##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 2474202127 HG02083_chrY 71487452 + 1594 71480139 HG002_chrY 62432599 + 2 62432577 1
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1640	1	0
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43	4	0
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33	0	8
23	0	4
12	8	0
542	0	1
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584	1	0
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985	0	28
503	2	0
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7	2	0
817	5	0
1407	2097	0
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81	39	0
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41	0	6
81	0	3
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191	1	0
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1559	17	14
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540	0	296
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2483	8	0
10476	2	0
195	52	0
117	0	52
11905	2	0
8493	15	0
2488	2	0
1928	0	1
16961	0	2
25935	0	1
22165	0	2
18399	2	0
10425	1	0
34394	0	2
9936	0	1
177	0	6
5521	0	12
13675	1	0
3023	0	1
10426	3	0
13047	0	2
13240	0	1
3230	4	0
1696	0	2
15790	66	0
104	0	66
71	0	22
9875	1	0
4938	3	0
1514	0	1
60710	0	3
25288	4	0
3763	1	0
70609	2	0
30	18	0
19449	1	0
2635	12	0
130	9	0
65	0	12
6	9	0
45	3	0
17	1	0
2	0	1
49319	0	1
48587	0	5
28	3	9
32444	1	0
86978	0	2
20725	18	0
9867	0	6
114	0	2
1981	2	0
5186	0	2
13087	2	0
120	0	2
4560	18	0
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31304	2	0
3151	4	0
5824	0	1
11354	0	2
3125	44	0
9882	0	2
10243	1	0
5675	0	3
4	0	20265
4318	2	0
117	4	0
20267	2	0
7167	6	0
28758	1	0
471	13	0
356	1	0
3303	1	0
393	4	0
96	8	0
4580	0	18
2556	2	0
30	0	4
838	1	0
1505	0	3
783	0	30
1940	0	1
3402	1	0
470	11	0
1	2	0
356	1	0
2002	5	0
1813	2	0
21	1	0
6982	1	0
117	0	2
26	6	0
3006	1	0
124	28	0
1116	0	1
823	1	0
1284	1	0
2327	3	0
258	0	13
356	0	1
3303	0	1
491	0	4
4602	18	0
2540	0	2
26	4	0
842	0	1
1505	3	0
786	20	0
3545	0	1
1795	0	1
471	0	13
356	0	1
2000	5	0
1109	3	0
191	0	1
428	0	2
106	2	0
4013	4	0
526	18	0
11540	0	1
3661	1	0
393	2	0
7244	2	0
30	0	6
836	1	0
1505	0	3
2723	0	1
3402	1	0
471	14	0
356	2	0
3692	6	0
100	4	0
4609	0	18
2412	1	0
143	2	0
846	1	0
1505	0	3
6154	1	0
471	13	0
7	1	0
349	2	0
1211	0	3
2515	0	2
4274	1	0
2931	0	2
26	8	0
838	0	1
1505	3	0
658	1	0
137	32	2
1925	1	0
1284	1	0
2327	3	0
258	0	13
356	0	1
3303	0	1
534	0	6
7121	2	0
5077	0	1
1607	0	1
5746	3	0
191	0	1
495	0	4
4051	4	0
3109	0	4
5071	1	0
1440	1	0
6106	1	0
390	0	2
99	0	2
7160	0	4
6	2	0
846	1	0
1505	0	3
2723	0	1
3402	1	0
470	11	0
1	2	0
356	1	0
2002	5	0
1694	8	0
96	4	0
4582	0	18
2439	1	0
143	2	0
14	0	2
830	1	0
1505	0	3
6158	1	0
470	11	0
1	3	0
356	2	0
2000	0	5
1693	0	2
101	4	0
4602	18	0
2540	0	2
26	0	6
846	0	1
1505	3	0
786	16	0
7	6	0
1930	1	0
3402	0	1
470	0	11
1	0	2
356	0	1
3303	0	1
450	0	1
73	0	12
4559	18	0
6815	1	0
4709	0	1
4052	0	12
14	0	109
19	0	40601
4013	0	4
3110	0	2
11313	0	5
1716	4	0
4664	0	18
2439	1	0
117	0	2
26	4	0
240	0	121744
2894	0	6
6204	0	1
1212	0	3
2580	0	6
10304	2	0
43	0	121774
1101	0	1
4227	0	1
471	0	13
356	0	1
3723	2	0
110	2	0
6982	0	1
133	0	4
854	0	1
2294	4	0
9	2	0
9303	0	4
581	0	4
93	0	8
10364	0	4
20273	8	0
5861	1	0
2378	0	5
8932	2	0
16948	1	0
43	0	4
17988	2	0
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1258	0	4
4211	1	0
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2182	8	0
42450	1	0
2274	1	0
31504	0	2
6919	0	2
33965	2	0
25859	0	29
372	0	2
3009	31	0
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33175	6	0
175	0	2
1143	1	0
4296	0	1
10737	1	0
3528	0	2
13063	2	0
4319	9	0
17099	0	4
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34135	2	0
29546	0	8
27185	0	2
2079	0	1
2256	0	1
1165	0	1
8831	1	0
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52143	477344	311619
29328	10	0
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860	5	0
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2530	0	5
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87	0	15
834	0	5
191	10	0
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347	0	5
1841	0	10
105	0	5
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4660	0	20
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725	0	5
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5610	0	10
383	0	15
415	5	0
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763	5	0
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772	5	0
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249	5	0
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189	5	0
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2311	10	0
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18	5	0
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380	5	0
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1165	5	0
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457	5	0
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22	0	2
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101	2	0
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5095	5	0
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1431	5	0
44	0	5
2200	0	10
536	15	0
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93	0	5
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50	0	5
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120	0	10
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374	5	0
13	5	0
34347	5	0
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13	0	4
28	0	2
17	0	1
12538	0	1
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32528	0	5
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265	5	0
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5030	0	5
572	5	0
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191	654	0
603	0	5
164	0	23077
2918	14	14
19	1606	5
184	1	0
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1100	0	5565
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574	10	0
5577	0	5
4432	0	5
497	5	0
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640	5	0
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10279	0	11091
737	10	0
42	20	0
519	0	25
208	0	5
788	5	0
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4273	9438	17719
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1765	0	5
1358	0	5
4194	0	10
195	1	0
92	1	0
209	0	1
820	0	5
597	55	0
28	1	0
1831	0	5
93	0	5
258	224362	198286
470	1378	0
506	0	5
667	0	15
694	4119	0
2	5	0
6826	0	5
1130	0	1373
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199	0	1
2237	39103	12984
29726	0	10
5562	0	5
1926	5	0
54	22304	0
3642	0	5
5779	5	0
10	5	0
1667	0	5
35	0	5
1	0	5
926	0	10
700	0	1
2201	10	0
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5541	0	35
136	1	0
1065	0	15
1473	11060	0
693	49751	5473
1675	0	10
570	0	5
3163	0	5
1250	0	3
523	0	5
581	25	0
810	0	10
2366	0	5
2354	0	5
3206	5	0
1778	0	5
206	5575	0
370	5	0
4816	0	10
148	5	0
601	0	10
5007	0	5
6081	0	5
4460	3	0
7711	5553	0
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1643	0	5
380	10	0
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1290	7653	0
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765	0	5
37	0	5
748	0	1
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552	0	10
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775	1	0
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305	0	369
1598	0	10
731	0	5
510	25	0
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790	10	0
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838	5	0
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1263	0	10
37	0	10
325	27062	3601
29	0	20
395	0	15
1152	0	15
226	0	15
69	0	25
1974	10997	3245
339	0	20
29	26722	0
397	0	15
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234	0	15
69	0	15
3081	5	0
1980	5	0
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2012	0	20
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2023	10	0
4	0	5
3787	0	5
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3131	0	5
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2010	0	5
2443	10	0
47	0	5
1751	20	0
2013	5	0
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1808	0	5
3869	15	0
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6292	5	0
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491	0	5
3336	4	0
3934	17144	25802
484	0	25
20	0	30
1414	0	5
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76	5	0
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213	0	10
220	15	0
25	65	0
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282	5	0
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5157	0	5
1210	5	0
195	10	0
1533	5	0
1659	5	0
3861	28	0
5571	1	0
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1441	0	1
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32	0	20
6584	2	0
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4062	8	0
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696	4	0
20112	0	1
1071	0	1
1776	31	0
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3715	1	0
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1135	8	0
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369	1	0
557	8	0
516	4	0
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68232	3	0
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122	8	0
28623	10	0
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595	0	2
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1355	0	8
88	4	0
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63	8	0
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428	0	1
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28	1	0
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2222	2	0
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109	1	0
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3521	1	0
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49	8	0
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3710	0	2
4972	1	0
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5648	1	0
1075	3	0
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11	0	1
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2975	0	1
930	8	0
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3429	1	0
35033	2	0
3757	0	1
18	1	0
5383	1	0
6458	0	3
5704	2	0
24	0	2
16	4	0
4651	4	0
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7714	0	1
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2757	1	0
3485	0	15
2	4	0
13	0	1
32109	0	1
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755	0	1
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71	1	0
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4	0	16
13	3	0
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39	0	1
74	4	0
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172	0	12
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44918	0	1
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8	0	1
52	4	0
4	0	8
1086	2	0
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60	0	1
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972	0	5
13	0	5
14956	1	0
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379	2	0
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762	1	0
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670	0	4
21	4	0
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18757	1	0
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876	0	1
252	3	0
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42	0	2
8270	1	0
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32	0	4
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5159	20	0
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34	0	4
658	0	4
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1742	8	0
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490	0	1
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34119	1	0
3726	7532	602230
501	1	0
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21	0	2
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8091	2	0
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3742	1	0
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27	23	0
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17582	1	0
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3959	1	0
486	1	0
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42	6	0
572	0	4
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36	0	36
27	0	64
5099	0	1
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2218	1	0
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685	1	0
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9310	37495	29501
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78	0	1
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11257	2	0
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10658	21537	12410
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332	0	7
3	7	0
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34	4	0
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687	1	0
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11	77	0
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14	0	2
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3875	1	0
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33	16	0
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6165	9570	57
435	1	0
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58	2138	2138
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474	1	0
253	0	10
538	0	5
623	0	10
154	5	0
1043	1	0
202	0	3127
526	0	12407
3835	1	0
6755	5	0
5751	0	10
3221	5	0
6333	5	0
10619	5	0
13449	8162	2649
6	0	5
10	0	280
11097	0	5
2754	0	10
211	0	1
352	5	0
2151	0	5
14	0	5
156	2	0
532	20	0
1684	0	15
335	10	0
5	5	0
695	30	0
249	0	5
1749	5	0
36	0	10
720	10	0
2003	10	0
31	15	0
700	30	0
2029	0	5
47	0	1
156	0	1
6	1	0
488	30	0
698	0	5
965	0	15
346	30	0
715	10	0
254	0	5
1409	15	0
320	5	0
4	0	5
1016	5	0
1744	0	5
31	0	5
47	0	1
936	0	5
1822	1	0
156	1	0
2179	15	0
355	0	20
998	5	0
1731	0	5
16	0	5512
5505	0	15
77	0	1
2408	0	1
1272	5	0
1335	16553	2764
422	15	0
16	0	10
47	1	0
216	1	0
455	0	10
230	0	11047
20	0	10
30	0	2753
672	15	0
345	15	0
347	0	15
361	5	0
818	0	10
147	0	10
3159	0	10
1339	5	0
13	0	10
548	1147632	1131850
22	10	0
1267	5	0
438	1	0
474	10	0
9	15	5
1066	0	5
270	0	10
652	15	0
8	3544	0
684	1	0
4329	5	0
1239	27233	20100
1805	5	0
7842	1	0
5687	32302	14503
521	15	0
583	0	5
685	0	15
163	0	1
103	0	10
15	0	5
1966	0	15
1458	1	0
67	3309	17519
14390	8961	1901
687	1	0
300	0	5
7	0	10
3200	0	3500
7362	0	5
16998	15	0
686	0	5
8346	3521	3536
2220	0	5
3	0	3529
4790	0	25
2043	0	1
165	5	7097
30	20	0
4963	39819	5937
6973	0	1
270	0	1
9262	1	1
9481	1	0
7971	0	1
458	3019	13650
4130	5	0
6408	17745	0
711	20	0
1733	10	0
1804	5	0
1779	0	10
393	0	5
2324	0	5
452	15	0
5697	0	5
918	0	5
1237	10	0
1361	15	0
2211	15	0
2270	5	0
1183	1	0
44	10	0
810	41530727	32045929
5521	5	0
3598	0	290
6788	0	5
3603	5	0
1780	12369	1712
63	45	0
8	25	0
6363	25	0
13327	0	5
397	19840	2913
5552	4823	7243
6027	0	3
1105	0	9668
6922	0	2
1	2422	0
5	0	2
600	1	0
690	2417	0
14357	7457	7457
8082	0	10
693	15	0
105	1	0
1002	0	10
781	15	0
122	10243	4284
812	15	0
11612	7060	0
4516	0	5
14455	5	0
542	10	0
51	1	0
1303	0	4494
11036	5	0
7114	5	0
7165	5	0
13856	15	0
1032	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
40	0	5
2519	0	7
988	0	5
45	3564	0
1749	5	0
22	0	10
3559	10	0
1536	17610	0
237	10	0
138	0	10613
327	1	0
3054	0	5
1802	0	10
1753	15	0
10	5	0
1781	0	10
1737	5	0
31	10	0
147	0	7113
3406	25	0
1746	5	0
1743	0	10
15	4	3548
1730	56695	31848
16022	10	0
4676	0	2414
10706	21078	6604
5398	60325	99215
10211	0	1
10149	25	0
1881	1	0
8740	0	25
835	185	3705
2515	0	25
22	0	15
3333	15	0
3685	0	25
3370	15	0
3506	15	0
164	25	0
1646	40	0
1849	25	0
1644	40	0
1875	25	0
1059	1	0
494	0	20
120	5152	1592
80	0	15
1233	1	0
494	0	20
1957	25	0
1644	40	0
1672	0	15
994	3520	0
814	40	0
1851	25	0
1658	40	0
1666	0	15
1814	40	0
1672	0	15
11718	0	1
494	20	0
66	40	0
15175	15	0
689	0	15
387	5	0
7860	0	3514
45	0	155
114	0	3609
2029	0	5
8069	3503	0
5828	0	15
24	15	0
40	0	10
321	5	0
4402	0	3498
552	30	0
218	0	1
46	0	5
178	5	0
14	0	1
1567	5	0
389	1	0
490	0	5
1048	4	0
1	1	0
940	0	5
620	5	0
389	1	0
1527	5	0
14	0	1
1576	0	14027
3469	5	0
32709	5	0
21087	2	0
56	0	5385
43699	4	0
149	4	0
4	12	0
3333	0	1
11555	0	2
2765	0	21
23	0	3
10945	0	3
16383	8	0
34972	5	0
3008	2	0
12789	0	36
1774	0	1
1087	2	0
2677	12	0
4328	10	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
3695	0	1
2723	4	0
45	0	6
11	0	3
2374	1	0
4546	0	1
401	0	1
10396	2	0
7215	0	1
4831	2	0
15807	0	33
22742	0	1
28566	0	1
52316	0	2
256	1	0
14297	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	5	0
4050	6	0
42	6	0
125	38	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	3
159	47	0
31	132	0
742	38	2
66	0	7
9	0	17
36	0	34
2	0	8
30	7	0
7	0	6
1	7	0
27	30	0
1	0	1
30	0	7
12	0	9
29	16	116
10	0	1
10	4	0
12	0	2
36	0	1
22	1	0
38	0	5
6	0	1
5	0	1
12	13	1
30	270	81
19	30	7
16	0	1
18	21	3
15	22	5
12	14	4
9	1	0
1	5	0
7	23	0
39	0	2
10	0	2
31	4	0
7	0	2
6	25	9
30	0	4
9	8	0
12	142	0
3	0	2
22	35	0
3	1	0
27	5	0
33	1	0
8	6	0
24	0	1
1	0	4
6	5	0
47	3	0
15	3	0
44	23	20
27	3	0
38	0	18
1	3	0
21	3	0
59	65	23
27	0	3
61	3	0
15	9	0
78	5	0
95	0	1
50	101	15
11	0	2
79	2	0
1	1	0
3	1	0
6	1	0
19	4	0
42	2	0
32	4	0
66	4	0
70	4	0
60	0	1
4	0	1
2	1651	0
56	0	5
53

chain 56512613 HG02083_chrY_random0000391 602631 + 1 602631 HG002_chrY 62432599 - 43282440 43884970 2
5340	0	1
9565	1	0
32658	1	0
9920	0	2
23726	0	4
41718	2	0
6718	7	0
8	1	0
21786	1	0
5535	1	0
5063	0	1
4088	1	0
2508	0	1
9553	0	8
2005	6	0
23153	1	0
2904	0	3
2156	1	0
1495	1	0
15319	3	0
26307	2	0
942	1	0
1541	0	8
1494	0	1
1	0	1
1	0	1
12	0	2
9557	25	0
6	4	0
10120	8	0
109	8	0
39072	2	0
1	8	0
47	3	0
59	13	0
10120	4	0
6	25	0
7035	0	6
9	0	2
2520	1	0
1524	12	0
1529	1	0
916	2	0
23927	2	0
2383	3	0
9025	1	0
6293	0	1
3625	3	0
2125	3372	3372
4072	0	12
2858	8	0
32	2	0
11359	1	0
2252	8	0
1952	0	8
9600	1	0
11653	1	0
27342	0	5
1	0	7
6725	2	0
24753	0	1
7263	0	1
3305	0	1
11660	0	1
16615	0	1
40237	1	0
31845	8	8
23

chain 201400 HG02083_chrY 71487452 + 25160820 25162942 HG002_chrY 62432599 - 36784196 36786318 3
2122

chain 2683 HG02083_chrY 71487452 + 12560501 12560529 HG002_chrY 62432599 + 12511308 12511336 4
28

chain 1084 HG02083_chrY 71487452 + 71476352 71476366 HG002_chrY 62432599 + 62430959 62430973 5
14

chain 1055 HG02083_chrY 71487452 + 11766501 11766512 HG002_chrY 62432599 + 11945862 11945873 6
11