##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 2097166744 HG03654_chrY 51076144 + 1025 51068483 HG002_chrY 62432599 + 2 62432577 1
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42	0	3
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24	540	0
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4	54	0
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48	4	0
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1559	17	14
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540	0	296
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1483	231	0
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1926	1	0
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40	0	2
830	1	0
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356	1	0
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43	0	40601
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67	4	0
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2287	0	1
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7465	10	0
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13	3	0
1	0	3
39	0	1
74	8	0
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2467	2	0
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2437	46215	46210
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13	0	5
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3569	1	0
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71	19	0
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18	0	2
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88	4	0
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7	7	0
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46	0	2
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4072	3366	3367
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44	1	0
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1	0	1
1494	4	0
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648	39674	39663
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1622	0	1
1087	2	0
2677	1	5
7834	0	2
59801	0	2
10395	2	0
11128	4	0
919	0	1
3144	18	0
8900	1	0
764	80	0
2998	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	12	0
272	0	1
2725	2	0
4392	0	1
9625	1	0
11492	1	0
9884	4	0
253	1	0
73	0	1
10647	1	0
1366	0	1
1509	2	0
347	0	3
255	2	0
11013	1	0
168	0	1
782	1	0
7835	0	2
15	2	0
8958	0	4
138	2	0
5226	1	0
1856	2	0
11572	58	0
27	58	0
745	6	0
99	10	16
107	7	0
1	0	1
75	1	0
24	1	0
6	1	0
13	4	35
30	0	1
10	0	1
29	4	0
5	0	19
2	8	0
12	2	1
31	5	0
3	1	0
15	0	5
5	8	0
13	0	5
12	0	1
13	11	36
12	1	0
1	22	0
25	139	44
19	22	12
4	0	1
18	22	3
17	10	0
18	8	0
1	3	0
9	1	0
1	5	0
17	1	0
31	6	0
5	1	0
38	4	0
8	0	1
7	0	1
4	18	3
31	0	1
11	8	0
9	169	8
6	2	0
16	49	0
3	1	0
6	1	0
21	5	0
23	10	12
6	6	0
48	0	10
14	22	11
15	3	0
47	0	5
12	3	0
27	3	0
10	1	0
31	0	5
6	8	0
5	3	0
21	3	0
1	2	0
58	17	0
2	0	2
4	1	0
5	3	0
9	19	0
28	0	2
38	0	3
9	0	3
24	9	0
22	0	1
11	0	1
130	1	0
8	0	1
50	110	28
36	0	3
40	2	0
4	1	0
25	4	0
36	0	6
24	0	1
7	4	0
43	0	1
1	0	4
17	4	0
70	4	0
30	0	1
29	0	1
6	1668	1
56	0	5
53

chain 25296003 HG03654_chrY_random0000103 268060 + 0 268060 HG002_chrY 62432599 - 39175796 39443863 2
1838	0	1
18002	4	0
38175	0	6
18394	1	0
3264	0	28
152	2	0
247	2	0
268	0	2
525	26	0
27864	2	1
1279	0	20
3812	4	0
1616	12	0
13117	0	4
11242	0	2
25554	0	1
49755	2	0
52490	1	0
12	1	0
383	1	0
13

chain 5612223 HG03654_chrY_random0000202 108111 + 31657 107667 HG002_chrY 62432599 + 55767075 55838096 3
4778	0	5
3559	5	0
8016	15	0
3598	0	1
3058	5	0
694	0	10
1066	0	5
1808	120	7217
6988	0	5
8	3563	0
3573	0	5
173	1447	0
12298	10	0
404	0	15
754	8	0
556	0	5
2071	0	3564
1488	5	0
1612	10643	0
412	1	0
1039	0	1
2235

chain 4353976 HG03654_chrY 51076144 + 17038517 17084731 HG002_chrY 62432599 - 45214480 45260689 4
29427	2	0
2440	0	2
17	8	0
2478	0	4
239	0	4
180	4	0
2741	1	0
8677

chain 3742564 HG03654_chrY 51076144 + 19409292 19448959 HG002_chrY 62432599 - 42850342 42889998 5
19965	4	0
6526	4	0
4702	1	0
5797	2	0
2666

chain 2683 HG03654_chrY 51076144 + 12402123 12402151 HG002_chrY 62432599 + 12511308 12511336 6
28