..... 
>A/Nagasaki/HA-44/2009/08/20         . ..... ... ............. .........E..... 
>A/Changsha/78/2009/06/29            . ..... ... ............. .........E..... 
>A/Ancona/05/2009/07/12              . ..... ... ............. .........E..... 
>A/Catalonia/S1632/2009/10/28        . ..... ... ............. .........E..... 
>A/Catalonia/S1161/2009/07/28        . ..... ... ............. .........E..... 
>A/Catalonia/S1604/2009/10/26        . ..... ... ............. .........E..... 

>A/Catalonia/NS2001/2009/08/03       - ----- ... ............. .........G..... 
>A/Catalonia/NS1706/2009/07/29       . ..... ... ............. .........G..... 
>A/Catalonia/NS2008/2009/08/03       . ..... ... ............. .........G..... 
>A/Texas/05/2009/04/15               . ..... ... ............. .........G..... 
>A/Texas/11/2009/04/23               . ..... ... ............. .........G..... 
>A/Mexico/InDRE4114/2009/            . ..... ... ............. .........G..... 
>A/Mexico/InDRE4114/2009/            . ..... ... ............. .........G..... 
>A/New York/04/2009/04               . ..... ... ............. .........G..... 
>A/Sao Paulo/53206/2009/07/19        . ..... ... ............. .........G..... 
>A/Sao Paulo/53225/2009/08/01        . ..... ... ............. .........G..... 
>A/Georgia/01/2009/04/27             . ..... ... ............. .........G..... 
>A/Zhejiang-Yiwu/11/2009/09/06       . ..... ... ............. .........G..... 
>A/Zhejiang/DTID-ZJU02/2009/09/07    . ..... ... ............. .........G..... 
>A/Zhejiang/DTID-ZJU03/2009/09/07    . ..... ... ............. .........G..... 
>A/Mexico/3955/2009/04/02            . ..... ... ............. .........G..... 

>A/New York/4099/2009/06/13          . ..... ... ............. .........N..... 
>A/New York/4576/2009/07/08          . ..... ... ............. .........N..... 
>A/Sao Paulo/53845/2009/08/02        . ..... ... ............. .........N..... 
>A/Sao Paulo/53838/2009/08/01        . ..... ... ............. .........N..... 

>A/Nebraska/02/2009/04               . ..... ... ............. .........X..... 
>A/California/13/2009/04/21          . ..... ... ............. .........X..... 
>A/Texas/10/2009/04/23               . ..... ... ............. .........X..... 
>A/New York/31/2009/04/24            . ..... ... ............. .........X..... 
>A/Texas/04/2009/04/14               . ..... ... ............. .........XX.... 
>A/California/07/2009/04/09          . ..... ... ............. .........XX.... 
>A/Singapore/GP2312/2009/07/31       . ..... ... ............. .........XXXX.. 

>A/Singapore/ON141/2009/06/02        . ..... ... ............. ........G...... 
>A/Singapore/ON1118/2009/07/09       . ..... ... ............. ........X...... 
>A/Singapore/GP2695/2009/08/06       . ..... ... ............. ........X...... 
>A/Singapore/GP2687/2009/08/06       . ..... ... ............. ........X....X. 
>A/Singapore/ON2081/2009/09/13       . ..... ... ............. ........X..XXX. 
>A/Singapore/ON1187/2009/07/15       . ..... ... ............. ........XX.X.X. 
>A/Singapore/GP2641/2009/08/05       . ..... ... ............. .......XXX.XX.. 
>A/Singapore/GP2651/2009/08/05       . ..... ... ............. .......XXX.XX.. 
>A/Sto Domingo/WR1057N/2009/07/02    . ..... ... ............. ..T............ 
>A/Hiroshima/201/2009/06/17          . ..... ... ............. ..T......G..... 
>A/Pennsylvania/14/2009/             . ..... ... ............. ..X............ 
>A/Auckland/1/2009/04/25             . ..... ... ..........I.. ............... 
>A/California/04/2009/06/05          . ..... ... ..........I.. ............... 
>A/Singapore/TLL38/2009/08/06        . ..... ... ..........I.. ............... 
>A/Singapore/TLL40/2009/08/08        . ..... ... ..........I.. ............... 
>A/Singapore/TLL42/2009/08/08        . ..... ... ..........I.. ............... 
>A/New York/35/2009/04/25            . ..... ... ..........J.. ............... 
>A/South Carolina/10/2009/04/26      . ..... ... ..........J.. ............... 
>A/Hiroshima/230/2009/06/25          . ..... ... ..........J.. ............... 
>A/New York/11/2009/04/25            . ..... ... ..........J.. .........X..... 
>A/Catalonia/S1384/2009/09/17        . ..... ... .........G... ............... 
>A/Chengdu/18/2009/07/26             . ..... ... .......R..... ............... 
>A/Singapore/ON1138/2009/07/13       . ..... ... ......G...... ............... 
>A/Sao Paulo/53823/2009/08/01        . ..... ... ....I........ ............... 
>A/New York/3502/2009/05/16          . ..... ... ....N........ ............... 
>A/Utsunomiya/2/2009/06/16           . ..... ... ....N........ ............... 
>A/Utsunomiya/1/2009/06/16           . ..... ... ....N........ ............... 
>A/Niigata/700/2009/06/22            . ..... ... ....N........ ............... 
>A/Catalonia/S1369/2009/09/15        . ..... ... ....N........ .........E..... 
>A/Catalonia/S1187/2009/07/30        . ..... ... ....N........ .........E..... 
>A/swine/Singapore-Q/M168/2009/      . ..... ... ...N......... ............... 
>A/New York/28/2009/04               . ..... ... ...X......... ............... 
>A/Kansas/03/2009/04/24              . ..... ... ..X.......... ............... 
>A/New York/17/2009/04               . ..... ... ..X.......... ............... 
>A/New York/27/2009/04               . ..... ... ..X.......... ............... 
>A/New York/18/2009/                 . ..... ... ..X.......... ..........X.... 
>A/Singapore/ON313/2009/06/19        . ..... ... X.....X...... ............... 
>A/Colombia/08/2009/04/25            . ..... ... XXXXXXXXXXXXX ............... 
>A/Osaka/180/2009/                   . ..... ..I ............. ............... 
>A/Osaka/1/2009/05/16                . ..... ..I ............. ............... 
>A/Singapore/ON1163/2009/07/14       . ..... ..I ............. ............... 
>A/Michigan/06/2009/                 . ...T. ... ............. ............... 
>A/Wisconsin/629-D01445/2009/05/24   . ...T. ... ............. ............... 
>A/Italy/128/2009/06/20              . ...T. ... ............. ............... 
>A/Toronto/T0106/2009/07/07          . ...T. ... ............. ............... 
>A/Shanghai/60T/2009/05/28           . ...T. ... ............. ............... 
>A/Ancona/04/2009/07/01              . ...T. ... ............. ...T........... 
>A/Catalonia/S1169/2009/07/28        . ...T. ... ............. ...T........... 
>A/New York/12/2009/04/25            . ...V. ... ............. ............... 
>A/New York/12/2009/04/25            . ...X. ... ............. ............... 
>A/Wisconsin/629-D02064/2009/05/22   . .A... ... ............. ............... 
>A/Indiana/09/2009/04/22             . .I... ... ............. ............... 
>A/Michigan/04/2009/04/24            . .I... ... ............. ............... 
>A/Michigan/05/2009/05/05            . .I... ... ............. ............... 
>A/New York/3573/2009/05/21          . .I... ... ............. ............... 
>A/New York/3576/2009/05/21          . .I... ... ............. ............... 
>A/New York/3654/2009/05/26          . .I... ... ............. ............... 
>A/Tokushima/1/2009/06/02            . .I... ... ............. ............... 
>A/New York/4014/2009/06/10          . .I... ... ............. ............... 
>A/Singapore/GP2316/2009/07/31       . X.... .X. ..........X.. .X..........XX. 
>A/Sw/Alberta/OTH-33-24/2009/05/03   . ..... ... ............H .......M....... 
>A/Sw/Alberta/OTH-33-21/2009/05/05   . ..... ... ............. .......M....... 
>A/Sw/Alberta/OTH-33-3/2009/05/03    . ..... ... ............. .........V..... 
                                     ------------------------------------------
                                     Y GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM 
                                     111111111111112222222222222222222222222222
                                     004455556667990000000000113333333333444444
                                     898901237890890123456789010123456789012345








    Code:
    receptor binding domain of influenza-A viruses  (Nov. 2006)

positions 98,134-138,153-155,184-196,216-230 in hemagglutinin
(H3-numbering)


count,species-serotype,amino-acids at these positions,representative sequence
-----------------------------------------------------------------------------------------------------
                 Y GVTAA WIT HPPTTSEQQSLYQ EIAARPKVRGQAGRM
   9 A-H1N1:     Y GVTAA WIT HPPTTSEQQSLYQ EIAARPKVRGQAGRM     A/turkey/Minnesota/1661/81(H1N1)
   4 A-H1N1:     . ..... ... .....N....... ...............    A/pintail duck/Alberta/210/2002(H1N1)

                .....S.S..L.....NIGD.RA..H....K.....D.E..I
 325 H-H1N1:     Y GVSAS WLT HPPNIGDQRALYH EIAKRPKVRDQEGRI     A/Wyoming/4/2003(H1N1)
  64 H-H1N1:     . ..T.. ... ..S.......I.. ...............    A/Switzerland/5389/95 (H1N1)
  44 H-H1N1:     . ..... ... ......N...... ...............    A/Yokohama/62/2002(H1N1)
  35 H-H1N2:     . ..... ... .........T... ..T............    A/Scotland/15/02(H1N2)
  26 H-H1N1:     . ..T.. ... ..S..E..KTI.R .........N.....    A/Ohio/201/1983(H1N1)
  22 H-H1N1:     . ..... ... ........K.... ...............    A/New York/4/2006(H1N1)
  17 H-H1N1:     . ..T.. ... ..S..E..KTI.R ...E.....G.A...    A/USSR/92/77(H1N1)
  16 H-H1N1:     . ..T.. ... ..S.......I.. .........G.....    A/Taiwan/01/1986(H1N1)
  13 H-H1N1:     . ..T.. ... ..S.M.....I.. ...............    A/Yokohama/24/2000(H1N1)
  12 H-H1N2:     . ..... ... ......N..T... ..T............    A/Switzerland/3100/2002(H1N2)
   8 H-H1N1:     . ..T.. ... ..S.......I.. ..T............    A/New York/694/1995(H1N1)
   8 H-H1N2:     . ..... ... ......N..T..N ...............    A/Wisconsin/12/2001(H1N2)
   7 H-H1N1:     . ..... ... ..S...V...I.. .........G.....    A/Nanchang/9/1996(H1N1)
   7 H-H1N1:     . ..T.. ... ..S..R....I.. ...............    A/Suita/1/89/(R)(H1N1)
   7 H-H1N1:     . ..T.. ... ..S.M.....I.. ...R...........    A/South Australia/64/2000(H1N1)
   7 H-H1N2:     . ..... ... .........T..N ...............    A/Yokohama/47/2002(H1N2)
   5 H-H1N1:     . ..... ... ......B...... ...............    A/Wellington/18/2000(H1N1)
   5 H-H1N1:     . ..... ... ..S.......I.. ...............    A/Singapore/15/96(H1N1)
   5 H-H1N1:     . ..T.. ... ..S..E..KTI.R ...............    A/Memphis/7/1980(H1N1)
   4 H-H1N1:     - ..... ... ............. ...............    A/Shiraz/22/2005(H1N1)
   4 H-H1N1:     . ..... ... ............. .........N.....    A/South Canterbury/35/2000(H1N1)
   4 H-H1N1:     . ..... ... ..S...V...I.. ...............    A/Nanchang/17/1996(H1N1)
   4 H-H1N1:     . ..T.A ... ....SKE.QN..Q ...E.......A..M    A/Puerto Rico/8/34(H1N1)
   4 H-H1N1:     . ..T.A ... ..S.SK..QNI.Q ...E.......A..M    A/PR/8/34(HON1)
   4 H-H1N1:     . ..T.. ... ..S..E..KTI.R .........G.....    A/Fiji/15899/83)]

                ....AT.A..IV....TSN..QS..Q....A.....G.A..M
  11 S-H1N1:     Y GATAA WIV HPPTSNDQQSLYQ EIAARPKVRGQAGRM     A/swine/Nederweert/13O/96(H1N1)
  11 S-H1N1:     . .V... .L. .....T....... ...............    A/swine/Wisconsin/1/61(H1N1)
  10 S-H1N1:     . ..... ... ....N........ ...............    A/Swine/Netherlands/477/93(H1N1)
   6 S-H1N1:     . .V... .L. .....T....... ...T...........    A/Swine/Indiana/1726/1988(H1N1)
   6 S-H1N2:     . .V... .L. ..S..A....... ...T.....D.....    A/Swine/Ohio/891/01(H1N2)
   5 S-H1N1:     . .V... .L. .....T....... ...S...........    A/Swine/Wisconsin/457/98(H1N1)
   4 S-H1N1:     . ..... ... .....S....... ...........T...    A/swine/Best/5R/96(H1N1)
   4 S-H1N1:     . .I... ... ....TS....... ........K......    A/Swine/Netherlands/12/85(H1N1)
   4 S-H1N1:     . .T.S. ... ....N........ ...............    A/swine/Someren/14M/96(H1N1)
   4 S-H1N2:     - .V... .L. .....A....... ...T.....D.....    A/SW/OH/7802/00(H1N2)

                ....GSR...LT...NDDTE.RT.......T....N..G...
  11 A-H2N3:     Y GGSRA WLT HPNDDTEQRTLYQ EIATRPKVNGQGGRM     A/Pintail duck/Alberta/293/77 (H2N3)
   6 A-H2N2:     . ..... ... ....E........ ...............    A/mallard/Potsdam/178-4/83 (H2N2)
   6 A-H2N5:     - ----- ... ....E....A... ......E....R...    A/tern/Australia/91/2004(H2N5)
   5 A-H2N3:     . ..... ... .....A....... ...............    A/Silky chicken/PA/9600897/96 (H2N3)
   4 A-H2N2:     . ..... ... .....A....... ...............    A/guinea/NJ/3070/91 (H2N2)
   4 A-H2N9:     . ..... ... ............. ...............    A/teal/Alberta/16/97(H2N9)

                ......K..........EA...A.......A......L.S..
   5 H-H2N2:     Y GGSKA WLT HPNDEAEQRALYQ EIAARPKVNGLGSRM     A/Taiwan/1/67(H2N2)
   4 H-H2N2:     . ...M. ... ............. ...............    A/Taiwan/1964(H2N2)
   4 H-H2N2:     . ...R. ... .....T...T... ...T........G..    A/Japan/305/1957(H2N2)
   4 H-H2N2:     . ...R. ... .....T...T... ...T...........    A/Victoria/15681/59 (H2N2)
   4 H-H2N2:     . ...R. ... .....T...T... ...T......Q.G..    A/Leningrad/134/57 (H2N2)

                ......N........STNQ..TN..V.N.GS..W.R.QSG.I
  13 A-H3N8:     Y GGSNA WLT HPSTNQEQTNLYV NIGSRPWVRGQSGRI     A/pintail duck/ALB/169/1980(H3N8)
   6 A-H3N2:     . ..... ... ............. ...............    A/pintail duck/ALB/86/1976(H3N2)
   5 A-H3N2:     . ...G. ... .........T... ......L........    A/duck/Korea/S9/03(H3N2)
   4 A-H3N8:     . ...S. ... ............. ...............    A/mallard/Alberta/127/00(H3N8)

                ....R.G.........S.....K..I.......L........
   3 C-H3N8:     Y GRSGA WLT HPSSNQEQTKLYI NIGSRPLVRGQSGRI     A/canine/Texas/1/2004(H3N8)

                .................................W........
  16 E-H3N8:     Y GRSGA WLT HPSSNQEQTKLYI NIGSRPWVRGQSGRI     A/equine/Wisconsin/1/03(H3N8)
  15 E-H3N8:     . ..... ... .....K....... ...............    A/equine/Suffolk/89(H3N8)
   8 E-H3N8:     . ..... ... .....N....... ...............    A/Equine/LaPlata/1/93(H3N8)
   8 E-H3N8:     . ..... ... ......Q..E... ...............    A/equine/Oklahoma/2000(H3N8)

                ....T.S........GTDSD.IS..A.......R..DV.S..
 347 H-H3N2:     Y GTSSA WLT HPGTDSDQISLYA NIGSRPRVRDVSSRI     A/Western Australia/50/2003(H3N2)
 300 H-H3N2:     . ..... ..H ..S.......... ......W..G.....    A/Western Australia/9/2000(H3N2)
 223 H-H3N2:     . ..... ... .....N....... ..........IP...    A/Zhejiang/546/04(H3N2)
 197 H-H3N2:     . ..... ..H ............. ......W..G.....    A/Western Australia/36/2002(H3N2)
 122 H-H3N2:     . ...Y. ..H ..S.....T.... ......W..G.....    A/Wellington/3/97(H3N2)
 116 H-H3N2:     . ...Y. ..H ..S.....T...V ......W..G.....    A/Yokohama/68/96(H3N2)
 108 H-H3N2:     . .K.Y. ..H ..S.....T...V ......W..GI....    A/West_Virginia/1/95(H3N2)
  81 H-H3N2:     . ..... ..H ..S.....T.... ......W..G.....    A/zhejiang/06/99(H3N2)
  65 H-H3N2:     . .K.Y. ..H ..S.....T...V ......W..GL....    A/Texas/57/93(H3N2)
  65 H-H3N2:     . ..... ... ....YN....... ..........IP...    A/Western Australia/78/2005(H3N2)
  64 H-H3N2:     . .E.Y. ..H ..S..RE.T...V ......W..GL....    A/Victoria/2/90(H3N2)
  58 H-H3N2:     . ..... ... .....N....... ...........P...    A/Zhejiang/95/03(H3N2)
  57 H-H3N2:     . ..... ... .....N...F... .........NIP...    A/Zhejiang/209/05(H3N2)
  53 H-H3N2:     . .K.Y. ..H ..S.....T...V ...F..W..GL....    A/New York/752/1993(H3N2)
  45 H-H3N2:     . .K.Y. ..H ..S.....T...V D..Y..W..GL....    A/Texas/5/94(H3N2)
  44 H-H3N2:     . ..... ... ....NN....... ..........IP...    A/Whanganui/69/2004(H3N2)
  43 H-H3N2:     . .G.Y. ..Y ..S..KE.TN..V ......W..GL....    A/Wellington/4/85(H3N2)
  36 H-H3N2:     . .G.Y. ..H ..S..RE.TN..V ......W..GL....    A/Wellington/5/89(H3N2)
  34 H-H3N2:     . .G.Y. ..H ..S.....T...V ......W..GQ....    A/Yokohama/73/92(H3N2)
  33 H-H3N2:     . ..... ..H ............. ...............    A/zhejiang/8/2002(H3N2)
  30 H-H3N2:     . .G.Y. ..H ..S.....T...V ......W..GL....    A/Stockholm/12/92(H3N2)
  28 H-H3N2:     . ..... ..H ............. ....G.W..G.....    A/New York/97/2002(H3N2)
  25 H-H3N2:     . ...F. ..H ..S.....T.... ......W..G.....    A/Zhejiang/18/98(H3N2)
  25 H-H3N2:     . ...Y. ..H ..S.....T...V ......W..GI....    A/Washington/5/96(H3N2)
  23 H-H3N2:     . .D.Y. ..H ..S..RE.T...I ......W..GL....    A/Wellington/66/92(H3N2)
  22 H-H3N2:     . .G.N. ... ..S.NQE.T...V ......W..GL....    A/Northern Territory/1960(H3N2)
  21 H-H3N2:     . .G.N. ..Y ..S..QE.T...V ......W..GL....    A/Udorn/72(H3N2)
  17 H-H3N2:     . .G.Y. ..H ..I..RE.TN..V ......W..GL....    A/Tokyo/1276/(H3N2)
  15 H-H3N2:     . ..... ..H ..S.......... ......W..G...I.    A/Taiwan/0275/2000 (H3N2)
  15 H-H3N2:     . ..... ... ............. ..........I....    A/Western Australia/58/2004(H3N2)
  14 H-H3N2:     . .G.Y. ..H ..S..R..T...V ......W..GQ....    A/Shanghai/24/90(H3N2)
  13 H-H3N2:     - ..... ..H ..S.......... ......W..G.....    A/Zaragoza/RR658/00(H3N2)
  13 H-H3N2:     . .G.Y. ..Y ..S..KE.TN..V ...P..W..GL....    A/Stockholm/4/(H3N2)
  13 H-H3N2:     . ..... ... .........N... ...........P...    A/Zhejiang/80/03(H3N2)
  13 H-H3N2:     . ...Y. ..H ..S.....T...V ......W..G...I.    A/Wisconsin/3/96(H3N2)
  12 H-H3N2:     . .G... ..Y ..S..KE.TD..V .V....W..GL...V    A/Rotterdam/5828/77(H3N2)
  12 H-H3N2:     . ..... ... ............. ...........P...    A/Zhejiang/92/03(H3N2)
  11 H-H3N2:     . .G.Y. ..Y ..S..KE.TN..V .V....W..GL....    A/Texas/1/77(H3N2)
  11 H-H3N2:     . .K.Y. ..H ..S.....T...V ......W..GQ....    A/Wuzhou/1/94(H3N2)
  11 H-H3N2:     . ..... ..H ............. ..........I....    A/StaCatarina/327/02(H3N2)
  10 H-H3N2:     - ...Y. ..H ..S.....T...V ......W..G.....    A/Madrid/SO1747/98(H3N2)
  10 H-H3N2:     . ..... ... .....N....... ...............    A/Waikato/108/2003(H3N2)
   9 H-H3N2:     . .E.Y. ..H ..I..RE.T...V ......W..GL....    A/Washington/15/91(H3N2)
   9 H-H3N2:     . .G.N. ..Y ..S..QE.TN..V ......W..GL....    A/Port Chalmers/73(H3N2)
   9 H-H3N2:     . ..... ... .....N..T.... ..........IP...    A/Waikato/2/2005(H3N2)
   8 H-H3N2:     - ...Y. ..H ..S.....T.... ......W..G.....    A/San Sebastian/RR390/98(H3N2)
   8 H-H3N2:     . .E.Y. ..H ..S..RE.T...I ......W..GL....    A/Stockholm/20/91(H3N2)
   8 H-H3N2:     . ..... ..H ............. ......W..G...K.    A/Western Australia/35/2002(H3N2)
   8 H-H3N2:     . ..... ... ............. ..........X....    A/New York/473/2003(H3N2)
   7 H-H3N2:     . .K.YS ..H ..S.....T...V D..Y..W..GL....    A/Spain/378/95(H3N2)
   7 H-H3N2:     . ...F. ..H ........T.... ......W..G.....    A/Virginia/21817/99(H3N2)
   7 H-H3N2:     . ..... ..H ..S.......... ......W..G...K.    A/South Australia/147/99(H3N2)
   7 H-H3N2:     . ..... ..H ..S.....T.... ......W..GI....    A/Neuquen/V690/98(H3N2)
   7 H-H3N2:     . ..... ... .....N....... ..........I....    A/Zhejiang/550/04(H3N2)
   7 H-H3N2:     . ..... ... .....N....... S......I...P...    A/Turkey/2108/2005(H3N2)
   7 H-H3N2:     . ...Y. ..H ..S.....T.I.V ......W..GI....    A/zhejiang/10/98(H3N2)
   6 H-H3N2:     . .K.Y. ..H ..S.....T...V ...F..W..GQ....    A/Vermont/3/94(H3N2)
   6 H-H3N2:     . ..... ..H ............. ......W..G...I.    A/United Kingdom/C4-13/2003(H3N2)
   6 H-H3N2:     . ..... ..H ..S.......... ....G.W..G.....    A/South Australia/71/2000(H3N2)
   6 H-H3N2:     . ..... ... .....N...F... S........NIP...    A/Sri Lanka/146/2005(H3N2)
   6 H-H3N2:     . ...Y. ..H ..S.....T.I.V ......W..G.....    A/Wuzhou/19/96(H3N2)
   5 H-H3N2:     - ..... ... ............. ...............    A/Yilan/566/04(H3N2)
   5 H-H3N2:     . .G.Y. ..Y ..S.EKE.TN..V ......W..GL....    A/Stockholm/10/85(H3N2)
   5 H-H3N2:     . .K.Y. ..H ..S.....T...V D..Y..W..GQ....    A/Paris/363/95(H3N2)
   5 H-H3N2:     . .K.YS ..H ..S.....T...V ......W..GL....    A/Stockholm/1/93(H3N2)
   5 H-H3N2:     . .K.YT ..H ..S.....T...V ......W..GL....    A/Wyoming/1/93(H3N2)
   4 H-H3N2:     . .E.Y. ..H ..S..RE.TK..V ......W..GL....    A/Beijing/353/89(H3N2)
   4 H-H3N2:     . .G.Y. ..H ..S..RE.TK..V ......W..GL....    A/Colorado/2/(H3N2)
   4 H-H3N2:     . .G.Y. ..H ..S..RE.TN..V ......W..GQ....    A/Czechoslovakia/19/89(H3N2)
   4 H-H3N2:     . .G.Y. ..Y ..I.EKE.TN..V ......W..GL....    A/Stockholm/8/(H3N2)
   4 H-H3N2:     . .G.YT ..Y ..S..KE.TN..V ......W..GL....    A/Memphis/7/85(H3N2)
   4 H-H3N2:     . .K.Y. ..H ..S.....T...V ...F..W..GL..G.    A/Pennsylvania/9/93(H3N2)
   4 H-H3N2:     . .K.Y. ..H ..S.....T...V ...Y..W..GL....    A/Washington/26/93(H3N2)
   4 H-H3N2:     . .K.YS ..H ..S.....T...V ...F..W..GL....    A/Washington/41/93(H3N2)
   4 H-H3N2:     . .K.YS ..H ..S.....T...V ......W..GI....    A/New York/635/1996(H3N2)
   4 H-H3N2:     . .K.YX ..H ..S.....T...V ......W..GL....    A/New York/772/1993(H3N2)
   4 H-H3N2:     . ..... ... .....N....... ..........XP...    A/Finland/484/2004 (H3N2)
   4 H-H3N2:     . ..... ... ............. ......K...I....    A/Stockholm/26/2002(H3N2)
   4 H-H3N2:     . ..... ... ............. .......I.......    A/South Korea/C5-4/2002(H3N2)
   4 H-H3N2:     . ..... ... ........T...V ......W..G.....    A/Kyongbuk/320/2002(H3N2)
   4 H-H3N2:     . ....S ..H ............. ......W..G.....    A/New York/216/2003(H3N2)
   4 H-H3N2:     . ...Y. ..H ..S.....TR..V ......W..GI....    A/Guangzhou/6/96(H3N2)
   4 H-H3N2:     . ...Y. ..H ..S.....T.... ......W..G...I.    A/Sydney/05/97-like(H3N2)
   4 H-H3N2:     . ...Y. ..H ..S...V.T...V ......W..GI....    A/Nanchang/933/95(H3N2)
   4 H-H3N2:     . ...Y. ..H ..S...V.T...V ......W..G.....    A/thailand/94/96(H3N2)
   4 H-H3N2:     . ...Y. ..H ..S.N...T.... ......W..G.....    A/Seoul/69/97(H3N2)

                ....G.N....Y...S..RE..N..V..V....W..GL....
   8 S-H3N2:     Y GGSNA WLY HPSTDREQINLYV NVGSRPWVRGLSSRI     A/Swine/Netherlands/L2/93(H3N2)
   6 S-H3N2:     . ...S. ... ............. ...............    A/Swine/Spain/39139/2002(H3N2)
   6 S-H3N2:     . ...YS ..H .....S..TS... .I........I....    A/Swine/Texas/4199-2/98(H3N2)
   6 S-H3N2:     . .S.Y. ..H ..G...D.T.... .I........V..I.    A/swine/Quebec/Biovet1/05(H3N2)
   4 S-H3N2:     . .T.S. ..H .....SD..SV.A .I........I....    A/swine/Guangdong/5/2003(H3N2)
   4 S-H3N2:     . .T.Y. ..H .....SD.TS... .I........V..I.    A/Swine/Wisconsin/14094/99(H3N2)

                ....K.G....K......T..T...K..I........Q.G..
  27 A-H4N6:     Y GKSGA WLK HPSTDTEQTNLYK NIGSRPWVRGQSGRI     A/pintail/Alberta/269/2001(H4N6)
  10 A-H4N2:     . ..... ... ............. ...............    A/pintail duck/ALB/599/1979(H4N2)
  10 A-H4N8:     . ..... ... ............. ...............    A/pintail duck/ALB/220/1977(H4N8)

                .....................................L.S..
   2 S-H4N6:     Y GKSGA WLK HPSTDTEQTNLYK NIGSRPWVRGLSSRI     A/Swine/Ontario/01911-2/99 (H4N6)

                ....V.S....I..SNDAA...K..Q.K.AT.SK.N.Q.G.M
 249 A-H5N1:     Y GVSSA WLI HSNDAAEQTKLYQ KIATRSKVNGQSGRM     A/white-backed munia/Hong Kong/2469/2006(H5N1)
 203 A-H5N1:     . ..... ... .P........... R..............    A/white peafowl/Bangkok/Thailand/CU-29/04(H5N1)
 201 A-H5N1:     . ..... ... .P.......R... ...............    A/wild duck/Shanghai/59/04(H5N1)
 115 A-H5N1:     . ..... ... .P........... ...............    A/tree sparrow/Henan/4/2004(H5N1)
  40 A-H5N1:     . ..... ... .P.NE....R... ...............    A/grey heron/Hong Kong/837/2004(H5N1)
  38 A-H5N1:     . ..... ... .P........... E....P.........    A/Silky Chicken/Hong Kong/p17/97 (H5N1)
  30 A-H5N1:     . ..... ... .P......I.... ...............    A/tree sparrow/Henan/3/2004(H5N1)
  30 A-H5N2:     . ..... ... .P......I.... E....P.........    A/chicken/Taiwan/1209/03(H5N2)
  30 A-H5N2:     . ..... ... .P........... E....P.........    A/wigeon/Ohio/379/1988(H5N2)
  25 A-H5N3:     . ..... ... .P........... E....P.........    A/teal/Italy/3812/2005(H5N3)
  22 A-H5N1:     . ..... ... .P..E....R... ...............    A/Quail/Shantou/911/05(H5N1)
  13 A-H5N1:     . ..... ... .P......I.... T..............    A/goose/Guiyang/337/2006(H5N1)
  11 A-H5N1:     . ..... ... .P.......RI.. ...............    A/Duck/Hunan/191/05(H5N1)
  10 A-H5N1:     . ..... ... .P.NE........ ...............    A/goose/Guangxi/3714/2005(H5N1)
  10 A-H5N9:     . ..... ... .P........... E....P.........    A/mallard/Sweden/80/02(H5N9)
   9 A-H5N1:     - ..... ... ............. ...............    A/goose/Yunnan/3359/2006(H5N1)
   7 A-H5N1:     - ..... ... .P.......R... ...............    A/turkey/Suzdalka/Nov-01/05(H5N1)
   7 A-H5N1:     . ...A. ... .P........... R..............    A/wild bird/Vietnam/434/2005(H5N1)
   7 A-H5N2:     . ..... ... .P........... E....PR........    A/duck/NY/44018-2/00(H5N2)
   6 A-H5N1:     . ...A. ... .P........... ...............    A/slaty-backed gull/Shandong/59/04(H5N1)
   6 A-H5N1:     . ..... ... .P..E....R... ..............I    A/quail/Viet Nam/15/2005(H5N1)
   6 A-H5N1:     . ..... ... ........I.... ...............    A/goose/Shantou/11989/2006(H5N1)
   6 A-H5N2:     . ..... ... .P......A.... I....P.........    A/Chicken/Pennsylvania/10210/86(H5N2)
   6 A-H5N2:     . ..... ... .P......A.... .....P.........    A/Turkey/Virginia/6962/83(H5N2)
   6 A-H5N2:     . ..... ... ............. .....PQ....R...    A/chicken/Guatemala/45511-5/00 (H5N2)
   5 A-H5N1:     . ..... ... .P...T....... ...............    A/goose/Guiyang/3610/2005(H5N1)
   5 A-H5N1:     . ..... ... .P.N.E....... ......R........    A/Goose/Hong Kong/ww491/2000(H5N1)
   4 A-H5N1:     . ..... ... .P......I.... R..............    A/Hatay/2004/(H5N1)
   4 A-H5N1:     . ..... ... .P........... ..............I    A/goose/China/F3/2004(H5N1)
   4 A-H5N1:     . ..... ... .P...T....... R..............    A/chicken/Thailand/Kamphaengphet-3-07/2005(H5N1)
   4 A-H5N2:     . ..... ... .P........... .....P........I    A/emu/Texas/39442/93(H5N2)
   4 A-H5N2:     . ..... ... .P......V.... V....PR........    A/chicken/Puebla/231-5284/98 (H5N2)
   4 A-H5N6:     . ..... ... .P........... E....P.........    A/mallard/Sweden/40/02(H5N6)

                ..............P............R..............
   2 C-H5N1:     Y GVSSA WLI HPNDAAEQTKLYQ RIATRSKVNGQSGRM     A/dog/Thailand-Suphanburi/KU-08/04(H5N1)

                ...........................E....P.........
   3 E-H5N2:     Y GVSSA WLI HPNDAAEQTKLYQ EIATRPKVNGQSGRM     A/environment/NY/5626-2/98(H5N2)

                ......................R....K....S.........
   1 F-H5N1:     Y GVSSA WLI HPNDAAEQTRLYQ KIATRSKVNGQSGRM     A/feline/Indonesia/CDC1/2006(H5N1)

                ..........................................
  45 H-H5N1:     Y GVSSA WLI HPNDAAEQTRLYQ KIATRSKVNGQSGRM     A/Indonesia/CDC742/2006(H5N1)
  18 H-H5N1:     . ..... ... .........K... R..............    A/Viet Nam/DN-33/2004(H5N1)
  15 H-H5N1:     . ..... ... .........K... E....P.........    A/Hong Kong/486/97(H5N1)
   4 H-H5N1:     . ..... ... ............. ...........N...    A/Hong Kong/213/03(H5N1)

                ......................K....R..............
   1 L-H5N1:     Y GVSSA WLI HPNDAAEQTKLYQ RIATRSKVNGQSGRM     A/leopard/Suphanburi/Thailand/Leo-1/04(H5N1)

                ...........................K..............
   2 S-H5N1:     Y GVSSA WLI HPNDAAEQTKLYQ KIATRSKVNGQSGRM     A/swine/Fujian/F1/2001(H5N1)

                ...........................R..............
   8 T-H5N1:     Y GVSSA WLI HPNDAAEQTKLYQ RIATRSKVNGQSGRM     A/tiger/Thailand/SPB-1(H5N1)

                ...........................E....P.........
   2 U-H5N2:     Y GVSSA WLI HPNDAAEQTKLYQ EIATRPKVNGQSGRM     A/unknown/NY/118547-11/01(H5N2)

                .....T....IK...P.EV..AN..G....D..PA...R..I
  14 A-H6N8:     Y GVTSA WIK HPPDEVEQANLYG EIADRPPANGQRGRI     A/Redhead/Alberta/291/94(H6N8)
  10 A-H6N1:     . ...K. ... ....TN..NT... ...A..AV.......    A/turkey/Germany/R30/99(H6N1)
  10 A-H6N2:     . ..S.. ... ....TN..NT... ...A..AV.......    A/duck/Hong Kong/3600/99 (H6N2)
  10 A-H6N2:     . ...K. ... ....TN..NT... ...A..AV.......    A/turkey/Canada/63(H6N2)
   9 A-H6N1:     . ...N. ... ....TTV.D.... ...A..AV....S..    A/duck/Taiwan/WB239/03(H6N1)
   9 A-H6N2:     . ..... ... ............. ...............    A/pintail/Ohio/351/1987(H6N2)
   8 A-H6N5:     . ...K. ... ....TN..NT... ...A..AV.......    A/turkey/Germany/R43/98(H6N5)
   8 A-H6N8:     . ...K. ... ....TN..NT... ...A..AV.......    A/turkey/France/01062/2001(H6N8)
   7 A-H6N1:     . .T.RS ... ...NTD..DT... ...A..AV.......    A/Teal/Hong Kong/W312/97(H6N1)
   6 A-H6N1:     . ...N. ... ....TTV.DT... ...A..AV....S..    A/chicken/Taiwan/1215/01(H6N1)
   6 A-H6N2:     . ...R. ... ....TDA.N.... ...A..VV.......    A/chicken/California/905/01(H6N2)
   5 A-H6N2:     . ...R. ... ....TNA.N.... ..SA..VV.......    A/Chicken/California/6643/2001(H6N2)
   5 A-H6N2:     . ..... ... ....DN....... ...S...V.......    A/pintail duck/ALB/133/1978(H6N2)
   5 A-H6N3:     . ..... ... ............. ...............    A/mallard duck/ALB/76/1985(H6N3)
   5 A-H6N6:     . ..... ... ............. .......V.......    A/widgeon/ALB/256/1982(H6N6)
   4 A-H6N2:     . ..... ... ............. ...G...........    A/shoveler/ALB/114/1985(H6N2)
   4 A-H6N5:     . ...R. ... ....TN..NT... ...A..AV.......    A/Shearwater/Australia/1/72(H6N5)

                ....A.....LN..SESVS..TK....SPGA.--------..
  39 A-H7N2:     Y GATSA WLN HSESVSEQTKLYG SPGAR--------RI     A/turkey/VA/67/02(H7N2)
  22 A-H7N1:     . ..... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Italy/977/99 (H7N1)
  22 A-H7N1:     . .T..T ... ..G.TT....... ...E.PQVNGQSG..    A/turkey/Italy/5074/99 (H7N1)
  20 A-H7N7:     . ..... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Germany/R11/01(H7N7)
  15 A-H7N3:     . ..... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Oregon/1971(H7N3)
  14 A-H7N3:     . ..... ... ..G.AT....... .....PQVNGQSG..    A/Turkey/Colorado/13356/91 (H7N3)
   8 A-H7N2:     . .T... ... ............. .T.............    A/Chicken/Pennsylvania/13552-1/98 (H7N2)
   8 A-H7N7:     . ...N. ... ..G.TT....... .....PQVNGQSG..    A/Mallard/Sweden/93/02(H7N7)
   7 A-H7N1:     . ..... ... ..G.TA....... .....PQVNGQSG..    A/parrot/England/1174/94(H7N1)
   7 A-H7N2:     . ..... ... ..G.......... .....PQVNGQSG..    A/Chicken/Rhode Island/4328/95 (H7N2)
   6 A-H7N3:     . .V... ... ..G.AN....... .....PQVNGQSG..    A/turkey/Chile/4418/02(H7N3)
   5 A-H7N1:     . .T... ... ..G.TT....... .....PQVNGQSG..    A/turkey/Italy/4857/99 (H7N1)
   4 A-H7N1:     . ..... ... ..V.TT....... .L...PQVNGQSG..    A/turkey/Italy/4042/99 (H7N1)
   4 A-H7N1:     . ..... ... ..V.TT....... .....PQVNGQSG..    A/turkey/Italy/2715/99 (H7N1)
   4 A-H7N2:     . ..... ... ............. N..............    A/guineafowl/NY/4649-18/2006(H7N2)
   4 A-H7N3:     . ..... ... ..G.AN....... .....PQVNGQSG..    A/Quail/Arkansas/16309-7/94 (H7N3)
   4 A-H7N3:     . ....S ... ..G.TT...R... .....PQVNGQSG..    A/peregrine falcon/U.A.E./188/2384/98(H7N3)
   4 A-H7N7:     - ----- --- ..G.TT....... .....PQVNGQSG..    A/Mongolia/736/02(H7N7)

                ....E..........G.TA...R....N..P.PQINGQSG..
   6 E-H7N7:     Y GETSA WLN HSGSTAEQTRLYG NPGPRPQINGQSGRI     A/equine/Sao Paulo/1/76(H7N7)

                ....A......S......T...K....S..A...V.......
   1 H-H7N1:     Y GATSA WLS HSGSTTEQTKLYG SPGARPQVNGQSGRI     A/Hong Kong/301/78(H7N1)

                ....T......N..........R...................
   1 S-H7N7:     Y GTTSA WLN HSGSTTEQTRLYG SPGARPQVNGQSGRI     A/seal/Mass/1/80(H7N7)

                .....SK....K..PPD.K...T..K.NI.P..L.R..Q..M
   7 A-H8N4:     Y GTSKA WLK HPPDTKEQTTLYK NIGPRPLVRGQQGRM     A/Turkey/Ontario/6118/68(H8N4)

                ...........T....TDTA..N..T.L.......N.L...I
  39 A-H9N2:     Y GTSKA WLT HPPTDTAQTNLYT LIGPRPLVNGLQGRI     A/Silky Chicken/Hong Kong/SF44/99(H9N2)
  17 A-H9N2:     . ..... ... ............I V......A.......    A/turkey/Tzur Moshe/1565/04(H9N2)
  17 A-H9N2:     . ..... ... ......V...... ...............    A/wild duck/Nanchang/2-0480/2000(H9N2)
  16 A-H9N2:     . ..... ... ......E.....K V.........Q....    A/mallard/Alberta/321/88(H9N2)
  14 A-H9N2:     . ..... ... ......E.M...K V.........Q....    A/silky chicken/Korea/S3/03(H9N2)
  13 A-H9N2:     - ----- --- ----........I V......A.......    A/turkey/Shadmot Dvorah/1567(H9N2)
  11 A-H9N2:     - ----- --- ----..E.....I V.........Q....    A/turkey/Sapir/1199/02(H9N2)
  11 A-H9N2:     . ..... ... ......V...... ..........Q....    A/duck/Hubei/W1/2004(H9N2)
  10 A-H9N2:     - ----- --- ----........I V..............    A/turkey/Kfar Vitkin/616/02 (H9N2)
  10 A-H9N2:     . ..... ... ............. V.........Q....    A/chicken/Shandong/7/96(H9N2)
   9 A-H9N2:     . ..... ... ............I V..............    A/turkey/Kfar Vitkin/616/02 (H9N2)
   8 A-H9N2:     . ..... ... ............. M.........Q....    A/Chicken/Shanghai/F/98(H9N2)
   7 A-H9N2:     - ----- --- ----........I V......A..Q....    A/turkey/Nahalal/1547/04(H9N2)
   6 A-H9N2:     - ----- --- -...E.......I M.........Q....    A/chicken/Iran8/01(H9N2)
   6 A-H9N2:     . ..... ... ............. V..............    A/quail/Nanchang/2-0460/2000(H9N2)
   6 A-H9N2:     . ..... ... ......E.....I V.........Q....    A/turkey/Yedidia/911/02(H9N2)
   6 A-H9N2:     . ..... ... ......T...... ...............    A/Quail/Shanghai/8/96(H9N2)
   6 A-H9N2:     . ..... ... ......V...... V.........Q....    A/Chicken/Sichuan/5/97(H9N2)
   6 A-H9N2:     . ...R. ... ......E.....K V.........Q....    A/turkey/Germany/R33/96(H9N2)
   6 A-H9N2:     . ...R. ... ....Y.E.....I V..............    A/Quail/Hong Kong/SSP10/99(H9N2)
   5 A-H9N1:     . ..... ... .....AE.....K V.........Q....    A/mallard/Alberta/743/83(H9N1)
   5 A-H9N2:     . ..... ... ............I V......A..Q....    A/turkey/Gyvat Haim Ehud/1544/03(H9N2)
   5 A-H9N2:     . ..... ... ......E.I...K V.....P...Q....    A/chicken/SNU0146/2000(H9N2)
   5 A-H9N2:     . ..... ... ......T...... ..........Q....    A/chicken/Yunnan/Xie-1/1999(H9N2)
   5 A-H9N2:     . ..... ... ......T...... V.........Q....    A/duck/Nanjing/2/97(H9N2)
   5 A-H9N2:     . ...R. ... ......V..E... M.........Q....    A/Chicken/Shijiazhuang/2/99(H9N2)
   4 A-H9N2:     . ..... ... .....AE.....K V.........Q....    A/Duck/Hong Kong/366/78(H9N2)
   4 A-H9N2:     . ..... ... ............. ..........Q....    A/Chicken/Yunnan/1/99(H9N2)
   4 A-H9N2:     . ..... ... ......E.I...K V.........Q....    A/duck/Hokkaido/49/98(H9N2)
   4 A-H9N2:     . ..... ... N............ S..............    A/Duck/Shantou/2144/00(H9N2)
   4 A-H9N2:     . ...R. ... ......E..D..K V.........Q....    A/Turkey/Wisconsin/66(H9N2)

                ......R..........Y.E.....I.V..............
   3 H-H9N2:     Y GTSRA WLT HPPTYTEQTNLYI VIGPRPLVNGLQGRI     A/Hong Kong/1074/99(H9N2)

                ......K..........D...M...K...........Q....
   4 S-H9N2:     Y GTSKA WLT HPPTDTEQMNLYK VIGPRPLVNGQQGRI     A/swine/Korea/S83/2004(H9N2)
   4 S-H9N2:     . ..... ... ......V.T...T ..........LH...    A/Swine/Hong Kong/9/98(H9N2)

                .....T.....K...SSTQ.KND..G..V.A..Q....S...
  17 A-H10N:     Y GTTKA WLK HPSSTQEKNDLYG VVGARPQVNGQSGRI     A/Shorebird/Taiwan/31-4/99)]

                .............................R............
   1 M-H10N:     Y GTTKA WLK HPSSTQEKNDLYG VVRARPQVNGQSGRI     /Mink/4(HA)/H10N4/Sweden/1984

                ....V.A....I...ATLK.HQ...K.EIST..K....A..M
  12 A-H11N:     Y GVTAA WLI HPATLKEHQDLYK EISTRPKVNGQAGRM     A/swan/Shimane/48/1997(H11N2)

                ....TSK....T...P.SD.QVK....N.GP..L.R..Q...
   6 A-H12N:     Y GTSKA WLT HPPTSDEQVKLYK NIGPRPLVRGQQGRM     A/ruddy turnstone/DE/97/2000(H12N5)

                .....TS...FI...VSV..TKT..V.ET.V..GYN..RSW.
   3 A-H13N:     Y GTTSA WFI HPVSVDETKTLYV ETGVRPGYNGQRSWM     A/Gull/Maryland/704/77(H13N6)

                ....SS....LK...S.DN.QTD..K.NI.S..RVRN.SGRI
   1 A-H14N:     Y GSSSA WLK HPSSDNEQTDLYK NIGSRPRVRNQSGRI     A/mallard duck/Astrakhan/263/1982(H14N5)

                ....AT.....S..S..LD..NK..G.SP.A..K.NG.A...
   5 A-H15N:     Y GATSA WLS HSSSLDEQNKLYG SPGARPKVNGQAGRI     A/wedge-tailed shearwater/Western Australia/2576/1979(H15N9)

                .F..T.AS...V..PDTEATA....V.EI.T.-IGD..RSWM
   3 A-H16N:     F GTTAS WLV HPDTEATANKLYV EIGTR-IGDGQRSWM     A/black-headed gull/Sweden/4/99(H16N3)
    I'm interested in expert panflu damage estimates
    my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

    Comment

    • #32
      Re: swine flu sequences (thread from h5n1experts)

      -----------------posted:2009/11/19-----------------

      Code:
                                           0000000001111122 00000011111111112222 00000000001111112 00000000000000000000001111111 0000111111 000000001111 00000000 000000000  
                                     0345567890245901 33777901344666671111 12345578890223890 00111124444555556667780002445 2355112223 223377891233 22346678 001345677  
                                     4564462715015866 02799655336478970889 95092551440035939 03134465679136771252991185066 9522141247 030124058134 13390969 774647409  
                                     2746717821722013 02058980291870636473 82658839025066341 67455831088647692083662407843 8124836781 483612840524 31320612 058794089  
-codon-position----------------------  2 1112 1121     12   21 2 1  1                     2   1  112111       21 121   1   1  22 1     1 1111 1          21 1 11211 1  
---Index-----------------------------CCGGCGAGGAGCGGGG ACCGTAATCAATTGAACCCG TAGACTAGACCCTCCTT GGACCCCGCAAACAGACGTAGCGCGACCG GGAGCGAGGC CGTGGAACGTCA GAGGGCCG GTCATGCTA  
   1 >A/******/index/2009/02/01      ................ .................... ................. ............................. .......... ............ ........ .........  
   3 >A/WI/629-D01844/2009/06/15     ...A.......T.... G.....G.......G..T.. C..G.C...T....... ....A.......T................ .......... .A........T. ........ .........  
   4 >A/WI/629-D01313/2009/05/08     ...A.......T.... G.....G.......G..... C..G............. ....A........................ .......... .A........T. ........ .........  
   5 >A/WI/629-D01619/2009/06/15     ...A.......T.... G.....G.......G..... C..G............. ....A........................ .......... .A........T. ........ .........  
   6 >A/WI/629-D02013/2009/05/30     ...A.......T.... G.....G.......G..... C..G............. ....A........................ .......... .A........T. ........ .........  
   7 >A/WI/629-D00022/2009/06/02     ...A.......T.... G.....G.......G..T.. C..G.C...T....... ....A.......T................ .......... .A........T. ........ .........  
   8 >A/WI/629-D02220/2009/06/21     ...A.......T.... G.....G.......G..... C..G............. ....A..................T..... .......... .A........T. ........ .........  
   9 >A/WI/629-S0252/2009//          .T.A............ GT....G............. ................. ....A........G..............A .......... ............ ........ ........G  
  10 >A/WI/629-D02263/2009/06/12     .T.A............ GT....G............. ................. ....A........G..............A .......... ............ ........ ........G  
  11 >A/WI/629-D00724/2009/06/01     .T.A............ GT....G............. ................. ....A........G..............A .......... ............ .....Y.. ........G  
  12 >A/WI/629-S0035/2009//          .T.A............ GT....G............. ................. ....A........G..............A .......... ............ ........ ........G  
  13 >A/WI/629-D02312/2009/05/02     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  14 >A/WI/629-D02452/2009/05/08     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  15 >A/WI/629-D01226/2009/05/04     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  16 >A/WI/629-D00790/2009/05/04     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  17 >A/WI/629-D00722/2009/05/19     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  18 >A/WI/629-D01606/2009/05/03     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  19 >A/WI/629-D00725/2009/06/04     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  20 >A/WI/629-S0319/2009//          ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  21 >A/WI/629-D01154/2009/05/13     ...AA........... .................... ................. .A.................G.T....... .......... ............ ........ .........  
  22 >A/WI/629-D00244/2009/05/02     ................ .................... ................. ............................. ...AT..... ............ ........ .........  
   2 >A/WI/09/2009/04/27             ---------------- -------------------- ----------------- ........................A.... ....T..... ............ ........ ---------  
  23 >A/WI/629-D02473/2009/05/03     ................ ...............G.... ................. ............................. .......... ............ ........ .........  

 189 >A/Cancun-NY/Index/2009/04/15   ...............A .................... ................. ..................A.......T.. A....A..A. ...A.G...... ...AA... ...G.....  
  24 >A/WI/629-D01147/2009/06/14     ...............A .................... ....T..A......... .......A..........A.......TT. A....A..A. ...A.G...... ...AA... .C.G.....  
  25 >A/WI/629-D01445/2009/05/24     ...............A .................... ....T..A......... .......A..........A.......TT. A....A..A. ...A.G...... ...AA... .C.G.....  

  39 >A/WI/629-D01664/2009/06/03     ..............A. ..........T......... ................. .................A........T.. A....A...T ...A.G.T.... .....T.A .........  
  65 >A/WI/629-D00658/2009/06/04     ................ ........T........... ................. .................A........T.. A....A.... ...A.G.T.... .....T.A .........  
  26 >A/WI/629-D01764/2009/05/04     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  27 >A/WI/629-D00228/2009/05/06     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  28 >A/WI/629-D02206/2009/05/23     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  29 >A/WI/629-D01773/2009/04/30     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  30 >A/WI/629-D00428/2009/06/20     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... A....T.A .........  
  31 >A/WI/629-D01308/2009/05/01     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .......C.  
  32 >A/WI/629-D01189/2009/05/02     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .......C.  
  33 >A/WI/629-D02262/2009/05/02     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .......C.  
  34 >A/WI/629-D00119/2009/06/14     ........A....... .................... ................. ................T.........T.. A.G..A.... ...A.G.T.... .....T.A .........  
  35 >A/WI/629-D01779/2009/05/28     ........A....... .................... ................. ................T.........T.. A.G..A.... ...A.G.T.... .....T.A .........  
  36 >A/WI/629-D01861/2009/05/01     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  37 >A/WI/629-D02427/2009/05/20     ................ ....C.....T......... ................. ..........................T.. A....A...T ...A.G.T.... .....T.A .........  
  38 >A/WI/629-D00367/2009/06/02     ................ ....C.....T......... ................. ..........................T.. A....A...T ...A.G.T.... .....T.A .........  
  40 >A/WI/629-D00496/2009/06/20     ..............A. ..........T......... C..G............. ..........................T.. A....A...T ...A.G.T.... .....T.A .........  
  41 >A/WI/629-S0255/2009//          ..............A. ..........T......... ................. ..........................T.. A....A...T ...A.G.T.C.. .....T.A .........  
  42 >A/WI/629-D00426/2009/05/29     ..............A. ..........T......... ................. ..........................T.. A....A...T ...A.G.T.... .....T.A .........  
  43 >A/WI/629-D02324/2009/05/25     ................ ..........T......... ................. ..........................T.. A....A...T ...A.GGT.... .....T.A .........  
  44 >A/WI/629-S0314/2009//          ................ ..........T......... ................. ..........................T.. A....A...T ...A.GGT.... .....T.A ....C....  
  45 >A/WI/629-D02292/2009/06/30     ................ ..........T......... ................. ..........................T.. A....A...T ...A.GGT.... .....T.A ....C....  
  46 >A/WI/629-D01837/2009/05/14     ................ ..........T......... ................. ..........................T.. A....A...T ...A.G.T.... .....T.A .........  
  47 >A/WI/629-D01505/2009/04/28     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  48 >A/WI/629-D00064/2009/05/14     ............A... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  49 >A/WI/629-D00179/2009/05/10     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  50 >A/WI/629-S0202/2009//          ................ ...................A ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  51 >A/WI/629-D01414/2009/06/27     ................ ...................A ................. ....................T.....T.. AA...A.... ..CA.G.T.C.. .....T.A .........  
  52 >A/WI/629-D02276/2009/05/27     ................ .................... ................. .........G..........T.....T.. AA...A.... ...A.G.T.C.. .....T.A .........  
  53 >A/WI/629-D00665/2009/06/13     ................ .................... ................. ...T................T.....T.. AA...A.... ...A.G.T.... .....T.A .........  
  54 >A/WI/629-D02068/2009/06/08     ................ .................... ................. ...T................T.....T.. AA...A.... ...A.G.T.... .....T.A .........  
  55 >A/WI/629-S0189/2009//          ................ .................... ................. ...T................T.....T.. AA...A.... ...A.G.T.... .....T.A .........  
  56 >A/WI/629-D00905/2009/05/08     ................ .................... ................. ....................T.....T.. AA...A.... ...A.G.T.... .....T.A .........  
  57 >A/WI/629-D00396/2009/05/04     ................ .................... ................. ....................T.....T.. AA...A.... ...A.G.T.... .....T.A .........  
  58 >A/WI/629-D01083/2009/05/28     ................ .................... ...........T..... ..G.................T.....T.. AA.A.A.... ...AAG.T.... .....T.A .........  
  59 >A/WI/629-D02213/2009/05/29     ................ ........T........... ...........T..... ..G.................T.....T.. AA.A.A.... ...AAG.T.... .....T.A .........  
  60 >A/WI/629-S0229/2009//          ................ ........T........... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  61 >A/WI/629-D00989/2009/05/17     ................ ........T........... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  62 >A/WI/629-D00451/2009/05/23     ................ ........T........... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  63 >A/WI/629-S0173/2009//          ................ ........T........... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
  64 >A/WI/629-D00949/2009/05/27     ................ ........T........... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  66 >A/WI/629-S0220/2009//          ................ ........T........... ................. A.........................T.. A....A.... ...A.G.T.... .....T.A .........  
  67 >A/WI/629-D01152/2009/06/15     ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  68 >A/WI/629-S0293/2009//          ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  69 >A/WI/629-S0197/2009//          ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  70 >A/WI/629-S0203/2009//          ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  71 >A/WI/629-D00541/2009/06/16     ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  72 >A/WI/629-D00196/2009/06/13     ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  73 >A/WI/629-S0464/2009//          ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  74 >A/WI/629-S0206/2009//          ................ ........T.........T. ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  75 >A/WI/629-D02024/2009/06/22     ................ ........T......G.... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  76 >A/WI/11/2009/05/04             ---------------- -------------------- ----------------- ..........................T.. A....A.... ...A.G.T.... -------- ---------  
  77 >A/WI/629-S0148/2009//          ..A...T......... ................T... ................C ..........................T.. A....A.... ...A.G.T.... .G...T.A .........  
  78 >A/WI/629-D01199/2009/06/09     ..A...T......... ................T... ................C ..........................T.. A....A.... ...A.G.T.... .G...T.A .........  
  79 >A/WI/629-D00160/2009/05/19     ..A...T......... .................... ................C ..........................T.. A....A.... ...A.G.T.... .G...T.A .........  
  80 >A/WI/629-D00807/2009/05/04     ..A...T......... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  81 >A/WI/629-D02272/2009/05/04     ......T......... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  82 >A/WI/629-D00767/2009/04/30     ......T......... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  83 >A/WI/629-D02432/2009/05/04     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  84 >A/WI/629-D00714/2009/05/04     ................ ...A................ ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  85 >A/WI/629-D00575/2009/05/16     ................ ...A................ ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  86 >A/WI/629-D00997/2009/05/14     ................ ...A........C....... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  87 >A/WI/629-S0339/2009//          ................ ...A........C....... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  88 >A/WI/629-S0226/2009//          ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  89 >A/WI/629-D00447/2009/04/30     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  90 >A/WI/629-D02361/2009/04/30     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  91 >A/WI/629-D00698/2009/05/27     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... A....T.A .........  
  92 >A/WI/629-D00967/2009/05/16     ............A... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  93 >A/WI/629-D00750/2009/04/30     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  94 >A/WI/629-D02408/2009/05/02     ..........A..... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  95 >A/WI/629-D01793/2009/05/01     ..........A..... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  96 >A/WI/629-D02064/2009/05/22     ................ .................... ............C.... .........G................T.. A....A.... ...A.G.T.... .....T.A .........  
  97 >A/WI/629-D01919/2009/05/09     ................ .................... ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  98 >A/WI/629-D00752/2009/05/19     ................ .................... ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
  99 >A/WI/629-D01521/2009/05/20     ................ .................... ............C.... ......A...................T.. A....A.... T..A.G.T.... .....T.A .........  
 100 >A/WI/629-D00941/2009/06/01     ................ .................... ............C.... ......A...................T.. A....A.... T..A.G.T.... .....T.A .........  
 101 >A/WI/629-D01894/2009/05/26     ................ .................... ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 102 >A/WI/629-D01296/2009/05/03     ................ .....C.............. ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 103 >A/WI/629-D01909/2009/05/08     T............... .....C.............. ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 104 >A/WI/629-D00117/2009/05/28     T............... .....C.............. ............C.... ...............G..........T.. A....A.... ...A.G.T.... .....T.A .........  
 105 >A/WI/629-S0143/2009//          T............... .....C.............. ............C.... ...............G..........T.. A....A.... ...A.G.T.... .....T.A .........  
 106 >A/WI/629-D01725/2009/06/01     T............... .....C.............. ............C.... ...............G..........T.. A....A.... ...A.G.T.... .....T.A .........  
 107 >A/WI/629-D01880/2009/05/04     ................ .....C.............. ............C.... ..........................T.. A....A.... ..CA.G.T.... .....T.A .........  
 108 >A/WI/629-D01810/2009/05/04     ................ .....C.............. ............C.... ........................A.T.. A....A.... ...A.G.T.... .....T.A .........  
 109 >A/WI/629-D00487/2009/05/07     ................ .....C.............. ............C.... ..........................T.. A....A.... .....G.T.... .....T.A .........  
 110 >A/WI/629-D01017/2009/05/03     ................ .....C.............. ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 111 >A/WI/629-D02425/2009/05/04     ................ .....C.............. ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 112 >A/WI/629-D01980/2009/05/02     ................ .....C.............. ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 113 >A/WI/629-D01851/2009/05/12     ................ .................... ............C.... ........T.................T.. A....A.... ...A.G.T.... .....T.A .....A...  
 114 >A/WI/629-D01642/2009/04/29     ................ .................... ............C.... ........T.................T.. A....A.... ...A.G.T.... .....T.A .....A...  
 115 >A/WI/629-S0208/2009//          ................ .................... ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 116 >A/WI/629-S0435/2009//          ................ .................... ............C.... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 117 >A/WI/629-D00015/2009/04/30     ................ .................... ................. ...........G..............T.. A....A.... ...A.G.T.... .....T.A .........  
 118 >A/WI/629-D00349/2009/05/04     ................ .................... ................. ...........G..............T.. A....A.... ...A.G.T.... .....T.A .........  
 119 >A/WI/629-D02141/2009/04/30     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 120 >A/WI/629-D00084/2009/05/19     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 121 >A/WI/629-D00677/2009/05/01     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 122 >A/WI/629-D01962/2009/05/04     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 123 >A/WI/629-D01486/2009/04/29     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 124 >A/WI/629-D00933/2009/05/02     ..........A..... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 125 >A/WI/10/2009/05/04             ---------------- -------------------- ----------------- ..........................T.. A....A.... ...A.G.T.... .....T.A ---------  
 126 >A/WI/629-D01295/2009/05/15     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 127 >A/WI/629-D01817/2009/05/01     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 128 >A/WI/629-D01482/2009/05/10     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 129 >A/WI/629-D01529/2009/04/30     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 130 >A/WI/629-D00008/2009/06/04     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 131 >A/WI/629-D00378/2009/05/04     ................ .................... ......G.......... ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 132 >A/WI/629-D01735/2009/05/02     ................ .................... ......G.......... ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 133 >A/WI/629-D00498/2009/05/03     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 134 >A/WI/629-S0279/2009//          ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 135 >A/WI/629-D01839/2009/05/15     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 136 >A/WI/629-D00978/2009/05/14     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 137 >A/WI/629-D01058/2009/05/04     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 138 >A/WI/629-D00869/2009/05/03     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 139 >A/WI/629-D01787/2009/05/20     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ..A......  
 140 >A/WI/629-D00223/2009/05/30     ................ .................... ..........T...... ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 141 >A/WI/08/2009/04/27             ---------------- -------------------- ----------------- ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 142 >A/WI/629-D01326/2009/06/11     ................ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 143 >A/WI/629-S0248/2009//          ................ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 144 >A/WI/629-S0146/2009//          ................ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 145 >A/WI/629-D02144/2009/05/28     ................ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 146 >A/WI/629-D00101/2009/06/08     .......A........ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 147 >A/WI/629-S0086/2009//          .......A........ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 148 >A/WI/629-S0247/2009//          ................ .................... ................. ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 149 >A/WI/629-D00829/2009/05/28     ................ .................... ..........T...... ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 150 >A/WI/629-D01883/2009/05/27     .....T.......... .................... ..........T...... ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 151 >A/WI/629-S0410/2009//          .....T.......... .................... .G............... ......................A...T.. A....A.... ...A.G.T.... .....T.A .........  
 152 >A/WI/629-D02298/2009/05/22     ................ .................... .G............... ..........................T.. A....A.A.. ...A.G.T.... .....T.A A........  
 153 >A/WI/629-D01734/2009/06/16     ................ .................... .G............... ..........................T.. A....A.A.. ...A.G.T.... .....T.A A........  
 154 >A/WI/629-S0201/2009//          ................ .................... .G............... ..........................T.. A....A.A.. ...A.G.T.... .....T.A A........  
 155 >A/WI/629-D00434/2009/05/16     ................ .................... .G............... ..........................T.. A....A.A.. ...A.G.T.... .....T.A A........  
 156 >A/WI/629-D02455/2009/05/02     ................ .................... ................. ..........................T.. A....AG... ...A.G.T.... .....T.A .........  
 157 >A/WI/629-D01558/2009/04/30     ................ .................... ................. ..........................T.. A....AG... ...A.G.T.... .....T.A .........  
 158 >A/WI/629-D02063/2009/06/18     ................ .................... ................. .........................GT.. A....AG... ...A.G.T.... .....T.A .........  
 159 >A/WI/629-S0269/2009//          ................ .................... ................. .........................GT.. A....AG... ...A.G.T...G .....T.A .........  
 160 >A/WI/629-D00453/2009/06/04     ................ ..T................. ..A.....G........ .........................GT.. A....AG... ...A.G.T...G .....T.A .........  
 161 >A/WI/629-D00017/2009/06/04     ................ ..T................. ..A.....G........ A.........................T.. A....A.... ...A.G.T.... .....T.A .........  
 162 >A/WI/629-S0245/2009//          ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 163 >A/WI/629-D01092/2009/05/03     .........G...... .......C.....A...... ................. .....T........A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 164 >A/WI/629-D01055/2009/05/09     .........G...... .......C...C.A...... ................. .....T........A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 165 >A/WI/629-D01618/2009/06/13     .........G...A.. .......C.....A...... ..............T.. .....T........A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 166 >A/WI/629-D01262/2009/05/28     .........G...A.. .......C.....A...... ..............T.. .....T........A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 167 >A/WI/629-D00579/2009/06/08     .........G...A.. .......C.....A...... ................. .....T........A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 168 >A/WI/629-D02227/2009/05/16     .........G...... .......C...C.A...... ................. .....T........A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 169 >A/WI/629-D01305/2009/05/13     .........G...... .......C.....A...... ................. ..............A...........T.. A....A.... ...A.G.T.... .....T.A .........  
 170 >A/WI/629-D01705/2009/05/03     ................ .................... ................. ......T...................T.. A....A.... ...A.G.T.... .....T.A .........  
 171 >A/WI/629-D00592/2009/06/02     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A ......T..  
 172 >A/WI/629-D00374/2009/06/01     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... A....T.A ......T..  
 173 >A/WI/629-S0186/2009//          ................ .................... ................. .......................T..T.. A....A.... ...A.G.T.... A....T.A .........  
 174 >A/WI/629-D01886/2009/05/27     ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... A....T.A .........  
 175 >A/WI/629-D01903/2009/06/05     ................ .................... ................. ..........................T.. A....A.... ...A.G.TA... A....T.A .........  
 176 >A/WI/629-D01026/2009/05/28     ................ .................... ................. ..........................T.. A....A.... ...A.G.TA... A....T.A .........  
 177 >A/WI/629-S0222/2009//          ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... A....T.A .........  
 178 >A/WI/629-S0280/2009//          ................ .................... ................. ..........................T.. A....A.... ...A.G.T.... A....T.A .........  
 179 >A/WI/12/2009/05/07             ---------------- -------------------- ----------------- ..........................T.. ---------- ...A.G.T.... -------- ---------  
 180 >A/WI/629-S0345/2009//          ......T......... .................... ................. ..........................T.. A....A.... ...A.G.T.... .....T.A .........  
 181 >A/WI/07/2009/04/27             ---------------- -------------------- ----------------- ..........................T.. ---------- ...A.G.T.... -------- ---------  
 182 >A/WI/629-S0254/2009//          ................ .............A...... .............T... ..........................T.. A....AG... ...A.G.T.... .....T.A .........  
 183 >A/WI/629-D01415/2009/05/04     ................ .........G.......... .............T... ..........................T.. A....AG... ...A.G.T.... .....T.A .........  
 184 >A/WI/629-D01251/2009/05/04     ................ .........G.......... .............T... ..........................T.. A....AG... ...A.G.T.... .....T.A .........  
 185 >A/WI/629-D00183/2009/05/04     ................ .........G.......... .............T... .......................T..T.. A....AG... ...A.G.T.... .....T.A .........  
 186 >A/WI/629-D02028/2009/05/01     ................ .................... ................. ..........................T.. A....AG... ...A.G.T.... .....T.A .........  
 187 >A/WI/629-D01847/2009/05/29     ................ .................... ...............C. ..........C...............T.. A....A.... ...A.G.T.... ..A..TTA .........  
 188 >A/WI/629-D00916/2009/06/14     ................ .................... ...............C. ..........C...............T.. A....A.... ...A.G.T.... ..A..TTA .........  
 189 >A/Cancun-NY/Index/2009/04/15   ...............A .................... ................. ..................A.......T.. A....A..A. ...A.G...... ...AA... ...G.....  
                                                                                                                                                                       
---Index-----------------------------CCGGCGAGGAGCGGGG ACCGTAATCAATTGAACCCG TAGACTAGACCCTCCTT GGACCCCGCAAACAGACGTAGCGCGACCG GGAGCGAGGC CGTGGAACGTCA GAGGGCCG GTCATGCTA  
-codon-position----------------------  2 1112 1121     12   21 2 1  1                     2   1  112111       21 121   1   1  22 1     1 1111 1          21 1 11211 1  
                                     0000000001111122 00000011111111112222 00000000001111112 00000000000000000000001111111 0000111111 000000001111 00000000 000000000  
                                     0345567890245901 33777901344666671111 12345578890223890 00111124444555556667780002445 2355112223 223377891233 22346678 001345677  
                                     4564462715015866 02799655336478970889 95092551440035939 03134465679136771252991185066 9522141247 030124058134 13390969 774647409  
                                     2746717821722013 02058980291870636473 82658839025066341 67455831088647692083662407843 8124836781 483612840524 31320612 058794089
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment

      • #33
        Re: swine flu sequences (thread from h5n1experts)

        ---------------posted:2009/11/19-----------------

        Code:
                                             0000112 000112 00011 000000000111111 000111 000000000111 00000 00000   
                                     0158361 445091 15767 122556678014566 236112 223467788033 45669 02337   
                                     7799036 157598 86974 414074513670629 902144 481954609927 92060 97677   
                                     2749853 401859 01771 590760861838365 814838 036842277792 22047 49795   
-codon-position----------------------   2      12 2   2 1 1    112   1    11 2    11  1   2 1    11 1 111   
---Index-----------------------------TATAGGG GTGACT AAGGA CCATGGTATGGCGAT GGGCGG GAGTTAGGGGAC GGGCG TGAAA   
   1 >A/******/index/2009/02/01      ....... ...... ..... ............... ...... ............ ..... .....   
  13 >A/Texas/15/2009/04/15          ....... ...... ..... ............... ...... ............ ..... .....   
  39 >A/Arizona/03/2009/04/26        ------- ------ ----- ............... ------ ............ ..... -----   
  40 >A/Arizona/01/2009/04/22        ....... ...... ..... ............... ...... ............ ..... .....   
  41 >A/Arizona/04/2009/04/27        ------- ------ ----- ............... ------ ............ ..... -----   
  42 >A/Arizona/07/2009/05/07        ------- ------ ----- --------------- ...... ............ ----- .....   

   4 >A/Texas/06/2009/04/23          ....A.. .C.... ----- ..........A.A.. ...... ............ .A... ....G   
   5 >A/Texas/08/2009/04/24          ....A.. .C.... .C... ..........A.A.. ...... ............ .A... ....G   
   6 >A/Texas/05/2009/04/15          ....A.. .C.... .C... .......G..A.A.. ...... ............ .A... ....G   
   7 >A/Texas/11/2009/04/23          ------- ------ ----- .......G..A.A.. .A.... ...........T .A... -----   
   8 >A/Texas/10/2009/04/23          ------- ------ ----- .......R..A.A.. ...... ...........T .A... -----   
   9 >A/Texas/12/2009/04/24          ------- ------ ----- ..........A.A.. ...... ............ .A... -----   
  10 >A/Texas/22/2009/04/26          C...A.. .C.... .C.A. ..........A.A.. ...... A........... .A... C...G   
  11 >A/Texas/09/2009/04/25          C...A.. .C.... .C.A. ..........A.A.. ...... A........... .A... C...G   
  12 >A/Texas/04/2009/04/14          ....A.. .C.... .C... ..........A.A.. ...... ............ .A... ....G   

  28 >A/Texas/35/2009/05/08          ------- ------ ----- --------------- ...T.. ....C....... ----- .....   
  29 >A/Texas/42122969/2009//        ....... ....T. ....C ....A....A..... ...T.. ....C....... ..... .....   
  30 >A/Texas/07/2009/04/25          ....... ....T. ----- ....A....A..... ...T.. ........A... ..... .....   
  31 >A/Texas/28/2009/04/29          ------- ------ ----- ....A....A..... ...T.. ........A... ..... -----   
  32 >A/Texas/34/2009/05/12          ------- ------ ----- ....A....A..... ------ ........A... ..... -----   
  33 >A/Texas/36/2009/04/29          ------- ------ ----- ....A....A..... ------ ............ ..... -----   
  34 >A/Texas/29/2009/05/02          ------- ------ ----- ....A....A...G. ------ .......T.... ----- -----   
  35 >A/Texas/30/2009//              ------- ------ ----- ....A....A...G. ...T.. .......T.... ..... -----   
  36 >A/Arizona/02/2009/04/26        ....... ...... ..A.C ............... ...T.. ............ ..... .....   
  37 >A/Arizona/06/2009//            ------- ------ ----- ............... ...T.. .G.......... ..... -----   
  38 >A/Texas/42113095/2009//        ....... ...... ....C ............... ...T.. .G.......... ..... .....   
  43 >A/Texas/20/2009/04/25          ------- ------ ----- .T.C..........C ------ ............ ..... -----   
  44 >A/Texas/17/2009/04/24          ------- ------ ----- .T.C..........C .A.T.. ............ ..... -----   
  45 >A/Texas/37/2009/04/26          ------- ------ ----- .T.C..........C ------ ............ ..... -----   
  46 >A/New Mexico/04/2009/04/26     ....... ...... ....C ............... ...T.. ............ ..... .....   
   2 >A/Texas/47/2009//              ------- ------ ----- A.............. ------ ............ ----- -----   
  47 >A/Houston/9OS/2009/05/21       .....A. ..A... ....C A.......C...... ...T.. .G.......... ....A .....   
  48 >A/Houston/1OS/2009/05/13       .....A. ..A... ....C A.......C...... ...T.. .G.......... ....A .....   
  49 >A/Houston/2H/2009/05/18        .....A. ..A... ....C A.......C...... ...T.. .G.......... ....A .....   
  50 >A/Texas/42123701/2009//        ...G... ...GT. ....C ..T..T......... ...T.. ...C..A..A.. ...A. ...G.   
  51 >A/Texas/42191653/2009//        ...G... ...GT. ....C ..T..T......... ...T.. ...C..A..A.. ...A. ...G.   
   3 >A/Arizona/09/2009/05/19        ....... ------ G.A.C ............... ...T.. ............ ----- .....   

  14 >A/Texas/45062633/2009//        ......A ...... ..... ......A....T... A...AA ..A..G...... A.A.. ..G..   
  15 >A/Texas/43242018/2009//        ......A ...... G.... ......A....T... A...AA ..A..G...... A.A.. ..G..   
  16 >A/Arizona/05/2009/04/26        ------- ------ ----- --------------- ------ ..A..G...... A.A.. -----   
  17 >A/Texas/42152486/2009//        .TC...A A....C ..... ......A....T... A.A.AA ..A..G...... A.A.. .AG..   
  18 >A/Texas/43011033/2009//        .TC...A A....C ..... ......A....T... A.A.AA ..A..G...... A.A.. .AG..   
  19 >A/Texas/32/2009/05/11          ------- ------ ----- ......A....T... ------ ..A..G...... A.A.. -----   
  20 >A/Texas/42114261/2009//        .T....A .....C ..... ......A....T... A.A.AA ..A..G...... A.A.. .AG..   
  21 >A/Texas/42173957/2009//        .T....A .....C ..... ......A....T... A.A.AA ..A..G...... A.A.. .AG..   
  22 >A/Texas/42201824/2009//        .T....A .....C ..... ......A....T... A.A.AA ..A..G...... A.A.. .AG..   
  23 >A/Texas/39/2009/05/22          ------- ------ ----- ......A....T... ------ ..A..G...... ----- -----  
 
  24 >A/Texas/23/2009/04/27          ....... ...... ----- ...........T... A...A. ..A..G...... ..... .....   
  25 >A/Texas/19/2009/04/26          ------- ------ ----- ...........T... A...A. ..A..G....C. ..... .....   
  26 >A/Texas/33/2009/05/12          ------- ------ ----- --------------- ------ ..A..G....C. ..... -----  
  27 >A/Texas/31/2009/05/12          ------- ------ ----- ...........T... ------ ------------ ----- -----   

  52 >A/Cancun-NY/Index/2009/04/15   ......A ...... ..... ......A....T... A...AA ..A..G...... A.A.. ..G..   
                                                                                                            
---Index-----------------------------TATAGGG GTGACT AAGGA CCATGGTATGGCGAT GGGCGG GAGTTAGGGGAC GGGCG TGAAA   
-codon-position----------------------   2      12 2   2 1 1    112   1    11 2    11  1   2 1    11 1 111   
                                     0000112 000112 00011 000000000111111 000111 000000000111 00000 00000   
                                     0158361 445091 15767 122556678014566 236112 223467788033 45669 02337   
                                     7799036 157598 86974 414074513670629 902144 481954609927 92060 97677   
                                     2749853 401859 01771 590760861838365 814838 036842277792 22047 49795
        I'm interested in expert panflu damage estimates
        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

        Comment

        • #34
          Re: swine flu sequences (thread from h5n1experts)

          ---------------posted:2009/11/19---------------------

          Code:
                                               0000011111222 000000011112 0000111111 000000000111111111111111111 00011111111 0000000000011111 000000 0000000000 
                                     1125823567011 358888927992 0478034677 011122667122222233446666666 24911222334 2222345577900233 466789 1136778888 
                                     1144718771236 673458516594 3842900849 404616561722223335050467778 92414489553 4458114748549322 909613 5864243444 
                                     0456981743323 617452720551 7013851114 565766856367890109852497890 86383893674 7873640126447039 206073 3973489124 
-codon-position----------------------2 2   12  12   1 1    22   1  1   11   112 2122 2 12 11 1   1 12  1 12  2  1  12211  11   2       11    11112121 
---Index-----------------------------GGAGGAAAAATAG AGGCTAGTTCCT ACCCGTGAAC AGCGTCTGAGCAGTAGGCCCTGATCTA GCCCGGGGGCC GTCAGCACAGCAGACA GGCTTG CAACGTTATA 
   1 >A/******/index/2009/02/01      ............. ............ .......... ........................... ........... ................ ...... .......... 

 113 >A/MexCity/59/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G....T---- ------ ---------- 
 115 >A/MexCity/22/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 121 >A/MexCity/25/2009/05/02        ------------- ------------ ---------- --------------------------- ----------- ------G.....---- ------ ---------- 
 122 >A/MexCity/72/2009/05/04        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 132 >A/MexCity/28/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 138 >A/MexCity/34/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------GT....---- ------ ---------- 
 142 >A/MexCity/35/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 143 >A/MexCity/27/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 144 >A/MexCity/56/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 145 >A/MexCity/62/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 146 >A/MexCity/36/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 147 >A/MexCity/32/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 148 >A/MexCity/12/2009/05/01        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 149 >A/MexCity/51/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 150 >A/MexCity/14/2009/05/01        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 151 >A/MexCity/52/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 152 >A/MexCity/103/2009/05/04       ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 153 >A/MexCity/7/2009/05/01         ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 154 >A/MexCity/2/2009/05/01         ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 155 >A/MexCity/68/2009/05/05        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 156 >A/MexCity/30/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 157 >A/MexCity/21/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 161 >A/MexCity/104/2009/05/04       ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 163 >A/MexCity/24/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ------G.....---- ------ ---------- 
 159 >A/MexCity/75/2009/05/05        ------------- ------------ ---------- ---------.............----- ----------- ------G.G.T.---- ------ ---------- 
  92 >A/MexCity/44/2009/05/03        ------------- ------------ ---------- --------------------------- ----------- ------G.G...---- ------ ---------- 
  93 >A/MexCity/20/2009/05/01        ------------- ------------ ---------- ---------R............----- ----------- ------G.G...---- ------ ---------- 
  94 >A/MexCity/9/2009/05/01         ------------- ------------ ---------- ---------.............----- ----------- ------G.G...---- ------ ---------- 
  95 >A/MexCity/45/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G.G...---- ------ ---------- 
  96 >A/MexCity/54/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ------G.G...---- ------ ---------- 
  97 >A/MexCity/66/2009/05/05        ------------- ------------ ---------- ---------.............----- ----------- ------G.G...---- ------ ---------- 
  98 >A/MexCity/1/2009/05/01         ------------- ------------ ---------- ---------.............----- ----------- ------G.G...---- ------ ---------- 
 112 >A/MexCity/33/2009/05/02        ------------- ------------ ---------- ---------........T....----- ----------- ------G....G---- ------ ---------- 
 111 >A/MexCity/018/2009/05/10       .....G....... ............ .......... .................T......... ........... ...........G.... ...... .......... 

  60 >A/Mex/InDRE13495/2009/04/29    ...A......... ............ .......... ........................... ........... ................ ...... .......... 
  61 >A/MexCity/88/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
  62 >A/Mex/InDRE13494/2009/04/29    ............. ............ .......... ........................... ........... ................ ...... .......... 
  63 >A/MexCity/3/2009/05/01         ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 

  99 >A/MexCity/23/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 100 >A/Mex/4115/2009/04/07          ..G.......... ............ ...A.....T ........................... ........... ................ ...... .......... 
 101 >A/Mex/InDRE4115/2009//         ..G.......... ............ ...A...... ........................... ........... ................ ...... .......... 
 102 >A/MexCity/93/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 103 >A/MexCity/017/2009/05/09       ...A......... ............ .......... ........................... ........... .......T........ ...... .......... 
 104 >A/MexCity/19/2009/05/01        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 106 >A/MexCity/10/2009/05/01        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 107 >A/Mex/InDRE4487/2009/04/14     ..G.......... ............ ...A...... ........................... ........... ................ ...... .......... 
 109 >A/Mex/InDRE4114/2009//         ............. ............ .......... ........G.................. ........... ................ ...... .......... 
 110 >A/MexCity/009/2009/05/12       ...A......... ............ .......... ........................... ........... ................ ...... .......... 
 120 >A/MexCity/102/2009/05/02       ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 123 >A/MexCity/43/2009/05/03        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 125 >A/MexCity/80/2009/05/05        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 128 >A/MexCity/89/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 131 >A/MexCity/83/2009/05/01        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 133 >A/MexCity/91/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 135 >A/MexCity/101/2009/05/02       ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 137 >A/MexCity/95/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 139 >A/MexCity/84/2009/05/01        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 141 >A/MexCity/8/2009/05/01         ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 158 >A/MexCity/85/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 160 >A/MexCity/82/2009/05/05        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 
 162 >A/MexCity/29/2009/05/02        ------------- ------------ ---------- ---------.............----- ----------- ---------------- ------ ---------- 

  55 >A/Mex/4486/2009/04/14          .......G..... ............ ........C. .........------------------ ...T....... ................ ...... .......... 
  56 >A/Mex/3955/2009/04/03          ------------- ------------ ---------- ........GA......A....A..... ----------- ................ .....A ---------- 
  57 >A/Mex/4108/2009/04/03          ............. ............ ........C. .........A......A....A..... ...T....... ................ .....A .......... 
  58 >A/Mex/4269/2009/04/15          .......G..... ............ ........C. ........................... ...T....... ................ ...... .......... 
  59 >A/Mex/4627/2009/04/20          ------------- ------------ ---------- .........A................. ...T....... ................ ------ ---------- 
 105 >A/Mex/4646/2009/04/20          ............. ..........T. ---------- ........................... ...T....... ................ ...... ---------- 
 116 >A/Mex/6882/2009/04/26          ..........C.. ------------ ---------- --------------------------- ...T....... ---------------- ------ .......... 
 124 >A/MexCity/005/2009/05/08       ............. ..........T. ........C. ........................... ...T....... ................ ...... .......... 
 126 >A/Mex/47N/2009/04/25           ............. .A.......... ........C. ..A.C...................... ...T....... A..G.........G.. ...... .......... 
 127 >A/Mex/48N/2009/04/25           ............. .A.......... ........C. ..A.C...................... ...T....... A..G.........G.. ...... .......... 
 129 >A/Mex/4176/2009/04/13          ------------- ............ ........C. ........................... ...T....... .........A...... ------ .......... 
 130 >A/New Mex/04/2009/04/26        ..........C.. ............ ........C. ........................... ...T....... ................ ...... .......... 
 136 >A/MexCity/004/2009/05/08       .......G..... ........C... ........C. ........................... ...T....... .............G.. ...... .......... 
 140 >A/MexCity/015/2009/05/09       ............. .A.......... ........C. ..A........................ ...T....... ...G............ ...... .......... 

 108 >A/Mex/InDRE13547/2009/04/27    ............. ............ .......... .......A................... A.......... ..T............. ...... .......... 
 114 >A/Mex/4516/2009/04/25          ------------- ------------ ---------- --------------------------- A...A...... ---------------- .....A ---------- 
  15 >A/MexCity/WR1087T/2009/06/19   CA........... ............ .......... ......................T.... A..TA...... ....A...G......C ...... ......GTCT 
 134 >A/Mex/4593/2009/04/20          ------------- ------------ ---------- ........................... ----------- ....A...G....... ------ ---------- 
   2 >A/MexCity/WR1307N/2009/09/14   C...AG...G... ...T........ G.A.A.TT.. TA.A.A....GCCAGT..TT..T.... ATT.A..A.G. ....AT..G.....T. ...C.. ......GTCT 
   3 >A/MexCity/WR1301N/2009/09/12   C...AG...G... ...TG....... G.A.A.TT.. TA.A.A............TT..-ATAG ATT.A..A.G. ....AT..G.....T. ...C.. ......GTCT 
   4 >A/MexCity/63/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
   5 >A/MexCity/6/2009/05/01         ------------- ------------ ---------- ---------.........T...----- ----------- ------G.....---- ------ ---------- 
   6 >A/MexCity/37/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
   7 >A/MexCity/002/2009/05/08       .........G... ............ .......... ..................T........ A...A...... ....A...G....... ...... .......... 
   8 >A/MexCity/98/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
   9 >A/MexCity/003/2009/05/08       ...........G. ............ .......... ..................T........ A...A.A.... ....A...G.T..... ..T... .......... 
  10 >A/MexCity/006/2009/05/09       ...........G. ............ .......... ..................T........ A...A.A.... ....A...G.T..... ..T... ........-- 
  11 >A/MexCity/001/2009/05/07       ............. ............ .......... ..................T........ A...A...... ....A...G.T..... ..T... .......... 
  12 >A/MexCity/011/2009/05/09       ............. ............ .......... ..................T........ A...A...... ..T.A...G......C ...... .......... 
  13 >A/MexCity/012/2009/05/09       ............. ............ .......... ..................T.C...... A...A...... ....A...G......C ...... .....C.... 
  14 >A/Mex/4635/2009/04/20          ............. ............ .......... ..................T........ A...A...... ....A...R......C ...... ---------- 
  16 >A/Mex/4482/2009/04/14          ------------- ............ .......... ..................T........ A...A...... ....A...G....... ....C. .......... 
  17 >A/MexCity/77/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  18 >A/MexCity/46/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.....---- ------ ---------- 
  19 >A/MexCity/94/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  21 >A/MexCity/86/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  22 >A/MexCity/013/2009/05/09       ............. ............ .......... ..................T........ A...A...... ....A...G....... ...... .......... 
  23 >A/MexCity/76/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  24 >A/Mex/4604/2009/04/19          ............. ............ .......... ..................T........ A...A...... ....A...G....... ...... .......... 
  25 >A/MexCity/96/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  26 >A/MexCity/010/2009/05/09       ............. ............ .......... ..................T........ A...A...... ....A...G......C ...... ........-- 
  27 >A/MexCity/90/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  28 >A/MexCity/18/2009/05/01        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  29 >A/Mex/4283/2009/04/15          ------------- ------------ .......... ..................T........ A...A...... ---------------- ------ T......... 
  30 >A/MexCity/31/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  31 >A/MexCity/38/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  32 >A/MexCity/008/2009/05/10       ............. ............ .......... .......A..........T........ AT..A...... ....A...G....... ...... .......... 
  33 >A/MexCity/50/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  34 >A/Mex/4595/2009/04/20          ............. ------------ ---------- ..................T........ A...A...... ....A...G......C ------ T......... 
  35 >A/MexCity/100/2009/05/02       ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  41 >A/MexCity/97/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  42 >A/MexCity/007/2009/05/09       ............. .....GAC.... .......... ..................T........ A...A...... ....A...G....... ...... .......... 
  43 >A/MexCity/74/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  44 >A/MexCity/71/2009/05/04        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  45 >A/MexCity/49/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.GA..---- ------ ---------- 
  46 >A/MexCity/87/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  47 >A/Mex/4603/2009/04/19          ............. ............ .......... ..................T........ A...A...... ....R...G......C ....C. .......... 
  48 >A/MexCity/42/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  49 >A/MexCity/11/2009/05/01        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G.T.---- ------ ---------- 
  53 >A/MexCity/47/2009/05/03        ------------- ------------ ---------- --------------------------- ----------- ------G.G.T.---- ------ ---------- 
 117 >A/MexCity/70/2009/05/04        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G.T.---- ------ ---------- 
 118 >A/MexCity/13/2009/05/01        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G.T.---- ------ ---------- 
 119 >A/MexCity/15/2009/05/01        ------------- ------------ ---------- --------------------------- ----------- ------G.G.T.---- ------ ---------- 
  50 >A/MexCity/79/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  51 >A/Mex/InDRE13551/2009/04/28    ............. ............ ......A... ..................T........ A...A...... ....A...G....... ...... .......... 
  52 >A/MexCity/41/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  54 >A/MexCity/60/2009/05/03        ------------- ------------ ---------- ---------.........T.C.----- ----------- ---------------- ------ ---------- 
  64 >A/MexCity/106/2009/05/05       ------------- ------------ ---------- --------------------------- ----------- ------G.....---- ------ ---------- 
  65 >A/Mex/4502/2009/04/17          ------------- ............ ---------- ..................T........ ----------- ---------------- ------ ---------- 
  66 >A/Mex/4575/2009/04/20          ------------- ------------ ---------- ..................T........ ----------- ....A...G....... ------ ---------- 
  67 >A/Mex/InDRE13555/2009/04/29    ............. .....GAC.... .......... ..................T........ A...A...... ....A...G....... ...... .......... 
  68 >A/MexCity/81/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  69 >A/MexCity/40/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  70 >A/MexCity/99/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  71 >A/MexCity/67/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ------G..A..---- ------ ---------- 
  72 >A/MexCity/78/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  73 >A/MexCity/39/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  74 >A/MexCity/4/2009/05/01         ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  75 >A/MexCity/64/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  76 >A/MexCity/48/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  77 >A/MexCity/61/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  78 >A/MexCity/65/2009/05/05        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  79 >A/MexCity/69/2009/05/04        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  80 >A/MexCity/73/2009/05/04        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  81 >A/MexCity/105/2009/05/04       ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  83 >A/MexCity/26/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  84 >A/MexCity/57/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  85 >A/MexCity/53/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  86 >A/MexCity/92/2009/05/02        ------------- ------------ ---------- ---------.........T...----- ----------- ---------------- ------ ---------- 
  87 >A/MexCity/55/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  88 >A/MexCity/16/2009/05/01        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  89 >A/MexCity/58/2009/05/03        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  90 >A/MexCity/17/2009/05/01        ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 
  91 >A/MexCity/5/2009/05/01         ------------- ------------ ---------- ---------.........T...----- ----------- ------G.G...---- ------ ---------- 

  20 >A/MexCity/WR1100N/2009/06/29   CA..........A ............ .......... ......A...........T........ A...AA..... ....A...G....... AA.... ..G...GTCT 
  82 >A/MexCity/WR1306N/2009/09/02   C....G......A ............ .........T ......A...........T...-ATAG A...AA..... ....A...G....... AA.... ..G..CGTCT 
  36 >A/MexCity/WR1308T/2009/09/04   C....GG.G...A G.AT....G..C .T...C.... ......A...........T........ A...AA....T ....A...G...A... AA.... .GGTA.GTCT 
  37 >A/MexCity/WR1297N/2009/09/03   CA...GG.G...A G.ATG...GT.C .T...C.... ......A...GCCAGT..T...T.... A...AA....T ....A...G...A... AA.... .GGTA.GTCT 
  38 >A/MexCity/WR1311T/2009/09/10   C.....G.G...A G..TG...GT.C .T...C.... ......A...GCCAGT..T...T.... A...AA..A.T .C..A...G...A... AA.... .GGTA.GTCT 
  39 >A/MexCity/WR1310N/2009/09/09   C.....G.G...A G.......GT.C .T...C.... ......A...GCCAGT..T...G.... A...AA..A.T .C..A...G...A... AA.... .GGTA.GTCT 
  40 >A/MexCity/WR1312N/2009/09/10   C.....G.G...A G..T....GT.C .T...C.... ......A...........T...T.... A...AA..A.T .C..A...G...A... AA.... .GGTA.GTCT 

 164 >A/Cancun-NY/Index/2009/04/15   ............A ............ .......... ......A...........T........ A...AA..... ....A...G....... AA.... ..G....... 
                                                                                                                                                      
---Index-----------------------------GGAGGAAAAATAG AGGCTAGTTCCT ACCCGTGAAC AGCGTCTGAGCAGTAGGCCCTGATCTA GCCCGGGGGCC GTCAGCACAGCAGACA GGCTTG CAACGTTATA 
-codon-position----------------------2 2   12  12   1 1    22   1  1   11   112 2122 2 12 11 1   1 12  1 12  2  1  12211  11   2       11    11112121 
                                     0000011111222 000000011112 0000111111 000000000111111111111111111 00011111111 0000000000011111 000000 0000000000 
                                     1125823567011 358888927992 0478034677 011122667122222233446666666 24911222334 2222345577900233 466789 1136778888 
                                     1144718771236 673458516594 3842900849 404616561722223335050467778 92414489553 4458114748549322 909613 5864243444 
                                     0456981743323 617452720551 7013851114 565766856367890109852497890 86383893674 7873640126447039 206073 3973489124
          I'm interested in expert panflu damage estimates
          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

          Comment

          • #35
            Re: swine flu sequences (thread from h5n1experts)

            -------------posted:2010/01/03-------------

            amino-acids 134-138,153-155,184-196,216-230
            in H3 enumeration , add 14 for H1-enumeration


            RBDs of mxh6p with counts:

            Code:
            ................x................x.....   positions 190 and 225 marked with "x"
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM,1542
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVREQEGRM,82
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRGQEGRM,17
GVTAA WLV HPSTNADQQSLYQ EIAIRPKVRDQEGRM,13
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRDPEGRM,13
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRDREGRM,11
GITAA WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM,8
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVR-QEGRM,8
GVTTA WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM,7
----- WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM,6
----- --- HPSTSADQQSLYQ EIAIRPKVR------,5
GVTAA WLV HPSTSADQQSIYQ EIAIRPKVRDQEGRM,5
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRNQEGRM,5
----- --- ------------- EIAIRPKVRDQEGRM,4
GVTAA WLV HPSTSADQQSLYQ ---------------,4
GVTAA WLI HPSTSADQQSLYQ EIAIRPKVRDQEGRM,3
GVTAA WLV ------------- ---------------,3
GVTAA WLV HPRTSADQQSLYQ EIAIRPKVRDQEGRM,3
GVTAA WLV HPSTSADQQSQYQ EIAIRPKVRDQEGRM,3
...

            RBDs of h1x with counts:
            Code:
            ................x................x.....
GVSAS WLT HPPNIGDQRALYH EIAKRPKVRDQEGRI,1103
GVSAS WLT HPPNIGDQKALYH EIAKRPKVRDQEGRI,519
GVSAS WLT HPPNIGDQMTLYH EIAKRPKVRDQEGRI,194
GVSAS WLT HPPNIGNQRALYH EIAKRPKVRDQEGRI,118
GVTAS WLT HPSNIGDQRAIYH EIAKRPKVRDQEGRI,79
GVTAA WLV HPPTSTDQQSLYQ EIAARPKVRGQAGRM,77
GVSAS WLT HPPNIVPQKTLYR EIAKRPKVRDQEGRI,49
GVTAA WLV HPSTSADQQSLYQ EIATRPKVRDQAGRM,47
GVSAS WLT HPPNIGDQRTLYH EITKRPKVRDQEGRI,45
GVTAS WLT HPSNIEDQKTIYR EIAKRPKVRNQEGRI,45
GVSAS WLT HPPNIGNQKALYH EIAKRPKVRDQEGRI,43
GVSAS WLT HPPNIVDQKTLYR EIAKRPKVRDQEGRI,41
GVSAS WLT HPPNIVNQKTLYR EIAKRPKVRDQEGRI,33
GVSAS WLT HPPNIADQKTLYH EIAKRPKVRDQEGRI,32
----- --- ------------- ---------------,30
GVSAS WLT HPPNIGDQRALYH ---------------,30
GVTAS WLT HPSNIGDQRAIYH ---------------,25
GVTAA WLV HPPTSTDQQSLYQ EIATRPKVRGQAGRM,24
GVSAS WLT HPPSINDQKTLYH EIAKRPKVRDQEGRI,22
GVTAS WLT HPSNIGDQRAIYH EIAKRPKVRGQEGRI,21
GVSAS WLT HPPNIGVQRALYH EIAKRPKVRDQEGRI,20
GVSAS WLT HPPNIENQRTLYH EITKRPKVRDQEGRI,19
GVTAS WLT HPSNIEDQKTIYR EIAERPKVRGQAGRI,19
GVSAS WLT HPPNIGPQKALYH EIAKRPKVRDQEGRI,18
GVSAS WLT HPPNIGPQRALYH EIAKRPKVRDQEGRI,18
GVSAS WLT HPPNIGDQKTLYH EIAKRPKVRDQEGRI,17
GVSAS WLT HPPNIGNQRTLYH EITKRPKVRDQEGRI,17
GVSAS WLT NPPNIGDQKALYH EIAKRPKVRDQEGRI,17
GVTAS WLT HPSNMGDQRAIYH EIAKRPKVRDQEGRI,17
GVSAS WLT HPPNIGDQRAL-- ---------------,16
GVSAS WLT HPPN--------- ---------------,14
GVSAS WLT HPPNIGVQKALYH EIAKRPKVRDQEGRI,14
GVSAS WLT HPPNINDQKALYH EIAKRPKVRDQEGRI,14
GVTAS WLT HPSNMGDQRAIYH EIARRPKVRDQEGRI,14
GVSAS WLT HPPSISDQKTLYH EIAKRPKVRDQEGRI,13
GVTAA WLV HPPTSTDQQTLYQ EIAARPKVRDQAGRM,13
GVSAS WLT HPPNIGDQRALYH EIAKRPKVRNQEGRI,11
GVSAS WLT HPPNIGNQMTLYH EIAKRPKVRDQEGRI,11
GVSAS WLT HPPNIGDQNTLYH EIAKRPKVRDQEGRI,10
GVSAS WLT HPPNIGGQKALYH EIAKRPKVRDQEGRI,9
GVTAA WLI HPSTSADQQSLYQ EIATRPKVRDQAGRM,9
GVTAS WLT HPSNIEDQKTIYR EIAKRPKVRDQEGRI,9
GVSAS WLT HPPNIGAQKALYH EIAKRPKVRDQEGRI,8
GVSAS WLT HPPNIGNQRTLYN EIAKRPKVRDQEGRI,8
GVTAS WLT HPSNIGDQRAIYH EITKRPKVRDQEGRI,8
GVTAS WLT HPSNIRDQRAIYH EIAKRPKVRDQEGRI,8
GVSAS WLT HPPNIGDQRTLYN EIAKRPKVRDQEGRI,7
GVSAS WLT HPPSISDQKTLYH EVAKRPKVRDQEGRI,7
GVSAS WLT HPSNIGVQRAIYH EIAKRPKVRGQEGRI,7
GVTAA WLT HPPNSKEQQNLYQ EIAERPKVRDQAGRM,7
GVTAA WLV HPPTSNDQQSLYQ EIAARPKVRGQAGRM,7
GVTAS WLT HPSNIEDQKTIYR EIAKRPKVRGQEGRI,7
GVSAS WLT HPPNIANQKTLYH EIAKRPKVRDQEGRI,6
GVSAS WLT HPPNIGDQRALYH EIAKRPKVRGQEGRI,6
GVSAS WLT HPPNIGDQRTLYY EIAKRPKVRDQEGRI,6
GVSAS WLT HPPNIRDQRALYH EIAKRPKVRDQEGRI,6
GVSAS WLT HPPTIGDQSTLYH EIAKRPKVRDQEGRI,6
GVTAA WLT HPSNIEDQKTLYR EIAERPKVRGQAGRI,6
GVTAA WLV HPPTSADQQSLYQ EIATRPKVRDQAGRM,6
GVTSA WLV HPPTSTDQQSLYQ EIATRPKVRGQAGRM,6
GGSAS WLT HPPNIGDQRALYH EIAKRPKVRDQEGRI,5
GVSAS WLT HPPDIGPQKTLYH EIAKRPKVRDQEGRI,5
GVSAS WLT HPPNIAPQKTLYH EIAKRPKVRDQEGRI,5
GVSAS WLT HPPNIGDQRALYH EIAKRPKVRDREGRI,5
GVSAS WLT HPPNIGVQMTLYH EIAKRPKVRDQEGRI,5
GVSAS WLT HPPSISNQKTLYH EVAKRPKVRDQEGRI,5
GVSAS WLT HPSNIGDQRAIYH EIAKRPKVRDQEGRI,5
GVTAA WLT HPSNIKDQQTLYQ EIAERPKVRGQAGRM,5
GVTAA WLV HPPTSTDQQSLYQ EIASRPKVRGQAGRM,5
GVTAA WLV HPSTSADQQSLYQ EIAIRPKVRDQEGRM,5
GVSAS WLT HPPDIGNQKTLYH EIAKRPKVRDQEGRI,4
GVSAS WLT HPPNIGDQKALYH EIAKRPKVRGQEGRI,4
GVSAS WLT HPPNIGDQRALYH EITKRPKVRDQEGRI,4
GVSAS WLT HPPNIGNQKTLYH EIAKRPKVRDQEGRI,4
GVSAS WLT HPPNIGPQMTLYH EIAKRPKVRDQEGRI,4
GVSAS WLT HPSNIGDQRALYH EIAKRPKVRDQEGRI,4
GVSAS WLT HPSNIGVQRAIYH EIAKRPKVRDQEGRI,4
GVTAA WLT HPSNIGDQRAIYH EIAKRPKVRGQEGRI,4
GVTAA WLT HPSNSKDQQNIYQ EIAERPKVRDQAGRM,4
GVTAA WLV HPPTSADQQSLYQ EIATRPKVRNQAGRM,4
GVTAS WLT HPSNIGDQRAIYH EIAKRPKVRNQEGRI,4
GVTAS WLT HPSNIRDQRAIYH EIAKRPKVRGQEGRI,4
...
            I'm interested in expert panflu damage estimates
            my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

            Comment

            • #36
              Re: swine flu sequences (thread from h5n1experts)

              ---------------posted:2010/03/14-------------------

              [11] Nelson M, Spiro D, Wentworth D, Beck E, Fan J, et al. (2009) The early diversification of Influenza A/H1N1pdm. PLoS Currents Influenza

              Page not available - PMC
              http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2773564/?tool=pubmed



              amino-acid markers:
              1:S224P*(PA),S100P*(HA),A214T*(HA),V338I*(HA),
              2:M581L*(PA),T373I(NP)
              3:
              4:V649I*(PB2),I667T(PB1),V100I(NP),V106I(NA),E63K( NS2)
              5:V100I*(NP),V106I*(NA),N248D(NA)
              6:K2E(HA),Q310H*(HA),V100I(NP),V106I(NA),N248D(NA)
              7:S220T(HA),V100I*(NP),V106I(NA),N248D*(NA),I123V( NS1)


              3 must be my "original Meico"
              7 must be my "Cancun"
              2 must be my "Northern"
              1 must be my "early USA"
              4 must be my "Japan"
              5 must be my "pre-Cancun"
              6 must be my "Wisconsin" (?)

              (where is my airplane-SC-Cancun2 ?)



              7 substrains H1N1, India study:
              Genetic Characterization of the Influenza A Pandemic (H1N1) 2009 Virus Isolates from India - FluTrackers News and Information
              http://www.flutrackers.com/forum/showthread.php?p=346828#post346828


              * Clade 1 included amongst others the California/04/2009 and California/07/2009 isolates

              * Clade 2 included isolates from Mexico, California, Canada, France, Germany, Netherlands, China and multiple US states

              * clade 3 - France, England, Russia, China, Canada, Mexico and the US states;

              * clade 4?two east Asian countries, Korea and Japan;

              * clade 5?Canada, China, Japan, the USA (mainly Wisconsin isolates) with an addition of Thailand and

              *clade 6?Canada, Italy, China, Japan with new additions of Germany, Taiwan, Thailand and few US states.

              * clade 7 which was the largest clade included isolates from Canada, China, Japan, Germany, Italy, Luxembourg, Russia and several states of the USA with Taiwan, Denmark, Singapore, Malaysia, Central and South America getting added.
              I'm interested in expert panflu damage estimates
              my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

              Comment

              • #37
                Re: swine flu sequences (thread from h5n1experts)

                Thank you Gsgs for also posting these on FluTrackers.

                Comment

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