##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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34	0	71
1191	1	0
171	308	0
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677	8	0
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73	0	4
230	0	54
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5	0	4
881	0	3
2851	1	0
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184	0	21
43	12	0
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658	0	1
354	0	3
336	1	0
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10	2	0
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1285	0	1
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2	11	0
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52	2	1
24	8	0
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65	2	0
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755	4	0
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60	511	0
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1435	3	0
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1401	0	1190
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5	5	0
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6	15	191
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46	0	1
19	209	194
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54	1	0
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211	0	62
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3	78	0
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61	0	7
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16	148	0
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1	10	0
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14	162	357
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183	17	0
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23	0	4
12	8	0
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584	1	0
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341	8	0
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2	4	0
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3868	86	46
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39	52	12
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15	1	0
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1	6	0
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52	8	67
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17	10	545
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37	2	0
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34	4	0
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2121	1	0
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3600	42	8
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1454	41493	13146
3455	15	0
75	5	0
1279	0	15
1318	5	0
845	0	15
82	0	5
818	5	0
9717	0	15
1458	8104	4575
1042	3554	0
6458	0	2415
170	9134	13900
8046	2416	0
3164	4979	0
25980	35124	25615
3757	5615	2046
2357	0	25
3872	3534	0
9754	16418449	31885530
3426	0	20
4280	5	0
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10199	15	0
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194	0	10
22	5	0
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830	1	0
1347	0	3574
2216	0	1
887	7133	0
1831	5236	1712
71	25	0
1145	0	1
5217	25	0
13729	17425	2913
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15614	7457	7457
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11612	7045	0
31	0	3530
2217	0	5
229	15	0
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156	15	0
499	0	5
333	0	10
87	0	1
706	0	15
1323	0	7072
339	648	22898
433	0	10
208	15	0
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1265	2982	2987
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1103	0	10
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48	0	1
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1837	7081	0
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673	0	5
4280	5	0
134	0	15
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1377	0	7091
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84	0	10
739	0	7
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1777	10	0
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16	0	25
4	7047	0
5392	1	0
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138	0	10613
327	1	0
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1802	0	10
1763	5	0
3220	0	20
20	0	15
253	0	5
173	0	7113
1638	10	0
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1746	5	0
1768	0	3554
19	1	6
1725	5	0
750	0	3549
1061	10	0
1504	65863	34043
69	0	15
1499	0	10
16673	2	0
312	3	0
239	0	1
416	1	0
1382	0	2414
13705	5289	47686
1276	0	15
2243	0	1
167	61729	86456
22285	577	28596
6075	0	20
20055	5	0
19713	0	5
2322	0	10
2198	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
13988	5	0
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32615	0	4
3444	0	1
5649	2	0
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10987	0	3
16383	10	0
34972	5	0
3008	2	0
6752	1	0
3573	0	10
2632	3	10
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2677	2	0
7839	0	2
52414	0	1
7386	0	2
38249	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
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6099	0	1
73	12	0
272	0	2
2724	2	0
4392	0	1
9625	1	0
21629	1	0
73	0	1
10647	1	0
1366	0	1
1509	2	0
9	1	0
338	0	3
255	4	0
11013	1	0
168	0	1
782	1	0
16952	2	0
5226	1	0
1381	1	0
475	0	1
3574	0	6
7438	0	1
579	0	58
687	6	0
106	6	0
193	1	0
40	0	8
78	0	1
36	0	12
24	0	1
16	0	1
1	2	0
7	0	5
41	0	1
4	12	0
1	0	1
13	5	0
43	132	35
13	78	18
21	7	0
7	18	0
29	0	1
2	3	0
17	10	6
15	30	14
7	19	0
5	1	0
36	7	0
27	0	1
15	4	0
5	11	16
34	122	29
19	40	9
12	0	5
7	5	0
23	18	54
6	0	1
21	20	39
31	0	5
18	18	14
12	2	0
6	3	0
33	0	1
7	0	5
5	7	1
5	3	0
9	0	1
11	3	0
9	0	2
41	0	1
6	13	0
2	0	2
9	15	10
27	0	3
15	3	28
18	3	0
12	1	3
22	0	1
1	0	54
5	8	0
28	0	1
2	0	47
12	0	1
6	1	0
5	0	5
34	55	12
14	0	2
27	2	0
14	0	4
34	2	0
29	4	0
13	0	1
22	0	6
30	8	4
27	0	5
32	4	0
12	0	1
11	0	8
6	0	3
25	1	0
4	4	0
17	0	5
9	346	121
37

chain 340365517 HG00321_chrY 45747808 + 6250848 9877805 HG002_chrY 62432599 - 52562439 56521946 2
72	2	0
17847	0	4
43	1	0
13799	2	0
10400	2	0
1681	0	5
38985	2	0
20166	6	0
110	2	0
8792	0	1
7053	0	121806
153	0	1
4207	0	8
3795	0	1
358	0	1
3885	0	1
1926	2	16
9	0	14
2894	0	121744
2824	0	18
4586	2	0
99	0	2
390	1	0
1303	0	5
6244	1	0
12198	0	40601
47	4	0
105	0	2
390	0	1
10837	1	0
1781	2	0
7127	0	2
110	0	2
422	0	1
3303	0	1
356	0	2
1	0	11
470	0	1
3402	1	0
1930	6	0
7	24	0
786	3	0
1505	0	1
846	0	6
26	0	2
2931	1	0
4205	0	6
101	0	2
1693	0	5
786	0	3
1211	1	0
356	3	0
1	11	0
470	1	0
5370	0	2
786	0	3
1505	1	0
830	0	2
14	2	0
143	1	0
2439	0	18
4582	4	0
96	6	0
3696	2	0
356	3	0
1	11	0
470	1	0
3402	0	1
2723	0	3
1505	1	0
840	0	6
26	2	0
7142	0	4
99	0	2
390	1	0
3661	0	1
2444	1	0
6511	0	4
2557	18	0
540	0	20277
4030	0	6
112	2	0
422	0	1
1301	5	0
2002	0	1
356	0	13
258	3	0
2327	1	0
1284	1	0
1927	22	0
137	1	0
658	3	0
1505	0	1
838	8	0
26	0	2
2556	18	0
4543	2	0
110	0	2
8778	0	1
1138	0	6
783	0	3
1505	1	0
989	1	0
2412	0	18
4609	4	0
100	8	0
1692	5	0
2000	1	0
356	13	0
471	1	0
3402	0	1
2723	0	3
1505	1	0
838	0	4
30	2	0
7144	0	2
98	2	0
393	1	0
12618	6	0
3110	4	0
4013	2	0
110	0	6
420	0	1
191	3	0
1109	5	0
2000	0	1
356	0	13
471	0	1
1795	0	1
3545	30	0
786	3	0
1505	0	1
842	4	0
26	0	2
2556	18	0
2602	2	0
1988	2	0
94	0	4
393	0	1
3303	0	1
356	0	13
258	3	0
2327	1	0
1284	1	0
824	1	0
1116	14	0
124	1	0
658	3	0
1505	0	1
840	0	2
26	0	2
2556	18	0
4543	1	0
19	0	2
115	0	4
8749	0	4
1113	0	30
5719	0	18
4580	10	0
96	2	0
3696	1	0
356	13	0
471	1	0
3402	0	1
2723	0	3
1505	1	0
872	2	0
3082	0	4
4054	0	6
98	4	0
393	1	0
191	0	3
3467	0	1
2278	1	0
1607	1	0
8181	4	0
4054	6	0
96	0	4
587	3	0
3737	0	3
210	0	1
1795	0	1
322	0	1
1284	0	1
12210	0	2
4181	0	13
254	3	0
207	0	1
1797	0	1
1608	1	0
2724	3	0
1508	0	1
821	4	0
32	0	2
2565	18	0
4551	4	0
110	0	2
3716	1	0
364	13	0
472	1	0
2117	1	0
1284	1	0
1940	26	0
124	1	0
658	3	0
1505	0	1
820	2	0
22	8	0
26	0	2
2556	18	0
468	0	40623
4116	0	2
9998	0	2
25986	18	0
4544	0	6
3843	1	0
2636	0	1
3579	2	0
8332	2	0
2097	0	6
9867	18	0
10	2	0
44375	0	2
74758	1	0
21010	0	3
32	0	1
10427	0	10
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21457	0	1
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19307	1	0
2	2	0
143	9	0
51	0	12
67	6	0
2635	1	0
6340	0	6
6502	2	0
6601	8	0
30	2	0
66973	1	0
3059	0	4
573	1	0
3763	2	0
25288	0	3
60710	0	1
11	1	0
16316	0	22
93	0	44
527	0	1
17064	4	0
3660	2	0
12811	0	2
23473	0	1
16702	0	8
5521	0	6
10116	2	0
19136	1	0
25683	2	0
18399	0	2
9815	0	1
25951	0	4
6527	1	0
5803	0	2
18890	2	0
2488	6	0
8870	36	0
11528	0	52
117	26	0
95	0	7
5487	1	0
5082	8	0
4611	0	2
39564	0	3
9072	1	0
4290	5	0
3592	1	0
15906	4	0
13943	0	4
407	20	0
45522	0	3
33	6	0
107	12	0
115355	0	4
86	12	0
3161	0	1
42153	1	0
12510	1	0
3955	0	1
31152	15	0
5572	1	0
18854	0	1
12418	0	1
2652	0	1
43025	0	1
7511	0	1
95512	0	1
13643	0	1
57902	2	0
35768	8	0
108344	0	5
4382	0	1
1702	20	0
56	4	0
51	1	0
57086	1	0
16998	0	5
2668	0	5
73362	1	0
3069	1	0
31410	0	1
4027	0	6
23915	0	4
25327	0	1
8648	0	2
13739	300	0
177	100	0
9505	1	0
27488	16	0
39989	1	0
24040	2	0
20	3	7
24069	2	0
24165	8	0
170	0	4
46	0	4
36147	0	1
49414	0	2
14937	2	0
7346	0	2
42897	1	0
29197	1	0
2752	4	0
21613	6	0
3965	0	2
1271	0	1
20409	0	1
4501	0	8
250	0	1
1372	0	1
21869	0	8
20126	0	1
13893	1	0
74394	0	1
15803	1	0
1056	0	1
9201	0	10
339	1	0
6946	0	12
21711	1	0
28597	12	0
2673	0	1
50462	1	0
23657	0	1
3606	1	0
43350	0	1
2839	0	1
50474	0	1
35599	0	1
14355	1	0
3747	0	1
37886	3	0
53583	0	2
25427	1	0
67402	0	4
11393	0	2
20405	8	0
39543	1	0
11284	0	2
4	0	2
77	0	8
1640	2	0
15854	2	0
16924	2	0
79572	2	0
2479	0	4
1159	0	10004
4056	4	0
59	8	0
12214	0	9
2308	0	3
5864	0	27
113	0	2
28	0	3
27	0	3
252	29	0
41	29	0
4770	0	1
11167	0	1
5950	4	0
5732	8	0
17684	1603	0
322	0	1
2755	2	0
1755	0	1
3328	26	0
59	2	0
43	0	2
26	0	6
2	4	0
172	8	0
176	0	1
364	0	1
2701	0	2
687	4	0
1023	0	14
306	1	0
1673	0	2
2334	0	1
1400	0	4
32	1	3
886	0	2
320	0	1
375	2	0
2675	20324	0
1628	0	9
6424	0	1
285	18	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 153870163 HG00321_chrY_random0000028 1637430 + 369 1637079 HG002_chrY 62432599 - 35636409 37266058 3
1722	0	1
3985	2	0
7920	1	0
21190	0	1
3505	0	1
17150	0	1
2156	12	0
4054	9	0
2564	1	0
7381	1	0
31793	4	0
3	0	2
58	0	4
22479	0	16
9746	0	3
16579	0	1
10182	1	0
4369	0	8
21	0	2
475	0	4
14728	4	0
14444	1	0
909	1	0
18132	1	0
2261	1	0
10190	0	1
3992	0	2
18875	1	0
9931	1	0
10850	0	4
663	0	1
842	1	0
18800	0	12
1827	1	0
2434	1	0
10415	1	0
5276	0	1
12004	16	0
36	0	4
18294	0	3
12	0	9
6	15	0
61	0	6
9195	3	0
4881	0	2
17537	1	0
10125	1	0
35771	0	1
831	0	1
893	0	1
12376	0	2
271	0	2
34	8	2
5201	0	10
1063	3	0
1571	3	0
4705	1	0
904	0	1
1738	0	7
366	0	1
4854	2	0
1930	0	1
3339	1	0
8867	0	2
6508	0	1
7059	1	0
7558	1	0
2464	0	1
4557	0	6
16	2	0
11460	2	0
7743	0	2
407	0	1
4842	0	2
2718	0	2
7193	1	0
16904	0	1
2705	0	1
213	1	0
7065	1	0
5047	2	0
13	4	0
9159	0	1
13519	1	0
2076	1	0
5193	2	0
10975	1	0
4700	1	0
17665	4	0
5407	6	0
2864	9	0
14816	2	0
212	8	0
15111	0	1
1939	4	0
4747	1	0
478	2	0
46	0	2
7163	1	0
518	1	0
30687	0	24
1753	0	1
912	2	0
1664	2	0
1406	0	8
4934	0	4
13665	2	0
688	0	2
16450	0	4
3825	0	1
7404	0	1
3048	4	0
1807	0	3
26963	0	4
821	1	0
9867	0	1
6780	0	2
5111	1	0
33755	0	1
12562	0	1
6974	0	2
7852	0	1
3315	0	1
125	0	4
22207	2	0
62270	0	1
2148	1	0
3261	2	0
6879	0	2
3264	0	1
471	1	0
17302	3	0
6170	0	12
67	0	8
38	2	0
63	8	0
17	0	4
96	0	28
3360	0	4
3343	0	23
480	1	0
24376	0	2
8311	4	0
5425	0	2
5830	0	3
4132	8	0
17366	1	0
14206	4769	0
435	0	1
33719	1	0
4460	0	1
33319	1	0
15335	1	0
407	2	0
1567	1	0
30995	2385	0
4302	1	0
12368	1	0
2016	0	1
15351	2	0
4129	0	3
1667	8	0
6543	0	4
3042	0	4
33160	1	0
15177	1	0
4358	2	0
16550	1	0
69251	1	0
16316	1	0
20215	0	20
15	0	2
4614	12	0
25563	1	0
32131	1	0
8081	0	1
59490	0	2
26715	2	0
12072	0	2
14676	0	1
3986	1	0
4010

chain 327277 HG00321_chrY 45747808 + 19236201 19239658 HG002_chrY 62432599 - 43575590 43579047 4
3457