genome.fa.s54.2.7.7.80.10.50.1000.11.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: Scaffold54
Parameters: 2 7 7 80 10 50 1000
Length:  3629595

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   

This is table  11  of  20  ( 2342 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)
1742454--1742493	15	2.5	16	88	8	55	57	0	2	40	1.12
1742454--1742496	16	2.6	17	85	10	63	55	0	2	41	1.12
1742892--1742924	14	2.2	16	89	10	52	57	12	0	30	1.35
1743686--1743724	11	3.5	11	78	0	51	56	5	7	30	1.49
1743724--1743753	14	2.1	14	93	0	51	66	6	0	26	1.16
1743744--1743787	19	2.2	19	84	8	52	65	4	0	29	1.12
1743748--1743826	29	2.7	30	77	13	74	63	3	0	32	1.12
1743830--1743884	4	13.8	4	77	11	51	0	18	0	81	0.68
1743826--1743887	17	3.5	17	80	10	79	0	17	0	82	0.67
1743828--1743884	23	2.6	23	84	15	84	0	17	0	82	0.67
1748035--1748060	13	2.0	13	100	0	52	38	0	0	61	0.96
1748077--1748139	20	2.9	22	73	23	62	55	0	0	44	0.99
1748084--1748150	22	3.0	23	76	10	68	55	0	0	44	0.99
1748432--1748460	14	2.0	15	93	6	51	79	0	0	20	0.74
1748450--1748565	32	3.8	32	68	15	91	56	1	0	41	1.16
1748503--1748543	20	2.0	20	86	9	57	60	0	0	39	0.96
1750058--1750083	13	2.0	13	100	0	52	38	0	23	38	1.55
1753438--1753473	2	17.5	2	94	5	63	50	2	0	47	1.15
1753599--1753640	14	3.1	13	83	10	57	40	4	11	42	1.63
1758386--1758468	24	3.3	24	69	15	62	39	0	0	60	0.97
1759116--1759150	16	2.1	18	89	10	56	48	0	0	51	1.00
1761146--1761202	23	2.5	24	80	5	73	49	3	1	45	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1763830--1763873	21	2.0	21	86	4	61	81	0	9	9	0.87
1765805--1765840	17	2.0	17	89	10	54	44	2	8	44	1.48
1771183--1771241	2	29.5	2	96	0	109	47	0	1	50	1.11
1771548--1771765	34	6.5	34	85	5	282	40	27	7	24	1.82
1771546--1771765	67	3.3	67	88	1	323	40	27	7	24	1.82
1776181--1776396	34	6.4	34	85	5	287	40	26	7	25	1.83
1776179--1776396	67	3.2	67	88	1	310	40	26	7	25	1.82
1777019--1777044	2	13.0	2	100	0	52	50	0	0	50	1.00
1780998--1781028	3	10.3	3	92	0	53	70	0	29	0	0.87
1780998--1781034	12	3.1	12	92	0	56	70	0	29	0	0.88
1781573--1781602	3	10.0	3	100	0	60	66	0	33	0	0.92
1787964--1788030	23	3.2	23	62	37	60	38	5	0	55	1.25
1787971--1788038	24	3.2	24	63	30	62	36	8	0	54	1.32
1787943--1788046	40	2.6	39	87	4	147	38	7	0	53	1.30
1794021--1794046	2	13.0	2	100	0	52	50	0	0	50	1.00
1794018--1794091	18	3.9	19	68	16	55	40	0	1	58	1.07
1794936--1794964	14	2.1	14	100	0	58	58	0	0	41	0.98
1796471--1796538	22	3.2	22	79	10	70	36	0	1	61	1.05
1796477--1796533	24	2.4	24	74	11	62	35	0	0	64	0.93
1798389--1798418	13	2.2	13	94	5	51	53	0	0	46	1.00
1798382--1798428	14	3.7	13	78	13	53	53	0	0	46	1.00
1798382--1798432	13	4.0	12	78	19	50	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1799159--1799185	12	2.2	12	100	0	54	92	0	0	7	0.38
1802007--1802043	18	1.9	19	89	10	58	35	0	0	64	0.94
1801997--1802057	29	2.1	28	85	14	81	37	0	0	62	0.96
1806521--1806605	2	44.5	2	75	17	65	45	3	2	48	1.32
1809457--1809513	22	2.6	22	78	8	64	47	0	1	50	1.11
1809474--1809514	20	2.2	19	87	12	59	48	0	0	51	1.00
1809795--1809831	14	2.4	16	86	13	51	40	0	0	59	0.97
1810236--1810292	27	2.1	27	100	0	114	49	24	7	19	1.73
1810705--1810734	12	2.5	12	94	0	51	53	0	0	46	1.00
1811291--1811318	2	14.0	2	100	0	56	50	0	0	50	1.00
1812186--1812238	8	6.8	8	75	25	51	60	0	0	39	0.97
1812176--1812238	21	3.2	21	79	20	66	58	0	0	41	0.98
1832478--1832514	13	2.9	14	84	15	53	62	5	0	32	1.18
1832469--1832516	25	2.0	24	87	4	69	62	4	0	33	1.14
1833170--1833220	20	2.5	20	81	12	59	50	1	3	43	1.31
1835481--1835522	2	21.0	2	100	0	84	50	0	0	50	1.00
1838657--1838704	22	2.2	21	78	10	53	52	0	6	41	1.27
1840111--1840155	22	2.0	22	87	8	65	42	0	0	57	0.98
1841111--1841142	2	16.0	2	93	0	55	0	50	3	46	1.17
1844580--1844613	14	2.4	14	100	0	68	17	0	17	64	1.29
1844642--1844697	25	2.2	26	81	15	73	58	1	0	39	1.08
1845043--1845092	11	4.2	12	73	16	50	62	0	2	36	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1845065--1845108	20	2.2	21	80	19	58	63	0	6	29	1.20
1845542--1845578	3	12.3	3	100	0	74	32	0	0	67	0.91
1847183--1847209	2	13.5	2	100	0	54	51	0	0	48	1.00
1847699--1847729	2	15.5	2	93	0	53	45	0	3	51	1.17
1852180--1852222	22	1.9	23	90	4	70	37	0	0	62	0.95
1853364--1853448	6	14.0	6	81	1	71	17	38	2	41	1.63
1857184--1857259	39	1.9	39	100	0	152	44	21	17	17	1.86
1859146--1859170	5	5.0	5	100	0	50	80	0	20	0	0.72
1859755--1859957	102	2.0	102	96	1	372	26	11	33	28	1.91
1861209--1861240	5	6.4	5	92	0	55	78	0	21	0	0.76
1863036--1863114	2	39.5	2	79	0	77	48	8	1	41	1.42
1863051--1863113	24	2.6	24	89	0	99	49	11	1	38	1.48
1865360--1865418	26	2.3	26	96	0	109	25	18	10	45	1.81
1872353--1872381	14	2.1	14	93	6	51	37	0	6	55	1.27
1872797--1872821	13	1.9	13	100	0	50	40	0	0	60	0.97
1876721--1876786	23	2.9	23	76	13	64	48	1	1	48	1.20
1880212--1880275	32	2.0	32	96	0	119	40	14	12	32	1.83
1880980--1881017	20	1.9	20	89	10	60	36	0	0	63	0.95
1880990--1881014	11	2.3	11	100	0	50	36	0	0	64	0.94
1882647--1882700	23	2.3	24	76	17	60	35	11	7	46	1.67
1883430--1883485	28	2.1	26	83	6	67	35	0	3	60	1.14
1884408--1884432	11	2.3	11	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1884729--1884769	2	20.5	2	84	0	55	0	58	0	41	0.98
1884912--1884967	14	3.6	14	75	25	51	55	0	0	44	0.99
1884894--1884965	32	2.2	33	85	9	103	56	0	0	43	0.99
1891089--1891249	39	4.1	39	73	9	132	42	5	10	40	1.63
1891622--1891789	87	1.9	85	83	5	212	44	7	13	35	1.72
1894043--1894070	12	2.3	12	100	0	56	42	0	14	42	1.45
1894165--1894279	33	3.4	34	70	24	89	55	9	0	33	1.38
1894163--1894379	72	3.0	70	83	5	256	53	12	1	32	1.47
1894337--1894420	26	3.4	25	74	12	93	57	10	0	32	1.33
1895870--1895933	30	2.1	30	82	5	76	37	0	4	57	1.19
1896814--1896904	13	6.9	13	69	25	59	59	1	1	38	1.12
1896809--1896906	27	3.6	27	77	10	83	61	1	1	36	1.10
1896859--1896913	17	3.2	17	74	20	51	63	1	1	32	1.15
1896850--1896908	19	3.0	20	79	18	61	64	1	1	32	1.13
1897137--1897182	18	2.6	18	79	10	58	58	2	0	39	1.10
1901338--1901372	3	11.7	3	100	0	70	65	0	0	34	0.93
1901849--1901896	3	16.0	3	100	0	96	66	0	0	33	0.92
1902251--1902320	28	2.5	27	90	4	104	50	7	1	41	1.39
1914231--1914264	9	3.8	9	88	0	50	88	0	11	0	0.52
1924432--1924460	2	15.0	2	92	7	51	48	0	0	51	1.00
1925592--1925631	21	1.9	21	85	10	55	47	0	5	47	1.24
1929634--1929687	22	2.4	22	87	3	72	44	0	3	51	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1929677--1929747	32	2.2	32	85	2	90	47	0	4	47	1.21
1929725--1929775	21	2.4	22	80	12	61	50	0	5	43	1.26
1929829--1929867	12	3.2	12	88	0	51	46	0	7	46	1.31
1929912--1929951	14	3.1	14	73	26	52	57	0	0	42	0.98
1929910--1929943	10	3.5	10	92	4	52	55	0	0	44	0.99
1929912--1929996	24	3.5	24	82	4	91	54	1	0	44	1.07
1929909--1929981	33	2.2	33	83	13	89	56	1	0	42	1.08
1929907--1930011	24	4.4	23	77	12	72	54	0	0	44	1.06
1932772--1932835	27	2.3	28	81	7	78	51	0	0	48	1.00
1932778--1932825	15	3.1	15	79	5	60	45	0	0	54	0.99

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20