##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 2160555278 NA18879_chrY 49516307 + 3 49512541 HG002_chrY 62432599 + 5 62432577 1
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125	0	4
30	0	4
69	0	12
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56	0	3
27	0	16
147	20	0
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63	0	4
232	0	20
165	4	0
181	4	0
69	0	18
16	0	12
1437	1	0
518	3	0
167	5	0
659	2	0
84	0	8
1328	1	0
606	6	3
305	0	1
1520	2	0
323	4	0
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1081	0	2
9	0	1
241	0	135
211	10	0
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37	0	1
1540	0	1
613	2	0
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7	2	0
513	1	0
1121	4	0
801	0	2
540	0	38
43	8	0
31	8	0
77	113	43
1331	0	1
2076	0	2
2814	8	0
46	5	0
173	0	2
539	0	10
2629	0	3
4162	4	0
5022	0	9
1537	6	0
58	52	0
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749	0	3
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1510	16	0
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300	0	1
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77	0	21
9	0	2
55	21	0
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69	29	0
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79	29	0
58	0	8
8	4	0
106	132	3
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2	4	0
18	4	0
669	0	1
341	0	4
1292	2	0
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14	0	5
1040	0	95
882	1	0
284	9	0
863	0	1
2752	1	0
4	9	0
559	3	0
779	1	0
345	170	0
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909	4	0
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392	1	0
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334	0	1
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441	0	1
58	0	1
866	3	15
54	0	8
17	0	27
7	40	0
2496	5	0
3139	1	0
892	0	6
369	829	0
979	0	389
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68	1	0
3515	133	0
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56	10	0
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15	2	0
7	0	4
157	0	5
1137	1	0
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798	4	0
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686	1	0
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4	0	4
51	3	0
8	169	8
63	4	0
1317	308	0
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87	4	0
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9	8	47
32	17	0
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5924	49	0
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550	0	1
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2418	20	110
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8	2	58
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10	29	0
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1374	1	0
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1302	0	2
933	0	370
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1643	7	0
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1831	1	0
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91	104	0
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10	0	9
719	0	1
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60	0	4
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27	0	3
64	1	0
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3127	0	10
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28	2	0
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7	155	0
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1572	1	0
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39	0	7
15	0	11
53	1	0
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60	3	0
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43	0	8
4	4	0
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68	0	4
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19	0	4
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13	12	0
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27	1	0
552	0	2
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982	0	2
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292	0	4
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35	1	0
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2120	3	0
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389	0	1
1365	0	1
2695	1	0
2429	0	2
691	1	0
1899	0	4
1940	0	152
1528	3	0
10	9	20
11	14	0
3889	1	0
419	2	0
27	4	0
856	1	0
640	2	0
860	1	0
4289	0	1
1685	0	2
3039	4	0
16	4	0
81	0	4
66	12	0
213	0	4
294	4	0
28	0	8
47	50	30
16	8	0
21	20	0
148	4	0
2564	0	1
298	9	0
396	0	1
1176	40	0
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69	5	0
13	4	0
21	72	7
9	0	15
13	16	0
4	5	0
35	13	0
11	3	0
6	7	0
30	26	0
13	0	5
9	0	10
26	3	0
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18	3	0
2	1	0
22	3	0
5	18	0
3	9	0
5	9	0
8	35	0
93	4	0
10	5	0
9	46	0
63	8	3
97	0	16
1047	0	1
74	3	0
278	1	0
1820	1	0
319	0	1
2592	1	0
920	0	5
1134	0	8
1319	0	12
176	4	0
17	4	0
67	0	4
76	0	4
146	4	0
1264	0	4
250	0	4
18	4	0
3722	12	0
52	0	4
2738	3	0
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22	8	0
3032	0	1
299	0	2
1167	1	0
600	0	5
814	1	0
631	0	1
1655	0	1
277	4	0
781	0	5
211	10	0
576	1	0
314	2	0
2456	1	0
293	2	0
2	8	0
1179	0	2
9	0	2
971	0	1
795	0	1
187	4	0
9	0	4
434	4	0
40	4	0
907	0	5
161	1	0
7	3	0
2671	0	1
604	0	1
816	4	0
1051	4	0
1765	1	0
155	1	0
571	0	4
219	28	0
5	8	0
1569	1	0
72	0	12
118	2	0
312	1	0
4	11	0
499	0	3
1905	1	0
47	0	1
170	1	0
767	0	69
113	0	5
1378	4	0
989	0	3
1349	0	1
1519	2	0
1254	0	2
366	1	0
3413	4	0
197	0	4
186	0	8
4136	0	337
287	4	0
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512	4	0
636	2	0
907	1	0
232	0	10
18	0	5
216	0	1
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66	0	10
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53	0	1
99	0	1
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58	1	0
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73	0	15
34	0	20
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6031	0	21
968	0	2
271	47	0
48	47	0
6856	374	0
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1053	0	2
74	0	2
30	9	0
9	1	0
784	0	1
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896	0	35
63	10	771
69	28	0
1718	0	1
658	0	4
182	4	0
6267	1	0
209	0	1
571	1	0
2820	0	1
1489	0	124
127	62	0
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437	0	4
5	0	22
403	0	2
280	1	0
587	0	1
829	15	0
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252	2	0
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1782	1	0
63	2	0
345	0	1
62	165	0
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897	0	1
1516	1	0
298	4	0
2635	8	0
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163	1	0
448	0	1
944	133	0
13	0	266
878	0	1
135	1	0
13	1	0
1510	0	9
933	0	1
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3057	2	0
2747	5	0
388	2	0
4	0	6
22	1	30
5	4	0
1854	1	0
1136	0	1
2653	0	18
259	0	296
1546	0	1
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21	0	2
3040	4	0
98	1	0
503	0	2
141	2	0
1062	0	1
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298	0	1
1163	1	0
1793	12	0
2	36	0
53	18	0
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2	10	0
6	8	0
2	2	0
16	0	2
35	0	2
13	78	0
21	1	0
1	9	0
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46	4	0
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15	3	0
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10	10	0
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6	8	0
6	2	0
8	3	0
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15	0	1
32	8	6
7	26	0
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10	4	0
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30	16	8
17	0	1
18	0	1
7	0	2
34	3	0
1	1	0
18	2	0
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1	51	0
9	6	0
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24	0	2
5	0	1
7	0	2
28	2	0
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28	2	0
8	4	0
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11	0	1
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16	2	0
14	0	1
1	2	0
44	1	0
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34	5	0
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1	9	0
57	0	1
50	0	2
2	16	0
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33	0	5
1	0	16
6	55	0
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2	5	0
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10	0	6
10	0	6
9	0	1
1	3	0
47	4	0
3	0	8
22	24	0
40	2	0
2	12	0
36	4	0
29	18	16
36	20	0
10	269	0
48	0	2
64	12	0
1529	0	2
3421	4	0
303	0	2
1972	0	1
5	0	6
1145	11	0
186	0	4
1928	1	0
572	1	0
328	0	2
2183	0	2
2303	255	0
21	501	0
2096	1	0
8006	0	22
745	4	0
614	1	0
448	0	2
329	0	2
91	3	0
168	0	20
446	0	4
3968	0	4
2082	0	2
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143	0	3
99	0	4
43	0	4
128	4	0
79	4	0
912	0	4
257	0	4
2468	0	1
508	0	6
2997	0	2
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11	15	0
861	2	0
1089	1	0
1837	0	1
54	0	3
34	0	4
105	60	0
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5	0	1
35	0	18
3	0	1
9	0	97
9	2	0
4	0	5
1	0	7
3	1	0
20	2	0
419	0	9
4	35	0
158	0	32
128	0	74
6	0	6
1418	0	6
9	13	14
723	0	1
550	1	0
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3775	1	0
157	0	1
2568	0	12
3918	0	30
2951	0	1
872	0	5
584	0	45
487	0	1
1142	0	4
1736	0	1
287	0	1
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626	0	1
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523	0	1
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22	0	4
4405	3	0
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880	1	0
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13	4	0
222	0	2
743	0	2
439	1	0
2550	0	4
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154	28	0
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302	8	0
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1665	14	0
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102	4	0
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23	0	2
210	0	12
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148	0	2
1015	4	0
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39	4	0
542	0	1
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187	0	1
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149	1	0
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1915	3	0
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6	0	3
4	0	3
39	3	0
84	0	3
4978	275	682
630	0	62
5	0	1
285	58	0
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169	0	2
1546	3	0
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795	0	2
306	0	1
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1267	0	1
1	0	1
540	0	296
1671	1	0
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1415	4	0
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684	5	0
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4740	0	3
1064	1	0
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691	0	1
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341	8	0
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1536	67	44
852	3	0
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979	0	1
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1594	1	0
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1232	3	0
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264	2	0
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568	1	0
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145	0	4
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296	0	4
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1231	1	0
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623	0	1
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772	12	23
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9	19	48
546	1	0
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7	25	6
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15	1	0
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17	1	0
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76	0	5
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3108	3	0
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1536	0	1
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44	0	87
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39454	0	1
3932	1	0
1432	0	5
286	5	0
2966	5	0
44	0	5
2200	0	20
526	5	0
235	15	0
93	0	15
87	0	10
305	0	5
222	0	15
373	15	0
878	0	5
459	5	0
160	5	0
85	5	0
86	0	10
941	5	0
513	0	5
373	5	0
266	0	5
451	5	0
792	0	5
246	5	0
13	5	0
20989	0	1
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36854	0	2
30	0	2
17	0	1
12538	0	1
5524	0	1
16929	0	12
392	8	0
2984	1	0
1510	1	0
4954	0	1
158	1	0
4441	1	0
32529	0	5
3165	0	10
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265	0	5
1504	0	5
8798	0	5
1630	20	0
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5589	0	5
572	5	0
3173	5	0
1863	5	0
566	0	5
5030	5	0
572	10	0
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1656	0	5
3954	5	0
572	0	10
5035	0	5
572	15	0
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1623	0	5
4531	5	0
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5598	0	5
10198	0	5
12	0	5
6182	0	5
25	10	0
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530	10	0
574	10	0
5618	5	0
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497	5	0
957	5	0
152	0	1
335	3	0
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301	0	1
354	0	12421
1436	0	5591
2506	0	5
3766	0	10
3018	1	0
1042	0	11091
2638	5	0
588	0	5
2273	1378	0
81	15	0
906	0	1378
10	0	1842
3	0	5
8	7359	0
121	24632	12166
995	0	5
1769	5	0
1335	10	0
5548	0	5
2444	0	5
21	11431	15545
1	2602	0
10	5	0
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595	0	1
381	5	0
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312	0	1
908	0	5
1833	1	0
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874	30	0
1963	181916	165622
20257	0	15
3533	0	1373
231	0	5
699	0	1377
263	40866	20093
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565	10	0
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33	5531	0
1440	1	0
467	0	10
3376	0	5
264	0	5
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54	5581	0
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1880	0	10
5566	5	0
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700	0	1
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499	20	0
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5541	0	15
156	1	0
1065	0	15
1473	11095	0
693	31146	8892
3259	0	3
289	10	0
234	0	20
566	25	0
3054	0	5
73	0	5
1593	10	0
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549	0	25
5175	5574	0
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5531	0	5
5010	3	0
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62	5	0
2110	7671	0
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1290	7658	0
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2710	0	5
6736	10	0
809	5	0
4825	0	20
1890	0	5
263	7531	0
18	20	0
526	0	5
748	0	1
4070	0	30
2650	15	0
775	1	0
2786	5	0
3159	5	0
1575	1	0
1951	5	0
3980	10	0
793	20	0
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8	10	0
305	0	369
215	0	10
1373	0	10
731	0	5
510	25	0
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280	0	20
495	10	0
2749	0	10
838	5	0
3917	5	0
4533	0	5
720	7491	0
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1999	10967	3245
339	0	20
29	19100	0
397	0	15
1145	0	15
234	0	15
69	0	15
3081	10	0
2018	0	5
1788	10	0
3770	35	0
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3862	0	20
1747	15	0
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51	0	3816
3815	0	5
3803	0	10
1751	5	0
675	0	15
1349	5	0
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579	5	0
1427	10	0
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1770	0	5
679	0	15
84	0	15
1217	0	10
29	0	2423
33	0	5
1751	5	0
29	0	1
608	15	0
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1263	10	0
39	5	0
1759	10	0
658	15	0
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61	0	25
1243	0	5
1808	0	5
780	5	0
1302	0	10
9348	0	10
5721	0	5
1846	0	5
796	10	0
1216	1	0
380	1	3696
12	0	15
6	0	55
1434	10	0
775	20	0
608	10	0
640	0	3851
6319	0	5
4446	0	5
3336	4	0
4449	5	0
2747	0	15
195	10	0
7047	0	10
1242	5	0
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3472	5	0
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2161	5	0
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5415	5	0
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1752	0	5
5825	0	5
853	10	0
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57	10	0
188	0	5
50	0	5
2473	5	0
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4604	5	0
955	10	0
807	5	0
376	1	0
2094	0	5
2888	0	20
1281	5	0
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3071	5	0
43	5	0
1470	5	0
4126	0	5
329	10	0
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1835	25	0
81	5	0
760	20	0
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25	55	0
1519	5	0
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1741	5	0
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6034	0	5
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1533	0	5
479	0	5
428	10	0
569	0	1
172	0	5
53	0	5
610	5	0
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2223	1	0
6054	5	0
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298	1	0
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25	8	0
8573	0	4
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696	6	0
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2847	0	6
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6622	1	0
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949	0	20
3703	1	0
1031	0	12
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5531	0	2
782	2	0
5557	1	0
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6437	4	0
1902	8	0
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968	0	12
926	4	0
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12899	1	0
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7520	0	1
8796	4	0
2017	0	1
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122	4	0
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6367	20	0
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1063	0	1
5638	1	0
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5194	1	0
1394	0	1
32033	0	1
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9141	4	0
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6638	13	0
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1	1	0
6799	0	4
14627	0	1
4860	4	0
1363	0	1
45633	11	0
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28	0	4
1061	0	4
1451	4	0
49	4	0
67	8	0
996	1	0
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39833	1	0
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2909	6	0
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402	0	451
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2927	0	2
26	1	0
37881	0	1
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31321	1	0
1768	4	0
2603	0	4
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7633	1	0
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13616	1	0
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185	0	1
5817	2	0
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684	0	2
468	1	0
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151	1	0
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118	0	1
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253	2	0
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161	1542	0
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3482	1	0
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2265	0	1
5484	0	10
8557	0	5
18521	0	1
8558	0	3
40	2	0
7480	1	0
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4647	1	0
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682	2	0
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156	2	0
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5559	4	0
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8794	1	0
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339	0	1
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18	2	0
21238	0	2
623	0	8
34478	1	0
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3058	0	12
46467	0	8
55	8	0
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33619	6	0
5933	0	1
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4787	0	1
399	0	16
314	9	0
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5583	4	0
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486	20	0
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2882	8	0
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5	0	20
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351	2	0
3965	0	3
1384	4	0
49	4	0
11530	3411	3411
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2195	1	0
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355	0	2
5555	0	5
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561	0	1
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3591	4	0
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5831	1	0
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1475	5	0
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11014	1	0
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18363	0	1
4313	3	0
677	21	0
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11953	2	0
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10529	8	0
6828	2	0
21	2	0
2	19	0
21	23	0
153	0	69
1225	1	0
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37	0	14
5839	0	8
1189	0	2
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640	2	0
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15	1	0
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3473	0	1
5504	2	0
4897	0	1
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5591	0	1
292	0	2
13330	1	0
2445	28	0
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66	2	0
3714	0	2
4972	0	1
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6627	1	0
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938	1	0
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2000	3	0
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10125	0	2
26	0	1
16	2	0
6	14	0
5336	0	6
4230	1	0
4069	0	1
8914	7	0
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5597	0	4
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2784	0	4
114	8	0
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1690	0	8
843	1	0
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3678	2	0
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771	0	5
1734	0	4
786	12	0
2970	1	0
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238	4	0
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283	0	4
5756	5	0
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47	0	1
4	12	0
2	4	0
2166	4	0
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4401	0	41
474	4	0
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610	8	0
4980	1	0
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1351	2	0
58	2	0
1699	1	0
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7835	1	0
8887	1	0
3949	4	0
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24617	2	0
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151	1	0
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328	12	0
67	0	8
7905	1	0
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6723	0	1
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5169	0	1
4536	1	0
280	0	1
2976	0	1
41162	2	0
32	4	0
3757	0	1
18	1	0
587	12642	12645
580	0	1
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17	0	1
3712	2	0
42	7	0
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23191	0	1
3691	0	1
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7	0	2
2283	0	1
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1992	1	0
3227	2	0
2	24	0
7077	8	0
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6440	35	0
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534	2	0
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52	8	0
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3088	2	0
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1539	46208	46210
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135	0	4
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3074	0	1
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37111	1	0
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11	7	0
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35364	8378	266748
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15459	1	0
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6230	3	0
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6	5	3
10	2	0
28	0	1
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4754	30	0
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3480	23	0
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54	0	3
20	4	0
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229	2	0
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24	0	2
3742	1	0
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86	1	0
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27	21	0
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2794	22	0
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3632	1	0
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551	1	0
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588	9	0
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5	20	0
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3925	326	0
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686	0	1
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154	5224	0
293	0	1
66	1	0
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133	38299	83458
498	0	2
78	0	1
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3	0	3
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15791	11569	1077
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157	20410	12410
3219	2	2126
41	125	0
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24	19	1
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6	0	6
26	12	0
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483	10	0
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11662	1	0
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364	0	2
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2596	1	0
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323	0	2
4637	1	0
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25	0	4
11215	0	4
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1586	3	0
3838	0	4
1289	0	17
7	0	1
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19	3	55
13	11	0
25	0	2
13	2	0
13	0	2
13	2	0
8	0	15
18	0	2
167	0	2
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20763	1	0
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23	0	6
9870	1	0
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64	8	0
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391	1	0
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847	11	0
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2264	1	0
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288	0	3
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4101	1	0
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105	0	1
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3	10	0
464	0	4
16541	1	0
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6813	1	0
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611	3	0
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3833	0	1
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1723	0	1
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37	0	2
4867	0	4
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5	4	0
9987	1	0
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7	2384	0
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4812	15370	3437
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13431	24534542	37493860
2304	15	0
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1676	1	0
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14	5079	1599
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828	6988	0
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3459	7012	0
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172	1	0
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1776	0	3
2033	0	1
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866	1	0
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45	0	6
11	0	3
2374	1	0
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915	2	0
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658	16	0
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13897	4	0
8845	0	1
31465	1	0
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4751	0	1
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334	4	0
258	4	0
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615	1	0
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15	2	0
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713	0	1
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240	0	4
807	0	3
4169	0	1
1543	2	0
475	0	2
3526	0	6
41	0	6
36	6	0
125	38	0
1489	1251	0
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4424	0	6
120	1	0
466	2	0
162	47	0
58	29	0
715	41	225
28	0	1
30	0	7
12	36	122
12	0	1
17	0	1
22	4	1
11	0	2
15	0	6
15	0	4
22	0	5
7	0	5
18	0	5
6	0	1
19	1	0
23	0	1
6	0	6
14	18	0
6	44	23
13	55	17
28	17	0
2	0	2
12	0	1
18	24	3
15	36	3
14	17	13
92	4	0
7	0	2
6	18	21
7	7	0
34	86	2
11	1	0
16	35	0
1	0	5
24	5	0
23	0	12
6	6	0
24	47	59
15	3	0
10	57	54
10	0	21
36	24	17
21	3	0
10	0	50
1	0	2
9	3	0
37	0	3
15	3	28
18	3	0
15	9	0
22	106	252
21	0	1
35	2	0
29	4	0
36	0	6
16	0	51
29	0	1
1	4	0
12	0	1
2	0	1
11	0	7
34	401	70
56	0	5
53

chain 13578655 NA18879_chrY_random0000089 290567 + 1 147579 HG002_chrY 62432599 + 18706043 18853552 2
23033	1	0
9544	8	0
52	0	12
4204	1	0
11359	2	0
2760	6	0
130	0	9
766	1	0
165	0	1
357	0	1
17	0	1
2767	3372	3372
2125	6	0
3625	0	1
6293	1	0
9025	3	0
2383	2	0
21606	0	1
2318	0	2
2445	16	0
1464	0	1
10	2	1
2568	0	2
9	6	0
7041	25	0
6	4	0
10120	13	0
54	0	1
4	3	0
48	2	0
17806

chain 13145558 NA18879_chrY_random0000089 290567 + 147580 290567 HG002_chrY 62432599 - 43575591 43718532 3
21262	2	0
1	0	4
43	3	0
4	0	1
54	13	0
10120	4	0
6	25	0
9620	0	1
1475	12	0
1527	0	2
3236	1	0
6137	1	0
15470	2	0
2383	3	0
9025	1	0
6293	1	0
5751	3372	3372
1537	0	3
2461	0	3
65	0	2
1	0	13
129	6	0
2728	4	0
11391	1	0
4204	0	12
52	8	0
9544	1	0
11653	0	1
3355

chain 4355568 NA18879_chrY 49516307 + 17439893 17486100 HG002_chrY 62432599 - 45214480 45260689 4
10582	1	0
15839	0	1
5445	2	0
2497	0	4
11841

chain 1190969 NA18879_chrY 49516307 + 17053724 17066364 HG002_chrY 62432599 - 45634118 45646761 5
1386	0	6
6455	1	0
4090	2	0
706

chain 322611 NA18879_chrY 49516307 + 15189835 15193243 HG002_chrY 62432599 - 47507067 47510475 6
3408