genome.fa.s4.2.7.7.80.10.50.1000.7.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  7  of  31  ( 3628 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)
1628330--1628354	13	1.9	13	100	0	50	56	0	4	40	1.18
1629514--1629553	2	20.0	2	100	0	80	50	0	0	50	1.00
1635793--1635862	35	2.0	35	100	0	140	40	14	5	40	1.69
1636603--1636638	16	2.2	16	90	0	54	66	0	0	33	0.92
1643124--1643173	24	2.1	24	96	0	91	52	10	12	26	1.70
1643313--1643365	25	2.1	25	82	6	63	39	1	1	56	1.21
1644347--1644412	37	1.9	34	82	14	82	30	1	1	66	1.10
1652772--1652802	2	15.5	2	100	0	62	51	0	0	48	1.00
1653623--1653662	2	20.0	2	84	0	53	47	5	0	47	1.24
1656769--1656793	2	12.5	2	100	0	50	48	0	0	52	1.00
1672382--1672458	38	2.0	38	97	0	145	40	9	20	29	1.83
1676173--1676212	2	20.0	2	100	0	80	50	0	50	0	1.00
1677465--1677514	24	2.2	24	85	7	68	46	8	2	44	1.44
1678294--1678357	27	2.2	29	81	15	80	23	6	10	59	1.54
1681575--1681634	20	3.1	19	73	22	52	63	5	0	31	1.16
1710469--1710535	20	3.3	20	71	19	57	38	4	5	50	1.47
1711165--1711211	15	2.9	16	87	9	69	40	0	0	59	0.97
1711526--1711557	2	16.0	2	100	0	64	50	0	0	50	1.00
1712061--1712112	16	2.9	18	78	18	56	69	1	3	25	1.16
1717936--1717971	3	12.0	3	87	0	54	0	33	0	66	0.92
1719730--1719773	23	1.9	24	90	9	74	36	2	0	61	1.09
1719729--1719780	23	2.3	23	83	6	70	44	1	0	53	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1727021--1727046	4	6.5	4	100	0	52	23	0	0	76	0.78
1727747--1727788	22	2.0	22	85	4	59	47	4	9	38	1.57
1728038--1728062	6	4.2	6	100	0	50	32	0	0	68	0.90
1729537--1729567	15	2.1	15	94	5	55	35	9	0	54	1.33
1729703--1729757	21	2.8	20	86	8	76	58	0	0	41	0.98
1729703--1729755	13	3.8	15	72	22	53	56	0	0	43	0.99
1729703--1729771	21	3.4	20	82	11	61	57	0	1	40	1.07
1731929--1731977	19	2.5	20	83	6	55	51	2	2	44	1.24
1733310--1733360	11	4.5	11	76	16	50	33	0	1	64	1.05
1736369--1736424	28	2.0	28	86	6	78	50	1	0	48	1.11
1737135--1737175	22	2.0	21	85	9	57	46	2	0	51	1.14
1746539--1746600	32	2.0	32	90	3	99	41	11	11	35	1.77
1747921--1748002	28	2.9	27	77	13	69	60	3	0	35	1.14
1753298--1753337	17	2.4	17	91	0	62	37	0	2	60	1.11
1753306--1753345	17	2.4	17	95	0	71	35	0	0	65	0.93
1753296--1753350	26	2.1	27	83	10	69	32	0	1	65	1.03
1753409--1753446	19	2.1	18	90	9	60	47	0	0	52	1.00
1754346--1754394	20	2.4	21	76	10	57	57	0	8	34	1.29
1754396--1754420	2	12.5	2	100	0	50	52	0	0	48	1.00
1754723--1754774	21	2.5	19	80	17	59	34	0	0	65	0.93
1754797--1754855	30	1.9	31	86	3	84	52	1	6	38	1.38
1756582--1756611	7	4.3	7	91	0	51	30	0	26	43	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1757481--1757586	52	2.0	52	85	3	142	40	7	9	42	1.66
1761472--1761519	23	2.0	24	88	4	71	56	0	0	43	0.99
1761465--1761529	26	2.5	25	79	18	71	50	0	0	49	1.00
1762521--1762549	2	14.5	2	100	0	58	48	0	0	51	1.00
1762549--1762580	2	16.0	2	100	0	64	0	0	50	50	1.00
1767141--1767227	45	1.9	46	90	2	140	47	8	8	36	1.63
1767141--1767238	45	2.2	44	87	7	135	45	8	8	37	1.64
1768112--1768157	3	15.3	3	100	0	92	67	0	0	32	0.91
1768571--1768602	2	16.0	2	100	0	64	50	0	0	50	1.00
1771558--1771628	23	3.0	24	72	15	58	42	2	1	53	1.24
1771703--1771747	21	2.1	22	83	4	56	71	0	0	28	0.87
1772014--1772049	2	18.0	2	94	0	63	47	0	2	50	1.15
1772373--1772424	18	3.1	16	81	10	59	42	0	0	57	0.98
1772361--1772433	16	4.6	16	71	18	55	43	0	0	56	0.99
1772383--1772460	31	2.4	32	81	16	90	42	1	0	56	1.07
1776856--1776907	22	2.4	22	80	0	59	46	3	3	46	1.39
1777444--1777503	28	2.1	28	87	0	84	51	1	0	46	1.10
1780122--1780159	2	19.0	2	100	0	76	50	0	0	50	1.00
1780741--1780775	2	17.5	2	87	0	52	48	2	0	48	1.16
1782773--1782874	34	3.0	34	81	7	91	50	0	3	45	1.27
1788765--1788832	20	3.6	19	75	13	68	54	0	2	42	1.15
1788838--1788891	25	2.3	23	79	17	65	31	3	0	64	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1789164--1789202	18	2.2	17	86	4	51	48	2	0	48	1.15
1792534--1792589	22	2.5	23	85	5	71	62	0	3	33	1.12
1792921--1792953	12	2.8	12	86	4	50	57	0	0	42	0.98
1793676--1793737	21	3.0	21	77	11	74	66	0	33	0	0.92
1793705--1793790	5	17.4	5	81	9	61	74	0	25	0	0.82
1793688--1793731	16	2.7	15	86	10	52	68	0	31	0	0.90
1793698--1793791	25	3.8	24	76	23	90	73	0	26	0	0.84
1793693--1793790	10	9.9	10	70	16	53	72	0	27	0	0.85
1793713--1793791	19	4.2	19	69	15	65	74	0	25	0	0.82
1793708--1793791	29	2.9	29	74	11	84	75	0	25	0	0.81
1794557--1794599	22	2.0	21	86	13	61	46	0	0	53	1.00
1798118--1798191	2	37.0	2	94	0	67	37	0	12	50	1.40
1798406--1798455	15	3.4	15	83	10	59	38	0	2	60	1.09
1798778--1798819	22	1.9	22	90	9	68	35	0	2	61	1.09
1798800--1798842	18	2.3	18	84	4	50	34	2	2	60	1.22
1798809--1798872	23	2.7	22	81	11	74	39	1	0	59	1.07
1798897--1798938	21	2.0	22	85	4	59	61	0	0	38	0.96
1807930--1807973	21	2.1	21	100	0	88	27	15	22	34	1.95
1808000--1808049	15	3.3	15	74	20	50	40	0	0	60	0.97
1808006--1808045	17	2.4	17	82	0	53	37	0	0	62	0.95
1809199--1809231	17	1.9	17	88	11	50	27	6	0	66	1.15
1809363--1809388	2	13.0	2	100	0	52	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1811610--1811648	13	2.9	13	84	3	51	7	10	0	82	0.86
1815992--1816203	115	1.9	112	89	4	327	33	19	14	33	1.92
1815992--1816218	114	2.0	115	87	6	327	34	18	14	32	1.91
1816405--1816433	2	14.5	2	100	0	58	51	48	0	0	1.00
1819025--1819068	21	2.1	21	100	0	88	27	15	22	34	1.95
1819095--1819128	17	2.1	16	88	5	50	44	0	0	55	0.99
1820292--1820324	17	1.9	17	88	11	50	27	6	0	66	1.15
1820452--1820480	2	15.0	2	92	7	51	0	48	0	51	1.00
1822700--1822738	13	2.9	13	84	3	51	7	10	0	82	0.86
1827086--1827297	115	1.9	112	89	4	327	33	19	14	33	1.92
1827086--1827312	114	2.0	115	87	6	327	34	18	14	32	1.91
1827498--1827526	2	14.5	2	100	0	58	51	48	0	0	1.00
1832165--1832376	115	1.9	112	89	4	327	33	19	14	33	1.92
1832165--1832391	114	2.0	115	87	6	327	34	18	14	32	1.91
1832577--1832605	2	14.5	2	100	0	58	51	48	0	0	1.00
1838176--1838202	2	13.5	2	100	0	54	48	0	0	51	1.00
1838464--1838488	2	12.5	2	100	0	50	0	48	0	52	1.00
1838488--1838519	2	16.0	2	100	0	64	50	0	0	50	1.00
1847096--1847247	77	1.9	78	85	5	209	50	8	7	33	1.62
1848420--1848475	16	3.7	15	79	9	51	30	8	1	58	1.39
1848433--1848470	16	2.4	16	90	0	58	23	7	2	65	1.32
1854823--1854866	20	2.2	20	84	8	54	47	11	2	38	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1869312--1869353	21	2.0	21	90	0	66	40	19	16	23	1.91
1869314--1869359	21	2.2	21	84	0	56	43	21	15	19	1.87
1879273--1879312	2	20.0	2	89	0	62	47	2	0	50	1.14
1879775--1879807	2	16.5	2	100	0	66	48	0	0	51	1.00
1880454--1880506	24	2.2	24	83	6	63	64	3	0	32	1.12
1882808--1882862	16	3.4	16	79	20	69	58	1	0	40	1.09
1882808--1882875	16	4.2	17	75	20	65	58	1	0	39	1.07
1885636--1885670	2	17.5	2	93	0	61	48	0	2	48	1.16
1887031--1887074	20	2.2	20	84	8	54	54	0	0	45	0.99
1890080--1890115	2	18.0	2	100	0	72	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