##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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881	0	3
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43	9	0
31	0	1
658	0	1
354	0	3
336	1	0
2017	26	0
1027	1	0
534	0	8
5812	103	16
39	23	0
13	1	0
3	33	0
391	1	0
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588	0	1
1066	0	1
2424	0	4
2358	90	0
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2100	0	4
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1400	0	1
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27	60	0
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197	0	2
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1431	0	3
2026	1	0
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41	8	0
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5	4	0
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823	1	0
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65	2	0
571	0	3
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686	0	2
67	4	0
1751	1	0
119	38	0
2231	0	4
696	20	0
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36	0	309
2402	28	0
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547	1	0
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7989	4	0
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14	0	5
2325	0	13
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297	0	4
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52	0	4
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457	4	0
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3	20	0
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73	4	0
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2584	2	0
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5086	1	0
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316	1	0
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7	155	0
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58	4	0
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48	12	0
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1269	1	0
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13	12	0
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75	0	9
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16	20	0
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61	0	4
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22	0	5
66	10	27
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4	10	0
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49	1	0
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17	0	25
63	1	0
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44	0	1
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17	0	1
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26	69	105
563	0	4
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8	0	2
49	0	4
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234	341	342
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167	0	1
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309	8	0
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10	27	23
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34	0	1
64	0	1
12	2	0
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86	2	0
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8	0	5
8	0	8
182	0	62
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92	4	0
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15	0	4
8773	0	14
21	0	8
102	0	4
274	0	4
14	24	1
35	0	1
3	0	4
4	2	0
3234	1	0
1559	0	1
1647	0	1
1524	0	1
1170	0	1
1594	59	0
838	4	0
5493	6	0
33	0	1
732	8	0
248	0	4
3907	0	1
1930	0	1
849	168	0
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882	0	4
2847	1	0
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1592	0	10
6310	3	0
161	0	2
901	1	0
11	1	0
296	2	0
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1	8	0
229	0	4
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3	2	0
19	2	0
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112	0	4
1250	26	11
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149	0	5
743	4	0
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397	0	136
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614	6	0
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889	18	0
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7	1	73
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17	0	2
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6	2	0
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384	0	2
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1093	1	0
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623	0	1
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97	41	0
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248	40	327
57	0	41
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24	8	0
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772	12	23
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257	0	1
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704	1	0
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19	4	19
8	28	0
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14	17	185
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48	1	0
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15	20	70
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42	0	1
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44	0	2
12	21	0
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12	3	0
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9	0	3
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7	0	9
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12	21	38
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15	1	0
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2519	0	24
489	2	0
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1527	6	0
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9	1	0
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8	8	73
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10	4	0
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8	1	0
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11	3	0
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4	7	53
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20	0	23
31	16	121
1733	0	2
1373	3	0
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199	1	0
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63	14	0
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957	2	0
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536	0	2
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2532	16	2
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56	2	0
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96	0	2
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5	114	205
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326	2	0
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48	0	2
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46	0	2
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59	1	0
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63	1	0
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84	2	0
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869	1	0
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72	8	0
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1	5	0
134	0	8
1677	1	0
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38	28	0
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9	1	0
7	36	35
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67	10	27
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67	1	0
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9	0	22
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94	12	0
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117	2	0
21	1	0
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26	4	0
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1505	3	0
658	1	0
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393	2	0
98	0	4
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2278	0	1
3467	3	0
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106	4	0
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8954	1	0
358	1	0
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2971	0	1
4055	1	0
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1505	0	3
787	26	0
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1211	0	3
2478	2	0
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588	0	6
93	4	0
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6511	1	0
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1505	0	3
787	28	0
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1	3	0
356	2	0
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1693	0	2
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26	0	6
846	0	1
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1930	1	0
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1	0	2
3660	0	1
424	2	0
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73	0	12
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16	0	109
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2546	2	0
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356	1	0
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6982	1	0
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22	4	0
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4207	1	0
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2584	6	0
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837	2668	104118
722	0	1
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2002	0	5
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9	2	16
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27	0	121774
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24	24	0
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1672	1	0
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15	0	8
3141	2	0
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5561	5	0
46582	1095462	311619
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597	529	17394
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8	7359	0
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818	12307	22120
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336	37167	143040
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325	22945	10781
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3757	0	35
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4090	1	0
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1973	0	1
3730	2	0
4693	2	0
11628	5	0
6929	0	1
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10717	2	0
67	4	0
3	2	0
4	2	0
2287	0	1
2757	1	0
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39	0	1
42	0	4
28	16	0
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12788	46225	46210
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70	0	4
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28	2	0
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735	0	1105
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4075	3373	3373
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48	4	0
2531	0	2
7039	25	0
6	4	0
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39072	4	0
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2368	1	0
5669	0	24
648	39675	39663
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3742	1	0
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5630	2	0
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11662	1	0
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6735	0	2
5079	1	0
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625	3	0
105	0	1
8071	0	9
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31581	1	1
563	0	1
1227	4	0
17981	0	1
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611	1	0
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1723	0	1
3988	2	0
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37273	0	2
8969	0	1
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30961	16	0
9987	1	0
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3267	0	3
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3702	1	0
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74	2	4
34	4	0
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3422	0	4
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7	2384	0
1126	1	0
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8842	1	0
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4887	10849	0
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15477	0	1
35	0	1
63	4919091	4816515
2248	975	0
28	284	0
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62	5	0
11	5	0
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187	1405	0
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14217	6038	2710
1493	15	0
601	0	15
3509	15	0
1680	28238	201672
3671	17214	7083
1	0	3013
40	3549	0
1932	0	1
105	0	5
18	0	5
1966	0	15
1525	2199	9301
4900	0	5
16	0	5
3292	19798	16291
687	1	0
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3200	0	3500
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8346	2	3546
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3381	20	0
4963	61358	22629
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393	0	5
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952	5	0
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810

chain 81974310 HG00512_chrY 81719894 + 80622999 81716301 HG002_chrY 62432599 + 61334266 62432577 2
5521	5	0
39	0	290
308	0	3559
8273	0	10
1776	5	0
2	5	0
1798	5	0
832	0	5
119	15	0
828	0	5
3	25	0
326	15	0
712	0	15
670	0	1
37	0	5
808	5	0
119	0	15
10	1	0
825	0	2544
12	0	5
21	0	225
13742	10172	2913
5552	9081	6663
2542	0	9671
11098	2	0
125	17800	872
5	0	2
600	1	0
690	2417	0
3861	4836	4836
5660	44070	38068
502	15	0
15376	5	0
542	10	0
51	1	0
1303	0	4494
11036	5	0
10651	10723	43
38	0	10
17393	15	0
354	0	5
673	0	5
4280	5	0
134	0	15
752	10	0
1178	0	17147
90	0	15
1692	0	3547
754	15	0
1073	2918	0
30	0	15
2519	0	7
8	18735	1030
7113	5	0
1758	42584	7048
1783	5	0
10651	0	5
173	0	7113
3396	0	10
9568	0	3549
8084	25	0
1306	20145	27218
6937	10	0
17796	16252	6604
12792	0	1
3986	0	10603
13174	0	5
20	2071	16205
3367	1	0
2105	0	1
1428	0	1
3534	1	0
6240	0	14139
30294	0	25
3519	25	0
5416	1	0
1645	25	0
3559	0	25
4371	185	3705
15593	1	0
2713	40	0
1849	25	0
1644	40	0
1686	0	15
1233	1	0
494	0	20
120	6417	13456
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8042	0	1
513	20	0
61	40	0
27068	0	1
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45	0	155
114	0	3609
2350	5	0
7753	3503	0
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1438	30	0
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32	0	3508
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1774	0	1
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407	1	0
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915	0	3
3142	14	0
8900	1	0
658	16	0
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16288	0	3
6451	0	1
343	0	2
4828	0	1
6	0	3
530	2	0
2613	1	0
1095	0	4
12695	0	1
6099	0	1
73	12	0
272	0	2
2724	2	0
4392	0	1
9625	1	0
21629	1	0
73	0	1
10647	1	0
1366	0	1
1509	2	0
9	1	0
338	0	3
255	3	0
11013	1	0
168	0	1
782	1	0
16952	2	0
5226	1	0
1381	1	0
4050	0	6
8018	58	0
745	6	0
106	6	0
3	0	6
184	1	0
43	0	1
3	0	1
5	1	12
43	0	1
38	0	2
12	115	166
12	0	2
42	60	11
21	7	6
7	18	0
16	0	1
18	8	2
12	0	43
17	11	23
12	7	0
5	0	1
9	0	1
15	4	0
7	0	2
6	22	578
24	3	0
15	9	0
22	65	397
15	4	0
66	4	0
70	4	0
60	0	1
4	0	1
58	0	5
53

chain 11101695 HG00512_chrY 81719894 + 24700963 24852038 HG002_chrY 62432599 - 38399346 38539790 3
17699	0	1
23	0	10850
4459	1	0
2454	1	0
4952	0	1
6999	1	0
715	0	4757
650	32265	6035
7	1	0
2251	0	1
4310	1	0
1457	0	10
1559	1	0
3724	1	0
3316	3	0
4363	4	0
862	0	1
9915	1	0
195	0	6
4132	12	0
1653	6	0
2516	0	1
3683	0	1
3434	0	4
8290	1	0
24833	0	1
229	1	0
95

chain 4354618 HG00512_chrY 81719894 + 17769017 17815241 HG002_chrY 62432599 - 45214480 45260689 4
13217	8	0
13204	1	0
5446	0	2
17	8	0
2478	0	4
239	4	0
11602

chain 3741743 HG00512_chrY 81719894 + 20138723 20178391 HG002_chrY 62432599 - 42850342 42889998 5
17408	4	0
2557	2	0
6526	6	0
10499	2	0
881	0	2
1783

chain 6804 HG00512_chrY 81719894 + 24860177 24860337 HG002_chrY 62432599 - 38539790 38542814 6
2	0	2864
158

chain 2683 HG00512_chrY 81719894 + 13132774 13132802 HG002_chrY 62432599 + 12511308 12511336 7
28