##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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4975	4	0
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57	4	0
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488	3	0
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403	0	2
28	2	0
907	3	0
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8	0	1
41	2	0
1035	4	0
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4	0	7
13	0	4
23	0	4
39	0	7
15	0	11
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11	0	4
46	0	1
2109	0	1
507	781	0
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8	1	0
28	21	0
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33	3	0
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12	8	15
11	0	2
19	0	7
346	0	1
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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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19	0	4
33	0	8
524	0	5
812	2	0
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86	12	0
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653	20	0
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54	82	42
677	7364	0
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2707	0	4
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37	0	10
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45	135	0
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712	2	0
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72	0	8
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3	5	0
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98	4	0
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16	1	0
70	24	358
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11	4	182
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9	49	8
3049	1	0
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211	0	62
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9	24	0
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3	51	0
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63	34	0
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16	39	2
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8	0	49
16	148	0
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460	10	0
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14	162	357
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704	9	0
32	0	12
42	0	2
1680	0	1
187	5	0
17	0	6
894	1	0
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699	1	0
443	250	0
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894	1	0
1831	0	1
2574	6	0
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12	16	0
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1351	0	40
299	0	40
501	40	0
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7800	5	0
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37	2	0
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268	0	1
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557	0	3
657	0	12
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8	0	12
34	4	0
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2121	1	0
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3367	0	1
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22	31	8
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17	0	1
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7	13	10
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24	5	23
81	0	1
89	0	1
31	0	1
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292	0	12
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6	0	1
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9	0	2
7	24	18
11	0	3
12	0	2
5	2	0
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11	0	1
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18	50	45
4	1	0
5	0	1
4	0	5
103	3	0
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163	1	0
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28	3	0
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3525	1	0
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5091	3	0
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37	0	34
8137	0	1
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668	0	1
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5563	0	14
2232	0	1014
43	0	4
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41	1	0
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6030	1	0
49	0	3
128	4	0
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5	0	5
9	0	22
15	0	12
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51	0	24
721	1	0
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1345	2	0
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69	2	0
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3849	0	19
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944	1	0
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4763	1	0
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49	0	8
1643	0	4
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6376	1	0
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483	0	7
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13	1	0
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15	0	16
216	1	0
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810	0	10
18	0	8
5548	4	0
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61	2	0
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144	8	0
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33	0	4
633	0	2
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3	0	9
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695	6	0
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37	0	2
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8220	0	1
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322	1603	0
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71	0	8
4	0	2
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3497	0	1
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277	300	0
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4	0	20265
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26	0	2
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108	0	6
4030	0	20277
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1926	1	0
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830	1	0
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786	0	32
1937	0	1
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2983	0	20314
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2414	1	0
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22	4	0
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357	0	1
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1794	2	0
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4570	18	0
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34	26	34
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52	0	7
3	7	0
10	0	1
443	125	0
24	1002	0
48	4	0
2	0	5
323	0	4
413	125	0
125	125	0
532	124	0
655	92407	25286
23351	29742	29504
494	0	2
78	0	1
130	0	1
133	0	1
115	4	0
3	0	3
3250	0	25
7982	2	0
7607	0	125
3001	0	124
2275	0	499
2159	1	1
3001	125	0
3030	0	625
47	0	999
16	0	125
123	0	125
78	0	125
145	875	0
26	1124	0
4320	0	125
4792	250	0
2344	0	250
3330	2624	0
52	3749	0
37	250	0
10199	0	125
3212	1918	2918
42	1000	0
9450	3376	0
98	0	250
2872	1	2125
41	125	0
1044	1	0
62	125	0
411	0	1
254	0	125
560	0	1
332	0	7
3	7	0
240	124	0
1300	1	0
1500	0	1
3400	0	375
9522	125	0
790	5874	0
33232	0	6
60907	0	4
32422	0	6
69702	0	2
19796	1	0
32009	1	0
47466	3	0
26794	1	0
38642	0	1
25017	0	8
21361	0	1
5936	0	1
41395	1	0
406	0	1
15124	0	4
19442	6	0
5878	8	0
38351	1	0
22499	0	4
7068	0	1
13926	0	3
8514	0	1
20794	0	6
62465	0	1
304	0	4
4681	0	9
2122	32296	32299
2096	3	0
4640	8	0
7056	0	1
5030	0	12
7229	0	1
14654	0	1
15689	0	4
21189	2	0
83	0	6
17649	4	0
4813	8	0
1624	0	1
9642	1	0
23335	0	1
29939	1	0
10929	0	1
23807	4	0
32	0	1
40255	0	8
3764	1	0
93523	0	1
1833	5	0
4	0	1
13	0	1
2	1	0
3	0	1
94168	1	0
16930	47074	0
9540	8	0
23507	0	2
14838	4	0
9799	6	0
21070	1	0
16987	6	0
158	0	2
39952	0	1
5844	1	0
17480	0	2
4	4	2
7744	10	0
56	12	2
10	2	0
10	0	2
15	1	0
10	1	0
54	17	0
28	0	1
77160	1	0
2518	0	1
6282	9	0
26738	2	0
44199	0	8
663	1	0
12771	0	1
11210	2	0
12329	1	0
11197	12	0
8871	1	0
3153	0	3
6076	0	2
11466	0	1
3870	0	10
483	10	0
3	0	7
11662	1	0
117	0	3
622	0	1
2687	0	1
4076	14	0
11658	1	0
2763	0	3
4549	0	1
14829	1	0
18150	1	0
1424	0	6
3802	0	1
10	0	6
19876	1	0
13243	2	0
13728	0	3
23223	0	21
2157	0	1
2803	2	0
30848	12	0
63	4	0
12452	0	2
14508	1	0
21670	0	2
27923	8513	0
100	2	0
94	0	2
20	0	1
6	18	0
211	3	0
147	0	1
15	3	0
120	0	2
69	5	0
79	1	0
69	0	3
5	0	1
158	0	4
288	0	1
40	1	0
200	146	0
5	2	0
22	18	0
61	2	0
131	1	0
72	0	12
9	1	0
5	2	0
48	0	1
315	0	14
104	2	0
111	0	1
69	0	7
3	0	5
20	0	9
28	0	1
53	3	0
50	2	0
72	0	2
25	7	0
232	1	0
53	28	0
4	0	32
53	2	0
114	3	0
386	42146	2085
307	0	3
60	0	2
73	1	0
124	1	0
646	3	0
15	0	8
416	4	0
77	0	1
61	2	0
192	1	0
30	1	0
144	0	2
73	0	1
135	1	0
9	0	1
64	1	0
51	0	1
90	1	0
184	0	1
145	1	0
176	0	1
26	15	0
112	1	0
20	1	0
216	1	0
133	3	0
23	2	0
134	3	0
52	4	0
14	3	0
59	0	19
2	3	0
71	6	0
57	1	0
30	0	1
12	0	1
36	0	1809
38	3	0
277	4	0
26	1	0
38	0	4
17	31	0
9	25	0
6	22	0
14	0	12
52	1	0
31	0	26
9	4	0
37	0	314
85	1	0
78	0	1
43	0	2
3	0	1
88	4	0
41	3	0
24	0	4
38	1	0
28	0	2
69	0	1
443	0	1
290	0	6
124	2	0
20	4	0
103	1	0
61	1	0
118	2	0
30	18	0
8	10	0
23	0	1
3	0	2
475	0	2
24	1	0
154	0	2
217	0	1
111	0	3
22	2	0
17	0	4
49	0	1
42	10	0
5	0	11
54	197	0
11	0	19
74	3	0
112	0	1
134	7	0
135	2	0
48	1	0
5	0	2
7	3	0
267	0	12
79	3	0
266	1	0
164	3	0
63	6	0
16	4	0
206	2	0
14	1	0
188	0	1
40	0	4
153	0	4
17	1	0
262	2	0
100	0	1
29	1	0
6	2	0
117	0	1
170	0	1
28	0	5
57	44	0
163	0	1
177	0	2
22	20	0
170	1	0
129	0	7
15	0	14
103	0	1
42	330	0
10	3	0
58	4	0
129	0	1502
76	1	0
88	0	17
140	0	1
83	0	1
209	5	0
88	17	0
5	0	15
23	0	1
26	0	1
82	12	0
79	325	0
27	3	0
31	0	2
32	3	0
59	0	13
118	0	3
55	4	0
161	1	0
38	10	0
10	0	68
7	0	4
12	0	2
98	1	0
43	0	11
3	16	0
63	4	0
249	0	1
53	0	4
20	0	60
130	0	2
8	1	0
295	1	0
188	0	2
295	0	4
72	0	22
46	0	4
93	0	1
253	0	4
38	1	0
27	0	3
12	107	0
26	0	6
32	0	2
91	4	0
27	3	0
176	3	0
53	1	0
26	0	4
60	0	5
57	0	6
103	0	1
105	0	1
17	2	0
92	0	1
51	1	0
310	12	0
138	1	0
109	0	1
86	0	6
267	0	3
73	0	1
550	0	4
46	6	0
609	1	0
46	1	0
146	1	0
18	1	0
44	4	0
71	1	0
73	0	4
577	0	2
141	0	1
240	1	0
15	0	1
148	0	2
211	1	0
25	3	0
116	2	0
76	0	1
104	11	0
116	0	4
3	3	0
139	0	1
109	0	1
116	0	1
188	0	5
213	1	0
192	0	1
37	0	1
10	0	1
37	0	1
50	1	0
5	0	2
178	0	3
120	2	0
98	0	1
251	2	0
28	0	1
57	1	0
23	466	6295
120	0	1
262	0	1
214	0	4
221	0	1
130	4	0
213	4	0
43	1	0
105	0	1
2	2	0
29	0	1
15	0	2
96	1	0
127	1056	0
244	0	1
60	0	7
439	0	1
41	1	0
235	11	0
7	0	1
690	0	1
254	0	1
16	36	0
97	1	0
234	0	2
27	0	1
33	4	0
1	0	5
121	2	0
25	1	0
73	0	1
50	4600	2764
121	12	0
77	12	0
117	4	0
176	0	1
95	8	0
91	0	3
210	6	0
2	0	8
75	0	8
117	0	15
117	1	0
31	0	3
197	0	1
107	75527	109875
386	0	3
114	0	2
53	32	0
4	0	28
67	0	1
218	0	7
25	2	0
72	0	2
50	0	3
53	1	0
28	9	0
20	5	0
3	7	0
69	1	0
111	0	2
104	14	0
315	1	0
48	0	2
5	0	1
9	12	0
72	0	1
131	0	2
61	0	6
22	0	2
5	0	152
200	0	1
40	1	0
288	4	0
158	1	0
5	3	0
69	0	1
79	0	5
69	2	0
120	0	3
15	1	0
147	0	3
211	0	14
2	0	4
4	1	0
20	2	0
94	0	2
113	0	8513
2075	0	1
25832	2	0
21691	1	0
14525	0	2
12416	4	0
97	8	0
35880	1	0
6932	0	2
29888	2	0
13267	0	1
8238	337	0
1551	1	0
48318	1	0
4556	3	0
14389	0	2
4101	1	0
2688	1	0
625	3	0
105	0	1
8071	0	8
23	0	1
4059	0	6
28080	0	1
19208	0	1
6338	8	0
4619	0	1
35	6	0
20213	0	2
43485	0	4
1723	0	1
3988	0	6
4916	0	4
45114	0	2
37275	1	0
40925	0	5
19466	1	0
5250	0	1
1689	0	2
7889	1	0
6683	0	2
600	1	0
5846	11	0
8550	0	1
1390	0	1
5	0	8
2577	0	2
7400	1	0
5547	18	0
51451	0	1
3267	0	3
10608	0	1
21455	0	1
2051	0	8
74	0	4
34	4	0
3519	0	4
3393	5	0
7155	1	0
6540	1	0
18673	0	1
754	0	4
3434	0	1
2015	1	0
1668	0	1
2516	2	0
912	0	1
737	0	3
4124	0	14
195	1	0
9044	0	3
39	0	3
827	1	0
2023	0	2
3200	2	0
2015	0	1
1198	0	8
3817	0	1
1568	0	1
14711	0	4757
15120	0	1
4459	0	10850
36832	10849	0
37962	0	1
1551	0	1
3805	8	0
1219	1	0
5217	0	1
2024	1	0
837	0	6
9287	0	6
4110	0	12
1677	0	2
9588	0	16
33129	5	0
3366	0	4
3388	4	8
49	4	0
43	0	12
8	4	0
2207	0	1
25138	0	2
6904	0	3
5432	1	0
49302	18	0
5547	1	0
9963	0	3
1396	1	0
8541	0	11
5841	0	1
596	2	0
3252	4	0
128	1	0
11170	0	8
19530	1	0
7973	1	0
16600	0	1
9171	0	1
5106	1	0
6792	1	0
2173	0	2
7681	0	1
814	4	0
18578	0	1
10197	0	2
3060	1	0
7397	1	0
3835	4	0
16455	2	0
710	0	2
13643	0	6
4905	2	0
1436	0	2
1645	0	1
923	1	0
2200	0	1
11298	2	0
18973	1	0
518	0	1
7163	0	4
5272	0	4
15627	3	0
1424	4	0
224	0	4
7159	0	1
9300	1	0
1226	0	6
4341	2	0
1065	0	4
17664	1	0
2120	1	0
6935	0	1
3805	1	0
2815	0	4
5191	0	1
20	1	0
2056	0	1
13519	1	0
9159	2	0
5060	0	1
7065	0	2
214	1	0
2705	1	0
16903	0	1
7194	8	0
2710	6	0
5250	1	0
19206	0	2
44	0	2
21616	1	0
20642	0	2
4856	1	0
366	9	0
1737	1	0
904	0	1
4705	0	3
2634	10	0
5201	0	8
1868	1	0
10817	1	0
893	1	0
831	1	0
34950	0	1
821	0	1
6317	1	0
3699	0	1
107	0	1
11500	0	1
922	0	1
9997	0	6
9259	0	15
4	0	1
1	0	1
2760	6	0
15515	16	0
79	3	2
12014	1	0
15691	3	0
2434	0	1
1827	16	0
19640	1	0
667	0	6
20777	0	1
18880	4	0
3988	1	0
10190	0	1
20379	0	2
913	0	1
25805	0	1
3377	0	2
481	4	0
19	6	0
4371	0	2
10182	1	0
16581	3	0
32300	0	1
6	0	8
31793	0	1
13953	12	0
19340	1	0
3514	1	0
17891	0	1
11219	0	1
18662	0	2
37342	0	3
1442	0	1
18149	0	1
25234	1	0
16107	0	1
8080	0	1
32131	1	0
25541	8	0
4671	0	2
18594	1	0
1621	1	0
16316	1	0
17607	2	0
1886	1	0
14064	6	0
35694	1	0
20908	1	0
12012	0	1
2991	20209169	36158925
64628	0	1
3534	1	0
3534	0	10604
7069	1	0
7069	1	0
6240	0	14139
2114	0	15
2235	0	1
1284	15	0
21094	25	0
3551	0	25
3519	25	0
5416	1	0
1584	0	1
3619	0	25
3511	0	25
1901	3560	0
1469	15	0
150	25	0
3370	0	15
150	0	25
3370	15	0
150	25	0
3370	0	15
150	0	25
3370	15	0
150	25	0
7037	0	15
4541	1	0
494	0	20
74	0	25
14	3495	14054
9902	0	1
513	20	0
61	40	0
13405	1	0
494	0	20
66	0	40
3148	10	0
13	20	0
225	15	0
64	0	40
61	1	0
323	1	0
739	15	0
784	20	0
300	0	10
156	45	0
122	0	20
8	0	3482
4	0	20
92	1	0
262	0	1
373	1	0
120	20	0
353	0	15
403	0	5
122	5	0
940	10	0
88	15	0
409	0	10
161	45	0
122	0	18
14255	0	1
7348	3503	0
129	5	0
2625	0	5
387	1	0
334	0	15
134	5	0
2199	0	15
24	15	0
3864	5	0
909	0	3498
552	30	0
2030	5	0
3498	5	0
3475	0	5
1020	5207	1704
14799	5	0
32709	5	0
18950	2	0
18698	0	2
32686	0	8
32	4	0
4	0	12
3321	0	1
11555	0	2
2765	0	5
10987	0	3
11089	1	0
5294	10	0
34972	5	0
15975	3	10
2710	4	0
2677	4	0
4328	12	0
928	1	0
6743	0	4
2378	1	0
172	1	0
16595	0	7
1874	19	0
1776	0	3
1309	1	0
724	0	1
3697	4	0
5522	0	2
1476	0	1
109	0	1
3452	0	1
2733	2	0
3695	0	1
2723	4	0
45	0	6
11	0	3
6920	0	1
401	0	3
8057	0	1
718	0	30
1588	0	4
7215	1	0
3909	0	4
915	2	0
3145	14	0
8900	1	0
658	0	32
74	80	0
666	2	0
6383	2	0
6458	0	3
5809	0	3
6451	0	1
343	0	2
4828	0	1
6	0	3
530	2	0
2613	1	0
1095	0	4
12695	0	1
6099	0	1
73	12	0
272	0	2
2724	2	0
4392	0	1
9625	1	0
21629	1	0
73	0	1
10647	1	0
1366	0	1
1509	2	0
347	0	1
257	2	0
11013	1	0
168	0	1
782	2	0
4479	0	1
5573	0	1
6898	2	0
5226	1	0
1856	0	1
11571	29	0
27	0	58
687	6	0
42	6	0
64	6	0
3	0	6
134	0	12
20	27	80
15	0	1
25	1	0
16	0	2
5	0	1
34	2	2
6	8	0
11	0	4
15	0	1
4	0	1
17	1	0
25	7	0
13	0	5
11	12	0
1	0	1
12	7	0
30	237	74
36	0	2
12	0	1
18	21	3
17	31	3
12	14	4
9	1	0
1	5	0
7	19	0
36	0	4
25	7	0
13	0	5
1	4	0
8	0	1
6	17	21
7	7	0
9	0	1
1	0	4
9	7	0
9	159	3
11	2	0
13	59	12
48	0	1
5	1	0
8	6	0
24	0	1
8	0	1
8	0	1
5	0	10
16	39	29
24	1	0
35	3	0
13	0	1
13	3	0
35	4	0
5	1	0
11	15	6
9	0	1
11	3	0
5	0	5
11	2	0
13	1	0
7	0	11
6	22	7
7	3	0
9	24	1
27	0	3
15	0	11
19	1	0
15	0	10
6	9	0
34	0	1
39	0	1
3	5	0
41	2	0
46	1	0
8	0	1
50	112	35
9	0	23
23	0	5
7	2	5
4	1	0
25	0	25
17	2	0
6	1	0
26	3	0
1	0	1
41	0	1
22	4	0
12	0	1
38	1	0
5	8	0
10	1	0
4	4	0
23	2	0
9	0	4
6	0	4
8	2	0
6	0	1
6	1680	1
56	0	5
53

chain 151754641 HG01099_chrY_random0000013 1673483 + 2015 1673447 HG002_chrY 62432599 - 35865814 37507190 2
83	1	0
6	0	1
253	1	0
65	0	1
119	1	0
121	0	1
81	0	1
7	0	1
66	1	0
100	1	0
142	0	1
29	0	1
178	0	1
91	1	0
24	0	1
65	1	0
89	1	0
198	1	0
207	1	0
5	0	1
195	1	0
138	0	1
76	1	0
238	0	1
39	0	3
291	1	0
28	0	1
390	0	1
440	1	0
296	1	0
593	1	0
8	0	1
19	0	1
381	1	0
39	0	1
10393	2	0
5797	4	0
20978	0	2
664	1	0
19650	0	4
1827	1	0
12849	1	0
5276	0	1
12004	16	0
15588	4	0
2761	0	9
70	0	3
14076	0	2
660	1	0
4456	1	0
12421	1	0
10125	1	0
35771	0	1
831	0	1
893	0	1
10817	0	1
1558	0	2
271	0	2
34	10	2
5201	0	10
7339	1	0
904	0	1
1745	1	0
366	0	1
6784	0	1
12206	0	2
6509	1	0
17081	0	1
4561	0	2
16	2	0
11460	2	0
7743	0	2
407	0	1
7556	0	8
7193	1	0
16904	0	1
2705	0	1
213	1	0
7065	1	0
5060	2	0
2604	0	1
6554	0	1
13519	1	0
2076	1	0
5193	4	0
2815	0	1
3805	2	0
14	0	1
4339	1	0
2580	0	1
2119	2	0
814	0	1
16850	4	0
5407	6	0
2864	8	0
15028	12	0
17051	4	0
4725	0	2
20	1	0
478	2	0
46	0	2
7163	1	0
518	1	0
30687	0	8
1769	0	1
912	1	0
3070	0	6
4936	0	4
13665	2	0
688	0	2
20279	0	1
7404	0	1
3048	4	0
28773	0	4
821	1	0
16648	0	2
5111	1	0
25781	0	1
7973	0	1
12562	0	1
6976	2	0
7852	0	1
3315	0	1
125	0	4
19676	0	4
16	0	10
2501	2	0
43303	0	1
21115	1	0
3169	0	1
6970	0	2
3264	0	1
471	1	0
17302	3	0
6170	0	20
105	2	0
63	12	0
13	4	0
4	4	0
100	0	20
3368	0	4
3343	5	0
7201	1	0
17678	0	2
13651	2	0
1	4	0
84	0	12
4144	0	2
932	0	1
741	0	18
4117	8	0
17366	0	1
13913	0	2385
727	1	0
2064	0	7153
6487	0	1
1224	0	2
13953	1	0
451	1	0
4460	0	1
308	21690	0
328	0	1
33005	0	21688
4589	0	1
2563	14342	0
805	0	2
2	0	1
4776	0	3
2118	4779	0
3686	2	0
1224	1	0
6523	2384	0
2036	0	1
310	19105	32
16307	0	1
3205	0	2
12138	0	6
4117	0	15
1667	6	0
2474	0	1
7114	0	4
33160	9	0
15177	2	0
4358	2	0
16550	1	0
35694	4	0
33557	1	0
17937	1	0
18630	0	1
4614	12	0
25563	1	0
28030	2	0
4101	0	2
9800	2	0
1114	0	520
70	0	3
4111	0	4
1105	0	1
2382	0	2
21349	0	2
5911	1	0
900	0	1
20296	0	1
28367	0	417
10003	0	2
2024	1	0
68604	8	0
4011	9	0
7359	1	0
34381	4	0
22552	0	2
8	0	4
201	1	0
1658	0	2
7883	0	1
26765	1	0
4817	0	2
46	0	8
3377	0	1
2514	1	0
8879	2	0
15327	0	1
5349	0	1
15029	0	1
14178	2	0
12884	2	0
5936

chain 13783818 HG01099_chrY 47743209 + 15932721 16078812 HG002_chrY 62432599 + 14937114 15083186 3
1388	0	7
287	1	0
321	1	0
1587	1	0
1762	2	0
355	0	2
5496	0	5
59	5	0
9604	2	0
560	0	2
1130	25	0
58841	0	4
4918	0	3
9822	8	0
29155	0	1
20717	0	2
44

chain 3742424 HG01099_chrY 47743209 + 20696769 20736463 HG002_chrY 62432599 - 42850342 42889998 4
19965	6	0
6518	10	0
8	22	0
13165

chain 3058483 HG01099_chrY 47743209 + 23129226 23161521 HG002_chrY 62432599 - 40507615 40539913 5
6287	0	1
5505	0	2
20503

chain 1095296 HG01099_chrY 47743209 + 16079347 16090925 HG002_chrY 62432599 + 14925532 14937110 6
11578

chain 427764 HG01099_chrY 47743209 + 24438912 24443423 HG002_chrY 62432599 - 39338719 39343231 7
2490	0	1
2021

chain 327277 HG01099_chrY 47743209 + 20007612 20011069 HG002_chrY 62432599 - 43575590 43579047 8
3457