genome.fa.s40.2.7.7.80.10.50.1000.14.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: Scaffold40
Parameters: 2 7 7 80 10 50 1000
Length:  3440810

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   

This is table  14  of  24  ( 2833 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)
1879317--1879353	15	2.4	15	86	4	56	56	2	0	40	1.13
1882341--1882383	21	2.0	21	100	0	86	37	9	9	44	1.69
1884342--1884368	13	2.1	13	100	0	54	14	7	22	55	1.64
1884557--1884594	18	2.1	18	90	0	58	21	0	0	78	0.74
1884555--1884593	7	5.6	7	96	0	60	23	0	0	76	0.78
1885841--1885954	57	2.0	57	86	3	158	43	10	10	35	1.74
1886532--1886565	4	8.0	4	87	12	50	50	2	0	47	1.16
1888665--1888697	2	16.5	2	100	0	66	48	0	0	51	1.00
1889259--1889318	30	2.0	30	96	0	111	45	13	21	20	1.85
1900392--1900455	10	6.7	10	72	13	55	43	0	0	56	0.99
1900393--1900440	22	2.2	21	85	3	60	41	0	0	58	0.98
1900413--1900467	18	3.2	17	79	20	62	41	0	0	58	0.98
1900413--1900468	17	3.4	17	79	16	57	41	0	0	58	0.98
1900426--1900491	32	2.0	35	85	8	93	42	0	3	54	1.15
1900510--1900547	13	2.9	13	88	0	58	36	0	0	63	0.95
1900640--1900700	18	3.3	18	78	15	63	57	0	1	40	1.08
1901362--1901402	11	3.6	11	83	3	55	46	4	0	48	1.23
1901357--1901402	22	2.1	21	84	11	65	47	4	0	47	1.21
1901749--1901789	15	2.7	15	85	10	57	29	0	4	65	1.13
1902013--1902075	23	2.7	23	72	18	58	39	12	1	46	1.52
1902795--1902827	17	2.0	17	88	5	50	45	0	0	54	0.99
1902790--1902832	22	2.0	22	86	9	61	48	0	2	48	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1902852--1902920	27	2.6	25	86	11	93	44	1	1	52	1.19
1903889--1903931	18	2.3	19	84	4	52	34	2	0	62	1.08
1907358--1907426	25	2.7	26	80	11	79	37	1	7	53	1.38
1907976--1908024	20	2.5	19	80	9	53	24	0	2	73	0.94
1908127--1908167	3	13.7	3	100	0	82	65	0	0	34	0.93
1908166--1908204	3	13.0	3	100	0	78	33	0	0	66	0.92
1909088--1909143	27	2.1	27	83	6	69	55	1	7	35	1.38
1909991--1910067	23	3.3	24	75	13	72	41	0	0	58	0.98
1910004--1910041	19	2.1	18	90	9	60	42	0	0	57	0.98
1909974--1910069	40	2.4	40	81	8	97	41	0	0	58	0.98
1909983--1910065	22	3.7	22	78	10	96	43	0	0	56	0.99
1910034--1910082	16	3.1	16	75	0	62	34	0	0	65	0.93
1910077--1910206	29	4.6	28	80	11	131	42	1	0	55	1.14
1910077--1910204	57	2.2	57	76	13	129	42	1	0	55	1.15
1910169--1910297	35	3.6	35	74	13	138	40	1	0	57	1.14
1910158--1910297	72	1.9	73	88	1	210	41	1	0	56	1.13
1910312--1910344	15	2.1	16	88	5	50	33	0	0	66	0.92
1912563--1912593	1	31.0	1	100	0	62	0	100	0	0	0.00
1918826--1918866	15	2.6	16	81	18	50	51	0	0	48	1.00
1919714--1919760	21	2.3	20	82	13	60	21	2	0	76	0.89
1919729--1919761	13	2.8	12	86	13	50	21	0	0	78	0.75
1919714--1919766	21	2.6	19	77	16	52	22	3	0	73	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1920067--1920093	4	6.8	4	100	0	54	25	0	0	74	0.83
1920332--1920383	16	3.3	16	74	15	54	55	0	0	44	0.99
1920409--1920477	30	2.4	29	85	9	88	50	0	0	49	1.00
1920569--1920616	18	2.7	17	78	15	53	50	2	0	47	1.12
1920588--1920654	29	2.4	28	81	18	77	58	1	0	40	1.07
1920569--1920658	28	3.1	29	76	19	89	55	1	0	43	1.07
1921309--1921350	21	1.9	22	85	9	59	54	0	0	45	0.99
1921940--1922009	35	1.9	36	82	5	88	51	0	0	48	1.00
1922506--1922582	14	5.6	14	76	11	70	48	0	9	42	1.35
1922516--1922593	40	2.0	38	90	5	120	47	0	7	44	1.31
1922698--1922726	10	2.7	11	89	10	51	31	0	6	62	1.22
1922764--1922884	22	5.3	21	71	15	89	58	0	1	38	1.14
1922798--1922921	37	3.5	35	71	17	96	52	0	3	43	1.23
1922896--1922952	27	2.1	27	84	12	73	61	5	0	33	1.18
1922771--1922939	70	2.4	70	92	2	279	55	0	2	41	1.17
1923440--1923543	33	3.2	32	82	5	127	22	39	13	25	1.90
1923591--1923777	63	3.0	63	83	1	232	24	44	11	20	1.84
1924861--1924894	17	1.9	18	94	5	61	38	0	0	61	0.96
1925120--1925172	19	2.7	20	74	11	56	52	0	0	47	1.00
1927171--1927214	23	1.9	23	86	9	63	52	0	2	45	1.13
1928054--1928089	16	2.3	15	95	4	63	61	0	0	38	0.96
1928039--1928097	22	2.7	21	80	12	57	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)
1928192--1928274	26	3.1	26	80	15	89	53	1	1	44	1.16
1928274--1928315	15	2.9	15	89	6	61	66	2	0	30	1.04
1931770--1931826	29	2.0	29	86	6	80	35	0	1	63	1.05
1932047--1932097	14	3.2	15	78	16	50	58	0	0	41	0.98
1932455--1932522	11	6.3	11	73	10	59	61	1	0	36	1.05
1932463--1932589	43	2.8	45	70	14	118	59	0	0	40	0.98
1932465--1932558	32	2.9	32	78	13	95	58	0	0	41	0.98
1932511--1932584	16	4.6	16	77	15	55	56	0	0	43	0.99
1932465--1932585	18	7.2	18	71	22	86	59	0	0	40	0.97
1932774--1932951	16	11.0	17	62	23	55	34	1	1	62	1.10
1932820--1932873	20	2.8	19	80	8	65	38	0	0	61	0.96
1932820--1932876	18	3.1	18	85	10	62	40	0	0	59	0.97
1932828--1932939	32	3.5	31	75	10	102	35	0	0	63	1.01
1932788--1932934	11	12.9	11	64	16	50	34	0	0	64	1.03
1932911--1932953	18	2.2	20	80	8	54	37	4	0	58	1.19
1933518--1933550	16	2.0	17	88	5	50	30	3	0	66	1.06
1934991--1935027	20	1.9	18	89	10	56	51	0	0	48	1.00
1935197--1935247	26	1.9	25	84	11	66	45	0	0	54	0.99
1935225--1935285	17	3.8	16	79	10	63	45	0	0	54	1.00
1935555--1935618	6	10.5	6	86	3	92	59	0	0	40	0.97
1935541--1935614	12	6.2	12	84	7	62	58	0	0	41	0.98
1936242--1936282	18	2.3	18	91	8	66	31	2	7	58	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1936394--1936433	20	2.1	19	85	4	53	25	5	7	62	1.42
1936638--1936692	24	2.3	24	100	0	110	67	3	3	25	1.23
1936865--1936900	11	3.1	11	92	8	54	30	0	0	69	0.89
1937529--1937570	22	1.9	22	90	0	66	52	0	0	47	1.00
1938314--1938357	20	2.3	20	81	11	58	36	0	9	54	1.32
1939553--1939580	2	14.0	2	100	0	56	50	0	0	50	1.00
1939769--1939823	24	2.3	24	87	6	76	52	7	5	34	1.52
1940543--1940587	2	22.5	2	82	17	58	46	2	2	48	1.26
1940975--1941122	32	4.4	33	74	18	101	39	0	0	59	1.07
1940974--1941122	50	2.9	49	76	13	133	39	0	0	59	1.07
1942615--1942663	14	3.4	14	78	13	55	40	0	0	59	0.98
1942648--1942714	21	3.0	21	79	12	64	38	4	1	55	1.29
1942868--1942962	18	5.4	16	69	24	59	43	1	1	54	1.14
1942838--1942907	17	4.4	15	73	22	54	32	1	1	64	1.11
1942865--1942935	19	4.1	16	75	20	63	40	1	1	56	1.17
1942977--1943008	2	16.0	2	93	0	55	46	0	0	53	1.00
1943168--1943201	16	2.1	16	88	0	50	61	2	2	32	1.26
1944793--1944836	18	2.4	19	76	3	54	43	0	6	50	1.29
1944975--1945044	30	2.6	26	80	14	79	47	0	2	50	1.16
1944993--1945060	25	2.7	25	78	14	70	48	2	1	47	1.26
1945070--1945108	19	2.0	21	85	10	55	48	0	0	51	1.00
1947794--1947835	10	4.2	10	81	6	50	59	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1948567--1948620	23	2.4	21	76	11	54	53	0	0	46	1.00
1948814--1948874	14	4.6	13	76	15	54	59	0	0	40	0.98
1948836--1948871	12	2.9	12	87	4	54	69	0	0	30	0.89
1948814--1948867	14	3.9	14	81	13	67	61	0	0	38	0.96
1950619--1950680	22	2.8	22	81	15	83	16	17	3	62	1.45
1952161--1952238	25	3.0	26	77	7	77	48	0	0	51	1.00
1955572--1955625	27	2.0	27	96	0	99	35	18	14	31	1.91
1959682--1959707	13	2.0	13	100	0	52	38	15	15	30	1.88
1959760--1959822	19	3.7	18	74	24	64	36	17	11	34	1.85
1959746--1959803	13	4.0	13	74	23	53	32	15	15	36	1.89

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