##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 2514729868 HG02027_chrY 67671062 + 16 28079264 HG002_chrY 62432599 + 2 27976408 1
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831	2	0
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17	0	27
7	40	0
974	0	1
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70	1	0
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30	257	0
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73	0	4
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823	1	0
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18	0	5
52	0	1
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153	0	1
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75	0	5
58	1	0
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99	0	1
73	0	15
34	0	20
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6031	0	21
968	0	1
272	141	0
48	47	0
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658	0	4
243	12	0
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3472	1	0
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28	0	1
571	1	0
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316	6	4
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67	0	2
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54	8	0
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30	0	1
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38	2	0
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8	0	2
38	0	8
4	0	30
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7	291	340
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118	12	0
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294	0	6
1608	0	2
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178	0	4
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2162	4	0
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17	0	15
58	31	82
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42	0	1
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75	0	14
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1439	5	8
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1559	17	14
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20	30	106
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7249	5	0
195	10	0
2017	5	0
1175	5	0
9432	1	0
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13732	0	1
2223	1	0
7495	0	1
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6635	1	0
1969	0	4
4062	16	0
3948	4	0
696	2	0
836	1	0
2354	0	1
16921	0	1
2848	28	0
19709	4	0
14513	2	0
7882	8	0
19600	6	1
422	8	0
949	0	8
3715	1	0
25803	5	0
5542	0	2
1134	0	4
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1951	0	2
4433	0	6
2010	4	0
1902	12	0
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3435	0	3
935	8	0
81	4	0
435	4	0
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68232	1	0
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4763	4	0
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43	0	4
75	20	0
84	4	0
39389	1	0
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5194	0	1
1393	0	1
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8627	0	2
6636	13	0
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469	4	0
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7752	2	0
1093	0	4
1451	12	0
49	0	4
63	4	0
107180	0	1
10657	0	6
12914	1	0
4385	0	12
428	0	1
6107	1	0
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8167	0	451
14746	1	0
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584	0	1
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15671	2	0
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33050	0	1
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67637	1	0
109	1	0
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684	0	2
468	1	0
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230	1	0
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47	1	0
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151	1	0
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5	1	0
118	0	1
50	0	3
253	2	0
342	0	1
161	1542	0
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4896	1	0
1771	1	0
2266	2	0
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5	0	5
30977	1	0
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3663	1	0
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683	2	0
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28	2	0
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5559	2	0
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3521	1	0
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1305	4	0
49	4	0
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59	4	0
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3	6	0
4378	1	0
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400	0	10
320	20	0
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5901	1	0
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79	0	4
5975	0	4
2054	0	2
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1617	29	0
1524	0	12
8339	1	0
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2	2	0
3179	0	2
118	0	26
207	2	0
3965	0	1
1386	0	4
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3910	0	12
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1392	0	3
2195	1	0
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5545	0	15
9596	0	8
561	0	1
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6960	0	1
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2567	2	0
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3248	1	0
4314	0	6
671	9	0
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63	2	0
23	0	2
11583	1	0
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1424	1	0
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17934	0	1
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37	0	8
7042	2	0
39449	3	0
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640	2	0
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15	1	0
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284	4	0
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9	0	1
3	0	1
288	0	2
15775	21	0
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7958	2	0
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161	3	0
66	0	2
3712	0	2
10222	1	0
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6627	1	0
850	1	0
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940	1	0
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2986	1	0
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6621	2	0
22	2	0
1700	8	0
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4068	0	1
8914	7	0
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5597	0	4
13839	1	0
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185	0	4
11	16	0
2541	1	0
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826	5	0
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693	0	8
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44	0	8
2160	4	0
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8000	1	0
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1540	0	1
1873	2	0
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614	4	0
4980	1	0
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4311	1	0
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7835	1	0
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3949	2	0
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926	1	0
6580	6	0
8935	1	0
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12	0	2
27764	18	0
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919	10	0
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328	20	0
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6723	0	23
5633	4	0
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4816	0	1
2976	0	1
930	0	10
40222	2	0
32	2	0
3757	0	35
5367	1	0
6458	0	3
1957	0	32
2	0	1
3712	2	0
21	0	4
17	4	0
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67	0	2
7	0	2
2283	0	1
2757	1	0
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19197	0	5
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7763	1	0
5701	0	4
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7768	1	0
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12615	8	0
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21764	1	0
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766	0	1
26489	0	4
14681	1	0
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8436	2	0
6457	1	0
2264	4	0
6	4	0
8278	0	16
13	3	0
1	0	3
48	4	0
66	4	0
11196	0	4
13441	1	0
14040	8	0
239	0	4
2478	8	0
17	0	2
18650	12	0
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5292	4	0
4119	0	1
7110	4	0
74	0	4
8	0	1
52	4	0
4	0	16
1078	2	0
6613	2	0
9269	2	0
972	0	5
13	0	5
14956	1	0
4740	1	0
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379	0	6
19540	1	0
3036	0	2
22404	0	2
8505	1	0
20737	5	0
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16686	0	2
30	2	0
3142	1	0
14742	1	0
8355	0	2
8552	17	0
2064	2	0
4024	1	0
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19892	1	0
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20572	0	1
6329	0	1
1009	0	4
19911	2	0
25	0	2
3569	2	0
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1127	1	0
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7243	1	0
7123	0	1
32196	1	0
2394	1	0
4292	4	0
609	8	0
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325	1	0
1390	15	0
3422	0	1
28913	0	4
13058	5	0
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8140	8	0
16360	1	0
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1351	0	2
30569	2	0
11642	0	2
25498	2	0
73	19	0
1631	1	0
23827	0	1
4474	0	1
16	1	0
3517	0	1
6326	1	0
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1193	1	0
40	0	2
189	0	1
8635	0	1
1560	0	2
34742	0	1
14580	2	0
67	1	0
1981	6	0
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708	2	0
1188	0	1
7736	0	8
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27840	0	1
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32	0	2
8720	0	1
1657	0	2
13386	0	1
6749	1	0
6447	0	4
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5134	4	0
17	1	0
1	2	0
11	20	0
15615	0	2
961	3	0
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14744	0	8
72	18	8
616	0	4
24049	0	8
58	0	4
32	0	2
2	0	6
33113	0	1
9819	0	4
7161	1	0
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430	4	0
9473	0	1
3522	0	1
83622	0	19
6696	0	3
6220	1	0
11987	6	0
25452	0	1
21221	3	0
13565	8	0
4538	1	0
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5480	1	0
3476	1	0
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4414	2	0
6698	1	0
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571	0	1
9370	8	0
34123	1	0
3425	0	1
36811	0	1
16615	0	1
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27197	0	1
31635	1	0
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9544	8	0
13	0	2
41	0	8
1952	8	0
2252	1	0
11359	2	0
32	2	0
2858	0	3
4079	3374	3374
2125	3	0
9919	1	0
9025	3	0
2383	4	0
1379	1	0
22548	2	0
916	1	0
1529	16	0
1476	6	0
2579	0	2
7039	25	0
6	4	0
10120	8	0
59	3	0
47	4	0
1	2	0
17806	3457	3457
17809	12	0
109	8	0
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6	25	0
7008	2	0
2549	0	1
27927	4	0
2383	3	0
15319	1	0
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218	0	1
6421	0	3
16492	6	0
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4	8	0
9504	0	2
6596	0	1
5063	1	0
5535	1	0
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8	7	0
6718	1	0
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1644	3	0
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6712	1	0
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3128	1	0
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5510	1	0
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6231	3	0
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5632	0	2
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6410	0	1
39	2	0
21	0	2
4325	1	0
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8416	0	1
2532	1	0
6275	0	1
996	0	1
2421	7523	307020
1450	1	0
7309	1	0
29049	4	0
141	0	8
11919	0	2
5661	2	0
23	1	0
1	1	0
10765	2	0
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1800	1	0
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2119	1	0
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26161	1	0
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1414	1	0
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6954	0	10
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7269	2	0
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8712	0	1
8159	0	4
2444	6	0
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42	12	0
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1675	1	0
7415	0	1
5671	0	2
21254	0	1
14663	4	0
9	0	64
1592	1	0
3507	0	1
1794	1	0
3346	0	2
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5248	0	1
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12464	15	0
2996	2	0
275	1	0
33015	5	0
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22237	2	0
34	0	2
26756	1	0
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5733	0	7
6844	0	4
8374	2	0
2989	1	0
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695	0	1
5945	0	1
16244	0	1
7227	17	0
53656	0	5
32687	0	8
6895	0	1
18829	1	0
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1960	0	1
44930	2	0
6472	0	3
1186	1	0
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874	0	1
6580	0	1
2739	2	0
555	1	0
2161	0	1
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668	1	0
176	10	0
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5795	0	1129
7864	0	2759
20005	0	123
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6034	37743	29501
498	0	2
78	0	1
130	0	1
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115	4	0
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11257	2	0
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3030	0	625
47	0	999
16	0	125
123	0	125
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145	875	0
26	1124	0
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17	0	500
408	0	1125
1205	2000	0
52	3999	0
37	250	0
2505	0	999
10032	1918	2918
2089	1	0
7403	4847	5345
390	0	125
570	1	0
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411	0	1
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560	0	1
332	0	7
3	7	0
240	124	0
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790	4249	0
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3982	0	2
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18743	1	0
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780	0	1
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5936	0	1
5540	1	0
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713	0	1
304	0	4
36	4	0
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7233	1	0
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34	4	0
7825	0	1
9736	8	0
57	4	0
4813	8	0
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655	1	0
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4	4	2
7744	10	0
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11	77	0
40	1	0
1	10	0
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1583	5	0
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26	0	4
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5	0	16
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34	4	0
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740	3	0
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3214	0	8
3817	0	1
1567	0	2
14061	9570	57
435	1	0
158	0	4757
12667	1	0
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20499	2138	2138
94	1	0
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23822	7433	281
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4	4	0
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1	0	4
48	2	0
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4001	0	3
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49	0	15
6	7	0
2761	4	0
15515	0	16
63	4	0
13790	1	0
3502	1	0
10415	1	0
4262	0	4
19636	2	0
667	2	0
1848	0	3
24929	0	4
12880	4	0
34558	0	1
15327	0	12
11381	0	1
3377	0	4
326	37	0
4543	1	0
25740	1	0
1025	0	1
7883	0	2
1859	0	8
22	0	4
22467	4	0
61	0	8
41736	9	0
4011	12	0
51965	0	1
16638	0	1
2023	0	2
12072	0	2
22059	1	0
4654	0	1
14599	0	2
31634	0	1
2223	2	0
3490	10	0
6801	0	1
740	0	1
8080	0	1
32131	1	0
19246	1	0
6295	4	0
4669	0	4
20824	1	0
15707	1	0
4082	0	1
13524	2	0
32	2	0
33272	1	0
18340	1	0
15147	3	0
1403	2	0
4358	1	0
15177	0	11
24860	1	0
7541	1	0
748	8	0
6620	0	1
497	0	1
2474	4	0
16782	4	0
1161	0	1
3206	0	2
8601	2	0
7737	16691	0
2347	9536	0
6523	1	0
1224	2	0
5804	0	3
8149	0	1
4589	0	21688
15812	2	0
35	1	0
58	2138	2138
63	0	1
35	0	1
15191	21694	0
4769	1	0
451	1	0
13953	0	2
1224	0	1
6487	0	7153
2064	1	0
19040	0	2
15350	2	0
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4156	1	0
5413	0	12
8312	0	1
24860	0	19
3343	0	4
3372	0	16
93	0	3
4	12	0
17	8	0
101	0	8
75	0	4
2483	1	0
24725	0	2
67172	1	0
7387	2	0
2569	13	0
1392	1	0
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604	2	0
6683	0	1
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6970	0	1
12562	0	1
7973	0	1
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6780	0	1
2190	0	1
7676	1	0
821	0	4
28773	2	0
3048	0	1
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20279	0	1
689	6	0
23	0	2
7058	0	1
6581	2	0
4896	0	2
48	12	0
3070	2	0
912	0	1
1777	4	0
8468	0	3
606	3	0
340	3	0
2318	0	2
18950	2	0
518	1	0
7163	6	0
526	1	0
20	0	2
4725	4	0
15621	0	1
1429	8	0
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25119	0	1
814	1	0
4700	1	0
8159	1	0
2816	0	4
5189	0	1
32016	0	1
4862	1	0
17521	1	0
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12995	2	0
11460	2	0
16	2	0
4563	0	1
10012	1	0
4936	0	1
2132	0	1
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12206	0	1
22353	2	0
34	0	2
271	0	1
35294	0	5
17839	1	0
19283	0	1
19260	15	0
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71	4	0
27696	1	0
2434	1	0
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2312	1	0
17342	1	0
664	2	0
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14184	1	0
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19	4	0
4377	1	0
26762	0	1
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1857	0	4
64296	0	3
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3297	1	0
50043	0	1
13878	0	6
41080	3	0
2	0	2
3740	1	0
14825	1	0
2861	0	1
5948	0	1
48710	0	1
2673	0	1
6296	0	4
24891	0	1
608	3	0
33309	0	10
28	6	0
15912	4	0
17373	1	0
31936	1	0
19327	0	1
1207	0	1
1974	1	0
3985	0	1
16267	1	0
27	0	6
41	12	0
13240	1	0
5039	1	0
49354	2	0
20051	0	6
26283	2	0
4386	0	1
18078	1	0
5088	0	1
629	2	0
8228	19	15
33	0	2
14351	0	4
38133	1	0
19805	4	0
10804	0	4
9936	0	1
2685	1	0
562	4	0
22977	1	0
13659	0	1
17487	0	1
27883	0	399
18141	0	5
11983	0	10
2779	14525	161
1352	5	0
376	0	1
10	1	0
542	5	0
88	0	1
15	1	0
437	0	5
1391	0	5
860	1	0
64	0	10
2825	2878	0
659	0	1
1209	0	10
562	0	5
482	15	0
24	5745	0
532	0	10
64	0	1
2276	10	0
1609	0	20
1790	0	5
11	0	5
64	0	1
1002	20	0
324	5	0
925	10	0
2867	0	5
16	10	0
2847	15	0
558	0	10
1815	5	0
505	0	5
2863	0	15
1023	0	1
601	20	0
332	5	0
1924	0	1
1359	0	5
500	0	10
1023	0	1
598	20	0
1241	10	0
548	0	10
1067	20	0
1269	5	0
532	10	0
64	1	0
1169	0	10
1063	0	15
533	5	0
16	5	0
61	1	0
400	0	1
1359	0	5
505	5	0
548	0	10
2336	5	0
596	1	0
1002	0	20
1248	5	0
547	0	10
2306	25	0
1023	1	0
1359	5	0
507	5	0
538	0	10
468	1	0
3671	10	0
561	0	5
495	20	0
1023	1	0
1364	5	0
497	0	10
620	0	1
400	1	0
1359	5	0
1068	10	0
54	1	0
2245	0	15
547	10	0
65	0	1
1002	20	0
1800	10	0
2316	0	10
552	10	0
1801	0	5
510	0	5
547	10	0
1068	20	0
1253	0	5
1625	20	0
1243	5	0
622	1	0
2252	0	15
543	0	10
1069	20	0
446	0	2873
1325	2873	0
2890	10	0
8	2878	0
2865	0	10
1128	22054	7938
173	1	0
6155	0	15
2425	0	20
1362	0	2
1755	10	0
3934	10	0
672	0	6262
1631	0	10
6211	0	6252
24	0	5
40	0	5
18140	0	6216
474	10	0
30	5	0
81	10	0
1319	0	5
617	0	1
1048	0	5
26	0	10
1261	10	0
560	0	3114
1267	0	10
189	15	0
706	0	1
1276	0	5
949	0	20
153	15	0
227	1	0
2318	0	6240
398	0	15
157	15	0
227	1	0
2548	5	0
148	10	0
783	0	5
5	0	5
1378	0	5
48	20	0
739	5	0
113	5	10
40	0	12442
800	5	0
564	0	1
821	0	12465
595	10	0
290	5	0
22	5	0
789	0	5
98	0	1
721	10	0
1501	10	0
79	1	0
726	0	5
1408	20	0
897	5	0
11492	0	5
623	0	10
1136	0	6193
4638	1	0
1640	0	1
5114	5	0
4776	5	0
975	0	10
3221	5	0
16952	5	0
8423	0	20
5006	8162	2649
6	0	5
10	0	280
5902	0	2763
1	0	2769
420	0	1
2005	0	5
550	5	0
14	5	0
131	30	0
2200	2	0
532	20	0
2002	10	0
732	20	0
2034	0	15
700	0	20
2245	0	1
2517	0	10
206	1	0
488	20	0
1668	0	15
346	20	0
715	10	0
254	0	5
1409	15	0
320	5	0
4	0	5
1016	5	0
1785	15	0
2727	0	5
1463	0	5
820	5	0
126	8	8
357	0	5
2729	10	0
26	0	5512
66	1	0
2681	10	0
1000	0	5
1758	0	10
3759	5	0
1745	0	5
85	0	1
8221	5	0
2461	0	1
5793	0	5
2065	15	0
2035	0	30
332	0	15
708	0	15
615	0	5
314	0	5
389	10	0
1766	0	10
548	22069	0
10571	16945	24048
2130	0	4
19172	0	41
3524	51	0
7016	0	5
339	0	1
11241	5	0
685

chain 66923156 HG02027_chrY 67671062 + 66925331 67667037 HG002_chrY 62432599 + 61647336 62432577 2
22	0	10
13371	0	10
2609	10	0
17796	16252	6604
21274	1	0
21207	0	10603
7069	1	0
7069	1	0
1254	25	0
4986	0	14139
2092	25	0
3557	15	0
2235	1	0
1194	0	1
5874	1	0
179	5	0
946	10	0
86	15	0
414	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
2723	25	0
3356	0	15
7086	0	15
5574	1	0
9600	185	3705
2350	0	15
150	0	25
15766	40	0
1849	25	0
1644	40	0
1686	0	15
1233	1	0
494	0	20
120	0	14039
1666	0	15
11724	0	1
28181	0	3514
45	0	155
114	0	3609
10103	3503	0
5828	0	15
24	15	0
371	5	0
7014	5	0
1438	30	0
2030	10	0
389	1	0
1297	0	1
245	4	0
1566	5	0
389	1	0
1527	5	0
950	0	5
1020	1	0
447	2636	13156
3509	5	0
30419	0	2
2288	5	0
37648	0	2
32577	20	0
9499	1	0
8310	0	10
10982	0	3
16383	12	0
37980	2	0
18364	2	0
4328	12	0
7671	0	4
2378	1	0
172	1	0
5936	1	0
660	0	1
11879	19	0
1776	0	3
2033	0	1
3697	2	0
866	1	0
4656	0	1
1477	0	1
109	0	1
2373	1	0
1036	1	0
43	0	1
1026	2	0
1707	1	0
3695	0	2
2722	3	0
45	0	6
11	0	3
2374	1	0
4546	0	1
401	0	1
8120	0	5
407	1	0
1864	4	0
7215	0	1
3912	0	4
915	0	1
3144	16	0
8900	1	0
658	0	16
3088	0	33
14142	0	1
3703	2	0
4896	0	1
28220	0	1
52662	4	0
14555	2	0
2146	1	0
3373	6	0
2040	0	2
6976	0	4
68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
4172	0	1
1543	3	0
475	0	1
3574	6	0
42	6	0
125	38	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	2
160	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
10	4	0
12	0	2
15	0	6
15	0	1
22	1	0
25	7	1
28	44	15
30	0	6
6	5	0
6	62	2
6	0	1
17	125	29
10	0	5
19	18	0
2	0	2
12	0	1
18	22	3
11	31	9
15	8	0
1	3	0
9	1	0
1	5	0
7	22	0
41	7	0
27	0	1
15	4	0
7	0	2
6	17	21
19	142	29
19	45	12
21	6	35
6	1	0
33	0	1
30	0	7
12	19	0
15	3	0
44	0	1
19	3	0
27	3	0
2	1	0
8	1	0
17	1	0
13	23	17
21	3	0
45	1	0
16	0	2
9	3	0
9	19	0
18	2	0
10	0	2
15	0	4
15	1	43
15	109	224
11	0	2
79	2	0
29	4	0
36	0	6
24	0	1
1	0	37
35	4	0
70	4	0
60	0	1
6	1608	1
56	0	5
53

chain 15197349 HG02027_chrY_random0000474 287639 + 126552 287637 HG002_chrY 62432599 + 19542601 19703643 3
2666	4	0
10499	12	0
6526	4	0
20569	0	16
8087	2	0
83	2	0
14790	0	2
3742	2	0
16236	1	0
1312	0	1
86	1	0
27644	0	1
5681	1	0
6906	1	0
27	24	0
4754	2	0
739	1	0
15391	0	1
2542	1	0
650	0	1
3145	1	0
4155	1	0
454	1	0
47	0	1
1034	1	0
119	1	0
155	1	0
13	1	0
905	0	1
648	1	0
21	1	0
1392

chain 11946318 HG02027_chrY_random0000474 287639 + 1 126551 HG002_chrY 62432599 - 42723810 42850342 4
17236	0	1
24077	0	5
6088	1	0
840	1	0
5681	0	1
27644	1	0
86	0	1
1312	1	0
13032	1	0
3204	1	0
3742	0	2
133	2	0
14657	2	0
83	2	0
8103	16	0
604

chain 327277 HG02027_chrY 67671062 + 19174672 19178129 HG002_chrY 62432599 - 43575590 43579047 5
3457

chain 201400 HG02027_chrY 67671062 + 25744859 25746981 HG002_chrY 62432599 - 36784196 36786318 6
2122

chain 201400 HG02027_chrY 67671062 + 24118158 24120280 HG002_chrY 62432599 - 38399346 38401468 7
2122

chain 1346 HG02027_chrY 67671062 + 67668311 67668325 HG002_chrY 62432599 + 62432585 62432599 8
14