genome.fa.s25.2.7.7.80.10.50.1000.9.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   

This is table  9  of  56  ( 6609 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)
1732141--1732173	2	17.0	2	87	6	50	48	3	0	48	1.17
1734445--1734486	19	2.3	18	91	4	66	80	2	0	16	0.81
1735346--1735389	21	2.1	21	95	0	79	38	13	11	36	1.81
1736993--1737045	2	26.5	2	88	7	81	0	47	1	50	1.12
1738443--1738477	2	17.5	2	100	0	70	48	0	0	51	1.00
1739428--1739506	42	1.9	42	86	2	115	51	2	6	39	1.41
1754941--1754970	11	2.7	11	94	0	51	20	0	6	73	1.05
1757353--1757401	21	2.3	22	92	3	82	32	0	2	65	1.04
1757362--1757421	23	2.5	25	74	20	65	36	0	0	63	0.95
1757351--1757422	21	3.4	23	78	14	75	37	0	1	61	1.05
1757737--1757766	2	15.0	2	100	0	60	50	0	50	0	1.00
1757768--1757801	2	17.0	2	100	0	68	50	0	0	50	1.00
1758182--1758258	23	3.5	24	72	19	69	42	0	0	57	0.99
1758183--1758270	17	5.3	17	68	10	56	40	0	0	59	0.98
1758185--1758286	50	2.2	45	82	8	114	40	0	1	56	1.17
1760054--1760090	20	1.9	19	89	10	58	29	0	0	70	0.88
1761341--1761375	18	1.9	18	88	11	54	62	0	2	34	1.10
1761963--1762010	22	2.2	21	77	3	51	52	0	0	47	1.00
1761967--1762069	52	2.0	52	83	11	131	47	0	0	52	1.00
1763735--1763782	21	2.3	21	89	7	71	56	0	2	41	1.11
1764089--1764155	29	2.5	25	74	23	64	52	4	2	40	1.37
1764098--1764156	29	2.0	31	84	12	81	52	3	3	40	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1766520--1766564	20	2.2	20	92	0	72	28	15	24	31	1.96
1774488--1774548	9	6.8	9	77	7	61	31	1	0	67	1.01
1774800--1774877	19	3.8	20	75	14	70	56	1	0	42	1.07
1775030--1775061	16	2.0	17	88	11	50	56	0	3	40	1.15
1776901--1776951	11	4.5	11	75	15	50	64	0	0	35	0.94
1776903--1776951	20	2.5	20	76	6	55	65	0	0	34	0.93
1776905--1776984	25	3.2	25	79	13	94	61	0	0	38	0.96
1776901--1777020	16	7.4	16	71	23	56	59	0	0	40	1.03
1776931--1777004	32	2.2	34	85	7	98	56	0	1	41	1.07
1776949--1777007	16	3.6	17	80	13	70	55	0	1	42	1.09
1776944--1777018	32	2.2	34	88	6	109	54	0	1	44	1.08
1778899--1778955	29	2.0	28	86	3	78	36	1	0	61	1.07
1779048--1779152	33	3.2	33	70	15	110	47	1	7	42	1.43
1779052--1779175	64	1.9	65	93	1	214	47	2	7	42	1.44
1779059--1779161	32	3.1	34	69	16	99	50	2	5	40	1.41
1782310--1782367	30	1.9	30	89	6	91	34	0	0	65	0.93
1782333--1782371	20	2.1	18	85	9	51	33	0	0	66	0.92
1782376--1782424	8	6.2	8	81	18	59	44	0	0	55	0.99
1782395--1782430	14	2.7	13	91	8	63	47	0	0	52	1.00
1784323--1784373	11	4.5	11	75	15	50	64	0	1	33	1.05
1784415--1784482	30	2.3	30	87	5	93	47	0	5	47	1.26
1788155--1788292	68	2.0	69	84	1	179	42	13	12	32	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1788372--1788428	30	1.9	30	88	0	87	36	12	0	50	1.40
1789769--1789819	20	2.5	21	81	12	61	43	5	1	49	1.38
1790033--1790066	10	3.4	10	91	0	50	38	0	11	50	1.39
1791054--1791084	16	1.9	16	100	0	62	45	6	6	41	1.55
1803770--1804071	152	2.0	149	97	1	568	48	21	14	16	1.81
1808270--1808306	3	12.7	3	94	5	67	70	0	0	29	0.88
1809287--1811117	617	3.0	614	90	3	2831	39	20	15	24	1.91
1811183--1811207	9	2.8	9	100	0	50	44	0	12	44	1.41
1819868--1819964	31	3.2	31	63	16	85	36	12	7	44	1.70
1819873--1819991	60	2.0	62	96	3	224	36	14	6	42	1.72
1823283--1823360	40	2.0	40	82	5	95	57	2	0	39	1.12
1823675--1823733	23	2.6	23	86	7	77	42	0	1	55	1.09
1823754--1823778	8	3.1	8	100	0	50	36	0	0	64	0.94
1827778--1827830	21	2.5	21	96	0	97	35	7	35	20	1.81
1830343--1830369	13	2.1	13	100	0	54	59	0	0	40	0.98
1830433--1830497	15	4.4	15	77	9	71	66	3	0	30	1.07
1832349--1832382	11	3.0	11	91	8	59	35	0	0	64	0.94
1832343--1832383	6	6.8	6	81	18	50	31	0	2	65	1.05
1832442--1832492	25	2.0	25	81	7	59	29	0	3	66	1.09
1832446--1832477	16	1.9	17	93	6	57	31	0	3	65	1.08
1832439--1832534	27	3.4	27	75	12	77	32	0	3	64	1.09
1835161--1835185	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1838365--1838397	16	2.1	16	94	0	57	54	15	0	30	1.41
1839473--1839518	22	2.1	21	88	11	67	34	10	0	54	1.36
1839568--1839614	14	3.3	14	83	13	60	42	0	0	57	0.98
1839737--1839777	21	2.0	21	85	4	57	65	14	4	14	1.42
1839949--1839992	17	2.5	17	79	17	54	52	2	2	43	1.26
1839944--1840002	22	2.7	23	77	15	61	52	1	1	44	1.21
1841402--1841436	18	1.9	18	88	11	54	22	0	2	74	0.95
1841403--1841460	23	2.4	23	83	13	73	27	0	1	70	0.97
1841847--1841912	28	2.3	30	80	12	86	33	1	0	65	1.02
1841847--1841907	29	2.1	29	87	6	88	32	1	0	65	1.02
1841952--1841985	14	2.3	15	90	5	52	41	0	5	52	1.25
1841979--1842035	15	3.8	14	77	11	60	50	1	0	47	1.11
1841986--1842070	31	2.7	30	82	10	91	54	1	2	42	1.21
1842023--1842247	104	2.2	104	91	0	369	56	1	5	36	1.34
1842217--1842259	22	1.9	23	90	4	70	72	0	4	23	1.04
1846034--1846074	19	2.0	21	86	9	59	43	2	2	51	1.28
1846351--1846396	17	2.8	16	83	6	56	56	0	0	43	0.99
1847126--1847202	38	2.0	38	89	0	118	25	9	16	48	1.76
1850249--1850275	13	2.1	13	100	0	54	29	14	0	55	1.40
1864791--1864840	2	25.0	2	87	0	73	48	0	4	48	1.20
1865384--1865439	3	18.7	3	96	0	103	66	0	1	32	1.03
1865724--1865768	11	4.1	11	77	11	56	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1866344--1866391	19	2.3	22	75	10	57	60	0	2	37	1.09
1867552--1867636	29	2.9	28	72	16	82	40	2	0	57	1.11
1869480--1869529	14	3.4	14	76	15	55	50	0	0	50	1.00
1869455--1869528	31	2.5	28	84	8	85	51	0	0	48	1.00
1869411--1869552	10	14.4	10	69	20	61	44	1	0	53	1.14
1870815--1870847	2	16.5	2	100	0	66	51	0	0	48	1.00
1871390--1871424	16	2.2	16	94	0	61	40	8	22	28	1.84
1879327--1879433	52	2.1	52	90	0	169	49	15	13	21	1.78
1880348--1880372	13	1.9	13	100	0	50	88	0	12	0	0.53
1888077--1888136	22	2.7	23	80	14	81	48	5	0	46	1.24
1888077--1888137	23	2.7	22	78	16	72	49	4	0	45	1.23
1888392--1888433	12	3.6	12	80	3	50	30	0	2	66	1.04
1890877--1891147	42	6.5	42	77	5	260	23	25	22	27	2.00
1890866--1891147	126	2.2	126	81	2	316	24	24	22	27	2.00
1895605--1895725	60	2.0	60	100	0	242	32	16	19	31	1.94
1901562--1901613	26	2.0	26	85	14	72	40	0	1	57	1.10
1901571--1901633	29	2.4	27	82	15	71	47	0	0	52	1.00
1901562--1901621	24	2.4	24	83	10	68	43	0	1	55	1.10
1901614--1901722	38	2.9	38	73	11	107	54	2	0	42	1.21
1903459--1903498	2	20.0	2	94	0	71	50	2	0	47	1.14
1904622--1904661	21	2.0	21	85	5	55	50	0	2	47	1.14
1907410--1907440	13	2.4	13	94	0	53	41	3	0	54	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1912091--1912178	32	2.8	33	76	10	78	54	1	4	39	1.28
1912620--1912823	112	1.8	112	88	2	311	46	1	3	48	1.28
1914044--1914089	22	2.1	22	84	8	58	39	0	0	60	0.97
1915347--1915390	19	2.3	19	84	7	54	43	2	2	52	1.26
1916251--1916277	13	2.1	13	100	0	54	25	7	7	59	1.51
1918497--1918521	10	2.5	10	100	0	50	36	0	0	64	0.94
1919017--1919055	2	19.5	2	91	0	60	46	2	2	48	1.29
1920447--1920542	15	6.2	15	68	23	56	39	0	0	60	0.97
1920446--1920502	29	2.0	29	90	10	91	35	0	0	64	0.93
1920491--1920540	15	3.2	16	76	23	61	44	0	0	56	0.99

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   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56