##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 1779090795 HG03732_chrY 52035213 + 1245 52030553 HG002_chrY 62432599 + 2 62432577 1
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23	0	6
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8	4	0
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1029	2	0
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17	0	27
7	40	0
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68	1	0
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1831	1	0
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43	0	4
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75	0	9
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1334	8	0
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21	273	360
40	2	0
14	0	4
126	0	2
16	8	0
1487	0	2
13	0	3
3421	0	9
294	0	6
1608	0	2
342	11	0
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20158	0	1
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102	0	4
2055	0	2
588	1	0
162	0	1
4523	4	0
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637	0	8
501	0	4
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269	4	0
79	4	0
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2225	0	2
1735	0	7
847	0	1
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853	5	0
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4	18	0
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5	0	8
8	0	1
9	22	64
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15	2	0
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25	0	1
12	0	1
22	0	1
6	16	13
86	12	0
53	51	0
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16	0	18
68	0	1
6	0	14
177	0	26
6	0	118
1065	1	0
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176	0	5
964	0	12
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164	0	3
4	1	0
4727	1	0
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183	17	0
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23	0	4
12	8	0
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4739	0	3
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102	0	4
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1569	30	11
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743	4	0
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623	0	1
51	0	121
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24	8	0
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772	12	23
18	59	58
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7	1	0
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704	1	0
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65	32	0
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11	16	0
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37	0	1
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4	2	17
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6	12	0
43	32	0
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6	24	0
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24	1	0
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42	0	3
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60	13	0
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4	4	3
12	44	15
11	0	1
1	0	6
15	1	0
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1527	6	0
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31	1	36
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199	1	0
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44	0	87
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7	34	35
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6684	0	5
467	0	5
138	0	5
736	5	0
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2681	10	0
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18	5	0
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11	2	0
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297	0	5
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19	0	10
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21	32360	47635
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251	10	1378
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13	0	1
1927	28598	14932
8180	8511	5770
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8	10	0
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479	0	10
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1363	0	5
6569	28723	1275
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34	0	5
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1746	24818	16546
2715	5	0
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28	5	0
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33	5535	0
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264	0	10
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44	38885	0
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1453	0	15
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4	10	0
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1	0	5
5515	15	0
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96	1	0
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1473	11060	0
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228	36564	8892
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76	0	5
1304	0	3
289	10	0
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32	15	0
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6030	0	10
37	0	10
325	7641	10781
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8	0	5
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24	0	2423
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3955	5	0
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3934	34300	25802
484	0	25
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29	0	4
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12	0	2
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4075	3371	3372
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50	249	1
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4	1356	87
30

chain 346946989 HG03732_chrY 52035213 + 6288930 9982178 HG002_chrY 62432599 - 52562439 56521946 2
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43	1	0
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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
1981	0	2
114	0	6
9867	18	0
10	2	0
3131	12	0
27	2	0
17557	0	2
23658	0	2
70950	0	6
24806	3	9
32	0	1
718	2	0
9709	0	10
38150	0	1
5172	1	0
10330	1	0
18472	1	0
15365	3	0
45	15	0
6	0	12
65	9	0
2765	2	0
19449	8	0
30	2	0
19898	2	0
37608	0	1
13102	1	0
3763	26	0
25288	0	3
53684	4	0
13479	1	0
8455	2	0
17473	0	2
1696	4	0
16471	0	2
13047	3	0
10426	0	1
6180	0	2
10520	0	8
1850	0	2
3669	0	6
177	0	1
9936	0	2
44819	2	0
18399	0	2
6229	1	0
2083	0	1
1489	0	14
38285	0	2
21378	18	0
20398	0	52
117	26	0
10671	8	0
4355	4	0
12877	0	1
24378	2	0
2563	0	6
4059	0	4
5009	1	0
25604	1	0
4144	6	0
8394	16	0
11600	1	0
33916	0	9
140	3	0
44660	0	1
70784	12	0
57825	1	0
3955	0	1
12745	4	0
18407	5	0
53	4	0
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
55	4	1
35799	0	16
101600	4	0
39	4	0
6607	5	0
4382	0	1
1660	3	0
42	12	0
106	4	0
1	1	0
2645	0	4
50564	6	0
20876	10	0
20	5	0
29683	0	1
26414	1	0
19917	1	0
16019	4	0
22494	26	0
23915	0	4
47144	50	0
119	225	0
37624	16	0
8186	0	4
23423	0	8
3845	0	4
28559	46	27
18	2	0
21	0	2
31720	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
54525	0	1
2752	4	0
19674	0	3
1936	10	0
26	2	0
3937	0	4
21681	0	1
4505	0	4
250	0	1
1372	0	1
42911	1	0
24021	6	0
55098	2	0
25121	0	1
16504	0	4
21711	1	0
22183	1	0
6414	8	0
2673	0	1
50462	1	0
27263	0	1
4369	1	0
38981	0	1
2839	0	1
40239	0	1
10234	0	1
53702	0	1
24999	2	0
32240	15775	0
88569	1	0
1535	1	0
22438	0	2
14515	0	6
11393	0	2
8083	4	0
12322	6	0
50837	0	4
1719	4	0
112350	2	0
2479	0	4
1769	0	2
13444	11	11
66251	1603	0
13440	0	1
18361	1	0
569	1	0
1721	0	4
311	0	1
311	1	0
292

chain 12137763 HG03732_chrY 52035213 + 24235618 24396439 HG002_chrY 62432599 - 38399346 38539790 3
17084	0	1
614	0	1
31	10848	0
4887	0	5
5572	0	3
352	0	1
4481	1	0
452	1	0
6954	0	1
7714	0	4757
650	20341	6035
7	1	0
2251	0	1
4310	1	0
1457	0	11
1558	1	0
3724	1	0
3316	4	0
3200	0	1
1162	0	2
860	0	1
9915	1	0
195	0	4
4134	15	0
740	0	1
912	2	0
2516	0	1
1668	1	0
2015	0	1
3430	0	8
754	0	1
32368	0	6
224	1	0
95

chain 3058952 HG03732_chrY 52035213 + 22110370 22142667 HG002_chrY 62432599 - 40507615 40539913 4
6287	0	1
26010

chain 327277 HG03732_chrY 52035213 + 18929350 18932807 HG002_chrY 62432599 - 43575590 43579047 5
3457

chain 321414 HG03732_chrY 52035213 + 14997809 15001213 HG002_chrY 62432599 - 47507067 47510475 6
2617	0	4
787

chain 6804 HG03732_chrY 52035213 + 24404578 24404738 HG002_chrY 62432599 - 38539790 38542814 7
2	0	2864
158

chain 2683 HG03732_chrY 52035213 + 12611505 12611533 HG002_chrY 62432599 + 12511308 12511336 8
28