##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 1799002050 HG04157_chrY 45011078 + 920 43408076 HG002_chrY 62432599 + 2 62432577 1
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2595	23	0
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41	2	0
1031	0	4
2859	1	0
1459	4	0
118	0	2
3245	12	0
2794	538	0
3998	2	0
3741	4	0
12	4	0
43	0	8
4	4	0
29	4	0
112	4	0
13	4	0
58	4	0
302	4	0
14	4	0
68	0	4
48	4	0
32	0	4
19	0	4
33	0	8
524	0	5
621	29	0
191	2	0
243	0	1
305	2	0
1016	0	2
1482	1	0
36	4	0
18	0	14
98	0	3
1	0	1
13	12	0
24	12	0
21	0	36
27	1	0
554	14	0
147	0	1
637	0	4
4	0	8
851	526	0
443	16	0
60	0	1
239	0	1
153	2	0
362	2	0
387	0	3
960	0	270
3628	0	4
316	0	1
896	0	6
5122	0	2
4173	0	1
1082	0	259
2940	1	0
11	0	4
28	0	4
61	1	0
30	4	16
2177	0	3
538	0	4
124	0	18
776	0	18
2033	3	0
1869	0	4
41	0	6
484	0	1
1234	0	2
1381	135	0
205	5	0
2006	0	1
184	0	536
4	0	1
1200	148	0
557	0	885
86	0	590
276	0	295
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
5446	0	1
716	0	1
1591	1	0
823	0	200
393	0	520
3516	0	107
37	10	10
27	0	188
5	0	162
22	0	324
37	21	0
149	6	73
157	0	4
163	0	4
1253	1	0
1337	0	20
37	5	0
7	0	5
30	0	10
9	5	29
707	2	0
1777	0	2
166	1	0
9927	1	0
2036	106	0
1069	0	4
3392	108	0
88	0	72
7332	2	0
442	0	2
77	7	0
154	0	1
2240	318	0
3344	2	0
330	0	2
36	0	317
7	0	22
321	0	4
263	0	6
94	4	0
24	124	0
3	8	0
151	0	8
113	142	0
141	0	6
966	0	1
1215	49	0
1827	0	2
305	0	1
16	14	0
1504	1	0
14	0	2
940	0	1
28	0	8
14	0	1
394	2	0
47	0	1
3	1	0
169	0	26
71	0	1
17	0	2
279	0	3
26	0	1
588	4	0
622	1	0
249	6	0
259	1	0
735	6	46
28	0	60
78	0	25
1	5	0
11	10	15
43	1	0
2	4	0
253	0	2
85	0	1
22	1	0
47	1	0
7	0	3
2	0	1
30	0	2
27	0	10
44	0	3
34	20	0
39	1	0
1	4	0
892	0	1
719	2	0
138	1	0
2328	0	1
591	0	1
363	0	1
178	0	2
142	0	2
82	0	1
834	2	0
171	0	1
1476	0	1
65	0	1
125	0	1
6	0	4
3	0	2
91	0	1
95	0	4
29	5	0
234	1939	1962
93	0	4
143	0	23
5	0	4
264	4	0
282	0	1
115	0	1
396	0	2
317	0	1
400	0	5
282	0	1
225	0	1
118	0	1
212	0	2
6	1	0
92	4	0
42	4	0
50	0	2
12	3	0
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211	0	4
335	0	1
200	0	1
55	0	2
47	0	1
16	0	1
171	0	2
89	0	1
8	1	0
6	0	1
4	0	3
1	0	1
28	0	54
3	1	0
5	0	1
3	3	0
31	3	0
11	120	75
17	54	14
12	0	7
12	145	14
52	20	0
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12	15	0
9	0	1
12	0	1
6	37	11
15	20	0
6	2	0
4	4	0
15	37	0
9	208	0
3	1	0
9	3	1
64	13	0
7	13	0
18	0	1
8	2	0
10	127	0
14	1	0
6	2	0
13	6	0
9	25	6
11	25	0
10	6	0
8	24	12
10	0	1
8	81	10
9	16	0
5	1	0
1	0	2
23	58	0
1	0	1
2	0	1
12	88	13
13	0	1
5	12	0
7	41	14
33	0	1
1	19	0
3	0	2
7	3	0
13	13	0
19	0	2
3	0	5
7	0	1
6	144	91
23	15	9
31	11	0
3	0	1
7	1	0
7	1	0
15	231	19
4	0	1
6	27	0
6	0	1
27	0	1
49	0	1
1	0	1
23	0	3
9	0	1
25	0	1
3	0	2
7	2	0
7	6	3
45	0	1
33	1	0
2	0	2
13	1	0
1	0	2
8	1	0
16	0	23
12	0	1
13	338	0
8	0	3
10	1	0
22	0	1
38	1	0
63	0	2
30	175	0
58	21	22
16	60	0
12	60	72
8	3	0
6	0	3
7	6	0
5	0	4
6	0	6
17	4	0
12	0	1
6	0	7
9	0	1
12	527	76
49	0	1
416	0	1
975	0	1
550	0	1
534	0	1
509	0	1
3	0	1
184	0	1
41	0	1
166	0	1
375	0	1
930	0	208
1029	0	1
206	0	3
4	0	39
31	105	0
26	20	33
5	0	3
8	0	5
8	0	8
182	0	62
8	19	0
33	0	19
9	24	0
11	0	5
3	4	0
58	42	0
16	18	0
11	27	0
8	2	21
8	27	0
481	0	1
642	0	1
27	0	3
213	41	0
35	0	5
311	28	0
56	29	0
28	1	0
63	313	167
812	2	0
2	83	0
169	0	1
603	1	0
2114	0	5
24	0	10
8	0	1
13	0	10
13	0	5
15	0	10
577	2	0
1225	1	0
1521	0	74
1117	0	1
214	1	0
538	0	1
973	30	0
152	2	0
38	0	2
34	2	0
17	0	11
49	6	0
6	0	2
322	0	1
641	0	1
1156	20	0
12	15	0
10	0	2
14	0	2
830	4	0
9	0	1
531	0	8
1023	3	0
1420	4	0
542	1	0
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
13	4	0
19	31	0
7	9	0
98	2	0
454	0	10
55	0	4
127	4	0
57	0	34
112	0	4
146	4	0
840	1	0
470	3	0
975	0	13
5	2	0
76	0	14
2787	0	1
549	3	0
1797	15	0
2090	0	8
1016	1	0
397	0	4
435	0	6
13	5	0
1271	1	0
2160	1	0
1707	0	1
337	4	0
80	0	8
7463	0	4
510	4	0
748	8	0
368	0	4
11	12	0
1682	0	1
5770	11	0
2	0	92
27	0	3
25	0	40
32	0	40
20	0	2
13	0	37
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
324	1	0
952	0	4
319	0	38
505	0	4
2720	4	0
42	0	4
67	15	0
963	0	1
705	2	0
941	2	0
249	0	2
442	0	6
162	0	5
14	35	0
53	15	0
58	0	5
9	0	5
146	5	0
105	0	10
669	1	0
8	0	2
525	0	1
876	0	8
28	0	4
484	4	0
63	4	0
73	4	0
190	56	0
48	0	84
1853	440	0
4956	2	0
3316	0	18
48	2	0
1878	0	2
910	114	0
401	0	228
1398	3	0
706	0	1
1426	0	2
170	0	244
1137	0	1
17	0	5
1	10	0
579	1	0
683	183	0
424	0	1
861	0	1
105	0	5
309	0	2
23	0	1
294	0	1
146	1	0
474	1	0
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2	2	0
889	7	0
317	1	0
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461	1	0
630	0	3
882	0	1
1091	0	4
181	8	0
1236	1	0
376	1	0
1369	0	3
420	0	1
2	0	1
696	0	3
14	3	0
329	0	1
46	24	50
15	0	6
9	0	9
42	47	2
10	0	4
1064	0	1
16045	0	57
534	155	98
5331	0	364
1110	429	87
3350	0	117
18	0	78
1	0	1
10	0	159
2740	0	1
296	0	3
580	0	1
189	0	2
2112	0	1
659	0	19
68	30	87
54	123	9
29	54	320
793	0	4
5	0	4
247	4	0
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975	1	0
313	0	1
1343	1	0
74	0	1042
472	1	0
170	0	2
1436	20	0
163	0	1
174	3	0
727	30	0
836	1	0
308	1	0
90	4	0
1179	1	0
107	34	0
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790	1	0
343	0	4
424	258	0
756	0	1
143	0	1
131	0	1
73	2	0
5824	164	0
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324	2	0
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1128	1	0
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1329	0	5
229	0	1
1807	0	1
242	0	1
742	0	1
601	6	20
8	0	4
532	1	0
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141	0	1
140	0	3
27	1	0
1027	0	3
111	0	3
359	0	18
717	0	7
4592	142	0
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15	48	0
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52	72	0
22	0	2
94	2	0
46	0	2
63	70	0
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396	1	0
3223	0	12
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44	0	1630
48	0	232
21917	0	4
26	0	29
5868	0	4
2241	57	0
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48	0	27
2625	4	0
561	0	4
937	0	4
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4533	4	0
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7	0	4
9	6	0
4	0	10
17	0	4
1	0	4
35	13	11
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553	0	4
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175	0	2
33	0	4
2243	0	4
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90	2	0
573	0	1
2781	0	12
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586	20	0
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86	0	4
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1966	4	0
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331	12	0
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1668	0	2
305	2	0
463	1	0
3022	1	0
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299	63	0
394	0	1
9499	0	38
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4660	0	4
703	4	0
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4478	0	4
158	0	4
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8	28	0
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12	0	1
8	24	0
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161	0	12
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1324	0	16
12	0	189
2018	0	1
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2068	0	1
870	1	0
426	22	0
3115	4	0
256	3	0
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691	1	0
627	4	0
4906	56	20
1415	3	0
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392	0	2
402	2	0
1523	2	0
1450	0	1
3698	0	1
823	0	5
857	0	7
1026	0	39
1576	0	4
76	12	0
21	8	0
2	8	0
290	4	0
97	0	8
62	12	0
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81	0	1
59	0	8
290	4	0
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18	12	0
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16	8	0
167	3	2
6141	1	0
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582	4	0
4054	1	0
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286	3	0
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1169	1	0
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3101	1	0
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781	0	1
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3062	19	3
1179	1	0
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817	0	1
153	0	1
784	1	0
11	1	0
188	4	0
487	4	0
907	7	0
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54	4	12
63	4	0
35	0	4
211	0	4
64	8	0
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739	1	0
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65	4	0
18	2	0
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1641	0	12
5391	14	0
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769	4	0
38	0	1
3306	0	1
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5297	1	0
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55	0	8
5	4	0
1796	4	0
512	3	0
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25	0	6
569	2	0
907	1	0
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18	0	5
335	10	0
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62	20	0
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54	1	0
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33	0	1
125	0	1
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58	1	0
130	0	1
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3	0	1
73	0	15
34	0	20
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4064	0	1
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387	0	1
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166	0	1
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88	0	1
842	0	1
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185	0	1
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1280	0	1
80	0	2
18	1	0
538	1	0
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749	0	1
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48	1	0
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37	1	0
489	0	1
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161	0	1
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644	373	0
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364	0	1
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435	0	1
379	0	1
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1326	0	1
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15	7	0
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23	99972	59881
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2	6	0
75	1	0
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75	0	1
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103	0	1
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42	1	0
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1	1	0
57	0	3
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14	23	23
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22	0	1
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16	0	1
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21	26	26
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10	2	0
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14	6	0
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14	28	0
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2	0	6
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8	1	0
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20	0	1
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3	0	31
10	0	4
6	1	0
7	0	1
14	0	4
4	0	2
2	0	2
6	0	4
13	299	360
13	0	13
19	29	43
64	0	1
21	12	0
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21	1	0
62	1	0
71	1	0
377	1	0
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191	1	0
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448	0	1
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2303	255	0
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588	1	0
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2998	0	2
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17	8	17
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139	13	0
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1676	2	0
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662	6	0
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1106	1	0
190	2	0
7816	0	1
1765	0	1
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502	1	0
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664	30	0
119	780	0
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753	7	0
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1774	0	4
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1531	5	0
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33	0	15
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881	0	1378
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258	2858	9672
1	2601	0
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293	13127	21444
2275	5	0
7573	307477	181037
4584	5	0
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206	7172	0
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12788	46200	46210
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10	0	1
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25	20	0
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42	4	0
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69	7536	283378
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648	39665	39663
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361	51599	52855
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64	40	0
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323	0	1
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24	15	0
371	5	0
3493	5	0
909	0	3498
552	30	0
5528	5	0
3475	5	0
32	0	3508
3459	27750	6724
759	1	0
456	0	20
550	1	0
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15740	0	70
12638	0	1
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1854	5	0
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12	17	0
99	0	4
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2410	1	0
351	0	9
1716	0	1
1445	1	0
7821	0	3
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34737	0	1
214	15	0
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2677	8	0
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6743	0	4
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172	1	0
5936	1	0
12540	19	0
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2374	1	0
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407	1	0
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3143	18	0
8900	1	0
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3356	5	0
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68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
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162	0	8
1373	4	0
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42	6	0
125	38	0
1489	1251	0
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66	0	7
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27	24	0
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29	16	116
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10	4	0
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36	0	1
22	1	0
38	0	5
6	0	1
5	0	1
12	13	1
30	266	73
34	18	0
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12	0	1
18	21	3
13	39	7
12	31	14
7	24	0
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43	8	0
5	0	1
6	7	0
3	0	1
8	5	0
7	4	0
7	0	2
6	23	9
12	13	0
31	177	17
22	41	0
9	1	0
21	5	0
33	1	0
22	0	4
8	0	4
6	5	0
47	20	0
15	3	0
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37	0	1
2	0	5
7	7	0
5	4	0
13	0	1
13	3	0
25	0	1
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2	0	2
7	3	0
1	0	7
13	3	0
27	1	0
18	1	0
14	17	0
2	0	2
9	3	0
9	33	1
18	0	1
8	0	3
42	0	1
17	0	10
6	9	0
47	1	0
36	8	0
46	0	1
43	0	1
50	95	28
62	0	5
7	2	5
4	1	0
25	4	0
35	30	0
39	4	0
52	2	0
84	4	0
47	0	2
11	0	1
6	1634	1
56	0	5
53

chain 336363401 HG04157_chrY 45011078 + 6322440 9908581 HG002_chrY 62432599 - 52562439 56521946 2
17919	0	4
43	1	0
13799	6	0
3147	0	2
8932	0	5
8239	4	0
2294	0	1
830	0	8
22	0	4
16	0	2
4	0	2
2	6	0
7129	8	0
100	0	2
1697	5	0
2358	1	0
1	11	0
16271	0	2
20167	6	0
8902	0	1
4227	4	0
29	2	0
787	0	2
2008	0	121806
153	0	1
8010	0	1
358	0	1
2278	1	0
2431	0	1
1102	2	16
9	0	14
2894	0	121744
238	0	2
26	0	2
2556	0	18
375	1	0
4207	0	4
1794	0	5
786	0	3
1570	1	0
3885	1	0
5071	2	0
22	0	2
121	1	0
6982	0	40601
45	0	2
99	0	8
390	0	1
12616	0	20
6	0	4
7099	6	0
112	6	0
424	0	1
5940	1	0
1607	1	0
823	0	1
1899	3	0
2346	0	12
26	0	2
2556	18	0
4574	0	12
51	0	1
1744	0	5
8195	0	4
10322	2	0
96	2	0
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3794	0	1
356	0	13
471	0	1
1961	1	0
1440	1	0
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2925	1	0
144	0	20277
478	0	1
3551	0	8
110	0	2
420	0	1
3304	1	0
358	1	0
269	3	0
210	1	0
2117	1	0
1284	1	0
1925	28	2
137	1	0
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117	1	0
7092	0	2
1723	5	0
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7	13	0
471	1	0
3402	0	1
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783	0	3
1505	1	0
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26	2	0
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98	2	0
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102	0	2
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96	0	2
393	0	1
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258	3	0
2327	1	0
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106	0	2
3696	1	0
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470	1	0
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783	0	3
1505	1	0
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526	0	4
4050	8	0
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393	1	0
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840	0	4
28	2	0
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2556	18	0
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96	0	4
395	0	1
191	3	0
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3545	32	0
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13	0	81155
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112	0	8
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29434	2	0
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407	28	0
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140	3	0
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86	4	0
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18407	15	0
45	0	8
5519	2	0
12331	1	0
6524	4	0
6137	46	0
2	2	0
8	22	0
6271	0	1
2652	0	1
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7511	0	1
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9811	0	1
3281	0	1
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13643	0	1
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1043	2	0
35768	4	0
69986	0	1
31747	0	8
6597	0	10
4382	0	1
1702	8	0
56	12	0
15	4	0
2681	0	4
50558	0	6
20876	5	0
7525	0	1
27569	2	0
40940	1	0
16019	4	0
22494	22	0
13783	1	0
35463	0	1
8650	2	0
12628	0	1
314	0	50
746	300	0
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22589	2	0
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4275	0	1
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4055	1	0
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19478	1	0
1215	0	1
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18	2	0
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14	21	0
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36147	0	1
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12	2	0
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4053	1	0
2218	4	0
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17516	1	0
59618	2	0
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1159	0	10004
4048	11	15
52	4	0
12214	0	9
2308	0	3
5864	0	27
113	0	2
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27	0	3
252	29	0
41	29	0
55	0	2
4713	0	1
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5732	4	0
17684	1602	0
322	0	1
2755	2	0
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3328	32	0
59	2	0
43	0	2
26	0	6
2	2	0
172	8	0
176	0	1
364	0	1
1701	0	1
999	0	2
687	4	0
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306	1	0
1673	0	2
2334	0	1
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32	1	3
886	0	2
320	0	1
375	2	0
2675	20326	0
8061	0	1
285	20	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 190525291 HG04157_chrY 45011078 + 23692537 25741196 HG002_chrY 62432599 - 37108802 39148525 3
21517	1	0
6703	1	0
8081	0	1
1720	2	0
1114	0	520
70	0	3
4109	0	6
1105	0	1
29646	1	0
900	0	1
10420	1	0
1195	0	1
8680	0	1
1442	0	3
3786	0	7
21475	0	2
12072	0	2
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7920	0	1
3298	0	1
2098	1	0
15793	1	0
3514	1	0
19336	0	4
25	4	0
13928	0	1
31793	0	8
22505	0	12
1904	0	2
7884	2	0
16581	1	0
10182	0	2
4371	4	0
4	4	0
15	2	0
427	0	2
54	2	0
3377	0	1
11352	2	0
41	6	0
13927	0	1
327	1	0
157	0	1
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18117	0	1
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10190	1	0
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195	0	1
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667	2	0
19640	16	0
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309	0	8
1	2	0
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270	0	1
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4	0	4
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4113	2	0
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2013	1	0
1219	8	0
5357	2	0
10139	0	2384
16217	5467	3090
2728	0	2
3403	10848	0
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18864	0	1
715	0	4757
158	1	0
435	14327	57
14061	0	20
1549	0	1
3817	0	8
1198	0	1
2015	3	0
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1301	3	0
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97	4	0
34	0	8
24057	1	0
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4922	6	0
3988	0	1
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9454	0	1
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610	0	2
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105	3	0
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24824	0	1
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4807	1	0
20467	0	1
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2130	10	19
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13136	0	1
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4057	1	0
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180	0	1
346	0	1
92	0	1
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215	8	0
3	0	1
31	0	4
58	4	0
146	1	0
72	0	1
1125	1	0
100	0	1
77

chain 28236196 HG04157_chrY_random0000150 299179 + 0 299171 HG002_chrY 62432599 - 39158449 39457709 4
9	0	1
282	1	0
39	0	1
145	1	0
360	0	1
12	0	1
51	1	0
68	0	2
38	0	1
593	0	1
4818	0	3
59443	2	0
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21097	0	24
626	0	52
50	11	0
326	0	28
56	0	2
28	0	2
12	2	0
80	0	56
47	0	13
26	2	0
14	11	0
13	28	0
92	0	26
116	26	0
34	26	0
27830	2	0
1300	4	0
3812	2	0
1616	15	0
13117	0	4
11242	0	2
259	4	0
25295	0	1
13275	10	0
66042	0	4
30762	0	3
5412	0	3
104	1	0
51	0	1
9	0	1
361	1	0
147	0	1
40	1	0
283

chain 19105313 HG04157_chrY_random0000167 302706 + 27 206285 HG002_chrY 62432599 + 18650814 18857009 5
510	0	2
7263	0	1
9891	0	15
14847	1	0
6780	0	2
38951	1	0
9544	8	0
56	0	8
1952	6	0
2252	1	0
9364	1	0
1995	2	0
32	4	0
2858	0	3
4076	3378	3378
2124	6	0
9919	1	0
9025	3	0
1738	1	0
645	4	0
3698	0	1
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3236	0	1
1528	8	0
1447	0	9
19	2	1
48	5	0
1691	1	0
829	0	2
9	2	0
5085	0	1
1955	25	0
6	4	0
10120	13	0
59	3	0
47	4	0
1	2	0
21263

chain 15084202 HG04157_chrY 45011078 + 43904487 44231130 HG002_chrY 62432599 + 28547125 28874456 6
2102	5	0
7055	0	5
7060	0	5
1865	1	0
1273	0	3529
38812	15	0
228	15	0
10721	17625	0
7	25	0
20197	0	3185
1	0	349
600	6598	6619
12883	0	1
3353	2419	0
16	13744	4083
7	1	0
1464	0	5
80	2	0
633	0	4
33	5	0
1201	2	0
102	1	0
437	0	2
525	0	6
1	4	0
146	0	5
29	1	0
993	0	1
274	0	1
437	2	0
5323	5	0
5252	0	5
754	0	2625
10534	7147	0
1739	7152	0
919	1	0
244	0	3568
18	0	5
28	0	5
3531	0	10
7090	0	10
10	0	5
36	0	20
1356	10	0
54	1	0
343	5	0
12	64611	103027
284	15	0
132	1	0
1478	0	15
775	10	0
357	15	0
737	0	15
323	0	1
1595	1	0
873	15	0
719	0	5
3	0	5
263	10	0
299	1	0
1064	15	0
812	0	10
191	40152	33219
1493	15	0
4125	15	0
1680

chain 8388574 HG04157_chrY_random0000167 302706 + 206285 295321 HG002_chrY 62432599 - 43579047 43668005 7
17806	2	0
1	8	0
106	13	0
10120	4	0
6	25	0
7041	2	0
2531	4	0
48	4	1
19	0	9
1447	20	0
1528	0	1
3236	1	0
13436	0	8
4464	0	1
3698	4	0
645	1	0
1738	3	0
9025	1	0
9919	6	0
2124

chain 4353970 HG04157_chrY 45011078 + 18274435 18320634 HG002_chrY 62432599 - 45214480 45260689 8
7914	0	2
5301	0	4
18646	0	4
2493	0	4
423	4	0
11418

chain 3741100 HG04157_chrY 45011078 + 20369323 20408981 HG002_chrY 62432599 - 42850342 42889998 9
8542	0	1
11422	4	0
6522	0	4
4702	1	0
5797	4	0
881	0	2
1783

chain 1190324 HG04157_chrY 45011078 + 17888304 17900949 HG002_chrY 62432599 - 45634118 45646761 10
1386	0	6
6455	1	0
3040	1	0
1050	6	0
706

chain 322611 HG04157_chrY 45011078 + 16024493 16027901 HG002_chrY 62432599 - 47507067 47510475 11
3408