##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 1871603514 HG02602_chrY 55325284 + 656 55321263 HG002_chrY 62432599 + 2 62432577 1
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7	40	0
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11	163	360
62	12	0
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16	8	0
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7	1	0
178	0	4
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572	0	1
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23	0	180
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1569	0	756
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266	0	43
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447	0	4
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5	0	1
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761	0	1
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501	0	4
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280	8	5
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18	2	0
830	10	0
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2424	0	1
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2	2	0
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12	8	0
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1483	231	0
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69	0	2
665	4	0
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76	0	1
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7	0	4
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623	0	1
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63	41	0
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24	4	0
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3894	104	52
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8	0	3
1014	1	0
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1	3	0
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39	52	12
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15	1	0
7	33	0
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1	6	0
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9	0	29
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37	2	0
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56	4	0
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9875	1	0
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4	6	0
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4030	0	20277
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356	0	1
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1716	4	0
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2	388	0
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11530	3411	3411
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287	1	0
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355	0	2
6818	1	0
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561	0	1
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12	0	2
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18	1	0
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13	0	5
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3569	1	0
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704	0	4
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19	1	0
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15892	873208	5393272
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2	8139	0
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7	20341	6035
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63	6019841	1617272
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790	7507	350
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385	3945	3945
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14553	1	0
2146	1	0
3356	2	0
17	2	0
2040	0	1
6977	0	4
68	0	4
6	2	0
37	0	4
134	4	0
716	3	0
4172	0	1
162	0	8
1373	3	0
475	0	1
3574	6	0
42	6	0
125	38	0
1489	1250	0
1129	0	3
4424	0	6
120	1	0
466	0	2
160	47	0
31	103	0
742	38	2
66	0	7
9	0	17
36	0	34
2	0	8
30	7	0
14	8	0
27	24	0
1	0	1
30	0	7
12	0	9
29	16	116
10	0	1
10	4	0
12	0	2
36	0	1
25	0	5
17	7	1
12	0	5
6	0	1
5	0	1
12	77	51
6	0	1
35	51	17
30	0	2
12	0	2
37	27	19
22	19	687
9	3	0
15	9	0
22	106	252
57	2	0
29	4	0
36	0	6
24	0	1
1	0	37
35	4	0
70	4	0
60	0	1
6	1608	1
56	0	5
53

chain 447710161 HG02602_chrY 55325284 + 19431450 24539158 HG002_chrY 62432599 - 38399346 43256012 2
17084	0	1
614	0	1
31	10849	0
4479	1	0
411	0	2
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	2384	0
7	1	0
2251	0	1
4310	1	0
1457	0	10
1559	1	0
3724	1	0
1300	0	1
2015	5	0
4363	0	2
860	0	1
9915	1	0
195	0	6
4132	15	0
1653	4	0
2516	0	1
1668	14	0
84	0	6
1925	0	1
3438	4	0
754	0	1
32368	0	14
3379	0	4
3330	8	0
35	4	0
44	0	3
10	0	8
39	0	4
46	4	0
34	2	8
70	16	0
27221	0	2
6901	0	3
3267	0	1
56998	1	0
9967	0	20
30961	0	8
104609	0	4
30746	0	1
695	0	6
13666	0	4
4922	6	0
3988	0	1
1723	0	4
466	3	0
33624	0	10
8774	1	0
611	0	2
1619	0	1
18593	4	0
4655	4	0
6338	0	1
19208	0	1
24186	0	1
3895	0	4
4059	0	1
23	0	8
8071	0	1
105	3	0
625	1	0
2688	1	0
4101	0	2
12290	1	0
39641	1	0
1442	0	3
23676	0	1
26959	0	3
2130	10	19
909	1	0
20069	1	0
101	0	2
4976	0	2
30799	0	8
12505	0	2
5451	0	3
30762	4	0
28984	0	1
27590	1	0
2797	0	24
443	0	28
152	2	0
247	2	0
184	0	28
15	0	13
28	0	2
122	0	56
47	0	13
26	2	0
14	13	0
13	54	0
92	0	52
90	26	0
34	26	0
27826	0	4
5112	7	0
1616	14	0
13117	0	4
11217	0	2
25579	0	1
13275	5	0
36480	2	0
60328	0	3
5413	0	2
7428	2	0
2458	0	1
2565	4	0
63	12	0
232	1	0
35577	0	21
117	0	1
1663	0	1
18404	0	1
897	16	7
15863	2	0
36941	0	3
43796	1	0
4430	2	0
5151	8	0
4076	0	1
2687	0	1
622	0	3
117	1	0
12163	0	2
3870	0	1
11466	0	2
6076	0	3
12024	12	0
11197	1	0
2174	321	0
7283	23539	0
2872	0	4
11206	0	1
13434	0	4
44203	4	0
26732	0	6
6282	0	1
79673	0	12
101	0	2
10	2	0
11	11	0
1	1	0
22	12	0
18	77	0
11	2	0
5	10	0
7036	1	0
1	1	0
20	1	0
687	4	2
4	0	2
5181	0	1
15940	0	4
2198	0	1
40063	0	3
17033	1	0
9721	1	0
4532	2	0
1204	12	0
15412	2	0
38347	12	0
9540	71264	326
72136	0	1
40493	0	1
2711	0	4
44684	1	0
16656	1	0
15713	0	1
18721	0	1
39092	4	0
32	0	2
23773	0	1
10929	1	0
29939	0	1
34602	8	0
4813	4	0
53	0	4
5565	0	3
1146	1	0
3022	0	1
1877	0	16
5932	2	0
32	0	4
21268	0	8
15689	0	1
21854	0	4
12125	8	0
4640	1	0
8384	0	1
5505	0	4
1257	0	1
21374	1	0
4989	0	1
62469	0	2
29309	0	3
13926	0	1
7072	4	0
66728	2	0
34977	1	0
41395	0	1
5936	0	1
20524	1	0
799	12	0
16385	1	0
8677	0	2
51921	1	0
13515	14	0
33584	1	0
13882	1	0
40254	0	1
11551	0	1
69702	0	6
32422	0	4
60870	2	0
43	2	0
34022	125	0
13197	0	126
1871	0	125
2775	1	0
1044	125	0
41	21381	17755
13536	250	0
37	3749	0
52	2624	0
4515	0	500
909	250	0
9237	1124	0
26	875	0
145	0	125
78	0	125
123	0	125
16	0	999
47	0	625
984	0	250
871	0	375
157	0	1249
294	0	125
333	1	0
246	1	0
70	5868	3869
247	0	125
6490	0	1
6136	2	0
2201	498	0
195	1	0
518	1	0
82	0	2
286	0	1
15	7	0
6	0	7
137	0	249
27	0	1
269	0	2
280	0	1
266	0	125
239	0	1
28	0	124
330	1496	0
225	0	2
124	2	0
293	0	125
122	3	1001
16	5	0
2	0	5
102	1	0
292	0	124
307	0	123
603	0	2
164	0	1
124	1	0
523	0	247
434	2	0
283	10	9
80	0	2
105	1	0
267	2	0
158	0	3
3	4	0
83	0	2
164	0	1
130	0	1
244	1	0
98	0	1
63	0	125
43	28134	29505
324	0	1
239	0	85
5	0	39
192	0	1
176	0	250
12252	0	125
9658	65659	3
22154	0	1
3048	67398	0
20986	0	123
27067	0	125
3436	0	1129
5795	125	0
2121	8273	0
702	0	872
104	0	5
2	5	0
180	872	0
23428	1	0
20163	2	0
2759	0	1
6580	0	1
874	1	0
10523	9	0
1420	0	1
1340	0	1
17451	5	0
3839	1	0
51302	4	0
19716	0	1
22212	1	0
2441	0	1
1960	3	0
21375	1	0
31924	1	0
46021	0	1
482	0	1
6420	2	0
10443	2	0
75905	16	0
7227	0	1
18844	1	0
3346	0	1
14440	0	3
43282	2	0
8374	0	4
24994	0	1
15506	0	4
2901	0	1
90916	1	0
275	2	0
3035	10	0
12425	0	4
21202	1	0
16872	0	2
7920	0	2
3346	1	0
5302	0	1
1591	0	64
4	20	0
5	4	0
18	0	20
14625	0	1
13364	1	0
7890	0	2
5671	0	1
9090	3	0
23258	0	8
9101	0	1
3958	0	12
576	8	0
1856	0	2
8161	0	1
8712	0	1
20144	0	1
13069	0	1
2810	1	0
7269	0	2
33984	0	10
21189	10	0
18193	17	0
22223	2	0
44763	1	0
5933	0	4
31118	2	0
7837	0	4
67367	0	2
990	2	0
13666	1	0
4333	4	0
2334	1	0
2119	0	3
7981	0	2
18413	1	0
15409	0	2
23	0	2
15859	5	13
20	0	5
5663	2	0
50534	2	0
3003	2	0
2627	14	2
4032	0	12
4234	2	0
2725	0	5
5673	1	0
726	0	2
14322	3	0
15906	0	1
7754	0	1
3192	0	1
20884	14	0
6093	1	0
840	1	0
5681	0	1
27644	1	0
1399	1	0
16236	1	0
3742	0	2
131	0	2
14740	2	0
8095	0	8
604	39678	39663
644	0	28
8037	4	0
14738	2	0
104	2	0
7000	1	0
14320	1	0
29907	23	0
10409	0	4
20882	1	0
2532	0	1
8416	1	0
15906	0	3
14249	2	0
23	4	0
6450	0	5
10944	2	2
57	4	0
2627	2	0
5934	0	4
25159	0	2
21311	6	0
3182	0	4
4513	0	1
6293	0	1
10914	2	0
46662	3	0
13595	0	4
7776	0	2
35	5	0
10639	1	0
15459	0	12
4399	0	1
6711	1	0
10967	1	0
952	6	0
1314	1	0
2873

chain 76677424 HG02602_chrY 55325284 + 24639265 25451291 HG002_chrY 62432599 - 35962327 36786318 3
84	1	0
519	1	0
36	1	0
302	1	0
130	1	0
349	1	0
240	0	1
16	1	0
41	0	1
24	1	0
89	2	0
29	0	1
23	0	1
241	1	0
122	1	0
89	0	1
148	1	0
18	1	0
541	1	0
592	0	1
125	1	0
963	1	0
213	1	0
673	1	0
148	1	0
988	0	1
1165	0	1
89	0	1
88	0	1
8313	4	0
9270	6	0
9998	0	1
72693	0	2
34	2	0
82	0	2
6861	1	0
8257	1	0
5221	2	0
2	2	0
1926	0	3
18	2	0
12188	0	2
6508	0	1
7059	1	0
10022	0	1
4561	0	2
16	2	0
11460	2	0
7743	0	2
407	0	1
4842	0	2
2718	0	2
7193	1	0
16903	0	2
2705	0	1
213	1	0
7065	2	0
5060	2	0
22679	1	0
1454	1	0
67	1	0
555	1	0
11814	2	0
14	0	1
1692	0	1
2646	1	0
2580	0	1
2119	2	0
814	0	1
16850	4	0
1065	0	1
4341	6	0
2864	6	0
15028	12	0
21776	0	2
20	1	0
478	2	0
46	0	2
7163	1	0
518	1	0
30687	0	4
1773	0	1
912	1	0
1720	0	5
1345	0	6
4936	0	4
13665	2	0
688	0	2
16450	0	4
3825	0	1
7404	0	1
3048	4	0
28773	0	4
821	1	0
9867	0	1
6780	0	2
5111	1	0
25781	0	1
7973	0	1
12562	0	1
14828	0	1
3315	0	1
125	0	4
19676	4	0
2531	2	0
64419	1	0
10140	0	2
3264	0	1
471	2	0
17246	0	4
52	3	0
4135	1	0
2035	0	16
63	0	4
42	2	0
63	8	0
17	4	0
100	0	12
3376	0	4
3343	0	22
24857	0	2
7535	1	0
776	4	0
5340	2	0
1	4	0
84	0	14
1668	1	0
2474	0	2
1674	0	15
4120	2	0
214	0	1
9908	1	0
860	2	0
1159	0	1
3207	0	3
2013	0	1
1219	0	8
83	0	1
3722	0	1
1545	13	0
1473	0	1
4314	1	0
1555	398	12320
1446	0	1
6265	0	1
6999	1	0
4952	0	1
6913	1	0
17722

chain 30680227 HG02602_chrY_random0000675 332917 + 1 332472 HG002_chrY 62432599 - 43396101 43728521 4
15991	2	0
3	1	0
5	1	0
21786	1	0
10598	0	1
4088	1	0
2508	0	2
9508	8	0
44	0	16
1997	2	0
13649	0	4
2857	6	0
11706	1	0
16814	3	0
2364	4	0
3717	0	1
21167	1	0
1545	0	4
1449	0	1
48	0	1
12	0	2
9557	25	0
6	4	0
10120	13	0
17918	3457	3457
17806	2	0
48	3	0
59	13	0
10120	4	0
6	25	0
7050	0	2
2568	2	1
10	0	1
8	0	9
1439	0	8
2445	0	2
20226	1	0
6082	3	0
12643	1	0
8426	3372	3372
4072	0	12
70	0	3
2785	6	0
11391	1	0
2252	4	0
1952	0	24
40	8	0
9544	1	0
2512	0	1
5641	0	1
16843

chain 10681098 HG02602_chrY_random0000669 170326 + 57127 170326 HG002_chrY 62432599 + 18289135 18402363 5
1874	0	12
34	0	4
9423	0	1
65872	0	1
21278	0	13
6696	0	3
907	1	0
3918	1	0
500	0	1
14	0	1
323	1	0
556	1	0
647	1	0
428	1	0
7	1	0
715

chain 3742489 HG02602_chrY 55325284 + 24133473 24173144 HG002_chrY 62432599 + 19542601 19582257 6
2666	2	0
10499	8	0
6526	4	0
4450	1	0
15515

chain 372467 HG02602_chrY 55325284 + 26160940 26164885 HG002_chrY 62432599 - 36078953 36082898 7
3945

chain 327146 HG02602_chrY_random0000675 332917 + 179531 182988 HG002_chrY 62432599 + 18853552 18857009 8
3457

chain 322611 HG02602_chrY 55325284 + 14838161 14841569 HG002_chrY 62432599 - 47507067 47510475 9
3408

chain 2683 HG02602_chrY 55325284 + 12451830 12451858 HG002_chrY 62432599 + 12511308 12511336 10
28

chain 1346 HG02602_chrY 55325284 + 55322488 55322502 HG002_chrY 62432599 + 62432585 62432599 11
14