##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 2146855236 HG04115_chrY 53778708 + 52985 53770397 HG002_chrY 62432599 + 25897 62432577 1
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218	0	48
1831	2	0
303	0	1
165	0	1
873	0	4
905	1	0
1515	0	830
4	1	0
12	0	55
350	0	2
868	0	4
1692	0	52
91	104	0
73	52	0
3745	0	4
10	0	9
719	0	1
1605	0	13
938	0	1
714	0	1
621	3	0
704	0	4
10	0	4
60	398	0
28	93	0
81	951	0
93	10	0
20	176	4
53	71	0
9	26	0
321	0	6
125	6	0
76	0	2
22	2	0
192	0	4
60	0	4
1280	0	4
29	1	0
2151	0	5
302	1	0
276	0	12
36	4	0
457	4	0
77	4	0
3	20	0
103	0	4
32	4	0
14	4	0
27	8	0
540	4	0
172	0	4
2584	1	0
669	1	0
3	1	0
35	3	0
3833	4	0
23	3	0
1222	0	8
431	0	2
907	12	0
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2595	24	0
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531	0	4
316	1	0
31	1	0
7	155	0
93	0	1
328	1	0
949	1	0
125	1	0
702	0	2
8700	8	0
2859	1	0
964	0	13
247	0	8
104	2	0
4	0	7
13	0	4
23	0	4
39	0	7
15	0	11
53	1	0
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4183	2	0
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119	2	0
651	0	4
659	0	1
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3741	4	0
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43	0	8
4	4	0
29	4	0
112	4	0
71	4	0
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14	4	0
68	0	4
48	8	0
32	0	4
19	0	4
37	0	4
524	0	5
812	1	0
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2890	0	4
95	36	0
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17	0	36
575	0	6
147	0	1
657	0	4
30	15	65
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23	16	0
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14	1	0
666	4208	0
18	534	8
717	0	1
515	2	0
387	0	3
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3628	0	4
316	0	1
896	0	6
3859	1	0
1263	0	2
871	0	1
2191	4	0
1110	0	1
1082	0	259
2738	4	0
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61	1	0
30	6	16
9	0	2
2169	1	0
831	0	5
2675	3	0
1867	0	6
31	0	16
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
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2950	4	0
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366	2	0
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45	135	0
2745	1	0
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7760	0	107
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5	0	162
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37	21	0
149	6	73
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163	0	4
2560	0	4
26	0	20
37	5	0
7	0	5
30	0	10
9	5	29
707	2	0
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6478	2	0
2	0	4
143	0	3
351	0	1
273	0	1
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3917	106	0
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635	4	0
57	4	0
53	0	4
38	4	0
1899	0	4
96	12	0
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10	0	36
99	0	2
284	1	0
2	1	0
35	1	0
146	0	252
69	396	35
717	0	72
108	0	1
4	0	1
69	1	0
932	0	2
146	4	0
5712	2	0
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5584	2	0
32	2	0
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13	0	1
1	0	14
588	0	6
94	4	0
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157	0	2
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834	0	1
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1	10	0
78	0	16
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315	1	0
61	0	4
503	0	6
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11	0	1
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43	0	3
5	0	2
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11	0	2
2	0	28
7	0	3
80	0	1
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5	0	1
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19	0	2
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3	80	0
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6	0	1
7	0	1
3	0	1
7	0	1
7	0	3
19	37	79
14	0	1
563	0	3
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58	1	0
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638	1	0
1233	5	0
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188	0	4
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80	0	12
28	0	8
502	8	0
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83	4	0
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562	2	0
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37	0	2
50	0	1
94	0	5
29	5	0
234	1464	1475
580	0	4
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5	0	4
264	4	0
797	1	0
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846	0	2
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12	6	0
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202	0	1
47	0	4
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98	1	0
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3	1	0
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3	3	0
31	3	0
12	0	8
8	162	10
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2	44	0
14	1	3
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16	0	6
25	155	0
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9	277	0
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9	3	0
52	0	2
59	1	0
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5	3	3
44	0	1
64	58	0
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2	0	1
18	67	4
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7	49	13
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1	19	0
74	1	0
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12	0	1
12	0	1
6	22	10
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6	1	0
78	0	2
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36	136	8
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56	4	0
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4	0	7
19	0	1
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4	0	7
6	13	0
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3	165	0
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88	0	1
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21	166	0
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40	1	0
1	0	4
16	62	0
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9	1	0
7	25	17
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7	6	0
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17	4	0
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2	1	0
7	18	9
7	0	1
13	0	24
1	0	1
12	0	2
6	508	29
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31	105	0
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5	0	3
8	0	5
8	0	8
182	0	62
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58	45	0
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8	27	0
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213	41	0
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63	37	0
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32	4	0
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53	60	0
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1165	0	9
4	0	3
4	0	4
141	0	2
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72	0	1
27	0	2
147	0	2
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72	0	18
2788	1	0
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1285	0	4
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1247	1	0
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705	1	0
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304	0	4
6457	2	0
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1	10	0
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68	30	87
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5868	0	4
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2625	4	0
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4752	1	0
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54	292	1
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2120	3	0
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2519	1	0
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96	0	1
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14	162	357
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743	0	2
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11	4	0
123	0	8
171	4	0
17	3	0
1022	8	0
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54	0	2
66	4	0
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198	0	2
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21	0	2
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2293	0	4
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891	0	4
48	0	2
1015	4	0
78	4	0
481	4	0
33	0	8
581	0	1
731	0	1
638	1	0
1441	0	9
584	3	0
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985	0	28
503	2	0
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1742	1	0
1670	3743	0
6310	3	0
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738	1	4
539	0	296
1686	0	2
1415	4	0
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684	0	3
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1334	1	0
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2287	231	0
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131	0	4
274	0	4
14	24	1
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3	0	4
4	2	0
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732	8	0
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29	0	8
69	0	2
665	4	0
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1	8	0
229	0	4
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40	0	4
630	4	0
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14	0	2
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772	12	23
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257	0	1
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704	1	0
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47	1	0
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43	1	0
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67	7	2
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37	3	10
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26	0	1
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16	16	0
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2	177	0
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15	1	0
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8	8	73
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31	1	36
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8	1	0
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1	0	7
20	0	62
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20	13	66
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31	16	121
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1373	3	0
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199	1	0
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63	14	0
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46	0	180
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80	1	0
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1677	1	0
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7	8	33
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9	1	0
7	28	23
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67	10	27
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67	1	0
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4	0	39
69	3	0
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1922	22	0
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4	0	20265
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12	2668	104118
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285	0	1
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35	0	8
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1465	1	0
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640	1	0
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288	4	0
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22	0	2
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12	0	2
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17	0	4
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2479	3	21
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47	0	3
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64	0	8
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13	0	5
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3569	1	0
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162	12	0
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14	0	1
52	3	0
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1	7	0
88	8	0
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46	0	4
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34	0	4
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70	0	12
4072	3372	3372
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20	2	0
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644	39678	39663
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315	1	0
48	0	2
5	0	1
9	12	0
72	0	1
131	0	2
61	0	6
29	0	152
200	0	1
40	1	0
288	4	0
158	1	0
5	3	0
69	0	1
79	0	5
69	2	0
120	0	3
15	1	0
147	0	3
211	0	14
2	0	4
4	1	0
20	2	0
94	0	2
113	0	8513
27908	4	0
30762	0	2
5452	0	2
7415	1	0
2455	1	0
2546	4	0
149	0	4
30743	0	2
4976	0	2
101	1	0
20069	1	0
909	10	19
2130	0	3
26959	0	1
25121	1	0
39641	1	0
12290	0	2
4101	1	0
2688	1	0
625	3	0
105	0	1
8071	0	8
23	0	1
4059	0	4
3895	0	1
24186	0	1
19208	0	1
6338	4	0
4655	4	0
18593	0	1
1618	0	3
611	1	0
8774	0	10
33624	3	0
466	0	4
1723	0	1
3988	6	0
4922	0	4
13666	0	6
695	0	1
30746	0	4
104609	0	8
6773	0	1
24187	0	20
9967	1	0
56998	0	1
3267	0	3
6901	0	2
3234	1	0
1066	0	1
20960	1	0
1960	16	0
70	2	8
34	4	0
46	0	4
39	0	8
4	4	0
6	0	3
44	4	0
35	4	0
3330	0	4
3379	0	14
33123	8	0
3438	0	1
1925	0	6
84	16	0
1668	0	1
2516	4	0
1653	15	0
4132	0	6
195	1	0
9915	0	1
860	0	2
4363	5	0
2015	0	1
1300	1	0
3724	1	0
1558	0	11
1457	1	0
4310	0	1
2251	1	0
7	2384	0
1126	1	0
5052	0	1
506	0	4757
715	0	1
6998	0	1
4952	1	0
2002	1	0
452	1	0
10409	0	1
412	1	0
4479	10849	0
31	0	1
614	0	1
17084	28568987	37324310
71	25	0
6363	25	0
13729	12588	2913
959	6425	11256
2987	0	1
3372	2	0
79	2	0
1111	0	2
174	0	4835
10750	2	0
994	0	2
1	2	0
5	0	2
600	1	0
690	2419	0
3861	4836	4836
5659	31008	41568
2711	5	0
229	0	15
111	1	0
156	0	15
499	5	0
333	10	0
87	1	0
706	15	0
1716	1	0
640	0	15
349	0	20
919	0	5
1340	48556	172223
6886	10	0
2952	0	26846
35158	0	5
20	2071	16205
3367	1	0
3534	0	1
3534	1	0
6240	0	14139
9022	5	0
28351	25	0
1881	1	0
8740	0	25
1901	3534	0
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3370	15	0
150	25	0
18673	1	0
494	0	20
74	0	25
14	5079	1599
1328	1	0
494	0	20
66	0	40
6176	3495	0
3748	0	1
527	20	0
47	40	0
29907	20	0
28076	0	15
1129	3484	0
129	5	0
2606	0	5
3088	0	15
24	15	0
371	5	0
3493	5	0
909	0	3498
552	30	0
5528	5	0
3475	5	0
32	0	3508
1878	0	1
12109	5	0
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18741	0	2395
3769	5	0
18950	2	0
16252	0	2
2444	0	2
8382	12705	0
24195	0	4
149	0	4
3329	0	1
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26	1	0
5880	0	2
2765	1	0
10992	0	3
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48301	0	10
2433	3	0
21	0	36
2862	4	0
2677	6	0
4328	12	0
928	1	0
6743	0	4
2378	1	0
172	1	0
18476	19	0
1776	0	3
1309	1	0
724	0	1
1972	4	0
1725	5	0
866	1	0
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109	0	1
3452	0	1
1026	2	0
5402	0	1
2723	1	0
45	0	9
8	0	3
1978	0	1
5343	0	1
8059	0	1
2336	4	0
7219	1	0
3909	0	4
915	0	1
3144	30	0
8900	1	0
26537	0	1
48984	0	3
48597	1	0
3356	0	3
14	2	0
6284	1	0
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106	0	2
160	0	4
24	0	4
68	0	4
6	2	0
37	0	4
134	2	0
4888	0	1
1543	4	0
475	0	2
3646	0	6
5	0	6
77	19	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	2
160	47	0
31	74	0
27	58	0
715	42	0
30	6	0
38	0	7
20	1	0
40	9	10
28	0	8
30	0	5
9	13	0
27	24	0
1	0	1
6	1	0
24	0	7
20	0	1
1	0	5
23	1	12
6	1	0
13	0	1
8	8	26
30	0	2
9	0	1
15	2	0
3	0	1
10	4	1
11	0	2
17	0	4
15	0	1
18	2	0
4	1	0
38	0	5
12	0	1
7	7	6
15	1	0
20	0	1
12	203	82
23	0	1
18	26	3
17	35	19
9	1	0
1	5	0
12	1	0
5	1	0
17	2	14
13	0	5
6	8	0
6	1	0
13	4	0
7	29	17
43	8	0
10	125	2
27	65	9
21	27	35
6	6	0
26	0	4
6	5	0
46	1	0
1	20	0
15	3	0
22	0	1
41	3	0
13	0	1
13	3	0
51	8	1
5	3	0
21	3	0
21	2	0
8	0	5
7	0	11
7	17	0
2	0	2
4	1	0
5	3	0
9	25	1
27	0	3
14	0	4
43	3	0
15	5	0
22	0	4
52	5	0
33	0	1
53	1	0
8	0	1
50	108	35
10	0	5
57	2	0
4	1	0
25	4	0
42	2	0
6	1	0
26	4	0
66	4	0
70	4	0
17	0	5
38	0	1
7	1658	0
56	0	5
53

chain 10913755 HG04115_chrY 53778708 + 24292322 24429347 HG002_chrY 62432599 - 38401468 38539790 2
63	0	1
35	0	1
15477	0	1
23	0	10850
4459	1	0
2454	1	0
4938	0	1
13	0	1
6999	1	0
715	0	4757
650	20341	6035
7	1	0
2251	0	1
4310	1	0
1457	0	10
1559	1	0
3724	1	0
967	1	0
2349	4	0
3200	0	1
2024	0	1
9915	1	0
4333	15	0
740	0	1
912	2	0
2516	0	1
1668	15	0
84	0	6
1925	0	1
3430	0	8
754	0	1
32368	0	6
224	1	0
95

chain 4800894 HG04115_chrY_random0001211 148016 + 9924 125627 HG002_chrY 62432599 - 33305182 33403118 3
13729	0	15
354	5	0
8510	3685	10787
39	0	15
1966	0	5
18	0	5
105	0	1
1932	3554	0
40	0	3013
1	20880	10755
6421	1	0
9647	1602	0
1	29150	20099
1239	5	0
4329	1	0
684	3544	0
8	15	0
652	0	10
270	0	5
1066	15	5
9	10	0
912	5	0
1267	10	0
22

chain 3988312 HG04115_chrY_random0001149 58768 + 2138 45070 HG002_chrY 62432599 + 29138267 29198836 4
6122	0	5
7084	5	0
1	10	0
241	0	15
2208	0	7070
379	15	0
457	0	15
219	15	0
494	14	0
754	0	20
13	10	0
5	0	15
10	0	10581
1129	15	0
23732

chain 3742489 HG04115_chrY 53778708 + 19566642 19606313 HG002_chrY 62432599 - 42850342 42889998 5
15515	1	0
4450	4	0
6526	8	0
10499	2	0
2666

chain 3638990 HG04115_chrY_random0001150 54943 + 707 39944 HG002_chrY 62432599 + 29141962 29198836 6
2427	0	5
7084	5	0
1	10	0
241	0	15
2208	0	7070
379	15	0
457	0	15
219	15	0
494	14	0
754	0	20
13	10	0
5	0	15
10	0	10581
1129	15	0
23732

chain 3431641 HG04115_chrY_random0001133 71433 + 548 50782 HG002_chrY 62432599 + 28656321 28701953 7
10654	2419	0
16	10669	4081
2	0	1760
15201	0	5
754	0	2625
279	0	15
10240

chain 2744179 HG04115_chrY_random0001067 46679 + 1867 43437 HG002_chrY 62432599 + 29113027 29144019 8
292	5	0
16	0	1
337	0	15
147	0	1
13581	11955	1377
10	15	0
69	1	0
1132	1	0
300	0	5
7	0	10
13	0	5
505	0	14
2753	15	0
4256	14	0
6146

chain 1945963 HG04115_chrY_random0001070 34130 + 13299 34128 HG002_chrY 62432599 + 29128794 29149616 9
10	15	0
69	1	0
1132	1	0
300	0	5
7	0	10
13	0	5
505	0	14
2753	15	0
4256	14	0
6516	0	5
5222

chain 1727732 HG04115_chrY_random0001157 72006 + 3184 72006 HG002_chrY 62432599 - 33193407 33235653 10
8430	1	0
1027	0	1
8454	49019	22444
1294	1	0
596

chain 427764 HG04115_chrY 53778708 + 23405800 23410311 HG002_chrY 62432599 - 39338719 39343231 11
2490	0	1
2021

chain 327146 HG04115_chrY 53778708 + 18877550 18881007 HG002_chrY 62432599 - 43575590 43579047 12
3457

chain 322611 HG04115_chrY 53778708 + 14945789 14949197 HG002_chrY 62432599 - 47507067 47510475 13
3408

chain 6804 HG04115_chrY 53778708 + 24437486 24437646 HG002_chrY 62432599 - 38539790 38542814 14
2	0	2864
158

chain 2683 HG04115_chrY 53778708 + 12559430 12559458 HG002_chrY 62432599 + 12511308 12511336 15
28