##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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1572	1	0
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41	2	0
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74	0	1
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43	0	8
4	4	0
29	4	0
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71	4	0
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68	0	4
44	0	4
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62	4	0
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7549	0	4
39	0	8
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1200	148	0
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45	135	0
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34	0	12
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712	2	0
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299	0	3
12129	106	0
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335	2	0
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4571	1	0
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70	4	145
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234	2306	2368
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59	0	4
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8	152	10
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14	95	75
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3	352	0
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13	560	75
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1434	1	0
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16	148	0
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738	1	0
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7	0	4
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7	0	24
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13	77	0
8	231	0
361	1	0
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341	4	0
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1	11	0
3432	0	2
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280	0	1
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1	8	0
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614	6	0
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548	0	23
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704	1	0
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23	50	7
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1	169	0
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11	3	0
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31	12	121
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160	0	3
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63	14	0
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961	2	0
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72	8	0
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1677	1	0
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34	0	20
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67	10	27
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67	1	0
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9	0	22
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207	3	0
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356	0	1
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1298	0	1
390	4	0
115	0	2
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620	0	1
823	0	1
1284	0	1
322	0	1
1795	0	1
210	0	3
3737	3	0
587	0	2
98	8	0
4054	4	0
8181	1	0
1607	1	0
5746	0	3
191	1	0
393	6	0
98	0	6
4054	0	4
3082	2	0
28	2	0
844	1	0
1505	0	3
2723	0	1
3402	1	0
471	13	0
356	1	0
3696	4	0
96	10	0
4580	0	18
5719	0	30
9866	0	4
115	0	2
19	1	0
4559	18	0
2540	0	2
26	4	0
842	0	1
1505	3	0
658	1	0
124	14	0
1116	1	0
824	1	0
1284	1	0
2327	3	0
258	0	13
356	0	1
3303	0	1
393	0	4
94	0	2
4604	18	0
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26	6	0
842	0	1
1505	3	0
786	32	0
3545	0	1
1795	0	1
471	0	13
356	0	1
2000	5	0
1109	3	0
191	0	1
428	0	2
106	2	0
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3110	10	0
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1303	1	0
393	4	0
98	0	2
1212	2	0
5932	2	0
30	0	4
838	1	0
1505	0	3
6126	1	0
471	13	0
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3692	8	0
100	8	0
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8198	5	0
1835	2	0
4559	18	0
2568	4	0
2344	3	0
658	1	0
3348	1	0
2117	1	0
210	3	0
269	1	0
3662	0	1
422	4	0
2	0	2
106	0	8
4030	0	20277
2952	1	0
117	0	2
3164	30	0
9	0	2
1926	1	0
1440	1	0
2444	1	0
1570	0	3
2580	0	6
4209	1	0
6098	50	0
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96	4	0
4582	0	18
2556	2	0
36	0	6
830	1	0
1505	0	3
786	0	32
1937	0	1
3402	1	0
470	11	0
1	2	0
356	1	0
2000	0	5
1693	4	0
103	6	0
7170	0	10
5071	1	0
7968	0	4
112	2	0
4168	1	0
14276	5	0
1301	0	1
497	0	2
45	0	40601
6982	1	0
121	0	2
22	4	0
2348	3	0
786	30	0
1937	1	0
3885	1	0
358	1	0
2001	0	5
1794	0	2
4209	1	0
375	0	18
2556	0	2
26	4	0
240	0	121744
602	0	1
1505	3	0
786	6	0
39	2	0
5329	0	1
472	0	14
355	0	2
3794	0	6
4209	0	1
383	18	0
4525	0	3
1183	0	4
37	0	121774
1103	0	1
4227	0	1
471	0	13
356	0	1
3723	4	0
26	0	1
73	0	10
4559	18	0
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133	0	4
2360	0	3
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1113	1	0
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471	0	13
356	0	1
3744	0	1
51	0	18
19	4	0
4567	18	0
2540	0	6
4	0	20
866	1	0
1505	0	3
794	2	34
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3402	1	0
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1	1	0
356	1	0
3303	1	0
396	0	2
100	6	0
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3360	3	0
555	0	4
3074	6	0
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22	0	4
6	0	6
10	0	8
1186	0	1
1149	0	3
786	0	28
1937	0	1
3409	1	0
486	1	0
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2023	0	5
715	3	0
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1	2	0
53	1	0
51	12	0
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3147	6	0
13799	1	0
43	0	4
17988	2	0
239	0	1
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3415	6	0
9519	0	2
8435	2	0
1753	0	9
46028	0	6
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69020	0	1
6362	0	10
21749	0	2
35125	10004	0
4029	4	0
70	0	12
12213	6	0
2309	3	0
5859	0	4
114	2	0
27	3	0
28	3	0
27	7	0
7	0	29
21	0	5
82	5	0
23	0	5
147	0	29
3020	31	0
1723	1	0
11168	1	0
5950	0	4
5719	0	8
10468	4	0
8537	1	0
616	1	0
2755	0	2
1755	1	0
3315	0	28
72	0	2
43	2	0
26	8	6
172	0	8
176	1	0
364	1	0
423	1	0
1272	1	0
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687	0	4
1019	13	0
310	0	1
1673	2	0
2334	1	0
1398	6	0
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320	1	0
375	0	2
2711	0	20323
1592	9	0
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285	0	20
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19	0	8
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3263	0	12
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39330	1	0
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2082	0	6
3468	0	5
3706	0	4
30235	0	344
12293	323363	311619
28743	5	0
1696	0	10
297	5	0
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844	0	5
932	0	5
844	0	5
191	15	0
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110	0	30
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4025	0	25
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69	0	10
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3390	0	5
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5439	0	5
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777	10	0
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1418	0	10
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19016	1	0
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8	7359	0
121	24622	12166
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2842	212519	185079
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557	0	30
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1	0	5
926	0	10
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202	0	25
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1912	0	40
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1473	11026	0
693	36631	8892
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76	0	5
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1999	10942	3245
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690	0	10
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3081	10	0
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10	9	0
14	0	235
8	55	0
16	25	0
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13	15	0
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12	15	0
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56	0	21
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6	50	0
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1751	15	0
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397	3731	3822
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3934	34325	25802
484	0	25
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2725	0	5
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12960	3411	3411
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5724

chain 23529861 200085_chrY_random0000119 253111 + 0 253111 HG002_chrY 62432599 + 18721531 18974539 2
5032	0	1
1176	1	0
1336	1	0
9600	0	8
1952	4	0
2252	1	0
11391	6	0
2785	0	3
70	0	3
4081	3367	3367
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1	2	0
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46	0	1
11	1	0
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13291	1	0
305	2	0
592	2	0
1435	4	0
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2527

chain 11117366 200085_chrY 52434251 + 23995515 24134662 HG002_chrY 62432599 - 38399346 38539790 3
17699	0	1
23	0	10850
6913	1	0
4938	0	1
13	0	1
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715	0	4757
650	20341	6035
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2251	0	1
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912	2	0
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754	0	1
32368	0	8
222	1	0
95

chain 3058316 200085_chrY 52434251 + 21777931 21810224 HG002_chrY 62432599 - 40507615 40539913 4
6287	0	1
5505	0	4
20501

chain 1311479 200085_chrY 52434251 + 1183064 1196965 HG002_chrY 62432599 + 963794 977702 5
1343	1	0
132	0	2
299	0	3
166	1	0
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649	0	1
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466	0	2
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514	0	4
857	0	1
1069

chain 1057892 200085_chrY 52434251 + 1121021 1133110 HG002_chrY 62432599 + 899681 911270 6
18	797	8
477	0	1
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151	0	2
362	2	0
387	0	3
960	0	270
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327	0	2
4	0	1
105	1	0
653	0	1
7	2	0
2391	0	3
195	0	2
558

chain 779666 200085_chrY 52434251 + 1170212 1178452 HG002_chrY 62432599 + 950852 959093 7
268	0	1
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657	0	1
5306	1	0
19	1	0
18	5	0
3	0	4
399

chain 739914 200085_chrY 52434251 + 1201730 1209535 HG002_chrY 62432599 + 982291 990101 8
576	1	0
2666	0	1
1355	4	5
809	0	1
1	0	1
1461	0	2
450	0	1
4	1	0
477

chain 708455 200085_chrY 52434251 + 1142712 1150270 HG002_chrY 62432599 + 921144 928704 9
9	0	2
1990	1	0
374	0	1
169	3	5
1519	2	0
155	0	3
1464	3	0
424	1	0
763	0	1
681

chain 442665 200085_chrY 52434251 + 1217468 1222179 HG002_chrY 62432599 + 997348 1002078 10
157	0	2
32	1	0
344	0	1
132	0	5
3	3	0
11	0	1
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688	0	1
702	2	0
436	0	14
2192

chain 435873 200085_chrY 52434251 + 1197070 1201658 HG002_chrY 62432599 + 977702 982291 11
256	0	1
4332

chain 427764 200085_chrY 52434251 + 23111088 23115599 HG002_chrY 62432599 - 39338719 39343231 12
2490	0	1
2021

chain 400688 200085_chrY 52434251 + 1103202 1107440 HG002_chrY 62432599 + 887735 891978 13
500	0	2
34	0	2
888	0	2
2448	1	0
367

chain 394360 200085_chrY 52434251 + 1134373 1138544 HG002_chrY 62432599 + 912535 916705 14
872	3	0
376	1	0
1813	0	2
611	0	1
495

chain 355893 200085_chrY 52434251 + 1178452 1182213 HG002_chrY 62432599 + 959148 962906 15
594	1	0
461	3	0
1820	0	1
882

chain 354572 200085_chrY 52434251 + 1159792 1163575 HG002_chrY 62432599 + 940261 944356 16
719	0	313
113	2	0
429	1	0
1683	0	2
836

chain 350016 200085_chrY 52434251 + 1212326 1216036 HG002_chrY 62432599 + 992575 996296 17
189	0	4
322	0	3
15	9	0
3	0	17
169	3	0
2744	1	0
255

chain 322611 200085_chrY 52434251 + 14974784 14978192 HG002_chrY 62432599 - 47507067 47510475 18
3408

chain 311725 200085_chrY 52434251 + 1109433 1112754 HG002_chrY 62432599 + 893943 897268 19
191	2	0
242	0	2
867	0	1
3	0	3
2016

chain 303922 200085_chrY 52434251 + 1167009 1170209 HG002_chrY 62432599 + 947653 950852 20
2514	1	0
685

chain 294733 200085_chrY 52434251 + 1150270 1153406 HG002_chrY 62432599 + 928708 931857 21
41	0	6
485	3	0
1233	0	3
385	0	7
240	0	1
247	1	0
501

chain 258910 200085_chrY 52434251 + 1139629 1142364 HG002_chrY 62432599 + 918050 920788 22
1491	0	2
773	0	1
471

chain 234251 200085_chrY 52434251 + 1000541 1003171 HG002_chrY 62432599 + 1008342 1010945 23
1	5	0
11	10	15
43	1	0
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49	0	2
28	0	1
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19	0	1
99	0	10
81	20	0
5	1	0
34	1	0
1	3	0
1612	1	0
138	3	0
80	1	0
58	5	0
7	0	5
18

chain 233658 200085_chrY 52434251 + 1209535 1212008 HG002_chrY 62432599 + 990103 992575 24
72	2	0
433	2	0
1530	0	1
5	0	1
339	0	1
90

chain 230034 200085_chrY 52434251 + 1157295 1159791 HG002_chrY 62432599 + 935994 940261 25
557	0	885
86	0	590
276	0	295
952	0	1
625

chain 225833 200085_chrY 52434251 + 1153541 1155943 HG002_chrY 62432599 + 931857 934253 26
205	5	0
1627	0	1
379	2	0
184

chain 185231 200085_chrY 52434251 + 1165030 1167009 HG002_chrY 62432599 + 945674 947652 27
191	2	0
446	1	0
366	0	1
8	1	0
6	0	1
254	0	1
704

chain 175225 200085_chrY 52434251 + 1107444 1109404 HG002_chrY 62432599 + 891978 893943 28
12	4	0
43	0	8
4	4	0
29	4	0
112	4	0
71	4	0
302	4	0
14	4	0
68	0	4
44	0	4
32	0	4
19	0	4
37	0	4
524	0	5
621

chain 152040 200085_chrY 52434251 + 1222247 1223858 HG002_chrY 62432599 + 1002100 1003711 29
1504	1	0
15	0	1
91

chain 119302 200085_chrY 52434251 + 1133111 1134373 HG002_chrY 62432599 + 911270 912531 30
160	1	0
1101

chain 118522 200085_chrY 52434251 + 1163579 1164895 HG002_chrY 62432599 + 944356 945674 31
168	0	4
366	2	0
600	2	0
133	0	2
45

chain 111976 200085_chrY 52434251 + 1225132 1226341 HG002_chrY 62432599 + 1005006 1006240 32
47	0	1
3	1	0
169	0	26
89	0	2
279	3	0
21	0	1
56	1	0
540

chain 111725 200085_chrY 52434251 + 1155943 1157147 HG002_chrY 62432599 + 934789 935994 33
499	0	1
705

chain 101379 200085_chrY 52434251 + 1138544 1139629 HG002_chrY 62432599 + 916709 917791 34
198	4	0
2	0	2
632	1	0
248

chain 80273 200085_chrY 52434251 + 1226345 1227215 HG002_chrY 62432599 + 1006240 1007111 35
622	0	1
248

chain 76447 200085_chrY 52434251 + 1227221 1228035 HG002_chrY 62432599 + 1007111 1007924 36
590	1	0
223

chain 74763 200085_chrY 52434251 + 1113526 1114324 HG002_chrY 62432599 + 898029 898830 37
147	0	1
552	0	2
99

chain 71018 200085_chrY 52434251 + 1114427 1115235 HG002_chrY 62432599 + 898895 899681 38
13	2	0
54	8	4
25	16	0
690

chain 67055 200085_chrY 52434251 + 1182345 1183062 HG002_chrY 62432599 + 963072 963794 39
5	0	5
712

chain 65713 200085_chrY 52434251 + 1216373 1217061 HG002_chrY 62432599 + 996633 997321 40
688

chain 63399 200085_chrY 52434251 + 1223866 1224576 HG002_chrY 62432599 + 1003711 1004452 41
23	4	0
363	0	3
4	0	33
221	2	0
26	0	1
67

chain 58527 200085_chrY 52434251 + 1112885 1113524 HG002_chrY 62432599 + 897391 898029 42
69	2	0
15	1	0
265	0	2
287

chain 39179 200085_chrY 52434251 + 1224714 1225130 HG002_chrY 62432599 + 1004589 1005006 43
22	0	1
394

chain 31970 200085_chrY 52434251 + 1216036 1216371 HG002_chrY 62432599 + 996298 996633 44
335

chain 28297 200085_chrY 52434251 + 1142368 1142675 HG002_chrY 62432599 + 920788 921098 45
245	0	4
18	1	0
43

chain 15160 200085_chrY 52434251 + 1228035 1228192 HG002_chrY 62432599 + 1007925 1008082 46
157

chain 12040 200085_chrY 52434251 + 1224577 1224710 HG002_chrY 62432599 + 1004452 1004589 47
61	0	4
72

chain 9332 200085_chrY 52434251 + 1182247 1182345 HG002_chrY 62432599 + 962960 963058 48
98

chain 7925 200085_chrY 52434251 + 1112754 1112845 HG002_chrY 62432599 + 897272 897367 49
29	0	4
62

chain 6804 200085_chrY 52434251 + 24142801 24142961 HG002_chrY 62432599 - 38539790 38542814 50
2	0	2864
158

chain 5989 200085_chrY 52434251 + 1114336 1114401 HG002_chrY 62432599 + 898830 898895 51
65

chain 3328 200085_chrY 52434251 + 1182213 1182247 HG002_chrY 62432599 + 962914 962948 52
34

chain 2802 200085_chrY 52434251 + 1142676 1142706 HG002_chrY 62432599 + 921098 921128 53
30

chain 2683 200085_chrY 52434251 + 12588448 12588476 HG002_chrY 62432599 + 12511308 12511336 54
28

chain 2292 200085_chrY 52434251 + 1112849 1112873 HG002_chrY 62432599 + 897367 897391 55
24

chain 1696 200085_chrY 52434251 + 1217065 1217085 HG002_chrY 62432599 + 997321 997341 56
20

chain 1446 200085_chrY 52434251 + 1103171 1103186 HG002_chrY 62432599 + 887704 887719 57
15

chain 1127 200085_chrY 52434251 + 29553598 29553614 HG002_chrY 62432599 + 29226428 29226444 58
16