##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 2173161838 HG00609_chrY 71946244 + 5 71941250 HG002_chrY 62432599 + 26 62432577 1
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7	0	4
58	28	0
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1232	9	0
292	0	1
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73	0	4
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5	0	4
87	8	0
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658	0	1
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39	8	0
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2592	0	4
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67	29	0
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119	73	649
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160	0	4
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1643	7	0
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1831	1	0
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719	0	1
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60	402	0
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851	526	0
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1435	3	0
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3891	1	0
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447	47	154
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3031	0	1
8	1	0
585	5	29
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292	0	4
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35	1	0
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1065	1	0
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9537	16	0
14253	0	1
13218	1	0
2278	2	0
7093	0	50
100	100	0
177	300	0
454	225	0
119	50	0
173	0	50
12943	2	0
8650	0	1
25327	0	4
23915	20	0
4033	0	1
18460	2	0
12950	1	0
3069	1	0
18191	0	1
32372	2	0
25451	5	0
20	5	0
74030	5	0
95	4	0
15	16	0
56	4	0
5	0	2
35	4	0
1660	0	1
10989	0	8
58953	1	0
42678	0	4
99	4	0
35746	12	0
22	2	0
5936	2	0
51966	0	1
13643	2	0
80751	0	1
4933	1	0
9828	0	1
7511	0	1
43025	0	1
2652	0	1
6234	22	0
6184	0	1
18854	1	0
5519	0	12
77	20	0
1197	0	5
17169	4	0
12745	0	1
3955	1	0
57825	16	0
69099	0	1
13038	0	1
33306	12	0
140	0	3
45522	20	0
407	0	6
23684	1	0
9786	5	0
4259	1	0
9072	0	3
35687	1	0
4135	4	0
4355	8	0
10643	0	9
12093	2	0
5131	1	0
3362	3	0
2488	10	0
18890	0	2
25935	1	0
13853	0	1
8312	0	2
4782	1	0
13617	2	0
32638	2	0
12181	0	4
9934	0	2
176	0	6
5521	0	12
16698	0	1
10426	3	0
13047	0	2
16471	4	0
1696	0	2
16031	0	22
7	32	0
9868	3	0
6452	0	1
60710	0	3
25288	22	0
3763	1	0
12508	1	0
58101	2	0
30	10	0
13103	3	0
6346	1	0
2635	9	0
67	0	12
196	1	0
8	0	4
49310	0	1
38150	0	15
8	0	4
9692	2	0
38	0	1
679	2	0
29262	0	6
90196	0	2
17557	2	0
27	8	0
3131	12	0
10	18	0
485	1	0
8992	1	0
390	0	14
106	6	0
1983	2	0
985	0	1
1632	18	0
2540	0	2
26	0	14
2346	0	3
783	0	20
10	0	12
1106	1	0
2431	0	1
2278	1	0
358	0	1
3303	0	1
418	0	6
25	1	0
79	0	16
1941	0	2
985	1	0
1241	1	0
2957	6	0
840	0	1
1505	3	0
786	30	0
5823	0	1
4052	10	0
43	0	1
52	6	0
4205	0	1
391	18	0
2568	6	0
3135	0	2
5373	1	0
471	13	0
356	1	0
3708	0	4
86	4	0
4118	0	40623
484	18	0
2540	0	2
26	4	0
22	2	0
820	0	1
1505	3	0
658	1	0
2064	1	0
1284	1	0
6669	0	2
7252	0	2
6342	0	1
325	0	1
1797	0	1
4525	2	0
117	4	0
20167	0	2
7265	6	0
13106	2	0
20271	4	0
10317	0	16
1130	1	0
8750	0	4
26	0	2
87	6	0
21	1	0
1941	2	0
5158	0	2
26	6	0
842	0	1
1505	3	0
658	1	0
124	32	0
1940	1	0
1284	1	0
2327	3	0
258	0	13
356	0	1
2000	5	0
1303	0	1
491	0	4
7170	10	0
5071	0	1
1607	0	1
5746	3	0
620	0	2
106	2	0
4013	4	0
14425	5	0
1696	6	0
98	0	4
7025	1	0
989	1	0
1505	0	3
787	30	0
1112	0	1
8745	2	0
100	4	0
10319	0	8
8192	5	0
1835	2	0
4559	18	0
2568	4	0
3002	1	0
3348	1	0
2117	1	0
210	3	0
269	0	1
4084	2	0
116	0	2
4030	0	20277
3097	0	6
6509	1	0
2444	1	0
358	1	0
3694	4	0
101	0	4
7025	1	0
989	1	0
1505	0	3
787	24	0
5339	1	0
470	11	0
1	3	0
356	1	0
1211	0	3
2578	2	0
4207	1	0
375	0	18
5722	0	2
8197	0	5
1693	0	2
7271	0	8
12620	0	1
424	2	0
106	0	6
12198	1	0
7938	0	4
103	0	4
43	0	40601
16083	1	0
3667	1	0
413	2	0
4289	1	0
375	0	18
2556	0	2
26	4	0
842	0	1
1505	3	0
783	32	0
5350	0	1
4545	0	2
108	6	0
4570	18	0
2546	0	2
20	4	0
831	0	1
1508	3	0
793	22	0
1931	1	0
3405	1	0
465	12	0
8	1	0
356	1	0
3719	8	0
110	2	0
4570	0	18
2414	1	0
132	0	2
29	4	0
3122	31	3
1114	0	1
815	1	0
3405	0	1
465	0	12
364	0	1
3302	0	1
412	2	0
112	0	4
4570	18	0
2546	0	4
28	6	0
821	0	1
1508	3	0
813	0	10
8175	5	0
1709	0	2
76	0	2
21	2	0
4583	18	0
2578	0	2
3123	0	20
1931	0	1
3892	0	1
3650	1	0
390	0	2
103	4	0
4586	0	18
2594	0	2
8944	1	0
358	1	0
2003	0	5
1691	0	2
10412	0	4
6206	0	1
1212	0	3
2499	0	2
79	0	6
10304	2	0
43	0	121774
1101	0	1
4227	0	1
471	0	13
356	0	1
3723	2	0
110	2	0
6982	0	1
133	0	4
6	2	0
2354	0	3
786	0	16
1937	0	1
7970	2	0
70	0	8
7136	0	6
4	0	20
866	1	0
1505	0	3
794	2	34
1103	0	1
4227	1	0
470	11	0
1	2	0
356	1	0
3303	1	0
396	0	2
235	0	1
3360	3	0
3633	6	0
2	0	2
30	0	8
10	0	8
2336	0	3
786	0	28
1937	0	1
2005	229109	5831
100	0	2
7272	2	0
3149	2	0
13799	1	0
43	0	4
12728	1	0
5260	2	0
11134	8	0
88114	0	1
1262	4	0
4211	2	0
10609	2	0
1194	0	4
2186	12	0
18134	0	4
19362	2	0
45649	0	2
2575	2	0
31390	2	0
5185	0	4
70	0	12
20588	0	29
3383	31	0
18794	2	0
33175	2	0
175	0	2
1143	1	0
4296	0	1
10737	1	0
16593	2	0
27	0	2
4290	9	0
27213	0	4
14825	0	4
63681	0	12
27181	0	2
2079	0	1
2256	0	1
22063	6	0
49854	3	0
11950	1	0
11358	1	0
34944	0	4
350	0	2
52143	481367	326879
13483	0	10
575	5	0
1111	0	10
297	10	0
573	5	0
27	5	0
857	0	5
744	0	5
922	0	5
849	5	0
850	10	0
87	0	10
839	5	0
196	15	0
1950	5	0
347	0	5
1841	0	10
105	0	10
1244	10	0
896	0	5
595	0	5
630	5	0
4030	0	25
2222	10	0
1568	0	5
843	10	0
69	0	5
3993	0	15
337	0	5
383	0	5
2063	0	5
3390	0	5
2220	0	10
383	0	5
282	10	0
143	5	0
881	0	10
758	5	0
757	1876	0
281	0	5
5439	0	5
2619	5	0
2145	0	5
1349	0	10
258	5	0
474	0	10
1327	0	5
1226	0	5
1784	0	10
11585	15	0
2184	5	0
333	5	0
1282	0	5
514	5	0
2036	15	0
2562	5	0
2525	0	10
2412	5	0
1740	20	0
2004	0	5
3884	0	5
2540	0	5
1530	0	5
43	5	0
5950	5	0
1923	0	5
4025	15	0
1033	0	5
409	0	5
2205	5	0
2709	0	5
2383	5	0
2058	0	5
6910	0	5
397	5	0
1149	0	10
802	5	0
5701	5	0
1555	0	5
850	5	0
4328	0	5
207	0	5
422	0	5
232	5	0
1732	0	5
2054	10	0
2063	5	0
5452	5	0
2220	5	0
1115	0	10
2876	0	5
442	5	0
242	0	5
6668	5	0
10155	5	0
4007	5	0
143	0	5
736	5	0
21745	0	5
892	5	0
1082	0	5
2350	0	5
2681	5	0
618	0	5
8591	0	10
2358	0	5
2139	0	5
1350	10	0
624	20	0
1867	0	5
2002	5	0
178	10	0
1707	1	0
2162	15	0
885	0	15
23445	30	0
4053	0	5
24741	0	5
6848	5	0
3561	5	0
1331	0	5
2652	0	10
1440	10	0
380	20	0
326	0	5
18	5	0
269	5	0
702	5	0
2365	0	5
9464	10	0
6564	0	10
597	5	0
30	5	0
2281	5	0
1154	0	5
5867	0	5
2742	10	0
138	0	5
380	5	0
3584	0	10
6749	0	25
1165	0	10
1198	0	10
1454	0	10
16072	0	5
1561	5	0
9448	0	1
6415	2	0
22	0	2
13360	0	2
17879	2	0
19370	1	0
11620	1	0
5938	1	0
56483	0	10
16891	2	0
1158	0	2
46903	0	1
7139	0	1
12819	0	1
26634	0	1
5095	0	5
264	0	10
1801	0	15
1431	5	0
44	0	5
297	0	5
1898	0	5
541	10	0
235	10	0
93	0	5
97	0	5
537	0	5
383	10	0
878	0	5
619	10	0
85	25	0
86	0	5
120	0	5
588	10	0
746	0	10
368	0	5
177	0	5
535	5	0
187	10	0
477	0	5
123	5	0
251	5	0
27382	0	1
23320	1	0
19878	0	1
5555	16	0
854	0	1
8858	4	0
16046	0	1
5571	0	2
14	0	1
1	0	2
12538	0	1
5524	1	0
26782	0	1
4599	2	0
32529	0	5
15474	3	0
265	0	5
4784	5	0
5523	0	5
1630	15	0
11522	0	5
22918	25	0
5594	0	5
572	10	0
4299	0	5607
1303	15	0
265	0	5
4752	5	0
5615	5	0
572	0	10
5035	0	5
5622	0	10
11203	5	0
1641	0	5
5598	0	5
4595	0	5
628	0	5
3101	15	0
19	5	0
2446	0	5
25	10	0
5059	0	15
427	15	0
5000	10	0
574	10	0
5577	0	5
4437	5	0
497	5	0
561	5	0
5608	0	5
640	5	0
4959	5	0
552	0	15
62	10	0
585	20	0
1867	6198	0
21351	0	5
12387	1378	0
81	15	0
906	0	1378
10	0	1842
3	0	5
8	7359	0
121	19102	12166
995	0	5
1788	0	10
198	6	0
19	0	5
68	1	0
209	0	1
801	10	5
556	5	0
12	15	0
63	1	0
818	24090	35219
1069	5	0
93	0	15
10629	0	4
208	0	1
2511	0	5
1373	5	0
299	15	0
2195	1	0
196	5	0
40	0	15
336	27899	143368
357	1	0
34	0	5
392	0	15
965	0	5
9907	0	15
1462	60488	34361
8227	5	0
5732	0	5
7179	5	0
3652	0	5
5294	0	5
264	0	5
1926	0	10
44	22299	0
3642	0	5
5198	5	0
360	0	5
9	0	5
202	0	20
574	0	1
540	5	0
542	0	5
1486	0	15
2134	0	5
244	0	5
5	0	5
1120	5	0
568	5	0
944	10	0
516	0	15
161	1	0
1988	5	0
213	0	20
579	0	1
540	5	0
559	25	0
1459	0	15
1603	0	1
265	15	0
1465	0	5
151	5	0
579	0	10
11	0	5
3233	0	5
358	15	0
213	5	0
1661	5	0
45	5	0
3049	0	1
530	5	0
4	0	5
1912	0	40
131	1	0
836	0	15
214	0	15
1473	11041	0
693	36658	8892
2004	0	5
1250	0	3
1109	20	0
5545	0	5
5565	5	0
4816	0	10
148	5	0
601	0	10
5007	0	5
10546	3	0
1084	10	0
5002	0	10
1615	5553	0
4846	10	0
2615	7671	0
1538	5	0
1290	7658	0
7514	5	0
9726	0	20
509	0	5
1285	0	5
3015	5	0
2430	0	5
281	20	0
526	0	5
748	0	1
4090	0	10
2650	5	0
775	1	0
2062	1	0
724	5	0
3159	10	0
785	0	5
785	1	0
1951	5	0
3980	10	0
793	10	0
1299	15	0
8	10	0
305	0	369
1598	0	10
731	0	5
510	25	0
1873	0	10
790	10	0
2749	0	10
838	5	0
721	5	0
3193	0	15
1263	0	5
42	0	10
325	11462	10781
339	0	20
29	26546	0
1107	0	5
793	5	0
3081	10	0
1975	0	5
1831	5	0
2023	5	0
1747	10	0
2003	5	0
3872	0	15
1747	15	0
1993	0	5
1846	0	10
1983	10	0
1816	0	15
2023	10	0
4	0	5
3772	5	0
31	0	10
1751	5	0
675	0	15
1349	5	0
1782	10	0
1998	0	5
1803	5	0
579	5	0
1427	5	0
1790	10	0
1998	0	5
1831	5	0
1998	5	0
16	11376	0
17	30	0
1775	5	0
4458	10	0
47	0	5
1751	15	0
740	5	0
665	0	3831
603	0	5
5677	0	5
7576	0	5
2040	0	5
3676	0	5
7588	5	0
2648	5	0
3059	25	0
818	0	5
11496	15	0
3832	4	0
7196	0	15
195	5	0
10704	0	5
3472	0	5
2686	5	0
698	0	5
1724	0	10
301	0	15
2129	0	20
2529	0	5
6478	5	0
7381	0	5
2161	5	0
16850	15	0
18844	0	5
853	5	0
1361	0	15
173	5	0
2533	5	0
815	0	5
2228	5	0
4138	5	0
376	1	0
19	0	10
4958	0	10
3291	10	0
3076	10	0
1513	5	0
4460	5	0
2319	0	5
1840	0	5
76	5	0
973	0	15
220	20	0
25	60	0
1519	5	0
702	0	10
2687	5	0
1314	0	5
282	5	0
4971	10	0
2967	5	0
3545	0	5
2484	0	5
1210	15	0
195	10	0
1533	5	0
1659	5	0
9432	1	0
7273	3	0
13732	0	1
2223	1	0
6054	0	5
1436	0	1
14230	2	0
32	0	2
6602	1	0
1969	0	4
4062	12	0
3948	4	0
696	2	0
836	1	0
2354	0	1
11557	0	1
5363	0	1
2848	30	0
19709	8	0
14513	2	0
7882	4	0
19600	16	1
422	12	0
4672	1	0
1031	0	12
24760	0	3
5539	0	1
1135	0	4
10506	0	4
1951	0	2
4433	2	0
3918	12	0
13994	0	1
3435	0	3
935	12	0
14415	0	4
42788	0	4
54645	0	8
206	4	0
31356	4	0
8033	1	0
8484	0	1
10948	1	0
51859	0	5
6588	0	1
25757	1	0
22681	12	0
29434	0	1
11772	0	1
15265	13	0
20437	1	0
2065	2	0
27894	0	2
6795	50	0
11697	0	2
469	4	0
19021	8	0
16675	0	1
13108	6	0
17213	10	0
26336	3	0
13369	0	1
7752	2	0
1093	0	4
1451	8	0
49	0	4
12050	0	5
95188	0	1
7747	1	0
2910	0	6
17299	0	12
428	0	1
6107	1	0
7034	0	8
11970	0	451
1919	0	1
12826	1	0
125	4	0
37172	1	0
584	0	1
14966	0	3
34911	0	1
3950	4	0
5161	0	1
34569	0	1
14286	0	1
4288	0	5
15671	2	0
28307	0	4
7381	1	0
26054	1	0
136237	0	1
7108	0	1
50234	1	0
17403	1	0
109	1	0
188	13	0
684	0	2
468	1	0
1150	0	1
230	1	0
225	11	0
47	1	0
160	0	4
151	1	0
205	1	0
5	1	0
118	0	1
50	0	3
253	2	0
342	0	1
161	1542	0
23424	2	0
6667	1	0
2266	1	0
14042	0	5
5	0	5
18521	0	1
8558	3	0
2979	0	2
11833	0	15
32196	1	0
28578	0	5
29189	1	0
683	2	0
57368	1	0
23228	0	4
26	0	10
10035	0	1
6711	0	5
3521	1	0
36628	0	2
8270	4	0
1305	36	0
49	8	0
11331	0	1
20038	0	3
52408	0	1
42834	3	0
48718	2	0
18758	0	3
46476	0	16
47	0	4
11779	4	0
4378	1	0
50199	1	0
400	0	9
321	21	0
10077	0	1
33398	2	0
54907	0	1
44384	0	18
41698	0	4
165	8	0
3051	0	1
3006	0	4
2054	0	2
4148	4	0
11585	0	1
21179	0	4
1617	29	0
1524	0	12
8339	1	0
1292	0	15
2319	0	2
2	2	0
3179	0	2
351	2	0
3965	0	1
1386	0	4
14355	0	12
12197	0	4
1394	0	1
287	1	0
1908	1	0
1762	2	0
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7978	1	0
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4314	0	6
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63	2	0
23	0	2
19905	4	0
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17378	2	0
2	19	0
21	23	0
153	0	69
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6169	4	0
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28660	3	0
37	0	8
7042	2	0
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636	2	0
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15	1	0
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288	4	0
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15773	21	0
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23	0	4
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45	0	2
3712	0	1
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43	2	0
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12	0	2
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1	6	0
12861	1	0
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2	0	1
3712	2	0
21	0	4
17	4	0
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6455	1	0
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5	0	4
105	0	4
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239	0	4
2497	2	0
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60	0	1
6387	2	0
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13	0	5
19696	1	0
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379	0	6
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30	2	0
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25	0	2
3569	1	0
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317	1	0
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1255	1	0
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73	19	0
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6749	1	0
6447	0	8
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1	7	0
36	0	2
42	2	0
8	4	0
616	0	4
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2	0	6
1742	20	0
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426	0	12
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26	0	2
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4414	2	0
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1652	1	0
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571	0	1
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2013	8	0
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2858	0	3
4079	3374	3374
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39072	8	0
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6	25	0
9557	0	3
11	0	1
1	0	1
1496	0	4
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49	8	0
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648	39673	39663
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3	7	0
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34	2	0
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7	34647	6035
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82	0	6
28	7	0
1	0	1
25	0	12
38	1	0
108	0	1
10	0	1
15	2	0
3	0	1
58	0	54
3	1	0
6	0	5
6	0	1
5	0	1
17	148	74
14	72	17
15	8	6
7	18	0
16	0	1
12	0	1
5	21	3
11	28	7
14	0	1
2	8	0
18	24	0
10	1	0
31	8	0
43	27	43
24	8	0
12	123	0
3	0	2
12	0	1
9	43	10
20	5	0
23	0	12
6	1	0
6	0	23
53	3	5
11	3	0
29	1	0
7	5	16
12	3	0
21	2	0
6	3	0
9	0	1
41	8	1
5	4	0
9	0	1
11	3	0
61	0	2
4	1	0
5	3	0
9	25	1
17	2	0
10	0	2
27	1	0
9	0	5
5	1	0
16	3	0
15	5	9
13	0	1
51	0	1
3	5	0
87	1	0
4	0	12
10	1	0
33	58	35
9	0	23
40	2	0
4	1	0
25	4	0
36	0	6
32	4	0
66	4	0
70	4	0
60	0	1
6	1608	1
56	0	5
53

chain 12753284 HG00609_chrY 71946244 + 24398292 24547195 HG002_chrY 62432599 - 38399346 38539790 2
2221	1	0
15478	0	1
31	10850	0
4887	0	5
10409	2	0
452	1	0
2002	1	0
4952	0	1
6999	1	0
715	0	4757
506	0	1
5052	1	0
1126	2384	0
7	1	0
2251	0	1
4310	1	0
1457	0	10
1559	1	0
3724	1	0
1300	1	0
2016	4	0
5225	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	4	0
8290	1	0
24833	0	25
205	1	0
95

chain 3743036 HG00609_chrY 71946244 + 19749754 19789420 HG002_chrY 62432599 - 42850342 42889998 3
19965	4	0
6526	2	0
10499	4	0
2666

chain 6804 HG00609_chrY 71946244 + 24555334 24555494 HG002_chrY 62432599 - 38539790 38542814 4
2	0	2864
158

chain 1346 HG00609_chrY 71946244 + 71942884 71942898 HG002_chrY 62432599 + 62432585 62432599 5
14