##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 1724160259 HG04160_chrY 50818595 + 23 50813539 HG002_chrY 62432599 + 2 62432577 1
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670	1	0
1637	1	0
1378	0	1
14	0	5
1040	0	95
882	1	0
5718	510	0
1323	0	10
909	4	0
1674	3	0
490	0	1
3214	2	0
1156	0	4
225	0	9
112	0	4
852	52	18
107	2	0
40	2	0
1025	0	4
1735	1	0
1797	4	0
1300	0	9
1377	0	5
5748	1	0
876	1	0
2532	0	1
68	1	0
6348	2	0
7	0	4
101	0	3
6	0	2
7692	134	0
859	1	0
559	0	1
2125	308	0
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1622	0	1
864	1	0
5069	0	4
677	8	0
21	0	8
73	0	4
230	0	54
25	0	4
5	0	4
87	8	0
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2851	1	0
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184	0	21
43	6	0
31	0	1
658	0	1
354	0	3
336	1	0
2017	26	0
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18	45	0
27	90	0
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45	135	0
18	0	45
2100	0	4
1749	4	0
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411	0	4
7231	8	8
54	2	31
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14	3	0
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4038	4	0
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11	1	0
81	0	816
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20	0	4
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54	0	16
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220	0	4
5	0	4
40	4	0
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35	0	1
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34	4	0
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528	0	142
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434	0	9
3	0	706
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174	12	0
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1643	7	0
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1436	68	0
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4	1	0
12	0	55
350	0	2
2345	3	0
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91	104	0
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4869	1	0
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3	4	0
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1222	0	8
431	0	2
907	6	0
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313	1	0
874	1	0
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13	0	4
23	0	4
39	0	7
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693	0	1
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4	0	1
14	0	2
23	0	3
5818	1	0
74	0	1
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43	0	8
4	4	0
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19	0	4
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524	0	5
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2	0	1
4	4	0
37	0	2
680	4208	0
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5067	4	0
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7	0	4
2169	1	0
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37	0	10
484	0	1
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4	0	1
1200	148	0
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45	135	0
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34	0	12
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712	2	0
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178	0	1
162	4	0
20	375	7
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17	2	0
1113	1	0
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78	0	342
1116	1	0
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301	0	4
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55	0	1
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98	0	5
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73	4	0
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5	23	0
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41	0	5
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22	1	0
865	1	0
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1233	5	0
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288	0	1
1156	4	0
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468	6	0
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653	4	0
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1214	0	4
29	5	0
210	24	24
690	8	0
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21	0	4
80	0	10
57	0	1
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13	4	0
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3	1	0
201	51	0
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41	25	0
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59	0	19
87	0	12
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7	1	0
1	0	7
8	0	20
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46	3	0
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12	0	1
12	0	1
12	0	182
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49	0	1
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11	1	0
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99	1	0
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3057	1	0
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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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9	24	0
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3	4	0
58	45	0
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8	27	0
481	0	1
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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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52	38	2
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13	0	10
13	0	5
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577	2	0
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3	0	1
66	4	0
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175	1	0
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396	0	4
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1023	2	0
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61	0	7
160	0	2
2135	28	0
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4	0	3
4	0	4
141	0	2
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26	4	0
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1434	1	0
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16	128	0
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12	21	0
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323	0	6
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145	1161	285
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35	13	11
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6559	0	4
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67	0	4
5470	0	4
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582	8	0
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215	2	0
576	1	0
3062	15	3
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1984	1	0
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1569	1	0
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426	1	0
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85	1290	1301
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47	0	6
44	3	0
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171	0	3
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24	540	0
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39	52	12
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25	10	0
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574	5	0
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4934	5	0
561	5	0
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14034	1	5505
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1057	1378	0
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2947	5563	5553
2736	0	5
1358	0	5
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7653	0	5
359	5	0
28	0	1
59	5	0
381	10	0
1526	1	1374
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1943	1362	0
15	3962	3961
1080	0	1
2442	5	0
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594	0	1358
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1672	15	0
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5499	0	5
3370	58804	65749
8180	8516	5770
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40	0	15
8	10	0
1350	5	0
129	0	190
479	0	10
1023	0	16101
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17	0	5
1363	0	5
6569	31473	1275
357	1	0
34	0	5
8250	0	5
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6494	1373	0
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265	4154	1
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654	15	0
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745	5	0
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33	5550	0
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264	0	10
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44	38890	0
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1453	0	15
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4	10	0
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779	0	5
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45	0	5
96	1	0
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1473	11060	0
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228	36574	8892
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76	0	5
1304	0	3
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1285	7653	0
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57	0	5
297	369	0
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4745	5	0
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1772	5	0
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24	0	2423
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1264	0	5
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3934	34325	25802
484	0	25
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32	0	4
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3	1	0
4669	1	0
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31432	0	4
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6588	0	1
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28	0	2
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55481	1	0
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6536	1	0
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11	0	2
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6629	1	0
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118	0	1
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6663	1	0
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287	1	0
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39	0	4
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1960	0	1
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1420	5	0
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874	0	1
6580	0	1
2739	2	0
20183	1	0
176	5	0
24462	655	655
2121	125	0
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4619	0	1129
30628	0	123
2453	381	0
18533	63654	0
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22154	64408	0
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176	0	1
192	0	39
5	0	85
239	0	1
324	29131	29505
43	0	125
63	0	1
98	1	0
244	0	1
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164	0	2
83	4	0
3	0	3
158	2	0
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80	10	9
283	2	0
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523	1	0
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603	0	123
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2	5	0
16	3	1001
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225	1496	0
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266	0	1
280	0	2
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27	0	249
137	0	7
6	7	0
15	0	1
286	0	2
82	1	0
518	1	0
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15791	8321	1077
1924	125	0
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47	0	999
16	0	125
123	0	125
78	0	125
145	875	0
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5627	0	250
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3300	15691	7065
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41	125	0
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332	0	7
3	7	0
240	124	0
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30	0	8
23091	0	32
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17847	1	0
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13926	0	3
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62443	0	1
344	4	0
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2123	32298	32299
2096	2	0
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3952	1	0
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32	2	0
5932	0	16
1877	0	1
3022	1	0
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5565	0	4
4866	8	0
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29939	1	0
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30	2	0
32	4	0
137551	0	1
112630	71270	326
9540	10	0
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4532	1	0
9721	1	0
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3120	0	1
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4	4	2
708	1	0
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1559	0	1
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6940	1	0
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9788	0	2
3644	0	1
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483	10	0
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11662	1	0
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622	0	1
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4076	8	0
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36941	2	0
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17	0	21
4961	2	0
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5413	0	3
30762	0	2
27923	8513	0
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94	0	2
20	0	1
6	18	0
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69	5	0
79	1	0
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5	0	1
158	0	4
288	0	1
40	1	0
200	140	0
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22	12	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
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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
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53	2	0
114	3	0
386	42012	2085
307	0	3
60	0	2
73	1	0
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646	3	0
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416	4	0
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61	2	0
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64	1	0
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90	1	0
184	0	1
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71	6	0
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17	31	0
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52	1	0
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9	4	0
37	0	314
85	1	0
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43	0	2
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88	4	0
41	3	0
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38	1	0
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69	0	1
443	0	1
290	0	6
124	2	0
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61	1	0
118	2	0
30	16	0
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23	0	1
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475	0	2
24	1	0
154	0	2
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22	2	0
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49	0	1
42	10	0
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54	189	0
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74	3	0
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134	7	0
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48	1	0
5	0	2
7	3	0
267	0	12
79	3	0
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164	3	0
63	6	0
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206	2	0
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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
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28	0	5
57	44	0
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22	20	0
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103	0	1
42	336	0
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58	4	0
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76	1	0
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140	0	1
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209	5	0
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23	0	1
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82	12	0
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32	3	0
59	0	13
118	0	3
55	4	0
161	1	0
38	10	0
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7	0	4
12	0	2
98	1	0
43	0	11
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63	4	0
249	0	1
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130	0	2
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295	1	0
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72	0	22
46	0	4
93	0	1
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38	1	0
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103	0	1
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139	0	1
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50	1	0
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178	0	3
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23	466	6295
120	0	1
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96	1	0
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690	0	1
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16	36	0
97	1	0
234	0	2
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33	4	0
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121	2	0
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73	0	1
50	4600	2764
121	12	0
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95	8	0
91	0	3
210	6	0
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75	0	8
117	0	15
117	1	0
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197	0	1
107	75518	109875
386	0	3
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67	0	1
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69	1	0
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104	14	0
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72	0	1
131	0	2
61	0	6
29	0	152
200	0	1
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288	4	0
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5	3	0
69	0	1
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69	2	0
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94	0	2
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101	1	0
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909	10	19
2130	0	3
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3275	1	0
11254	2	0
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30961	1	0
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23	0	1
4059	0	4
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9983	1	0
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32164	1	0
1960	20	0
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39	0	8
57	4	0
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3330	0	4
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35	0	1
63	4764832	4551689
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608	6651	6611
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355	0	1
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243	20556	13969
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36	8918	54290
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2797	13824	11384
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19549	0	1
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4	13388	7434
17945	887	8005
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1840	0	1
233	5	0
1041	0	3504
7273	16127	99637
5299	5	0
3544	15	5
2695	1	0
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1234	29170	20099
1	1601	0
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1212	28722	14503
40	3554	0
1932	0	1
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8	6878	17519
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5231	10102	5875
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1139	15	0
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17167	39807	5937
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71	20845672	32147291
71	20	0
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13729	12587	2913
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1318	4836	7254
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4165	72270	261723
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2804	897	4432
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67	0	8
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8979	6	0
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2765	0	23
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2433	3	0
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1774	0	1
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2378	1	0
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6920	0	1
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8057	0	1
718	0	30
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11481	1	0
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65	0	1
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24	102	215
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60	0	1
6	1648	1
54	1	7
53

chain 335107077 HG04160_chrY 50818595 + 6243400 9814760 HG002_chrY 62432599 - 52562439 56521946 2
17506	20	223258
153	0	1
240	0	4
43	1	0
560	0	5
329	0	1
54	1	0
124	0	1
2621	0	1
124	1	0
78	0	30
51	0	1
43	0	14
92	388	0
2	0	7
281	1	0
96	0	1
598	0	491
17	1	0
23	1	0
53	0	5
40	0	4
89	0	5
233	1	0
337	0	1
44	6	0
138	0	1
141	1	0
370	0	2
613	0	3
355	0	4
154	0	1
327	0	1
722	1	0
81	0	1
532	6	0
42	22	0
14	22	0
22	1	0
2812	0	1
1102	2	2
23	0	14
786	3	0
664	1	0
1694	2	0
20	4	0
117	0	1
655	0	2
1782	18	0
4656	3	1
32	0	4
1691	0	5
3566	2668	104118
12	0	1
2935	2	0
9312	0	12
51	0	1
49	2	0
1693	0	5
2000	0	1
356	0	2
1	0	11
470	0	1
3402	1	0
824	1	0
6831	18	0
4543	0	12
24	0	2
49	0	1
22	0	2
4551	0	1
5337	28	0
793	3	0
400	0	3
1105	0	1
821	6	0
2994	0	1
1241	1	0
984	0	2
1983	0	8
69	0	2
412	0	1
3302	0	1
355	0	1
9	0	12
465	0	1
1797	0	1
2424	1	0
1930	3	0
1508	0	1
855	0	2
2948	1	0
4211	0	4
101	0	6
390	0	1
3304	1	0
358	1	0
3885	1	0
1937	30	0
3134	4	0
26	0	2
117	1	0
6982	2	0
112	4	0
424	0	1
1301	5	0
11317	0	10
7170	2	0
99	0	4
390	1	0
1303	0	5
2000	1	0
356	2	0
1	11	0
470	1	0
5340	0	32
786	0	3
1505	1	0
830	0	6
10	2	0
26	2	0
2556	0	18
4582	12	0
96	6	0
3696	1	0
356	2	0
1	11	0
470	1	0
3402	0	1
2723	0	3
1505	1	0
846	4	0
6	0	4
2553	18	0
8403	0	1
356	0	13
471	0	1
1961	1	0
1440	1	0
1926	0	2
9	32	0
786	3	0
1505	0	1
872	0	2
2925	1	0
144	0	20277
4030	0	8
106	0	2
2	2	0
422	0	1
2089	0	3
1570	1	0
269	3	0
210	1	0
2117	1	0
1284	1	0
1925	32	2
137	1	0
3002	8	0
26	0	2
117	1	0
6982	8	0
534	1	0
3303	1	0
356	12	0
471	1	0
3402	0	1
1940	0	28
783	0	3
1505	1	0
842	0	4
26	2	0
7156	4	0
100	6	0
1692	5	0
8166	26	0
5723	18	0
4688	6	0
7940	1	0
8181	4	0
4013	2	0
106	0	2
428	0	1
191	3	0
1099	0	10
2000	0	1
356	0	13
471	0	1
1795	0	1
1607	0	1
5071	8	0
7170	0	4
98	2	0
393	0	1
1293	0	10
2000	0	1
356	0	13
258	3	0
2327	1	0
1284	1	0
1940	34	0
124	1	0
658	3	0
1505	0	1
842	6	0
26	0	2
2556	18	0
4543	1	0
21	10	0
87	0	2
26	0	4
8750	1	0
1130	0	16
10317	2	0
33377	6	0
4825	0	1
2441	2	0
20154	2	0
109	2	0
4339	0	20265
4	0	3
5551	32	0
124	1	0
658	3	0
1505	0	1
842	4	0
26	0	2
2931	1	0
93	0	40623
4114	0	4
86	0	4
3708	1	0
356	13	0
471	1	0
5373	0	2
5719	18	0
375	0	1
4205	10	0
52	0	1
43	10	0
3693	0	1
356	0	14
471	0	1
5340	32	0
786	3	0
1505	0	1
840	6	0
2957	1	0
1241	1	0
985	0	2
1941	0	16
79	1	0
25	0	6
418	0	1
3662	1	0
2278	0	1
2431	1	0
1106	0	12
10	0	20
783	0	3
2346	0	14
26	0	2
2556	18	0
2602	2	0
2097	0	6
9867	18	0
10	2	0
3131	12	0
27	2	0
17557	0	2
23658	0	2
70950	0	6
24808	0	2
2	0	3
28	0	5
718	2	0
9709	0	10
38150	0	1
5172	1	0
10330	1	0
18472	1	0
15348	1	0
5	0	2
10	3	0
45	12	0
83	6	0
130	6	0
2635	1	0
19449	10	0
30	2	0
19898	2	0
50711	1	0
3763	25	0
25288	0	3
53684	4	0
8541	3	0
4938	1	0
8455	2	0
1420	0	22
71	0	66
104	66	0
15790	0	2
1696	4	0
16471	0	2
13047	3	0
10426	0	1
6180	0	2
10508	0	20
1850	0	2
3669	0	6
177	0	1
54757	2	0
18399	0	2
9802	0	14
5382	5	0
32903	0	2
18890	2	0
2488	18	0
20398	0	52
10788	8	0
17232	0	1
24378	2	0
2560	0	9
4059	0	4
5009	1	0
25604	1	0
4144	6	0
8394	16	0
11600	1	0
33910	0	15
137	0	3
115359	4	0
86	20	0
57825	1	0
3955	0	1
12745	4	0
18407	5	0
45	0	8
5519	1	0
18853	0	2
6184	22	0
6234	0	1
2652	0	1
43025	0	1
7511	0	1
14761	0	1
94394	0	1
57902	2	0
22	4	0
35746	8	0
91	0	12
101600	4	0
6641	0	5
4382	0	1
1702	12	0
106	4	0
1	1	0
2645	0	4
43674	4	0
6890	6	0
20876	10	0
20	5	0
29683	0	1
26414	1	0
19917	1	0
16019	4	0
22494	8	0
23915	0	4
46921	0	50
746	300	0
277	0	50
36843	16	0
8186	0	4
10598	0	4
12821	0	8
3845	0	4
28559	2	0
20	3	7
18	2	0
21	0	2
23050	8	0
8670	0	17
16456	4	0
82	0	8
130	0	4
30383	1	0
5764	0	1
368	0	4
49042	0	2
14937	2	0
24915	0	1
31117	0	1
23407	0	1
2752	4	0
21613	8	0
26	2	0
3937	0	4
2083	1	0
19598	0	1
4505	0	4
250	0	1
1372	0	1
42911	1	0
24021	6	0
55098	2	0
25121	0	1
38219	1	0
22183	1	0
6410	0	4
2673	0	1
50462	1	0
27263	0	1
15230	0	1
28119	0	1
2839	0	1
40239	0	1
10233	0	2
53702	0	1
24999	2	0
32240	15775	0
16016	0	2
52108	1	0
20443	1	0
23973	0	2
110	2	0
14411	2	0
11393	0	2
8083	4	0
12322	6	0
50815	0	2
2	0	2
6	0	2
4	0	2
2	4	0
1723	2	0
63821	1	0
48529	2	0
2479	0	4
1769	0	2
13444	19	11
52	12	0
66199	1603	0
13440	0	1
18361	1	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 36999278 HG04160_chrY_random0000188 392421 + 0 392421 HG002_chrY 62432599 - 42678378 43070760 3
102	1	0
118	0	1
10	1	0
90	1	0
66	1	0
11	0	1
310	0	1
64	1	0
24	1	0
6	0	2
350	0	2
165	1	0
61	1	0
116	0	1
143	4	0
558	1	0
1493	0	1
3578	2	0
2	8	0
47	1	0
3985	0	12
4234	2	0
2725	5	0
5678	1	0
726	0	12
35	2	0
8703	0	9
3247	0	1
25978	0	1
19323	2	0
4754	17	0
27	1	0
6066	1	0
840	1	0
5681	0	1
23141	0	1
4502	1	0
1399	1	0
13032	1	0
3204	1	0
3742	0	2
131	0	2
14740	2	0
8091	0	12
16119	1	0
4450	4	0
6478	0	2
46	2	0
10499	4	0
3345	8	0
8037	4	0
14738	2	0
3078	1	0
4026	1	0
14320	1	0
29907	23	0
3480	1	0
6933	23	0
4754	2	0
27548	1	0
29666	2	0
21	0	2
21	0	2
6394	0	5
49	0	5
10987	0	2
4	0	10
5630	0	4
2923	0	8
3820	0	1
3708

chain 12134023 HG04160_chrY 50818595 + 23826148 23986968 HG002_chrY 62432599 - 38399346 38539790 4
17084	0	1
614	0	1
31	10847	0
4887	0	5
5572	0	3
352	0	1
4481	1	0
452	1	0
2002	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	11
1558	1	0
300	1	0
3424	1	0
3316	3	0
4363	0	2
860	0	1
9915	1	0
195	0	6
4132	15	0
740	0	1
912	2	0
2516	0	1
1668	2	0
2015	0	1
3430	0	8
754	0	1
32368	0	7
223	1	0
95

chain 3058952 HG04160_chrY 50818595 + 21627630 21659927 HG002_chrY 62432599 - 40507615 40539913 5
6287	0	1
26010

chain 428205 HG04160_chrY 50818595 + 22961045 22965557 HG002_chrY 62432599 - 39338719 39343231 6
4512

chain 322480 HG04160_chrY 50818595 + 14865875 14869283 HG002_chrY 62432599 - 47507067 47510475 7
3408

chain 6804 HG04160_chrY 50818595 + 23995107 23995267 HG002_chrY 62432599 - 38539790 38542814 8
2	0	2864
158

chain 2683 HG04160_chrY 50818595 + 12479517 12479545 HG002_chrY 62432599 + 12511308 12511336 9
28