##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 2144183287 NA18534_chrY 77637201 + 0 24480900 HG002_chrY 62432599 + 8 24033253 1
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29	0	4
1906	0	1
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489	0	48
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14	0	5
2338	6	0
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22	2	0
69	0	6
1323	0	4
61	4	0
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29	1	0
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302	1	0
7	8	0
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436	4	0
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41	8	0
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26	0	2
882	0	3
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893	0	2
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41	2	0
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22	4	0
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74	0	1
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43	0	8
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68	0	4
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634	6	0
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54	0	8
21	16	0
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61	1	0
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7	0	4
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41	0	6
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585	5	29
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10	0	5
70	5	0
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1768	6	0
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17	5	0
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46	354	167
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120	1	0
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653	4	0
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1214	0	4
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8	0	5
8	0	8
182	0	62
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8	27	0
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213	41	0
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395	1	0
30	419	200
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13	0	10
13	0	5
15	0	10
577	2	0
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322	0	1
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535	0	4
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61	0	7
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1044	0	4
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207	1	0
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7	12	0
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1445	63	0
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1374	0	8
614	6	0
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889	18	0
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322	0	1
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111	183	0
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70	3	0
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735	0	4
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267	25	0
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70	2	0
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18	0	3
58	0	1
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2174	12	0
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1093	1	0
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623	0	1
51	0	121
97	41	0
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459	0	3
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772	12	23
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704	1	0
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1	169	0
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15	52	12
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10	0	4
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2519	0	24
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31	1	36
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8	1	0
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20	1	51
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20	13	66
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31	16	121
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199	1	0
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63	14	0
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957	1	0
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96	0	2
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581	1	0
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1	5	0
134	0	8
1677	1	0
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538	1	0
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12	24	137
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79	15	7
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7	8	33
38	28	0
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9	1	0
4	7	26
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67	1	0
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4	0	39
69	3	0
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15	4	0
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48	11	11
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4	0	20265
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41	0	40601
4168	1	0
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1505	3	0
786	30	0
1937	1	0
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470	0	11
1	0	2
356	0	1
2000	0	5
1794	0	4
4582	0	18
2584	2	0
5071	0	1
12	2668	104118
3566	0	5
1691	0	2
105	0	6
7019	0	1
117	2	0
26	0	4
3134	0	14
9	2	16
1102	0	1
5068	0	1
1212	0	3
2580	0	8
10345	0	121774
1101	0	1
4227	0	1
471	0	13
356	0	1
3723	2	0
110	6	0
6982	0	1
133	0	4
854	0	1
2294	4	0
9	2	0
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581	0	4
93	4	0
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9857	2	0
102	0	2
10312	18	0
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2378	0	5
8932	2	0
16948	1	0
43	0	4
17988	2	0
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5732	3	0
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1262	4	0
4211	1	0
547	1	0
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2575	4	0
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372	0	2
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1312	1	0
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5297	1	0
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97	0	2
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52	0	4
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34135	2	0
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5551	0	10
46582	873552	311619
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580	5	0
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12538	0	1
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4569	0	5
7813	1378	0
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2736	0	1373
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122	260088	155929
8180	21644	6499
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119	190	0
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571	19080	27282
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694	4119	0
2	5	0
15335	0	1
120	44051	16546
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206	5570	0
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325	19204	3601
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8	11457	3245
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4075	3372	3372
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5335	2	0
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401	1	0
510	0	1
1479	0	1
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150	1	0
135	1	0
898	35972	261548
26453	1	0
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909	10	19
2130	0	3
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567	1	0
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11314	0	1
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4556	3	0
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23	0	1
3585	0	7
3	10	0
464	0	12
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24186	0	1
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2672	0	1
6338	8	0
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611	1	0
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34251	0	8
1723	0	1
912	1	0
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4867	0	4
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46244	1	0
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5547	18	0
51451	0	1
3267	0	3
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1952	0	8
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34	4	0
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12789	1	0
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912	0	1
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1163	1	0
3200	4	0
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3724	1	0
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1457	1	0
4310	0	1
2251	1	0
7	39415	6035
650	0	4757
715	1	0
6999	0	1
4952	1	0
2454	2	0
4459	0	10850
23	0	1
17699

chain 68448285 NA18534_chrY 77637201 + 75697707 76438550 HG002_chrY 62432599 - 158 785263 2
15	0	1
25	2	5
43	0	8
4	0	5
10	4	0
7	0	8
16	0	51
9	0	4
3	0	6
35	8	30
12	0	5
17	85	73
48	0	1
1	0	1
23	0	1
5	0	7
7	0	1
17	0	1
33	10	20
23	0	1
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3	0	1
13	5	9
10	0	4
19	14	55
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6	0	3
11	2	0
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16	4	0
14	1	0
19	1	0
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18	23	37
13	0	1
5	0	5
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13	19	0
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39	0	1
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11	0	3
27	1	0
21	5	12
18	57	12
22	155	8
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6	0	2
7	4	0
15	0	1
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5	7	0
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41	20	0
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12	39	5
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17	89	27
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12	7	1
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66	38	2
657	0	58
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120	0	6
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1972	0	1
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1309	0	3
1776	19	0
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172	1	0
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142	0	36
12789	2	0
37980	18	0
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2763	0	4
11555	0	1
36065	2	0
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32709	5	0
10529	758	4270
770	4	0
195	0	5
44	0	1
1298	1	0
416	5	0
3475	5	0
5528	30	0
1438	5	0
331	0	10
3180	5	0
3493	5	0
371	15	0
24	0	15
3088	0	5
2606	5	0
129	3484	0
10103	0	3609
114	0	155
45	0	3514
24126	40	0
41	20	0
519	0	1
11718	0	15
1672	40	0
1627	25	0
1860	3528	14047
120	0	20
494	1	0
1233	0	15
1686	40	0
1630	25	0
1863	40	0
5151	25	0
165	15	0
7080	15	0
3370	0	25
2515	185	3705
835	0	25
3511	0	25
3543	25	0
1661	1	0
5400	25	0
3535	0	25
518	0	5
29771	0	14139
2705	0	1
2243	0	15
1276	1	0
7069	1	0
7069	0	10603
66859	10	0
16044

chain 24639858 NA18534_chrY_random0000138 261195 + 2 261195 HG002_chrY 62432599 + 22992423 23253644 3
479	0	1
920	1	0
980	0	1
4392	1	0
12872	0	2
9842	1	0
19726	0	2
4	0	2
17467	4	0
18947	5	0
6462	1	0
6867	0	1
25276	0	4
274	0	2
11242	0	4
13117	0	7
1583	6	0
3838	0	4
1296	0	2
6764	1	0
19085	1	0
1979	26	0
34	26	0
287	2	0
196	2	0
12	0	2
28	0	2
888	0	58
21407	0	12
16305	0	2
12022	1	0
9840	2	0
16682

chain 12544339 NA18534_chrY 77637201 + 24480900 24630074 HG002_chrY 62432599 - 38401468 38539790 4
63	0	1
35	0	1
15477	0	1
31	10848	0
4887	0	5
10409	1	0
452	1	0
2002	1	0
4952	0	1
6998	0	1
715	0	4757
506	0	1
5052	1	0
1126	4769	0
7	1	0
2251	0	1
4310	1	0
1457	0	10
1559	1	0
3724	1	0
3316	5	0
3200	1	0
1163	2	0
862	0	1
9915	1	0
195	0	2
4136	15	0
1653	2	0
2516	0	1
1668	18	0
84	0	6
1925	0	1
3434	0	4
754	0	1
7360	1	0
175	1	0
24833	0	25
205	1	0
95

chain 9773202 NA18534_chrY 77637201 + 31670166 31873545 HG002_chrY 62432599 + 29089896 29276691 5
40	3554	0
2046	5	0
1986	0	15
1458	1	0
54	3565	3546
1329	3549	0
2230	0	5
7104	0	5
16	0	5
17676	8287	1907
687	1	0
300	0	5
7	0	10
3200	0	3500
7362	0	5
16998	15	0
457	0	15
219	15	0
494	14	0
754	0	20
13	10	0
12	0	5
606	2931	9978
2220	0	7053
3700	0	3554
3381	20	0
4963	49253	22629
6016	2	0
238	5	0
415	0	2422
206	1	0
8430	24208	24188
9	0	1
678	25	0
23	10	0
925	0	5
803	10	0
33	10	0
1756	0	15
490	0	1
1691	0	5
672	1	0
671	8	48
1390	15	0
2131	5	0
510	1	0
430	5	0
1024

chain 327177 NA18534_chrY 77637201 + 19436476 19439932 HG002_chrY 62432599 - 43575591 43579047 6
3456

chain 320916 NA18534_chrY 77637201 + 15504382 15507778 HG002_chrY 62432599 - 47507067 47510475 7
619	0	12
2777

chain 6804 NA18534_chrY 77637201 + 24638213 24638373 HG002_chrY 62432599 - 38539790 38542814 8
2	0	2864
158