genome.fa.s500.2.7.7.80.10.50.1000.9.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: Scaffold500
Parameters: 2 7 7 80 10 50 1000
Length:  2046043

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  9  of  10  ( 1137 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)
1713259--1713324	22	2.9	22	75	11	62	59	0	0	40	0.98
1713304--1713341	20	1.9	19	89	5	58	60	0	0	39	0.97
1717541--1717576	3	11.7	3	94	5	63	66	0	0	33	0.92
1720113--1720162	3	16.7	3	95	0	91	66	0	2	32	1.03
1725819--1725847	2	14.5	2	100	0	58	51	48	0	0	1.00
1729085--1729114	5	6.0	5	100	0	60	60	0	0	40	0.97
1734684--1734732	2	25.0	2	91	4	82	46	0	0	53	1.00
1739061--1739095	2	18.5	2	88	11	56	54	0	0	45	0.99
1739335--1739359	12	2.1	12	100	0	50	0	8	0	92	0.40
1743228--1743342	57	2.0	57	91	0	185	34	24	10	30	1.89
1745982--1746180	102	2.0	102	87	0	290	32	23	14	30	1.94
1752162--1752211	24	2.1	24	85	14	68	36	0	0	64	0.94
1764560--1764595	2	18.0	2	100	0	72	50	0	50	0	1.00
1765490--1765518	7	4.1	7	100	0	58	72	0	0	27	0.85
1765600--1765693	45	2.1	45	100	0	188	28	6	25	39	1.80
1771001--1771035	2	17.5	2	93	0	61	48	0	0	51	1.00
1771202--1771275	21	3.6	19	89	8	94	51	5	0	43	1.24
1771210--1771275	21	3.2	21	93	4	109	53	6	0	40	1.26
1776199--1776265	25	2.8	23	82	13	66	64	2	1	31	1.18
1776329--1776492	17	10.6	17	67	24	73	42	0	1	56	1.10
1776350--1776398	24	2.1	24	82	17	59	40	0	0	59	0.98
1776329--1776396	16	4.0	17	74	11	50	39	0	1	58	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1776355--1776407	26	2.1	24	82	6	61	43	0	1	54	1.11
1776435--1776487	21	2.7	20	77	8	63	37	0	1	60	1.08
1776359--1776498	23	6.0	23	67	22	69	44	0	1	54	1.09
1776445--1776509	25	2.6	25	75	20	73	38	0	3	58	1.14
1776685--1776745	25	2.5	23	75	17	61	49	0	0	50	1.00
1776697--1776747	23	2.2	24	86	10	70	50	0	0	49	1.00
1776763--1776813	25	2.0	25	85	7	68	41	3	0	54	1.19
1776775--1776831	23	2.4	24	79	5	62	35	8	1	54	1.42
1777056--1777080	2	12.5	2	100	0	50	48	0	0	52	1.00
1785081--1785117	3	12.3	3	94	0	65	62	2	0	35	1.10
1785541--1785576	2	18.0	2	100	0	72	50	0	50	0	1.00
1795466--1795508	3	14.3	3	95	0	77	30	0	2	67	1.03
1796222--1796298	37	2.1	39	85	7	106	57	2	0	40	1.13
1796365--1796408	9	4.8	9	78	15	54	72	0	0	27	0.85
1796431--1796457	14	1.9	14	100	0	54	62	0	0	37	0.95
1796468--1796534	30	2.2	29	79	10	73	58	0	0	41	0.98
1800925--1800958	2	17.0	2	100	0	68	50	0	0	50	1.00
1808979--1809028	2	25.0	2	95	0	91	48	0	0	52	1.00
1810379--1810412	5	6.8	5	93	0	59	58	0	2	38	1.13
1811963--1812085	42	2.8	43	78	18	128	32	0	1	65	1.08
1812009--1812084	12	6.8	11	76	22	70	30	0	0	69	0.88
1811986--1812088	20	4.8	23	74	24	100	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1811987--1812081	33	3.0	33	79	14	103	32	0	0	67	0.91
1812017--1812067	17	3.2	16	77	20	54	29	0	0	70	0.87
1811986--1812131	43	3.5	40	76	18	120	36	0	0	63	0.95
1811986--1812131	22	6.9	20	70	21	95	36	0	0	63	0.95
1812869--1812922	19	3.0	18	81	7	56	61	0	0	38	0.96
1813308--1813361	2	26.5	2	81	3	63	50	1	7	40	1.41
1824269--1824345	22	3.4	23	77	10	88	50	2	0	46	1.15
1824317--1824388	28	2.5	28	80	8	74	56	2	0	40	1.13
1825259--1825338	2	40.0	2	74	16	60	46	1	3	48	1.28
1825407--1825465	30	2.0	30	86	6	84	52	3	1	42	1.28
1826275--1826305	2	15.5	2	100	0	62	51	0	0	48	1.00
1828399--1828425	2	13.5	2	100	0	54	0	48	0	51	1.00
1838588--1838627	2	20.0	2	100	0	80	50	0	0	50	1.00
1839791--1839817	1	27.0	1	100	0	54	0	0	0	100	0.00
1840130--1840154	13	1.9	13	100	0	50	52	8	8	32	1.60
1849323--1850570	178	7.0	178	96	0	2214	33	16	10	40	1.82
1853169--1853208	21	1.9	21	89	0	62	45	0	0	55	0.99
1853169--1853221	21	2.5	21	84	3	52	47	0	0	52	1.00
1853276--1853307	16	2.0	16	93	0	55	46	0	0	53	1.00
1854236--1854261	2	13.0	2	100	0	52	50	0	0	50	1.00
1860961--1860994	5	6.6	5	86	6	50	38	17	5	38	1.74
1862784--1862819	2	18.0	2	100	0	72	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1863277--1863304	3	9.3	3	100	0	56	67	0	0	32	0.91
1863461--1863492	3	10.7	3	93	0	55	34	3	0	62	1.11
1864282--1864347	28	2.2	29	84	12	82	57	1	3	37	1.23
1865363--1865388	4	6.5	4	100	0	52	76	0	0	23	0.78
1872379--1872432	2	27.0	2	96	0	99	50	1	0	48	1.11
1873153--1873195	4	10.8	4	89	0	59	44	6	0	48	1.29
1873195--1873219	2	12.5	2	100	0	50	52	0	48	0	1.00
1875416--1875466	24	2.1	24	82	7	59	33	13	9	43	1.77
1877782--1877824	19	2.3	19	84	8	52	51	0	9	39	1.34
1877884--1877935	22	2.2	24	86	10	72	55	0	3	40	1.18
1883624--1883682	2	31.0	2	90	10	97	52	0	0	47	1.00
1890107--1890145	2	19.5	2	83	0	51	48	0	7	43	1.31
1890107--1890145	12	3.2	12	92	0	60	48	0	7	43	1.31
1890593--1890622	3	10.0	3	100	0	60	33	0	0	66	0.92
1892017--1892079	16	3.9	16	72	2	54	33	1	0	65	1.03
1892093--1892165	38	1.9	38	88	0	110	47	4	2	45	1.36
1892289--1892341	17	2.9	18	78	21	65	32	1	0	66	1.03
1892296--1892360	31	2.2	29	81	15	80	32	3	0	64	1.09
1895164--1895190	4	6.8	4	100	0	54	74	0	0	25	0.83
1899707--1899767	2	31.0	2	83	3	79	42	6	0	50	1.28
1907063--1907094	3	10.7	3	93	0	55	31	0	3	65	1.08
1907196--1907243	18	2.7	18	96	0	87	20	27	35	16	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1910421--1910450	2	15.0	2	100	0	60	50	0	0	50	1.00
1910704--1910794	47	1.9	47	93	0	155	37	17	16	28	1.92
1911141--1911333	96	2.0	96	92	2	325	32	13	17	36	1.89
1913844--1913880	2	18.5	2	100	0	74	51	0	0	48	1.00
1914302--1914326	2	12.5	2	100	0	50	48	0	0	52	1.00
1914428--1914462	2	17.5	2	100	0	70	51	48	0	0	1.00
1914798--1914824	4	6.8	4	100	0	54	22	0	0	77	0.76
1914942--1914966	2	12.5	2	100	0	50	0	48	0	52	1.00
1915044--1915068	2	12.5	2	100	0	50	0	52	0	48	1.00
1915068--1915093	2	13.0	2	100	0	52	50	50	0	0	1.00
1916004--1916040	6	6.2	6	87	0	56	0	48	0	51	1.00
1921618--1921717	48	2.1	48	88	3	148	40	12	13	35	1.81
1928426--1928473	24	2.0	24	100	0	96	41	25	8	25	1.83
1929733--1929759	13	2.1	13	100	0	54	40	14	14	29	1.86
1929812--1929874	19	3.7	18	72	24	64	36	17	11	34	1.85
1929804--1929874	32	2.2	32	92	0	124	36	18	11	33	1.86
1930316--1930348	16	2.1	16	100	0	66	39	0	36	24	1.56
1932219--1932267	21	2.4	21	82	3	64	40	4	0	55	1.19
1932221--1932273	21	2.5	22	81	6	63	37	3	0	58	1.16
1937193--1937512	159	2.0	159	96	1	588	19	19	13	47	1.82
1938485--1938509	1	25.0	1	100	0	50	100	0	0	0	0.00
1947480--1947508	14	2.0	15	93	6	51	0	82	17	0	0.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1948870--1948900	2	15.5	2	93	0	53	45	3	0	51	1.17
1955280--1955359	31	2.7	30	76	7	83	46	3	2	47	1.34
1957934--1957971	6	6.3	6	87	0	58	23	0	50	26	1.50
1957937--1957972	12	3.0	12	100	0	72	25	0	50	25	1.50
1958031--1958067	5	7.4	5	93	0	56	24	40	0	35	1.55
1958458--1958521	17	4.1	17	76	13	66	54	0	0	45	0.99
1958508--1958552	22	2.0	22	83	8	56	42	2	2	53	1.25
1963183--1963220	3	12.7	3	100	0	76	31	0	0	68	0.90
1963931--1963959	6	4.8	6	100	0	58	17	17	17	48	1.82
1965841--1965869	3	9.7	3	100	0	58	34	34	0	31	1.58

Tables:   1   2   3   4   5   6   7   8   9   10