##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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1643	7	0
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41	2	0
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43	0	8
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20	16	6
240	0	121744
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24	24	0
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2970	1	0
693	0	8
49	8	0
17925	0	8
4759	0	4
238	8	0
2616	0	4
5756	5	0
4414	2	0
2192	0	8
45	1	0
2171	4	0
1137	4	0
4879	1	0
19589	0	2
9636	1	0
28029	0	1
21996	4	0
18592	10	0
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4980	0	13
16534	2	0
11	2	0
62698	0	1
1351	2	0
58	2	0
22110	0	3
15358	0	1
4311	1	0
6259	0	6
5444	0	1
36039	0	1
7836	1	0
8887	1	0
3949	2	0
24366	0	4
158	4	0
926	1	0
6580	8	0
8935	2	0
52401	14	0
24354	0	1
26105	0	10
12316	4	0
328	12	0
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7321	1	0
17942	6	0
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5633	4	0
5816	0	1
9698	0	1
4816	0	1
2976	0	1
930	4	0
40264	2	0
3757	0	35
1275	0	2
4090	1	0
6458	0	3
5704	2	0
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6929	1	0
3692	0	2
10717	2	0
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2757	1	0
12298	0	8
23319	0	1
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10709	12	0
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23594	0	2
12615	0	4
1160	0	1
21764	1	0
14267	8	0
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7961	1	0
6396	1	0
766	0	1
19803	6	0
5827	2	0
859	0	2
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10644	1	0
4742	1	0
4429	1	0
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8435	2	0
6385	0	1
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530	0	2
7734	0	4
4	0	16
13	5	9
42	8	1
34	0	4
28	16	0
7094	0	1
4101	0	4
3090	2	0
10351	2	0
2437	46231	46210
10554	0	1
5292	0	4
4115	1	0
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66	4	0
48	0	4
1111	2	0
6613	2	0
533	8	0
8736	2	0
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13	0	5
19696	2	0
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379	0	6
862	2	0
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28	2	0
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8552	18	0
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460	2	0
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5718	2	0
2079	1	0
3278	0	8
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25	0	2
3569	2	0
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8529	4	0
4727	1	0
12599	1	0
6341	1	0
7212	0	4
79	16	0
18204	1	0
851	0	1105
3289	0	1
28913	0	4
13058	10	0
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12268	1	0
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51757	1	0
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4068	1	0
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71	19	0
1631	1	0
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4491	1	0
3517	0	1
6326	1	0
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1523	3	0
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34	0	2
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37	0	2
2819	0	1
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32	0	4
8718	0	1
1657	2	0
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6749	1	0
6447	0	4
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5163	12	0
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961	3	0
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6312	1	0
1	7	0
80	0	2
6	8	0
616	0	4
24145	0	20
1738	8	0
937	1	0
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430	0	12
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3522	0	1
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50358	0	1
34786	0	8
7797	0	12
19548	1	0
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11899	3	0
1655	1	0
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8426	0	3
23046	1	0
3	0	1
27354	1	0
3498	1	0
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13	0	12
11	0	28
1952	4	0
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32	2	0
2858	0	3
4079	3375	3375
2124	6	0
9919	1	0
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1529	12	0
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10	2	1
2568	0	2
7050	25	0
6	4	0
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59	3	0
47	4	0
1	2	0
17806	3457	3457
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109	10	0
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6	25	0
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2547	0	1
13	0	1
48	0	1
19	0	1
2978	2	0
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1495	1	0
5063	1	0
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2007	0	12
4	0	8
44	8	0
9508	0	2
2508	1	0
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5063	1	0
5535	1	0
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8	7	0
6718	0	1
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9743	1	0
1844	0	2
8645	1	0
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6712	1	0
1387	0	1
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3128	1	0
3473	1	0
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666	1	0
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195	1	0
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5632	4	0
4	2	0
4038	2	0
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6450	2	0
23	2	0
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840	1	0
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77	4	0
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881	4	0
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8087	2	0
83	2	0
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3742	2	0
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45	0	2
726	1	0
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141	0	8
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1	1	0
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550	0	1
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89	0	15
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18	4	0
5	20	0
4	0	64
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695	0	1
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337	32996	29501
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78	0	1
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3	7	0
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22	0	4
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36	8	0
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34	2	0
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32153	70943	326
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63	4791209	4794680
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33	164	8
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24	1	0
8	1	0
33	0	1
8	0	1
5	0	10
24	25	9
7	3	0
36	27	28
10	0	21
6	1	0
11	1	0
30	15	6
21	3	0
7	1	0
14	2	0
8	0	5
25	17	0
2	0	2
9	32	10
27	0	3
18	1	0
43	3	0
12	1	3
74	0	1
3	5	0
43	0	35
17	0	1
13	0	1
36	104	15
11	0	2
76	0	1
2	2	0
29	4	0
74	4	0
34	2	0
32	4	0
12	0	1
57	4	0
4	0	6
50	0	1
4	0	1
58	0	5
53

chain 11106757 HG02056_chrY 61667361 + 24473619 24619920 HG002_chrY 62432599 - 38399346 38539790 2
17699	0	1
23	0	10850
4459	1	0
2454	1	0
4952	0	1
6999	1	0
715	0	4757
650	27498	6035
7	1	0
2251	0	1
4310	1	0
1457	0	10
1559	1	0
3724	1	0
3316	3	0
4363	4	0
862	0	1
9915	1	0
195	0	4
4134	21	0
1653	4	0
2516	0	1
1668	1	0
2015	0	1
3434	0	4
8290	1	0
24833	0	18
212	1	0
95

chain 4355379 HG02056_chrY 61667361 + 17488237 17534467 HG002_chrY 62432599 - 45214480 45260689 3
13217	8	0
13204	1	0
5446	4	0
2497	0	4
239	12	0
11602

chain 327277 HG02056_chrY 61667361 + 19168822 19172279 HG002_chrY 62432599 - 43575590 43579047 4
3457

chain 6804 HG02056_chrY 61667361 + 24628059 24628219 HG002_chrY 62432599 - 38539790 38542814 5
2	0	2864
158

chain 2683 HG02056_chrY 61667361 + 12852095 12852123 HG002_chrY 62432599 + 12511308 12511336 6
28

chain 1346 HG02056_chrY 61667361 + 61664224 61664238 HG002_chrY 62432599 + 62432585 62432599 7
14