##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 2532636572 HG02514_chrY 75184911 + 78 75173572 HG002_chrY 62432599 + 359 62432577 1
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7	0	29
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29	4	0
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359	56	0
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7	40	0
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572	0	389
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32	0	6
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10	168	204
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13	2	0
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5364	1	0
3131	2	0
2420	0	1
269	1	0
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2303	255	0
21	501	0
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283	816	0
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338	0	22
745	4	0
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91	3	0
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282	8	5
11	0	2
859	0	1
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114	3	0
51	8	56
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11	19	0
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29	0	1
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5	0	1
1	0	6
138	13	0
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65	15	0
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65	16	0
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6	0	118
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318	0	1
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3423	0	1
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1237	1	0
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563	0	1
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119	780	0
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6204	3	0
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19	4	19
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47	1	0
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58	21	0
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15	52	12
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15	1	0
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6271	22	0
8	2	0
2	46	0
26	0	24
1076	0	2
1	0	18
4990	0	2
18853	1	0
5519	0	12
77	5	0
1197	0	5
17169	4	0
11332	1	0
1413	0	1
3955	1	0
21002	1	0
20934	0	1
15888	12	0
86	0	20
115479	0	3
45522	8	0
407	0	4
23686	0	12
14033	1	0
9057	0	3
12	0	6
4852	0	1
34966	0	4
1868	1	0
2483	8	0
10671	26	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	4
10524	0	1
3158	1	0
3023	0	1
10426	3	0
13047	0	2
13240	0	1
3230	4	0
1696	0	2
15894	22	0
10034	1	0
4938	3	0
1514	0	1
7026	2	0
3370	0	2
50312	0	3
25288	21	0
3763	1	0
70609	2	0
30	12	0
19449	2	0
2635	9	0
130	9	0
65	0	12
6	24	0
45	3	0
11	0	1
5	1	0
49322	0	1
48587	0	1
32	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
11880	0	1
14089	0	12
17203	2	0
3151	8	0
17179	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	8	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	14	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
989	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
112	0	1
2818	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
4030	0	20277
2483	0	16
598	0	2
4249	1	0
2264	1	0
6496	4	0
101	0	10
7152	0	4
6	2	0
846	1	0
1505	0	3
6126	1	0
470	11	0
1	2	0
356	1	0
3303	1	0
489	6	0
4582	0	18
2556	2	0
26	2	0
10	0	6
830	1	0
1505	0	3
786	0	4
1965	0	1
3402	1	0
470	11	0
1	3	0
356	2	0
3698	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	10
16	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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15057	0	1
73056	0	1
1258	0	4
4758	1	0
11256	0	8
2182	8	0
44724	1	0
31504	0	2
6919	0	2
33965	2	0
5271	8	0
20588	0	29
372	0	2
3009	31	0
18794	2	0
33175	8	0
175	0	2
1143	1	0
4296	0	1
10737	1	0
3528	0	2
13063	2	0
4319	9	0
6728	0	1
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34135	2	0
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27185	0	2
2079	0	1
2256	0	1
1165	0	1
8831	1	0
47589	1	0
26281	1	0
11358	1	0
35298	0	2
52143	415582	311619
28743	0	5
580	10	0
1111	0	20
860	5	0
27	5	0
857	5	0
3380	10	0
87	0	5
844	0	5
191	10	0
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347	0	5
1841	0	15
100	0	5
1249	5	0
896	15	0
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4660	0	30
2217	10	0
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2872	0	10
730	0	5
1026	5	0
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5610	0	10
383	0	15
415	5	0
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758	5	0
757	1876	0
281	0	5
256	0	20
6924	5	0
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732	0	5
1332	0	5
1226	0	5
3221	0	10
772	5	0
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8130	15	0
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249	5	0
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4152	20	0
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21	0	5
189	5	0
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807	5	0
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892	5	0
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178	5	0
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2311	10	0
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18	5	0
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380	25	0
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2293	5	0
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22	0	2
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387	5	0
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2200	0	10
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13	0	4
28	0	2
17	0	1
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4784	5	0
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572	5	0
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191	654	0
603	0	5
164	0	23077
2918	14	14
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184	1	0
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4273	9438	17719
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195	1	0
92	1	0
209	0	1
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597	55	0
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1831	0	5
93	0	5
258	69146	67869
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877	0	1
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3528	0	1
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1369	5	0
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1391	5	0
4677	109521	87462
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667	0	15
694	4119	0
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7961	0	1373
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699	0	1377
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195	5	0
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184	5	0
562	0	9
24	5	0
19	1	0
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2037	5507	0
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33	5550	0
1440	1	0
467	5	0
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311	0	5
1879	5	0
54	5566	0
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1880	5	0
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3624	0	5
1912	0	25
45	0	5
96	1	0
1065	0	15
1473	11060	0
693	49751	5473
1675	0	10
570	0	5
3163	0	5
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523	0	5
581	25	0
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206	5575	0
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6081	0	5
4460	3	0
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380	10	0
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1919	5	0
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10	0	5
770	1	0
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197	7531	0
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2099	0	20
2158	7177	0
18	20	0
516	0	15
3566	5	0
721	5	0
532	0	30
1861	10	0
789	5	0
775	1	0
880	3800	3584
339	0	20
416	0	15
686	0	5
461	0	15
217	0	15
77	4	34
756	1	0
532	15	0
305	0	369
5	20	0
11	3792	3237
360	0	20
405	0	15
1137	0	15
234	0	15
60	1	21
1290	10	0
340	3785	3589
339	0	20
416	0	15
682	0	10
465	0	15
234	0	15
61	0	10
1267	15	0
373	3785	3589
339	0	20
416	0	15
696	0	10
451	0	15
211	0	15
84	0	35
1243	0	15
57	0	5
297	369	0
1606	5	0
721	5	0
552	0	10
720	22552	0
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786	5	0
1295	15	0
327	0	369
8	10776	3245
388	26797	0
397	0	15
700	5	0
1172	0	15
2687	15	0
1975	0	5
3849	0	5
1747	10	0
2003	15	0
3872	0	15
1747	10	0
1993	0	10
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1983	5	0
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2023	10	0
3796	5	0
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1349	10	0
1782	0	5
1993	0	10
42	0	5
1751	10	0
579	5	0
3217	10	0
1998	0	10
1826	10	0
2014	26637	0
17	25	0
1775	5	0
2010	0	5
1808	5	0
635	10	0
47	0	5
1751	20	0
2013	5	0
39	5	0
2519	10	0
1268	0	5
1808	0	5
3869	15	0
7571	0	10
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818	0	5
7536	5	0
3960	5	0
491	0	5
3336	4	0
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306	0	15
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540	0	30
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5559	10	0
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4963	0	5
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1840	0	5
76	10	0
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213	0	10
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25	65	0
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697	0	5
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2604	5	0
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5157	0	5
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9432	1	0
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2223	1	0
6054	5	0
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32	0	20
6584	1	0
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4062	12	0
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696	2	0
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1776	27	0
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418	20	0
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3715	1	0
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372	1	0
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122	8	0
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18568	47957	12570
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2986	1	0
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43	2	0
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70	12	0
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788	8	0
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238	8	0
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56	8	0
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4871	1	0
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156	4	0
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270	6	0
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11	0	1
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67	2	0
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2	4	0
13	0	1
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755	0	1
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39	0	1
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4	0	8
1086	2	0
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60	0	1
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13	0	5
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379	6	0
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32	0	4
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1742	8	0
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4	0	4
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4075	3372	3372
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8	7	0
6718	1	0
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1	0	1
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6165	9570	57
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99	2138	2138
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58	2138	2138
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41	2	0
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437	0	5
1067	20	0
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80	0	2
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13	17	2
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901	20	0
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1241	15	0
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532	10	0
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526	5	0
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54	1	0
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81	1	0
2252	0	15
543	0	10
1069	20	0
446	0	2873
1325	2873	0
2890	10	0
8	2878	0
2865	0	10
1128	22054	7938
173	1	0
5881	15	0
196	3131	0
78	0	15
2425	0	20
7053	10	0
672	0	6262
1152	0	3131
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5417	0	5
40	0	5
34179	0	5
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155	5	0
113	5	10
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725	5	0
139	10	0
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15807	0	1
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2305	5	0
6633	0	1
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623	0	10
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4638	1	0
6755	5	0
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3221	5	0
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13449	8162	2649
6	0	5
10	0	280
11	20	0
16	0	5
725	10	0
2008	0	5
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739	0	10
33	0	1
2020	10	0
312	0	2763
1	0	2769
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564	5	0
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304	0	5
761	10	0
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1998	25	0
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291	1	0
253	1159871	1162432
1805	5	0
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3439	1	0
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13	2022	19796
12113	8961	1901
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4847	1	4840
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810	42946282	32045929
5521	5	0
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3333	0	1
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337	0	1
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13428	58	0
27	49	15
730	6	0
106	6	0
82	0	6
105	1	0
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30	0	1
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8	2	0
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20	8	0
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96	0	1
5	0	1
13	5	0
15	1	0
14	5	0
1	0	6
12	88	7
18	56	5
14	73	17
28	17	0
16	0	1
18	21	3
17	10	0
3	1	0
15	8	0
1	3	0
9	1	0
1	5	0
48	6	0
43	39	24
52	167	8
22	46	9
21	5	0
23	18	54
46	1	0
1	20	0
15	3	0
64	3	0
27	3	0
57	3	0
21	3	0
59	17	0
2	0	2
9	3	0
9	25	1
27	0	3
61	3	0
15	9	0
78	5	0
95	0	1
50	101	15
11	0	2
79	2	0
29	4	0
36	0	6
32	4	0
66	4	0
70	4	0
60	0	1
6	1668	1
56	0	5
53

chain 6315138 HG02514_chrY 75184911 + 30891937 31009397 HG002_chrY 62432599 + 29060059 29163364 2
10	5	0
6671	0	1
2965	1	0
5687	25155	14503
40	3554	0
1932	0	1
128	0	5
1966	0	15
1273	0	15
237	2199	9301
4900	0	5
16	0	5
3584	5	0
14098	8961	1901
687	1	0
300	0	5
7	0	10
3200	0	3500
7362	0	5
9576	8592	5094
14	14	0
2314	15	0
691	25	0
494	14	0
754	0	20
13

chain 6042257 HG02514_chrY 75184911 + 29298340 29434908 HG002_chrY 62432599 + 29173965 29288337 3
2220	0	5
3	0	3529
4790	0	25
2043	0	1
165	5	7097
30	20	0
4963	39814	5937
3010	0	2418
71	18385	11134
6075	2	0
238	5	0
415	0	2422
206	1	0
7971	0	1
458	10812	14326
1655	5	0
1011	0	15
774	0	15
12	0	5
1737	0	10
21	0	9
1	0	1
1072	1	0
716	15	0
1757	0	10
954	15	0
798	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

chain 326836 HG02514_chrY 75184911 + 18876490 18879946 HG002_chrY 62432599 - 43575590 43579047 4
818	0	1
2638

chain 201400 HG02514_chrY 75184911 + 25735936 25738058 HG002_chrY 62432599 - 36784196 36786318 5
2122

chain 201400 HG02514_chrY 75184911 + 24116233 24118355 HG002_chrY 62432599 - 38399346 38401468 6
2122

chain 1055 HG02514_chrY 75184911 + 11688867 11688878 HG002_chrY 62432599 + 11945862 11945873 7
11