genome.fa.s4.2.7.7.80.10.50.1000.5.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   

This is table  5  of  31  ( 3628 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1152775--1152830	28	2.0	28	89	0	85	35	23	7	33	1.82
1154972--1155036	19	3.4	19	79	16	80	53	0	0	46	1.00
1158916--1158950	2	17.0	2	94	5	61	48	2	0	48	1.16
1158950--1158978	2	14.5	2	100	0	58	0	0	48	51	1.00
1159334--1159360	2	13.5	2	100	0	54	51	0	0	48	1.00
1159568--1159731	81	2.0	81	96	0	301	37	21	20	20	1.94
1165594--1165629	17	2.1	17	90	10	56	41	0	0	58	0.98
1165624--1165658	3	11.7	3	100	0	70	31	0	0	68	0.90
1174915--1174939	12	2.1	12	100	0	50	32	16	8	44	1.76
1184576--1184646	34	2.1	34	87	10	101	59	0	1	39	1.06
1188310--1188334	13	1.9	13	100	0	50	64	0	8	28	1.22
1190720--1190750	15	2.0	16	93	6	55	70	0	0	29	0.87
1190848--1190970	34	3.6	34	83	2	158	27	7	22	42	1.80
1193028--1193143	56	2.1	55	80	9	128	47	2	4	45	1.36
1193126--1193154	12	2.3	13	94	5	51	62	3	0	34	1.12
1199327--1199374	24	2.0	25	84	12	64	52	0	0	47	1.00
1209174--1209208	2	17.5	2	93	0	61	48	0	48	2	1.16
1209547--1209589	21	2.0	22	86	4	61	60	0	0	39	0.97
1209785--1209944	52	3.2	49	77	13	166	52	4	1	41	1.32
1210087--1210120	13	2.5	14	90	4	52	55	0	0	44	0.99
1210279--1210355	21	3.7	20	70	17	66	53	1	1	44	1.17
1210295--1210526	51	4.5	52	78	9	233	54	4	1	40	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1210334--1210526	49	3.7	51	79	11	187	55	5	1	38	1.29
1210999--1211053	22	2.5	21	88	5	83	40	7	5	47	1.54
1211224--1211248	9	2.8	9	100	0	50	80	0	0	20	0.72
1211428--1211470	21	2.0	21	82	8	52	37	6	4	51	1.50
1211783--1211812	16	1.9	16	93	6	53	50	0	0	50	1.00
1212254--1212470	34	6.4	34	83	2	249	25	6	26	41	1.79
1212254--1212469	102	2.1	101	87	4	301	25	6	25	42	1.79
1216878--1217096	34	6.5	34	85	2	244	26	8	24	40	1.83
1216878--1217096	102	2.2	101	86	1	303	26	8	24	40	1.83
1217284--1217324	18	2.3	18	86	0	64	14	0	2	82	0.76
1217284--1217324	12	3.5	11	84	15	55	14	0	2	82	0.76
1222700--1222729	14	2.1	14	100	0	60	40	6	13	40	1.71
1224839--1224904	33	1.9	34	88	11	100	62	0	1	36	1.05
1224829--1224917	25	3.4	25	73	17	83	60	0	1	38	1.04
1233403--1233486	27	2.7	33	71	17	90	58	0	0	41	0.98
1238385--1238425	5	8.2	5	94	0	73	58	0	2	39	1.11
1244056--1244097	21	2.0	21	90	9	68	59	0	0	40	0.97
1250989--1251054	12	5.2	12	71	12	51	39	0	1	59	1.07
1250979--1251050	26	2.8	26	80	4	92	41	0	1	56	1.07
1265125--1265196	37	1.9	37	91	0	117	27	16	9	45	1.79
1269827--1269869	22	2.0	22	86	4	61	37	18	18	25	1.94
1270154--1270193	3	13.3	3	94	0	71	0	30	2	67	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1270987--1271026	21	1.9	21	85	10	55	80	12	2	5	0.98
1271617--1271668	25	2.1	25	82	7	61	32	0	1	65	1.04
1274654--1274685	2	16.0	2	100	0	64	50	0	0	50	1.00
1277774--1277802	8	3.8	8	95	4	51	89	0	0	10	0.48
1277970--1278003	11	3.1	11	84	16	52	58	0	0	41	0.98
1279184--1279257	19	4.4	17	74	22	66	54	2	1	41	1.23
1280869--1280905	3	12.3	3	100	0	74	32	0	0	67	0.91
1281431--1281459	14	2.0	15	93	6	51	13	10	0	75	1.04
1282207--1282257	9	5.4	10	79	13	54	54	7	1	35	1.40
1287446--1287486	3	13.7	3	100	0	82	34	0	0	65	0.93
1292668--1292707	2	20.0	2	89	0	53	57	0	0	42	0.98
1311581--1311631	21	2.4	21	80	9	59	52	0	1	45	1.12
1313319--1313376	23	2.5	24	86	5	75	39	1	1	56	1.19
1313518--1313586	34	2.0	34	94	0	120	27	31	11	28	1.92
1313605--1313630	8	3.2	8	100	0	52	0	15	26	57	1.38
1313929--1313978	20	2.5	20	80	3	57	58	2	0	40	1.10
1314427--1314464	15	2.4	17	86	8	53	52	0	0	47	1.00
1314572--1314598	4	6.8	4	100	0	54	22	0	0	77	0.76
1314935--1315006	24	3.2	23	75	9	69	55	1	0	43	1.08
1314995--1315042	21	2.3	22	78	10	55	39	0	0	60	0.97
1315007--1315032	12	2.2	12	100	0	52	30	0	0	69	0.89
1315003--1315047	21	2.1	21	84	8	56	33	0	2	64	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1315464--1315502	18	2.3	18	86	8	55	64	2	0	33	1.08
1315524--1315557	15	2.2	16	90	10	54	52	0	2	44	1.16
1315626--1315682	25	2.4	24	77	16	64	61	1	0	36	1.07
1318952--1319023	23	3.2	21	81	18	67	61	0	4	34	1.16
1320160--1320300	69	2.0	69	91	2	230	27	22	26	22	1.99
1328265--1328331	12	5.7	12	77	19	61	34	0	0	65	0.93
1328264--1328341	22	3.6	22	77	14	74	37	0	0	62	0.95
1331109--1331147	20	2.0	20	85	5	53	48	12	12	25	1.77
1333262--1333335	39	1.9	38	81	8	87	37	0	2	59	1.12
1333248--1333317	31	2.3	31	81	11	83	38	0	2	58	1.13
1337103--1337153	16	3.1	17	75	13	52	45	0	3	50	1.20
1339848--1339881	3	11.3	3	100	0	68	32	0	0	67	0.91
1340908--1340956	17	2.6	17	84	12	53	71	4	0	24	1.03
1343892--1343989	14	7.2	14	80	10	123	63	1	2	33	1.13
1343894--1344001	27	4.0	27	80	8	130	62	0	1	35	1.13
1343891--1344021	41	3.2	40	86	8	176	60	1	2	35	1.19
1343892--1344001	14	8.1	13	80	8	121	62	0	1	34	1.12
1344074--1344123	12	4.0	13	75	15	52	66	0	0	34	0.92
1347904--1347936	15	2.1	16	88	5	50	45	0	9	45	1.35
1347920--1347978	22	2.7	22	75	12	68	45	0	1	52	1.10
1347957--1347992	13	2.8	13	100	0	72	52	0	0	47	1.00
1366048--1366103	24	2.4	23	79	5	67	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1366062--1366100	12	3.5	11	83	16	53	51	0	0	48	1.00
1367907--1367932	2	13.0	2	100	0	52	50	0	0	50	1.00
1368065--1368101	19	2.0	20	89	10	60	45	0	2	51	1.15
1370522--1370591	25	2.7	27	82	12	76	51	0	0	48	1.00
1370522--1370585	23	2.7	24	79	13	62	53	0	0	46	1.00
1372850--1372874	3	8.3	3	100	0	50	68	0	32	0	0.90
1374307--1374349	17	2.6	16	79	17	52	53	0	0	46	1.00
1376941--1377007	12	5.8	11	75	15	55	50	0	1	47	1.10
1383828--1384026	101	2.0	101	100	0	398	45	10	13	31	1.77
1408741--1408772	2	16.0	2	100	0	64	50	0	0	50	1.00
1411405--1411460	21	2.7	21	83	5	69	39	5	0	55	1.23
1412079--1412145	9	7.2	9	75	24	52	62	1	0	35	1.04
1412102--1412154	27	2.0	27	88	7	81	62	1	0	35	1.06
1412094--1412147	9	6.2	8	81	14	63	62	1	0	35	1.06
1412094--1412147	17	3.1	17	80	19	67	62	1	0	35	1.06
1412079--1412147	35	1.9	37	88	11	108	62	1	0	36	1.04
1418687--1418734	24	1.9	26	83	8	64	50	0	0	50	1.00
1418690--1418757	35	1.9	36	88	8	104	48	0	0	51	1.00
1418719--1418770	20	2.6	20	79	8	61	48	0	0	51	1.00
1418725--1418793	23	3.0	24	77	12	65	44	0	1	53	1.09
1418687--1418775	15	5.5	15	70	19	56	48	0	0	51	1.00
1418697--1418775	17	4.9	16	73	14	65	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1419305--1419415	11	10.4	11	70	16	56	61	1	0	36	1.07
1419302--1419364	11	5.9	11	76	14	60	63	1	0	34	1.04
1419322--1419395	37	2.0	36	84	10	96	63	1	0	35	1.03
1419345--1419386	14	2.9	14	80	13	50	64	2	0	33	1.07
1419375--1419431	8	6.4	9	82	13	66	56	1	0	42	1.10
1419375--1419437	27	2.4	27	82	15	78	53	1	0	44	1.10
1420823--1420851	2	14.5	2	100	0	58	48	0	0	51	1.00
1423736--1423799	28	2.3	28	97	0	119	23	17	6	53	1.66
1431954--1432006	3	17.7	3	100	0	106	67	0	32	0	0.91
1432550--1432621	10	8.1	8	77	19	56	38	0	0	61	0.96

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31