Announcement

**gsgs** · April 28, 2009, 07:39 AM

Re: swine flu sequences, data only

differences in promille to other selected genomes for each of the 8 segments.
Some segments may be partial only, zeros indicate non-available segments

updated 29.4.

Code:

 32 >A/California/04/2009-04-01/(H1N1)                   
  1:151,107,118,492,162,497, 66,308   A/Ck/Germany/n/1949(H10N7)
  2:153,135,117,497,162,498, 81,152   A/fowl/Dobson/1927(H7N7)
  3:153,250,116,549,164,  0, 79,151   A/Ck/Brescia/1902(H7N7)
  4:153,134,116,499,168,171, 90,153   A/FPV/Rostock/34(H7N1)
  5:150,131,116,500,164,168, 88,151   A/fowl/Rostock/45/1934(H7N1)
  6:148,124,118,501,157,463, 76,163   A/turkey/England/1963(H7N3)
  7:153,130, 80,365,157,485, 69,158   A/duck/Germany/1215/1973(H2N3)
  8:155,127, 93,369,155,482, 66,166   A/tern/South Africa/1961(H5N3)
  9:146,108,106,368,159,133, 72,160   A/Ck/Scotland/1959(H5N1)
 10:156,144,100,351,168,148, 91,162   A/human/China/GD02/06(H5N1)
 11:153,145,110,361,170,149, 88,158   A/Bar-h Gs/Qinghai/62/05(H5N1)
 12:160,138, 93,354,168,145, 90,174   A/duck/Shandong/093/2004(H5N1)
 13:153,133, 90,382,151,143, 76,301   A/duck/Taiwan/0526/72(H6N1)
 14:154,135, 95,383,151,142, 76,299   A/chicken/Taiwan/G2/87(H6N1)
 15:153,132, 73,376,164,434, 76,166   A/shearwater/Australia/1/1973(H6N5)
 16: 98,126, 96,463,164,435, 91,159   A/pintail/Alberta/49/2003(H12N5)
 17:103,121,  0,488,164,361, 92,150   A/mallard duck/ALB/581/1983(H4N4)
 18:114,180,139,451,166,357, 87,158   A/turkey/Ontario/6118/1968(H8N4)
 19:114,180,139,451,166,357, 87,158   A/turkey/Ontario/6118/1968(H8N4)
 20: 93,111,139,432,158,504, 92,163   A/turkey/Wisconsin/1/1966(H9N2)
 21:108,118,145,432,160,507, 94,163   A/turkey/Wisconsin/66(H9N2)
 22:112,114,140,429,166,508, 90,295   A/Turkey/California/189/66(H9N2)
 23: 92,100,123,500,158,490, 92,291   A/turkey/Oregon/1971(H7N3)
 24: 49, 60, 58,500,  0,  0,  0,  0   A/swine/Minnesota/SG-00241/2007(H1N1)
 25: 49, 50, 57, 62, 54,199,120, 50   A/swine/OH/511445/2007(H1N1)
 26: 49, 51, 57,500,  0,  0,  0,  0   A/swine/Illinois/SG-00244/2007(H1N1)
 27: 50, 50, 57, 63, 55,199,120, 54   A/swine/Ohio/24366/07(H1N1)
 28: 47, 49,  0, 64,  0,205,128,  0   A/swine/Ohio/C62006/06(H1N1)
 29: 48, 51, 58,500,  0,  0,  0,  0   A/swine/Minnesota/SG-00240/2007(H1N1)
 30: 46, 47, 46, 89, 44,201,124, 51   A/Iowa/CEID23/2005(H1N1)
 31: 34, 31, 44, 54, 36,201,119, 45   A/Wisconsin/10/98(H1N1)
 32:  0,  0,  0,  0,  0,  0,  0,  0   A/California/04/2009-04-01/(H1N1)
 33: 51, 53, 54,500,  0,  0,  0,  0   A/swine/Minnesota/SG-00238/2006(H1N1)
 34: 30, 36, 45, 49, 31,503,113, 41   A/Turkey/MO/24093/99(H1N2)
 35: 30, 34, 37,500,  0,  0,  0,  0   A/mallard duck/South Dakota/Sg-00125/2007(H3N2)
 36: 96,131, 67,479,164,443, 90,290   A/pintail/Alaska/779/2005(H3N8)
 37:153,130, 85,489,156,441, 62,300   A/duck/Chabarovsk/1610/1972(H3N8)
 38:156,107, 92,490,151,442, 70,164   A/Dk/UKR/1/1963(H3N8)
 39:150,120,119,495,150,448, 84,157   A/quail/Italy/1117/1965(H10N8)
 40:149,116,108,499,158,494, 75,162   A/duck/Czechoslovakia/1956(H4N6)
 41:148,113, 98,418,167,493, 74,166   A/duck/England/1956(H11N6)
 42:110,174,143,433,172,485, 96,297   A/duck/Memphis/546/1974(H11N9)
 43:101,122,143,387,164,496,114,152   A/pintail duck/ALB/189/1982(H6N6)
 44: 82,121,146,243,164,137, 97,146   A/pigeon/MN/1407/1981(H1N1)
 45: 83,123,142,242,167,136, 88,153   A/pintail duck/ALB/219/1977(H1N1)
 46: 83,123,142,242,167,136, 88,153   A/pintail duck/ALB/219/1977(H1N1)
 47: 80,118,121,240,168,136, 98,147   A/mallard duck/ALB/127/1977(H1N1)
 48: 98,118,129,241,160,138, 89,151   A/mallard duck/ALB/46/1977(H1N1)
 49: 92,121,123,242,172,145, 97,152   A/mallard duck/Tennessee/11464/1985(H1N1)
 50: 96,126,127,246,166,150, 92,151   A/mallard/Ohio/56/1999(H1N1)
 51: 96,126,126,246,166,150, 92,151   A/pintail/Ohio/25/1999(H1N1)
 52: 95,126,125,246,166,150, 93,151   A/green-winged teal/Ohio/72/1999(H1N1)
 53: 95,126,125,246,166,150, 92,150   A/mallard/Ohio/66/1999(H1N1)
 54:100,130, 94,251,164,151, 93,158   A/mallard/MD/170/2002(H1N1)
 55:100,131, 92,251,160,150, 91,158   A/mallard/MD/02-181/2002(H1N1)
 56:100,131, 92,251,161,150, 91,159   A/mallard/MD/382/2002(H1N1)
 57:100,130, 93,251,162,152, 92,159   A/mallard/MD/369/2002(H1N1)
 58:100,130, 93,251,162,152, 92,159   A/mallard/MD/390/2002(H1N1)
 59:101,131, 92,251,161,150, 91,160   A/mallard/MD/02-375/2002(H1N1)
 60:102,130, 92,252,162,151, 91,159   A/mallard/Maryland/350/2002(H1N1)
 61:101,131, 92,252,162,150, 91,159   A/mallard/MD/02-359/2002(H1N1)
 62:100,130, 92,251,160,151, 92,160   A/mallard/MD/161/2002(H1N1)
 63:100,130, 92,251,160,151, 91,160   A/mallard/MD/02-184/2002(H1N1)
 64:100,130, 92,251,160,150, 92,160   A/mallard/MD/163/2002(H1N1)
 65:101,131, 92,251,162,151, 92,159   A/mallard/MD/406/2002(H1N1)
 66:100,128, 95,249,161,152, 94,158   A/mallard/MD/168/2002(H1N1)
 67: 81,126, 92,250,166,150, 92,159   A/mallard/MD/403/2002(H1N1)
 68: 74,122, 77,243,161,148, 93,152   A/mallard/Ohio/171/1990(H1N1)
 69: 78,122, 75,243,167,146, 89,150   A/mallard duck/ALB/322/1988(H1N1)
 70: 73,127, 76,245,163,145, 97,293   A/turkey/SD/7034/1986(H1N1)
 71: 74,127, 76,243,165,145, 91,252   A/blue winged teal/LA/B228/1986(H1N1)
 72: 87,125, 92,242,160,154, 89,295   A/mallard/ALB/201/1998(H1N1)
 73: 99,120,125,248,171,156, 97,293   A/pintail duck/Alberta/210/2002(H1N1)
 74: 85,120,128,242,167,136, 90,290   A/mallard duck/ALB/965/1979(H1N1)
 75: 80,121,123,248,165,142, 95,293   A/green-winged teal/Ohio/430/1987(H1N1)
 76: 79,118, 72,242,163,139, 92,290   A/pintail duck/ALB/238/1979(H1N1)
 77: 88,132, 54,245,170,148, 92,295   A/blue-winged teal/Alberta/141/1992(H1N1)
 78:106,129, 94,248,171,158, 96,297   A/muscovy duck/New York/21211-5/2005(H1N1)
 79:106,121, 95,251,168,158, 96,294   A/swine/Saskatchewan/18789/02(H1N1)
 80: 96,127, 85,242,161,149, 90,294   A/duck/NJ/7717-70/1995(H1N1)
 81: 94,129, 78,245,157,201, 96,295   A/turkey/MO/21939/1987(H1N1)
 82:103,124, 81,246,163,152,103,152   A/quail/IN/38685/1993(H1N1)
 83: 60,129, 81,248,160,150, 92,156   A/black duck/Ohio/95/1993(H1N1)
 84: 60,130, 81,249,161,150, 92,152   A/mallard/Ohio/118/1993(H1N1)
 85:108,138, 80,250,160,150, 97,146   A/duck/NY/13152-13/1994(H1N1)
 86:158,128,125,246,158, 80, 50,171   A/swine/Germany/2/1981(H1N1)=1578
 87:158,136,132,255,156, 82, 43,179   A/swine/Virginia/670/1987(H1N1)
 88:158,136,131,253,155, 81, 44,179   A/swine/Virginia/671/1987(H1N1)
 89:170,149,147,258,166, 88, 51,188   A/Swine/Spain/50047/2003(H1N1)
 90:164,147,144,258,164, 80, 59,189   A/swine/Spain/51915/2003(H1N1)
 91:161,145,144,259,159, 80, 60,185   A/swine/Spain/53207/2004(H1N1)
 92:178,136,141,488,163,507, 22,188   A/swine/Hong Kong/5190/99(H3N2)
 93:153, 82,164,490,157,503,118,182   A/Russia/WO0200884/72(H3N2)
 94:159, 64,171,497,176,505,135,183   A/Texas/UR06-0356/2007(H3N2)
 95:148,106,165,366,154,510,116,164   A/Japan/305/57(H2N2)
 96:139,178,158,213,136,197,106,162   A/Alaska/1935(H1N1)
 97:146,177,157,215,150,193,112,157   A/Hickox/1940(H1N1)
 98:152,185,169,229,154,202,118,168   A/swine/Henan/01/06(H1N1)
 99:150,186,169,229,156,201,126,169   A/swine/Tianjin/01/04(H1N1)
100:165,191,172,234,157,216,126,179   A/Kansas/UR06-0068/2007(H1N1)
101:166,250,  0,238,  0,213,131,  0   A/swine/Ohio/K1130/06(H1N1)
102:168,250,  0,243,  0,215,132,  0   A/swine/Ohio/K1207/06(H1N1)
103:126,176,155,182,120,168, 88,143   A/Brevig Mission/1/1918(H1N1)
104:126,176,155,182,120,168, 88,143   A/Brevig Mission/1/1918(H1N1)
105:136,180,157,172,109,163,102,128   A/swine/Jamesburg/1942(H1N1)
106:137,182,156,175,112,158,106,132   A/swine/1931(H1N1)
107:137,182,156,175,112,158,106,132   A/Sw/1931(H1N1)
108:142,183,155,167,104,173,105,131   A/swine/Ohio/23/1935(H1N1)
109:146,192,173,131, 83,195,113,109   A/swine/Wisconsin/1/1957(H1N1)
110:149,190,172,123, 81,196,109,107   A/swine/Wisconsin/1/1961(H1N1)
111:153,192,172,120, 76,196,110,103   A/swine/Wisconsin/2/1966(H1N1)
112:157,189,175,121, 80,197,109, 98   A/swine/Wisconsin/1/1967(H1N1)
113:158,194,176,120, 83,197,111,106   A/swine/Wisconsin/2/1970(H1N1)
114:158,196,175,116, 75,199,104, 94   A/swine/Wisconsin/1/1971(H1N1)
115:160,195,179,121, 82,198,115, 89   A/swine/Illinois/1/1975(H1N1)
116:161,196,179,121, 82,198,115, 89   A/swine/Tennessee/1/1975(H1N1)
117:158,195,178,109, 71,199,110, 90   A/swine/Tennessee/19/1976(H1N1)
118:156,193,179,109, 72,197,113, 89   A/swine/Iowa/1/1976(H1N1)
119:155,195,178,109, 70,196,113, 87   A/swine/Tennessee/3/1976(H1N1)
120:155,196,178,109, 70,196,113, 87   A/swine/Tennessee/10/1976(H1N1)
121:155,195,179,109, 70,196,113, 87   A/swine/Tennessee/7/1976(H1N1)
122:158,192,178,117, 68,201,118, 88   A/swine/Tennessee/62/1977(H1N1)
123:160,192,178,116, 68,200,116, 91   A/swine/Tennessee/25/1977(H1N1)
124:159,192,178,119, 64,202,118, 95   A/swine/Tennessee/96/1977(H1N1)
125:160,192,179,119, 64,202,118, 95   A/swine/Iowa/100/1977(H1N1)
126:157,191,179,118, 67,201,115, 85   A/swine/Tennessee/61/1977(H1N1)
127:158,191,178,119, 68,196,111, 88   A/swine/Tennessee/79/1977(H1N1)
128:161,196,181,121, 75,197,112, 81   A/swine/Tennessee/11/1978(H1N1)
129:161,196,181,121, 75,198,112, 81   A/swine/Tennessee/9/1978(H1N1)
130:161,196,181,121, 75,197,112, 81   A/swine/Tennessee/10/1978(H1N1)
131:160,195,180,117, 74,196,110, 88   A/swine/Tennessee/64/1977(H1N1)
132:160,195,180,117, 74,196,110, 88   A/swine/Tennessee/65/1977(H1N1)
133:159,194,179,108, 71,199,111, 87   A/swine/Tennessee/17/1976(H1N1)
134:159,194,178,108, 71,199,111, 87   A/swine/Tennessee/15/1976(H1N1)
135:161,194,178,107, 76,198,112, 88   A/swine/Tennessee/86/1977(H1N1)
136:158,195,179,112, 72,198,111, 85   A/swine/Tennessee/3/1978(H1N1)
137:159,196,178,108, 72,199,115, 90   A/swine/Wisconsin/30747/1976(H1N1)
138:160,198,177,116, 76,205,112, 94   A/swine/Kyoto/3/1979(H1N1)
139:158,196,178,111, 72,199,115, 97   A/swine/Tennessee/10/1977(H1N1)
140:157,196,178,109, 74,199,106, 90   A/swine/Kentucky/1/1976(H1N1)
141:161,196,178,109, 76,200,110, 87   A/swine/Iowa/4/1976(H1N1)
142:160,193,178,114, 76,197,112, 90   A/swine/Iowa/1/1977(H1N1)
143:157,198,180,113, 78,201,115, 89   A/swine/Arizona/148/1977(H1N1)
144:157,198,180,113, 78,201,115, 89   A/swine/Tennessee/112/1977(H1N1)
145:157,198,180,113, 77,201,116, 89   A/swine/Tennessee/105/1977(H1N1)
146:157,198,180,113, 78,201,115, 89   A/swine/Tennessee/106/1977(H1N1)
147:157,198,180,113, 78,201,115, 88   A/swine/Tennessee/109/1977(H1N1)
148:157,198,180,114, 78,201,115, 88   A/swine/Tennessee/118/1977(H1N1)
149:160,194,177,109, 72,197,112, 87   A/swine/Minnesota/27/1976(H1N1)
150:160,194,177,109, 72,198,112, 89   A/swine/Minnesota/24/1975(H1N1)
151:163,194,176,109, 74,200,111, 89   A/swine/Tennessee/49/1977(H1N1)
152:161,197,177,111, 73,198,111, 90   A/swine/Tennessee/19/1977(H1N1)
153:161,197,177,111, 73,198,109, 90   A/swine/Tennessee/21/1977(H1N1)
154:162,197,177,111, 74,199,111, 90   A/swine/Tennessee/37/1977(H1N1)
155:162,197,177,112, 73,200,110, 89   A/swine/Tennessee/31/1977(H1N1)
156:163,196,178,114, 76,199,112, 88   A/swine/Tennessee/7/1978(H1N1)
157:159,197,177,105, 72,198,110, 91   A/swine/Nebraska/123/1977(H1N1)
158:157,192,176,111, 76,202,116, 92   A/swine/Tennessee/48/1977(H1N1)
159:159,192,178,108, 74,201,112, 89   A/swine/Tennessee/23/1976(H1N1)
160: 73, 44,182,130, 50,206,123,107   A/swine/Ontario/53518/03(H1N1)
161:173, 58,190,122, 70,209,130, 98   A/swine/Ontario/23866/04(H1N1)
162:173,219,175,115, 64,199,129, 89   A/swine/Ontario/57561/03(H1N1)
163:172,196,164,111, 78,201,129,102   A/swine/Alberta/56626/03(H1N1)
164:167,197,184, 71, 43,198,115, 56   A/swine/California/T9001707/1991(H1N1)
165:167,196,179, 72, 42,202,113, 52   A/turkey/IA/21089-3/1992(H1N1)
166:167,196,179, 71, 46,199,117, 54   A/swine/Iowa/24297/1991(H1N1)
167:165,196,180, 70, 47,197,117, 54   A/swine/Maryland/23239/1991(H1N1)
168:165,197,179, 78, 45,199,115, 58   A/swine/Iowa/17672/1988(H1N1)
169:164,196,180, 78, 49,197,114, 59   A/turkey/NC/19762/1988(H1N1)
170:164,194,181, 85, 65,206,110, 81   A/swine/Iowa/1/1987(H1N1)
171:163,193,179, 81, 62,200,113, 83   A/swine/Kansas/3228/1987(H1N1)
172:166,196,181, 79, 48,197,113, 81   A/swine/Iowa/31483/1988(H1N1)
173:165,195,180, 78, 64,194,114, 66   A/swine/Wisconsin/1915/1988(H1N1)
174:163,194,178, 81, 62,201,113, 82   A/swine/Kansas/3024/1987(H1N1)
175:166,195,180, 82, 62,200,116, 79   A/swine/Iowa/1/1985(H1N1)
176:166,195,181, 82, 62,201,116, 79   A/swine/Iowa/3/1985(H1N1)
177:166,195,181, 82, 62,201,116, 79   A/swine/Iowa/2/1985(H1N1)
178:164,196,184, 95, 54,202,110, 78   A/swine/Iowa/2/1987(H1N1)
179:164,195,178,104, 66,201,116, 72   A/swine/Wisconsin/11/1980(H1N1)
180:165,194,177,104, 68,201,117, 76   A/swine/Ontario/1/1981(H1N1)
181:164,193,178,105, 68,201,117, 73   A/swine/Ontario/7/1981(H1N1)
182:163,193,178,105, 68,201,119, 75   A/swine/Ontario/6/1981(H1N1)
183:164,194,177,105, 68,201,117, 73   A/swine/Ontario/2/1981(H1N1)
184:163,193,178,105, 68,201,117, 73   A/swine/Ontario/4/1981(H1N1)
185:165,193,177,105, 68,201,117, 73   A/swine/Ontario/3/1981(H1N1)
186:160,193,177,107, 63,202,113, 85   A/swine/Wisconsin/8/1980(H1N1)
187:159,196,177,102, 62,201,113, 87   A/swine/Wisconsin/661/1980(H1N1)
188:159,196,178,103, 62,201,113, 85   A/swine/Wisconsin/629/1980(H1N1)
189:159,196,177,103, 62,201,113, 85   A/swine/Wisconsin/641/1980(H1N1)
190:160,196,177,103, 62,201,113, 87   A/swine/Wisconsin/663/1980(H1N1)
191:165,191,179, 89, 66,201,120, 95   A/swine/Iowa/1/1986(H1N1)
192:162,196,177,102, 61,199,109, 90   A/swine/Minnesota/5892-7/1979(H1N1)
193:158,198,180,108, 77,202,113, 83   A/turkey/KS/4880/1980(H1N1)
194:158,198,181,108, 77,202,115, 82   A/chicken/PA/35154/1991(H1N1)
195:161,195,179,106, 75,201,113, 89   A/swine/Tennessee/8/1978(H1N1)
196:161,195,177,104, 76,202,113, 81   A/swine/Tennessee/4/1978(H1N1)
197:161,196,177,104, 76,199,113, 81   A/swine/Tennessee/2/1978(H1N1)
198:160,195,176,102, 76,201,113, 78   A/swine/Tennessee/82/1977(H1N1)
199:160,195,176,102, 76,201,113, 78   A/swine/Tennessee/88/1977(H1N1)
200:160,195,176,102, 76,200,113, 79   A/swine/Tennessee/84/1977(H1N1)
201:159,195,177,102, 76,201,114, 81   A/swine/Tennessee/5/1978(H1N1)
202:160,194,176,103, 76,201,113, 78   A/swine/Tennessee/87/1977(H1N1)

**gsgs** · April 28, 2009, 07:40 AM

Re: swine flu sequences, data only

closest other sequences in the 8 segments
(data from Jan.2009, segment2 maybe only Jan.2007)
columns are:

.difference in 1/100 percent
......#different nucleotides
.........length of common alignment
.............number in my list
.....................sequence name

Code:

   0    0 2280 6904 California/04/2009-04-01/(H1N1)

----PB2----------------------------------------------------------
 304   24  787 2897 Turkey/MO/24093/99(H1N2)
 306   69 2249 3703 mallard Dk/South Dakota/Sg-00127/07(H3N2)
 306   69 2249 3704 mallard Dk/South Dakota/Sg-00128/07
 307   69 2246 3702 pintail Dk/South Dakota/Sg-00126/07(H3N2)
 307   69 2247 3701 mallard Dk/South Dakota/Sg-00125/07(H3N2)
 321   50 1557 2887 Sw/Texas/4199-2/98(H3N2)
 333   52 1557 2888 Sw/Minnesota/9088-2/98(H3N2)
 333   52 1557 2895 Sw/Iowa/8548-1/98
 342   78 2280 3760 Sw/Korea/JNS06/04(H3N2)
 343   54 1573 2894 Wisconsin/10/98(H1N1)
 346   79 2280 3705 Sw/Minnesota/55551/00(H1N2)
--------PB1-----------------------------------------------------
 312   71 2271 5644 Wisconsin/10/98(H1N1)
 340   77 2259 5652 mallard Dk/South Dakota/Sg-00125/07(H3N2)
 351   80 2274 5656 Sw/Indiana/9K035/99(H1N2)
 365   83 2271 5638 Sw/Nebraska/209/98(H3N2)
 365   83 2271 5639 Sw/Iowa/533/99(H3N2)
 365   83 2271 5640 Sw/Iowa/569/99(H3N2)
 365   83 2271 5641 Sw/Minnesota/593/99(H3N2)
 369   84 2271 5657 Sw/Korea/CAN04/05(H3N2)
 369   84 2274 5675 Dk/NC/91347/01(H1N2)
 374   43 1149 4066 Sw/Minnesota/9088-2/98(H3N2)
 374   43 1149 4068 Sw/Iowa/8548-1/98
 374   85 2271 5668 Sw/Illinois/100085A/01(H1N2)
 374   85 2271 5670 Sw/Ohio/891/01(H1N2)
 378   86 2271 5654 Sw/Iowa/930/01(H1N2)
 378   86 2271 5682 Sw/Korea/CY04/07(H3N2)
 378   86 2271 5683 Sw/Korea/CY05/07(H3N2)
 382   44 1149 4067 Sw/Texas/4199-2/98(H3N2)
 383   87 2271 5658 Sw/Korea/CAS07/05(H3N2)
 383   87 2271 5659 Sw/Korea/CAS09/06(H3N2)
 383   87 2271 5690 Sw/Indiana/P12439/00(H1N2)
----------PA--------------------------------------------------------
 370   79 2130 4925 mallard duck/South Dakota/Sg-00128/2007
 370   79 2131 4923 pintail duck/South Dakota/Sg-00126/2007(H3N2)
 373   79 2117 4922 mallard duck/South Dakota/Sg-00125/2007(H3N2)
 381   79 2073 4924 mallard duck/South Dakota/Sg-00127/2007(H3N2)
 390   84 2151 2977 Swine/Nebraska/209/98 (H3N2)
 390   84 2151 2978 Swine/Iowa/533/99 (H3N2)
 390   84 2151 2979 Swine/Iowa/569/99 (H3N2)
 390   84 2151 2980 Swine/Minnesota/593/99 (H3N2)
 390   84 2151 3015 Swine/Illinois/100084/01 (H1N2)
 399   86 2151 3011 Swine/Minnesota/55551/00 (H1N2)
-----------HA-----------------------------------------------------
 470   80 1700  344 Swine/Indiana/P12439/00 (H1N2)
 482   82 1700  280 Swine/Indiana/9K035/99 (H1N2)
 500   85 1700  504 Turkey/MO/24093/99(H1N2)
 505   86 1700 2468 swine/Minnesota/1192/2001(H1N2)
 511   87 1700  339 Swine/Ohio/891/01(H1N2)
 517   88 1700  549 SW/MN/23124-T/01(H1N2)
 517   88 1700 2115 swine/Guangxi/17/2005(H1N2)
 529   90 1700  550 SW/MN/23124-S/01(H1N2)
 529   90 1700  552 SW/MN/16419/01(H1N2)
 535   91 1700  345 Swine/Illinois/100085A/01 (H1N2)
 542   56 1032  296 Wisconsin/10/98 (H1N1)
--------NP----------------------------------------------------------
 250   13  520 6925 Sw/Oklahoma/18717/99(H3N2)
 251   13  516 6921 Sw/Colorado/23619/99(H3N2)
 262   14  533 6922 Sw/Wisconsin/14094/99(H3N2)
 262   14  533 6924 Sw/Illinois/21587/99(H3N2)
 263   14  531 6923 Sw/Oklahoma/18089/99(H3N2)
 312   16  512 6926 Sw/NorthCarolina/16497/99(H3N2)
 316   31  980 6927 Turkey/MO/24093/99(H1N2)
 329   48 1457 6963 Sw/Iowa/533/99(H3N2)
 336   49 1457 6961 Sw/Indiana/P12439/00(H1N2)
 336   49 1457 6969 Sw/Korea/CY04/07(H3N2)
 336   49 1457 6970 Sw/Korea/CY05/07(H3N2)
 337   33  979 6928 Sw/Texas/4199-2/98(H3N2)
 337   33  979 6929 Sw/Iowa/8548-1/98
 339   19  560 6972 SW/NC/45319/99(H1N2)
 339   19  560 6973 SW/NC/17366/01(H1N2)
 339   19  560 6974 SW/CO/17871/01(H1N2)
 343   50 1457 6971 Sw/Korea/CY09/07(H3N2)
----------NA--------------------------------------------------------
 589   83 1409 1741 Sw/England/195852/92(H1N1)
 652   92 1409 1742 Sw/Germany/Vi5698/95(H1N1)
 712   98 1376 1746 Sw/Belgium/74/85(H1N1)
 751  101 1344 1773 Sw/Ille et Vilaine/1455/99(H1N1)
 753  105 1394 1772 Sw/Cotes d'Armor/1488/99(H1N1)
 754  106 1404 1749 Italy/1424-4/95(H1N1)
 765  108 1410 1737 Sw/Belgium/1/83(H1N1)
 777  104 1338 1777 Sw/Italy/1492/97(H1N1)
 786  103 1310 1778 Sw/Italy/1513-8/98(H1N1)
 787  111 1410 1739 turkey/France/87075/87(H1N1)
 787  111 1410 1788 Sw/Italy/53949/04(H1N1)
 787  111 1410 1789 Sw/Italy/65296/04(H1N1)
 794  112 1410 1738 Sw/Finistere/3616/84(H1N1)
 795  102 1282 1750 Sw/Italy/1424-3/95(H1N1)
 801  113 1410 1736 Sw/Lot/2979/82(H1N1)
 801  113 1410 1790 Sw/Spain/53207/04(H1N1)
 801  113 1410 1791 Sw/Italy/247578/04(H1N1)
 801  113 1410 1793 Sw/Spain/51915/03(H1N1)
 812  106 1305 1774 Cotes d'Armor/1121/00(H1N1)
 815  115 1410 1794 Sw/Virginia/671/1987(H1N1)
------------M--------------------------------------------------------
 230   22  955 2735 Sw/HK/5190/99(H3N2)
 230   22  955 2736 Sw/HK/5200/99(H3N2)
 230   22  955 2737 Sw/HK/5212/99(H3N2)
 261   25  955 2739 Sw/HK/1197/02(H3N2)
 261   25  955 2740 Sw/HK/1144/02(H3N2)
 272   26  955 2738 Sw/HK/9745/01(H3N2)
 272   26  955 2743 HK/1774/99(H3N2)
 293   28  955 2741 Sw/HK/7982/00(H3N2)
 314   30  955 2742 Sw/HK/9296/01(H3N2)
 345   33  955 2721 Sw/Leipzig/145/92(H3N2)
 366   35  955 2726 Sw/Cotes d'Armor/1482/99(H1N1)
 397   38  955 2722 wild boar/Germany/WS169/06(H3N2)
 397   38  955 2727 Sw/Italy/1521/98(H1N2)
----------NS--------------------------------------------------
 346   29  838 6427 Sw/Texas/4199-2/98(H3N2)
 346   29  838 6428 Sw/Minnesota/9088-2/98(H3N2)
 357   30  838 6429 Sw/Iowa/8548-1/98
 381   32  838 6444 Sw/Indiana/9K035/99(H1N2)
 395   33  835 6436 Sw/North Carolina/98225/01(H1N2)
 395   33  835 6437 Sw/Minnesota/55551/00(H1N2)
 395   33  835 6445 SW/MN/3327/00(H1N2)
 395   33  835 6453 SW/IN/14810-T/01(H1N2)
 395   33  835 6454 SW/IN/14810-S/01(H1N2)
 395   33  835 6455 Sw/Korea/CAS09/06(H3N2)
 407   34  835 6456 Sw/Korea/CAN04/05(H3N2)
 407   34  835 6457 Sw/Korea/CAS07/05(H3N2)
 407   34  835 6467 Sw/Korea/CAS08/05(H1N1)
 407   34  835 6506 Sw/Iowa/930/01(H1N2)
 417   35  838 6430 Sw/Nebraska/209/98(H3N2)
 417   35  838 6438 Turkey/MO/24093/99(H1N2)
 417   35  838 6483 turkey/OH/313053/04(H3N2)

**gsgs** · April 28, 2009, 07:42 AM

Re: swine flu sequences, data only

Code:

p0 e0 f0 h0 s1
maxl=59
#differences
                                                             1   2   3   4   5   6   7   PB2 PB1  PA  HA  NP  NA   M  NS
----------------------------------------------------------------------------------------------------------------------------------
  1 >A/Texas/04/2009(H1N1),2009-04-14,m16,x                  0   0   6   8   6   8   5     0   0   0  18   5   4   7   0    10#    4    4659   5327      1:>A/Texas/04/2009(H1N1),2009-04-14,m16,x               
  2 >A/Texas/05/2009(H1N1),2009-04-15,m16,x                  0   0   9  12   9  12   5     0   0  11  18   5   4   8   5    10#    6    6435   5421      2:>A/Texas/05/2009(H1N1),2009-04-15,m16,x               
  3 >A/California/06/2009(H1N1),2009-04-16,f41,m1            6   9   0  12  18  21   5    20   8  10  22   6   0   4   0    13#   10    7796   5529      3:>A/California/06/2009(H1N1),2009-04-16,f41,m1         
  4 >A/California/05/2009(H1N1),2009-03-30,f09,c1            8  12  12   0  12  18   7     9   6  10  17  14   8   8   0    11#    9    8800   5528      4:>A/California/05/2009(H1N1),2009-03-30,f09,c1         
  5 >A/California/07/2009(H1N1),2009-04-09,m54,m1            6   9  18  12   0   2   1     9   4  10  18   0   0   4   0    10#    6    6729   5597      5:>A/California/07/2009(H1N1),2009-04-09,m54,m1         
  6 >A/California/04/2009(H1N1),2009-04-01,m10,cx            8  12  21  18   2   0   0     9   6  10  21   5   5   2   5     9#    8    9032   5527      6:>A/California/04/2009(H1N1),2009-04-01,m10,cx         
  7 >A/California/09/2009(H1N1),2009-04-15,m07,original      5   5   5   7   1   0   0     0   0   0  23   0   5   4   0    10#    3    2993   5201      7:>A/California/09/2009(H1N1),2009-04-15,m07,original   
---------------------------------------------------------------------------------------------------------------------------------------------
                                                             1   2   3   4   5   6   7     6   3   7  19   5   3   5   1


#differences in total to index
#differences in total to index , considering only polymorphisms that occur more than once in this table
#differences in total to index, where defined
#differences in total to index, where defined, considering only polymorphisms that occur more than once in this table


                                                          0011122 0011 00011 00000111 001 01 00 0 
                                                          4427800 8977 55679 02368015 261 20 05 7 
                                                          2815779 2105 68748 29649176 861 84 02 7 
                                                          0185203 5518 18016 28601233 298 34 82 5 
-codon-position------------------------------------------- 1    2        11  11 1 1     2 1  2  1 
---Index--------------------------------------------------AGATCCG CCAG AATAG CTGGGGGG ACC AA TG A 
  1 >A/Texas/04/2009(H1N1),2009-04-14,m16,x               ------- ---- ----- ......AA ... .. -A -       21     21 ,      3      3      1:>A/Texas/04/2009(H1N1),2009-04-14,m16,x               
  2 >A/Texas/05/2009(H1N1),2009-04-15,m16,x               ------- ---- C.... ......AA ... .. .A G       16     16 ,      5      5      2:>A/Texas/05/2009(H1N1),2009-04-15,m16,x               
  3 >A/California/06/2009(H1N1),2009-04-16,f41,m1         GA.CTTA .TG. .G.C. A.A..... ..T -- .. -       16     16 ,     13     13      3:>A/California/06/2009(H1N1),2009-04-16,f41,m1         
  4 >A/California/05/2009(H1N1),2009-03-30,f09,c1         ....T.. A... .G.C. A....... CTT G. C. -       11     11 ,     10     10      4:>A/California/05/2009(H1N1),2009-03-30,f09,c1         
  5 >A/California/07/2009(H1N1),2009-04-09,m54,m1         ..G.... .... ..C.T .C..AA.. --- -- .. -       12     12 ,      6      6      5:>A/California/07/2009(H1N1),2009-04-09,m54,m1         
  6 >A/California/04/2009(H1N1),2009-04-01,m10,cx         ..G.... ...A ..C.T .C.AAA.. ... .G -. .       10     10 ,      9      9      6:>A/California/04/2009(H1N1),2009-04-01,m10,cx         
  7 >A/California/09/2009(H1N1),2009-04-15,m07,original   ------- ---- ----- .C.AA--- --- .G .. -       27     27 ,      4      4      7:>A/California/09/2009(H1N1),2009-04-15,m07,original   
                                                                                                  
---Index--------------------------------------------------AGATCCG CCAG AATAG CTGGGGGG ACC AA TG A 
-codon-position------------------------------------------- 1    2        11  11 1 1     2 1  2  1 
                                                          0011122 0011 00011 00000111 001 01 00 0 
                                                          4427800 8977 55679 02368015 261 20 05 7 
                                                          2815779 2105 68748 29649176 861 84 02 7 
                                                          0185203 5518 18016 28601233 298 34 82 5

**gsgs** · April 29, 2009, 03:09 AM

Re: swine flu sequences, data only

34 new (partial) sequences uploaded, but only from USA

differences in HA1:

Code:

                                                          00000000111 
                                                          00236689000 
                                                          23964599000 
                                                          27860816156 
-codon-position-------------------------------------------111 11  2 1 
---Index--------------------------------------------------CGTGGTGCGGA 
  1 >A/Texas/04/2009(H1N1),2009-04-14,m16,x               ........... 
  2 >A/Texas/05/2009(H1N1),2009-04-15,m16,x               ........... 
  3 >A/California/06/2009(H1N1),2009-04-16,f41,m1         A..A....... 
  4 >A/California/05/2009(H1N1),2009-03-30,f09,c1         A.......... 
  5 >A/California/07/2009(H1N1),2009-04-09,m54,m1         ..C...A.... 
  6 >A/California/04/2009(H1N1),2009-04-01,m10,cx         ..C.A.A.... 
  7 >A/California/09/2009(H1N1),2009-04-15,m07,original   ..C.A.A---- 
  8 >A/New York/19/2009(H1N1)                             .....A..... 
  9 >A/Kansas/03/2009(H1N1)                               .A.....T.-- 
 10 >A/New York/20/2009(H1N1)                             -....A.T.AG 
 11 >A/Ohio/07/2009(H1N1)                                 -....A...AG 
 12 >A/Ohio/07b/2009(H1N1)                                -....A..A-- 
                                                                      
---Index--------------------------------------------------CGTGGTGCGGA 
-codon-position-------------------------------------------111 11  2 1 
                                                          00000000111 
                                                          00236689000 
                                                          23964599000 
                                                          27860816156

**gsgs** · May 1, 2009, 02:02 AM

Re: swine flu sequences, data only

Code:

                                          0000000000001111111  
                                          0011123667890000145  
                                          2323396455990001706  
                                          2780186086161562383  
-codon-position---------------------------112121 11   2 11 1   
---Index----------------------------------CGTACTGGTGGCGGAGGCG  
  1 >A/California/04/2009(H1N1)           .....C.A..A....A...  
  2 >A/California/09/2009(H1N1)           .....C.A..A--------  
  3 >A/California/07/2009(H1N1)           .....C....A....A...  
  4 >A/California/08/2009(H1N1)           .....C....A....A...  
  5 >A/California/07/2009(H1N1)           .....C....A....A...  
  6 >A/Toronto/3178/2009(H1N1)            --.....------------  
  7 >A/Toronto/3181/2009(H1N1)            -----..------------  
  8 >A/Toronto/3184/2009(H1N1)            -----..------------  
  9 >A/California/05/2009(H1N1)           A..................  
 10 >A/California/10/2009(H1N1)           A..................  
 11 >A/California/06/2009(H1N1)           A.....A............  
 12 >A/Auckland/1/2009(H1N1)              --...............T.  
 13 >A/New York/19/2009(H1N1)             ........A........T.  
 14 >A/Toronto/3141/2009(H1N1)            -------.A.......---  
 15 >A/Toronto/3145/2009(H1N1)            -------.A.......---  
 16 >A/Toronto/3146/2009(H1N1)            -------.A.......---  
 17 >A/Ohio/07/2009(H1N1)                 -.......A...A------  
 18 >A/Regensburg/Germany/01/2009(H1N1)   --.......A.........  
 19 >A/Texas/05/2009(H1N1)                ................A.A  
 20 >A/Texas/04/2009(H1N1)                ................A.A  
 21 >A/Kansas/03/2009(H1N1)               .A.........T.------  
 22 >A/New York/20/2009(H1N1)             -.......A..T.AG----  
 23 >A/Ohio/07/2009(H1N1)                 -.......A....AG----  
 24 >A/Toronto/3170/2009(H1N1)            --CGT..------------  
                                                               
---Index----------------------------------CGTACTGGTGGCGGAGGCG  
-codon-position---------------------------112121 11   2 11 1   
                                          0000000000001111111  
                                          0011123667890000145  
                                          2323396455990001706  
                                          2780186086161562383

Code:

>gi|227809829|gb|FJ966082| /Human/4 (HA)/H1N1/USA/2009/04/01/ Influenza A virus (A/California/04/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227831758|gb|FJ966952| /Human/4 (HA)/H1N1/USA/2009/03/30/ Influenza A virus (A/California/05/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227831773|gb|FJ966959| /Human/4 (HA)/H1N1/USA/2009/04/15/ Influenza A virus (A/Texas/05/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227831775|gb|FJ966960| /Human/4 (HA)/H1N1/USA/2009/04/16/ Influenza A virus (A/California/06/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227831800|gb|FJ966971| /Human/4 (HA)/H1N1/USA/2009/04/15/ Influenza A virus (A/California/09/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|227831807|gb|FJ966974| /Human/4 (HA)/H1N1/USA/2009/04/09/ Influenza A virus (A/California/07/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227831825|gb|FJ966982| /Human/4 (HA)/H1N1/USA/2009/04/14/ Influenza A virus (A/Texas/04/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227977098|gb|FJ969509| /Human/4 (HA)/H1N1/USA/2009/// Influenza A virus (A/New York/19/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227977103|gb|FJ969511| /Human/4 (HA)/H1N1/USA/2009/04/08/ Influenza A virus (A/California/10/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227977127|gb|FJ969521| /Human/4 (HA)/H1N1/USA/2009/04/24/ Influenza A virus (A/Ohio/07/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|227977131|gb|FJ969523| /Human/4 (HA)/H1N1/USA/2009/04/24/ Influenza A virus (A/Kansas/03/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|227977159|gb|FJ969535| /Human/4 (HA)/H1N1/USA/2009/04/24/ Influenza A virus (A/Ohio/07/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|227977171|gb|FJ969540| /Human/4 (HA)/H1N1/USA/2009/04/09/ Influenza A virus (A/California/07/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|227977175|gb|FJ969542| /Human/4 (HA)/H1N1/USA/2009/// Influenza A virus (A/New York/20/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228017757|gb|FJ971076| /Human/4 (HA)/H1N1/USA/2009/04/09/ Influenza A virus (A/California/08/2009(H1N1)) segment 4 hemagglutinin (HA) gene, complete cds
>gi|228481045|gb|FJ973557| /Human/4 (HA)/H1N1/New Zealand/2009/04/25/ Influenza A virus (A/Auckland/1/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228495369|gb|FJ974021| /Human/4 (HA)/H1N1/Germany/2009/04/27/ Influenza A virus (A/Regensburg/Germany/01/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551499|gb|FJ974022| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3181/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551501|gb|FJ974023| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3170/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551503|gb|FJ974024| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3184/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551505|gb|FJ974025| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3178/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551507|gb|FJ974026| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3141/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551509|gb|FJ974027| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3145/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds
>gi|228551511|gb|FJ974028| /Human/4 (HA)/H1N1/Canada/2009/04// Influenza A virus (A/Toronto/3146/2009(H1N1)) segment 4 hemagglutinin (HA) gene, partial cds

**gsgs** · May 1, 2009, 03:28 AM

Re: swine flu sequences, data only

this is continued here:

http://www.zonegrippeaviaire.com/showthread.php?t=25600

where I can edit posts indefinitely

**gsgs** · May 6, 2009, 01:38 AM

Re: swine flu sequences, data only

also here now :

h5n1experts.org - h5n1experts Resources and Information.

http://h5n1experts.org/forum/showthread.php?p=1101

h5n1experts.org is your first and best source for all of the information you’re looking for. From general topics to more of what you would expect to find here, h5n1experts.org has it all. We hope you find what you are searching for!

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swine flu sequences, data only

swine flu sequences, data only

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