##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 2154013429 HG01457_chrY 51813559 + 469 24775126 HG002_chrY 62432599 + 2 24031131 1
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39	24	0
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588	0	1
571	1	0
5632	45	0
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483	225	0
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45	135	0
1786	4	0
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7646	8	8
54	2	31
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2753	4	0
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81	0	816
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220	0	4
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649	2	0
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2524	1	0
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91	104	0
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10	0	9
719	0	1
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3256	1	0
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3599	1	0
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316	1	0
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7	155	0
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41	2	0
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2712	538	0
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33	0	8
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7	0	4
2166	0	3
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44	0	12
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1840	1	0
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9	5	29
707	2	0
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292	0	4
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35	1	0
407	108	0
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24	36	0
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69	1	0
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12	4	46
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8	1	0
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73	1	0
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690	8	0
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100	10	0
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24	301	357
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2721	1	0
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807	0	150
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2734	1	0
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4734	2	0
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13	4	0
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753	7	0
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73	0	4
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102	4	0
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39	0	4
538	0	1
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584	1	0
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539	0	2
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548	0	22
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623	0	1
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772	12	23
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6	5	0
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1	4	0
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15	1	0
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8	0	57
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3	0	1
2955	0	3
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1	0	3
20	3	0
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6	8	0
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894	0	5
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12	16	0
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44	0	87
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23	6	544
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34	4	0
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8	0	12
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5583	8	0
54907	0	1
2876	1	0
3709	0	2
486	14	0
48696	0	1
37	1	0
23	1	0
26161	2	0
4278	20	0
79	12	0
5979	0	4
2054	0	3
4147	0	8
8549	1	0
3028	6	0
2785	2	0
19861	25	0
155	29	0
12	1	2
934	1	0
586	0	2
2882	8	0
5459	1	0
1275	0	5
5	0	20
5502	0	2
351	2	0
3965	0	6
1430	4	0
10398	0	1
16112	12	0
1403	0	4
2195	1	0
1762	2	0
355	0	2
5555	0	5
1230	1	0
5476	8	0
2898	2	0
1692	25	0
12420	1	0
46421	0	4
11149	0	3
11569	1	0
40149	2	0
1746	0	1
1481	5	0
3293	0	2
8581	0	2
11014	1	0
4846	0	2
18362	0	1
4313	3	0
677	15	0
18925	0	14
1055	8	0
43873	0	1
26922	1	0
6025	2	0
5196	4	0
31182	0	2
3377	0	1
12579	4	0
65	0	6
17	6	0
11585	1	0
8322	4	0
1891	0	1
17357	2	0
21	0	2
21	2	0
21	0	2
1424	1	0
48862	0	4
14764	1	0
2917	2	0
37	0	14
7036	0	2
19042	0	2
4027	0	1
977	0	1
28937	1	0
3783	0	2
640	2	0
26690	1	0
18002	0	4
12502	0	1
5882	3	0
15	1	0
27872	1	0
8087	2	0
8978	2	0
4897	0	1
5400	1	0
21392	0	1
3295	0	8
377	0	8
9198	0	1
292	0	4
13328	1	0
1354	0	2
1089	21	0
8106	0	2
17907	0	4
7958	6	0
21167	0	4
14590	0	1
161	2	0
66	4	0
3714	0	2
4972	0	1
7966	0	1
15730	0	4
383	26	0
46018	0	1
7477	1	0
21718	0	2
938	1	0
14662	0	1
2598	0	1
12742	0	1
11135	2	0
47	2	0
19	0	2
2000	3	0
14159	0	4
3548	1	0
6577	0	2
39	8	0
4	2	0
6	10	0
16	0	2
5318	0	4
4232	3	0
4069	0	1
8914	7	0
5257	4	0
5597	0	4
13839	1	0
15354	0	2
49073	2	0
800	0	4
2898	4	0
82	12	0
1690	0	8
40824	0	8
3682	2	0
23205	1	0
8778	0	8
826	5	0
1692	0	4
786	8	0
2970	1	0
693	0	8
22741	4	0
242	4	0
2616	0	4
10170	4	0
2153	5	0
95	4	0
2168	4	0
1137	4	0
4879	1	0
21227	0	5
57506	0	41
474	4	0
6923	0	6
5094	1	0
6569	10	0
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612	8	0
4980	0	1
8072	0	1
4643	1	0
3841	4	0
62698	0	1
1409	10	0
1699	1	0
4689	1	0
10132	0	1
25262	1	0
6259	0	4
5446	0	1
16221	1	0
7785	0	1
19869	1	0
8887	1	0
3949	6	0
24528	4	0
926	1	0
6580	2	0
8935	0	4
52397	27	0
24354	0	1
26131	69	0
2591	0	1
151	1	0
9885	16	0
21884	0	4
1274	0	4
4475	1	0
6255	2	0
5058	1	0
8193	2	0
13240	0	8
9639	4	0
56714	3	0
2805	4	0
2851	4	0
5816	0	1
4527	0	1
5170	0	1
4816	0	1
2976	0	1
930	8	0
8353	1	0
31879	2	0
32	2	0
3757	0	1
22	1	0
1289	2	0
4090	1	0
6455	0	6
1968	0	1
5	3	0
2319	0	1
1410	2	0
42	5	0
16	0	1
4634	2	0
11628	20	0
6929	0	1
13068	0	3
1339	2	0
67	0	2
7	0	8
2277	0	1
1675	0	1
1081	1	0
1992	1	0
3227	2	0
2	24	0
7077	4	0
881	0	1
22445	0	1
18619	1	0
5701	0	4
10709	4	0
23796	4	0
18	0	4
7485	4	0
3789	4	0
317	0	1
368	0	2
11337	1	0
23594	0	1
8495	0	2
5283	0	1
17280	1	0
4484	1	0
14267	0	4
6577	35	0
4	3	0
3005	0	1
15124	0	1
3930	0	2
21698	2	0
859	0	2
8387	0	1
10645	1	0
4742	1	0
4429	0	1
3069	0	1
8435	2	0
6385	1	0
72	1	0
2264	4	0
540	0	4
6651	0	2
1087	0	16
61	0	4
11262	0	4
3090	2	0
10351	1	0
2437	46210	46210
10554	0	1
1054	1	0
1151	0	2
3085	2	0
4119	1	0
7111	0	4
139	0	12
7695	2	0
533	8	0
2348	1	0
14830	2	0
3077	0	1
9171	1	0
10645	1	0
8001	0	1
379	6	0
6698	0	4
38286	0	4
8684	0	4
11190	0	2
5523	4	0
3837	5	0
7777	0	2
2488	4	0
16686	0	2
3172	1	0
13012	2	0
10085	0	4
14638	1	0
26241	0	29
5689	2	0
2883	1	0
2474	8	0
4946	0	1
22969	0	4
18612	0	1
1323	0	2
3569	11	0
1158	8	0
16671	18	0
2501	0	7
41721	0	4
13891	1	0
14366	0	1
39274	0	4
213	20	0
18204	0	1
107	0	4
1736	0	5
3392	0	1
18462	2	0
10451	0	4
13058	25	0
20350	0	8
1166	0	1
6969	0	4
6160	2	0
10196	0	4
54154	12	0
11642	0	2
1129	0	3
24439	19	0
1631	1	0
5955	3	0
14772	0	1
11108	0	1
19041	3	0
1194	1	0
17	0	3
20	4	0
2	4	0
3074	0	1
7337	2	0
248	2	0
19	0	2
4776	1	0
3438	1	0
36789	0	1
4026	2	0
14	0	1
52	0	2
1979	1	0
13493	0	1
3819	0	2
8315	0	1
16268	1	0
7737	0	12
11604	0	3
17522	0	1
2350	0	1
7968	0	1
5549	5	0
25368	0	14
20	0	4
8718	0	1
21795	2	0
32312	0	8
4948	0	4
178	0	4
25	16	0
15615	1	0
963	1	0
13553	0	1
1782	0	1
2511	25	5
88	8	0
616	0	4
5931	0	12
18106	0	20
50	6	0
28	0	6
2	0	6
1734	0	8
10922	1	0
20449	0	1
9819	0	4
174	0	1
20277	0	12
422	0	4
9469	0	1
210	0	1
8004	1	0
57608	4	0
3	4	0
4	6	0
21315	0	19
24906	6	0
25452	0	1
5709	1	0
15512	0	2
13388	0	1
174	4	0
1491	0	1
6313	5	0
14080	1	0
5480	0	1
17719	0	3
11907	0	3
1652	1	0
3997	0	1
491	0	1
8472	0	1
977	0	4
20362	0	1
6005	1	0
11176	1	0
25048	1	0
8942	0	2
2820	0	1
15570	1	0
2767	1	0
6726	1	0
6519	0	1
7263	0	1
9517	0	1
9657	0	2
5576	2	0
6722	1	0
3	0	1
8	0	4
37659	1	0
1336	1	0
9544	8	0
52	0	12
1952	4	0
2252	1	0
11391	2	0
2728	6	0
130	0	9
4075	3371	3372
5751	1	0
6293	1	0
9025	3	0
2383	6	0
3699	1	0
11771	1	0
6137	1	0
4765	16	0
1476	8	0
48	0	1
2519	0	2
9	8	0
7041	25	0
6	4	0
10120	13	0
59	3	0
47	4	0
1	2	0
5629	0	1
12176	3457	3457
17809	0	4
105	13	0
4525	4	0
5595	4	0
6	25	0
9557	0	1
11	6	0
2	0	1
48	0	1
2998	0	1
3258	1	0
6137	1	0
15470	6	0
2383	3	0
15319	2	0
1495	1	0
2153	0	6
2904	1	0
218	0	1
6424	6	1
129	6	0
2729	0	2
33	0	2
13596	2	0
2011	0	8
6	4	2
48	8	0
4	12	0
9505	0	1
1330	1	0
1178	1	0
4088	0	1
5062	0	1
5535	1	0
21747	4	0
39	4	0
5	1	0
3	7	0
6718	2	0
15245	0	1
9485	0	1
10591	1	0
9940	0	1
2766	0	1
5829	0	1
11585	0	4
15807	0	1
19160	1	0
3425	1	0
23244	0	1
2452	1	0
8427	0	4
970	0	1
353	0	15
26155	0	3
11115	0	8
15459	1	0
5828	0	1
4810	5	0
6359	1	2
1452	8	0
49	0	3
151	0	1
13395	0	1
46661	0	4
10910	0	1
1075	0	2
6230	3	0
3500	2	0
13702	0	1
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6861	0	4
18290	0	4
2927	2	0
16637	0	5
6448	0	2
14272	0	3
24322	0	1
2532	1	0
16128	2	0
4754	24	0
6093	1	0
840	1	0
3480	23	0
25319	1	0
4588	2	0
14320	1	0
3425	1	0
3679	2	0
14659	0	2
77	4	0
229	0	2
671	1	0
7135	0	12
660	39666	39663
604	4	0
8103	2	0
22	0	3
58	0	2
14655	2	0
133	0	2
3534	1	0
208	1	0
12632	0	1
3603	1	0
1312	0	1
86	1	0
4502	0	1
23141	0	1
5681	1	0
6906	1	0
27	21	0
4754	2	0
19323	0	1
7754	0	1
25787	0	4
4437	0	2
4422	1	0
8941	0	12
4034	2	0
5630	6	0
38607	0	4
1724	1	0
15862	0	6
19	4	9
15888	0	2
1444	0	1
355	0	1
4917	0	1
13381	1	0
7980	2	0
5742	0	6
7977	0	3
2119	1	0
2334	4	0
18989	0	2
7248	1	0
20228	2	0
147	0	8
47577	8	0
58418	1	0
23400	1	0
10460	8	0
11763	23	0
18193	18	0
8033	1	0
6231	0	4
6954	0	10
33950	0	3
3632	1	0
239	4	0
6209	4	0
13068	0	2
20144	0	1
8712	0	1
10019	4	0
319	0	1
268	12	0
12414	0	6
42	12	0
572	0	4
4947	0	1
6767	0	1
11572	7	0
9090	0	1
2284	1	0
3387	0	2
21254	0	1
10745	4	0
3918	4	0
5	20	0
4	0	64
1589	0	3
5302	1	0
3346	0	2
255	1	0
9905	1	0
7729	2	0
19291	0	1
8816	0	3
3925	325	0
1133	1	0
7426	10	0
2976	2	0
6870	1	0
26420	5	0
8868	4	0
22241	0	2
32	2	0
26758	0	6
2896	0	2
73718	3	0
18445	6	0
8293	1	0
6150	0	2
5944	0	1
16244	0	1
7227	19	0
85	0	1
68301	0	1
3680	0	3
21180	0	1
18829	0	1
27191	1	0
17495	1	0
1095	1	0
29323	0	1
7345	0	1
17667	1	0
27263	2	0
14476	2	0
40170	0	10
16721	0	1
654	0	1
1340	0	1
1420	0	2
10521	1	0
874	0	1
6315	0	1
264	0	1
2739	6	0
20183	1	0
176	5	0
20178	125	0
7060	125	0
5795	0	1129
3759	0	754
3351	0	2759
23564	0	125
3052	0	1
14372	27080	25203
22465	0	372
513	53667	29501
498	0	2
78	0	1
130	0	1
133	0	1
115	4	0
3	0	3
11257	2	0
15791	11693	1077
1924	125	0
3030	0	625
47	0	999
16	0	125
123	0	125
78	0	125
145	875	0
26	1124	0
9237	250	0
3733	0	375
1816	2625	0
11308	250	0
2317	5752	1
2858	33272	14896
41	124	0
1044	1	0
62	125	0
411	0	1
254	0	125
560	0	1
332	0	7
3	7	0
240	124	0
1067	4	879
854	0	1
9522	250	0
102	125	0
2402	2132	7
633	0	104
3	0	21
412	91	91
95	0	125
334	0	1
4	1	0
17	1	0
6022	0	1
27423	8	0
60913	0	4
32422	0	6
27606	0	2
42094	0	2
36121	1	0
15684	1	0
47466	0	8
7492	0	2
2281	0	1
2872	0	1
858	0	1
33124	1	0
18796	0	1
21768	1	0
3249	4	0
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21620	0	1
10130	0	1
3765	0	1
27345	0	24
4264	0	1
15157	4	0
5878	6	0
38351	1	0
4704	1	0
14576	0	1
2683	0	1
7188	0	1
417	0	1
10712	0	1
3213	0	3
29309	2	0
62471	0	1
304	4	0
4685	0	11
2120	32298	32299
2096	2	0
4640	12	0
35	4	0
12052	12	0
20959	0	1
936	0	1
15689	4	0
21276	2	0
17598	0	8
4554	1	0
308	12	0
34602	0	1
9797	0	3
20139	1	0
10929	0	1
23773	0	2
32	4	0
24591	1	0
36117	1	0
29476	0	13
21041	0	4
18293	0	1
8047	0	1
19589	0	2
93365	47074	0
9540	2	0
23507	0	4
11203	0	1
10315	0	1
3115	2	0
8673	0	1
12396	1	0
14487	1	0
2500	9	0
11702	8	0
28410	0	1
23324	9	8
6192	0	1
1551	81	16
52	2	0
24	0	3
10	0	6
12	0	12
10	0	1
11	0	69
10817	0	4
47549	1	0
21270	0	1
6282	0	6
21464	0	1
946	2	0
4321	0	2
47320	0	1
6672	0	2
3644	0	1
11210	2	0
23526	4	0
12024	0	3
6076	0	2
8682	2	0
2784	0	1
3870	0	10
483	10	0
3	0	7
11662	1	0
117	0	3
622	0	1
2687	0	1
4076	6	0
3497	2	0
8761	0	1
6714	0	1
71347	2	0
15863	16	7
897	0	1
13123	0	2
7061	0	21
4961	2	0
18448	1	0
1353	0	2
3710	1	0
7294	36	0
2670	2	0
15302	0	2
9092	1	0
10617	0	7
11046	0	4
79317	0	1
25554	20	0
25	0	4
11215	0	4
13117	0	6
1584	6	0
3838	0	24
1276	0	2
27828	26	0
34	26	0
55	235	179
13	0	2
12	2	0
322	15	0
1224	48	0
19995	1	0
39259	12	0
21691	1	0
9071	0	1
5453	0	2
9870	2	0
2575	0	4
112	0	8
7266	1	0
3664	0	2
391	1	0
141	0	1
847	12	0
11694	0	2
9551	0	1
2264	1	0
10234	1	0
9835	1	0
909	10	19
2130	0	3
13692	2	0
11673	0	2
1592	0	1
77052	0	6
4097	1	0
1704	2	0
984	1	0
625	3	0
105	0	1
8071	1	0
4091	0	4
6676	2	0
9865	1	0
30750	0	1
6338	4	0
4655	10	0
18592	0	2
1619	0	2
611	1	0
33417	0	1
9456	0	4
1723	0	1
3988	8	0
4922	0	4
45114	0	4
104609	0	6
14568	0	2
16393	0	8
9979	1	0
5547	18	0
44109	0	3
7339	0	1
3267	0	4
10607	0	1
17493	1	0
3512	0	1
450	1	0
2055	0	4
78	6	0
34	4	0
46	0	4
47	8	0
57	4	0
35	20	0
3330	0	4
922	0	1
2464	0	6
13694	0	1
11138	2	0
8290	8	0
5454	2	0
4185	2	0
5783	0	8
195	1	0
9089	3	0
826	0	1
860	0	2
4363	6	0
3316	1	0
5282	0	11
1457	1	0
4310	0	1
2251	1	0
7	18446	6521
898	1	0
4075	0	2
498	0	4
53	0	1
67	0	1
37	1	0
7	14	0
3	1	0
26	1	0
143	1	0
430	6	0
207	4	0
11	1	0
124	4	0
71	0	2
1195	0	1
4779	0	1
4952	1	0
2454	1	0
4459	0	10850
23	0	1
15477	0	1
99

chain 61232462 HG01457_chrY 51813559 + 51119562 51808821 HG002_chrY 62432599 + 61659781 62432577 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
843	0	2413
832	2	0
244	0	2
2293	0	7
134	0	2
677	19295	0
11095	0	45932
882	0	15
5763	0	1
3534	1	0
3534	0	1
2720	0	10604
9169	15	0
2235	1	0
1284	0	15
1262	5	0
150	0	1
436	15	0
566	0	5
3350	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
88	15	0
402	0	10
168	45	0
122	0	20
103	1	0
13353	25	0
3356	0	15
2045	1	0
1569	0	3535
3471	0	15
150	0	25
542	0	7080
18078	609	0
3573	1	0
494	0	20
74	0	25
14	4064	28603
5838	0	1
494	20	0
66	40	0
2934	1	0
494	0	20
66	0	40
1717	0	10
124	25	0
17852	5	0
19	5	0
8	0	15
7119	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
477	0	15
1060	5	0
7	5	0
416	1	0
31	1	0
416	2627	13156
463	1	0
456	0	20
2570	5	0
18258	0	3
9750	0	5
4693	5	0
37648	0	2
32577	12	0
153	0	12
3321	0	1
5649	2	0
5906	0	6
2761	0	9
1716	0	1
1445	1	0
5036	4	0
2785	0	3
16383	0	2
5080	0	1
6449	0	4
32849	1	0
347	1	0
1401	0	1
2171	0	10
4264	0	1
1087	2	0
2677	2	0
4328	10	0
928	1	0
62386	0	2
10395	2	0
15192	14	0
8900	1	0
658	0	32
74	80	0
666	2	0
6383	2	0
6458	0	3
5809	0	3
6451	0	1
343	0	2
4828	0	1
6	0	3
530	2	0
2613	1	0
1095	0	4
12695	0	1
6099	0	1
73	14	0
272	0	2
2724	2	0
4392	0	1
9625	1	0
35831	0	1
28915	2	0
5226	1	0
1381	0	1
4049	6	0
42	6	0
125	38	0
1489	1251	0
1129	0	3
5236	0	58
687	6	0
99	7	7
175	13	42
7	0	157
11	0	1
4	0	1
11	17	14
9	0	19
19	0	1
56	65	12
19	0	1
17	120	49
12	0	1
18	1	0
20	10	0
18	13	1
17	24	0
18	0	17
3	0	1
45	4	0
7	0	2
6	17	21
18	1	13
15	0	2
19	57	13
20	5	0
23	10	12
6	1	0
6	0	23
7	5	0
46	1	0
1	3	0
15	3	0
1	0	4
39	0	1
2	0	5
12	3	0
27	3	0
10	1	0
11	1	0
19	1	0
17	5	170
24	3	0
15	9	0
22	102	252
57	2	0
4	1	0
25	4	0
36	0	6
24	0	1
1	0	37
35	4	0
70	2	5
55	0	1
6	1539	1
56	0	5
53

chain 12750435 HG01457_chrY 51813559 + 24775126 24924045 HG002_chrY 62432599 - 38399346 38539790 3
17084	0	1
614	0	1
31	10845	0
4887	0	5
5572	0	3
352	0	1
4481	1	0
452	1	0
2002	1	0
4952	0	1
6998	0	1
715	0	4757
506	0	1
3489	0	3
1560	1	0
1126	2384	0
7	1	0
2251	0	1
4310	1	0
1457	0	11
1558	1	0
3724	1	0
3316	5	0
4363	0	2
860	0	1
826	3	0
9089	1	0
195	0	12
4126	15	0
740	1	0
3429	0	1
1668	13	0
84	0	6
1925	0	1
3438	8	0
8290	2	0
11138	0	1
13694	0	1
229	1	0
95

chain 4354526 HG01457_chrY 51813559 + 17806684 17852893 HG002_chrY 62432599 - 45214480 45260689 4
13217	0	4
18646	2	0
153	1	0
2587	8	0
17	0	3
164	0	4
11414

chain 3741729 HG01457_chrY 51813559 + 20177515 20217174 HG002_chrY 62432599 - 42850342 42889998 5
8542	0	1
11422	2	0
6526	2	0
10499	2	0
881	0	2
1783

chain 3058047 HG01457_chrY 51813559 + 22588326 22620623 HG002_chrY 62432599 - 40507615 40539913 6
6287	0	1
26010

chain 327277 HG01457_chrY 51813559 + 19488383 19491840 HG002_chrY 62432599 - 43575590 43579047 7
3457

chain 6804 HG01457_chrY 51813559 + 24932184 24932344 HG002_chrY 62432599 - 38539790 38542814 8
2	0	2864
158

chain 1346 HG01457_chrY 51813559 + 51810250 51810264 HG002_chrY 62432599 + 62432585 62432599 9
14