##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 2134102955 HG01252_chrY 56573349 + 4 29899456 HG002_chrY 62432599 + 88 29288337 1
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893	0	2
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659	0	1
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43	0	8
4	4	0
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75	0	9
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9	4	182
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1434	1	0
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156	0	41
248	40	327
63	41	0
262	0	40
168	1	0
186	42	0
301	41	0
2837	0	1
3459	0	4
165	0	4
1875	1	0
1123	0	1
501	1	0
3881	0	1
713	0	2
24	4	0
696	4	0
3894	98	52
41	6	0
552	1	0
46	4	0
18	2	0
779	3	0
130	0	2
8	0	3
1014	1	0
7	1	0
127	0	1
640	0	1
2916	0	2
19	6	0
155	12	0
95	15	0
31	0	2
27	0	5
21	15	0
15	1	0
15	5	0
15	1	0
47	1	0
1	3	0
28	2	680
33	32	3
20	1	0
12	0	11
63	1	0
11	1	0
4	1	0
42	5	3
11	0	1
15	1	0
15	0	1
31	0	1
39	52	12
13	0	6
15	1	0
7	33	0
3040	1	0
6703	0	1
710	4	0
330	0	4
1396	6	0
1098	0	24
21	0	1
50	7	0
12	8	0
20	0	21
12	3	0
41	1	0
4	2	0
48	0	4
14	2	0
43	0	11
12	0	1
24	4	0
12	0	1
24	0	4
16	1	0
20	0	1
39	0	1
28	0	1
8	1	0
75	0	3
1	6	0
2	1	0
52	0	18
1	0	1
3	0	3
14	0	1
42	0	8
36	21	34
19	4	0
10	0	3
62	0	4
41	0	1
22	0	1
52	0	3
17	3	0
29	4	1
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28	0	3
2	0	6
76	0	5
2	0	4
2	1	0
12	0	23
3	3	0
10	1	0
42	0	8
12	4	0
46	0	4
3	0	1
3131	3	0
28	0	3
336	3	0
15	0	3
63	14	0
301	6	0
725	0	12
300	0	1
2366	0	2
1142	1	0
1869	1	0
1538	0	1
3506	30	0
485	2	0
1663	0	2
704	9	0
86	0	2
1680	0	1
187	4	0
17	0	6
894	1	0
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699	1	0
443	250	0
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894	1	0
1831	0	1
2574	6	0
2	0	4
12	16	0
4109	1	0
1351	0	40
299	0	40
501	40	0
1879	1	0
7800	5	0
1349	16	0
186	10	545
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1	0	2
37	2	0
198	18	0
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10	0	2
20	0	1
17	4	0
1329	0	5
268	0	1
7433	0	3
1360	2	0
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131	0	2
12	1	0
614	0	1
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556	0	3
657	0	12
859	2	0
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311	8	0
1183	0	12
215	12	0
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8	0	12
34	4	0
215	0	8
2121	1	0
462	0	2
862	4	0
2	0	5
6491	20	0
3414	0	1
946	0	1
2529	0	2
1023	0	6
3	17	0
10	1	0
18	0	3
7	47	28
38	19	2
13	1	0
2	1	0
1	0	1
17	0	1
10	13	10
11	0	3
19	2	0
17	0	1
1	0	8
5	0	2
37	0	3
7	0	2
8	0	12
464	6	0
12	0	3
1	0	16
9	0	1
60	27	97
6	0	1
15	4	27
7	0	1
12	0	1
3	0	1
11	1	0
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5	0	2
12	1	0
13	17	36
13	0	4
5	0	1
8	1	0
2	15	0
6	0	4
8	7	6
12	41	0
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25	2	0
4	1	0
5	0	1
4	0	39
978	1	0
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1760	1	0
8	5	0
6938	0	4
163	1	0
1759	14	0
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16767	0	2257
261	0	1
2599	0	1
759	1	0
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909	3	0
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176	1	0
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3972	2	0
296	1	0
2466	2	0
716	106	0
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9	106	0
1272	1	0
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397	1	0
863	1	0
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734	0	1
454	0	10
280	0	2
326	1	0
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172	1	0
6838	0	3
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6516	1	0
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510	101	0
691	0	4
1313	0	2
936	0	1
22	0	4
4373	2	0
588	1	0
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872	0	14
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345	0	1
1662	3	0
117	0	49
43	0	100
3446	0	2
16	0	1
2910	0	1
32	3	0
9605	1	0
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2685	1	49
9	0	4
24	0	34
1526	0	5
3683	1	0
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1700	1	0
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33	0	16
668	1	0
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94	4	0
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6775	0	2
4725	1	0
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2287	0	2
379	8	0
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756	1	0
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10	1	0
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1742	0	1
964	1	0
2545	1	0
6223	1	0
121	2	0
11	34	0
2041	5	0
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4742	1	0
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953	1	0
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4932	3	0
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13	0	3
134	1	0
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23	9	0
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49	0	3
128	4	0
203	3	200
5	0	5
9	0	22
15	0	12
14	33	16
51	0	24
721	1	0
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601	0	1
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323	0	1
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1345	2	0
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69	2	0
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1298	9	0
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6	0	2
6818	0	1
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3674	20	0
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944	1	0
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21	0	8
373	1	0
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57	0	1
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4	0	1
3472	64	0
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55	0	2
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7911	1	0
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100	100	0
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2894	0	14
9	2	16
1926	0	1
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4816	0	1
2976	0	1
930	0	4
8349	1	0
31879	2	0
32	2	0
3757	0	1
18	1	0
4	1	0
583	12642	12645
586	2	0
2319	0	1
1410	2	0
42	5	0
16	0	1
4634	0	6
11622	15	0
6929	0	1
4685	0	3
9722	2	0
76	0	2
2283	0	1
1675	0	1
1081	1	0
1992	1	0
3227	2	0
2	24	0
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18	0	4
7485	4	0
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368	0	2
3918	3	0
7419	1	0
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21764	1	0
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6581	35	0
4	3	0
3005	0	2
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72	1	0
2264	4	0
540	0	10
6645	0	2
1091	0	4
17	0	4
52	4	0
58	0	8
11196	0	4
3090	2	0
12788	46215	46210
10554	0	1
2205	0	2
3085	2	0
4119	1	0
7111	0	8
135	0	4
7703	0	2
531	8	0
2348	1	0
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4430	2	0
4740	1	0
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378	6	0
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16715	4	0
3837	5	0
7777	0	2
2488	4	0
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3172	1	0
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14640	1	0
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8573	1	0
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4946	0	1
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3569	6	0
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779	4	0
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79	8	0
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1166	0	1
88	1	0
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6160	2	0
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25071	2	0
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2936	0	1
21429	2	0
73	19	0
1631	1	0
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1194	1	0
17	0	3
20	4	0
2	4	0
10412	2	0
248	2	0
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4776	1	0
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4026	2	0
14	0	1
52	0	2
1979	0	1
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39	0	2
8270	0	1
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5110	1	0
3876	1	0
3861	0	12
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7968	0	1
5549	5	0
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36	4	0
8720	0	1
1657	2	0
20138	1	0
6447	4	0
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4944	0	4
178	0	4
25	20	0
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963	1	0
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2511	25	5
88	12	0
616	0	4
5931	0	12
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60	0	2
28	0	6
2	0	6
1613	0	1
124	0	4
10922	1	0
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176	0	1
12412	1	0
7865	0	12
422	4	0
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210	0	1
8004	1	0
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21494	6	0
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6313	5	0
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4414	1	0
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1850	12	0
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5576	1	0
6722	1	0
7	0	1
39003	1	0
9544	4	0
52	0	12
1952	4	0
2252	1	0
11391	6	0
2728	6	0
130	0	6
4072	3377	3378
5751	1	0
6293	1	0
9025	3	0
2383	6	0
3699	2	0
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7039	25	0
6	4	0
5585	4	0
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59	3	0
43	0	4
1	2	0
39122	4	0
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61	0	1
3940	2	0
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3699	6	0
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1495	1	0
2153	0	6
2904	1	0
218	0	1
6415	0	9
130	6	0
2731	2	0
33	0	2
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48	8	0
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5	1	0
3	7	0
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8427	0	4
970	0	1
353	0	15
6680	2	0
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8100	1	0
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6230	3	0
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2532	1	0
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54	0	3
20	4	0
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881	2	0
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671	0	2
229	2	0
83	0	2
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107	0	2
24	0	2
3742	1	0
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840	1	0
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27	22	0
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45	0	2
4422	1	0
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5630	6	0
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141	0	4
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23	0	2
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5742	0	6
7977	0	3
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8030	1	0
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3632	1	0
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551	2	0
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268	6	0
3959	1	0
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42	12	0
568	0	8
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2284	1	0
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5	20	0
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1589	0	3
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3925	325	0
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6315	0	1
264	0	1
2739	6	0
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226	0	1250
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43	0	1
146	1	0
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69	1	0
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3052	0	1
14372	107189	78054
498	0	2
78	0	1
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11257	2	0
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9614	11569	1078
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145	875	0
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32	6	0
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386	42188	2085
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107	75527	109875
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14568	0	2
16393	0	4
9983	1	0
5547	18	0
44109	0	3
7339	0	1
3267	0	3
10608	0	1
16627	0	1
4828	1	0
2059	12	0
58	2	20
34	4	0
42	0	8
39	0	12
53	4	0
35	12	0
3330	0	4
3391	0	2
33123	12	0
3438	0	1
1925	0	6
84	12	0
1668	0	1
3429	1	0
740	15	0
4130	0	8
195	1	0
9915	0	1
860	0	2
4363	6	0
1196	0	1
2119	1	0
3724	1	0
1558	0	11
1457	1	0
4310	0	1
2251	1	0
7	2384	0
1126	1	0
1560	0	3
3489	0	1
506	0	4757
715	0	1
6998	0	1
3586	0	3
3365	1	0
452	1	0
4481	0	1
352	0	3
5572	0	5
4887	10845	0
31	0	1
614	0	1
17084	4955403	5026806
9647	1	0
1582	15060	15594
1	0	3013
40	3570	0
1932	0	1
103	0	10
15	0	5
1966	0	15
1525	2199	9301
1372	10	0
3528	0	5
16	0	5
3292	18005	46273
1846	0	5
241	15	0
1185	14	0
754	0	20
13	10	0
5	0	15
10	0	10581
7010	25	0
1171	15	0
1072	0	5
1777	5	0
1570	0	1
190	5	0
1773	5	0
706	0	15
864	0	1
8516	0	1
8	25478	6118
3010	0	2418
71	18362	13533
1083	0	2
2591	2	0
238	5	0
415	0	2422
206	1	0
4405	7564	4025
6594	15	0
4042	0	25
8058	0	10
1935	1	0
3524	24821	0
9	0	1
678	25	0
23	10	0
925	0	5
81	1	0
722	10	0
33	10	0
171	0	20
1181	15	0
384	0	15
923	0	5
851	0	10
5318	0	5
3553	0	5
918	0	5
1237	10	0
1361	15	0
2211	15	0
2270	5	0
1183	1	0
44	10	0
810

chain 48684966 HG01252_chrY 56573349 + 55645462 56212761 HG002_chrY 62432599 + 61659781 62299219 2
12	0	5
5692	0	2
2542	0	2414
392	1	0
1752	5	0
1166	1	0
3279	0	2414
858	0	2
3613	0	2
3012	0	7
134	0	2
677	31360	0
11095	0	45932
882	0	15
5763	0	1
3534	1	0
3534	0	1
2705	0	14139
4364	0	1
1284	15	0
351	5	0
1884	1	0
7069	1	0
179	5	0
946	10	0
91	16	16
393	0	5
156	45	0
122	0	20
2691	10	0
88	15	0
402	0	10
168	45	0
122	0	20
103	1	0
9809	0	25
176	0	2
3341	25	0
3535	25	0
1881	1	0
671	0	7095
809	0	15
150	0	25
542	0	7080
18800	5	0
2851	1	0
494	0	20
74	0	25
14	5063	26107
8334	0	1
494	20	0
66	40	0
2934	1	0
494	0	20
66	0	40
1717	0	10
124	25	0
25013	5	0
6990	5	0
763	3502	0
9731	5	0
3521	5	0
1438	30	0
2030	15	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
1543	4	0
770	758	4270
2451	0	15
457	5	0
605	10	0
447	1	0
436	0	10
21	3742	7236
17109	0	3
9750	0	5
4693	5	0
37648	0	2
36063	0	1
11555	0	4
2763	0	5
1720	0	1
1445	1	0
5036	4	0
2785	0	3
16383	2	0
5082	0	1
6449	0	4
33196	1	0
1401	0	1
2171	0	10
4264	0	1
1087	2	0
2677	4	0
4328	12	0
928	1	0
27773	19	0
1776	0	3
2033	0	1
1972	4	0
1725	6	0
866	1	0
16126	0	1
2723	1	0
45	0	6
7336	0	2
8119	0	5
407	1	0
1864	8	0
7215	0	1
4831	0	2
3143	14	0
8900	1	0
658	32	0
3104	0	33
21154

chain 10843111 HG01252_chrY 56573349 + 24713950 24862914 HG002_chrY 62432599 - 38401468 38539790 3
99	0	1
15477	0	1
23	0	10850
4459	1	0
2454	1	0
4952	0	1
4779	0	1
1195	0	2
71	4	0
124	1	0
11	4	0
207	6	0
430	1	0
143	1	0
26	1	0
3	14	0
7	1	0
37	0	1
67	0	1
53	0	4
498	0	2
52	0	4757
158	1	0
435	32321	6092
7	1	0
2251	0	1
4310	1	0
1457	0	11
1558	0	1
3723	1	0
1300	0	1
2015	6	0
4363	0	2
860	0	1
826	3	0
9089	1	0
195	0	12
4126	15	0
740	0	1
912	0	2
2514	0	1
1668	2	0
6208	0	1
7535	2	0
24833	0	1
229	1	0
95

chain 4353624 HG01252_chrY 56573349 + 17739751 17785965 HG002_chrY 62432599 - 45214480 45260689 4
21782	0	1
7644	2	0
2459	8	0
2478	0	8
235	8	0
184	0	4
11414

chain 3058579 HG01252_chrY 56573349 + 22517804 22550101 HG002_chrY 62432599 - 40507615 40539913 5
6287	0	1
26010

chain 1190744 HG01252_chrY 56573349 + 17353625 17366265 HG002_chrY 62432599 - 45634118 45646761 6
1386	0	6
6455	1	0
4090	2	0
706

chain 427764 HG01252_chrY 56573349 + 23827406 23831917 HG002_chrY 62432599 - 39338719 39343231 7
2490	0	1
2021

chain 322611 HG01252_chrY 56573349 + 15489765 15493173 HG002_chrY 62432599 - 47507067 47510475 8
3408

chain 6804 HG01252_chrY 56573349 + 24871053 24871213 HG002_chrY 62432599 - 38539790 38542814 9
2	0	2864
158