##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 2261428406 HG005_chrY 58743069 + 7523 58739039 HG002_chrY 62432599 + 4406 62432577 1
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5	4	0
377	0	4
358	4	0
1015	7	0
343	0	3
26	0	4
66	0	4
277	28	0
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425	0	4
14	0	4
70	4	0
62	24	0
45	0	4
84	8	0
194	0	4
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18	0	8
29	4	0
11	4	0
100	20	0
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7	20	0
54	0	4
8	0	19
90	4	0
16	12	0
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16	0	1
6820	8	8
54	2	31
2642	0	11
1355	1	0
43	0	1
8	12	2
23	8	0
35	8	0
8	3	0
5	4	0
1192	0	4
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2753	4	0
1740	2	0
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81	0	816
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199	4	0
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20	0	4
24	0	8
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54	0	16
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46	16	0
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4	0	8
220	0	4
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40	4	0
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123	0	4
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3	1	0
176	0	4
34	4	0
52	0	4
649	2	0
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174	4	0
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1207	0	2
36	0	309
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1133	1	0
361	0	2
7	28	0
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1369	0	1
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480	1	0
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1643	7	0
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1773	0	96
60	0	96
489	0	48
7715	0	8
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3341	3	0
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32	0	3
3833	4	0
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1222	0	8
431	0	2
907	9	0
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3695	0	1
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43	0	8
56	0	4
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58	4	0
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68	0	4
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54	8	4
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4419	0	2
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9	0	2
37	0	2
2495	5	0
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3531	3	0
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37	21	0
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2556	0	8
38	0	8
1	0	3
94	0	14
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712	2	0
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292	0	4
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2132	1	0
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355	0	4
1247	1	0
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1560	0	4
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99	0	2
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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
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5712	2	0
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9	0	3
65	7	0
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2240	318	0
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865	2	0
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680	8	0
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143	0	16
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105	1	0
861	0	2
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16	26	0
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61	0	4
41	0	3
11	0	1
447	0	6
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22	1	0
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7	45	6
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3	679	0
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24	1	0
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8	3	0
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14	0	15
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30	0	2
8	2	0
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38	1	0
1	4	0
85	10	0
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58	2	0
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83	4	0
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1040	60	0
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1287	0	58
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6	1	0
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92	0	2
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75	38	152
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9	0	26
86	0	61
3	0	1
8	0	168
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164	171	181
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2341	1	0
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5	0	3
8	0	5
8	0	8
182	0	62
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8	27	0
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213	41	0
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367	29	0
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63	37	0
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1334	0	5
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967	30	0
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322	0	1
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4	0	2
159	1	0
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330	0	4
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1044	0	4
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7	12	0
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1	10	0
1262	179	0
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4640	0	4
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32	19	22
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6	26	5
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2	388	0
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8	7359	0
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7978	2	0
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7416	0	2
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160	1	0
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170	0	4
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111	3	0
28	0	3
532	18	0
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21	2	0
2319	0	4
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1889	0	1
17357	2	0
197	0	69
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37	0	16
6407	1	0
627	0	2
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640	2	0
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374	1	0
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2093	3	0
15	1	0
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288	4	0
93	0	4
25272	30	0
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16	0	4
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7722	1	0
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161	4	0
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4972	0	1
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6630	26	0
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45	2	0
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41	2	0
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2	0	20
1676	0	8
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114	8	0
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62	4	0
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782	12	0
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84	4	0
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158	8	0
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13	0	2
1276	4	0
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1	0	3
1280	2	0
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67	0	2
7	0	14
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38	18	0
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17	0	8
1086	2	0
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691	0	4
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684	2	0
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75	16	0
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37	0	2
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25	4	0
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3	7	0
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46	4	0
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4064	3381	3381
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3	6	0
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660	39676	39663
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59	0	13
118	0	3
55	4	0
161	1	0
38	10	0
10	0	68
7	0	4
12	0	2
98	1	0
43	0	11
3	16	0
63	4	0
249	0	1
53	0	4
20	0	60
130	0	2
8	1	0
295	1	0
188	0	2
295	0	4
72	0	22
46	0	4
93	0	1
253	0	4
38	1	0
27	0	3
12	107	0
26	0	6
32	0	2
91	4	0
27	3	0
176	3	0
53	1	0
26	0	4
60	0	5
57	0	6
103	0	1
105	0	1
17	2	0
92	0	1
51	1	0
310	12	0
138	1	0
109	0	1
86	0	6
267	0	3
73	0	1
550	0	4
46	6	0
609	1	0
46	1	0
146	1	0
18	1	0
44	4	0
71	1	0
73	0	4
577	0	2
141	0	1
240	1	0
15	0	1
148	0	2
211	1	0
25	3	0
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76	0	1
104	11	0
116	0	4
3	3	0
139	0	1
109	0	1
116	0	1
188	0	5
213	1	0
192	0	1
37	0	1
10	0	1
37	0	1
50	1	0
5	0	2
178	0	3
120	2	0
98	0	1
251	2	0
28	0	1
57	1	0
23	466	6295
120	0	1
262	0	1
214	0	4
221	0	1
130	4	0
213	4	0
43	1	0
105	0	1
2	2	0
29	0	1
15	0	2
96	1	0
127	1056	0
244	0	1
60	0	7
439	0	1
41	1	0
235	11	0
7	0	1
690	0	1
254	0	1
16	36	0
97	1	0
234	0	2
27	0	1
33	4	0
1	0	5
121	2	0
25	1	0
73	0	1
50	4600	2764
121	12	0
77	12	0
117	4	0
176	0	1
95	8	0
91	0	3
210	6	0
2	0	8
75	0	8
117	0	15
117	1	0
31	0	3
197	0	1
107	75531	109875
386	0	3
114	0	2
53	32	0
4	0	28
67	0	1
218	0	7
25	2	0
72	0	2
50	0	3
53	1	0
28	9	0
20	5	0
3	7	0
69	1	0
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104	14	0
315	1	0
48	0	2
5	0	1
9	12	0
72	0	1
131	0	2
61	0	6
22	0	2
5	0	152
200	0	1
40	1	0
288	4	0
158	1	0
5	3	0
69	0	1
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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
18068	1	0
33911	2	0
6691	0	3
322	0	1
5126	0	4
12445	0	4
25	0	4
35	4	0
32	0	24
10930	0	2
391	1	0
141	0	1
847	12	0
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6735	0	2
5079	1	0
20069	1	0
909	10	19
2130	0	3
26959	0	1
43268	1	0
30305	4	0
2374	1	0
1105	4	0
4103	1	0
2688	1	0
625	3	0
105	0	1
2513	2	0
5558	1	0
4091	0	4
8	0	1
28073	0	1
19208	0	1
6338	4	0
4655	6	0
18592	0	2
1619	0	2
9268	0	1
14253	0	1
10505	0	1
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1723	0	1
3988	6	0
4922	0	2
8362	0	1
5305	0	2
699	0	1
30746	0	2
31104	0	1
21349	0	1
3324	0	1
48831	0	8
15168	1	0
5846	11	0
9947	0	8
9979	1	0
5547	18	0
54719	0	14
6892	2	0
18	2	0
3216	1	0
24045	2	20
34	4	0
97	8	0
4	4	0
53	4	0
35	8	0
3330	0	4
17088	1	0
29067	2	0
913	1	0
4876	0	2
9284	3	0
2851	0	1
3200	3	0
8609	1	0
8026	20342	6035
650	0	4757
715	1	0
2089	0	4780
5082	0	1
11296	1	0
1567	0	2
4890	10849	0
15609	2138	2138
94	1	0
24785	15351	10839
399	1	0
56	0	8
45	1	0
27	0	1
218	0	6
31	0	1
570	6	0
145	1	0
18	0	7
4	7	0
499	2	0
680	0	1
67	0	3
123	0	1
9	0	1
4	0	4
207	0	6
429	0	1
182	3	4768
97	1	0
41	1	0
18	1	0
501	2	0
210	1	0
549	1	0
55	0	8
40	1	0
32	0	1
215	0	6
35	0	1
270	10085	298
366	0	2384
7690	1	0
5357	8	0
1219	1	0
2013	1	0
6069	0	3
9285	0	8
4110	0	12
742	1	0
935	0	2
6158	1	0
3442	0	4
8289	0	1
11156	1	0
13683	1	0
3366	0	4
3388	4	8
49	4	0
43	0	12
8	4	0
193	8	0
23918	1	0
3264	2	0
6877	0	3
3274	1	0
2158	1	0
49302	18	0
5547	1	0
9946	8	0
20	1	0
1396	1	0
14990	2	0
3252	4	0
128	1	0
11170	0	8
48849	1	0
12538	1	0
5960	0	1
74032	0	1
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4903	12	0
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4301	12	0
23123	0	1
7616	1	0
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46	2	0
22279	0	4
220	0	4
7159	0	1
7662	5	0
8276	0	2
14298	4	0
3368	2	0
2120	1	0
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7272	0	1
13257	1	0
262	1	0
8259	0	2
898	0	4
8199	1	0
3923	0	1
4022	5	0
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4842	0	1
407	0	1
19205	0	2
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2133	0	1
309	1	0
25190	1	0
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2641	1	0
4706	0	3
2634	9	0
5200	2	0
1	0	8
1868	1	0
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5115	0	1
4882	0	9
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55	3	0
6	0	15
6	9	0
2761	2	0
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71	12	0
17292	1	0
12849	0	1
1827	4	0
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14178	0	1
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15327	0	12
1063	1	0
10318	0	1
3377	0	6
5979	0	5
9329	0	3
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6867	1	0
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1859	0	4
26	0	4
14698	1	0
7830	0	8
34377	1	0
4800	1	0
189	0	2
2368	3	0
3986	4	0
25	8	0
40745	0	7
11213	0	1
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12072	0	2
3361	0	1
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3486	0	2
7540	0	1
8080	0	1
32131	1	0
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23267	1	0
11258	0	2
6677	1	0
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1854	1	0
3770	1	0
10294	4	0
35694	1	0
20908	1	0
12012	0	1
2991	2483715	3624954
1468	0	1
1196	15544	2083
687	1	0
300	0	5
7	0	10
3290	15	0
8935	15	0
1837	0	5
5335	0	10
8809	30	0
2844	15	0
9037	3521	3536
2189	0	10
349	0	15
2112	15	0
1078	5	0
7391	0	15
11712	75769	54006
7014	1	0
3524	14180	0
711	5	0
1733	5	0
33	10	0
1061	0	1
694	0	15
923	0	5
2650	5	0
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452	15	0
1800	15	0
841	1	0
435	0	5
817	7136	0
402	7135	3
1015	0	15
859	0	1
427	0	5
1237	10	0
1361	5	0
932	0	5
1274	15	0
646	0	1
671	0	5
947	5	0
1183	1	0
44	10	0
810	29335314	32358999
22	0	10
21630	2413	0
4760	1	0
7150	26129	6850
10879	0	31794
1092	0	15
5769	0	1
2804	898	4432
6901	0	1
3534	1	0
6240	0	14139
26743	25	0
3551	0	25
8935	1	0
671	0	7095
974	0	25
835	185	3705
5055	0	10
11431	15	0
164	25	0
1646	40	0
1670	0	15
236	5	0
4506	1	0
494	0	20
74	0	25
14	4049	28603
4735	0	15
7054	25	0
32766	3503	0
771	0	1
2258	0	15
2783	0	15
24	15	0
371	5	0
7014	5	0
1438	30	0
2030	15	0
389	1	0
1297	0	1
245	4	0
1566	5	0
389	1	0
1527	5	0
1591	0	14027
423	1	0
456	0	20
2570	5	0
29715	2	0
2994	5	0
37648	0	2
13119	3	0
19458	4	0
153	12	0
3333	0	1
1282	1	0
8525	1	0
1748	0	4
2763	1	0
1725	0	1
1445	1	0
7821	0	3
11089	0	1
5293	12	0
34757	0	1
214	15	0
3008	2	0
12768	3	0
21	0	36
2862	2	0
2677	0	2
4326	14	0
928	1	0
9297	1	0
12705	0	1
5770	19	0
1776	0	3
2033	0	1
3697	2	0
866	1	0
6134	0	1
109	0	1
2373	1	0
1036	1	0
43	0	1
1026	2	0
1707	1	0
3695	0	1
2723	4	0
45	0	6
11	0	3
2374	1	0
4546	0	1
401	0	1
10396	2	0
12047	2	0
3145	12	0
8900	1	0
658	32	0
3104	0	33
4018	1	0
12270	0	3
6451	0	1
343	0	2
4828	0	1
6	0	3
530	2	0
2613	1	0
1095	0	4
12695	0	1
6099	0	1
73	12	0
272	0	2
2724	2	0
4392	0	1
9625	1	0
21629	1	0
73	0	1
10647	1	0
1366	0	1
1509	2	0
347	0	3
255	3	0
11013	1	0
168	0	1
782	1	0
4759	6	0
12193	2	0
5226	1	0
5431	0	12
8012	0	58
687	6	0
106	6	0
183	6	34
7	0	157
9	0	54
6	0	1
2	0	5
6	0	1
5	0	1
17	2	32
12	0	2
4	23	0
1	1	0
19	49	4
14	68	17
21	7	0
5	0	1
17	0	2
17	1	0
2	5	0
14	108	160
40	1	0
1	4	0
5	0	2
22	51	9
14	5	84
28	21	39
39	0	1
2	0	5
12	3	0
27	3	0
57	5	170
24	3	0
15	9	0
78	5	0
33	0	1
2	0	47
12	0	1
50	104	50
57	2	0
29	4	0
36	0	6
24	0	1
1	0	37
35	4	0
70	4	0
60	0	1
6	1608	1
56	0	5
53

chain 3741539 HG005_chrY 58743069 + 19926811 19966480 HG002_chrY 62432599 - 42850342 42889998 2
8542	0	1
11422	4	0
6526	10	0
10499	2	0
881	0	2
1783

chain 428205 HG005_chrY 58743069 + 23612347 23616859 HG002_chrY 62432599 - 39338719 39343231 3
4512

chain 327277 HG005_chrY 58743069 + 19237696 19241153 HG002_chrY 62432599 - 43575590 43579047 4
3457

chain 322611 HG005_chrY 58743069 + 15306266 15309674 HG002_chrY 62432599 - 47507067 47510475 5
3408

chain 201400 HG005_chrY 58743069 + 24503935 24506057 HG002_chrY 62432599 - 38399346 38401468 6
2122

chain 2683 HG005_chrY 58743069 + 12919786 12919814 HG002_chrY 62432599 + 12511308 12511336 7
28

chain 1346 HG005_chrY 58743069 + 58740168 58740182 HG002_chrY 62432599 + 62432585 62432599 8
14