##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 1734870153 HG03492_chrY 54517012 + 531 54510384 HG002_chrY 62432599 + 2 62432577 1
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1435	3	0
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1146	135	0
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874	4	0
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688	4	0
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69	20	0
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4	0	2
279	0	10
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6	1	0
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54	1	0
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84	22	346
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14	5	0
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2985	1	0
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1072	0	4
75	8	0
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814	0	2021
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894	1	0
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24	0	2
152	0	3
1715	1	0
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1552	102	0
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4478	0	4
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14	161	357
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23	1	0
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46	0	20
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62	1	0
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37	0	3
1	4	0
7	3	0
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18	4	0
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15	1	0
7	33	0
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710	4	0
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1626	1	0
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11	3	0
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42	0	4
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20	3	0
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50	0	2
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568	0	1
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12	16	0
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73	2	0
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89	2	358
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39	0	22
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9	0	1
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55	0	2
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716	70	146
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128	4	0
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5	0	5
9	0	22
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1373	1	0
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2518	4	0
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5	0	5
18521	1	0
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11530	3415	3411
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287	1	0
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644	39676	39663
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1	10	0
241	0	15
2208	0	7070
379	15	0
457	0	15
219	15	0
494	14	0
754	0	20
13	10	0
5	0	15
10	0	10581
1129	15	0
5513	7053	0
368	25	0
17851	49019	22444
2987	0	2
5465	0	1
1027	1	0
8430	9163	3533
5	0	2096
17456	0	10
37	0	10
345	0	3514
3209	0	10
393	0	5
672	1	0
690	0	10
14	0	5
933	0	5
452	15	0
5697	0	5
918	0	5
1237	10	0
1361	15	0
2211	15	0
2270	5	0
1183	1	0
44	10	0
810	23955067	31992147
568	15	0
878	15	0
1702	3529	0
4648	0	1
2093	5	0
8004	10	0
12688	0	20
4260	0	20
3521	0	5
6961	1	0
6372	0	5
7557	5	0
637	0	3559
2921	5	0
3559	0	5
3574	5	0
1809	12349	1712
71	25	0
6363	25	0
13729	12588	2913
959	6425	11256
2987	0	1
3372	2	0
79	2	0
1111	0	2
174	0	4835
10750	2	0
994	0	2
1	2	0
5	0	2
600	1	0
690	2419	0
3861	4836	4836
5659	45224	41568
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	40374	172223
6886	10	0
2952	0	26846
35158	0	5
20	2071	16205
3367	1	0
3534	0	1
3534	1	0
6240	0	14139
9022	5	0
28351	25	0
1881	1	0
5204	0	25
3450	0	1
60	0	25
1901	3535	0
1469	15	0
7080	15	0
150	25	0
3370	0	15
150	0	25
5172	0	25
8	0	15
1656	15	0
8237	1	0
494	0	20
74	0	25
14	5079	1599
1328	1	0
494	0	20
66	0	40
6176	3495	0
253	0	1
494	20	0
66	40	0
2934	0	1
527	20	0
47	40	0
29907	20	0
28076	0	15
1129	3484	0
129	5	0
2606	0	5
3088	0	15
24	15	0
371	5	0
3493	5	0
909	0	3498
552	30	0
5528	5	0
3475	5	0
32	0	3508
1878	0	1
12109	5	0
7804	15	0
18741	0	2395
3769	5	0
18950	2	0
16252	0	2
2444	0	2
8382	12705	0
24348	0	4
3329	0	1
5649	2	0
26	1	0
5880	0	2
2765	1	0
10992	0	3
16383	0	4
48301	0	10
2433	3	0
21	0	36
5539	0	2
4326	12	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	5	0
866	1	0
6335	1	0
9791	0	1
2723	2	0
45	0	6
1324	0	1
6011	0	1
8120	0	5
407	1	0
1864	10	0
7215	0	1
3912	0	4
915	0	2
3143	14	0
8900	1	0
658	32	0
3104	0	33
16288	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	11	0
272	0	2
2724	2	0
4392	0	1
9625	1	0
7862	1	0
10510	0	2
3002	4	0
253	1	0
73	0	1
13870	0	2
11269	1	0
168	0	1
782	1	0
16952	2	0
5226	1	0
1856	0	1
12343	6	0
106	6	0
116	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
20	8	0
91	0	5
6	0	1
5	0	1
28	1	0
2	4	0
25	55	8
6	0	1
17	53	6
12	75	17
28	22	12
4	0	1
18	21	3
17	10	0
7	32	22
91	4	0
7	29	17
52	158	8
19	45	12
54	1	0
14	12	30
38	0	5
3	1	0
1	3	0
15	3	0
1	0	4
59	3	0
13	0	1
13	3	0
57	3	0
21	3	0
27	0	3
21	0	3
5	17	0
2	0	2
9	3	0
9	25	1
27	0	3
35	0	5
21	3	0
15	9	0
137	0	7
1	0	5
23	0	1
50	101	15
11	0	2
79	2	0
29	4	0
36	0	6
32	4	0
45	0	4
17	4	0
70	4	0
60	0	1
6	1664	1
56	0	5
53

chain 339106131 HG03492_chrY 54517012 + 6249748 9846266 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	0
31	0	8
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
5071	16	6
2578	0	18
526	0	4
4056	6	0
101	2	0
390	1	0
1303	0	5
2000	0	1
4243	1	0
1937	22	0
786	3	0
402	0	3
1100	0	1
842	4	0
22	0	2
2560	18	0
4543	0	4
110	0	4
4545	0	1
5337	42	0
793	3	0
1508	0	1
821	6	0
2574	0	18
1644	1	0
984	0	2
1983	0	8
483	0	1
3302	1	0
356	1	0
2285	0	1
2424	1	0
1114	10	0
3180	0	2
132	1	0
7029	0	2
497	0	1
19745	2	0
112	0	4
7968	1	0
5071	0	10
7168	0	2
103	4	0
1693	0	5
2000	2	0
356	3	0
1	11	0
470	1	0
3402	0	1
1937	0	32
786	0	3
1505	1	0
830	0	2
40	2	0
2556	0	18
4582	4	0
96	2	0
9862	30	0
6098	1	0
4209	0	6
2580	0	3
1570	1	0
2444	1	0
1440	1	0
1926	0	2
9	34	0
3138	2	0
26	0	2
117	1	0
2952	0	20277
4030	0	8
110	6	0
422	0	1
794	0	2
2508	1	0
358	1	0
269	3	0
210	1	0
2117	1	0
3348	1	0
3002	2	0
7127	8	0
110	2	0
424	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	6	0
100	4	0
1692	5	0
8166	26	0
5723	18	0
4688	6	0
7940	1	0
8181	4	0
4013	4	0
728	3	0
5746	0	1
1607	0	1
5071	10	0
7170	0	4
98	4	0
393	0	1
1303	5	0
2000	0	1
356	0	13
258	3	0
2327	1	0
1284	1	0
1940	32	0
124	1	0
658	3	0
1505	0	1
842	6	0
26	0	2
2556	18	0
4543	1	0
21	8	0
87	0	2
26	0	4
8750	1	0
1130	0	16
10317	2	0
33377	6	0
7165	0	2
100	2	0
20154	4	0
109	2	0
4339	0	20265
4	0	3
5675	1	0
10243	0	2
1701	0	5
2839	1	0
5337	30	0
3123	0	4
2582	0	18
396	1	0
17334	2	0
7215	2	0
13135	6	0
7261	2	0
15590	18	0
1616	1	0
2928	0	10
112	10	0
422	0	1
8992	0	1
485	0	6
32	0	4
3144	0	2
5186	2	0
2097	0	6
9867	18	0
10	2	0
20715	0	2
23658	0	2
70950	0	6
24765	0	2
25	1	9
9	1	5
23	0	10
10437	5	0
38150	0	1
33974	1	0
15348	1	0
5	0	1
11	3	0
45	12	0
83	6	0
20	0	2
108	6	0
2635	1	0
6343	0	3
13095	0	8
30	4	0
19898	2	0
50711	1	0
3763	5	0
25288	0	3
30091	1	0
23593	4	0
13479	1	0
9875	0	22
49	0	88
104	66	0
15790	0	2
1696	4	0
16471	0	2
13047	3	0
10426	0	1
16698	0	12
1850	0	2
3669	0	6
177	0	1
9938	2	0
44819	2	0
13606	0	11
4782	0	2
9802	0	14
38285	0	2
18890	2	0
2488	21	0
20398	0	104
10736	8	0
2483	1	0
1919	0	5
206	2	0
36998	1	0
2554	0	15
9072	1	0
29748	6	0
8394	12	0
45522	0	3
115585	24	0
36802	1	0
21023	1	0
3955	0	1
12745	4	0
18407	5	0
5572	1	0
18854	0	1
6087	0	24
26	46	0
2	2	0
8	22	0
6271	0	1
2652	0	1
43025	0	1
7511	0	1
14455	1	0
306	0	1
51049	1	0
29701	0	1
13643	0	1
57902	2	0
18	0	4
35841	0	8
101600	4	0
11028	0	1
1694	0	8
56	4	0
2696	0	4
71440	5	0
20	5	0
29683	0	1
26414	1	0
19917	1	0
16019	4	0
18460	0	1
1930	0	1
2102	26	0
23915	0	4
33974	0	4
3675	1	0
9268	0	50
173	50	0
44	50	0
75	425	0
454	300	0
177	0	75
25	0	50
36843	16	0
8182	0	8
23423	0	8
3845	0	4
4501	0	18
3086	0	1
20953	21	27
18	2	0
31743	0	17
16456	8	0
86	0	4
80	0	4
46	0	4
30383	1	0
5764	0	1
24636	0	4
24774	0	2
14937	2	0
24915	0	1
19281	2	0
37997	4	0
21613	8	0
3965	0	2
21681	0	1
4501	0	8
250	0	1
1372	0	1
21877	4	0
35316	1	0
2720	1	0
7019	6	0
19198	0	1
4007	2	0
5256	1	0
26634	0	2
11719	2	0
13402	0	1
38219	1	0
11790	0	1
10392	1	0
9087	0	1
42051	1	0
8411	1	0
39247	0	1
22882	2	0
8484	0	1
2839	0	1
15242	0	1
26611	0	1
8619	0	1
23107	0	3
30592	0	1
24999	2	0
10259	0	2
29189	0	1
8803	0	4
17825	2	0
34283	2	0
20443	1	0
16969	0	1
21522	0	4
11393	0	2
8083	4	0
12320	0	2
50837	4	0
75	0	8
43	4	0
1597	6	0
15854	4	0
96496	2	0
2479	0	4
1769	0	4
13438	11	15
48	0	4
12220	0	3
53976	1603	0
13440	0	1
15512	0	1
2848	1	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 38561793 HG03492_chrY_random0000921 408392 + 357 408031 HG002_chrY 62432599 - 39104204 39511975 3
5151	0	1
124	0	1
6624	0	2
30799	0	12
12501	0	2
5451	0	3
30762	4	0
28984	0	1
27590	1	0
2797	0	24
443	0	28
152	2	0
247	2	0
197	0	2
2	0	11
70	0	2
209	0	15
26	2	0
14	13	0
13	0	28
64	0	26
116	26	0
34	26	0
27828	0	3
5111	8	0
1616	13	0
13117	0	4
11217	0	2
25	4	0
25554	0	1
13275	5	0
36480	2	0
60328	0	3
5413	0	2
12515	0	8
35801	0	21
117	0	1
1535	0	1
127	0	1
5137

chain 10913416 HG03492_chrY 54517012 + 23982200 24119219 HG002_chrY 62432599 - 38401468 38539790 4
63	0	1
35	0	1
15477	0	1
23	0	10850
4459	1	0
2454	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
3724	1	0
967	1	0
2349	4	0
3200	0	1
2024	0	1
9915	1	0
4333	12	0
740	0	1
912	2	0
2516	0	1
1668	14	0
84	0	6
1925	0	1
3430	0	8
754	0	1
32368	0	7
223	1	0
95

chain 3742526 HG03492_chrY 54517012 + 19560023 19599692 HG002_chrY 62432599 - 42850342 42889998 5
15515	1	0
4450	4	0
6526	6	0
10499	2	0
2666

chain 327146 HG03492_chrY 54517012 + 18870940 18874397 HG002_chrY 62432599 - 43575590 43579047 6
3457

chain 322143 HG03492_chrY 54517012 + 14939183 14942595 HG002_chrY 62432599 - 47507067 47510475 7
2617	4	0
791

chain 6804 HG03492_chrY 54517012 + 24127358 24127518 HG002_chrY 62432599 - 38539790 38542814 8
2	0	2864
158

chain 2683 HG03492_chrY 54517012 + 12552849 12552877 HG002_chrY 62432599 + 12511308 12511336 9
28