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] | in orf3b, Spike and orf8 but especially variable in Spike S1 and orf8 which were previously shown to be recombination hot spots. | 7,794 | 7,922 | [
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2220,
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193,
193,
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529,
545,
29613,
16989,
272,
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7001,
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23,
4502,
399,
64875,
1767,
3632,
248,
24325,
24,
384,
3669,
9482,
271,
241,
4583,
273,
1999,
25,
707,
55995,
325,
35429,
1448,
965,
204,
19,
384,
518,
5906,
20,
10837,
272,
241,
3377,
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19003,
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1190,
5632,
1309,
314,
12840,
271,
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16236,
19639,
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1806,
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1037,
779,
24,
8458,
1999,
451,
416,
1314,
1104,
15381,
388,
248,
1144,
601,
13,
204,
19,
28,
20,
204,
25,
605,
2065,
2376,
2505,
6847,
996,
9407,
1487,
11027,
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and compare this to the actual model | 23,274 | 23,363 | [
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1
] |
[
4773,
916,
46915,
25,
241,
80,
8825,
84,
650,
5305,
272,
3082,
3328,
42,
1620,
807,
1018,
369,
5044,
37,
317,
7365,
5136,
40740,
49916,
2738,
42,
193,
193,
12659,
7561,
17794,
25,
17747,
6825,
25,
24084,
88,
25,
6298,
83,
25,
16162,
26,
4111,
78,
26,
34067,
26,
7141,
46,
32943,
58838,
28,
26,
193,
193,
40853,
37,
261,
34,
78,
27869,
27,
64531,
34236,
36,
79,
2237,
80,
29,
76,
35,
77,
2034,
7262,
2034,
33,
80,
43264,
33,
79,
42194,
31,
78,
193,
193,
43382,
37,
526,
518,
351,
303,
23,
18574,
331,
14292,
49108,
257,
23,
302,
12334,
285,
38,
31506,
895,
16368,
23,
12946,
16368,
493,
14292,
42657,
6018,
23,
38505,
462,
14292,
17080,
23,
58078,
302,
14292,
7501,
47135,
23,
401,
387,
851,
11832,
38,
302,
14413,
14927,
23,
15739,
1718,
38,
703,
4486,
23,
4653,
341,
14292,
331,
2775,
381,
4410,
23,
10732,
3604,
10387,
193,
7499,
37,
204,
626,
27,
24,
3519,
24,
2102,
193,
40144,
37,
204,
696,
25,
19469,
28,
26,
35048,
25,
91,
404,
79,
25,
1321,
48955,
30,
193,
34729,
37,
32067,
24,
1546,
193,
193,
12053,
37,
636,
807,
1018,
369,
5044,
6429,
304,
241,
26026,
24,
18682,
11525,
47147,
325,
504,
241,
2084,
1242,
2549,
272,
7305,
273,
6255,
16026,
3783,
23,
22061,
23,
29218,
23,
28960,
23,
30871,
23,
491,
22820,
23,
273,
19255,
1492,
35561,
25,
22731,
271,
17512,
5798,
23,
3050,
1902,
35055,
413,
650,
3713,
272,
3434,
275,
2993,
4704,
7404,
273,
1988,
275,
701,
27506,
17729,
272,
204,
853,
32,
600,
3924,
273,
272,
2600,
272,
204,
853,
34,
25,
10944,
23,
3508,
2913,
413,
650,
7805,
272,
248,
2522,
2941,
272,
18770,
10169,
427,
2245,
16302,
2698,
25,
16174,
23,
629,
304,
658,
9200,
379,
44337,
2820,
25,
1743,
248,
4141,
275,
267,
11525,
3247,
5218,
23,
248,
26409,
2704,
4071,
335,
248,
520,
8393,
273,
16767,
12309,
19029,
8541,
248,
2138,
275,
267,
3227,
9200,
25,
529,
414,
1856,
23,
360,
39147,
248,
3941,
6921,
783,
9592,
25,
193,
193,
5854,
37,
636,
807,
1018,
369,
5044,
6429,
204,
19,
3992,
32747,
65,
770,
241,
26026,
24,
18682,
47147,
5740,
431,
2926,
5502,
275,
51550,
273,
52496,
32719,
204,
19,
57,
5172,
1656,
20,
345,
241,
17528,
319,
39460,
11799,
5861,
325,
6255,
636,
807,
1018,
369,
5044,
16026,
204,
19,
3992,
32747,
49,
770,
504,
650,
16292,
3151,
7404,
23,
5798,
23,
273,
3434,
275,
2600,
272,
3050,
1762,
204,
70,
28,
23,
204,
29,
23,
204,
30,
72,
204,
25,
8165,
32747,
65,
304,
267,
19255,
1256,
349,
24,
18682,
6429,
204,
19,
23408,
39892,
20,
273,
304,
22964,
271,
7305,
8708,
431,
317,
39935,
241,
80,
8825,
84,
23,
248,
29357,
7736,
16026,
13536,
1322,
204,
70,
31,
23,
204,
32,
72,
204,
25,
8165,
32747,
65,
7228,
304,
9673,
431,
6362,
6168,
1765,
23,
537,
41169,
701,
9871,
679,
11038,
1106,
876,
204,
70,
33,
72,
204,
25,
390,
3783,
3418,
701,
1536,
427,
248,
9486,
452,
5842,
50545,
12065,
3599,
275,
35733,
273,
64135,
23,
273
] | [
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
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1,
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1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
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1,
1,
1,
1,
1,
1,
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1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
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1,
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1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1
] | for over 300 | 9,392 | 9,404 | [
0,
0,
0,
0,
0,
0,
0,
0,
0,
0,
1,
1,
1,
1,
1,
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1,
1,
1,
1,
1,
1,
1,
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1,
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1,
1,
1,
1,
1,
1,
1,
1,
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1,
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1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1,
1
] |
[
1562,
304,
248,
4807,
275,
38107,
39892,
12586,
42,
65,
3598,
24,
65,
410,
2033,
24290,
9133,
34021,
23979,
1061,
193,
193,
12659,
7561,
17794,
25,
17747,
6825,
25,
24084,
88,
25,
6298,
83,
25,
16162,
26,
4111,
78,
26,
34067,
26,
7141,
46,
34599,
39894,
33,
26,
193,
193,
40853,
37,
261,
33,
79,
29,
1622,
77,
29,
705,
3828,
79,
47493,
54616,
29,
18637,
7262,
81,
35,
76,
42273,
19822,
22715,
77,
4821,
77,
193,
193,
43382,
37,
9084,
364,
23,
20797,
317,
14292,
5736,
91,
7102,
23,
302,
25,
5169,
193,
7499,
37,
204,
626,
31,
24,
3739,
24,
3924,
193,
40144,
37,
204,
696,
25,
34314,
27,
26,
97,
42267,
25297,
32,
193,
34729,
37,
32067,
24,
1546,
193,
193,
12053,
37,
10744,
248,
9865,
275,
267,
272,
34761,
9200,
325,
504,
650,
11367,
312,
204,
41,
1223,
909,
23,
248,
23076,
6429,
5758,
271,
2887,
47921,
273,
14830,
7782,
25,
25495,
9359,
275,
33250,
23076,
6429,
20895,
273,
248,
27768,
275,
627,
20895,
14327,
5571,
248,
12792,
275,
5310,
14810,
325,
9789,
313,
241,
3185,
335,
33250,
23076,
20895,
25,
7947,
23,
629,
304,
241,
4902,
662,
312,
627,
23,
14379,
11109,
14810,
39567,
1206,
3517,
24,
539,
682,
4425,
271,
3144,
248,
662,
312,
262,
715,
89,
684,
8536,
2009,
275,
16767,
23076,
14810,
25,
2737,
3919,
33435,
6429,
24,
298,
297,
2033,
14810,
362,
267,
15424,
5647,
271,
15613,
272,
34761,
14810,
875,
6429,
32117,
6596,
7863,
6112,
275,
23076,
61527,
23,
830,
427,
11839,
14734,
23076,
17436,
23,
1093,
8960,
272,
248,
4436,
275,
248,
12586,
325,
418,
2413,
9407,
5861,
8511,
25,
529,
1594,
23,
241,
1488,
297,
2033,
9200,
1764,
9526,
4763,
275,
248,
9200,
271,
3370,
275,
33545,
422,
20343,
963,
345,
248,
13930,
18732,
14764,
4425,
427,
23076,
6429,
7228,
25,
10299,
23,
248,
3205,
271,
13990,
28091,
6429,
32117,
271,
4634,
5946,
23076,
14810,
724,
1586,
248,
42513,
2895,
4419,
241,
12656,
9200,
12040,
1542,
455,
23076,
17436,
25,
735,
1856,
451,
2178,
14366,
6429,
24,
298,
297,
2033,
14810,
312,
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1
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] |
[
1562,
304,
248,
758,
2260,
23,
31627,
24,
54524,
1838,
2336,
7893,
47147,
272,
1216,
7133,
273,
1986,
10860,
11576,
42,
780,
12873,
290,
341,
2046,
32413,
20963,
275,
204,
31,
24,
273,
204,
32,
24,
1620,
4755,
90,
24,
29,
24,
60171,
24,
57,
24,
70,
28,
24,
31806,
24,
28,
16376,
35161,
1985,
56557,
20,
1015,
257,
24,
29,
24,
1985,
72,
4570,
101,
311,
1910,
1542,
23496,
5345,
193,
193,
12659,
7561,
17794,
25,
17747,
6825,
25,
24084,
88,
25,
6298,
83,
25,
16162,
26,
4111,
78,
26,
34067,
26,
7141,
46,
32433,
21635,
31,
26,
193,
193,
40853,
37,
261,
27,
80,
33,
333,
81,
5831,
79,
4975,
80,
31083,
6991,
76,
29,
81,
34213,
80,
1868,
80,
29650,
2617,
310,
54692,
13418,
193,
193,
43382,
37,
1193,
308,
344,
8884,
9208,
23,
29603,
6233,
38,
337,
1974,
259,
285,
9208,
23,
51369,
76,
38,
49653,
86,
23,
531,
18768,
38,
2109,
2907,
47867,
23,
317,
768,
38,
10909,
530,
3095,
23,
462,
1032,
7508,
38,
319,
907,
86,
23,
1031,
9884,
38,
462,
1006,
558,
86,
23,
52242,
193,
7499,
37,
204,
626,
32,
24,
3091,
24,
1030,
193,
40144,
37,
204,
696,
25,
13200,
32,
26,
626,
32,
26,
34042,
45806,
193,
34729,
37,
32067,
24,
1546,
193,
193,
12053,
37,
317,
2559,
275,
7598,
42514,
204,
29,
24,
60171,
24,
57,
24,
70,
28,
24,
31806,
24,
28,
16376,
35161,
1985,
56557,
20,
1015,
257,
24,
29,
24,
1985,
72,
4570,
101,
311,
1910,
398,
17552,
345,
16702,
8833,
32413,
7836,
1542,
1373,
6077,
51330,
275,
17036,
51465,
24,
20023,
574,
48128,
44726,
42902,
359,
204,
19,
15107,
5345,
20,
273,
302,
25,
42902,
359,
7103,
4724,
204,
34821,
1313,
345,
248,
5515,
273,
1932,
1873,
12543,
25,
390,
5865,
8833,
32413,
10533,
398,
6636,
431,
1072,
47783,
966,
339,
1968,
1698,
427,
43068,
14766,
4817,
11216,
24,
4406,
61781,
13761,
25,
390,
8833,
32413,
429,
46786,
275,
15199,
204,
32,
24,
28515,
90,
24,
29,
24,
60171,
24,
57,
24,
35388,
29,
62,
14898,
30,
24,
46747,
24,
28,
24,
31806,
24,
28,
24,
102,
70,
31,
16376,
1970,
340,
11027,
252,
279,
13498,
20,
35161,
1985,
72,
56557,
104,
3945,
257,
24,
29,
24,
1985,
72,
4570,
101,
29998,
204,
19,
28,
81,
770,
409,
24,
102,
19,
29,
62,
14898,
28,
24,
35388,
31,
24,
77,
397,
51874,
1985,
20,
56557,
54283,
30,
24,
46747,
24,
28,
24,
1448,
630,
36577,
24,
29,
24,
1985,
47120,
31,
24,
28515,
90,
24,
29,
24,
60171,
4570,
101,
29998,
204,
19,
28,
82,
770,
273,
204,
31,
24,
28515,
90,
24,
57,
24,
102,
19,
29,
62,
14898,
28,
24,
35388,
30,
23,
31,
24,
79,
479,
4755,
51874,
1985,
20,
56557,
54283,
30,
24,
46747,
24,
28,
24,
1448,
630,
36577,
24,
29,
24,
1985,
47120,
29,
24,
60171,
4570,
101,
29998,
204,
19,
28,
83,
20,
398,
5305,
431,
601,
24,
23961,
31535,
335,
241,
2297,
10533,
275,
248,
14625,
6686,
271,
204,
28,
99,
23,
204,
29,
99,
23,
273,
204
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1
] | Methicillin-resistant Staphylococcus aureus (MRSA) | 1,919 | 1,969 | [
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24246,
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1856,
3730,
42,
1620,
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1018,
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5044,
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5136,
40740,
49916,
2738,
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12659,
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1985,
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1562,
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27172,
59676,
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19722,
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] |
[
1830,
1902,
304,
248,
370,
5475,
65,
26082,
42,
56364,
26082,
32388,
273,
53818,
4655,
3549,
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12659,
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17794,
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17747,
6825,
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24084,
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6298,
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16162,
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34067,
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17414,
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193,
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40853,
37,
261,
32,
6991,
30,
81,
5175,
2378,
26541,
37873,
6869,
3668,
79,
50425,
80,
55684,
366,
32,
81,
516,
6746,
6869,
193,
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43382,
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16721,
540,
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12975,
10012,
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432,
6602,
327,
23,
2345,
367,
14292,
336,
43630,
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1193,
316,
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943,
382,
14292,
1521,
257,
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1814,
553,
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301,
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2883,
7664,
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8776,
409,
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7491,
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361,
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4826,
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43767,
1058,
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7499,
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3091,
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3627,
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40144,
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696,
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15711,
33,
26,
94,
9811,
3306,
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33813,
24,
27530,
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101,
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34729,
37,
32067,
24,
1546,
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193,
12053,
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41569,
51834,
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6823,
1345,
523,
14466,
39892,
204,
19,
51,
5475,
65,
20,
304,
267,
1355,
2887,
275,
13241,
13930,
8056,
272,
2115,
1770,
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21884,
26082,
32388,
9526,
1286,
13071,
275,
10042,
2863,
273,
35055,
23,
585,
304,
416,
1304,
1777,
335,
1072,
24,
2257,
9719,
19740,
25,
18490,
46403,
37,
703,
1416,
241,
204,
29,
24,
244,
2491,
10642,
4717,
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3039,
1407,
6055,
32388,
2082,
271,
5017,
248,
2615,
26082,
19740,
275,
2505,
370,
5475,
65,
20895,
23,
12822,
1373,
1072,
24537,
204,
19,
44,
29,
23,
341,
28,
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1562,
304,
20712,
272,
8910,
42,
25399,
1364,
34330,
3069,
273,
44573,
21163,
275,
12731,
32911,
529,
3044,
1998,
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648,
1800,
81,
8250,
2003,
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37,
49356,
263,
45456,
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28566,
2562,
51178,
14457,
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12659,
7561,
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18900,
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2086,
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37,
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24,
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193,
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12053,
37,
1800,
81,
8250,
2003,
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204,
19,
63,
423,
770,
304,
248,
772,
12731,
22474,
30908,
6984,
312,
2820,
275,
12731,
26,
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2634,
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2672,
271,
3869,
271,
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1913,
533,
95,
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7402,
6192,
25,
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23,
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21913,
335,
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59985,
99,
10970,
23825,
272,
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2634,
25,
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267,
11526,
41134,
4313,
23,
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3035,
241,
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335,
1462,
24,
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6078,
10277,
23,
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23,
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26367,
18289,
44337,
3743,
1542,
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3988,
12707,
275,
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20895,
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1014,
15411,
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618,
30294,
2740,
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23219,
1104,
427,
301,
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5724,
679,
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335,
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5205,
409,
15466,
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847,
38546,
23,
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37148,
23,
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359,
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8384,
24,
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4352,
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40741,
9482,
1192,
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15466,
19979,
255,
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6928,
23,
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30,
504,
2879,
312,
2515,
2138,
345,
241,
627,
12731,
22474,
30908,
335,
6899,
44337,
20440,
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7865,
5793,
273,
14831,
3069,
5353,
648,
11022,
8250,
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16359,
23,
414,
2220,
15623,
248,
9233,
275,
56105,
3035,
43031,
23,
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325,
414,
4313,
765,
314,
1042,
272,
5463,
11526,
41134,
24,
3039,
13149,
22474,
29933,
1542,
12731,
273
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[
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