##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 1908279479 NA20870_chrY 48476143 + 8 48471225 HG002_chrY 62432599 + 3 62432577 1
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531	0	4
286	0	1
29	1	0
31	1	0
7	124	0
93	0	1
328	1	0
246	4	0
703	1	0
827	0	2
314	1	0
1646	0	2
1187	1	0
5	0	4
4465	0	1
41	2	0
3894	1	0
10135	0	4
659	0	1
817	2	0
3741	4	0
12	4	0
43	0	8
56	0	4
85	4	0
13	4	0
58	4	0
302	4	0
14	4	0
68	0	4
48	8	0
32	0	4
19	0	4
37	0	4
524	0	5
811	0	1
243	0	1
305	1	0
2670	0	4
10	20	0
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21	0	2
14	0	2
595	6	0
702	0	3
13	0	3
7	2	1
6	2	0
11	4	0
39	0	4
11	39	4
45	4	0
17	12	0
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54	16	0
4	8	0
23	14	0
2	16	0
690	789	0
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60	0	1
239	0	1
153	2	0
362	2	0
4680	0	1
487	0	1
80	0	3
316	0	1
900	0	2
49	3	0
1249	0	8
1750	22	0
2066	0	2
871	0	1
2189	0	2
178	4	0
932	0	1
833	0	1
248	0	259
195	1	0
2543	4	0
25	0	4
173	1	0
11	0	4
93	0	8
22	6	16
2177	0	3
538	0	4
124	0	18
776	0	18
2033	3	0
1867	0	6
29	0	18
484	0	1
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1381	135	0
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4	0	1
1200	148	0
557	0	885
86	0	590
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2088	0	1
208	0	313
112	0	1
2950	4	0
168	0	4
366	2	0
600	2	0
133	0	2
45	135	0
2745	1	0
2701	0	1
716	0	1
1591	1	0
823	0	200
393	0	520
3065	0	4
379	3	0
68	0	107
37	10	10
58	0	55
107	0	162
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271	0	3
1566	1	0
1307	0	4
26	0	20
37	5	0
7	0	5
30	0	10
9	5	29
707	2	0
1777	0	2
12129	106	0
4553	0	72
72	0	72
7632	1	0
5816	2	0
32	4	0
347	2	0
654	0	6
363	4	0
20	379	7
157	0	2
4571	2	0
6	1	0
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1504	1	0
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52	8	0
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27	25	5
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59	8	0
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10	1	0
61	0	8
6	0	8
54	0	8
423	0	6
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124	5	0
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363	1	0
59	0	1
2	0	4
85	0	1
6	0	1
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43	20	0
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1	4	0
615	0	2
995	1	0
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1445	4	0
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130	2	0
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34	0	6
84	0	2
90	4	0
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14	66	0
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4	0	2
279	0	10
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50	60	0
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58	0	1
67	5	0
224	2638	2712
591	0	2
649	0	4
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859	0	1
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6	1	0
92	4	0
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11	0	2
74	0	2
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47	1	0
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8	1	0
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12	0	8
8	388	23
14	1	3
24	120	25
9	64	0
4	7	0
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6	7	0
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6	9	0
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8	24	12
10	0	1
8	26	0
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4	48	0
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9	44	5
35	19	0
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13	92	75
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15	240	19
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41	0	1
42	4	0
1	9	0
18	1	0
61	0	2
1	0	1
41	0	1
61	0	1
11	0	1
3	0	22
10	0	2
1	0	1
9	0	1
3	352	0
145	196	32
76	0	4
16	62	0
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9	0	1
9	1	0
7	25	17
13	3	0
3	0	8
5	6	0
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17	4	0
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6	0	7
9	0	1
13	554	75
438	1	0
28	0	1
244	6	0
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1691	0	208
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5	0	3
211	0	62
8	19	0
33	0	19
9	24	0
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3	4	0
37	45	21
16	18	0
8	3	0
3	78	0
8	2	21
8	27	0
1775	29	0
28	1	0
63	34	0
94	0	1
36	1	0
16	39	2
830	2	0
2	83	0
169	1	0
604	1	0
2114	0	5
24	0	15
3	0	1
13	0	10
13	0	5
15	0	10
577	2	0
1225	1	0
1521	0	74
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538	0	1
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34	2	0
17	0	11
49	4	0
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322	0	1
641	0	1
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870	1	0
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481	0	4
38	0	16
1023	3	0
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12	0	2
439	0	1
905	0	3
1205	1	93
387	0	2
1165	0	9
4	0	3
4	0	4
141	0	2
37	0	2
220	2	0
72	0	1
27	0	2
147	0	2
69	14	0
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454	0	10
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127	4	0
57	0	34
112	0	4
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840	1	0
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76	0	14
3337	2	0
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1413	0	4
435	0	6
13	5	0
5384	4	0
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80	0	4
7467	0	4
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11	12	0
1682	0	1
5834	120	0
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3346	0	1
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1322	0	4
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6451	2	0
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1398	3	0
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6	0	1
814	0	2021
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67	1	0
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56	0	46
2821	0	1
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2559	429	87
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3086	1	0
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35	0	4
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68	0	1
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1266	1	0
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373	0	4
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609	2	12
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152	0	3
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42	7	0
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146	3	2
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1553	1	0
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114	2	0
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83	175	0
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57	0	4
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63	1	0
1826	0	5
86	0	5
280	106382	120209
2403	0	5
780	0	10
5348	0	5
5399	3638	0
1	0	887
852	0	1378
11042	16008	3641
7605	0	5
1134	0	5
264	0	15
1293	0	5
3171	57268	13797
685	1	0
34	0	5
1372	0	5
1338	0	1
27	5	0
4134	0	5
2732	5	0
3147	20574	17815
5003	17060	11543
4019	5	0
11632	5	0
9117	20	0
33	5555	0
1440	1	0
467	5	0
3386	0	5
311	0	5
1879	0	5
49	39017	0
3632	0	15
1931	0	10
5515	0	10
3630	5	0
1926	15	0
3614	5	0
249	5	0
5732	0	15
760	0	5
4565	10	0
574	1	0
540	0	5
578	0	15
3167	0	10
401	0	5
244	0	10
1112	0	10
536	5	0
3417	14479	8892
1869	0	5
76	0	5
1304	0	3
289	10	0
234	0	15
571	15	0
3186	0	5
1773	5	0
618	5	0
798	0	10
4144	0	5
206	5565	0
370	15	0
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148	5	0
601	0	10
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580	5	0
1904	15	0
3597	0	5
4460	3	0
7711	5553	0
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1147	0	1
5951	0	1
181	20	0
791	40	0
11	30	0
757	0	1
507	25	0
634	0	110
225	0	1
2224	20	0
415	0	30
469	1	0
3484	10	0
32	5	0
330	0	369
1598	0	5
1261	5	0
2677	0	5
770	1	0
515	0	5
2278	5	0
737	5	0
520	0	20
2176	20	0
526	0	5
4819	0	30
1861	10	0
789	5	0
775	1	0
880	3795	3584
339	0	20
416	0	15
1152	0	15
217	0	15
77	4	34
756	1	0
837	0	369
5	20	0
11	3802	3237
360	0	20
405	0	15
1137	0	15
234	0	15
60	1	21
1282	15	0
8	10	0
340	3795	3589
339	0	20
416	0	15
682	0	10
465	0	15
234	0	15
61	0	10
1640	3795	3589
339	0	20
416	0	15
696	5	0
461	0	15
211	0	15
84	0	35
1243	5	0
47	0	10
325	11447	10781
339	0	20
426	0	15
695	0	5
445	0	15
234	0	15
69	0	15
1288	0	5
3806	0	5
3768	15	0
1790	5	0
2374	0	3826
1437	5	0
1993	0	20
51	0	3816
1778	0	10
2023	10	0
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2016	0	5
1772	5	0
675	0	15
24	15	0
61	18	3
1261	10	0
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694	15	0
61	18	3
1240	0	5
1803	0	15
15	0	1328
9	0	10
8	0	5
2406	5	0
755	25	0
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1831	5	0
758	30	0
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33	5	0
1775	5	0
2010	0	30
9	0	2423
32	0	7657
320	0	3856
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3676	0	5
3888	5	0
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3059	5	0
813	0	10
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780	0	10
3950	5	0
491	0	5
3336	4	0
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4896	5	0
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1034	0	5
6634	0	5
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329	10	0
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1284	15	0
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682	10	0
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2484	0	5
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479	0	5
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9427	1	0
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5499	0	1
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2223	1	0
7495	0	1
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32	0	6
1396	0	1
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4062	0	12
3936	4	0
696	4	0
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6896	1	0
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378	0	1
1071	1	0
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3719	1	0
1031	0	8
1	0	1
24762	5	0
4899	1	0
643	2	0
1136	0	8
10030	0	1
1	0	1
469	0	4
1951	0	2
4433	0	4
17908	0	1
2446	21	0
989	0	6
932	8	0
81	4	0
435	4	0
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80592	0	4
3954	0	4
2260	2	0
412	1	0
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122	4	0
31440	4	0
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6588	0	1
32033	0	1
66239	0	2
5307	0	1
1328	13	0
22502	2	0
8432	8	0
19462	0	2
4744	0	9113
47	0	4
34	26	34
926	4	0
3590	0	2
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26336	3	0
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7752	2	0
28	0	2
1063	0	4
1355	0	8
88	8	0
116	4	0
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40	0	2
95351	0	1
7747	0	1
2909	0	6
17299	0	12
25548	0	451
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15671	2	0
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7385	0	17
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6358	1	0
750	0	2
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109	1	0
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684	0	2
468	1	0
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47	1	0
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5	1	0
118	0	1
50	0	3
253	2	0
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161	1542	0
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5	0	5
45	0	5
30009	0	2
916	1	0
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18	0	3
15366	1	0
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683	1	0
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28	0	2
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1162	1	0
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1303	4	0
49	0	8
83773	0	1
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59	0	8
11775	0	2
31559	4	0
6439	2	0
3398	0	3
13176	1	0
400	0	9
321	16	0
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26	0	2
18915	1	0
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79	0	20
5959	0	4
2054	0	2
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3028	3	0
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9198	1	0
325	1	0
297	0	5
1431	4	0
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2195	1	0
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6818	1	0
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4918	0	3
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3228	5	0
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38539	0	3
111	0	3
560	0	3
18959	4	0
1032	8	0
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6025	2	0
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3972	2	0
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63	2	0
23	0	2
11513	1	0
8392	4	0
1891	0	1
17313	21	0
65	0	2
21	2	0
153	0	69
7577	1	0
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8583	0	2
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35	0	4
64460	1	0
26042	1	0
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5719	3	0
15	2	0
79923	0	4
288	4	0
93	0	4
9495	0	2
15775	34	0
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7958	14	0
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161	2	0
3780	0	2
29057	26	0
645	0	1
45372	0	1
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805	1	0
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4099	0	2
938	1	0
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25	2	0
18	2	0
22	4	0
1700	0	8
3612	0	8
8297	0	1
2333	0	1
6580	7	0
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5597	0	4
13839	1	0
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114	0	8
74	20	0
33389	1	0
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2522	0	4
786	8	0
3663	0	4
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4822	0	5
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7415	5	0
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52	0	4
2164	4	0
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58	6	0
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5445	0	1
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7837	1	0
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862	1	0
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12	0	2
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324	0	4
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348	0	3
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2792	1	0
51	4	0
5816	0	1
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4816	0	1
2976	0	1
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163	0	13
3581	0	1
5401	1	0
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24	0	2
16	4	0
4	12	0
12	0	1
10	0	8
4616	8	0
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1203	0	4
4041	0	5
6924	1	0
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993	3	0
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67	4	0
7	2	0
2287	0	1
2757	1	0
1992	1	0
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300	0	1
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758	0	1
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4	0	16
13	3	0
1	0	3
39	0	1
74	4	0
7094	0	1
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12788	46205	46210
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2205	0	2
3085	4	0
4119	1	0
7111	0	8
66	0	4
8	0	1
52	4	0
4	0	8
1086	2	0
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60	0	1
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13	0	5
10524	1	0
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379	0	2
866	0	2
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906	1	0
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8552	17	0
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27908	4	0
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3569	4	0
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1311	4	0
44229	6	0
1554	1	0
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392	0	4
130	0	4
79	4	0
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8325	10	0
3422	0	1
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7929	4	0
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523	0	2
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14	0	1
52	3	0
1981	4	0
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43	0	2
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2693	1	0
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7727	0	4
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4871	1	0
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32	0	2
10378	6	0
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5134	4	0
29	8	0
4877	0	15
8724	0	1
1998	0	2
961	1	0
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88	0	4
612	4	0
24053	0	20
48	0	2
30	0	4
1689	0	1
1	0	1
58	8	0
116	4	0
10806	1	0
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7865	4	0
434	4	0
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3082	0	1
6448	0	1
47712	5	0
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40	0	1
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3404	2	0
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9063	1	0
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1893	2	0
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3707	1	0
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333	2	0
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15570	1	0
2767	1	0
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6533	1	0
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6722	1	0
3	0	1
8	0	4
38995	1	0
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4	0	2
2007	4	0
2252	1	0
11391	6	0
2728	0	12
39	1	0
6	0	3
42	11	0
27	0	4
77	0	3
4001	3373	3373
2124	6	0
9919	1	0
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17908	1	0
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3	0	9
8	0	1
10	12	1
48	1	0
2531	0	2
7039	25	0
6	4	0
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4	0	1
4	3	0
47	44	0
1	2	0
34484	0	4
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1846	0	10
7701	0	1
13	0	1
1	0	1
1496	0	20
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6081	3	0
15319	1	0
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5063	1	0
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33	0	2
13596	2	0
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2508	1	0
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5888	1	0
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44	0	5
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1060	4	0
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664	39671	39663
604	0	8
8095	4	0
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3742	1	0
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6399	0	5
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42	6	0
572	0	4
23288	1	0
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8	4	0
1623	0	1
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38071	0	7
12464	20	0
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34	0	2
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2287	20	0
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10499	1	0
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57	0	125
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6702	125	0
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2479	499	0
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12081	97703	25203
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7641	19402	29501
498	0	2
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11257	2	0
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145	875	0
26	1124	0
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1360	17412	12410
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332	0	7
3	6	0
311	0	125
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53539	1	0
7372	0	4
32422	0	3
27609	0	2
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2115	32299	32299
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545	0	1
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216	1	0
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23	0	1
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58	2138	2138
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59	0	20
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16	25063	14586
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56	0	5
53

chain 338298647 NA20870_chrY 48476143 + 6244292 9850803 HG002_chrY 62432599 - 52562439 56521946 2
17919	0	4
43	1	0
16944	0	4
8932	0	5
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97	2	0
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117	0	1
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2291	1	0
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1940	20	0
124	1	0
658	3	0
1505	0	1
842	4	0
2584	18	0
4543	1	0
21	2	0
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783	0	3
1505	1	0
989	1	0
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4580	6	0
96	2	0
1694	5	0
2002	1	0
356	13	0
471	1	0
3402	0	1
2723	0	3
1505	1	0
844	6	0
28	4	0
7144	0	2
98	2	0
393	1	0
12615	10	0
3113	4	0
4054	2	0
98	0	2
395	0	1
191	3	0
1107	5	0
712	0	1
1289	0	1
356	0	13
471	0	1
1795	0	1
3545	28	0
786	3	0
1505	0	1
842	4	0
26	0	2
2556	18	0
2602	2	0
1953	0	2
13	0	81155
22	0	4
68	0	4
14	0	4
8762	1	0
1130	0	18
5719	18	0
375	0	1
4205	2	0
52	0	1
43	4	0
3693	0	1
356	0	14
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1505	0	1
840	6	0
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538	0	1
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17	3	0
45	12	0
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67	6	0
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30	2	0
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121	300	0
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50833	0	8
71	0	8
1640	10	0
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2479	0	4
1159	0	10004
4052	19	11
52	8	0
12214	0	9
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5864	0	27
113	0	2
28	0	3
27	0	3
252	29	0
41	29	0
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5950	8	0
5732	4	0
17684	1602	0
322	0	1
2755	2	0
1755	0	1
3328	26	0
59	2	0
43	0	2
26	0	6
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172	8	0
176	0	1
364	0	1
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999	0	2
687	4	0
1023	0	14
306	1	0
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32	1	3
886	0	2
320	0	1
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2675	20325	0
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285	12	0
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1721	0	4
311	0	1
311	1	0
292

chain 126268065 NA20870_chrY 48476143 + 24459841 25808163 HG002_chrY 62432599 - 35428670 36784196 3
5794	3	0
609	1	0
1617	2	0
18609	2	0
13639	0	1
54659	0	1
2122	0	1
10487	2	0
21349	0	1
18427	0	1
10119	0	9
25268	6	0
1961	0	1
36692	1	0
3298	0	1
40754	0	4
45739	0	4
13431	1	0
9119	0	8
9749	1	0
21546	0	1
9586	0	6
502	4	0
14728	2	0
2741	1	0
47190	1	0
18680	4	0
19783	0	2
1195	2	0
20318	12	0
4261	1	0
27736	8	0
15548	8	0
2840	0	3
19193	0	1
12534	0	1
32596	0	3
27287	0	1
271	0	2
34	2	0
5212	0	1
1732	1	0
902	2	0
373	3945	3945
385	0	2
904	0	1
1745	2	0
5221	2	0
2	4	0
1928	0	1
12206	0	2
23590	0	1
16039	2	0
7743	0	2
7968	0	4
7193	1	0
19824	1	0
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24735	1	0
5211	0	2
6621	2	0
14	0	1
1693	1	0
2646	1	0
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814	0	1
17916	1	0
5567	1	0
1638	5	0
15028	20	0
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546	2	0
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3048	2	0
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49305	0	1
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6879	0	2
38	2	0
3226	0	1
471	1	0
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63	4	0
46	2	0
63	12	0
17	4	0
100	0	16
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3343	0	14
24865	0	1
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84	0	14
1668	1	0
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1672	0	15
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214	0	1
9090	0	3
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860	2	0
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2013	0	1
1219	0	8
83	0	1
3722	0	2
1544	10	0
1473	0	1
4314	1	0
1555	398	12320
1446	0	1
6265	0	1
4084	2	0
119	6761	2006
790	1	0
4952	0	1
6913	1	0
15500	0	1
99

chain 37272838 NA20870_chrY 48476143 + 24040228 24434720 HG002_chrY 62432599 + 25702901 26097477 4
1678	0	1
29610	4	0
4117	0	18
1674	0	2
4142	0	14
84	4	0
1	2	0
5328	0	12
8311	0	2
17678	1	0
7181	0	20
3343	0	4
3380	0	8
100	8	0
17	8	0
6358	3	0
17773	0	1
3264	0	2
74559	2	0
2569	5	0
1392	1	0
8550	0	11
5842	0	1
604	2	0
6683	0	1
7852	0	2
6974	0	1
12562	0	1
6905	0	5
1063	0	1
30891	0	3
6780	0	1
2191	1	0
7676	1	0
821	0	4
28773	4	0
3048	0	1
7404	0	1
20279	0	1
689	6	0
23	0	2
7058	0	1
6581	0	2
4894	0	2
3118	3	0
912	0	1
1757	0	20
9077	3	0
340	2	0
2320	2	0
204

chain 4354067 NA20870_chrY 48476143 + 17170503 17216707 HG002_chrY 62432599 - 45214480 45260689 5
13217	0	4
16206	0	2
4935	0	8
235	8	0
2925	1	0
8677

chain 3742518 NA20870_chrY 48476143 + 19541400 19581064 HG002_chrY 62432599 - 42850342 42889998 6
19965	4	0
6526	2	0
10499	2	0
2666

chain 3059133 NA20870_chrY 48476143 + 21971477 22003775 HG002_chrY 62432599 - 40507615 40539913 7
6287	0	1
4953	1	0
21057

chain 2144432 NA20870_chrY 48476143 + 25840163 25863310 HG002_chrY 62432599 + 25667431 25697734 8
3485	0	1
4952	1	0
1140	35	7192
8444	1	0
2387	1	0
2381	0	1
320

chain 1646206 NA20870_chrY 48476143 + 25808163 25825576 HG002_chrY 62432599 + 25646281 25663694 9
17413

chain 372803 NA20870_chrY 48476143 + 25110138 25114083 HG002_chrY 62432599 + 26349701 26353646 10
3945

chain 201400 NA20870_chrY 48476143 + 23988381 23990503 HG002_chrY 62432599 - 36784196 36786318 11
2122