genome.fa.s38.2.7.7.80.10.50.1000.13.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: Scaffold38
Parameters: 2 7 7 80 10 50 1000
Length:  2073527

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   

This is table  13  of  15  ( 1750 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)
1785411--1785488	32	2.5	30	75	17	86	60	0	0	39	0.97
1785426--1785478	14	3.1	18	70	30	53	54	0	0	45	0.99
1785558--1785593	17	2.1	17	100	0	72	33	30	11	25	1.90
1785783--1785825	20	2.3	19	88	8	61	65	2	0	32	1.06
1786261--1786363	16	6.2	16	67	15	50	65	0	0	33	1.06
1786303--1786388	27	2.8	32	75	16	94	56	0	0	43	0.99
1786345--1786393	17	2.8	18	77	22	59	51	0	0	48	1.00
1792502--1792569	27	2.6	27	79	13	79	60	0	0	39	0.97
1792502--1792569	26	2.5	26	81	11	84	60	0	0	39	0.97
1793724--1793774	27	1.9	26	88	4	75	62	5	0	31	1.19
1793724--1793781	27	2.1	27	84	6	73	62	6	0	31	1.22
1796490--1796566	17	4.2	18	76	19	70	55	1	0	42	1.07
1796490--1796550	27	2.3	27	80	5	70	54	0	0	45	1.00
1796474--1796552	34	2.3	35	80	8	92	54	0	2	43	1.14
1796982--1797046	25	2.5	25	80	14	78	47	0	1	50	1.10
1798384--1798452	22	3.0	23	76	18	72	46	1	0	52	1.09
1798753--1798800	18	2.5	19	80	12	55	52	0	2	45	1.12
1798868--1798901	3	11.7	3	93	6	61	32	0	0	67	0.91
1798872--1798900	14	2.1	14	100	0	58	34	0	0	65	0.93
1798869--1798901	17	1.9	17	100	0	66	33	0	0	66	0.92
1802396--1802434	20	2.0	20	84	0	51	53	0	10	35	1.35
1803543--1803583	20	2.0	20	90	0	64	34	9	7	48	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1805535--1805599	33	2.0	33	100	0	130	43	21	18	16	1.88
1805851--1805899	16	3.1	16	77	11	55	55	22	0	22	1.44
1806907--1806980	11	6.5	11	74	20	55	44	0	0	55	0.99
1806899--1806978	24	3.2	23	69	26	63	41	0	1	57	1.07
1806907--1806979	34	2.1	34	82	7	85	43	0	0	56	0.99
1806907--1806982	6	13.2	6	70	18	54	44	0	0	55	0.99
1807490--1807519	15	2.0	15	93	0	51	76	0	0	23	0.78
1808505--1808560	21	2.5	22	75	21	55	50	0	0	50	1.00
1810529--1810560	14	2.3	14	94	0	55	50	3	0	46	1.17
1811228--1811289	22	2.8	21	73	9	61	33	6	3	56	1.41
1811598--1811626	14	2.1	14	100	0	58	55	6	0	37	1.27
1813554--1813594	16	2.7	15	85	10	57	63	0	0	36	0.95
1815163--1815205	12	3.5	12	84	6	59	39	0	0	60	0.97
1815147--1815200	25	2.2	25	87	6	76	38	0	0	61	0.96
1815169--1815209	15	2.9	14	86	13	57	39	0	0	60	0.96
1816323--1816361	20	2.0	20	89	0	60	35	0	7	56	1.28
1818986--1819037	24	2.0	26	82	14	63	48	1	0	50	1.12
1819001--1819044	12	3.7	12	79	11	54	50	0	0	50	1.00
1819483--1819518	19	1.9	19	94	5	65	52	0	0	47	1.00
1819480--1819524	19	2.5	17	80	19	56	57	0	0	42	0.98
1819520--1819552	15	2.1	17	88	11	52	48	0	0	51	1.00
1819977--1820021	23	2.0	23	86	0	63	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1822303--1822366	32	2.1	30	83	11	78	56	6	4	32	1.45
1824201--1824240	21	2.0	21	85	5	55	45	0	0	55	0.99
1826482--1826529	2	24.5	2	78	4	53	52	0	2	45	1.12
1827868--1827918	20	2.5	20	78	12	59	54	0	0	45	0.99
1828372--1828414	3	14.3	3	100	0	86	32	0	0	67	0.91
1831596--1831631	2	18.0	2	100	0	72	50	0	50	0	1.00
1833882--1833923	18	2.3	19	84	12	61	30	0	2	66	1.04
1833943--1833972	12	2.6	11	90	10	51	33	6	3	56	1.42
1834375--1834448	23	3.8	19	74	20	64	36	0	1	62	1.04
1834375--1834449	18	3.8	18	75	23	62	37	0	1	61	1.05
1834983--1835072	34	2.7	33	78	11	87	44	1	0	54	1.07
1835022--1835087	10	6.5	10	74	22	50	34	0	0	65	0.93
1835036--1835085	11	5.3	9	76	23	50	34	0	0	66	0.92
1835121--1835193	8	9.0	8	77	16	71	41	0	0	58	0.98
1835120--1835156	9	4.2	9	93	6	67	45	0	0	54	1.00
1835120--1835191	23	3.0	23	86	12	92	43	0	0	56	0.99
1835234--1835260	13	2.1	13	100	0	54	44	0	0	55	0.99
1835232--1835279	17	3.1	16	85	14	66	45	0	0	54	0.99
1835286--1835335	26	1.9	26	95	0	91	36	0	0	64	0.94
1835287--1835332	17	2.6	17	81	18	51	34	0	0	65	0.93
1835284--1835332	8	5.6	9	75	20	50	34	0	0	65	0.93
1837101--1837140	21	1.9	21	89	0	62	50	2	0	47	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1837131--1837158	2	14.0	2	100	0	56	50	0	0	50	1.00
1837175--1837218	22	2.0	22	95	0	79	29	18	20	31	1.96
1841339--1841394	21	2.5	22	85	8	78	48	0	0	51	1.00
1841451--1841483	13	2.4	14	90	10	50	24	0	0	75	0.80
1843851--1843894	21	2.1	21	87	8	63	54	0	0	45	0.99
1843860--1843903	21	2.0	22	82	4	54	65	0	0	34	0.93
1845911--1845964	3	18.0	3	100	0	108	66	0	0	33	0.92
1851038--1851081	19	2.2	20	88	4	63	40	0	0	59	0.98
1851021--1851082	22	3.0	22	75	20	69	38	0	0	61	0.96
1851061--1851111	17	3.1	17	83	10	70	45	0	3	50	1.20
1852070--1852099	15	2.0	15	93	0	51	60	3	0	36	1.14
1853132--1853176	22	2.0	24	82	8	58	55	2	0	42	1.12
1853196--1853233	15	2.5	15	95	0	67	44	5	0	50	1.24
1853478--1853522	19	2.4	19	84	0	54	44	0	6	48	1.29
1853801--1853874	30	2.5	28	77	14	67	40	1	9	48	1.44
1857324--1857361	19	2.0	19	89	0	58	47	0	0	52	1.00
1857323--1857370	23	2.0	23	84	11	62	47	0	0	52	1.00
1857355--1857398	18	2.4	19	85	11	56	56	0	0	43	0.99
1857468--1857558	45	2.0	45	85	8	121	50	2	1	46	1.20
1857568--1857603	18	1.9	19	94	5	65	5	13	0	80	0.88
1858343--1858376	16	2.1	17	88	5	52	50	0	0	50	1.00
1858852--1858878	3	9.0	3	100	0	54	33	33	0	33	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1859127--1859180	19	2.7	20	75	13	58	44	0	1	53	1.11
1859191--1859241	27	2.0	25	84	7	66	64	1	1	31	1.15
1859598--1859624	11	2.5	11	100	0	54	66	7	0	25	1.17
1859664--1859702	19	2.0	20	90	5	62	61	0	0	38	0.96
1859664--1859731	18	3.7	19	79	13	61	57	0	0	42	0.98
1859978--1860031	3	18.0	3	96	0	99	31	33	1	33	1.69
1862943--1863036	47	2.0	47	89	0	143	23	27	14	34	1.94
1863768--1863811	2	22.0	2	100	0	88	50	0	0	50	1.00
1863857--1863898	15	2.4	19	77	22	56	33	4	2	59	1.31
1863861--1863899	18	2.4	16	87	12	53	35	5	2	56	1.35
1864732--1864787	20	2.8	20	71	13	51	57	1	0	41	1.09
1865266--1865344	16	4.8	16	67	11	52	62	0	1	36	1.04
1865303--1865354	19	2.6	20	72	9	52	55	0	0	44	0.99
1865701--1865736	14	2.6	14	90	0	54	66	0	2	30	1.06
1865830--1865965	42	3.3	41	81	4	146	20	22	13	43	1.87
1866160--1866193	13	2.7	13	86	4	52	52	0	0	47	1.00
1866642--1866762	46	2.7	45	78	11	131	33	15	14	35	1.89
1866642--1866761	45	2.6	46	76	11	129	34	15	15	35	1.89
1870551--1870600	19	2.6	19	87	9	66	62	0	0	38	0.96
1873117--1873158	22	1.9	22	95	0	75	80	0	19	0	0.70
1873195--1873247	17	2.8	19	74	25	51	37	0	0	62	0.96
1873170--1873247	40	2.0	37	83	11	95	34	0	1	64	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1873524--1873565	21	2.0	21	86	9	59	23	2	9	64	1.35
1874152--1874760	311	1.9	313	89	3	942	35	9	7	48	1.62
1874777--1874822	4	11.8	4	81	4	58	78	0	21	0	0.76
1874776--1874826	12	4.3	12	82	2	68	80	0	19	0	0.71
1874775--1874826	8	6.0	8	76	14	50	78	0	21	0	0.74
1874914--1874958	16	2.8	17	84	15	60	26	0	4	68	1.08
1874976--1875003	13	2.2	13	100	0	56	21	0	0	78	0.75
1876639--1876669	1	31.0	1	100	0	62	0	0	0	100	0.00
1877014--1877052	19	2.1	18	85	4	51	56	0	7	35	1.28
1878790--1878815	2	13.0	2	100	0	52	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15