##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 2502342476 HG04199_chrY 54872857 + 20 54867598 HG002_chrY 62432599 + 2 62432577 1
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1369	0	1
1094	2	0
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480	1	0
28	0	5
1906	0	1
1584	962	2
8	1250	0
103	48	0
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155	48	0
144	687	109
42	0	1
2115	1	0
304	1	0
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5332	0	52
91	104	0
73	52	0
3745	0	4
10	0	9
719	0	1
1618	1	0
938	0	1
714	0	1
621	3	0
782	4	0
28	63	2
79	30	0
93	0	18
297	0	4
322	0	2
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1202	0	4
61	4	0
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2038	0	5
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32	0	4
457	4	0
77	4	0
3	20	0
103	0	4
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463	0	4
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2584	2	0
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431	0	2
907	6	0
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8	0	1
41	2	0
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85	0	7
22	4	0
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2638	4	0
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74	0	1
770	0	2
21	0	24
3741	4	0
12	4	0
43	0	8
4	4	0
29	4	0
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14	4	0
68	0	4
80	0	4
19	0	4
37	0	4
524	0	5
621	29	0
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27	1	0
554	10	0
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653	12	0
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748	789	0
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153	1	0
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3060	0	1
487	0	1
79	0	4
316	0	1
896	0	6
3859	1	0
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1082	0	259
2738	4	0
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61	1	0
30	4	16
7	0	4
2168	0	1
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39	0	8
484	0	1
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366	2	0
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446	1	0
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1624	1	0
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1591	1	0
823	0	200
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379	3	0
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37	10	10
58	0	55
107	0	162
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271	0	3
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34	0	12
936	0	2
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292	0	4
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538	0	1
2132	1	0
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46	4	0
355	0	4
1247	1	0
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635	4	0
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38	4	0
335	0	4
1560	0	4
96	12	0
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99	0	2
111	0	72
101	1	0
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35	1	0
407	108	0
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24	36	0
9	327	2
84	180	0
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33	0	1
4	0	1
69	1	0
699	5	0
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146	4	0
5712	2	0
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656	0	4
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20	377	7
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309	2	0
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106	2	0
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52	2	57
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97	5	0
262	1	0
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81	20	0
39	1	0
1	4	0
7	0	1
252	0	1
1489	2	0
7664	15	5
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797	2	0
2033	0	4
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204	75	363
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88	1	0
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10	0	168
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1336	0	5
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13	0	10
13	0	5
15	0	10
6540	0	4
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439	0	1
908	1	0
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32	56	28
78	60	0
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5783	0	2
3337	2	0
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1413	0	4
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13	5	0
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11	12	0
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46	0	40
36	0	1
6	0	148
102	0	1
9	1	0
20	66	87
1563	2	0
39	10	0
1758	1	0
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952	0	4
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1917	0	1
872	0	4
34	0	5
3309	2	0
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306	0	3
1928	1	0
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910	114	0
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1398	3	0
706	0	1
247	2	0
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137	0	1
824	0	1
35	0	2
420	0	1
24	1	0
441	1	0
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6	0	1
814	0	2021
521	0	1
5964	15	0
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88	0	1
846	1	0
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534	155	98
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2240	429	87
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69	0	39
103	0	78
2740	0	1
296	0	3
771	0	1
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642	38	0
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797	4	0
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45	0	8
20	4	0
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28	4	0
947	1	0
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1343	1	0
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1436	16	0
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894	1	0
21	0	5
219	1	0
107	34	0
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341	5	0
2899	0	1
143	0	1
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73	2	0
3646	2992	2299
6	5	0
324	3	0
553	0	1
311	2	0
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57	4	100
118	2	0
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22	0	2
112	4	0
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2499	4	0
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35	13	11
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5	0	4
128	0	4
605	1	0
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60	103747	4711
48	152	0
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2519	1	0
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96	0	1
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69	5	0
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64	4	0
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10	2	168
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19	13	40
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28	240	357
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1569	26	11
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344	0	773
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5943	6	0
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5	0	2
76	0	1
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9	0	26
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58	0	1
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7	5	77
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623	0	1
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39	52	12
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15	1	0
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37	2	0
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356	0	1
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7668	2668	104118
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788	0	5
1691	0	4
33	3	0
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153	0	121806
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1272	1	0
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52143	1125038	311619
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21	154709	190674
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34	0	5
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23	49936	18818
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1	5551	0
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7263	0	1
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30840	1	0
5642	0	1
2512	1	0
9544	8	0
13	0	12
15	0	24
1952	4	0
2252	1	0
11391	2	0
2808	0	3
46	0	4
4081	3374	3375
2122	9	0
3625	0	1
6293	1	0
9025	3	0
2383	6	0
22591	0	1
5256	0	6
2573	0	2
7039	25	0
6	4	0
10120	13	0
59	3	0
47	12	0
1	2	0
38817	2	0
255	8	0
50	1	0
59	13	0
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6	25	0
7008	2	0
2549	0	3
11	0	1
3	0	1
1	0	3
1490	0	20
37803	0	1
6293	1	0
1495	1	0
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2904	1	0
6628	0	15
2859	0	2
33	0	2
13596	2	0
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44	8	0
4	8	0
9504	0	2
2508	1	0
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1540	1	0
9058	1	0
21747	4	0
39	1	0
6	0	1
6719	0	1
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7311	1	0
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9919	0	1
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3719	1	0
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9911	1	0
5667	6	0
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9878	0	3
8099	0	1
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6601	1	0
8858	1	0
602	1	0
6731	0	1
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11984	0	1
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3184	3	0
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2927	4	0
5634	0	2
4040	20	0
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2731	0	15
39	0	5
6396	2	0
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7772	0	1
643	0	1
2532	1	0
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6933	1	0
3480	23	0
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6838	0	56
859	1	0
237	1	0
47	0	16
15	0	3
39	0	1
44	1	0
18	3	0
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12	0	1
218	0	1
110	1	0
49	85788	223413
24338	0	6
954	4	0
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23	0	2
33822	0	4
4810	1	0
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50696	1	0
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2481	1	0
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3632	1	0
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9765	0	1
3676	1	0
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8712	0	1
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585	0	3
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42	6	0
556	0	20
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4380	4	0
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5	20	0
4	0	64
1592	1	0
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3346	0	2
7921	0	1
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6662	1	0
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16254	8	11
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5988	1	0
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874	0	1
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592	0	1
2739	4	0
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3273	0	3
12390	125	0
5795	0	1129
7864	0	2759
63997	2	0
2320	66910	0
23351	36231	29500
498	0	2
78	0	1
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115	4	0
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11257	2	0
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16	0	125
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78	0	125
145	875	0
26	1124	0
9237	250	0
872	3913	1288
3641	2372	123
52	3749	0
37	250	0
13536	4484	2859
59	624	0
42	1000	0
2047	1	0
690	0	1875
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560	0	1
332	0	7
3	7	0
240	124	0
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32422	3	0
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13	0	2
3416	1	0
7419	1	0
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26774	1	0
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845	1	0
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5936	0	1
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5028	0	3
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20769	0	1
344	8	0
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4639	8	0
35	4	0
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7233	1	0
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2448	1	0
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34	4	0
7825	0	1
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32978	0	1
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23839	0	1
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41538	1	0
55612	0	1
15479	70943	326
33047	4	0
14840	2	0
9799	4	0
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37	0	3
11653	2	0
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5844	1	0
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4	4	2
687	1	0
22	0	1
7039	0	12
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24	0	3
6	0	4
14	0	2
2	0	12
22	0	58
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37858	1	0
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26726	2	0
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3175	0	23529
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6076	0	2
11466	0	1
3870	0	10
483	10	0
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3592	2	0
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622	0	1
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4076	8	0
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5413	0	3
6639	1	0
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27921	8513	0
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20	0	1
6	18	0
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69	5	0
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5	0	1
158	0	4
288	0	1
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25	7	0
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53	2	0
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386	41693	2085
307	0	3
60	0	2
73	1	0
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416	4	0
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26	15	0
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71	6	0
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36	0	1809
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52	1	0
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9	4	0
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43	0	2
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88	4	0
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38	1	0
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69	0	1
443	0	1
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124	2	0
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475	0	2
24	1	0
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22	2	0
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49	0	1
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7	3	0
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17	1	0
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28	0	5
57	44	0
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42	325	0
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76	1	0
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140	0	1
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23	0	1
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82	12	0
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3	16	0
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91	4	0
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577	0	2
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139	0	1
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50	1	0
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178	0	3
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28	0	1
57	1	0
23	466	6295
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96	1	0
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439	0	1
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690	0	1
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16	36	0
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33	4	0
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121	2	0
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73	0	1
50	4600	2764
121	12	0
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95	8	0
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210	6	0
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75	0	8
117	0	15
117	1	0
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197	0	1
107	75520	109875
386	0	3
114	0	2
53	32	0
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67	0	1
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25	2	0
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69	1	0
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9	12	0
72	0	1
131	0	2
61	0	6
22	0	2
5	0	152
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69	2	0
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4	1	0
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94	0	2
113	0	8513
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35824	1	0
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6211	8	0
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34	4	0
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104	4	0
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1567	0	2
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614	0	1
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99	2138	2138
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18999	10847	0
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1675	0	4
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3380	8	16
92	0	12
8	4	0
126	0	8
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4852	1	0
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31793	1	0
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8228	0	6
6	10	0
3	2	0
72	2	0
14310	0	8
18549	4	0
19584	1	0
30609	0	4
13184	4	0
36636	0	1
17486	0	2
46423	0	5
2829	2873	0
34	0	5
19581	0	55
1070	0	1
1209	0	10
3940	15	0
1625	0	20
324	0	5
909	0	15
1625	20	0
324	5	0
925	15	0
1609	0	20
1238	0	5
1622	20	0
741	0	5
495	15	0
1625	0	20
738	5	0
1057	0	10
65	0	1
1002	5	0
13	17	2
1233	0	5
1957	5	0
901	15	0
548	0	10
64	0	1
1019	0	2878
2264	0	1
601	20	0
738	0	5
516	0	10
532	10	0
64	1	0
400	0	1
601	20	0
1274	5	0
514	5	0
16	5	0
61	1	0
1002	0	20
167	0	10
1061	0	10
1023	0	1
601	20	0
738	0	5
1122	1	0
1002	0	20
1248	10	0
547	0	10
2306	20	0
548	0	10
465	1	0
601	0	20
738	5	0
507	15	0
1016	1	0
1364	0	5
505	0	5
558	0	10
1057	20	0
167	10	0
1061	10	0
540	0	10
473	1	0
1364	5	0
1528	1	0
601	0	20
738	5	0
505	0	5
558	10	0
54	1	0
1740	0	5
510	0	5
547	10	0
1068	20	0
1800	10	0
1068	20	0
1248	0	10
552	10	0
1063	20	0
1238	0	20
1615	20	0
1238	0	20
531	0	10
1084	20	0
1238	0	5
531	0	10
81	1	0
2810	0	10
1069	20	0
446	0	2873
7088	0	10
1128	2883	0
13992	5	0
196	3121	0
7	432	0
2521	0	10
815	10	0
6910	0	6262
1152	0	3131
3569	0	6252
24	0	5
40	0	5
33416	1	0
763	0	5
11545	0	5
6840	3101	0
5988	3101	0
383	5	0
169	30	0
1338	1	0
854	20	0
893	0	5
172	0	10
632	5	0
554	0	1
3963	3121	0
4009	5	0
22	5	0
16919	1	0
1593	5	0
153	5	0
162	0	10
51	5	0
27	0	10
23	0	1
1041	1	0
155	65	0
148	1	0
530	0	5
912	1	0
45	0	15
142	0	10
58	5	0
29	0	10
1361	0	12407
1567	1	0
2268	1	0
6755	5	0
5751	0	10
3221	5	0
16952	5	0
13347	0	5
97	8162	2649
6	0	5
10	0	280
2425	0	15
325	0	5
1015	0	5
2334	0	2763
166	0	10
2034	0	5
2404	0	15
909	5	0
131	30	0
249	0	5
1800	10	0
146	2	0
2529	0	5
2735	0	5
16502	30	0
79	1	0
156	1	0
2179	15	0
355	0	15
62	0	1
156	0	1
546	1	0
237	5	0
1405	0	15
306	10	0
5	0	5
16	0	5507
24	5	0
47	1	0
923	0	5
1753	15	0
77	1	0
2686	0	10
77	0	1
923	0	5
1743	10	0
87	1	0
923	5	0
1745	0	5
85	0	1
2685	15	0
16	0	10
2718	0	2758
10359	15	0
723	5	0
720	10	0
954	0	15
708	0	15
615	0	5
314	0	5
389	10	0
2067	1	0
253	16538	4
10571	20474	24048
2130	0	4
1423	0	3534
2151	4	0
1408	0	5
6030	1093186	1046335
1035	0	15
1283	5	0
915	0	5
1247	0	3528
4506	1	0
486	7157	21191
22	10	0
1262	0	5
912	10	0
9	15	0
40	10	0
326	0	15
1415	0	5
207	15	0
590	0	5
97	1	0
140	10	0
700	15	0
3429	0	1
39	0	5
15	0	5
155	0	216
863	90683	79946
440	10	0
20	5	0
41	15	0
1764	5	0
17	6	0
1	3521	0
3130	1	0
1917	26114	2083
687	1	0
300	0	5
7	0	10
3290	15	0
10759	6054	9594
4833	0	15
2574	15	0
691	5	0
3419	0	1
4926	3521	3536
6652	7028	0
368	25	0
2222	0	5
16	0	5
3713	3538	3538
8352	77284	24041
4604	2	0
238	5	0
415	0	2422
206	1	0
8430	5645	5645
5019	5	0
18692	0	7121
823	0	5
399	3581	3
1889	0	1
427	0	5
1237	10	0
443	0	1
917	5	0
932	0	5
1274	15	0
1318	0	5
947	5	0
1183	1	0
44	10	0
810	21597	25172
1042	3554	0
6458	2411	2411
6828	0	7246
99	1283	8537
1089	0	5
1480	4979	0
19657	1	0
15883	0	1
2120	25743	24607
1288	0	15
81	3534	0
2383	0	1
4951	0	5
3554	0	5
148	0	1
8474	23938503	32224543
6937	0	10
17786	18658	6604
11095	0	45932
882	0	15
5763	0	1
3534	1	0
6240	0	14139
7884	1	0
7069	1	0
179	5	0
946	10	0
91	15	0
16	25	0
393	0	5
156	45	0
122	0	20
583	0	5
95	1	0
55	1	0
432	0	15
566	5	0
940	10	0
101	15	0
8	25	0
381	0	10
168	45	0
122	0	20
103	1	0
2544	0	15
3699	25	0
3362	0	15
174	0	25
3346	0	15
1794	0	40
9	0	320
3174	0	40
197	1	0
671	0	7095
974	0	25
215	0	21200
1366	20	0
65	40	0
6427	1	0
494	0	20
74	0	25
14	4064	28603
2343	0	1
494	20	0
66	40	0
15812	3502	0
5882	0	10
442	15	0
1848	0	15
2762	5	0
8	0	15
379	0	1
326	31	14166
5828	0	15
24	15	0
371	5	0
7014	5	0
1438	30	0
2030	10	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
447	2636	13156
3509	5	0
17221	4	0
3423	0	3
12062	5	0
22242	0	1
15405	0	2
32631	17	0
5	0	30
60	4	0
4	4	0
38	4	0
3295	1	0
809	0	1
8998	1	0
1748	0	2
2765	0	26
10966	0	3
16383	5	0
30876	1	0
19872	3	0
21	0	3
1807	0	1
1087	2	0
2677	0	2
4326	16	0
928	1	0
31585	1	0
23459	0	3
7339	0	2
22442	1	0
15807	0	33
11481	1	0
11261	0	1
28566	0	2
52315	0	2
14553	2	0
2146	1	0
3356	1	0
17	6	0
2040	0	1
6977	0	4
68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
4172	0	1
1543	4	0
475	0	1
3574	6	0
42	6	0
125	38	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	2
160	47	0
31	74	0
742	38	2
66	0	7
9	0	17
36	0	34
2	0	8
30	7	0
14	8	0
27	24	0
1	0	1
30	0	7
12	0	9
29	16	116
10	0	1
10	4	0
12	0	2
36	0	1
22	1	0
38	0	5
6	0	1
5	0	1
12	13	1
30	0	6
6	5	0
8	18	0
24	86	29
36	0	2
12	0	1
20	5	0
18	10	0
15	19	14
60	8	0
31	4	0
7	0	2
6	23	9
14	2	385
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 5859262 HG04199_chrY_random0000138 90854 + 0 62096 HG002_chrY 62432599 - 42827845 42889998 2
726	1	0
472	1	0
1258	1	0
11334	2	0
6838	0	56
1197	0	12
20569	4	0
6526	2	0
10499	2	0
1254	0	2
1410

chain 4356244 HG04199_chrY 54872857 + 17925124 17971330 HG002_chrY 62432599 - 45214480 45260689 3
13217	4	0
12115	0	3
9029	0	4
11841

chain 2713635 HG04199_chrY_random0000138 90854 + 62097 90838 HG002_chrY 62432599 + 19582257 19610999 4
604	0	4
8099	2	0
14740	2	0
133	0	2
3742	1	0
1418

chain 1191845 HG04199_chrY 54872857 + 17539018 17551659 HG002_chrY 62432599 - 45634118 45646761 5
1386	0	3
6458	1	0
4796

chain 428205 HG04199_chrY 54872857 + 23898657 23903169 HG002_chrY 62432599 - 39338719 39343231 6
4512

chain 321938 HG04199_chrY 54872857 + 15675052 15678464 HG002_chrY 62432599 - 47507067 47510475 7
2617	4	0
791

chain 201175 HG04199_chrY 54872857 + 24763788 24765910 HG002_chrY 62432599 - 38399346 38401468 8
2122

chain 2683 HG04199_chrY 54872857 + 13288831 13288859 HG002_chrY 62432599 + 12511308 12511336 9
28