##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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29	4	0
1674	3	0
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76	0	2
359	56	0
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831	2	0
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225	0	9
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852	52	12
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1069	2	0
654	1	0
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442	1	0
57	0	2
871	3	10
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17	0	27
7	40	0
5635	1	0
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6348	2	0
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2047	1	0
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18	22	49
63	4	0
1339	308	0
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60	390	0
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49	0	2
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1200	148	0
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560	0	4
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75	0	9
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35	1	0
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69	1	0
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3740	318	0
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4796	5694	23404
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1	0	2
356	0	1
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110	0	2
4559	18	0
2540	0	2
26	4	0
842	0	1
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402	3	0
786	24	0
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3402	0	1
471	0	13
356	0	1
3303	0	1
390	0	4
51	0	1
51	0	16
2971	0	20314
1228	0	1
2966	2	0
24	0	2
2	4	0
4239	1	0
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4551	0	2
22	0	1
49	0	2
24	0	12
4559	18	0
6815	1	0
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2358	0	5
1303	1	0
413	2	0
78	6	0
4056	0	4
526	0	18
2584	0	2
1196	0	1
3872	0	1
12	2668	104118
3566	0	5
1691	0	4
32	3	1
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655	0	1
117	4	0
1714	1	0
664	3	0
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35	2	0
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42	6	0
532	0	1
81	1	0
722	0	1
327	0	1
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613	0	2
370	1	0
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44	0	1
337	1	0
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89	0	4
22	0	5
71	1	0
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17	0	491
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96	1	0
281	0	7
2	388	0
92	0	14
43	0	1
51	0	30
78	1	0
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54	0	1
329	0	5
560	1	0
43	0	4
240	0	1
153	20	223258
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546	0	1
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35125	10004	0
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114	2	0
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27	7	0
7	0	29
21	0	5
82	5	0
23	0	5
147	0	29
3020	31	0
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5719	0	8
10468	4	0
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72	0	2
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26	8	6
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364	1	0
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687	0	4
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2711	0	20323
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7592	0	1
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3473	5	0
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12293	317738	311619
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1181	1	0
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19016	1	0
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8	7359	0
121	19102	12166
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2852	129701	120200
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5	0	25
102	9616	0
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926	0	10
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202	0	25
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1912	0	40
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76	0	5
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8	11462	3245
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10	9	0
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6	50	0
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1135	12	0
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18	0	8
7481	4	0
5818	1	0
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377	1	0
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530	2	0
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13	3	0
1	0	3
110	0	4
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74	4	0
4	0	1
1158	2	0
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3569	0	1
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79	8	0
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1732	0	5
1913	1	0
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773	0	1
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7225	3	0
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173	2	0
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32	0	4
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44	0	2
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60	8	0
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907	1	0
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1378	1	0
574	4	0
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4075	3372	3373
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46	2	0
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17806	3457	3457
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1	0	1
1494	0	24
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44	8	0
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53	0	2
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3742	1	0
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86	1	0
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27	27	0
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18	4	11
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42	6	0
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185	48603	6037
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6360	2	0
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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
5488	0	15
156	5046	7458
173	0	5
7	10242	14904
812	15	0
11612	7060	0
67	0	15
794	0	15
115	5	0
2594	15	0
5659	0	7072
394	1	0
632	0	15
369	0	15
898	0	5
812	0	5
42	10	0
51	1	0
373	53109	168744
5845	1	0
1041	10	0
2952	0	26846
15876	1	0
3534	0	1
3534	1	0
3534	1	0
4811	0	15
3363	5	0
2415	0	10603
3534	0	1
167	3504	0
12	0	5
954	0	10
81	0	15
416	10	0
152	0	45
125	20	0
92	0	1
1459	1	0
656	0	1
6412	1	0
1254	25	0
4986	0	14139
2092	25	0
3557	15	0
2235	1	0
1194	0	1
5874	1	0
179	5	0
946	10	0
86	15	0
414	0	5
156	45	0
122	0	20
583	0	5
150	1	0
432	0	15
566	5	0
940	10	0
101	15	0
8	25	0
381	0	10
168	45	0
122	0	20
103	1	0
2723	25	0
3356	0	15
7086	0	15
3693	25	0
1881	1	0
1480	0	15
3520	0	15
174	0	25
4078	0	7080
21651	1	0
494	0	20
74	0	25
14	5079	1599
1328	1	0
494	0	20
66	0	40
6429	0	1
494	20	0
66	40	0
13419	0	1
513	20	0
61	40	0
51377	0	5
14	0	5
387	1	0
334	0	15
134	5	0
2199	0	15
24	15	0
777	1	0
334	0	15
134	5	0
3513	0	3498
552	30	0
2419	1	0
341	0	15
129	5	0
8828	21497	10994
3805	5	0
7804	15	0
24905	5	0
37648	0	2
32577	4	0
153	4	0
3333	0	1
5649	6	0
26	1	0
5880	0	4
2763	2	0
10992	0	6
16380	2	0
48305	0	10
5352	4	0
2677	2	0
4328	2	0
928	1	0
6743	0	4
2378	1	0
172	1	0
18476	19	0
1776	0	3
1309	1	0
724	0	1
1972	4	0
1725	3	0
5522	0	2
1476	0	1
109	0	1
3452	0	1
2733	2	0
3695	0	1
2723	3	0
45	0	6
11	0	3
6920	0	1
401	0	3
10394	2	0
50629	0	1
80883	0	2
16699	1	0
3356	0	3
14	2	0
6284	1	0
2438	2	0
106	0	2
160	0	4
24	0	4
68	0	4
6	2	0
37	0	4
134	2	0
4888	0	1
1543	3	0
475	0	3
3645	0	6
5	0	6
77	19	0
1489	1251	0
1129	0	3
4424	0	6
120	1	0
466	0	2
160	47	0
31	103	0
27	58	0
715	42	0
30	6	0
38	0	7
20	1	0
40	9	10
28	0	8
30	0	5
9	13	0
27	24	0
1	0	1
6	1	0
24	0	7
50	1	12
6	1	0
13	0	1
8	8	26
30	0	2
9	0	8
8	2	0
3	0	1
10	4	1
11	0	2
6	8	0
28	0	54
9	0	5
6	0	1
5	0	1
7	56	55
6	1	0
19	20	5
14	0	1
7	52	29
9	0	2
12	0	1
21	15	0
17	66	728
9	3	0
1	0	4
10	9	0
15	0	4
46	0	13
3	0	33
7	0	35
9	1	0
4	0	12
10	1	0
33	61	195
15	4	0
43	0	1
1	0	4
17	4	0
51	1	0
15	412	156
30	1	0
2	4	0
20

chain 11271091 HG00096_chrY 52898475 + 23998796 24149877 HG002_chrY 62432599 - 38399346 38539790 2
17699	0	1
23	0	10850
6913	1	0
4938	0	1
13	0	1
6999	1	0
105	0	1
53	0	4
552	0	2381
638	1	0
67	4	0
123	1	0
13	4	0
207	6	0
429	1	0
145	1	0
20	1	0
8	15	0
46	0	1
62	0	1
60	0	4
498	0	2
210	1	0
435	29933	6092
7	1	0
2251	0	1
3446	1	0
864	1	0
1457	0	11
1558	1	0
3724	1	0
3316	5	0
3200	1	0
1163	0	2
860	0	1
9915	1	0
195	0	8
4130	12	0
740	0	1
912	2	0
2516	0	1
3683	0	1
3438	12	0
33123	0	7
223	1	0
95

chain 3058316 HG00096_chrY 52898475 + 21781183 21813476 HG002_chrY 62432599 - 40507615 40539913 3
6287	0	1
5505	0	4
20501

chain 427764 HG00096_chrY 52898475 + 23114365 23118876 HG002_chrY 62432599 - 39338719 39343231 4
2490	0	1
2021

chain 327277 HG00096_chrY 52898475 + 18600492 18603949 HG002_chrY 62432599 - 43575590 43579047 5
3457

chain 322611 HG00096_chrY 52898475 + 14668721 14672129 HG002_chrY 62432599 - 47507067 47510475 6
3408

chain 6804 HG00096_chrY 52898475 + 24158016 24158176 HG002_chrY 62432599 - 38539790 38542814 7
2	0	2864
158

chain 2683 HG00096_chrY 52898475 + 12282361 12282389 HG002_chrY 62432599 + 12511308 12511336 8
28