genome.fa.s36.2.7.7.80.10.50.1000.12.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: Scaffold36
Parameters: 2 7 7 80 10 50 1000
Length:  4808052

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   

This is table  12  of  28  ( 3342 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)
1898632--1898679	19	2.6	18	81	12	62	45	2	0	52	1.12
1898700--1898739	20	2.2	17	86	13	53	42	0	0	57	0.98
1898703--1898740	18	2.0	19	90	10	60	47	0	0	52	1.00
1899152--1899184	13	2.4	14	90	5	50	36	0	0	63	0.95
1902379--1902413	3	11.7	3	93	0	61	28	0	2	68	1.04
1908109--1908150	13	3.3	13	76	6	50	64	2	0	33	1.07
1908100--1908160	25	2.4	25	76	10	70	59	1	0	39	1.08
1908126--1908225	49	2.1	46	81	9	112	53	5	2	40	1.34
1908249--1908325	40	1.9	40	89	0	118	51	7	5	35	1.53
1908843--1908884	21	2.0	21	90	4	68	16	19	14	50	1.79
1913652--1913677	2	13.0	2	100	0	52	50	0	0	50	1.00
1915439--1915490	22	2.3	22	77	9	52	61	1	0	36	1.07
1916647--1916696	20	2.4	20	80	6	55	40	0	4	56	1.18
1916651--1916703	23	2.2	24	80	19	65	39	0	3	56	1.17
1917131--1917168	20	1.9	20	84	10	51	68	0	2	28	1.03
1917164--1917209	14	3.5	14	80	14	53	45	0	0	54	0.99
1917167--1917231	24	2.7	24	82	2	76	44	1	0	53	1.09
1919543--1919727	50	3.7	49	81	4	192	37	18	11	31	1.87
1920563--1920599	16	2.3	16	95	0	65	51	2	0	45	1.15
1920713--1920793	28	2.9	27	81	10	83	28	2	9	59	1.42
1920731--1920793	27	2.3	28	86	8	85	31	1	9	57	1.40
1924056--1924113	23	2.7	22	84	10	75	65	0	1	32	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1926128--1926164	18	2.1	19	85	10	51	21	13	8	56	1.63
1926153--1926322	84	2.0	84	94	0	295	35	11	2	51	1.51
1928464--1928501	20	2.0	20	89	5	60	36	0	2	60	1.11
1929145--1929178	17	2.0	17	88	0	50	47	0	0	52	1.00
1930502--1930536	2	17.5	2	100	0	70	48	0	0	51	1.00
1932566--1932591	3	8.7	3	100	0	52	30	0	0	69	0.89
1932768--1932815	2	24.0	2	100	0	96	50	0	0	50	1.00
1935977--1936003	2	13.5	2	100	0	54	48	0	0	51	1.00
1936097--1936137	2	20.5	2	94	0	73	46	0	2	51	1.14
1937310--1937339	8	3.8	8	90	0	51	63	0	0	36	0.95
1937380--1937450	35	2.2	32	83	16	85	32	5	0	61	1.19
1937760--1937802	2	21.5	2	95	0	77	2	48	0	48	1.14
1937802--1937829	2	14.0	2	100	0	56	50	0	0	50	1.00
1938219--1938266	16	3.1	16	84	3	62	72	2	0	25	0.95
1938203--1938254	26	2.0	25	88	7	77	65	3	0	30	1.10
1938211--1938266	27	2.1	26	83	3	67	71	1	0	26	0.96
1938259--1938320	32	1.9	32	86	0	88	53	1	1	43	1.20
1938270--1938325	16	3.5	16	77	18	62	50	1	0	48	1.11
1939641--1939678	2	19.0	2	100	0	76	50	0	0	50	1.00
1939821--1940277	227	2.0	227	98	0	878	38	15	15	30	1.89
1941354--1941776	214	2.0	214	99	0	837	37	12	17	32	1.87
1946756--1946781	8	3.2	8	100	0	52	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1946852--1946897	20	2.3	20	81	7	58	54	0	0	45	0.99
1952319--1952384	12	5.8	12	68	18	52	34	1	0	63	1.04
1952325--1952388	21	2.9	22	81	11	69	39	3	0	57	1.14
1952786--1952845	31	1.9	31	86	6	86	51	0	1	46	1.10
1952803--1952873	25	2.9	24	83	8	81	50	0	0	49	1.00
1952841--1952932	22	4.2	21	70	19	64	50	1	0	48	1.08
1952822--1952881	23	2.6	22	78	19	61	51	0	0	48	1.00
1952848--1952881	11	3.0	11	95	4	59	52	0	0	47	1.00
1952893--1952931	11	3.7	10	83	10	51	46	2	0	51	1.14
1952893--1952931	16	2.4	16	82	0	51	46	2	0	51	1.14
1953138--1953168	13	2.4	13	100	0	62	83	0	16	0	0.64
1953386--1953414	3	9.7	3	100	0	58	0	31	0	68	0.89
1953429--1953474	24	1.9	24	100	0	92	36	34	6	21	1.80
1954647--1954693	25	2.0	22	84	15	60	31	17	17	34	1.92
1961056--1961084	14	2.0	15	93	6	51	37	0	0	62	0.96
1961508--1961566	30	2.0	28	81	12	66	28	1	0	69	0.98
1962554--1962583	4	7.8	4	92	7	53	23	0	0	76	0.78
1965548--1965574	8	3.4	8	100	0	54	88	0	0	11	0.50
1967481--1967559	35	2.2	36	81	2	88	67	1	2	29	1.12
1967953--1967995	23	1.9	22	86	13	61	65	2	2	30	1.18
1968475--1968519	23	1.9	24	86	4	65	26	15	6	51	1.68
1969036--1969511	158	3.0	158	97	0	889	38	11	8	42	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1970041--1970138	37	2.8	34	74	8	97	29	2	27	40	1.67
1976002--1976203	52	3.9	52	87	5	284	31	16	18	33	1.94
1976191--1976217	13	2.1	13	100	0	54	29	14	14	40	1.86
1976278--1976302	13	1.9	13	100	0	50	32	16	16	36	1.90
1976360--1976401	21	2.0	21	90	0	66	35	14	14	35	1.86
1978381--1978405	12	2.1	12	100	0	50	16	0	44	40	1.47
1978430--1978471	22	1.9	22	90	0	66	23	7	30	38	1.82
1979524--1979584	22	2.7	22	78	9	61	42	1	13	42	1.53
1980046--1980153	48	2.2	49	80	3	112	41	27	15	14	1.87
1980046--1980154	32	3.4	32	83	0	119	41	28	15	14	1.87
1980046--1980154	16	6.8	16	73	0	92	41	28	15	14	1.87
1983591--1983626	18	2.0	18	100	0	72	38	33	0	27	1.57
1984559--1984674	59	2.0	59	87	3	171	42	16	12	28	1.85
1984704--1984768	30	2.3	29	76	21	68	43	0	0	56	0.99
1985754--1985837	37	2.3	37	97	0	159	33	33	15	17	1.92
1985865--1985895	16	1.9	16	93	0	53	38	29	22	9	1.86
1993196--1993280	41	2.1	41	86	0	116	30	21	12	35	1.91
1993355--1993792	152	2.9	153	89	1	682	15	25	18	40	1.90
1993695--1993890	98	2.0	100	90	4	315	14	21	19	43	1.87
1995116--1995158	16	3.0	14	81	15	52	46	0	0	53	1.00
1998177--1998211	2	17.5	2	100	0	70	51	0	0	48	1.00
1999451--1999509	25	2.3	25	80	11	66	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)
1999465--1999535	17	4.0	18	75	23	62	56	0	1	42	1.08
1999487--1999529	20	2.1	21	80	20	56	55	0	2	41	1.12
1999489--1999535	19	2.4	21	83	16	66	55	0	2	42	1.12
1999875--1999939	30	2.1	32	83	13	82	58	1	1	38	1.17
2001551--2001679	38	3.4	38	84	0	150	32	12	24	31	1.92
2001589--2001696	38	2.8	37	84	5	135	29	12	26	31	1.92
2006242--2006319	38	2.1	38	92	0	129	28	11	29	30	1.92
2006247--2006392	38	3.8	38	75	10	111	28	12	26	32	1.92
2007293--2007345	16	3.2	17	82	12	67	69	1	0	28	0.99
2008010--2008044	16	2.1	17	89	5	54	57	2	2	37	1.29
2008385--2008422	3	12.7	3	94	0	67	31	0	2	65	1.06
2009518--2009563	24	2.0	23	82	4	56	36	4	8	50	1.53
2010424--2010455	15	2.1	16	94	5	57	0	6	18	75	1.01
2013170--2013213	2	22.0	2	100	0	88	50	0	0	50	1.00
2015400--2015457	23	2.7	21	82	12	82	44	0	0	55	0.99
2015414--2015465	23	2.3	23	83	6	61	44	0	1	53	1.11
2015813--2015869	2	29.5	2	75	7	55	50	1	1	45	1.22
2015827--2015857	13	2.4	13	94	0	53	58	0	0	41	0.98
2015813--2015869	15	3.6	16	81	9	62	50	1	1	45	1.22
2015827--2015864	13	2.9	13	81	14	51	57	0	0	42	0.98
2017498--2017578	17	4.9	16	73	8	65	50	0	2	46	1.14
2017528--2017592	18	3.2	18	74	25	67	55	0	3	41	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
2029936--2030000	26	2.5	26	70	2	60	38	0	1	60	1.07
2031602--2031638	2	18.5	2	100	0	74	48	0	0	51	1.00
2031681--2031717	2	18.5	2	94	0	65	45	0	2	51	1.15
2032294--2032341	19	2.5	19	86	3	60	29	2	0	68	1.01
2033761--2033800	18	2.1	18	86	13	53	32	0	0	67	0.91
2033858--2033902	19	2.4	18	85	10	63	60	2	0	37	1.09
2034207--2034245	18	2.2	18	86	9	53	48	0	0	51	1.00
2034455--2034571	30	3.9	31	74	17	90	55	0	0	44	0.99
2034454--2034574	56	2.1	58	82	11	144	56	0	0	43	0.99
2035253--2035472	100	2.2	101	85	0	298	31	16	15	35	1.91

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