##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
chain 2175118136 HG03209_chrY 54733247 + 11098 54725625 HG002_chrY 62432599 + 8 62432577 1
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58	8	0
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76	0	726
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44	4	0
56	0	3
31	0	12
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63	0	4
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62	0	20
142	0	1
18	0	4
181	4	0
69	0	18
8	0	20
2384	1	0
397	2	0
84	0	11
1325	1	0
35	8	0
571	3	0
3	1	0
305	0	1
1520	2	0
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1334	0	135
211	12	0
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39	0	1
1540	0	1
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1332	0	1
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93	0	4
1872	8	0
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539	0	8
2631	0	2
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6568	6	0
58	87	0
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79	29	0
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38	16	0
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96	0	4
76	0	2
14	0	6
20	0	1
648	0	1
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3414	1	0
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29	4	0
1674	3	0
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2701	2	0
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112	0	4
854	26	0
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1	13	0
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1081	1	0
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54	0	8
17	0	27
7	40	0
5035	0	1
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689	0	1
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2890	1	0
3458	2	0
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30	0	28
459	1	0
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8	0	2
25	2	31
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2067	4	12
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33	0	2
823	1	0
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899	2	0
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24	7	0
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1584	480	0
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2338	3	0
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27	0	3
64	1	0
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3105	0	4
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74	0	1
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68	0	4
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524	0	5
621	29	0
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34	0	8
630	6	0
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93	0	8
22	8	16
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2950	4	0
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45	135	0
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6459	4	0
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3031	0	1
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75	0	9
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635	4	0
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45	253	248
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6451	2	0
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104	2	0
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367	0	2
683	16	0
54	0	18
917	0	12
6	0	3
760	3	0
38	0	1
1172	0	2
1440	1	0
692	0	5
11	0	2
3763	4	0
2566	0	4
524	3	0
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127	0	1
895	4	0
13	7	3
39	0	8
5	4	0
16	16	0
1780	4	0
1148	2	0
1064	45	0
53	21	0
22	0	10
99	37	37
54	0	2
31	0	24
111	20	0
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65	11	6
66	0	12
8	0	5
4	0	10
39	0	1
29	68	0
39	0	1
30	0	1
213	5	0
75	0	5
58	1	0
130	0	1
99	0	1
19	5	0
64	0	5
50	0	1
28	0	20
6031	0	21
968	0	1
314	113	0
6	47	0
6023	0	1
832	374	0
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1053	0	2
74	0	2
30	10	0
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784	0	1
797	2	0
1921	0	9
896	0	35
63	10	771
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243	12	0
1184	1	0
323	1	0
4699	1	0
209	0	1
571	1	0
2820	0	1
1489	0	124
451	1	0
4	2	0
446	0	22
3389	0	10
1346	2	0
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3577	0	1
495	2	0
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963	1	0
63	2	0
81	0	165
162	82	0
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468	0	2
40	0	3
895	0	3
258	1	0
1691	0	4
55	3	0
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1740	0	3
1584	0	3
163	1	0
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13	1	0
490	1	0
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23	2	0
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938	2	0
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1743	0	1
40	4	0
82	6	0
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82	2	0
172	0	2
6	0	4
58	2	0
985	0	20
119	0	2
586	0	117
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22	1	30
5	5	0
1854	1	0
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1619	0	2
28	0	3044
153	0	1
806	2	0
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1163	1	0
1713	1	0
78	52	5
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5	0	1
7	0	4
3	7	0
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2	2	0
39	1	0
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5	18	14
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31	1	0
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4	0	2
7	0	1
31	19	0
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6	4	0
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18	0	1
8	1	0
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7	19	0
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5	4	0
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5	5	0
6	1	0
4	31	25
26	2	0
4	0	1
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37	3	0
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3	0	2
9	0	2
15	1	0
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6	7	0
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9	1	0
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36	0	2
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6	55	0
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37	2	0
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29	457	202
1502	0	3
3421	0	1
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471	0	8
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1275	4	0
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848	3	0
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61	2	0
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4	13	0
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4	34	0
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1418	0	6
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727	0	1
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56	0	2
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4	0	3810
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254	0	2
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150	924	0
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287	0	3
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37	0	3
37	0	3
49	0	3
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84	0	3
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376	0	348
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5803	1	0
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691	0	1
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202	469	7
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62	11	12
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1594	1	0
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743	4	0
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154	4	0
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37	2	0
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34	7	0
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288	0	3
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59	8	0
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86	12	0
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33	0	10
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2	46	0
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4	0	20265
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52143	962750	326879
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263	40866	20093
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124	15	0
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18	0	10
1440	1	0
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3376	0	5
264	0	10
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44	22289	0
3642	0	5
1880	0	10
5566	5	0
3640	0	5
1921	15	0
970	10	0
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700	0	1
1687	15	0
499	20	0
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5541	0	15
156	1	0
1065	0	15
1473	11095	0
693	31146	8892
3259	0	3
289	10	0
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566	35	0
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73	0	5
1593	10	0
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5175	5569	0
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92	5	0
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6736	10	0
5634	0	20
1890	0	5
263	7531	0
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748	0	1
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2650	15	0
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8	10	0
305	0	369
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720	7496	0
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790	10	0
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339	0	20
29	19090	0
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69	0	15
3081	10	0
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1788	10	0
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3862	0	20
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679	0	15
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29	0	2423
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380	1	3696
12	0	15
6	0	55
1434	10	0
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53	0	5
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3703	1	0
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968	0	12
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81	4	0
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29430	0	1
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1	1	0
6799	0	4
14627	0	1
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6211	3	0
28	0	4
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20	0	8
1496	4	0
67	4	0
996	1	0
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2909	6	0
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29733	1	0
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185	0	1
5817	2	0
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684	0	2
468	1	0
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5	1	0
118	0	1
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3894	1	0
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682	2	0
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18	2	0
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623	0	8
34478	1	0
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314	11	0
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11530	3411	3411
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4313	3	0
677	18	0
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88	0	6
11579	1	0
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2	19	0
21	23	0
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5839	0	8
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65	27	0
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6	14	0
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7905	1	0
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583	12642	12645
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2	24	0
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6440	35	0
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17	8	0
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30	0	5
3392	0	1
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3074	0	1
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20130	1	0
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7	7	0
1	0	3
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65	0	3
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1537	3372	3372
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6	5	3
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563	4	0
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9090	0	1
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5	20	0
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133	38423	83458
498	0	2
78	0	1
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3	0	3
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15791	11569	1077
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26	1124	0
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157	20410	12410
3219	2	2126
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57	4	0
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32	2	0
32	1	0
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349	1	0
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10	2	0
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15	1	0
10	1	0
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483	10	0
3	0	7
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4076	6	0
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141	1	0
364	0	2
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70	0	4
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322	0	3
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25	0	3
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7	0	1
27988	2	0
16	0	2
19	3	55
13	11	0
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13	2	0
13	0	2
13	2	0
8	0	15
18	0	2
167	0	2
460	0	52
20763	1	0
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23	0	6
9870	1	0
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64	20	0
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391	1	0
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288	0	3
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3	10	0
464	0	4
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1	0	2
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5	4	0
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13431	29275644	37493860
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4742	1	0
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14	5084	1599
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264	10	0
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114	0	5
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38	1	0
1497	10	0
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63	3482	0
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828	6988	0
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552	30	0
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14	0	1
1537	5	0
7	5	0
32	0	3508
3459	7012	0
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91	0	1
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436	0	10
1065	1	0
1997	1	0
456	0	20
2570	5	0
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491	5	0
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191	4	0
3295	0	1
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1419	1	0
1346	0	8
1717	0	1
1445	1	0
7821	0	3
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34972	5	0
3008	2	0
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6036	0	36
463	2	0
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2378	1	0
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348	0	3
7570	0	1
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45	0	6
11	0	3
1978	0	1
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22742	0	1
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3116	1	0
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17	2	0
2040	0	1
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68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
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162	0	8
1373	4	0
475	0	3
11569	29	0
27	0	58
687	6	0
45	0	12
49	6	0
193	1	0
30	1	0
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1	0	2
43	0	1
10	0	1
15	2	0
3	0	1
10	4	0
55	0	1
11	13	6
20	12	5
7	1	0
6	0	5
11	28	15
23	0	1
6	193	48
14	75	17
21	31	7
35	1	0
2	5	0
18	143	105
15	4	0
8	0	1
6	23	9
43	182	17
22	49	9
21	5	0
33	1	0
3	0	4
27	0	4
6	5	0
15	0	4
21	26	22
64	3	0
1	0	1
25	3	0
52	16	13
13	3	0
25	0	1
3	0	5
7	0	11
7	17	0
2	0	2
9	3	0
8	35	2
27	0	3
15	0	11
19	1	0
16	3	0
15	9	0
85	108	154
11	0	2
17	0	5
57	2	0
4	1	0
25	4	0
42	2	0
6	1	0
26	4	0
37	1	0
29	4	0
56	8	0
14	4	0
54	1	0
14	1650	0
56	0	5
53

chain 1190969 HG03209_chrY 54733247 + 17308578 17321218 HG002_chrY 62432599 - 45634118 45646761 2
1386	0	6
6455	1	0
4090	2	0
706

chain 322611 HG03209_chrY 54733247 + 15444736 15448144 HG002_chrY 62432599 - 47507067 47510475 3
3408