##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 2262117183 HG00329_chrY 56090397 + 16 56086227 HG002_chrY 62432599 + 88 62432577 1
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62	8	0
29	16	0
690	5786	0
18	797	8
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239	0	1
153	2	0
362	2	0
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500	0	1
487	0	1
82	0	1
316	0	1
894	0	8
49	1	0
5073	0	2
871	0	1
3301	0	1
1082	0	259
2738	4	0
18	0	4
318	4	16
48	0	2
5641	3	0
1867	0	6
31	0	16
484	0	1
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1381	135	0
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4	0	1
1200	148	0
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2950	4	0
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45	135	0
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2389	4	0
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107	0	162
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557	0	4
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33	0	36
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274	108	0
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9891	318	0
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298	0	2
33	3	352
322	2	0
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16	813	11
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966	0	1
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301	0	4
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965	0	1
15	0	1
12	162	347
63	2	0
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59	50	0
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8	2	0
81	20	0
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855	3	0
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1233	5	0
4748	2284	2236
44	0	23
5	0	4
264	4	0
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12	0	8
8	277	23
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1	26	0
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4	0	1
5	35	0
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8	28	17
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4	48	0
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14	94	75
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12	248	19
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4	0	7
174	0	1
3	353	0
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76	0	4
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7	25	17
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8	0	1
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6	528	29
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2005	83	39
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482	0	4
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8	0	49
16	148	0
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67	10	0
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146	5	0
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669	1	0
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1853	440	0
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697	0	2
14	3	0
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12	21	0
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8	0	8
323	0	6
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743	3	0
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1539	91	0
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1034	0	1
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1352	2	12
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136	4	0
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67	0	9
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34	32	0
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1	3	0
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38	28	81
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30	1	0
7	0	3
5	4	0
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47	2	1
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10	16	0
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28	11	0
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11	22	16
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1	0	4
22	13	16
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12	0	2
31	1	0
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6	16	0
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32	172	38
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4	0	2
6	0	1
5	5	0
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28	1	0
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7	3	0
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4	4	3
15	52	12
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15	1	0
7	22	0
70	0	1
14	0	1
111	1	0
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371	1	0
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3	1	0
109	0	1
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31	1	36
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8	0	3
4	0	26
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22	0	1
1	0	7
11	3	0
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42	24	106
14	0	36
18	16	121
1733	0	2
1373	3	0
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199	1	0
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63	14	0
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536	0	2
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80	1	0
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12	128	24
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14	78	0
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2	6	0
18	167	244
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8	0	4
5	0	3
14	0	1
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18	137	46
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32	1	0
4	39	2
11	0	3
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8	1	0
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65	14	0
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19	19	35
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8	1	0
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8	31	8
18	137	104
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20	17	0
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16	16	0
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9	0	22
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3357	31	0
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46582	977412	311619
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129	9018	50484
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9	9449	8046
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141	7500	322946
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94	0	1
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65	1	0
44	1	0
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648	39675	39663
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65	4	0
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267	42124	29541
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11257	2	0
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173	5	0
9363	5	0
3089	5	0
4508	0	6197
263	0	10
538	0	5
623	0	10
1202	1	0
474	1	0
253	0	10
1330	5	0
232	0	1
2864	5	0
176	0	15
875	0	1
480	0	1
105	3092	0
148	0	12407
3835	1	0
6755	5	0
2895	5	0
2856	0	10
3221	5	0
16952	5	0
16098	2474	0
8579	0	15
2804	0	5
3328	5	0
131	20	0
33	0	1
1985	0	15
20	10	0
146	2	0
532	30	0
2734	20	0
2003	0	5
16502	25	0
79	1	0
156	1	0
2179	15	0
355	0	20
5	0	5
47	0	1
156	0	1
783	5	0
435	0	5
965	0	15
306	10	0
26	10	0
61	1	0
1024	0	2764
1656	15	0
73	1	0
2681	5	0
1000	0	5
1758	0	10
3759	5	0
1745	0	5
85	0	1
2263	385	16943
311	0	1
318	0	5
5235	1	0
253	16538	4
2590	10	0
7981	31369	24284
13915	0	5
2529	1236317	1140961
40	3559	0
1932	0	1
105	0	5
18	0	5
1966	0	15
1512	5	0
13	10153	24397
10100	1	0
300	0	5
7	0	10
3290	15	0
6663	0	1
4108	0	5
7084	5	0
1	10	0
2464	0	7070
379	15	0
691	10	0
1878	5	0
6468	3526	3536
2220	0	7053
3700	0	3554
8344	67119	64544
4233	0	15
490	0	1
429	0	7121
2624	0	5
918	0	5
1237	10	0
1361	15	0
2211	15	0
2270	5	0
1183	1	0
44	10	0
810	32270	25172
1146	0	5
6349	2411	2411
5477	0	2
264	0	1
1087	0	4834
43	5	0
792	1	0
227	2	0
1446	1281	6121
1826	2420	0
281	2	0
2883	4979	0
17962	0	1
9508	1	0
10190	19914	1008
4717	11758	8209
12057	3534	0
7335	0	5
2414	27422647	32245133
791	0	2414
392	1	0
1752	5	0
1166	1	0
1035	0	7
199	5	0
656	1	0
1382	0	2414
15	0	1317
1	0	3505
110	2	0
244	0	2
2167	0	2
2285	0	3
9543	1	42398
1075	0	15
2243	0	1
1660	10	0
9	30	0
1042	0	1
442	15	0
380	1	0
1276	0	15
2243	0	1
7068	0	1
2720	0	10604
9169	15	0
24645	0	25
3519	25	0
5416	1	0
1584	0	1
7722	0	7080
15224	40	0
1849	25	0
1644	40	0
1686	0	15
1233	1	0
494	0	20
120	3488	14047
6347	10	0
3555	0	1
513	20	0
61	40	0
21668	10	0
26974	3503	0
5828	0	15
24	15	0
371	5	0
4402	0	3498
552	30	0
2030	5	0
3498	5	0
3475	5	0
32	0	14027
3469	5	0
32709	5	0
442	0	3
37203	0	2
32577	4	0
109	0	8
36	0	8
3325	0	1
11555	0	2
2765	0	6
314	0	1
10671	0	3
9579	1	0
6804	14	0
37980	2	0
18364	4	0
4328	4	0
10053	1	0
18648	19	0
1776	0	3
1309	1	0
724	0	1
1972	4	0
1725	5	0
866	1	0
16126	0	1
2768	0	6
7336	0	2
8119	0	5
407	1	0
1864	6	0
7215	0	1
3912	0	4
915	0	3
15804	0	33
11481	1	0
4807	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	2
2724	3	0
4392	0	1
9625	1	0
21629	1	0
73	0	1
10647	1	0
1366	0	1
1518	1	0
338	0	3
255	2	0
11013	1	0
951	1	0
16690	0	2
7342	1	0
7794	0	2
3776	29	0
27	0	58
687	6	0
106	6	0
82	0	6
49	0	45
23	14	50
10	0	6
6	0	4
12	2	0
8	0	1
6	0	5
6	0	1
22	4	0
12	0	2
17	5	0
17	0	54
9	0	5
6	0	1
4	17	0
1	0	1
17	1	25
19	0	2
6	0	1
17	86	35
26	21	6
12	0	1
12	25	9
17	23	19
9	1	0
1	5	0
12	1	0
48	7	0
31	4	0
7	23	29
40	95	8
22	40	9
21	5	0
33	1	0
8	1	0
5	6	31
38	0	5
4	20	0
59	0	1
2	0	5
12	3	0
13	0	1
2	0	80
9	3	0
61	0	2
4	1	0
5	3	0
9	25	1
27	0	3
14	0	4
15	1	43
78	4	0
33	0	1
2	0	47
12	0	1
50	101	15
11	0	2
74	2	5
4	1	0
25	4	0
36	0	6
32	4	0
66	4	0
70	4	0
60	0	1
6	1668	1
56	0	5
53

chain 16209069 HG00329_chrY_random0000046 340549 + 7 175567 HG002_chrY 62432599 + 18678070 18853552 2
468	1	0
259	0	1
232	0	1
233	0	1
161	0	1
358	0	1
821	0	1
157	0	1
238	0	1
482	0	1
29	1	0
535	0	1
605	0	1
684	3	0
6725	0	3
1	0	1
4	0	4
27342	1	0
3498	0	1
5641	0	1
12056	8	0
52	0	12
1952	4	0
2252	1	0
11359	2	0
32	4	0
2858	3	0
4075	3382	3382
2124	6	0
9919	1	0
9025	3	0
2383	4	0
23927	4	0
916	1	0
1529	4	0
1524	2	0
9572	25	0
6	4	0
10120	12	0
59	3	0
47	12	0
1	2	0
17806

chain 15221948 HG00329_chrY_random0000046 340549 + 175567 340549 HG002_chrY 62432599 - 43575590 43740479 3
21263	2	0
1	12	0
47	3	0
59	13	0
10120	4	0
6	25	0
9571	0	1
3053	1	0
24843	6	0
2383	3	0
9025	1	0
6293	0	1
3625	6	0
2125	3371	3372
4075	0	9
2858	2	0
32	2	0
11359	1	0
2252	4	0
2016	12	0
56	3	0
10824	2	0
6818	0	1
26646	0	1
120	0	1
87	1	0
499	0	1
36	1	0
67	1	0
30	1	0
42	1	0
421	0	1
178	1	0
179	1	0
446	1	0
46

chain 7198256 HG00329_chrY_random0000064 79074 + 0 79017 HG002_chrY 62432599 - 62027104 62108890 4
453	0	2
229	0	1
23	0	145
90	0	464
56	0	348
49	421	58
278	0	1
40	0	1
294	1	0
364	1	0
528	1	0
3028	0	4
117	8	0
905	4	0
2119	1	0
915	0	4
102	0	32
1100	417	0
1404	4	0
1294	123	0
2231	1	0
3409	0	1
11	0	1
951	0	3
14	4	0
348	8	0
51	0	2
75	3	0
881	0	8
44	0	12
10	4	0
4	0	14
2	0	8
712	0	2
602	0	9
632	156	0
198	18	0
1436	0	6
282	0	2
34	0	2
222	0	3
1087	0	1
419	1	0
256	0	8
29	1	0
225	0	2
3	0	333
6	0	1
13	1	0
20	0	1
81	0	67
10	1	0
28	0	1
46	0	1
20	1	0
37	0	2
40	6	0
12	0	7
10	0	2
4	0	15
59	0	1
5	0	14
27	37	0
11	0	2
39	0	8
24	0	105
21	0	2
10	4	11
44	0	2
7	0	14
8	3	0
61	2	0
6	0	9
25	2	0
15	1	0
50	2	0
20	4	1
44	0	2
2	0	65
103	0	196
29	2	0
36	0	67
425	1	0
47	0	36
53	2	0
73	2	0
47	0	65
10	2	0
65	2	0
155	4	0
18	1	15
11	2	0
27	0	1
37	0	2
5	0	33
27	2	0
13	1	0
56	0	130
132	2	0
15	0	1
5	0	65
61	0	1
7	1	0
109	2	0
65	2	0
65	0	2
65	0	2
65	2	0
11	0	65
186	2	0
252	0	67
77	2	0
65	0	2
21	0	64
109	0	465
74	2	0
197	0	2
110	0	2
82	4	0
248	1	0
747	0	62
390	1	0
2275	0	4
630	12	0
288	4	0
24	0	1
1	0	3
48	8	0
147	0	72
2557	0	1
316	0	5
487	0	1
209	5	2
606	0	1
790	1	0
1329	8	140
1863	88	0
4096	0	4
686	1	0
338	2	0
322	0	1
296	0	1
450	2	0
836	0	1
112	0	80
331	4	0
8	8	0
259	1	0
1657	0	2
3947	54	0
1605	1	0
150	1	0
8483	0	21
1073	0	4
23	0	4
47	3	0
155	0	4
21	0	12
181	0	58
831	0	1
7	0	1
1433	240	2
167	1	0
2297	57	61
464	0	2
96	21	20
123	0	1
199	0	1
55	0	9
98	0	3
155	0	23
4	0	88
5	9	0
38	39	29
21	38	0
116	0	1
264	1	0
52	0	1
43	1	0
45	0	1
96	0	1
41	0	1
77	0	3
12	0	9
268	0	2
176	0	68
54	1	0
67	0	101
54	0	1
22	0	51
16	0	154
6	0	17
9	0	1
19	1	0
2	0	172
6	0	13
4	0	26
13	13	0
52	0	119
13	0	34
8	0	24
7	0	1
4	0	25
2	0	17
41	0	25
72	9	0
44

chain 3742329 HG00329_chrY 56090397 + 19632343 19672011 HG002_chrY 62432599 - 42850342 42889998 5
19965	4	0
6526	4	0
10499	4	0
2666

chain 427764 HG00329_chrY 56090397 + 23422599 23427110 HG002_chrY 62432599 - 39338719 39343231 6
2490	0	1
2021