##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 1883522205 HG02647_chrY 54649369 + 107 54644084 HG002_chrY 62432599 + 2 62432577 1
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1194	2	0
179	10	0
76	2	0
49	0	2
183	0	15
652	20	6
18	6	0
15	2	0
7	0	4
58	28	0
1241	1	0
291	0	2
6212	134	0
859	1	0
559	0	1
172	0	1
232	0	22
381	4	0
1339	309	0
1738	0	1
5344	3	0
589	0	4
677	8	0
21	0	8
311	0	50
34	0	4
60	3	0
27	8	0
794	0	3
2851	1	0
814	3	0
437	0	6
728	0	6
174	0	18
50	0	6
31	0	1
526	1	0
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11	0	1
344	0	1
336	1	0
2017	26	0
614	0	1
124	1	0
288	0	1
521	0	20
1869	54	0
74	2	0
3880	29	5
1632	3	0
775	0	1
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2409	0	450
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123	45	0
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5	4	0
377	0	4
1373	7	0
343	0	3
26	0	4
66	0	4
277	28	0
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422	0	8
14	0	4
70	4	0
62	24	0
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278	0	4
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18	0	8
29	4	0
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54	0	4
8	0	19
90	4	0
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2614	0	4
845	0	1
147	0	1
1251	0	2
1719	27	0
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54	9	32
149	0	27
1	0	2
10	29	0
65	27	0
3793	4	12
2237	0	370
65	2	0
1385	4	0
940	1	0
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991	2	0
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608	0	4
4649	4	0
174	24	0
10357	0	1
37	0	309
580	1	0
171	308	0
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607	1	0
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2464	2	0
654	0	3
1612	0	3
2	0	2
24	7	0
264	7	0
1584	531	2
38	0	288
70	48	144
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158	1	0
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815	34	0
1401	0	1
1781	0	1
3632	0	8
1692	0	52
91	104	0
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18	0	1
719	0	1
1618	4	0
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60	0	4
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3	20	0
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2583	0	1
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27	0	3
64	1	0
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316	1	0
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7	155	0
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1572	1	0
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4124	2	0
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43	0	8
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68	0	4
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581	2	0
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690	789	0
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320	8	0
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3048	1	0
30	8	16
2179	0	1
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484	0	1
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1381	135	0
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1867	295	0
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3898	0	1
2373	4	0
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366	2	0
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45	135	0
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1624	1	0
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716	0	1
1591	1	0
823	0	200
41	0	1160
3210	2	0
18	0	107
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5	0	162
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37	21	0
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1253	1	0
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2612	0	1
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18	4	0
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63	1	0
14	5	0
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449	0	1
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1247	2	0
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546	4	0
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57	4	0
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38	4	0
1363	2	0
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35	1	0
146	0	252
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24	46	9
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362	0	1
65	0	1
899	0	2
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321	0	4
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133	3	139
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363	0	3
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315	1	0
61	0	8
499	0	6
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1240	1	0
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2	4	0
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359	1	0
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615	0	1
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264	4	0
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6	1	0
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3	0	1
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23	0	1
10	61	184
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6	18	0
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3	198	0
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1709	26	0
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84	1	0
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577	3	0
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1057	0	4
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2240	429	87
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7104	1	0
33724	2	0
6459	0	1
5663	2	0
4278	24	0
6058	0	4
2054	0	2
4148	0	4
58	0	4
11519	1	0
2785	4	0
19861	25	0
155	29	0
1532	0	4
2220	2	0
662	8	0
2378	0	1
3077	0	1
1287	0	20
5855	2	0
1766	1	0
1902	0	1
296	0	6
1381	12	0
49	4	0
26511	12	0
12	4	0
1388	0	7
286	0	1
1908	2	0
1762	2	0
5912	0	5
1257	0	1
3068	0	1
2379	8	0
668	2	0
2230	2	0
1692	25	0
215	0	55
58571	0	4
14491	0	1
8229	3	0
14313	1	0
6865	1	0
18969	0	2
3228	5	0
3293	1	0
1167	4	0
7416	0	1
3327	1	0
319	1	0
12215	8	0
5341	1	0
9775	0	1
3247	1	0
325	0	1
3988	3	0
65	0	12
600	0	3
5781	0	1
1536	0	1
11640	4	0
1032	4	0
5974	1	0
18726	7	0
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21096	1	0
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5196	4	0
28147	0	1
3034	0	1
3930	2	0
1807	0	1
10285	0	4
19	4	0
14088	3	0
3753	5	0
2066	8	0
1891	0	2
14876	0	1
2154	0	3
291	23	0
8	0	2
21	2	0
94	0	2
1395	2	0
23476	0	1
4249	2	0
5512	0	2
4643	0	2
11423	0	1
6512	0	1
3078	0	2
7645	5	0
37	0	20
15	0	2
6386	1	0
627	0	2
2233	1	0
1670	0	2
10919	1	0
3140	0	3
6082	0	1
5732	2	0
3419	0	4
3239	1	0
1536	2	0
1467	1	0
13540	1	0
3879	0	3
543	2	0
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4279	2	0
8225	0	1
163	0	4
5715	3	0
15	1	0
20555	0	1
7316	6	0
17065	2	0
35278	4	0
93	0	4
9193	4	0
302	10	0
15777	16	0
4202	4	0
3904	0	4
17882	1	0
23	0	4
7958	8	0
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6624	1	0
1102	0	1
6867	0	1
227	0	22
3692	0	2
726	1	0
28331	26	0
645	0	1
3175	2	0
15655	4	0
2590	1	0
8506	1	0
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4594	0	1
6422	0	1
204	1	0
850	1	0
18732	20	0
2986	2	0
940	1	0
17032	1	0
229	0	8
12735	0	1
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19	0	2
2000	9	0
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2524	4	0
146	4	0
2800	2	0
500	0	1
6576	0	4
1763	0	4
4047	2	0
3805	3	0
4069	0	1
1099	1	0
7815	7	0
5256	0	3
5595	0	4
8108	1	0
5731	1	0
8399	1	0
4773	0	1
2181	0	1
15084	1	0
33887	1	2
101	0	2
798	0	4
2898	0	4
78	12	0
1690	0	2
849	1	0
18980	0	2
20999	0	14
6230	0	1
11318	1	0
7996	0	18
7399	1	0
2697	0	4
66	0	4
760	15	0
1692	0	6
4447	0	8
49	4	0
20243	1	0
2449	0	4
238	0	4
2319	0	10
6043	0	5
4409	0	2
2190	8	0
56	0	8
2160	4	0
1137	0	8
4871	1	0
15029	0	1
6197	20	0
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22817	15	0
1545	0	1
1873	2	0
9964	1	0
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6568	15	0
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604	8	0
4980	0	2
16556	6	0
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1301	0	2
20	0	4
72	0	2
8	10	0
34548	0	1
7234	1	0
6259	0	3
2769	2	0
2678	0	1
11419	1	0
4802	1	0
3309	2	0
4476	0	2
12031	2	0
7837	1	0
7772	1	0
5064	4	0
4318	0	1
770	0	11
2745	0	4
16517	2	0
1088	4	0
6580	0	8
8927	1	0
1460	0	1
23160	0	1
4136	1	0
16864	0	1
6778	11	0
24354	0	1
26131	39	0
2743	1	0
9557	0	4
324	12	0
64	0	12
7904	1	0
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6165	1	0
8973	7	0
10125	4	0
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25009	0	1
7628	0	1
5347	1	0
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8982	4	0
6725	0	1
5604	0	1
50	4	0
5816	0	1
8386	0	4
1274	23	0
34	0	1
4536	1	0
280	0	1
2976	0	1
930	6	0
12861	1	0
24957	3	0
941	2	0
1473	0	6
26	5	0
3467	0	352
544	12644	12645
580	0	11
2314	0	3
1408	2	0
24	0	2
16	4	0
16	0	1
10	0	8
1456	2	0
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36	4	0
2372	2	0
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3691	0	1
993	0	3
8380	3	0
472	1	0
870	4	0
67	4	0
3	2	0
4	2	0
2287	0	1
1675	0	1
1081	1	0
1992	1	0
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4859	0	16
15199	0	1
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5677	0	12
11	0	4
9338	0	1
1370	16	0
21735	1	0
2079	0	8
7481	0	4
28	4	0
4074	0	1
3939	0	1
348	3	0
7419	1	0
8974	1	0
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1326	0	1
8495	0	3
5282	0	1
21764	1	0
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6577	35	0
4	3	0
3005	0	1
1115	1	0
6847	0	1
6395	0	1
765	0	1
3930	2	0
3039	1	0
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6044	6	0
379	0	13
7997	0	1
15387	1	0
4429	3	0
3341	0	1
7194	10	0
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7133	0	2
1592	0	4
530	0	2
7746	0	4
21	3	0
5	0	3
11306	0	8
3086	2	0
2216	0	1
7904	0	3
225	0	2
897	0	1
604	0	6
929	46212	46210
1540	0	2
9012	0	2
1053	1	0
4238	0	4
4115	1	0
7111	0	4
139	0	12
1082	2	0
8565	2	0
868	0	1
60	0	1
6387	2	0
972	5	0
7470	1	0
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4739	1	0
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366	6	0
868	2	0
5710	1	0
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8501	0	1
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2363	0	2
1728	0	1
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3708	0	2
8552	20	0
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18694	4	0
7546	0	23
5695	0	2
2881	0	2
2444	4	0
28	4	0
4946	0	1
9182	8	0
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955	12	0
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6955	1	0
3126	2	0
25	0	4
3567	0	3
1155	8	0
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6928	1	0
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79	20	0
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80	0	12
15	0	8
1697	0	5
30	0	5
3392	0	1
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91	0	2
5002	0	2
1075	2	0
8	4	0
903	0	3
8264	1	0
641	1	0
632	0	8
3952	0	1
9101	15	0
4426	0	1
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1170	0	1
88	0	1
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207	0	4
4128	2	0
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173	2	0
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5470	1	0
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19	4	0
16	0	2
534	0	1
549	0	3
7626	0	1
360	0	19
394	1	0
1876	0	2
4871	0	1
9216	0	4
69	19	0
1631	1	0
3667	0	1
2287	3	0
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5351	4	0
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3517	0	1
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1161	2	0
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1192	1	0
40	0	2
1266	4	0
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1979	0	1
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38	0	2
8270	0	2
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1451	0	2
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4948	1	0
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5549	5	0
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3469	0	1
1657	0	8
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4403	1	0
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5130	0	4
25	12	0
4877	3	0
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961	0	4
15332	0	2
2514	5	0
1	7	0
88	8	0
616	0	8
24047	0	2
36	0	4
22	0	4
26	0	20
1160	4	0
690	0	4
31255	2	0
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9320	1	0
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3188	0	6
3499	0	3
907	0	1
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7977	10	0
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4920	1	0
865	1	0
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4414	1	0
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11908	3	0
1655	1	0
2724	0	1
2360	8	0
7330	0	1
290	1	0
256	0	2
976	4	0
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6874	0	2
652	0	2
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7263	0	1
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300	0	6
5576	4	0
6722	1	0
3	0	7
1	0	5
3	0	1
62	19	0
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39	0	4
13	0	12
11	0	28
1952	4	0
2252	1	0
9364	1	0
1995	4	0
32	4	0
2858	0	30
4054	3372	3372
2125	6	0
6300	0	1
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3698	0	1
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916	2	0
1529	16	0
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9	8	0
7041	25	0
6	4	0
10120	11	0
54	0	4
48	8	0
1	2	0
5642	1	0
12164	6520454	6792729
17413	14583	3737
3485	0	1
3078	2	0
1874	1	0
790	6761	2006
119	2	0
4084	0	1
6265	0	1
1446	398	12320
1555	1	0
4314	0	1
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3722	0	1
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2019	1	0
840	3	0
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210	0	4
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84	4	0
1	2	0
1923	0	1
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8136	1	0
176	0	1
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3343	0	4
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100	12	0
17	12	0
57	0	2
50	4	0
63	0	16
2035	1	0
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470	0	2
3266	2	0
7943	1	0
2197	1	0
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1392	1	0
8550	0	11
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604	3	0
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7973	0	1
663	0	1
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21000	2	0
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48	12	0
3981	0	2
1745	0	32
432	1	0
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7799	2	0
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1774	1	0
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524	0	1
19	0	2
4725	4	0
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1428	8	0
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1086	1	0
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814	2	0
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14	2	0
3805	0	1
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535	0	1
66	0	1
769	0	5
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179	1	0
67	0	1
955	0	2
3905	0	1
212	0	1
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9470	1	0
7434	1	0
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2708	4	0
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397	2	0
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16	0	4
949	1	0
762	1	0
2848	0	1
935	5	0
1529	1	0
13	1	0
7535	4	0
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1930	2	0
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1737	0	2
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2634	0	10
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34	0	2
271	0	1
1559	0	1
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451	0	4
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53	0	2
15	0	6
64	0	3
2694	2	0
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2040	2	0
5587	1	0
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780	1	0
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12716	1	0
9517	0	1
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37	2	0
8824	1	0
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2067	0	12
38	0	2
427	0	2
4398	2	0
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29506	1	0
2735	4	0
67	4	0
39174	1	0
6569	4	0
49	12	0
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3824	0	1
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3296	1	0
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11	0	2
11387	0	1
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1442	0	1
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2374	1	0
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28	8	0
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142	0	1
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221	1	0
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15707	1	0
679	0	1
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29	0	4
39	0	2
511	12703	10
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364	1	0
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9082	4	0
5638	0	1
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358	0	2
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2011	0	2
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2	0	2
7	0	6
5479	0	1
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562	4	0
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445	2893	0
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656	1	2869
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562	0	5
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48	4	0
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40	3	2941
158	0	1
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65	0	1
27	1	0
98	0	5
62	10	0
6	0	5
92	0	20
129	351	0
26	10	0
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53

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1315	1	0
8672	0	1
17488	0	2
2169	1	0
16820	4	0
2334	1	0
2119	0	3
5800	0	1
2176	0	6
20438	0	3
6663	1	0
6718	0	2
1864	0	4
14010	5	19
18	0	7
5661	0	2
12068	8	0
29609	0	4
5926	0	8
2919	4	0
5630	2	0
4034	0	10
4207	0	6
23	0	1
2724	0	15
4404	0	1
1258	1	0
726	0	6
41	0	2
34791	0	1
3144	0	1
3192	0	1
14511	0	1
879	0	2
732	4	0
5	0	4
10843	1	0
840	1	0
2923	0	1
2757	0	1
27644	1	0
73	0	14
1312	1	0
3603	0	1
12632	1	0
3742	0	2
22	0	4
107	10	0
14740	4	0
8125	4	0
7036	1	0
2088	0	1
11422	4	0
1944	0	1
4533	0	2
46	4	0
10499	6	0
881	0	2
2458	0	4
8037	6	0
77	0	2
14659	6	0
104	0	4
6996	1	0
14320	2	0
4588	1	0
25319	23	0
3480	1	0
840	1	0
10845	0	2
5	4	0
15412	92	0
11

chain 17274189 HG02647_chrY_random0000803 200595 + 0 183151 HG002_chrY 62432599 - 39159995 39343231 3
307	0	2
230	0	1
20	0	1
16	0	1
165	0	1
14	0	1
470	1	0
385	0	1
286	0	1
2652	0	1
323	0	2
4612	1	0
2003	0	1
24146	2	0
14045	0	2
24128	0	6
94	6	0
20955	0	2
2	0	20
768	0	52
584	0	2
101	13	0
53	11	0
105	0	52
11	0	2
77	26	0
34	26	0
258	0	28
4699	0	1
16078	1	0
6712	0	2
52	6	1
6727	6	0
13117	0	4
11216	0	3
23	0	2
259	8	0
3623	1	0
21672	0	1
2021

chain 11672475 HG02647_chrY 54649369 + 19844717 19974330 HG002_chrY 62432599 - 43575590 43707112 4
15621	1	0
5642	2	0
1	8	0
48	0	4
54	12	0
10120	4	0
6	25	0
7041	8	0
2527	0	4
48	6	0
1476	16	0
2445	0	2
20226	1	0
3699	4	0
2383	3	0
9025	1	0
4016	1	0
1214	1	0
1063	0	10
696	0	3
749	0	1424
744	6	0
2130	3364	3367
524	1	0
346	1	0
424	0	4
54	1	0
887	8	0
525	0	4
245	0	317
671	0	3
77	0	4
19	0	12
21	0	1
19	0	42
3	0	12
222	0	1
38	1	0
63	0	2
98	0	3
39	1	0
78	0	4
514	0	1
978	0	1
380	2	0
293	0	32
61	0	6
114	4	0
195	2	0
84	0	2
52	0	2
30	0	2
205	1	0
766	0	1
65	1	0
417	0	6
753	0	1
123	1	0
837	3	0
1804	4	0
115	0	1
46	0	2
18	1	0
640	0	1
184	5	0
425	1	0
389	0	3
3963	0	1
58	1	0
1039	1	0
31	0	6
854	0	1
96	4	0
193	0	32
2	0	2
156	3	0
414	1	0
2	0	25
235	0	1
943	1	0
85	0	1
150	8	0
23	0	11
13	0	1
26	11	0
81	0	1
233	0	10
331	0	1
156	0	29
103	0	23
406	0	1
1681	0	1
201	0	6
378	1	0
282	4	0
780	1	0
58	1	0
644	0	5
344	1	0
168	1	0
434	1	0
279	0	4
184	0	4
498	0	1
60	0	2
338	1	0
97	8	3
1270	4	0
373	0	3
146	0	1
286	3	0
596	0	1
1078	3	0
2	0	1
197	0	7
31	0	2
161	1	0
658	1	0
419

chain 10176701 HG02647_chrY_random0000804 107798 + 1 107797 HG002_chrY 62432599 + 22984554 23092360 5
1388	0	1
2001	0	1
9471	0	1
14651	0	2
16844	0	4
12716	2	0
10730	0	1
1864	0	2
37158	0	1
369	1	0
601

chain 4508568 HG02647_chrY 54649369 + 26310684 26365171 HG002_chrY 62432599 - 36729698 36784196 6
283	4768	0
5204	0	1
4768	1	0
9441	1415	6195
1140	1	0
1874	2	0
3078	0	1
22413	0	1
99

chain 4349747 HG02647_chrY 54649369 + 18163169 18209380 HG002_chrY 62432599 - 45214480 45260689 7
7914	2	0
5303	0	4
13200	0	1
3005	4	0
26	2	0
2414	4	0
2497	0	8
235	0	4
180	8	0
2741	0	1
8676

chain 1190376 HG02647_chrY 54649369 + 17777098 17789740 HG002_chrY 62432599 - 45634118 45646761 8
1386	0	6
6455	1	0
4090	4	0
706

chain 2683 HG02647_chrY 54649369 + 13485953 13485981 HG002_chrY 62432599 + 12511308 12511336 9
28

chain 1055 HG02647_chrY 54649369 + 12685555 12685566 HG002_chrY 62432599 + 11945862 11945873 10
11