##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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275	0	16
243	2	0
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14	0	5
1040	0	95
882	1	0
284	10	0
863	0	1
694	0	3
2055	1	0
4	8	0
559	3	0
779	1	0
345	170	0
131	510	0
170	340	0
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909	4	0
1674	3	0
490	0	1
76	0	2
3136	2	0
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230	1	0
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921	16	0
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442	1	0
58	0	1
824	1	0
52	3	5
54	0	8
17	0	27
7	40	0
1718	0	4
70	1	0
296	4	0
3546	0	1
876	1	0
2532	0	1
68	1	0
2890	1	0
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76	2	0
49	0	2
183	0	15
652	1	0
5	3	0
1	10	0
33	2	0
7	0	4
58	28	0
1241	1	0
291	0	2
3215	0	2
2995	134	0
859	1	0
559	0	1
172	0	1
1781	2	0
171	308	0
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5887	3	0
1045	0	3
336	1	0
2017	26	0
629	0	402
522	0	16
1869	0	25
9698	1	0
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980	114	69
327	0	45
360	0	45
141	45	0
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827	0	1
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377	0	4
317	0	6
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1391	4	0
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57	0	4
428	0	4
69	0	4
15	4	0
95	0	72
28	12	0
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3442	7	0
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1719	16	18
216	0	29
66	27	0
1	6	0
120	0	2
75	0	2
1790	2	0
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1519	3	0
474	3	0
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58	6	0
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11	4	0
8	3	0
5	4	0
18	0	1
1210	0	2
2753	4	0
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81	0	816
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220	0	4
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52	0	8
645	2	0
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174	12	0
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5865	2	0
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1643	7	0
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174	48	0
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1333	0	830
4	1	0
12	0	55
350	0	2
868	0	4
1473	3	0
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91	104	0
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27	0	3
666	1	0
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1222	0	8
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893	0	2
2595	20	0
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531	0	4
316	1	0
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7	155	0
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874	1	0
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41	2	0
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39	0	7
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3332	4	0
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2771	538	0
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43	0	8
4	4	0
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58	4	0
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68	0	4
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33	0	8
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34	0	8
33	0	2
2	0	12
581	10	0
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690	789	0
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4079	4	0
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93	0	8
22	2	16
7	0	4
982	0	2
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365	5	0
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37	0	10
484	0	1
1235	0	1
1381	135	0
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634	45	0
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324	61	0
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628	1	0
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1435	3	0
338	0	2
312	0	1
3271	4	0
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13	0	4
1783	1	0
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716	0	1
1591	1	0
815	160	0
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1991	0	1
8	1	0
564	4	0
21	5	29
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9	5	0
10	0	5
65	0	5
712	2	0
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6454	0	1
189	2	0
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143	0	3
351	0	1
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63	1	0
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80	4	0
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82	4	0
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546	4	0
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38	4	0
295	0	4
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33	0	107
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33	0	1
4	0	1
69	1	0
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77	7	0
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2240	318	0
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36	0	317
9	0	20
319	0	6
114	2	0
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133	5	139
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112	0	2
849	0	1
702	1	0
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1	5	0
52	8	0
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72	0	4
28	0	1
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373	2	0
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66	0	2
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1027	1235	1236
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16	39	2
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54	4	12
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22	8	0
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37	4	0
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743	1	0
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1341	0	3
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4	0	4
426	2	0
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170	1	0
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7	0	20
128	1	0
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335	10	0
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153	0	1
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58	1	0
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874	174	0
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1419	2	0
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1740	0	3
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56	3	0
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65	15	0
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2077	0	12
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624	0	3
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82	7	55
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4	54	0
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2444	0	5
21	11421	15545
1	1229	0
10	5	0
149	5	0
595	0	1
381	5	0
381	10	0
150	1	0
312	0	1
908	0	5
1833	1	0
1943	1373	0
613	0	15
246	30	0
1963	179352	165622
20257	0	15
3290	0	4128
63	40871	20093
2922	5	0
1097	10	0
7415	0	15
124	15	0
11069	15	0
2126	15	0
33	5531	0
1440	1	0
467	0	10
3376	0	5
264	0	5
1926	5	0
54	5581	0
3642	0	5
1880	0	10
9206	0	5
1921	15	0
970	10	0
2893	10	0
2644	0	10
700	0	1
1687	15	0
499	20	0
7197	0	5
3624	0	5
1912	0	15
156	1	0
1065	0	15
1473	11095	0
693	31151	8892
3259	0	3
289	10	0
234	0	20
566	30	0
3054	0	5
73	0	5
1593	10	0
256	0	10
549	0	25
5175	5574	0
370	30	0
4974	10	0
601	0	10
5007	0	5
5531	0	5
5010	3	0
528	15	0
556	0	5
5494	1	0
92	5	0
859	5	0
4638	5	0
385	10	0
443	5	0
2172	7671	0
1538	5	0
1290	7658	0
7099	20	0
415	10	0
2710	0	5
6736	10	0
809	5	0
4825	0	20
1890	0	5
263	7536	0
18	20	0
526	0	5
748	0	1
4070	0	30
2650	15	0
775	1	0
2786	5	0
3159	5	0
1575	1	0
1951	5	0
3980	10	0
793	20	0
1299	15	0
8	10	0
305	0	369
215	0	10
1373	0	10
731	0	5
510	25	0
1873	0	5
280	0	20
495	10	0
2749	0	10
838	5	0
3917	5	0
4533	0	5
720	7496	0
1141	0	5
790	10	0
1999	10972	3245
339	0	20
29	19090	0
397	0	15
1145	0	15
234	0	15
69	0	15
3081	15	0
2023	5	0
1788	5	0
3770	10	0
2003	0	5
366	0	3826
1437	20	0
1993	0	20
51	0	3816
1788	15	0
3798	0	5
2016	0	5
1772	5	0
675	0	15
3131	10	0
1998	0	10
1798	10	0
579	5	0
3217	10	0
1998	0	5
1831	5	0
3801	0	5
679	0	15
84	0	15
1217	0	10
29	0	2423
33	0	5
1751	15	0
740	0	25
1248	5	0
39	5	0
1759	0	5
653	15	0
26	0	15
61	0	25
1243	0	5
56	10	0
1752	0	25
34	0	1
3814	15	0
2377	3812	3731
1458	0	15
1960	1	0
80	0	5
1202	5	0
368	0	10
2096	0	5
1846	0	10
683	0	15
93	0	5
8	0	10
1218	5	0
3700	5	0
1873	5	0
775	10	0
608	10	0
686	15	0
1765	5	0
8359	0	5
4446	0	5
3336	4	0
4449	5	0
2747	0	15
195	10	0
7047	0	10
1242	5	0
2405	0	5
3472	5	0
2691	0	5
2422	0	5
3510	0	10
1479	0	5
1250	10	0
2391	0	5
2783	0	10
39	5	0
4108	5	0
2234	0	10
1029	0	5
2161	5	0
16850	15	0
5415	5	0
5837	0	10
1752	0	5
5825	0	5
853	5	0
1304	20	0
57	10	0
188	0	5
50	0	5
2473	5	0
815	0	5
195	0	5
217	0	15
4172	5	0
955	20	0
807	5	0
376	1	0
2094	0	5
2888	0	20
1281	5	0
2000	0	5
3071	5	0
43	5	0
1470	5	0
4126	0	5
296	0	5
28	5	0
2319	0	10
1835	20	0
81	5	0
760	15	0
218	0	10
220	10	0
25	60	0
1519	5	0
702	0	5
2692	5	0
1314	0	10
1741	5	0
4279	10	0
1231	5	0
964	5	0
6034	0	5
1210	5	0
195	5	0
1533	0	5
479	0	5
428	10	0
569	0	1
230	0	5
610	5	0
8759	2	0
7273	2	0
13732	0	1
2223	1	0
6054	5	0
1441	0	2
298	1	0
13931	0	6
26	6	0
1402	1	0
5202	1	0
1969	0	6
1571	0	1
2488	8	0
3948	8	0
696	6	0
836	0	1
2353	0	1
16921	0	2
2847	0	6
612	0	2
13894	0	1
5194	8	0
6622	1	0
7891	1	0
7882	8	0
2829	0	1
16771	4	0
422	8	0
949	0	20
3703	1	0
1031	0	12
24760	0	12
5530	0	1
783	2	0
5557	1	0
7260	0	20
6431	4	0
1902	4	0
3553	25	0
10441	1	0
2447	0	21
968	0	6
932	8	0
14415	0	4
12899	1	0
1181	0	1
12631	1	0
16076	2	0
32965	0	1
10813	0	1
10869	0	4
126	4	0
22255	0	1
6367	15	0
2817	0	4
1071	0	1
5638	1	0
14371	2	0
49880	0	1
8359	0	5
5194	1	0
1394	0	1
32033	0	1
45838	0	1
9141	4	0
11259	4	0
6638	13	0
22502	2	0
7969	4	0
19925	0	2
11691	0	1
1	1	0
6799	0	4
14627	0	1
4860	12	0
1363	0	1
45633	12	0
26336	3	0
13369	1	0
7753	3	0
28	0	4
1061	0	4
1500	4	0
67	4	0
996	1	0
42765	0	1
39833	1	0
7791	0	3
15791	0	1
7747	0	1
2909	6	0
12920	1	0
4385	0	12
13570	0	8
11970	0	451
11790	0	1
2927	0	2
37907	0	1
49880	0	1
39586	1	0
4095	0	1
14286	0	1
19964	2	0
31321	1	0
1768	4	0
2603	0	3
29734	1	0
28573	4	0
22929	0	1
48001	0	2
13616	1	0
19432	0	1
7108	0	1
185	0	1
5817	4	0
44231	0	1
17511	1	0
188	13	0
684	0	2
468	1	0
1150	0	1
230	1	0
225	11	0
47	1	0
160	0	4
151	1	0
205	1	0
5	1	0
118	0	1
50	0	3
253	2	0
342	0	1
161	1542	0
20433	1	0
2991	0	4
3482	1	0
1410	0	1
4036	0	1
14051	0	5
18521	0	1
8558	0	3
2976	0	4
914	1	0
3626	1	0
7291	0	6
681	15	0
2333	1	0
13037	1	0
11502	0	5
4647	1	0
5909	1	0
22717	5	0
4373	1	0
14308	1	0
10465	0	1
682	2	0
8816	0	1
71649	0	2
156	2	0
10047	0	1
5559	4	0
4678	1	0
10310	0	4
26314	0	2
8270	0	2
1303	4	0
7493	1	0
38422	1	0
37575	0	1
339	0	1
15942	0	2
19239	0	2
18	2	0
21238	0	2
623	0	8
34478	1	0
15699	0	1
3058	0	6
46473	0	4
11842	0	2
4376	0	3
33619	6	0
5933	0	1
5855	0	1
5187	0	16
314	10	0
10077	0	1
27788	0	2
25	2	0
5583	0	4
36	0	2
2267	1	0
26055	2	0
26543	0	1
2865	1	0
3720	0	2
486	20	0
79196	20	0
1666	4	0
4392	0	4
2054	0	2
15733	6	0
2785	2	0
19861	25	0
155	29	0
1530	0	6
2882	8	0
5459	1	0
1295	0	10
5502	0	2
351	2	0
3965	0	1
1386	4	0
49	4	0
11530	3411	3411
1135	0	1
10442	0	4
1388	0	7
2195	1	0
1762	2	0
355	0	2
5555	0	5
1257	0	1
3068	0	1
2379	8	0
3459	0	1
1130	25	0
36731	1	0
22114	4	0
9309	0	1
1839	0	3
3591	4	0
7978	1	0
6406	1	0
26386	1	0
7357	2	0
1746	0	7
1475	5	0
3293	0	2
1165	4	0
2500	0	1
4915	0	2
11014	1	0
19962	0	1
3247	0	1
4313	3	0
677	15	0
19994	8	0
76821	2	0
5196	2	0
28147	1	0
3035	0	1
15958	2	0
11673	1	0
8322	4	0
1891	0	1
10529	4	0
6828	2	0
21	2	0
2	19	0
21	23	0
153	0	69
1225	0	1
37882	0	2
28699	0	14
5839	0	8
1189	0	2
19042	0	2
5005	0	1
15397	0	1
13539	1	0
3783	0	2
640	2	0
57198	0	1
5882	3	0
15	1	0
27872	1	0
8087	2	0
3473	0	1
5504	2	0
4897	0	1
34088	2	0
5591	0	1
292	0	2
13330	1	0
2445	27	0
25992	3	0
23	0	4
7958	4	0
21167	0	4
14590	0	1
161	2	0
47	2	0
19	2	0
3714	0	2
4972	0	1
21908	0	1
2175	26	0
46018	0	1
6627	1	0
850	1	0
21718	0	2
938	1	0
14662	0	1
2598	0	1
12742	0	1
11182	2	0
19	0	2
2000	3	0
14159	0	4
3548	0	1
6621	2	0
6	10	0
5336	0	6
8299	0	1
8914	7	0
5257	2	0
5597	0	8
13835	1	0
15354	0	3
31931	1	0
11805	0	1
6135	2	0
2784	4	0
200	12	0
1690	0	8
843	1	0
4015	0	1
35965	0	10
3680	2	0
2554	0	1
19314	0	3
10111	0	16
771	0	5
7	5	0
1727	0	4
786	4	0
2970	1	0
693	0	4
19299	0	1
3445	0	4
238	4	0
2328	0	5
283	0	4
10170	0	2
2190	0	4
52	4	0
2168	4	0
1137	12	0
4879	1	0
21227	0	4
36025	0	1
17079	0	1
4401	0	41
474	4	0
6923	0	3
11666	30	0
15150	0	6
608	4	0
4980	1	0
12717	1	0
3841	4	0
11614	1	0
51084	0	1
1351	2	0
58	2	0
1699	1	0
40084	3	0
6259	0	3
5447	0	1
16813	0	1
7192	0	1
12032	0	2
7835	1	0
8887	1	0
3949	4	0
24528	12	0
926	1	0
6580	0	4
6344	0	1
2586	0	4
35235	2	0
17162	16	0
2536	4	0
21818	0	1
26131	44	0
2591	0	1
151	1	0
9557	8	0
328	12	0
67	0	8
7905	1	0
13904	0	6
6159	1	0
19098	12	0
26558	0	1
27280	1	0
19037	0	2
6723	0	19
2786	4	0
2851	4	0
5816	0	1
1798	0	1
2728	0	2
5169	0	1
4816	0	1
2976	0	1
930	8	0
40232	4	0
32	4	0
1437	0	1
2319	0	1
18	1	0
4	1	0
583	12642	12645
586	6	0
3730	2	0
42	7	0
16	0	1
4634	2	0
18557	0	1
14410	4	0
2361	0	1
1675	0	1
1081	1	0
1992	1	0
3227	2	0
2	24	0
7077	4	0
881	0	1
22445	0	1
24320	0	4
10709	4	0
2431	0	1
5932	1	0
15432	8	0
18	0	4
7485	8	0
4106	0	1
1711	1	0
9996	1	0
14079	0	1
9514	0	1
1911	2	0
6584	0	1
4120	0	4
1160	0	1
21764	1	0
14267	16	0
123	0	18
6440	35	0
4	3	0
18130	0	1
3930	0	2
30946	0	1
9259	0	3
10554	0	1
3069	0	1
7465	10	0
2628	0	2
4725	1	0
72	1	0
2264	4	0
540	2	0
6655	0	2
1001	0	1
110	0	4
52	4	0
66	4	0
11196	0	6
3088	2	0
11249	1	0
1539	46214	46210
1540	1	0
898	1	0
8116	0	1
2205	0	2
32	0	1
3052	4	0
4119	1	0
7111	0	4
70	4	0
47	0	1
17	8	0
89	0	1
7621	6	0
533	12	0
2348	1	0
6388	2	0
972	0	5
13	0	5
10524	0	2
4262	2	0
168	1	0
4740	1	0
18646	0	2
378	0	4
35768	0	1
9215	0	4
19878	4	0
5525	4	0
11614	0	2
2488	4	0
16686	0	2
3172	2	0
13012	2	0
10085	0	6
8548	17	0
32329	0	29
7726	0	4
17	4	0
3299	4	0
4946	0	1
22969	0	4
16785	1	0
3151	0	2
3569	0	3
1155	8	0
16671	18	0
2501	0	7
41721	2	0
13895	1	0
14366	0	1
39274	4	0
217	8	0
18204	0	1
152	0	1
1669	5	0
3422	0	1
18462	2	0
10451	0	4
670	4	0
25	0	4
12359	15	0
6714	1	0
13636	0	4
1170	0	1
88	0	1
11012	1	0
2032	2	0
10196	0	3
2398	0	1
21185	0	1
30570	0	7
11635	0	2
1129	0	3
24366	2	0
73	19	0
1631	1	0
31836	0	1
6326	0	1
11963	1	0
1985	4	0
2	4	0
3074	0	1
7363	52	0
239	2	0
4780	1	0
3438	1	0
36789	0	1
4026	2	0
14	0	1
52	0	2
1979	1	0
13493	0	1
3819	0	5
40	0	2
8270	0	1
11154	4	0
12851	0	4
11612	0	5
27840	0	1
5549	5	0
9707	3	0
15661	0	2
32	0	4
8718	0	1
1657	0	8
20130	1	0
16981	1	0
1896	0	4
13431	0	4
5134	0	4
25	8	0
15615	3	0
963	0	1
184	1	0
13368	0	1
4294	27	5
88	12	0
616	0	4
5931	0	12
18172	0	4
26	0	20
1722	0	16
10922	1	0
20449	0	1
9819	0	4
174	0	1
6986	1	0
5426	1	0
7865	0	12
422	4	0
9473	0	1
3082	1	0
440	1	0
4693	1	0
57615	4	0
62	0	8
21245	0	19
12894	6	0
37464	0	1
21221	0	3
13387	0	1
174	0	8
1483	0	1
6313	5	0
4867	1	0
5230	0	1
16066	0	4
4414	1	0
6698	0	3
13562	1	0
3997	0	1
4324	0	1
4639	0	1
977	0	12
20354	0	1
10039	1	0
3717	1	0
6083	1	0
16502	2	0
5888	1	0
11764	1	0
9741	0	1
7528	1	0
14313	0	1
7263	0	1
31475	1	0
11	7	0
1	0	3
43	4	0
37617	1	0
1336	1	0
9544	12	0
44	0	20
4204	1	0
11359	2	0
2760	6	0
130	0	9
4075	3372	3372
2125	6	0
3625	0	1
6293	1	0
9025	3	0
2383	2	0
21606	0	1
4765	16	0
1437	0	1
6	3	0
11	0	1
9	1	0
11	2	0
48	0	1
2519	0	2
9	6	0
7041	25	0
6	4	0
10120	13	0
54	0	1
4	3	0
48	2	0
17806	3457	3457
17918	13	0
10120	4	0
6	25	0
7008	0	2
2547	0	1
62	0	1
1449	0	4
4804	1	0
6137	1	0
15470	2	0
2383	3	0
15319	2	0
1495	1	0
2153	0	6
2904	1	0
4105	0	3
2529	0	6
130	6	0
2764	0	2
13614	2	4
1997	0	12
44	8	0
4	12	0
9505	0	1
2508	1	0
4088	0	1
10598	1	0
21747	4	0
39	5	0
5	1	0
3	7	0
6718	0	1
24730	0	1
40714	0	4
32994	0	1
1465	0	1
17681	0	2
9493	0	1
10875	0	8
970	0	1
2497	1	0
2126	0	1
3837	1	0
4305	12	0
196	0	1
1644	3	0
11917	0	2
11111	0	12
15459	1	0
5828	1	0
4811	10	0
6359	1	2
1452	0	8
195	0	1
13395	0	2
5478	0	2
15740	1	0
25440	0	6
10908	0	1
1075	0	2
6230	3	0
3500	0	2
24476	1	0
6	5	3
18681	1	0
23326	0	1
9186	4	0
23	4	0
4368	8	0
9881	0	3
15906	1	0
8416	0	1
18660	2	0
4754	16	0
6093	1	0
840	1	0
3480	23	0
25319	1	0
4588	2	0
14320	1	0
3217	0	1
3886	2	0
14659	0	2
54	0	3
20	4	0
8037	0	4
2458	0	2
881	2	0
10499	12	0
6526	2	0
4450	1	0
6972	0	1
16347	1	0
671	0	2
229	2	0
83	0	2
14655	0	2
105	0	2
24	0	2
3534	1	0
208	1	0
16236	1	0
1399	1	0
27644	0	1
2757	0	1
2923	1	0
6906	1	0
27	21	0
4750	0	4
19323	0	1
3144	0	1
30397	0	4
4384	0	8
43	0	4
6404	5	0
6959	0	12
4032	6	0
2	2	0
5630	2	0
2927	4	0
6490	1	0
29049	12	0
141	0	4
17586	0	4
21	0	1
1	0	1
15869	0	2
23	0	2
20100	1	0
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24	1	0
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12	0	1
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12	59	9
17	68	4
14	75	17
26	20	6
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18	24	3
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25	4	0
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36	5	0
6	0	1
39	1	0
1	20	0
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2	4	0
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59	64	23
27	0	3
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33	5	0
95	0	1
50	106	15
11	0	2
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29	4	0
36	0	6
32	4	0
66	4	0
70	4	0
60	0	1
6	1666	1
56	0	5
53

chain 12752553 NA19705_chrY 53625916 + 25341098 25490023 HG002_chrY 62432599 - 38399346 38539790 2
17084	0	1
614	0	2
30	10847	0
4888	0	4
10409	1	0
452	1	0
2002	1	0
4952	0	1
6998	0	1
715	0	4757
506	0	1
6178	2384	0
7	1	0
950	1	0
1301	0	1
4310	1	0
1457	0	11
1558	1	0
3724	1	0
3316	4	0
3200	0	1
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9914	1	0
195	0	6
4132	15	0
740	1	0
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2516	0	1
1668	14	0
84	0	6
1925	0	1
3438	8	0
754	0	1
18673	0	1
13694	0	8
222	1	0
95

chain 4357157 NA19705_chrY 53625916 + 18464373 18510586 HG002_chrY 62432599 - 45214480 45260689 3
31867	4	0
14342

chain 1190969 NA19705_chrY 53625916 + 18078210 18090850 HG002_chrY 62432599 - 45634118 45646761 4
1386	0	6
6455	1	0
4090	2	0
706

chain 327177 NA19705_chrY 53625916 + 20146119 20149575 HG002_chrY 62432599 - 43575591 43579047 5
3456

chain 322611 NA19705_chrY 53625916 + 16214366 16217774 HG002_chrY 62432599 - 47507067 47510475 6
3408

chain 6926 NA19705_chrY 53625916 + 25498162 25498322 HG002_chrY 62432599 - 38539790 38542814 7
2	0	2864
158