##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 5316585661 HG003_chrY 59253811 + 12241 59250094 HG002_chrY 62432599 + 5105 62432577 1
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27	90	0
45	90	0
45	135	0
1435	4	0
1090	4	0
1391	4	0
789	0	8
738	4	0
385	0	8
1941	0	4
1483	0	14
147	0	1
1252	0	1
1719	27	0
149	0	2
83	0	29
8	2	58
27	0	4
29	1	7
27	6	0
27	0	2
27	0	27
1	0	2
10	29	0
8	0	2
121	27	0
52	0	2
211	0	4
1400	2	0
14	3	0
1519	3	0
474	3	0
11	1	0
58	6	0
19	23	0
13	0	11
11	4	0
8	3	0
5	4	0
18	0	1
1167	0	2
4	0	4
858	1	0
306	0	124
1500	4	0
1739	3	0
1	2	0
92	0	816
11	0	4
199	4	0
45	2	0
1024	0	4
3	0	4
6	0	8
2	0	4
46	8	0
23	0	4
54	0	16
36	12	0
18	0	4
18	0	4
46	16	0
96	4	0
4	0	8
220	0	4
5	0	4
40	4	0
77	4	0
15	0	133
104	0	4
28	0	4
9	0	8
106	0	4
35	0	1
3	1	0
176	0	4
34	4	0
52	0	4
649	2	0
3	0	1
528	0	142
195	0	71
95	0	141
1103	0	2
434	0	9
3	0	706
262	0	1
264	0	3
33	0	4
103	0	12
59	12	0
4444	8	0
107	12	0
3802	23	0
2004	0	1
37	0	309
898	0	1
4621	2	0
624	1	0
29	0	4
1643	7	0
876	4	0
1161	0	96
60	0	96
1436	68	0
158	204	0
891	0	2
184	0	1
166	1	0
1782	4	0
181	0	1
1333	0	830
4	1	0
12	0	55
350	0	2
872	4	0
1473	3	0
219	0	52
91	104	0
73	52	0
9163	0	2
200	0	4
4989	4	0
4017	3	0
4540	4	0
23	3	0
1222	0	8
431	0	2
907	12	0
894	0	1
2594	0	1
11887	0	3
8	0	1
41	2	0
1035	8	0
4202	0	2
85	0	7
22	4	0
253	19	0
473	0	1
1463	8	0
507	773	0
537	2	0
49	21	0
14	4	0
60	3	0
8	14	0
11	0	5
16	0	3
4	0	1
14	0	2
19	0	7
346	0	1
2895	2	0
168	0	2
712	2	0
334	0	1
1359	1	0
4633	4	0
12	4	0
43	0	8
4	4	0
29	4	0
112	4	0
13	4	0
58	4	0
302	4	0
14	4	0
68	0	4
80	0	4
19	0	4
33	0	8
524	0	5
812	2	0
243	0	1
1321	0	2
1482	1	0
36	4	0
18	0	14
98	0	3
1	0	1
13	20	0
24	12	0
4	4	0
17	0	36
27	1	0
554	12	0
147	0	1
649	0	4
851	526	0
443	16	0
60	0	1
239	0	1
153	1	0
362	2	0
387	0	3
960	0	270
3628	0	4
316	0	1
896	0	6
3859	1	0
1263	0	2
871	0	1
3301	0	1
1082	0	259
3048	0	8
45	0	4
2168	0	1
365	10	0
153	0	1
2497	0	4
491	1	0
1867	0	6
31	0	16
484	0	1
1232	0	4
1586	4	0
75933	0	1
110	0	1
247	9	0
9	5	0
15	0	1
15	0	15
368	1	0
8835	1	1
3294	0	1
4226	0	4
13	0	7
77994	0	1
250	0	1
79024	0	1
6539	0	1
25669	0	1
1286	0	1
38	0	11
8	2	0
9	0	2
6	0	2
14	0	10
4	1	0
9	0	13
13	0	14
8	0	1
4	0	2
1	8	0
2396	0	1
204840	0	4
10514	0	1
9956	3	2
55	0	8
5	4	0
1326	0	1
312	1	0
2424	0	1
10	0	1
257	0	1
70785	0	2
7768	0	1
9060	1	0
937	0	1
144	0	1
6	0	1
577	0	1
45	0	2
24	1	0
301	0	2
1	1	0
242	22	0
48	0	2
14	1	0
3	0	24
72	0	2
20	0	17
1	0	2
21	0	1
11	0	2
31	12	0
11	1	0
1	13	0
15	0	2
41	0	1
91	4	0
14	0	1
20	0	8
201	0	2
31	0	1
23	0	1
10	0	5
2	0	17
20	14	0
69	0	1
1119	0	2
317	0	2
1451	0	1
105	0	1
2443	0	1
3421	0	2
5	0	1
1	0	1
20054	0	1
19098	1	0
861	1	0
3322	2	0
10	0	12
18	2	0
61887	0	2
47483	0	1
17340	0	4
11	0	3
1	11	0
34	0	2
85359	0	2
5440	0	1
27173	0	2
9336	1	0
22183	0	1
17360	1	0
4	1	0
45	2	0
75	3	0
39	52	12
13	0	6
15	1	0
7	33	0
9942	0	1
4027	0	4
163	0	1
114	0	4
21516	1	0
64771	1	0
790	0	1
234	0	1
51	1	0
274	0	1
756	1	0
423	1	0
160	1	0
1839	0	1
73	1	0
10	1	0
6	0	2
1	4	0
6	2	0
5	1	0
120365	0	1
137877	1	0
164286	0	1
172497	0	1
472892	0	1
48073	0	2
127482	0	2
159405	0	2
234867	0	2
246829	0	1
346690	1	0
236299	0	2
386159	0	2
204571	1	0
20548	0	1
93022	0	2
195997	0	1
152341	0	2
93245	0	1
50303	0	1
91035	2	0
2	0	2
59350	0	1
109462	0	1
312471	0	2
58937	0	1
179067	1	0
92297	0	1
171593	0	1
425142	0	1
731024	0	1
80536	0	1
649408	1	0
92853	6	0
65	0	12
51	3	0
17	1	0
2	0	1
97907	0	1
32	0	1
86607	0	1
286770	0	2
19	1	0
584279	0	1
204825	0	1
143538	4	0
213289	0	1
251366	166603	166603
179461	0	10
469326	0	1
614482	5845	5845
669108	0	1
45285	0	1
129088	0	1
2426	1	0
1113566	0	1
496897	1	0
232235	2	0
208831	0	1
29352	0	1
9815	10	4
10220	0	1
196126	0	2
237472	1	0
37	0	2
64462	1	0
477727	1	0
95381	0	2
423777	1	0
40136	0	1
223246	0	1
65991	0	1
7721	1	0
12223	0	1
37600	0	2
247886	1	0
8010	0	2
48355	3	0
52	4	0
388108	1	0
388282	0	1
75997	0	1
59530	0	1
43204	0	2
83610	0	1
43571	0	1
68	4	2
32	0	2
2	0	6
1669	0	2
8	0	1
3	0	1
230357	0	1
21369	0	5
10699	0	1
44137	0	1
115885	0	1
105811	3	0
4079	3372	3372
51305	0	2
7662	0	1
71115	0	1
132551	0	1
45262	0	1
8596	0	1
98043	0	1
130848	0	1
245787	0	2
71361	0	1
86	1	0
181558	0	1
65146	0	1
91236	2	0
122232	0	2
55183	0	2
10079	0	1
302509	0	1
628715	29500	29500
235958	0	1
309612	0	1
177566	0	1
698311	0	1
431168	0	1
15303	0	1
27624	0	1
2861	10504	296961
39	0	1
1030	1	0
143605	2067201	3686624
12726	0	2
137144	0	2
340922	0	6262
1641	10	0
1058881	4	3548
2548477	0	5
1393045	225786	217970
10	0	2
1163697	0	5
164546	0	5
151169	0	3529
1167450	2422	0
1699236	0	2
203	1	0
538811	5	0
882750	1	0
349267	5	0
1561652	5	0
9703242	2416	0
37858	0	2418
123	0	2
978171	5	0
398571	5	0
386417	9655	0
678825	5	0
739071	3524	0
1895827	2419	0
1498289	0	4840
708894	10	0
89032	5	0
202549	5	0
24810	154995	1398424
860	0	1
1215995	2	0
337075	1	0
1176	10	0
372638	0	1
897675	0	2
185010	0	1
81141	0	1
35997	0	1
11571	29	0
27	0	58
687	6	0
99	10	16
863	1	0
10	0	1
1183	688	0
56	0	5
53

chain 154295606 HG003_chrY_random0000146 1632668 + 323 1632668 HG002_chrY 62432599 + 25377245 27009601 2
58	0	1
435	0	1
397	1	0
606	0	3
15707	1	0
153888	2	0
15351	0	1
158354	0	1
35846	0	1
24878	0	1
30983	0	1
271776	0	2
114515	0	1
8008	0	1
29231	1	0
326863	0	1
215107	0	1
3298	1	0
214964	0	1
608	0	1
9292	1	0
673	0	1
9	1	0
612	1	0
280	0	1
278	1	0
54	0	1
232	13	13
19

chain 25467047 HG003_chrY_random0000132 269783 + 1 269783 HG002_chrY 62432599 - 39175933 39445722 3
50	0	1
14	0	1
159	1	0
202	0	1
117	1	0
259	0	1
152	1	0
7	0	1
79658	0	52
90	26	0
34	26	0
27830	0	1
156422	0	1
1215	0	1
1955	0	1
1322	0	1
241