genome.fa.s3.2.7.7.80.10.50.1000.13.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: Scaffold3
Parameters: 2 7 7 80 10 50 1000
Length:  6198200

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   32   

This is table  13  of  32  ( 3795 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)
1725483--1725532	17	2.9	17	80	13	59	32	2	4	62	1.25
1726986--1727034	13	3.5	13	81	10	53	75	2	2	20	1.00
1727776--1727838	20	3.0	21	73	17	60	60	0	1	38	1.07
1728058--1728086	15	2.0	15	93	6	51	44	0	0	55	0.99
1728125--1728175	20	2.5	20	80	6	57	47	3	1	47	1.32
1728170--1728225	5	11.8	5	75	11	55	33	0	0	66	0.92
1728170--1728225	23	2.4	23	87	3	76	33	0	0	66	0.92
1728164--1728228	28	2.2	29	83	5	87	38	0	0	61	0.96
1733846--1733890	19	2.4	19	88	7	65	55	2	0	42	1.12
1736970--1737045	28	2.6	28	83	10	82	32	3	0	63	1.13
1737289--1737372	38	2.2	38	85	8	107	51	0	1	47	1.08
1742674--1742714	19	2.2	19	86	8	57	65	0	2	31	1.05
1742674--1742720	8	5.0	10	78	21	57	65	0	2	31	1.04
1742731--1742775	16	2.7	17	80	13	58	53	0	0	46	1.00
1742705--1742791	33	2.6	32	82	12	88	52	1	1	44	1.15
1743434--1743475	2	21.0	2	90	0	66	0	47	4	47	1.23
1744939--1745039	37	2.7	36	89	6	157	39	9	35	14	1.80
1745081--1745133	27	2.0	27	92	0	88	47	7	9	35	1.64
1745747--1745832	44	1.9	45	95	2	156	43	15	17	24	1.87
1746188--1746240	27	2.0	27	92	0	88	35	9	7	47	1.64
1746280--1746382	37	2.8	37	86	2	145	16	30	8	44	1.78
1748122--1748281	84	1.9	83	91	3	259	29	14	17	38	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1748243--1748310	29	2.3	29	100	0	136	29	10	13	47	1.75
1757855--1758379	259	2.0	259	100	0	1050	37	21	11	29	1.88
1759569--1759608	17	2.3	18	95	4	73	35	7	20	37	1.81
1762015--1762064	26	1.9	26	84	8	66	76	10	0	14	1.03
1762826--1762871	21	2.2	21	88	0	65	60	0	0	39	0.97
1762834--1762888	21	2.7	21	83	8	60	60	1	1	36	1.18
1763067--1763207	33	4.1	35	77	16	127	56	2	1	40	1.20
1763139--1763235	25	3.8	25	72	5	88	55	1	0	43	1.06
1762986--1763196	31	6.6	32	68	18	118	54	1	2	40	1.26
1763178--1763222	19	2.3	21	75	21	53	57	2	0	40	1.11
1765091--1765115	11	2.3	11	100	0	50	92	0	8	0	0.40
1771953--1771985	2	16.5	2	100	0	66	48	0	0	51	1.00
1772424--1772467	23	2.0	23	86	4	63	40	0	0	59	0.98
1774051--1774081	9	3.3	9	95	4	53	51	0	0	48	1.00
1775639--1775667	5	6.0	5	92	8	51	82	0	17	0	0.66
1784092--1784162	36	1.9	37	86	8	101	49	0	0	50	1.00
1784060--1784172	46	2.4	48	80	12	128	47	0	0	52	1.00
1784590--1784641	10	5.3	10	73	13	54	53	3	0	42	1.19
1784941--1784972	15	2.0	17	88	11	50	62	0	0	37	0.95
1787109--1787177	32	2.1	32	84	10	86	44	0	0	55	0.99
1787120--1787211	8	10.8	9	72	15	63	40	0	0	59	0.97
1787119--1787192	32	2.2	32	85	9	94	43	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1787539--1787565	2	13.5	2	100	0	54	48	0	0	51	1.00
1789505--1789534	15	2.0	15	100	0	60	33	0	0	66	0.92
1790227--1790277	18	2.9	17	75	13	50	45	0	0	54	0.99
1791091--1791136	19	2.5	19	89	6	69	58	0	0	41	0.98
1791455--1791496	20	2.0	21	86	13	61	26	0	2	71	0.98
1791501--1791542	17	2.4	18	80	11	52	50	0	2	47	1.14
1791481--1791565	27	3.2	27	72	8	75	42	0	2	55	1.12
1792049--1792126	41	1.9	41	82	10	97	47	0	0	52	1.00
1793024--1793282	50	5.2	50	93	0	430	28	20	19	30	1.97
1797679--1797937	50	5.2	50	92	0	412	28	20	19	31	1.97
1799352--1799394	21	2.1	20	86	4	59	37	0	0	62	0.95
1799362--1799422	32	2.0	30	84	12	79	40	0	0	59	0.98
1799434--1799472	13	2.9	15	78	21	50	33	0	0	66	0.92
1799403--1799485	10	7.7	11	67	17	50	38	0	0	61	0.96
1807447--1807486	3	13.3	3	100	0	80	32	0	0	67	0.91
1808343--1808398	28	2.0	28	100	0	112	50	10	0	39	1.37
1811954--1811983	2	15.0	2	100	0	60	50	0	0	50	1.00
1813364--1813402	11	3.5	11	82	3	51	43	5	0	51	1.24
1813559--1813623	22	3.3	19	69	22	53	53	0	0	46	1.00
1818669--1818735	16	4.3	16	75	11	68	62	0	0	37	0.95
1818685--1818709	7	3.6	7	100	0	50	48	0	0	52	1.00
1818658--1818718	30	2.0	31	87	9	90	54	0	0	45	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1819396--1819508	30	3.8	30	76	13	108	44	4	8	42	1.55
1819396--1819508	59	1.9	59	83	3	147	44	4	8	42	1.55
1826664--1826698	2	17.5	2	100	0	70	51	0	48	0	1.00
1829662--1829690	3	9.7	3	100	0	58	31	0	0	68	0.89
1829954--1830010	17	3.0	19	80	19	66	42	0	0	57	0.98
1830352--1830491	70	2.0	70	91	0	226	38	12	10	39	1.76
1830828--1830854	2	13.5	2	100	0	54	48	0	0	51	1.00
1840432--1840475	23	1.9	23	82	17	56	56	2	0	40	1.11
1844009--1844036	3	9.3	3	100	0	56	67	0	0	32	0.91
1844383--1844434	18	3.1	16	81	13	59	34	0	3	61	1.14
1845267--1845322	22	2.7	21	73	15	53	46	0	0	53	1.00
1845681--1845754	15	5.1	15	69	25	52	41	2	1	54	1.23
1851744--1851834	33	2.7	33	73	14	87	50	2	0	47	1.13
1872754--1872786	12	2.8	12	90	0	57	39	42	18	0	1.50
1873356--1873457	51	2.0	51	96	0	186	17	25	22	34	1.96
1880002--1880061	30	2.0	30	100	0	120	40	26	13	20	1.89
1885121--1885168	18	2.7	18	80	9	53	39	0	0	60	0.97
1885143--1885186	22	2.0	22	86	4	63	36	0	0	63	0.95
1885168--1885198	16	1.9	16	93	0	53	54	0	0	45	0.99
1885301--1885383	32	2.8	29	83	8	112	44	0	1	54	1.08
1885298--1885383	19	4.4	19	72	15	59	46	0	1	52	1.08
1888005--1888039	13	2.6	13	90	4	52	65	0	5	28	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1888021--1888059	18	2.2	18	85	0	51	58	0	2	38	1.12
1888033--1888059	9	3.0	9	100	0	54	55	0	0	44	0.99
1888221--1888262	20	2.1	20	86	0	57	38	0	0	61	0.96
1893738--1893766	14	2.1	14	100	0	58	0	0	65	34	0.93
1893914--1893943	3	10.0	3	100	0	60	66	0	0	33	0.92
1893999--1894037	20	2.0	20	89	0	60	38	0	0	61	0.96
1895297--1895345	21	2.3	21	96	0	89	46	10	18	24	1.79
1904626--1904696	37	1.9	37	94	5	126	53	18	16	11	1.72
1907837--1907886	26	2.0	24	84	7	64	62	0	0	38	0.96
1907854--1907896	19	2.1	22	87	12	65	69	0	0	30	0.88
1907858--1907913	20	3.0	18	77	12	60	62	0	1	35	1.06
1907845--1907934	39	2.3	37	76	14	92	61	0	1	37	1.04
1908006--1908051	23	2.0	23	87	8	67	43	0	2	54	1.12
1919223--1919252	2	15.0	2	100	0	60	50	0	0	50	1.00
1920627--1920664	18	2.2	18	86	9	53	57	0	2	39	1.12
1989803--1989955	75	2.0	75	93	5	263	21	20	7	49	1.74
1990520--1990664	71	2.0	73	94	2	258	38	12	15	33	1.85
1992881--1993058	89	2.0	89	94	0	311	21	19	15	43	1.87
1996706--1996749	11	4.1	11	79	5	54	34	2	0	63	1.07
1996698--1996751	21	2.7	19	75	13	54	35	1	0	62	1.06
2002952--2003009	30	1.9	30	89	3	89	56	0	0	43	0.99
2002951--2003021	26	2.5	29	82	11	85	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2003255--2003305	23	2.4	22	84	15	63	29	3	0	66	1.09
2003661--2003693	17	1.9	17	88	11	50	48	0	6	45	1.27
2003688--2003747	23	2.5	26	76	15	65	65	1	0	33	1.03
2003720--2003753	17	2.0	17	88	0	50	64	2	0	32	1.08
2016463--2016487	8	3.1	8	100	0	50	48	0	0	52	1.00
2016494--2016524	16	1.9	16	93	0	53	45	3	0	51	1.17
2016883--2016909	6	4.5	6	100	0	54	85	0	0	14	0.61
2016959--2017010	2	26.0	2	100	0	104	50	0	0	50	1.00
2017566--2017601	2	19.5	2	83	16	51	50	0	0	50	1.00
2017566--2017601	19	1.9	18	88	5	54	50	0	0	50	1.00

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   32