##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
##gapPenalties=axtChain O=400 E=30
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93	0	4
1872	12	0
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3374	0	9
1739	0	6
1709	0	1
3330	0	9
174	0	1
1596	96	0
503	0	1
39	1	0
1193	0	31
101	84	8
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275	0	16
243	2	0
670	1	0
1637	1	0
1378	0	1
14	0	5
1040	0	95
408	0	8
466	1	0
284	10	0
863	0	1
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2059	0	15
1323	1	0
2687	0	2
29	4	0
1674	3	0
490	0	1
437	56	0
20	0	56
831	1	0
3018	0	12
230	1	0
26	0	4
921	16	0
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2804	1	0
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12	0	12
442	1	0
57	0	2
881	8	0
54	0	8
17	0	27
7	40	0
6504	0	7
796	0	2
572	0	389
30	257	0
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171	308	0
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3353	3	0
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4030	0	3
104	0	1
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1912	1	0
5632	45	0
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3639	0	4
283	8	0
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54	2	31
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11	1	0
39	10	13
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8	3	0
5	4	0
1192	0	4
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823	1	0
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65	2	0
571	0	3
1	0	55
755	4	0
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743	20	0
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15	4	0
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4823	8	0
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36	0	309
898	0	1
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361	0	2
7	28	0
51	20	0
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359	0	1
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480	1	0
29	0	4
1643	7	0
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91	104	0
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10	0	9
719	0	1
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2040	0	4
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60	392	0
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1203	4	0
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29	1	0
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14	4	0
27	8	0
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105	0	4
395	4	0
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57	4	0
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39	0	7
15	0	11
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4	0	1
14	0	2
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346	0	1
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74	0	1
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43	0	8
4	4	0
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68	0	4
80	0	4
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524	0	5
621	29	0
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653	12	13
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680	4208	0
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83	1	0
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61	1	0
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22	4	16
7	0	4
3000	0	5
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1200	148	0
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45	135	0
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6023	2	0
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107	0	162
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75	0	9
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722	2	0
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635	4	0
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99	0	2
284	1	0
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35	1	0
146	0	252
69	396	35
717	0	72
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4	0	1
69	1	0
932	0	2
146	4	0
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5584	2	0
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325	2	0
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88	0	3
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54	0	1
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237	1385	1370
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71	2	0
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8	149	10
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3	185	0
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6559	0	4
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6	0	4
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16	2	0
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14	0	8
4	0	30
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16	0	2
28	272	357
46	0	10
6	28	0
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94	12	0
1528	0	3
3421	13	0
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761	0	1
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280	8	5
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859	4	0
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11	22	62
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61	0	1
6	16	13
86	12	0
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68	0	1
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1065	1	0
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4	1	0
4727	1	0
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540	0	296
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684	7	0
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55	1	0
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39	52	12
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15	1	0
7	33	0
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42	0	8
8	1	0
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8	25	38
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7	1	0
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3745	0	4
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734	1	0
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48	0	176
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89	2	0
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48	184	0
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19	6	0
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6413	3	200
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98	0	2
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30	0	4
838	1	0
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658	1	0
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747	0	20277
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7023	1	0
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787	28	0
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356	1	0
1211	0	3
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99	0	2
45	0	40601
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39	2	0
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37	0	121774
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82	5	0
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147	0	29
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12293	294457	311619
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8	7359	0
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2852	129701	120200
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2166	42074	8892
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3757	0	1
18	1	0
5383	1	0
6458	0	3
1974	1	0
3730	2	0
16321	5	0
6929	1	0
3692	0	2
10717	2	0
2361	0	1
2757	1	0
5219	2	0
2	24	0
7077	4	0
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13464	0	4
10709	8	0
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18	0	8
7481	4	0
5818	1	0
9996	1	0
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1327	0	1
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21764	1	0
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9590	0	1
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8435	2	0
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2341	0	4
8274	0	16
13	3	0
1	0	3
110	0	4
11196	0	2
4257	1	0
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2437	6	0
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2485	0	4
596	6	0
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4	0	1
60	4	0
1098	2	0
9433	1	0
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3076	0	1
19816	2	0
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866	0	4
44116	0	2
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5355	0	4
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14920	2	0
25	0	2
3569	1	0
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1364	1	0
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7294	8	0
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34	0	2
580	1	0
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3956	0	1
9101	10	0
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7933	4	0
207	4	0
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29079	4	0
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25498	2	0
73	19	0
1631	1	0
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5935	0	1
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5165	0	4
12348	1	0
773	0	1
9170	3	0
3493	2	0
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3565	2	0
14	0	1
52	3	0
1981	2	0
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21	0	2
173	2	0
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5110	1	0
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11612	0	2
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32	0	4
10376	2	0
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6732	1	0
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8	3	0
11	1	0
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4919	0	4
236	8	0
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961	2	0
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1	7	0
56	1	0
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60	0	2
32	0	2
2	0	6
44	0	2
1555	0	1
2	0	35
103	8	0
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105	0	4
41075	2	0
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9469	0	1
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907	1	0
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87294	8	0
48	0	16
1378	1	0
574	4	0
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2858	0	12
4072	3372	3373
2124	6	0
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44	1	0
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9	0	2
5083	0	1
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43	0	4
1	2	0
17806	3457	3457
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6	25	0
9557	0	3
11	3	9
1490	0	24
2467	2	0
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2904	1	0
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70	0	3
2788	4	0
33	0	2
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5	1	0
3	6	0
6718	0	1
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17314	1	0
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33728	2	0
53	0	2
8212	1	0
2732	0	5
49	0	5
6396	2	0
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840	1	0
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3317	2	0
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8095	2	0
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107	2	0
26	0	2
3742	1	0
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86	1	0
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6906	1	0
27	21	0
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2542	1	0
650	0	1
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726	1	0
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2	2	0
5630	4	0
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16993	4	0
141	4	0
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18	5	13
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23	0	2
15409	1	0
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7981	0	3
2119	1	0
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990	0	2
67367	0	12
7829	3	0
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13	1	0
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7269	1	0
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2432	0	12
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42	6	0
560	0	16
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5789	1	0
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12464	15	0
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275	1	0
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32	2	0
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482	0	1
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874	0	1
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84	1	0
592	0	125
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670	1	0
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43	0	1
81	0	4
43	0	1
164	0	2
24	0	1
185	48603	6037
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239	0	1
324	34492	29505
43	0	125
63	0	1
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83	4	0
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158	2	0
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16	3	1001
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137	0	7
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286	0	2
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332	0	7
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2121	32294	32299
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3592	1	0
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386	42095	2085
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600	1	0
690	2419	0
3861	4836	4836
4277	28826	42950
2711	5	0
229	0	15
111	1	0
156	0	15
499	5	0
333	10	0
87	1	0
706	15	0
1716	1	0
640	0	15
349	0	20
919	0	5
1340	48567	172223
5845	1	0
1041	10	0
2952	0	26846
6409	2	3521
154	0	15
1282	0	10603
18633	1	0
4819	0	15
1505	897	4432
975	5	0
2392	1	0
3534	0	1
175	0	5
1074	25	0
2280	1	0
4789	25	0
1451	0	14139
5559	0	1
89	15	0
2235	1	0
7069	1	0
179	5	0
946	10	0
91	15	0
16	25	0
393	0	5
156	45	0
122	0	20
583	0	5
150	1	0
432	0	15
566	5	0
940	10	0
101	15	0
8	25	0
381	0	10
168	45	0
122	0	20
103	1	0
2544	0	15
3699	25	0
3362	0	15
174	0	25
3519	25	0
3356	0	15
2045	1	0
1480	0	15
7080	0	15
150	0	25
835	185	3705
9595	0	25
1646	0	40
1684	15	0
1802	0	25
8	0	15
1656	15	0
8871	3503	14047
9902	0	1
513	20	0
61	40	0
48642	3484	0
129	5	0
2606	0	5
3088	0	15
24	15	0
371	5	0
3493	5	0
909	0	3498
552	30	0
5528	5	0
3475	5	0
32	0	3508
1878	0	1
12109	5	0
7804	15	0
24905	5	0
37648	0	2
32577	8	0
3486	0	1
5649	2	0
26	1	0
5880	0	4
2763	0	3
10989	0	6
16380	0	2
48303	0	10
2433	3	0
21	0	36
1774	0	1
1087	2	0
2677	1	5
4323	14	0
928	1	0
6743	0	4
2550	1	0
6251	0	3
6451	0	1
5770	19	0
1776	0	3
2033	0	1
3697	2	0
866	1	0
6134	0	1
109	0	1
2373	1	0
1036	1	0
43	0	1
1026	2	0
1707	1	0
6419	4	0
45	0	6
11	0	3
2374	1	0
4546	0	1
10798	2	0
12047	1	0
12703	16	0
3104	0	33
22742	0	1
28566	0	1
52316	0	2
14553	1	0
2146	1	0
3356	3	0
17	2	0
2040	0	1
6977	0	4
68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
4172	0	1
162	0	8
1373	4	0
475	0	2
3573	6	0
42	6	0
125	38	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	1
161	47	0
31	74	0
742	38	2
66	0	7
9	0	17
36	0	34
2	0	8
30	7	0
14	8	0
27	24	0
1	0	1
30	0	7
12	0	9
29	16	116
10	0	1
8	0	2
12	0	2
15	0	6
15	0	1
30	0	29
17	18	0
1	0	1
13	1	0
4	1	25
13	57	13
18	108	36
28	18	0
2	0	2
12	0	2
17	196	289
10	0	12
39	0	1
30	21	39
31	0	5
3	0	1
19	4	0
27	3	0
51	8	1
5	3	0
21	3	0
59	39	531
24	0	1
1	0	37
33	0	1
1	4	0
30	0	1
37	397	154
30	1	0
2	4	0
5	21	0
10

chain 11117037 HG00126_chrY 52517795 + 24074427 24213570 HG002_chrY 62432599 - 38399346 38539790 2
17699	0	1
23	0	10850
4459	1	0
2454	1	0
4938	0	1
13	0	1
6999	1	0
715	0	4757
650	20341	6035
7	1	0
2251	0	1
3446	1	0
864	1	0
1457	0	12
1557	1	0
3724	1	0
3316	5	0
3200	1	0
1163	0	2
860	0	1
9915	1	0
195	0	10
4128	12	0
740	0	1
912	2	0
2516	0	1
1668	1	0
2015	0	1
3438	8	0
33123	0	7
223	1	0
95

chain 3057525 HG00126_chrY 52517795 + 21786287 21818580 HG002_chrY 62432599 - 40507615 40539913 3
6287	0	1
5505	0	4
806	1	0
451	0	1
19243

chain 427764 HG00126_chrY 52517795 + 23190034 23194545 HG002_chrY 62432599 - 39338719 39343231 4
2490	0	1
2021

chain 327277 HG00126_chrY 52517795 + 18610923 18614380 HG002_chrY 62432599 - 43575590 43579047 5
3457

chain 322611 HG00126_chrY 52517795 + 14679158 14682566 HG002_chrY 62432599 - 47507067 47510475 6
3408

chain 6804 HG00126_chrY 52517795 + 24221709 24221869 HG002_chrY 62432599 - 38539790 38542814 7
2	0	2864
158

chain 2683 HG00126_chrY 52517795 + 12292846 12292874 HG002_chrY 62432599 + 12511308 12511336 8
28

chain 1036 HG00126_chrY 52517795 + 52514566 52514587 HG002_chrY 62432599 + 62431277 62431299 9
12	0	1
9