##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
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302	1	0
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269	0	12
493	4	0
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32	4	0
14	4	0
27	8	0
32	0	4
105	0	4
395	4	0
172	0	4
3256	1	0
3807	0	4
57	4	0
23	3	0
917	2	0
313	3	0
403	0	2
28	8	0
907	15	0
894	0	1
2595	11	0
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181	0	1
531	0	4
286	0	1
29	1	0
31	1	0
7	123	0
93	0	1
328	1	0
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722	0	5
85	0	1
14	0	1
480	0	1
222	0	1
314	1	0
6695	0	101
1590	4	0
2859	1	0
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484	22	0
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359	2	0
4	0	7
13	0	4
23	0	4
39	0	7
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53	1	0
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60	3	0
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16	0	3
4	0	1
14	0	2
19	0	7
346	0	1
10104	4	0
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43	0	8
4	4	0
29	4	0
112	4	0
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58	4	0
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14	4	0
68	0	4
48	4	0
32	0	4
19	0	4
33	0	8
524	0	5
812	2	0
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1482	1	0
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98	0	3
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13	12	0
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27	1	0
554	24	0
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653	4	0
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896	0	6
1753	0	1
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871	0	1
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1082	0	259
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61	1	0
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7	0	4
2166	0	3
80	35	0
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98	0	1
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44	0	12
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89	12	0
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41	0	6
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1098	1	0
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1591	1	0
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233	4	0
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2564	8	0
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292	0	4
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538	0	1
2132	1	0
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46	4	0
1881	106	0
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3392	108	0
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7776	1	0
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658	0	2
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20	371	7
1385	0	2
1214	49	0
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121	7	0
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7	0	1
104	0	1
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9	0	1
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3	0	1
12	0	1
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36	51	95
22	0	3
10	0	1
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12	0	1
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9	0	1
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17	14	60
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7	1	0
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39	0	1
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16	7	30
16	2	0
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30	79	38
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7	2	0
2	0	1
31	0	1
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10	0	1
34	0	1
11	54	106
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17	0	1
213	0	1
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79	1	0
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38	1	0
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56	0	2
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428	1	0
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48	0	1
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54	0	3
319	1	0
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76	0	2
54	0	2
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62	4	0
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501	1	0
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51	5	0
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217	1656	1655
143	0	1
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8	0	4
59	0	1
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48	1	0
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42	0	1
66	0	5
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57	0	1
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81	3	0
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92	1	0
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4	0	3
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12	65	22
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2	54	0
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39	18	0
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5	13	0
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17	0	6
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28	148	134
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3	235	0
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14	8	133
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6	522	24
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2240	843	0
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65	0	205
3531	0	1
2112	0	1
659	0	19
197	107	12
38	290	328
785	0	4
256	4	0
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1070	2	0
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174	1	0
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1	4	0
863	1	0
1596	0	12
73	29	0
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67	0	2
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5	0	3
6	0	3
1659	1	0
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323	0	1
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34	0	4
24	0	2
152	0	3
1715	1	0
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70	1	0
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141	0	1
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43	1	0
61	0	3
142	16	0
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46	28	52
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732	1	0
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563	0	36
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309	1	0
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43	1	0
881	0	1
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5868	0	2
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48	0	27
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937	0	4
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7	0	4
9	6	0
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17	0	4
1	0	4
35	13	11
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24	0	4
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33	0	4
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523	63	0
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14	0	4
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592	0	2
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4640	4	0
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52	0	3
79	0	1
2439	4	0
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691	1	0
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4904	16	20
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402	2	0
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81	0	8
62	16	0
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817	0	1
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1613	0	4
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4	0	4
114	2	0
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3771	18	0
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335	10	0
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58	1	0
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572	0	4
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55	115	10
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163	80	0
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55	3	0
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1739	0	4
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47	0	2
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23	1	0
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10	2	168
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14	1	0
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9	0	2
42	2	0
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26	2	0
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14	0	8
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28	256	357
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6	28	0
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94	12	0
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39	52	12
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4	0	20265
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1065	0	15
2166	42099	8892
1869	0	5
76	0	5
1304	0	3
289	10	0
234	0	10
576	15	0
3186	0	5
3189	0	10
4144	0	5
206	5565	0
370	5	0
2759	0	5560
450	0	5
1616	0	5
4	0	5
193	5	0
528	0	10
42	5	0
993	10	0
8973	3	0
7711	5553	0
4846	10	0
505	5	0
2054	1	0
1594	0	5
2941	0	1
181	25	0
791	35	0
768	0	1
507	30	0
663	0	1
321	15	0
5	5	0
540	0	5
830	0	5
739	0	5
11	0	11
58	20	0
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494	1	0
290	0	20
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775	0	5
6736	5	0
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1232	0	5
5661	5	0
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260	25	0
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2754	0	5
4755	0	5
1270	0	5
3248	0	10
720	7506	0
1936	10	0
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793	5	0
1240	0	10
1281	0	15
535	10	0
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1831	20	0
1980	5	0
5648	10	0
2012	0	20
1747	20	0
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3824	5	0
1831	5	0
3803	5	0
2016	0	5
1772	5	0
675	0	15
1349	10	0
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2387	5	0
1422	0	5
7655	5	0
1770	0	5
679	0	15
84	0	15
1217	0	5
1267	0	1190
33	0	5
1751	25	0
1405	0	3831
603	0	5
1808	0	5
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3666	0	15
1846	0	10
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3700	5	0
2648	5	0
3059	10	0
818	0	5
5745	0	1
1790	0	10
4441	0	10
3331	4	0
3934	34325	25802
484	0	25
20	0	30
2725	0	5
19	1	0
5	15	0
450	10	0
139	5	0
459	5	0
1596	20	0
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2161	5	0
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4422	0	10
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2204	0	10
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1735	0	5
5559	15	0
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3291	5	0
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1513	5	0
3881	0	10
536	0	5
28	5	0
1266	15	0
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225	5	0
25	60	0
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772	5	0
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5397	0	5
190	5	0
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9427	1	0
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2223	1	0
6054	0	5
1436	0	1
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4064	4	0
3948	8	0
696	4	0
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2848	23	0
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796	0	2
13715	2	0
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3715	1	0
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8211	1	0
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3914	4	0
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947	0	3
935	8	0
81	0	4
431	4	0
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26712	1	0
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41565	1	0
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6588	0	1
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1225	0	1
7752	4	0
28	0	4
2420	4	0
55630	1	0
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7747	0	1
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1171	1	0
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6972	0	4
6664	0	1
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19964	2	0
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7381	2	0
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67746	1	0
188	13	0
684	0	2
468	1	0
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47	1	0
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151	1	0
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118	0	1
50	0	3
253	2	0
342	0	1
161	1542	0
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893	6	0
1373	0	1
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2979	0	2
916	3	0
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3017	1	0
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58455	1	0
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1303	20	0
49	0	4
83777	0	1
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59	8	0
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4376	14	0
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330	15	0
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5714	1	0
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684	0	14
26	0	2
18590	1	0
325	0	1
2253	0	12
9565	1	0
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16399	4	0
79	4	0
5979	0	4
2054	0	2
4148	0	4
11581	1	0
2785	2	0
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948	1	0
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5	0	20
5502	0	2
351	2	0
910	1	0
2433	1	0
325	1	0
297	0	5
12961	3411	3411
11574	0	8
1389	0	6
287	1	0
321	1	0
1587	1	0
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355	0	2
5555	0	5
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674	3	0
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63	2	0
23	0	2
19905	4	0
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4787	1	0
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80	0	46
165	2	0
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1424	1	0
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640	1	0
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381	0	8
3607	2	0
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66	0	2
3712	0	2
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426	1	0
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74	12	0
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287	8	0
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91	0	4
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4875	1	0
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84	4	0
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7835	1	0
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8921	1	0
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12	0	2
27764	7	0
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64	12	0
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7909	1	0
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263	2	0
11	0	2
1276	8	0
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5635	1	0
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1974	1	0
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7	2	0
2287	0	1
2757	1	0
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2	24	0
30404	0	1
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18	0	8
7481	4	0
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13	3	0
1	0	3
110	0	4
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4	0	1
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4727	4	0
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52	4	0
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2	0	6
1742	8	0
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907	1	0
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27343	1	0
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399	7549	291379
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8212	1	0
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3742	1	0
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185	48603	6037
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2819	0	6
5	0	9
19660	4	0
7072	0	1
13926	0	3
21299	1	0
8010	0	14
62457	0	1
304	0	4
4681	0	10
2121	32294	32299
2096	3	0
4640	8	0
35	4	0
33948	0	1
15689	0	8
21268	0	4
32	2	0
5932	0	16
1877	0	1
3022	1	0
1146	0	3
5565	4	0
57	8	0
4813	4	0
34602	0	1
29939	1	0
34737	2	0
19867	1	0
37947	0	1
32369	1	0
39351	1	0
8048	0	1
40493	0	1
72136	70945	326
9540	10	0
38347	2	0
9799	6	0
6817	2	0
4532	1	0
9721	1	0
16987	6	0
40112	0	1
349	1	0
22975	0	2
4	4	2
708	1	0
5484	1	0
1552	10	0
5	2	0
11	77	0
40	1	0
1	11	0
11	2	0
90	0	57
10828	0	4
68819	0	1
33020	2	0
44205	0	2
9960	0	1
3473	0	1
11208	0	2
23526	12	0
12024	0	3
6076	0	2
11466	0	1
3870	0	10
483	10	0
3	0	7
11662	1	0
117	0	3
622	0	1
2687	0	1
4076	4	0
5151	2	0
48226	0	9
52798	16	7
897	0	1
20068	0	1
98	0	2
17	0	21
2157	1	0
13634	11	0
9000	2	0
10965	0	12
12556	0	2
5412	0	4
29071	0	4
1687	0	2
27923	8513	0
100	2	0
94	0	2
20	0	1
6	18	0
211	3	0
147	0	1
15	3	0
120	0	2
69	5	0
79	1	0
69	0	3
5	0	1
158	0	4
288	0	1
40	1	0
200	140	0
5	2	0
22	6	0
61	2	0
131	1	0
72	0	12
9	1	0
5	2	0
48	0	1
315	0	14
104	2	0
111	0	1
69	0	7
3	0	5
20	0	9
28	0	1
53	3	0
50	2	0
72	0	2
25	7	0
232	1	0
53	28	0
4	0	32
53	2	0
114	3	0
386	42152	2085
307	0	3
60	0	2
73	1	0
124	1	0
646	3	0
15	0	8
416	4	0
77	0	1
61	2	0
192	1	0
30	1	0
144	0	2
73	0	1
135	1	0
9	0	1
64	1	0
51	0	1
90	1	0
184	0	1
145	1	0
176	0	1
26	15	0
112	1	0
20	1	0
216	1	0
133	3	0
23	2	0
134	3	0
52	4	0
14	3	0
59	0	19
2	3	0
71	6	0
57	1	0
30	0	1
12	0	1
36	0	1809
38	3	0
277	4	0
26	1	0
38	0	4
17	31	0
9	25	0
6	22	0
14	0	12
52	1	0
31	0	26
9	4	0
37	0	314
85	1	0
78	0	1
43	0	2
3	0	1
88	4	0
41	3	0
24	0	4
38	1	0
28	0	2
69	0	1
443	0	1
290	0	6
124	2	0
20	4	0
103	1	0
61	1	0
118	2	0
38	10	0
23	0	1
3	0	2
475	0	2
24	1	0
154	0	2
217	0	1
111	0	3
22	2	0
17	0	4
49	0	1
42	10	0
5	0	11
54	193	0
11	0	19
74	3	0
112	0	1
134	7	0
135	2	0
48	1	0
5	0	2
7	3	0
267	0	12
79	3	0
266	1	0
164	3	0
63	6	0
16	4	0
206	2	0
14	1	0
188	0	1
40	0	4
153	0	4
17	1	0
262	2	0
100	0	1
29	1	0
6	2	0
117	0	1
170	0	1
28	0	5
57	44	0
163	0	1
177	0	2
22	20	0
170	1	0
129	0	7
15	0	14
103	0	1
42	336	0
10	3	0
58	4	0
129	0	1502
76	1	0
88	0	17
140	0	1
83	0	1
209	5	0
88	17	0
5	0	15
23	0	1
26	0	1
82	12	0
79	327	0
27	3	0
31	0	2
32	3	0
4	0	1
54	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
116	2	0
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	75523	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
111	0	2
104	14	0
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	4
321	1	0
5129	0	2
12509	0	4
7322	1	0
23477	0	2
28206	0	3
13692	2	0
78030	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	6	0
18593	0	1
1619	0	2
611	1	0
8774	0	10
33624	4	0
468	0	2
1723	0	1
3988	0	16
37	0	2
4867	0	4
13666	0	6
695	0	3
30744	0	2
104611	0	8
30961	4	0
9987	1	0
5547	18	0
51451	0	1
3267	0	3
34112	0	12
70	2	8
34	4	0
42	0	8
39	0	8
57	4	0
35	4	0
3330	0	4
3393	6	0
32368	0	1
754	12	0
3438	0	1
1925	0	6
84	17	0
1668	0	1
2516	4	0
1653	12	0
4132	0	6
195	1	0
9915	0	1
860	0	2
4363	6	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
4481	0	1
352	0	3
5572	0	5
4887	10848	0
31	0	1
614	0	1
14862	0	1
35	0	1
63	27523084	37324720
823	0	5
119	15	0
833	5	0
3	25	0
326	15	0
6037	25	0
13729	10173	2913
5552	4825	7243
5780	2	0
79	2	0
1111	0	2
174	0	4835
10750	2	0
994	0	2
1	2422	0
5	0	2
600	1	0
690	2419	0
3861	4836	4836
3453	35	30
794	28826	42950
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	53050	172223
5845	1	0
1041	10	0
2952	0	26846
15876	1	0
3534	0	1
3534	1	0
3534	1	0
4811	0	15
3363	5	0
2415	0	10603
3534	0	1
167	3504	0
12	0	5
954	0	10
81	0	15
416	10	0
152	0	45
125	20	0
92	0	1
1459	1	0
656	0	1
6412	1	0
1254	25	0
4986	0	14139
2092	25	0
3557	15	0
2235	1	0
1194	0	1
5874	1	0
179	5	0
946	10	0
86	15	0
414	0	5
156	45	0
122	0	20
583	0	5
150	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
2723	25	0
3356	0	15
7086	0	15
3693	25	0
1881	1	0
1480	0	15
3520	0	15
174	0	25
4078	0	7080
21651	1	0
494	0	20
74	0	25
14	5079	1599
1328	1	0
494	0	20
66	0	40
6429	0	1
494	20	0
66	40	0
13419	0	1
513	20	0
61	40	0
51377	0	5
14	0	5
387	1	0
334	0	15
134	5	0
2199	0	15
24	15	0
777	1	0
334	0	15
134	5	0
3513	0	3498
552	30	0
2419	1	0
341	0	15
129	5	0
8828	21497	10994
3805	5	0
7804	15	0
24905	5	0
37648	0	2
32577	8	0
153	0	8
3325	0	1
5649	6	0
26	1	0
5880	0	4
2763	0	2
10990	0	6
16380	0	2
34970	5	0
13333	0	10
2433	3	0
21	0	36
2862	4	0
7005	8	0
4255	1	0
3416	0	4
1517	4	0
861	1	0
18648	19	0
1776	0	3
1309	1	0
724	0	1
1972	4	0
1725	4	0
5522	0	2
1476	0	1
109	0	1
3452	0	1
2733	2	0
3695	0	1
2723	4	0
45	0	6
11	0	3
6920	0	1
401	0	3
10394	4	0
27854	0	33
11481	1	0
4807	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	3	0
4392	0	1
9177	0	4
444	1	0
21629	1	0
73	0	1
10647	1	0
1366	0	1
1509	2	0
347	0	2
256	2	0
11013	1	0
951	1	0
7835	0	2
15	2	0
9100	2	0
5226	1	0
1381	1	0
475	1	0
11599	29	0
745	6	0
106	6	0
3	0	6
107	7	0
1	0	1
75	1	0
52	0	10
1	0	2
43	0	1
10	0	1
15	2	0
3	0	1
10	4	0
14	0	12
22	0	54
9	0	5
6	0	1
5	0	1
16	2	33
12	0	2
24	58	4
14	75	17
30	0	2
12	0	1
18	1	0
2	5	0
18	10	0
15	14	4
9	1	0
1	5	0
25	0	17
3	0	1
45	4	0
7	0	2
6	23	9
14	3	555
24	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 26855238 HG01261_chrY_random0000118 288367 + 65 288367 HG002_chrY 62432599 - 43425064 43713267 2
550	0	1
1299	2	0
1924	0	1
5047	1	0
5535	1	0
5063	0	1
4088	1	0
2508	0	2
9508	8	0
1483	1	0
574	2	0
13649	0	2
2859	0	6
11700	1	0
3772	1	0
13042	3	0
2364	4	0
3716	0	2
20225	2	0
942	1	0
1549	4	0
1494	0	1
1	0	1
1	0	1
11	0	3
7613	0	1
1943	25	0
6	4	0
10120	14	0
5741	0	1
27809	0	1
5629	2	0
1	4	0
47	3	0
59	15	0
10120	4	0
6	25	0
7050	0	2
2519	0	1
42	0	6
1468	0	8
28755	3	0
12643	1	0
8426	3372	3372
4081	0	3
70	0	3
2785	6	0
11391	1	0
2252	4	0
1952	0	4
60	8	0
9544	1	0
1336	1	0
1176	0	1
6046	0	2
1183

chain 11270258 HG01261_chrY 52239270 + 23806352 23957435 HG002_chrY 62432599 - 38399346 38539790 3
17699	0	1
23	0	10850
4459	1	0
2454	1	0
4938	0	1
13	0	1
6999	1	0
105	0	1
53	0	4
552	0	2381
638	1	0
67	4	0
123	1	0
13	4	0
207	6	0
429	1	0
145	1	0
20	1	0
8	15	0
46	0	1
62	0	1
60	0	4
498	0	2
210	1	0
435	29933	6092
7	1	0
2251	0	1
3446	1	0
864	1	0
1457	0	11
1558	1	0
3724	1	0
3316	5	0
3200	1	0
1163	0	2
860	0	1
9915	1	0
195	0	8
4130	12	0
740	0	1
912	2	0
2516	0	1
1668	1	0
2015	0	1
3438	12	0
33123	0	7
223	1	0
95

chain 3058316 HG01261_chrY 52239270 + 21588757 21621050 HG002_chrY 62432599 - 40507615 40539913 4
6287	0	1
5505	0	4
20501

chain 427764 HG01261_chrY 52239270 + 22921943 22926454 HG002_chrY 62432599 - 39338719 39343231 5
2490	0	1
2021

chain 322611 HG01261_chrY 52239270 + 14755346 14758754 HG002_chrY 62432599 - 47507067 47510475 6
3408

chain 6804 HG01261_chrY 52239270 + 23965574 23965734 HG002_chrY 62432599 - 38539790 38542814 7
2	0	2864
158

chain 2683 HG01261_chrY 52239270 + 12368965 12368993 HG002_chrY 62432599 + 12511308 12511336 8
28

chain 1015 HG01261_chrY 52239270 + 1016401 1016419 HG002_chrY 62432599 + 1024836 1024854 9
18