genome.fa.s52.2.7.7.80.10.50.1000.8.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: Scaffold52
Parameters: 2 7 7 80 10 50 1000
Length:  1774672

Tables:   1   2   3   4   5   6   7   8   9   

This is table  8  of  9  ( 1067 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)
1448491--1448550	20	3.1	18	79	15	57	70	3	1	25	1.12
1448586--1448721	12	11.8	12	69	16	83	62	1	0	35	1.10
1448586--1448651	22	3.0	23	79	18	77	66	1	0	31	1.01
1453078--1453134	21	2.8	20	76	5	62	42	3	7	47	1.47
1453144--1453220	20	3.9	19	83	9	84	41	0	3	54	1.19
1453185--1453250	29	2.2	30	81	2	80	37	1	7	53	1.39
1453216--1453341	46	2.7	47	87	3	173	42	1	8	47	1.44
1453326--1453376	20	2.6	19	85	11	68	43	1	0	54	1.11
1473451--1473490	19	2.1	19	100	0	80	65	0	10	25	1.24
1474181--1474222	2	22.0	2	90	9	70	50	0	0	50	1.00
1477662--1477701	6	7.2	6	83	11	50	55	0	0	45	0.99
1478278--1478334	11	5.1	11	76	2	60	36	1	0	61	1.07
1478278--1478334	22	2.5	22	94	2	96	36	1	0	61	1.07
1478872--1478907	6	6.0	6	100	0	72	66	0	33	0	0.92
1479080--1479150	21	3.6	21	72	22	64	54	0	0	45	0.99
1479112--1479145	16	2.0	18	88	11	54	52	0	0	47	1.00
1490804--1490854	22	2.3	23	79	3	59	47	3	0	49	1.20
1492139--1492166	2	14.0	2	100	0	56	50	0	0	50	1.00
1499665--1499698	2	17.0	2	100	0	68	50	0	0	50	1.00
1500037--1500086	17	3.1	17	76	23	54	58	2	0	40	1.10
1500486--1500528	22	1.9	22	90	4	68	60	0	0	39	0.97
1501240--1501281	14	3.1	13	86	6	57	61	0	0	38	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1501248--1501281	13	2.5	14	95	4	61	64	0	0	35	0.94
1502122--1502237	47	2.4	48	80	7	130	47	1	1	49	1.22
1502545--1502594	23	2.1	23	85	3	64	54	0	0	46	1.00
1506603--1506637	3	12.0	3	93	6	63	68	0	0	31	0.90
1511004--1511041	17	2.2	18	85	4	51	63	5	5	26	1.37
1511357--1511382	2	13.0	2	100	0	52	0	50	0	50	1.00
1513420--1513480	29	2.1	30	84	3	79	45	0	0	54	1.00
1514987--1515073	24	3.3	26	76	12	72	34	4	11	49	1.60
1518151--1518184	16	2.0	17	88	11	52	26	8	11	52	1.67
1518233--1518280	20	2.5	20	86	3	62	58	0	0	41	0.98
1519684--1519761	20	3.9	20	86	6	113	61	0	2	35	1.10
1520668--1520762	42	2.3	42	98	0	181	45	13	10	30	1.77
1524732--1524791	30	2.0	29	81	9	68	25	10	6	58	1.55
1524845--1524912	27	2.5	27	84	11	86	41	0	0	58	0.98
1524868--1524941	33	2.3	33	86	9	100	35	0	1	63	1.03
1524868--1524956	33	2.8	32	80	11	87	34	0	1	64	1.01
1524914--1524967	27	1.9	29	81	7	67	31	0	1	66	1.02
1525160--1525219	22	2.7	23	72	15	63	46	0	0	53	1.00
1525171--1525222	21	2.5	21	87	6	70	46	0	0	53	1.00
1525208--1525237	15	2.1	15	93	6	53	56	0	0	43	0.99
1525238--1525341	17	6.4	16	84	7	129	53	1	0	44	1.11
1525237--1525333	22	4.5	20	70	13	68	53	2	0	44	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1525253--1525303	22	2.3	22	89	3	75	54	0	0	45	0.99
1525235--1525341	33	3.3	32	85	5	144	54	1	0	43	1.11
1525531--1525573	17	2.6	16	85	10	52	53	0	0	46	1.00
1526195--1526236	2	20.5	2	85	4	57	47	2	2	47	1.28
1533663--1533878	34	6.4	34	86	1	274	25	7	26	40	1.83
1533663--1533880	67	3.2	66	84	2	292	25	7	26	40	1.82
1533663--1533878	101	2.1	101	90	1	335	25	7	26	40	1.83
1538295--1538512	34	6.5	34	87	1	278	25	7	26	40	1.83
1538295--1538514	67	3.3	66	85	2	296	25	7	26	40	1.82
1538295--1538512	101	2.2	101	90	1	339	25	7	26	40	1.83
1544619--1544908	52	5.6	51	80	2	319	25	11	32	30	1.91
1553244--1553325	2	41.0	2	100	0	164	50	0	0	50	1.00
1553365--1553402	2	19.0	2	100	0	76	50	0	0	50	1.00
1555059--1555154	49	2.0	49	81	4	113	38	4	13	43	1.63
1555880--1555961	43	1.9	42	83	11	105	34	15	14	35	1.89
1558913--1558979	28	2.5	29	81	11	81	62	2	1	32	1.19
1559104--1559157	14	3.8	14	76	9	56	0	18	1	79	0.82
1559929--1560016	28	3.1	28	76	11	81	38	1	0	60	1.04
1559943--1560014	36	1.9	36	86	8	99	38	1	0	59	1.06
1559942--1560021	20	4.2	19	78	15	76	37	1	0	61	1.04
1559937--1560027	20	4.4	21	70	26	70	38	1	0	60	1.04
1559949--1560054	28	4.0	28	73	20	77	37	0	0	60	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1559964--1560045	23	3.6	22	80	15	78	36	1	0	62	1.03
1559936--1560055	51	2.3	51	83	9	138	37	0	0	60	1.08
1566024--1566059	18	2.0	18	88	0	54	58	2	0	38	1.13
1570910--1570967	18	3.3	18	70	13	50	46	0	0	53	1.00
1570965--1571037	31	2.3	32	78	17	82	58	0	2	38	1.12
1572661--1572703	16	2.7	17	82	13	56	60	0	2	37	1.10
1581508--1581584	20	4.2	20	68	20	60	42	0	3	53	1.19
1583782--1583836	16	3.4	17	75	25	55	43	0	0	56	0.99
1583779--1583876	33	3.1	33	76	15	91	44	0	0	55	0.99
1583862--1583918	13	4.5	13	75	22	50	36	0	0	63	0.95
1594162--1594239	40	2.0	39	92	2	129	20	24	15	39	1.91
1595321--1595369	2	24.5	2	87	0	71	42	0	4	53	1.20
1600363--1600393	2	15.5	2	100	0	62	48	0	0	51	1.00
1600958--1601010	25	2.1	26	82	3	63	52	0	0	47	1.00
1601328--1601378	23	2.2	24	85	3	68	62	0	1	35	1.06
1601315--1601400	40	2.2	40	81	10	97	59	0	1	39	1.05
1601371--1601395	11	2.3	11	100	0	50	76	0	0	24	0.80
1601778--1601834	19	3.0	19	73	14	55	66	0	0	33	0.92
1602005--1602065	2	30.5	2	93	0	104	47	0	3	49	1.18
1603916--1603949	14	2.5	14	85	4	52	38	0	0	61	0.96
1603911--1603950	21	1.9	21	90	10	64	35	2	0	62	1.09
1607099--1607166	33	2.0	33	85	2	91	17	11	11	58	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1612591--1612634	2	22.0	2	90	0	70	47	2	0	50	1.13
1615177--1615230	29	1.9	29	85	7	76	42	1	0	55	1.10
1615764--1615818	23	2.4	24	78	9	60	56	0	0	43	0.99
1618487--1618555	34	2.1	34	88	2	104	20	11	10	57	1.62
1627105--1627136	3	10.7	3	100	0	64	68	0	31	0	0.90
1627327--1627385	4	16.2	4	92	3	67	28	0	0	71	0.87
1627482--1627529	23	2.0	25	84	12	64	20	8	2	68	1.26
1630625--1630781	22	7.9	20	66	17	87	36	1	2	58	1.23
1630729--1630787	21	2.9	22	87	9	81	32	0	0	67	0.91
1630729--1630787	5	11.4	5	76	20	59	32	0	0	67	0.91
1630740--1630782	12	3.6	12	90	6	61	32	0	0	67	0.91
1631260--1631299	20	2.0	21	85	5	55	62	0	2	35	1.09
1633340--1633379	21	2.0	20	85	5	53	15	10	2	72	1.21
1634062--1634095	17	2.0	17	88	11	52	44	0	0	55	0.99
1640164--1640196	13	2.6	13	95	4	59	42	0	0	57	0.98
1640204--1640245	19	2.2	19	83	8	50	54	0	0	45	0.99
1640925--1640969	13	3.4	13	79	14	56	60	0	0	40	0.97
1640930--1640977	17	2.8	17	75	12	53	58	0	0	41	0.98
1641409--1641557	5	29.2	5	68	17	60	38	1	0	59	1.06
1641458--1641540	32	2.6	32	78	1	94	38	0	0	61	0.96
1641437--1641557	11	10.9	12	68	17	66	38	0	0	61	1.02
1641654--1641688	18	2.1	17	89	10	54	51	2	11	34	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1642083--1642117	3	12.0	3	93	6	63	31	0	0	68	0.90
1642989--1643028	14	2.9	14	84	0	53	47	0	0	52	1.00
1643332--1643361	2	15.0	2	100	0	60	50	0	0	50	1.00
1644133--1644167	16	2.2	16	94	0	61	45	0	2	51	1.16
1644444--1644482	17	2.3	17	86	8	53	28	5	0	66	1.12
1644680--1644729	21	2.5	22	75	15	54	50	0	0	50	1.00
1644684--1644743	16	3.9	16	78	10	63	46	0	1	51	1.10
1644684--1644743	32	1.9	30	86	6	84	46	0	1	51	1.10
1644690--1644753	32	2.0	31	81	3	74	50	0	1	48	1.10
1644990--1645027	2	19.0	2	100	0	76	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9