##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 2322175647 HG01074_chrY 51860611 + 404 51855272 HG002_chrY 62432599 + 2 62432577 1
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283	8	0
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3354	0	29
35	2	31
190	29	0
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121	27	0
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1633	0	2
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1519	3	0
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52	8	0
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11	4	0
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5	4	0
18	0	1
1167	0	2
4	0	4
31	0	4
823	1	0
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81	0	816
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199	4	0
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4	0	8
220	0	4
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40	4	0
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176	0	4
34	4	0
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649	2	0
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3	0	706
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174	4	0
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1207	0	3
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899	1	0
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1643	7	0
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57	0	192
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1831	1	0
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91	104	0
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10	0	9
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57	4	0
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41	2	0
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46	0	1
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346	0	1
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33	0	8
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6	23	0
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54	82	42
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2707	0	4
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45	135	0
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712	2	0
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5	0	1
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12	29	0
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5	0	448
10	43	200
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37	0	2
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4	3	0
40	22	356
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42	0	1
9	46	8
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29	3	0
2	105	0
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211	0	62
8	19	0
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9	24	0
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3	4	0
37	45	21
16	18	0
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3	51	0
8	2	21
8	27	0
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63	34	0
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16	39	2
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96	0	2
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16	148	0
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2821	0	1
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11	1	0
4	1	0
42	5	3
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7	25	6
33	52	12
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15	1	0
7	33	0
3040	1	0
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64	4	0
330	0	4
1396	6	0
830	18	0
2	8	0
266	0	24
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50	7	0
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41	1	0
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48	0	4
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16	1	0
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8	1	0
32	0	4
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1	6	0
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52	0	18
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9	0	29
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36	21	34
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3	4	0
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62	0	4
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10	0	1
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49	0	1
1	0	7
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5	3	0
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2	0	6
76	0	5
18	3	0
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12	4	0
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63	14	0
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50	0	2
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894	1	0
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12	16	0
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37	2	0
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72	18	0
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34	4	0
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8	0	12
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9	0	1
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42430	807688	326879
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13	32974	4914
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8	7359	0
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341	3820	3749
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1979	1	0
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38	0	2
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7737	0	8
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5549	5	0
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32	0	4
8718	0	1
21795	1	0
6447	8	0
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4948	0	4
178	0	4
25	12	0
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88	12	0
616	0	4
5931	0	12
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1744	0	1
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210	0	1
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7	0	1
39003	1	0
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48	8	0
52	0	12
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130	0	9
4070	3376	3377
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5585	4	0
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1	2	0
17806	3457	3457
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105	12	0
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6415	0	9
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4	4	0
9505	0	1
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6718	0	1
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671	1	0
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664	39676	39663
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5630	6	0
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513	38602	29501
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11257	2	0
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24284	0	4
34	6	0
1873	0	1
14038	0	2
52245	0	2
15708	1	0
679	0	1
1207	0	1
5959	0	1
16267	3	0
33	2	0
39	0	2
18279	1	0
57640	0	1
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6333	0	6
28	0	20
6479	2	0
5738	2	0
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14407	1	0
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13	2	0
14388	0	2
10542	1	0
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11548	1	0
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4039	2	0
562	4	0
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515	10	0
173	0	2878
2827	2878	0
307	0	1
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119	1	0
406	15	0
3311	1	0
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589	0	10
610	0	10
1049	15	0
24	5725	0
1609	0	20
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1128	10510	4774
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7	432	0
191	0	10
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155	5	0
123	10	0
40	0	12442
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128	10	0
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1429	20	0
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133	0	10
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479	0	1
240	10	0
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263	0	3092
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1408	20	0
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3782	3107	0
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1136	0	6193
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6601	326	0
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85	0	1
2263	16978	16943
63	5	0
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544	8261	4
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7976	22664839	33666509
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138	0	10613
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124	3559	0
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342	0	15
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1446	3547	3557
364	5	0
1725	3539	0
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38	10	0
1395	15	0
363	0	10
530	3549	0
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865	15	0
5616	100778	44293
28	0	10
5671	0	2
2542	0	2414
392	1	0
1752	5	0
1166	1	0
3279	0	2414
550	0	3
305	0	2
6627	0	7
134	0	2
677	19295	0
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882	0	15
2229	1	0
3534	0	1
3534	1	0
3534	0	1
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1078	0	10604
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2272	1	0
179	5	0
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156	45	0
122	0	20
583	0	5
150	1	0
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402	0	10
168	45	0
122	0	20
103	1	0
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215	0	21200
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2851	1	0
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14	0	14054
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66	40	0
6429	1	0
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124	25	0
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552	30	0
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28	7	1
23	0	1
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1	0	1
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21	47	5
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6	1	0
7	70	17
28	18	0
35	23	3
32	14	4
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31	8	0
12	7	0
5	0	1
25	37	24
53	160	10
9	0	1
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14	5	0
34	0	3
4	6	0
36	5	0
6	0	1
39	1	0
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29	1	0
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4	0	5
18	3	0
51	15	6
21	3	0
41	0	11
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4	1	0
5	3	0
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27	0	2
36	0	5
5	1	0
16	3	0
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24	0	54
33	0	1
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12	0	1
50	101	15
11	0	2
62	0	5
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24	0	1
1	0	37
35	4	0
70	2	5
55	0	1
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56	0	5
53

chain 127011681 HG01074_chrY 51860611 + 24741062 26102556 HG002_chrY 62432599 - 35428670 36784196 2
5794	1	0
20835	8	0
4665	0	4
6296	0	1
19226	1	0
11523	1	0
9874	2	0
4044	1	0
2624	0	2
10040	0	1
9123	0	2
3485	6	0
8816	0	2
2	3	0
12530	1	0
27108	1	0
1442	0	6
3792	0	7
19789	1	0
1680	2	0
28810	0	1
6530	0	11
3302	1	0
3298	0	1
40705	0	4
23	0	13
9	0	4
45739	4	0
63	0	4
22491	0	4
1859	0	2
7887	0	1
26762	2	0
4377	2	0
21	0	2
427	0	2
14778	0	6
5815	0	1
8458	1	0
22925	1	0
12724	0	2
18680	4	0
10190	2	0
780	1	0
9996	0	14
664	1	0
842	1	0
16499	0	1
2308	0	4
4261	1	0
10415	1	0
5276	0	1
1168	0	1
10863	0	12
12169	0	1
6124	0	3
12	0	9
58	0	15
14076	0	2
1976	1	0
7830	5	0
7731	1	0
2441	1	0
7684	1	0
16381	0	1
19389	0	1
831	0	1
893	0	1
10817	0	1
1559	0	1
271	0	2
34	10	2
5201	0	10
2634	3	0
4705	1	0
904	0	1
1737	0	8
5221	2	0
2	4	0
1928	0	1
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16039	2	0
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407	0	1
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2714	0	6
27017	1	0
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13	4	0
3728	1	0
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814	0	1
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883	4	0
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7616	1	0
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1777	0	1
3982	10	0
4944	0	2
13665	4	0
68697	0	1
7436	0	1
1534	0	1
58405	0	2
40892	0	1
57031	1	0
3261	1	0
6919	2	0
3226	0	2
470	1	0
17302	3	0
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47	0	2
10	0	4
42	2	0
63	12	0
17	12	0
100	0	16
3372	0	4
3343	0	5
24874	0	2
7535	1	0
776	12	0
5340	2	0
1	4	0
84	0	14
1668	1	0
4150	0	15
4120	4	0
214	0	1
9090	3	0
818	1	0
860	2	0
4367	0	2
2014	0	1
1310	0	1
3722	0	1
1545	10	0
1473	0	1
4314	1	0
2273	0	1
4768	0	1
2381	1	0
2387	1	0
9441	1415	6195
1140	1	0
4951	0	2
3485	14586	3737
15191	0	1
99

chain 12819456 HG01074_chrY 51860611 + 26349250 26484867 HG002_chrY 62432599 + 25894114 26029742 3
9991	1	0
9685	0	4
125	0	1
3315	0	1
7852	2	0
6976	0	1
12562	0	1
7973	0	1
25781	1	0
5111	0	2
6780	0	1
9867	1	0
821	0	4
28773

chain 8390630 HG01074_chrY 51860611 + 26193479 26282300 HG002_chrY 62432599 + 25738325 25827164 4
1676	2	0
2474	1	0
1668	0	14
84	4	0
1	2	0
5340	12	0
8313	1	0
24873	0	6
3343	0	4
3372	0	16
100	4	0
4	4	0
13	12	0
63	2	0
42	0	4
59	0	20
6170	3	0
17773	0	1
13406

chain 6381884 HG01074_chrY 51860611 + 24648204 24715931 HG002_chrY 62432599 + 26029742 26097477 5
3048	0	1
7404	0	1
20279	0	1
689	6	0
23	0	2
7058	0	1
6581	0	2
4893	9	2
3119	2	0
912	0	1
1757	0	20
9077	3	0
340	1	0
2320	2	0
204

chain 5403964 HG01074_chrY 51860611 + 26282301 26339333 HG002_chrY 62432599 + 25827164 25884196 6
57032

chain 4352226 HG01074_chrY 51860611 + 17543917 17590103 HG002_chrY 62432599 - 45214480 45260689 7
13217	0	8
2775	2	0
13427	4	0
262	0	21
2157	0	4
2736	4	0
11602

chain 3741866 HG01074_chrY 51860611 + 19914805 19954474 HG002_chrY 62432599 - 42850342 42889998 8
8542	0	1
11422	2	0
6526	8	0
10499	6	0
881	0	2
1783

chain 1646673 HG01074_chrY 51860611 + 26102556 26119969 HG002_chrY 62432599 + 25646281 25663694 9
17413

chain 1140911 HG01074_chrY 51860611 + 26177225 26189359 HG002_chrY 62432599 + 25722048 25734186 10
1159	2	0
860	1	0
840	3	0
36	0	9
9023	0	1
210

chain 1071039 HG01074_chrY 51860611 + 26142990 26156232 HG002_chrY 62432599 + 25675869 25689134 11
1140	1632	1656
119	2	0
4084	0	1
6265

chain 936668 HG01074_chrY 51860611 + 26339334 26349250 HG002_chrY 62432599 + 25884196 25894110 12
7387	2	0
2527

chain 834526 HG01074_chrY 51860611 + 26158076 26166974 HG002_chrY 62432599 + 25702901 25711788 13
1555	1	0
4314	0	1
1473	11	0
1544

chain 789752 HG01074_chrY 51860611 + 26134554 26142989 HG002_chrY 62432599 + 25667431 25675869 14
3485	0	1
4063	0	2
887

chain 663088 HG01074_chrY 51860611 + 26166974 26174020 HG002_chrY 62432599 + 25711790 25718838 15
3722	0	1
1310	0	1
2014

chain 427764 HG01074_chrY 51860611 + 23590553 23595064 HG002_chrY 62432599 - 39338719 39343231 16
2490	0	1
2021

chain 387413 HG01074_chrY 51860611 + 26189359 26193479 HG002_chrY 62432599 + 25734190 25738310 17
4120

chain 327277 HG01074_chrY 51860611 + 19225687 19229144 HG002_chrY 62432599 - 43575590 43579047 18
3457

chain 322143 HG01074_chrY 51860611 + 15293863 15297275 HG002_chrY 62432599 - 47507067 47510475 19
2617	4	0
791

chain 301627 HG01074_chrY 51860611 + 26174020 26177225 HG002_chrY 62432599 + 25718840 25722045 20
3205

chain 201400 HG01074_chrY 51860611 + 24255242 24257364 HG002_chrY 62432599 - 36784196 36786318 21
2122

chain 137940 HG01074_chrY 51860611 + 26156232 26157678 HG002_chrY 62432599 + 25689135 25690581 22
1446

chain 1005 HG01074_chrY 51860611 + 1008720 1008734 HG002_chrY 62432599 + 1025194 1025209 23
9	0	1
5